bluuebunny/crossref_metadata_2025_split huggingface dataset:
A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent homologous recombination
Authors: Pang Tin Yau 
Published: March 2020

Abstract
Background A frequent event in the evolution of prokaryotic genomes is homologous recombination, where a foreign DNA stretch replaces a genomic region similar in sequence. Recombination can affect the relative position of two genomes in a phylogenetic reconstruction in two different ways: (i) one genome can recombine with a DNA stretch that is similar to the other genome, thereby reducing their pairwise sequence divergence; (ii) one genome can recombine with a DNA stretch from an outgroup genome, increasing the pairwise divergence. While several recombination-aware phylogenetic algorithms exist, many of these cannot account for both types of recombination; some algorithms can, but do so inefficiently. Moreover, many of them reconstruct the ancestral recombination graph (ARG) to help infer the genome tree, and require that a substantial portion of each genome has not been affected by recombination, a sometimes unrealistic assumption. Results Here, we propose a coarse-graining approach for phylogenetic reconstruction (CGP), which is recombination-aware but forgoes ARG reconstruction. It accounts for the tendency of a higher effective recombination rate between genomes with a lower phylogenetic distance. It is applicable even if all genomic regions have experienced substantial amounts of recombination, and can be used on both nucleotide and amino acid sequences. CGP considers the local density of substitutions along pairwise genome alignments, fitting a model to the empirical distribution of substitution density to infer the pairwise coalescent time. Given all pairwise coalescent times, CGP reconstructs an ultrametric tree representing vertical inheritance. Based on simulations, we show that the proposed approach can reconstruct ultrametric trees with accurate topology, branch lengths, and root positioning. Applied to a set of E. coli strains, the reconstructed trees are most consistent with gene distributions when inferred from amino acid sequences, a data type that cannot be utilized by many alternative approaches. Conclusions The CGP algorithm is more accurate than alternative recombination-aware methods for ultrametric phylogenetic reconstructions.
Weight Development Between Age 5 And 10 Years And Its Associations With Dietary Patterns At Age 5 In The Abcd Cohort
Authors: Rashid Viyan , Streppel Martinette T , Engberink Marielle F. , Weijs Peter J.M. , Nicolaou Mary , Verhoeff Arnoud P. 
Published: March 2020

Abstract
Background: Social inequalities in bodyweight start early in life and track into adulthood. Dietary patterns are an important determinant of weight development in children, towards both overweight and underweight. T herefore, w e aimed to examine weight development between age 5 and 10 years by ethnicity, SES and thereafter by BMI category at age 5, to explore its association with dietary patterns at age 5.

Methods: Participants were 1 765 children from the Amsterdam Born Children and their Development (ABCD) cohort that had valid data on BMI at age 5 and 10 and diet at age 5. Linear mixed model analysis was used to examine weight development between age 5 and 10 years and to assess if four previously identified dietary patterns at age 5 (snacking, full-fat, meat and healthy) were associated with weight development. Analyses were adjusted for relevant confounders, stratified by ethnicity and SES and thereafter stratified per BMI category at age 5.

Results: Overall, weight decreased in Dutch and high SES children and increased in non-Dutch and low/middle SES children. Across the range of bodyweight categories at age 5, we observed a conversion to normal weight, which was stronger in Dutch and high SES children but less pronounced in non-Dutch and low/middle SES children. Overall, the observed associations between weight development and dietary patterns were mixed with some unexpected findings: a healthy dietary pattern was positively associated with weight development in most groups, regardless of ethnicity and SES (e.g. Dutch B 0.084, 95% CI 0.038;0.130 and high SES B 0.096, 95% CI 0.047;0.143) whereas the full-fat pattern was negatively associated with weight development (e.g. Dutch B -0.069, 95% CI -0.114;-0.024 and high SES B -0.072, 95% CI -0.119;-0.026).

Conclusions: We observed differential weight development per ethnic and SES group. Our results indicate that each ethnic and SES group follows its own path of weight development. Associations between dietary patterns and weight development showed some unexpected findings; follow-up research is needed to understand the association between dietary patterns and weight development.

Keywords: BMI, body mass index, thinness, normal weight, overweight, obesity, socio-economic position, ethnicity, children, young children.
Higher Prevalence of Obesity among Children with Functional Abdominal Pain Disorders
Authors: Galai Tut , Moran-Lev Hadar , Cohen Shlomi , Ben-Tov Amir , Levy Dina , Weintraub Yael , Amir Achiya , Segev Or , Yerushalmy-Feler Anat 
Published: March 2020

Abstract
Background

Functional abdominal pain (FAP) disorders are one of the most common gastrointestinal disorders in children. We aimed to define the association between obesity and functional abdominal pain (FAP) disorders and to assess differences between overweight/obese children and normal weight children with FAP disorders.

Methods

We conducted a retrospective study of children (2-18 years old) with a clinical diagnosis of FAP who were followed-up in our pediatric gastroenterology unit between 1/2016-10/2018. FAP disorders were defined according to the ROME IV criteria. Body mass index (BMI) percentiles were defined by CDC standards. Patients with BMIs ≥85th percentile were designated as being overweight/obese. A population control group was obtained from the 2015-2016 Israel national health survey.

Results

Data from 173 children with FAP disorders (median age 11.5 years, 114 females) were included. Seventy-one children (41%) were classified as having functional abdominal pain-NOS, 67 (38.7%) as having irritable bowel syndrome (IBS), and 35 (20.2%) has having functional dyspepsia. Fifty-three children (30.6%) were classified as being overweight/obese.

Adolescents with FAP disorders had a significantly higher prevalence of overweight/obesity compared to controls (39.5% vs. 30%, respectively, p = 0.04). Children with FAP and overweight were older [12.4 (range 9.8-15.3) vs. 10.8 (7.4-14.1) years, p = 0.04] and had more hospitalizations due to FAP (20.8% vs. 7.6%, p = 0.01) compared to Children with FAP and normal weight.

Conclusions

Adolescents with FAP had higher prevalence of overweight/obesity compared to controls. Future studies are warranted to raise awareness of weight issues in FAP and determine the effect of weight loss on FAP.
Amaryllidaceae alkaloids with anti-Trypanosoma cruzi activity
Authors: Martinez-Peinado Nieves , Cortes-Serra Nuria , Torras-Claveria Laura , Pinazo Maria-Jesus , Gascon Joaquim , Bastida Jaume , Alonso-Padilla Julio 
Published: March 2020

Abstract
Background: Chagas disease, caused by the protozoan Trypanosoma cruzi, is a neglected disease that affects ~7 million people worldwide. Development of new drugs to treat the infection remains a priority since those currently available have frequent side effects and limited efficacy at the chronic stage. Natural products provide a pool of diversity structures to lead the chemical synthesis of novel molecules for this purpose. Herein we analyzed the anti- T. cruzi activity of 9 alkaloids derived from plants of the Amaryllidaceae family. Methods: the activity of each alkaloid was assessed by means of an anti- T. cruzi phenotypic assay. We further evaluated the compounds that inhibited the parasite growth on two distinct cytotoxicity assays to discard those that were toxic to host cells and assure parasite selectivity. Results: we identified a single compound (hippeastrine 2 ) that was selectively active against the parasite yielding selectivity indexes of 12.7 and 35.2 against Vero and HepG2 cells, respectively. Moreover, it showed specific activity against the amastigote stage (IC 50 = 3.31 μM). Conclusions: results reported here suggest that natural products are an interesting source of new compounds for the development of drugs against Chagas disease.
Modified trapdoor procedures using autogenous tricortical iliac graft without preserving the broken cartilage to treat osteonecrosis of the femoral head: A Prospective Cohort Study With Historical Controls
Authors: Cheng Qi , Zhao Fengchao , Xu Shizhuang , Zheng Li , Zheng Xin 
Published: March 2020

Abstract
Background The aim of the present study was to investigate clinical and radiological outcomes of autologous tricortical iliac graft through a window created at the femoral head, without suturing the opened articular cartilage to treat osteonecrosis of the femoral head (ONFH), called modified trapdoor procedures. Methods A total of 59 consecutive patients (67 hips; 36 males and 23 females) with ONFH were included in this study, which was conducted during the period from April 2009 to March 2012. Patient age ranged from 27 to 46 years old, with mean age of 36.3 years. Harris hip scores (HHS) were used to evaluate hip function pre- and postoperatively. Anteroposterior and frog-position X-rays and magnetic resonance imaging (MRI) were conducted to evaluate lesion location, size, and ARCO stage. Clinical failure was defined as score < 80 points or treatment by total hip arthroplasty(THA). Radiographic failure was defined as a > 3 mm of collapse in the hip. This group was retrospectively matched according to the ARCO stage, extent, location, etiology of the lesion, average age, gender, and preoperative Harris hip score to a group of 59 patients (67 hips) who underwent the“light bulb”approach during March 2007 to April 2009. Results Mean follow-up was 91.2 ± 13.6 months (range, 75–115 months). Mean HHS was 91.3 ± 4.5, compared with 83.1± 4.5 in the “light bulb” cohort at the 6 years follow-up examination ( P < 0.001). At the 6 years follow-up, for modified trapdoor procedures, five hips (8.5%) were classified as clinical failure, and 3 hips underwent total hip arthroplasty; Seven hips were classified as (10.4%) radiographic failure.The clinical and radiographic failure of the hips treated with the modified trapdoor procedure was significantly lower than that of the hips treated with the “light bulb” procedure (p < 0.05). Survival of the joint was not significantly related to the location of the femoral head lesion between two groups, but there was better clinical and radiographic results in modified trapdoor procedures with Size-C and the ARCO stage III. Conclusion The study demonstrated superior medterm clinical results in ONFH with the use of autologous tricortical iliac block graft through a femoral head window, without suturing the opened articular cartilage. The results of this femoral head-preserving procedure in patients with postcollapse osteonecrosis and large lesion are superior to those of the “light bulb” procedure treatment.
Positive results for patients with COVID-19 discharged from hospital in Chongqing, China
Authors: Deng Wang , Guang Tian-wen , Yang Mei , Li Jian-rong , Jiang De-peng , Li Chang-yi , Wang Dao-Xin 
Published: March 2020

Abstract
Since December 2019 , more than 80 thousand patients with coronavirus disease 2019 (COVID-19) has been confirmed in China. With the increasing number of recovered patients, more attention should be paid to the follow-up of patients. In the study, 576 patients with COVID-19 discharged from hospital in Chongqing, China from January 24, 2020, to March 10, 2020 were evaluated by viral nucleic acid tests for SARS-CoV-2 to determine if they could be released from quarantine at home. Among the 576 patients, 61 patients (10.6%) had positive results for severe acute respiratory syndrome coronavirus 2. We aimed to analyze the demographics, clinical characteristics and treatment of 61 patients. Criteria for hospital discharge or discontinuation of quarantine would be updated with the progress of clinical evidence and experience accumulation.
Modulation of inflammatory factors predicts the outcome following spinal cord injury
Authors: Yu Zepeng , Sun Xingwei , Xia Rui , Chen Qian , Wu Qin , Zheng Weiwei 
Published: March 2020

Abstract
BACKGROUND : The correlation between inflammatory responses caused by spinal cord injury (SCI) and the prognosis of patients with SCI still remains controversial. METHODS : In the present study, we preliminary investigated the serum levels of interleukin (IL)-4, IL-10, major histocompatibility complex (MHC)-I and inducible nitric oxide synthase (iNOS), and compared the serum IL-4 and IL-10 expression in rats of high BBB scores with these of low Basso-Beattie-Bresnahan(BBB) scores. Besides, the infiltration of macrophage and the axonal regeneration of the injuried spinal cord were observed from day10 to day30. RESULTS : We found that higher serum levels of IL-4 and IL-10 can reflect the restorability degree of SCI and could be potential biomarkers for the prognosis of SCI. The infiltration of M2 subtype of macrophage and the axons regrowth might contribute to better prognosis. CONCLUSIONS ： Collectively, the current study demonstrates that the serum levels of IL-4 and IL-10 are preliminary adopted as serologic markers to forecast SCI, and high serum levels of IL-4 and IL-10 may indicate a better prognosis. Moreover, the way to promote macrophage polarization from M1 to M2 may contribute to better axonal regeneration.
Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae
Authors: Kehlet-Delgado Hanna , Häse Claudia , Mueller Ryan S 
Published: March 2020

Abstract
Background: Vibriosis has been implicated in major losses of larvae at shellfish hatcheries. However, the species of Vibrio responsible for disease in aquaculture settings and their associated virulence genes are often variable or undefined. Knowledge of the specific nature of these factors is essential to developing a better understanding of the environmental and biological conditions that lead to larvae mortality events in hatcheries. We tested the virulence of 51 Vibrio strains towards Pacific Oyster (Crassostreae gigas) larvae and sequenced draft genomes of 42 hatchery-associated vibrios to determine groups of orthologous genes associated with virulence and to determine the phylogenetic relationships among pathogens and non-pathogens of C. gigas larvae.Results: V. coralliilyticus strains were the most prevalent pathogenic isolates. A phylogenetic logistic regression model identified over 500 protein-coding genes correlated with pathogenicity. Many of these genes had straightforward links to disease mechanisms, including predicted hemolysins, proteases, and multiple Type 3 Secretion System genes, while others appear to have possible indirect roles in pathogenesis and may be more important for general survival in the host environment. Multiple metabolism and nutrient acquisition genes were also identified to correlate with pathogenicity, highlighting specific features that may enable pathogen survival within C. gigas larvae. Conclusions: These findings have important implications on the range of pathogenic Vibrio sp. found in oyster-rearing environments and the genetic determinants of virulence in these populations.
Causes of Lower Extremity Weaknesses After Posterior Lumber Spine Fusion Surgery and Therapeutic Effects of Active Surgical Exploration
Authors: Wang Rui , Li Chunde , Yi Xiaodong , Lu Hailin , Wang Yu , Li Hong 
Published: March 2020

Abstract
Background : This study was aimed at investigating the causes of lower extremity weaknesses after posterior lumber spine fusion surgery, and looking at subsequent treatment strategies. Methods : Patients who underwent posterior lumber spine fusion surgery in the Peking University First Hospital between Jan 2009 and Dec 2018 were counted. Those who needed secondary surgery because of subsequent lower extremity weaknesses were selected. CT scans and MRIs were used to evaluate the reasons for weaknesses before secondary surgery. Muscle strength was evaluated after surgery. Results: Thirty patients (30/4078, 0.74%) required a secondary surgery because of lower extremity weaknesses after posterior lumber spine fusion surgery. The main causes of weakness were: (1) internal fixation malposition and loosening (11 patients, 36%); (2) epidural hematomas (9 patients, 30%); (3) insufficient decompression (5 patients，17%) ; (4) and nerve root edemas (5 patients，17%). Weakness occurred on average 2.9 days after surgery (1-9 days). Twenty-seven patients (90%) got improved muscle strength after their secondary surgery. Conclusions : Iatrogenic neurologic deficits and lower extremity weaknesses were rare complications after posterior lumber spine fusion surgeries, but important to recognize and manage. The main causes of weakness were internal fixation malposition and loosening, epidural hematomas, insufficient decompression or root edemas. There may be positive, therapeutic effects to subsequent, active surgical exploration.
Genetic polymorphism and natural selection of circumsporozoite protein in Myanmar Plasmodium vivax
Authors: Võ Tuấn Cường , Lê Hương Giang , Kang Jung-Mi , Moe Mya , Naw Haung , Myint Moe Kyaw , Lee Jinyoung , Sohn Woon-Mok , Kim Tong-Soo , Na Byoung-Kuk 
Published: March 2020

Abstract
Background: Circumsporozoite surface protein (CSP) of malaria parasites has been recognized as one of the leading vaccine candidates. Clinical trials of vaccines for vivax malaria incorporating Plasmodium vivax CSP (PvCSP) have demonstrated their effectiveness in preventing malaria, at least in part. However, genetic diversity of PvCSP in the natural population is still a major concern.Methods: A total of 171 blood samples collected from patients infected with Plasmodium vivax in Myanmar analysed in this study. The gene for PvCSP was amplified by polymerase chain reaction, followed by T&A cloning and sequencing. Polymorphic characteristics and natural selection of Myanmar PvCSP population in Myanmar were analysed using DNASTAR, MEGA6 and DnaSP programs. The polymorphic pattern and natural selection of publicly accessible global PvCSP sequences were also comparatively analysed.Results: Myanmar PvCSP sequences were divided into two subtypes VK210 and VK247 comprising 143 and 28 sequences, respectively. The VK210 subtypes showed higher levels of genetic diversity and polymorphism than the VK247 subtypes. The N-terminal non-repeat region of PvCSP displayed limited genetic variations in the global population. Different patterns of octapeptide insertion (ANKKAEDA in VK210 and ANKKAGDA in VK247) and tetrapeptide repeat motif (GGNA) were identified in the C-terminal region of global PvCSP population. Meanwhile, the central repeat region (CRR) of Myanmar and global PvCSP, both in VK210 and VK247 variants, was highly polymorphic. The high level of genetic diversity in the CRR has been attributed to the different numbers, types and combinations of peptide repeat motifs (PRMs). Interestingly, 27 and 5 novel PRMs were found in Myanmar VK210 and VK247 variants, respectively.Conclusion: Comparative analysis of the global PvCSP population suggests a complex genetic profile of PvCSP in the global population. These results widen understanding of the genetic make-up of PvCSP in the global P. vivax population and provide valuable information for the development of a vaccine based on PvCSP.
Plasma, Urine and Tissue Concentrations of Flunixin and Meloxicam in Pigs
Authors: Nixon Emma , Mays Travis P. , Routh Patricia A. , Yeatts James L. , Fajt Virginia R. , Hairgrove Thomas , Baynes Ronald 
Published: March 2020

Abstract
Background: The objective of this study was to compare plasma and urine concentrations of flunixin and meloxicam in pigs, in order to determine urine withdrawal intervals for animals at livestock shows where urine is routinely tested for these drugs. Fourteen Yorkshire/Landrace cross pigs were housed in individual metabolism cages to facilitate complete urine collection. All animals were randomly divided into one of two treatment groups and received either 2.2 mg/kg flunixin or 0.4 mg/kg meloxicam via intramuscular injection. Plasma and urine were collected and analyzed by UPLC-MS/MS. Pigs were humanely euthanized when meloxicam/flunixin could no longer be detected in two consecutive urine samples, and liver and kidneys were collected to quantify any potential residues.Results: Drug levels in urine reached peak concentrations between 4 and 8 h post-dose for both flunixin and meloxicam. Flunixin urine concentrations were higher than maximum levels determined in plasma. Urine concentrations for flunixin and meloxicam were last detected above the limit of quantification (LOQ) at 120 h (0.0005 μg/mL) and 48 h (0.001 μg/mL), respectively. Mean apparent elimination half-life in plasma was 5.00 ± 1.89 h and 3.22 ± 1.52 h for flunixin and meloxicam, respectively. Six of seven pigs had detectable liver concentrations of flunixin (range 0.0001-0.0012 μg/g) following negative urine samples at 96 and 168 h, however all samples at 168 h were below the FDA tolerance level (0.03 μg/g). Meloxicam was detected in a single liver sample at necropsy (0.0054 μg/g) at 72 h but was below the EU MRL (0.065 μg/g) which was used to determine a safety level when FDA tolerance or FSIS testing limits were not established. Urine concentrations did not relate to liver residues at the single slaughter time Conclusions: This data suggests that pigs given a single intramuscular dose of meloxicam at 0.4 mg/kg or flunixin at 2.2 mg/kg are unlikely to have tissue residues above the US FDA tolerance or EU MRL following negative urine testing. This information will assist in generating withdrawal intervals for these NSAIDs for show pigs that might undergo a urine test by the livestock show authorities.
Brazing of transparent polycrystalline Al2O3 and GH99 with the assistance of (Cu, Ni) solid solution cladding layer
Authors: Zhang Bo , Zhang Lixia , Sun Zhan , Feng Jicai 
Published: March 2020

Abstract
In this study, pure Cu foil was firstly vacuum cladding on the GH99 alloy (GH99) surface to prepare a (Cu, Ni) solid solution layer. By varying the cladding temperatures, (Cu, Ni) solid solution layers with different Ni contents were achieved. The vacuum cladding process was then followed by vacuum brazing of the Cu-coated GH99 to transparent polycrystalline Al 2 O 3 (TPA). Typical microstructure of the TPA/Cu-cladding GH99 brazed joint was characterized. The effects of different cladding temperatures on microstructural evolution and mechanical response of the brazed joints were discussed. By varying the cladding temperature, different thickness of the reaction layer at the braze filler/TPA interfaces can be achieved, which shows a strong correlation with the mechanical performance of the brazed joint. The maximum shear strength of the brazed joint reached 103 MPa when the cladding temperature was 1105 ºC. Compared with the directly brazed joint, shear strength was improved by 472%.