bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zmat2 in mammals: conservation and diversification among genes and Pseudogenes
Authors: Rotwein Peter , Baral Kabita 
Published: January 2020

Abstract
Background
Recent advances in genetics and genomics present unique opportunities for enhancing our understanding of mammalian biology and evolution through detailed multi-species comparative analysis of gene organization and expression. Yet, of the more than 20,000 protein coding genes found in mammalian genomes, fewer than 10% have been examined in any detail. Here we elucidate the power of data available in publicly-accessible genomic and genetic resources by querying them to evaluate Zmat2, a minimally studied gene whose human ortholog has been implicated in spliceosome function and in keratinocyte differentiation.

Results
We find extensive conservation in coding regions and overall structure of Zmat2 in 18 mammals representing 13 orders and spanning ~ 165 million years of evolutionary development, and in their encoded proteins. We identify a tandem duplication in the Zmat2 gene and locus in opossum, but not in other monotremes, marsupials, or other mammals, indicating that this event occurred subsequent to the divergence of these species from one another. We also define a collection of Zmat2 pseudogenes in half of the mammals studied, and suggest based on phylogenetic analysis that they each arose independently in the recent evolutionary past.

Conclusions
Mammalian Zmat2 genes and ZMAT2 proteins illustrate conservation of structure and sequence, along with the development and diversification of pseudogenes in a large fraction of species. Collectively, these observations also illustrate how the focused identification and interpretation of data found in public genomic and gene expression resources can be leveraged to reveal new insights of potentially high biological significance.
Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor
Authors: Cogburn Larry A. , Trakooljul Nares , Wang Xiaofei , Ellestad Laura E. , Porter Tom E. 
Published: January 2020

AbstractBackgroundThe fasting-refeeding perturbation has been used extensively to reveal specific genes and metabolic pathways that control energy metabolism in the chicken. Most global transcriptional scans of the fasting-refeeding response in liver have focused on juvenile chickens that were 1, 2 or 4 weeks old. The present study was aimed at the immediate post-hatch period, in which newly-hatched chicks were subjected to fasting for 4, 24 or 48 h, then refed for 4, 24 or 48 h, and compared with a fully-fed control group at each age (D1-D4).ResultsVisual analysis of hepatic gene expression profiles using hierarchical and K-means clustering showed two distinct patterns, genes with higher expression during fasting and depressed expression upon refeeding and those with an opposing pattern of expression, which exhibit very low expression during fasting and more abundant expression with refeeding. Differentially-expressed genes (DEGs), identified from five prominent pair-wise contrasts of fed, fasted and refed conditions, were subjected to Ingenuity Pathway Analysis. This enabled mapping of analysis-ready (AR)-DEGs to canonical and metabolic pathways controlled by distinct gene interaction networks. The largest number of hepatic DEGs was identified by two contrasts: D2FED48h/D2FAST48h (968 genes) and D2FAST48h/D3REFED24h (1198 genes). The major genes acutely depressed by fasting and elevated upon refeeding includedANGTPL, ATPCL, DIO2, FASN, ME1, SCD, PPARG, SREBP2andTHRSPA—a primary lipogenic transcription factor. In contrast, major lipolytic genes were up-regulated by fasting or down-regulated after refeeding, includingALDOB, IL-15, LDHB, LPIN2, NFE2L2, NR3C1, NR0B1, PANK1, PPARA, SERTAD2andUPP2.ConclusionsTranscriptional profiling of liver during fasting/re-feeding of newly-hatched chicks revealed several highly-expressed upstream regulators, which enable the metabolic switch from fasted (lipolytic/gluconeogenic) to fed or refed (lipogenic/thermogenic) states. This rapidhomeorheticshift of whole-body metabolism from a catabolic-fasting state to an anabolic-fed state appears precisely orchestrated by a small number of ligand-activated transcription factors that provide either a fasting-lipolytic state (PPARA, NR3C1, NFE2L2, SERTAD2, FOX01, NR0B1, RXR)or a fully-fed and refed lipogenic/thermogenic state (THRSPA, SREBF2, PPARG, PPARD, JUN, ATF3, CTNNB1).THRSPAhas emerged as the key transcriptional regulator that drives lipogenesis and thermogenesis in hatchling chicks, as shown here in fed and re-fed states.
Quantitative trait loci analysis of seed oil content and composition of wild and cultivated soybean
Authors: Yao Yanjie , You Qingbo , Duan Guozhan , Ren Jianjun , Chu Shanshan , Zhao Junqing , Li Xia , Zhou Xinan , Jiao Yongqing 
Published: January 2020

Abstract
Background
Soybean oil is a major source of edible oil, and the domestication of wild soybean has resulted in significant changes in oil content and composition. Extensive efforts have been made to identify genetic loci that are related to soybean oil traits. The objective of this study was to identify quantitative trait loci (QTLs) related to soybean seed oil and compare the fatty acid composition between wild and cultivated soybean.

Results
Using the specific-locus amplified fragment sequencing (SLAF-seq) method, a total of 181 recombinant inbred lines (RILs) derived from a cross between wild soybean ZYD00463 (Glycine soja) and cultivated soybean WDD01514 (Glycine max) were genotyped. Finally, a high-density genetic linkage map comprising 11,398 single-nucleotide polymorphism (SNP) markers on 20 linkage groups (LGs) was constructed. Twenty-four stable QTLs for seed oil content and composition were identified by model-based composite interval mapping (CIM) across multiple environments. Among these QTLs, 23 overlapped with or were adjacent to previously reported QTLs. One QTL, qPA10_1 (5.94–9.98 Mb) on Chr. Ten is a novel locus for palmitic acid. In the intervals of stable QTLs, some interesting genes involved in lipid metabolism were detected.

Conclusions
We developed 181 RILs from a cross between wild soybean ZYD00463 and cultivated soybean WDD01514 and constructed a high-density genetic map using the SLAF-seq method. We identified 24 stable QTLs for seed oil content and compositions, which includes qPA10_1 on Chr. 10, a novel locus for palmitic acid. Some interesting genes in the QTL regions were also detected. Our study will provide useful information for scientists to learn about genetic variations in lipid metabolism between wild and cultivated soybean.
Sequential Paleotetraploidization shaped the carrot genome
Authors: Wang Jinpeng , Yu Jigao , Li Yuxian , Wei Chendan , Guo He , Liu Ying , Zhang Jin , Li Xiuqing , Wang Xiyin 
Published: January 2020

AbstractBackgroundCarrot (Daucus carota subsp. carotaL.) is an important root crop with an available high-quality genome. The carrot genome is thought to have undergone recursive paleo-polyploidization, but the extent, occurrences, and nature of these events are not clearly defined.ResultsUsing a previously published comparative genomics pipeline, we reanalysed the carrot genome and characterized genomic fractionation, as well as gene loss and retention, after each of the two tetraploidization events and inferred a dominant and sensitive subgenome for each event. In particular, we found strong evidence of two sequential tetraploidization events, with one (Dc-α) approximately 46–52 million years ago (Mya) and the other (Dc-β) approximately 77–87 Mya, both likely allotetraploidization in nature. The Dc-β event was likely common to all Apiales plants, occurring around the divergence of Apiales-Bruniales and after the divergence of Apiales-Asterales, likely playing an important role in the derivation and divergence of Apiales species. Furthermore, we found that rounds of polyploidy events contributed to the expansion of gene families responsible for plastidial methylerythritol phosphate (MEP), the precursor of carotenoid accumulation, and shaped underlying regulatory pathways. The alignment of orthologous and paralogous genes related to different events of polyploidization and speciation constitutes a comparative genomics platform for studying Apiales, Asterales, and many other related species.ConclusionsHierarchical inference of homology revealed two tetraploidization events that shaped the carrot genome, which likely contributed to the successful establishment of Apiales plants and the expansion of MEP, upstream of the carotenoid accumulation pathway.
Development of a senior-specific, citizen-oriented healthcare service system in South Korea based on the Canadian 48/6 model of care
Authors: Kim Yoon-Sook , Lee Jongmin , Moon Yeonsil , Kim Hee Joung , Shin Jinyoung , Park Jae-Min , Uhm Kyeong Eun , Kim Kyoung Jin , Yoo Jung A. , Oh Yun Kyoung , Byeon Pilsuk , Lee Kunsei , Han Seol-Heui , Choi Jaekyung 
Published: January 2020

AbstractBackgroundIn the age of aging, Korea’s current medical delivery system threatens to increase the number of medical and caring refugees. This study attempts to develop an integrated senior citizen-oriented healthcare service system in which daily care, professional care, and rehabilitation are organically organized between medical institutions and local communities, thereby meeting the daily life needs of the elderly and inducing well-being, wellness, and well-dying.MethodsTo develop the integrated healthcare system, data collection and analyses were conducted through a systematic review, literature review, benchmarking, focus group interviews, and expert consultation.ResultsThe senior-specific, citizen-oriented healthcare service system developed in this study is designed to screen patients aged 65 or older within 24 h of being admitted, using the Geriatric Screening for Care-10. If there is reason for concern as a result of the screening, further evaluation is performed through assessment. Doctors and nurses create a care plan and a discharge plan based on the results from the screening and assessment. The nurse further uses the screening to monitor the patient’s condition before discharge. Based on the screening results at the time of discharge, a transitional care plan is prepared and provided to elderly patients and/or their families. This process enables a systematic link between medical institutions and community resources, aiming for the continuous management of health issues. It also establishes a multidisciplinary treatment plan that considers patients and their families so that diseases common to the elderly are diagnosed and treated promptly.ConclusionsThe most important issue for the elderly is to be able to live healthily and independently for the rest of their lives through well-being, wellness, and well-dying. The senior-specific, citizen-oriented healthcare service proposed in this study is an integrated medical treatment system for elderly users the implementation of which requires the daily care, professional care, and rehabilitation of elderly members of society to be organically organized according to the role of the patients, their families, and the caregiver.
The association between cognition and gait in a representative sample of very old people – the influence of dementia and walking aid use
Authors: Öhlin Jerry , Ahlgren Anders , Folkesson Robert , Gustafson Yngve , Littbrand Håkan , Olofsson Birgitta , Toots Annika 
Published: January 2020

Abstract
Background
Cognition has been related with gait speed in older adults; however, studies involving the oldest age group, where many have mobility disability and cognitive impairment, are few. The aim was to investigate the association between global cognitive function and gait speed in a representative sample of very old people, and whether the association was affected by dementia, and walking aid use.

Method
This cross-sectional study included 1317 participants, mean age 89.4 years, and 68% women, from the Umeå85+/Gerontological Regional Database. Self-paced gait speed was measured over 2.4 m, with or without walking aids, and global cognitive function with the Mini-Mental State Examination (MMSE). The association between cognition and gait speed was analyzed using multiple linear regression and stratified according to dementia. The influence of missing gait speed values was explored using multiple imputation. An interaction analysis was performed to investigate the influence of walking aid use.

Results
In comprehensively adjusted analyses, MMSE associated with gait speed (unstandardized β (β) 0.011 m/s, 95% Confidence Interval [CI] = 0.009, 0.013, p < 0.001) in the total sample. No association was found in people with dementia (β 0.003 m/s, 95%CI = 0.000, 0.006, p = 0.058), until missing gait speed values were compensated for by multiple imputation (β 0.007 m/s, 95% [CI] = 0.002, 0.011, p = 0.002). In interaction analysis the use of walking aids attenuated the association between cognition and gait speed (β − 0.019 m/s, 95%CI = − 0.024, − 0.013, p < 0.001).

Conclusion
Global cognitive function appears to associate with gait speed in very old people. However, in people with dementia selection bias was indicated since unless missing gait speed values were accounted for no association was observed. Walking aid use attenuated cognitive load, which may not apply to walking in daily activities, and requires further investigation.
Molecular characterization of metallo-β-lactamase- producing carbapenem-resistant Enterobacter cloacae complex isolated in Heilongjiang Province of China
Authors: Zhao Yongxin , Zhang Jisheng , Fu Yanjun , Li Chunjiang , Hu Kewang , Su Shanshan , Yu Lan , Guo Yuhang , Fu Yu , Zhang Xiaoli 
Published: January 2020

Abstract
Background
Enterobacter cloacae complex (ECC) is one of the most common extended-spectrum β-lactamase and carbapenemase-producing pathogen that threatens millions of the elderly and vulnerable sick persons. The objective of this study was to perform the molecular characteristics of the carbapenem-resistant E. cloacae complex (CREC) emerged in Heilongjiang Province of China.

Methods
Six CREC strains were isolated from the patients with infectious diseases. The identities of ECC isolates were confirmed by sequencing the polymerase chain reaction (PCR) products of 16S rRNA gene. The characterization of the CREC isolates were analyzed by sequencing PCR products of the carbapenemase, ampC and fluoroquinolone resistance genes and performing multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole genome sequencing.

Results
All 6 isolates harbored multiple resistance genes. Of them, 5 carried metallo-β-lactamases and one was blaKPC-2-positive. The levofloxacin and ciprofloxacin-resistant strains had substitutions of gyrA83, gyrA87, and parC80 in the quinolone-resistance determining regions. The MLST analyses revealed that 6 isolates belonged to five sequence types (ST520, ST528, ST1119, ST1120, and ST93) while the PFGE patterns of the isolates fallen into four clusters. The strain ST1120 was found to carry two separated plasmids that encode blaNDM-1 and blaIMP-4.

Conclusions
Our study, for the first time, identified a CREC strain that co-produces blaNDM-1 and blaIMP-4 in the Northeast China. Our finding emphasizes an urgent need for more intensive surveillance and precaution measures to prevent the CERC spread.
Exploring womens’ experiences and decision making about physical activity during pregnancy and following birth: a qualitative study
Authors: Findley Amy , Smith Debbie M. , Hesketh Kathryn , Keyworth Chris 
Published: January 2020

AbstractBackgroundPhysical activity (PA) tends to decline during pregnancy, and remains low in the early postpartum period, despite the known physical and psychological benefits. This study aimed to explore: (1) women’s experiences of PA during pregnancy and following birth; and (2) decision-making processes related to PA during this time.MethodsSemi-structured telephone interviews were conducted with 16 women who were either pregnant or had recently given birth. Interviews were transcribed verbatim and analysed using thematic analysis.ResultsThere were two over-arching themes: (1) ownership of body, which consisted of the sub-themes: others try to take ownership, important to maintain fitness into pregnancy and motherhood, expectations of PA, and pressure to conform; and (2) unknown territory, which consisted of the sub-themes: engaging in PA with caution, and unclear advice. Decision-making about PA during pregnancy was influenced by: pressure from others who felt responsible to protect the woman from coming to harm; pressure from social media to lose weight postpartum; participant’s beliefs about the benefits of maintaining fitness and participants expectations of how active they thought they would be able to be during pregnancy. Participants felt that pregnancy was an ‘unknown territory’ in terms of the unfamiliar feelings in their body and the inability to continually monitor their baby for reassurance of baby’s health. Advice received from midwives was often lacking, or not tailored to the individual. Advice from friends and family was often regarded as incorrect, but still caused doubt and fear of PA during pregnancy.ConclusionsThese findings contribute to the understanding of women’s experiences of PA during pregnancy and post-partum, and their decision-making processes about PA during pregnancy. Developing accurate and tailored advice as part of midwifery care, that considers the physical and psychological aspects of engaging in PA during pregnancy, will help to ensure that women are supported to make informed decisions about their PA behaviour.
A cross-sectional study of the prevalence and factors associated with symptoms of perinatal depression and anxiety in Rwanda
Authors: Umuziga Marie Providence , Adejumo Oluyinka , Hynie Michaela 
Published: January 2020

Abstract
Background
Perinatal depression and anxiety are increasingly recognized as important public health issues in low and middle-income countries such as Rwanda and may have negative consequences for both mothers and their infants. Maternal mental health may be particularly challenged in Rwanda because of the prevalence of risk factors such as poverty, low education levels, negative life events and marital problems. However, there are limited data about perinatal depression and anxiety symptoms in Rwanda. This study thus aimed to explore the prevalence of symptoms of perinatal depression and anxiety in Rwanda, and factors associated with them.

Methods
A sample of 165 women in the perinatal period (second and third trimester of pregnancy, up to 1 year postnatal) were interviewed individually over 1 month in October 2013. Women were interviewed at 5 of 14 health centres in the Eastern Province or the affiliated district hospital. Participants answered socio-demographic questions and scales measuring symptoms of perinatal depression (EPDS: Edinburgh Postnatal Depression Scale) and anxiety (SAS: Zung Self-rating Anxiety Scale).

Results
Among women in the antenatal period (N = 85), 37.6% had symptoms indicating possible depression (EPDS ≥10) and 28.2% had symptoms associated with clinical levels of anxiety (SAS > 45). Among women within the postnatal period (N = 77), 63.6% had symptoms of possible depression, whereas 48,1% had symptoms of probable anxiety. Logistic regression showed that symptoms of postnatal depression were higher for respondents who had four or more living children relative to those having their first child (Odds Ratio: 0.07, C.I. = 0.01–0.42), and for those with a poor relationship with their partner (Odds Ratio: .09, C.I. =0.03–0.25). Any lifetime exposure to stressful events was the only predictor of symptoms of postnatal anxiety (Odds Ratio = 0.20, C.I. = 0.09–0.44).

Conclusions
Symptoms of postnatal depression and anxiety were prevalent in this Rwandan sample and most strongly predicted by interpersonal and social factors, suggesting that social interventions may be a successful strategy to protect against maternal mental health problems in the Rwandan context.
Prelabor rupture of membranes and the association with cerebral palsy in term born children: a national registry-based cohort study
Authors: Mynarek Maren , Bjellmo Solveig , Lydersen Stian , Strand Kristin Melheim , Afset Jan Egil , Andersen Guro L. , Vik Torstein 
Published: January 2020

AbstractBackgroundGuidelines regarding management of prelabor rupture of membranes (PROM) at term vary between immediate induction and expectant management. A long interval between PROM and delivery increases the risk for perinatal infections. Severe perinatal infections are associated with excess risk for cerebral palsy (CP) and perinatal death. We investigated if increasing intervals between PROM and delivery were associated with perinatal death or CP.MethodsEligible to participate in this population-based cohort-study were term born singletons without congenital malformations born in Norway during 1999–2009. Data was retrieved from the Medical Birth Registry of Norway (MBRN) and the Cerebral Palsy Register of Norway. In line with the registration in the MBRN, intervals between PROM and delivery of more than 24 h was defined as ‘prolonged’ and intervals between 12 and 24 h as ‘intermediate’. Outcomes were stillbirth, death during delivery, neonatal mortality and CP. Logistic regression was used to calculate odds ratio (OR) with 95% confidence intervals (CI) for adverse outcomes in children born after prolonged and intermediate intervals, compared with a reference group comprising all children born less than 12 h after PROM or without PROM.ResultsAmong 559,972 births, 34,759 children were born after intermediate and 30,332 were born after prolonged intervals. There was no association between increasing intervals and death during delivery or in the neonatal period, while the prevalence of stillbirths decreased with increasing intervals. Among children born after intermediate intervals 38 (0.11%) had CP, while among those born after prolonged intervals 46 (0.15%) had CP. Compared with the reference group, the OR for CP was 1.16 (CI; 0.83 to 1.61) after intermediate and 1.61 (CI; 1.19 to 2.18) after prolonged intervals. Adjusting for antenatal factors did not affect these associations. Among children with CP the proportion with diffuse cortical injury and basal ganglia pathology on cerebral MRI, consistent with hypoxic-ischemic injuries, increased with increasing intervals.ConclusionIntervals between PROM and delivery of more than 24 h were associated with CP, but not with neonatal mortality or death during delivery. The inverse association with stillbirth is probably due to reverse causality.