bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection
Authors: Hoque Ahasanul , Fiedler Jason D. , Rahman Mukhlesur 
Published: August 2020

AbstractBackgroundA sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6200 SNP markers.ResultsAll the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (averageH = 0.22 andI = 0.34). The pairwiseFstcomparison revealed a great degree of divergence (Fst > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 andp < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r = 0.251, 0.349 respectively andp < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance.ConclusionsTo maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest (Fst > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.
Genetic architecture and genomic selection of female reproduction traits in rainbow trout
Authors: D’Ambrosio J. , Morvezen R. , Brard-Fudulea S. , Bestin A. , Acin Perez A. , Guéméné D. , Poncet C. , Haffray P. , Dupont-Nivet M. , Phocas F. 
Published: August 2020

AbstractBackgroundRainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, to determine the genetic architecture of these traits by the identification of quantitative trait loci (QTL), and to assess the expected efficiency of a pedigree-based selection (BLUP) or genomic selection for these traits.ResultsA pedigreed population of 1343 trout were genotyped for 57,000 SNP markers and phenotyped for seven traits at 2 years of age: spawning date, female body weight before and after spawning, the spawn weight and the egg number of the spawn, the egg average weight and average diameter. Genetic parameters were estimated in multi-trait linear animal models. Heritability estimates were moderate, varying from 0.27 to 0.44. The female body weight was not genetically correlated to any of the reproduction traits. Spawn weight showed strong and favourable genetic correlation with the number of eggs in the spawn and individual egg size traits, but the egg number was uncorrelated to the egg size traits. The genome-wide association studies showed that all traits were very polygenic since less than 10% of the genetic variance was explained by the cumulative effects of the QTLs: for any trait, only 2 to 4 QTLs were detected that explained in-between 1 and 3% of the genetic variance. Genomic selection based on a reference population of only one thousand individuals related to candidates would improve the efficiency of BLUP selection from 16 to 37% depending on traits.ConclusionsOur genetic parameter estimates made unlikely the hypothesis that selection for growth could induce any indirect improvement for female reproduction traits. It is thus important to consider direct selection for spawn weight for improving egg production traits in rainbow trout breeding programs. Due to the low proportion of genetic variance explained by the few QTLs detected for each reproduction traits, marker assisted selection cannot be effective. However genomic selection would allow significant gains of accuracy compared to pedigree-based selection.
Cytosine methylations in the promoter regions of genes involved in the cellular oxidation equilibrium pathways affect rice heat tolerance
Authors: He Chao , Zhang Hong-Yu , Zhang Yong-Xin , Fu Pei , You Li-Li , Xiao Wen-Bo , Wang Zhao-Hai , Song Hai-Yan , Huang Ying-Jin , Liao Jiang-Lin 
Published: August 2020

AbstractBackgroundHigh temperatures, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that tolerate HNTs. DNA methylation may represent a potential avenue for HNT-tolerant rice strain development, as this mechanism regulates gene activity and cellular phenotype in response to adverse environmental conditions without changing the nucleotide sequence.ResultsAfter HNT exposure, the methylation patterns of cytosines in the CHH context differed noticeably between two coisogenic rice strains with significantly different levels in heat tolerance. Methylation differences between strains were primarily observed on successive cytosines in the promoter or downstream regions of transcription factors and transposon elements. In contrast to the heat-sensitive rice strain, the regions 358–359 bp and 2–60 bp downstream of two basal transcriptional factors (TFIID subunit 11andmediator of RNA polymerase II transcription subunit 31, respectively) were fully demethylated in the heat-tolerant strain after HNT exposure. In the heat-tolerant strain, HNTs reversed the methylation patterns of successive cytosines in the promoter regions of various genes involved in abscisic acid (ABA)-related reactive oxygen species (ROS) equilibrium pathways, including the pentatricopeptide repeat domain genePPR(LOC_Os07g28900) and the homeobox domain genehomeobox(LOC_Os01g19694). Indeed,PRRexpression was inhibited in heat-sensitive rice strains, and the methylation rates of the cytosines in the promoter region ofPRRwere greater in heat-sensitive strains as compared to heat-tolerant strains.ConclusionsAfter HNT exposure, cytosines in the CHH context were more likely than cytosines in other contexts to be methylated differently between the heat-sensitive and heat-tolerant rice strains. Methylation in the promoter regions of the genes associated with ABA-related oxidation and ROS scavenging improved heat tolerance in rice. Our results help to clarify the molecular mechanisms underlying rice heat tolerance.
Implications of AB0 blood group in hypertensive patients with covid-19
Authors: Sardu Celestino , Marfella Raffaele , Maggi Paolo , Messina Vincenzo , Cirillo Paolo , Codella Vinicio , Gambardella Jessica , Sardu Antonio , Gatta Gianluca , Santulli Gaetano , Paolisso Giuseppe 
Published: August 2020

AbstractBackgroundHypertension is the most frequent co-morbidity in patients with covid-19 infection, and we might speculate that a specific blood group could play a key role in the clinical outcome of hypertensive patients with covid-19.MethodsIn this prospective study, we compared 0 vs. non-0 blood group in hypertensive patients with covid-19 infection. In these patients, we evaluated inflammatory and thrombotic status, cardiac injury, and death events.ResultsPatients in non-0 (n = 92) vs. 0 blood group (n = 72) had significantly different values of activated pro-thrombin time, D-dimer, and thrombotic indexes as Von Willebrand factor and Factor VIII (p < 0.05). Furthermore, patients in non-0 vs. 0 blood group had higher rate of cardiac injury (10 (13.9%) vs. 27 (29.3%)) and death, (6 (8.3%) vs. 18 (19.6%)), (p < 0.05). At the multivariate analysis, Interleukin-6 (1.118, CI 95% 1.067–1.171) and non-0 blood group (2.574, CI 95% 1.207–5.490) were independent predictors of cardiac injury in hypertensive patients with covid-19. D-dimer (1.082, CI 95% 1.027–1.140), Interleukin-6 (1.216, CI 95% 1.082–1.367) and non-0 blood group (3.706, CI 95% 1.223–11.235) were independent predictors of deaths events in hypertensive patients with covid-19.ConclusionsTaken together, our data indicate that non-0 covid-19 hypertensive patients have significantly higher values of pro-thrombotic indexes, as well as higher rate of cardiac injury and deaths compared to 0 patients. Moreover, AB0 blood type influences worse prognosis in hypertensive patients with covid-19 infection.
BK virus-associated nephropathy in a lung transplant patient: case report and literature review
Authors: Crowhurst Thomas , Nolan James , Faull Randall , Holmes Mark , Holmes-Liew Chien-Li 
Published: August 2020

AbstractBackgroundBK virus-associated nephropathy (BKVAN) is a relatively common cause of renal dysfunction in the first six months after renal transplantation. It arises from reactivation of the latent and usually harmless BK virus (BK virus) due to immunosuppression and other factors including some that are unique to renal transplantation such as allograft injury. BKVAN is much rarer in non-renal solid organ transplantation, where data regarding diagnosis and management are extremely limited.Case presentationWe report a case of a 58-year-old man found to have worsening renal dysfunction nine months after bilateral sequential lung transplantation for chronic obstructive pulmonary disease (COPD). He had required methylprednisolone for acute allograft rejection but achieved good graft function. Urine microscopy and culture and renal ultrasound were normal. BK virus PCR was positive at high levels in urine and blood. Renal biopsy subsequently confirmed BKVAN. The patient progressed to end-stage renal failure requiring haemodialysis despite reduction in immunosuppression, including switching mycophenolate for everolimus, and the administration of intravenous immunoglobulin (IVIG).ConclusionsThis very rare case highlights the challenges presented by BK virus in the non-renal solid organ transplant population. Diagnosis can be difficult, especially given the heterogeneity with which BKV disease has been reported to present in such patients, and the optimal approach to management is unknown. Balancing reduction in immunosuppression against prevention of allograft rejection is delicate. Improved therapeutic options are clearly required.
Nasal carriage of Staphylococcus aureus in farm animals and breeders in north of Morocco
Authors: Mourabit Nadira , Arakrak Abdelhay , Bakkali Mohammed , Zian Zeineb , Bakkach Joaira , Laglaoui Amin 
Published: August 2020

Abstract
Background
The objectives of this study were to determine for the first time, in Morocco, the nasal carriage rate, antimicrobial susceptibility profiles and virulence genes of Staphylococcus. aureus isolated from animals and breeders in close contact.

Methods
From 2015 to 2016, 421 nasal swab samples were collected from 26 different livestock areas in Tangier. Antimicrobial susceptibility phenotypes were determined by disk diffusion according to EUCAST 2015. The presence of nuc, mecA, mecC, lukS/F-PV, and tst genes were determined by Polymerase Chain Reaction (PCR) for all isolates.

Results
The overall S. aureus nasal carriage rate was low in animals (9.97%) and high in breeders (60%) with a statistically significant difference, (OR = 13.536; 95% CI = 7.070–25.912; p < 0.001). In general, S. aureus strains were susceptible to the majority of antibiotics and the highest resistance rates were found against tetracycline (16.7% in animals and 10% in breeders). No Methicillin-Resistant S. aureus (MRSA) was detected in animals and breeders. A high rate of tst and lukS/F-PV genes has been recovered only from animals (11.9 and 16.7%, respectively).

Conclusion
Despite the lower rate of nasal carriage of S. aureus and the absence of MRSA strains in our study, S. aureus strains harbored a higher frequency of tst and lukS/F-PV virulence genes, which is associated to an increased risk of infection dissemination in humans. This highlights the need for further larger and multi-center studies to better define the transmission of the pathogenic S. aureus between livestock, environment, and humans.
Radiation exposure of a mobile 3D C-arm with large flat-panel detector for intraoperative imaging and navigation - an experimental study using an anthropomorphic Alderson phantom
Authors: Naseri Yashar , Hubbe Ulrich , Scholz Christoph , Brönner Johannes , Krüger Marie T. , Klingler Jan-Helge 
Published: August 2020

Abstract
Background
Intraoperative 3-dimensional (3D) navigation is increasingly being used for pedicle screw placement. For this purpose, dedicated mobile 3D C-arms are capable of providing intraoperative fluoroscopy-based 3D image data sets. Modern 3D C-arms have a large field of view, which suggests a higher radiation exposure. In this experimental study we therefore investigate the radiation exposure of a new mobile 3D C-arm with large flat-panel detector to a previously reported device with regular flat-panel detector on an Alderson phantom.

Methods
We measured the radiation exposure of the Vision RFD 3D (large 30 × 30 cm detector) while creating 3D image sets as well as standard fluoroscopic images of the cervical and lumbar spine using an Alderson phantom. The dosemeter readings were then compared with the radiation exposure of the previous model Vision FD Vario 3D (smaller 20 × 20 cm detector), which had been examined identically in advance and published elsewhere.

Results
The larger 3D C-arm induced lower radiation exposures at all dosemeter sites in cervical 3D scans as well as at the sites of eye lenses and thyroid gland in lumbar 3D scans. At ​​male and especially female gonads in lumbar 3D scans, however, the larger 3D C-arm showed higher radiation exposures compared with the smaller 3D C-arm. In lumbar fluoroscopic images, the dosemeters near/in the radiation field measured a higher radiation exposure using the larger 3D C-arm.

Conclusions
The larger 3D C-arm offers the possibility to reduce radiation exposures for specific applications despite its larger flat-panel detector with a larger field of view. However, due to the considerably higher radiation exposure of the larger 3D C-arm during lumbar 3D scans, the smaller 3D C-arm is to be recommended for short-distance instrumentations (mono- and bilevel) from a radiation protection point of view. The larger 3D C-arm with its enlarged 3D image set might be used for long instrumentations of the lumbar spine. From a radiation protection perspective, the use of the respective 3D C-arm should be based on the presented data and the respective application.
Prevalence of chronic kidney disease and its associated factors in Malaysia; findings from a nationwide population-based cross-sectional study
Authors: Saminathan Thamil Arasu , Hooi Lai Seong , Mohd Yusoff Muhammad Fadhli , Ong Loke Meng , Bavanandan Sunita , Rodzlan Hasani Wan Shakira , Tan Esther Zhao Zhi , Wong Irene , Rifin Halizah Mat , Robert Tania Gayle , Ismail Hasimah , Wong Norazizah Ibrahim , Ahmad Ghazali , Ambak Rashidah , Othman Fatimah , Abd Hamid Hamizatul Akmal , Aris Tahir 
Published: August 2020

Abstract
Background
The prevalence of chronic kidney disease (CKD) in Malaysia was 9.07% in 2011. We aim to determine the current CKD prevalence in Malaysia and its associated risk factors.

Methods
A population-based study was conducted on a total of 890 respondents who were representative of the adult population in Malaysia, i.e., aged ≥18 years old. Respondents were randomly selected using a stratified cluster method. The estimated glomerular filtration rate (eGFR) was estimated from calibrated serum creatinine using the CKD-EPI equation. CKD was defined as eGFR < 60 ml/min/1.73m2 or the presence of persistent albuminuria if eGFR ≥60 ml/min/1.73m2.

Results
Our study shows that the prevalence of CKD in Malaysia was 15.48% (95% CI: 12.30, 19.31) in 2018, an increase compared to the year 2011 when the prevalence of CKD was 9.07%. An estimated 3.85% had stage 1 CKD, 4.82% had stage 2 CKD, and 6.48% had stage 3 CKD, while 0.33% had stage 4–5 CKD. Hypertension (aOR 3.72), diabetes mellitus (aOR 3.32), increasing BMI (aOR 1.06), and increasing age (aOR 1.06) were significantly associated with CKD.

Conclusion
Our study has shown that CKD has become one of the leading public health issues in Malaysia. Thus, there is an urgent need to screen for CKD and prevent its progression, associated morbidity, and mortality at the national level.
Clinical and genetic characteristics of autosomal recessive polycystic kidney disease in Oman
Authors: Al Alawi Intisar , Molinari Elisa , Al Salmi Issa , Al Rahbi Fatma , Al Mawali Adhra , Sayer John A. 
Published: August 2020

Abstract
Background
There is a high prevalence of rare genetic disorders in the Middle East, and their study provides unique clinical and genetic insights. Autosomal recessive polycystic kidney disease (ARPKD) is one of the leading causes of kidney and liver-associated morbidity and mortality in Oman. We describe the clinical and genetic profile of cohort of ARPKD patients.

Methods
We studied patients with a clinical diagnosis of ARPKD (n = 40) and their relatives (parents (n = 24) and unaffected siblings (n = 10)) from 32 apparently unrelated families, who were referred to the National Genetic Centre in Oman between January 2015 and December 2018. Genetic analysis of PKHD1 if not previously known was performed using targeted exon PCR of known disease alleles and Sanger sequencing.

Results
A clinical diagnosis of ARPKD was made prenatally in 8 patients, 21 were diagnosed during infancy (0–1 year), 9 during early childhood (2–8 years) and 2 at later ages (9–13 years). Clinical phenotypes included polycystic kidneys, hypertension, hepatic fibrosis and splenomegaly. Twenty-four patients had documented chronic kidney disease (median age 3 years). Twenty-four out of the 32 families had a family history suggesting an autosomal recessive pattern of inherited kidney disease, and there was known consanguinity in 21 families (66%). A molecular genetic diagnosis with biallelic PKHD1 mutations was known in 18 patients and newly identified in 20 other patients, totalling 38 patients from 30 different families. Two unrelated patients remained genetically unsolved. The different PKHD1 missense pathogenic variants were: c.107C > T, p.(Thr36Met); c.406A > G, p.(Thr136Ala); c.4870C > T, p.(Arg1624Trp) and c.9370C > T, p.(His3124Tyr) located in exons 3, 6, 32 and 58, respectively. The c.406A > G, p.(Thr136Ala) missense mutation was detected homozygously in one family and heterozygously with a c.107C > T, p.(Thr36Met) allele in 5 other families. Overall, the most commonly detected pathogenic allele was c.107C > T; (Thr36Met), which was seen in 24 families.

Conclusions
Molecular genetic screening of PKHD1 in clinically suspected ARPKD cases produced a high diagnostic rate. The limited number of PKHD1 missense variants identified in ARPKD cases suggests these may be common founder alleles in the Omani population. Cost effective targeted PCR analysis of these specific alleles can be a useful diagnostic tool for future cases of suspected ARPKD in Oman.
Rural-urban differences in the mental health of perinatal women: a UK-based cross-sectional study
Authors: Ginja Samuel , Jackson Katherine , Newham James J. , Henderson Emily J. , Smart Debbie , Lingam Raghu 
Published: August 2020

AbstractBackgroundInternational data suggest that living in a rural area is associated with an increased risk of perinatal mental illness. This study tested the association between rurality and risk for two mental illnesses prevalent in perinatal women - depression and anxiety.MethodsUsing a cross-sectional design, antenatal and postnatal women were approached by healthcare professionals and through other networks in a county in Northern England (UK). After providing informed consent, women completed a questionnaire where they indicated their postcode (used to determine rural-urban status) and completed three outcome measures: the Edinburgh Postnatal Depression Scale (EPDS), the Whooley questions (depression measure), and the Generalised Anxiety Disorder 2-item (GAD-2). Logistic regression models were developed, both unadjusted and adjusted for potential confounders, including socioeconomic status, social support and perinatal stage.ResultsTwo hundred ninety-five participants provided valid data. Women in rural areas (n = 130) were mostly comparable to their urban counterparts (n = 165). Risk for depression and/or anxiety was found to be higher in the rural group across all models: unadjusted OR 1.67 (0.42) 95% CI 1.03 to 2.72,p = .038. This difference though indicative did not reach statistical significance after adjusting for socioeconomic status and perinatal stage (OR 1.57 (0.40), 95% CI 0.95 to 2.58,p = .078), and for social support (OR 1.65 (0.46), 95% CI 0.96 to 2.84,p = .070).ConclusionsData suggested that women in rural areas were at higher risk of depression and anxiety than their urban counterparts. Further work should be undertaken to corroborate these findings and investigate the underlying factors. This will help inform future interventions and the allocation of perinatal services to where they are most needed.