bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Allplex™ Entero-DR assay for detection of antimicrobial resistance determinants from bacterial cultures
Authors: Mojica María Fernanda , De La Cadena Elsa , Correa Adriana , Appel Tobias Manuel , Pallares Christian José , Villegas María Virginia 
Published: March 2020

Abstract
Objective
To evaluate the sensitivity and specificity of the Allplex™ Entero-DR, a quantitative PCR-based method, for the detection of β-lactamase-encoding genes and vancomycin-resistance determinants in 156 previously characterized Gram-negative bacilli and Enterococcus spp. from bacterial cultures.

Result
The method had 100% sensitivity and between 92 and 100% of specificity for identifying blaKPC, blaVIM, blaIMP, blaNDM, blaOXA-48-like, blaCTX-M and vanA. In nine isolates, unspecific amplifications were detected. The Ct of these false positives was above 33. The Ct of the correctly identified bla and van genes did not surpass 28 and 30, respectively. None of the clinical isolates included as negative controls yielded any amplification. Therefore, the Allplex™ Entero-DR assay is a highly accurate test for the detection of important antibiotic resistance determinants. With this assay, reliable results can be obtained within 3 h. However, according to our data, samples with Ct values greater than 33 should be considered with caution.
Evaluation of the yeast surface display system for screening of functional nanobodies
Authors: Kajiwara Kaho , Aoki Wataru , Ueda Mitsuyoshi 
Published: March 2020

AbstractYeast surface display is a powerful technology used to isolate and engineer proteins to improve their activity, specificity, and stability. In this method, gene expression is regulated by promoters, and secretion efficiency is affected by secretion signals. Furthermore, both the accessibility and activity of the displayed proteins are affected by the length of anchor proteins. The ideal promoter, secretion signal, and anchor protein combination depend on the proteins of interest. In this study, we optimized a yeast surface display suitable for nanobody evaluation. We designed five display systems that used different combinations of promoters, secretion signals, and anchor proteins. Anti-hen egg-white lysozyme nanobody was used as the model nanobody. The amount of nanobodies displayed on yeast cells, the number of antigens bound to the displayed nanobodies, and the display efficiency were quantified. Overall, we improved the yeast display system for nanobody engineering and proposed its optimization.
SARS-CoV-2 and COVID-19: The most important research questions
Authors: Yuen Kit-San , Ye Zi -Wei , Fung Sin-Yee , Chan Chi-Ping , Jin Dong-Yan 
Published: March 2020

AbstractCoronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Here we highlight nine most important research questions concerning virus transmission, asymptomatic and presymptomatic virus shedding, diagnosis, treatment, vaccine development, origin of virus and viral pathogenesis.
HCC-derived EGFR mutants are functioning, EGF-dependent, and erlotinib-resistant
Authors: Sueangoen Natthaporn , Tantiwetrueangdet Anchalee , Panvichian Ravat 
Published: March 2020

Abstract
Background
Epidermal growth factor receptor (EGFR) has emerged as an important therapeutic target. Overexpression of EGFR is frequently observed in hepatocellular carcinoma (HCC) and EGFR activation has been proven to be a potential determinant of primary resistance of HCC cells to sorafenib. In our previous study, we found 13 missense mutations in EGFR exon 19–23 from hepatocellular carcinoma (HCC) tissues, but the functions of these mutations have not been determined. This study aims to determine the kinase activity and sensitivity to erlotinib, a 1st-generation EGFR-tyrosine kinase inhibitor (TKI), of seven HCC-derived mutants (K757E, N808S, R831C, V897A, P937L, T940A, and M947T).

Results
Using transduction of pBabe-puro retroviral vector with or without EGFR, we constructed and determined the function of EGFRs in NIH-3T3 cells stably harboring each of the seven mutants, as well as the erlotinib-sensitive L858R-mutant, the erlotinib-resistant T790M-mutant, and EGFR wild type (WT). Our results indicate that the seven mutants are functioning, EGF-dependent, EGFRs. Cells harboring six of the seven mutants could generate some level of EGFR phosphorylation in the absence of EGF, indicating some constitutive kinase activity, but all of the seven mutants remain primarily EGF-dependent. Our results demonstrate that erlotinib induces differential degree of apoptosis and autophagy among cells harboring different EGFRs: complete apoptosis and autophagy (cleavage of both caspase-3 and PARP, and marked LC3-II increment) in L858R-mutant; partial apoptosis and autophagy (only cleavage of caspase-3, and moderate LC3-II increment) in WT and HCC-derived mutants; and no apoptosis and minimal autophagy (no cleavage of caspase-3 and PARP, and minimal LC3-II increment) in T790M-mutant. The seven HCC-derived mutants are erlotinib-resistant, as treatment with erlotinib up to high concentration could only induce partial inhibition of EGFR phosphorylation, partial or no inhibition of AKT and ERK phosphorylation, and partial apoptosis and autophagy.

Conclusion
The seven HCC-derived EGFR mutants in this study are functioning, EGF-dependent, and erlotinib-resistant. Erlotinib induces differential degree of apoptosis and autophagy among cells harboring different EGFRs. The degree of inhibition of EGFR phosphorylation by erlotinib is the determining factor for the degree of apoptosis and autophagy amongst cells harboring EGFR mutants. This study paves the way for further investigation into the sensitivity of these HCC-derived mutants to the 3rd-generation irreversible EGFR-TKI, osimertinib.
Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision?
Authors: Jing Tian-Zhong , Qi Feng-Hui , Wang Zhi-Ying 
Published: March 2020

AbstractBackgroundThe insect gut microbiota has been shown to contribute to the host’s digestion, detoxification, development, pathogen resistance, and physiology. However, there is poor information about the ranking of these roles. Most of these results were obtained with cultivable bacteria, whereas the bacterial physiology may be different between free-living and midgut-colonizing bacteria. In this study, we provided both proteomic and genomic evidence on the ranking of the roles of gut bacteria by investigating the anal droplets from a weevil,Cryptorhynchus lapathi.ResultsThe gut lumen and the anal droplets showed qualitatively and quantitatively different subsets of bacterial communities. The results of 16S rRNA sequencing showed that the gut lumen is dominated by Proteobacteria and Bacteroidetes, whereas the anal droplets are dominated by Proteobacteria. From the anal droplets, enzymes involved in 31 basic roles that belong to 7 super roles were identified by Q-TOF MS. The cooperation between the weevil and its gut bacteria was determined by reconstructing community pathway maps, which are defined in this study. A score was used to rank the gut bacterial roles. The results from the proteomic data indicate that the most dominant role of gut bacteria is amino acid biosynthesis, followed by protein digestion, energy metabolism, vitamin biosynthesis, lipid digestion, plant secondary metabolite (PSM) degradation, and carbohydrate digestion, while the order from the genomic data is amino acid biosynthesis, vitamin biosynthesis, lipid digestion, energy metabolism, protein digestion, PSM degradation, and carbohydrate digestion. The PCA results showed that the gut bacteria form functional groups from the point of view of either the basic role or super role, and the MFA results showed that there are functional variations among gut bacteria. In addition, the variations between the proteomic and genomic data, analyzed with the HMFA method from the point of view of either the bacterial community or individual bacterial species, are presented.ConclusionThe most dominant role of gut bacteria is essential nutrient provisioning, followed by digestion and detoxification. The weevil plays a pioneering role in diet digestion and mainly digests macromolecules into smaller molecules which are then mainly digested by gut bacteria.
The relationship between the Ottawa Valve Collapse Scale (OVCS) and clinical outcomes in septoplasty patients
Authors: Staibano Phillip , Bonaparte James P. 
Published: March 2020

The Ottawa Valve Collapse scale (OVCS) was developed to classify the severity of nasal valve collapse (NVC) in patients with nasal obstruction. The goal of this study was to determine, in patients who have nasal obstruction due to a septal deviation, whether those with a higher OVCS grade will have a reduced improvement in patient-centered clinical outcomes at one-year following septoplasty with inferior turbinate diathermy compared to those with a normal or lower OVCS grade. This study was a prospective study of 78 patients who completed an assessment using the NOSE questionnaire before and at one-year following the surgical intervention. A repeated-measures ANOVA was used to asses for differences in scores between OVCS groups. There was a significant improvement in NOSE scores one year post-septoplasty ( p < 0.01). There was no difference in NOSE score improvement when comparing the grades of the OVCS at one-year (F = 0.09, p = 0.968). Though the OVCS was designed to categorize the severity of NVC preoperatively, there is no evidence that it is helpful in predicting which patients will demonstrate poor results following septoplasty. Future studies are required to further evaluate the OVCS and whether complimentary assessments will improve its clinical utility.
Mechanisms of accidental fall injuries and involved injury factors: a registry-based study
Authors: Unguryanu Tatiana Nikolaevna , Grjibovski Andrej Mechislavovich , Trovik Tordis Agnete , Ytterstad Børge , Kudryavtsev Alexander Valerievich 
Published: March 2020

AbstractBackgroundFalls are the leading cause of injury-related morbidity and mortality worldwide, but fall injury circumstances differ by age. We studied the circumstances of accidental fall injuries by age in Shenkursk District, Northwest Russia, using the data from the population-based Shenkursk Injury Registry.MethodsData on accidental fall injuries (hereafter: fall injuries) occurring in January 2015–June 2018 were extracted from the Shenkursk Injury Registry (N = 1551) and categorized by age group (0–6, 7–17, 18–59, and 60+ years). The chi-square test and ANOVA were used to compare descriptive injury variables across age groups, and a two-step cluster analysis was performed to identify homogeneous groups of fall injuries by preceding circumstances.ResultsHalf of recorded fall injuries in the 0–6 year age group occurred inside dwellings (49%). The largest cluster of falls (64%) mainly included climbing up or down on home furnishings. In the 7–17 year age group, public outdoor residential areas were the most common fall injury site (29%), and the largest cluster of falls (37%) involved physical exercise and sport or play equipment. Homestead lands or areas near a dwelling were the most typical fall injury sites in the age groups 18–59 and 60+ years (31 and 33%, respectively). Most frequently, fall injury circumstances in these groups involved slipping on ice-covered surfaces (32% in 18–59 years, 37% in 60+ years).ConclusionThe circumstances of fall injuries in the Shenkursk District varied across age groups. This knowledge can be used to guide age-specific preventive strategies in the study area and similar settings.
STRsearch: a new pipeline for targeted profiling of short tandem repeats in massively parallel sequencing data
Authors: Wang Dong , Tao Ruiyang , Li Zhiqiang , Pan Dun , Wang Zhuo , Li Chengtao , Shi Yongyong 
Published: March 2020

Abstract
Background
Short tandem repeats (STRs) are important polymorphism makers for human identification and kinship analyses in forensic science. With the continuous development of massively parallel sequencing (MPS), more laboratories have utilized this technology for forensic applications. Existing STR genotyping tools, mostly developed for whole-genome sequencing data, are not effective for MPS data. More importantly, their backward compatibility with the conventional capillary electrophoresis (CE) technology has not been evaluated and guaranteed.

Results
In this study, we developed a new end-to-end pipeline called STRsearch for STR-MPS data analysis. The STRsearch can not only determine the allele by counting repeat patterns and INDELs that are actually in the STR region, but it also translates MPS results into standard STR nomenclature (numbers and letters). We evaluated the performance of STRsearch in two forensic sequencing datasets, and the concordance with CE genotypes was 75.73 and 75.75%, increasing 12.32 and 9.05% than the existing tool named STRScan, respectively. Additionally, we trained a base classifier using sequence properties and used it to predict the probability of correct genotyping at a given locus, resulting in the highest accuracy of 96.13%.

Conclusions
All these results demonstrated that STRsearch was a better tool to protect the backward compatibility with CE for the targeted STR profiling in MPS data. STRsearch is available as open-source software at https://github.com/AnJingwd/STRsearch.
Minilaparotomy for malfunctioning peritoneal dialysis catheter by nephrologists: experiences at two centers
Authors: Sakurada Tsutomu , Kohatsu Kaori , Yamada Shohei , Sato Hirotaka , Kojima Shigeki , Koitabashi Kenichiro , Kaneshiro Nagayuki , Shibagaki Yugo 
Published: March 2020

AbstractCatheter malfunction is one of the most important complications of peritoneal dialysis (PD). We have performed minilaparotomy for catheter repair by nephrologists. This study aimed to evaluate the effectiveness and safety of the surgery. The surgery was performed 11 times on 10 PD patients with catheter malfunction (3 man, 7 women; mean age 54.3 ± 14.6 years; 4 diabetes, 3 glomerulonephritis, 3 other) at two hospitals. All patients had inflow and/or outflow obstruction. One patient had inserted the PD catheter using conventional surgical technique, and the remaining nine patients had used Moncrief-Popovich technique. Seven patients with catheters embedded using the Moncrief-Popovich technique showed catheter occlusion at the time of externalization. The remaining three patients experienced catheter obstruction 6.0 ± 2.9 months after commencing PD. The cause of obstruction was fibrin in six patients, wrapping by fimbriae of the fallopian tube in two patients, omentum wrapping in two patients. One patient had no blockage in the catheter. Operative time was 97 ± 46 min, and no intraoperative complications were observed. PD was interrupted for 5.9 ± 3.0 days and was resumed without leakage in all patients. However, catheter malfunction recurred in one patient 3 months after the surgery. The mean hospital stay was 22.4 ± 14.7 days. Minilaparotomy by nephrologists is a safety and suitable for the management of catheter malfunction. In addition, it is necessary to always consider the possibility that the catheter has been occluded at the time of externalization in the Moncrief-Popovich technique.
Impact of soil application with humic acid and foliar spray of milagro bio-stimulant on vegetative growth and mineral nutrient uptake of Nonpareil almond young trees under Nubaria conditions
Authors: Abourayya Mahmoud Sami , Kaseem Nabila Elbadawy , Mahmoud Thanaa Shaban Mohamed , Rakha Amal Masoad , Eisa Ramadan Ahmed , Amin Osama Abdelfattah 
Published: March 2020

Abstract
Background
At present, agricultural production management techniques focus on greater commitment to environmental sustainability. As such, this study was carried out during two successive seasons (2018 and 2019) to investigate the impact of two natural bio-stimulant substances: humic acid (H) and milagro (M) on vegetative growth and nutritional status of Nonpareil almond young trees grown in Experimental Research Station of National Research Centre, Nubaria, El Behera governorate, Egypt. Three-year-old uniform trees were treated at the beginning of growth season by soil application of humic acid (H) and foliar spray of milagro (M) bio-stimulant. There were ten treatments as follows: control (untreated seedlings),10 g humic acid plus 10 ml/l milagro, 20 g humic acid plus 10 ml/l milagro, 30 g humic acid plus 10 ml/l milagro,10 g humic acid plus 20 ml/l milagro, 20 g humic acid plus 20 ml/l milagro, 30 g humic acid plus 20 ml/l milagro, 10 g humic acid plus 30 ml/l milagro, 20 g humic acid plus 30 ml/l milagro, and 30 g humic acid plus 30 ml/l milagro.

Results
The results showed that different treatments improved the vegetative growth of seedlings, stem length, diameter, number of branches and leaves, leaf area, leaf fresh and dry weight, and specific leaf dry weight as well as leaf chlorophylls and minerals content comparing with untreated young trees.

Conclusions
Soil application of 30 g humic acid along with 30 ml/l milagro per young tree as foliar spray was the promising treatment as a new fertilization technique that is non-chemical, low-cost, and environmentally safe for improving growth and nutritional status of Nonpareil almond young trees under Nubaria conditions.
Postoperative change in patellofemoral alignment following closing-wedge distal femoral osteotomy performed for valgus osteoarthritic knees
Authors: Akaoka Yusuke , Nakayama Hiroshi , Iseki Tomoya , Kanto Ryo , Tensho Keiji , Yoshiya Shinichi 
Published: March 2020

Abstract
Purpose
To evaluate the postoperative change in patellar position after medial closed distal femoral osteotomy (DFO) performed for valgus osteoarthritic knees.

Methods
The study included 21 consecutive knees in 20 patients undergoing DFO. A minimum of 2-year follow-up data was obtained for all subjects with a mean follow-up period of 42 months (range 31–59 months). The patellar position was evaluated on plain radiographs preoperatively, 1-year postoperatively, and 2-year postoperatively. For patellar height, the modified Insall–Salvati Index (mISI), modified Caton–Deschamps Index (mCDI) and modified Blackburne–Peel Index (mBPI) were measured on the standing lateral radiographs. Patellofemoral alignment on the axial plane was assessed on skyline views with 30° flexion based on the measurements for lateral patellar tilt (LPT) and lateral patellar shift (LPS). Measured values at pre- and postoperative phases were statistically compared using a two-way analysis of variance.

Results
All indices including mISI, mCDI, mBPI, LPT and LPS showed no statistically significant postoperative changes.

Conclusion
Medial closed-wedge DFO performed for valgus osteoarthritic knees did not significantly influence patellofemoral alignment either on the sagittal or axial plane. Therefore, to highlight the clinical relevance of our findings, medial closed-wedge DFO for the valgus knee does not adversely affect the patellofemoral joint.

Level of evidence
Level IV, case series.
Seismic stratigraphy interpretation by deep convolutional neural networks: A semisupervised workflow
Authors: Di Haibin , Li Zhun , Maniar Hiren , Abubakar Aria 
Published: March 2020

Depicting geologic sequences from 3D seismic surveying is of significant value to subsurface reservoir exploration, but it is usually time- and labor-intensive for manual interpretation by experienced seismic interpreters. We have developed a semisupervised workflow for efficient seismic stratigraphy interpretation by using the state-of-the-art deep convolutional neural networks (CNNs). Specifically, the workflow consists of two components: (1) seismic feature self-learning (SFSL) and (2) stratigraphy model building (SMB), each of which is formulated as a deep CNN. Whereas the SMB is supervised by knowledge from domain experts and the associated CNN uses a similar network architecture typically used in image segmentation, the SFSL is designed as an unsupervised process and thus can be performed backstage while an expert prepares the training labels for the SMB CNN. Compared with conventional approaches, the our workflow is superior in two aspects. First, the SMB CNN, initialized by the SFSL CNN, successfully inherits the prior knowledge of the seismic features in the target seismic data. Therefore, it becomes feasible for completing the supervised training of the SMB CNN more efficiently using only a small amount of training data, for example, less than 0.1% of the available seismic data as demonstrated in this paper. Second, for the convenience of seismic experts in translating their domain knowledge into training labels, our workflow is designed to be applicable to three scenarios, trace-wise, paintbrushing, and full-sectional annotation. The performance of the new workflow is well-verified through application to three real seismic data sets. We conclude that the new workflow is not only capable of providing robust stratigraphy interpretation for a given seismic volume, but it also holds great potential for other problems in seismic data analysis.
Activated pathogenic Th17 lymphocytes induce hypertension following high-fructose intake in Dahl salt-sensitive (SS) but not Dahl salt-resistant (SR) rats
Authors: Lee Eunjo , Kim Namkyung , Kang Jinjoo , Yoon Sangwon , Lee Hae-Ahm , Jung Hanna , Kim Sang-Hyun , Kim Inkyeom 
Published: March 2020

Objectives: High-salt or high-fructose intakes are risk factors for hypertension via oxidative stress and inflammation. T helper (Th)17 lymphocytes play an important role in the development of hypertension. We tested the hypothesis that activation of pathogenic Th17 lymphocytes induces hypertension after high-fructose intake in Dahl salt-sensitive (SS) but not Dahl salt-resistant (SR) rats.Methods: Eight-week-old male SS and SR rats were offered 20% fructose solution or tap water only for 4 weeks. Systolic blood pressure was measured by the tail-cuff method. T lymphocytes (Th17 and T regulatory (Treg)) profiling was determined via flow cytometry. The expression of Th17 -related (interleukin (IL)-17A, IL-17RA,IL-23R and retinoic acid receptor-related orphan receptor (ROR) γt) and Treg-related (IL-10, CD25, forkhead box (Fox)P3, and TGF-ß) factors were measured via ELISA or qRT-PCR. Th17 lymphocytes isolated from high fructose-fed SS rats were intraperitoneally injected into recipient SS and SR rats. Moreover, recombinant IL-23 protein was subcutaneously injected into SS and SR rats to induce hypertension.Results: High-fructose intake induced hypertension via the activation of pathogenic Th17 lymphocytes in SS but not SR rats. Injection of activated Th17 lymphocytes isolated from fructose-fed SS rats induced hypertension via increase of serum IL-17A in only recipient SS rat. In addition, injection of IL-23 induced hypertension via activation of pathogenic Th17 lymphocytes in only SS rats.Conclusion: Activation of pathogenic Th17 lymphocytes induces hypertension after high-fructose intake in SS but not SR rats. These results implicate that immunologic tolerance plays an important role in the protection against hypertension in SR.