bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are the Fingerprints of WTO Staff on Panel Rulings a Problem? A Reply to Joost Pauwelyn and Krzysztof Pelc
Authors: Steinbach Armin 
Published: August 2022

Abstract
By employing stylometric data analysis, Joost Pauwelyn and Krzysztof Pelc underpin the narrative of a power-mongering World Trade Organization (WTO) Secretariat. As ‘holder of the pen’ in writing WTO rulings, the Secretariat would absorb control over WTO adjudicators and the dispute settlement procedure. This reply disagrees. First, with stylometric analysis informing style rather than substance, this technique does not encrypt the intellectual ownership of WTO rulings, nor does it offer account of the deliberation between bureaucrats and adjudicators. Second, with public power typically deriving legitimacy from both political or judicial accountability as well as rational and de-politicized bureaucracies, an assertive WTO Secretariat under the direction of panellists is normatively desirable. Third, a WTO Secretariat pursuing consistent application of the growing WTO acquis does not impair the members-driven adjudication process.
Girls start life on an uneven playing field
Authors: Marphatia Akanksha A , Saville Naomi S , Manandhar Dharma S , Cortina-Borja Mario , Reid Alice M , Wells Jonathan C K 
Published: August 2022

AbstractBackground and objectivesEvolutionary research on the sex ratio at birth (SRB) has focused on explaining variability within and between populations, and whether parental fitness is maximized by producing daughters or sons. We tested predictors of SRB in a low-income setting, to understand whether girls differ from boys in their likelihood of being born into families with the capacity to invest in them, which has implications for their future health and fitness.MethodologyWe used data from a cluster randomized control trial from lowland rural Nepal (16 115 mother-child dyads). We applied principal component analysis to extract two composite indices reflecting maternal socio-economic and reproductive (parity, age) capital. We fitted mixed-effects logistic regression models to estimate odds ratios of having a girl in association with these individual factors and indices.ResultsThe SRB was 112. Compared to the global reference SRB (105), there were seven missing girls per 100 boys. Uneducated, early-marrying, poorer and shorter mothers were more likely to give birth to girls. Analysing composite maternal indices, lower socio-economic and reproductive capital were independently associated with a greater likelihood of having a girl.Conclusions and implicationsIn this population, girls start life facing composite disadvantages, being more likely than boys to be born to mothers with lower socio-economic status and reproductive capital. Both physiological and behavioural mechanisms may contribute to these epidemiological associations. Differential early exposure by sex to maternal factors may underpin intergenerational cycles of gender inequality, mediated by developmental trajectory, education and socio-economic status.
Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions
Authors: Aira Manuel , Pérez-Losada Marcos , Crandall Keith A , Domínguez Jorge 
Published: August 2022

Abstract
Host evolutionary history is a key factor shaping the earthworm cast microbiome, although its effect can be shadowed by the earthworm’s diet. To untangle dietary from taxon effects, we raised nine earthworm species on a uniform diet of cow manure and compared cast microbiome across species while controlling for diet. Our results showed that, under controlled laboratory conditions, earthworm microbiomes are species-specific, more diverse than that of the controlled diet, and mainly comprised of native bacteria (i.e. not acquired from the diet). Furthermore, diet has a medium to large convergence effect on microbiome composition since earthworms shared 16%–74% of their bacterial amplicon sequence variants (ASV). The interspecies core microbiome included 10 ASVs, while their intraspecies core microbiomes were larger and varied in ASV richness (24%–48%) and sequence abundance across earthworm species. This specificity in core microbiomes and variable degree of similarity in bacterial composition suggest that phylosymbiosis could determine earthworm microbiome assembly. However, lack of congruence between the earthworm phylogeny and the microbiome dendrogram suggests that a consistent diet fed over several generations may have weakened potential phylosymbiotic effects. Thus, cast microbiome assembly in earthworms seem to be the result of an interplay among host phylogeny and diet.
Correlations of expression of nuclear and mitochondrial genes in triploid fish
Authors: Cui Jialin , Zhang Hong , Gao Xin , Zhang Xueyin , Luo Mengxue , Ren Li , Liu Shaojun 
Published: August 2022

Abstract
The expression of nuclear and mitochondrial genes, as well as their coordinated control, regulates cell proliferation, individual development, and disease in animals. However, the potential coregulation between nuclear and mitochondrial genes is unclear in triploid fishes. The two triploids (R2C and RC2) with distinct mitochondrial genomes but similar nuclear genomes exhibit different embryonic development times and growth rates. They are an excellent model for studying how nuclear and mitochondrial genes coordinate. Here, we performed the mRNA-seq of four stages of embryonic development (blastula, gastrula, segmentation, and hatching periods) in the two triploids (R2C and RC2) and their diploid inbred parents (red crucian carp and common carp). After establishing the four patterns of mitochondrial and nuclear gene expression, 270 nuclear genes regulated by mitochondrial genes were predicted. The expression levels of APC16 and Trim33 were higher in RC2 than in R2C, suggesting their potential effects on regulating embryonic development time. In addition, 308 differentially expressed genes filtered from the list of nuclear-encoded mitochondrial genes described by Mercer et al. in 2011 were considered potential genes for which nuclear genes regulate mitochondrial function. The findings might aid in our understanding of the correlation between mitochondrial and nuclear genomes as well as their synergistic effects on embryonic development.
An enhancer variant associated with breast cancer susceptibility in Black women regulates TNFSF10 expression and antitumor immunity in triple-negative breast cancer
Authors: Han Yoo Jane , Zhang Jing , Hardeman Ashley , Liu Margaret , Karginova Olga , Romero Roger , Khramtsova Galina F , Zheng Yonglan , Huo Dezheng , Olopade Olufunmilayo I 
Published: August 2022

Abstract
Women of African ancestry have the highest mortality from triple-negative breast cancer (TNBC) of all racial groups. To understand the genomic basis of breast cancer in the populations, we previously conducted genome-wide association studies and identified single nucleotide polymorphisms (SNPs) associated with breast cancer in Black women. In this study, we investigated the functional significance of the top associated SNP rs13074711. We found the SNP served as an enhancer variant and regulated TNFSF10 (TRAIL) expression in TNBC cells, with a significant association between the SNP genotype and TNFSF10 expression in breast tumors. Mechanistically, rs13074711 modulated the binding activity of c-MYB at the motif and thereby controlled TNFSF10 expression. Interestingly, TNFSF10 expression in many cancers was consistently lower in African Americans compared with European Americans. Furthermore, TNFSF10 expression in TNBC was significantly correlated with the expression of antiviral immune genes and was regulated by type I interferons (IFNs). Accordingly, loss of TNFSF10 resulted in a profound decrease in apoptosis of TNBC cells in response to type I IFNs and poly(I:C), a synthetic analogue of double stranded virus. Lastly, in a syngeneic mouse model of breast cancer, TNFSF10-deficiency in breast tumors decreased tumor-infiltrated CD4+ and CD8+ T cell quantities. Collectively, our results suggested that TNFSF10 plays an important role in the regulation of antiviral immune responses in TNBC, and the expression is in part regulated by a genetic variant associated with breast cancer in Black women. Our results underscore the important contributions of genetic variants to immune defense mechanisms.
Smooth and Polyhedral Norms via Fundamental Biorthogonal Systems
Authors: Dantas Sheldon , Hájek Petr , Russo Tommaso 
Published: August 2022

Abstract
Let $\mathcal {X}$ be a Banach space with a fundamental biorthogonal system, and let $\mathcal {Y}$ be the dense subspace spanned by the vectors of the system. We prove that $\mathcal {Y}$ admits a $C^\infty $-smooth norm that locally depends on finitely many coordinates (LFC, for short), as well as a polyhedral norm that locally depends on finitely many coordinates. As a consequence, we also prove that $\mathcal {Y}$ admits locally finite, $\sigma $-uniformly discrete $C^\infty $-smooth and LFC partitions of unity and a $C^1$-smooth locally uniformly rotund norm. This theorem substantially generalises several results present in the literature and gives a complete picture concerning smoothness in such dense subspaces. Our result covers, for instance, every weakly Lindelöf determined Banach space (hence, all reflexive ones), $L_1(\mu )$ for every measure $\mu $, $\ell _\infty (\Gamma )$ spaces for every set $\Gamma $, $C(K)$ spaces where $K$ is a Valdivia compactum or a compact Abelian group, duals of Asplund spaces, or preduals of Von Neumann algebras. Additionally, under Martin Maximum MM, all Banach spaces of density $\omega _1$ are covered by our result.
A scoping review of publicly available language tasks in clinical natural language processing
Authors: Gao Yanjun , Dligach Dmitriy , Christensen Leslie , Tesch Samuel , Laffin Ryan , Xu Dongfang , Miller Timothy , Uzuner Ozlem , Churpek Matthew M , Afshar Majid 
Published: August 2022

Abstract

Objective
To provide a scoping review of papers on clinical natural language processing (NLP) shared tasks that use publicly available electronic health record data from a cohort of patients.

Materials and Methods
We searched 6 databases, including biomedical research and computer science literature databases. A round of title/abstract screening and full-text screening were conducted by 2 reviewers. Our method followed the PRISMA-ScR guidelines.

Results
A total of 35 papers with 48 clinical NLP tasks met inclusion criteria between 2007 and 2021. We categorized the tasks by the type of NLP problems, including named entity recognition, summarization, and other NLP tasks. Some tasks were introduced as potential clinical decision support applications, such as substance abuse detection, and phenotyping. We summarized the tasks by publication venue and dataset type.

Discussion
The breadth of clinical NLP tasks continues to grow as the field of NLP evolves with advancements in language systems. However, gaps exist with divergent interests between the general domain NLP community and the clinical informatics community for task motivation and design, and in generalizability of the data sources. We also identified issues in data preparation.

Conclusion
The existing clinical NLP tasks cover a wide range of topics and the field is expected to grow and attract more attention from both general domain NLP and clinical informatics community. We encourage future work to incorporate multidisciplinary collaboration, reporting transparency, and standardization in data preparation. We provide a listing of all the shared task papers and datasets from this review in a GitLab repository.
Give and take: Effects of genetic admixture on mutation load in endangered Florida panthers
Authors: Ochoa Alexander , Onorato David P , Roelke-Parker Melody E , Culver Melanie , Fitak Robert R 
Published: August 2022

AbstractGenetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e. proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e. non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida × Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest that introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.
Multiplex Polymerase Chain Reaction Reveals Unique Trends in Pathogen and Parasitoid Infestations of Alfalfa Leafcutting Brood Cells
Authors: Clements Justin , Haylett Maggie , Nelson Brenda , Shumate Silas , Young Nicole , Bradford Benjamin , Walsh Doug , Lamour Kurt 
Published: August 2022

AbstractThe alfalfa leafcutting bee Megachile rotundata Fabricius (HYMENOPTERA: Megachilidae) is an important pollinator for multiple agricultural seed commodities in the United States. M. rotundata is a solitary cavity nesting bee that forms brood nests where its larvae can develop. During the developmental stages of growth, brood can be preyed upon by multiple different fungal pathogens and insect predators and parasitoids, resulting in the loss of the developing larvae. Larval loss is a major concern for alfalfa (Medicago sativa L.) seed producers because they rely on pollination services provided by M. rotundata. Reduced pollination rates result in lower yields and increased production costs. In the present study, we examined the taxonomic composition of organisms found within M. rotundata brood cells using a multiplex PCR assay which was developed for the detection of bacterial, fungal, and invertebrate pests and pathogens of M. rotundata larvae. Known pests of M. rotundata were detected, including members of the fungal genus Ascosphaera, the causative agent of chalkbrood. The presence of multiple Ascosphaera species in a single brood cell was observed, with potential implications for chalkbrood disease management. The multiplex assay also identified DNA from more than 2,400 total species, including multiple predators and pathogenetic species not previously documented in association with M. rotundata brood cells.
Law Matters—Less Than We Thought
Authors: Klerman Daniel , Spamann Holger 
Published: August 2022

AbstractIn a pre-registered 2 × 2 × 2 factorial between-subject randomized lab experiment with 61 federal judges, we test if the law influences judicial decisions, if it does so more under a rule than under a standard, and how its influence compares to that of legally irrelevant sympathies. Participating judges received realistic materials and a relatively long period of time (50 min) to decide an auto accident case. We find at best weak evidence that the law matters or that rules constrain more than standards, and no evidence of a sympathy effect. (JEL K00, K13, K40, K41)
Quantitative Analysis of Vertical Transmission of Maternal SARS-CoV-2 Antibodies to Neonates and Young Infants Following Immunization During Pregnancy
Authors: Golan Naama , Ashkenazi Shai , Davidovich Rotem , Levinsky Alina , Bar Chaim Adina , Abu Hamad Ramzia , Raveh Omer , Yitzhaki Shai , Livni Gilat 
Published: August 2022

Abstract
Serum antibody levels to SARS-CoV-2 in infants born to mothers who had received 2 doses of the BNT2b2 vaccine during pregnancy correlated positively with increasing gestational age at vaccination (P &lt; .01) and negatively with increasing time from vaccination (P &lt; .01), with a significant drop in infants aged &gt;60 days (P = .045).
Predictors of Septic Shock or Bacteremia in Children Experiencing Febrile Neutropenia Post-Chemotherapy
Authors: Avilés-Robles Martha , Schnur Jennifer J , Dorantes-Acosta Elisa , Márquez-González Horacio , Ocampo-Ramírez Luis A , Chawla Nitesh V 
Published: August 2022

Abstract

Background
Febrile neutropenia (FN) is an early indicator of infection in oncology patients post-chemotherapy. We aimed to determine clinical predictors of septic shock and/or bacteremia in pediatric cancer patients experiencing FN and to create a model that classifies patients as low-risk for these outcomes.

Methods
This is a retrospective analysis with clinical data of a cohort of pediatric oncology patients admitted during July 2015 to September 2017 with FN. One FN episode per patient was randomly selected. Statistical analyses include distribution analysis, hypothesis testing, and multivariate logistic regression to determine clinical feature association with outcomes.

Results
A total of 865 episodes of FN occurred in 429 subjects. In the 404 sampled episodes that were analyzed, 20.8% experienced outcomes of septic shock and/or bacteremia. Gram-negative bacteria count for 70% of bacteremias. Features with statistically significant influence in predicting these outcomes were hematological malignancy (P &lt; .001), cancer relapse (P = .011), platelet count (P = .004), and age (P = .023). The multivariate logistic regression model achieves AUROC = 0.66 (95% CI 0.56–0.76). The optimal classification threshold achieves sensitivity = 0.96, specificity = 0.33, PPV = 0.40, and NPV = 0.95.

Conclusions
This model, based on simple clinical variables, can be used to identify patients at low-risk of septic shock and/or bacteremia. The model’s NPV of 95% satisfies the priority to avoid discharging patients at high-risk for adverse infection outcomes. The model will require further validation on a prospective population.
Maize sterility gene DRP1 encodes a desiccation-related protein that is critical for Ubisch bodies and pollen exine development
Authors: Hu Mingjian , Li Yunfei , Zhang Xiangbo , Song Weibin , Jin Weiwei , Huang Wei , Zhao Haiming 
Published: August 2022

Abstract
Desiccation tolerance is a remarkable feature of pollen, seeds, and resurrection-type plants. Exposure to desiccation stress can cause sporophytic defects, resulting in male sterility. Here, we report the novel maize sterility gene DRP1 (Desiccation-Related Protein 1), which was identified by bulked-segregant analysis sequencing and encodes a desiccation-related protein. Loss of function of DRP1 results in abnormal Ubisch bodies, defective tectum of the pollen exine, and complete male sterility. Our results suggest that DRP1 may facilitate anther dehydration to maintain appropriate water status. DRP1 is a secretory protein that is specifically expressed in the tapetum and microspore from the tetrad to the uninucleate microspore stage. Differentially expressed genes in drp1 are enriched in Gene Ontology terms for pollen exine formation, polysaccharide catabolic process, extracellular region, and response to heat. In addition, DRP1 is a target of selection that appears to have played an important role in the spread of maize from tropical/subtropical to temperate regions. Taken together, our results suggest that DRP1 encodes a desiccation-related protein whose loss of function causes male sterility. Our findings provide a potential genetic resource that may be used to design crops for heterosis utilization.
Clinician Perceptions of Transition From Legacy Electronic Health Record to MHS GENESIS: A Pilot Study
Authors: Knobloch Glynnis , Milliren Anna , Winnie Kirsten 
Published: August 2022

ABSTRACT

Introduction
The implementation of a new electronic health record (EHR) presents significant challenges as users navigate a new interface. Our institution was an early adopter of MHS GENESIS (MHSG), the MHS’s new EHR. This study investigated provider perceptions of usability and the prevalence of burnout during an EHR transition from the Legacy system (LEHR) utilizing online, anonymous surveys before implementation and at several points post-implementation.

Materials and Methods
Clinician satisfaction, perceptions of EHR impact on safety, communication, reliability, and chart completion were assessed on five-point Likert scales. Usability was assessed using the validated System Usability Scale (SUS). Burnout prevalence was assessed using a validated single-item measure. Data were gathered via online, anonymous surveys before implementation and at 1, 3-6, and 9-12 months post “Go-Live.”

Results
Of 367 clinicians, 56 responded to the baseline survey; on average, 29% of responses were positive (i.e., satisfied or very satisfied) with LEHR. Following implementation, an average of 47%, 37%, and 47% of responses were positive for MHSG at 1 months (n = 42), 6 months (n = 55), and 12 months (n = 30), respectively. The mean SUS for LEHR was 48 (on a scale of 1-100); for MHSG, the mean SUS was 48 (1 month), 41 (6 months), and 44 (12 months). The burnout rate was reported as 39% (baseline), 26% (1 month), 33% (6 months), and 37% (12 months).

Conclusions
Perceptions of system usability, physician satisfaction, and burnout were not remarkably different between the two systems. Study results imply a need for further investigation as to why most clinicians continue to be unsatisfied with MHSG and wish to return to LEHR and whether or how this EHR transition contributed to burnout or if other factors are more contributory in this population. Future studies could also explore whether changes in the clinician interface, training, or implementation process impact clinician satisfaction, burnout, and desire to return to LEHR, or if these measures change with longer follow-up or in more varied populations.