Novel Port Placement in Robot-Assisted DIEP Flap Harvest Improves Visibility and Bilateral DIEP Access: Early Controlled Cohort Study

SUMMARY

To minimize donor-site damage, robot-assisted (RA) deep inferior epigastric perforator (DIEP) flap harvest has been suggested. Current robotic approaches favor port placement, which either does not allow a bilateral DIEP flap harvest through the same ports or necessitates additional scars. In this article, the authors propose a modification of port configuration. In a retrospective controlled cohort study, RA-DIEP and conventional DIEP surgery were compared. The perforator and pedicle were visualized conventionally until the level behind the rectus abdominis muscle. Next, the robotic system was installed to dissect the retromuscular pedicle. The authors assessed patient age; body mass index; history of smoking, diabetes mellitus, and hypertension; and additional surgical time. The length of the anterior rectus sheath (ARS) incision was measured. Pain was quantified using the visual analogue scale. Donor-site complications were assessed. Thirteen RA-DIEP flaps (11 unilateral and two bilateral) and 87 conventional DIEP flaps were harvested without flap loss. The bilateral DIEP flaps were raised without readjustments of the ports. The mean time for pedicle dissection was 53.2 ± 13.4 minutes. The length of the ARS incision was significantly shorter in the RA-DIEP group (2.67 ± 1.13 cm versus 8.14 ± 1.69 cm; 304.87% difference; P < 0.0001). There was no statistical difference in postoperative pain (day 1: 1.9 ± 0.9 versus 2.9 ± 1.6, P = 0.094; day 2: 1.8 ± 1.2 versus 2.3 ± 1.5, P = 0.319; day 3: 1.6 ± 0.9 versus 2.0 ± 1.3, P = 0.444). Preliminary results show that the authors' RA-DIEP approach is safe and allows dissection of bilateral RA-DIEP flaps with short ARS incision lengths.

CLINICAL QUESTION/LEVEL OF EVIDENCE

Therapeutic, III.

Estimation of Effect Heterogeneity in Rare Events Meta-Analysis

The paper outlines several approaches for dealing with meta-analyses of count outcome data. These counts are the accumulation of occurred events, and these events might be rare, so a special feature of the meta-analysis is dealing with low counts including zero-count studies. Emphasis is put on approaches which are state of the art for count data modelling including mixed log-linear (Poisson) and mixed logistic (binomial) regression as well as nonparametric mixture models for count data of Poisson and binomial type. A simulation study investigates the performance and capability of discrete mixture models in estimating effect heterogeneity. The approaches are exemplified on a meta-analytic case study investigating the acceptance of bibliotherapy.

Diastolic dysfunction in individuals with and without heart failure with preserved ejection fraction

AIM

Left ventricular diastolic dysfunction (DD), a common finding in the general population, is considered to be associated with heart failure with preserved ejection faction (HFpEF). Here we evaluate the prevalence and correlates of DD in subjects with and without HFpEF in a middle-aged sample of the general population.

METHODS AND RESULTS

From the first 10,000 participants of the population-based Hamburg City Health Study (HCHS), 5913 subjects (mean age 64.4 ± 8.3 years, 51.3% females), qualified for the current analysis. Diastolic dysfunction (DD) was identified in 753 (12.7%) participants. Of those, 11.2% showed DD without HFpEF (ALVDD) while 1.3% suffered from DD with HFpEF (DDwHFpEF). In multivariable regression analysis adjusted for major cardiovascular risk factors, ALVDD was associated with arterial hypertension (OR 2.0, p < 0.001) and HbA1c (OR 1.2, p = 0.007). Associations of both ALVDD and DDwHFpEF were: age (OR 1.7, p < 0.001; OR 2.7, p < 0.001), BMI (OR 1.2, p < 0.001; OR 1.6, p = 0.001), and left ventricular mass index (LVMI). In contrast, female sex (OR 2.5, p = 0.006), atrial fibrillation (OR 2.6, p = 0.024), CAD (OR 7.2, p < 0.001) COPD (OR 3.9, p < 0.001), and QRS duration (OR 1.4, p = 0.005) were strongly associated with DDwHFpEF but not with ALVDD.

CONCLUSION

The prevalence of DD in a sample from the first 10,000 participants of the population-based HCHS was 12.7% of whom 1.3% suffered from HFpEF. DD with and without HFpEF showed significant associations with different major cardiovascular risk factors and comorbidities warranting further research for their possible role in the formation of both ALVDD and DDwHFpEF.

Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome

Escherichia coli is an important cause of bloodstream infections (BSI), which is of concern given its high mortality and increasing worldwide prevalence. Finding bacterial genetic variants that might contribute to patient death is of interest to better understand infection progression and implement diagnostic methods that specifically look for those factors. E. coli samples isolated from patients with BSI are an ideal dataset to systematically search for those variants, as long as the influence of host factors such as comorbidities are taken into account. Here we performed a genome-wide association study (GWAS) using data from 912 patients with E. coli BSI from hospitals in Paris, France. We looked for associations between bacterial genetic variants and three patient outcomes (death at 28 days, septic shock and admission to intensive care unit), as well as two portals of entry (urinary and digestive tract), using various clinical variables from each patient to account for host factors. We did not find any association between genetic variants and patient outcomes, potentially confirming the strong influence of host factors in influencing the course of BSI; we however found a strong association between the papGII operon and entrance of E. coli through the urinary tract, which demonstrates the power of bacterial GWAS when applied to actual clinical data. Despite the lack of associations between E. coli genetic variants and patient outcomes, we estimate that increasing the sample size by one order of magnitude could lead to the discovery of some putative causal variants. Given the wide adoption of bacterial genome sequencing of clinical isolates, such sample sizes may be soon available.

Cardiovascular risk factors, living and ageing in Halle: the CARLA study

The CARLA study (Cardiovascular Disease, Living and Ageing in Halle) is a longitudinal population-based cohort study of the general population of the city of Halle (Saale), Germany. The primary aim of the cohort was to investigate risk factors for cardiovascular diseases based on comprehensive cardiological phenotyping of study participants and was extended to study factors associated with healthy ageing. In total, 1779 probands (812 women and 967 men, aged 45–83 years) were examined at baseline (2002–2005), with a first and second follow-up performed 4 and 8 years later. The response proportion at baseline was 64.1% and the reparticipation proportion for the first and second follow-up was 86% and 77% respectively. Sixty-four percent of the study participants were in retirement while 25% were full- or partially-employed and 11% were unemployed at the time of the baseline examination. The currently running third follow-up focuses on the assessment of physical and mental health, with an intensive 4 h examination program, including measurement of cardiovascular, neurocognitive, balance and gait parameters. The data collected in the CARLA Study resulted in answering various research questions in over 80 publications, of which two thirds were pooled analyses with other similar population-based studies. Due to the extensiveness of information on risk factors, subclinical conditions and evident diseases, the biobanking concept for the biosamples, the cohort representativeness of an elderly population, and the high level of quality assurance, the CARLA cohort offers a unique platform for further research on important indicators for healthy ageing.

MFmap: A semi-supervised generative model matching cell lines to tumours and cancer subtypes

Translating in vitro results from experiments with cancer cell lines to clinical applications requires the selection of appropriate cell line models. Here we present MFmap (model fidelity map), a machine learning model to simultaneously predict the cancer subtype of a cell line and its similarity to an individual tumour sample. The MFmap is a semi-supervised generative model, which compresses high dimensional gene expression, copy number variation and mutation data into cancer subtype informed low dimensional latent representations. The accuracy (test set F₁ score >90%) of the MFmap subtype prediction is validated in ten different cancer datasets. We use breast cancer and glioblastoma cohorts as examples to show how subtype specific drug sensitivity can be translated to individual tumour samples. The low dimensional latent representations extracted by MFmap explain known and novel subtype specific features and enable the analysis of cell-state transformations between different subtypes. From a methodological perspective, we report that MFmap is a semi-supervised method which simultaneously achieves good generative and predictive performance and thus opens opportunities in other areas of computational biology.

Systematic review and meta-analysis of diagnostic studies of proximal surface caries

AIM

This systematic review and meta-analysis aimed to assess the diagnostic accuracy and reliability of commonly used caries detection methods for proximal caries diagnostics. Visual examination (VE), bitewing radiography (BWR), laser fluorescence (LF), and fibre-optic transillumination (FOTI) were considered in detail.

MATERIAL AND METHODS

PRISMA guidelines for the reporting of systematic reviews and meta-analyses were applied. The mnemonic PIRDS (problem, index test, reference test, diagnostic and study type) concept was used to guide the literature search. Next, studies that met the inclusion criteria were stepwise selected and evaluated for their quality with a risk of bias (RoB) assessment tool. Studies with low/moderate bias and sufficient reporting were considered for meta-analysis. The pooled sensitivity (SE), specificity (SP), diagnostic odds ratio (DOR), and area under the ROC curve (AUC) were calculated.

RESULTS

From 129 studies meeting the selection criteria, 31 in vitro studies and five clinical studies were finally included in the meta-analysis. The AUC values for in vitro VE amounted to 0.84 (caries detection) and 0.85 (dentin caries detection). BWR ranged in vitro from 0.55 to 0.82 (caries detection) and 0.81-0.92 (dentin caries detection). LF showed higher AUC values for overall caries detection (0.91) and dentin caries detection (0.83) than did other methods. Clinical data are limited.

CONCLUSION

The number of diagnostic studies with low/moderate RoB was found to be low and indicates a need for high-quality, well-designed caries diagnostic studies.

CLINICAL RELEVANCE

BWR and LF showed good diagnostic performance on proximal surfaces. However, because of the low number of includable clinical studies, these data should be interpreted with caution.

Towards novel osteoarthritis biomarkers: Multi-criteria evaluation of 46,996 segmented knee MRI data from the Osteoarthritis Initiative

Convolutional neural networks (CNNs) are the state-of-the-art for automated assessment of knee osteoarthritis (KOA) from medical image data. However, these methods lack interpretability, mainly focus on image texture, and cannot completely grasp the analyzed anatomies' shapes. In this study we assess the informative value of quantitative features derived from segmentations in order to assess their potential as an alternative or extension to CNN-based approaches regarding multiple aspects of KOA. Six anatomical structures around the knee (femoral and tibial bones, femoral and tibial cartilages, and both menisci) are segmented in 46,996 MRI scans. Based on these segmentations, quantitative features are computed, i.e., measurements such as cartilage volume, meniscal extrusion and tibial coverage, as well as geometric features based on a statistical shape encoding of the anatomies. The feature quality is assessed by investigating their association to the Kellgren-Lawrence grade (KLG), joint space narrowing (JSN), incident KOA, and total knee replacement (TKR). Using gold standard labels from the Osteoarthritis Initiative database the balanced accuracy (BA), the area under the Receiver Operating Characteristic curve (AUC), and weighted kappa statistics are evaluated. Features based on shape encodings of femur, tibia, and menisci plus the performed measurements showed most potential as KOA biomarkers. Differentiation between non-arthritic and severely arthritic knees yielded BAs of up to 99%, 84% were achieved for diagnosis of early KOA. Weighted kappa values of 0.73, 0.72, and 0.78 were achieved for classification of the grade of medial JSN, lateral JSN, and KLG, respectively. The AUC was 0.61 and 0.76 for prediction of incident KOA and TKR within one year, respectively. Quantitative features from automated segmentations provide novel biomarkers for KLG and JSN classification and show potential for incident KOA and TKR prediction. The validity of these features should be further evaluated, especially as extensions of CNN-based approaches. To foster such developments we make all segmentations publicly available together with this publication.

Preparatory delta phase response is correlated with naturalistic speech comprehension performance

While human speech comprehension is thought to be an active process that involves top-down predictions, it remains unclear how predictive information is used to prepare for the processing of upcoming speech information. We aimed to identify the neural signatures of the preparatory processing of upcoming speech. Participants selectively attended to one of two competing naturalistic, narrative speech streams, and a temporal response function (TRF) method was applied to derive event-related-like neural responses from electroencephalographic data. The phase responses to the attended speech at the delta band (1-4 Hz) were correlated with the comprehension performance of individual participants, with a latency of - 200-0 ms relative to the onset of speech amplitude envelope fluctuations over the fronto-central and left-lateralized parietal electrodes. The phase responses to the attended speech at the alpha band also correlated with comprehension performance but with a latency of 650-980 ms post-onset over the fronto-central electrodes. Distinct neural signatures were found for the attentional modulation, taking the form of TRF-based amplitude responses at a latency of 240-320 ms post-onset over the left-lateralized fronto-central and occipital electrodes. Our findings reveal how the brain gets prepared to process an upcoming speech in a continuous, naturalistic speech context.

Average semivariance yields accurate estimates of the fraction of marker-associated genetic variance and heritability in complex trait analyses

The development of genome-informed methods for identifying quantitative trait loci (QTL) and studying the genetic basis of quantitative variation in natural and experimental populations has been driven by advances in high-throughput genotyping. For many complex traits, the underlying genetic variation is caused by the segregation of one or more ‘large-effect’ loci, in addition to an unknown number of loci with effects below the threshold of statistical detection. The large-effect loci segregating in populations are often necessary but not sufficient for predicting quantitative phenotypes. They are, nevertheless, important enough to warrant deeper study and direct modelling in genomic prediction problems. We explored the accuracy of statistical methods for estimating the fraction of marker-associated genetic variance (p) and heritability (HM2) for large-effect loci underlying complex phenotypes. We found that commonly used statistical methods overestimate p and HM2. The source of the upward bias was traced to inequalities between the expected values of variance components in the numerators and denominators of these parameters. Algebraic solutions for bias-correcting estimates of p and HM2 were found that only depend on the degrees of freedom and are constant for a given study design. We discovered that average semivariance methods, which have heretofore not been used in complex trait analyses, yielded unbiased estimates of p and HM2, in addition to best linear unbiased predictors of the additive and dominance effects of the underlying loci. The cryptic bias problem described here is unrelated to selection bias, although both cause the overestimation of p and HM2. The solutions we described are predicted to more accurately describe the contributions of large-effect loci to the genetic variation underlying complex traits of medical, biological, and agricultural importance.

The contributions of individual genes to the phenotypic variation observed for genetically complex traits has been an ongoing and important challenge in biology, medicine, and agriculture. While many genes have statistically undetectable effects, those with large effects often warrant in-depth study and can be important predictors of complex phenotypes such as disease risk in humans or disease resistance in domesticated plants and animals. The genes identified through associations with genetic markers in complex trait analyses typically account for a fraction of the heritable variation, a genetic parameter we called ‘marker heritability’. We discovered that textbook statistical methods systematically overestimate marker heritability and thus overestimate the contributions of specific genes to the phenotypic variation observed for complex traits in natural and experimental populations. We describe the source of the upward bias, validate our findings through computer simulation, describe methods for bias-correcting estimates of marker heritability, and illustrate their application through empirical examples. The statistical methods we describe supply investigators with more accurate estimates of the contributions of specific genes or networks of interacting genes to the heritable variation observed in complex trait studies.

Role of circulating angiogenin levels in portal hypertension and TIPS

Background

Pathogenesis of portal hypertension is multifactorial and includes pathologic intrahepatic angiogenesis, whereby TIPS insertion is an effective therapy of portal hypertension associated complications. While angiogenin is a potent contributor to angiogenesis in general, little is known about its impact on TIPS function over time.

Methods

In a total of 118 samples from 47 patients, angiogenin concentrations were measured in portal and inferior caval vein plasma at TIPS insertion (each blood compartment n = 23) or angiographic intervention after TIPS (each blood compartment n = 36) and its relationship with patient outcome was investigated.

Results

Angiogenin levels in the inferior caval vein were significantly higher compared to the portal vein (P = 0.048). Ten to 14 days after TIPS, inferior caval vein angiogenin level correlated inversely with the portal systemic pressure gradient (P<0.001), measured invasively during control angiography. Moreover, patients with TIPS revision during this angiography, showed significantly lower angiogenin level in the inferior caval vein compared to patients without TIPS dysfunction (P = 0.01).

Conclusion

In cirrhosis patients with complications of severe portal hypertension, circulating levels of angiogenin are derived from the injured liver. Moreover, angiogenin levels in the inferior caval vein after TIPS may predict TIPS dysfunction.

Consensus based framework for digital mobility monitoring

Digital mobility assessment using wearable sensor systems has the potential to capture walking performance in a patient's natural environment. It enables monitoring of health status and disease progression and evaluation of interventions in real-world situations. In contrast to laboratory settings, real-world walking occurs in non-conventional environments and under unconstrained and uncontrolled conditions. Despite the general understanding, there is a lack of agreed definitions about what constitutes real-world walking, impeding the comparison and interpretation of the acquired data across systems and studies. The goal of this study was to obtain expert-based consensus on specific aspects of real-world walking and to provide respective definitions in a common terminological framework. An adapted Delphi method was used to obtain agreed definitions related to real-world walking. In an online survey, 162 participants from a panel of academic, clinical and industrial experts with experience in the field of gait analysis were asked for agreement on previously specified definitions. Descriptive statistics was used to evaluate whether consent (> 75% agreement as defined a priori) was reached. Of 162 experts invited to participate, 51 completed all rounds (31.5% response rate). We obtained consensus on all definitions ("Walking" > 90%, "Purposeful" > 75%, "Real-world" > 90%, "Walking bout" > 80%, "Walking speed" > 75%, "Turning" > 90% agreement) after two rounds. The identification of a consented set of real-world walking definitions has important implications for the development of assessment and analysis protocols, as well as for the reporting and comparison of digital mobility outcomes across studies and systems. The definitions will serve as a common framework for implementing digital and mobile technologies for gait assessment and are an important link for the transition from supervised to unsupervised gait assessment.

Aη-α and Aη-β peptides impair LTP ex vivo within the low nanomolar range and impact neuronal activity in vivo

BACKGROUND

Amyloid precursor protein (APP) processing is central to Alzheimer's disease (AD) etiology. As early cognitive alterations in AD are strongly correlated to abnormal information processing due to increasing synaptic impairment, it is crucial to characterize how peptides generated through APP cleavage modulate synapse function. We previously described a novel APP processing pathway producing η-secretase-derived peptides (Aη) and revealed that Aη-α, the longest form of Aη produced by η-secretase and α-secretase cleavage, impaired hippocampal long-term potentiation (LTP) ex vivo and neuronal activity in vivo.

METHODS

With the intention of going beyond this initial observation, we performed a comprehensive analysis to further characterize the effects of both Aη-α and the shorter Aη-β peptide on hippocampus function using ex vivo field electrophysiology, in vivo multiphoton calcium imaging, and in vivo electrophysiology.

RESULTS

We demonstrate that both synthetic peptides acutely impair LTP at low nanomolar concentrations ex vivo and reveal the N-terminus to be a primary site of activity. We further show that Aη-β, like Aη-α, inhibits neuronal activity in vivo and provide confirmation of LTP impairment by Aη-α in vivo.

CONCLUSIONS

These results provide novel insights into the functional role of the recently discovered η-secretase-derived products and suggest that Aη peptides represent important, pathophysiologically relevant, modulators of hippocampal network activity, with profound implications for APP-targeting therapeutic strategies in AD.

Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia

BACKGROUND

Repeat elements constitute a large proportion of the human genome and recent evidence indicates that repeat element expression has functional roles in both physiological and pathological states. Specifically for cancer, transcription of endogenous retrotransposons is often suppressed to attenuate an anti-tumor immune response, whereas aberrant expression of heterochromatin-derived satellite RNA has been identified as a tumor driver. These insights demonstrate separate functions for the dysregulation of distinct repeat subclasses in either the attenuation or progression of human solid tumors. For hematopoietic malignancies, such as Acute Myeloid Leukemia (AML), only very few studies on the expression/dysregulation of repeat elements were done.

METHODS

To study the expression of repeat elements in AML, we performed total-RNA sequencing of healthy CD34 + cells and of leukemic blast cells from primary AML patient material. We also developed an integrative bioinformatic approach that can quantify the expression of repeat transcripts from all repeat subclasses (SINE/ALU, LINE, ERV and satellites) in relation to the expression of gene and other non-repeat transcripts (i.e. R/G ratio). This novel approach can be used as an instructive signature for repeat element expression and has been extended to the analysis of poly(A)-RNA sequencing datasets from Blueprint and TCGA consortia that together comprise 120 AML patient samples.

RESULTS

We identified that repeat element expression is generally down-regulated during hematopoietic differentiation and that relative changes in repeat to gene expression can stratify risk prediction of AML patients and correlate with overall survival probabilities. A high R/G ratio identifies AML patient subgroups with a favorable prognosis, whereas a low R/G ratio is prevalent in AML patient subgroups with a poor prognosis.

CONCLUSIONS

We developed an integrative bioinformatic approach that defines a general model for the analysis of repeat element dysregulation in physiological and pathological development. We find that changes in repeat to gene expression (i.e. R/G ratios) correlate with hematopoietic differentiation and can sub-stratify AML patients into low-risk and high-risk subgroups. Thus, the definition of a R/G ratio can serve as a valuable biomarker for AML and could also provide insights into differential patient response to epigenetic drug treatment.

Vertical clinging and leaping induced evolutionary rate shifts in postcranial evolution of tamarins and marmosets (Primates, Callitrichidae)

BACKGROUND

Callitrichids comprise a diverse group of platyrrhine monkeys that are present across South and Central America. Their secondarily evolved small size and pointed claws allow them to cling to vertical trunks of a large diameter. Within callitrichids, lineages with a high affinity for vertical supports often engage in trunk-to-trunk leaping. This vertical clinging and leaping (VCL) differs from horizontal leaping (HL) in terms of the functional demands imposed on the musculoskeletal system, all the more so as HL often occurs on small compliant terminal branches. We used quantified shape descriptors (3D geometric morphometrics) and phylogenetically-informed analyses to investigate the evolution of the shape and size of the humerus and femur, and how this variation reflects locomotor behavior within Callitrichidae.

RESULTS

The humerus of VCL-associated species has a narrower trochlea compared with HL species. It is hypothesized that this contributes to greater elbow mobility. The wider trochlea in HL species appears to correspondingly provide greater stability to the elbow joint. The femur in VCL species has a smaller head and laterally-oriented distal condyles, possibly to reduce stresses during clinging. Similarly, the expanded lesser trochanters visible in VCL species provide a greater lever for the leg retractors and are thus also interpreted as an adaptation to clinging. Evolutionary rate shifts to faster shape and size changes of humerus and femur occurred in the Leontocebus clade when a shift to slower rates occurred in the Saguinus clade.

CONCLUSIONS

Based on the study of evolutionary rate shifts, the transition to VCL behavior within callitrichids (specifically the Leontocebus clade) appears to have been an opportunity for radiation, rather than a specialization that imposed constraints on morphological diversity. The study of the evolution of callitrichids suffers from a lack of comparative analyses of limb mechanics during trunk-to-trunk leaping, and future work in this direction would be of great interest.

Recruitment of phospholipase Cγ1 to the non-structural membrane protein pK15 of Kaposi Sarcoma-associated herpesvirus promotes its Src-dependent phosphorylation

Kaposi Sarcoma-associated herpesvirus (KSHV) causes three human malignancies, Kaposi Sarcoma (KS), Primary Effusion Lymphoma (PEL) and the plasma cell variant of multicentric Castleman’s Disease (MCD), as well as an inflammatory cytokine syndrome (KICS). Its non-structural membrane protein, pK15, is among a limited set of viral proteins expressed in KSHV-infected KS tumor cells. Following its phosphorylation by Src family tyrosine kinases, pK15 recruits phospholipase C gamma 1 (PLCγ1) to activate downstream signaling cascades such as the MEK/ERK, NFkB and PI3K pathway, and thereby contributes to the increased proliferation and migration as well as the spindle cell morphology of KSHV-infected endothelial cells. Here, we show that a phosphorylated Y⁴⁸¹EEVL motif in pK15 preferentially binds into the PLCγ1 C-terminal SH2 domain (cSH2), which is involved in conformational changes occurring during the activation of PLCγ1 by receptor tyrosine kinases. We determined the crystal structure of a pK15 12mer peptide containing the phosphorylated pK15 Y⁴⁸¹EEVL motif in complex with a shortened PLCγ1 tandem SH2 (tSH2) domain. This structure demonstrates that the pK15 peptide binds to the PLCγ1 cSH2 domain in a position that is normally occupied by the linker region connecting the PLCγ1 cSH2 and SH3 domains. We also show that longer pK15 peptides containing the phosphorylated pK15 Y⁴⁸¹EEVL motif can increase the Src-mediated phosphorylation of the PLCγ1 tSH2 region in vitro. This pK15-induced increase in Src-mediated phosphorylation of PLCγ1 can be inhibited with the small pK15-derived peptide which occupies the PLCγ1 cSH2 domain. Our findings thus suggest that pK15 may act as a scaffold protein to promote PLCγ1 activation in a manner similar to the cellular scaffold protein SLP-76, which has been shown to promote PLCγ1 activation in the context of T-cell receptor signaling. Reminiscent of its positional homologue in Epstein-Barr Virus, LMP2A, pK15 may therefore mimic aspects of antigen-receptor signaling. Our findings also suggest that it may be possible to inhibit the recruitment and activation of PLCγ1 pharmacologically.

Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) causes three human malignancies (Kaposi Sarcoma, Primary Effusion Lymphoma, Multicentric Castleman’s Disease) and an inflammatory condition, KICS. One of its non-structural membrane proteins, pK15, is expressed in tumor cells and has previously been shown to contribute to its ability to reactivate from latency and to its pathogenetic properties in endothelial cells by recruiting the cellular signaling enzyme phospholipase Cγ1 (PLCγ1). Here we investigate the interaction of pK15 with PLCγ1, report the structure of a PLCγ1 domain in complex with a pK15 peptide and show that pK15 primes PLCγ1 for phosphorylation by the cellular kinase Src. We also show that the pK15-dependent activation of PLCγ1 can be inhibited with a small peptide. Our findings therefore identify the pK15-PLCγ1 interaction as a putative druggable target and provide the basis for the development of small molecule inhibitors that could perhaps serve to inhibit KSHV replication and pathogenesis.

A Roman provincial city and its contamination legacy from artisanal and daily-life activities

Roman metal use and related extraction activities resulted in heavy metal pollution and contamination, in particular of Pb near ancient mines and harbors, as well as producing a global atmospheric impact. New evidence from ancient Gerasa (Jerash), Jordan, suggests that small-scale but intense Roman, Byzantine and Umayyad period urban, artisanal, and everyday site activities contributed to substantial heavy metal contamination of the city and its hinterland wadi, even though no metal mining took place and hardly any lead water pipes were used. Distribution of heavy metal contaminants, especially Pb, observed in the urban soils and sediments within this ancient city and its hinterland wadi resulted from aeolian, fluvial, cultural and post-depositional processes. These represent the contamination pathways of an ancient city-hinterland setting and reflect long-term anthropogenic legacies at local and regional scales beginning in the Roman period. Thus, urban use and re-use of heavy metal sources should be factored into understanding historical global-scale contaminant distributions.

Learning divisive normalization in primary visual cortex

Divisive normalization (DN) is a prominent computational building block in the brain that has been proposed as a canonical cortical operation. Numerous experimental studies have verified its importance for capturing nonlinear neural response properties to simple, artificial stimuli, and computational studies suggest that DN is also an important component for processing natural stimuli. However, we lack quantitative models of DN that are directly informed by measurements of spiking responses in the brain and applicable to arbitrary stimuli. Here, we propose a DN model that is applicable to arbitrary input images. We test its ability to predict how neurons in macaque primary visual cortex (V1) respond to natural images, with a focus on nonlinear response properties within the classical receptive field. Our model consists of one layer of subunits followed by learned orientation-specific DN. It outperforms linear-nonlinear and wavelet-based feature representations and makes a significant step towards the performance of state-of-the-art convolutional neural network (CNN) models. Unlike deep CNNs, our compact DN model offers a direct interpretation of the nature of normalization. By inspecting the learned normalization pool of our model, we gained insights into a long-standing question about the tuning properties of DN that update the current textbook description: we found that within the receptive field oriented features were normalized preferentially by features with similar orientation rather than non-specifically as currently assumed.

Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints

We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a multilateration algorithm that harnesses sets of interconnected spin label pairs to identify optimal rotamer ensembles at each residue that fit the DEER decay in the time domain. Benchmarked relative to data analysis packages, the algorithm yields comparable distance distributions with the advantage that fitting the DEER decay and rotamer ensemble optimization are coupled. We demonstrate this approach by modeling the protonation-dependent transition of the multidrug transporter PfMATE to an inward facing conformation with a deviation to the experimental structure of less than 2Å Cα RMSD. By decreasing spin label rotamer entropy, this approach engenders more accurate Rosetta models that are also more closely clustered, thus setting the stage for more robust modeling of protein conformational changes.

Data-driven model reduction of agent-based systems using the Koopman generator

The dynamical behavior of social systems can be described by agent-based models. Although single agents follow easily explainable rules, complex time-evolving patterns emerge due to their interaction. The simulation and analysis of such agent-based models, however, is often prohibitively time-consuming if the number of agents is large. In this paper, we show how Koopman operator theory can be used to derive reduced models of agent-based systems using only simulation data. Our goal is to learn coarse-grained models and to represent the reduced dynamics by ordinary or stochastic differential equations. The new variables are, for instance, aggregated state variables of the agent-based model, modeling the collective behavior of larger groups or the entire population. Using benchmark problems with known coarse-grained models, we demonstrate that the obtained reduced systems are in good agreement with the analytical results, provided that the numbers of agents is sufficiently large.

Towards enhancing coral heat tolerance: a "microbiome transplantation" treatment using inoculations of homogenized coral tissues

BACKGROUND

Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding.

RESULTS

Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 °C). One hundred twelve (Pocillopora sp.) and sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context.

CONCLUSIONS

Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. Video abstract.

Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition

Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, P_o concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.

Genotype-driven therapeutic developments in Parkinson's disease

BACKGROUND

Remarkable advances have been reached in the understanding of the genetic basis of Parkinson's disease (PD), with the identification of monogenic causes (mPD) and a plethora of gene loci leading to an increased risk for idiopathic PD. The expanding knowledge and subsequent identification of genetic contributions fosters the understanding of molecular mechanisms leading to disease development and progression. Distinct pathways involved in mitochondrial dysfunction, oxidative stress, and lysosomal function have been identified and open a unique window of opportunity for individualized treatment approaches. These genetic findings have led to an imminent progress towards pathophysiology-targeted clinical trials and potentially disease-modifying treatments in the future.

MAIN BODY OF THE MANUSCRIPT

In this review article we will summarize known genetic contributors to the pathophysiology of Parkinson's disease, the molecular mechanisms leading to disease development, and discuss challenges and opportunities in clinical trial designs.

CONCLUSIONS

The future success of clinical trials in PD is mainly dependent on reliable biomarker development and extensive genetic testing to identify genetic cases. Whether genotype-dependent stratification of study participants will extend the potential application of new drugs will be one major challenge in conceptualizing clinical trials. However, the latest developments in genotype-driven treatments will pave the road to individualized pathophysiology-based therapies in the future.

Gluten intake and metabolic health: conflicting findings from the UK Biobank

PURPOSE

The impact of gluten intake on metabolic health in subjects without celiac disease is unclear. The present study aimed to assess the association between gluten intake and body fat percentage (primary objective), as well as a broad set of metabolic health markers.

METHODS

Gluten intake was estimated in 39,927 participants of the UK Biobank who completed a dietary questionnaire for assessment of previous 24-h dietary intakes. Multiple linear regression analyses were performed between gluten intake and markers of metabolic health with Holm adjustment for multiple comparisons.

RESULTS

Median gluten intake was 9.7 g/day (male: 11.7 g/day; female: 8.2 g/day; p < 0.0001). In multiple linear regression analysis, association between gluten intake and percentage body fat was negative in males (β = - 0.028, p = 0.0020) and positive in females (β = 0.025, p = 0.0028). Furthermore, gluten intake was a negative predictor of total cholesterol (male: β = - 0.031, p = 0.0154; female: β = - 0.050, p < 0.0001), high-density lipoprotein cholesterol (male: β = - 0.052, p < 0.0001; female: β = - 0.068, p < 0.0001), and glomerular filtration rate (sexes combined: β = - 0.031, p < 0.0001) in both sexes. In females only, gluten intake was positively associated with waist circumference (β = 0.041, p < 0.0001), waist-to-height ratio (β = 0.040, p < 0.0001), as well as body mass index (β = 0.043, p < 0.0001), and negatively related to low-density lipoprotein cholesterol (β = - 0.035, p = 0.0011). A positive association between gluten intake and triglycerides was observed in males only (β = 0.043, p = 0.0001).

CONCLUSION

This study indicates that gluten intake is associated with markers of metabolic health. However, all associations are weak and not clinically meaningful. Limiting gluten intake is unlikely to provide metabolic health benefits for a population in total.

Collective behavior of thermophoretic dimeric active colloids in three-dimensional bulk

Colloids driven by phoresis constitute one of the main avenues for the design of synthetic microswimmers. For these swimmers, the specific form of the phoretic and hydrodynamic interactions dramatically influences their dynamics. Explicit solvent simulations allow the investigation of the different behaviors of dimeric Janus active colloids. The phoretic character is modified from thermophilic to thermophobic, and this, together with the relative size of the beads, strongly influences the resulting solvent velocity fields. Hydrodynamic flows can change from puller-type to pusher-type, although the actual flows significantly differ from these standard flows. Such hydrodynamic interactions combined with phoretic interactions between dimers result in several interesting phenomena in three-dimensional bulk conditions. Thermophilic dimeric swimmers are attracted to each other and form large and stable aggregates. Repulsive phoretic interactions among thermophobic dimeric swimmers hinder such clustering and lead, together with long- and short-ranged attractive hydrodynamic interactions, to short-lived, aligned swarming structures.

A deep cascaded segmentation of obstructive sleep apnea-relevant organs from sagittal spine MRI

Purpose

The main purpose of this work was to develop an efficient approach for segmentation of structures that are relevant for diagnosis and treatment of obstructive sleep apnea syndrome (OSAS), namely pharynx, tongue, and soft palate, from mid-sagittal magnetic resonance imaging (MR) data. This framework will be applied to big data acquired within an on-going epidemiological study from a general population.

Methods

A deep cascaded framework for subsequent segmentation of pharynx, tongue, and soft palate is presented. The pharyngeal structure was segmented first, since the airway was clearly visible in the T1-weighted sequence. Thereafter, it was used as an anatomical landmark for tongue location. Finally, the soft palate region was extracted using segmented tongue and pharynx structures and used as input for a deep network. In each segmentation step, a UNet-like architecture was applied.

Results

The result assessment was performed qualitatively by comparing the region boundaries obtained from the expert to the framework results and quantitatively using the standard Dice coefficient metric. Additionally, cross-validation was applied to ensure that the framework performance did not depend on the specific selection of the validation set. The average Dice coefficients on the test set were \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$0.89\pm 0.03$$\end{document}0.89±0.03, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$0.87\pm 0.02$$\end{document}0.87±0.02, and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$0.79\pm 0.08$$\end{document}0.79±0.08 for tongue, pharynx, and soft palate tissues, respectively. The results were similar to other approaches and consistent with expert readings.

Conclusion

Due to high speed and efficiency, the framework will be applied for big epidemiological data with thousands of participants acquired within the Study of Health in Pomerania as well as other epidemiological studies to provide information on the anatomical structures and aspects that constitute important risk factors to the OSAS development.

Societies in balance: Monumentality and feasting activities among southern Naga communities, Northeast India

Among various Naga communities of Northeast India, megalithic building and feasting activities played an integral role in the different and intertwined dimensions of social and political organisation until very recently. During a collaborative fieldwork in 2016, we visited different village communities in the southern areas of Nagaland and recorded local knowledge about the function and social implications of megalithic building activities. The preserved knowledge of the monuments themselves and their embeddedness in complex feasting activities and social structures illustrate the multifaceted character of megalithic building. The case study of Nagaland highlights how the construction of megalithic monuments may fulfil very different functions in societies characterised by institutionalised hierarchies than in those that have a more egalitarian social organisation. The case study of southern Naga communities not only shows the importance of various dimensions and courses of action–such as sharing and cooperation, competitive behaviour, and the influence of economic inequality–, but also the importance of social networks and different layers of kinship. The multifaceted and interwoven character of megalithic building activities in this ethnoarchaeological case study constitutes an expansion for the interpretation of archaeological case studies of monumentality.

Is the lack of smartphone data skewing wealth indices in low-income settings?

BACKGROUND

Smartphones have rapidly become an important marker of wealth in low- and middle-income countries, but international household surveys do not regularly gather data on smartphone ownership and these data are rarely used to calculate wealth indices.

METHODS

We developed a cross-sectional survey module delivered to 3028 households in rural northwest Burkina Faso to measure the effects of this absence. Wealth indices were calculated using both principal components analysis (PCA) and polychoric PCA for a base model using only ownership of any cell phone, and a full model using data on smartphone ownership, the number of cell phones, and the purchase of mobile data. Four outcomes (household expenditure, education level, and prevalence of frailty and diabetes) were used to evaluate changes in the composition of wealth index quintiles using ordinary least squares and logistic regressions and Wald tests.

RESULTS

Households that own smartphones have higher monthly expenditures and own a greater quantity and quality of household assets. Expenditure and education levels are significantly higher at the fifth (richest) socioeconomic status (SES) quintile of full model wealth indices as compared to base models. Similarly, diabetes prevalence is significantly higher at the fifth SES quintile using PCA wealth index full models, but this is not observed for frailty prevalence, which is more prevalent among lower SES households. These effects are not present when using polychoric PCA, suggesting that this method provides additional robustness to missing asset data to measure underlying latent SES by proxy.

CONCLUSIONS

The lack of smartphone data can skew PCA-based wealth index performance in a low-income context for the top of the socioeconomic spectrum. While some PCA variants may be robust to the omission of smartphone ownership, eliciting smartphone ownership data in household surveys is likely to substantially improve the validity and utility of wealth estimates.

Reassessment of the enigmatic ruminant Miocene genus Amphimoschus Bourgeois, 1873 (Mammalia, Artiodactyla, Pecora)

Amphimoschus is an extinct Eurasian ruminant genus, mostly recorded in Europe, without a close living relative and, hence, an unknown systematic position. This genus is known from around 50 localities from the late early to the middle Miocene. Two species were described during 180 years, but since their first description during the late 19^th century and early 20^th century, hardly any detailed taxonomic work has been done on the genus. Over the years, extensive collecting and excavating activities have enriched collections with more and more complete material of this still rare and enigmatic animal. Most interestingly, a number of skull remains have been unearthed and are promising in terms of providing phylogenetic information. In the present paper, we describe cranial material, the bony labyrinth, the dentition through 780 teeth and five skulls from different ontogenetic stages. We cannot find a clear morphometric distinction between the supposedly smaller and older species Amphimoschus artenensis and the supposedly younger and larger species A. ponteleviensis. Accordingly, we have no reason to retain the two species and propose, following the principle of priority (ICZN chapter 6 article 23), that only A. ponteleviensis Bourgeois, 1873 is valid. Our studies on the ontogenetic variation of Amphimoschus does reveal that the sagittal crest may increase in size and a supraorbital ridge may appear with age. Despite the abundant material, the family affiliation is still uncertain.

Accurate identification and quantification of commensal microbiota bound by host immunoglobulins

BACKGROUND

Identifying which taxa are targeted by immunoglobulins can uncover important host-microbe interactions. Immunoglobulin binding of commensal taxa can be assayed by sorting bound bacteria from samples and using amplicon sequencing to determine their taxonomy, a technique most widely applied to study Immunoglobulin A (IgA-Seq). Previous experiments have scored taxon binding in IgA-Seq datasets by comparing abundances in the IgA bound and unbound sorted fractions. However, as these are relative abundances, such scores are influenced by the levels of the other taxa present and represent an abstract combination of these effects. Diversity in the practical approaches of prior studies also warrants benchmarking of the individual stages involved. Here, we provide a detailed description of the design strategy for an optimised IgA-Seq protocol. Combined with a novel scoring method for IgA-Seq datasets that accounts for the aforementioned effects, this platform enables accurate identification and quantification of commensal gut microbiota targeted by host immunoglobulins.

RESULTS

Using germ-free and Rag1^-/- mice as negative controls, and a strain-specific IgA antibody as a positive control, we determine optimal reagents and fluorescence-activated cell sorting (FACS) parameters for IgA-Seq. Using simulated IgA-Seq data, we show that existing IgA-Seq scoring methods are influenced by pre-sort relative abundances. This has consequences for the interpretation of case-control studies where there are inherent differences in microbiota composition between groups. We show that these effects can be addressed using a novel scoring approach based on posterior probabilities. Finally, we demonstrate the utility of both the IgA-Seq protocol and probability-based scores by examining both novel and published data from in vivo disease models.

CONCLUSIONS

We provide a detailed IgA-Seq protocol to accurately isolate IgA-bound taxa from intestinal samples. Using simulated and experimental data, we demonstrate novel probability-based scores that adjust for the compositional nature of relative abundance data to accurately quantify taxon-level IgA binding. All scoring approaches are made available in the IgAScores R package. These methods should improve the generation and interpretation of IgA-Seq datasets and could be applied to study other immunoglobulins and sample types. Video abstract.

The nuclear lamina is a hub for the nuclear function of Jacob

Jacob is a synapto-nuclear messenger protein that couples NMDAR activity to CREB-dependent gene expression. In this study, we investigated the nuclear distribution of Jacob and report a prominent targeting to the nuclear envelope that requires NMDAR activity and nuclear import. Immunogold electron microscopy and proximity ligation assay combined with STED imaging revealed preferential association of Jacob with the inner nuclear membrane where it directly binds to LaminB1, an intermediate filament and core component of the inner nuclear membrane (INM). The association with the INM is transient; it involves a functional nuclear export signal in Jacob and a canonical CRM1-RanGTP-dependent export mechanism that defines the residing time of the protein at the INM. Taken together, the data suggest a stepwise redistribution of Jacob within the nucleus following nuclear import and prior to nuclear export.

DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures

BACKGROUND

The discovery of robust and trans-ethnically replicated DNA methylation markers of metabolic phenotypes, has hinted at a potential role of epigenetic mechanisms in lipid metabolism. However, DNA methylation and the lipid compositions and lipid concentrations of lipoprotein sizes have been scarcely studied. Here, we present an epigenome-wide association study (EWAS) (N = 5414 total) of mostly lipid-related metabolic measures, including a fine profiling of lipoproteins. As lipoproteins are the main players in the different stages of lipid metabolism, examination of epigenetic markers of detailed lipoprotein features might improve the diagnosis, prognosis, and treatment of metabolic disturbances.

RESULTS

We conducted an EWAS of leukocyte DNA methylation and 226 metabolic measurements determined by nuclear magnetic resonance spectroscopy in the population-based KORA F4 study (N = 1662) and replicated the results in the LOLIPOP, NFBC1966, and YFS cohorts (N = 3752). Follow-up analyses in the discovery cohort included investigations into gene transcripts, metabolic-measure ratios for pathway analysis, and disease endpoints. We identified 161 associations (p value < 4.7 × 10-10), covering 16 CpG sites at 11 loci and 57 metabolic measures. Identified metabolic measures were primarily medium and small lipoproteins, and fatty acids. For apolipoprotein B-containing lipoproteins, the associations mainly involved triglyceride composition and concentrations of cholesterol esters, triglycerides, free cholesterol, and phospholipids. All associations for HDL lipoproteins involved triglyceride measures only. Associated metabolic measure ratios, proxies of enzymatic activity, highlight amino acid, glucose, and lipid pathways as being potentially epigenetically implicated. Five CpG sites in four genes were associated with differential expression of transcripts in blood or adipose tissue. CpG sites in ABCG1 and PHGDH showed associations with metabolic measures, gene transcription, and metabolic measure ratios and were additionally linked to obesity or previous myocardial infarction, extending previously reported observations.

CONCLUSION

Our study provides evidence of a link between DNA methylation and the lipid compositions and lipid concentrations of different lipoprotein size subclasses, thus offering in-depth insights into well-known associations of DNA methylation with total serum lipids. The results support detailed profiling of lipid metabolism to improve the molecular understanding of dyslipidemia and related disease mechanisms.

Gamma-delta T cells stimulate IL-6 production by pancreatic stellate cells in pancreatic ductal adenocarcinoma

INTRODUCTION

The immunosuppressive tumor microenvironment promotes progression of pancreatic ductal adenocarcinoma (PDAC). γδ T cells infiltrate the pancreatic tumor stroma and support tumorigenesis through αβ T cell inhibition. Pancreatic stellate cell (PSC) activation contributes to pancreatic fibrosis in PDAC, limiting the delivery and efficacy of therapeutic agents. Whether γδ T cells have direct effects on PSC activation is unknown.

METHODS

In this study, we analyzed tumor tissue from 68 patients with PDAC and determined the frequency and location of γδ T cells using immunohistochemistry and immunofluorescence. PDAC samples from the TCGA database with low and high TRGC2 expression were correlated with the expression of extracellular matrix genes. Further, PSCs were isolated from pancreatic tumor tissue and co-cultured with γδ T cells for 48 hours and cytokine production was measured using a cytometric bead array.

RESULTS

γδ T cells infiltrated the pancreatic tumor stroma and were located in proximity to PSCs. A high infiltration of γδ T cells was associated with increased expression of several extracellular matrix genes in human PDAC. In vitro, γδ T cells stimulated IL-6 production by PDAC-derived PSCs.

CONCLUSION

γδ T cells activated PSCs and modulation of this interaction may enhance the efficacy of combinational therapies in human PDAC.

Quantification of nematic cell polarity in three-dimensional tissues

How epithelial cells coordinate their polarity to form functional tissues is an open question in cell biology. Here, we characterize a unique type of polarity found in liver tissue, nematic cell polarity, which is different from vectorial cell polarity in simple, sheet-like epithelia. We propose a conceptual and algorithmic framework to characterize complex patterns of polarity proteins on the surface of a cell in terms of a multipole expansion. To rigorously quantify previously observed tissue-level patterns of nematic cell polarity (Morales-Navarrete et al., eLife 2019), we introduce the concept of co-orientational order parameters, which generalize the known biaxial order parameters of the theory of liquid crystals. Applying these concepts to three-dimensional reconstructions of single cells from high-resolution imaging data of mouse liver tissue, we show that the axes of nematic cell polarity of hepatocytes exhibit local coordination and are aligned with the biaxially anisotropic sinusoidal network for blood transport. Our study characterizes liver tissue as a biological example of a biaxial liquid crystal. The general methodology developed here could be applied to other tissues and in-vitro organoids.

The roles of ascending sensory signals and top-down central control in the entrainment of a locomotor CPG

Previous authors have proposed two basic hypotheses about the factors that form the basis of locomotor rhythms in walking insects: sensory feedback only or sensory feedback together with rhythmic activity of small neural circuits called central pattern generators (CPGs). Here we focus on the latter. Following this concept, to generate functional outputs, locomotor control must feature both rhythm generation by CPGs at the level of individual joints and coordination of their rhythmic activities, so that all muscles are activated in an appropriate pattern. This work provides an in-depth analysis of an aspect of this coordination process based on an existing network model of stick insect locomotion. Specifically, we consider how the control system for a single joint in the stick insect leg may produce rhythmic output when subjected to ascending sensory signals from other joints in the leg. In this work, the core rhythm generating CPG component of the joint under study is represented by a classical half-center oscillator constrained by a basic set of experimental observations. While the dynamical features of this CPG, including phase transitions by escape and release, are well understood, we provide novel insights about how these transition mechanisms yield entrainment to the incoming sensory signal, how entrainment can be lost under variation of signal strength and period or other perturbations, how entrainment can be restored by modulation of tonic top-down drive levels, and how these factors impact the duty cycle of the motor output.

Monitor-based exoscopic 3D4k neurosurgical interventions: a two-phase prospective-randomized clinical evaluation of a novel hybrid device

Background

Promoting a disruptive innovation in microsurgery, exoscopes promise alleviation of physical strain and improved image quality through digital visualization during microneurosurgical interventions. This study investigates the impact of a novel 3D4k hybrid exoscope (i.e., combining digital and optical visualization) on surgical performance and team workflow in preclinical and clinical neurosurgical settings.

Methods

A pre-clinical workshop setting has been developed to assess usability and implementability through skill-based scenarios (neurosurgical participants n = 12). An intraoperative exploration in head and spine surgery (n = 9) and a randomized clinical study comparing ocular and monitor mode in supratentorial brain tumor cases (n = 20) followed within 12 months. Setup, procedure, case characteristics, surgical performance, and user experience have been analyzed for both ocular group (OG) and monitor group (MG).

Results

Brain tumor cases using frontal, frontoparietal, or temporal approaches have been identified as favorable use cases for introducing exoscopic neurosurgery. Mean monitor distance and angle were 180 cm and 10°. Surgical ergonomics when sitting improved significantly in MG compared with OG (P = .03). Hand-eye coordination required familiarization in MG. Preclinical data showed a positive correlation between lateral camera inclination and impact on hand-eye coordination (r_s = 0.756, P = .01). There was no significant added surgical time in MG. Image quality in current generation 3D4k monitors has been rated inferior to optic visualization yet awaits updates.

Conclusions

The hybrid exoscopic device can be integrated into established neurosurgical workflows. Currently, exoscopic interventions seem most suited for cranial tumor surgery in lesions that are not deep-seated. Ergonomics improve in monitor mode compared to conventional microsurgery.

Electronic supplementary material

The online version of this article (10.1007/s00701-020-04361-2) contains supplementary material, which is available to authorized users.

Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures

We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ -convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels.

Convergence rates of Gaussian ODE filters

A recently introduced class of probabilistic (uncertainty-aware) solvers for ordinary differential equations (ODEs) applies Gaussian (Kalman) filtering to initial value problems. These methods model the true solution x and its first q derivatives a priori as a Gauss-Markov process X , which is then iteratively conditioned on information about x ˙ . This article establishes worst-case local convergence rates of order q + 1 for a wide range of versions of this Gaussian ODE filter, as well as global convergence rates of order q in the case of q = 1 and an integrated Brownian motion prior, and analyses how inaccurate information on x ˙ coming from approximate evaluations of f affects these rates. Moreover, we show that, in the globally convergent case, the posterior credible intervals are well calibrated in the sense that they globally contract at the same rate as the truncation error. We illustrate these theoretical results by numerical experiments which might indicate their generalizability to q ∈ { 2 , 3 , … } .

Microtubule instability driven by longitudinal and lateral strain propagation

Tubulin dimers associate longitudinally and laterally to form metastable microtubules (MTs). MT disassembly is preceded by subtle structural changes in tubulin fueled by GTP hydrolysis. These changes render the MT lattice unstable, but it is unclear exactly how they affect lattice energetics and strain. We performed long-time atomistic simulations to interrogate the impacts of GTP hydrolysis on tubulin lattice conformation, lateral inter-dimer interactions, and (non-)local lateral coordination of dimer motions. The simulations suggest that most of the hydrolysis energy is stored in the lattice in the form of longitudinal strain. While not significantly affecting lateral bond stability, the stored elastic energy results in more strongly confined and correlated dynamics of GDP-tubulins, thereby entropically destabilizing the MT lattice.

The STRIPAK signaling complex regulates dephosphorylation of GUL1, an RNA-binding protein that shuttles on endosomes

The striatin-interacting phosphatase and kinase (STRIPAK) multi-subunit signaling complex is highly conserved within eukaryotes. In fungi, STRIPAK controls multicellular development, morphogenesis, pathogenicity, and cell-cell recognition, while in humans, certain diseases are related to this signaling complex. To date, phosphorylation and dephosphorylation targets of STRIPAK are still widely unknown in microbial as well as animal systems. Here, we provide an extended global proteome and phosphoproteome study using the wild type as well as STRIPAK single and double deletion mutants (Δpro11, Δpro11Δpro22, Δpp2Ac1Δpro22) from the filamentous fungus Sordaria macrospora. Notably, in the deletion mutants, we identified the differential phosphorylation of 129 proteins, of which 70 phosphorylation sites were previously unknown. Included in the list of STRIPAK targets are eight proteins with RNA recognition motifs (RRMs) including GUL1. Knockout mutants and complemented transformants clearly show that GUL1 affects hyphal growth and sexual development. To assess the role of GUL1 phosphorylation on fungal development, we constructed phospho-mimetic and -deficient mutants of GUL1 residues. While S180 was dephosphorylated in a STRIPAK-dependent manner, S216, and S1343 served as non-regulated phosphorylation sites. While the S1343 mutants were indistinguishable from wild type, phospho-deficiency of S180 and S216 resulted in a drastic reduction in hyphal growth, and phospho-deficiency of S216 also affects sexual fertility. These results thus suggest that differential phosphorylation of GUL1 regulates developmental processes such as fruiting body maturation and hyphal morphogenesis. Moreover, genetic interaction studies provide strong evidence that GUL1 is not an integral subunit of STRIPAK. Finally, fluorescence microscopy revealed that GUL1 co-localizes with endosomal marker proteins and shuttles on endosomes. Here, we provide a new mechanistic model that explains how STRIPAK-dependent and -independent phosphorylation of GUL1 regulates sexual development and asexual growth.

Fingolimod as a Treatment in Neurologic Disorders Beyond Multiple Sclerosis

Fingolimod is an approved treatment for relapsing-remitting multiple sclerosis (MS), and its properties in different pathways have raised interest in therapy research for other neurodegenerative diseases. Fingolimod is an agonist of sphingosine-1-phosphate (S1P) receptors. Its main pharmacologic effect is immunomodulation by lymphocyte homing, thereby reducing the numbers of T and B cells in circulation. Because of the ubiquitous expression of S1P receptors, other effects have also been described. Here, we review preclinical experiments evaluating the effects of treatment with fingolimod in neurodegenerative diseases other than MS, such as Alzheimer's disease or epilepsy. Fingolimod has shown neuroprotective effects in different animal models of neurodegenerative diseases, summarized here, correlating with increased brain-derived neurotrophic factor and improved disease phenotype (cognition and/or motor abilities). As expected, treatment also induced reductions in different neuroinflammatory markers because of not only inhibition of lymphocytes but also direct effects on astrocytes and microglia. Furthermore, fingolimod treatment exhibited additional effects for specific neurodegenerative disorders, such as reduction of amyloid-β production, and antiepileptogenic properties. The neuroprotective effects exerted by fingolimod in these preclinical studies are reviewed and support the translation of fingolimod into clinical trials as treatment in neurodegenerative diseases beyond neuroinflammatory conditions (MS).

Dendritic integration in olfactory bulb granule cells upon simultaneous multispine activation: Low thresholds for nonlocal spiking activity

The inhibitory axonless olfactory bulb granule cells form reciprocal dendrodendritic synapses with mitral and tufted cells via large spines, mediating recurrent and lateral inhibition. As a case in point for dendritic transmitter release, rat granule cell dendrites are highly excitable, featuring local Na+ spine spikes and global Ca2+- and Na+-spikes. To investigate the transition from local to global signaling, we performed holographic, simultaneous 2-photon uncaging of glutamate at up to 12 granule cell spines, along with whole-cell recording and dendritic 2-photon Ca2+ imaging in acute juvenile rat brain slices. Coactivation of less than 10 reciprocal spines was sufficient to generate diverse regenerative signals that included regional dendritic Ca2+-spikes and dendritic Na+-spikes (D-spikes). Global Na+-spikes could be triggered in one third of granule cells. Individual spines and dendritic segments sensed the respective signal transitions as increments in Ca2+ entry. Dendritic integration as monitored by the somatic membrane potential was mostly linear until a threshold number of spines was activated, at which often D-spikes along with supralinear summation set in. As to the mechanisms supporting active integration, NMDA receptors (NMDARs) strongly contributed to all aspects of supralinearity, followed by dendritic voltage-gated Na+- and Ca2+-channels, whereas local Na+ spine spikes, as well as morphological variables, barely mattered. Because of the low numbers of coactive spines required to trigger dendritic Ca2+ signals and thus possibly lateral release of GABA onto mitral and tufted cells, we predict that thresholds for granule cell-mediated bulbar lateral inhibition are low. Moreover, D-spikes could provide a plausible substrate for granule cell-mediated gamma oscillations.

Bassoon inhibits proteasome activity via interaction with PSMB4

Abstract

Proteasomes are protein complexes that mediate controlled degradation of damaged or unneeded cellular proteins. In neurons, proteasome regulates synaptic function and its dysfunction has been linked to neurodegeneration and neuronal cell death. However, endogenous mechanisms controlling proteasomal activity are insufficiently understood. Here, we describe a novel interaction between presynaptic scaffolding protein bassoon and PSMB4, a β subunit of the 20S core proteasome. Expression of bassoon fragments that interact with PSMB4 in cell lines or in primary neurons attenuates all endopeptidase activities of cellular proteasome and induces accumulation of several classes of ubiquitinated and non-ubiquitinated substrates of the proteasome. Importantly, these effects are distinct from the previously reported impact of bassoon on ubiquitination and autophagy and might rely on a steric interference with the assembly of the 20S proteasome core. In line with a negative regulatory role of bassoon on endogenous proteasome we found increased proteasomal activity in the synaptic fractions prepared from brains of bassoon knock-out mice. Finally, increased activity of proteasome and lower expression levels of synaptic substrates of proteasome could be largely normalized upon expression of PSMB4-interacting fragments of bassoon in neurons derived from bassoon deficient mice. Collectively, we propose that bassoon interacts directly with proteasome to control its activity at presynapse and thereby it contributes to a compartment-specific regulation of neuronal protein homeostasis. These findings provide a mechanistic explanation for the recently described link of bassoon to human diseases associated with pathological protein aggregation.

Graphic Abstract

Presynaptic cytomatrix protein bassoon (Bsn) interacts with PSMB4, the β7 subunit of 20S core proteasome, via three independent interaction interfaces. Bsn inhibits proteasomal proteolytic activity and degradation of different classes of proteasomal substrates presumably due to steric interference with the assembly of 20S core of proteasome. Upon Bsn deletion in neurons, presynaptic substrates of the proteasome are depleted, which can be reversed upon expression of PSMB4-interacting interfaces of Bsn. Taken together, bsn controls the degree of proteasome degradation within the presynaptic compartment and thus, contributes to the regulation of synaptic proteome

Electronic supplementary material

The online version of this article (10.1007/s00018-020-03590-z) contains supplementary material, which is available to authorized users.

OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling

In this study, we propose a new open-source simulation platform that comprises computer-aided design and computer-aided engineering tools for highly automated evaluation of electric field distribution and neural activation during Deep Brain Stimulation (DBS). It will be shown how a Volume Conductor Model (VCM) is constructed and examined using Python-controlled algorithms for generation, discretization and adaptive mesh refinement of the computational domain, as well as for incorporation of heterogeneous and anisotropic properties of the tissue and allocation of neuron models. The utilization of the platform is facilitated by a collection of predefined input setups and quick visualization routines. The accuracy of a VCM, created and optimized by the platform, was estimated by comparison with a commercial software. The results demonstrate no significant deviation between the models in the electric potential distribution. A qualitative estimation of different physics for the VCM shows an agreement with previous computational studies. The proposed computational platform is suitable for an accurate estimation of electric fields during DBS in scientific modeling studies. In future, we intend to acquire SDA and EMA approval. Successful incorporation of open-source software, controlled by in-house developed algorithms, provides a highly automated solution. The platform allows for optimization and uncertainty quantification (UQ) studies, while employment of the open-source software facilitates accessibility and reproducibility of simulations.

Directed acyclic graphs and causal thinking in clinical risk prediction modeling

BACKGROUND

In epidemiology, causal inference and prediction modeling methodologies have been historically distinct. Directed Acyclic Graphs (DAGs) are used to model a priori causal assumptions and inform variable selection strategies for causal questions. Although tools originally designed for prediction are finding applications in causal inference, the counterpart has remained largely unexplored. The aim of this theoretical and simulation-based study is to assess the potential benefit of using DAGs in clinical risk prediction modeling.

METHODS

We explore how incorporating knowledge about the underlying causal structure can provide insights about the transportability of diagnostic clinical risk prediction models to different settings. We further probe whether causal knowledge can be used to improve predictor selection in clinical risk prediction models.

RESULTS

A single-predictor model in the causal direction is likely to have better transportability than one in the anticausal direction in some scenarios. We empirically show that the Markov Blanket, the set of variables including the parents, children, and parents of the children of the outcome node in a DAG, is the optimal set of predictors for that outcome.

CONCLUSIONS

Our findings provide a theoretical basis for the intuition that a diagnostic clinical risk prediction model including causes as predictors is likely to be more transportable. Furthermore, using DAGs to identify Markov Blanket variables may be a useful, efficient strategy to select predictors in clinical risk prediction models if strong knowledge of the underlying causal structure exists or can be learned.

A guide for studying among-individual behavioral variation from movement data in the wild

Animal tracking and biologging devices record large amounts of data on individual movement behaviors in natural environments. In these data, movement ecologists often view unexplained variation around the mean as "noise" when studying patterns at the population level. In the field of behavioral ecology, however, focus has shifted from population means to the biological underpinnings of variation around means. Specifically, behavioral ecologists use repeated measures of individual behavior to partition behavioral variability into intrinsic among-individual variation and reversible behavioral plasticity and to quantify: a) individual variation in behavioral types (i.e. different average behavioral expression), b) individual variation in behavioral plasticity (i.e. different responsiveness of individuals to environmental gradients), c) individual variation in behavioral predictability (i.e. different residual within-individual variability of behavior around the mean), and d) correlations among these components and correlations in suites of behaviors, called 'behavioral syndromes'. We here suggest that partitioning behavioral variability in animal movements will further the integration of movement ecology with other fields of behavioral ecology. We provide a literature review illustrating that individual differences in movement behaviors are insightful for wildlife and conservation studies and give recommendations regarding the data required for addressing such questions. In the accompanying R tutorial we provide a guide to the statistical approaches quantifying the different aspects of among-individual variation. We use movement data from 35 African elephants and show that elephants differ in a) their average behavior for three common movement behaviors, b) the rate at which they adjusted movement over a temporal gradient, and c) their behavioral predictability (ranging from more to less predictable individuals). Finally, two of the three movement behaviors were correlated into a behavioral syndrome (d), with farther moving individuals having shorter mean residence times. Though not explicitly tested here, individual differences in movement and predictability can affect an individual's risk to be hunted or poached and could therefore open new avenues for conservation biologists to assess population viability. We hope that this review, tutorial, and worked example will encourage movement ecologists to examine the biology of individual variation in animal movements hidden behind the population mean.

Ubiquitin activation is essential for schizont maturation in Plasmodium falciparum blood-stage development

Ubiquitylation is a common post translational modification of eukaryotic proteins and in the human malaria parasite, Plasmodium falciparum (Pf) overall ubiquitylation increases in the transition from intracellular schizont to extracellular merozoite stages in the asexual blood stage cycle. Here, we identify specific ubiquitylation sites of protein substrates in three intraerythrocytic parasite stages and extracellular merozoites; a total of 1464 sites in 546 proteins were identified (data available via ProteomeXchange with identifier PXD014998). 469 ubiquitylated proteins were identified in merozoites compared with only 160 in the preceding intracellular schizont stage, suggesting a large increase in protein ubiquitylation associated with merozoite maturation. Following merozoite invasion of erythrocytes, few ubiquitylated proteins were detected in the first intracellular ring stage but as parasites matured through trophozoite to schizont stages the apparent extent of ubiquitylation increased. We identified commonly used ubiquitylation motifs and groups of ubiquitylated proteins in specific areas of cellular function, for example merozoite pellicle proteins involved in erythrocyte invasion, exported proteins, and histones. To investigate the importance of ubiquitylation we screened ubiquitin pathway inhibitors in a parasite growth assay and identified the ubiquitin activating enzyme (UBA1 or E1) inhibitor MLN7243 (TAK-243) to be particularly effective. This small molecule was shown to be a potent inhibitor of recombinant PfUBA1, and a structural homology model of MLN7243 bound to the parasite enzyme highlights avenues for the development of P. falciparum specific inhibitors. We created a genetically modified parasite with a rapamycin-inducible functional deletion of uba1; addition of either MLN7243 or rapamycin to the recombinant parasite line resulted in the same phenotype, with parasite development blocked at the schizont stage. Nuclear division and formation of intracellular structures was interrupted. These results indicate that the intracellular target of MLN7243 is UBA1, and this activity is essential for the final differentiation of schizonts to merozoites.

Digital versus analogue record systems for mass casualty incidents at sea-Results from an exploratory study

Objective

Mis-triage may have serious consequences for patients in mass casualty incidents (MCI) at sea. The purpose of this study was to assess outcome, reliability and validity of an analogue and a digital recording system for triage of a MCI at sea.

Methods

The study based on a triage exercise conducted with a cross-over-design. Forty-eight volunteers were presented a fictional MCI with 50 cases. The volunteers were randomly assigned to start with the analogue (Group A, starting with the analogue followed by the digital system) or digital system (Group B, starting with the digital followed by the analogue system). Triage score distribution and agreement between the triage methods and a predefined standard were reported. Reliability was analysed using Cronbach’s Alpha and Cohen’s Kappa. Validity was measured through sensitivity, specificity and predictive value. Treatment, period and carry-over-effects were analysed using a linear mixed-effects model.

Results

The number of patients triaged (total: n = 3545) with the analogue system (n = 1914; 79.75%) was significantly higher (p = 0.001) than with the digital system (n = 1631; 67.96%). A trend towards a higher percentage of correct triages with the digital system was observed (p = 0.282). Ratio of under-triage was significantly smaller with the digital system (p = 0.001). Validity measured with Cronbach’s Alpha and Cohen’s Kappa was higher with the digital system. So was sensitivity (category; green: 80.67%, yellow: 73.24%, red: 83.54%; analogue: green: 93.28%, yellow: 82.36%, red: 94.04%) and specificity of the digital system (green: 78.07%, yellow: 63.75%, red: 66.25%; analogue: green: 85.50%, yellow: 79.88%, red: 91.50%). Comparing the predictive values and accuracy, the digital system showed higher scores than the analogue system. No significant patterns of carry-over-effects were observed.

Conclusions

Significant differences were found for the number of triages comparing the analogue and digital recording system. The digital system has a slightly higher reliability and validity than the analogue triage system.

Morphological and physiological characterization of filamentous Lentzea aerocolonigenes: Comparison of biopellets by microscopy and flow cytometry

Cell morphology of filamentous microorganisms is highly interesting during cultivations as it is often linked to productivity and can be influenced by process conditions. Hence, the characterization of cell morphology is of major importance to improve the understanding of industrial processes with filamentous microorganisms. For this purpose, reliable and robust methods are necessary. In this study, pellet morphology and physiology of the rebeccamycin producing filamentous actinomycete Lentzea aerocolonigenes were investigated by microscopy and flow cytometry. Both methods were compared regarding their applicability. To achieve different morphologies, a cultivation with glass bead addition (Ø = 969 μm, 100 g L-1) was compared to an unsupplemented cultivation. This led to two different macro-morphologies. Furthermore, glass bead addition increased rebeccamycin titers after 10 days of cultivation (95 mg L-1 with glass beads, 38 mg L-1 without glass beads). Macro-morphology and viability were investigated through microscopy and flow cytometry. For viability assessment fluorescent staining was used additionally. Smaller, more regular pellets were found for glass bead addition. Pellet diameters resulting from microscopy followed by image analysis were 172 μm without and 106 μm with glass beads, diameters from flow cytometry were 170 and 100 μm, respectively. These results show excellent agreement of both methods, each considering several thousand pellets. Furthermore, the pellet viability obtained from both methods suggested an enhanced metabolic activity in glass bead treated pellets during the exponential production phase. However, total viability values differ for flow cytometry (0.32 without and 0.41 with glass beads) and confocal laser scanning microscopy of single stained pellet slices (life ratio in production phase of 0.10 without and 0.22 with glass beads), which is probably caused by the different numbers of investigated pellets. In confocal laser scanning microscopy only one pellet per sample could be investigated while flow cytometry considered at least 50 pellets per sample, resulting in an increased statistical reliability.

NCX1 represents an ionic Na+ sensing mechanism in macrophages

Inflammation and infection can trigger local tissue Na+ accumulation. This Na+-rich environment boosts proinflammatory activation of monocyte/macrophage-like cells (MΦs) and their antimicrobial activity. Enhanced Na+-driven MΦ function requires the osmoprotective transcription factor nuclear factor of activated T cells 5 (NFAT5), which augments nitric oxide (NO) production and contributes to increased autophagy. However, the mechanism of Na+ sensing in MΦs remained unclear. High extracellular Na+ levels (high salt [HS]) trigger a substantial Na+ influx and Ca2+ loss. Here, we show that the Na+/Ca2+ exchanger 1 (NCX1, also known as solute carrier family 8 member A1 [SLC8A1]) plays a critical role in HS-triggered Na+ influx, concomitant Ca2+ efflux, and subsequent augmented NFAT5 accumulation. Moreover, interfering with NCX1 activity impairs HS-boosted inflammatory signaling, infection-triggered autolysosome formation, and subsequent antibacterial activity. Taken together, this demonstrates that NCX1 is able to sense Na+ and is required for amplifying inflammatory and antimicrobial MΦ responses upon HS exposure. Manipulating NCX1 offers a new strategy to regulate MΦ function.