bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Creation of a Pediatric Surgical Checklist for Adult Providers
Authors: Rapolti Diana , Kisa Phyllis , Situma Martin , Nico Elsa , Lobe Thom , Sims Thomas , Ozgediz Doruk , Klazura Greg 
Published: September 2023

Abstract

Purpose: To address the need for a pediatric surgical checklist for adult providers.
Background: Pediatric surgery is unique due to the specific needs and many tasks that are employed in the care of adults require accommodations for children. There are some resources for adult surgeons to perform safe pediatric surgery and to assist such surgeons in pediatric emergencies, we created a straightforward checklist based on current literature. We propose a surgical checklist as the value of surgical checklists has been validated through research in a variety of applications,
Methods: Literature review on PubMed to gather information on current resources for pediatric surgery, all papers on surgical checklists describing their outcomes as of October 2022 were included to prevent a biased overview of the existing literature. Interviews with multiple pediatric surgeons were conducted for the creation of a checklist that is relevant to the field and has limited bias.
Results: 42 papers with 8529061 total participants were included. The positive impact of checklists was highlighted throughout the literature in terms of outcomes, financial cost and team relationship. Certain care checkpoints emerged as vital checklist items: antibiotic administration, anesthetic considerations, intraoperative hemodynamics and postoperative resuscitation. The result was the creation of a checklist that is not substitutive for existing WHO surgery checklists but additive for adult surgeons who must operate on children in emergencies.
Conclusion: The outcomes measured throughout the literature are varied and thus provide both a nuanced view of a variety of factors that must be taken into account and are limited in the amount of evidence for each outcome. We hope to implement the checklist developed to create a standard of care for pediatric surgery performed in low resource settings by adult surgeons and further evaluate its impact on emergency pediatric surgery outcomes.
Funding: Fulbright Fogarty Fellowship, GHES NIH FIC D43 TW010540
Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity
Authors: Davies Bryan , Randall Justin , Vieira Luiz , Wilke Claus 
Published: September 2023

Abstract

Antimicrobial peptides commonly act by disrupting bacterial membranes, but also frequently damage mammalian membranes. Deciphering the rules governing membrane selectivity is critical to understanding their function and enabling their therapeutic use. Past attempts to decipher these rules have failed because they cannot interrogate adequate peptide sequence variation. To overcome this problem, we develop deep mutational surface localized antimicrobial display (dmSLAY), which reveals comprehensive positional residue importance and flexibility across an antimicrobial peptide sequence. We apply dmSLAY to Protegrin-1, a potent yet toxic antimicrobial peptide, and identify thousands of sequence variants that positively or negatively influence its antibacterial activity. Further analysis reveals that avoiding large aromatic residues and eliminating disulfide bound cysteine pairs while maintaining membrane bound secondary structure greatly improves Protegrin-1 bacterial specificity. Moreover, dmSLAY datasets enable machine learning to expand our analysis to include over 5.7 million sequence variants and reveal full Protegrin-1 mutational profiles driving either bacterial or mammalian membrane specificity. Our results describe an innovative, high-throughput approach for elucidating antimicrobial peptide sequence-structure-function relationships which can inform synthetic peptide-based drug design.
Inferring the chronic copper deficiency stress responsive network and comparative analysis with excessive copper stress in grapevine
Authors: Liu Siyu , Lin Yilin , Yang Yuxian , Xia Jiaxin , Niu Mingxu , Hakeem Abdul , Fang Xiang , Ren Yanhua , Wang Xicheng , Fang Jinggui , Shangguan Lingfei 
Published: September 2023

Abstract

Copper is an essential trace element in grapevine growth, and lack of it will cause damage to grapevines. While there have been studies on the mechanism of grapevine tolerance to excessive copper stress, there is a lack of systematic reports on the regulation mechanism of copper deficiency stress. To explore the adaptive response and regulatory mechanism of ‘Shine Muscat’ (‘SM’) grapevines leave growth to copper deficiency, we treated the seedlings with Hoagland's nutrient solution without copper ions for a long time. Firstly, it was found that ‘SM’ grapevines were indeed affected by copper deficiency stress through the leaf symptoms and physiological data. Then, 657 up-regulated and 527 down-regulated differentially expressed genes (DEGs) and 72 differentially accumulated metabolites (DAMs, 31 up-regulated and 41 down-regulated) were identified between control and copper deficiency treatment. Copper ion transportation, photosynthetic pathway, antioxidant system, flavonoid metabolism and phytohormone metabolism were identified as the primary response systems in ‘SM’ grapevine. Several genes, including FRO4, ABCs, CHLP, APX, GPX, and PK, were found to play a crucial role in the response of ‘SM’ grapevine to copper deficiency stress. Furthermore, there were notable differences in copper uptake and transportation, chlorophyll degradation, flavonoid synthesis and metabolites, and ABA content between copper deficiency and excess stress. These results will be beneficial to gain insights with copper deficiency regulation and stress-responsive strategies in grapevines.
A Prospective, controlled, pilot study of personalized add-on Ayurveda treatment in high-risk Type II Diabetes COVID-19 patients
Authors: Kumar Somit , Eranezhanth Sujith Subash , Vishwanathan Vinod Kumar , Kakarla Mitravinda Sai , Chenthamarakshan Chaithanya , Selvaraj Lakshmiprabha , Satheeshan Balagopal , Unniappan Indulal , Purushotham Balaji , Pīrāgs Valdis , Furst Daniel E 
Published: September 2023

Abstract
Objective
In hospitalized mild to moderate COVID-19 Patients with Type 2 diabetes, we evaluated the efficacy of add-on customized Ayurveda intervention as compared to Standard of Care (SOC) in ameliorating symptoms, ICU admission and Ventilator support plus IL6 and CRP over 15 days.
Methods
In this quasi-experimental trial, 24 participants per arm diagnosed with COVID-19 by RT-PCR, aged 18 to 75 years, fulfilling the inclusion/exclusion criteria were inducted. The subjects were allocated, depending on their own voluntary choice to SOC plus Ayurveda (group 1) or SOC alone (group 2) for 15 days. The analyses used the Cochran-Mantel-Haenszel test, Multivariate ANOVA plus within group Repeated Measures ANOVA and Cochran’s Q test.
Results
Of the 13 symptoms, cough (p = 0.04), general weakness (p = 0.02), and sore throat (p = 0.02) were statistically significantly different across the groups, with Group I(add-on) improving better than Group II(SOC). IL-6 dropped rapidly in Group1 by 7 days (p = 0.006) Group 2 caught up by day 15.(p = 0.001). CRP improved more slowly than IL-6. The time to maximum change was not statistically different for IL-6 and CRP between the groups at day 15. There were no differences in AEs to Ayurveda added SOC group.
Conclusion
In this exploratory pilot study, cough, weakness and sore throat improved more in the add-on Ayurveda than in the SOC. IL-6 concentrations declining more rapidly in the add-on Ayurveda. Clinical and laboratory AEs suggested no additional toxicity of add-on Ayurveda treatments. This study supports the need for a randomized, double-blind trial.
Role of biochar in mitigating nickel stress in spinach (Spinacea oleracea L.) plants
Authors: Haider Arslan , Ahmad Muhammad Sajid Aqeel , Riffat Alia 
Published: September 2023

Abstract

Increasing nickel (Ni) concentration in plant cells causes physiological, metabolic and cellular alterations, which causes severe damage to the plants. Among various strategies to reduce Ni toxicity in plants, the use of biochar (BC) is very feasible method as it has potential to immobilize Ni which ultimately causes soil remediation. The present study was conducted to determine the role of BC in mitigating Ni stress. Two varieties of spinach (Desi and Green Gold), were subjected to BC (16.25 and 32.5 g) and Ni (5 mM) treatment. Results revealed that the length, fresh and dry weight of shoot and root were improved by application of BC at 32.5 g, however, application of Ni reduced all studied growth parameters. Among photosynthetic pigments, chlorophyll (chl) a, chl b, total chl and carotenoids were also improved at 32.5 g BC under Ni stress conditions. Biochar reduced the concentration of malondialdehyde (MDA) and hydrogen peroxide (H2O2) at 32.5 g by increasing enzymatic antioxidant superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) while, Ni stress raised the concentration of MDA and H2O2. Among organic osmolytes, BC at 32.5 g improved the concentration of glycine betain, total soluble proteins and total soluble sugars and lowered the toxic effects of Ni stress. The uptake of mineral ions such as Ca2+ and K+ were improved and Na+ concentration was reduced by applying BC at 32.5 g under Ni stress conditions. In conclusion, the application of BC at 32.5 g/ pot enhanced plant growth, photosynthetic pigments, osmolytes, antioxidants, ionic contents and lowered oxidative stress determinants to ameliorate Ni stress condition.
Genome-wide association studies for identification of novel QTLs related to four agronomic traits in Horsegram (Macrotyloma uniflorum)
Authors: Sharma Ankita , Chahota Rakesh Kumar 
Published: September 2023

Abstract
Horsegram (Macrotyloma uniflorum) is an important legume crop well adapted to harsh environments and has significant nutritional value. It is also well recognised due to its nutritional value, health benefits, drought tolerance, and ability to improve soil fertility. It is a versatile crop used in various dishes and is a valuable addition to any diet. However, in-depth molecular analysis must be improved to understand the molecular architecture regulating the essential traits. To achieve this, the study utilized a genome-wide association mapping approach using 88 horsegram accessions genotyped with 55656 single nucleotide polymorphisms (SNPs). A total of 54271 SNPs were mapped to the reference genome. Phenotypic data were collected for four agronomic and yield-related traits Plant height, Days to maturity, days to flowering and number of branches per plant. These traits played a significant role in plant growth, development, protection, and crop yield. The study identified 79 significant SNP-trait associations for the traits under study. The identified SNPs were in 8 chromosomes. The study also identified several novel genomic regions associated with the traits considered, providing new insights into the genetic basis of these essential traits in horse gram. Overall, the study highlights the potential of genome-wide association mapping for identifying genomic regions associated with important agronomic and yield-related traits in horsegram. This could facilitate the development of improved horsegram varieties through marker-assisted breeding programs and overcoming the morphological selection of desirable genotypes in the background of narrow genetic base.
Phylogenetic characterization of UPEC and its relation with serotyping, distribution of virulence factors, antimicrobial resistance pattern and biofilm formation ability: An apparent elucidation of the bacterial nature
Authors: Oskouie Arezoo Noie , Hasani Alka , Rezaee Mohammad Ahangarzadeh , Hasani Akbar , Saleh Parviz , Soltani Elghar 
Published: September 2023

Abstract

Extensive heterogeneity in O-serogroups, phylogenetic types, possession of plethora resistance mechanisms, and virulence factors have all accreted Uropathogenic Escherichia coli (UPEC) to achieve a landmark as an attractive pathogen and a survival advantage. The present research aimed at a comprehensive approach investigating antibiotic susceptibility, biofilm capability, serotyping, phylogenetic typing, and virulence factors of 102 UPEC isolates. O-serotyping and virulence genotyping was conducted to detect 14 serogroups and 8 virulence genes including molecular predictors of UPEC strains. Phylogenetic groups were identified at molecular level and analyzed to evaluate whether these strains belonged to one lineage or extended widely among hospital patients. The analysis revealed that the majority of the strains belonged to the phylogenetic groups B2, D/E and serotype O25. The number of virulence factors and antibiotic resistance exhibited was significantly high in groups B2 and serogroup O25/O15 compared to other groups. Among the 74 multidrug-resistant isolates, 56.7% belonged to the phylogenetic group B2. Significantly, isolates belonging to phylogroup B2, serogroup O25 and those harbored fimH and papE/F virulence factors formed biofilm. In conclusion, our study observed the dissemination of UPEC among several serotypes and phylogenetic groups. Strong biofilm index suggests a characteristic feature of UPEC isolates.
Enhancing the clinical reasoning of new graduate nurses: An experimental study using pre-test and post-test measures
Authors: Tan Hui Luan , Eng Chui Lee , Tan Delphine Hui Fang , Oh Hui Yen , Loo Benny Kai Guo 
Published: September 2023

Abstract
Background: This study examined the development of clinical reasoning abilities among new graduate nurses in a hospital setting. A blended learning approach incorporating a serious gaming platform, Socratic questioning, self-assessment, and facilitator feedback was used to improve their ability to reason clinically in actual patient cases.
Method: This study used a blended learning approach to examine how including a serious gaming platform, Socratic questioning, self-assessment, and facilitator feedback impacted the clinical reasoning abilities of new graduate nurses when evaluating patient cases. We conducted a Paired Sample t-test using a validated rubric to evaluate the potential enhancement of clinical reasoning abilities.
Results: The results showed a noticeable disparity in the scores of clinical reasoning from the initial pre-test to the first post-test (M= -6.54 SD = 5.754) (t = -5.334, df = 21, p = 0.000), and from the initial pre-test to the second post-test (M = -9.54 SD = 5.115) (t = -8.752, df = 21, p = 0.000), at a significance level of 0.05, with p value less than 0.05. The study found that the effect size, d, was 0.53 indicating a medium effect size. In addition to quantitative data, nurses' perceptions of the blended learning approach incorporating the serious gaming platform, Socratic questioning, self-written case scenarios, and facilitator feedback were also reported to provide qualitative insights into the approach's effectiveness for nurses.
Conclusions: Study findings suggest that integrating a serious gaming platform (thinking aloud), self-assessment, facilitator feedback (using self-written case scenarios), and Socratic questioning effectively enhanced the clinical reasoning skills of nurses. Specifically, nurses were better able to form well-supported reasons and judgments when evaluating patient cases. These findings suggest that using a serious gaming platform with Socratic questions can enhance nurses' clinical reasoning skills through written and oral discussions.
Prediction of antibiotic resistance genes and resistance mechanisms of Pseudomonas syringae pv. actinidiae strain L211 based on whole-genome sequencing
Authors: YANG Rui , WANG Linluo-sha , YANG Shuai , SHI Lin-fang , PENG Qing-zhong 
Published: September 2023

Abstract

The objective of this paper was to analyze of antibiotic resistance genes and mechanisms of antibiotic resistance in the causal agent of kiwifruit bacterial canker in western China. Pseudomonas syringae pv. actinidiae (Psa) strain L211, previously isolated from canker-infected kiwifruit (Actinidia chinensis)and identified in the laboratory, was used as the study material for whole-genome sequencing and annotation of gene functions. The antibiotic resistance genes and resistance mechanisms were predicted by comparison with the CARD database, and verified by antibiotic sensitivity tests. Our results showed that in total, 482 resistance genes were predicted in the strain L211 genome involved in resistance to28 antibiotics. Thepredicted genes were classified in six categories of resistance mechanisms, namely antibiotic efflux, antibiotic inactivation, antibiotic target alteration, antibiotic target protection, reduced antibiotic penetration, and mixed resistance mechanisms. Resistance was mainly characterized as active efflux, β-lactamase degradation, mutation of target genes, plasmid mediated, and reduced biofilm permeability. Antibiotic sensitivity tests revealed that strain L211 was resistant to carbenicillin, cefadroxil, clindamycin, isoniazid, sulfadiazine, bacitracin, norfloxacin, dapsone, and chloramphenicol, and sensitive to oxytetracycline, streptomycin, triclosan, and rifampin. Psa may be a broad-spectrum antibiotic-resistant bacterium, with antibiotic efflux as its main resistance mechanism.Multiple resistance mechanisms were predicted to act in concert, resulting in increased antibiotic resistance and resistance to multiple antibiotics. Frequent use of agricultural antibiotics is interpreted to have led to proliferation in resistance genes that target two antibiotics.To avoid further increase in the resistance spectrum of Psa, the use of chemical antibiotics in agriculture should be strictly controlled.
A graph-based Gaussian Mixture Variational Autoencoder improves metagenome binning for short contigs
Authors: Zhang Lu , Zhang Zhenmiao , Rao Mingxing , Huang Yufen 
Published: September 2023

Abstract
Grouping contigs from the same genome together through metagenome binning is crucial in reconstructing metagenome-assembled genomes (MAGs). While existing metagenome binning methods have successfully produced near-complete MAGs for long contigs with lengths exceeding 2Kb, they typically neglect short contigs in binning due to their inability to process the unstable conventional sequence composition features of short contigs.

We developed DeepMetaBin, a contig binning method that utilizes a graph-based Gaussian Mixture Variational Autoencoder (GMVAE) to group short (1Kb-2Kb) and long contigs (>2Kb) together. DeepMetaBin starts by generating a k-nearest neighbor graph (k-NN) for contigs based on their sequence composition features and removes noise nodes based on preliminary clustering and label propagation. Next, edges in the refined k-NN are incorporated as “must-links” to stabilize the embedding of short contigs in GMVAE. Finally, Gaussian Mixture Model is used to group the contigs into super clusters in the low-dimensional space, followed by involving single-copy genes as “cannot-links” to facilitate the division of these super clusters using constraint k-means.

We extensively evaluated DeepMetaBin by comparing its performance with six existing metagenome binning tools using simulated and real microbial communities. DeepMetaBin achieved the highest F1 scores for most of the single-sample and multi-sample metagenome binning tasks. It addressed the current practice in the research community of omitting short contigs during modeling and was the only tool that achieved state-of-art performance on both F1 scores and the number of near-complete MAGs.
Formation Behaviors and Selective Separation of the Binary (SF6+N2) Gas Mixtures Using Hydroquinone Clathrate
Authors: Yoon Sang Jun , Yoon Ji-Ho , Lee Jong-Won 
Published: September 2023

Abstract
After reacting hydroquinone (HQ) powder with pure sulfur hexafluoride (SF6) and nitrogen (N2), and binary gas mixtures of (SF6 + N2) with various compositions at experimental pressures of 20 bar and 40 bar, the HQ samples are analyzed using a series of analytic methods to obtain both qualitative and quantitative information. As a result, it was found that N2 can be enclathrated into cavities of the formed HQ clathrate if the simplified partial pressure of N2 is sufficiently large (occupation of 10% per one cavity when the simplified partial pressure is 32 bar, and occupation of 40% per one cavity when the pressure of pure N2 is 40 bar). In addition, additional experiments were performed to evaluate the N2 storage in the clathrate depending on the experimental pressure. When the pressure of pure N2 was increased up to 80 bar, the occupation per one clathrate cage was calculated to be 55%, which corresponded to 18.7 L of N2 at STP conditions per 1 kg of HQ. Because higher pressure is required to form the HQ clathrate and the stored amount of gas molecules is smaller compared with other technologies such as adsorption or hydrate-based process, a lot of additional investigations will be necessary, focusing on reducing energy consumption and increasing the gas storage.
Improving Stay-green Traits and Related Physiological Metabolism Increased the Rice Yield under Long-term Warming in Cool Region
Authors: Ma Ke , Zhou Yuanyuan , Ma Yao , Zhang Taoren 
Published: September 2023

Abstract
Research on the effect of long-term warming on rice in cool region is still rare. This study used the widely cultivated japonica rice Jiyang100 in Northeast China as the experiment material. We set up warming treatments at three growth stages of rice in the field: the tillering-panicle initiation stage (T1), the whole growth stage (T2) and the grain-filling stage (T3). The rice yield showed a trend of T1 > T2 > T3 > CK in both years. The positive effects of T1, T2 and T3 on the total number of spikelets per hole significantly increased the yield, with average increased by 11.5%, 9.9% and 6.5%, respectively. Each warming treatment had significant positive effect on the stay-green traits, photosynthesis, sucrose synthesis, and nitrogen metabolism of rice. The yield was significantly positively correlated with SPAD, soluble sugar content, sucrose content, SPS, NR, GS, and GOGAT activity. The physiological models constructed by SPAD and sucrose content could explain the changes of the yield (R2=0.704). The stay-green traits had significant correlation between carbon and nitrogen metabolism, and it played a pivotal role in them. Wherein, SPAD had significant positive correlation with soluble sugar content, soluble protein content, NR, GS, GOGAT and GDH activity, and significant negative correlation with AI activity. The stay-green ability had significant positive correlation with Pn, soluble sugar content and soluble protein content. The above results indicated that the coupling interaction of stay-green traits, nitrogen metabolism and carbon metabolism increased the sink capacity potential and sink storage supply capacity, which was the reason for the increase in rice yield under long-term warming in cool region.