bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes
Authors: Vernette Caroline , Lecubin Julien , Sánchez Pablo ,   Tara Oceans Coordinators, Acinas Silvia G , Babin Marcel , Bork Peer , Boss Emmanuel , Bowler Chris , Cochrane Guy , de Vargas Colomban , Gorsky Gabriel , Guidi Lionel , Grimsley Nigel , Hingamp1 Pascal , Iudicone Daniele , Jaillon Olivier , Kandels-Lewis Stefanie , Karp-Boss Lee , Karsenti Eric , Not Fabrice , Ogata Hiroyuki , Poulton Nicole , Pesant Stéphane , Sardet Christian , Speich Sabrina , Stemmann Lars , Sullivan Matthew B , Sunagawa Shinichi , Wincker Patrick , Sunagawa Shinichi , Delmont Tom O , Acinas Silvia G , Pelletier Eric , Hingamp Pascal , Lescot Magali 
Published: May 2022

Abstract
Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.
Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks
Authors: Emelianova Mariia , Gainullina Anastasiia , Poperechnyi Nikolay , Loboda Alexander , Artyomov Maxim , Sergushichev Alexey 
Published: May 2022

AbstractMultiple high-throughput omics techniques provide different angles on systematically quantifying and studying metabolic regulation of cellular processes. However, an unbiased analysis of such data and, in particular, integration of multiple types of data remains a challenge. Previously, for this purpose we developed GAM web-service for integrative metabolic network analysis. Here we describe an updated pipeline GATOM and the corresponding web-service Shiny GATOM, which takes as input transcriptional and/or metabolomic data and finds a metabolic subnetwork most regulated between the two conditions of interest. GATOM features a new metabolic network topology based on atom transition, which significantly improves interpretability of the analysis results. To address computational challenges arising with the new network topology, we introduce a new variant of the maximum weight connected subgraph problem and provide a corresponding exact solver. To make the used networks up-to-date we upgraded the KEGG-based network construction pipeline and developed one based on the Rhea database, which allows analysis of lipidomics data. Finally, we simplified local installation, providing R package mwcsr for solving relevant graph optimization problems and R package gatom, which implements the GATOM pipeline. The web-service is available at https://ctlab.itmo.ru/shiny/gatom and https://artyomovlab.wustl.edu/shiny/gatom.
AllerCatPro 2.0: a web server for predicting protein allergenicity potential
Authors: Nguyen Minh N , Krutz Nora L , Limviphuvadh Vachiranee , Lopata Andreas L , Gerberick G Frank , Maurer-Stroh Sebastian 
Published: May 2022

Abstract
Proteins in food and personal care products can pose a risk for an immediate immunoglobulin E (IgE)-mediated allergic response. Bioinformatic tools can assist to predict and investigate the allergenic potential of proteins. Here we present AllerCatPro 2.0, a web server that can be used to predict protein allergenicity potential with better accuracy than other computational methods and new features that help assessors making informed decisions. AllerCatPro 2.0 predicts the similarity between input proteins using both their amino acid sequences and predicted 3D structures towards the most comprehensive datasets of reliable proteins associated with allergenicity. These datasets currently include 4979 protein allergens, 162 low allergenic proteins, and 165 autoimmune allergens with manual expert curation from the databases of WHO/International Union of Immunological Societies (IUIS), Comprehensive Protein Allergen Resource (COMPARE), Food Allergy Research and Resource Program (FARRP), UniProtKB and Allergome. Various examples of profilins, autoimmune allergens, low allergenic proteins, very large proteins, and nucleotide input sequences showcase the utility of AllerCatPro 2.0 for predicting protein allergenicity potential. The AllerCatPro 2.0 web server is freely accessible at https://allercatpro.bii.a-star.edu.sg.
Clinical and Immunological Markers of Pulmonary Impairment Among People With HIV in India
Authors: Baidya Anurima , Sangle Shashikala , Marbaniang Ivan , Kulkarni Vandana , Deshpande Prasad , Nimkar Smita , Chavan Amol , Salvi Sonali , Lokhande Rahul , Kadam Dileep , Gupta Amita , Mave Vidya , Gupte Akshay N 
Published: May 2022

Abstract

Background
Despite antiretroviral therapy, chronic lung diseases remain an important source of morbidity and mortality in people with HIV (PWH). We sought to identify clinical and immunological markers of pulmonary impairment among PWH in India.

Methods
Two hundred ten adult PWH receiving antiretroviral therapy (ART) were prospectively evaluated for 3 years. Plasma concentrations of interleukin (IL)-6, IL-10, tumor necrosis factor alpha, D-dimer, C-reactive protein, soluble (s)CD14, and sCD163 were measured at enrollment. We used multivariable linear and logistic regression to measure the association of baseline and time-varying clinical and immunological variables with spirometry-defined chronic obstructive pulmonary disease (COPD), restrictive spirometry pattern (RSP), preserved ratio impaired spirometry (PRISm), forced expiratory volume in 1 second (FEV1), and forced vital capacity (FVC) during the third year of follow-up.

Results
After adjusting confounders, females were 7 times more likely to have RSP (95% CI, 2.81 to 17.62; P &lt; .001) and 22 times more likely to have PRISm (95% CI, 7.42 to 69.92; P &lt; .001) compared with men. Higher IL-6 concentrations were associated with lower FEV1 z-scores (β, −0.14 per log-higher; 95% CI, −0.29 to 0.008; P = .06) and higher odds of COPD (adjusted odds ratio [aOR], 2.66 per log-higher; 95% CI, 1.16 to 6.09; P = .02). Higher D-dimer concentrations were associated with lower FVC z-scores (β, −0.40 per log-higher; 95% CI, −0.78 to −0.01; P = .04). Conversely, higher IL-10 concentrations were associated with lower odds of PRISm (aOR, 0.76 per log-higher; 95% CI, 0.59 to 0.99; P = .04).

Conclusions
Female sex, higher concentrations of IL-6 and D-dimer, and lower concentrations of IL-10 were associated with pulmonary impairment in adult PWH receiving ART in India.
Quantification and Progress Over Time of Specific Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2 in Breast Milk of Lactating Women Vaccinated With BNT162b2 Pfizer-BioNTech Coronavirus Disease 2019 Vaccine (LacCOVID)
Authors: Esteve-Palau Erika , Gonzalez-Cuevas Araceli , Guerrero M Eugenia , Garcia-Terol Clara , Alvarez M Carmen , Garcia Geneva , Moreno Encarna , Medina Francisco , Casadevall David , Diaz-Brito Vicens 
Published: May 2022

Abstract

Background
Several observational studies demonstrated the passage of postvaccine antibodies through breast milk in women vaccinated against coronavirus disease 2019 (COVID-19), mostly with messenger RNA (mRNA)–based vaccines, but lacked long-term data.

Methods
A 6-month prospective cohort study was performed to determine severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine–induced antibody levels in the breast milk of 33 lactating healthcare workers at different timepoints after mRNA BNT162b2 Pfizer-BioNTech COVID-19 vaccination. Moreover, we examined the correlation of SARS-CoV-2 antibody levels between serum and breast milk, adverse events related to vaccination, and rate of SARS-CoV-2 infections.

Results
Mothers’ median age was 38 (interquartile range [IQR], 36–39) years and 15 (IQR, 10–22) months for infants. Median (IQR) SARS-CoV-2 immunoglobulin G (IgG) spike protein subunit S1 (S1) vaccine–induced levels at different timepoints for serum–milk pairs were 519 (234–937) to 1 (0–2.9) arbitrary units (AU)/mL at 2 weeks after first dose and 18 644 (9923–29 264) to 78 (33.7–128), 12 478 (6870–20 801) to 50.4 (24.3–104), 4094 (2413–8480) to 19.9 (10.8–51.9), 1350 (831–2298) to 8.9 (7.8–31.5) AU/mL at 2, 4, 12 and 24 weeks after second dose, respectively. We observed a positive correlation of antibody levels between serum and breast milk, no serious adverse events related to vaccination, and 2 (6%) COVID-19 vaccine breakthrough infections.

Conclusions
Women vaccinated with Pfizer-BioNTech transmit antibodies into breast milk with a positive correlation with serum levels. Both decreased over time in a 6-month follow-up.
Understanding the mechanics of complex topology of the 3D printed Anthill architecture
Authors: Kushwaha Brijesh , Kumar Avinash , Ambekar Rushikesh S , Arya Vinay , Negedu Solomon Demiss , Bakshi Deep , Olu Femi Emmanuel , Sastri Ayyagari Ravi , Pal Varinder , Sadasivuni Kishor Kumar , Pugno Nicola M , Bakli Chirodeep , Tiwary Chandra S 
Published: May 2022

Abstract
The present work aimed to investigate the deformation behavior of complex ant mound architectures under compression. We have used the cement casting method to extract four different ant nest morphologies. These casted cement structures were digitalized using a 3D micro-computer tomography scan. The digitized structures were simulated under different loading conditions using finite-element methods (FEMs). In order to supplement the numerical understanding, the digital architectures were 3D printed and experimentally tested under uniaxial loading conditions. Ants produce a variety of complex architectures for adapting to the surrounding environment and ants’ needs. Ant mound consists of at least one pillar with a broad base tapered toward its tip. Anthill architectures have unique topological features. Mechanical strength of ant mould can be 600 times enhanced by tuning topology. Thickness and angle of pillars have huge effect on load-bearing property. The branched structures can endure larger stress and deform in the process under a volumetric pressure application, making them sacrificial units for extreme disasters like floods and earthquakes. The 3D printing experiments and FEMs simulations are needed to tackle the complex ant mound architectures and appear in good agreement, suggesting a robust design and thus the possibility of constructing anthill-inspired civil buildings with a tree-trunk-like geometry.
Reliability, Validity, and Responsiveness of the Craniocervical Flexion Test in People Who Are Asymptomatic and Patients With Nonspecific Neck Pain: A Systematic Review and Meta-Analysis
Authors: Romeo Antonio , Baccini Marco , Carreras Giulia , Sagripanti Marco , Ruggeri Martina , Pillastrini Paolo , Di Bari Mauro 
Published: May 2022

Abstract

Objective
Among the tests designed to evaluate neck neuromuscular function, the craniocervical flexion test (CCFT) assesses the function of the deep cervical flexor muscles (DCFs). The purpose of this study was to conduct a review and meta-analysis of published articles about all measurement properties of the different CCFT versions (CCFT Activation Score [CCFT-AS], CCFT Performance Index [CCFT-PI], CCFT Cumulative Performance Index [CCFT-CPI], and CCFT alternative procedures for measuring activation level (CCFT1) or endurance (CCFT2) in people who were asymptomatic and people with nonspecific neck pain.

Methods
PubMed Central, MEDLINE, CINAHL, Scopus, Web of Science, and Google Scholar were searched from inception to June 30, 2020. Studies were selected if they reported data on reliability, validity, and/or responsiveness of the CCFT in adults who were asymptomatic or who had nonspecific neck pain. Two reviewers independently selected the studies, conducted quality assessment, and extracted the results. All meta-analyses used a random-effects model.

Results
Twenty-one studies met the inclusion criteria. The rating of interrater reliability (assessed for CCFT-AS and CCFT-CPI) was positive only for using the test at a group level. The same rating was ascribed to the intrarater reliability of CCFT-AS, CCFT1, and CCFT2, whereas CCFT-PI and CCFT-CPI showed positive intrarater reliability for assessment of individuals as well. CCFT validity was rated as positive for expressly assessing DCF action when measuring DCF activation through electromyography—not through ultrasonography—or craniocervical flexion motion as well as for differentiating patients who were asymptomatic and patients who had nonspecific neck pain (only the AS version). CCFT validity was rated as negative for investigating the CCFT performance correlation with the severity of nonspecific neck pain. CCFT responsiveness was rated as negative.

Conclusions
The CCFT is a potentially useful tool for detecting impairment in DCF control and identifying patients who have nonspecific neck pain and who would benefit from a targeted intervention. However, the limited reliability affects its suitability for that purpose. Further research on the reliability of different CCFT versions in which the raters are thoroughly trained is strongly recommended.

Impact
The CCFT might help to detect impairment in DCF control and identify patients who have nonspecific neck pain and who would benefit from a targeted intervention. However, the poor reliability of most versions of the test greatly limits its application in clinical practice. Only CCFT-PI and CCFT-CPI seem reliable enough to help in clinical decision-making at the individual level.
Adipose tissue distribution is associated with cardio-metabolic alterations in adult patients with juvenile-onset dermatomyositis
Authors: Marstein Henriette S , Witczak Birgit N , Godang Kristin , Schwartz Thomas , Flatø Berit , Bollerslev Jens , Sjaastad Ivar , Sanner Helga 
Published: May 2022

AbstractObjectivesPrimary aims were to compare adipose tissue distribution in adult patients with juvenile-onset DM (JDM), with matched controls. Secondary aims were to explore how adipose tissue distribution is associated with cardio-metabolic status (cardiac dysfunction and metabolic syndrome) in patients.MethodsThirty-nine JDM patients (all aged ≥18 y, mean age 31.7 y and 51% female) were examined mean 22.7 y (s.d. 8.9 y) after disease onset and compared with 39 age/sex-matched controls. In patients, disease activity and lipodystrophy were assessed by validated tools and use of prednisolone noted. In all participants, dual-energy X-ray absorptiometry (DXA) and echocardiography were used to measure visceral adipose tissue (VAT)(g) and cardiac function, respectively. Risk factors for metabolic syndrome were measured and associations with adipose tissue distribution explored. For primary and secondary aims, respectively, P-values ≤0.05 and ≤0.01 were considered significant.ResultsPatients exhibited a 2.4-fold increase in VAT, and reduced HDL-cholesterol values compared with controls (P-values ≤ 0.05). Metabolic syndrome was found in 25.7% of the patients and none of the controls. Cardiac dysfunction (systolic and/or diastolic) was found in 23.7% of patients and 8.1% of controls (P = 0.07). In patients, VAT levels were correlated with age, disease duration and occurrence of metabolic syndrome and cardiac dysfunction. Occurrence of lipodystrophy (P = 0.02) and male sex (P = 0.04) tended to be independently associated with cardiac dysfunction.ConclusionAdults with JDM showed more central adiposity and cardio-metabolic alterations than controls. Further, VAT was found increased with disease duration, which was associated with development of cardio-metabolic syndrome.
Impaired Hematopoietic Stem/Progenitor Cell Traffic and Multi-organ Damage in Diabetes
Authors: Fadini Gian Paolo , Albiero Mattia 
Published: May 2022

Abstract
During antenatal development, hematopoietic stem/progenitor cells (HSPCs) arise from a specialized endothelium and migrate from the extraembryonic mesoderm to the fetal liver before establishing hematopoiesis in the bone marrow (BM). It is still debated whether, in adulthood, HSPCs display such ontologic overlap with vascular cells and capacity for endothelial differentiation. Yet, adult HSPCs retain a prominent migratory activity and traffic in the bloodstream to secondary lymphoid organs and all peripheral tissues, before eventually returning to the BM. While patrolling parenchymatous organs, HSPCs locate close to the vasculature, where they establish local hematopoietic islands and contribute to tissue homeostasis by paracrine signals. Solid evidence shows that diabetes mellitus jeopardizes the traffic of HSPCs from BM to the circulation and peripheral tissues, a condition called “mobilopathy.” A reduction in the levels of circulating HSPCs is the most immediate and apparent consequence, which has been consistently observed in human diabetes, and is strongly associated with future risk for multi-organ damage, including micro- and macro-angiopathy. But the shortage of HSPCs in the blood is only the visible tip of the iceberg. Abnormal HSPC traffic results from a complex interplay among metabolism, innate immunity, and hematopoiesis. Notably, mobilopathy is mechanistically connected with diabetes-induced myelopoiesis. Impaired traffic of HSPCs and enhanced generation of pro-inflammatory cells synergize for tissue damage and impair the resolution of inflammation. We herein summarize the current evidence that diabetes affects HSPC traffic, which are the causes and consequences of such alteration, and how it contributes to the overall disease burden.
Managing severe acute and necrotizing pancreatitis
Authors: Van Wieren Alizabeth , Guild Michelle , Raucci Nicole , Meyer Sharon 
Published: May 2022

ABSTRACT
Acute pancreatitis is associated with significant morbidity and mortality, and is one of the most common gastrointestinal disorders requiring hospitalization. This article describes current concepts in the diagnosis and management of severe acute and necrotizing pancreatitis. Management of this disease requires IV fluids, pain control, and advanced medical and interventional care. Early identification and intervention may help to prevent patient morbidity and mortality.
Coagulopathy Underlying Rotational Thromboelastometry Derangements in Trauma Patients: A Prospective Observational Multicenter Study
Authors: Dujardin Romein W. G. , Kleinveld Derek J. B. , Gaarder Christine , Brohi Karim , Davenport Ross A. , Curry Nicola , Stanworth Simon , Johansson Pär I. , Stensballe Jakob , Maegele Marc , Juffermans Nicole P. 
Published: May 2022

Background
Viscoelastic hemostatic assays such as rotational thromboelastometry (ROTEM) are used to guide treatment of trauma induced coagulopathy. The authors hypothesized that ROTEM derangements reflect specific coagulation factor deficiencies after trauma.

Methods
This was a secondary analysis of a prospective cohort study in six European trauma centers in patients presenting with full trauma team activation. Patients with dilutional coagulopathy and patients on anticoagulants were excluded. Blood was drawn on arrival for measurement of ROTEM, coagulation factor levels, and markers of fibrinolysis. ROTEM cutoff values to define hypocoagulability were as follows: EXTEM clotting time greater than 80 s, EXTEM clot amplitude at 5 min less than 40 mm, EXTEM lysis index at 30 min less than 85%, FIBTEM clot amplitude at 5 min less than 10 mm, and FIBTEM lysis index at 30 min less than 85%. Based on these values, patients were divided into seven deranged ROTEM profiles and compared to the reference group (ROTEM values within reference range). The primary endpoint was coagulation factors levels and fibrinolysis.

Results
Of 1,828 patients, 732 (40%) had ROTEM derangements, most often consisting of a combined decrease in EXTEM and FIBTEM clot amplitude at 5 min, that was present in 217 (11.9%) patients. While an isolated EXTEM clotting time greater than 80 s had no impact on mortality, all other ROTEM derangements were associated with increased mortality. Also, coagulation factor levels in this group were similar to those of patients with a normal ROTEM. Of coagulation factors, a decrease was most apparent for fibrinogen (with a nadir of 0.78 g/l) and for factor V levels (with a nadir of 22.8%). In addition, increased fibrinolysis can be present when the lysis index at 30 min is normal but EXTEM and FIBTEM clot amplitude at 5 min is decreased.

Conclusions
Coagulation factor levels and mortality in the group with an isolated clotting time prolongation are similar to those of patients with a normal ROTEM. Other ROTEM derangements are associated with mortality and reflect a depletion of fibrinogen and factor V. Increased fibrinolysis can be present when the lysis index after 30 min is normal.

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