bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide
Authors: Jackson Daniel J. , Cerveau Nicolas , Posnien Nico 
Published: June 2024

AbstractMany questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the ‘scientific status’ of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
Molecular surveillance for dengue serotypes among the population living in Moyen-Ogooué province, Gabon; evidence of the presence of dengue serotype 1
Authors: Bikangui Rodrigue , Parkouda Soulemane , More Ayong , Magossou Mbadinga Marien Veraldy , Boussoukou Ismael Piérrick Mikelet , Ondo Georgelin Nguema , Nkoma Anne Marie Mouina , Adamou Rafiou , Honkpehedji Yabo Josiane , Rossatanga Elie Gide , Ushijima Yuri , Abe Haruka , Lell Bertrand , Dejon-Agobé Jean Claude , Yasuda Jiro , Adegnika Ayola Akim 
Published: June 2024

Abstract
Background
Despite dengue virus (DENV) outbreak in Gabon a decade ago, less is known on the potential circulation of DENV serotypes in the country. Previous studies conducted in some areas of the country, are limited to hospital-based surveys which reported the presence of some cases of serotype 2 and 3 seven years ago and more recently the serotype 1. As further investigation, we extend the survey to the community of Moyen Ogooué region with the aim to assess the presence of the dengue virus serotypes, additionally to characterize chikungunya (CHIKV) infection and describe the symptomatology associated with infections.

Method
A cross-sectional survey was conducted from April 2020 to March 2021. The study included participants of both sexes and any age one year and above, with fever or history of fever in the past seven days until blood collection. Eligible volunteers were clinically examined, and blood sample was collected for the detection of DENV and CHIKV using RT-qPCR. Positive samples were selected for the target sequencing.

Results
A total of 579 volunteers were included. Their mean age (SD) was 20 (20) years with 55% of them being female. Four cases of DENV infection were diagnosed giving a prevalence of 0.7% (95%CI: 0.2–1.8) in our cohort while no case of CHIKV was detected. The common symptoms and signs presented by the DENV cases included fatigue, arthralgia myalgia, cough, and loss of appetite. DENV-1was the only virus detected by RT-qPCR.

Conclusion
Our results confirm the presence of active dengue infection in the region, particularly DENV-1, and could suggest the decline of DENV-2 and DENV-3. Continuous surveillance remains paramount to comprehensively describe the extent of dengue serotypes distribution in the Moyen-Ogooué region of Gabon.
Graph analysis uncovers an opposing impact of methylphenidate on connectivity patterns within default mode network sub-divisions
Authors: Daood Maryana , Magal Noa , Peled-Avron Leehe , Nevat Michael , Ben-Hayun Rachel , Aharon-Peretz Judith , Tomer Rachel , Admon Roee 
Published: June 2024

Abstract
Background
The Default Mode Network (DMN) is a central neural network, with recent evidence indicating that it is composed of functionally distinct sub-networks. Methylphenidate (MPH) administration has been shown before to modulate impulsive behavior, though it is not yet clear whether these effects relate to MPH-induced changes in DMN connectivity. To address this gap, we assessed the impact of MPH administration on functional connectivity patterns within and between distinct DMN sub-networks and tested putative relations to variability in sub-scales of impulsivity.

Methods
Fifty-five right-handed healthy adults underwent two resting-state functional MRI (rs-fMRI) scans, following acute administration of either MPH (20 mg) or placebo, via a randomized double-blind placebo-controlled design. Graph modularity analysis was implemented to fractionate the DMN into distinct sub-networks based on the impact of MPH (vs. placebo) on DMN connectivity patterns with other neural networks.

Results
MPH administration led to an overall decreased DMN connectivity, particularly with the auditory, cinguloopercular, and somatomotor networks, and increased connectivity with the parietomedial network. Graph analysis revealed that the DMN could be fractionated into two distinct sub-networks, with one exhibiting MPH-induced increased connectivity and the other decreased connectivity. Decreased connectivity of the DMN sub-network with the cinguloopercular network following MPH administration was associated with elevated impulsivity and non-planning impulsiveness.

Conclusion
Current findings highlight the intricate effects of MPH administration on DMN rs-fMRI connectivity, uncovering its opposing impact on distinct DMN sub-divisions. MPH-induced dynamics in DMN connectivity patterns with other neural networks may account for some of the effects of MPH administration on impulsive behavior.
Mis-localization of endogenous TDP-43 leads to ALS-like early-stage metabolic dysfunction and progressive motor deficits
Authors: Hu Yiying , Hruscha Alexander , Pan Chenchen , Schifferer Martina , Schmidt Michael K. , Nuscher Brigitte , Giera Martin , Kostidis Sarantos , Burhan Özge , van Bebber Frauke , Edbauer Dieter , Arzberger Thomas , Haass Christian , Schmid Bettina 
Published: June 2024

Abstract

Background
The key pathological signature of ALS/ FTLD is the mis-localization of endogenous TDP-43 from the nucleus to the cytoplasm. However, TDP-43 gain of function in the cytoplasm is still poorly understood since TDP-43 animal models recapitulating mis-localization of endogenous TDP-43 from the nucleus to the cytoplasm are missing.

Methods
CRISPR/Cas9 technology was used to generate a zebrafish line (called CytoTDP), that mis-locates endogenous TDP-43 from the nucleus to the cytoplasm. Phenotypic characterization of motor neurons and the neuromuscular junction was performed by immunostaining, microglia were immunohistochemically localized by whole-mount tissue clearing and muscle ultrastructure was analyzed by scanning electron microscopy. Behavior was investigated by video tracking and quantitative analysis of swimming parameters. RNA sequencing was used to identify mis-regulated pathways with validation by molecular analysis.

Results
CytoTDP fish have early larval phenotypes resembling clinical features of ALS such as progressive motor defects, neurodegeneration and muscle atrophy. Taking advantage of zebrafish’s embryonic development that solely relys on yolk usage until 5 days post fertilization, we demonstrated that microglia proliferation and activation in the hypothalamus is independent from food intake. By comparing CytoTDP to a previously generated TDP-43 knockout line, transcriptomic analyses revealed that mis-localization of endogenous TDP-43, rather than TDP-43 nuclear loss of function, leads to early onset metabolic dysfunction.

Conclusions
The new TDP-43 model mimics the ALS/FTLD hallmark of progressive motor dysfunction. Our results suggest that functional deficits of the hypothalamus, the metabolic regulatory center, might be the primary cause of weight loss in ALS patients. Cytoplasmic gain of function of endogenous TDP-43 leads to metabolic dysfunction in vivo that are reminiscent of early ALS clinical non-motor metabolic alterations. Thus, the CytoTDP zebrafish model offers a unique opportunity to identify mis-regulated targets for therapeutic intervention early in disease progression.
The role of big data management, data registries, and machine learning algorithms for optimizing safe definitive surgery in trauma: a review
Authors: Pape Hans-Christoph , Starr Adam J. , Gueorguiev Boyko , Wanner Guido A. 
Published: June 2024

AbstractDigital data processing has revolutionized medical documentation and enabled the aggregation of patient data across hospitals. Initiatives such as those from the AO Foundation about fracture treatment (AO Sammelstudie, 1986), the Major Trauma Outcome Study (MTOS) about survival, and the Trauma Audit and Research Network (TARN) pioneered multi-hospital data collection. Large trauma registries, like the German Trauma Registry (TR-DGU) helped improve evidence levels but were still constrained by predefined data sets and limited physiological parameters. The improvement in the understanding of pathophysiological reactions substantiated that decision making about fracture care led to development of patient’s tailored dynamic approaches like the Safe Definitive Surgery algorithm. In the future, artificial intelligence (AI) may provide further steps by potentially transforming fracture recognition and/or outcome prediction. The evolution towards flexible decision making and AI-driven innovations may be of further help. The current manuscript summarizes the development of big data from local databases and subsequent trauma registries to AI-based algorithms, such as Parkland Trauma Mortality Index and the IBM Watson Pathway Explorer.
The clock gene BHLHE40 and atypical CCNG2 control androgen-induced cellular senescence as a novel tumor suppressive pathway in prostate cancer
Authors: Heidari Horestani Mehdi , Atri Roozbahani Golnaz , Baniahmad Aria 
Published: June 2024

Abstract
Background
The androgen receptor (AR) is a drug target used to inhibit AR and prostate cancer (PCa) growth. Surprisingly, treatment with supraphysiological androgen level (SAL), used in bipolar androgen therapy, inhibits growth of PCa suggesting a tumor-suppressive activity by SAL. SAL was shown to induce cellular senescence in PCa.

Methods
RNA-seq and transcriptome analysis, ChIP-seq, human 3D PCa spheroids, mouse xenografted castration-resistant PCa, knockdown and overexpression, Co-immunoprecipitation (Co-IP), translocation analysis, immune detection, qRT-PCR, protein–protein interaction modelling.

Results
Here, mice xenografts with castration-resistant PCa tumors show that SAL inhibits cancer growth in vivo suggesting that SAL activates a tumor-suppressive mechanism. RNA-seq and ChIP-seq revealed the clock gene BHLHE40 is a novel direct AR target. Compared to adjacent human prostate tissues, the expression of BHLHE40 is reduced in PCa tumors and associated with reduced survival. Knockdown suggests that BHLHE40 mediates SAL-induced cellular senescence including tumor spheroids. Interestingly, a large overlap of differentially expressed gene sets was identified between BHLHE40 and SAL leading to the identification of four classes of SAL-BHLHE40 transcriptome landscapes. Co-IP and modelling suggest binding of BHLHE40 to AR and their co-translocation into nucleus by SAL treatment. Further, RNA-seq and ChIP-seq analysis indicate that the atypical tumor suppressive cyclin G2 emerged as a novel downstream target of BHLHE40 and a mediator of SAL-induced cellular senescence.

Conclusions
The data provide evidence of the tumor suppressive activity of SAL and a novel signaling by the AR-BHLHE40-CCNG2 axis for androgen-induced cellular senescence, linking circadian rhythm factor to androgen signaling as a novel tumor suppressive pathway.
Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
Authors: Masood Daniall , Ren Luyao , Nguyen Cu , Brundu Francesco G. , Zheng Lily , Zhao Yongmei , Jaeger Erich , Li Yong , Cha Seong Won , Halpern Aaron , Truong Sean , Virata Michael , Yan Chunhua , Chen Qingrong , Pang Andy , Alberto Reyes , Xiao Chunlin , Yang Zhaowei , Chen Wanqiu , Wang Charles , Cross Frank , Catreux Severine , Shi Leming , Beaver Julia A. , Xiao Wenming , Meerzaman Daoud M. 
Published: June 2024

Abstract
Background
Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study, we benchmark the performance of cancer CNV calling by six most recent and commonly used software tools on their detection accuracy, sensitivity, and reproducibility. In comparison to other orthogonal methods, such as microarray and Bionano, we also explore the consistency of CNV calling across different technologies on a challenging genome.

Results
While consistent results are observed for copy gain, loss, and loss of heterozygosity (LOH) calls across sequencing centers, CNV callers, and different technologies, variation of CNV calls are mostly affected by the determination of genome ploidy. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we establish a high confident CNV call set for the reference cancer cell line (HCC1395).

Conclusions
NGS technologies and current bioinformatics tools can offer reliable results for detection of copy gain, loss, and LOH. However, when working with a hyper-diploid genome, some software tools can call excessive copy gain or loss due to inaccurate assessment of genome ploidy. With performance matrices on various experimental conditions, this study raises awareness within the cancer research community for the selection of sequencing platforms, sample preparation, sequencing coverage, and the choice of CNV detection tools.
Longitudinal tracking of hemocyte populations in vivo indicates lineage relationships and supports neural progenitor identity in adult neurogenesis
Authors: Edwards Alex J. , Beltz Barbara S. 
Published: June 2024

AbstractAdult neurogenesis, which takes place in both vertebrate and invertebrate species, is the process by which new neurons are born and integrated into existing functional neural circuits, long after embryonic development. Most studies in mammals suggest that self-renewing stem cells are the source of the new neurons, although the extent of self-renewal is a matter of debate. In contrast, research in the crayfish Procambarus clarkii has demonstrated that the neural progenitors producing adult-born neurons are capable of both self-renewing and consuming (non-self-renewing) divisions. However, self-renewing divisions are relatively rare, and therefore the production of adult-born neurons depends heavily on progenitors that are not replenishing themselves. Because the small pool of neural progenitors in the neurogenic niche is never exhausted throughout the long lives of these animals, we hypothesized that there must also be an extrinsic source of these cells. It was subsequently demonstrated that the neural progenitors originate in hemocytes (blood cells) produced by the immune system that travel in the circulation before ultimately integrating into niches where the neural lineage begins. The current study examines the developmental lineage of the three hemocyte types — hyaline (HC), semigranular (SGC) and granular (GC) cells — with the goal of understanding the origins of the progenitor cells that produce adult-born neurons. Longstanding qualitative metrics for hemocyte classification were validated quantitatively. Then, in a longitudinal study, proliferation markers were used to label the hemocytes in vivo, followed by sampling the circulating hemocyte population over the course of two months. Hemolymph samples were taken at intervals to track the frequencies of the different hemocyte types. These data reveal sequential peaks in the relative frequencies of HCs, SGCs and GCs, which were identified using qualitative and quantitative measures. These findings suggest that the three hemocyte types comprise a single cellular lineage that occurs in the circulation, with each type as a sequential progressive stage in hemocyte maturation beginning with HCs and ending with GCs. When combined with previously published data, this timeline provides additional evidence that HCs serve as the primary neural progenitor during adult neurogenesis in P. clarkii.
Magnitude and associated factors of occupational hazard exposures among sanitary workers: Propose RASM model for risk mitigation for the public hospitals, eastern Ethiopia
Authors: Tolera Sina Temesgen , Assefa Nega , Geremew Abraham , Toseva Elka , Gobena Tesfaye 
Published: June 2024

Abstract
Background
Hospital sanitation workers (SWs) are exposed to numerous occupational hazards due to workplace conditions such as unsafe and unhygienic working environment in the hospitals. Therefore, knowing magnitude, types and source of occupational hazard exposures with their determinants are very significant for further mitigations.

Methods
Hospital based cross-sectional study design was conducted in public hospitals, eastern Ethiopia from 1st May to August 30th, 2023. 809 SWs participated. Data was entered into Epi Data Version 3.1 and Stata 17MP version used for analysis. Descriptive analysis was applied to describe the data. While, multilevel logistic regression was explored to determine the association between outcome and independents among at individual level (model 1), at hospitals (model 2) and combination of the two (model 3). The crude odds ratio (COR) and adjusted odds ratio (AOR) for models 2 and 3 were reported. Variables with an AOR with a 95% confidence interval (CI) at a p-value < 0.05 were reported.

Result
Out of 809 SWs, 729 (90.11%) responded. The overall magnitude of self-reported occupational hazard exposures among SWs was 63.65% (95% CI 0.60–0.67). Of this, biological, chemical, and ergonomic hazards accounted for 82.44%, 74.76%, and 70.92%, respectively. The multilevel logistic regression shows that having social recognition (AOR: 0.37, 95% CI 0.14, 0.91), neutral attitude (AOR: 0.48, 95% CI 0.17, 1.41) as compared to negative attitude. The model also found that SWs those supervised could reduce the likelihood of occupational hazard exposures by 50% times (AOR: 0.50, 95% CI 0.18, 1.38) as compared to non-supervised SWs. The final model predicted the variation of occupational hazard exposures among sanitary workers from the hospitals to hospitals was 26.59%.

Conclusions
The concluded that hospital sanitary workers are facing biological, chemical, ergonomic, physical, psychological, mechanical, and electrical hazards. This study’s findings predicted that dissatisfied with their environment, working more than 8 hr per a day, a negative attitude towards workplace risks and inadequate supervision may serve as contributing factors for the likelihood of occupational hazard exposures among these groups. Thus, the study suggested that hospitals could reduce these hazard risks if they implement the Risk Assessment and Safety Management (RASM) model, which includes multi-modal strategies, indicators and tripartite philosophy.
The association of social networks and depression in community-dwelling older adults: a systematic review
Authors: Reiner Amelie , Steinhoff Paula 
Published: June 2024

Abstract
Background and objective
Depression is a globally prevalent mental condition, particularly among older adults. Previous research has identified that social networks have a buffering effect on depression. Existing systematic reviews have either limited their research to specific geographic areas or provided evidence from over a decade ago. The vast body of recent literature particularly from the last decade emphasizes the need for a comprehensive review. This systematic review aims to analyze the association of structural aspects of social networks and depression in older adults.

Methods
The electronic databases APA PsycINFO, ProQuest, PSYINDEX, PubMed, Scopus, SocINDEX, and Web of Science were searched from date of data base inception until 11 July 2023. Studies were eligible for inclusion if they reported on community-dwelling older adults (defined as a mean age of at least 60 years old), had an acceptable definition for depression, referred to the term social network in the abstract, and were published in English. Quality was appraised using the Newcastle Ottawa Scale for cross-sectional and longitudinal studies. Outcome data were extracted independently from each study and analyzed by direction of the relationship, social network domain and cross-sectional or longitudinal study design.

Results
In total, 127 studies were included. The study categorizes structural network aspects into seven domains and finds that larger and more diverse networks, along with closer social ties, help mitigate depression. The literature on the relationships between depression and network density, homogeneity, and geographical proximity is scarce and inconclusive.

Discussion and implications
Despite inconsistent findings, this review highlights the importance of quantifying complex social relations of older adults. Limitations of this review include publication and language bias as well as the exclusion of qualitative research. Further research should use longitudinal approaches to further investigate the reciprocal relationship between social networks and depression. Following this review, interventions should promote the integration of older adults in larger and more diverse social settings.
Other: This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Grant [454899704]. This systematic review was pre-registered. The review-protocol can be accessed at https://doi.org/10.17605/OSF.IO/6QDPK.
Biochar supplementation altered the expression of antioxidant proteins in rice leaf chloroplasts under high-temperature stress
Authors: Huang Min , Yin Xiaohong , Chen Jiana , Cao Fangbo 
Published: June 2024

AbstractIn order to identify the key antioxidant defense systems used to cope with high-temperature stress in rice leaf chloroplasts following biochar supplementation, the present study compared the expression levels of chloroplast proteins related to antioxidant defense in high-temperature stressed rice leaves between without (C0) and with biochar supplementation (C40; 40 g biochar kg–1 soil). A total of sixteen differentially expressed antioxidant chloroplastic proteins were identified. Among them, three antioxidant enzyme proteins and eight thioredoxin proteins were 62–123% and 37–225% higher under the C40 treatment compared to C0, respectively. These results suggest that both antioxidant enzymes and the thioredoxin system are central to the biochar-mediated protection of rice leaves exposed to high-temperature stress.