bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-centre experience of an early cannulation graft for haemodialysis access
Authors: Sutaria Rupesh , Gilbert James A 
Published: March 2020

Introduction: As the demographics of the population changes, increasing challenges are being faced in providing reliable access for dialysis. This article reports on the outcomes from the largest series to date using the early cannulation graft Flixene in a single centre. Methods: Between May 2012 and March 2018, 141 Flixene grafts were placed for dialysis access. The outcomes of the arteriovenous grafts were reviewed retrospectively from electronically held records and imaging. Results: In 75 patients, placement of Flixene graft was performed on an emergency basis and in 66 patients on a planned elective list. The 12-month primary, assisted primary and secondary patency rates were 48.7%, 56.6% and 83.6%, respectively. Eight (5.7%) patients developed infections of the graft during the follow-up period. Conclusion: In our experience, we have found the use of the early cannulation graft Flixene to be safe with a low complication rate and favourable patency rates. We believe these early cannulation grafts provide a useful addition for vascular access surgeons preventing the use of tunnelled lines and providing more flexibility in the timing of placing a graft for dialysis.
Adherence to laboratory monitoring among people taking oral drugs for multiple sclerosis: A Canadian population-based study
Authors: Ng Huah Shin , Kingwell Elaine , Zhu Feng , Zhang Tingting , Marrie Ruth Ann , Carruthers Robert , Tremlett Helen 
Published: March 2020

Objective: To examine laboratory testing adherence by persons initiating an oral disease-modifying therapy (DMT) for multiple sclerosis (MS). Methods: Population-based health administrative and laboratory data were accessed in British Columbia, Canada, to identify everyone filling their first prescription for dimethyl fumarate (DMF), fingolimod or teriflunomide (2011–2015). The proportion of people adherent to each drug monograph’s recommended laboratory monitoring schedule, pre- and on-DMT, was estimated. The association between patient characteristics and adherence was examined using multivariable logistic regression. Results: A total of 1016 people were included (DMF 567, fingolimod 253 and teriflunomide 196). The proportions of people adherent to pre-DMT liver and lymphocyte tests ranged from 88% to 91% and 91% to 94%, respectively, while 77% adhered to pre-DMF urinalysis. Adherence to the first on-DMT liver test was 89% for DMF (within 6 months), 61% for fingolimod (within 3 months) and 40% for teriflunomide (within 1 month). Men were less likely than women to have pre-DMF urinalysis (adjusted odds ratio (aOR); 95% confidence interval (CI): 0.40–0.95) or on-DMF liver (aOR: 0.46; 95% CI: 0.23–0.95) or lymphocyte (aOR: 0.47; 95% CI: 0.22–0.98) tests. Conclusions: Adherence to recommended laboratory testing was high (>77%) before oral DMT initiation, but lower once on drug. There is a need to understand the long-term consequences of suboptimal laboratory monitoring and sex differences in the DMT-treated MS population.
Dual VEGF inhibition with sorafenib and bevacizumab as salvage therapy in metastatic colorectal cancer: results of the phase II North Central Cancer Treatment Group study N054C (Alliance)
Authors: Xie Hao , Lafky Jacqueline M. , Morlan Bruce W. , Stella Philip J. , Dakhil Shaker R. , Gross Gerald G. , Loui William S. , Hubbard Joleen M. , Alberts Steven R. , Grothey Axel 
Published: March 2020

Background: Bevacizumab (BEV), a monoclonal antibody against vascular endothelial growth factor-A (VEGF-A), is a standard component of medical therapy of metastatic colorectal cancer (mCRC). Activation of alternative angiogenesis pathways has been implicated in resistance to BEV. This phase II study examines the activity of combined vertical blockade of VEGF signaling with sorafenib and BEV as salvage therapy in patients with progressive disease (PD) on all standard therapy in mCRC. Methods: mCRC patients with documented PD on standard therapy, received sorafenib (200 mg orally twice daily, days 1–5 and 8–12) and BEV (5 mg/kg intravenously, day 1) every 2 weeks. Primary endpoint was 3-month progression-free survival (PFS) rate and secondary endpoints were overall survival (OS), response rate (RR), safety, and feasibility. Results: Of the 83 patients enrolled, 79 were evaluable. Of these, 42 (53%) were progression-free at 3 months. Median PFS was 3.5 months and median OS was 8.3 months. One patient had a partial response and 50 patients (63.3%) had at least one stable tumor assessment. Of 79 evaluable patients, 54 (68%) experienced grade 3/4 adverse events (AEs) at least possibly related to treatment. Most frequent grade 3/4 AEs were: fatigue (24.1%), hypertension (16.5%), elevated lipase (8.9%), hand-foot skin reaction (8.9%), diarrhea (7.6%), and proteinuria (7.6%). Reasons for treatment discontinuation were PD (72%), AEs (18%), patient refusal (8%), physician decision (1%), and death (1%). Conclusions: The combination of BEV and sorafenib as salvage therapy in heavily pretreated mCRC patients is tolerable and manageable, with evidence of promising activity. ClinicalTrials.gov identifier: NCT00826540, URL: http://clinicaltrials.gov/ct2/show/NCT00826540
PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data
Authors: Zhang Jianbo , Panthee Dilip R. 
Published: March 2020

Abstract
Background
Bulked segregant analysis (BSA), coupled with next-generation sequencing, allows the rapid identification of both qualitative and quantitative trait loci (QTL), and this technique is referred to as BSA-Seq here. The current SNP index method and G-statistic method for BSA-Seq data analysis require relatively high sequencing coverage to detect significant single nucleotide polymorphism (SNP)-trait associations, which leads to high sequencing cost.

Results
We developed a simple and effective algorithm for BSA-Seq data analysis and implemented it in Python; the program was named PyBSASeq. Using PyBSASeq, the significant SNPs (sSNPs), SNPs likely associated with the trait, were identified via Fisher’s exact test, and then the ratio of the sSNPs to total SNPs in a chromosomal interval was used to detect the genomic regions that condition the trait of interest. The results obtained this way are similar to those generated via the current methods, but with more than five times higher sensitivity. This approach was termed the significant SNP method here.

Conclusions
The significant SNP method allows the detection of SNP-trait associations at much lower sequencing coverage than the current methods, leading to ~ 80% lower sequencing cost and making BSA-Seq more accessible to the research community and more applicable to the species with a large genome.
Phenology-dependent cold exposure and thermal performance of Ostrinia nubilalis ecotypes
Authors: Wadsworth Crista B. , Okada Yuta , Dopman Erik B. 
Published: March 2020

AbstractBackgroundUnderstanding adaptation involves establishing connections between selective agents and beneficial population responses. However, relatively little attention has been paid to seasonal adaptation, in part, because it requires complex and integrative knowledge about seasonally fluctuating environmental factors, the effects of variable phenology on exposure to those factors, and evidence for temporal specialization. In the European corn borer moth,Ostrinia nubilalis, sympatric pheromone strains exploit the same host plant (Zea mays) but may genetically differ in phenology and be reproductively “isolated by time.” Z strain populations in eastern North America have been shown to have a prolonged larval diapause and produce one annual mating flight (July), whereas E strain populations complete an earlier (June) and a later (August) mating flight by shortening diapause duration. Here, we find evidence consistent with seasonal “adaptation by time” between these ecotypes.ResultsWe use 12 years of field observation of adult seasonal abundance to estimate phenology of ecotype life cycles and to quantify life-stage specific climatic conditions. We find that the observed reduction of diapause duration in the E strain leads their non-diapausing, active life stages to experience a ~ 4 °C colder environment compared to the equivalent life stages in the Z strain. For a representative pair of populations under controlled laboratory conditions, we compare life-stage specific cold tolerance and find non-diapausing, active life stages in the E strain have as much as a 60% greater capacity to survive rapid cold shock. Enhanced cold hardiness appears unrelated to life-stage specific changes in the temperature at which tissues freeze.ConclusionsOur results suggest that isolation by time and adaptation by time may both contribute to population divergence, and they argue for expanded study in this species of allochronic populations in nature experiencing the full spectrum of seasonal environments. Cyclical selective pressures are inherent properties of seasonal habitats. Diverse fluctuating selective agents across each year (temperature, predation, competition, precipitation, etc.) may therefore be underappreciated drivers of biological diversity.
Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil
Authors: Klonowska Agnieszka , Moulin Lionel , Ardley Julie Kaye , Braun Florence , Gollagher Margaret Mary , Zandberg Jaco Daniel , Marinova Dora Vasileva , Huntemann Marcel , Reddy T. B. K. , Varghese Neha Jacob , Woyke Tanja , Ivanova Natalia , Seshadri Rekha , Kyrpides Nikos , Reeve Wayne Gerald 
Published: March 2020

Abstract
Background
Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems.

Results
The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance.

Conclusions
STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
Positive staining of the immunoligand B7-H6 in abnormal/transformed keratinocytes consistently accompanies the progression of cervical cancer
Authors: Gutierrez-Silerio Gloria Yareli , Franco-Topete Ramon Antonio , Haramati Jesse , Navarrete-Medina Eduardo Miguel , Gutierrez-Franco Jorge , Bueno-Topete Miriam Ruth , Bastidas-Ramirez Blanca Estela , Ramos-Marquez Martha Eloisa , del Toro-Arreola Susana 
Published: March 2020

Abstract
Background
B7-H6 has been revealed as an endogenous immunoligand expressed in a variety of tumors, but not expressed in healthy tissues. Heretofore, no studies have been reported describing B7-H6 in women with cervical cancer. To investigate this question, our present study was conducted.

Results
This retrospective study comprised a total of 62 paraffinized cervical biopsies, which were distributed in five groups: low-grade squamous intraepithelial lesions (LSIL), high-grade squamous intraepithelial lesions (HSIL), squamous cervical carcinoma (SCC), uterine cervical adenocarcinoma (UCAC), and a group of cervicitis (as a control for non-abnormal/non-transformed cells). Cervical sections were stained by immunohistochemistry to explore the expression of B7-H6, which was reported according to the immunoreactive score (IRS) system. We observed a complete lack of B7-H6 in LSIL abnormal epithelial cells. Interestingly, B7-H6 began to be seen in HSIL abnormal epithelial cells; more than half of this group had B7-H6 positive cells, with staining characterized by a cytoplasmic and membranous pattern. B7-H6 in the SCC group was also seen in the majority of the sections, showing the same cytoplasmic and membranous pattern. Strong evidence of B7-H6 was notably found in UCAC tumor columnar cells (in 100% of the specimens, also with cytoplasmic and membranous pattern). Moreover, consistent B7-H6 staining was observed in infiltrating plasma cells in all groups.

Conclusions
B7-H6 IRS positively correlated with disease stage in the development of cervical cancer; additionally, B7-H6 scores were found to be even higher in the more aggressive uterine cervical adenocarcinoma, suggesting a possible future therapeutic target for this cancer type.
Influence of exogenous ascorbic acid and glutathione priming on mitochondrial structural and functional systems to alleviate aging damage in oat seeds
Authors: Xia Fangshan , Cheng Hang , Chen Lingling , Zhu Huisen , Mao Peisheng , Wang Mingya 
Published: March 2020

AbstractBackgroundLoss of vigor caused by seed aging adversely affects agricultural production under natural conditions. However, priming is an economical and effective method for improving the vigor of aged seeds. The objective of this study was to test the effectiveness of exogenous ascorbic acid (ASC) and glutathione (GSH) priming in the repairing of aged oat (Avena sativa) seeds, and to test the hypothesis that structural and functional systems in mitochondria were involved in this process.ResultsOat seeds were artificially aged for 20 days at 45 °C, and were primed with solutions (1 mmol L− 1) of ASC, GSH, or ASC + GSH at 20 °C for 0.5 h before or after their aging. Seed germination, antioxidant enzymes in the ASC-GSH cycle, cytochrome c oxidase (COX) and mitochondrial malate dehydrogenase (MDH) activities, and the mitochondrial ultrastructures of the embryonic root cells were markedly improved in aged oat seeds through post-priming with ASC, GSH, or ASC + GSH, while their malondialdehyde and H2O2contents decreased significantly (P < 0.05).ConclusionOur results suggested that priming with ASC, GSH, or ASC + GSH after aging could effectively alleviate aging damage in oat seeds, and that the role of ASC was more effective than GSH, but positive effects of post-priming with ASC and GSH were not superior to post-priming with ASC in repairing aging damage of aged oat seeds. However, pre-priming with ASC, GSH, or ASC + GSH was not effective in oat seeds, suggesting that pre-priming with ASC, GSH, or ASC + GSH could not inhibit the occurrence of aging damage in oat seeds.
Intestinal flora imbalance affects bile acid metabolism and is associated with gallstone formation
Authors: Wang Qiang , Hao Chenjun , Yao Wenchao , Zhu Defu , Lu Haifeng , Li Long , Ma Biao , Sun Bei , Xue Dongbo , Zhang Weihui 
Published: March 2020

AbstractBackgroundThe gut microbiota participates in the metabolism of substances and energy, promotes the development and maturation of the immune system, forms the mucosal barrier, and protects the host from pathogen attacks. Although the pathogenesis of cholesterol gallstones is still not clear, studies have suggested that gut microbiota dysbiosis plays an important role in their formation.MethodsMicrobial DNA from faeces of normal control patients and those of patients with calculi was subjected to 16S rRNA gene sequencing to detect gene expression changes in intestinal microbes. ELISA kits were used to measure free bile acids, secondary bile acids and coprostanol according to the manufacturer’s instructions. The relationship between flora and their metabolites was then analysed.ResultsIn the gallstone group, the diversity of intestinal bacteria and the abundances of certain phylogroups were significantly decreased (p < 0.05), especiallyFirmicutes(p < 0.05), the largest phylum represented by the gut microbiota. This study found an increase in free bile acids (p < 0.001) and secondary bile acids (p < 0.01) in the enterohepatic circulation. Bile salt hydrolase activity was not related to the abundances of BSH-active bacteria. 7a-dehydroxylating gut bacteria were significantly increased (p < 0.01), whereas cholesterol-lowering bacteria were significantly reduced (p < 0.05). TheRuminococcus gnavusgroup could be used as a biomarker to distinguish the gallstone group from the control group.ConclusionWe conclude that intestinal flora imbalance affects bile acid and cholesterol metabolism and is associated with gallstone formation.
Pre-frailty factors in community-dwelling 40–75 year olds: opportunities for successful ageing
Authors: Gordon S. J. , Baker N. , Kidd M. , Maeder A. , Grimmer K. A. 
Published: March 2020

Abstract
Background
There is little known about pre-frailty attributes or when changes which contribute to frailty might be detectable and amenable to change. This study explores pre-frailty and frailty in independent community-dwelling adults aged 40–75 years.

Methods
Participants were recruited through local council networks, a national bank and one university in Adelaide, Australia. Fried frailty phenotype scores were calculated from measures of unintentional weight loss, exhaustion, low physical activity levels, poor hand grip strength and slow walking speed. Participants were identified as not frail (no phenotypes), pre-frail (one or two phenotypes) or frail (three or more phenotypes). Factor analysis was applied to binary forms of 25 published frailty measures Differences were tested in mean factor scores between the three Fried frailty phenotypes and ROC curves estimated predictive capacity of factors.

Results
Of 656 participants (67% female; mean age 59.9 years, SD 10.6) 59.2% were classified as not frail, 39.0% pre-frail and 1.8% frail. There were no gender or age differences. Seven frailty factors were identified, incorporating all 25 frailty measures. Factors 1 and 7 significantly predicted progression from not-frail to pre-frail (Factor 1 AUC 0.64 (95%CI 0.60–0.68, combined dynamic trunk stability and lower limb functional strength, balance, foot sensation, hearing, lean muscle mass and low BMI; Factor 7 AUC 0.55 (95%CI 0.52–0.59) comprising continence and nutrition. Factors 3 and 4 significantly predicted progression from pre-frail to frail (Factor 3 AUC 0.65 (95% CI 0.59–0.70)), combining living alone, sleep quality, depression and anxiety, and lung function; Factor 4 AUC 0.60 (95%CI 0.54–0.66) comprising perceived exertion on exercise, and falls history.

Conclusions
This research identified pre-frailty and frailty states in people aged in their 40s and 50s. Pre-frailty in body systems performance can be detected by a range of mutable measures, and interventions to prevent progression to frailty could be commenced from the fourth decade of life.
Epidemiological changes in measles infections in southern China between 2009 and 2016: a retrospective database analysis
Authors: Zheng Huizhen , Jia Katherine Min , Sun Riyang , Hu Pui , Wang Maggie Haitian , Zee Benny Chung-Ying , Liang Wenjia , Chong Ka Chun 
Published: March 2020

Abstract
Background
The incidence rate of measles in China reached a nadir in 2012 after 2 supplementary immunization activities (SIAs) were undertaken in 2009 and 2010. However, the disease began re-emerging in 2013, with a high prevalence rate observed in 2013–2014 in the southern province of Guangdong. In this study, we assessed the changes that occurred in measles epidemiology during 2009–2016, particularly between 2009 and 2011 (when the influence of the SIAs were in full effect) and between 2012 and 2016 (when this influence subsided).

Methods
Data from 22,362 patients with measles diagnosed between 2009 and 2016, and whose diagnoses were confirmed clinically and/or with laboratory testing, were extracted from the National Infectious Disease Monitoring Information System. Descriptive analyses were performed, and changes in epidemiological characteristics between 2009 and 2011 and 2012–2016 were compared.

Results
There was a substantial surge in 0–8-month-old patients after 2012; the incidence rate increased from 4.0 per 100,000 population in 2011 (10.3% of the total) to 280 per 100,000 population in 2013 (32.8% of the total). Patients aged 0–6 years represented 73.4% of the total increase between 2011 and 2013. Compared with 2009–2011, adults aged ≥25 years accounted for a higher proportion of patients in 2013 and after (p < 0.01), and were highest in 2016 (31% of the patient total).

Conclusion
Despite the remarkable results achieved by SIAs in terms of providing herd immunity, the 2013 resurgence of measles revealed insufficient immunization coverage among children. Therefore routine immunization programs should be strengthened, and supplementary vaccinations targeting adults should also be contemplated.