bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intersectionality and women's participation in peace negotiations
Authors: Sapiano Jenna , Jin Xianan , Heathcote Gina 
Published: November 2024

Abstract
The Women, Peace and Security resolutions have consistently called for women's increased participation at all levels in institutions and mechanisms for preventing, managing and resolving conflict. Despite a long history of feminist interventions to disrupt categories of gender as a stagnant, ahistorical or geographically consistent structure, rationales for women's inclusion continue to rest on problematic narratives and assumptions. We draw on twenty-nine interviews with practitioners whom we asked to speak about their experiences in peace negotiations and the expectations placed on women involved in these processes. The problematic narratives and assumptions we identify on the basis of these interviews and academic literature have the effect of diminishing women's agency and, thus, their ability to participate in peace negotiations on their terms. Women contribute positively to the durability of peace and the inclusion of gender provisions in agreements. Still, when women's identities are constructed as one-dimensional, the benefits of women's inclusion remain paradoxically a cause for celebration and a partial gain. In this article, we apply theories of intersectionality, informed by Black and African feminisms, to expose women's subject positions that may be made invisible because of assumptions that continue to be associated with calls for women's participation in peace negotiations.
Commitment and compromise in Danish cyber and tech diplomacy
Authors: Jacobsen Jeppe T 
Published: November 2024

Abstract
This article explores the emergence of norm promotion strategies through an in-depth, partly autobiographical case-study spanning almost a decade of Danish cyber and tech diplomacy. The article engages the norms literature in International Relations and highlights the significance of the frequently overlooked internal negotiations that take place within the bureaucratic structures of norm entrepreneurs. Despite Denmark's favourable position and aspiration to become a norm entrepreneur in cyberspace, internal dynamics characterized by varying levels of commitment and compromise in negotiations over cyber norm promotion strategies resulted in both failed norm promotion attempts and fundamental alterations to a previously successful initiative. The article advocates for increasing analytical attention to the internal dynamics of norm entrepreneurs, positing that such examination not only offers a more nuanced perspective on the initial stages of a norm's life-cycle, but also furnishes an additional indication of a norm's robustness. Methodologically tracing the practices of civil servants as they negotiate their continuing commitment to norm-entrepreneurial strategies, particularly in response to domestic political changes or external events, provides norms scholars with valuable insight into the potential weakening or strengthening of a norm.
Variability of interobserver interpretation of selected helminth ova in the development of a training image set
Authors: Chua Rupert Stephen Charles S , Henderson Kiersten A , de Guzman Lorenzo Maria C , Foss Vicki , Schub Nathaniel , Bell Cameron , Medina John Robert C , Siao Taggart G , Mistica Myra S , Belleza Maria Luz B , Modequillo Marie Cris R , Torres Nadine Joyce C , Belizario Vicente Y 
Published: November 2024

Abstract

Background
Diagnosis of soil-transmitted helminthiasis and schistosomiasis for surveillance relies on microscopic detection of ova in Kato–Katz (KK) prepared slides. Artificial intelligence (AI)-based platforms for parasitic eggs may be developed using a robust image set with defined labels by reference microscopists. This study aimed to determine interobserver variability among reference microscopists in identifying parasite ova.

Methods
Images of parasite ova taken from KK prepared slides were labelled according to species by two reference microscopists (M1 and M2). A third reference microscopist (M3) labelled images when the first two did not agree. Frequency, percent agreement, κ statistics and variability score (VS) were generated for analysis.

Results
M1 and M2 agreed on 89.24% of the labelled images (κ=0.86, p&lt;0.001). M3 had agreement with M1 and M2 (κ=0.30, p&lt;0.001 and κ=0.28, p&lt;0.001), resolving 89.29% of disagreement between them. The labelling of Schistosoma japonicum had the highest VS (κ=0.487, p=0.101) among the targeted ova. Reference microscopists were able to reliably reach consensus in 99.0% of the dataset.

Conclusions
Training AI using this image set may provide more objective and reliable readings compared with that of reference microscopists.
Maintaining Ocean ecosystem health with hydrocarbonoclastic microbes
Authors: Wang Wanpeng , Zhi Bin , Wang Yong , Shao Zongze 
Published: November 2024

Abstract
Accidental spills and persisting hydrocarbon pollution caused by petroleum exploitation have deeply disrupted marine ecosystems, including those in the deep oceans and the Arctic Ocean. While physicochemical methods are available for emergency cleanup, microorganisms are ultimately responsible for mineralizing the hydrocarbons. The understanding of environmental effects on the composition and efficiency of hydrocarbon-degrading microbial communities has greatly improved current microorganism-based remediation strategies. This review summarizes recent findings on the physiology, metabolism, and ecology of marine obligate hydrocarbonoclastic microorganisms. Strategies for improved biotechnological solutions based on the use of hydrocarbon-degrading microbes are discussed for hydrocarbon remediation in marine water columns, sediments, beaches, and the Arctic.
Combining polynomial regression with unsupervised machine learning on wafer-level packaging reliability prediction
Authors: Liao H H , Su Qinghua , Chiang K N 
Published: November 2024

ABSTRACT
The benefits of wafer-level packaging include better thermal dissipation, lower latency and reduced space consumption. Accelerated thermal cycling test (ATCT) is a regulation that determines whether a product is ready for mass production, but it takes a long time and is costly to perform. The design-on-simulation approach can reduce the number of ATCT experiments and shorten the design cycle. However, the simulation method must be verified before it can be treated as an experiment; if the simulation consistently matches experiments at close range, it can also be treated as an experiment. In addition, the verified simulation method can be used to develop a machine learning (ML) database and obtain an artificial intelligence model for long-term reliability prediction. Due to its effectiveness in solving nonlinear problems with relatively short computation times, polynomial regression (PR) is used in this study as ML model. Results show combining PR with an unsupervised learning algorithm, K-means, can produce more accurate predictions.
DNAproDB: an updated database for the automated and interactive analysis of protein–DNA complexes
Authors: Mitra Raktim , Cohen Ari S , Sagendorf Jared M , Berman Helen M , Rohs Remo 
Published: November 2024

Abstract
DNAproDB (https://dnaprodb.usc.edu/) is a database, visualization tool, and processing pipeline for analyzing structural features of protein–DNA interactions. Here, we present a substantially updated version of the database through additional structural annotations, search, and user interface functionalities. The update expands the number of pre-analyzed protein–DNA structures, which are automatically updated weekly. The analysis pipeline identifies water-mediated hydrogen bonds that are incorporated into the visualizations of protein–DNA complexes. Tertiary structure-aware nucleotide layouts are now available. New file formats and external database annotations are supported. The website has been redesigned, and interacting with graphs and data is more intuitive. We also present a statistical analysis on the updated collection of structures revealing salient patterns in protein–DNA interactions.
NusG-dependent RNA polymerase pausing is a common feature of riboswitch regulatory mechanisms
Authors: Jayasinghe Oshadhi T , Ritchey Laura E , Breil Thomas , Newman Paxton , Yakhnin Helen , Babitzke Paul 
Published: November 2024

Abstract
Transcription by RNA polymerase is punctuated by transient pausing events. Pausing provides time for RNA folding and binding of regulatory factors to the paused elongation complex. We previously identified 1600 NusG-dependent pauses throughout the Bacillus subtilis genome, with ∼20% localized to 5′ leader regions, suggesting a regulatory role for these pauses. We examined pauses associated with known riboswitches to determine whether pausing is a common feature of these mechanisms. NusG-dependent pauses in the fmnP, tenA, mgtE, lysP and mtnK riboswitches were in strategic positions preceding the critical decision between the formation of alternative antiterminator or terminator structures, which is a critical feature of transcription attenuation mechanisms. In vitro transcription assays demonstrated that pausing increased the frequency of termination in the presence of the cognate ligand. NusG-dependent pausing also reduced the ligand concentration required for efficient termination. In vivo expression studies with transcriptional fusions confirmed that NusG-dependent pausing is a critical component of each riboswitch mechanism. Our results indicate that pausing enables cells to sense a broader range of ligand concentrations for fine-tuning riboswitch attenuation mechanisms.
scImmOmics: a manually curated resource of single-cell multi-omics immune data
Authors: Li Yan-Yu , Zhou Li-Wei , Qian Feng-Cui , Fang Qiao-Li , Yu Zheng-Min , Cui Ting , Dong Fu-Juan , Cai Fu-Hong , Yu Ting-Ting , Li Li-Dong , Wang Qiu-Yu , Zhu Yan-Bing , Tang Hui-Fang , Hu Bao-Yang , Li Chun-Quan 
Published: November 2024

Abstract
Single-cell sequencing technology has enabled the discovery and characterization of subpopulations of immune cells with unique functions, which is critical for revealing immune responses under healthy or disease conditions. Efforts have been made to collect and curate single-cell RNA sequencing (scRNA-seq) data, yet an immune-specific single-cell multi-omics atlas with harmonized metadata is still lacking. Here, we present scImmOmics (https://bio.liclab.net/scImmOmics/home), a manually curated single-cell multi-omics immune database constructed based on high-quality immune cells with known immune cell labels. Currently, scImmOmics documents &gt;2.9 million cell-type labeled immune cells derived from seven single-cell sequencing technologies, involving 131 immune cell types, 47 tissues and 4 species. To ensure data consistency, we standardized the nomenclature of immune cell types and presented them in a hierarchical tree structure to clearly describe the lineage relationships within the immune system. scImmOmics also provides comprehensive immune regulatory information, including T-cell/B-cell receptor sequencing clonotype information, cell-specific regulatory information (e.g. gene/chromatin accessibility/protein/transcription factor states within known cell types, cell-to-cell communication and co-expression networks) and immune cell responses to cytokines. Collectively, scImmOmics is a comprehensive and valuable platform for unraveling the heterogeneity and diversity of immune cells and elucidating the specific regulatory mechanisms at the single-cell level.
Molecular basis for thermogenesis and volatile production in the titan arum
Authors: Zulfiqar Alveena , Azhar Beenish J , Shakeel Samina N , Thives Santos William , Barry Theresa D , Ozimek Dana , DeLong Kim , Angelovici Ruthie , Greenham Kathleen , Schenck Craig A , Schaller G Eric 
Published: November 2024

Abstract
The titan arum (Amorphophallus titanum), commonly known as the corpse flower, produces the largest unbranched inflorescence in the world. Its rare blooms last only a few days and are notable both for their burst of thermogenic activity and for the odor of rotting flesh by which they attract pollinators. Studies on the titan arum can therefor lend insight into the mechanisms underlying thermogenesis as well as the production of sulfur-based volatiles, about which little is known in plants. Here, we made use of transcriptome and metabolite analyses to uncover underlying mechanisms that enable thermogenesis and volatile production in the titan arum. The ability to perform thermogenesis correlated with the expression of genes involved in bypass steps for the mitochondrial electron transport chain, in particular alternative oxidase expression, and through our analysis is placed within the context of sugar transport and metabolism. The major odorants produced by the titan arum are dimethyl disulfide and dimethyl trisulfide, and we identified pathways for sulfur transport and metabolism that culminate in the production of methionine, which our analysis identifies as the amino acid substrate for production of these odorants. Putrescine, derived from arginine, was identified as an additional and previously unrecognized component of the titan arum's odor. Levels of free methionine and putrescine were rapidly depleted during thermogenesis, consistent with roles in production of the titan arum's odor. Models for how tissues of the titan arum contribute to thermogenesis and volatile production are proposed.
Directionality and representativeness are differentiable components of stereotypes in large language models
Authors: Nicolas Gandalf , Caliskan Aylin 
Published: November 2024

Abstract
Representativeness is a relevant but unexamined property of stereotypes in language models. Existing auditing and debiasing approaches address the direction of stereotypes, such as whether a social category (e.g. men, women) is associated more with incompetence vs. competence content. On the other hand, representativeness is the extent to which a social category's stereotypes are about a specific content dimension, such as Competence, regardless of direction (e.g. as indicated by how often dimension-related words appear in stereotypes about the social category). As such, two social categories may be associated with competence (vs. incompetence), yet one category's stereotypes are mostly about competence, whereas the other's are mostly about alternative content (e.g. Warmth). Such differentiability would suggest that direction-based auditing may fail to identify biases in content representativeness. Here, we use a large sample of social categories that are salient in American society (based on gender, race, occupation, and others) to examine whether representativeness is an independent feature of stereotypes in the ChatGPT chatbot and SBERT language model. We focus on the Warmth and Competence stereotype dimensions, given their well-established centrality in human stereotype content. Our results provide evidence for the construct differentiability of direction and representativeness for Warmth and Competence stereotypes across models and target stimuli (social category terms, racialized name exemplars). Additionally, both direction and representativeness uniquely predicted the models' internal general valence (positivity vs. negativity) and human stereotypes. We discuss implications for the use of AI in the study of human cognition and the field of fairness in AI.
QRISK3 and SCORE2 are equally reliable predictors of carotid plaques in patients with systemic lupus erythematosus
Authors: Ferraz-Amaro Iván , Heras-Recuero Elena , Quevedo-Abeledo Juan C , Llorca Javier , González-Gay Miguel Á 
Published: November 2024

Abstract

Objectives
Cardiovascular (CV) disease is the leading cause of death among patients with SLE. This study aimed to compare the performance of QRESEARCH risk estimator version 3 (QRISK3) and the Systematic Coronary Risk Evaluation-2 (SCORE2) scores to identify SLE patients at high risk of CV events, as indicated by the presence of carotid plaques.

Methods
Subclinical atherosclerosis was evaluated using carotid US in 365 SLE patients. QRISK3 and SCORE2 were calculated. The relationship between these scores and the presence of carotid plaques was analysed by treating the scores as continuous and categorical variables, as well as separately and in combination. Logistic regression and area under the receiver operating characteristic curve (AUC) analyses were used to assess their predictive accuracy.

Results
The discriminatory capacity of QRISK3, with an AUC of 0.770 (95% CI 0.720, 0.821), and SCORE2, with an AUC of 0.800 (95% CI 0.753, 0.843), for carotid plaque was similar, with no statistically significant difference (P = 0.070). However, when examining the association of both calculators considered continuously and together with their interaction, the discriminatory capacity of this combination was significantly greater than that of QRISK3 alone (P = 0.034) but did not differ from SCORE2 (P = 0.71).

Conclusion
QRISK3 and SCORE2 are equally reliable predictors of carotid plaques in SLE patients. The combination of both calculators offers significantly better discrimination than QRISK3 alone but shows no significant difference when compared with SCORE2 alone. Therefore, SCORE2 alone, without the need for additional tools, can be used to identify patients with SLE who are at high risk of CV events.
Tolvaptan safety in autosomal-dominant polycystic kidney disease; a focus on idiosyncratic drug-induced liver injury liabilities
Authors: Hammond Sean , Meng Xiaoli , Barber Jane , Mosedale Merrie , Chadwick Amy , Watkins Paul B , Naisbitt Dean J 
Published: November 2024

Abstract
Tolvaptan is a vasopressin V2 receptor antagonist which has proven to be an effective and mostly well-tolerated agent for the treatment of autosomal-dominant polycystic kidney disease. However, its administration is associated with rare but serious idiosyncratic liver injury, which has warranted a black box warning on the drug labels and frequent monitoring of liver blood tests in the clinic. This review outlines mechanistic investigations that have been conducted to date and constructs a working narrative as an explanation for the idiosyncratic drug-induced liver injury (IDILI) events that have occurred thus far. Potential risk factors which may contribute to individual susceptibility to DILI reactions are addressed, and key areas for future investigative/clinical development are highlighted.
Peripubertal exposure to oxyfluorfen, a diphenyl herbicide, delays pubertal development in the male rat by antagonizing androgen receptor activity
Authors: Murr Ashley S , Buckalew Angela R , Devane Grace , Bailey Jarod R , Ford Jermaine L , Gray Leon Earl , Stoker Tammy E 
Published: November 2024

Abstract
We recently identified the herbicide oxyfluorfen as an inhibitor of iodide uptake by the sodium iodide symporter, a key step in thyroid hormone synthesis, using in vitro assays. We also observed a suppression of serum T4 and T3 in juvenile rats exposed orally to oxyfluorfen for 4 to 8-d. The purpose of the present study was to further evaluate the effects of an extended 31-d oral exposure using a male pubertal rat study (15 to 500 mg/kg). Oxyfluorfen delayed puberty at all doses (1.3 to 3.5-d) suppressing ventral prostate at 62.5 mg/kg and above and seminal vesicle weights at 31.25 mg/kg and above with no effect on testosterone or luteinizing hormone. Serum T4 and T3 were suppressed by all doses up to 80%, with a linear increase in serum TSH. Based on delayed puberty without changes in testosterone, we hypothesized that oxyfluorfen interferes with androgen receptor (AR) function. Results from our Hershberger study, with oxyfluorfen (62.5 and 125 mg/kg) co-treated with testosterone propionate (TP, 1 mg/kg) for 10-d showed 3 of 5 of the androgenic tissue weights were suppressed compared with TP alone indicating AR antagonism. We next confirmed this effect in an in vitro AR transcriptional activation reporter assay (0 to 20 μM) with 125 pM 5αDH-11-ketotestosterone and found concentration-dependent inhibition of AR luminescence activity (EC50 1.75 µM) without cytotoxicity. Thus, this study confirms the endocrine-disrupting mechanism of oxyfluorfen using in vitro and in vivo evaluations of the thyroid hormone and AR pathways. This abstract does not necessarily reflect U.S. EPA policy.
Breathy Vocal Quality, Background Noise, and Hearing Loss: How Do These Adverse Conditions Affect Speech Perception by Older Adults?
Authors: Shen Jing , Heller Murray Elizabeth 
Published: November 2024

Objectives:
Although breathy vocal quality and hearing loss are both prevalent age-related changes, their combined impact on speech communication is poorly understood. This study investigated whether breathy vocal quality affected speech perception and listening effort by older listeners. Furthermore, the study examined how this effect was modulated by the adverse listening environment of background noise and the listener’s level of hearing loss.

Design:
Nineteen older adults participated in the study. Their hearing ranged from near-normal to mild-moderate sensorineural hearing loss. Participants heard speech material of low-context sentences, with stimuli resynthesized to simulate original, mild-moderately breathy, and severely breathy conditions. Speech intelligibility was measured using a speech recognition in noise paradigm, with pupillometry data collected simultaneously to measure listening effort.

Results:
Simulated severely breathy vocal quality was found to reduce intelligibility and increase listening effort. Breathiness and background noise level independently modulated listening effort. The impact of hearing loss was not observed in this dataset, which can be due to the use of individualized signal to noise ratios and a small sample size.

Conclusion:
Results from this study demonstrate the challenges of listening to speech with a breathy vocal quality. Theoretically, the findings highlight the importance of periodicity cues in speech perception in noise by older listeners. Breathy voice could be challenging to separate from the noise when the noise also lacks periodicity. Clinically, it suggests the need to address both listener- and talker-related factors in speech communication by older adults.