bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes
Authors: González-Castellano Inés , Manfrin Chiara , Pallavicini Alberto , Martínez-Lage Andrés 
Published: October 2019

Abstract

Background
The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns.

Results
A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species.

Conclusions
This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.
Phenotypic and molecular characterization of Hessian fly resistance in diploid wheat, Aegilops tauschii
Authors: Nemacheck Jill A. , Schemerhorn Brandon J. , Scofield Steven R. , Subramanyam Subhashree 
Published: October 2019

Abstract

Background
The Hessian fly (Mayetiola destructor), belonging to the gall midge family (Cecidomyiidae), is a devastating pest of wheat (Triticum aestivum) causing significant yield losses. Despite identification and characterization of numerous Hessian fly-responsive genes and associated biological pathways involved in wheat defense against this dipteran pest, their functional validation has been challenging. This is largely attributed to the large genome, polyploidy, repetitive DNA, and limited genetic resources in hexaploid wheat. The diploid progenitor Aegilops tauschii, D-genome donor of modern-day hexaploid wheat, offers an ideal surrogate eliminating the need to target all three homeologous chromosomes (A, B and D) individually, and thereby making the functional validation of candidate Hessian fly-responsive genes plausible. Furthermore, the well-annotated sequence of Ae. tauschii genome and availability of genetic resources amenable to manipulations makes the functional assays less tedious and time-consuming. However, prior to utilization of this diploid genome for downstream studies, it is imperative to characterize its physical and molecular responses to Hessian fly.

Results
In this study we screened five Ae. tauschii accessions for their response to the Hessian fly biotypes L and vH13. Two lines were identified that exhibited a homozygous resistance response to feeding by both Hessian fly biotypes. Studies using physical measurements and neutral red staining showed that the resistant Ae. tauschii accessions resembled hexaploid wheat in their phenotypic responses to Hessian fly, that included similarities in larval developmental stages, leaf and plant growth, and cell wall permeability. Furthermore, molecular responses, characterized by gene expression profiling using quantitative real-time PCR, in select resistant Ae. tauschii lines also revealed similarities with resistant hexaploid wheat.

Conclusions
Phenotypic and molecular characterization of Ae. tauschii to Hessian fly infestation revealed resistant accessions that shared similarities to hexaploid wheat. Resembling the resistant hexaploid wheat, the Ae. tauschii accessions mount an early defense strategy involving defense proteins including lectins, secondary metabolites and reactive oxygen species (ROS) radicals. Our results reveal the suitability of the diploid progenitor for use as an ideal tool for functional genomics research in deciphering the wheat-Hessian fly molecular interactions.
Comparison of postoperative pain between patients who underwent primary and repeated cesarean section: a prospective cohort study
Authors: Duan Guangyou , Yang Guiying , Peng Jing , Duan Zhenxin , Li Jie , Tang Xianglong , Li Hong 
Published: October 2019

Abstract

Background
The differences in post-operative pain are unclear between the primiparas who underwent a primary cesarean section and multiparas who underwent their first repeat cesarean section. The study aimed to explore the possible differences in postoperative pain between primiparas and multiparas.

Methods
A prospective cohort study was performed only including women who underwent cesarean deliveries under spinal anesthesia. Postoperative patient-controlled intravenous analgesia (PCIA) was administered to all subjects with 0.2 mg/kg hydromorphone and 4 mg/kg flurbiprofen; the pump was programmed as 2.0 mL/h background infusion with a loading dose of 1 mL and a lockout period of 15 min. Postoperative incision and visceral pain intensity were evaluated using the visual analogue scale, and inadequate analgesia was defined as a visual analogue scale score ≥ 40 during 48 h post-operation. Additionally, the patients’ pain statuses in postoperative week 1 and week 4 were also assessed during follow-up via telephone.

Results
From January to May 2017, a total of 168 patients (67 primiparas and 101 multiparas) were included. The relative risk for multiparas to experience inadequate analgesia on incision pain was 0.42 (95% CI: 0.25 to 0.74) compared to primiparas. In patients aged < 30 years, inadequate analgesia on visceral pain was higher in multiparas than in primiparas (RR, 3.56 [1.05 to 12.04], P = 0.025). There was no significant difference in the combined incidence of inadequate analgesia in both types of pain between the multiparas and primiparas (33.7% vs. 40.2%, P = 0.381). No difference was found in PCIA use between the two groups (111.1 ± 36.0 mL vs. 110.9 ± 37.3 mL, P = 0.979). In addition, a significantly higher incidence of pain was noted 4 weeks post-surgery in primiparas than that in multiparas (62.2% vs. 37.7%, P = 0.011).

Conclusion
Multiparas who underwent their first repeat cesarean section have a lower for inadequate analgesia on incision pain during the first 48 h after surgery than primiparas. Multiparas aged under 30 years may be more prone to experiencing postoperative inadequate analgesia on visceral pain.

Trail Registration
ClinicalTrial.gov: NCT03009955, Date registered: December 30, 2016.
Canadian in-hospital mortality for patients with emergency-sensitive conditions: a retrospective cohort study
Authors: Berthelot Simon , Lang Eddy S. , Quan Hude , Stelfox Henry T. 
Published: October 2019

Abstract

Background
The emergency department (ED) sensitive hospital standardized mortality ratio (ED-HSMR) measures risk-adjusted mortality for patients admitted to hospital with conditions for which ED care may improve health outcomes. This study aimed to describe in-hospital mortality across Canadian provinces using the ED-HSMR.

Methods
Hospital discharge data were analyzed from April 2009 to March 2012. The ED-HSMR was calculated as the ratio of observed deaths among patients with emergency-sensitive conditions in a hospital during a year (2010–11 or 2011–12) to the expected deaths for the same patients during the reference year (2009–10), multiplied by 100. The expected deaths were estimated using predictive models fitted from the reference year. Aggregated provincial ED-HSMR values were calculated. A HSMR value above or below 100 respectively means that more or fewer deaths than expected occurred within a province.

Results
During the study period, 1,335,379 patients were admitted to hospital in Canada with an emergency-sensitive condition as the most responsible diagnosis. More in-hospital deaths (95% confidence interval) than expected were respectively observed for the years 2010–11 and 2011–12 in Newfoundland [124.3 (116.3–132.6); & 117.6 (110.1–125.5)] and Nova Scotia [116.4 (110.7–122.5) & 108.7 (103.0–114.5)], while mortality was as expected in Prince Edward Island [99.9 (86.5–114.8) & 100.7 (87.5–115.3)] and Manitoba [99.2 (94.5–104.1) & 98.3 (93.5–103.3)], and less than expected in all other provinces and territories.

Conclusions
Our study revealed important variation in risk-adjusted mortality for patients admitted to hospital with emergency-sensitive conditions among Canadian provinces. The ED-HSMR may be a useful outcome indicator to complement existing process indicators in measuring ED performance.

Trial registration
N/A – Retrospective cohort study.
BUGSnet: an R package to facilitate the conduct and reporting of Bayesian network Meta-analyses
Authors: Béliveau Audrey , Boyne Devon J. , Slater Justin , Brenner Darren , Arora Paul 
Published: October 2019

Abstract

Background
Several reviews have noted shortcomings regarding the quality and reporting of network meta-analyses (NMAs). We suspect that this issue may be partially attributable to limitations in current NMA software which do not readily produce all of the output needed to satisfy current guidelines.

Results
To better facilitate the conduct and reporting of NMAs, we have created an R package called “BUGSnet” (Bayesian inference Using Gibbs Sampling to conduct a Network meta-analysis). This R package relies upon Just Another Gibbs Sampler (JAGS) to conduct Bayesian NMA using a generalized linear model. BUGSnet contains a suite of functions that can be used to describe the evidence network, estimate a model and assess the model fit and convergence, assess the presence of heterogeneity and inconsistency, and output the results in a variety of formats including league tables and surface under the cumulative rank curve (SUCRA) plots. We provide a demonstration of the functions contained within BUGSnet by recreating a Bayesian NMA found in the second technical support document composed by the National Institute for Health and Care Excellence Decision Support Unit (NICE-DSU). We have also mapped these functions to checklist items within current reporting and best practice guidelines.

Conclusion
BUGSnet is a new R package that can be used to conduct a Bayesian NMA and produce all of the necessary output needed to satisfy current scientific and regulatory standards. We hope that this software will help to improve the conduct and reporting of NMAs.
Family medicine vocational training and career satisfaction in Hong Kong
Authors: Lee K. P. , Wong C. , Chan D. , Kung K. , Luk L. , Wong M. C. S. , Chao D. , Leung V. , Chan C. W. , Ko W. , Leung T. F. , Chan Y. H. , Fung H. T. , Lee M. K. , Wong S. Y. S. 
Published: October 2019

AbstractBackgroundPostgraduate vocational training in family medicine (FM) is essential for physicians to build capacity and develop quality primary care. Inadequate standards in training and curriculum development can contribute to poor recruitment and retention of doctors in primary care. This study aimed to investigate: 1) the satisfaction level of doctors regarding vocational training in family medicine and associated demographics; and 2) the satisfaction level of doctors regarding their family medicine career and associated factors.MethodThis is a cross sectional study of all family medicine physicians across all government-funded primary care clinics (GOPCs). The study questionnaire consisted of items from a standardized and validated physician survey named the Physician Worklife Survey (PWS) (Konrad et al., Med Care, 1999). We selected three scales (7 items) relating to global job satisfaction, global career satisfaction and global specialty (family medicine) satisfaction with additional items on training and demographics. All significant variables in bivariate analyses were further examined using stepwise logistic regression.ResultsOut of 424 eligible family medicine physicians, 368 physicians successfully completed the questionnaire. The response rate was 86.8%. Most participants were male (52.6%), were aged between 35 and 44 years (55.5%), were FM specialists (42.4%), graduated locally (86.2%), and had postgraduate qualifications. Eighty-two percent (82%) of participants were satisfied with their training. Having autonomy and protected time for training were associated with satisfaction with FM training. Satisfaction with family medicine as a career was correlated with physicians’ satisfaction with their current job. Doctors who did not enroll in training (p < 0.001) and physicians who were older (p = 0.023) were significantly less satisfied. Stepwise multivariate regression showed that doctors who subjectively believed their training as “broad and in depth’ had higher career satisfaction (p < 0.001).ConclusionOverall, the satisfaction level of physicians on current family medicine training in Hong Kong was high. Having autonomy and protected time for training is associated with higher training satisfaction levels. Perceiving FM training as “broad and in-depth” is associated with higher family medicine career satisfaction.
Prevalence and determinants of frailty in the absence of disability among older population: a cross sectional study from rural communities in Nepal
Authors: Yadav Uday Narayan , Tamang Man Kumar , Thapa Tarka Bahadur , Hosseinzadeh Hassan , Harris Mark Fort , Yadav Krishna Kumar 
Published: October 2019

AbstractBackgroundLongevity and frailty have significant implications for healthcare delivery. They increase demands for healthcare service and surge risk of hospitalization. Despite gaining global attention, determinants of frailty have remained unmeasured in the rural community settings in Nepal. This study aimed to address this gap by accessing the prevalence and determinants of frailty in the absence of disability among older population living in rural communities in eastern Nepal.MethodsWe conducted a cross-sectional analytical study of 794 older adults aged ≥60 living in the rural part of Sunsari and Morang district of eastern Nepal between January and April in 2018. Multi-stage cluster sampling was applied to recruit the study participants. Study measures included socio-demographics; Frail Non-disabled scale (FiND) measuring frailty, Barthel’s Index measuring basic activities of daily living and Geriatric depression scale. Determinants of frailty in the absence of disability were identified using generalized estimating equation (GEE).ResultsAbout 65% of the participants self-reported the presence of frailty in the absence of disability. In the adjusted models, those from underprivileged ethnic groups, lack of daily physical exercise, presence of depressive symptoms and those not getting enough social support from family were found to be significantly associated with frailty among older participants.ConclusionsThe prevalence of frailty in the absence of disability was high among rural community old population living in eastern Nepal. Our findings suggest that need of frailty awareness (both for clinicians and general public), so as to avoid negative consequences. To reduce the healthcare burden early screening frailty in primary care has potentials to prevent implications of frailty in Nepal.
Low seroprevalence of Zika virus infection among adults in Southern Taiwan
Authors: Chien Yu-Wen , Ho Tzu-Chuan , Huang Pei-Wen , Ko Nai-Ying , Ko Wen-Chien , Perng Guey Chuen 
Published: October 2019

AbstractBackgroundWe recently conducted a serosurvey of newly arrived workers in Taiwan from four Southeast Asian countries which revealed that 1% of the migrant workers had laboratory-confirmed recent Zika virus (ZIKV) infection. Taiwan, whereAedesmosquitoes are prevalent, has a close relationship with Southeast Asian countries. Up to now, 21 imported cases of ZIKV infection have been reported in Taiwan, but there has been no confirmed indigenous case. The aim of this serosurvey was to assess whether there was unrecognized ZIKV infections in Taiwan.MethodsA total of 212 serum samples collected in a cross-sectional seroepidemiologic study conducted during the end of the 2015 dengue epidemic in Tainan, Taiwan, were analyzed. Anti-ZIKV IgM and IgG were tested using commercial enzyme-linked immunosorbent assays (ELISAs). Plaque reduction neutralization tests (PRNTs) for ZIKV and four dengue virus (DENV) serotypes were performed for samples with positive anti-ZIKV antibodies. A confirmed case of ZIKV infection was defined by ZIKV PRNT90titer ratio ≥ 4 compared to four DENV serotypes.ResultsThe mean age of the 212 participants was 54.0 years (standard deviation 13.7 years), and female was predominant (67.0%). Anti-ZIKV IgM and IgG were detected in 0 (0%) and 9 (4.2%) of the 212 participants, respectively. For the 9 samples with anti-ZIKV IgG, only 1 sample had 4 times higher ZIKV PRNT90titers compared to PRNT90titers against four dengue virus serotypes; this individual denied having traveled abroad.ConclusionsThe results suggest that undetected indigenous ZIKV transmission might have occurred in Taiwan. The findings also suggest that the threat of epidemic transmission of ZIKV in Taiwan does exist due to extremely low-level of herd immunity. Our study also indicates that serological tests for ZIKV-specific IgG remain a big challenge due to cross-reactivity, even in dengue non-endemic countries.
Hepatitis C virus infection: a challenge in the complex management of two cases of multidrug-resistant tuberculosis
Authors: Musso Maria , Mosti Silvia , Gualano Gina , Mencarini Paola , Urso Rocco , Ghirga Piero , Rianda Alessia , Del Nonno Franca , Goletti Delia , Palmieri Fabrizio 
Published: October 2019

Abstract

Background
Multidrug-resistant tuberculosis (MDR-TB) requires lengthy use of second-line drugs, burdened by many side effects. Hepatitis C virus (HCV) chronic infection increases risk of drug-induced liver injury (DILI) in these patients. Data on MDR-TB patients with concurrent HCV chronic infection treated at the same time with second-line antitubercular drugs and new direct-acting antivirals (DAAs) are lacking. We evaluate if treating at the same time HCV infection and pulmonary MDR-TB is feasible and effective.

Cases presentation
In this study, we described two cases of patients with pulmonary MDR-TB and concurrent HCV chronic infection cured with DAAs at a Tertiary Infectious Diseases Hospital in Italy. During antitubercular treatment, both patients experienced a DILI before treating HCV infection.
After DAAs liver enzymes normalized and HCV RNA was undetectable. Then antitubercular regimen was started according to the institutional protocol, drawn up following WHO MDR-TB guidelines. It was completed without further liver side effects and patients were declared cured from both HCV infection and MDR-TB.

Conclusions
We suggest to consider treatment of chronic hepatitis C with DAAs as a useful intervention for reintroduction of second-line antitubercular agents in those patients who developed DILI, reducing the risk of treatment interruption when re-exposed to these drugs.
Comparison of conventional and Si-photomultiplier-based PET systems for image quality and diagnostic performance
Authors: Oddstig Jenny , Leide Svegborn Sigrid , Almquist Helen , Bitzén Ulrika , Garpered Sabine , Hedeer Fredrik , Hindorf Cecilia , Jögi Jonas , Jönsson Lena , Minarik David , Petersson Richard , Welinder Annika , Wollmer Per , Trägårdh Elin 
Published: October 2019

Abstract

Background
A new generation of positron emission tomography with computed tomography (PET-CT) was recently introduced using silicon (Si) photomultiplier (PM)-based technology. Our aim was to compare the image quality and diagnostic performance of a SiPM-based PET-CT (Discovery MI; GE Healthcare, Milwaukee, WI, USA) with a time-of-flight PET-CT scanner with a conventional PM detector (Gemini TF; Philips Healthcare, Cleveland, OH, USA), including reconstruction algorithms per vendor’s recommendations.

Methods
Imaging of the National Electrical Manufacturers Association IEC body phantom and 16 patients was carried out using 1.5 min/bed for the Discovery MI PET-CT and 2 min/bed for the Gemini TF PET-CT. Images were analysed for recovery coefficients for the phantom, signal-to-noise ratio in the liver, standardized uptake values (SUV) in lesions, number of lesions and metabolic TNM classifications in patients.

Results
In phantom, the correct (> 90%) activity level was measured for spheres ≥17 mm for Discovery MI, whereas the Gemini TF reached a correct measured activity level for the 37-mm sphere. In patient studies, metabolic TNM classification was worse using images obtained from the Discovery MI compared those obtained from the Gemini TF in 4 of 15 patients. A trend toward more malignant, inflammatory and unclear lesions was found using images acquired with the Discovery MI compared with the Gemini TF, but this was not statistically significant. Lesion-to-blood-pool SUV ratios were significantly higher in images from the Discovery MI compared with the Gemini TF for lesions smaller than 1 cm (p < 0.001), but this was not the case for larger lesions (p = 0.053). The signal-to-noise ratio in the liver was similar between platforms (p = 0.52). Also, shorter acquisition times were possible using the Discovery MI, with preserved signal-to-noise ratio in the liver.

Conclusions
Image quality was better with Discovery MI compared to conventional Gemini TF. Although no gold standard was available, the results indicate that the new PET-CT generation will provide potentially better diagnostic performance.