bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Violence We Unsee: Human Rights Erasures in Supply Chain Capitalism
Authors: Georgi F Richard 
Published: January 2025

Abstract
Violence caused by business practices along global value chains have inflicted myriad forms of massive harm and posed far-reaching regulatory challenges. The role that human rights could play in rendering corporate violence visible, remediable, and litigable remains quite contested. On the one hand, debates on business and human rights have driven a regulatory revolution over the last decade that is associated with the rise of the human rights due diligence (HRDD) norm. On the other hand, this revolution has been largely ignored by scholars in critical international political sociology; indeed, many critical scholars maintain that human rights are ineffective toward, or complicit in violent neoliberalism. This article bridges the scholarly divide by harnessing insights from the political, historical, and legal critique of rights to expose the inherent limitations of HRDD as the new hope for remedying corporate violence globally. Through a spectral lens, I explore foundational assumptions about the taxonomy of (un-)seeing corporate violence; business subjectivity and (ir-)responsibility for violence; and the epistemology of rendering knowledge on corporate violence (in-)admissible. This article contributes to multidisciplinary and pragmatic research on governing supply chain capitalism, understanding HRDD as a potentially powerful tool—provided it is accompanied by reforms tackling discourses, structures, and knowledges that condition corporate violence.
De Facto States and COVID-19: New Comparative Insights into Governmental Capacity to Act
Authors: Berg Eiki , Pegg Scott , Toomla Raul 
Published: January 2025

Abstract
This paper takes advantage of the exogenous shock of the COVID-19 pandemic to study de facto state agency. It builds upon previous scholarship on de facto states’ integration into international society by employing seven case studies while developing an independent capacity index. We argue that the COVID-19 pandemic is ideally suited to this task because it provided a powerful exogenous, non-conflict-related shock to all seven of our case studies, thus allowing for a valuable diagnostic tool from which to view how de facto states responded. We develop and test four specific theoretical hypotheses that offer different suggestions as to how well or how poorly individual de facto states might be expected to respond to the pandemic. Our empirical findings reveal Taiwan in a class by itself, followed by Northern Cyprus, Kosovo, and Transnistria with lesser agency, and finally, Abkhazia, Somaliland, and Nagorno-Karabakh with extremely limited agency.
Decrypting the phylogeny and metabolism of microbial dark matter in green and red Antarctic snow
Authors: Ren Ze , Luo Wei , Li Huirong , Ding Haitao , Zhang Yunlin 
Published: January 2025

Abstract
Antarctic snow harbors diverse microorganisms, including pigmented algae and bacteria, which create colored snow patches and influence global climate and biogeochemical cycles. However, the genomic diversity and metabolic potential of colored snow remain poorly understood. We conducted a genome-resolved study of microbiomes in colored snow from 13 patches (7 green and 6 red) on the Fildes Peninsula, Antarctica. Using metagenome assembly and binning, we reconstructed 223 metagenome-assembled genomes (MAGs), with 91% representing previously unexplored microbes. Green snow (GS) and red snow (RS) showed distinct MAGs profile, with Polaromonas and Ferruginibacter as the most abundant genera, respectively. GS exhibited higher alpha diversity with more unique and enriched MAGs, while RS showed greater variability with higher beta diversity. All MAGs contained genes encoding auxiliary activities (AAs), carbohydrate esterases (CEs), glycoside hydrolases (GHs), and glycosyl transferases (GTs), indicating microbial degradation of complex carbon substrates. The most abundant enzymes included GT2 (cellulose synthase), GT4 (sucrose synthase), CE1 (acetyl xylan esterase), GT41 (peptide beta-N-acetylglucosaminyltransferase), and CE10 (arylesterase). GS had a higher abundance of GTs, whereas RS was enriched in GHs. Furthermore, 56% of MAGs contained genes for inorganic nitrogen cycling, with 18 gene families involved in assimilatory nitrate reduction, dissimilatory nitrate reduction, and denitrification. Potential coupling of nitrogen cycling and carbohydrate metabolism was observed at both genome and community levels, suggesting close links between these pathways, particularly through nitrate reduction during carbohydrate degradation. This study enhances our understanding of microbial metabolic functions in polar ecosystems and highlights their roles in maintaining Antarctic ecological stability.
Effects of simvastatin on the mevalonate pathway and cell wall integrity of Staphylococcus aureus
Authors: Cortês Iago Torres , Silva Kátia de Pádua , Cogo-Müller Karina 
Published: January 2025

Abstract

Aims
To investigate the effects of simvastatin as an antimicrobial, considering its influence on the mevalonate pathway and the bacterial cell wall of S. aureus.

Methods and Results
S. aureus ATCC 29213 and 33591 were exposed to simvastatin in the presence of exogenous mevalonate to determine whether mevalonate could reverse the inhibition. S. aureus was also treated with simvastatin and gene expression analysis assays were performed to evaluate genes associated with the mevalonate pathway (mvaA, mvaS, mvaK1, and mvaK2), peptidoglycan synthesis (uppS, uppP, and murG), and cell wall stress (vraX, sgtB, and tcaA). Transmission electron microscopy was used to identify the presence of morphological changes. The data were compared using two-way ANOVA and Bonferroni post-test, or the Mann–Whitney test. Addition of exogenous mevalonate was able to partially or completely reverse the inhibition caused by simvastatin. A significant increase of the vraX gene and a reduction of the mvaA gene were observed, together with changes in bacterial morphology.

Conclusion
Simvastatin can exert its antimicrobial effect by means of changes in the cell wall associated with the mevalonate pathway.
Sprouty2/4 deficiency disrupts early signaling centers impacting chondrogenesis in the mouse forelimb
Authors: Dalecka Linda , Hruba Eva , Andrasova Marketa , Steklikova Klara , Pavlikova Zuzana , Kucerova Klara , Szotkowska Tereza , Bartos Martin , Buchtova Marcela , Tucker Abigail Saffron , Hovorakova Maria 
Published: January 2025

Abstract
The FGF signaling pathway plays an important role in the regulation of limb development, controlling cell migration, proliferation, differentiation, and apoptosis. Sprouty proteins act as antagonists of the FGF pathway and control the extent of FGF signaling as part of a negative feedback loop. Sprouty2/4 deficient mice evince defects in endochondral bone formation and digit patterning in their forelimbs, with pathogenesis recently related to ciliopathies. To understand the mechanisms behind these pathologies, the limb defects in Sprouty2+/−;Sprouty4−/− male and female mice were characterized and correlated to the dynamic expression patterns of Sprouty2 and Sprouty4, and the impact on the main signaling centers of the limb bud was assessed. Sprouty2 and Sprouty4 exhibited dynamic expressions during limb development. Interestingly, despite similar expression patterns in all limbs, the hindlimbs did not evince any obvious alterations in development, while the forelimbs showed consistent phenotypes of variable severity. Prenatally as well as postnatally, the left forelimb was significantly more severely affected than the right one. A broad variety of pathologies was present in the autopodium of the forelimb, including changes in digit number, size, shape, and number of bones, hand clefts, and digit fusions. Ectopic ossification of bones and abnormal bone fusions detected in micro-CT scans were frequently observed in the digital as well as in the carpal and metacarpal areas. Sprouty2+/−;Sprouty4−/− limb buds showed patchy loss of Fgf8 expression in the apical ectodermal ridge, and a loss of tissue underlying these regions. The zone of polarizing activity was also impacted, with lineage analysis highlighting a change in the contribution of Sonic hedgehog expressing cells. These findings support the link between Sproutys and Hedgehog signaling during limb development and highlight the importance of Sprouty2 and Sprouty4 in controlling early signaling centers in the limb.
Assessing hybridization between non-native Procambarus clarkii (Girard, 1852) and native Procambarus troglodytes (Le Conte, 1855) (Decapoda: Astacidea: Cambaridae) in Atlantic drainages of the southeastern USA
Authors: Kendrick Michael , Walker Matt , Darden Tanya 
Published: January 2025

Abstract
Crayfishes play important ecological and economic roles in the southeastern USA, with non-native crayfishes threatening many native species. While hybridization of crayfish species is observed in both wild and captive populations for some crayfishes, evidence for hybridization in the genus Procambarus Ortmann, 1905 is limited. The red swamp crayfish (Procambarus clarkii (Girard, 1852)) and the eastern red swamp crayfish (Procambarus troglodytes(Le Conte, 1855)) are two closely related crayfishes native to different basins in the southeastern USA. We used genetic markers to assess the potential for hybridization in these two crayfishes in the North Carolina and South Carolina, USA. A total of 292 specimens were collected with morphological identification distinguishing 134 P. clarkii and 158 P. troglodytes individuals from syntopic (i.e., co-occurring) and allopatric populations. Genetic microsatellite data was used to determine that no individuals were documented as hybrids in our collections and there was no indication of recent or rampant hybridization between P. clarkii and P. troglodytes at any of the sampling locations. A limited laboratory experiment showed successful mating and egg fertilization but failed to produce viable hybrid offspring. Although historical successful hybridization was not documented in our study, mating events between the two species resulting in inviable offspring may be having detrimental ecological consequences for populations of the native P. troglodytes that warrant additional exploration.
Multi-sample long-read nanopore sequencing of Agabus bipustulatus (Coleoptera: Dytiscidae: Agabinae) mitogenome produces effectively reliable data for downstream analyses
Authors: Bielikova Olena , Vargovčík Ondrej , Čiamporová-Zaťovičová Zuzana , Čiampor Fedor 
Published: January 2025

Abstract
Mitochondrial genomes are a rich source of data for various downstream analyses such as population genetics, phylogeny, and systematics. Today it is possible to assemble rapidly large numbers of mitogenomes, mainly employing next-generation sequencing and third-generation sequencing. However, verification of the correctness of the generated sequences is often lacking, especially for noncoding, length-variable parts. Here we have assembled the mitochondrial genome (mitogenome) from four specimens of Agabus bipustulatus (L.) using long-read nanopore sequence data. The use of the latest nanopore chemistry (V14) combined with a comprehensive error correction workflow enabled the generation of mitogenomes with high accuracy and reproducibility, as tested on four samples. The resulting mitogenome is 17,876 bp long, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Differences in the control region length between samples were minimal. The arrangement of protein-coding genes, transfer RNAs, and ribosomal RNAs is similar to that of the ancestral insect mitogenome. Finally, we used the assembled, well-supported mitogenomes in the phylogenetic analysis of a part of the Dytiscidae related to the studied species and confronted the results with previous hypotheses. Conflicting estimates of their phylogeny suggest that considerably more robust data are required for a plausible sketch of their evolutionary history. Our research has confirmed that readily available third-generation sequencing technologies, such as Oxford Nanopore Technologies, combined with long-read sequencing, offer a highly efficient, reliable, and cost-effective approach to generate complete mitogenomes and potentially other longer regions of the genome. The use of reliable data will ultimately contribute to a deeper understanding and improved conservation strategies for diving beetles and other organisms.
Application of machine learning for detecting high fall risk in middle-aged workers using video-based analysis of the first 3 steps
Authors: Sakane Naoki , Yamauchi Ken , Kutsuna Ippei , Suganuma Akiko , Domichi Masayuki , Hirano Kei , Wada Kengo , Ishimaru Masashi , Hosokawa Mitsuharu , Izawa Yosuke , Matsumura Yoshihiro , Hozumi Junichi 
Published: January 2025

Abstract
Objectives: Falls are among the most prevalent workplace accidents, necessitating thorough screening for susceptibility to falls and customization of individualized fall prevention programs. The aim of this study was to develop and validate a high fall risk prediction model using machine learning (ML) and video-based first 3 steps in middle-aged workers.
Methods: Participants to provide training data (n = 190, mean [SD] age = 54.5 [7.7] years, 48.9% male) and validation data (n = 28, age = 52.3 [6.0] years, 53.6% male) were enrolled in this study. Pose estimation was performed using a marker-free deep pose estimation method called MediaPipe Pose. The first 3 steps, including the movements of the arms, legs, trunk, and pelvis, were recorded using an RGB camera, and the gait features were identified. Using these gait features and fall histories, a stratified k-fold cross-validation method was used to ensure balanced training and test data, and the area under the curve (AUC) and 95% CI were calculated.
Results: Of 77 gait features in the first 3 steps, we found 3 gait features in men with an AUC of 0.909 (95% CI, 0.879-0.939) for fall risk, indicating an “excellent” (0.9-1.0) classification, whereas we determined 5 gait features in women with an AUC of 0.670 (95% CI, 0.621-0.719), indicating a “sufficient” (0.6-0.7) classification.
Conclusions: These findings suggest that fall risk prediction can be developed based on ML and the first 3 steps in men; however, the accuracy was only “sufficient” in women. Further development of the formula for women is required to improve its accuracy in the middle-aged working population.
Analytic natural gradient updates for Cholesky factor in Gaussian variational approximation
Authors: Tan Linda S L 
Published: January 2025

Abstract
Natural gradients can improve convergence in stochastic variational inference significantly but inverting the Fisher information matrix is daunting in high dimensions. Moreover, in Gaussian variational approximation, natural gradient updates of the precision matrix do not ensure positive definiteness. To tackle this issue, we derive analytic natural gradient updates of the Cholesky factor of the covariance or precision matrix and consider sparsity constraints representing different posterior correlation structures. Stochastic normalized natural gradient ascent with momentum is proposed for implementation in generalized linear mixed models and deep neural networks.
The role of mobile DNA elements in the dynamics of plant genome plasticity
Authors: Emmerson Robyn , Catoni Marco 
Published: January 2025

Abstract
Plants host a range of DNA elements capable of self-replication. These molecules, usually associated with the activity of transposable elements or viruses, are found integrated in the genome or in the form of extrachromosomal DNA. The activity of these elements can impact genome plasticity by a variety of mechanisms, including the generation of structural variants, the shuffling of regulatory or coding DNA sequences across the genome, and DNA endoduplication. This plasticity can dynamically alter gene expression and genome stability, ultimately affecting plant development or the response to environmental changes. While the activation of these elements is often considered deleterious to the genome, their role in creating variation is important in adaptation and evolution. Moreover, the mechanisms by which mobile DNA proliferates have been exploited for plant engineering, or contributed to understand how desirable traits can be generated in crops. In this review, we discuss the origins and the roles of mobile DNA element activity on genome plasticity and plant biology, as well as their potential function and current application in plant biotechnology.
Mapping dusty galaxy growth at z &gt; 5 with FRESCO: detection of Hα in submm galaxy HDF850.1 and the surrounding overdense structures
Authors: Herard-Demanche Thomas , Bouwens Rychard J , Oesch Pascal A , Naidu Rohan P , Decarli Roberto , Nelson Erica J , Brammer Gabriel , Weibel Andrea , Xiao Mengyuan , Stefanon Mauro , Walter Fabian , Matthee Jorryt , Meyer Romain A , Wuyts Stijn , Reddy Naveen , Rowland Lucie , van Leeuwen Ivana , Haro Pablo Arrabal , Dannerbauer Helmut , Shapley Alice E , Chisholm John , van Dokkum Pieter , Labbe Ivo , Illingworth Garth , Schaerer Daniel , Shivaei Irene 
Published: January 2025

ABSTRACT
We report the detection of a 13$\sigma$ H$\alpha$ emission line from HDF850.1 at $z=5.188\pm 0.001$ using the FRESCO (First Reionization Era Spectroscopically Complete Observations) NIRCam F444W grism observations. Detection of H$\alpha$ in HDF850.1 is noteworthy, given its high far-infrared (IR) luminosity, substantial dust obscuration, and the historical challenges in deriving its redshift. HDF850.1 shows a clear detection in the F444W imaging data, distributed between a northern and southern component, mirroring that seen in [C ii] from the Plateau de Bure Interferometer. Modelling the spectral energy distribution of each component separately, we find that the northern component has a higher mass, star formation rate (SFR), and dust extinction than the southern component. The observed H$\alpha$ emission appears to arise entirely from the less-obscured southern component and shows a similar $\Delta$v$\sim$ + 130 ${\rm{km\,s}}^{-1}$ velocity offset to that seen for [C ii] relative to the source systemic redshift. Leveraging H$\alpha$-derived redshifts from FRESCO observations, we find that HDF850.1 is forming in one of the richest environments identified to date at $z\gt 5$, with 100 $z=5.17$–5.20 galaxies distributed across 13 smaller structures and a $\sim$(15 cMpc)$^3$ volume. Based on the evolution of analogous structures in cosmological simulations, the $z=5.17$–5.20 structures seem likely to collapse into a single $\gt 10^{14}$${\rm M}_{\odot }$ cluster by $z\sim 0$. Comparing galaxy properties forming within this overdensity with those outside, we find the masses, SFRs, and $UV$ luminosities inside the overdensity to be clearly higher. The prominence of H$\alpha$ line emission from HDF850.1 and other known highly obscured $z\gt 5$ galaxies illustrates the potential of NIRCam-grism programs to map both the early build-up of IR-luminous galaxies and overdense structures.
Young onset chronic inflammatory back pain: A diagnostic dilemma between axial spondylitis and diffuse idiopathic skeletal hyperostosis
Authors: Namas Rajaie , Al Qassimi Sarah , Alameri Jawahir , Alawadhi Fatema , Memisoglu Esat , Almarzooqi Ahlam 
Published: January 2025

ABSTRACT
Diffuse idiopathic skeletal hyperostosis (DISH) and axial spondyloarthritis (axSpA) share similarities in both clinical presentation and radiological findings, making the diagnostic process challenging. We report the case of a 30-year-old male with a long-standing history of back pain with an initial diagnosis of young-onset DISH. However, a diagnosis of axSpA was ultimately pursued based on his age and clinical presentation. This was further supported by improvement in both Ankylosing Spondylitis Disease Activity Score with Erythrocyte Sedimentation Rate (ASDAS-ESR) and Ankylosing Spondylitis Disease Activity Score with C-Reactive Protein (ASDAS-CRP) scores at his 6- and 12-month follow-ups on ixekizumab. Early and accurate diagnosis of axSpA, followed by appropriate treatment, is essential in preventing complications and improving patient outcomes.
(Un)Sustainable Science: Greening Practices in Research, Clinical Microbiology, and Veterinary Laboratories Locally and Globally
Authors: Bayrau Bethel Alebel , Buyukcangaz Esra , Sadarangani Sapna P , Ondigo Bartholomew N , Prinzi Andrea , LaBeaud A Desiree 
Published: January 2025

Abstract
Health care, veterinary, and research facilities produce tremendous amounts of waste and account for a significant proportion of their institutions’ energy and water use. The majority of municipal solid waste produced by these facilities gets unsustainably disposed of, including exportation to lower-income countries, and most of the plastic waste is nonrecyclable and nondegradable. The produced waste not only results in excessive carbon emissions harming planetary health but also poses direct harm to human health, broadens global inequities, and produces avoidable economic costs. Greening up laboratories by reducing waste production and water and energy use offers many benefits and does not have to be time or resource intensive. Sustainable practices to green up laboratories include reusing materials, decreasing energy use by choosing low-energy settings and shutting off equipment when not in use, installing low-flow faucets to decrease water use, proper sorting of waste, environmentally conscious purchases of supplies, and avoiding unnecessary medical and veterinary tests.
Chronic Hepatitis B and COVID-19 Clinical Outcomes in the United States: A Multisite Retrospective Cohort Study
Authors: Yendewa George A , Olasehinde Temitope , Mulindwa Frank , Salata Robert A , Mohareb Amir M , Jacobson Jeffrey M 
Published: January 2025

Abstract

Background
There is conflicting evidence regarding the impact of chronic hepatitis B virus (HBV) on SARS-CoV-2 outcomes. Additionally, the impact of SARS-CoV-2 vaccination and variant periods on outcomes in HBV/SARS-CoV-2 coinfection remain unexplored.

Methods
We utilized the TriNetX database to compare adults with HBV/SARS-CoV-2 (vs SARS-CoV-2 alone) across 97 US healthcare systems from 2020 to 2023. We assessed the odds of all inpatient hospitalizations, intensive care unit admissions, mechanical ventilation, 30-day, 90-day, and overall mortality. In sensitivity analyses, we excluded HIV, hepatitis C virus, and transplant cases and stratified the HBV/SARS-CoV-2 cohort by cirrhosis status. We applied propensity score matching to address confounding and reported odds ratios (OR) with 95% confidence intervals (CI).

Results
Of 4 206 774 individuals with SARS-CoV-2, about 0.2% (8293) were HBV/SARS-CoV-2. Individuals with HBV/SARS-CoV-2 (vs SARS-CoV-2 alone) had higher odds of intensive care unit admissions (OR, 1.18; 95% CI, 1.02–1.36), 90-day (OR, 1.22; 95% CI, 1.01–1.41) and overall mortality (OR, 1.18; 95% CI, 1.06–1.33). In sensitivity analyses, those with HBV/SARS-CoV-2 and cirrhosis had a 2.0- to 2.50-fold higher odds of adverse outcomes. Notably, even individuals with HBV/SARS-CoV-2 without cirrhosis had higher odds of mortality. Vaccinated (vs unvaccinated) individuals with HBV/SARS-CoV-2 had 57%, 54%, and 29% reduction in 30-day, 90-day, and overall mortality, respectively. The pre-Delta variant period was associated with higher odds of hospitalization compared to the Omicron but not the Delta period.

Conclusions
Chronic HBV was associated with worse SARS-CoV-2 outcomes, whereas SARS-CoV-2 vaccination reduced the likelihood of adverse outcomes.