bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting horizontal gene transfer: a probabilistic approach
Authors: Sevillya Gur , Adato Orit , Snir Sagi 
Published: March 2020

Abstract
Background
Horizontal gene transfer (HGT) is the event of a DNA sequence being transferred between species not by inheritance. HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic novelty resulting in antibiotic resistance or the outbreak of virulent strains. Detection of HGT and the mechanisms responsible and enabling it, is hence of prime importance.Existing algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from its recipient genome. Closely related species pose an even greater challenge as most genes are very similar and therefore, the phylogenetic signal is weak anyhow. Notwithstanding, the importance of detecting HGT between such organisms is extremely high for the role of HGT in the emergence of new highly virulent strains.

Results
In a recent work we devised a novel technique that relies on loss of synteny around a gene as a witness for HGT. We used a novel heuristic for synteny measurement, SI (Syntent Index), and the technique was tested on both simulated and real data and was found to provide a greater sensitivity than other HGT techniques. This synteny–based approach suffers low specificity, in particular more closely related species. Here we devise an adaptive approach to cope with this by varying the criteria according to species distance. The new approach is doubly adaptive as it also considers the lengths of the genes being transferred. In particular, we use Chernoff bound to decree HGT both in simulations and real bacterial genomes taken from EggNog database.

Conclusions
Here we show empirically that this approach is more conservative than the previous χ2 based approach and provides a lower false positive rate, especially for closely related species and under wide range of genome parameters.
Gene expression analysis reveals the tipping points during infant brain development for human and chimpanzee
Authors: Tang Hui , Tang Ying , Zeng Tao , Chen Luonan 
Published: March 2020

Abstract
Background
Postpartum developmental delay has been proposed as an important phenotype of human evolution which contributes to many human-specific features including the increase in brain size and the advanced human-specific cognitive traits. However, the biological processes and molecular functions underlying early brain development still remain poorly understood, especially in human and primates.

Results
In this paper, we comparatively and extensively studied dorsolarteral prefrontal cortex expression data in human and chimpanzee to investigate the critical processes or biological events during early brain development at a molecular level. By using the dynamic network biomarker (DNB) model, we found that there are tipping points around 3 months and 1 month, which are crucial periods in infant human and chimpanzee brain development, respectively. In particular, we shown that the human postnatal development and the corresponding expression changes are delayed 3 times relative to chimpanzee, and we also revealed that many common biological processes are highly involved in those critical periods for both human and chimpanzee, e.g., physiological system development functions, nervous system development, organismal development and tissue morphology. These findings support that the maximal rates of brain growth will be in those two critical periods for respective human and primates. In addition, different from chimpanzee, our analytic results also showed that human can further develop a number of advanced behavior functions around this tipping point (around 3 months), such as the ability of learning and memory.

Conclusion
This work not only provides biological insights into primate brain development at a molecular level but also opens a new way to study the criticality of nonlinear biological processes based on the observed omics data.
Genome-wide identification of loci associated with growth in rainbow trout
Authors: Ali Ali , Al-Tobasei Rafet , Lourenco Daniela , Leeds Tim , Kenney Brett , Salem Mohamed 
Published: March 2020

AbstractBackgroundGrowth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully explored in rainbow trout.ResultsA previously developed 50 K gene-transcribed SNP chip, containing ~ 21 K SNPs showing allelic imbalances potentially associated with important aquaculture production traits including body weight, muscle yield, was used for genotyping a total of 789 fish with available phenotypic data for bodyweight gain. Genotyped fish were obtained from two consecutive generations produced in the NCCCWA growth-selection breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform a genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with bodyweight gain. Using genomic sliding windows of 50 adjacent SNPs, 247 SNPs associated with bodyweight gain were identified. SNP-harboring genes were involved in cell growth, cell proliferation, cell cycle, lipid metabolism, proteolytic activities, chromatin modification, and developmental processes. Chromosome 14 harbored the highest number of SNPs (n = 50). An SNP window explaining the highest additive genetic variance for bodyweight gain (~ 6.4%) included a nonsynonymous SNP in a gene encoding inositol polyphosphate 5-phosphatase OCRL-1. Additionally, based on a single-marker GWA analysis, 33 SNPs were identified in association with bodyweight gain. The highest SNP explaining variation in bodyweight gain was identified in a gene coding for thrombospondin-1 (THBS1) (R2 = 0.09).ConclusionThe majority of SNP-harboring genes, including OCRL-1 and THBS1, were involved in developmental processes. Our results suggest that development-related genes are important determinants for growth and could be prioritized and used for genomic selection in breeding programs.
Multi-locus phylogeny and taxonomy of an unresolved, heterogeneous species complex within the genus Golovinomyces (Ascomycota, Erysiphales), including G. ambrosiae, G. circumfusus and G. spadiceus
Authors: Qiu Peng-Lei , Liu Shu-Yan , Bradshaw Michael , Rooney-Latham Suzanne , Takamatsu Susumu , Bulgakov Timur S. , Tang Shu-Rong , Feng Jing , Jin Dan-Ni , Aroge Temitope , Li Yu , Wang Li-Lan , Braun Uwe 
Published: March 2020

Abstract
Background
Previous phylogenetic analyses of species within the genus Golovinomyces (Ascomycota, Erysiphales), based on ITS and 28S rDNA sequence data, revealed a co-evolutionary relationship between powdery mildew species and hosts of certain tribes of the plant family Asteraceae. Golovinomyces growing on host plants belonging to the Heliantheae formed a single lineage, comprised of a morphologically differentiated complex of species, which included G. ambrosiae, G. circumfusus, and G. spadiceus. However, the lineage also encompassed sequences retrieved from Golovinomyces specimens on other Asteraceae tribes as well as other plant families, suggesting the involvement of a plurivorous species. A multilocus phylogenetic examination of this complex, using ITS, 28S, IGS (intergenic spacer), TUB2 (beta-tubulin), and CHS1 (chitin synthase I) sequence data was carried out to clarify the discrepancies between ITS and 28S rDNA sequence data and morphological differences. Furthermore, the circumscription of species and their host ranges were emended.

Results
The phylogenetic and morphological analyses conducted in this study revealed three distinct species named, viz., (1) G. ambrosiae emend. (including G. spadiceus), a plurivorous species that occurs on a multitude of hosts including, Ambrosia spp., multiple species of the Heliantheae and plant species of other tribes of Asteraceae including the Asian species of Eupatorium; (2) G. latisporus comb. nov. (≡ Oidium latisporum), the closely related, but morphologically distinct species confined to hosts of the Heliantheae genera Helianthus, Zinnia, and most likely Rudbeckia; and (3) G. circumfusus confined to Eupatorium cannabinum in Europe.

Conclusions
The present results provide strong evidence that the combination of multi-locus phylogeny and morphological analysis is an effective way to identify species in the genus Golovinomyces.
Novel myocardial markers GADD45G and NDUFS5 identified by RNA-sequencing predicts left ventricular reverse remodeling in advanced non-ischemic heart failure: a retrospective cohort study
Authors: Iwahana Togo , Okada Sho , Kanda Masato , Oshima Motohiko , Iwama Atsushi , Matsumiya Goro , Kobayashi Yoshio 
Published: March 2020

Abstract
Background
Left ventricular reverse remodeling (LVRR) has been detected in non-ischemic dilated cardiomyopathy (NIDCM) patients following optimal treatment. However, its prediction with only conventional modalities is often difficult. This study sought to examine whether RNA sequencing (RNA-seq) of myocardium tissue samples could predict LVRR in NIDCM.

Methods
A total of 17 advanced NIDCM patients with left ventricular ejection fraction (LVEF) below 30% who underwent cardiac biopsy from Left ventricle (LV) were prospectively recruited. They received optimal treatment and followed with echocardiogram every 6 months. Based on LVRR status after 12 months of treatment, patients were divided into the reverse remodeling (RR) or non-RR group. Tissue samples were analyzed by RNA-seq, and a functional analysis of differentially expressed genes was carried out.

Results
There were eight and nine patients in the RR and non-RR groups, respectively. No difference was found in age, sex, disease duration, LV end-diastolic diameter, and LVEF between the two groups. There were 155 genes that were differentially expressed between the two groups. Nicotinamide adenine dinucleotide ubiquinone oxidoreductase subunit (NDUF)S5 and Growth arrest and DNA-damage-inducible protein (GADD)45G, along with several genes related to the mitochondrial respiratory chain and ribosome, were significantly downregulated in the RR as compared to the non-RR group.

Conclusion
GADD45G and NDUFS5 are potential biomarkers for LVRR in patients with advanced NIDCM.
Recombinant Klotho protein enhances cholesterol efflux of THP-1 macrophage-derived foam cells via suppressing Wnt/β-catenin signaling pathway
Authors: Liu Wei , Chen Xiujuan , Wu Min , Li Lin , Liu Jiani , Shi Jing , Hong Tian 
Published: March 2020

Abstract
Background
Atherosclerosis (AS) is the basis of cardiovascular diseases, characterized by chronic inflammatory and lipid metabolism disorders. Although the anti-inflammatory effect of Klotho in AS has been clearly shown, its lipid-lowering effect is unclear. In this study, we examined the effects of recombinant Klotho (Re-KL) protein on lipid accumulation in foam cells.

Methods
THP-1 cells were exposed to 100 nM phorbol myristate acetate for 24 h and then to oxidized low-density lipoprotein (ox-LDL; 80 mg/mL) to induce foam cell formation. Subsequently, the foam cells were incubated with Re-KL and/or DKK1, an inhibitor of the Wnt/β-catenin pathway.

Results
Oil red O staining and cholesterol intake assay revealed that the foam cell model was constructed successfully. Pre-treatment of the foam cells with Re-KL decreased total cholesterol level, up-regulated the expression of ATP binding cassette transporter A1 (ABCA1) and G1 (ABCG1), and down-regulated the expression of acyl coenzyme a-cholesterol acyltransferase 1 (ACAT1) and members of the scavenger family (SR-A1 and CD36). In addition, the expression of Wnt/β-catenin pathway-related proteins in foam cells was significantly decreased by the stimulus of Re-KL. Interestingly, the effect of Re-KL was similar to that of DKK1 on foam cells.

Conclusions
The Re-KL-induced up-regulation of reverse cholesterol transport capacity promotes cholesterol efflux and reduces lipid accumulation by suppressing the Wnt/β-catenin pathway in foam cells.
Identifying long-term psychological distress from single measures: evidence from a nationally representative longitudinal survey of the Australian population
Authors: Welsh J. , Korda R. J. , Banks E. , Strazdins L. , Joshy G. , Butterworth P. 
Published: March 2020

AbstractBackgroundSingle time-point assessments of psychological distress are often used to indicate chronic mental health problems, but the validity of this approach is unclear. The aims of this study were to investigate how a single assessment of distress relates to longer-term assessment and quantify misclassification from using single measures to indicate chronic distress.MethodsData came from the Household, Income and Labour Dynamics in Australia Survey, a nationally representative study of Australian adults. Psychological distress, measured with the Kessler10 and categorised into low (scores:10- < 12), mild (12- < 16), moderate (16- < 22) and high (22–50), has been assessed in the Survey biennially since wave 7. Among respondents who were aged ≥25 years and participated in all waves in which distress was measured, we describe agreement in distress categories, and using a mixed linear model adjusting for age and sex we estimate change in scores, over a two-, four-, six- and eight-year follow-up period. We applied weights, benchmarked to the Australian population, to all analyses.ResultsTwo-years following initial assessment, proportions within identical categories of distress were 66.0% for low, 54.5% for mild, 44.0% for moderate and 50.3% for high, while 94.1% of those with low distress initially had low/mild distress and 81.4% with high distress initially had moderate/high distress. These patterns did not change materially as follow-up time increased. Over the full eight-year period, 77.3% of individuals with high distress initially reported high distress on ≥1 follow-up occasion. Age-and sex- adjusted change in K10 scores over a two-year period was 1.1, 0.5, − 0.7 and − 4.9 for low, mild, moderate and high distress, respectively, and also did not change materially as follow-up time increased.ConclusionIn the absence of repeated measures, single assessments are useful proxies for chronic distress. Our estimates could be used in bias analyses to quantify the magnitude of the bias resulting from use of single assessments to indicate chronic distress.
False positive finding from malignancy-like lesions on FDG PET/CT: case report of tuberculosis patients
Authors: Hutomo Febby , Yudistiro Ryan , Mulyanto Ivana Dewi , Budiawan Hendra 
Published: March 2020

Abstract
Background
The F-18 fluorodeoxyglucose positron emission/computed tomography (FDG PET/CT) has become an established diagnostic imaging for malignancy. However, there are other diseases that can also be identified with FDG, some of them are infections such as tuberculosis.

Case presentation
In this case report, two patients showed multiple hypermetabolic tuberculosis lesions on FDG PET/CT, with one of the patients having history of malignancy. The objective of the present case report is to emphasize the need to use other differential diagnosis techniques for tuberculosis especially in tuberculosis-endemic countries when interpreting FDG PET/CT.

Conclusion
By analyzing diagnostic imaging alone, there is a high chance of misinterpreting asymptomatic tuberculosis patient as having malignancy. Therefore, there is need for correlation with clinical data as well as other imaging modalities and PET/CT with more specific tracer in order to differentiate malignancy from benign disease such as tuberculosis.
Renal medullary carcinoma masquerading as renal infection: a case report
Authors: Huang Zhong-Ming , Wang Hai , Ji Zhi-Gang 
Published: March 2020

Abstract
Background
Renal medullary carcinoma is a rare and aggressive tumor and often seen in young adults with sickle cell hemoglobinopathies.

Case presentation
We report a case of renal medullary carcinoma in a 29-year old male patient with an occupying renal lesion who presented with fever, flank pain and hematuria. The patient received intensive antibiotics treatment, but no improvement was seen. The symptoms disappeared after laparoscopic radical left nephrectomy. Postoperative pathological study showed that the mass was renal medullary carcinoma.

Conclusions
Our case suggests that renal medullary carcinoma should be considered in differential diagnoses of patients with occupying renal lesions who have fever of unknown origin.
The association of kidney function and cognitive decline in older patients at risk of cardiovascular disease: a longitudinal data analysis
Authors: Zijlstra Laurien E. , Trompet Stella , Mooijaart Simon P. , van Buren Marjolijn , Sattar Naveed , Stott David J. , Jukema J. Wouter 
Published: March 2020

Abstract
Background
Chronic kidney disease (CKD) has been identified as a significant direct marker for cognitive decline, but controversy exists regarding the magnitude of the association of kidney function with cognitive decline across the different CKD stages. Therefore, the aim of this study was to investigate the association of kidney function with cognitive decline in older patients at high risk of cardiovascular disease, using data from the PROspective Study of Pravastatin in the Elderly at Risk (PROSPER).

Methods
Data of 5796 patients of PROSPER were used. Strata were made according to clinical stages of CKD based on estimated glomerular filtration rate; < 30 ml/min/1.73m2 (stage 4), 30-45 ml/min/1.73m2 (stage 3b), 45-60 ml/min/1.73m2 (stage 3a) and ≥ 60 ml/min/1.73m2 (stage 1–2). Cognitive function and functional status was assessed at six different time points and means were compared at baseline and over time, adjusted for multiple prespecified variables. Stratified analyses for history of vascular disease were executed.

Results
Mean age was 75.3 years and 48.3% participants were male. Mean follow-up was 3.2 years. For all cognitive function tests CKD stage 4 compared to the other stages had the worst outcome at baseline and a trend for faster cognitive decline over time. When comparing stage 4 versus stage 1–2 over time the estimates (95% CI) were 2.23 (0.60–3.85; p = 0.009) for the Stroop-Colour-Word test, − 0.33 (− 0.66–0.001; p = 0.051) for the Letter-Digit-Coding test, 0.08 (− 0.06–0.21; p = 0.275) for the Picture-Word-Learning test with immediate recall and − 0.07 (− 0.02–0.05; p = 0.509) for delayed recall. This association was most present in patients with a history of vascular disease. No differences were found in functional status.

Conclusion
In older people with vascular burden, only severe kidney disease (CKD stage 4), but not mild to modest kidney disease (CKD stage 3a and b), seem to be associated with cognitive impairment at baseline and cognitive decline over time. The association of severe kidney failure with cognitive impairment and decline over time was more outspoken in patients with a history of vascular disease, possibly due to a higher probability of polyvascular damage, in both kidney and brain, in patients with proven cardiovascular disease.
Psychiatric disorders in children and adolescents in a middle-income Latin American country
Authors: Caqueo-Urízar Alejandra , Flores Jerome , Escobar Carolang , Urzúa Alfonso , Irarrázaval Matías 
Published: March 2020

AbstractBackgroundChild and adolescent mental health has scarcely been studied in developing countries, though it is an important aspect of health. Mental health problems in youth often continue into adulthood if not diagnosed or treated in time.MethodsTheSistema de Evaluación de Niños y Adolescentes (SENA)[Child and Adolescent Evaluation System] was used to evaluate mental health indicators in a sample of students in Northern Chile. Two age-appropriate versions of the assessment were applied to a total sample of 5043 students, which included an elementary education sample of 1953 schoolchildren from fourth grade through sixth grade (ages 8 to 13 years), and a Secondary School sample of 3090 schoolchildren from seventh grade (the last year of elementary school) through the last year of Secondary school (senior high school) (ages 12 to 19 years). For each group, the version of the assessment used was determined by the students’ grade level. Both samples included municipal, government-subsidized, and private schools.ResultsIn this student population, depression, anxiety, and behavioral disorders were the main mental health problems identified, and indicators revealed a progressive increase in cases over the years, coinciding with the global epidemiological scenario. Males showed a greater presence of externalizing behaviors related to mental health problems associated with aggression and defiant behavior. However, females showed the highest number of mental health issues overall, especially regarding problems related to internalization. There are significant differences between school types.ConclusionsOur sample population analysis indicates that early intervention is necessary for the diagnosis and treatment of youth, with the goal of reducing the probability that psychiatric disorders will be prolonged, evolving, and worsening in adulthood.
LncRNA MAGI2-AS3 is downregulated in non-small cell lung cancer and may be a sponge of miR-25
Authors: Sui Yutong , Chi Wencheng , Feng Li , Jiang Jiakang 
Published: March 2020

Abstract
Background
This study aimed to investigate the role of lncRNA MAGI2-AS3 in non-small cell lung cancer (NSCLC).

Methods
Expression levels of MAGI2-AS3 and RECK mRNA in two types of tissues (non-tumor and NCSLC) were measured by qPCR. To further investigate the interaction between MAGI2-AS3 and RECK, MAGI2-AS3 and RECK expression vectors were transfected into H1993 cells.

Results
We found that MAGI2-AS3 and RECK were upregulated and positively correlated in NSCLC. In NSCLC cells, MAGI2-AS3 overexpression led to upregulated RECK. Bioinformatics analysis showed that MAGI2-AS3 may bind miR-25, which can directly target RECK. In NSCLC cells, miR-25 overexpression led to downregulated RECK and attenuated the effects of MAGI2-AS3 overexpression, while MAGI2-AS3 and miR-25 failed to affect each other. Cell invasion and migration analysis showed decreased NSCLC cell invasion and migration rates after MAGI2-AS3 and RECK overexpression. MiR-25 showed opposite role and reduced the effects of MAGI2-AS3 overexpression.

Conclusion
Therefore, MAGI2-AS3 may sponge miR-25 to upregulate RECK, thereby inhibiting NSCLC cell invasion and migration.

Trial registration
HLJCM20163358592, registered by First Affiliated Hospital, Heilongjiang University of Chinese Medicine at March 3, 2016, prospectively.