bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why More Biologists Must Embrace Quantitative Modeling
Authors: Milligan Brook G , Rohde Ashley T 
Published: May 2024

Synopsis
Biology as a field has transformed since the time of its foundation from an organized enterprise cataloging the diversity of the natural world to a quantitatively rigorous science seeking to answer complex questions about the functions of organisms and their interactions with each other and their environments. As the mathematical rigor of biological analyses has improved, quantitative models have been developed to describe multi-mechanistic systems and to test complex hypotheses. However, applications of quantitative models have been uneven across fields, and many biologists lack the foundational training necessary to apply them in their research or to interpret their results to inform biological problem-solving efforts. This gap in scientific training has created a false dichotomy of “biologists” and “modelers” that only exacerbates the barriers to working biologists seeking additional training in quantitative modeling. Here, we make the argument that all biologists are modelers and are capable of using sophisticated quantitative modeling in their work. We highlight four benefits of conducting biological research within the framework of quantitative models, identify the potential producers and consumers of information produced by such models, and make recommendations for strategies to overcome barriers to their widespread implementation. Improved understanding of quantitative modeling could guide the producers of biological information to better apply biological measurements through analyses that evaluate mechanisms, and allow consumers of biological information to better judge the quality and applications of the information they receive. As our explanations of biological phenomena increase in complexity, so too must we embrace modeling as a foundational skill.
Historical climate drivers and species’ ecological niche in the Beaufort Sea food web
Authors: Sora Kristen J , Wabnitz Colette C C , Steiner Nadja S , Sumaila U Rashid , Hoover Carie , Niemi Andrea , Loseto Lisa L , Li Mi-Ling , Giang Amanda , Gillies Emma , Cheung William W L 
Published: May 2024

Abstract
Climate change impacts have been particularly acute and rapid in the Arctic, raising concerns about the conservation of key ecologically and culturally significant species (e.g. beluga whales, Arctic cod), with consequences for the Indigenous community groups in the region. Here, we build on an Ecopath with Ecosim model for the Canadian Beaufort Sea Shelf and Slope to examine historical (1970–2021) changes in the ecological dynamics of the food web and key species under climate change. We compare the individual and cumulative effects of (i) increased sea surface temperature; (ii) reduced sea ice extent; (iii) ocean deoxygenation; and (iv) changing ocean salinity in the ecosystem models. We found that including salinity time series in our ecosystem models reduced the diversity found within the ecosystem, and altered the trophic levels, biomass, and consumption rates of some marine mammal and fish functional groups, including the key species: beluga whales, as well as Arctic and polar cods. Inclusion of the dissolved oxygen time series showed no difference to ecosystem indicators. The model findings reveal valuable insights into the attribution of temperature and salinity on Arctic ecosystems and highlight important factors to be considered to ensure that existing conservation measures can support climate adaptation.
Disavowing an Implied Term of Fairness
Authors: Brodie Douglas 
Published: May 2024

Abstract
In the Court of Appeal decision in Burn v Alder Hey (Burn), there are obiter suggestions that the employment contract contains an implied term that would require the employer to act fairly during a disciplinary process. In an article in this journal, Collins and Golding (the authors) endorse this direction of travel and explore what they see as a number of advantages that would accrue for employees (and other workers) should the courts hold that such a term is indeed part of the law of contract. This article seeks to argue that recognition of the term would be misguided.
The Capsular Polysaccharide Obstructs Wall Teichoic Acid Functions in Staphylococcus aureus
Authors: Lehmann Esther , van Dalen Rob , Gritsch Lisa , Slavetinsky Christoph , Korn Natalya , Rohmer Carina , Krause Daniela , Peschel Andreas , Weidenmaier Christopher , Wolz Christiane 
Published: May 2024

Abstract

Background
The cell envelope of Staphylococcus aureus contains 2 major secondary cell wall glycopolymers: capsular polysaccharide (CP) and wall teichoic acid (WTA). Both CP and WTA are attached to the cell wall and play distinct roles in S. aureus colonization, pathogenesis, and bacterial evasion of host immune defenses. We aimed to investigate whether CP interferes with WTA-mediated properties.

Methods
Strains with natural heterogeneous expression of CP, strains with homogeneous high CP expression, and CP-deficient strains were compared regarding WTA-dependent phage binding, cell adhesion, IgG deposition, and virulence in vivo.

Results
WTA-mediated phage adsorption, specific antibody deposition, and cell adhesion were negatively correlated with CP expression. WTA, but not CP, enhanced the bacterial burden in a mouse abscess model, while CP overexpression resulted in intermediate virulence in vivo.

Conclusions
CP protects the bacteria from WTA-dependent opsonization and phage binding. This protection comes at the cost of diminished adhesion to host cells. The highly complex regulation and mostly heterogeneous expression of CP has probably evolved to ensure the survival and optimal physiological adaptation of the bacterial population as a whole.
Longitudinal Analysis of Nursing Home Residents’ T-Cell Responses After SARS-CoV-2 mRNA Vaccinations Shows Influence of Biological Sex and Infection History
Authors: Smith Carson L , Didion Elise , Aung Htin , Tamilselvan Banumathi , Bej Taissa , Oyebanji Oladayo A , Shive Carey L , Wilson Brigid M , Cameron Mark , Cameron Cheryl , Gravenstein Stefan , Canaday David H 
Published: May 2024

Abstract

Background
Vaccines and vaccine boosting have blunted excess morbidity and mortality from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in older nursing home residents (NHR). However, the impact of repeated vaccination on the T-cell response based on biological sex and prior infection of NHR remain understudied.

Methods
We examined T-cell responses to SARS-CoV-2 mRNA vaccines in a cohort of NHR and healthcare workers (HCW) over 2 years. We used interferon-γ ELIspot and flow cytometry to assess T-cell response before, 2 weeks, and 6 months after the initial series and each of 2 booster vaccines. We analyzed these data longitudinally with mixed-effect modeling and also examined subsets of our cohorts for additional changes in T-cell effector function.

Results
Prior SARS-CoV-2 infection and female sex contributed to higher T-cell response in NHR but not HCW. When looking across time points, NHR but not HCW with prior infection had significantly higher T-cell responses than infection-naive subjects. These patterns of response were maintained across multiple booster vaccinations.

Conclusions
These results suggest that the age, multimorbidity, and/or frailty of the NHR cohort may accentuate sex and infection status differences in T-cell response to mRNA vaccination.
The Effect of Gastrointestinal Graft-Versus-Host Disease and Diarrhea on the Pharmacokinetic Profile of Sotrovimab in Hematopoietic Stem Cell Transplant Recipients
Authors: Boonyaratanakornkit Jim , Wang Qianwen , Nader Ahmed , Kimball Louise , Stevens-Ayers Terry , Levkova Marta , Blazevic Rachel , Nguyen Jeanette , Wright Jennifer , Castor Jared , Greninger Alexander L , Ford Emily , Mielcarek Marco , Fordred Shelley , Han Jennifer , Boeckh Michael , Waghmare Alpana 
Published: May 2024

Abstract

Background
Monoclonal antibodies (mAbs) are utilized broadly to treat cancer and infectious diseases, and mAb exposure (serum concentration over time) is one predictor of overall treatment efficacy. Herein, we present findings from a clinical trial evaluating the pharmacokinetics of the long-acting mAb sotrovimab targeting severe acute respiratory syndrome coronavirus 2 in hematopoietic cell transplant (HCT) recipients.

Methods
All participants received an intravenous infusion of sotrovimab within 1 week prior to initiating the pretransplant preparative regimen. The serum concentration of sotrovimab was measured longitudinally for up to 24 weeks posttransplant.

Results
Compared to non-HCT participants, we found that mAb clearance was 10% and 26% higher in autologous and allogeneic HCT recipients, respectively. Overall sotrovimab exposure was approximately 15% lower in HCT recipients compared to non-HCT recipients. Exposure was significantly reduced in HCT recipients who developed diarrhea and lower gastrointestinal graft-versus-host disease (GVHD) posttransplant.

Conclusions
These data show that sotrovimab exposure may be reduced in HCT recipients, possibly related to increased gastrointestinal clearance in patients with GVHD. This phenomenon has implications for dose selection and duration of efficacy with sotrovimab and potentially other mAbs in this vulnerable patient population. Thus, mAb dose regimens developed in non-HCT populations may have to be optimized when applied to HCT populations.
Metabolic potential of Nitrososphaera-associated clades
Authors: Bei Qicheng , Reitz Thomas , Schädler Martin , Hodgskiss Logan H , Peng Jingjing , Schnabel Beatrix , Buscot François , Eisenhauer Nico , Schleper Christa , Heintz-Buschart Anna 
Published: May 2024

Abstract
Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014–2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.
Narratives of Blended Experience
Authors: Flint Tom , O’Keefe Brian , Mastermaker Mike , Sturdee Miriam , Benyon David 
Published: May 2024

Abstract
This paper focuses on interaction across and between the physical/digital divide. We use blending theory to design for these situations, otherwise known as conceptual integration. Initially, this paper offers a discussion of the literature around blends. From this literature, we applied Benyon’s (Benyon, 2014) proposition of conceptual integration in mixed reality spaces (Blended Spaces) to consider interactions with the digital that complement the physical. We investigated blended spaces in partnership with undergraduate students during a live theatre festival. Our collaborators designed applications that applied blending principles, employing techniques drawn from speculative design. Outputs consist of speculative, narrative storyboards that use data gathered directly from stakeholder interviews and over 380 festival visitors. Our work led us to propose reworking Blended Spaces into a model that novice designers could easily conceive and apply. The work we conducted highlighted the need to consider user transitions from physical to digital and back again and highlighted the experiential nature of this type of interaction.
A general framework for developing computable clinical phenotype algorithms
Authors: Carrell David S , Floyd James S , Gruber Susan , Hazlehurst Brian L , Heagerty Patrick J , Nelson Jennifer C , Williamson Brian D , Ball Robert 
Published: May 2024

Abstract

Objective
To present a general framework providing high-level guidance to developers of computable algorithms for identifying patients with specific clinical conditions (phenotypes) through a variety of approaches, including but not limited to machine learning and natural language processing methods to incorporate rich electronic health record data.

Materials and Methods
Drawing on extensive prior phenotyping experiences and insights derived from 3 algorithm development projects conducted specifically for this purpose, our team with expertise in clinical medicine, statistics, informatics, pharmacoepidemiology, and healthcare data science methods conceptualized stages of development and corresponding sets of principles, strategies, and practical guidelines for improving the algorithm development process.

Results
We propose 5 stages of algorithm development and corresponding principles, strategies, and guidelines: (1) assessing fitness-for-purpose, (2) creating gold standard data, (3) feature engineering, (4) model development, and (5) model evaluation.

Discussion and Conclusion
This framework is intended to provide practical guidance and serve as a basis for future elaboration and extension.
JWST MIRI and NIRCam unveil previously unseen infrared stellar populations in NGC 6822
Authors: Nally Conor , Jones Olivia C , Lenkić Laura , Habel Nolan , Hirschauer Alec S , Meixner Margaret , Kavanagh P J , Boyer Martha L , Ferguson Annette M N , Sargent B A , Nayak Omnarayani , Temim Tea 
Published: May 2024

ABSTRACT
NGC 6822 is a nearby (∼490 kpc) non-interacting low-metallicity (0.2 Z⊙) dwarf galaxy which hosts several prominent H ii regions, including sites of highly embedded active star formation. In this work, we present an imaging survey of NGC 6822 conducted with the Near Infrared Camera (NIRCam) and Mid-Infrared Instrument (MIRI) onboard JWST. We describe the data reduction, source extraction, and stellar population identifications from combined near- and mid-infrared (IR) photometry. Our NIRCam observations reach 7 mag deeper than previous JHKs surveys of this galaxy, which were sensitive to just below the tip of the red giant branch (TRGB). These JWST observations thus reveal for the first time in the near-IR the red clump stellar population and extend nearly 3 mag deeper. In the mid-IR, we observe roughly 2 mag below the TRGB with the MIRI F770W and F1000W filters. With these improvements in sensitivity, we produce a catalogue of ∼900 000 point sources over an area of ∼6.0 × 4.3 arcmin2. We present several NIRCam and MIRI colour–magnitude diagrams and discuss which colour combinations provide useful separations of various stellar populations to aid in future JWST observation planning. Finally, we find populations of carbon- and oxygen-rich asymptotic giant branch stars which will assist in improving our understanding of dust production in low-metallicity, early Universe analogue galaxies.
Does the fundamental metallicity relation evolve with redshift? I: the correlation between offsets from the mass-metallicity relation and star formation rate
Authors: Garcia Alex M , Torrey Paul , Ellison Sara , Grasha Kathryn , Hernquist Lars , Zovaro Henry R M , Chen Qian-Hui , Hemler Z S , Kewley Lisa J , Nelson Erica J , Wright Ruby J 
Published: May 2024

ABSTRACT
The scatter about the mass-metallicity relation (MZR) has a correlation with the star formation rate (SFR) of galaxies. The lack of evidence of evolution in correlated scatter at z ≲ 2.5 leads many to refer to the relationship between mass, metallicity, and SFR as the Fundamental Metallicity Relation (FMR). Yet, recent high-redshift (z &gt; 3) JWST observations have challenged the fundamental (i.e. redshift-invariant) nature of the FMR. In this work, we show that the cosmological simulations Illustris, IllustrisTNG, and Evolution and Assembly of GaLaxies and their Environment (EAGLE) all predict MZRs that exhibit scatter with a secondary dependence on SFR up to z = 8. We introduce the concept of a ‘strong’ FMR, where the strength of correlated scatter does not evolve with time, and a ‘weak’ FMR, where there is some time evolution. We find that each simulation analysed has a statistically significant weak FMR – there is non-negligible evolution in the strength of the correlation with SFR. Furthermore, we show that the scatter is reduced an additional ∼10–40 per cent at z ≳ 3 when using a weak FMR, compared to assuming a strong FMR. These results highlight the importance of avoiding coarse redshift binning when assessing the FMR.
The oldest stars with low neutron-capture element abundances and origins in ancient dwarf galaxies
Authors: Andales Hillary Diane , Santos Figueiredo Ananda , Fienberg Casey Gordon , Mardini Mohammad K , Frebel Anna 
Published: May 2024

ABSTRACT
We present a detailed chemical abundance and kinematic analysis of six extremely metal-poor (−4.2 ≤ [Fe/H] ≤−2.9) halo stars with very low neutron-capture abundances ([Sr/H] and [Ba/H]) based on high-resolution Magellan/MIKE spectra. Three of our stars have [Sr/Ba] and [Sr/H] ratios that resemble those of metal-poor stars in ultra-faint dwarf galaxies (UFDs). Since early UFDs may be the building blocks of the Milky Way, extremely metal-poor halo stars with low, UFD-like Sr and Ba abundances may thus be ancient stars from the earliest small galactic systems that were accreted by the proto-Milky Way. We label these objects as Small Accreted Stellar System (SASS) stars, and we find an additional 61 similar ones in the literature. A kinematic analysis of our sample and literature stars reveals them to be fast-moving halo objects, all with retrograde motion, indicating an accretion origin. Because SASS stars are much brighter than typical UFD stars, identifying them offers promising ways towards detailed studies of early star formation environments. From the chemical abundances of SASS stars, it appears that the earliest accreted systems were likely enriched by a few supernovae whose light element yields varied from system to system. Neutron-capture elements were sparsely produced and/or diluted, with r-process nucleosynthesis playing a role. These insights offer a glimpse into the early formation of the Galaxy. Using neutron-capture elements as a distinguishing criterion for early formation, we have access to a unique metal-poor population that consists of the oldest stars in the universe.
The mutation R107Q alters mtSSB ssDNA compaction ability and binding dynamics
Authors: Martucci Martial , Moretton Amandine , Tarrés-Solé Aleix , Ropars Virginie , Lambert Louise , Vernet Patrick , Solà Maria , Falkenberg Maria , Farge Geraldine , van den Wildenberg Siet 
Published: May 2024

Abstract
Mitochondrial single-stranded DNA-binding protein (mtSSB) is essential for mitochondrial DNA (mtDNA) replication. Recently, several mtSSB variants have been associated with autosomal dominant mitochondrial optic atrophy and retinal dystrophy. Here, we have studied at the molecular level the functional consequences of one of the most severe mtSSB variants, R107Q. We first studied the oligomeric state of this variant and observed that the mtSSBR107Q mutant forms stable tetramers in vitro. On the other hand, we showed, using complementary single-molecule approaches, that mtSSBR107Q displays a lower intramolecular ssDNA compaction ability and a higher ssDNA dissociation rate than the WT protein. Real-time competition experiments for ssDNA-binding showed a marked advantage of mtSSBWT over mtSSBR107Q. Combined, these results show that the R107Q mutation significantly impaired the ssDNA-binding and compacting ability of mtSSB, likely by weakening mtSSB ssDNA wrapping efficiency. These features are in line with our molecular modeling of ssDNA on mtSSB showing that the R107Q mutation may destabilize local interactions and results in an electronegative spot that interrupts an ssDNA-interacting-electropositive patch, thus reducing the potential mtSSB-ssDNA interaction sites.
Stress-induced nucleoid remodeling in Deinococcus radiodurans is associated with major changes in Heat Unstable (HU) protein dynamics
Authors: Vauclare Pierre , Wulffelé Jip , Lacroix Françoise , Servant Pascale , Confalonieri Fabrice , Kleman Jean-Philippe , Bourgeois Dominique , Timmins Joanna 
Published: May 2024

Abstract
Bacteria have developed a wide range of strategies to respond to stress, one of which is the rapid large-scale reorganization of their nucleoid. Nucleoid associated proteins (NAPs) are believed to be major actors in nucleoid remodeling, but the details of this process remain poorly understood. Here, using the radiation resistant bacterium D. radiodurans as a model, and advanced fluorescence microscopy, we examined the changes in nucleoid morphology and volume induced by either entry into stationary phase or exposure to UV-C light, and characterized the associated changes in mobility of the major NAP in D. radiodurans, the heat-unstable (HU) protein. While both types of stress induced nucleoid compaction, HU diffusion was reduced in stationary phase cells, but was instead increased following exposure to UV-C, suggesting distinct underlying mechanisms. Furthermore, we show that UV-C-induced nucleoid remodeling involves a rapid nucleoid condensation step associated with increased HU diffusion, followed by a slower decompaction phase to restore normal nucleoid morphology and HU dynamics, before cell division can resume. These findings shed light on the diversity of nucleoid remodeling processes in bacteria and underline the key role of HU in regulating this process through changes in its mode of assembly on DNA.
SEMA 2.0: web-platform for B-cell conformational epitopes prediction using artificial intelligence
Authors: Ivanisenko Nikita V , Shashkova Tatiana I , Shevtsov Andrey , Sindeeva Maria , Umerenkov Dmitriy , Kardymon Olga 
Published: May 2024

Abstract
Prediction of conformational B-cell epitopes is a crucial task in vaccine design and development. In this work, we have developed SEMA 2.0, a user-friendly web platform that enables the research community to tackle the B-cell epitopes prediction problem using state-of-the-art protein language models. SEMA 2.0 offers comprehensive research tools for sequence- and structure-based conformational B-cell epitopes prediction, accurate identification of N-glycosylation sites, and a distinctive module for comparing the structures of antigen B-cell epitopes enhancing our ability to analyze and understand its immunogenic properties. SEMA 2.0 website https://sema.airi.net is free and open to all users and there is no login requirement. Source code is available at https://github.com/AIRI-Institute/SEMAi