Vocabulary Matters: An Annotation Pipeline and Four Deep Learning Algorithms for Enzyme Named Entity Recognition

Enzymes are indispensable in many biological processes, and with biomedical literature growing exponentially, effective literature review becomes increasingly challenging. Natural language processing methods offer solutions to streamline this process. This study aims to develop an annotated enzyme corpus for training and evaluating enzyme named entity recognition (NER) models. A novel pipeline, combining dictionary matching and rule-based keyword searching, automatically annotated enzyme entities in >4800 full-text publications. Four deep learning NER models were created with different vocabularies (BioBERT/SciBERT) and architectures (BiLSTM/transformer) and evaluated on 526 manually annotated full-text publications. The annotation pipeline achieved an F1-score of 0.86 (precision = 1.00, recall = 0.76), surpassed by fine-tuned transformers for F1-score (BioBERT: 0.89, SciBERT: 0.88) and recall (0.86) with BiLSTM models having higher precision (0.94) than transformers (0.92). The annotation pipeline runs in seconds on standard laptops with almost perfect precision, but was outperformed by fine-tuned transformers in terms of F1-score and recall, demonstrating generalizability beyond the training data. In comparison, SciBERT-based models exhibited higher precision, and BioBERT-based models exhibited higher recall, highlighting the importance of vocabulary and architecture. These models, representing the first enzyme NER algorithms, enable more effective enzyme text mining and information extraction. Codes for automated annotation and model generation are available from https://github.com/omicsNLP/enzymeNER and https://zenodo.org/doi/10.5281/zenodo.10581586.

Identification of genetic drivers of plasma lipoprotein size in the Diversity Outbred mouse population

Despite great progress in understanding lipoprotein physiology, there is still much to be learned about the genetic drivers of lipoprotein abundance, composition, and function. We used ion mobility spectrometry to survey 16 plasma lipoprotein subfractions in 500 Diversity Outbred mice maintained on a Western-style diet. We identified 21 quantitative trait loci (QTL) affecting lipoprotein abundance. To refine the QTL and link them to disease risk in humans, we asked if the human homologs of genes located at each QTL were associated with lipid traits in human genome-wide association studies. Integration of mouse QTL with human genome-wide association studies yielded candidate gene drivers for 18 of the 21 QTL. This approach enabled us to nominate the gene encoding the neutral ceramidase, Asah2, as a novel candidate driver at a QTL on chromosome 19 for large HDL particles (HDL-2b). To experimentally validate Asah2, we surveyed lipoproteins in Asah2-/- mice. Compared to wild-type mice, female Asah2-/- mice showed an increase in several lipoproteins, including HDL. Our results provide insights into the genetic regulation of circulating lipoproteins, as well as mechanisms by which lipoprotein subfractions may affect cardiovascular disease risk in humans.

A resonant sextuplet of sub-Neptunes transiting the bright star HD 110067

Planets with radii between that of the Earth and Neptune (hereafter referred to as 'sub-Neptunes') are found in close-in orbits around more than half of all Sun-like stars1,2. However, their composition, formation and evolution remain poorly understood3. The study of multiplanetary systems offers an opportunity to investigate the outcomes of planet formation and evolution while controlling for initial conditions and environment. Those in resonance (with their orbital periods related by a ratio of small integers) are particularly valuable because they imply a system architecture practically unchanged since its birth. Here we present the observations of six transiting planets around the bright nearby star HD 110067. We find that the planets follow a chain of resonant orbits. A dynamical study of the innermost planet triplet allowed the prediction and later confirmation of the orbits of the rest of the planets in the system. The six planets are found to be sub-Neptunes with radii ranging from 1.94R⊕ to 2.85R⊕. Three of the planets have measured masses, yielding low bulk densities that suggest the presence of large hydrogen-dominated atmospheres.

Parathyroidectomy trends and surgical trainee parathyroidectomy experience based on the Collaborative Endocrine Surgery Quality Improvement Program (CESQIP) database

BACKGROUND

The parathyroidectomy approach has shifted over the last few decades from routine bilateral to more commonly focused exploration. The purpose of this study is to assess the operative experience in parathyroidectomy for surgical trainees as well as overall parathyroidectomy trends.

METHODS

Data from the Collaborative Endocrine Surgery Quality Improvement Program (CESQIP) were analyzed between 2014 and 2019.

RESULTS

The overall distribution of focused versus bilateral parathyroidectomy remained stable (2014: 54 % focused and 46 % bilateral approach; 2019: 55 % focused and 45 % bilateral). Ninety three percent of procedures involved a trainee (fellow or resident) in 2014, this dropped to 74 % in 2019 (P < 0.005). Fellow involvement decreased significantly from 31 % to 17 % (P < 0.05) over the six-year period.

CONCLUSIONS

Resident exposure to parathyroidectomies mirrored that of practicing endocrine surgeons. This works highlights the opportunities to capture more information regarding the surgical trainee experience in endocrine surgeries.

Prediction of exercise respiratory limitation from pulmonary function tests

BACKGROUND

Evaluation of unexplained exercise intolerance is best resolved by cardiopulmonary exercise testing (CPET) which enables the determination of the exercise limiting system in most cases. Traditionally, pulmonary function tests (PFTs) at rest are not used for the prediction of a respiratory limitation on CPET.

OBJECTIVE

We sought cut-off values on PFTs that might, a priori, rule-in or rule-out a respiratory limitation in CPET.

METHODS

Patients who underwent CPET in our institute were divided into two groups according to spirometry: obstructive and non-obstructive. Each group was randomly divided 2:1 into derivation and validation cohorts respectively. We analyzed selected PFTs parameters in the derivation groups in order to establish maximal and minimal cut-off values for which a respiratory limitation could be ruled-in or ruled-out. We then validated these values in the validation cohorts.

RESULTS

Of 593 patients who underwent a CPET, 126 were in the obstructive and 467 in the non-obstructive group. In patients with obstructive lung disease, forced expiratory volume in 1 second (FEV1) ≥ 61% predicted could rule out a respiratory limitation, while FEV1 ≤ 33% predicted was always associated with a respiratory limitation. For patients with non-obstructive spirometry, FEV1 of ≥ 73% predicted could rule-out a respiratory limitation. Application of this algorithm might have saved up to 47% and 71% of CPETs in our obstructive and non-obstructive groups, respectively.

CONCLUSION

Presence or absence of a respiratory limitation on CPET can be predicted in some cases based on a PFTs performed at rest.

GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies

The GWAS Central resource gathers and curates extensive summary-level genome-wide association study (GWAS) data and puts a range of user-friendly but powerful website tools for the comparison and visualisation of GWAS data at the fingertips of researchers. Through our continued efforts to harmonise and import data received from GWAS authors and consortia, and data sets actively collected from public sources, the database now contains over 72.5 million P-values for over 5000 studies testing over 7.4 million unique genetic markers investigating over 1700 unique phenotypes. Here, we describe an update to integrate this extensive data collection with mouse disease model data to support insights into the functional impact of human genetic variation. GWAS Central has expanded to include mouse gene-phenotype associations observed during mouse gene knockout screens. To allow similar cross-species phenotypes to be compared, terms from mammalian and human phenotype ontologies have been mapped. New interactive interfaces to find, correlate and view human and mouse genotype-phenotype associations are included in the website toolkit. Additionally, the integrated browser for interrogating multiple association data sets has been updated and a GA4GH Beacon API endpoint has been added for discovering variants tested in GWAS. The GWAS Central resource is accessible at https://www.gwascentral.org/.

Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond

Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple "yes" or "no" responses to queries about the presence of a given variant in datasets hosted by Beacon providers. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a "lingua franca" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects.

Auto-CORPus: A Natural Language Processing Tool for Standardizing and Reusing Biomedical Literature

To analyse large corpora using machine learning and other Natural Language Processing (NLP) algorithms, the corpora need to be standardized. The BioC format is a community-driven simple data structure for sharing text and annotations, however there is limited access to biomedical literature in BioC format and a lack of bioinformatics tools to convert online publication HTML formats to BioC. We present Auto-CORPus (Automated pipeline for Consistent Outputs from Research Publications), a novel NLP tool for the standardization and conversion of publication HTML and table image files to three convenient machine-interpretable outputs to support biomedical text analytics. Firstly, Auto-CORPus can be configured to convert HTML from various publication sources to BioC. To standardize the description of heterogenous publication sections, the Information Artifact Ontology is used to annotate each section within the BioC output. Secondly, Auto-CORPus transforms publication tables to a JSON format to store, exchange and annotate table data between text analytics systems. The BioC specification does not include a data structure for representing publication table data, so we present a JSON format for sharing table content and metadata. Inline tables within full-text HTML files and linked tables within separate HTML files are processed and converted to machine-interpretable table JSON format. Finally, Auto-CORPus extracts abbreviations declared within publication text and provides an abbreviations JSON output that relates an abbreviation with the full definition. This abbreviation collection supports text mining tasks such as named entity recognition by including abbreviations unique to individual publications that are not contained within standard bio-ontologies and dictionaries. The Auto-CORPus package is freely available with detailed instructions from GitHub at: https://github.com/omicsNLP/Auto-CORPus.

Management of well appearing infants born to afebrile mothers with inadequate GBS prophylaxis: A retrospective comparison of the three approaches recommended by the COFN

BACKGROUND

There are three different approaches set forth by the Committee on the Fetus and Newborn (COFN) for managing asymptomatic neonates born to mothers with inadequate intrapartum antibiotic prophylaxis (IAP) for early-onset Group B Strep (GBS) infection. The first approach is that of categorical risk factor assessments, and recommends that asymptomatic infants born to afebrile mothers with inadequate IAP for GBS be monitored with clinical observation for 36-48 hours. The second approach recommends serial physical examinations and vital signs for 36-48 hours to closely monitor changes in clinical condition for all patients. The Kaiser Permanente EOS risk calculator (SRC) is an example of the third approach, a multivariate risk assessment, and it takes into consideration several perinatal risk factors. This multivariate risk assessment then provides recommendations for reassessment and management based on presume risk of the infant developing or having Early Onset Sepsis (EOS). The aim of our study was to compare these three recently published recommendations from the COFN for the management of asymptomatic neonates born to afebrile mothers with inadequate IAP for GBS.

STUDY DESIGN

This is a retrospective study of asymptomatic neonates with gestational age ≥35 weeks born to afebrile mothers with indicated inadequate IAP for GBS between April 2017 and July 2020. Management recommendations of the SRC were compared to the recommendations of categorical risk assessment and risk assessment based on clinical condition.

RESULTS

A total of 7,396 infants were born during the study period, 394 (5.3%. to mothers with inadequate IAP. Recommendations for these infants according to both the categorical risk factor guideline and the clinical condition guideline include extended, close observation. However, the SRC recommended routine newborn care for 99.7%.f these infants. None of the infants developed EOS.

CONCLUSION

The SRC recommend routine neonatal care without enhanced and prolonged observation for nearly all asymptomatic infants born to afebrile mothers with inadequate IAP. As none of the infants in this cohort had EOS, further studies in a larger cohort are needed to establish the safety of SRC in neonates born to mothers with inadequate IAP.

GA4GH: International policies and standards for data sharing across genomic research and healthcare

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Role of Chiral Two-Body Currents in ^{6}Li Magnetic Properties in Light of a New Precision Measurement with the Relative Self-Absorption Technique

A direct measurement of the decay width of the excited 0_{1}^{+} state of ^{6}Li using the relative self-absorption technique is reported. Our value of Γ_{γ,0_{1}^{+}→1_{1}^{+}}=8.17(14)_{stat.}(11)_{syst.}  eV provides sufficiently low experimental uncertainties to test modern theories of nuclear forces. The corresponding transition rate is compared to the results of ab initio calculations based on chiral effective field theory that take into account contributions to the magnetic dipole operator beyond leading order. This enables a precision test of the impact of two-body currents that enter at next-to-leading order.

Thyroid Cancer Identified After Positron Emission Tomography (PET) Shows Aggressive Histopathology

BACKGROUND

Incidental thyroid nodules with focal uptake on positron emission tomography (PET) have an increased risk for malignancy, with the majority being differentiated thyroid cancer (DTC). It is unclear whether these cancers have more aggressive histopathology compared with DTC diagnosed via other means.

METHOD

Electronic medical record of two medical centers was queried for the period of 2001-2016 to identify patients who underwent PET imaging for nonthyroid-related indications and who were found to have focal thyroid uptake. Patients who underwent thyroid nodule fine needle aspiration biopsy (FNAB) and subsequent thyroidectomy with a final diagnosis of DTC were further reviewed. A comparison group, matched for age, tumor type, and tumor size, was selected from consecutive patients who underwent surgery for DTC.

RESULTS

Among 35,124 PET scans reviewed, 227 (0.6%) patients were found to have focal thyroid uptake and underwent FNAB: Fourty-seven (21%) were found to have cancer (36 papillary thyroid cancer (PTC), 9 metastases, and 2 lymphoma). Sixty-seven patients proceeded to surgery: Thirty-one with FNAB of PTC and the rest with indeterminate FNAB necessitating diagnostic thyroidectomy. Compared with the control group, the PET PTC patients involved more men (54% versus 26%, P = 0.003), had more advanced tumor stage (P = 0.03), and had increased BRAF mutation on final pathology (78% versus 42%, P = 0.05).

CONCLUSIONS

This study demonstrates that DTC detected on PET is most commonly of the papillary type. Despite the small sample size, the results suggest that these PTC may be more aggressive than PTC detected through other means and more frequently harbor BRAF mutations.

ΔK=0 M1 Excitation Strength of the Well-Deformed Nucleus ^{164}Dy from K Mixing

The size of a ΔK=0 M1 excitation strength has been determined for the first time in a predominantly axially deformed even-even nucleus. It has been obtained from the observation of a rare K-mixing situation between two close-lying J^{π}=1^{+} states of the nucleus ^{164}Dy with components characterized by intrinsic projection quantum numbers K=0 and K=1. Nuclear resonance fluorescence induced by quasimonochromatic linearly polarized γ-ray beams provided evidence for K mixing of the 1^{+} states at 3159.1(3) and 3173.6(3) keV in excitation energy from their γ-decay branching ratios into the ground-state band. The ΔK=0 transition strength of B(M1;0_{1}^{+}→1_{K=0}^{+})=0.008(1)μ_{N}^{2} was inferred from a mixing analysis of their M1 transition rates into the ground-state band. It is in agreement with predictions from the quasiparticle phonon nuclear model. This determination represents first experimental information on the M1 excitation strength of a nuclear quantum state with a negative R-symmetry quantum number.

Long-Term Venovenous Connection for Extracorporeal Carbon Dioxide Removal (ECCO2R)-Numerical Investigation of the Connection to the Common Iliac Veins

Purpose

Currently used cannulae for extracorporeal carbon dioxide removal (ECCO₂R) are associated with complications such as thrombosis and distal limb ischemia, especially for long-term use. We hypothesize that the risk of these complications is reducible by attaching hemodynamically optimized grafts to the patient’s vessels. In this study, as a first step towards a long-term stable ECCO₂R connection, we investigated the feasibility of a venovenous connection to the common iliac veins. To ensure its applicability, the drainage of reinfused blood (recirculation) and high wall shear stress (WSS) must be avoided.

Methods

A reference model was selected for computational fluid dynamics, on the basis of the analysis of imaging data. Initially, a sensitivity analysis regarding recirculation was conducted using as variables: blood flow, the distance of drainage and return to the iliocaval junction, as well as the diameter and position of the grafts. Subsequently, the connection was optimized regarding recirculation and the WSS was evaluated. We validated the simulations in a silicone model traversed by dyed fluid.

Results

The simulations were in good agreement with the validation measurements (mean deviation 1.64%). The recirculation ranged from 32.1 to 0%. The maximum WSS did not exceed 5.57 Pa. The position and diameter of the return graft show the highest influence on recirculation. A correlation was ascertained between recirculation and WSS. Overall, an inflow jet directed at a vessel wall entails not only high WSS, but also a flow separation and thereby an increased recirculation. Therefore, return grafts aligned to the vena cava are crucial.

Conclusion

In conclusion, a connection without recirculation could be feasible and therefore provides a promising option for a long-term ECCO₂R connection.

GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies

The GWAS Central resource provides a toolkit for integrative access and visualization of a uniquely extensive collection of genome-wide association study data, while ensuring safe open access to prevent research participant identification. GWAS Central is the world's most comprehensive openly accessible repository of summary-level GWAS association information, providing over 70 million P-values for over 3800 studies investigating over 1400 unique phenotypes. The database content comprises direct submissions received from GWAS authors and consortia, in addition to actively gathered data sets from various public sources. GWAS data are discoverable from the perspective of genetic markers, genes, genome regions or phenotypes, via graphical visualizations and detailed downloadable data reports. Tested genetic markers and relevant genomic features can be visually interrogated across up to sixteen multiple association data sets in a single view using the integrated genome browser. The semantic standardization of phenotype descriptions with Medical Subject Headings and the Human Phenotype Ontology allows the precise identification of genetic variants associated with diseases, phenotypes and traits of interest. Harmonization of the phenotype descriptions used across several GWAS-related resources has extended the phenotype search capabilities to enable cross-database study discovery using a range of ontologies. GWAS Central is updated regularly and available at https://www.gwascentral.org.

Tumor-Targeted Drug Conjugates as an Emerging Novel Therapeutic Approach in Small Cell Lung Cancer (SCLC)

There are few effective therapies for small cell lung cancer (SCLC), a highly aggressive disease representing 15% of total lung cancers. With median survival <2 years, SCLC is one of the most lethal cancers. At present, chemotherapies and radiation therapy are commonly used for SCLC management. Few protein-targeted therapies have shown efficacy in improving overall survival; immune checkpoint inhibitors (ICIs) are promising agents, but many SCLC tumors do not express ICI targets such as PD-L1. This article presents an alternative approach to the treatment of SCLC: the use of drug conjugates, where a targeting moiety concentrates otherwise toxic agents in the vicinity of tumors, maximizing the differential between tumor killing and the cytotoxicity of normal tissues. Several tumor-targeted drug conjugate delivery systems exist and are currently being actively tested in the setting of SCLC. These include antibody-drug conjugates (ADCs), radioimmunoconjugates (RICs), small molecule-drug conjugates (SMDCs), and polymer-drug conjugates (PDCs). We summarize the basis of action for these targeting compounds, discussing principles of construction and providing examples of effective versus ineffective compounds, as established by preclinical and clinical testing. Such agents may offer new therapeutic options for the clinical management of this challenging disease in the future.

Gene loci associated with insulin secretion in islets from non-diabetic mice

Genetic susceptibility to type 2 diabetes is primarily due to β-cell dysfunction. However, a genetic study to directly interrogate β-cell function ex vivo has never been previously performed. We isolated 233,447 islets from 483 Diversity Outbred (DO) mice maintained on a Western-style diet, and measured insulin secretion in response to a variety of secretagogues. Insulin secretion from DO islets ranged >1,000-fold even though none of the mice were diabetic. The insulin secretory response to each secretagogue had a unique genetic architecture; some of the loci were specific for one condition, whereas others overlapped. Human loci that are syntenic to many of the insulin secretion QTL from mouse are associated with diabetes-related SNPs in human genome-wide association studies. We report on three genes, Ptpn18, Hunk and Zfp148, where the phenotype predictions from the genetic screen were fulfilled in our studies of transgenic mouse models. These three genes encode a non-receptor type protein tyrosine phosphatase, a serine/threonine protein kinase, and a Krϋppel-type zinc-finger transcription factor, respectively. Our results demonstrate that genetic variation in insulin secretion that can lead to type 2 diabetes is discoverable in non-diabetic individuals.

Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer

Genomic rearrangements are a hallmark of cancer biology and progression, allowing cells to rapidly transform through alterations in regulatory structures, changes in expression patterns, reprogramming of signaling pathways, and creation of novel transcripts via gene fusion events. Though functional gene fusions encoding oncogenic proteins are the most dramatic outcomes of genomic rearrangements, we investigated the relationship between rearrangements evidenced by fusion transcripts and local expression changes in cancer using transcriptome data alone. 9,953 gene fusion predictions from 418 primary serious ovarian cancer tumors were analyzed, identifying depletions of gene fusion breakpoints within coding regions of fused genes as well as an N-terminal enrichment of breakpoints within fused genes. We identified 48 genes with significant fusion-associated upregulation and furthermore demonstrate that significant regional overexpression of intact genes in patient transcriptomes occurs within 1 megabase of 78 novel gene fusions that function as central markers of these regions. We reveal that cancer transcriptomes select for gene fusions that preserve protein and protein domain coding potential. The association of gene fusion transcripts with neighboring gene overexpression supports rearrangements as mechanism through which cancer cells remodel their transcriptomes and identifies a new way to utilize gene fusions as indicators of regional expression changes in diseased cells with only transcriptomic data.

Shape transitions between and within Zr isotopes

The Zirconium isotopes across the N=56,58 neutron sub­shell closures have been of special interest since years, sparked by the near doubly-magic features of 96Zr and the subsequent rapid onset of collectivity with a deformed ground-state structure already in 100Zr. Recent state-of-the-art shell model approaches did not only correctly describe this shape-phase transition in the Zr isotopic chain, but alsothe coexistence of non-collective structures and pronounced collectivity especially in 96,98Zr. Theisotope 98Zr is located on the transition from spherical to deformed ground state structures. We summarize recent experimental work to obtain the B(E2) excitation strengths of the first 2+ state of98Zr, including a new experiment employing the recoil-distance Doppler-shift method following a two-neutron transfer reaction.

A stochastic microstructure model for particle reinforced aluminium matrix composites

Metal matrix composites are complex materials consisting of various phases which can display largely different mechanical properties. The deformation behaviour of these composites cannot be sufficiently modelled by averages or simple particle shapes due to the local stresses that occur on the particle edges. Therefore, a sophisticated model of the microstructure is needed. We introduce a method for stochastic modelling of a silicon carbide (SiC) particle reinforced aluminium matrix composite. The SiC particles are modelled by Laguerre polyhedra generated by densely packed spheres. The shape factors of the polyhedra have been fitted to the particle shapes observed in three-dimensional images. Particle elongation in extrusion direction and the observed log-normal volume distribution of the particles are included in the model by suitable scaling. An outlook is presented on how to model the grains of the polycrystalline aluminium matrix and intermetallic precipitates, which result from the strengthening mechanism of the matrix. LAY DESCRIPTION: Metal matrix composites are complex materials consisting of different phases which can display largely different mechanical properties. The deformation behaviour of these composites cannot be sufficiently modelled by averages or simple particle shapes due to the local stresses that occur on the particle edges. Therefore, a sophisticated model of the microstructure is needed. We introduce a method of stochastic modelling of a silicon carbide (SiC) particle reinforced aluminium matrix composite. The SiC particles are modelled by Laguerre polyhedra generated by densely packed spheres. The shape factors of the polyhedra have been fitted to the SiC shapes observed in three-dimensional images. Additionally, the polyhedra are scaled anisotropically to account for orientation anisotropy and to obtain a log-normal volume distribution. An outlook is presented on how to model the aluminium phase's grains and intermetallic precipitates, which result from the strengthening mechanism of the aluminium matrix alloy.

Effect of pre-operative methylprednisolone on orthostatic hypotension during early mobilization after total hip arthroplasty

BACKGROUND

Orthostatic hypotension (OH) and intolerance (OI) are common after total hip arthroplasty (THA) and may delay early mobilization. The pathology of OH and OI includes a dysregulated post-operative vasopressor response, by a hitherto unknown mechanism. We hypothesized that OI could be related to the inflammatory stress response which is inhibited by steroid administration. Consequently, this study evaluated the effect of a pre-operative high-dose methylprednisolone on OH and OI early after THA.

METHODS

Randomized, double-blind, placebo-controlled study in 59 patients undergoing elective unilateral THA with spinal anesthesia and a standardized multimodal analgesic regime. Patients were allocated (1 : 1) to pre-operative intravenous (IV) methylprednisolone (MP) 125 mg or isotonic saline (C). OH, OI and cardiovascular responses to sitting and standing were evaluated using a standardized mobilization protocol pre-operatively, 6, and 24 h after surgery. Systolic and diastolic arterial pressure and heart rate were measured non-invasively (Nexfin^® ). The systemic inflammation was monitored by the C-reactive protein (CRP) response.

RESULTS

At 6 h post-operatively, 11 (38%) versus 11 (37%) patients had OH in group MP and group C, respectively (RR 1.02 (0.60 to 1.75; P = 1.00)), whereas OI was present in 9 (31%) versus 13 (43%) patients (RR 0.76 (0.42 to 1.36; P = 0.42)), respectively. At 24 h post-operatively, the prevalence of OH and OI did not differ between groups, though CRP levels were significantly reduced in group MP (P < 0.001).

CONCLUSION

Pre-operative administration of 125 mg methylprednisolone IV did not reduce OH or OI compared with placebo despite a reduced inflammatory response.

Shell Evolution and E2 Collectivity: New Spectroscopic Information

New spectroscopic information on electric quadrupole collectivity has recently been obtained. We report on our identification of a coexisting deformed structure in the quasi-doubly closed-shell nucleus 96Zr from our measurement of a corresponding absolute E2 intraband transition strength in electron scattering reactions and its small mixing matrix element with the spherical ground state structure. The even-mass zirconium isotopes exhibit a first order quantum shape phase transition between neutron numbers 58 and 60. We have used photon scattering reactions for a first measurement of the E2 decay strength of the nuclear 1+ scissors mode. Evidence for its 2+ rotational excitation and its extraordinarily large rotational moment of inertia are presented.

E2 decay strength of the M1 scissors mode of ^{156}Gd and its first excited rotational state

The E2/M1 multipole mixing ratio δ_{1→2} of the 1_{sc}^{+}→2_{1}^{+} γ-ray decay in ^{156}Gd and hence the isovector E2 transition rate of the scissors mode of a well-deformed rotational nucleus has been measured for the first time. It has been obtained from the angular distribution of an artificial quasimonochromatic linearly polarized γ-ray beam of energy 3.07(6) MeV scattered inelastically off an isotopically highly enriched ^{156}Gd target. The data yield first direct support for the deformation dependence of effective proton and neutron quadrupole boson charges in the framework of algebraic nuclear models. First evidence for a low-lying J^{π}=2^{+} member of the rotational band of states on top of the 1^{+} band head is obtained, too, indicating a significant signature splitting in the K=1 scissors mode rotational band.

A data-driven approach links microglia to pathology and prognosis in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that lacks a predictive and broadly applicable biomarker. Continued focus on mutation-specific upstream mechanisms has yet to predict disease progression in the clinic. Utilising cellular pathology common to the majority of ALS patients, we implemented an objective transcriptome-driven approach to develop noninvasive prognostic biomarkers for disease progression. Genes expressed in laser captured motor neurons in direct correlation (Spearman rank correlation, p < 0.01) with counts of neuropathology were developed into co-expression network modules. Screening modules using three gene sets representing rate of disease progression and upstream genetic association with ALS led to the prioritisation of a single module enriched for immune response to motor neuron degeneration. Genes in the network module are important for microglial activation and predict disease progression in genetically heterogeneous ALS cohorts: Expression of three genes in peripheral lymphocytes - LILRA2, ITGB2 and CEBPD – differentiate patients with rapid and slowly progressive disease, suggesting promise as a blood-derived biomarker. TREM2 is a member of the network module and the level of soluble TREM2 protein in cerebrospinal fluid is shown to predict survival when measured in late stage disease (Spearman rank correlation, p = 0.01). Our data-driven systems approach has, for the first time, directly linked microglia to the development of motor neuron pathology. LILRA2, ITGB2 and CEBPD represent peripherally accessible candidate biomarkers and TREM2 provides a broadly applicable therapeutic target for ALS.

Whole-Body Diffusion Imaging Applying Simultaneous Multi-Slice Excitation

PURPOSE

The purpose of this study was to examine the feasibility of a fast protocol for whole-body diffusion-weighted imaging (WB-DWI) using a slice-accelerated echo-planar sequence, which, when using comparable image acquisition parameters, noticeably reduces measurement time compared to a conventional WB-DWI protocol.

MATERIALS AND METHODS

A single-shot echo-planar imaging sequence capable of simultaneous slice excitation and acquisition was optimized for WB-DWI on a 3 T MR scanner, with a comparable conventional WB-DWI protocol serving as the reference standard. Eight healthy individuals and one oncologic patient underwent WB-DWI. Quantitative analysis was carried out by measuring the apparent diffusion coefficient (ADC) and its coefficient of variation (CV) in different organs. Image quality was assessed qualitatively by two independent radiologists using a 4-point Likert scale.

RESULTS

Using our proposed protocol, the scan time of the WB-DWI measurement was reduced by up to 25.9 %. Both protocols, the slice-accelerated protocol and the conventional protocol, showed comparable image quality without statistically significant differences in the reader scores. Similarly, no significant differences of the ADC values of parenchymal organs were found, whereas ADC values of brain tissue were slightly higher in the slice-accelerated protocol.

CONCLUSION

It was demonstrated that slice-accelerated DWI can be applied to WB-DWI protocols with the potential to greatly reduce the required measurement time, thereby substantially increasing clinical applicability.

KEY POINTS

•Whole-body diffusion-weighted imaging (WB-DWI) using simultaneous multi-slice and blipped-CAIPIRINHA reduces the measurement time strongly without having a significant impact on image quality. •The reduction in measurement time might strongly contribute to the clinical applicability of WB-DWI. •However, further refinement of the slice-accelerated EPI sequence, and the WB-DWI protocol applying this sequence type seems necessary; and the value of such WB-DWI protocols for assessment of systemic oncological diseases needs to be investigated in further clinical studies.

Cafe Variome: general-purpose software for making genotype-phenotype data discoverable in restricted or open access contexts

Biomedical data sharing is desirable, but problematic. Data "discovery" approaches-which establish the existence rather than the substance of data-precisely connect data owners with data seekers, and thereby promote data sharing. Cafe Variome (http://www.cafevariome.org) was therefore designed to provide a general-purpose, Web-based, data discovery tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners, to make safe or sensitive content appropriately discoverable. Data fields or content of any type can be accommodated, from simple ID and label fields through to extensive genotype and phenotype details based on ontologies. The system provides a "shop window" in front of data, with main interfaces being a simple search box and a powerful "query-builder" that enable very elaborate queries to be formulated. After a successful search, counts of records are reported grouped by "openAccess" (data may be directly accessed), "linkedAccess" (a source link is provided), and "restrictedAccess" (facilitated data requests and subsequent provision of approved records). An administrator interface provides a wide range of options for system configuration, enabling highly customized single-site or federated networks to be established. Current uses include rare disease data discovery, patient matchmaking, and a Beacon Web service.

Abstract 34: AMH and AMHR2 regulate survival signaling, epithelial-mesenchymal transition (EMT) and resistance to HSP90 inhibition in non-small cell lung cancer (NSCLC)

In spite of encouraging advances in the treatment of lung cancer, the five-year survival rate has remained below 20 percent. Much of the mortality is associated with uncontrolled metastasis. Members of the TGF-ß/BMP superfamily have long been known to regulate progression and metastasis in NSCLC. In this study, we identify unexpected inputs into TGF-ß/BMP superfamily signaling that significantly modulate intrinsic tumor properties and drug response in NSCLC.

Anti-Mullerian Hormone (AMH) and its specific type II receptor, AMHR2, share common type I receptors with BMP, and regulate overlapping signaling outputs. AMH and AMHR2 have thus far predominantly been studied in the context of gonadal development, in regulation of the female reproductive cycle and in gynecological malignancies. However, using a focused RNAi library designed to detect genes associated with resistance to the HSP90 inhibitor ganetespib, siRNAs against AMH and AMHR2 sensitized 4 out of 5 and 3 out of 5 NSCLC cell lines to ganetespib, respectively. We for the first time confirmed autocrine expression of AMH and AMHR2 in this non-gonadal tumor environment.

TGF-ß and BMP signaling is important for the regulation of epithelial-mesenchymal transition (EMT). Strikingly, depletion of AMH/AMHR2 induced EMT-like features, including downregulation of cadherins, assumption of a mesenchymal morphology, and expression of mesenchymal markers, which are generally associated with resistance to chemotherapy. In contrast, inhibition of HSP90 selected for a more epithelial-like population of cells, as evident by increased E-Cadherin or P-Cadherin, and down regulation of mesenchymal markers such as vimentin and α-smooth muscle actin. To confirm that mesenchymal-like cells are indeed more responsive to HSP90 inhibition, we depleted E-cadherin or P-cadherin and again observed sensitization to ganetespib. We further found that AMH and AMHR2 did not confer sensitization to cisplatin.

These data suggested an unusual relationship between ganetespib control of cell growth and differentiation status. We further established that inhibition of HSP90 increased expression of AMH and AMHR2 as well as several of the type 1 receptors (ALK2, ALK3, ALK6) that are necessary for signaling by BMP. Mechanistically, AMH and AMHR2 depletion increased phosphorylation of SMAD proteins, but depressed activity of NF-kB and AKT, both critical regulators of EMT and survival. These results for the first time indicate the presence of an AMH-AMHR2-NFkB-AKT signaling axis of therapeutic relevance in NSCLC. Importantly, our results also suggest that AMH and AMHR2 may serve as biomarkers to predict resistance to HSP90 inhibitors, and that it may be beneficial to prime lung tumors with HSP90 inhibitors, to reverse EMT and decrease survival signaling, prior to treatment with chemotherapy.

Citation Format: Tim Beck, Emmanuelle Nicolas, Yan Zhou, Ilya Serebriiskii, Erica Golemis. AMH and AMHR2 regulate survival signaling, epithelial-mesenchymal transition (EMT) and resistance to HSP90 inhibition in non-small cell lung cancer (NSCLC). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 34. doi:10.1158/1538-7445.AM2015-34

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.

The BioMart community portal: an innovative alternative to large, centralized data repositories

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

Overview of the ARGOS X-ray framing camera for Laser MegaJoule

Commissariat à l'Énergie Atomique et aux Énergies Alternatives has developed the ARGOS X-ray framing camera to perform two-dimensional, high-timing resolution imaging of an imploding target on the French high-power laser facility Laser MegaJoule. The main features of this camera are: a microchannel plate gated X-ray detector, a spring-loaded CCD camera that maintains proximity focus in any orientation, and electronics packages that provide remotely-selectable high-voltages to modify the exposure-time of the camera. These components are integrated into an "air-box" that protects them from the harsh environmental conditions. A miniaturized X-ray generator is also part of the device for in situ self-testing purposes.

Survival after neoadjuvant chemotherapy with or without bevacizumab or everolimus for HER2-negative primary breast cancer (GBG 44-GeparQuinto)†

BACKGROUND

The GeparQuinto study showed that adding bevacizumab to 24 weeks of anthracycline-taxane-based neoadjuvant chemotherapy increases pathological complete response (pCR) rates overall and specifically in patients with triple-negative breast cancer (TNBC). No difference in pCR rate was observed for adding everolimus to paclitaxel in nonearly responding patients. Here, we present disease-free (DFS) and overall survival (OS) analyses.

PATIENTS AND METHODS

Patients (n = 1948) with HER2-negative tumors of a median tumor size of 4 cm were randomly assigned to neoadjuvant treatment with epirubicin/cyclophosphamide followed by docetaxel (EC-T) with or without eight infusions of bevacizumab every 3 weeks before surgery. Patients without clinical response to EC ± Bevacizumab were randomized to 12 weekly cycles paclitaxel with or without everolimus 5 mg/day. To detect a hazard ratio (HR) of 0.75 (α = 0.05, β = 0.8) 379 events had to be observed in the bevacizumab arms.

RESULTS

With a median follow-up of 3.8 years, 3-year DFS was 80.8% and 3-year OS was 89.7%. Outcome was not different for patients receiving bevacizumab (HR 1.03; P = 0.784 for DFS and HR 0.974; P = 0.842 for OS) compared with patients receiving chemotherapy alone. Patients with TNBC similarly showed no improvement in DFS (HR = 0.99; P = 0.941) and OS (HR = 1.02; P = 0.891) when treated with bevacizumab. No other predefined subgroup (HR+/HER2-; locally advanced (cT4 or cN3) or not; cT1-3 or cT4; pCR or not) showed a significant benefit. No difference in DFS (HR 0.997; P = 0.987) and OS (HR 1.11; P = 0.658) was observed for nonearly responding patients receiving paclitaxel with or without everolimus overall as well as in subgroups.

CONCLUSIONS

Long-term results, in opposite to the results of pCR, do not support the neoadjuvant use of bevacizumab in addition to an anthracycline-taxane-based chemotherapy or everolimus in addition to paclitaxel for nonearly responding patients.

CLINICAL TRIAL NUMBER

NCT 00567554, www.clinicaltrials.gov.

Medical preparedness, incidents, and group dynamics during the analog MARS2013 mission

Participants on spaceflights and international scientific analog Mars missions can encounter medical incidents (accidents, illnesses) and psychological issues (e.g., stress, group interaction, sleep disturbance, emotions). The aim of this study was to examine these parameters in a field crew living in a desert environment similar to Mars (Group 1) and in Mission Support Center (MSC) personnel on "Earth" (Group 2) during a 4-week mission. Of the 107 medical interventions in the field, 73 mainly minor incidents together with four near accidents and 29 medical checkup interventions were recorded. Of the 32 medical interventions, medical treatments for 23 incidents of minor severity were necessary in Group 2. Injuries (Group 1: 1.4/100 h, Group 2: 0.1/100 h) were significantly increased in the field, and illnesses (Group 1: 0.3/100 h, Group 2: 3.0/100 h) in the MSC personnel. Causes of accidents and illnesses are described. Psychological results show that emotions and stress remained stable in both groups. Sympathy, social competence, teamwork, and leadership showed high scores. These scores were lower on "Earth" but significantly increased in the last weeks. The Sahara's nighttime coldness was reflected in an increased wake-up frequency, and a longer sleeping time peaked in the third week, probably as a result of overfatigue. MARS2013 was a successful mission with highly motivated participants and minor medical incidents. For future analog missions and possibly long-distance open-space missions, some recommendations in terms of medical and psychological preparedness are made to reduce risks for field crew members and MSC personnel.

Opioid maintenance therapy in Switzerland: an overview of the Swiss IMPROVE study

BACKGROUND/AIMS

Switzerland's drug policy model has always been unique and progressive, but there is a need to reassess this system in a rapidly changing world. The IMPROVE study was conducted to gain understanding of the attitudes and beliefs towards opioid maintenance therapy (OMT) in Switzerland with regards to quality and access to treatment. To obtain a "real-world" view on OMT, the study approached its goals from two different angles: from the perspectives of the OMT patients and of the physicians who treat patients with maintenance therapy. The IMPROVE study collected a large body of data on OMT in Switzerland. This paper presents a small subset of the dataset, focusing on the research design and methodology, the profile of the participants and the responses to several key questions addressed by the questionnaires.

METHODS

IMPROVE was an observational, questionnaire-based cross-sectional study on OMT conducted in Switzerland. Respondents consisted of OMT patients and treating physicians from various regions of the country. Data were collected using questionnaires in German and French. Physicians were interviewed by phone with a computer-based questionnaire. Patients self-completed a paper-based questionnaire at the physicians' offices or OMT treatment centres.

RESULTS

A total of 200 physicians and 207 patients participated in the study. Liquid methadone and methadone tablets or capsules were the medications most commonly prescribed by physicians (60% and 20% of patient load, respectively) whereas buprenorphine use was less frequent. Patients (88%) and physicians (83%) were generally satisfied with the OMT currently offered. The current political framework and lack of training or information were cited as determining factors that deter physicians from engaging in OMT. About 31% of OMT physicians interviewed were ≥60 years old, indicating an ageing population. Diversion and misuse were considered a significant problem in Switzerland by 45% of the physicians.

CONCLUSION

The subset of IMPROVE data presented gives a present-day, real-life overview of the OMT landscape in Switzerland. It represents a valuable resource for policy makers, key opinion leaders and drug addiction researchers and will be a useful basis for improving the current Swiss OMT model.

WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing

Motivation: Copy number variations (CNVs) are a major source of genomic variability and are especially significant in cancer. Until recently microarray technologies have been used to characterize CNVs in genomes. However, advances in next-generation sequencing technology offer significant opportunities to deduce copy number directly from genome sequencing data. Unfortunately cancer genomes differ from normal genomes in several aspects that make them far less amenable to copy number detection. For example, cancer genomes are often aneuploid and an admixture of diploid/non-tumor cell fractions. Also patient-derived xenograft models can be laden with mouse contamination that strongly affects accurate assignment of copy number. Hence, there is a need to develop analytical tools that can take into account cancer-specific parameters for detecting CNVs directly from genome sequencing data.

Results: We have developed WaveCNV, a software package to identify copy number alterations by detecting breakpoints of CNVs using translation-invariant discrete wavelet transforms and assign digitized copy numbers to each event using next-generation sequencing data. We also assign alleles specifying the chromosomal ratio following duplication/loss. We verified copy number calls using both microarray (correlation coefficient 0.97) and quantitative polymerase chain reaction (correlation coefficient 0.94) and found them to be highly concordant. We demonstrate its utility in pancreatic primary and xenograft sequencing data.

Availability and implementation: Source code and executables are available at https://github.com/WaveCNV. The segmentation algorithm is implemented in MATLAB, and copy number assignment is implemented Perl.

Contact:lakshmi.muthuswamy@gmail.com

Supplementary information:Supplementary data are available at Bioinformatics online.