bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput analysis suggests differences in journal false discovery rate by subject area and impact factor but not open access status
Authors: Hall L. M. , Hendricks A. E. 
Published: December 2020

AbstractBackgroundA low replication rate has been reported in some scientific areas motivating the creation of resource intensive collaborations to estimate the replication rate by repeating individual studies. The substantial resources required by these projects limits the number of studies that can be repeated and consequently the generalizability of the findings. We extend the use of a method from Jager and Leek to estimate the false discovery rate for 94 journals over a 5-year period usingpvalues from over 30,000 abstracts enabling the study of how the false discovery rate varies by journal characteristics.ResultsWe find that the empirical false discovery rate is higher for cancer versus general medicine journals (p = 9.801E−07, 95% CI: 0.045, 0.097; adjusted mean false discovery rate cancer = 0.264 vs. general medicine = 0.194). We also find that false discovery rate is negatively associated with log journal impact factor. A two-fold decrease in journal impact factor is associated with an average increase of 0.020 in FDR (p = 2.545E−04). Conversely, we find no statistically significant evidence of a higher false discovery rate, on average, for Open Access versus closed access journals (p = 0.320, 95% CI − 0.015, 0.046, adjusted mean false discovery rate Open Access = 0.241 vs. closed access = 0.225).ConclusionsOur results identify areas of research that may need additional scrutiny and support to facilitate replicable science. Given our publicly available R code and data, others can complete a broad assessment of the empirical false discovery rate across other subject areas and characteristics of published research.
Three functional mutation sites affect the immune response of pigs through altering the expression pattern and IgV domain of the CD4 protein
Authors: Zhang Weiya , Ni Juan , Zhang Jie , Zhang Lu , Zhou Huanhuan , Zhao Changzhi , Zhu Mengjin , Wang Haiyan , Han Jianlin , Li Xinyun , Zhao Shuhong 
Published: December 2020

AbstractBackgroundThe CD4 protein is an important surface marker of T lymphocytes, which can mediate the antigen presentation process by interacting with MHC II and TCR molecules in human and mouse.ResultsIn this study, two haplotypes (A and B) of theCD4gene were found within Chinese indigenous and Western commercial pig breeds. These two haplotypes were defined by 22 fully linked SNPs in the CDS region of theCD4gene. The expression level and localization of the CD4 protein were significantly different between haplotypes A and B. Transcriptome analysis revealed that the immune response-related genes and signaling pathways were down-regulated in genotype AA. Finally, three linked functional SNPs were identified, which affected the expression level and membrane localization of the CD4 protein in pigs. These three SNPs led to the replacements of two amino acids in the IgV1 domain of the CD4 protein, and related to the function of the CD4 protein in the immune response.ConclusionThese three linked SNPs were the key functional mutation sites in theCD4gene, which played important roles in the immune response, and could be utilized as new molecular markers in breeding for disease resistance in pigs.
Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus
Authors: Baeza J. Antonio 
Published: December 2020

AbstractBackgroundWhole mitogenomes or short fragments (i.e., 300–700 bp of thecox1gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ‘primer walking’ or ‘long PCR’ followed by Sanger sequencing or Illumina short-read low-coverage whole genome (LC-WGS) sequencing with or without prior enrichment of mitochondrial DNA. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I first tested whether mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a ‘gold’ standard reference mitogenome retrieved from the same individual using Illumina sequencing. Third and lastly, I tested if the long-read assemblies are useful for mitophylogenomics and barcoding research. To accomplish these goals, I used the Caribbean spiny lobsterPanulirus argus, an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region.ResultsLC-WGS using a MinION ONT device and variousde-novoandreference-basedassembly pipelines retrieved a complete and highly accurate mitogenome for the Caribbean spiny lobsterPanulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not ‘perfect’, phylogenetic analyses using entire mitogenomes or a fragment of thecox1gene demonstrated that mitogenomes assembled using long reads reliably identify the sequenced specimen as belonging toP. argusand distinguish it from other related species in the same genus, family, and superorder.ConclusionsThis study serves as aproof-of-conceptfor the future implementation of in-situ surveillance protocols using the MinION to detect mislabeling inP. argusacross its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income countries.
Under fire-simultaneous volatilome and transcriptome analysis unravels fine-scale responses of tansy chemotypes to dual herbivore attack
Authors: Clancy Mary V. , Haberer Georg , Jud Werner , Niederbacher Bishu , Niederbacher Simon , Senft Matthias , Zytynska Sharon E. , Weisser Wolfgang W. , Schnitzler Jörg-Peter 
Published: December 2020

Abstract
Background
Tansy plants (Tanacetum vulgare L.) are known for their high intraspecific chemical variation, especially of volatile organic compounds (VOC) from the terpenoid compound group. These VOCs are closely involved in plant-insect interactions and, when profiled, can be used to classify plants into groups known as chemotypes. Tansy chemotypes have been shown to influence plant-aphid interactions, however, to date no information is available on the response of different tansy chemotypes to simultaneous herbivory by more than one insect species.

Results
Using a multi-cuvette system, we investigated the responses of five tansy chemotypes to feeding by sucking and/or chewing herbivores (aphids and caterpillars; Metopeurum fuscoviride Stroyan and Spodoptera littoralis Boisduval). Herbivory by caterpillars following aphid infestation led to a plant chemotype-specific change in the patterns of terpenoids stored in trichome hairs and in VOC emissions. The transcriptomic analysis of a plant chemotype represents the first de novo assembly of a transcriptome in tansy and demonstrates priming effects of aphids on a subsequent herbivory. Overall, we show that the five chemotypes do not react in the same way to the two herbivores. As expected, we found that caterpillar feeding increased VOC emissions, however, a priori aphid infestation only led to a further increase in VOC emissions for some chemotypes.

Conclusions
We were able to show that different chemotypes respond to the double herbivore attack in different ways, and that pre-treatment with aphids had a priming effect on plants when they were subsequently exposed to a chewing herbivore. If neighbouring chemotypes in a field population react differently to herbivory/dual herbivory, this could possibly have effects from the individual level to the group level. Individuals of some chemotypes may respond more efficiently to herbivory stress than others, and in a group environment these “louder” chemotypes may affect the local insect community, including the natural enemies of herbivores, and other neighbouring plants.
Novel stromal biomarker screening in pancreatic cancer patients using the in vitro cancer-stromal interaction model
Authors: Nishida Yasunori , Nagatsuma Akiko Kawano , Kojima Motohiro , Gotohda Naoto , Ochiai Atsushi 
Published: December 2020

Abstract
Background
Stromal fibroblasts associated with pancreatic ductal adenocarcinoma (PDAC) play an important role in tumor progression through interactions with cancer cells. Our proposed combination strategies of in vitro and in silico biomarker screening through a cancer-stromal interaction model were previously identified several actin-binding proteins in human colon cancer stroma. The main aim of the present study was to identify novel prognostic markers in human PDAC stroma using our strategies.

Methods
Five primary cultivated fibroblasts from human pancreas were stimulated by two types of pancreatic cancer-cell-conditioned medium (Capan-1 and MIA PaCa-2) followed by gene expression analysis to identify up-regulated genes. Publicly available microarray data set concomitant with overall survival was collected and prognostic marker candidates were selected among the genes that were found to be up-regulated. The mRNA expression levels of the selected genes were evaluated in 5 human fresh PDAC tissues. Finally, survival analysis was performed based on immunohistochemical results on tissue microarrays consisting of 216 surgically resected PDAC tissues.

Results
The microarray data of the cancer-stromal interaction model revealed that 188 probes were significantly regulated in pancreatic fibroblasts. Further, six genes were selected using publicly available microarray data set, and a single Diaphanous-related formin-3 (DIAPH3), actin-binding protein, was identified as a stromal biomarker in PDAC fibroblasts by RNA validation analysis. DIAPH3 exhibited strong immunohistochemical expression in stromal fibroblasts. The high stromal expression of DIAPH3 was associated with shorter survival times of PDAC patients.

Conclusions
DIAPH3 was identified as a prognostic marker in PDAC fibroblasts using our biomarker screening strategies through the cancer-stromal interaction model, indicating that stromal actin-binding proteins might have an important biological role in cancer progression. These strategies were also available in PDAC, and can be used for stromal biomarker screening in various cancers.
Antimicrobial resistance among GLASS pathogens in conflict and non-conflict affected settings in the Middle East: a systematic review
Authors: Truppa Claudia , Abo-Shehada Mahmoud N. 
Published: December 2020

Abstract
Background
In spite of the evident general negative effects of armed conflict on countries’ health systems and populations’ health outcomes, little is known about similar impacts of conflicts on the spread of antimicrobial resistances (AMR). This review was to address this evidence gap and describe:

Patterns of AMR in the Middle East (ME) and resistance profiles of pathogens included in the Global AMR Surveillance System (GLASS) supported by the World Health Organization;

Differences in proportions of AMR isolates between conflict and non-conflict countries.

Methods
A systematic literature review was conducted following PRISMA guidelines and searching five electronic databases. Subject heading and free text were searched for “antimicrobial resistances” and “Middle East”, to identify observational studies on AMR published from January 2011 to June 2018. Data were extracted from included articles on a predefined set of variables. Percentages of AMR were analysed as median and interquartile ranges. Risk of bias was assessed using the Newcastle-Ottawa Scale.

Results
A total of 132 articles met the inclusion criteria. Included studies showed heterogeneity in study design, laboratory methods and standards for interpretation of results, and an overall high risk of bias. Main findings were the following:

High proportions of carbapenem resistance in Acinetobacter spp. (median 74.2%), and both carbapenem resistance (median 8.1 and 15.4% for E. coli and K. pneumoniae respectively) and ESBL-production (median 32.3 and 27.9% for E. coli and K. pneumoniae respectively) amongst Enterobacteriaceae. S. aureus isolates showed a median methicillin resistance percentage of 45.1%, while vancomycin resistance was almost absent. A median of 50% of the strains of S. pneumoniae showed non-susceptibility to penicillin.

Similar trends were observed in conflict and non-conflict affected countries.

Conclusions
There is a lack of standardization in the methodological approach to AMR research in the Middle East. The proportion of antibiotic resistances among specific GLASS pathogens is high, particularly among Acinetobacter spp.
Pneumococcal nasopharyngeal carriage among Bhutanese children hospitalized with clinical pneumonia: serotypes and viral co-infection
Authors: Jullien Sophie , Sharma Ragunath , Lhamu Mynak Mimi , Henares Desiree , Muñoz-Almagro Carmen , Bassat Quique 
Published: December 2020

Abstract
Background
Pneumococcal nasopharyngeal colonization (PNC) generally precedes pneumococcal disease. The purpose of this study was to determine the prevalence of PNC and to identify the pneumococcal serotypes circulating among Bhutanese children under five years of age admitted with clinical pneumonia, before the introduction of pneumococcal conjugate vaccine (PCV13) in the country. We also aimed to contribute to the understanding of the interplay between PNC and viral co-infection among this population.

Methods
This was a prospective study conducted at the Jigme Dorji Wangchuck National Referral Hospital in Bhutan over 12 consecutive months. Children aged 2 to 59 months admitted with WHO-defined clinical pneumonia were eligible for recruitment. We collected blood for bacterial culture and molecular identification of S. pneumoniae, and nasopharyngeal washing for screening of respiratory viruses, and for the detection and capsular typing of S. pneumoniae by real-time polymerase chain reaction (RT-PCR).

Results
Overall, 189 children were recruited, and PNC was tested in 121 of them (64.0%). PNC was found in 76/121 children (62.8%) and S. pneumoniae was identified in blood (both by culture and RT-PCR) in a single child. Respiratory viruses were detected in a similar proportion among children with (62/70; 88.6%) and without PNC (36/40; 90.0%; p = 1.000), but rhinovirus detection was less common among children with PNC (20/70; 28.6% versus 19/40; 47.5%; p = 0.046). Capsular typing identified 30 different serotypes. Thirty-nine children (51.3%) were colonised with two to five different serotypes. A third of the children presented with serotypes considered highly invasive. Over half of the children (44/76; 57.9%) were carrying at least one serotype included in PCV13.

Conclusions
This study provides baseline information on the status of PNC among Bhutanese children admitted with clinical pneumonia prior to the introduction of PCV13, which is valuable to monitor its potential impact. PCV13 could theoretically have averted up to 58% of the pneumococcal infections among the children in this study, suggesting a future role for the vaccine to significantly reduce the burden associated with S. pneumoniae in Bhutan.
Lactation challenges of resident physicians- results of a national survey
Authors: Peters Gabrielle W. , Kuczmarska-Haas Aleksandra , Holliday Emma B. , Puckett Lindsay 
Published: December 2020

Abstract
Background
There are unique challenges to parenting in residency and there is limited data to guide policy regarding lactation facilities and support for female physicians-in-training. We aimed to assess issues surrounding breast-feeding during graduate medical training for current residents or recent graduates from United States (US) residency programs.

Methods
A national cross-sectional survey was sent to current and recently graduated (2017 and later) female residents in June 2020. This questionnaire was administered using the Qualtrics Survey tool and was open to each participating woman’s organization for 4 weeks. Summary statistics were used to describe characteristics of all respondents and free-text responses were reviewed to identify common themes regarding avenues for improvement.

Results
Three hundred twelve women responded to the survey, representing a 15.6% response rate. The median duration of providing breastmilk was 9 months (IQR 6–12). 21% of residents reported access to usable lactation rooms within their training hospital, in which 12% reported a computer was present. 60% of lactating residents reported not having a place to store breast milk. 73% reported residency limited their ability to lactate, and 37% stopped prior to their desired goal. 40% reported their faculty and/or co-residents made them feel guilty for their decision to breastfeed, and 56% reported their difficulties with breastfeeding during residency impacted their mental health.

Conclusion
Residents who become mothers during training face significant obstacles to meeting their breastfeeding/pumping needs and goals. With these barriers defined, informed policy change can be instituted to improve the lactation experience for physicians-in-training.
Trends and correlates of cesarean section rates over two decades in Nepal
Authors: Bhandari Aliza K. C. , Dhungel Bibha , Rahman Mahbubur 
Published: December 2020

Abstract
Background
Cesarean section (CS) is a major component of emergency obstetric care. There has been a substantial rise in the rate of CS in private institutions in Nepal which might reflect the successful implementation of delivery schemes introduced by the government extended to the private organizations alternatively, it may also reflect the need for more public health care facilities to provide maternal and child health care services. Hence, the objective of this study was to examine the trends in institutional-based CS rates in Nepal along with its correlates over time.

Methods
We used the National Demographic and Health Survey (NDHS) data collected every 5 years, from 1996 to 2016. The trend in CS rates based on five waves of NDHS data along with its correlates were examined using multivariable logistic regression models after adjusting for socio-demographics and pregnancy-related variables.

Results
We included 20,824 reproductive-aged women who had a history of delivery within the past 5 years. The population-based CS rate increased from 0.9% in 1996 [95% CI: (0.6–1.2) %] to 10.2% in 2016 [95% CI: (8.9–11.6) %, p < 0.01] whereas the institutional-based CS rate increased from 10.4% in 1996 [95% CI: (8.3–12.9) %] to 16.4% in 2016 [95% CI: (14.5–18.5) %, p < 0.01]. Private institutions had a nearly 3-fold increase in CS rate (8.9% in 1996 [95% CI: (4.8–16.0) %] vs. 26.3% in 2016[95% CI: (21.9–31.3) %]. This was also evident in the trend analysis where the odds of having CS was 3.58 times higher [95% CI: (1.83–7.00), p < 0.01] in 2016 than in 1996 in the private sectors, while there was no evidence of an increase in public hospitals (10.9% in 1996 to 12.9% in 2016; p for trend > 0.05). Education of women, residence, wealth index, parity and place of delivery were significantly associated with the CS rate.

Conclusion
Nepal has observed a substantial increase in cesarean delivery over the 20 years, which might indicate a successful implementation of the safe motherhood program in addressing the Millennium Development Goals and Universal Health Care agenda on maternal and child health. However, the Nepal government should examine existing disparities in accessibility of emergency obstetric care services, such as differences in CS between public and private sectors, and promote equity in maternal and child health care services accessibility and utilization.
Accelerated fetal growth in early pregnancy and risk of preterm birth: a prospective cohort study
Authors: Elenis Evangelia , Wikström Anna-Karin , Simic Marija 
Published: December 2020

Abstract
Background
Preterm birth (occurring before 37 completed weeks of gestation) affects 15 million infants annually, 7.5% of which die due to related complications. The detection and early diagnosis are therefore paramount in order to prevent the development of prematurity and its consequences. So far, focus has been laid on the association between reduced intrauterine fetal growth during late gestation and prematurity. The aim of the current study was to investigate the association between accelerated fetal growth in early pregnancy and the risk of preterm birth.

Methods
This prospective cohort study included 69,617 singleton pregnancies without congenital malformations and with available biometric measurements during the first and second trimester. Estimation of fetal growth was based on measurements of biparietal diameter (BPD) at first and second trimester scan. We investigated the association between accelerated fetal growth and preterm birth prior to 37 weeks of gestation. The outcome was further stratified into very preterm birth (before 32 weeks of gestation) or moderate preterm birth (between 32 and 37 weeks of gestation) and medically induced or spontaneous preterm birth and was further explored.

Results
The odds of prematurity were increased among fetuses with accelerated BPD growth (> 90th centile) estimated between first and second ultrasound scan, even after adjustment for possible confounders (aOR 1.36; 95% CI 1.20–1.54). The findings remained significant what regards moderate preterm births but not very preterm births. Regarding medically induced preterm birth, the odds were found to be elevated in the group of fetuses with accelerated growth in early pregnancy (aOR 1.34; 95% CI 1.11–1.63). On the contrary, fetuses with delayed fetal growth exhibited lower odds for both overall and spontaneous preterm birth.

Conclusions
Fetuses with accelerated BPD growth in early pregnancy, detected by ultrasound examination during the second trimester, exhibited increased odds of being born preterm. The findings of the current study suggest that fetal growth in early pregnancy should be taken into account when assessing the risk for preterm birth.