bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differentially Expressed Heterogeneous Overdispersion Genes Testing for Count Data*
Authors: Yuan Yubai , Xu Qi , Wani Agaz , Dahrendor Jan , Wang Chengqi , Donglasan Janelle , Burgan Sarah , Graham Zachary , Uddin Monica , Wildman Derek , Qu Annie 
Published: February 2023

AbstractThe mRNA-seq data analysis is a powerful technology for inferring information from biological systems of interest. Specifically, the sequenced RNA fragments are aligned with genomic reference sequences, and we count the number of sequence fragments corresponding to each gene for each condition. A gene is identified as differentially expressed (DE) if the difference in its count numbers between conditions is statistically significant. Several statistical analysis methods have been developed to detect DE genes based on RNA-seq data. However, the existing methods could suffer decreasing power to identify DE genes arising from overdispersion and limited sample size. We propose a new differential expression analysis procedure: heterogeneous overdispersion genes testing (DEHOGT) based on heterogeneous overdispersion modeling and a post-hoc inference procedure. DEHOGT integrates sample information from all conditions and provides a more flexible and adaptive overdispersion modeling for the RNA-seq read count. DEHOGT adopts a gene-wise estimation scheme to enhance the detection power of differentially expressed genes. DEHOGT is tested on the synthetic RNA-seq read count data and outperforms two popular existing methods, DESeq and EdgeR, in detecting DE genes. We apply the proposed method to a test dataset using RNAseq data from microglial cells. DEHOGT tends to detect more differently expressed genes potentially related to microglial cells under different stress hormones treatments.
Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar)
Authors: Andres Kara J. , Liu Bingdi , Johnson Lauren E. , Kapuscinski Kevin L. , Moerke Ashley H. , Ling Fangqiong , Knouft Jason H. 
Published: February 2023

ABSTRACTMicrobiomes play an essential role in promoting host health and fitness, but the factors affecting variation in gut microbiomes among individuals are not fully understood. Investigating the microbiome under different conditions is needed to link gut microbiomes to host physiology and potentially design manipulations to improve rearing success of captive species. In this study, we characterized the gut microbiomes of Atlantic salmon (Salmo salar) in individuals at different life stages, vaccination status, and hatchery origin. Microbiomes differed between age-0 sub-adults and adults, with sub-adults exhibiting higher diversity and more similar communities when compared to adults. We also found that vaccines against bacterial kidney disease reduced gut microbial diversity within individual sub-adult salmon, resulting in dissimilar gut microbial communities among individuals. The diversity and structure of microbiomes did not differ between groups of adults that were reared in two different hatcheries and sampled from the wild. Sub-adults, particularly unvaccinated sub-adults, displayed a strong core microbiome present in the majority of individuals. Our results suggest that life stage and vaccination status are essential factors in the gut microbiome development of salmon. Conditions experienced during early life stages appear to have a strong influence on the microbiome, but differences among individuals at early life stages may be lost due to environmental factors experienced later in life. The plasticity of the microbiome throughout the life of individuals may have important implications for understanding host health, with potential applications for improving the rearing and reintroduction success of the ecologically and economically important Atlantic salmon.IMPORTANCEThe Atlantic salmon (Salmo salar) is a globally important fisheries and aquaculture species, but the factors affecting gut microbiomes of hatchery-reared fish are not fully understood. Our study explores the influence of life stage, vaccination status, and hatchery origin on the composition and structure of the Atlantic salmon gut microbiome. We found that life stage is an important driver of gut microbiome diversity, likely driven by differences in habitat and diet.Vaccination against bacterial kidney disease led to marked declines in gut microbial diversity within individuals, resulting in highly distinct gut microbial communities among individuals. Hatchery origin did not have a strong influence on adult Atlantic salmon captured from the wild. These findings suggest that life stage and vaccination drive variation in Atlantic salmon microbiomes, but the stability and long-term implications of such variation on host health should be considered in future microbiome research.
The autotransporter BafA contributes to the proangiogenic potential of Bartonella elizabethae
Authors: Suzuki Natsumi , Kumadaki Kayo , Tatematsu Kaoru , Doi Yohei , Tsukamoto Kentaro 
Published: February 2023

AbstractBartonella elizabethae is a rat‐borne zoonotic bacterium that causes human infectious endocarditis or neuroretinitis. Recently, a case of bacillary angiomatosis (BA) resulting from this organism was reported, leading to speculation that B. elizabethae may also trigger vasoproliferation. However, there are no reports of B. elizabethae promoting human vascular endothelial cell (EC) proliferation or angiogenesis, and to date, the effects of this bacterium on ECs are unknown. We recently identified a proangiogenic autotransporter, BafA, secreted from B. henselae and B. quintana, which are recognized as Bartonella spp. responsible for BA in humans. Here, we hypothesized that B. elizabethae also harbored a functional bafA gene and examined the proangiogenic activity of recombinant B. elizabethae–derived BafA. The bafA gene of B. elizabethae, which was found to share a 51.1% amino acid sequence identity with BafA of B. henselae and 52.5% with that of B. quintana in the passenger domain, was located in a syntenic region of the genome. The recombinant protein of the N‐terminal passenger domain of B. elizabethae‐BafA facilitated EC proliferation and capillary structure formation. Furthermore, it upregulated the receptor signaling pathway of vascular endothelial growth factor, as observed in B. henselae‐BafA. Taken together, B. elizabethae–derived BafA stimulates human EC proliferation and may contribute to the proangiogenic potential of this bacterium. So far, functional bafA genes have been found in all BA‐causing Bartonella spp., supporting the key role BafA may play in BA pathogenesis.
Predictors of clinical experience performance in occupational therapy and physiotherapy: A scoping review
Authors: Horwitz Heidi M. , Struckmeyer Linda R. , MacPherson Kevin L. , Morgan‐Daniel Jane , Gerry Grace , Myers Christine 
Published: February 2023

AbstractIntroductionSuccessful completion of clinical education experiences is a graduation requirement for students in occupational therapy and physical therapy programmes. A scoping review was conducted to determine what is known about possible clinical experience performance predictors and to find associated research gaps.MethodsThe search included one hand‐searched journal and seven databases, which were used to identify related relevant studies: CINAHL, Education Database, Education Source, Education Resources Information Center (ERIC), PubMed, REHABDATA, and Web of Science. A research librarian guided the search process, and the review's reporting is structured by the Preferred Reporting Items for Systematic reviews and Meta‐Analyses extension for Scoping Reviews (PRISMA‐ScR) Checklist. Studies were included if they contained predictors of clinical experience success indicated by validated performance evaluation tools that were scored by clinical instructors. A multidisciplinary team reviewed the title, abstract, and full text for inclusion and conducted thematic data synthesis to categorise findings.FindingsTwenty‐six articles met the inclusion criteria. The majority of articles were of correlational design and included single institutions. Seventeen articles included occupational therapy, eight included physical therapy, with only one article including both programmes. Four categories of predictors of clinical experience success were identified: pre‐admission variables, academic preparation, learner characteristics, and demographics. Each of the main categories included three to six subcategories. Key findings included the following: (a) The most common cited predictors in clinical experiences are academic preparation and learner characteristics, (b) more experimental design studies are needed to determine the causal relationship between predictors and clinical experience success, and (c) future research is needed on ethnic disparities and clinical experience success.ConclusionFindings from this review show that possible predictors of clinical experience success include a wide range of factors when correlating success with a standardised tool. Academic preparation and learner characteristics were the most investigated predictors. There were only a small number of studies that found a correlation with pre‐admission variables. The findings of this study suggest that students' academic achievement may be a critical element of clinical experience preparation. Future research using experimental designs and across institutions is needed to determine the main predictors for student success.
Transformation or tumor heterogeneity: Mutations in EGFR, SOX2, TP53, and RB1 persist in the histological rapid conversion from lung adenocarcinoma to small‐cell lung cancer
Authors: Hao Lidan , Chen Haiyang , Wang Lili , Zhou Hanqiong , Zhang Zhe , Han Jing , Hou Jiabao , Zhu Yichen , Zhang He , Wang Qiming 
Published: February 2023

AbstractThe transformation from non‐small‐cell lung cancer (NSCLC) to small‐cell lung cancer (SCLC) is one of the mechanisms of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR‐TKIs) resistance. Previous studies exhibited that the median transformation time was 17.8 months for NSCLC to SCLC. Here we introduced a case of lung adenocarcinoma (LADC) with EGFR19 exon deletion mutation in which the pathological transformation emerged only 1 month after lung cancer surgery and receiving EGFR‐TKI inhibitor. Eventually, the pathological examination confirmed the patient experienced a transformation from LADC to SCLC with EGFR, tumor protein p53 (TP53), RB transcriptional corepressor 1 (RB1), and SRY‐box transcription factor 2 (SOX2) mutation. Although the transformation of LADC with EGFR‐mutant into SCLC after targeted therapy was frequent, the pathological results of most patients were only biopsy specimens, which cannot rule out the existence of mixed pathological components of the primary tumor. In this case, the patient's postoperative pathology was sufficient to exclude the probability of mixed tumor components, confirming that the patient's pathological change was indeed transformation from LADC to SCLC. In addition, primary drug resistance in such a short time after surgery and osimertinib‐targeted therapy has not been reported before. We detected the molecular state of this patient before and after SCLC transformation through targeted gene capture and high‐throughput sequencing, and also found for the first time that the mutations of EGFR, TP53, RB1, and SOX2 continue to exist before and after transformation, but the mutation abundance is different. In our paper, the occurrence of small‐cell transformation is affected largely by these gene mutations.
Machine‐reeling technology diffusion in early Meiji Japan's silk industry
Authors: Moriwaki Shota 
Published: February 2023

AbstractUsing 1880 s panel data from Yamanashi and Gifu prefectures in Japan, we estimated the diffusion factors and total factor productivity (TFP) in machine‐reeling technology in Japan's silk‐reeling sector. While the cost of distance through the traditional highway from the Shimosuwa‐shuk post town in the Nagano Prefecture has a negative correlation with technology diffusion, the correlation of silk production per population is positive. Machine‐reeling technology is raw‐material‐intensive and does not show increasing returns to scale. While the TFP in Yamanashi is higher than in Gifu, machine‐reeling output expansion is larger in the latter.
Colonial companies and the cost of introducing Indian immigrants into Fiji, 1884–1916
Authors: Persaud Alexander 
Published: February 2023

AbstractUsing Fiji as a case study, I conduct the first cost accounting of government‐run Indian indentureship in the nineteenth and twentieth centuries. I analyse multiple official data sources and estimate the total cost of bringing Indians to Fiji was £926,851, roughly a fifth of Fiji's reported expenditure. Businesses funded 92.6% of this cost. However, business payments to the government do not appear in official Blue Books. Incorporating business payments shows that both official revenue and expenditure were underestimated by 15%. My results show how one part of colonialism was funded and how colonial fiscal capacity may be underestimated more broadly.
Effects of dietary organic or inorganic iron concentrations on productive performance, egg quality, blood measurements, and tissue iron concentrations in aged laying hens
Authors: Kim Jong Hyuk , Kim Hyun Woo , Kwon Chan Ho , Kwon Sung Hoon , Kil Dong Yong 
Published: February 2023

AbstractThe objective of the current experiment was to investigate the effects of dietary organic or inorganic iron (Fe) concentrations on productive performance, egg quality, blood measurements, and tissue Fe concentrations in aged laying hens. A total of three hundred fifty 60‐week‐old Hy‐Line Brown laying hens were allotted to one of five dietary treatments with seven replicates. Each replicate had 10 consecutive cages. Organic Fe (Fe‐Gly) or inorganic Fe (FeSO4) was added to the basal diet at the levels of 100 or 200 mg/kg Fe. Diets were fed on an ad libitum basis for 6 weeks. Results indicated that supplementation of organic or inorganic Fe in diets increased (p < 0.05) eggshell color and feather Fe concentrations compared with no supplementation of Fe in diets. An interaction was found (p < 0.05) between Fe sources and supplemental levels in diets for egg weight, eggshell strength, and Haugh unit. Hens fed diets supplemented with organic Fe had greater (p < 0.05) eggshell color and hematocrit than those fed diets supplemented with inorganic Fe. In conclusion, dietary supplementation of organic Fe increases the eggshell color of aged laying hens. High supplemental levels of organic Fe in diets improve egg weight in aged laying hens.
The Informative Value of Key Audit Matters in the Audit Report: Understanding the Impact of the Audit Firm and KAM Type
Authors: Gambetta Nicolás , Sierra‐García Laura , García‐Benau María Antonia , Novejarque‐Civera Josefina 
Published: February 2023

AbstractThis paper examines whether the readability (and hence informative value) of key audit matters (KAM) varies according to the audit firm and the KAM type disclosed, a question of vital importance for stakeholders, whose effective decision‐making depends on the quality of information received. Our analysis shows that the informative value of KAM matter and KAM audit procedures varies according to the audit firm responsible. This informative value also depends on whether the KAM is related to entity‐ or accounting‐level risks. This study contributes to the KAM and audit quality literature by showing how these factors impact on the informative value of the expanded audit report. Furthermore, in the context of the agency, institutional and self‐presentation theories and the real effects hypothesis, we discuss auditors’ incentives to increase or decrease the informative value of the expanded audit report.
A qualitative study of young people's lived experiences of suicide and self‐harm: intentionality, rationality and authenticity
Authors: Marzetti Hazel , McDaid Lisa , O'Connor Rory 
Published: February 2023

BackgroundSuicide is a leading cause of death amongst young people and a major public health concern. Although increasing research has identified contributory and protective factors affecting youth suicide, less is known about how young people make sense of suicidal distress themselves.MethodsUsing semi‐structured interview methods and reflexive thematic analysis, this study explores how 24 young people aged 16–24 in Scotland, UK made sense of their lived experiences of suicidal thoughts and feelings, self‐harm, and suicide attempts.ResultsIntentionality, rationality, and authenticity formed our central themes. Suicidal thoughts were categorised by participants dependent on their intention to act on them; a distinction often used to downplay the significance of early suicidal thoughts. Escalating suicidal feelings were then described as almost rational responses to adversities; whereas suicide attempts appeared to be described as more impulsive. These narratives seemed to be somewhat shaped by dismissive attitudes participants experienced in response to their suicidal distress, both from professionals and within their close networks. This impacted how participants articulated distress and asked for support.ConclusionSuicidal thoughts that participants articulated as lacking the intention to act could represent key opportunities for early clinical intervention to prevent suicide. In contrast, stigma, difficulties communicating suicidal distress and dismissive attitudes could serve as barriers to seeking help, and, therefore, additional efforts should be made to ensure young people feel comfortable seeking help.
The 5C model: A proposed continuous quality improvement framework for volunteer dental services in remote Australian Aboriginal communities
Authors: Patel Jilen , Nattabi Barbara , Long Robyn , Durey Angela , Naoum Steven , Kruger Estie , Slack‐Smith Linda 
Published: February 2023

AbstractObjectivesAboriginal and Torres Strait Islander communities in remote parts of Australia are some of the most underserviced communities in regard to oral health care. These communities rely on volunteer dental programmes such as the Kimberley Dental Team to fill the gaps in care, however, there are no known continuous quality improvement (CQI) frameworks to guide such organizations to ensure that they are delivering high‐quality, community‐centred, culturally appropriate care. This study proposes a CQI framework model for voluntary dental programmes providing care to remote Aboriginal communities.MethodsRelevant CQI models wherein the (i) behaviour of interest was quality improvement, and (ii) the health context was volunteer services in Aboriginal communities were identified from the literature. The conceptual models were subsequently augmented using a ‘best fit’ framework and the existing evidence synthesized to develop a CQI framework that aims to guide volunteer dental services to develop local priorities and enhance current dental practice.ResultsA cyclical five‐phase model is proposed starting with consultation and moving through the phases of data collection, consideration, collaboration and celebration.ConclusionsThis is the first proposed CQI framework for volunteer dental services working with Aboriginal communities. The framework enables volunteers to ensure that the quality of care provided is commensurate with the community needs and informed by community consultation. It is anticipated that future mixed methods research will enable formal evaluation of the 5C model and CQI strategies focusing on oral health among Aboriginal communities.
Dietary nitrate improves jaw bone remodelling in zoledronate‐treated mice
Authors: Pan Wen , Gu Jianyu , Xu Shihan , Zhang Chunmei , Wang Jinsong , Wang Songlin , Xu Junji 
Published: February 2023

AbstractBisphosphonate‐related osteonecrosis of the jaw (BRONJ) is a serious complication that occurs in patients with osteoporosis or metastatic bone cancer treated with bisphosphonate. There is still no effective treatment and prevention strategy for BRONJ. Inorganic nitrate, which is abundant in green vegetables, has been reported to be protective in multiple diseases. To investigate the effects of dietary nitrate on BRONJ‐like lesions in mice, we utilized a well‐established mouse BRONJ model, in which tooth extraction was performed. Specifically, 4 mM sodium nitrate was administered in advance through drinking water to assess the short‐ and long‐term effects on BRONJ. Zoledronate injection could induce severe healing inhibition of the tooth extraction socket, while addition of pretreating dietary nitrate could alleviate the inhibition by reducing monocyte necrosis and inflammatory cytokines production. Mechanistically, nitrate intake increased plasma nitric oxide levels, which attenuated necroptosis of monocytes by downregulating lipid and lipid‐like molecule metabolism via a RIPK3 dependent pathway. Our findings revealed that dietary nitrate could inhibit monocyte necroptosis in BRONJ, regulate the bone immune microenvironment and promote bone remodelling after injury. This study contributes to the understanding of the immunopathogenesis of zoledronate and supports the feasibility of dietary nitrate for the clinical prevention of BRONJ.
Prediction of movement difficulties at 5 years from parent report at 2 years in children born extremely preterm
Authors: Costa Raquel , Aubert Adrien M. , Seppänen Anna‐Veera , Ådén Ulrika , Sarrechia Iemke , Zemlin Michael , Cuttini Marina , Männamaa Mairi , Pierrat Véronique , van Heijst Arno , Barros Henrique , Zeitlin Jennifer , Johnson Samantha ,   the SHIPS research group
Published: February 2023

AbstractAimTo assess the predictive validity of parent‐reported gross motor impairment (GMI) at age 2 years to detect significant movement difficulties at age 5 years in children born extremely preterm.MethodData were from 556 children (270 males, 286 females) born at less than 28 weeks' gestation in 2011 to 2012 in 10 European countries. Parent report of moderate/severe GMI was defined as walking unsteadily or unable to walk unassisted at 2 years corrected age. Examiners assessed significant movement difficulties (score ≤ 5th centile on the Movement Assessment Battery for Children, Second Edition) and diagnoses of cerebral palsy (CP) were collected by parent report at 5 years chronological age.ResultsAt 2 years, 66 (11.9%) children had moderate/severe GMI. At 5 years, 212 (38.1%) had significant movement difficulties. Parent reports of GMI at age 2 years accurately classified CP at age 5 years in 91.0% to 93.2% of children. Classification of moderate/severe GMI at age 2 years had high specificity (96.2%; 95% confidence interval 93.6–98.0) and positive predictive value (80.3%; 68.7–89.1) for significant movement difficulties at age 5 years. However, 74.5% of children with significant movement difficulties at 5 years were not identified with moderate/severe GMI at age 2 years, resulting in low sensitivity (25.1%; 19.4–31.5).InterpretationThis questionnaire may be used to identify children born extremely preterm who at age 2 years have a diagnosis of CP or movement difficulties that are likely to have a significant impact on their functional outcomes at age 5 years.