bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of temperature on proliferation of myoblasts from donor piglets with different thermoregulatory maturities
Authors: Metzger Katharina , Dannenberger Dirk , Tuchscherer Armin , Ponsuksili Siriluck , Kalbe Claudia 
Published: June 2021

Abstract
Background
Climate change and the associated risk for the occurrence of extreme temperature events or permanent changes in ambient temperature are important in the husbandry of farm animals. The aim of our study was to investigate the effects of permanent cultivation temperatures below (35 °C) and above (39 °C, 41 °C) the standard cultivation temperature (37 °C) on porcine muscle development. Therefore, we used our porcine primary muscle cell culture derived from satellite cells as an in vitro model. Neonatal piglets have limited thermoregulatory stability, and several days after birth are required to maintain their body temperature. To consider this developmental step, we used myoblasts originating from thermolabile (five days of age) and thermostable piglets (twenty days of age).

Results
The efficiency of myoblast proliferation using real-time monitoring via electrical impedance was comparable at all temperatures with no difference in the cell index, slope or doubling time. Both temperatures of 37 °C and 39 °C led to similar biochemical growth properties and cell viability. Only differences in the mRNA expression of myogenesis-associated genes were found at 39 °C compared to 37 °C with less MYF5, MYOD and MSTN and more MYH3 mRNA. Myoblasts grown at 35 °C are smaller, exhibit higher DNA synthesis and express higher amounts of the satellite cell marker PAX7, muscle growth inhibitor MSTN and metabolic coactivator PPARGC1A. Only permanent cultivation at 41 °C resulted in higher HSP expression at the mRNA and protein levels. Interactions between the temperature and donor age showed that MYOD, MYOG, MYH3 and SMPX mRNAs were temperature-dependently expressed in myoblasts of thermolabile but not thermostable piglets.

Conclusions
We conclude that 37 °C to 39 °C is the best physiological temperature range for adequate porcine myoblast development. Corresponding to the body temperatures of piglets, it is therefore possible to culture primary muscle cells at 39 °C. Only the highest temperature of 41 °C acts as a thermal stressor for myoblasts with increased HSP expression, but it also accelerates myogenic development. Cultivation at 35 °C, however, leads to less differentiated myoblasts with distinct thermogenetic activity. The adaptive behavior of derived primary muscle cells to different cultivation temperatures seems to be determined by the thermoregulatory stability of the donor piglets.
LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival
Authors: Goering Raeann , Engel Krysta L. , Gillen Austin E. , Fong Nova , Bentley David L. , Taliaferro J. Matthew 
Published: June 2021

AbstractBackgroundThe sequence content of the 3′ UTRs of many mRNA transcripts is regulated through alternative polyadenylation (APA). The study of this process using RNAseq data, though, has been historically challenging.ResultsTo combat this problem, we developed LABRAT, an APA isoform quantification method. LABRAT takes advantage of newly developed transcriptome quantification techniques to accurately determine relative APA site usage and how it varies across conditions. Using LABRAT, we found consistent relationships between gene-distal APA and subcellular RNA localization in multiple cell types. We also observed connections between transcription speed and APA site choice as well as tumor-specific transcriptome-wide shifts in APA isoform abundance in hundreds of patient-derived tumor samples that were associated with patient prognosis. We investigated the effects of APA on transcript expression and found a weak overall relationship, although many individual genes showed strong correlations between relative APA isoform abundance and overall gene expression. We interrogated the roles of 191 RNA-binding proteins in the regulation of APA isoforms, finding that dozens promote broad, directional shifts in relative APA isoform abundance both in vitro and in patient-derived samples. Finally, we find that APA site shifts in the two classes of APA, tandem UTRs and alternative last exons, are strongly correlated across many contexts, suggesting that they are coregulated.ConclusionsWe conclude that LABRAT has the ability to accurately quantify APA isoform ratios from RNAseq data across a variety of sample types. Further, LABRAT is able to derive biologically meaningful insights that connect APA isoform regulation to cellular and molecular phenotypes.
Exome-based investigation of the genetic basis of human pigmentary glaucoma
Authors: van der Heide Carly , Goar Wes , Meyer Kacie J. , Alward Wallace L. M. , Boese Erin A. , Sears Nathan C. , Roos Ben R. , Kwon Young H. , DeLuca Adam P. , Siggs Owen M. , Gonzaga-Jauregui Claudia , Sheffield Val C. , Wang Kai , Stone Edwin M. , Mullins Robert F. , Anderson Michael G. , Fan Bao Jian , Ritch Robert , Craig Jamie E. , Wiggs Janey L. , Scheetz Todd E. , Fingert John H. 
Published: June 2021

Abstract
Background
Glaucoma is a leading cause of visual disability and blindness. Release of iris pigment within the eye, pigment dispersion syndrome (PDS), can lead to one type of glaucoma known as pigmentary glaucoma. PDS has a genetic component, however, the genes involved with this condition are largely unknown. We sought to discover genes that cause PDS by testing cohorts of patients and controls for mutations using a tiered analysis of exome data.

Results
Our primary analysis evaluated melanosome-related genes that cause dispersion of iris pigment in mice (TYRP1, GPNMB, LYST, DCT, and MITF). We identified rare mutations, but they were not statistically enriched in PDS patients. Our secondary analyses examined PMEL (previously linked with PDS), MRAP, and 19 other genes. Four MRAP mutations were identified in PDS cases but not in controls (p = 0.016). Immunohistochemical analysis of human donor eyes revealed abundant MRAP protein in the iris, the source of pigment in PDS. However, analysis of MRAP in additional cohorts (415 cases and 1645 controls) did not support an association with PDS. We also did not confirm a link between PMEL and PDS in our cohorts due to lack of reported mutations and similar frequency of the variants in PDS patients as in control subjects.

Conclusions
We did not detect a statistical enrichment of mutations in melanosome-related genes in human PDS patients and we found conflicting data about the likely pathogenicity of MRAP mutations. PDS may have a complex genetic basis that is not easily unraveled with exome analyses.
High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach
Authors: Bhattarai Gehendra , Yang Wei , Shi Ainong , Feng Chunda , Dhillon Braham , Correll James C. , Mou Beiquan 
Published: June 2021

Abstract
Background
Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16.

Results
Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP.

Conclusions
Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.
A newly identified linear epitope on non-RBD region of SARS-CoV-2 spike protein improves the serological detection rate of COVID-19 patients
Authors: Zhang Yunwen , Yang Zhengrong , Tian Sicheng , Li Baisheng , Feng Tiejian , He Jianfan , Jiang Min , Tang Xiujuan , Mei Shujiang , Li Hao , Zhong Yifan , Li Guilian , Tang Mingyuan , Liu Sijing , Tang Tian , Wang Chuan , Wang Xiaohui 
Published: June 2021

Abstract
Background
Serological test is helpful in confirming and tracking infectious diseases in large population with the advantage of fast and convenience. Using the specific epitope peptides identified from the whole antigen as the detection antigen is sensitive and relatively economical. The development of epitope peptide-based detection kits for COVID-19 patients requires comprehensive information about epitope peptides. But the data on B cell epitope of SARS-CoV-2 spike protein is still limited. More importantly, there is a lack of serological data on the peptides in the population. In this study, we aimed to identify the B cell epitope peptides of spike protein and detect the reactivity in serum samples, for further providing data support for their subsequent serological applications.

Results
Two B cell linear epitopes, P104 and P82, located in non-RBD region of SARS-CoV-2 S protein were identified by indirect ELISA screening of an overlapping peptide library of the S protein with COVID-19 patients’ convalescent serum. And the peptides were verified by testing with 165 serum samples. P104 has not been reported previously; P82 is contained in peptide S21P2 reported before. The positive reaction rates of epitope peptides S14P5 and S21P2, the two non-RBD region epitopes identified by Poh et al., and P82 and P104 were 77.0%, 73.9%, 61.2% and 30.3%, respectively, for 165 convalescent sera, including 30 asymptomatic patients. Although P104 had the lowest positive rate for total patients (30.3%), it exhibited slight advantage for detection of asymptomatic infections (36.7%). Combination of epitopes significantly improved the positive reaction rate. Among all combination patterns, (S14P5 + S21P2 + P104) pattern exhibited the highest positive reaction rate for all patients (92.7%), as well as for asymptomatic infections (86.7%), confirming the feasibility of P104 as supplementary antigen for serological detection. In addition, we analyzed the correlation between epitopes with neutralizing antibody, but only S14P5 had a medium positive correlation with neutralizing antibody titre (rs = 0.510, P < 0.01).

Conclusion
Our research proved that epitopes on non-RBD region are of value in serological detection especially when combination more than one epitope, thus providing serological reaction information about the four epitopes, which has valuable references for their usage.
Long-term results after mitral valve surgery using minimally invasive versus sternotomy approach: a propensity matched comparison of a large single-center series
Authors: Cetinkaya Ayse , Geier Anna , Bramlage Karin , Hein Stefan , Bramlage Peter , Schönburg Markus , Choi Yeong-Hoon , Richter Manfred 
Published: June 2021

Abstract
Background
Mitral valve (MV) surgery has traditionally been performed by conventional sternotomy (CS), but more recently minimally invasive surgery (MIS) has become another treatment option. The aim of this study is to compare short- and long-term results of MV surgery after CS and MIS.

Methods
This study was a retrospective propensity-matched analysis of MV operations between January 2005 and December 2015.

Results
Among 1357 patients, 496 underwent CS and 861 MIS. Matching resulted in 422 patients per group. The procedure time was longer with MIS than CS (192 vs. 185 min; p = 0.002) as was cardiopulmonary bypass time (133 vs. 101 min; p < 0.001) and X-clamp time (80 vs. 71 min; p < 0.001). ‘Short-term’ successful valve repair was higher with MIS (96.0% vs. 76.0%, p < 0.001). Length of hospital stay was shorter in MIS than CS patients (10 vs. 11 days; p = 0.001). There was no difference in the overall 30-day mortality rate. Cardiovascular death was lower after MIS (1.2%) compared with CS (3.8%; OR 0.30; 95%CI 0.11–0.84). The difference did not remain significant after adjustment for procedural differences (aOR 0.40; 95%CI 0.13–1.25). Pacemaker was required less often after MIS (3.3%) than CS (11.2%; aOR 0.31; 95%CI 0.16–0.61), and acute renal failure was less common (2.1% vs. 11.9%; aOR 0.22; 95%CI 0.10–0.48). There were no significant differences with respect to rates of stroke, myocardial infarction or repeat MV surgery. The 7-year survival rate was significantly better after MIS (88.5%) than CS (74.8%; aHR 0.44, 95%CI 0.31–0.64).

Conclusion
This study demonstrates that good results for MV surgery can be obtained with MIS, achieving a high MV repair rate, low peri-procedural morbidity and mortality, and improved long-term survival.
Association between protoporphyrin IX and sarcopenia: a cross sectional study
Authors: Kao Chia-Chun , Yang Zhe-Yu , Chen Wei-Liang 
Published: June 2021

AbstractBackgroundAccording to the European Working Group on Sarcopenia in Older People (EWGSOP), the diagnosis of sarcopenia primarily focused on low muscle strength with the detection of low muscle quality and quantity as confirming index. Many studies had identified mitochondrial dysfunction as one of the multifactorial etiologies of sarcopenia. Yet, no study had investigated the role of biosynthetic pathway intermediate, which was found in mitochondria, in the development of sarcopenia. This study aimed to examine the association between protoporphyrin IX (PPIX) and components of sarcopenia.MethodThe present study enrolled 1172 participants without anemia between 1999 to 2002 from the National Health and Nutrition Examination Survey (NHANES) database. We employed the multivariable-logistic regression model to examine the relationship between PPIX and sarcopenia. Covariate adjustments were designated to each of the three models for further analysis of the relationship.ResultsIn the unadjusted model, PPIX was significantly associated with sarcopenia (OR = 3.910, 95% CI = 2.375, 6.439,Pvalue < 0.001). The significance persisted after covariate adjustments as observed in the fully adjusted model (OR = 2.537, 95% CI = 1.419, 4.537,Pvalue = 0.002).ConclusionsThe findings of this study suggested statistically significant association between PPIX and sarcopenia. Our study disclosed the potential of PPIX as a valuable indicator of sarcopenia.
Decline in independence after three years and its association with dietary patterns and IADL-related factors in community-dwelling older people: an analysis by age stage and sex
Authors: Kodama Sayuri , Hoshi Tanji , Kurimori Sugako 
Published: June 2021

Abstract
Background
Few studies have shown age stage and sex differences in the association among dietary patterns and various health factors related to disability in older people. This study aimed to reveal the differences of characteristics, including several dietary patterns, associated with a decline in independence over 3 years in community-dwelling independent older people. Specifically, we examined data by age stage, for people between 65 and 75 years (earlier-stage) and people aged 75 years or above (later-stage), and sex.

Methods
We conducted a nationwide longitudinal study of 25 Japanese prefectures from 2013 to 2016; 2250 participants’ complete data (1294 men and 956 women) were analyzed. Independence was evaluated based on instrumental activities of daily living (IADL) scores (maximum = 12). Dietary patterns were derived from a principal component analysis of the seven food groups. Baseline IADL-related factors linked to independence 3 years later were selected. Multiple logistic regression analysis for having low independence—without a full score of IADL 3 years after baseline—was conducted, adjusted for baseline IADL scores. Finally, to compare differences among age stage and sex groups, we used Multiple-Group Path Analysis.

Results
Participants with a full IADL score 3 years later were classified as high independence (69.6%), and those without the full score were classified as low independence (30.4%). Only the later-stage older peoples’ proportion of low independence 3 years later was significantly higher than those at baseline. A high meat frequency pattern was associated with a significantly higher risk of decline in independence 3 years later in later-stage older women. The earlier-stage older people showed that 18.5 ≤ BMI < 25 was associated with a lower risk, referring to BMI < 18.5. In the later-stage, exercising three or more times a week with enjoyment and fulfillment was associated with a significantly lower risk.

Conclusions
The IADL disability in older people aged 75 and over showed a rapid change. The different characteristics associated with the risk of decline in independence among age stage and sex were revealed. Targeting age stage and sex separately for community-based comprehensive supportive strategies would be necessary for a long life globally.
Ageing and dementia: age-period-cohort effects of policy intervention in England, 2006–2016
Authors: Kolpashnikova Kamila 
Published: June 2021

Abstract
Background
Dementia is one of the most critical challenges of our time. According to the Dementia Statistics Hub, only about 66 % of all UK residents with dementia were diagnosed in 2017–2018. Yet, there are reservations about the early diagnosis of dementia-related diseases. As a result, the UK National Screening Committee does not recommend systematic population screening of dementia, although case-finding strategies are still applied for high-risk groups.

Methods
This study added additional evidence of the effectiveness of the National Dementia Strategy and increased numbers of diagnosis of dementia on the younger cohorts of the older people, using the intrinsic estimator age-period-cohort (APC) models and the English Longitudinal Study of Ageing data.

Results
Age effects show that diagnosis increases in volume only among those aged 75 and above, suggesting that many of those aged below 75 might not be diagnosed in time. Period effects show that although there was an initial increase due to the new policy implementation, the trend stalled in later years, indicating that the increase might not have been even across the period when controlled for age and cohort. The study also shows that cohort effects indicate lower prevalence in younger cohorts controlled for age and period effects.

Conclusions
Although more research in diverse contexts is warranted, this study cautions against the abandonment of timely diagnosis, increased screening and case-finding, and shows some effectiveness of prevention strategies on the national level.
Carbapenem-resistant Enterobacter cloacae complex in a tertiary Hospital in Northeast China, 2010–2019
Authors: Chen Jingjing , Tian Sufei , Nian Hua , Wang Ruixuan , Li Fushun , Jiang Ning , Chu Yunzhuo 
Published: June 2021

Abstract
Background
Carbapenem-resistant Enterobacter cloacae complex (CREC) is a new emerging threat to global public health. The objective of the study was to investigate the clinical characteristics and molecular epidemiology of CREC infections in the medical center of northeast China.

Methods
Twenty-nine patients were infected/colonized with CREC during a ten-year period (2010–2019) by WHONET analysis. Antibiotic susceptibilities were tested with VITEK 2 and micro broth dilution method (for polymyxin B and tigecycline). Carbapenemase encoding genes, β-lactamase genes, and seven housekeeping genes for MLST were amplified and sequenced for 18 cryopreserved CREC isolates. Maximum likelihood phylogenetic tree was built with the concentrated sequences to show the relatedness between the 18 isolates.

Results
There was a rapid increase in CREC detection rate during the ten-year period, reaching 8.11% in 2018 and 6.48% in 2019. The resistance rate of CREC isolates to imipenem and meropenem were 100.0 and 77.8%, however, they showed high sensitivity to tigecycline, polymyxin B and amikacin. The 30-day crude mortality of CREC infection was 17.4%, indicating that it may be a low-virulence bacterium. Furthermore, molecular epidemiology revealed that ST93 was the predominant sequence type followed by ST171 and ST145, with NDM-1 and NDM-5 as the main carbapenemase-encoding genes. Moreover, E. hormaechei subsp. steigerwaltii and E. hormaechei subsp. oharae were the main species, which showed different resistance patterns.

Conclusion
Rising detection rate of CREC was observed in a tertiary hospital, which showed heterogeneity in drug resistance patterns, resistance genes, and MLST types. Effective infection prevention and control measures should be taken to reduce the spread of CREC.
Values and preferences for hepatitis C self-testing among people who inject drugs in Kyrgyzstan
Authors: Martínez-Pérez Guillermo Z. , Nikitin Danil S. , Bessonova Alla , Fajardo Emmanuel , Bessonov Sergei , Shilton Sonjelle 
Published: June 2021

Abstract
Background
The prevalence of hepatitis C virus (HCV) among people who inject drugs (PWID) continues to be a major public-health burden in this highly stigmatised population. To halt transmission of HCV, rapid HCV self-testing kits represent an innovative approach that could enable PWID to know their HCV status and seek treatment. As no HCV test has yet been licenced for self-administration, it is crucial to obtain knowledge around the factors that may deter or foster delivery of HCV self-testing among PWID in resource-constrained countries.

Methods
A qualitative study to assess values and preferences relating to HCV self-testing was conducted in mid-2020 among PWID in the Bishkek and Chui regions of Kyrgyzstan. Forty-seven PWID participated in 15 individual interviews, two group interviews (n = 12) and one participatory action-research session (n = 20). Responses were analysed using a thematic analysis approach with 4 predefined themes: awareness of HCV and current HCV testing experiences, and acceptability and service delivery preferences for HCV self-testing. Informants’ insights were analysed using a thematic analysis approach. This research received local ethics approval.

Results
Awareness of HCV is low and currently PWID prefer community-based HCV testing due to stigma encountered in other healthcare settings. HCV self-testing would be accepted and appreciated by PWID. Acceptability may increase if HCV self-testing: was delivered in pharmacies or by harm reduction associations; was free of charge; was oral rather than blood-based; included instructions with images and clear information on the test’s accuracy; and was distributed alongside pre- and post-testing counselling with linkage to confirmatory testing support.

Conclusions
HCV self-testing could increase awareness of and more frequent testing for HCV infection among PWID in Kyrgyzstan. It is recommended that peer-driven associations are involved in the delivery of any HCV self-testing. Furthermore, efforts should be maximised to end discrimination against PWID at the healthcare institutions responsible for confirmatory HCV testing and treatment provision.