Thoracic impedance pneumography in propofol-sedated patients undergoing percutaneous endoscopic gastrostomy (PEG) placement in gastrointestinal endoscopy: A prospective, randomized trial

STUDY OBJECTIVE

To assess the efficacy of an ECG-based method called thoracic impedance pneumography to reduce hypoxic events in endoscopy.

DESIGN

This was a single center, 1:1 randomized controlled trial.

SETTING

The trial was conducted during the placement of percutaneous endoscopic gastrostomy (PEG).

PATIENTS

173 patients who underwent PEG placement were enrolled in the present trial. Indication was oncological in most patients (89%). 58% of patients were ASA class II and 42% of patients ASA class III.

INTERVENTIONS

Patients were randomized in the standard monitoring group (SM) with pulse oximetry and automatic blood pressure measurement or in the intervention group with additional thoracic impedance pneumography (TIM). Sedation was performed with propofol by gastroenterologists or trained nurses.

MEASUREMENTS

Hypoxic episodes defined as SpO2 < 90% for >15 s were the primary endpoint. Secondary endpoints were minimal SpO2, apnea >10s/>30s and incurred costs.

MAIN RESULTS

Additional use of thoracic impedance pneumography reduced hypoxic episodes (TIM: 31% vs SM: 49%; p = 0.016; OR 0.47; NNT 5.6) and elevated minimal SpO2 per procedure (TIM: 90.0% ± 8.9; SM: 84.0% ± 17.6; p = 0.007) significantly. Apnea events >10s and > 30s were significantly more often detected in TIM (43%; 7%) compared to SM (1%; 0%; p < 0.001; p = 0.014) resulting in a time advantage of 17 s before the occurrence of hypoxic events. As a result, adjustments of oxygen flow were significantly more often necessary in SM than in TIM (p = 0.034) and assisted ventilation was less often needed in TIM (2%) compared with SM (9%; p = 0.053). Calculated costs for the additional use of thoracic impedance pneumography were 0.13$ (0.12 €/0.11 £) per procedure.

CONCLUSIONS

Additional thoracic impedance pneumography reduced the quantity and extent of hypoxic events with less need of assisted ventilation. Supplemental costs per procedure were negligible.

KEY WORDS

thoracic impedance pneumography, capnography, sedation, monitoring, gastrointestinal endoscopy, percutaneous endoscopic gastrostomy.

Frequency and spatial distribution of knock-down resistance (kdr) to pyrethroids in multiple oilseed rape pest species of the genus Ceutorhynchus

BACKGROUND

The protection of European oilseed rape (OSR) from damaging insects relies on pyrethroid insecticides, but the development of resistance in key coleopteran pests such as the pollen beetle (Brassicogethes aeneus) and the cabbage stem flea beetle (Psylliodes chrysocephala) has resulted in reduced effectiveness of these insecticides. The sodium channel gene mutation L1014F knock-down resistance (kdr) is a contributing factor in resistance to pyrethroids in B. aeneus and P. chrysocephala, but little is known about the status of resistance in weevils of the genus Ceutorhynchus (Coleoptera: Curculonidae). Therefore, the present study investigated pyrethroid susceptibility and the presence of the kdr mutation in four Ceutorhynchus species.

RESULTS

The kdr mutation in either its heterozygous or homozygous form was found in all investigated Ceutorhynchus species (C. picitarsis, C. pallidactylus, C. napi and C. obstrictus). Samples where pyrethroids in bioassays still provided control at 100% field rate or below contained kdr at frequencies of ≤12.5%, whilst bioassays using 100% field rate that did not control Ceutorhynchus populations contained homozygous resistant individuals at frequencies of greater than 55%. Field sampling demonstrated that kdr frequencies in populations of C. picitarsis and C. obstrictus collected from across France and Germany ranged from 0 to 100%.

CONCLUSION

The present study demonstrated the potential of all four Ceutorhynchus species tested to develop pyrethroid resistance via the L1014F (kdr) mutation. Although kdr frequency varies among species and geographic locations, the risk of loss of pyrethroid insecticide effectiveness is high. Integration of other control tools for resistance management is therefore needed. © 2023 Society of Chemical Industry.

Screening H3 Histone Acetylation in a Wild Bird, the House Sparrow (Passer Domesticus)

Epigenetic mechanisms are increasingly understood to have major impacts across ecology. However, one molecular epigenetic mechanism, DNA methylation, currently dominates the literature. A second mechanism, histone modification, is likely important to ecologically relevant phenotypes and thus warrants investigation, especially because molecular interplay between methylation and histone acetylation can strongly affect gene expression. There are a limited number of histone acetylation studies on non-model organisms, yet those that exist show that it can impact gene expression and phenotypic plasticity. Wild birds provide an excellent system to investigate histone acetylation, as free-living individuals must rapidly adjust to environmental change. Here, we screen histone acetylation in the house sparrow (Passer domesticus); we studied this species because DNA methylation was important in the spread of this bird globally. This species has one of the broadest geographic distributions in the world, and part of this success is related to the way that it uses methylation to regulate its gene expression. Here, we verify that a commercially available assay that was developed for mammals can be used in house sparrows. We detected high variance in histone acetylation among individuals in both liver and spleen tissue. Further, house sparrows with higher epigenetic potential in the Toll Like Receptor-4 (TLR-4) promoter (i.e., CpG content) had higher histone acetylation in liver. Also, there was a negative correlation between histone acetylation in spleen and TLR-4 expression. In addition to validating a method for measuring histone acetylation in wild songbirds, this study also shows that histone acetylation is related to epigenetic potential and gene expression, adding a new study option for ecological epigenetics.

A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits

BACKGROUND

Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments.

RESULTS

Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene.

CONCLUSIONS

In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.

What MRI Sequences are Necessary for Automated Neural Network-Based Metastasis Segmentation - An Ablation Study

PURPOSE/OBJECTIVE(S)

Brain metastasis (BM) delineation is a time-consuming process in both daily clinical practice and research. Automated BM segmentation algorithms can be used to assist in this task. Most approaches to brain tumor segmentation, such as algorithms trained on the BraTS challenge, use four magnetic resonance imaging (MRI) sequences as input, making them susceptible to missing or corrupted sequences and increase the number of sequences necessary for MRI RT planning. The goal of this project is to compare neural networks with different combinations of input sequences for the segmentation of the contrast-enhancing metastasis and the surrounding FLAIR hyperintense edema. All models were tested in a multicenter international external test cohort. This allows us to determine which MRI sequences are needed for effective automated segmentations.

MATERIALS/METHODS

In total, we had T1-weighted sequences without (T1) and with contrast enhancement (T1-CE), T2-weighted sequences (T2), and T2 fluid-attenuated inversion recovery (FLAIR) sequences from 339 patients with at least one brain metastasis from seven centers available. Preprocessing yielded co-registered, skull-stripped sequences with an isotropic resolution of 1 millimeter. The contrast-enhancing metastasis as well as the surrounding FLAIR hyperintense edema were manually segmented to create reference labels. A baseline 3D U-Net with all four sequences as well as six additional U-Nets with different clinically plausible combinations (T1-CE; T1; FLAIR; T1-CE+FLAIR; T1-CE+T1+FLAIR; T1-CE+T1) of input sequences were trained on a cohort of 239 patients from two centers and subsequently tested on an external cohort of 100 patients from the remaining five centers.

RESULTS

All models that included T1-CE in their selected sequences showed similar performance for metastasis segmentation with a median Dice similarity coefficient (DSC) of 0.93-0.96. T1-CE alone likewise achieved a performance of 0.96 (IQR 0.93-0.97). The model trained with only FLAIR performed worse (DSC = 0.73, IQR 0.54-0.84). For edema segmentation, models that included both T1-CE and FLAIR performed best (median DSC = 0.93), while the remaining four models without simultaneous inclusion of these two sequences (T1-CE; T1; FLAIR; T1-CE+T1) reached a median DSC of 0.81-0.89.

CONCLUSION

Automatic segmentation of brain metastases with less than four input sequences is feasible with minimal or no loss of quality. A T1-CE-only protocol suffices for metastasis segmentation. In contrast, for edema segmentation, the combination of T1-CE and FLAIR seems to be important. Missing either T1-CE or FLAIR decreases performance. These findings may improve future imaging routines by omitting unnecessary sequences, thus speeding up procedures in daily clinical practice while allowing for optimal neural network-based target definitions.

Hypofractionated Stereotactic Radiotherapy vs. Single Fraction Stereotactic Radiosurgery to the Resection Cavity of Brain Metastases after Surgical Resection (SATURNUS trial): A Prospective, Randomized Phase III Trial

PURPOSE/OBJECTIVE(S)

The brain is a common site for metastases. Resection of large or symptomatic metastases is followed by stereotactic radiotherapy to prevent local recurrence. The optimal fractionation scheme is subject of ongoing research. Supported by emerging retrospective data, we hypothesize that hypofractionated stereotactic radiotherapy (HFSRT) is superior to single-fraction stereotactic radiosurgery (SRS) in terms of local control (LC). We designed the SATURNUS trial to prospectively demonstrate the superiority of HFSRT over SRS after resection of brain metastases in terms of LC.

MATERIALS/METHODS

The SATURNUS trial is a prospective, randomized phase III trial, currently recruiting patients at a single institution. Patients are 1:1 allocated to HFSRT or SRS using permuted block randomization. Affiliation to the treatment arm is solely blinded to the neuroradiologist assessing therapy response. HFSRT will be delivered with 6 - 7 x 5 Gy and SRS with 1 x 12-20 Gy, prescribed to the surrounding isodose, depending on cavity size and proximity to structures at risk. For SRS, doses do not exceed the maximum doses according to RTOG 90-05. Case number calculation was based on own institutional data on HFSRT (mean LC rate of 88% at 12 months) and data from large phase III trials on SRS (pooled mean LC rate of 66% at 12 months). Using a Chi-squared test of equal proportions (odds ratio = 1), setting test significance level (α) to 0.05, and allocating an equal number of patients to both treatment arms, 114 patients are needed to detect the superiority of HFSRT in terms of LC at 12 months (primary endpoint) with a power of at least 80%. Estimating a dropout rate of 10%, the case number was set to 126. The trial was registered with clinicaltrials.gov (NCT05160818). The first patient was enrolled in May 2021 and recruitment is ongoing. Patients with up to three resected brain metastases are considered for study participation. Further eligibility criteria are histologically confirmed solid tumor disease, resection cavity diameter ≤ 4 cm, consent to perform adjuvant radiotherapy by an interdisciplinary tumor board, completed wound healing, resection within the last six weeks at the time of study inclusion, age ≥ 18 years, KPS ≥ 60%, adequate contraceptive measures for fertile women / men and written informed consent. Patients are followed up clinically and with MRI at 6 weeks and 3, 6, 9 and 12 months after treatment. LC is assessed according to RANO-BM. Toxicity (CTCAE v4.03) is assessed as a secondary endpoint. The rather broad dose corridors allowed within the trial do justice to clinical reality, however, may represent a limitation of the trial. They are therefore addressed with a predefined subgroup analysis, as will be cavity size, among others. Participation of further study centers is desired. To the best of our knowledge, the SATURNUS trial is the only randomized phase III trial adequately powered to detect the superiority of HFSRT over SRS with regard to LC for resected brain metastases.

RESULTS

To be determined.

CONCLUSION

To be determined.

Reconstruction of the Corticospinal Tract in Patients with Motor-Eloquent High-Grade Gliomas Using Multilevel Fiber Tractography Combined with Functional Motor Cortex Mapping

BACKGROUND AND PURPOSE

Tractography of the corticospinal tract is paramount to presurgical planning and guidance of intraoperative resection in patients with motor-eloquent gliomas. It is well-known that DTI-based tractography as the most frequently used technique has relevant shortcomings, particularly for resolving complex fiber architecture. The purpose of this study was to evaluate multilevel fiber tractography combined with functional motor cortex mapping in comparison with conventional deterministic tractography algorithms.

MATERIALS AND METHODS

Thirty-one patients (mean age, 61.5 [SD, 12.2] years) with motor-eloquent high-grade gliomas underwent MR imaging with DWI (TR/TE = 5000/78 ms, voxel size = 2 × 2 × 2 mm3, 1 volume at b = 0 s/mm2, 32 volumes at b = 1000 s/mm2). DTI, constrained spherical deconvolution, and multilevel fiber tractography-based reconstruction of the corticospinal tract within the tumor-affected hemispheres were performed. The functional motor cortex was enclosed by navigated transcranial magnetic stimulation motor mapping before tumor resection and used for seeding. A range of angular deviation and fractional anisotropy thresholds (for DTI) was tested.

RESULTS

For all investigated thresholds, multilevel fiber tractography achieved the highest mean coverage of the motor maps (eg, angular threshold = 60°; multilevel/constrained spherical deconvolution/DTI, 25% anisotropy threshold = 71.8%, 22.6%, and 11.7%) and the most extensive corticospinal tract reconstructions (eg, angular threshold = 60°; multilevel/constrained spherical deconvolution/DTI, 25% anisotropy threshold = 26,485 mm3, 6308 mm3, and 4270 mm3).

CONCLUSIONS

Multilevel fiber tractography may improve the coverage of the motor cortex by corticospinal tract fibers compared with conventional deterministic algorithms. Thus, it could provide a more detailed and complete visualization of corticospinal tract architecture, particularly by visualizing fiber trajectories with acute angles that might be of high relevance in patients with gliomas and distorted anatomy.

Methylation subgroup and molecular heterogeneity is a hallmark of glioblastoma: implications for biopsy targeting, classification and therapy

Background

Patients and methods

Results

Conclusions

•

Glioblastoma exhibits significant heterogeneity, from epigenome-wide methylation phenotypes to single molecular targets.

•

Phylogeny showed CDKN2A/B loss and gain of EGFR, PDGFRA, and CDK4 early in tumor development.

•

Intratumoral heterogeneity is of utmost importance for molecular classification as well as for defining therapeutic targets.

•

Assessing single biopsies underestimates the true molecular diversity in a tumor.

Epidemiology and reporting of osteoporotic vertebral fractures in patients with long-term hospital records based on routine clinical CT imaging

Osteoporotic vertebral fractures signify an increased risk of future fractures and mortality and can manifest the diagnosis of osteoporosis. We investigated the prevalence of vertebral fractures in routine CT of patients with long-term hospital records. Three out of ten patients showed osteoporotic vertebral fractures (VFs) corresponding to the highest rates reported in European population-based studies.

INTRODUCTION

VFs are a common manifestation of osteoporosis, which influences future fracture risk. Their epidemiology has been investigated in population-based studies. However, few studies report the prevalence of osteoporotic VF in patients seen in clinical routine and include all common fracture levels of the thoracolumbar spine. The purpose of this study was to investigate the prevalence of osteoporotic VF in patients with CT scans and long-term hospital records and identify clinical factors associated with prevalent VFs.

METHODS

All patients aged 45 years and older with a CT scan and prior hospital record of at least 5 years that were seen in the study period between September 2008 and May 2017 were reviewed. Imaging requirements were a CT scan with sagittal reformations including at least T6-L4. Patients with multiple myeloma were excluded. Fracture reading was performed using the Genant semi-quantitative method. Medical notes were reviewed for established diagnoses of osteoporosis and clinical information. Clinical factors (e.g. drug intake, chemotherapy, and mobility level) associated with prevalent VF were identified in logistic regression.

RESULTS

The study population consisted of 718 patients (228 women and 490 men; mean age 69.3 ± 10.1 years) with mainly cancer staging and angiography CT imaging. The overall prevalence of VFs was 30.5%, with non-significantly more men showing a fracture (32.5%) compared to women (26.3%; p > 0.05). Intake of metamizole for ≥ 3 months was significantly associated with a prevalent VF. Medical records did not include information about bone health in 90% of all patients. CT reports did mention a VF in only 24.7% of patients with a prevalent VF on CT review.

CONCLUSION

Approximately 30% of elderly patients with CT imaging and long-term hospital records showed VFs. Only one-quarter of these patients had VFs mentioned in CT reports. Osteoporosis management could be improved by consequent reporting of VFs in CT, opportunistic bone density measurements, and early involvement of fracture liaison services.

Differential Effects of Fingolimod and Natalizumab on Magnetic Resonance Imaging Measures in Relapsing-Remitting Multiple Sclerosis

Fingolimod and natalizumab are approved disease-modifying drugs in relapsing-remitting multiple sclerosis (RRMS). The two drugs have different modes of action and may therefore influence different aspects of MS-related tissue damage. In this retrospective cohort study, we longitudinally compared patients treated with fingolimod and patients treated with natalizumab by measures based on structural magnetic resonance imaging (MRI). We included patients with RRMS given that two standardized MRI scans under the same drug were available with an interval of at least 6 months both from therapy start to baseline scan and from baseline scan to follow-up scan. After matching for age, baseline and follow-up scans from 93 patients (fingolimod, 48; natalizumab, 45) were investigated. Mean follow-up time was 1.9 years. We determined the number of new white matter lesions as well as thalamic, cortical, and whole-brain atrophy. After scaling for time of the interscan interval, measures were analyzed by group comparisons and, to account for demographic and clinical characteristics, by multiple regression models and a binary logistic regression model. Compared to natalizumab, fingolimod treatment went along with more new white matter lesions (median [interquartile range, IQR] 0.0 [0.0; 0.7] vs. 0.0 [0.0; 0.0] /year; p < 0.01) whereas whole-brain atrophy was lower (median [IQR] 0.2 [0.0; 0.5] vs. 0.5 [0.2; 1.0] %/year; p = 0.01). These significant differences were confirmed by multiple regression models and the binary logistic regression model. In conclusion, our observation is compatible with stronger neuroprotective properties of fingolimod compared to natalizumab.

Electron Transfer Coupled to Conformational Dynamics in Cell Respiration

Cellular respiration is a fundamental process required for energy production in many organisms. The terminal electron transfer complex in mitochondrial and many bacterial respiratory chains is cytochrome c oxidase (CcO). This converts the energy released in the cytochrome c/oxygen redox reaction into a transmembrane proton electrochemical gradient that is used subsequently to power ATP synthesis. Despite detailed knowledge of electron and proton transfer paths, a central question remains as to whether the coupling between electron and proton transfer in mammalian mitochondrial forms of CcO is mechanistically equivalent to its bacterial counterparts. Here, we focus on the conserved span between H376 and G384 of transmembrane helix (TMH) X of subunit I. This conformationally-dynamic section has been suggested to link the redox activity with the putative H pathway of proton transfer in mammalian CcO. The two helix X mutants, Val380Met (V380M) and Gly384Asp (G384D), generated in the genetically-tractable yeast CcO, resulted in a respiratory-deficient phenotype caused by the inhibition of intra-protein electron transfer and CcO turnover. Molecular aspects of these variants were studied by long timescale atomistic molecular dynamics simulations performed on wild-type and mutant bovine and yeast CcOs. We identified redox- and mutation-state dependent conformational changes in this span of TMH X of bovine and yeast CcOs which strongly suggests that this dynamic module plays a key role in optimizing intra-protein electron transfers.

Outcomes after stereotactic radiosurgery of brain metastases in patients with malignant melanoma and validation of the melanoma molGPA

INTRODUCTION

Malignant melanoma is the third most common primary in the diagnosis of brain metastases. Stereotactic radiosurgery (SRS) is a well-established treatment option in limited brain disease. We analyzed outcomes of SRS with a particular focus on the graded prognostic assessment (GPA, melanoma molGPA), prognostic factors, and toxicity.

METHODS

We evaluated 173 brain metastases in 83 patients with malignant melanoma. All were treated with SRS median dose of 20 Gy prescribed to the 80 or 100% isodose line between 2002 and 2019. All patients were followed-up regularly, including contrast-enhanced brain imaging as well as clinical examination, initially 6 weeks after treatment, then in quarterly follow-up.

RESULTS

The median age was 61 years (range 27-80); 36 female and 47 male patients were treated. After a median follow-up of 5.7 months, median OS (overall survival) was 9.7 months 95%-KI 4.7-14.7). LC (local control) at 6 months, 12, 24 months was 89%, 86%, and 72%, respectively (median was not reached). Median DBC (distant brain control) was 8.2 months (95%-KI 4.7-11.7). For OS, a KPS ≥ 80%, a positive BRAF mutation status, a small PTV (planning target volume), the absence of extracranial metastases, as well as a GPA and melanoma molGPA > 2 were prognostic factors. In the MVA, a small PTV and a melanoma molGPA > 2 remained significant.

CONCLUSION

The present survival outcomes support the use of the disease-specific melanoma molGPA as reliable prognostic score. Favorable outcomes for SRS compared to other studies were observed. In the treatment of brain metastases of malignant melanoma patients, a multidisciplinary approach consisting of surgery, SRS, chemotherapy, and immunotherapy should be considered.

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a “One Health” perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a “One Health” perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

Basal Ganglia versus Peripheral Infarcts: Predictive Value of Early Fiber Alterations

BACKGROUND AND PURPOSE

Impairment of fiber integrity of the corticospinal tract in the subacute and chronic phases after ischemic stroke has been linked to poor motor outcome. The aim of the study was an assessment of fiber integrity in the acute poststroke phase and an evaluation of its association with the clinical course dependent on the infarction pattern (subtypes: peripheral versus basal ganglia infarction).

MATERIALS AND METHODS

All patients who underwent mechanical recanalization of a large-vessel occlusion in the anterior circulation and postinterventional DTI were included (n = 165). The fractional anisotropy index of the patient-specific corticospinal tract within the posterior limb of the internal capsule was correlated to clinical parameters (NIHSS scores/mRS at 90 days), and the interaction of stroke subtype (peripheral infarcts versus basal ganglia infarction) was tested in a moderation analysis.

RESULTS

The fractional anisotropy index was reduced in the acute poststroke phase with a correlation to clinical presentation, especially in case of peripheral infarcts (eg, with the NIHSS motor subscore: r = -0.4, P < .001). This correlation was absent for basal ganglia infarction (r = -0.008, P > .05). There was a significant association between the fractional anisotropy index and clinical outcome (mRS after 90 days, P < .01), which is moderated by stroke subtype with significant effects only for peripheral infarcts.

CONCLUSIONS

Corticospinal tract abnormalities can be observed in the early stage after mechanical recanalization and have prognostic capacity. This finding increases the clinical value of early DTI imaging parameters. Because the effects observed were limited to peripheral infarcts, further and longitudinal evaluation of fiber integrities within basal ganglia infarction is required.

A short history of thrombectomy - Procedure and success analysis of different endovascular stroke treatment techniques

Background

The historical development of interventional stroke treatment shows a wide variation of different techniques and materials used. Thus, the question of the present work is whether the technical and procedural differences of thrombectomy techniques lead to different technical and clinical results.

Methods and results

Analysis of a mixed retrospective/prospective database of all endovascular treated patients with an occlusion of the Carotid-T or M1 segment of the MCA at a single comprehensive stroke center since 2008. Patients were classified regarding the technical approach used. Six hundred sixty-eight patients were available for the final analysis. Reperfusion rates ranged between 56% and 100% depending on the technical approach. The use of balloon guide catheters and most recently the establishment of combination techniques using balloon guide catheters, aspiration catheters and stent retrievers have shown a further significant increase in the rates of successful recanalization, full recanalization and first-pass recanalization. Additionally, the technical development of interventional techniques has led to a subsequent drop in complications, embolization into previously unaffected territories in particular.

Conclusion

Technical success of MT has improved substantially over the past decade owing to improved materials and procedural innovations. Combination techniques including flow modulation have emerged to be the most effective approach and should be considered as a standard of care.

Level of evidence: Level 3, retrospective study.

Tracking and predicting U.S. influenza activity with a real-time surveillance network

Each year in the United States, influenza causes illness in 9.2 to 35.6 million individuals and is responsible for 12,000 to 56,000 deaths. The U.S. Centers for Disease Control and Prevention (CDC) tracks influenza activity through a national surveillance network. These data are only available after a delay of 1 to 2 weeks, and thus influenza epidemiologists and transmission modelers have explored the use of other data sources to produce more timely estimates and predictions of influenza activity. We evaluated whether data collected from a national commercial network of influenza diagnostic machines could produce valid estimates of the current burden and help to predict influenza trends in the United States. Quidel Corporation provided us with de-identified influenza test results transmitted in real-time from a national network of influenza test machines called the Influenza Test System (ITS). We used this ITS dataset to estimate and predict influenza-like illness (ILI) activity in the United States over the 2015-2016 and 2016-2017 influenza seasons. First, we developed linear logistic models on national and regional geographic scales that accurately estimated two CDC influenza metrics: the proportion of influenza test results that are positive and the proportion of physician visits that are ILI-related. We then used our estimated ILI-related proportion of physician visits in transmission models to produce improved predictions of influenza trends in the United States at both the regional and national scale. These findings suggest that ITS can be leveraged to improve "nowcasts" and short-term forecasts of U.S. influenza activity.

Gadolinium-Enhanced 3D T1-Weighted Black-Blood MR Imaging for the Detection of Acute Optic Neuritis

BACKGROUND AND PURPOSE

A 3D T1-weighted black-blood sequence was recently shown to improve the detection of contrast-enhancing lesions in the brain in patients with MS compared with a 3D T1-weighted MPRAGE sequence. We compared a contrast-enhanced 3D T1-weighted black-blood sequence with a dedicated orbital contrast-enhanced T1-weighted Dixon sequence in patients with acute optic neuritis.

MATERIALS AND METHODS

MR imaging data (3T) of 51 patients showing symptoms of acute optic neuritis were analyzed retrospectively, including whole-brain contrast-enhanced 3D T1-weighted black-blood and dedicated orbital coronal 2D or 3D contrast-enhanced T1-weighted Dixon sequences. Two neuroradiologists assessed the images for overall image quality, artifacts, diagnostic confidence, and visual contrast enhancement. Furthermore, the standardized contrast-to-noise ratio was calculated. The final diagnosis of acute optic neuritis was established on the basis of clinical presentation, visually evoked potentials, and optical coherence tomography.

RESULTS

Thirty of 51 patients were diagnosed with acute optic neuritis. Of those, 21 showed contrast-enhancing lesions in the optic nerves, similarly detectable on contrast-enhanced T1-weighted Dixon and contrast-enhanced T1-weighted black-blood images. Thus, the accuracy for each sequence was identical, with a resulting sensitivity of 70% and specificity of 90% or 100% (depending on the reader). Overall image quality, diagnostic confidence, visual contrast enhancement, and artifacts were rated similarly in contrast-enhanced 3D T1-weighted black-blood and dedicated orbital contrast-enhanced T1-weighted Dixon sequences. There was no significant difference (P = .27) in the mean standardized contrast-to-noise ratio between contrast-enhanced T1-weighted black-blood (1.76 ± 1.07) and contrast-enhanced T1-weighted Dixon (2.29 ± 2.49) sequences.

CONCLUSIONS

Contrast-enhanced 3D T1-weighted black-blood imaging is comparable in accuracy and qualitative/quantitative features with dedicated orbital contrast-enhanced T1-weighted Dixon imaging for the detection of acute optic neuritis. Therefore, when used, it has the potential to considerably shorten total patient imaging time.

Thrombus Histology of Basilar Artery Occlusions : Are There Differences to the Anterior Circulation?

BACKGROUND

For patients with acute vessel occlusions of the anterior circulation histopathology of retrieved cerebral thrombi has been reported to be associated to stroke etiology. Due to the relatively small incidence of posterior circulation stroke, exclusive histopathologic analyses are missing for this subgroup. The aim of the study was to investigate thrombus histology for patients with basilar artery occlusions and uncover differences to anterior circulation clots with respect to underlying etiology.

METHODS

A total of 59 basilar thrombi were collected during intracranial mechanical recanalization and quantitatively analyzed in terms of their relative fractions of the main constituents, e.g. fibrin/platelets (F/P), red (RBC) and white blood cells (WBC). Data were compared to histopathological analyses of 122 thrombi of the anterior circulation with respect to underlying pathogenesis.

RESULTS

The composition of basilar thrombi differed significantly to thrombi of the anterior circulation with an overall higher RBC amount (median fraction in % (interquartile range):0.48 (0.37-0.69) vs. 0.37 (0.28-0.50), p < 0.001) and lower F/P count (0.45 (0.21-0.58) vs. 0.57 (0.44-0.66), p < 0.001). Basilar thrombi composition did not differ between the different etiological stroke subgroups.

CONCLUSION

The results depict a differing thrombus composition of basilar thrombi in comparison to anterior circulation clots with an overall higher amount of RBC. This may reflect different pathophysiologic processes between anterior and posterior circulation thrombogenesis, e.g. a larger proportion of appositional thrombus growth in the posterior circulation.

Fly-Tox: A panel of transgenic flies expressing pest and pollinator cytochrome P450s

There is an on-going need to develop new insecticides that are not compromised by resistance and that have improved environmental profiles. However, the cost of developing novel compounds has increased significantly over the last two decades. This is in part due to increased regulatory requirements, including the need to screen both pest and pollinator insect species to ensure that pre-existing resistance will not hamper the efficacy of a new insecticide via cross-resistance, or adversely affect non-target insect species. To add to this problem the collection and maintenance of toxicologically relevant pest and pollinator species and strains is costly and often difficult. Here we present Fly-Tox, a panel of publicly available transgenic Drosophila melanogaster lines each containing one or more pest or pollinator P450 genes that have been previously shown to metabolise insecticides. We describe the range of ways these tools can be used, including in predictive screens to avoid pre-existing cross-resistance, to identify potential resistance-breaking inhibitors, in the initial assessment of potential insecticide toxicity to bee pollinators, and identifying harmful pesticide-pesticide interactions.

Inner retinal layer thinning in radiologically isolated syndrome predicts conversion to multiple sclerosis

BACKGROUND AND PURPOSE

Individuals with radiologically isolated syndrome (RIS) are at increased risk of converting to multiple sclerosis (MS). Early identification of later converters is crucial for optimal treatment decisions. The purpose of this study was to assess the predictive potential of optical coherence tomography (OCT) measures in individuals with RIS regarding conversion to MS.

METHODS

This prospective observational cohort study included 36 individuals with RIS and 36 healthy controls recruited from two German MS centers. All individuals received baseline OCT and clinical examination and were longitudinally followed over up to 6 years. The primary outcome measure was the conversion to MS.

RESULTS

During clinical follow-up of 46 (26-58) months (median, 25%-75% interquartile range), eight individuals with RIS converted to MS. Individuals converting to MS showed a thinning of the peripapillary retinal nerve fiber layer (pRNFL) and the common ganglion cell and inner plexiform layer (GCIP) at baseline and during follow-up. Individuals with a pRNFL of 99 µm or lower or a GCIP of 1.99 mm³ or lower were at a 7.5- and 8.0-fold risk for MS conversion, respectively, compared to individuals with higher measures. After correction for other known risk factors, Cox proportional hazards regression revealed a hazard ratio of 1.08 for conversion to MS for each 1 µm decline in pRNFL.

CONCLUSIONS

Reduction of the pRNFL might be a novel and independent risk factor for conversion to MS in individuals with RIS. OCT might be useful for risk stratification and therapeutic decision-making in individuals with RIS.

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Background

Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (H_P) and fixation index (F_ST)] and group-based F_ST approaches, which compare groups of breeds defined according to external traits and use/specialization/type.

Results

We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars.

Conclusions

Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.

Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

T1-Weighted Intensity Increase After a Single Administration of a Linear Gadolinium-Based Contrast Agent in Multiple Sclerosis

Purpose

Through analysis of T1-weighted (T1w) images this study investigated gadolinium (Gd) deposition in the brain after administration of a linear (gadopentetic acid) and a cyclic (gadoteric acid) gadolinium-based contrast agent (GBCA) in patients with multiple sclerosis (MS), a disorder frequently requiring magnetic resonance imaging (MRI) scans over years.

Methods

A total of 3233 T1w images (unenhanced with respect to the same scanning session) of 881 MS patients were retrospectively analyzed. After spatial normalization and intensity scaling using a sphere within the pons, differences of all pairs of subsequent scans were calculated and attributed to either linear (n = 2718) or cyclic (n = 385) or no GBCA (n = 130) according to the first scan. Regional analyses were performed, focusing on the dentate nucleus, and whole brain analyses. By 1‑sample t‑tests, signal intensity increases within conditions were searched for; conditions were compared by 2‑sample t‑tests. Furthermore, recent hypotheses on the reversibility of GBCA deposition were tested.

Results

In the dentate nucleus, a significant increase was observed only after administration of linear GBCA even after a single GBCA administration. This increase differed significantly (p < 0.001) from the other conditions (cyclic and no GBCA). Whole brain analyses revealed T1w signal increases only after administration of linear GBCA within two regions, the dentate nucleus and globus pallidus. Additional analyses did not indicate any decline of Gd deposition in the brain.

Conclusion

The data point towards Gd deposition in the brain after administration of linear GBCA even after a single administration.

Imaging glioma biology: spatial comparison of amino acid PET, amide proton transfer, and perfusion-weighted MRI in newly diagnosed gliomas

PURPOSE

Imaging glioma biology holds great promise to unravel the complex nature of these tumors. Besides well-established imaging techniques such O-(2-[18F]fluoroethyl)-L-tyrosine (FET)-PET and dynamic susceptibility contrast (DSC) perfusion imaging, amide proton transfer-weighted (APTw) imaging has emerged as a promising novel MR technique. In this study, we aimed to better understand the relation between these imaging biomarkers and how well they capture cellularity and vascularity in newly diagnosed gliomas.

METHODS

Preoperative MRI and FET-PET data of 46 patients (31 glioblastoma and 15 lower-grade glioma) were segmented into contrast-enhancing and FLAIR-hyperintense areas. Using established cutoffs, we calculated hot-spot volumes (HSV) and their spatial overlap. We further investigated APTw and CBV values in FET-HSV. In a subset of 10 glioblastoma patients, we compared cellularity and vascularization in 34 stereotactically targeted biopsies with imaging.

RESULTS

In glioblastomas, the largest HSV was found for APTw, followed by PET and CBV (p < 0.05). In lower-grade gliomas, APTw-HSV was clearly lower than in glioblastomas. The spatial overlap of HSV was highest between APTw and FET in both tumor entities and regions. APTw correlated significantly with cellularity, similar to FET, while the association with vascularity was more pronounced in CBV and FET.

CONCLUSIONS

We found a relevant spatial overlap in glioblastomas between hotspots of APTw and FET both in contrast-enhancing and FLAIR-hyperintense tumor. As suggested by earlier studies, APTw was lower in lower-grade gliomas compared with glioblastomas. APTw meaningfully contributes to biological imaging of gliomas.

Microstructural Integrity of Salvaged Penumbra after Mechanical Thrombectomy

BACKGROUND AND PURPOSE

There are sparse data on the microstructural integrity of salvaged penumbral tissue after mechanical thrombectomy of large-vessel occlusions. The aim of the study was to analyze possible microstructural alteration in the penumbra and their association with clinical symptoms as well as angiographic reperfusion success in patients undergoing mechanical thrombectomy.

MATERIALS AND METHODS

All patients who underwent mechanical thrombectomy for large-vessel occlusions in the anterior circulation and who received an admission CT perfusion together with postinterventional DTIs were included (n = 65). Angiographic reperfusion success by means of modified Thrombolysis in Cerebral Infarction (mTICI) scale and clinical outcome were recorded. Microstructural integrity was assessed by DTI evaluating the mean diffusivity index within the salvaged gray matter of the former penumbra.

RESULTS

The mean diffusivity index was higher in completely recanalized patients (mTICI 3: -0.001 ± 0.034 versus mTICI <3: -0.030 ± 0.055, P = .03). There was a positive correlation between the mean diffusivity index and NIHSS score improvement (r = 0.49, P = .003) and the mean diffusivity index was associated with midterm functional outcome (r = -0.37, P = .04) after adjustment for confounders. In mediation analysis, the mean diffusivity index and infarction growth mediated the association between reperfusion success and clinical outcomes.

CONCLUSIONS

The macroscopic salvaged penumbra included areas of microstructural integrity changes, most likely related to the initial hypoperfusion. These abnormalities were found early after mechanical thrombectomy, were dependent on angiographic results, and correlated with the clinical outcome. When confirmed, these findings prompt the evaluation of therapies for protection of the penumbral tissue integrity.

Etiology of recurrent large vessel occlusions treated with repeated thrombectomy

BACKGROUND

Repeated mechanical thrombectomy for acute stroke treatment in individual patients has been proven feasible. However, less is known about the etiology of recurrent vessel occlusions after prior thrombectomy. We aimed to understand if the etiology of such recurrent events differs from the first stroke.

METHODS

Retrospectively, we identified all patients at our center who received a repeated mechanical thrombectomy between 2007 and 2019. Clinical data were retrieved from medical records. Etiology of stroke was evaluated retrospectively, and angiographic studies were revisited.

RESULTS

Twenty-three patients (1.5%) were identified. Median age was 68 years (IQR 56-77). Median NIHSS at first admission was 11 points (IQR 5-15). In nine cases (39.1%), the recurrent vessel occlusion was located exactly at the same position as the prior occlusion. Overall, five (21.7%) patients had a remarkable extracranial pathology as likely cause of stroke recurrence. In 16 patients (69.6%), the etiology of the first stroke and its recurrence was considered as likely being the same, mostly of cardioembolic or unknown origin. In the seven remaining patients (30.4%), the cause of stroke possibly differed from the first event, with five patients (21.7%) having a postinterventional intracranial intimal lesion as possible cause of stroke.

CONCLUSION

Incidence of repeated thrombectomy was low. However, the high number of patients with known origin of stroke etiology raises the question how their monitoring may be optimized. The number of patients with remarkable extracranial pathologies or intracranial endothelial lesions supports current clinical practice to pay attention to final angiographic series.

Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models

Stochastic transmission dynamic models are needed to quantify the uncertainty in estimates and predictions during outbreaks of infectious diseases. We previously developed a calibration method for stochastic epidemic compartmental models, called Multiple Shooting for Stochastic Systems (MSS), and demonstrated its competitive performance against a number of existing state-of-the-art calibration methods. The existing MSS method, however, lacks a mechanism against filter degeneracy, a phenomenon that results in parameter posterior distributions that are weighted heavily around a single value. As such, when filter degeneracy occurs, the posterior distributions of parameter estimates will not yield reliable credible or prediction intervals for parameter estimates and predictions. In this work, we extend the MSS method by evaluating and incorporating two resampling techniques to detect and resolve filter degeneracy. Using simulation experiments, we demonstrate that an extended MSS method produces credible and prediction intervals with desired coverage in estimating key epidemic parameters (e.g. mean duration of infectiousness and R0) and short- and long-term predictions (e.g. one and three-week forecasts, timing and number of cases at the epidemic peak, and final epidemic size). Applying the extended MSS approach to a humidity-based stochastic compartmental influenza model, we were able to accurately predict influenza-like illness activity reported by U.S. Centers for Disease Control and Prevention from 10 regions as well as city-level influenza activity using real-time, city-specific Google search query data from 119 U.S. cities between 2003 and 2014.

Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F_ST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

Cost-Effectiveness of Alternative Uses of Polyvalent Meningococcal Vaccines in Niger: An Agent-Based Transmission Modeling Study

Background. Despite the introduction of an effective serogroup A conjugate vaccine (MenAfriVac™), sporadic epidemics of other Neisseria meningitidis serogroups remain a concern in Africa. Polyvalent meningococcal conjugate (PMC) vaccines may offer alternatives to current strategies that rely on routine infant vaccination with MenAfriVac plus, in the event of an epidemic, district-specific reactive campaigns using polyvalent meningococcal polysaccharide (PMP) vaccines. Methods. We developed an agent-based transmission model of N. meningitidis in Niger to compare the health effects and costs of current vaccination practice and 3 alternatives. Each alternative replaces MenAfriVac in the infant vaccination series with PMC and either replaces PMP with PMC for reactive campaigns or implements a one-time catch up campaign with PMC for children and young adults. Results. Over a 28-year period, replacement of MenAfriVac with PMC in the infant immunization series and of PMP in reactive campaigns would avert 63% of expected cases (95% prediction interval 49%-75%) if elimination of serogroup A is not followed by serogroup replacement. At a PMC price of $4/dose, this would cost $1412 ($81-$3510) per disability-adjusted life-year (DALY) averted. If serogroup replacement occurs, the cost-effectiveness of this strategy improves to $662 (cost-saving, $2473) per DALY averted. Sensitivity analyses accounting for incomplete laboratory confirmation suggest that a catch-up PMC campaign would also meet standard cost-effectiveness thresholds. Limitations. The assumption that polyvalent vaccines offer similar protection against all serogroups is simplifying. Conclusions. The use of PMC vaccines to replace MenAfriVac in routine infant immunization and in district-specific reactive campaigns would have important health benefits and is likely to be cost-effective in Niger. An additional PMC catch-up campaign would also be cost-effective if we account for incomplete laboratory reporting.

Opportunistic osteoporosis screening in multi-detector CT images via local classification of textures

Our study proposed an automatic pipeline for opportunistic osteoporosis screening using 3D texture features and regional vBMD using multi-detector CT images. A combination of different local and global texture features outperformed the global vBMD and showed high discriminative power to identify patients with vertebral fractures.

INTRODUCTION

Many patients at risk for osteoporosis undergo computed tomography (CT) scans, usable for opportunistic (non-dedicated) screening. We compared the performance of global volumetric bone mineral density (vBMD) with a random forest classifier based on regional vBMD and 3D texture features to separate patients with and without osteoporotic fractures.

METHODS

In total, 154 patients (mean age 64 ± 8.5, male; n = 103) were included in this retrospective single-center analysis, who underwent contrast-enhanced CT for other reasons than osteoporosis screening. Patients were dichotomized regarding prevalent vertebral osteoporotic fractures (noFX, n = 101; FX, n = 53). Vertebral bodies were automatically segmented, and trabecular vBMD was calculated with a dedicated phantom. For 3D texture analysis, we extracted gray-level co-occurrence matrix Haralick features (HAR), histogram of gradients (HoG), local binary patterns (LBP), and wavelets (WL). Fractured vertebrae were excluded for texture-feature and vBMD data extraction. The performance to identify patients with prevalent osteoporotic vertebral fractures was evaluated in a fourfold cross-validation.

RESULTS

The random forest classifier showed a high discriminatory power (AUC = 0.88). Parameters of all vertebral levels significantly contributed to this classification. Importantly, the AUC of the proposed algorithm was significantly higher than that of volumetric global BMD alone (AUC = 0.64).

CONCLUSION

The presented classifier combining 3D texture features and regional vBMD including the complete thoracolumbar spine showed high discriminatory power to identify patients with vertebral fractures and had a better diagnostic performance than vBMD alone.

Texture analysis of vertebral bone marrow using chemical shift encoding-based water-fat MRI: a feasibility study

This feasibility study investigated the spatial heterogeneity of the lumbar vertebral bone marrow using chemical shift encoding-based water-fat MRI. Acquired texture features like contrast and dissimilarity allowed for differentiation of pre- and postmenopausal women and may serve as imaging biomarkers in the future.

INTRODUCTION

While the vertebral bone marrow fat using chemical shift encoding water-fat magnetic resonance imaging (MRI) has been extensively studied, its spatial heterogeneity has not been analyzed yet. Therefore, this feasibility study investigated the spatial heterogeneity of the lumbar vertebral bone marrow by using texture analysis in proton density fat fraction (PDFF) maps.

METHODS

Forty-one healthy pre- and postmenopausal women were recruited for this study (premenopausal (n = 15) 30 ± 7 years, postmenopausal (n = 26) 65 ± 7 years). An eight-echo 3D spoiled gradient echo sequence was used for chemical shift encoding-based water-fat separation at the lumbar spine. Vertebral bodies L1 to L5 were manually segmented. Mean PDFF values and texture features were extracted at each vertebral level, namely variance, skewness, and kurtosis, using statistical moments and second-order features (energy, contrast, correlation, homogeneity, dissimilarity, entropy, variance, and sum average). Parameters were compared between pre- and postmenopausal women and vertebral levels.

RESULTS

PDFF was significantly higher in post- than in premenopausal women (49.37 ± 8.14% versus 27.76 ± 7.30%, p < 0.05). Furthermore, PDFF increased from L1 to L5 (L1 37.93 ± 12.85%, L2 38.81 ± 12.77%, L3 40.23 ± 12.72%, L4 42.80 ± 13.27%, L5 45.21 ± 14.55%, p < 0.05). Bone marrow heterogeneity based on texture analysis was significantly (p < 0.05) increased in postmenopausal women. Contrast and dissimilarity performed best in differentiating pre- and postmenopausal women (AUC = 0.97 and 0.96, respectively), not significantly different compared with PDFF (AUC = 0.97).

CONCLUSION

Conclusively, an increased bone marrow heterogeneity could be observed in postmenopausal women. In the future, texture parameters might provide additional information to detect and monitor vertebral bone marrow alterations due to aging or hormonal changes beyond conventional anatomic imaging.

Evidence for a white matter lesion size threshold to support the diagnosis of relapsing remitting multiple sclerosis

BACKGROUND

The number of white matter lesions (WML) in brain MRI is the most established paraclinical tool to support the diagnosis of multiple sclerosis (MS) and to monitor its course. Diagnostic criteria have stipulated a minimum detectable diameter of 3 mm per WML, although this threshold is not evidence-based. We aimed to provide a rationale for a WML size threshold for three-dimensional MRI sequences at 3 T by comparing patients with relapsing-remitting MS (RRMS) to control subjects (CS).

METHODS

We analyzed MR images from two cohorts, obtained at scanners from two different vendors, each comprising patients with RRMS and CS. Both cohorts were examined with FLAIR and T1w sequences. In total, 232 patients with RRMS (Expanded Disability Status Scale: mean = 1.6 ± 1.2; age: mean = 36 ± 10) as well as 116 age- and sex-matched CS were studied. We calculated odds ratios across WML volumes. The WML size threshold, which discriminated best between patients and CS, was estimated with receiver operating characteristic curve analysis.

RESULTS

In both cohorts, odds ratios increased continuously with increasing WML volumes, and discriminative power was highest at a WML size threshold corresponding to a diameter of about 3 mm.

CONCLUSION

The stipulated WML size threshold of 3 mm in diameter for the diagnostic criteria of MS seems a reasonable choice for three-dimensional MRI sequences at 3 T.

Effects of virtual tube current reduction and sparse sampling on MDCT-based femoral BMD measurements

This study investigates the impact of tube current reduction and sparse sampling on femoral bone mineral density (BMD) measurements derived from multi-detector computed tomography (MDCT). The application of sparse sampling led to robust and clinically acceptable BMD measurements. In contrast, BMD measurements derived from MDCT with virtually reduced tube currents showed a considerable increase when compared to original data.

INTRODUCTION

The study aims to evaluate the effects of radiation dose reduction by using virtual reduction of tube current or sparse sampling combined with standard filtered back projection (FBP) and statistical iterative reconstruction (SIR) on femoral bone mineral density (BMD) measurements derived from multi-detector computed tomography (MDCT).

METHODS

In routine MDCT scans of 41 subjects (65.9% men; age 69.3 ± 10.1 years), reduced radiation doses were simulated by lowering tube currents and applying sparse sampling (50, 25, and 10% of the original tube current and projections, respectively). Images were reconstructed using FBP and SIR. BMD values were assessed in the femoral neck and compared between the different dose levels, numbers of projections, and image reconstruction approaches.

RESULTS

Compared to full-dose MDCT, virtual lowering of the tube current by applying our simulation algorithm resulted in increases in BMD values for both FBP (up to a relative change of 32.5%) and SIR (up to a relative change of 32.3%). In contrast, the application of sparse sampling with a reduction down to 10% of projections showed robust BMD values, with clinically acceptable relative changes of up to 0.5% (FBP) and 0.7% (SIR).

CONCLUSIONS

Our simulations, which still require clinical validation, indicate that reductions down to ultra-low tube currents have a significant impact on MDCT-based femoral BMD measurements. In contrast, the application of sparse-sampled MDCT seems a promising future clinical option that may enable a significant reduction of the radiation dose without considerable changes of BMD values.

Diversity across major and candidate genes in European local pig breeds

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.

Use of daily Internet search query data improves real-time projections of influenza epidemics

Seasonal influenza causes millions of illnesses and tens of thousands of deaths per year in the USA alone. While the morbidity and mortality associated with influenza is substantial each year, the timing and magnitude of epidemics are highly variable which complicates efforts to anticipate demands on the healthcare system. Better methods to forecast influenza activity would help policymakers anticipate such stressors. The US Centers for Disease Control and Prevention (CDC) has recognized the importance of improving influenza forecasting and hosts an annual challenge for predicting influenza-like illness (ILI) activity in the USA. The CDC data serve as the reference for ILI in the USA, but this information is aggregated by epidemiological week and reported after a one-week delay (and may be subject to correction even after this reporting lag). Therefore, there has been substantial interest in whether real-time Internet search data, such as Google, Twitter or Wikipedia could be used to improve influenza forecasting. In this study, we combine a previously developed calibration and prediction framework with an established humidity-based transmission dynamic model to forecast influenza. We then compare predictions based on only CDC ILI data with predictions that leverage the earlier availability and finer temporal resolution of Wikipedia search data. We find that both the earlier availability and the finer temporal resolution are important for increasing forecasting performance. Using daily Wikipedia search data leads to a marked improvement in prediction performance compared to weekly data especially for a three- to four-week forecasting horizon.

AEgIS at ELENA: outlook for physics with a pulsed cold antihydrogen beam

The efficient production of cold antihydrogen atoms in particle traps at CERN's Antiproton Decelerator has opened up the possibility of performing direct measurements of the Earth's gravitational acceleration on purely antimatter bodies. The goal of the AEgIS collaboration is to measure the value of g for antimatter using a pulsed source of cold antihydrogen and a Moiré deflectometer/Talbot-Lau interferometer. The same antihydrogen beam is also very well suited to measuring precisely the ground-state hyperfine splitting of the anti-atom. The antihydrogen formation mechanism chosen by AEgIS is resonant charge exchange between cold antiprotons and Rydberg positronium. A series of technical developments regarding positrons and positronium (Ps formation in a dedicated room-temperature target, spectroscopy of the n=1-3 and n=3-15 transitions in Ps, Ps formation in a target at 10 K inside the 1 T magnetic field of the experiment) as well as antiprotons (high-efficiency trapping of [Formula: see text], radial compression to sub-millimetre radii of mixed [Formula: see text] plasmas in 1 T field, high-efficiency transfer of [Formula: see text] to the antihydrogen production trap using an in-flight launch and recapture procedure) were successfully implemented. Two further critical steps that are germane mainly to charge exchange formation of antihydrogen-cooling of antiprotons and formation of a beam of antihydrogen-are being addressed in parallel. The coming of ELENA will allow, in the very near future, the number of trappable antiprotons to be increased by more than a factor of 50. For the antihydrogen production scheme chosen by AEgIS, this will be reflected in a corresponding increase of produced antihydrogen atoms, leading to a significant reduction of measurement times and providing a path towards high-precision measurements.This article is part of the Theo Murphy meeting issue 'Antiproton physics in the ELENA era'.

AEg̅IS latest results

The validity of the Weak Equivalence Principle (WEP) as predicted by General Relativity has been tested up to astounding precision using ordinary matter. The lack hitherto of a stable source of a probe being at the same time electrically neutral, cold and stable enough to be measured has prevented highaccuracy testing of the WEP on anti-matter. The AEg̅IS (Antimatter Experiment: Gravity, Interferometry, Spectroscopy) experiment located at CERN's AD (Antiproton Decelerator) facility aims at producing such a probe in the form of a pulsed beam of cold anti-hydrogen, and at measuring by means of a moiré deflectometer the gravitational force that Earth's mass exerts on it. Low temperature and abundance of the H̅ are paramount to attain a high precision measurement. A technique employing a charge-exchange reaction between antiprotons coming from the AD and excited positronium atoms is being developed at AEg̅IS and will be presented hereafter, alongside an overview of the experimental apparatus and the current status of the experiment

Towards the first measurement of matter-antimatter gravitational interaction

The AEgIS (Antimatter Experiment: Gravity, Interferometry, Spectroscopy) is a CERN based experiment with the central aim to measure directly the gravitational acceleration of antihydrogen. Antihydrogen atoms will be produced via charge exchange reactions which will consist of Rydberg-excited positronium atoms sent to cooled antiprotons within an electromagnetic trap. The resulting Rydberg antihydrogen atoms will then be horizontally accelerated by an electric field gradient (Stark effect), they will then pass through a moiré deflectometer. The vertical deflection caused by the Earth's gravitational field will test for the first time the Weak Equivalence Principle for antimatter. Detection will be undertaken via a position sensitive detector. Around 103 antihydrogen atoms are needed for the gravitational measurement to be completed. The present status, current achievements and results will be presented, with special attention toward the laser excitation of positronium (Ps) to the n=3 state and the production of Ps atoms in the transmission geometry.

Pre- and Postcontrast 3D Double Inversion Recovery Sequence in Multiple Sclerosis: A Simple and Effective MR Imaging Protocol

BACKGROUND AND PURPOSE

The double inversion recovery sequence is known to be very sensitive and specific for MS-related lesions. Our aim was to compare the sensitivity of pre- and postcontrast images of 3D double inversion recovery and conventional 3D T1-weighted images for the detection of contrast-enhancing MS-related lesions in the brain to analyze whether double inversion recovery could be as effective as T1WI.

MATERIALS AND METHODS

A postcontrast 3D double inversion recovery sequence was acquired in addition to the standard MR imaging protocol at 3T, including pre- and postcontrast 3D T1WI sequences as well as precontrast double inversion recovery of 45 consecutive patients with MS or clinically isolated syndrome between June and December 2013. Two neuroradiologists independently assessed precontrast, postcontrast, and subtraction images of double inversion recovery as well as T1WI to count the number of contrast-enhancing lesions. Afterward, a consensus reading was performed. Lin concordance was calculated between both radiologists, and differences in lesion detectability were assessed with the Student t test. Additionally, the contrast-to-noise ratio was calculated.

RESULTS

Significantly more contrast-enhancing lesions could be detected with double inversion recovery compared with T1WI (16%, 214 versus 185, P = .007). The concordance between both radiologists was almost perfect (ρ_c = 0.94 for T1WI and ρ_c = 0.98 for double inversion recovery, respectively). The contrast-to-noise ratio was significantly higher in double inversion recovery subtraction images compared with T1-weighted subtraction images (double inversion recovery, 14.3 ± 5.5; T1WI, 6.3 ± 7.1; P < .001).

CONCLUSIONS

Pre- and postcontrast double inversion recovery enables better detection of contrast-enhancing lesions in MS in the brain compared with T1WI and may be considered an alternative to the standard MR imaging protocol.

Risk of Thrombus Fragmentation during Endovascular Stroke Treatment

BACKGROUND AND PURPOSE

Periprocedural thrombus fragmentation is a relevant risk in endovascular stroke treatment. Because factors influencing its occurrence are largely unknown, this study addresses a potential relationship between thrombus histology and clot stability.

MATERIALS AND METHODS

Eighty-five patients with anterior circulation stroke treated with thrombectomy were included in this retrospective study. The number and location of emboli after retrieving the primary thrombus, the number of maneuvers, and TICI scores were evaluated. H&E and neutrophil elastase staining of retrieved clots was performed, and semiquantitative measurements of thrombus components were correlated with procedural parameters.

RESULTS

An inverse correlation between maneuvers required for thrombus retrieval and the number of distal and intermediate emboli was observed (Spearman r, -0.23; P = .032). Younger patients were at higher risk for periprocedural thrombus fragmentation (Spearman r, -0.23; P = .032). Bridging thrombolysis tended to be associated with fewer maneuvers (2 vs 3, P = .054) but more emboli (1 vs 0, P = .067). While no consistent correlation between procedural parameters and red/white blood cells and fibrin-/platelet fractions could be found, higher amounts of neutrophil elastase-positive cells within the thrombus were independently associated with the occurrence of multiple emboli (adjusted OR, 4.6; 95% CI, 1.1-19.7; P = .041) and lower rates of complete recanalization (adjusted OR, 0.3; 95% CI, 0.1-0.9; P = .050).

CONCLUSIONS

Younger age, easy-to-retrieve thrombi, and bridging thrombolysis may be risk factors for periprocedural thrombus fragmentation. Findings from standard histologic stains did not provide insight into thrombectomy-relevant thrombus stability. However, higher neutrophil levels in the thrombus tissue were related to an increased risk of periprocedural thrombus fragmentation. This observation aligns with the proposed thrombolytic capacity of neutrophil elastase and points to its potential clinical relevance in the context of stroke thrombectomy.

MR Imaging of Individual Perfusion Reorganization Using Superselective Pseudocontinuous Arterial Spin-Labeling in Patients with Complex Extracranial Steno-Occlusive Disease

BACKGROUND AND PURPOSE

Patients with multiple stenoses or occlusions of the extracranial arteries require an individualized diagnostic approach. We evaluated the feasibility and clinical utility of a novel MR imaging technique for regional perfusion imaging in this patient group.

MATERIALS AND METHODS

Superselective pseudocontinuous arterial spin-labeling with a circular labeling spot enabling selective vessel labeling was added to routine imaging in a prospective pilot study in 50 patients (10 women, 70.05 ± 10.55 years of age) with extracranial steno-occlusive disease. Thirty-three had infarct lesions. DSC-MR imaging was performed in 16/50 (32%), and cerebral DSA, in 12/50 patients (24%). Vascular anatomy and the distribution of vessel stenoses and occlusions were defined on sonography and TOF-MRA. Stenoses were classified according to the NASCET criteria. Infarct lesions and perfusion deficits were defined on FLAIR and DSC-MR imaging, respectively. Individual perfusion patterns were defined on the superselective pseudocontinuous arterial spin-labeling maps and were correlated with vascular anatomy and infarct lesion localization.

RESULTS

The superselective pseudocontinuous arterial spin-labeling imaging sequence could be readily applied by trained technicians, and the additional scan time of 12.7 minutes was well-tolerated by patients. The detected vessel occlusions/stenoses and perfusion patterns corresponded between cerebral DSA and superselective pseudocontinuous arterial spin-labeling maps in all cases. Perfusion deficits on DSC-CBF maps significantly correlated with those on superselective pseudocontinuous arterial spin-labeling maps (Pearson r = 0.9593, P < .01). Individual collateral recruitment patterns were not predictable from the vascular anatomy in 71% of our patients.

CONCLUSIONS

Superselective pseudocontinuous arterial spin-labeling is a robust technique for regional brain perfusion imaging, suitable for the noninvasive diagnostics of individual perfusion patterns in patients with complex cerebrovascular disease.

Hypogyrification in obsessive-compulsive disorder

BACKGROUND

Previous studies hypothesized that neurodevelopmental risk factors may play a role in the pathogenesis of obsessive-compulsive disorder (OCD). Cortical folding has been shown to be a reliable indicator for normal and altered neurodevelopment, but in OCD it has barely been investigated up to now. The present study investigates whether alterations in gyrification are detectable in OCD and, if so, how these are associated with clinical characteristics.

METHOD

We compared the local Gyrification Index (lGI) between 75 OCD patients and 75 matched healthy subjects across the whole brain. In addition, for those regions exhibiting an altered lGI in patients we explored a potential relationship to symptom severity, age of onset, and influence of medication.

RESULTS

OCD patients had a significantly decreased lGI in right parietal, precentral but also insula, temporal, pars triangularis and rostral middle frontal regions compared to healthy subjects. A positive association with age of onset was found but no association with symptom severity. There was no effect of co-morbidity or medication.

CONCLUSIONS

The reduced gyrification found in OCD confirms previous findings in other psychiatric disorders and suggests that alterations may already occur during early stages of brain development. Our findings support the idea that altered cortical folding might represent a trait characteristic of the disorder although longitudinal studies are needed to clarify the trajectory of this morphological measure in OCD.

A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study

Background

Mathematical models are used to gain an integrative understanding of biochemical processes and networks. Commonly the models are based on deterministic ordinary differential equations. When molecular counts are low, stochastic formalisms like Monte Carlo simulations are more appropriate and well established. However, compared to the wealth of computational methods used to fit and analyze deterministic models, there is only little available to quantify the exactness of the fit of stochastic models compared to experimental data or to analyze different aspects of the modeling results.

Results

Here, we developed a method to fit stochastic simulations to experimental high-throughput data, meaning data that exhibits distributions. The method uses a comparison of the probability density functions that are computed based on Monte Carlo simulations and the experimental data. Multiple parameter values are iteratively evaluated using optimization routines. The method improves its performance by selecting parameters values after comparing the similitude between the deterministic stability of the system and the modes in the experimental data distribution. As a case study we fitted a model of the IRF7 gene expression circuit to time-course experimental data obtained by flow cytometry. IRF7 shows bimodal dynamics upon IFN stimulation. This dynamics occurs due to the switching between active and basal states of the IRF7 promoter. However, the exact molecular mechanisms responsible for the bimodality of IRF7 is not fully understood.

Conclusions

Our results allow us to conclude that the activation of the IRF7 promoter by the combination of IRF7 and ISGF3 is sufficient to explain the observed bimodal dynamics.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-017-0406-4) contains supplementary material, which is available to authorized users.

A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models

Stochastic transmission dynamic models are especially useful for studying the early emergence of novel pathogens given the importance of chance events when the number of infectious individuals is small. However, methods for parameter estimation and prediction for these types of stochastic models remain limited. In this manuscript, we describe a calibration and prediction framework for stochastic compartmental transmission models of epidemics. The proposed method, Multiple Shooting for Stochastic systems (MSS), applies a linear noise approximation to describe the size of the fluctuations, and uses each new surveillance observation to update the belief about the true epidemic state. Using simulated outbreaks of a novel viral pathogen, we evaluate the accuracy of MSS for real-time parameter estimation and prediction during epidemics. We assume that weekly counts for the number of new diagnosed cases are available and serve as an imperfect proxy of incidence. We show that MSS produces accurate estimates of key epidemic parameters (i.e. mean duration of infectiousness, R0, and Reff) and can provide an accurate estimate of the unobserved number of infectious individuals during the course of an epidemic. MSS also allows for accurate prediction of the number and timing of future hospitalizations and the overall attack rate. We compare the performance of MSS to three state-of-the-art benchmark methods: 1) a likelihood approximation with an assumption of independent Poisson observations; 2) a particle filtering method; and 3) an ensemble Kalman filter method. We find that MSS significantly outperforms each of these three benchmark methods in the majority of epidemic scenarios tested. In summary, MSS is a promising method that may improve on current approaches for calibration and prediction using stochastic models of epidemics.