bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Atlas of the DevelopingDrosophilaVisual System Glia and Subcellular mRNA Localization of Transcripts in Single Cells
Authors: Ferreira Amanda A. G. , Desplan Claude 
Published: August 2023

AbstractGlial cells are essential for proper nervous system development and function. To understand glial development and function, we comprehensively annotated glial cells in a single-cell mRNA-sequencing (scRNAseq) atlas of the developingDrosophilavisual system. This allowed us to study their developmental trajectories, from larval to adult stages, and to understand how specific types of glia diversify during development. For example, neuropil glia that are initially transcriptionally similar in larvae, split into ensheathing and astrocyte-like glia during pupal stages. Other glial types, such as chiasm glia change gradually during development without splitting into two cell types.The analysis of scRNA-seq allowed us to discover that the transcriptome of glial cell bodies can be distinguished from that of their broken processes. The processes contain distinct enriched mRNAs that were validated in vivo. Therefore, we have identified most glial types in the developing optic lobe and devised a computational approach to identify mRNA species that are localized to cell bodies or cellular processes.
Machine learning models for prediction of xenobiotic chemicals with high propensity to transfer into human milk
Authors: Vijayaraghavan Sudharsan , Lakshminarayanan Akshaya , Bhargava Naman , Ravichandran Janani , Vivek-Ananth R.P. , Samal Areejit 
Published: August 2023

AbstractBreast milk serves as a vital source of essential nutrients for infants. However, human milk contamination via transfer of environmental chemicals from maternal exposome is a significant concern for infant health. Machine learning based predictive toxicology models can be valuable in predicting chemicals with high propensity to transfer into human milk. To this end, we build such classification- and regression-based models by employing multiple machine learning algorithms and leveraging the largest curated dataset to date of 375 chemicals with known Milk to Plasma concentration (M/P) ratios. Our Support Vector Machine (SVM) based classifier outperforms other models in terms of different performance metrics, when evaluated on both (internal) test data and external test dataset. Specifically, the SVM based classifier on (internal) test data achieved a classification accuracy of 77.33%, specificity of 84%, sensitivity of 64%, and F-score of 65.31%. When evaluated on an external test dataset, our SVM based classifier is found to be generalizable with sensitivity of 77.78%. While we were able to build highly predictive classification models, our best regression models for predicting the M/P ratio of chemicals could achieve only moderate R2values on the (internal) test data. As noted in earlier literature, our study also highlights the challenges in developing accurate regression models for predicting the M/P ratio of xenobiotic chemicals. We have made our complete workflow, train and test datasets, and computer codes for the classification and regression models publicly available via a dedicated GitHub repository. Overall, this study attests the immense potential of predictive computational toxicology models in characterizing the myriad chemicals in the human exposome.
From forests to fields: investigatingCulicoides(Diptera: Ceratopogonidae) abundance and diversity in cattle pastures and adjacent woodlands
Authors: Steele Cassandra H. , McDermott Emily G. 
Published: August 2023

AbstractCulicoidesLatreille (Diptera: Ceratopogonidae) biting midges are hematophagous flies that feed on wild and domestic ruminants, and transmit many arboviruses, including bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV) circulating in the United States (US). They occupy a range of aquatic and semiaquatic habitats, and disperse short distances from their development sites. In the southeastern US there are limited studies on the abundance and diversity ofCulicoidesin wooded and adjacent livestock pasture habitats. In thus study, we characterizedCulicoidesdiversity and abundance within these distinct habitat types by setting BG-Sentinel and CDC miniature suction traps baited with CO2or UV-light in wooded and pasture habitats at two locations on a university beef farm in Savoy, AR. Traps were set once per week for nine weeks in August-October of 2021-2022. Fifteen species were collected during this study. The two most abundant species wereCulicoides haematopotusMalloch andCulicoides stelliferCoquillett. There was a significant effect of site and location onC. haematopotuscollections, and a significant effect and interaction of site and trap onC. stellifercollections. In the woods, significantly moreC. stelliferwere collected from the CDC-UV trap, while in the pasture, significantly more were collected in the CDC-CO2trap. These data suggest thatC. stellifer, a putative vector of BTV and EHDV in the southeast, may be traveling into the pasture to host-seek, whileC. haematopotusremains primarily in the woods. This study reveals community differences between these habitat types and implications forCulicoidescontrol.
Highly accurate and robust protein sequence design with CarbonDesign
Authors: Ren Milong , Yu Chungong , Bu Dongbo , Zhang Haicang 
Published: August 2023

AbstractProtein sequence design, the inverse problem of protein structure prediction, plays a crucial role in protein engineering. Although recent deep learning-based methods have shown promising advancements, achieving accurate and robust protein sequence design remains an ongoing challenge. Here, we present CarbonDesign, a new approach that draws inspiration from successful ingredients of AlphaFold for protein structure prediction and makes significant and novel developments tailored specifically for protein sequence design. At its core, CarbonDesign explores Inverseformer, a novel network architecture adapted from AlphaFold’s Evoformer, to learn representations from backbone structures and an amortized Markov Random Fields model for sequence decoding. Moreover, we incorporate other essential AlphaFold concepts into CarbonDesign: an end-to-end network recycling technique to leverage evolutionary constraints in protein language models and a multi-task learning technique to generate side chain structures corresponding to the designed sequences. Through rigorous evaluations on independent testing data sets, including the CAMEO and recent CASP15 data sets, as well as the predicted structures from AlphaFold, we show that CarbonDesign outperforms other published methods, achieving high accuracy in sequence generation. Moreover, it exhibits superior performance onde novobackbone structures obtained from recent diffusion generative models such as RFdiffusion and FrameDiff, highlighting its potential for enhancingde novoprotein design. Notably, CarbonDesign also supports zero-shot prediction of the functional effects of sequence variants, indicating its potential application in directed evolution-based design. In summary, our results illustrate CarbonDesign’s accurate and robust performance in protein sequence design, making it a promising tool for applications in bioengineering.
Gene-to-Gene Coordinated Regulation of Transcription and Alternative splicing by 3D Chromatin Remodeling upon NF-κB activation
Authors: Marie Paul , Ladet Julien , Bazire Matéo , Ameur Lamya Ben , Chahar Sanjay , Fontrodona Nicolas , Sexton Tom , Auboeuf Didier , Bourgeois Cyril F. , Mortreux Franck 
Published: August 2023

SummaryThe p65/RelA factor of NF-κB plays a pivotal role in coordinating gene expression in response to diverse stimuli, including viral infections. At the chromatin level, p65/RelA regulates gene transcription and alternative splicing (AS) through promoter enrichment and genomic exon occupancy, respectively. However, the mechanisms underlying the coordination of these processes across distinct genes remain elusive. In this study, we employed the HTLV-1 Tax oncoprotein, a potent activator of NF-κB, to investigate the integrative relationship between 3D chromatin architecture, NF-κB-regulated transcription and AS. Our analysis revealed that Tax induces a pronounced reorganization of the 3D genome, resulting in the formation of multigene complexes that comprise genes regulated either transcriptionally or through AS. Notably, we found that the Tax-induced gene-gene contact between the two master genesNFKBIAandRELAis associated with their differential regulation in gene expression and AS, respectively. Through dCas9-mediated approaches, we demonstrated thatNFKBIA-RELAinteraction is required for AS regulation and is caused by an intragenic enrichment of p65/RelA onRELA. Our findings shed light on new regulatory mechanisms upon HTLV-1 Tax and underscore the integral role of p65/RelA in coordinated regulation of NF-κB-responsive genes at both transcriptional and AS levels in the context of the 3D genome.
How heterogeneous wine lots result in a price discount relative to homogeneous lots
Authors: Breeden Joseph L. 
Published: August 2023

Purpose
The purpose of this study is to determine whether the fine wine market is efficient between homogeneous lots and heterogeneous lots.

Design/methodology/approach
Auction price data for homogeneous (or solid) lots of fine wines was analyzed to create price prediction models. Those models were used to predict the expected auction price for the bottles within heterogeneous lots. Lastly, models were created to explain and predict the differences between expected and realized prices for heterogenous wine lots.

Findings
The results show that large inefficiencies exist. The more complex and expensive the heterogeneous lot, the greater the discount relative to what would have been realized if the bottles had been sold individually. This discount can exceed 50% of the expected auction price.

Practical implications
Heterogeneous lots may arise as a practical requirement from the auction house. Restaurant buyers probably have little interest in such lots because of the inclusion of wines the restaurant will be unable to sell. Collectors may be uniquely positioned to benefit from this price discount.

Originality/value
These results are unique in the literature, because the price dynamics of heterogeneous (or mixed) lots of fine wines have not previously been studied.
Exploratory study of an ally training program for mental health support
Authors: Wendeln Beatrice Meda , Sheehan Lindsay 
Published: August 2023

Purpose
The purpose of this study was to evaluate the effects of an online mental health ally program on several measurements of readiness to help and stigma reduction. Allyship is one way to support people with mental health challenges beyond traditional care services.

Design/methodology/approach
The efficacy of the program was evaluated in pre and postintervention surveys (n = 26) including measures of self-care, help-seeking intentions, peer-support self-efficacy, advocacy, knowledge of resources and stigma. A within-subject, repeated measures design was conducted analyzing changes at completion. Twenty-six participants who completed the program (either with or without lived experience of mental illness) were included in the study. A subgroup of participants (n = 11) who reported lived experiences of mental illness were assigned additional measures of internalized stigma, stigma stress, stigma resistance and self-esteem.

Findings
Analysis of mean differences indicated a statistically significant change in scores pre and postcompletion. The program increased peer-support, help-seeking intentions and self-esteem, while reducing internalized stigma and stigma stress. Findings provide preliminary support for program effectiveness in training individuals to support others and themselves through mental health challenges.

Research limitations/implications
Trained allies might improve the lives of individuals with mental health challenges by reducing discrimination and improving social support. We discuss the implication of allies to complement the mental health system.

Originality/value
To the best of the authors’ knowledge, this is the first exploratory study on the efficacy of an online ally training program for individuals with mental illness. The NoStigmas Ally Program is a novel and original development in ally training.
Evaluating AI literacy proficiency among LIS researchers in ASEAN
Authors: A. Subaveerapandiyan , Paladhi Monali Mitra , Maruthaveeran Vijayalatchumy 
Published: August 2023

Purpose
This paper aims to investigate AI literacy proficiency among LIS researchers in Association of Southeast Asian Nations (ASEAN) countries. This study also aims to assess current proficiency levels, identify challenges and gaps, explore recommendations for improving skills and examine how researchers stay updated on AI advancements.

Design/methodology/approach
A structured questionnaire was used to collect data, then analysed using appropriate statistical methods.

Findings
Most respondents showed proficiency in various aspects of AI literacy for LIS research. However, some aspects, such as understanding AI concepts, ethical considerations and programming skills, had lower proficiency levels. Factors influencing AI literacy included limited resources for enhancement, lack of awareness and insufficient AI-related courses in LIS education.

Originality/value
This study presents an original assessment of AI literacy proficiency among LIS researchers in ASEAN countries, shedding light on the current state of AI knowledge in the region’s library and information science field. The findings identify specific gaps and challenges, offering valuable insights for policymakers, educators and stakeholders seeking to enhance AI literacy skills in this context.
More effect of ephemeral plant species diversity on aboveground biomass than functional diversity and functional composition
Authors: Guo Hao , Zhou Xiaobing , Tao Ye , Yin Jinfei , Lin Yajun , Zang Yongxin , Zhang Yuanming 
Published: August 2023

AbstractThe quantification of plant diversity–productivity relationships is essential for accurate productivity assessments. Global change drivers are altering resource availability and biodiversity. However, the extent to which multiple attributes of diversity (species, functions) buffer community productivity in response to the resource availability changes and the potential driver mechanisms of the diversity‐productivity relationship still needs to be the consensus. We investigated the ephemeral plant diversity–productivity relationships of different attributes along a precipitation gradient in the Gurbantunggut Desert, China. To evaluate the potential mechanisms by which diversity and functional composition affect aboveground productivity (niche complementarity and selection effect). Our results showed that (1) the variance of species richness (SR), Rao's quadratic entropy (RaoQ), community‐weighted mean of height (CWMH), and community‐weighted mean of leaf phosphorus concentration (CWMP) was larger among sites (variation between different sites) than subplots (variation between different subplots). Among subplots, the variance of community‐weighted mean of specific leaf area (CWMSLA), community‐weighted mean of leaf carbon concentration (CWMC), and community‐weighted mean of leaf nitrogen concentration (CWMN) was larger than the sites. (2) SR, RaoQ, CWMC, CWMN, CWMH, pH, and mean annual precipitation (MAP) collectively influenced the accumulation of aboveground biomass (AGB). (3) Species diversity and MAP have strongly affected AGB and accounted for 50% and 42%. The study confirms that SR is the optimal predictor of biomass in ephemeral plants. Complementation effects may be the primary mechanism explaining the relationship between biodiversity and productivity in the Gurbantunggut Desert, and thus the effect of plant diversity cannot be downplayed.
Treatment pattern and changes in oral glucocorticoid dose after tocilizumab treatment in patients with adult Still's disease: An analysis of a Japanese claims database
Authors: Kaneko Yuko , Kameda Hideto , Ikeda Kei , Yamashita Katsuhisa , Ozaki Ryoto , Tanaka Yoshiya 
Published: August 2023

AbstractAimIntravenous tocilizumab (TCZ‐IV) was approved for the treatment of adult Still's disease (ASD) in Japan in May 2019 based on its efficacy and safety in a phase III randomized controlled trial. This study determined treatment patterns in patients with ASD and assessed oral glucocorticoid (GC) dose changes after TCZ‐IV administration in Japanese clinical practice.MethodsPatients in the Medical Data Vision database aged 16 years or older with one or more of International Classification of Diseases, 10th revision codes M061 (ASD) or M082 (systemic juvenile idiopathic arthritis) during January 2017–March 2021 (cohort 1) and those initiating TCZ‐IV during May 2019–March 2021 (cohort 2) were included.ResultsIn cohort 1, the proportion of patients who were prescribed interleukin‐6 inhibitors (mainly TCZ‐IV) increased from 10.8% (January–April 2019 [before TCZ‐IV approval]; n = 2002) to 18.3% (January–March 2021 [after TCZ‐IV approval]; n = 2008). In cohort 2 (n = 193), 84.5% of patients were on oral GCs (≤5 mg/day: 23.8%) at index date (initial TCZ‐IV prescription date); 46/70 (65.7%) were on oral GC at 5 mg/day or higher 12 months after TCZ‐IV treatment (primary outcome). After 12 months of treatment, the TCZ‐IV retention rate was 73.6% and the TCZ‐IV administration interval was every 4 weeks and every 2 weeks in 31.9% and 27.7% of patients, respectively.ConclusionThe use of interleukin‐6 inhibitors increased by 7.5% points in Japanese patients with ASD ~2 years after TCZ‐IV approval, suggesting that an unmet medical need existed. This study suggests the potential GC‐sparing effect of TCZ‐IV in patients with ASD in clinical practice.
A case of discordant histology and expression of programmed death ligand 1 between primary tumor and brain metastases in adenosquamous carcinoma of the lung
Authors: Takagi Hironori , Muto Satoshi , Enta Akio , Fukuhara Mitsuro , Asano Shigeyuki , Shio Yutaka , Suzuki Hiroyuki 
Published: August 2023

AbstractA patient presented with vomiting and gait disturbance. Investigation revealed a single cerebellar tumor and another tumor in the upper lobe of the left lung. Based on the severe vomiting and gait disturbance, we removed the cerebellar tumor first, achieving resolution of symptoms. The cerebellar tumor was pathologically diagnosed as metastatic lung adenocarcinoma. No other metastases were identified, including in the mediastinal lymph nodes. We therefore resected the primary lung tumor. On final pathological analysis, the tumor in the upper lobe of the left lung was diagnosed as adenosquamous carcinoma with no lymph node metastasis. PD‐L1 expression was low in the primary lung adenosquamous carcinoma and high in the cerebellar metastasis. Furthermore, both tumors were KRASG12C‐positive. Tumor PD‐L1 expression is considered important for immune escape. In this case, adenocarcinoma cells in the primary adenosquamous carcinoma may have migrated to form a cerebellar metastasis. In advanced lung cancer, tumor growth may be observed in some lesions even when many other lesions are controlled by chemo‐ or immunotherapy. Biopsy to confirm histology and PD‐L1 expression is worth considering, depending on the location of the metastases and the invasiveness of the biopsy procedure.
Auditing with data and analytics: External reviewers' judgments of audit quality and effort
Authors: Emett Scott A. , Kaplan Steven E. , Mauldin Elaine G. , Pickerd Jeffrey S. 
Published: August 2023

AbstractAudit firms hesitate to take full advantage of data and analytics (D&A) audit approaches because they lack certainty about how external reviewers evaluate those approaches. We propose that external reviewers use an effort heuristic when evaluating audit quality, judging less effortful audit procedures as lower quality, which could shape how external reviewers evaluate D&A audit procedures. We conduct two experiments in which experienced external reviewers evaluate one set of audit procedures (D&A or traditional) within an engagement review, while holding constant the procedures' level of assurance. Our first experiment provides evidence that external reviewers rely on an effort heuristic when evaluating D&A audit procedures—they perceive D&A audit procedures as lower in quality than traditional audit procedures because they perceive them to be less effortful. Our second experiment confirms these results and evaluates a theory‐based intervention that reduces reviewers' reliance on the effort heuristic, causing them to judge quality similarly across D&A and traditional audit procedures.
Assessing protected area effectiveness in western Tanzania: Insights from repeated line transect surveys
Authors: Kiffner Christian , Giliba Richard A. , Fust Pascal , Loos Jacqueline , Waltert Matthias 
Published: August 2023

AbstractIn many parts of East Africa, wildlife populations have declined over the past decades. Given these trends, site‐based studies are needed to assess how protected areas with differing management strategies enable the effective conservation of wildlife populations. In Tanzania, game reserves are managed for tourist hunting, while national parks are managed for non‐consumptive wildlife‐based tourism. To assess the relative performance of these management strategies, we here focus on two areas: Rukwa Game Reserve (RGR) and Katavi National Park (KNP). Based on systematically designed line distance surveys in 2004 and 2021, we compared densities and group sizes of large mammal populations (African elephant, giraffe, buffalo, zebra, topi, and hartebeest) over time. Contrary to published ecosystem‐wide declines observed in numerous species which considered earlier baselines, we did not detect significant population declines between 2004 and 2021. While these new results showing apparent stable populations do not invalidate earlier studies on wildlife declines, they could indicate a stabilisation phase after declines. This highlights the importance of considering appropriate temporal baselines and historical contexts when assessing conservation effectiveness.
Hsa_circ_0015382 is involved in the pathogenesis of preeclampsia by mediating THBS2 expression
Authors: Wang Yang , Liu Lingfang , Wang Jiayao , Gao Yan 
Published: August 2023

AbstractBackgroundPreeclampsia (PE) is a hypertensive disorder of pregnancy that causes significant maternal and perinatal morbidity and mortality. Circular RNA (circRNA) hsa_circ_0015382 is associated with the pathogenesis of PE, but its underlying regulatory mechanism remains to be explored.MethodsRelative RNA levels of hsa_circ_0015382, microRNA‐616‐3p and thrombospondin‐2 (THBS2) were detected by quantitative reverse transcription‐polymerase chain reaction. In vitro regulatory effects of hsa_circ_0015382 on the proliferation, migration, invasion and angiogenesis of trophoblasts were evaluated by CCK‐8, flow cytometry for cell cycle, EdU, transwell, wound healing and HUVEC tube formation assays, respectively. Targeting interaction was verified by dual‐luciferase reporter and RNA immunoprecipitation assays.ResultsHsa_circ_0015382 was highly expressed in placental tissues from PE patients. Upregulation of hsa_circ_0015382 repressed trophoblast proliferation, migration, invasion and lowered trophoblast‐induced HUVEC tube formation. Hsa_circ_0015382 was validated as a miR‐616‐3p sponge and miR‐616‐3p targeted THBS2. Hsa_circ_0015382 could mediate trophoblast proliferation, migration, invasion and regulate trophoblast‐induced HUVEC tube formation by sponging miR‐616‐3p and regulating THBS2 expression.ConclusionHsa_circ_0015382 is associated with the pathogenesis of PPE by regulating the miR‐616‐3p/THBS2 axis.Highlights
Hsa_circ_0015382 is overexpressed in preeclampsia patients.
Hsa_circ_0015382 inhibits trophoblast proliferation, migration, invasion and decreases trophoblast‐induced HUVEC tube formation.
Hsa_circ_0015382 interacts with miR‐616‐3p to regulate THBS2 expression.