bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of somatic variant calling on matched FF and FFPE WGS from a metastatic prostate sample
Authors: Brienen Louise de Schaetzen van , Larmuseau Maarten , Eecken Kim Van der , Fostier Jan , Ost Piet , Marchal Kathleen 
Published: October 2019

Abstract
Background. Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, do collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artifacts might obfuscate the variant calling. To assess whether FFPE material can be used for cohort studies, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE Whole Genome Sequence (WGS) samples extracted from the same prostate metastatic tumor. Results. We first compared the calls between FF and FFPE, showing that on average 50% of the calls in FF are recovered in FFPE, with notable differences between variant callers. Remarkably, this overlap was better than the overlap between different variant callers on the same sample. Inspecting the Variant Allele Frequency (VAF), we observed that many of the calls common to FF and FFPE belonged to the same clonal subpopulation but were detected at a lower VAF in FFPE. We also demonstrated that these calls receive higher significance scores and are often identified by more than one variant caller. Based on this observation, we propose a simple heuristic to perform reliable variant calling in FFPE samples. Our heuristic identified 3684 common calls at a F1-score of 0.83. Conclusion. This study illustrates that when using the correct variant calling strategy, the overlap between the FF and FFPE sample in somatic SNVs increases to such an extent that a large fraction of the calls detected in the FFPE sample are contained in the FF sample and the number of variants unique to each sample remains restricted. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.
Dromedary camel CD14high MHCIIhigh monocytes display inflammatory properties and are reduced in newborn camel calves
Authors: Hussen Jamal , Shawaf Turke , Al-Mubarak Abdullah I. A. , Humam Naser Abdallah Al , Almathen Faisal , Schuberth Hans-Joachim 
Published: October 2019

Abstract
Background

in human and different animal species, blood monocytes are classified based on their expression pattern of different monocytic markers into phenotypically and functionally different subsets. In the current study, we used monoclonal antibodies to CD172a, CD14, CD163 and MHCII to identify monocyte subsets in peripheral blood of dromedary camels and to evaluate their phenotype and function.Results

similar to bovine and swine monocytes, camel CD172a can be used as a pan-monocyte marker. Based on CD14, CD163 and MHCII expression, camel CD172a+ monocytes were divided into three subsets: The major subpopulation of camel monocytes (mo-I) showed high expression of CD14 and CD163, but low expression of MHCII. A second subset of monocytes (mo-II) expressed highly all three markers, CD14, CD163 and MHCII. A third monocyte subset (mo-III) displayed low expression of CD14 and CD163 with high MHCII expression. The three monocyte subsets also showed different expression patterns of cell adhesion molecules. While the two MHCII high subsets (mo-II and mo-III) showed higher expression of CD11a in comparison to the MHCIIlow subset mo-I, CD18 and CD11b were highest expressed on the two CD14high subsets (mo-I and mo-II). Bacterial stimulation of camel leukocytes identified mo-II cells as an antimicrobial monocyte subset with the highest phagocytic and ROS production capacity. The comparison of monocyte counts and phenotype between newborn camel calves and adult camels revealed significantly reduced numbers of mo-II cells in newborn animals. Monocytes of newborns expressed significantly more CD172a and CD163 molecules but less CD14 and MHCII molecules than monocytes of adult camels.Conclusions

The analysis of phenotypic and functional properties suggests that camel monocyte subsets mo-I, mo-II and mo-III are counterparts of bovine classical, intermediate and non-classical monocytes respectively. Age related changes in camel monocyte numbers and phenotype were identified.
Utility of the optical quality analysis system for decision-making in Nd: YAG laser posterior capsulotomy in patients with light posterior capsule opacity
Authors: LU BO , Zhu Weijie , Fan Yu , Shi Dong , Ma Liwei 
Published: October 2019

Abstract
Background: To evaluate whether the Optical Quality Analysis System (OQAS) can serve as a valuable additional indicator for appropriate posterior capsulotomy referral.
Methods: One hundred and five eyes from 96 patients undergoing capsulotomy were divided into precapsulotomy logMAR CDVA ≤ 0.1 group and logMAR CDVA > 0.1 group. CDVA， and the Visual Function 14 index (VF-14) score were estimated before and 1 month after capsulotomy. Objective scattering index (OSI) value was measured by using the OQAS. Posterior capsule opacification (PCO) severity was assessed with Evaluation of PCO 2000 (EPCO 2000) software.
Results：In logMAR CDVA > 0.1 group, the correlations of OSI, logMAR CDVA, EPCO score and VF-14 score were very strong preoperatively. In logMAR CDVA ≤ 0.1 group, preoperatively, OSI was correlated with logMAR CDVA (r = 0.451), EPCO score (r = 0.789), and VF-14 score (r = 0.852). LogMAR CDVA has weak correlation with VF-14 score (r = -0.384) and EPCO score (r = 0.566). VF-14 score was correlated with EPCO score (r = -0.669). In the logMAR CDVA ≤ 0.1 group, there was no significant difference in logMAR CDVA between precapsulotomy and postcapsulotomy (P > 0.05). In the two groups, all the other optical quality parameters were significantly improved after capsulotomy (P < 0.05).
Conclusions：The OSI was useful for the evaluation of PCO and prediction of beneficial capsulotomy. Especially for patients with slight PCO and better visual acuity, OSI is more valuable than CDVA and a complete objectivity examination.
Trial registration: The study protocol was registered at the Chinese Clinical Trial Registry. Register: ChiCTR1800018842 (Registered Date: October 13th, 2018).
Keywords: Posterior capsule opacification, Objective scattering index, Capsulotomy, Visual Function 14 index, Visual outcomes
JM-1232(-) and propofol, a new combination of anesthetics with short-acting and non-cumulative preferable properties
Authors: Adachi Yushi Ueda , Taharabaru Saori , Higashi Michiko , Matsuda Naoyuki , Satomoto Maiko , Tamura Takahiro , Sato Aiji Boku , Okuda Masahiro 
Published: October 2019

Abstract
Background Drug interactions are significant in anesthesiology because drug combinations can potentially possess novel properties. The pharmacological advantages of a new combination of the benzodiazepine receptor agonist JM-1232(-) and propofol were investigated in mice.Methods Male adult mice were administered JM-1232(-) or propofol or combinations of the two drugs intravenously. Loss of the righting reflex was evaluated as achieving hypnosis, and the time until recovery of the reflex was measured as hypnosis time. After determining the ED50, doses double and triple the ED50 of propofol were injected with JM-1232(-) to compare hypnosis time. The injections were repeated four times, and the hypnosis times were compared. Flumazenil was administered separately immediately after the last dose was injected.Results The ED50 values ([95% confidence interval]) for hypnosis were 3.76 [3.36–4.10] for JM-1232(-) and 9.88 [8.03–11.58] mg kg-1 for propofol. Co-administration of 0.05 and 0.1 mg kg-1 JM-1232(-) reduced the ED50 values of propofol to 1.76 [1.21–2.51] and 1.00 [0.46–1.86] mg kg-1, respectively. The drug combination for hypnosis produced a supra-additive interaction. Hypnosis time was significantly shorter in the groups given the mixtures compared to each hypnotic administered alone. After repeated injections, hypnosis time with the mixtures showed smaller prolongation than that with the hypnotic alone. Flumazenil completely restored the recovery time after anesthesia.Conclusions The combination of JM-1232(-) and propofol showed a supra-additive interaction, and the reduced hypnotic dose contributed to a faster recovery even after multiple injections.
Socio-demographic factors associated with early sexual experience among South African female youth
Authors: Baruwa Ololade Julius , Amoateng Acheampong Yaw 
Published: October 2019

Abstract
Early sexual experiences affect the sexual and reproductive health of young persons because they put them at the risk of risky sexual behaviours including multiple sexual partners and inconsistent condom use. As a consequence, early sexual experiences increase the risk of unintended pregnancies and STIs, including HIV/AIDS. There has been limited research on the prevalence and socio-demographic determinants of early sexual experience in South Africa. Thus, this study aimed to fill the void by assessing the socio-demographic factors that are associated with early sexual experience among South African female youth using the 2016 South Africa Demographic and Health Survey (SADHS). Results showed that female youth with secondary (HR: 0.69, CI: 0.61-0.77) and higher (HR: 0.47, CI: 0.41-0.54) education had lower hazard risk of early sexual experience compared to those who had no education and primary education. Female youth between the ages of 25-34 (HR: 0.70, CI: 0.65-0.74) had hazard lower risk of early sexual experience compared to those from poor wealth index. Belonging to “other” population group reduced the hazard risk of early sexual experience among female youth compared to those belonging to African population group (HR: 0.87, CI: 0.77-0.98). Programs should target high-risk groups to delay early sexual initiation.
Patterns of Fish and Whale Consumption and Concentrations of Methylmercury in Hair Among Residents of Western Canadian Arctic Communities
Authors: Walker Emily Victoria , Yuan Yuan , Girgis Safwat , Goodman Karen J. 
Published: October 2019

Abstract
Background. Methylmercury contamination of the environment represents a substantial environmental health concern. Human exposure to methylmercury occurs primarily through consumption of fish and marine mammals. Heavily exposed subgroups include sport or subsistence fishers residing in Arctic communities. We aimed to estimate the association of fish/whale consumption patterns of Canadian Arctic subsistence fishers with the internal dose of methylmercury as measured in hair.
Methods. This research was conducted within ongoing community projects led by the CANHelp Working Group in Aklavik and Fort McPherson, Northwest Territories and Old Crow, YT. We interviewed each participant using a fish-focused food-frequency questionnaire during September-November 2016 and collected hair samples concurrently. Methylmercury was measured in the full-length of each hair sample using gas chromatography inductively-coupled plasma-mass spectrometry. Multivariable random-effects linear regression estimated beta-coefficients and 95% confidence intervals (CIs) for the effect of fish/whale consumption on hair-methylmercury concentrations.
Results. In total, 101 participants provided hair samples and diet data. The mean number of fish/whale species eaten by participants was 3.5 (SD:1.9). The mean hair-methylmercury concentration was 0.60μg/g (SD:0.47). Fish/whale consumption was positively associated with hair-methylmercury concentration, after adjusting for sex, hair length and use of permanent hair treatments. Hair-methylmercury concentrations among participants who consumed the most fish/whale in each season ranged from 0.30- 0.50μg/g higher than those who consumed <1 meal/week.
Conclusions. Hair-methylmercury concentrations were below the 6.0μg/g threshold for safe exposure defined by Health Canada, suggesting that fish/whale consumption patterns among participants are not increasing their risk of known serious health effects of methylmercury exposure.
Efficacy of Ursodeoxycholic Acid in Nonalcoholic Fatty Liver Disease: An Updated Meta-Analysis of Randomized Controlled Trials
Authors: Zhang Wenyue , Tang Yao , Huang Juan , Ren Hong , Yang Yixuan , Yang Qinbing , Hu Huaidong 
Published: October 2019

Abstract
Background Nonalcoholic fatty liver disease (NAFLD) is a kind of chronic liver disease among general population. Recent years, more and more new experiments have made the role of ursodeoxycholic acid (UDCA) become clearer. In this meta-analysis, we analyzed the efficacy of ursodeoxycholic acid (UDCA) for the treatment of nonalcoholic fatty liver disease (NAFLD). Methods We searched the Web of Science, Pubmed, Embase and Cochrane library databases for relavent studies published before March 1, 2019. We examined 134 randomized controlled trials (RCTs) that investigated the effectiveness of UDCA in NAFLD against placebo or other treatments. Next, we conducted meta-analysis by Stata(version 12.0) to examine the change among several indices: Alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyl transferase (GGT), Alkaline phosphatase (AP), total bilirubin and albumin. Results Following the application of different inclusion and exclusion criteria, 9 articles with 1106 participants were finally selected. The forest plot displayed that UDCA treatment can significantly decrease the ALT levels among the NAFLD patients (SMD=0.17,95%CI [0.03 to 0.3], P=0.07). However, UDCA treatment did not significantly affect the AST, GGT, AP, total bilirubin and albumin levels. Further, the subgroup analyses suggested the significant role of UDCA treatment in different geographical regions, age group and treatment duration (P=0.003 in people from Europe, P=0.001 in people older than 50 years and P=0.008 in longer duration(>6 months)). Conclusion In this study, several indices we analyzed among 9 articles. UDCA treatment was found beneficial in lowering the ALT levels in NAFLD patients. The remaining indices like AST, GGT, AP showed non-significant changes in this analysis. This could be attributed for the insufficient number of trials because all parameters were not analyzed in each individual RCT. Therefore, future meta-analysis will be required to fully confirm and validate the efficacy of UDCA in NAFL.
The significance of multidisciplinary classifications based on transbronchial pathology in possible idiopathic interstitial pneumonias
Authors: xu jian , Wang Weixue , Liu Chunfang , Feng Ruie , Zhao Junjun , Gao Na , Jiang Ling , Zhang Xiaolin , Han Xue , Ren Lina , Zhao Xiaohui , Liu Yuan 
Published: October 2019

Abstract
Background the multidisciplinary diagnosis based on clinic–radiologic–pathologic information had been widely used as the diagnostic gold standard for idiopathic interstitial pneumonias (IIPs). Surgical lung biopsy (SLB) had been recommended as the standard method to sample lung parenchymal lesions for suspected IIPs. Here, we attempted to show the diagnostic conﬁdence of multidisciplinary classifications based on transbronchial pathology including transbronchial lung cryobiopsy (TBLC), bronchoalveolar lavage fluid (BALF) and endobronchial ultrasound-guided transbronchial needle aspiration biopsy (EBUS-TBNA) in IIPs. Methods all new suspected interstitial lung diseases (ILD) were in-patient at the respiratory department of Dalian Municipal Central Hospital from June 2016 to December 2018. The multidisciplinary discussion (MDD) were made to exclude known causes of ILD and typical IPF depending on clinical, radiological information. The cases of atypical IPF, and possible IIPs were included and suggested to transbronchial pathological evaluation. Initial MDD classifications were made depending on clinical, radiological and transbronchial pathological information. The final MDD classifications was confirmed by following therapeutic effect. Results 70 subjects were eligible including 24 males and 46 females. The sampled lung parenchyma from TBLC were enough for confirmation of pathological diagnosis in 68.6% (48/70) cases. If the confirmed pathological evaluations through EBUS-TBNA and BALF were involved, 77.1% (54/70) cases had gotten the defined diagnosis. All cases were following up. Meanwhile, 60% was improved, 11.43% was relapsed when glucocorticoid was reduced to small dose or withdrawal, 14.29% was steady and 8.57% was progressed in which the diagnosis were modified in 4 cases. 94.3% initial MDD classifications based on transbronchial pathology were agreed with the final MDD, the difference of diagnostic yield wasn’t significant between initial and final MDD (Z=-1.414, p=0.157). Conclusion classifications of IIPs based on transbronchial pathology were useful and quite agreed with final MDD.
RNA-seq and two-dimensional gel electrophoresis revealed genomic and proteomic signatures during bacteriophage-host interactions in Pseudomonas aeruginosa
Authors: Tan Yinling , Zhong Qiu , Zhao Xia , Chen Canhuang , Li Yang , Le Shuai , Chen Ming 
Published: October 2019

Abstract
Background
Understanding the biological nature of bacteriophage is important in exploring the therapeutic and biotechnological potentials of bacteriophages. However, available information is limited to the infection processes on either model phages infecting Escherichia coli or lytic phages against pathogens. The interplay between lysogenic phage and its host was rarely studied.
Results
We investigated the interactions between Pseudomonas aeruginosa and a lysogenic bacteriophage PaP3 through RNA-seq and two-dimensional gel electrophoresis (2D-GE). Compared to the uninfected host, a total of 2,891 (51.3%) differentially expressed genes (DGEs) were identified, most of which were repressed by phages, including the changes in metabolic-related and virulence-associated genes. The RT-qPCR results showed consistent directional changes compared with the RNA-seq results. According to 2D-GE, phage structure proteins were detected after phage infection. The host proteins, such as flagella hook-associated proteins, disappeared gradually after phage infection and may be shut off by phage.
Conclusions All these indicate that although lysogenic phages do not immediately lyse the host, they play a significant regulatory role in the expression of host genes. Our findings provide an expanded view of the lysogenic phage infection processes and may offer potential targets for therapeutic intervention against P. aeruginosa infections.
Predicting Cover Crop Nitrogen Content with a Handheld Normalized Difference Vegetation Index Meter
Authors: White Charles M. , Bradley Brosi , Finney Denise M. , Kaye Jason P. 
Published: October 2019

Core Ideas
Cover crop biomass N content (CC‐N) can be estimated in the field with a handheld NDVI meter.
Separate calibration equations exist for different cover crop types in fall and spring.
Rapidly estimating CC‐N could facilitate management of N‐related services provided by cover crops.
Cover crop (CC) biomass nitrogen content (CC‐N; kg ha−1) is related to a number of ecosystem services but is rarely measured by farmers and agronomists because of the expense of sampling and analysis. We hypothesized that normalized difference vegetation index (NDVI) measured by a handheld meter could predict CC‐N. Using a dataset of 598 observations, we predicted fall biomass N with two separate calibrations for (i) clover‐type legumes and (ii) CCs consisting of brassicas (Brassica spp.), cereal grasses, vining legumes, and grass–legume–brassica mixtures. Spring biomass N was predicted with three separate calibrations for (i) cereal grain CCs, (ii) brassicas, and (iii) CCs consisting of pure legumes and grass–legume–brassica mixtures. Quality of the calibrations ranged from r2 = 0.72 to r2 = 0.87. Rapidly and inexpensively estimating CC‐N with an NDVI meter could enhance the ability of farmers and agronomists to routinely monitor and manage the N‐related ecosystem services provided by CCs.
Characterization of Excreted Salt from the Recretohalophytes Distichlis spicata and Spartina pectinata
Authors: Morris Logan , Yun Kassandra , Rutter Allison , Zeeb Barbara A. 
Published: October 2019

Recretohalophytes are salt‐tolerant plants that excrete excess salts through specialized glands on their leaf surfaces. They have the potential to be applied as a phytotechnology to remediate salt‐impacted soils by removing the salt from the soil and allowing it to be mobilized on the wind (haloconducted) and hence dispersed over a wide area where the salt ions will act as nutrients rather than pollutants. This study is the first to characterize the excreted salts of two recretohalophytic grasses, Spartina pectinata Bosc ex Link and Distichlis spicata (L.) Greene using scanning electron microscopy (SEM). At above‐optimal conditions for salt excretion (i.e., >65% humidity and >26°C), salt appeared on the stem and leaf surfaces as a sap‐like excretion that could not be easily mobilized. The mean diameter of the salt crystals excreted by S. pectinata (31 ± 24 μm) is significantly smaller than the diameter of those excreted by D. spicata (49 ± 22 μm) (p < 0.05). Spartina pectinata excreted significantly more salt crystals per unit area of plant surface (60 ± 41 crystals mm−2) than D. spicata (27 ± 16 crystals mm−2). These salt crystal characteristics can now be used to assist with determining the optimal species for haloconduction, and in particulate dispersal modeling systems to help determine the fate of the excreted salts once they become airborne by wind.Core Ideas
Recretohalophytes excrete salts that disperse via winds through “haloconduction.”
The mean diameter of excreted salt crystals varied by plant species.
The mean number of salt crystals per unit of leaf area varied by plant species.
Air particulate modeling can use this to assess the effectiveness of salt dispersal.
Salt excretion and dispersal may prove to be a useful form of salt remediation.
Current perspectives on fixed-dose ACE inhibitordiuretic combination therapy in the management of arterial hypertension
Authors: Gorokhovskaya G. N. , Yun V. L. , Martynov A. I. , Vasyuk Yu. A. , Moiseenko S. V. 
Published: October 2019

Despite our achievements in modern medicine, arterial hypertension (AH) remains one of the main causes of fatal complications, such as myocardial infarction and acute cerebrovascular accident leading to disability and mortality of patients, including those of working age. The prevalence of hypertension is significantly higher among old and senile age population, however, it has recently tended to increase in young and middle-aged people. Thus, the Russian epidemiological ESSE-RF study, in which representative sample of the Russian population aged 25–64 years were studied, showed that the prevalence of hypertension in individuals of that age group was 44%. It was predicted that the world’s burden of hypertension would increase by 15–20% to approximately 1.5 million people in the year 2015. Due to the high incidence of hypertension and complications associated with hypertension development, further study of pathogenetic mechanisms, development of diagnostic examination methods, prophylactic measures and the search for new treatment options with fixed-dose combination drugs is an important area of modern medicine. This article provides an overview of clinical studies of the components (lisinopril and indapamide) of a rational ACE inhibitor–diuretic combination and a clinical example.