bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quorum sensing activities and genomic insights of plant growth-promoting rhizobacteria isolated from Assam tea
Authors: Chopra Ankita , Mongad Dattatray , Satpute Surekha , Mazumder Pranab Behari , Rahi Praveen 
Published: November 2022

Abstract
Secretion of quorum sensing (QS) molecules is important for the effective colonization of host plants by plant growth-promoting rhizobacteria. The current study aims at the isolation and characterization of tea rhizosphere bacteria, which produce the QS molecules, acyl homoserine lactone (AHLs), along with multiple plant growth-promoting (PGP) activities. Thirty-one strains were isolated from the tea rhizosphere, and screening for PGP activities resulted in the selection of strains RTE1 and RTE4 with multiple PGP traits, inhibiting the growth of tea fungal pathogens. Both strains also showed production of AHL molecules while screened using two biosensor strains, Chromobacterium violaceum CV026 and Escherichia coli MT 102(jb132). The strains identified as Burkholderia cepacia RTE1 and Pseudomonas aeruginosa RTE4 based on genome-based analysis like phylogeny, dDDH, and fastANI calculation. Detailed characterization of AHLs produced by the strains using reverse-phase TLC, fluorometry, and LC-MS indicated that the strain RTE1 produced a short chain, C8, and a long chain C12 AHL, while RTE4 produced short-chain AHLS C4 and C6. Confocal microscopy revealed the formation of thick biofilm by RTE1 and RTE4 (18 µm and 23 µm, respectively). Additionally, we found several genes involved in QS, and PGP, inducing systemic resistance (ISR) activities such as lasI/R, qscR, pqq, pvd, aldH, acdS, phz, Sod, rml, and Pch, and biosynthetic gene clusters like N-acyl homoserine lactone synthase, terpenes, pyochelin, and pyocyanin. Based on the functional traits like PGP, biofilm formation and production of AHL molecules, and genetic potential of the strains B. cepacia RTE1 and P. aeruginosa RTE4 appear promising candidates to improve the health and growth of tea plantations.
Objective assessment of intraoperative skills for robot-assisted partial nephrectomy (RAPN)
Authors: Farinha Rui , Breda Alberto , Porter James , Mottrie Alexandre , Cleynenbreugel Ben , Sloten Jozef Vander , Mottaran Angelo , Gallagher Anthony 
Published: November 2022

Abstract
Background
RAPN training usually takes place in-vivo and methods vary across countries/ institutions. No common system exists to objectively assess trainee capacity to perform RAPN at predetermined performance levels prior to in-vivo practice. The identification of objective performance metrics for RAPN training is a crucial starting point to improve training and surgical outcomes.
Objective
The authors sought to examine the reliability, construct and discriminative validity of objective intraoperative performance metrics which best characterize optimal and suboptimal performance of a reference approach for training novice RAPN surgeons.
Design, setting, and participants:
Seven Novice and 9 Experienced RAPN surgeons videorecorded one or two independently performed RAPN procedures in the human. The videos were anonymized and two experienced urology surgeons were trained to reliably score RAPN performance, using previously developed metrics. The assessors were blinded to the performing surgeon, hospital and surgeon group. They independently scored surgeon RAPN performance. Novice and Experienced group performance scores were compared for procedure steps completed and errors made. Each group was divided at the median for Total Errors score, and subgroup scores (i.e., Novice HiErrs and LoErrs, Experienced HiErrs and LoErrs) were compared.
Results
The mean inter-rater reliability (IRR) for scoring was 0.95 (range 0.84–1). Compared with Novices, Experienced RAPN surgeons made 69% fewer procedural Total Errors. This difference was accentuated when LoErr Expert RAPN surgeon’s performance was compared with the HiErrs Novice RAPN surgeon’s performance with an observed 170% fewer Total Errors. GEARS showed poor reliability (Mean IRR = 0.44; range 0.0–0.8), for scoring RAPN surgical performance.
Conclusions
The RAPN procedure metrics reliably distinguish Novice and Experienced surgeon performances. They further differentiated performance levels within a group with similar experience. Reliable and valid metrics will underpin quality-assured novice RAPN surgical training.
Analysis of the efficacy of a single subumbilical stoma for bilateral cutaneous ureterostomy after radical cystectomy
Authors: fu zhenyu , Tian Zhen , Chen Yongchang , Jia Zongming , Wang Chengyu , Zhang Xuefeng , Zhang Weijie , Li Gang , Wei Xuedong , Huang Yuhua 
Published: November 2022

Abstract
Purpose: The efficacy and complications of bilateral cutaneous ureterostomy with a single subumbilical stoma were compared with those of cutaneous ureterostomy with two stomas and an ileal conduit.
Methods: The clinical data for 108 patients who received bilateral cutaneous ureterostomy with a single subumbilical stoma (ureterostomy with a single stoma group), cutaneous ureterostomy with two stomas (ureterostomy with two stomas group), or an ileal conduit (ileal conduit group) after radical cystectomywere retrospectively analysed. The operative time, pathological stage, survival status, perioperative complication rate, rate of successful first extubation, rehospitalization rate at 6 months after surgery,ostomy-related medical costs ,and postoperative quality of life were compared between the three groups of patients.
Results: A significant difference in the operative time was found between the three groups (P = 0.001). No significant differences in pathological stage, survival status, perioperative complication rate, rehospitalization rate at 6 months after surgery, or BCI score were identified among the three groups. The difference in the successful first extubation rate between the three groups of patients was significant (P = 0.001). Significant differences in ostomy-related medical costs were observed among the three groups of patients (P = 0.006).
Conclusion: The survival and complication rates of patients undergoing three different urinary diversion strategies after radical cystectomy were similar, but the operative time of the single-stoma group was shorter than that of the ileal conduit group. Compared with the two-stoma group, the single-stoma group had a significantly higher rate of successful first extubation and lower ostomy-related medical costs.
Chemical Rules for Optimization of Chemical Mutagenicity via Matched Molecular Pairs Analysis and Machine Learning Methods
Authors: Lou Chaofeng , Yang Hongbin , Deng Hua , Huang Mengting , Li Weihua , Liu Guixia , Lee Philip W. , Tang Yun 
Published: November 2022

Abstract
Chemical mutagenicity is a serious issue that needs to be addressed in early drug discovery. Over a long period of time, medicinal chemists have manually summarized a series of empirical rules for the optimization of chemical mutagenicity. However, given the rising amount of data, it is getting more difficult for medicinal chemists to identify the more comprehensive chemical rules behind the biochemical data. Herein, we integrated a large Ames mutagenicity data set with 8576 compounds to derive mutagenicity transformation rules for reversing Ames mutagenicity via matched molecular pairs analysis. A well-trained consensus model with a reasonable applicability domain was constructed, which showed favorable performance in the external validation set with an accuracy of 0.814. The model was used to assess the generalizability and validity of these mutagenicity transformation rules. The results demonstrated that these rules were of great practicability and could provide inspiration for the structural modifications of compounds with potential mutagenic effects. We also found that the local chemical environment of the attachment points of rules was critical for successful transformation. To facilitate the use of these mutagenicity transformation rules, we integrated them into ADMETopt2 (http://lmmd.ecust.edu.cn/admetsar2/admetopt2/), a free webserver for optimization of chemical ADMET properties. The above-mentioned approach would be extended to the optimization of other toxicity endpoints.
Nationwide analysis of COVID-19 death rate throughout the pandemic in Italy
Authors: Mattiuzzi Camilla , Lippi Giuseppe 
Published: November 2022

Abstract
Background: No definitive epidemiological evidence is available on SARS-CoV-2 lethality during the surge of different variants of concern (VoCs) and Coronavirus disease 2019 (COVID-19) vaccination in relation to Influenza virus fatality.
Methods: We collected and longitudinally analyzed official data about new COVID-19 cases and COVID-9 related deaths throughout the pandemic in Italy, which were then compared with the recent flu-related fatality rate.
Results: The mortality rate of COVID-19 has declined from 3.53% during predominance of the ancestral SARS-CoV-2 strain to 0.26-0.21% after surge of the new Omicron sublineages BA.1/2 and BA.4/5, when the nationwide COVID-19 vaccine coverage with primary cycle and booster doses has been concomitantly extended to 90.2% and 84.5% of the general population ≥12 years, respectively. The death rate of COVID-19 was approximately 11-fold higher than that of flu (i.e., 3.53% versus 0.32%) at the beginning of the pandemic, but has then become 36% lower after widespread COVID-19 vaccine coverage and surge of Omicron sublineages BA.4/5.
Conclusions: Although our data seem to underline a reassuring epidemiological scenario, with the death rate of COVID-19 currently lower than that of influenza in Italy, we reemphasize the importance of preventing further surge of aggressiveness (and potential lethality) of SARS-CoV-2, especially in the most vulnerable parts of the population.
Functional characterization and evaluation of multi-biological activities of water soluble polysaccharide from Periploca laevigata
Authors: Bkhairia Intidhar , Krayem Najeh , Dhibi Sabah , Ghorbel Sofiane , Ghamidi Othman Al , Ktari Naourez , Slima Sirine , salah Riadh Ben , Li Suming , Nasri Moncef , Hajji mohamed 
Published: November 2022

Abstract
The water-soluble polysaccharide was isolated from Periploca laevigata root barks and purified. The structurale, surface, functional properties, and biological activities of P. laevigata polysaccharide (PLP1) were investigated. Scanning electron microscopy (SEM), X-ray diffraction crystallography (XRD), were used for structurale characterization of PLP1.
SEM analysis suggested that the polysaccharide had irregular particle size with a large number of cavities, mostly seen as aggregates, and fibrous in nature. The samples had peaks at approximately 22°, and 38° 2θ degrees in the XRD pattern, which indicated both crystalline and amorphous structure. Functional properties of PLP1 were investigated based on water and oil holding capacity, solubility, emulsification activity, and foaming ability. Interestingly, PLP1 exhibited, a noticeable ability to emulsify corn and olive oil. Experimental analysis indicated that PLP1 able to decrease surface tension of water of 67.5 mN/m to 43.7 mN/m. On other trend, bioactivities evidenced that PLP1 is a potent protease and lipase inhibitor. The cell viability proved the cytoprotective effect of PLP1 on cell treated with hydrogen peroxide
H2O2, suppressing apoptosis and ameliorating oxidative lesions. The experimental data and multi functionality provides enough evidence and open many new possibilities for biomedicine and food applications.
Heterogeneity of quality of life in the later stages of first-episode psychosis recovery
Authors: Clarke Emily L. , Allott Kelly , Anderson Jacqueline F.I. , Gao Caroline X. , Filia Kate M. , Killackey Eoin , Cotton Sue M. 
Published: November 2022

Abstract
Purpose: First-episode psychosis (FEP) is characterised by wide heterogeneity in terms of symptom presentation and illness course. However, the heterogeneity of quality of life (QoL) in FEP is not well understood. We investigated whether subgroups can be identified using participants responses on four QoL domains (Physical Health, Psychological, Social Relationships, and Environmental) 18-months into the recovery phase of FEP. We then examined the discriminant validity of these subgroups with respect to clinical, cognitive, and functioning features of FEP.
Method: Demographic and clinical characteristics, QoL, cognition, and functioning were assessed in 100 people with FEP at the 18-month follow-up of a randomised controlled trial of Individual Placement Support, which aims to facilitate vocational recovery. QoL was measured using the World Health Organisation’s QoL-BRIEF. A two-stage clustering approach using Ward’s method and Squared Euclidean Distance with a k-means confirmation was conducted. Multinomial logistic regressions were used to establish external validity.
Results: Three QoL subgroups emerged: a ‘good’ subgroup with relatively high QoL across all domains (31%), an ‘intermediate’ subgroup with relatively low psychological QoL (48%) and a ‘poor’ subgroup with markedly low social relationship QoL (21%). Negative symptoms, depressive symptoms, social/occupational functioning and social inclusion at follow-up predicted subgroup membership. Sensitivity analysis found similar results.
Conclusion: Although some individuals with FEP have QoL comparable to individuals without mental-ill health, QoL can remain concerningly low despite treatment efforts. Future research on interventions that target factors associated with poor QoL, such as low social inclusion, is required to counteract prolonged poor QoL in FEP.
A piece in the SARS-CoV-2 genome mosaic: furin site on the spike protein
Authors: Romeu Antonio R. 
Published: November 2022

Abstract
The recent Smriti Mallapaty’work (Nature. News, 10 November 2022) highlights the role of recombination in the evolution of the SARS-CoV-2. It seems hard to deal the origin of the virus as a whole. The SARS-CoV-2genome is a mosaic of regions or parts, each with their own origin. The SARS-CoV-2’s closest known relative is a bat virus found in Laos called BANAL-52, which can therefore infect human cells. Furthermore, BANAL-52 don’t contain the so-called furin cleavage site on the spike protein that further aids the entry of SARS-CoV-2 into human cells. So, the furin site was a key piece in the virus “mosaic”. However, The SARS-CoV-2 furin site “gain-of-function” was being made against the CGG-CGG genetic footprint encoding the polybasic arginine dimer. For SARS-CoV-2 the only output to the CGG-CGGinstability is to proceed with synonymous substitutions (silent mutations) keeping the arginine dimer from the furin site. Theaim of this work is to provide updated data on the plausibility of this evolution in the coding of thatarginine dimer. Using the NCBI Virus database as a source of information, the sample of SARS-CoV-2 spike proteins, with releasedate November 1-10, 2022, shows that 78 out of 27281 (0.28 %) sequences show a synonymous base substitution in the CGG-CGG. This percentage is twice of samples retrieved in August 2022.
Application of a Gene Modular Approach for Clinical Phenotype Genotype Association and Sepsis Prediction using Machine Learning in Meningococcal Sepsis
Authors: Rashid Asrar , Uddin Mohammed , Sarpal Amrita , Shaikh M. Guftar , Benakatti Govind , Ismail Javed , Zaki Syed Ahmed , Hussain Amir 
Published: November 2022

Abstract
Background
Meningococcal Septic Shock (MSS) is a life-threatening condition, especially in Infants. Therefore the ability to track MSS pathogenesis during using temporal microarray data was explored. Gene Modular association analysis of Meningococcal Septic Shock time series data in infants was explored using WGCNA. 5 infants with Meningococcal Sepsis were admitted to PCC were recruited into the study. Secondary data analysis was completed on data points collected at 0, 4, 8, 12, 24, and 48 hours following admission. Machine Learning algorithms were also used to predict sepsis survival. These included Support Vector Machine (SVM), Naive Bayes, K-Nearest Neighbors (KNN), Decision Tree, Random Forest and ANN (Artificial Neural Network).
Results
WGCNA was applied to time-series transcriptome data (from the Arraygen Human 1.0 ST array platform) obtained from 5 PCC MSS cases. Log base 2 (log2) normalisation (ArrayExpress E-MEXP-3850) {Kwan, 2013 #49} was then undertaken on the gene expression data. Unsupervised hierarchical clustering was then applied with a heat map generated, indicating time points 0 and 48 hours as the most different in terms of gene expression. WGCNA was constructed using a soft threshold power of 6 based on network topology characteristics. Subsequently, 18 clusters (modules) were identified and compared to clinical parameters. From the adjacency matrix, a gene list was generated for each module which was significantly associated with clinical traits. Each gene list underwent gene enrichment analysis using g:profiler using the Fisher exact test for gene enrichment pathway analysis. The modules associated with Pediatric Logistic Organ Dysfunction (PELOD) score at 0, 24, and 48 hours showed a changing pattern of enriched pathways related to nuclear (p < 2e-08), cytoplasmic (p < 4e-05), and then extracellular gene regulation (p < 7e-17) for PELOD 0, 24 and 48 hours, respectively. The classification of survival and non-survival dataset using the proposed machine learning ANN technique achieved accuracies of 100% for both train and test data.
Conclusion
Time series transcriptomic analysis using WGCNA applied to a meningococcal septic shock dataset revealed an association between MSS clinical traits and major cellular processes activated through the study period of up-to 48 hours post admission. Using WGCNA, this study demonstrated the association of temporal clinical characteristics to changing cellular processes. Among ML algorithms, ANN generated the best accuracy in sepsis prediction. Thereby WCGNA and ML approached may provide a clinical linkage approach for precision management strategies in sepsis.
Implementation of the concept of healthy food in restaurants
Authors: Paska Mariia , Radzimovska Olga , Guzenko Iryna 
Published: November 2022

Food refers to the most important factors of the environment, which directly affect the human body throughout life. Proper nutrition is an important part of a balanced diet. The regime provides regular meals at certain hours at certain intervals, as well as the distribution of the daily diet by energy value during the day. Adherence to the diet ensures the rhythmic functioning of the digestive system, normal digestion and proper metabolism. The food ration should be composed so that its energy value covers the body's energy expenditure. The organization of a balanced diet is one of the most important factors in maintaining good health and improving efficiency. The diet should be composed so that its energy value covers the body's energy expenditure.
Promising in this regard is the introduction of the concept of healthy eating in the daily diet of athletes in various sports. After all, the trends of modern healthy eating show a growing interest among athletes in various sports.
The aim of research is to introduce the concept of healthy eating in sports and recreation and restaurants.
The following research methods were used in the work: observation analysis (diet), organoleptic evaluation, statistical data processing, consumer evaluation of finished restaurant products according to DSTU.
To fulfill our tasks of theoretical generalizations and experimental research, scientifically substantiated the introduction of the concept of healthy eating in the diets, as well as balanced the ingredient composition of the diet by developing and adding chopped semi-finished products using beef and raw materials.
In our work let’s offer an innovative model for the use of meatballs for health purposes in the diets of athletes with playing sports
Relationship of salinity, temperature, pH, and transparency to dissolved oxygen in the Bouregreg estuary (Morocco): First results
Authors: Haddout Soufiane , Priya K. L. , Hoguane A. M. , Casila Joan Cecilia C. , Ljubenkov I. 
Published: November 2022

Abstract
Dissolved oxygen (DO) concentration is an essential indicator for assessment of estuary ecosystems. According to our knowledge, there is no research on the depth profiles of the DO and associated water quality variables of the entire Bouregreg estuary (Morocco). Water samples were collected from three stations at 0.5-m depth intervals during high and low tides (10/11/2021, 20/03/2022, and 02/07/2022). Our study shows that the DO concentrations ranged between 5.5 and 11.8 mg/L and demonstrated an inconsistent stratification pattern. When the tide was high and low in most of the study area, the bottom layer had a higher concentration of DO than the surface layer. There was a relatively high concentration of DO in the bottom layer of the estuary and a relatively low concentration in the surface layer of the estuary due to a high rate of freshwater flow on the surface (the release of Sidi Mohammed Ben Abdellah dam and the existence of estuarine gravitational circulation). Salinity, pH, water temperature, and water transparency ranged from 19.4 to 35.8 ppt, 7.0 to 8.7, 17 to 23 °C, and 16 to 21 cm, respectively, considering the depth profiles in the study area. The study provides scientific support for ecology operation and considerable advances in understanding the ecosystem dynamics of the Bouregreg estuary.