bluuebunny/crossref_metadata_2025_split huggingface dataset:
CuGenDBv2: an updated database for cucurbit genomics
Authors: Yu Jingyin , Wu Shan , Sun Honghe , Wang Xin , Tang Xuemei , Guo Shaogui , Zhang Zhonghua , Huang Sanwen , Xu Yong , Weng Yiqun , Mazourek Michael , McGregor Cecilia , Renner Susanne S , Branham Sandra , Kousik Chandrasekar , Wechter W Patrick , Levi Amnon , Grumet Rebecca , Zheng Yi , Fei Zhangjun 
Published: October 2022

Abstract
The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for &gt;20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel ‘Genotype’ module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated ‘Expression’ module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.
ImmCluster: an ensemble resource for immunology cell type clustering and annotations in normal and cancerous tissues
Authors: Jiang Tiantongfei , Zhou Weiwei , Sheng Qi , Yu Jiaxin , Xie Yunjin , Ding Na , Zhang Yunpeng , Xu Juan , Li Yongsheng 
Published: October 2022

Abstract
Single-cell transcriptome has enabled the transcriptional profiling of thousands of immune cells in complex tissues and cancers. However, subtle transcriptomic differences in immune cell subpopulations and the high dimensionality of transcriptomic data make the clustering and annotation of immune cells challenging. Herein, we introduce ImmCluster (http://bio-bigdata.hrbmu.edu.cn/ImmCluster) for immunology cell type clustering and annotation. We manually curated 346 well-known marker genes from 1163 studies. ImmCluster integrates over 420 000 immune cells from nine healthy tissues and over 648 000 cells from different tumour samples of 17 cancer types to generate stable marker-gene sets and develop context-specific immunology references. In addition, ImmCluster provides cell clustering using seven reference-based and four marker gene-based computational methods, and the ensemble method was developed to provide consistent cell clustering than individual methods. Five major analytic modules were provided for interactively exploring the annotations of immune cells, including clustering and annotating immune cell clusters, gene expression of markers, functional assignment in cancer hallmarks, cell states and immune pathways, cell–cell communications and the corresponding ligand–receptor interactions, as well as online tools. ImmCluster generates diverse plots and tables, enabling users to identify significant associations in immune cell clusters simultaneously. ImmCluster is a valuable resource for analysing cellular heterogeneity in cancer microenvironments.
Temporalis muscle thickness predicts early relapse and short survival in primary CNS lymphoma
Authors: Bonm Alipi V , Menghini Anthony , Drolet Caroline E , Graber Jerome J 
Published: October 2022

AbstractBackgroundMost patients with primary CNS lymphoma (PCNSL) achieve durable remission whereas a minority die in the first year. Sarcopenia is a powerful predictor of mortality in the brain and systemic cancers. Temporalis muscle thickness (TMT) is a validated radiographic measure of sarcopenia. We hypothesized that patients with thin TMT at diagnosis would have early progression and short survival.MethodsTwo blinded operators retrospectively measured TMT in 99 consecutive brain MRIs from untreated patients with PCNSL.ResultsWe generated a receiver operator characteristic curve and chose a single threshold defining thin TMT in all patients as &lt;5.65 mm, at which specificity and sensitivity for 1-year progression were 98.4% and 29.7% and for 1-year mortality were 97.4% and 43.5% respectively. Those with thin TMT were both more likely to progress (P &lt; .001) and had higher rates of mortality (P &lt; .001). These effects were independent of the effect of age, sex, and Eastern Cooperative Oncology Group performance status in a cox regression. Memorial Sloan Kettering Cancer Center score did not predict progression-free survival or overall survival as well as TMT. Patients with thin TMT received fewer cycles of high-dose methotrexate and were less likely to receive consolidation but neither variable could be included in the Cox regression due to violation of the proportional hazards assumption.ConclusionsWe conclude that PCNSL patients with thin TMT are at high risk for early relapse and short survival. Future trials should stratify patients by TMT to avoid confounding.
High-efficiency nonlocal reflection-type vortex beam generation based on bound states in the continuum
Authors: Li Tongyu , Wang Jiajun , Zhang Wenjie , Wang Xinhao , Liu Wenzhe , Shi Lei , Zi Jian 
Published: October 2022

ABSTRACT
Momentum-space polarization vortices centered at symmetry-protected bound states in the continuum of a periodic structure, e.g. photonic crystal slab, provide a novel nonlocal approach to generate vortex beams. This approach enjoys a great convenience of no precise alignment requirements, although the generation efficiency of the nonlocal generators requires further optimization before the practical application. In this work, we propose a temporal-coupled-mode-theory-based guideline for high-efficiency nonlocal reflection-type vortex generator design. The conversion efficiency of the vortex beam is found to be limited by the ratio of the radiative loss to the intrinsic absorption in practical systems. To increase this ratio through mode selection and structure design, the photonic crystal slabs are theoretically designed and experimentally characterized, showing a maximum on-resonance conversion efficiency of up to 86%. Combining high efficiency with simple fabrication and no requirement for precise alignment, reflection-type photonic crystal slabs could offer a new and competitive way to generate vortex beams flexibly.
Analyzing Adherence to the 2016 Infectious Diseases Society of America Guidelines for Candidemia in Cancer Patients
Authors: Lehmann Dena M , Cohen Nina , Lin I-Hsin , Alexander Shane , Kathuria Ritu , Kerpelev Marina , Taur Ying , Seo Susan K 
Published: October 2022

Abstract

Background
Candidemia is associated with morbidity and mortality in cancer patients. We analyzed adherence to the 2016 Infectious Diseases Society of America (IDSA) candidiasis guidelines and the reasons for guideline nonadherence. We also investigated whether matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) improved time to effective antifungal therapy compared with historical data (median, 43.2 hours).

Methods
Cancer patients with candidemia between 1/1/17 and 12/31/19 were included. Adherence to 7 individual IDSA guideline components was assessed. Composite IDSA guideline adherence (defined as meeting ≥6 guideline components) was also assessed. Charts were reviewed to examine reasons for noncompliance.

Results
Of 157 patients with candidemia, 150 (95.5%) had infectious disease (ID) consultation. The median total time from blood culture collection to antifungal initiation was 42.1 hours. Excluding 39 patients with short treatment due to death, there was 100% adherence with surveillance blood cultures, followed by antifungal susceptibility testing (117/118, 99.2%), initial appropriate therapy (117/118, 99.2%), antifungal duration (110/118, 93.2%), line removal (82/91, 90.1%), eye exams (93/118, 78.8%), and step-down therapy (69/94, 73.4%). A quarter (30/118) did not meet composite IDSA guideline adherence. Univariate logistic regression suggested a relationship between poor cancer prognosis and incomplete adherence to the 2016 IDSA candidiasis guidelines (odds ratio, 8.6; 95% CI, 1.6–47).

Conclusions
The addition of MALDI-TOF did not shorten time to effective antifungal therapy. Nearly all patients were seen by ID for candidemia. Poor cancer prognosis was a common factor for incomplete composite adherence to the 2016 IDSA candidiasis guidelines.
Long-Term Virological Treatment Outcomes in Adolescents and Young Adults With Perinatally and Non-Perinatally Acquired Human Immunodeficiency Virus
Authors: Weijsenfeld Annouschka M , Smit Colette , Wit Ferdinand W N M , Mudrikova Tania , Nellen Jeannine F J B , van der Valk Marc , Pajkrt Dasja 
Published: October 2022

Abstract

Background
Long-term viral suppression on antiretroviral therapy (ART) is not established among all people with human immunodeficiency virus (PWH). Young adults (18–24 years) are recognized as a group vulnerable for suboptimal virological treatment outcomes. The aim of this study is to evaluate longitudinal virological treatment outcomes and to identify risk factors for virological failure (VF) among young adults with non-perinatally and perinatally acquired human immunodeficiency virus (HIV) in the Netherlands.

Methods
We included individuals registered in the national ATHENA observational cohort from 2000 until 2020 who had entered care before the age of 25 years, who had received ART for at least 6 months with at least 2 available HIV ribonucleic acid measurements between the age of 18 and 24 years. We compared VF between age groups 12–17, 18–24, and 25–30 years. A multivariable generalized linear mixed model was used to evaluate risk factors for VF. Analyses were stratified by HIV acquisition mode.

Results
In total, 1174 non-perinatally PWH and 157 perinatally PWH were included. In 2020, VF rate was 7% in non-perinatally PWH young adults and 19% in perinatally PWH young adults. The adjusted risk for VF was significantly higher in those aged 18–24 compared to 25–30 years in both non-perinatally PWH (odds ratio [OR], 1.27; 95% confidence interval [CI], 1.07–1.50) and perinatally PWH (OR, 2.34; 95% CI, 1.48–3.71).

Conclusions
Young adulthood is a vulnerable period, with increased risk for VF, especially for perinatally PWH. The probability of VF decreased over time, but less for perinatally PWH compared to non-perinatally PWH.
Evaluation of Severe Acute Respiratory Syndrome Coronavirus 2 Nucleocapsid Antigen in the Blood as a Diagnostic Test for Infection and Infectious Viral Shedding
Authors: Mathur Sujata , Davidson Michelle C , Anglin Khamal , Lu Scott , Goldberg Sarah A , Garcia-Knight Miguel , Tassetto Michel , Zhang Amethyst , Romero Mariela , Pineda-Ramirez Jesus , Diaz-Sanchez Ruth , Rugart Paulina , Chen Jessica Y , Donohue Kevin , Shak Joshua R , Chenna Ahmed , Winslow John W , Petropoulos Christos J , Yee Brandon C , Lambert Jeremy , Glidden David V , Rutherford George W , Deeks Steven G , Peluso Michael J , Andino Raul , Martin Jeffrey N , Kelly J Daniel 
Published: October 2022

Abstract

Background
SARS-CoV-2 nucleocapsid antigen can be detected in plasma, but little is known about its performance as a diagnostic test for acute SARS-CoV-2 infection or infectious viral shedding among nonhospitalized individuals.

Methods
We used data generated from anterior nasal and blood samples collected in a longitudinal household cohort of SARS-CoV-2 cases and contacts. Participants were classified as true positives if polymerase chain reaction (PCR) positive for SARS-CoV-2 and as true negatives if PCR negative and seronegative. Infectious viral shedding was determined by the cytopathic effect from viral culture. Stratified by 7 days after symptom onset, we constructed receiver operating characteristic (ROC) curves to describe optimized accuracy (Youden index), optimized sensitivity, and specificity.

Results
Of 80 participants, 58 (73%) were true positives while 22 (27%) were true negatives. Using the manufacturer's cutoff of 1.25 pg/mL for evaluating infection, sensitivity was higher from 0 to 7 days (77.6% [95% confidence interval {CI}, 64%–88.2%]) than from 8 to 14 days (43.2% [95% CI, 31.1%–54.5%]) after symptom onset; specificity was unchanged at 100% (95% CI, 88.1%–100%). This test had higher sensitivity (100% [95% CI, 88.4%–100%]) and lower specificity (65% [95% CI, 40.8%–84.6%]) for infectious viral shedding as compared with infection, particularly within the first week of symptom onset. Although the presence of N-antigen correlated with infectious viral shedding (r = 0.63; P &lt; .01), sensitivity still declined over time. Additional cutoffs from ROC curves were identified to optimize sensitivity and specificity.

Conclusions
We found that this SARS-CoV-2 N-antigen test was highly sensitive for detecting early but not late infectious viral shedding, making it a viable screening test for community-dwelling individuals to inform isolation practices.
Rice GLUCAN SYNTHASE-LIKE5 promotes anther callose deposition to maintain meiosis initiation and progression
Authors: Somashekar Harsha , Mimura Manaki , Tsuda Katsutoshi , Nonomura Ken-Ichi 
Published: October 2022

Abstract
Callose is a plant cell wall polysaccharide whose deposition is spatiotemporally regulated in various developmental processes and environmental stress responses. The appearance of callose in premeiotic anthers is a prominent histological hallmark for the onset of meiosis in flowering plants; however, the biological role of callose in meiosis remains unknown. Here, we show that rice (Oryza sativa) GLUCAN SYNTHASE LIKE5 (OsGSL5), a callose synthase, localizes on the plasma membrane of pollen mother cells (PMCs) and is responsible for biogenesis of callose in anther locules through premeiotic and meiotic stages. In Osgsl5 mutant anthers mostly lacking callose deposition, aberrant PMCs accompanied by aggregated, unpaired, or multivalent chromosomes were frequently observed and, furthermore, a considerable number of mutant PMCs had untimely progress into meiosis compared to that of wild-type PMCs. Immunostaining of meiosis-specific protein HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS2 in premeiotic PMCs revealed precocious meiosis entry in Osgsl5 anthers. These findings provide insights into the function of callose in controlling the timing of male meiosis initiation and progression, in addition to roles in microsporogenesis, in flowering plants.
Using theory to understand how policy change happens: Insights from agricultural research for development
Authors: Douthwaite Boru , Proietti Claudio , Polar Vivian , Thiele Graham 
Published: October 2022

Abstract
Influencing policy is an important scaling mechanism. However, if a program is to plausibly claim that it has or can influence policy, it needs to explain how. This is not straightforward because of the complex nature of policy change. Scholars suggest the use of theory to help answer the ‘how’ question. In this article, we show how, in practice, a middle-range policy change theory—Kingdon’s Policy Window theory—helped us model the workings of four outcome trajectories that produced agricultural policy outcomes in four cases. By providing a common framework, the middle-range theory helped accumulate learning from one evaluation to the next, generating specific and generalizable insights in the process. Accumulation learning in this way can help organizations become more convincing in the proposals they write to donors, more accountable and better able to identify and deliver on their goals.
Claims to (S)expertise in the British Sex Survey, c. 1960s–1990s
Authors: Jones Katherine 
Published: October 2022

Summary
This article focuses on one main producer of knowledge about sexual subjects in the twentieth century: the social sciences. Sociological interest in issues relating to sex and sexuality intensified in the 1950s, along with the rise of post-war social science deployed to gather information on a changing post-war British nation. Family planning surveys were central to this new academic sociology, and increasingly framed women respondents as experts on family planning practices. This article argues that social surveys related to contraceptive and sexual health practices became increasingly interested in questions of subjectivity from the 1970s, reflecting a broader shift in the social sciences. This led researchers to turn their attention towards men as valid contributors. In doing so, this article charts the development of sexual knowledge and makes broader interventions into the history of knowledge production, by providing insights into the changing ideas regarding legitimate sources of knowledge and expertise.
miRNA-141-5p Affects the Levels of Neutrophil Elastase in Preeclampsia by Regulating MAPK1
Authors: Cheng Keyan , Cui Jialei , Zhou Wenli , Liu Huiqiang , Yang Taotao , Wang Yonghong 
Published: October 2022

Abstract

Objective
The objective of this study was to investigate the expression levels of microRNA-141-5p(miRNA-141-5p), MAPK1 and neutrophil elastase in patients with and without preeclampsia (PE), and the relationship between miRNA-141-5p and MAPK1 with respect to the secretion of elastase by neutrophils in patients with PE.

Methods
Thirty patients with PE and 30 healthy pregnant (HP) women were recruited from The Second Hospital of Shanxi Medical University, Taiyuan, China, between February 2017 and July 2018. Neutrophils were isolated from 8 mL peripheral blood samples and cultured. We recorded neutrophil count and morphology during culture. Apoptosis was detected by flow cytometry in different groups at 0, 24, and 48 h. The expression levels of elastase were detected in neutrophils by enzyme-linked immunosorbent assay, whereas the expression levels of miRNA-141-5p in peripheral blood neutrophils were detected by real-time polymerase chain reaction. We used TargetScanHuman Release 7.2 to analyze the target genes of miRNA-141-5p. The expression of MAPK1 in peripheral blood neutrophils was detected by western blotting. Data were analyzed by SPSS version 21.0 software, and comparisons between groups were carried out with the Student t test.

Results
There was no significant difference between the PE and HP groups (P > 0.050) with regard to age or body mass index. The weight of newborns in the PE group (2846.00 ± 600.00 g) was significantly lower than that in the HP group (3055.00 ± 230.68 g). The number of neutrophilic granulocytes(NGs) in blood samples from the PE group was significantly higher than that in the HP group (P = 0.003). There was no significant difference between the groups with regard to morphology. Apoptosis in the PE group was delayed when compared with the HP group at different time points. The P value of apoptosis in the PE and HP groups were respectively 0.790, < 0.001 and 0.030 at 0 h, 24 h and 48 h. The expression levels of miRNA-141-5p in the PE group were significantly lower than those in the HP group (P < 0.050). The expression levels of MAPK1 in neutrophils from the PE group were significantly higher than those in the HP group (P < 0.050) by western blot. The expression levels of elastase in neutrophils from the PE group were significantly higher than those in the HP group (P < 0.050). Furthermore, the number of NGs in peripheral blood from the PE group was higher than that of the HP group; however, the levels of apoptosis were lower. The expression levels of miRNA-141-5p in NGs decreased, the expression of MAPK1 increased, and the secretion of neutrophil elastase in the NG medium increased in the PE group than those in the HP group.

Conclusion
Collectively, our analysis suggested that miRNA-141-5p may be involved in the pathogenesis of PE by regulating the MAPK1 signaling pathway to activate neutrophils and increase the secretion of elastase.
Impact of board attributes and managerial ownership on cash holdings: empirical evidence using GMM and quantile regressions
Authors: Talbi Dorra , Menchaoui Ines 
Published: October 2022

PurposeThe purpose of this study is to examine the impact of board attributes and managerial ownership on cash holdings.Design/methodology/approachThe present study examines a sample of 70 listed firms in Saudi Arabia observed during the period stretching from 2006 to 2016. To test the hypotheses, the authors used generalized method of moments and quantile regressions.FindingsThe empirical results reveal that corporate governance (CG) mechanisms are inefficient in the Saudi context. In fact, the authors found that board size, board independence, duality and managerial ownership impact positively and significantly cash holdings. Additionally, quantile regressions confirm the results that at certain thresholds, CG mechanisms are not efficient in protecting shareholders’ interests. Shariah compliance is found to moderate negatively and significantly the studied relationship.Originality/valueThis study helps to not only clarify and help decision-makers to see the importance of corporate cash management but also to identify the limits of the CG mechanisms put in place.
A literature review on digital content management: trends and future challenges
Authors: Rahman Md. Habibur , Ahmad Azree , Zakaria Sohaimi 
Published: October 2022

PurposeThe purpose of this study is to review the literature on digital content management (DCM) published between 2001 and 2021, as well as to provide insights and research directions for the future.Design/methodology/approachThis study followed the systematic literature review framework PRISMA for reviewing existing literature on DCM. The PRISMA checklist helps the researcher in refining the reporting of the review paper. Data was collected from Scopus and Web of Science (WoS) databases. A total of 136 documents were selected for analysis from Scopus and WoS.FindingsBased on current papers, this study attempted to discuss some key DCM trends and themes. Seven themes have been identified in the literature: virtual reality and its implications on DCM; personal DCM; microservices based DCM; model for DCM; DCM using Bluetooth Low Emergency technology; DCM software; and DCM codification. This study identifies influential authors, top contributing countries, top contributing institutions, most cited papers, most common title words and contributions by fields.Originality/valueThe findings of this study, as well as future research projects, open the path for more research and contributions to the field.