bluuebunny/crossref_metadata_2025 huggingface dataset:
Diet and the gut microbiome in patients with Parkinson’s disease
Authors: Kwon Dayoon , Zhang Keren , Paul Kimberly C. , Folle Aline D. , Del Rosario Irish , Jacobs Jonathan P. , Keener Adrienne M. , Bronstein Jeff M. , Ritz Beate
Published: April 2024

It has been suggested that gut microbiota influence Parkinson’s disease (PD) via the gut–brain axis. Here, we examine associations between diet and gut microbiome composition and its predicted functional pathways in patients with PD. We assessed gut microbiota in fecal samples from 85 PD patients in central California using 16S rRNA gene sequencing. Diet quality was assessed by calculating the Healthy Eating Index 2015 (HEI-2015) based on the Diet History Questionnaire II. We examined associations of diet quality, fiber, and added sugar intake with microbial diversity, composition, taxon abundance, and predicted metagenomic profiles, adjusting for age, sex, race/ethnicity, and sequencing platform. Higher HEI scores and fiber intake were associated with an increase in putative anti-inflammatory butyrate-producing bacteria, such as the genera Butyricicoccus and Coprococcus 1. Conversely, higher added sugar intake was associated with an increase in putative pro-inflammatory bacteria, such as the genera Klebsiella. Predictive metagenomics suggested that bacterial genes involved in the biosynthesis of lipopolysaccharide decreased with higher HEI scores, whereas a simultaneous decrease in genes involved in taurine degradation indicates less neuroinflammation. We found that a healthy diet, fiber, and added sugar intake affect the gut microbiome composition and its predicted metagenomic function in PD patients. This suggests that a healthy diet may support gut microbiome that has a positive influence on PD risk and progression.
Distinguishable short-term effects of tea and water drinking on human saliva redox
Authors: Meng Xiangyu , Chong Pik Han , Ke Lijing , Zhang Pengwei , Li Li , Song Binbin , Yu Zhaoshuo , Rao Pingfan
Published: April 2024

Food consumption can alter the biochemistry and redox status of human saliva, and the serving temperature of food may also play a role. The study aimed to explore the immediate (3 min) and delayed (30 min) effects of hot tea (57 ± 0.5 °C) ingestion and cold tea (8 ± 0.5 °C) ingestion on the salivary flow rate and salivary redox-relevant attributes. The saliva was collected from 20 healthy adults before, 3-min after and 30-min after the tea ingestion. The hot or cold deionised water at the same temperatures were used as control. The salivary flow rate and redox markers in hot tea (HBT), cold tea (CBT), hot water (HW) and cold water (CW) group were analysed and compared. The results demonstrated that neither the black tea nor the water altered the salivary flow rate; the black tea immediately increased the salivary thiol (SH) and malondialdehyde (MDA) content while reduced salivary uric acid (UA) significantly. The tea ingestion showed a tendency to elevate the ferric reducing antioxidant power (FRAP) in saliva, although not significantly. The water ingestion decreased the MDA content immediately and increased the UA level significantly. Cold water was found to induce a greater delayed increase in total salivary total protein (TPC) than the hot water. In conclusion, the black tea ingestion affects the redox attributes of human saliva acutely and significantly, while the temperature of drink makes the secondary contribution.
Chromosome-level genome assembly of the diploid oat species Avena longiglumis
Authors: Liu Qing , Xiong Gui , Wang Ziwei , Wu Yongxing , Tu Tieyao , Schwarzacher Trude , Heslop-Harrison John Seymour
Published: April 2024

Diploid wild oat Avena longiglumis has nutritional and adaptive traits which are valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly size of 3,960.97 Mb. A total of 40,845 protein-coding genes were annotated. The assembled genome was composed of 87.04% repetitive DNA sequences. Dotplots of the genome assembly (PI657387) with two published ALO genomes were compared to indicate the conservation of gene order and equal expansion of all syntenic blocks among three genome assemblies. Two recent whole-genome duplication events were characterized in genomes of diploid Avena species. These findings provide new knowledge for the genomic features of A. longiglumis, give information about the species diversity, and will accelerate the functional genomics and breeding studies in oat and related cereal crops.
Single-unit data for sensory neuroscience: Responses from the auditory nerve of young-adult and aging gerbils
Authors: Heeringa Amarins N.
Published: April 2024

This dataset was collected to study the functional consequences of age-related hearing loss for the auditory nerve, which carries acoustic information from the periphery to the central auditory system. Using high-impedance glass electrodes, raw voltage traces and spike times were recorded from more than one thousand single fibres of the auditory nerve of young-adult, middle-aged, and old Mongolian gerbils raised in a quiet environment. The dataset contains not only responses to simple acoustic stimuli to characterize the fibres, but also to more complex stimuli, such as speech logatomes in background noise and Schroeder-phase stimuli. A software toolbox is provided to search through the dataset, to plot various analysed outcomes, and to give insight into the analyses. This dataset may serve as a valuable resource to test further hypotheses about age-related hearing loss. Additionally, it can aid in optimizing available computational models of the auditory system, which can contribute to, or eventually even fully replace, animal experiments.
Essentiality, protein–protein interactions and evolutionary properties are key predictors for identifying cancer-associated genes using machine learning
Authors: Safadi Amro , Lovell Simon C. , Doig Andrew J.
Published: April 2024

The distinctive nature of cancer as a disease prompts an exploration of the special characteristics the genes implicated in cancer exhibit. The identification of cancer-associated genes and their characteristics is crucial to further our understanding of this disease and enhanced likelihood of therapeutic drug targets success. However, the rate at which cancer genes are being identified experimentally is slow. Applying predictive analysis techniques, through the building of accurate machine learning models, is potentially a useful approach in enhancing the identification rate of these genes and their characteristics. Here, we investigated gene essentiality scores and found that they tend to be higher for cancer-associated genes compared to other protein-coding human genes. We built a dataset of extended gene properties linked to essentiality and used it to train a machine-learning model; this model reached 89% accuracy and > 0.85 for the Area Under Curve (AUC). The model showed that essentiality, evolutionary-related properties, and properties arising from protein–protein interaction networks are particularly effective in predicting cancer-associated genes. We were able to use the model to identify potential candidate genes that have not been previously linked to cancer. Prioritising genes that score highly by our methods could aid scientists in their cancer genes research.
Antibacterial and antibiofilm activities of iodinated hydrocarbons against Vibrio parahaemolyticus and Staphylococcus aureus
Authors: Faleye Oluwatosin Oluwaseun , Faleye Olajide Sunday , Lee Jin-Hyung , Lee Jintae
Published: April 2024

Food-related illnesses have become a growing public concern due to their considerable socioeconomic and medical impacts. Vibrio parahaemolyticus and Staphylococcus aureus have been implicated as causative organisms of food-related infections and poisoning, and both can form biofilms which confer antibiotic resistance. Hence, the need for continuous search for compounds with antibiofilm and antivirulence properties. In this study, 22 iodinated hydrocarbons were screened for their antibiofilm activity, and of these, iodopropynyl butylcarbamate (IPBC) was found to effectively control biofilm formation of both pathogens with a MIC of 50 µg/mL which was bactericidal to V. parahaemolyticus and S. aureus. Microscopic studies confirmed IPBC inhibits biofilm formation of both bacteria and also disrupted their mixed biofilm formation. Furthermore, IPBC suppressed virulence activities such as motility and hemolytic activity of V. parahaemolyticus and the cell surface hydrophobicity of S. aureus. It exhibited a preservative potential against both pathogens in a shrimp model. IPBC disrupted the cell membrane of S. aureus and V. parahaemolyticus and differentially affected gene expressions related to biofilm formation and virulence. Additionally, it displayed broad-spectrum antibiofilm activities against other clinically relevant pathogens. These findings indicate IPBC offers a potential means of controlling infections mediated by Vibrio and Staphylococcus biofilms.
A novel multidrug-resistant cell line from a Chinese patient with pancreatic ductal adenocarcinoma
Authors: Tang Huan , Miao Xin , Yu Cheng , Chai Changpeng , Su Yuanhui , Li Lu , Yi Jianfeng , Ye Zhenzhen , Miao Long , Wang Zhengfeng , Zhang Hui , Xu Hao , Zhou Wence
Published: April 2024

Chemotherapy resistance poses clinical challenges in pancreatic cancer treatment. Developing cell lines resistant to chemotherapy is crucial for investigating drug resistance mechanisms and identifying alternative treatment pathways. The genetic and biological attributes of pancreatic cancer depend on its aetiology, racial demographics and anatomical origin, underscoring the need for models that comprehensively represent these characteristics. Here, we introduce PDAC-X2, a pancreatic cancer cell line derived from Chinese patients. We conducted a comprehensive analysis encompassing the immune phenotype, biology, genetics, molecular characteristics and tumorigenicity of the cell line. PDAC-X2 cells displayed epithelial morphology and expressed cell markers (CK7 and CK19) alongside other markers (E-cadherin, Vimentin, Ki-67, CEA and CA19-9). The population doubling time averaged around 69 h. In vivo, PDAC-X2 cells consistently maintained their tumorigenicity, achieving a 100% tumour formation rate. Characterised by a predominantly tetraploid karyotype, this cell line exhibited a complex genetic markup. Notably, PDAC-X2 cells demonstrated resistance to multiple drugs, including gemcitabine, paclitaxel, 5-fluorouracil and oxaliplatin. In conclusion, PDAC-X2 presents an invaluable preclinical model. Its utility lies in facilitating the study of drug resistance mechanisms and the exploration of alternative therapeutic approaches aimed at enhancing the prognosis of this tumour type.
Biallelic variants identified in 36 Pakistani families and trios with autism spectrum disorder
Authors: Khan Hamid , Harripaul Ricardo , Mikhailov Anna , Herzi Sumayah , Bowers Sonya , Ayub Muhammad , Shabbir Muhammad Imran , Vincent John B.
Published: April 2024

With its high rate of consanguineous marriages and diverse ethnic population, little is currently understood about the genetic architecture of autism spectrum disorder (ASD) in Pakistan. Pakistan has a highly ethnically diverse population, yet with a high proportion of endogamous marriages, and is therefore anticipated to be enriched for biallelic disease-relate variants. Here, we attempt to determine the underlying genetic abnormalities causing ASD in thirty-six small simplex or multiplex families from Pakistan. Microarray genotyping followed by homozygosity mapping, copy number variation analysis, and whole exome sequencing were used to identify candidate. Given the high levels of consanguineous marriages among these families, autosomal recessively inherited variants were prioritized, however de novo/dominant and X-linked variants were also identified. The selected variants were validated using Sanger sequencing. Here we report the identification of sixteen rare or novel coding variants in fifteen genes (ARAP1, CDKL5, CSMD2, EFCAB12, EIF3H, GML, NEDD4, PDZD4, POLR3G, SLC35A2, TMEM214, TMEM232, TRANK1, TTC19, and ZNF292) in affected members in eight of the families, including ten homozygous variants in four families (nine missense, one loss of function). Three heterozygous de novo mutations were also identified (in ARAP1, CSMD2, and NEDD4), and variants in known X-linked neurodevelopmental disorder genes CDKL5 and SLC35A2. The current study offers information on the genetic variability associated with ASD in Pakistan, and demonstrates a marked enrichment for biallelic variants over that reported in outbreeding populations. This information will be useful for improving approaches for studying ASD in populations where endogamy is commonly practiced.
Multilevel multinomial regression analysis of factors associated with birth weight in sub-Saharan Africa
Authors: Bezie Meklit Melaku , Tesema Getayeneh Antehunegn , Seifu Beminate Lemma
Published: April 2024

Birth weight significantly determines newborns immediate and future health. Globally, the incidence of both low birth weight (LBW) and macrosomia have increased dramatically including sub-Saharan African (SSA) countries. However, there is limited study on the magnitude and associated factors of birth weight in SSA. Thus, thus study investigated factors associated factors of birth weight in SSA using multilevel multinomial logistic regression analysis. The latest demographic and health survey (DHS) data of 36 sub-Saharan African (SSA) countries was used for this study. A total of a weighted sample of 207,548 live births for whom birth weight data were available were used. Multilevel multinomial logistic regression model was fitted to identify factors associated with birth weight. Variables with p-value < 0.2 in the bivariable analysis were considered for the multivariable analysis. In the multivariable multilevel multinomial logistic regression analysis, the adjusted Relative Risk Ratio (aRRR) with the 95% confidence interval (CI) was reported to declare the statistical significance and strength of association. The prevalence of LBW and macrosomia in SSA were 10.44% (95% CI 10.31%, 10.57%) and 8.33% (95% CI 8.21%, 8.45%), respectively. Maternal education level, household wealth status, age, and the number of pregnancies were among the individual-level variables associated with both LBW and macrosomia in the final multilevel multinomial logistic regression analysis. The community-level factors that had a significant association with both macrosomia and LBW were the place of residence and the sub-Saharan African region. The study found a significant association between LBW and distance to the health facility, while macrosomia had a significant association with parity, marital status, and desired pregnancy. In SSA, macrosomia and LBW were found to be major public health issues. Maternal education, household wealth status, age, place of residence, number of pregnancies, distance to the health facility, and parity were found to be significant factors of LBW and macrosomia in this study. Reducing the double burden (low birth weight and macrosomia) and its related short- and long-term effects, therefore, calls for improving mothers' socioeconomic status and expanding access to and availability of health care.
Prevalence of chronic kidney disease and its associated factors among diabetes mellitus patients in Dessie Referral Hospital, South Wollo, Ethiopia
Authors: Adem Mohammed , Mekonen Wondyefraw , Ausman Ahmed , Ahmed Mohammed , Yimer Ali
Published: April 2024

Diabetes mellitus shares a large proportion of kidney failure. Despite many patients suffering from diabetes mellitus and its complications in Dessie City, no study was conducted in the study area that shows the prevalence and associated factors of chronic kidney disease among diabetes mellitus patients. Therefore, this study aims to assess the prevalence of chronic kidney disease and its associated factors among adult diabetes mellitus patients attending Dessie Referral Hospital, South Wollo, Northeast Ethiopia. An institutional-based cross-sectional study was conducted at Dessie Referral Hospital among 267 randomly selected adult diabetic patients. Data were collected using questionnaires administered by interviewers. The glomerular filtration rate was estimated from serum creatinine levels. Data were entered into Epi-data version 4.6 and analyzed using SPSS version 26 software. Multi-variable logistic regression was used to determine the strength of association for the associated factors of chronic kidney disease. Variables with apvalue < 0.05 were used to ascertain statistically significant associations. A total of 267 diabetic patients participated in this study. About 104 (39%) of the respondents were female and from the total, 133 (48.1%) were hypertensive. The overall prevalence of chronic kidney disease in this study was 31.5% (95% CI 25.3–37.1%). Being older (p-value = 0.003) and having hypertension (p-value = 0.043) were significant factors for chronic kidney disease among diabetes mellitus patients. This study found a high prevalence (31.5%) of chronic kidney disease among diabetic patients. Older age, having hypertension, and elevated serum creatinine were statistically significant associated factors of chronic kidney disease among patients with diabetes mellitus. Thus, clinicians should be aware of the high prevalence of chronic kidney disease in Dessie City. Moreover, emphasis should be given for old age and hypertension as contributing factors to the high prevalence in diabetic patients.
SGD-OD: investigating the potential oxygen demand of submarine groundwater discharge in coastal systems
Authors: Moore Willard S. , Benitez-Nelson Claudia , Schutte Charles , Moody Amy , Shiller Alan , Sibert Ryan J. , Joye Samantha
Published: April 2024

Submarine groundwater discharge (SGD) supplies nutrients, carbon, metals, and radionuclide tracers to estuarine and coastal waters. One aspect of SGD that is poorly recognized is its direct effect on dissolved oxygen (DO) demand in receiving waters, denoted here as SGD-OD. Sulfate-mediated oxidation of organic matter in salty coastal aquifers produces numerous reduced byproducts including sulfide, ammonia, dissolved organic carbon and nitrogen, methane, and reduced metals. When these byproducts are introduced to estuarine and coastal systems by SGD and are oxidized, they may substantially reduce the DO concentration in receiving waters and impact organisms living there. We consider six estuarine and coastal sites where SGD derived fluxes of reduced byproducts are well documented. Using data from these sites we present a semiquantitative model to estimate the effect of these byproducts on DO in the receiving waters. Without continued aeration with atmospheric oxygen, the study sites would have experienced periodic hypoxic conditions due to SGD-OD. The presence of H2S supplied by SGD could also impact organisms. This process is likely prevalent in other systems worldwide.
Transcriptome and single-cell analysis reveal disulfidptosis-related modification patterns of tumor microenvironment and prognosis in osteosarcoma
Authors: Wang Linbang , Liu Yu , Tai Jiaojiao , Dou Xinyu , Yang Hongjuan , Li Qiaochu , Liu Jingkun , Yan Ziqiang , Liu Xiaoguang
Published: April 2024

Osteosarcoma (OS) is the most common malignant bone tumor with high pathological heterogeneity. Our study aimed to investigate disulfidptosis-related modification patterns in OS and their relationship with survival outcomes in patients with OS. We analyzed the single-cell-level expression profiles of disulfidptosis-related genes (DSRGs) in both OS microenvironment and OS subclusters, and HMGB1 was found to be crucial for intercellular regulation of OS disulfidptosis. Next, we explored the molecular clusters of OS based on DSRGs and related immune cell infiltration using transcriptome data. Subsequently, the hub genes of disulfidptosis in OS were screened by applying multiple machine models. In vitro and patient experiments validated our results. Three main disulfidptosis-related molecular clusters were defined in OS, and immune infiltration analysis suggested high immune heterogeneity between distinct clusters. The in vitro experiment confirmed decreased cell viability of OS after ACTB silencing and higher expression of ACTB in patients with lower immune scores. Our study systematically revealed the underlying relationship between disulfidptosis and OS at the single-cell level, identified disulfidptosis-related subtypes, and revealed the potential role of ACTB expression in OS disulfidptosis.
A novel method for evaluating mastoid defect regrowth after cochlear implantation
Authors: Hamed Nezar , Alahmadi Asma , Abdelsamad Yassin , Alballaa Abdulaziz , Almuhawas Fida , Allami Hussain , Almousa Hisham , Hagr Abdulrahman
Published: April 2024

This retrospective study examined mastoid defects resulting from cochlear implant (CI) surgery and their potential for spontaneous regrowth across different age groups. Spontaneous closure of mastoid defects has been observed in certain CI patients during revision surgery or through post-operative temporal bone computer tomography (TB-CT). The analysis encompassed 123 CI recipients, comprising 81.3% children and 18.7% adults, who underwent post-operative TB-CT scans. Using image adjustment software, the study measured mastoid defect areas and found a significant reduction in children's defects between the initial and subsequent scans. Notably, mastoid defect areas differed significantly between children and adults at both time points. Furthermore, the analysis revealed significant correlations between mastoid defect areas and the age at implantation as well as the time elapsed since the CI surgery and the first CT scan. This study provides valuable insights for evaluating CI patients scheduled for revision surgery by assessing potential surgical challenges and duration. Furthermore, it may have a pivotal role in evaluating patients who experience postauricular swelling subsequent to CI surgery.
Snapshot study of canine distemper virus in Bangladesh with on-site PCR detection and nanopore sequencing
Authors: Lanszki Zsófia , Islam Md. Shafeul , Shikder Md. Foisal , Sarder Md. Jalal Uddin , Khan Shahneaz Ali , Chowdhury Sharmin , Islam Md. Nurul , Tauber Zsófia , Tóth Gábor Endre , Jakab Ferenc , Kemenesi Gábor , Akter Sazeda
Published: April 2024

Canine distemper virus (CDV) is a highly contagious virus that affects domestic and wild animals, causing severe illness with high mortality rates. Rapid monitoring and sequencing can provide valuable information about circulating CDV strains, which may foster effective vaccination strategies and the successful integration of these into conservation programs. During two site visits in Bangladesh in 2023, we tested a mobile, deployable genomic surveillance setup to explore the genetic diversity and phylogenetic patterns of locally circulating CDV strains. We collected and analysed 355 oral swab samples from stray dogs in Rajshahi and Chattogram cities, Bangladesh. CDV-specific real-time RT-PCR was performed to screen the samples. Out of the 355 samples, 7.4% (10/135) from Rajshahi city and 0.9% (2/220) from Chattogram city tested positive for CDV. We applied a real-time RT-PCR assay and a pan-genotype CDV-specific amplicon-based Nanopore sequencing technology to obtain the near-completes. Five near-complete genome sequences were generated, with phylogenetic relation to the India-1/Asia-5 lineage previously identified in India. This is the first study to provide genomic data on CDV in Bangladesh and the first demonstration of a mobile laboratory setup as a powerful tool in rapid genomic surveillance and risk assessment for CDV in low resource regions.
Application of power-law committee machine to combine five machine learning algorithms for enhanced oil recovery screening
Authors: Yousefzadeh Reza , Kazemi Alireza , Al-Maamari Rashid S.
Published: April 2024

One of the main challenges in screening of enhanced oil recovery (EOR) techniques is the class imbalance problem, where the number of different EOR techniques is not equal. This problem hinders the generalization of the data-driven methods used to predict suitable EOR techniques for candidate reservoirs. The main purpose of this paper is to propose a novel approach to overcome the above challenge by taking advantage of the Power-Law Committee Machine (PLCM) technique optimized by Particle Swam Optimization (PSO) to combine the output of five cutting-edge machine learning methods with different types of learning algorithms. The PLCM method has not been used in previous studies for EOR screening. The machine learning models include the Artificial Neural Network (ANN), CatBoost, Random Forest (RF), K-Nearest Neighbors (KNN), and Support Vector Machine (SVM). The CatBoost is used for the first time in this work for screening of EOR methods. The role of the PSO is to find the optimal values for the coefficients and exponents of the power-law model. In this study, a bigger dataset than those in previous studies, including 2563 successful worldwide EOR experiences, was gathered. A bigger dataset improves the generalization of the data-driven methods and prevents overfitting. The hyperparameters of the individual machine-learning models were tuned using the fivefold cross-validation technique. The results showed that all the individual methods could predict the suitable EOR method for unseen cases with an average score of 0.868. Among the machine learning models, the KNN and SVM had the highest scores with a value of 0.894 and 0.892, respectively. Nonetheless, after combining the output of the models using the PLCM method, the score of the predictions improved to 0.963, which was a substantial increase. Finally, a feature importance analysis was conducted to find out the most influential parameters on the output. The novelty of this work is having shown the ability of the PLCM technique to construct an accurate model to overcome the class-imbalance issue in EOR screening by utilizing different types of data-driven models. According to feature importance analysis, oil gravity and formation porosity were recognized as the most influential parameters on EOR screening.
Study on time–frequency features of induced charge signals during the damage and failure process of coal medium
Authors: Lyu Jinguo , Li Shixu , Pan Yishan , Tang Zhi , Wang Xuebin , Xue Zhanpeng , Zhang Yanli , Qiao Yanfang
Published: April 2024

Monitoring and preventing coal-rock dynamic disasters are vital for safe mining. To investigate the time–frequency features of induced charge signals with coal damage and failure of roadways, the generation mechanism of free charge in loaded coal is analyzed and the induced charge monitoring test is conducted. According to the stress-induced charge-time curves, the time-domain features of charge signals at each loading stage are obtained. The wavelet threshold denoising approach and generalized Morse wavelet transform method are applied to denoise the raw signals and study the frequency-domain features. Further, the quantitative relationship between the de-noised induced charge signals and the degree of coal damage is established. The results show that the event number, amplitude and fluctuation degree of available induced charge signals are all at a low level in the compaction and elastic stages of the coal, which are mainly generated by the piezoelectric effect and predominantly represent discreteness. When entering the plastic and failure stages, the available signals are primarily produced by the crack propagation and triboelectric effects, with a significant increase in the event number, amplitude, and fluctuation degree. Then the induced charge signals gradually transit from discrete to continuous. Generally, the dominant frequency of the available induced charge signals during the coal damage process is concentrated at 0 ~ 11 Hz. The available induced charge is positively correlated with the degree of coal damage, which can perform the damage degree of coal mass, providing a new approach to evaluate the stability of roadway surrounding rocks.
Combined application of bacteriophages with a competitive exclusion culture and carvacrol with organic acids can reduce Campylobacter in primary broiler production
Authors: Peh E. , Szott V. , Reichelt B. , Friese A. , Ploetz M. , Roesler U. , Kittler S.
Published: April 2024

For reducing Campylobacter (C.) in the food production chain and thus the risk to the consumer, the combined application of different measures as a multiple-hurdle approach is currently under discussion. This is the first study to investigate possible synergistic activities in vivo, aiming at reducing intestinal C. jejuni counts by administering (i) bacteriophages (phages) in combination with a competitive exclusion (CE) product and (ii) carvacrol combined with organic acids. The combined application of the two selected phages (Fletchervirus phage NCTC 12673 and Firehammervirus phage vB_CcM-LmqsCPL1/1) and the CE product significantly reduced C. jejuni loads by 1.0 log10 in cecal and colonic contents as well as in cloacal swabs at the end of the trial (33 and 34 days post hatch). The proportion of bacterial isolates showing reduced phage susceptibility ranged from 10.9% (isolates from cecal content) to 47.8% (isolates from cloacal swabs 32 days post hatch) for the Fletchervirus phage, while all tested isolates remained susceptible to the Firehammervirus phage. The use of carvacrol combined with an organic acid blend (sorbic acid, benzoic acid, propionic acid, and acetic acid) significantly reduced Campylobacter counts by 1.0 log10 in cloacal swabs on day 30 only.
Novel Cu(II)-based metal–organic framework STAM-1 as a sulfur host for Li–S batteries
Authors: Niščáková V. , Almáši M. , Capková D. , Kazda T. , Čech O. , Čudek P. , Petruš O. , Volavka D. , Oriňaková R. , Fedorková A. S.
Published: April 2024

Due to the increasing demand for energy storage devices, the development of high-energy density batteries is very necessary. Lithium–sulfur (Li–S) batteries have gained wide interest due to their particularly high-energy density. However, even this type of battery still needs to be improved. Novel Cu(II)-based metal–organic framework STAM-1 was synthesized and applied as a composite cathode material as a sulfur host in the lithium–sulfur battery with the aim of regulating the redox kinetics of sulfur cathodes. Prepared STAM-1 was characterized by infrared spectroscopy at ambient temperature and after in-situ heating, elemental analysis, X-ray photoelectron spectroscopy and textural properties by nitrogen and carbon dioxide adsorption at − 196 and 0 °C, respectively. Results of the SEM showed that crystals of STAM-1 created a flake-like structure, the surface was uniform and porous enough for electrolyte and sulfur infiltration. Subsequently, STAM-1 was used as a sulfur carrier in the cathode construction of a Li–S battery. The charge/discharge measurements of the novel S/STAM-1/Super P/PVDF cathode demonstrated the initial discharge capacity of 452 mAh g−1 at 0.5 C and after 100 cycles of 430 mAh g−1, with Coulombic efficiency of 97% during the whole cycling procedure at 0.5 C. It was confirmed that novel Cu-based STAM-1 flakes could accelerate the conversion of sulfur species in the cathode material.
Technical, economic, and environmental feasibility of rice hull ash from electricity generation as a mineral additive to concrete
Authors: Ro Jin Wook , Cunningham Patrick R. , Miller Sabbie A. , Kendall Alissa , Harvey John
Published: April 2024

A circular economy based on symbiotic relationships among sectors, where the waste from one is resource to another, holds promise for cost-effective and sustainable production. This research explores such a model for the agriculture, energy, and construction sectors in California. Here, we develop new an understanding for the synergistic utilization mechanisms for rice hull, a byproduct from rice production, as a feedstock for electricity generation and rice hull ash (RHA) used as a supplementary cementitious material in concrete. A suite of methods including experimental analysis, techno-economic analysis (TEA), and life-cycle assessment (LCA) were applied to estimate the cost and environmental performance of the system. TEA results showed that the electricity price required for break even on expenses without selling RHA is $0.07/kWh, lower than the market price. As such, RHA may be available at little to no cost to concrete producers. Our experimental results showed the viability of RHA to be used as a supplementary cementitious material, meaning it can replace a portion of the cement used in concrete. LCA results showed that replacing 15% of cement with RHA in concrete can reduce carbon dioxide equivalent (CO2e) emissions by 15% while still meeting material performance targets. While the substitution rate of RHA for cement may be modest, RHA generated from California alone could mitigate 0.2% of total CO2e from the entire cement production sector in the United States and 1% in California.
The usefulness of quantitative 99mTc-HMPAO WBC SPECT/CT for predicting lower extremity amputation in diabetic foot infection
Authors: Park Soo Bin , Lim Chae Hong , Chun Dong-il , Kim Yong Jae , Kim Tae Hyong , Park Jung Mi
Published: April 2024

We investigated the usefulness of quantitative 99mTc-white blood cell (WBC) single photon emission computed tomography (SPECT)/computed tomography (CT) for predicting lower extremity amputation in diabetic foot infection (DFI). A total of 93 feet of 83 consecutive patients with DFI who underwent WBC SPECT/CT for treatment planning were retrospectively analysed. The clinical and SPECT/CT parameters were collected along with the measurements of the maximum standardized uptake value (SUVmax) at DFI. Statistical logistic regression analysis was performed to explore the predictors of LEA and receiver operating characteristic (ROC) curve was analysed to assess the predictive value of SPECT/CT. The independent predictors of amputation were previous amputation (OR 11.9), numbers of SPECT/CT lesions (OR 2.1), and SUVmax of DFI; either continuous SUVmax (1-increase) (OR 1.3) or categorical SUVmax > 1.1 (OR 21.6). However, the conventional SPECT/CT interpretation failed to predict amputation. In ROC analysis, the SUVmax yielded a fair predictor (area under the curve (AUC) 0.782) of amputation. The model developed from these independent predictors yielded an excellent performance for predicting amputation (AUC 0.873). Quantitative WBC SPECT/CT can provide new information useful for predicting the outcomes and guiding treatment for patients with DFI.
The dynamical perspective of soliton solutions, bifurcation, chaotic and sensitivity analysis to the (3+1)-dimensional Boussinesq model
Authors: Nadeem Muhammad , Islam Asad , Şenol Mehmet , Alsayaad Yahya
Published: April 2024

In this study, we examine multiple perspectives on soliton solutions to the (3+1)-dimensional Boussinesq model by applying the unified Riccati equation expansion (UREE) approach. The Boussinesq model examines wave propagation in shallow water, which is derived from the fluid dynamics of a dynamical system. The UREE approach allows us to derive a range of distinct solutions, such as single, periodic, dark, and rational wave solutions. Furthermore, we present the bifurcation, chaotic, and sensitivity analysis of the proposed model. We use planar dynamical system theory to analyze the structure and characteristics of the system’s phase portraits. The current study depends on a dynamic structure that has novel and unexplored results for this model. In addition, we display the behaviors of associated physical models in 3-dimensional, density, and 2-dimensional graphical structures. Our findings demonstrate that the UREE technique is a valuable mathematical tool in engineering and applied mathematics for studying wave propagation in nonlinear evolution equations.
All-fiber few-mode interference for complex azimuthal pattern generation
Authors: Gómez-Méndez Josué I. , Carrillo-Betancourt Rodolfo A. , May-Arrioja Daniel A. , Velázquez-Benítez Amado M. , Cuando-Espitia Natanael , Hernández-Cordero Juan
Published: April 2024

We report on an all-fiber setup capable of generating complex intensity patterns using interference of few guided modes. Comprised by a few-mode fiber (FMF) spliced to a multimodal interference (MMI) fiber device, the setup allows for obtaining different output patterns upon adjusting the phases and intensities of the modes propagating in the FMF. We analyze the output patterns obtained when exciting two family modes in the MMI device using different phase and intensity conditions for the FMF modal base. Using this simple experimental arrangement we are able to produce complex intensity patterns with radial and azimuthal symmetry. Moreover, our results suggest that this approach provides a means to generate beams with orbital angular momentum (OAM).
Male sexual dysfunction in patients with chronic kidney disease: a cross-sectional study
Authors: Fu Ruijie , He Peihua , Hong Weihong , Liang Yichun , Wang Wen , Yuan Shaoying , Liu Lichang
Published: April 2024

Sexual dysfunction is common in males with chronic kidney disease (CKD), but yet the prevalence and specific relationship between CKD and sexual dysfunction, especially premature ejaculation (PE), remain to be investigated in China; This study aims to examine the prevalence and association between CKD and sexual dysfunction in male patients in China; In this cross-sectional, non-interventional, observational study conducted at a single center. 72 male patients with CKD were enrolled. Data collection included socio-demographic information, assessments via the 5-item version of the International Index of Erectile Function (IIEF-5), the Chinese version of the Premature Ejaculation Diagnostic Tool, the Patient Health Quentionnnaire-9 and the General Anxiety Disorder-7. Data analysis was performed using R version 3.5.2 and SPSS software version 25.0; Among the 72 CKD patients, 56.9% experienced erectile dysfunction and 29.2% had PE. Various factors including estimated Glomerular Filtration Rate, Albumin-to-Creatinine Ratio, psychological aspects, medication use were found to be associated with sexual dysfunction in these CKD patients; Sexual dysfunction is prevalent in males with CKD and is, influenced by multiple factors. It is important for clinicians to focus on sexual dysfunction in this patient group and further investigate its underlying mechanisms.
TO-UGDA: target-oriented unsupervised graph domain adaptation
Authors: Zeng Zhuo , Xie Jianyu , Yang Zhijie , Ma Tengfei , Chen Duanbing
Published: April 2024

Graph domain adaptation (GDA) aims to address the challenge of limited label data in the target graph domain. Existing methods such as UDAGCN, GRADE, DEAL, and COCO for different-level (node-level, graph-level) adaptation tasks exhibit variations in domain feature extraction, and most of them solely rely on representation alignment to transfer label information from a labeled source domain to an unlabeled target domain. However, this approach can be influenced by irrelevant information and usually ignores the conditional shift of the downstream predictor. To effectively address this issue, we introduce a target-oriented unsupervised graph domain adaptive framework for graph adaptation called TO-UGDA. Particularly, domain-invariant feature representations are extracted using graph information bottleneck. The discrepancy between two domains is minimized using an adversarial alignment strategy to obtain a unified feature distribution. Additionally, the meta pseudo-label is introduced to enhance downstream adaptation and improve the model’s generalizability. Through extensive experimentation on real-world graph datasets, it is proved that the proposed framework achieves excellent performance across various node-level and graph-level adaptation tasks.
Unveiling the link between lactate metabolism and rheumatoid arthritis through integration of bioinformatics and machine learning
Authors: Yang Fan , Shen Junyi , Zhao Zhiming , Shang Wei , Cai Hui
Published: April 2024

Rheumatoid arthritis (RA) is a persistent autoimmune condition characterized by synovitis and joint damage. Recent findings suggest a potential link to abnormal lactate metabolism. This study aims to identify lactate metabolism-related genes (LMRGs) in RA and investigate their correlation with the molecular mechanisms of RA immunity. Data on the gene expression profiles of RA synovial tissue samples were acquired from the gene expression omnibus (GEO) database. The RA database was acquired by obtaining the common LMRDEGs, and selecting the gene collection through an SVM model. Conducting the functional enrichment analysis, followed by immuno-infiltration analysis and protein–protein interaction networks. The results revealed that as possible markers associated with lactate metabolism in RA, KCNN4 and SLC25A4 may be involved in regulating macrophage function in the immune response to RA, whereas GATA2 is involved in the immune mechanism of DC cells. In conclusion, this study utilized bioinformatics analysis and machine learning to identify biomarkers associated with lactate metabolism in RA and examined their relationship with immune cell infiltration. These findings offer novel perspectives on potential diagnostic and therapeutic targets for RA.
Molecular epidemiology and hematological profiles of hemoglobin variants in southern Thailand
Authors: Tepakhan Wanicha , Kanjanaopas Sataron , Sreworadechpisal Korntip , Penglong Tipparat , Sripornsawan Pornpun , Wangchauy Chaowanee , Nokkong Chadaporn , Kongkan Chulalak , Buathong Saristha
Published: April 2024

Data on hemoglobin (Hb) variants in southern Thailand are lacking. This study aimed to reassess the frequency of Hb variants and the clinical aspects of compound heterozygous Hb variant with other hemoglobinopathies. We enrolled 13,391 participants from ten provinces in southern Thailand during 2015–2022. Hb analysis was performed using capillary electrophoresis, and mutations in the HBA and HBB genes were identified using PCR or DNA sequencing. Hb variants were identified in 337 (2.5%) unrelated subjects. Nine β-chain variants, namely Hb Malay (76.9%), Hb C (10.1%), Hb D-Punjab (2.9%), Hb G-Makassar (2.3%), Hb Dhonburi (2.3%), Hb Tak (1.4%), Hb J-Bangkok (1.4%), Hb New York (0.3%), and Hb Hope (0.3%), and four α-chain variants—Hb G-Georgia (HBA1) (0.9%), Hb G-Georgia (HBA2) (0.3%), Hb Q-Thailand (0.6%), and Hb St. Luke’s-Thailand (0.3%)—were identified. The southern population exhibited a distinct spectrum of Hb variants compared to that observed in the populations from other areas. Several compound heterozygous genotypes were also identified. Combining Hb Malay with Hb E or high Hb F determinants did not require a blood transfusion. This study provides essential information for genetic counseling in thalassemia prevention and control programs in this region.
Real-time near infrared artificial intelligence using scalable non-expert crowdsourcing in colorectal surgery
Authors: Skinner Garrett , Chen Tina , Jentis Gabriel , Liu Yao , McCulloh Christopher , Harzman Alan , Huang Emily , Kalady Matthew , Kim Peter
Published: April 2024

Surgical artificial intelligence (AI) has the potential to improve patient safety and clinical outcomes. To date, training such AI models to identify tissue anatomy requires annotations by expensive and rate-limiting surgical domain experts. Herein, we demonstrate and validate a methodology to obtain high quality surgical tissue annotations through crowdsourcing of non-experts, and real-time deployment of multimodal surgical anatomy AI model in colorectal surgery.
Record-breaking fire weather in North America in 2021 was initiated by the Pacific northwest heat dome
Authors: Jain Piyush , Sharma Aseem Raj , Acuna Dante Castellanos , Abatzoglou John T. , Flannigan Mike
Published: April 2024

The 2021 North American wildfire season was marked by record breaking fire-conducive weather and widespread synchronous burning, extreme fire behaviour, smoke and evacuations. Relative to 1979–2021, the greatest number of temperature and vapor pressure deficit records were broken in 2021, and in July alone, 3.2 million hectares burned in Canada and the United States. These events were catalyzed by an intense heat dome that formed in late June over western North America that synchronized fire danger, challenging fire suppression efforts. Based on analysis of persistent positive anomalies of geopotential heights, the heat dome accounted for 21–34% of the total area burned in 2021. The event was 59% longer, 34% larger and had 6% higher maximum amplitude than the same event would have been without a warming climate. Climate change will continue to magnify heat dome events, increase fire danger, and enable extreme synchronous wildfire in forested areas of North America.
The value of unrealistic targets: why some climate activists are unwilling to abandon the 1.5 °C target
Authors: Hadden Jennifer , Prakash Aseem
Published: April 2024

Evidence is mounting that the 1.5 °C goal of the Paris Agreement is unrealistic. But, contrary to many in the scientific community, major NGOs have remained steadfast in their support for this target. We argue that this is because “unrealistic” or aspirational targets can serve important political objectives, including becoming focal points for coalition-building and broad-based mobilization and allowing for effective naming and shaming.
Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germline
Authors: Ohta Naoyuki , Christiaen Lionel
Published: April 2024

Transcription control is a major determinant of cell fate decisions in somatic tissues. By contrast, early germline fate specification in numerous vertebrate and invertebrate species relies extensively on RNA-level regulation, exerted on asymmetrically inherited maternal supplies, with little-to-no zygotic transcription. However delayed, a maternal-to-zygotic transition is nevertheless poised to complete the deployment of pre-gametic programs in the germline. Here, we focus on early germline specification in the tunicate Ciona to study zygotic genome activation. We first demonstrate that a peculiar cellular remodeling event excludes localized postplasmic Pem-1 mRNA, which encodes the general inhibitor of transcription. Subsequently, zygotic transcription begins in Pem-1-negative primordial germ cells (PGCs), as revealed by histochemical detection of elongating RNA Polymerase II, and nascent Mef2 transcripts. In addition, we uncover a provisional antagonism between JAK and MEK/BMPRI/GSK3 signaling, which controls the onset of zygotic gene expression, following cellular remodeling of PGCs. We propose a 2-step model for the onset of zygotic transcription in the Ciona germline and discuss the significance of germ plasm dislocation and remodeling in the context of developmental fate specification.
Highly stable localized surface plasmon resonance of Cu nanoparticles obtained via oxygen plasma irradiation
Authors: Fang Yingcui , Xu Bin , Wang Shuai , Liu Hongjun , Wang Jie , Si Mengting
Published: April 2024

A CuNPs@d-CuO core–shell structure with a ∼4 nm CuO layer was obtained by passivating CuNPs via highly active oxygen plasma irradiation. The LSPR is strong and stable in air over 180 days.
Biogenic derived egg shell and its derivatives as solid base heterogeneous catalysts for organic transformations: a comprehensive review
Authors: Naik Nagaraj S. , Divakar Swathi , M. S. Jyothi , Budagumpi Srinivasa , Balakrishna R. Geetha , Padaki Mahesh
Published: April 2024

The implication of employing green chemistry in synthetic chemistry has opened new doors of sustainability and innovation.