bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity of C4 photosynthesis pathway genes in Sorghum bicolor (L.)
Authors: Tao Yongfu , George-Jaeggli Barbara , Bouteille-Pallas Marie , Tai Shuaishuai , Cruickshank Alan , Jordan David , Mace Emma 
Published: October 2019

Abstract
Background C4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C3 and C4 species have elucidated the genetic diversity underpinning the C4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Results Here, we present the first genetic diversity survey of 8 known C4 gene families in an important C4 crop, Sorghum bicolor (L.) Moench using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C4 gene families varied more than 20-fold from the NADP-MDH gene family (θπ =0.2×10-3) to the PPDK gene family (θπ = 5.21×10-3). Genetic diversity of C4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C4 PPDK and CA genes, and balancing selection signals on C4 PPDK-RP and PEPC genes. Allelic distribution of these C4 genes was consistent with selection signals detected.Conclusions Domestication of sorghum has reshaped diversity of C4 pathway. A better understanding of the genetic diversity of this pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.
Sero-positivity and associated intrinsic and extrinsic drivers of Rift Valley fever occurrence in pastoral herds of Nigeria: A cross sectional survey
Authors: Alhaji Nma Bida , Aminu Jibrin , Lawan Mohammed Kabir , Babalobi Olutayo Olajide , Ghali-Mohammed Ibrahim , Odetokun Ismail Ayoade 
Published: October 2019

Abstract
Background: Rift Valley fever (RVF) is a vector-borne emerging zoonotic disease of animals and humans characterized by major socioeconomic losses to livestock farmers, with potential global public health threat. The study assessed herders’ existing knowledge, sero-prevalence and factors influencing the occurrence of RVF in cattle herds. Methods: A cross-sectional study using questionnaire and determination of IgM was conducted among pastoral herds. Frequencies and proportions were used for descriptive analysis. Categorical variables were presented as proportions and their associations determined by Chi-square tests. Associations were analyzed by univariable tests and multivariable logistic regressions analysis at 95% confidence level. Results: All 403 pastoralists (50.5±15.5 years) participated in this study with the majority of respondents being male, married and had no formal education. The majority of the pastoralists reported low knowledge about zoonotic RVF infections. The within-herd seropositivity of RVF in Nigeria is 5.6% which was higher under nomadic (7.4%) than agro-pastoral (3.8%) settings. All animal demographic characteristics of age, sex and breeds were not significantly (p>0.05) associated with occurrence of RVF in pastoral cattle herds. However, all the socio-ecological factors significantly (p<0.05) influenced RVF occurrence in pastoral settlements. However, availability of mosquitoes in the pastoral environments (OR=7.81; 95% CI: 4.85, 12.37), presence of rivers and streams in grazing fields (OR=10.80; 95% CI: 6.77, 17.34), high rainfall (OR=4.30; 95% CI: 2.74, 6.59), irrigated rice fields (OR=5.14; 95% CI: 3.21, 7.79) and bushy vegetation and (OR=6.11; 95% CI: 3.96, 9.43), animal movement (OR=2.2; 95% CI: 1.45, 3.25) and seasonal variations (OR=2.34; 95% CI: 1.55, 3.51) were more likely to influence RVF occurrence in pastoral herds. Conclusions: This study highlighted low levels of knowledge about RVF among surveyed pastoralists as well as socio-ecological factors contributory to RVF occurrence. This study illustrates recent circulation of RVFV in Nigeria and needs urgent interventions. This challenging gap calls for health education of these vulnerable populations on the socio-economic and health threats of RVF in the remote rural areas of developing countries, especially Africa.
Males are more sensitive to reward and less sensitive to loss than females among people with internet gaming disorder: fMRI evidence from a card-guessing task
Authors: Zhang Jialin , Hu Yan , Wang Ziliang , Du Xiaoxia , Dong Guangheng 
Published: October 2019

Abstract
Background Many studies have found an interesting issue in the Internet gaming disorder (IGD): males are always observed to be the majority. Explore why males are more vulnerable to IGD than females could help in understanding the underlying neural mechanism of IGD. Methods Data from functional magnetic resonance imaging (fMRI) were collected from 111 subjects (IGD: 29 male, 25 female; recreational gaming use (RGU): 36 male, 21 female) while they were performing a card-guessing task. We collected and compared their brain features when facing the win and loss conditions in different groups. Results For winning conditions, the gender × addiction group interaction results showed hyperactivity in the thalamus, parahippocampal gyrus and hypoactive inferior frontal gyrus (IFG) in the males with IGD relative to females. For lossing conditions, the gender × addiction group interaction results showed that compared to females with IGD, males with IGD showed decreased brain activities in the IFG and lingual gyrus. Conclusions Males and females showed opposite activation patterns in IGD degree and rewards/losses processing. And male IGD subjects are more sensitive to reward and less sensitive to loss than females, which might be the reason for the gender different rates on IGD. Keywords: Internet gaming disorder; Gender; Reward processing; Loss processing
Intraoperative electroencephalographic burst suppression may help to identify patients at risk for long-term adverse outcome: Findings from a homozygous twins case
Authors: Linassi Federico , Maran Eleonora , Kreuzer Matthias , Mazzarolo Anna Paola , Rosellini Edoardo , Zanatta Paolo , Carron Michele 
Published: October 2019

Abstract
Background: Postoperative cognitive dysfunction (POCD) presents a risk factor after general anesthesia, especially for old or cognitively impaired patients. Hence, strategies to identify possible patients at risk could help to decrease the rate of POCD. In this case report we relate the occurrence of electroencephalographic burst suppression and low bispectral indices to the development of neurocognitive decline after 12 months in one homozygous twin, whereas the other twin exhibited neither burst suppression nor neurocognitive decline. Case presentation: Two 68-year-old homozygous twins underwent the same surgical procedure with the same anesthetic regimens in comparable concentrations. For cognitive assessment, we applied a battery of neurocognitive tests at baseline (one day before surgery), at hospital discharge (three days after surgery), and 12 months after the procedure. The twins performed similarly in preoperative and discharge testing, but one twin showed worse test performance after 12 months. During surgery, we tested for possible connected consciousness by applying the isolated forearm technique (IFT). For assessment of the level of anesthesia and visual inspection of the EEG, we used the bispectral index (BIS). Neither of the twins showed signs of connected consciousness during anesthesia and the emergence tone to the return of a positive IFT response were similar. We observed lower intraoperative BIS indices for one twin. Furthermore, this twin also had two episodes of Burst Supppression. Vital parameters, particularly mean blood pressure, were stable and comparable during the entire duration of anaesthesia. The twin who exhibited Burst Suppression and lower BIS indices showed distinctly worse cognitive test scores after 12 months compared to baseline and discharge testing, indicating serious neurocognitive decline. The other twin’s cognitive performance did not decrease. Conclusions: We present findings from a unique scenario of homozygous twins with comparable lifestyles undergoing the same surgical intervention. The twin with neurocognitive decline had lower BIS values and multiple episodes of BSupp. These findings suggest that EEG monitoring under general anesthesia could help to identify frail brains that may be at increased risk of developing cognitive impairments.
Preoperative hypoalbuminemia was associated with acute kidney injury in high-risk patients following non-cardiac surgery: a retrospective cohort study
Authors: Li Nan , Qiao Hong , Guo Jing-Fei , Yang Hong-Yun , Li Xue-Ying , Li Shuangling , Wang Dong-Xin , Yang Li 
Published: October 2019

Abstract
Background:
Acute kidney injury (AKI) is a common complication following non-cardiac surgery with adverse short- and long- term morbidity and mortality. Evidence shows that hypoalbuminemia is associated with increased AKI risk in patients with infectious diseases and cancer and following cardiac surgery and transplant surgery. However, little evidence is available on non-cardiac surgery population. Thus, we investigated the association between preoperative hypoalbuminemia and AKI following non-cardiac surgery.
Methods:
We retrospectively assessed perioperative risk factors and preoperative serum albumin concentration in 729 consecutive adult patients who underwent non-cardiac surgery from July 1, 2017, to June 30, 2018. Each patient was categorized according to maximal Kidney Disease Improving Global Outcomes criteria based on creatinine changes and urine output within the first week after surgery. Multivariate Logistic regression models were used to analyze the association between preoperative hypoalbuminemia and postoperative AKI.
Results:
Of 729 patients, 188 (25.8%) developed AKI. AKI incidence was higher in patients with preoperative serum albumin <37.5 g/L than in those with preoperative serum albumin ≥37.5 g/L [35.9% (98/273) vs. 19.7% (90/456), P<0.001]. Multivariate logistic regression analysis showed that preoperative serum albumin <37.5 g/L (odds ratio 1.892; 95% confidence interval 1.238-2.891; P=0.003) was independently associated with postoperative AKI. Patients with preoperative serum albumin <37.5 g/L tended to have a higher but not significant ratio in AKI stage 2 (2.6% vs 1.1%, P=0.144) and much higher ratio in AKI stage 3 (4.8% vs 0.7%, P<0.001) than those with preoperative serum albumin ≥37.5 g/L. AKI patients had a higher in-hospital mortality rate [6.9% (13/188) vs. 0.2% (1/541), P<0.001]. Kaplan-Meier analysis revealed that the cumulative survival rate decreased with increasing AKI severity (P<0.001). Postoperative AKI was also associated with other worse outcomes, such as prolonged mechanical ventilation [53.4 (33.0, 73.8) vs 14.7 (11.1, 18.3) hours, P<0.001], intensive care unit stay [4.0 (3.1, 4.9) vs 2.0 (1.8, 2.3) days, P<0.001], postoperative hospital stay [17.8 (14.8, 20.9) vs 12.3 (11.3, 13.3) days, P<0.001], and higher total cost [13,453 (8,538, 20,228) vs 11,306 (6,277, 16,400) dollars, P<0.001].
Conclusions
Preoperative hypoalbuminemia was independently associated with AKI after non-cardiac surgery, and postoperative AKI was associated with poor outcomes.
Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis
Authors: Santos Karen Cristine Gonçalves Dos , Desgagné-Penix Isabel , Germain Hugo 
Published: October 2019

Abstract
Background: RNA sequencing allows the measuring of gene expression at a resolution unmet by expression arrays or RT-qPCR. It is however necessary to normalize sequencing data by library size, transcript size and composition, among other factors, before comparing expression levels. The use of internal control genes or spike-ins is advocated in the literature for scaling read counts, but the methods for choosing reference genes are mostly targeted at RT-qPCR studies and require a set of pre-selected candidate controls or pre-selected target genes.
Results: Here, we report an R-based script to select internal control genes based solely on read counts and gene sizes. This novel method first normalizes the read counts to Transcripts per Million (TPM) and then excludes weakly expressed genes using the DAFS script to calculate the cut-off. It then selects as references the genes with lowest TPM covariance. We used this method to pick custom reference genes for the differential expression analysis of three transcriptome sets from transgenic Arabidopsis plants expressing heterologous fungal effector proteins tagged with GFP (using GFP alone as the control). The custom reference genes showed lower covariance and fold change as well as a broader range of expression levels than commonly used reference genes. When analyzed with NormFinder, both typical and custom reference genes were considered suitable internal controls, but the expression of custom selected genes was more stable. geNorm produced a similar result in which most custom selected genes ranked higher (i.e. expression more stable) than commonly used reference genes.
Conclusions: The proposed method is innovative, rapid and simple. Since it does not depend on genome annotation, it can be used with any organism, and does not require pre-selected reference candidates or target genes that are not always available.
Escherichia Coli O157:H7: Distribution, molecular characterization, antimicrobial resistance patterns and source of contamination of sheep and goat carcasses at an export Abattoir, Mojdo, Ethiopia
Authors: Abreham Solomon , Teklu Akafete , Cox Eric , Tessema Tesfaye Sisay 
Published: October 2019

Abstract
Background : Cattle have been identified as a major reservoir of E. coli O157:H7 for human infection; the ecology of the organism in sheep and goats is less understood. This study was carried out to determine prevalence, source of infection, antibiotic resistance and molecular characterization of Escherichia coli O157: H7 isolated from sheep and goat.
Methods : Systematic random sampling was carried out at Modjo export abattoir, Ethiopia, from November 2012 to April 2013 to collect 408 samples from 72 sheep and 32 goats. Samples collected were skin swabs, fecal samples, intestinal mucosal swabs and the inside and outside part of carcasses as well as carcass in contacts such as workers hands, knife, hook and carcass washing water. Then, samples were processed following standard bacteriological procedures. Non-Sorbitol fermenting colonies were tested on latex agglutination test and the positives are subjected to PCR for detection of attaching and effacing genes ( eaeA) and shiga toxin producing genes ( stx1 and stx2 ). All E. coli O157:H7 isolates were checked for their susceptibility pattern towards 15 selected antibiotics.
Results : E. coli O157:H7 were detected in only 20/408 samples (4.9%). Among these 20 positive samples, 70% (14/20), 25% (5/20) and 5% (1/20) were from sheep, goats and knife samples, respectively. No significant associations were found between carcasses and the assumed sources of contaminations. Of all the 20 isolates virulence genes were found in 10 (50%) of them; 3 (15%) with only the eaeA gene and 7(35%) expressing eaeA and stx2 genes. All the isolates were susceptible to Norfloxacin (NOR) (100%).
Conclusions : The presence of virulence genes shows E. coli O157:H7 is a potential source of human infection in Ethiopia.
Key words : Abattoir, antibiotic sensitivity, CT-SMAC, E. coli O157:H7, IMS, Latex agglutination, multiplex PCR.
Cognitive impairments in patients with persistent symptoms attributed to Lyme disease
Authors: Berende Anneleen , Rentergem Joost Agelink van , Evers Andrea W. M. , Hofstede Hadewych J. M. ter , Vos Fidel J. , Kullberg Bart Jan , Kessels Roy P.C. 
Published: October 2019

Abstract
Background: Persistent symptoms attributed to Lyme borreliosis often include self-reported cognitive impairment. However, it remains unclear whether these symptoms can be substantiated by objective cognitive testing. Methods: For this observational study, cognitive performance was assessed in 280 adults with persistent symptoms attributed to Lyme borreliosis (as part of baseline data collected for the Dutch PLEASE study). Cognitive testing covered the five major domains: episodic memory, working memory/attention, verbal fluency, information-processing speed and executive function. Patients’ profiles of test scores were compared to a large age-, education- and sex-adjusted normative sample using multivariate normative comparison. Performance validity was assessed to detect suboptimal effort, and questionnaires were administered to measure self-reported cognitive complaints, fatigue, anxiety, depressive symptoms and several other psychological factors. Results: Of 280 patients, one was excluded as the test battery could not be completed. Of the remaining 279 patients, 239 (85.4%) displayed sufficient performance validity. Patients with insufficient performance validity felt significantly more helpless and physically fatigued, and less orientated. Furthermore, they had a lower education level and less often paid work. Of the total study cohort 5.7% (n=16) performed in the impaired range. Among the 239 patients who displayed sufficient performance validity, 2.9% (n=7) were classified as cognitively impaired. No association between subjective cognitive symptoms and objective impairment was found. Conclusions: Only a small percentage of patients with borreliosis-attributed persistent symptoms have objective cognitive impairment. Performance validity should be taken into account in neuropsychological examinations of these patients. Self-report questionnaires are insufficiently valid to diagnose cognitive impairment.
Rates and Predictors of Switching to Tenofovir alafenamide-containing ART in a nationwide cohort
Authors: Surial Bernard , Cavassini Matthias , Calmy Alexandra , Fehr Jan , Stöckle Marcel , Bernasconi Enos , Roth Bianca , Fux Christoph A. , Kovari Helen , Furrer Hansjakob , Rauch Andri , Wandeler Gilles 
Published: October 2019

Abstract
Background
Tenofovir alafenamide (TAF)-containing combinations were introduced in Switzerland after October 2016 and are recommended over tenofovir disoproxil fumarate (TDF) in patients with osteoporosis or impaired renal function.
Methods
We included all participants of the Swiss HIV Cohort Study on TDF-containing antiretroviral therapy with follow-up visits after January 2016. We determined the proportion of switches from TDF to TAF overall, and among patients with risk factors for TDF toxicity, including osteoporosis, impaired renal function or marked proteinuria. We used multivariable logistic regression to explore predictors of switching from TDF to TAF.
Results
We included 5’012 patients, of whom 652 (13.0%) had risk factors for TDF toxicity. A switch from TDF to TAF was undertaken in 2’796 (55.8%) individuals overall, and in 465 (71.3%) with risk factors. Predictors of switching to TAF were male sex (adjusted odds ratio 1.27, 95% confidence interval 1.07-1.50), age >50 years (1.43, 1.23-1.66) and the presence of risk factors for TDF toxicity (2.21, 1.77-2.75). In contrast, patients with non-nucleoside reverse transcriptase inhibitor (NNRTI)-based single-pill regimen (0.11, 0.09-0.13), those treated in non-tertiary centers (0.56, 0.46-0.70), as well as those with CD4 cell counts below 500/µL (0.77, 0.66-0.90) and with chronic hepatitis C infection (0.66, 0.54-0.80) were most likely to stay on TDF.
Conclusions
Over 50% of patients on TDF-containing therapy, including the majority of patients at risk for TDF toxicity, were switched to TAF within two years of its introduction in Switzerland. Individuals on NNRTI-based single-pill regimens were most likely to remain on TDF.
Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples
Authors: Bhagwate Aditya Vijay , Liu Yuanhang , Winham Stacey J. , McDonough Samantha J. , Stallings-Mann Melody L. , Heinzen Ethan P. , Davila Jaime I. , Vierkant Robert A. , Hoskin Tanya L. , Frost Marlene , Carter Jodi M. , Radisky Derek C. , Cunningham Julie M. , Degnim Amy , Wang Chen 
Published: October 2019

Abstract
Background: Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are sub-optimal, and resulting NGS-based genetics variant detections are prone to false positives. Evaluations of wet-lab and bioinformatics approaches are needed to optimize variant detection from FFPE samples.
Results: As a pilot study, we designed within-subject triplicate samples of DNA derived from paired FFPE and fresh frozen breast tissues to highlight FFPE-specific artifacts. For FFPE samples, we tested two FFPE DNA extraction methods to determine impact of wet-lab procedures on variant calling: QIAGEN QIAamp DNA Mini Kit ("QA"), and QIAGEN GeneRead DNA FFPE Kit ("QGR"). We also used negative-control (NA12891) and positive control samples (Horizon Discovery Reference Standard FFPE). All DNA sample libraries were prepared for NGS according to the QIAseq Human Breast Cancer Targeted DNA Panel protocol and sequenced on the HiSeq 4000. Variant calling and filtering were performed using QIAGEN Gene Globe Data Portal. Detailed variant concordance comparisons and mutational signature analysis were performed to investigate effects of FFPE samples compared to paired fresh frozen samples, along with different DNA extraction methods.
In this study, we found that five times or more variants were called with FFPE samples, compared to their paired fresh-frozen tissue samples even after applying molecular barcoding error-correction and default bioinformatics filtering recommended by the vendor. We also found that QGR as an optimized FFPE-DNA extraction approach leads to much fewer discordant variants between paired fresh frozen and FFPE samples. Approximately 92 % of the uniquely called FFPE variants were of low allelic frequency range (<5%), and collectively shared a “C>T|G>A” mutational signature known to be representative of FFPE artifacts resulting from cytosine deamination. Based on control samples and FFPE-frozen replicates, we derived an effective filtering strategy with associated empirical false-discovery estimates.
Conclusions: Through this study, we demonstrated feasibility of calling and filtering genetic variants from FFPE tissue samples using a combined strategy with molecular barcodes, optimized DNA extraction, and bioinformatics methods incorporating genomics context such as mutational signature and variant allelic frequency.