bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of hydantoin based Decaprenylphosphoryl-β-d-Ribose Oxidase (DprE1) inhibitors as antimycobacterial agents using computational tools
Authors: Mali Suraj N. , Pandey Anima , Bhandare Richie R. , Shaik Afzal B. 
Published: September 2022

AbstractTuberculosis (TB) is one of the emerging infectious diseases in the world. DprE1 (Decaprenylphosphoryl-β-d-ribose 2′-epimerase), an enzyme accountable for mycobacterial cell wall synthesis was the first drug gable target based on discoveries of inhibitors via HTS (high throughput screening). Since then, many literature reports have been published so far enlightening varieties of chemical scaffolds acting as inhibitors of DprE1. Herein, in our present study, we have developed statistically robust GA-MLR (genetic algorithm multiple linear regression), atom-based as well as field based-3D-QSAR models. Both atom-based as well as field based-3D-QSAR models (internally as well as externally validated) were obtained with robust Training set, R2 > 0.69 and Test set, Q2 > 0.50. We have also developed top ranked 5 point hypothesis AAAHR_1 among 14 CPHs (common pharmacophore hypotheses). We found that our dataset molecule had more docking score (XP mode = − 9.068 kcal/mol) than the standards isoniazid and ethambutol; when docked into binding pockets of enzyme 4P8C with Glide module. We further queried our best docked dataset molecule 151 for ligand based virtual screening using “SwissSimilarity” platform. Among 9 identified hits, we found ZINC12196803 had best binding energies and docking score (docking score = − 9.437 kcal/mol, MMGBSA dgBind = − 70.508 kcal/mol). Finally, our molecular dynamics studies for 1.2–100 ns depicts that these complexes are stable. We have also carried out in-silico ADMET predictions, Cardiac toxicity, ‘SwissTargetPredictions’ and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding energy calculations for further explorations of dataset as well as hit molecules. Our current studies showed that the hit molecule ZINC12196803 may enlighten the path for future developments of DprE1 inhibitors.
Influence of electrode potential, pH and NAD+ concentration on the electrochemical NADH regeneration
Authors: Aamer Emad , Thöming Jorg , Baune Michael , Reimer Nicholas , Dringen Ralf , Romero Manuela , Bösing Ingmar 
Published: September 2022

AbstractElectrochemical NAD+ reduction is a promising method to regenerate NADH for enzymatic reactions. Many different electrocatalysts have been tested in the search for high yields of the 1,4-isomer of NADH, the active NADH, but aside from electrode material, other system parameters such as pH, electrode potential and educt concentration also play a role in NADH regeneration. The effect of these last three parameters and the mechanisms behind their influence on NADH regeneration was systematically studied and presented in this paper. With percentages of active NADH ranging from 10 to 70% and faradaic efficiencies between 1 and 30%, it is clear that all three system parameters drastically affect the reaction outcome. As a proof of principle, the NAD+ reduction in the presence of pyruvate and lactate dehydrogenase was performed. It could be shown that the electrochemical NADH regeneration can also be done successfully in parallel to enzymatically usage of the regenerated cofactor.
Environment is associated with chytrid infection and skin microbiome richness on an amphibian rich island (Taiwan)
Authors: Schmeller Dirk S. , Cheng Tina , Shelton Jennifer , Lin Chun-Fu , Chan-Alvarado Alan , Bernardo-Cravo Adriana , Zoccarato Luca , Ding Tzung-Su , Lin Yu-Pin , Swei Andrea , Fisher Matthew C. , Vredenburg Vance T. , Loyau Adeline 
Published: September 2022

AbstractGrowing evidence suggests that the origins of the panzootic amphibian pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are in Asia. In Taiwan, an island hotspot of high amphibian diversity, no amphibian mass mortality events linked to Bd or Bsal have been reported. We conducted a multi-year study across this subtropical island, sampling 2517 individuals from 30 species at 34 field sites, between 2010 and 2017, and including 171 museum samples collected between 1981 and 2009. We analyzed the skin microbiome of 153 samples (6 species) from 2017 in order to assess any association between the amphibian skin microbiome and the probability of infection amongst different host species. We did not detect Bsal in our samples, but found widespread infection by Bd across central and northern Taiwan, both taxonomically and spatially. Museum samples show that Bd has been present in Taiwan since at least 1990. Host species, geography (elevation), climatic conditions and microbial richness were all associated with the prevalence of infection. Host life-history traits, skin microbiome composition and phylogeny were associated with lower prevalence of infection for high altitude species. Overall, we observed low prevalence and burden of infection in host populations, suggesting that Bd is enzootic in Taiwan where it causes subclinical infections. While amphibian species in Taiwan are currently threatened by habitat loss, our study indicates that Bd is in an endemic equilibrium with the populations and species we investigated. However, ongoing surveillance of the infection is warranted, as changing environmental conditions may disturb the currently stable equilibrium.
GnRH agonist-triggering ovulation in women with advanced age
Authors: Rahav Koren Roni , Miller Netanella , Moran Rimon , Decter Dean , Berkowitz Arie , Haikin Herzberger Einat , Wiser Amir 
Published: September 2022

AbstractThis study evaluates the effect of GnRH agonist (GnRHa) trigger for ovulation induction among women with advanced maternal age (AMA). This is a retrospective study performed at a single assisted reproductive technology centre, 2012 to 2020. A total of 306 patients with 515 IVF cycles who were triggered with GnRHa for Ovum Pick Up (OPU), were divided into two groups according to maternal age: age ≥ 40 and age < 40. The groups were compared for demographics, stimulation parameters of IVF treatment and IVF treatment outcomes. The patients in the age < 40 group were approximately 10 years younger than the patients in the age ≥ 40 group (31 ± 5.4 vs. 41.5 ± 1.3 years, p < 0.001). The age ≥ 40 group had significantly higher mean E2/retrieved oocytes ratio, compared to the age < 40 group (310.3 ± 200.6 pg/ml vs. 239 ± 168.2 pg/ml, p = 0.003), and a lower mean MII/retrieved oocyte (35 ± 37.8 vs. 43.4 ± 35.9, p = 0.05, respectively). Multivariable logistic regression analysis for E2/retrieved oocytes demonstrated that age < 40 and total dose of gonadotropins were significant variables. In conclusion, GnRHa for ovulation triggering in high responder patients prior to OPU appears to be a good option for AMA. However, this population is characterized by different parameters of ovarian response that require further evaluation.
Insight into the pulmonary molecular toxicity of heated tobacco products using human bronchial and alveolar mucosa models at air–liquid interface
Authors: Rahman Mizanur , Irmler Martin , Introna Micol , Beckers Johannes , Palmberg Lena , Johanson Gunnar , Upadhyay Swapna , Ganguly Koustav 
Published: September 2022

AbstractHeated tobacco products (HTP) are novel nicotine delivery products with limited toxicological data. HTP uses heating instead of combustion to generate aerosol (HTP-smoke). Physiologically relevant human bronchial and alveolar lung mucosa models developed at air–liquid interface were exposed to HTP-smoke to assess broad toxicological response (n = 6–7; ISO puffing regimen; compared to sham; non-parametric statistical analysis; significance: p < 0.05). Elevated levels of total cellular reactive oxygen species, stress responsive nuclear factor kappa-B, and DNA damage markers [8-hydroxy-2′-deoxyguanosine, phosphorylated histone H2AX, cleaved poly-(ADP-Ribose) polymerase] were detected in HTP-smoke exposed bronchial and/or alveolar models. RNA sequencing detected differential regulation of 724 genes in the bronchial- and 121 genes in the alveolar model following HTP-smoke exposure (cut off: p ≤ 0.01; fold change: ≥ 2). Common enriched pathways included estrogen biosynthesis, ferroptosis, superoxide radical degradation, xenobiotics, and α-tocopherol degradation. Secreted levels of interleukin (IL)1ꞵ and IL8 increased in the bronchial model whereas in the alveolar model, interferon-γ and IL4 increased and IL13 decreased following HTP-smoke exposure. Increased lipid peroxidation was detected in HTP-smoke exposed bronchial and alveolar models which was inhibited by ferrostatin-1. The findings form a basis to perform independent risk assessment studies on different flavours of HTP using different puffing topography and corresponding chemical characterization.
Simultaneous monitoring of mouse grip strength, force profile, and cumulative force profile distinguishes muscle physiology following surgical, pharmacologic and diet interventions
Authors: Munier Joseph J. , Pank Justin T. , Severino Amie , Wang Huan , Zhang Peixiang , Vergnes Laurent , Reue Karen 
Published: September 2022

AbstractGrip strength is a valuable preclinical assay to study muscle physiology in disease and aging by directly determining changes in muscle force generation in active laboratory mice. Existing methods to statistically evaluate grip strength, however, have limitations in the power and scope of the physiological features that are assessed. We therefore designed a microcontroller whose serial measure of resistance-based force enables the simultaneous readout of (1) peak grip strength, (2) force profile (the non-linear progress of force exerted throughout a standard grip strength trial), and (3) cumulative force profile (the integral of force with respect to time of a single grip strength trial). We hypothesized that muscle pathologies of different etiologies have distinct effects on these parameters. To test this, we used our apparatus to assess the three muscle parameters in mice with impaired muscle function resulting from surgically induced peripheral pain, genetic peripheral neuropathy, adverse muscle effects induced by statin drug, and metabolic alterations induced by a high-fat diet. Both surgically induced peripheral nerve injury and statin-associated muscle damage diminished grip strength and force profile, without affecting cumulative force profile. Conversely, genetic peripheral neuropathy resulting from lipin 1 deficiency led to a marked reduction to all three parameters. A chronic high-fat diet led to reduced grip strength and force profile when normalized to body weight. In high-fat fed mice that were exerted aerobically and allowed to recover for 30 min, male mice exhibited impaired force profile parameters, which female mice were more resilient. Thus, simultaneous analysis of peak grip strength, force profile and cumulative force profile distinguishes the muscle impairments that result from distinct perturbations and may reflect distinct motor unit recruitment strategies.
Phyto-Fenton remediation of a dichloro-diphenyl-trichloroethane contaminated site in Ha Tinh Province, Vietnam
Authors: Dang Hieu Minh , Vo Cong Huu , Inagaki Yoshihiko , Dao Nhung Thi , Tran Trinh Dinh , Tran Thao Minh , Nguyen Thinh Thi , Ho Hang Thi Thuy , Tran Vien Duc , Sakakibara Yutaka 
Published: September 2022

AbstractA field trial was conducted at a site in Cam Binh commune, Ha Tinh province, Vietnam, highly contaminated with organo-pesticides. The phyto-Fenton process was applied to remove pesticide residues in soils. In addition to magnetite (Fe3O4) materials added to the soils, fertilizers and elicitors for oxidative burst were also added in the different experimental treatments. Dichloro-diphenyl-trichloroethane (DDT) and isomers were removed in all experimental lots. The removal efficiency was highest in lot B1, a site where only iron materials were added. The removal efficiency and the final content of DDTs in B1 were 98.4% and 0.009 mg kg−1, respectively. In the presence of elicitors, the conversion of DDT to dichloro-diphenyl-dichloroethylene was more favorable. Analysis of soil properties indicated that the phyto-Fenton process can occur at neutral soil pH, and when there are only small changes in soil organic carbon content and cation exchange capacities. Shifts in the composition of the microbial communities were observed. Further studies on the interactions between materials added to soil, plants, and the soil microbiome are needed to understand the mechanism of action of the phyto-Fenton process during soil remediation.
Machine learning approaches for predicting arsenic adsorption from water using porous metal–organic frameworks
Authors: Abdi Jafar , Mazloom Golshan 
Published: September 2022

AbstractArsenic in drinking water is a serious threat for human health due to its toxic nature and therefore, its eliminating is highly necessary. In this study, the ability of different novel and robust machine learning (ML) approaches, including Light Gradient Boosting Machine (LightGBM), Extreme Gradient Boosting, Gradient Boosting Decision Tree, and Random Forest was implemented to predict the adsorptive removal of arsenate [As(V)] from wastewater over 13 different metal–organic frameworks (MOFs). A large experimental dataset was collected under various conditions. The adsorbent dosage, contact time, initial arsenic concentration, adsorbent surface area, temperature, solution pH, and the presence of anions were considered as input variables, and adsorptive removal of As(V) was selected as the output of the models. The developed models were evaluated using various statistical criteria. The obtained results indicated that the LightGBM model provided the most accurate and reliable response to predict As(V) adsorption by MOFs and possesses R2, RMSE, STD, and AAPRE (%) of 0.9958, 2.0688, 0.0628, and 2.88, respectively. The expected trends of As(V) removal with increasing initial concentration, solution pH, temperature, and coexistence of anions were predicted reasonably by the LightGBM model. Sensitivity analysis revealed that the adsorption process adversely relates to the initial As(V) concentration and directly depends on the MOFs surface area and dosage. This study proves that ML approaches are capable to manage complicated problems with large datasets and can be affordable alternatives for expensive and time-consuming experimental wastewater treatment processes.
Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes
Authors: Mackiewicz Paweł , Matosiuk Maciej , Świsłocka Magdalena , Zachos Frank E. , Hajji Ghaiet M. , Saveljev Alexander P. , Seryodkin Ivan V. , Farahvash Tarlan , Rezaei Hamid Reza , Torshizi Rasoul Vaez , Mattioli Stefano , Ratkiewicz Mirosław 
Published: September 2022

AbstractMitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genusCervusthat is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13Cervustaxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmedCervusto be monophyletic. Molecular dating based on several fossil calibration points revealed thatca. 2.6 Mya two main mitochondrial lineages ofCervusseparated in Central Asia, the Western (includingC. hangluandC. elaphus) and the Eastern (comprisingC. albirostris,C. canadensisandC. nippon). We also observed convergent changes in the composition of some mitochondrial genes inC. hangluof the Western lineage and representatives of the Eastern lineage. Several subspecies ofC. nipponandC. hangluhave accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B ofC. elaphuswas sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between differentCervusspecies as well as from the common ancestor of South Asian deer,Rusa timorensisandR. unicolor, to theCervusclade.
Differential expression of aqueous humor microRNAs in central retinal vein occlusion and its association with matrix metalloproteinases: a pilot study
Authors: Hong Eun Hee , Hwang Mina , Yu Hyoseon , Park Hyun-Hee , Cho Heeyoon , Koh Seong-Ho , Shin Yong Un 
Published: September 2022

AbstractThe aim of this study is to investigate the differential expression of microRNAs (miRNAs) in the aqueous humor (AH) of patients with central retinal vein occlusion (CRVO), and their association with AH matrix metalloproteinase (MMP) activity. Eighteen subjects, including 10 treatment naïve patients with CRVO and 8 control subjects, scheduled for intravitreal injection and cataract surgery, respectively, were included. AH samples were collected at the beginning of the procedure. A microarray composed of 84 miRNAs was performed to identify differentially expressed miRNAs in CRVO AH, which were further analyzed using bioinformatic tools to identify directly related cytokines/proteins. Eight miRNAs (hsa-mir-16-5p, hsa-mir-142-3p, hsa-mir-19a-3p, hsa-mir-144-3p, hsa-mir-195-5p, hsa-mir-17-5p, hsa-mir-93-5p, and hsa-mir-20a-5p) were significantly downregulated in the CRVO group. Bioinformatic analysis revealed a direct relationship among downregulated miRNAs, CRVO, and the following proteins: MMP-2, MMP-9, tumor necrosis factor, transforming growth factor beta-1, caspase-3, interleukin-6, interferon gamma, and interleukin-1-beta. Activities of MMP-2 and -9 in AH were detected using gelatin zymography, showing significant increase in the CRVO group compared to the control group (p < 0.01). This pilot study first revealed that MMP-2 and -9 were directly related to downregulated miRNAs and showed significant increase in activity in AH of patients with CRVO. Therefore, the relevant miRNAs and MMPs in AH could serve as potential biomarkers or therapeutic targets for CRVO.
Comparing two machine learning approaches in predicting lupus hospitalization using longitudinal data
Authors: Zhao Yijun , Smith Dylan , Jorge April 
Published: September 2022

AbstractSystemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease characterized by flares ranging from mild to life-threatening. Severe flares and complications can require hospitalizations, which account for most of the direct costs of SLE care. This study investigates two machine learning approaches in predicting SLE hospitalizations using longitudinal data from 925 patients enrolled in a multicenter electronic health record (EHR)-based lupus cohort. Our first Differential approach accounts for the time dependencies in sequential data by introducing additional lagged variables between consecutive time steps. We next evaluate the performance of LSTM, a state-of-the-art deep learning model designed for time series. Our experimental results demonstrate that both methods can effectively predict lupus hospitalizations, but each has its strengths and limitations. Specifically, the Differential approach can be integrated into any non-temporal machine learning algorithms and is preferred for tasks with short observation periods. On the contrary, the LSTM model is desirable for studies utilizing long observation intervals attributing to its capability in capturing long-term dependencies embedded in the longitudinal data. Furthermore, the Differential approach has more options in handling class imbalance in the underlying data and delivers stable performance across different prognostic horizons. LSTM, on the other hand, demands more class-balanced training data and outperforms the Differential approach when there are sufficient positive samples facilitating model training. Capitalizing on our experimental results, we further study the optimal length of patient monitoring periods for different prediction horizons.
Impact of old environmental burden in the Spiš region (Slovakia) on soil and home-grown vegetable contamination, and health effects of heavy metals
Authors: Musilová Janette , Franková Hana , Lidiková Judita , Chlpík Juraj , Vollmannová Alena , Árvay Július , Harangozo Ľuboš , Urminská Jana , Tóth Tomáš 
Published: September 2022

AbstractDue to several centuries of ongoing mining activities, Middle Spiš (Slovakia) is one of the areas with a damaged environment. The contents of Fe, Mn, Zn, Cu, Ni, Pb, Cd, and Hg were determined in the soils and home-grown vegetables (potatoes, carrots, tomatoes). Except for Pb, the contents of heavy metals in the soils of some plots were higher than the limit values. Based on the values of Contamination factor (Cf), Degree of contamination (Cdeg), Geo-accumulation index (Igeo), and Pollution load index (PLI), very high Fe, Cd, and Hg contamination (Cf ≥ 6), very high soil contamination (Cdeg ≥ 20), extremely heavy Fe and Hg contamination (Igeo > 5), resp. moderately pollution to non-pollution (1 < PLI ≤ 2) was found in all plots. In vegetable samples, the maximum levels were exceeded for Cu, Pb, Hg (potato), Pb (carrot, tomato), and Hg (carrot, plot E). Bioaccumulation factor values BAF > 1 were for Cu (carrots, potatoes). Estimated daily intake values for all heavy metals were lower than their tolerable daily intake. Chronic daily intake of heavy metals ranged 2.495E−06 (Hg)—0.1416 (Fe) mg/kg/day. Based on Hazard index values, potato consumption poses a risk (0.8068–1.3057). The results showed that the monitoring of soils and cultivated production is necessary for the investigated area.
Low-cost treated lignocellulosic biomass waste supported with FeCl3/Zn(NO3)2 for water decolorization
Authors: Kheradmand Asiyeh , Negarestani Mehrdad , Mollahosseini Afsaneh , Shayesteh Hadi , Farimaniraad Hamidreza 
Published: September 2022

AbstractDye pollution has always been a serious concern globally, threatening the lives of humans and the ecosystem. In the current study, treated lignocellulosic biomass waste supported with FeCl3/Zn(NO3)2was utilized as an effective composite for removing Reactive Orange 16 (RO16). SEM/EDAX, FTIR, and XRD analyses exhibited that the prepared material was successfully synthesized. The removal efficiency of 99.1% was found at an equilibrium time of 110 min and dye concentration of 5 mg L−1Adsorbent mass of 30 mg resulted in the maximum dye elimination, and the efficiency of the process decreased by increasing the temperature from 25 to 40 °C. The effect of pH revealed that optimum pH was occurred at acidic media, having the maximum dye removal of greater than 90%. The kinetic and isotherm models revealed that RO16 elimination followed pseudo-second-order (R2 = 0.9982) and Freundlich (R2 = 0.9758) assumptions. Surprisingly, the performance of modified sawdust was 15.5 times better than the raw sawdust for the dye removal. In conclusion, lignocellulosic sawdust-Fe/Zn composite is promising for dye removal.