bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches
Authors: Lo-Thong Ophélie , Charton Philippe , Cadet Xavier F. , Grondin-Perez Brigitte , Saavedra Emma , Damour Cédric , Cadet Frédéric 
Published: August 2020

AbstractMetabolic pathway modeling plays an increasing role in drug design by allowing better understanding of the underlying regulation and controlling networks in the metabolism of living organisms. However, despite rapid progress in this area, pathway modeling can become a real nightmare for researchers, notably when few experimental data are available or when the pathway is highly complex. Here, three different approaches were developed to model the second part of glycolysis of E. histolytica as an application example, and have succeeded in predicting the final pathway flux: one including detailed kinetic information (white-box), another with an added adjustment term (grey-box) and the last one using an artificial neural network method (black-box). Afterwards, each model was used for metabolic control analysis and flux control coefficient determination. The first two enzymes of this pathway are identified as the key enzymes playing a role in flux control. This study revealed the significance of the three methods for building suitable models adjusted to the available data in the field of metabolic pathway modeling, and could be useful to biologists and modelers.
Karyotype changes in long-term cultured tick cell lines
Authors: Kotsarenko Kateryna , Vechtova Pavlina , Lieskovska Jaroslava , Füssy Zoltán , Cabral-de-Mello Diogo C. , Rego Ryan O. M. , Alberdi Pilar , Collins Marisol , Bell-Sakyi Lesley , Sterba Jan , Grubhoffer Libor 
Published: August 2020

AbstractTick cell lines are an easy-to-handle system for the study of viral and bacterial infections and other aspects of tick cellular processes. Tick cell cultures are often continuously cultivated, as freezing can affect their viability. However, the long-term cultivation of tick cells can influence their genome stability. In the present study, we investigated karyotype and genome size of tick cell lines. Though 16S rDNA sequencing showed the similarity between Ixodes spp. cell lines at different passages, their karyotypes differed from 2n = 28 chromosomes for parental Ixodes spp. ticks, and both increase and decrease in chromosome numbers were observed. For example, the highly passaged Ixodes scapularis cell line ISE18 and Ixodes ricinus cell lines IRE/CTVM19 and IRE/CTVM20 had modal chromosome numbers 48, 23 and 48, respectively. Also, the Ornithodoros moubata cell line OME/CTVM22 had the modal chromosome number 33 instead of 2n = 20 chromosomes for Ornithodoros spp. ticks. All studied tick cell lines had a larger genome size in comparison to the genomes of the parental ticks. Thus, highly passaged tick cell lines can be used for research purposes, but possible differences in encoded genetic information and downstream cellular processes, between different cell populations, should be taken into account.
Cytochrome P450 inhibition potential and initial genotoxic evaluation of 14-O-[(4,6-diaminopyrimidine-2-yl)thioacetyl] mutilin
Authors: Fu Yunxing , Yi Yunpeng , Fan Yuan , Shang Ruofeng 
Published: August 2020

Abstract14-O-[(4,6-Diaminopyrimidine-2-yl)thioacetyl] mutilin (DPTM) is a promising drug candidate with excellent antibacterial activity against Gram-positive bacteria. The present study was designed to characterize its Cytochrome P450 (CYP) enzymes inhibition activities and the genotoxicity with the standard Ames test. We determined the inhibitory effects of DPTM on CYP1A2, CYP2D1/6, CYP2E1, CYP2C11/9 and CYP3A/4 in rat liver microsomes (RLMs) and in human liver microsomes (HLMs). The mRNA expressions of the above CYP isoforms and their transcriptional regulators were also evaluated using the Hep G2 cell model. The results showed DPTM exhibited a moderate inhibitory potential against CYP3A/4 (IC50 values of 10 ± 2 and 8 ± 2 μM, respectively) and weak against the other CYP enzymes based on their IC50 values. Compared to the control, CYP isoforms and their transcriptional regulators mRNA expressions significantly increased when the Hep G2 cells were treated with DPTM for a certain period of time. In the Ames test, Salmonella strains TA97, TA98, TA100, TA102 and TA1535 were treated with or without the metabolic activation (S9). Analysis showed the average number of revertant colonies per plate was less in double in the groups treated with DPTM than that in the negative control plate and showed no dose-related increase.
DNA barcodes for delineating Clerodendrum species of North East India
Authors: Gogoi Barbi , Wann S. B. , Saikia S. P. 
Published: August 2020

AbstractThe diversified genus of Clerodendrum with its complex evolutionary history leads to taxonomic mystification. Unlike traditional taxonomic methods, DNA barcoding could be a promising tool for the identification and conservation of Clerodendrum species. This study was attempted to develop an efficient barcode locus in Clerodendrum species of North East India. We evaluated four barcode candidates (ITS2, matK, rbcL, ycf1) and its combinations in different Clerodendrum species. The reliability of barcodes to distinguish the species were calculated using genetic pairwise distances, intra- and inter-specific diversity, barcode gap, and phylogenetic tree-based methods. The results exemplify that matK posse’s maximum number of variables and parsimony-informative sites (103/100), intra- (0.021 ± 0.001) and inter- (0.086 ± 0.005) specific divergences and species resolution rate (89.1%) followed by ITS2, ycf1, and rbcL. Among the combinatorial locus, ITS2 + matK showed the best species discrimination with distinctive barcode gaps. Therefore, we tentatively suggest that the combination of ITS2 + matK as core barcode for Clerodendrum and converted into quick response (QR) code. Hence, this finding indicates that DNA barcoding could provide consistent resources for species discrimination and resolve taxonomic controversies of the genus as well as set a preliminary assessment toward its biodiversity.
The grasper-integrated disposable flexible cystoscope is comparable to the reusable, flexible cystoscope for the detection of bladder cancer
Authors: Seyam Raouf M. , Zeitouni Omar M. , Alsibai Tarek M. , AlAyoub Abdulrahman J. , Al-Qassab Osamah M. , AlDeiry Mhd A. , Zino Ahmad O. , Hulwi Hasan S. , Mokhtar Alaa A. , Shahbaz Mahmoud , Junejo Noor N. , Alotaibi Mohamed F. , Alzahrani Hassan M. , Alothman Khaled I. , Alkhateeb Sultan S. , Al-Hussain Turki O. , Altaweel Waleed M. 
Published: August 2020

AbstractFlexible cystoscopy under local anaesthesia is standard for the surveillance of bladder cancer. Frequently, several reusable cystoscopes fail to reprocess. With the new grasper incorporated single-use cystoscope for retrieval of ureteric stents, we explored the feasibility of using it off-label for diagnosis and the detection of bladder cancer. Consecutive diagnostic flexible cystoscopies between Mar 2016 and Nov 2018 were reviewed comparing the reusable versus the disposable cystoscopes. A total of 390 patients underwent 1211 cystoscopies. Median age was 61.5 years (SD 14.2, 18.8–91.4), males 331 (84.9%) and females 59 (15.1%). Indication for cystoscopy was prior malignancy in 1183 procedures (97.7%), haematuria 19 (1.6%) or bladder mass 7 (0.6%). There were 608 reusable and 603 disposable cystoscopies. There was no significant difference between groups at baseline in age, sex, BMI, smoking status, or prior tumor risk category. There was no significant difference in positive findings (123/608, 20.2% vs 111/603, 18.4%, p = 0.425) or cancer detection rates (95/608, 15.6% vs 88/603, 14.4%, p 0.574) among the two groups, respectively. We conclude that the disposable grasper integrated cystoscope is comparable to reusable cystoscope in the detection of bladder cancer.
Impaired chondrocyte U3 snoRNA expression in osteoarthritis impacts the chondrocyte protein translation apparatus
Authors: Ripmeester Ellen G. J. , Caron Marjolein M. J. , van den Akker G. G. H. , Surtel Don A. M. , Cremers Andy , Balaskas Panagiotis , Dyer Philip , Housmans Bas A. C. , Chabronova Alzbeta , Smagul Aibek , Fang Yongxiang , van Rhijn Lodewijk W. , Peffers Mandy J. , Welting Tim J. M. 
Published: August 2020

AbstractAlthough pathways controlling ribosome activity have been described to regulate chondrocyte homeostasis in osteoarthritis, ribosome biogenesis in osteoarthritis is unexplored. We hypothesized that U3 snoRNA, a non-coding RNA involved in ribosomal RNA maturation, is critical for chondrocyte protein translation capacity in osteoarthritis. U3 snoRNA was one of a number of snoRNAs with decreased expression in osteoarthritic cartilage and osteoarthritic chondrocytes. OA synovial fluid impacted U3 snoRNA expression by affecting U3 snoRNA gene promoter activity, while BMP7 was able to increase its expression. Altering U3 snoRNA expression resulted in changes in chondrocyte phenotype. Interference with U3 snoRNA expression led to reduction of rRNA levels and translational capacity, whilst induced expression of U3 snoRNA was accompanied by increased 18S and 28S rRNA levels and elevated protein translation. Whole proteome analysis revealed a global impact of reduced U3 snoRNA expression on protein translational processes and inflammatory pathways. For the first time we demonstrate implications of a snoRNA in osteoarthritis chondrocyte biology and investigated its role in the chondrocyte differentiation status, rRNA levels and protein translational capacity.
Factors related to the psychological impact of malocclusion in adolescents
Authors: Iranzo-Cortés José Enrique , Montiel-Company José Maria , Bellot-Arcis Carlos , Almerich-Torres Teresa , Acevedo-Atala Claudia , Ortolá-Siscar José Carmelo , Almerich-Silla José Manuel 
Published: August 2020

AbstractTo study the association between orthodontic treatment need and the psychosocial impact of dental aesthetics in a sample of adolescents, as well as other associated factors. A transversal study was conducted on 1,158 adolescents (12–16 years old) examined at the schools selected for the 2018 epidemiological study on oral health in the Comunidad Valenciana (Spain). The need for orthodontic treatment was determined by DAI and IOTN. The psychosocial impact was established by the Psychosocial Impact of Dental Aesthetics Questionnaire (PIDAQ). Other variables considered were sex, social class, DMFT index and Body-Mass Index, and having previously worn or presently wearing an orthodontic device. A lineal regression statistical technique was applied to study the significant associations with the scoring obtained in PIDAQ. The PIDAQ scores revealed a significant and positive lineal relationship with regard to need for orthodontic treatment: DAI (ẞ = 0.20) and IOTN-DHC (ẞ = 4.87), in women (ẞ = 2.66) and a negative one for having previously worn an orthodontic device (ẞ = − 5.74). The rest of the variables had no statistical significance (p > 0.05). The psychosocial impact of dental aesthetics in adolescents is associated with the presence of malocclusion and the female sex, while the condition of having previously worn an orthodontic device reduces the psychosocial impact.
A network percolation-based contagion model of flood propagation and recession in urban road networks
Authors: Fan Chao , Jiang Xiangqi , Mostafavi Ali 
Published: August 2020

AbstractIn this study, we propose a contagion model as a simple and powerful mathematical approach for predicting the spatial spread and temporal evolution of the onset and recession of floodwaters in urban road networks. A network of urban roads resilient to flooding events is essential for the provision of public services and for emergency response. The spread of floodwaters in urban networks is a complex spatial–temporal phenomenon. This study presents a mathematical contagion model to describe the spatial–temporal spread and recession process of floodwaters in urban road networks. The evolution of floods within networks can be captured based on three macroscopic characteristics—flood propagation rate ($$\beta$$
β
), flood incubation rate ($$\alpha$$
α
), and recovery rate ($$\mu$$
μ
)—in a system of ordinary differential equations analogous to the Susceptible-Exposed-Infected-Recovered (SEIR) model. We integrated the flood contagion model with the network percolation process in which the probability of flooding of a road segment depends on the degree to which the nearby road segments are flooded. The application of the proposed model is verified using high-resolution historical data of road flooding in Harris County during Hurricane Harvey in 2017. The results show that the model can monitor and predict the fraction of flooded roads over time. Additionally, the proposed model can achieve 90% precision and recall for the spatial spread of the flooded roads at the majority of tested time intervals. The findings suggest that the proposed mathematical contagion model offers great potential to support emergency managers, public officials, citizens, first responders, and other decision-makers for flood forecast in road networks.
Identification of C3 as a therapeutic target for diabetic nephropathy by bioinformatics analysis
Authors: Tang ShuMei , Wang XiuFen , Deng TianCi , Ge HuiPeng , Xiao XiangCheng 
Published: August 2020

AbstractThe pathogenesis of diabetic nephropathy is not completely understood, and the effects of existing treatments are not satisfactory. Various public platforms already contain extensive data for deeper bioinformatics analysis. From the GSE30529 dataset based on diabetic nephropathy tubular samples, we identified 345 genes through differential expression analysis and weighted gene coexpression correlation network analysis. GO annotations mainly included neutrophil activation, regulation of immune effector process, positive regulation of cytokine production and neutrophil-mediated immunity. KEGG pathways mostly included phagosome, complement and coagulation cascades, cell adhesion molecules and the AGE-RAGE signalling pathway in diabetic complications. Additional datasets were analysed to understand the mechanisms of differential gene expression from an epigenetic perspective. Differentially expressed miRNAs were obtained to construct a miRNA-mRNA network from the miRNA profiles in the GSE57674 dataset. The miR-1237-3p/SH2B3, miR-1238-5p/ZNF652 and miR-766-3p/TGFBI axes may be involved in diabetic nephropathy. The methylation levels of the 345 genes were also tested based on the gene methylation profiles of the GSE121820 dataset. The top 20 hub genes in the PPI network were discerned using the CytoHubba tool. Correlation analysis with GFR showed that SYK, CXCL1, LYN, VWF, ANXA1, C3, HLA-E, RHOA, SERPING1, EGF and KNG1 may be involved in diabetic nephropathy. Eight small molecule compounds were identified as potential therapeutic drugs using Connectivity Map.
Occurrence of cold sensitivity in carpal tunnel syndrome and its effects on surgical outcome following open carpal tunnel release
Authors: Zimmerman Malin , Nyman Erika , Dahlin Lars B. 
Published: August 2020

AbstractCold sensitivity is common following nerve injuries in the upper extremity, but is less well studied in carpal tunnel syndrome (CTS). We investigated cold sensitivity in CTS and its effects on surgical outcome. A search of the Swedish National Registry for Hand Surgery (HAKIR) for open carpal tunnel releases (OCTR) from 2010–2016 identified 10,746 cases. Symptom severity questionnaires (HQ-8; HAKIR questionnaire 8, eight Likert-scale items scored 0–100, one item on cold sensitivity) and QuickDASH scores before and after surgery were collected. Patient mean age was 56 ± SD 16 years, and 7,150/10,746 (67%) were women. Patients with severe cold sensitivity (defined as cold intolerance symptom severity score > 70; n = 951), scored significantly higher on QuickDASH at all time points compared to those with mild cold sensitivity (cold intolerance symptom severity scores ≤ 30, n = 1,532); preoperatively 64 [50–75] vs. 40 [25–55], at three months 32 [14–52] vs. 18 [9–32] and at 12 months 25 [7–50] vs. 9 [2–23]; all p < 0.0001. Severe cold sensitivity predicted higher postoperative QuickDASH scores at three [12.9 points (95% CI 10.2–15.6; p < 0.0001)] and at 12 months [14.8 points (11.3–18.4; p < 0.0001)] compared to mild cold sensitivity, and adjustment for a concomitant condition in the hand/arm, including ulnar nerve compression, did not influence the results. Cold sensitivity improves after OCTR. A higher preoperative degree of cold sensitivity is associated with more preoperative and postoperative disability and symptoms than a lower degree of cold sensitivity, but with the same improvement in QuickDASH score.
Akupunktur und ihr Einfluss auf das Immunsystem – Hintergründe und Wirkungen beim landwirtschaftlichen Nutztier
Authors: Kuhlow Tim , Mohr Elmar 
Published: August 2020

ZusammenfassungIm Rahmen der vorliegenden Literaturstudie wurden die aktuellen Kenntnisse über den Zusammenhang zwischen Akupunkturbehandlung und Reaktion des Immunsystems zusammengefasst. Die Akupunktur spricht über eine Kopplung von Nerven- und Immunsystem sowohl unspezifische angeborene als auch spezifische Abwehrmechanismen an. Diesbezüglich wurden 69 wissenschaftliche Studien herangezogen und ausgewertet. Die Ergebnisse lassen darauf schließen, dass über eine Stimulation peripherer Nervenbahnen an definierten Punkten eine Immunmodulation erfolgt. Primär wird dabei der angeborene unspezifische Teil des Immunsystems angesprochen. Einer der zu diesem Zweck häufig genannten Akupunkturpunkte ist Ma 36.
Forward and Retro Locomotion Training on Anthropometrical Body
Compositions and Aerobic Performance
Authors: Kachanathu Shaji John , Al-Kheraif Abdulaziz A. , Alenazi Aqeel M , Hafez Ashraf R , Nuhmani Shibili , Algarni Abdulrahman D 
Published: August 2020

Abstract
Background Forward and retro locomotion on a treadmill is a common tool
for lower extremity rehabilitation in the clinical setting. The purpose of this
study was to evaluate effect on anthropometrical body composition adaptations
and aerobic performance during forward and retro locomotion training on a
treadmill at 10-degree inclinations.
Methods A convenience sample of 30 healthy male subjects with mean age of
20.93±2.54 years, participated in the study. Subjects were divided into
2 groups, Forward Locomotion Group (FLG) and Retro Locomotion Group (RLG)
(n=15) and performed forward and retro locomotion training on a
treadmill at 10-degree inclination respectively for duration of 6 weeks. Study
outcomes such as aerobic performance and anthropometrical body composition were
measured at pre and post intervention phases.
Results Although both FLG and RLG training improved aerobic performance
significantly. However, RLG reported a significant improvement as compared to
FLG in the above parameters. Whereas, anthropometrical body composition changes
are not found to be significant even after 6 weeks of intervention in both
groups.
Conclusion Both the forward and retro locomotion training improved
aerobic performance but not the body composition variables, also retro
locomotion training was more effective than forward locomotion in improving
aerobic performance.
The Prevalence of Joint Hypermobility among High School and University Students
Authors: Kashif Muhammad , Albalwi Abdulaziz Aoudh , Fatima Nisar , Fatima Nasreen 
Published: August 2020

Abstract
Background Joint hypermobility (JH) prevails worldwide, especially in
children and females, although its consequences have been neglected and
understated by health care practitioners. JH can lead to musculoskeletal
injuries, which can have serious negative effects on a person’s health.
This topic has not been sufficiently studied in Pakistan so this study will help
in filling the gap.
Objective This study aims to determine the prevalence of asymptomatic
joint hypermobility, among high school and university students, at 2
institutions in Pakistan.
Methodology A total of 1,749 students, with an average age of 16.96
(range 14–26), who studied at Dar e Arqam School or Riphah International
University in Faisalabad were examined. The Beighton criteria system was used to
determine the prevalence of JH on the basis of minor criteria for hypermobility
(1/9–3/9 joints, indicating localized and peripheral
hypermobility) and major criteria (4/9 joints or above 4 joints,
indicating generalized hypermobility).
Results The results showed that the prevalence of JH in female students
studying in high school was 61.9%, and in female university students,
the prevalence was 58.4%. Minor hypermobility was most common among
university students in their 5th to 8th semester (60.3%), while major
hypermobility occurred most frequently in high school students of 9th grade
(80.1%). In addition, the results of the study established that joint
hypermobility was most common in the elbow joint on the right side: 673
(94.7%) male and 1,002 (96.5%) female students.
Conclusion The prevalence of common hypermobility, especially generalized
hypermobility, was high among female high school students compared to university
students, and hypermobility in the right trunk and elbow joint was more common
compared to other joints.
Ocular Sarcoidosis
Authors: Sève Pascal , Jamilloux Yvan , Tilikete Caroline , Gerfaud-Valentin Mathieu , Kodjikian Laurent , El Jammal Thomas 
Published: August 2020

AbstractSarcoidosis is one of the leading causes of inflammatory eye disease. Any part of the eye and its adnexal tissues can be involved. Uveitis and optic neuropathy are the main manifestations, which may require systemic treatment. Two groups of patients with sarcoid uveitis can be distinguished: one of either sex and any ethnicity in which ophthalmological findings are various and another group of elderly Caucasian women with mostly chronic posterior uveitis. Clinically isolated uveitis revealing sarcoidosis remains a strictly ocular condition in a large majority of cases. Although it can be a serious condition involving functional prognosis, early recognition in addition to a growing therapeutic arsenal (including intravitreal implant) has improved the visual prognosis of the disease in recent years. Systemic corticosteroids are indicated when uveitis does not respond to topical corticosteroids or when there is bilateral posterior involvement, especially macular edema. In up to 30% of the cases that require an unacceptable dosage of corticosteroids to maintain remission, additional immunosuppression is used, especially methotrexate. As with other forms of severe noninfectious uveitis, monoclonal antibodies against tumor necrosis factor-α have been used. However, only very rarely does sarcoid uveitis fail to respond to combined corticosteroids and methotrexate therapy, a situation that should suggest either poor adherence or another granulomatous disease. Optic neuropathy often affects women of African and Caribbean origins. Some authors recommend that patients should be treated with high-dose of corticosteroids and concurrent immunosuppression from the onset of this manifestation, which is associated with a poorer outcome.