bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments
Authors: Liu Zi Hao , Teixeira João M C , Zhang Oufan , Tsangaris Thomas E , Li Jie , Gradinaru Claudiu C , Head-Gordon Teresa , Forman-Kay Julie D 
Published: December 2023

Abstract

Summary
The Local Disordered Region Sampling (LDRS, pronounced loaders) tool is a new module developed for IDPConformerGenerator, a previously validated approach to model intrinsically disordered proteins (IDPs). The IDPConformerGenerator LDRS module provides a method for generating all-atom conformations of intrinsically disordered protein regions at N- and C-termini of and in loops or linkers between folded regions of an existing protein structure. These disordered elements often lead to missing coordinates in experimental structures or low confidence in predicted structures. Requiring only a pre-existing PDB or mmCIF formatted structural template of the protein with missing coordinates or with predicted confidence scores and its full-length primary sequence, LDRS will automatically generate physically meaningful conformational ensembles of the missing flexible regions to complete the full-length protein. The capabilities of the LDRS tool of IDPConformerGenerator include modeling phosphorylation sites using enhanced Monte Carlo-Side Chain Entropy, transmembrane proteins within an all-atom bilayer, and multi-chain complexes. The modeling capacity of LDRS capitalizes on the modularity, the ability to be used as a library and via command-line, and the computational speed of the IDPConformerGenerator platform.

Availability and implementation
The LDRS module is part of the IDPConformerGenerator modeling suite, which can be downloaded from GitHub at https://github.com/julie-forman-kay-lab/IDPConformerGenerator. IDPConformerGenerator is written in Python3 and works on Linux, Microsoft Windows, and Mac OS versions that support DSSP. Users can utilize LDRS’s Python API for scripting the same way they can use any part of IDPConformerGenerator’s API, by importing functions from the “idpconfgen.ldrs_helper” library. Otherwise, LDRS can be used as a command line interface application within IDPConformerGenerator. Full documentation is available within the command-line interface as well as on IDPConformerGenerator’s official documentation pages (https://idpconformergenerator.readthedocs.io/en/latest/).
Artificial intelligence-assisted quantification and assessment of whole slide images for pediatric kidney disease diagnosis
Authors: Feng Chunyue , Ong Kokhaur , Young David M , Chen Bingxian , Li Longjie , Huo Xinmi , Lu Haoda , Gu Weizhong , Liu Fei , Tang Hongfeng , Zhao Manli , Yang Min , Zhu Kun , Huang Limin , Wang Qiang , Marini Gabriel Pik Liang , Gui Kun , Han Hao , Sanders Stephan J , Li Lin , Yu Weimiao , Mao Jianhua 
Published: December 2023

Abstract

Motivation
Pediatric kidney disease is a widespread, progressive condition that severely impacts growth and development of children. Chronic kidney disease is often more insidious in children than in adults, usually requiring a renal biopsy for diagnosis. Biopsy evaluation requires copious examination by trained pathologists, which can be tedious and prone to human error. In this study, we propose an artificial intelligence (AI) method to assist pathologists in accurate segmentation and classification of pediatric kidney structures, named as AI-based Pediatric Kidney Diagnosis (APKD).

Results
We collected 2935 pediatric patients diagnosed with kidney disease for the development of APKD. The dataset comprised 93 932 histological structures annotated manually by three skilled nephropathologists. APKD scored an average accuracy of 94% for each kidney structure category, including 99% in the glomerulus. We found strong correlation between the model and manual detection in detected glomeruli (Spearman correlation coefficient r = 0.98, P &lt; .001; intraclass correlation coefficient ICC = 0.98, 95% CI = 0.96–0.98). Compared to manual detection, APKD was approximately 5.5 times faster in segmenting glomeruli. Finally, we show how the pathological features extracted by APKD can identify focal abnormalities of the glomerular capillary wall to aid in the early diagnosis of pediatric kidney disease.

Availability and implementation
https://github.com/ChunyueFeng/Kidney-DataSet.
FunctanSNP: an R package for functional analysis of dense SNP data (with interactions)
Authors: Ren Rui , Fang Kuangnan , Zhang Qingzhao , Ma Shuangge 
Published: December 2023

Abstract

Summary
Densely measured SNP data are routinely analyzed but face challenges due to its high dimensionality, especially when gene–environment interactions are incorporated. In recent literature, a functional analysis strategy has been developed, which treats dense SNP measurements as a realization of a genetic function and can ‘bypass’ the dimensionality challenge. However, there is a lack of portable and friendly software, which hinders practical utilization of these functional methods. We fill this knowledge gap and develop the R package FunctanSNP. This comprehensive package encompasses estimation, identification, and visualization tools and has undergone extensive testing using both simulated and real data, confirming its reliability. FunctanSNP can serve as a convenient and reliable tool for analyzing SNP and other densely measured data.

Availability and implementation
The package is available at https://CRAN.R-project.org/package=FunctanSNP.
TADA: taxonomy-aware dataset aggregator
Authors: Hägglund Emil , Andersson Siv G E , Guy Lionel 
Published: December 2023

Abstract

Summary
The profusion of sequenced genomes across the bacterial and archeal domains offers unprecedented possibilities for phylogenetic and comparative genomic analyses. In general, phylogenetic reconstruction is improved by the use of more data. However, including all available data is (i) not computationally tractable, and (ii) prone to biases, as the abundance of genomes is very unequally distributed over the biological diversity. Thus, in most cases, subsampling taxa to build a phylogeny is necessary. Currently, though, there is no available software to perform that handily. Here we present TADA, a taxonomic-aware dataset selection workflow that allows sampling across user-defined portions of the prokaryotic diversity with variable granularity, while setting constraints on genome quality and balance between branches.

Availability and implementation
TADA is implemented as a snakemake workflow and is freely available at https://github.com/emilhaegglund/TADA.
Plasma lipidomics reveal systemic changes persistent throughout early life following a childhood burn injury
Authors: Kierath Eva , Ryan Monique , Holmes Elaine , Nicholson Jeremy K , Fear Mark W , Wood Fiona M , Whiley Luke , Gray Nicola 
Published: December 2023

Abstract

Background
Non-severe paediatric burns can result in poor long-term health outcomes. This occurs even in cases with good acute burn-related outcomes, including minimal scarring. The mechanisms that underpin the transition from non-severe burn to sustained negative long-term health impacts are currently unknown. However, sustained metabolic and immune changes have been observed in paediatric burn studies, suggesting these changes may be important.
The plasma lipidome consists of a rich pool of bioactive metabolites that play critical roles in systemic processes including molecular signalling and inflammation. We hypothesised that changes in the plasma lipidome may reflect underlying changes in health status and be linked to long-term health after burn trauma.

Methods
This study analysed the lipidome in children who had previously experienced a non-severe burn, compared to non-injured controls. Thirty-three participants were recruited between the ages of 5 and 8 years who had experienced a non-severe burn between the ages of 1 and 3 years. Plasma samples were also collected from a non-injured, healthy, age and gender matched control group (n = 21). Plasma lipids were measured using reversed-phase liquid chromatographymass spectrometery (LC-MS).

Results
In total 838 reproducible lipid species from 19 sub-classes passed quality control procedures and progressed to statistical analysis. Analysis of individual lipid metabolites showed significantly higher concentrations of lysophosphatidylethanolamines and phosphatidylethanolamines, and significantly lower concentrations in myristic, palmitic and palmitoleic acids in the plasma of those who had experienced burn injury compared to controls.

Conclusion
Long-term changes in the lipid profile may give insight into the mechanisms underlying poor long-term health subsequent to non-severe burn injury. Further work to investigate the relationship between long-term pathology and lipidomic changes may lead to a better understanding of the causes of secondary morbidity post-burn and to clinical intervention to reduce the long-term health burden of burn trauma.
A case report of myocardial infarction in a young transgender man with testosterone therapy: raising awareness on healthcare issues in the transgender community and a call for further research
Authors: Connelly Paul J , Osmanska Joanna , Lee Matthew M Y , Delles Christian , McEntegart Margaret B , Byrne John 
Published: December 2023

Abstract

Background
People who are transgender may utilize masculinizing or feminizing gender-affirming hormonal therapy. Testosterone and oestrogen receptors are expressed throughout the cardiovascular system, yet the effects of these therapies on cardiovascular risk and outcomes are largely unknown. We report the case of a young transgender man with no discernible cardiovascular risk factors presenting with an acute coronary syndrome.

Case summary
A 31-year-old transgender man utilizing intramuscular testosterone masculinizing gender-affirming hormonal therapy presented with central chest pain radiating to the left arm. He had no past medical history of hypertension, dyslipidaemia, diabetes, or smoking. Electrocardiography demonstrated infero-septal ST depression, and high-sensitivity troponin-I was elevated and increased to 19 686 ng/L. He was diagnosed with a non–ST-segment elevation myocardial infarction. Inpatient coronary angiography confirmed a critical focal lesion in the mid right coronary artery, which was managed with two drug-eluting stents. Medical management (i.e. aspirin, ticagrelor, atorvastatin, ramipril, and bisoprolol) and surveillance of residual plaque disease evident in the long tubular left main stem, proximal left anterior descending, and proximal circumflex vessels was undertaken. The masculinizing gender-affirming hormonal therapy was continued.

Discussion
Despite a greater awareness of the potential risk of increased cardiovascular disease in transgender people, the fundamental lack of data regarding cardiovascular outcomes in transgender people may be contributing to healthcare inequalities in this population. We must implement better training, awareness, and research into transgender cardiovascular health to facilitate equitable and evidence-based outcomes.
A national overview of nonprofit hospital community benefit programs to address the social determinants of health
Authors: Franz Berkeley , Burns Ashlyn , Kueffner Kristin , Bhardwaj Meeta , Yeager Valerie A , Singh Simone , Puro Neeraj , Cronin Cory E 
Published: December 2023

Abstract
Decades of research have solidified the crucial role that social determinants of health (SDOH) play in shaping health outcomes, yet strategies to address these upstream factors remain elusive. The aim of this study was to understand the extent to which US nonprofit hospitals invest in SDOH at either the community or individual patient level and to provide examples of programs in each area. We analyzed data from a national dataset of 613 hospital community health needs assessments and corresponding implementation strategies. Among sample hospitals, 69.3% (n = 373) identified SDOH as a top-5 health need in their community and 60.6% (n = 326) reported investments in SDOH. Of hospitals with investments in SDOH, 44% of programs addressed health-related social needs of individual patients, while the remaining 56% of programs addressed SDOH at the community level. Hospitals that were major teaching organizations, those in the Western region of the United States, and hospitals in counties with more severe housing problems had greater odds of investing in SDOH at the community level. Although many nonprofit hospitals have integrated SDOH-related activities into their community benefit work, stronger policies are necessary to encourage greater investments at the community-level that move beyond the needs of individual patients.
What works in sanitation promotion?
Authors: Aunger Robert 
Published: December 2023

AbstractPromotion appears to be the least effective but is nevertheless often the only available, means to achieve increased access to sanitation services, especially at scale, in lower-income countries. A cursory examination of the history of past and present approaches to sanitation promotion, including sanitation marketing, community development, community-led total sanitation and public health, shows that they have a variety of features and characteristics which make them distinctive. Unfortunately, rigorous evaluation has not kept pace with this proliferation of approaches, so it is difficult to recommend any one approach over the others, based on empirical performance in a range of circumstances. However, I argue that a ‘hybrid’ approach which exhibits a number of salient features from all of the previous approaches is likely to be a good bet. I present a recent example of such a hybrid programme which proved to significantly increase the rate of improved sanitation coverage through promotion (without subsidy of any kind) at scale in Tanzania. I suggest other sanitation promotion programs may want to think about adopting similar practices in their own programming going forward.
The Wehrmacht’s Complicity in Late-War Genocide: The Palmnicken Massacre and the Military in East Prussia, 1944–1945
Authors: Willems Bastiaan 
Published: December 2023

Abstract
By examining the death marches from Stutthof’s East Prussian subcamps in January 1945 and the following “Palmnicken Massacre,” this article retraces the role of the Wehrmacht in late-war genocidal violence. Scholars have established the complicity of Wehrmacht soldiers in acts of genocide during their stay on the Eastern Front, and documented the racist mindset that underpinned their behavior. Yet no such research exists on the final year of the war. From Summer 1944 until May 1945, the Wehrmacht’s main task was to defend its home soil. Scholarship has thus focused more on the military’s defense of Germany rather than their willingness to support the regime’s genocidal demands. This article argues that many Wehrmacht commanders were fully aware of the genocide perpetrated in their midst during the war’s final months, and when called upon, different Wehrmacht commanders actively assisted the SS in carrying out the regime’s racist mission even at the very end of the war. Finally, the author reveals how the military attempted to conceal these acts of violence throughout the postwar years.
Carbohydrate nutrition associated with health of overwintering honey bees
Authors: Quinlan Gabriela , Döke Mehmet Ali , Ortiz-Alvarado Yarira , Rodriguez-Gomez Norma , Koru Yilmaz Berk , Underwood Robyn 
Published: December 2023

Abstract
In temperate climates, honey bees rely on stored carbohydrates to sustain them throughout the winter. In nature, honey serves as the bees’ source of carbohydrates, but when managed, beekeepers often harvest honey and replace it with cheaper, artificial feed. The effects of alternative carbohydrate sources on colony survival, strength, and individual bee metabolic health are poorly understood. We assessed the impacts of carbohydrate diets (honey, sucrose syrup, high-fructose corn syrup, and invert syrup) on colony winter survival, population size, and worker bee nutritional state (i.e., fat content and gene expression of overwintered bees and emerging callow bees). We observed a nonsignificant trend for greater survival and larger adult population size among colonies overwintered on honey compared to the artificial feeds, with colonies fed high-fructose corn syrup performing particularly poorly. These trends were mirrored in individual bee physiology, with bees from colonies fed honey having significantly larger fat bodies than those from colonies fed high-fructose corn syrup. For bees fed honey or sucrose, we also observed gene expression profiles consistent with a higher nutritional state, associated with physiologically younger individuals. That is, there was significantly higher expression of vitellogenin and insulin-like peptide 2 and lower expression of insulin-like peptide 1 and juvenile hormone acid methyltransferase in the brains of bees that consumed honey or sucrose syrup relative to those that consumed invert syrup or high-fructose corn syrup. These findings further our understanding of the physiological implications of carbohydrate nutrition in honey bees and have applied implications for colony management.
Effect on genetic diversity of the absence of intraspecies preference in 2 sympatric Reticulitermes termite species (Isoptera: Rhinotermitidae)
Authors: Wu Jia , Dong Ya-Nan , Niu Tong , Wang Huan , Hassan Ali , Du Bei 
Published: December 2023

Abstract
The recombinant genotypes that can be produced when closely related species mate improve the genetic diversity of the population. Among closely related species, the link between interspecific reproduction behaviors and genetic diversity has barely been studied. Reticulitermes chinensis and R. flaviceps, which live close to each other, were used as research subjects in our study to find out how preferring conspecifics affects reproductive behavior between species. We discovered that neither R. chinensis nor R. flaviceps displayed preference behavior for conspecifics. Males of R. chinensis and R. flaviceps chased and groomed not only intraspecific females but also interspecific females. In a brief period of time, 2 mating behaviors, intra- and interspecific mating, were also observed. There were no significant differences in the duration of each behavior (tandem, grooming, and mating) between interspecies and intraspecies partners. Moreover, genetic analysis showed both interspecific mating and intraspecific mating can produce living offspring when the 2 types of mating occur in a colony. Our findings showed that there was no obvious intraspecific preference between the 2 species of termite Reticulitermes when it came to tandem, grooming, and mating, which not only makes it easier for interspecific hybridization to occur but also sheds light on the genetic diversity.
Glycogen synthase kinase 3 signaling in neural regeneration in vivo
Authors: Zhang Jing , Yang Shu-Guang , Zhou Feng-Quan 
Published: December 2023

Abstract
Glycogen synthase kinase 3 (GSK3) signaling plays important and broad roles in regulating neural development in vitro and in vivo. Here, we reviewed recent findings of GSK3-regulated axon regeneration in vivo in both the peripheral and central nervous systems and discussed a few controversial findings in the field. Overall, current evidence indicates that GSK3β signaling serves as an important downstream mediator of the PI3K–AKT pathway to regulate axon regeneration in parallel with the mTORC1 pathway. Specifically, the mTORC1 pathway supports axon regeneration mainly through its role in regulating cap-dependent protein translation, whereas GSK3β signaling might be involved in regulating N6-methyladenosine mRNA methylation-mediated, cap-independent protein translation. In addition, GSK3 signaling also plays a key role in reshaping the neuronal transcriptomic landscape during neural regeneration. Finally, we proposed some research directions to further elucidate the molecular mechanisms underlying the regulatory function of GSK3 signaling and discover novel GSK3 signaling-related therapeutic targets. Together, we hope to provide an updated and insightful overview of how GSK3 signaling regulates neural regeneration in vivo.
Impaired dNKAP function drives genome instability and tumorigenic growth in Drosophila epithelia
Authors: Guo Ting , Miao Chen , Liu Zhonghua , Duan Jingwei , Ma Yanbin , Zhang Xiao , Yang Weiwei , Xue Maoguang , Deng Qiannan , Guo Pengfei , Xi Yongmei , Yang Xiaohang , Huang Xun , Ge Wanzhong 
Published: December 2023

Abstract
Mutations or dysregulated expression of NF-kappaB-activating protein (NKAP) family genes have been found in human cancers. How NKAP family gene mutations promote tumor initiation and progression remains to be determined. Here, we characterized dNKAP, the Drosophila homolog of NKAP, and showed that impaired dNKAP function causes genome instability and tumorigenic growth in a Drosophila epithelial tumor model. dNKAP-knockdown wing imaginal discs exhibit tumorigenic characteristics, including tissue overgrowth, cell-invasive behavior, abnormal cell polarity, and cell adhesion defects. dNKAP knockdown causes both R-loop accumulation and DNA damage, indicating the disruption of genome integrity. Further analysis showed that dNKAP knockdown induces c-Jun N-terminal kinase (JNK)-dependent apoptosis and causes aberrant cell proliferation in distinct cell populations. Activation of the Notch and JAK/STAT signaling pathways contributes to the tumorigenic growth of dNKAP-knockdown tissues. Furthermore, JNK signaling is essential for dNKAP depletion-mediated cell invasion. Transcriptome analysis of dNKAP-knockdown tissues confirmed the misregulation of signaling pathways involved in promoting tumorigenesis and revealed abnormal regulation of metabolic pathways. dNKAP knockdown and oncogenic Ras, Notch, or Yki mutations show synergies in driving tumorigenesis, further supporting the tumor-suppressive role of dNKAP. In summary, this study demonstrates that dNKAP plays a tumor-suppressive role by preventing genome instability in Drosophila epithelia and thus provides novel insights into the roles of human NKAP family genes in tumor initiation and progression.