bluuebunny/crossref_metadata_2025_split huggingface dataset:
SGLT2 inhibitors among patients with heart failure with preserved ejection fraction: A meta-analysis of randomised controlled trials
Authors: Jaiswal Akash , Jaiswal Vikash , Ang Song Peng , Hanif Muhammad , Vadhera Ananya , Agrawal Vibhor , Kumar Tushar , Nair Anagha M. , Borra VamsikalyanReddy , Garimella Vamsi , Ishak Angela , Wajid Zarghoona , Song David , Attia Abdelrahman M. , Huang Helen , Aguilera Alvarez Victor Hugo , Shrestha Abhigan Babu , Biswas Monodeep 
Published: September 2023

Background:
Sodium-glucose co-transporter 2 (SGLT2) inhibitors have been recommended in the practice guidelines for the treatment of patients with heart failure with reduced ejection fraction; however, their effects among patients with preserved ejection fraction have been debatable.

Objective:
We aim to evaluate the SGLT2 inhibitor effect among patients with heart failure with reduced ejection fraction, including DELIVER and EMPEROR-Preserved trials.

Methods:
We performed a systematic literature search using the PubMed, Embase, Scopus, and Cochrane libraries for relevant articles from inception until August 30th, 2022. Statistical analysis was performed by calculating hazard ratio (HR) using the random effect model with a 95% confidence interval (CI) and probability value (P). Statistical significance was met if 95% CI does not cross numeric “1” and P < .05.

Results:
Six studies with a total of 15,989 total patients were included in the final analysis. The mean age of patients enrolled in SGLT2 inhibitors and placebo was 69.13 and 69.37 years, respectively. The median follow-up duration was 2.24 years. SGLT2 inhibitors reduced composite cardiovascular mortality or first hospitalization for heart failure (HR, 0.80 [95% CI: 0.74–0.87], P < .001, I
2 = 0%), heart failure hospitalization (HR, 0.74 [95% CI: 0.67–0.82], P < .001, I
2 = 0%) compared with placebo. However, all-cause mortality (HR, 0.97 [95% CI: 0.89–1.06], P = .54, I
2 = 0%) and cardiovascular mortality (HR, 0.96 [95% CI: 0.82–1.13), P = .66, I
2 = 35.09%] were comparable between both groups.

Conclusion:
Our study finding shows that SGLT2 inhibitors significantly reduced the risk of first HF hospitalization or cardiovascular death and HF hospitalization; however, all-cause mortality was comparable between the groups.
Bioinformatics analysis of copper death gene in diabetic immune infiltration
Authors: Lu Zhimin , Ding Ling , Zhang Sen , Jiang Xing , Wang Qinglu , Luo Ying , Tian Xuewen 
Published: September 2023

Background:
Copper plays an important role in the human body and is potentially related to the development of diabetes. The mechanism of copper death gene regulating immune infiltration in diabetes has not been studied.

Methods:
Download microarray data from healthy normal and diabetic patients from the GEO database. The identification of differentially expressed genes (DEGs) was analyzed by gene enrichment. Using String online database and Cytoscape software to interact with the protein interaction network and make visual analysis. Using Wilcox analyze the correlation between the copoer death gene and diabetic mellitus. Analysis of the correlation between immune penetration cells and functions, and the difference between the diabetes group and the control group, screening the copper death gene associated with diabetes, and predicting the upper top of microRNA (miRNA) through the Funrich software.

Results:
According to the identification of differential genes in 25 samples of GSE25724 and GSE95849 data sets, 328 differential genes were identified by consensus, including 190 up-regulated genes and 138 down-regulated genes (log2FC = 2, P < .01). KEGG results showed that neurodegeneration-multiple disease pathways were most significantly upregulated, followed by Huntington disease. According to Cytohubba, the TOP10 genes HCK, FPR1, MNDA, AQP9, TLR8, CXCR1, CSF3R, VNN2, TLR4, and CCR5 are down-regulated genes, which are mostly enriched in neutrophils. Immunoinfiltration-related heat maps show that Macrophage was strongly positively correlated with Activated dendritic cell, Mast cell, Neutrophil, and Regulatory T cell showed a strong positive correlation. Neutrophil was strongly positively correlated with Activated dendritic cell, Mast cell, and Regulatory T cell. Differential analysis of immune infiltration showed that Neutroph, Mast cell, Activated B cell, Macrophage and Eosinophil were significantly increased in the diabetic group. Central memory CD4 T cell (P < .001), Plasmacytoid dendritic cell, Immature dendritic cell, and Central memory CD8 T cell, etal were significantly decreased. DBT, SLC31A1, ATP7A, LIAS, ATP7B, PDHA1, DLST, PDHB, GCSH, LIPT1, DLD, FDX1, and DLAT genes were significantly associated with one or more cells and their functions in immune invasion. Forty-one miRNA.

Conclusions:
Copper death is closely related to the occurrence of diabetes. Copper death genes may play an important role in the immune infiltration of diabetes.
Medial patellofemoral ligament reconstruction appears to be a better treatment than repair, proximal realignment, or conservative management for primary patellar dislocation: A network meta-analysis
Authors: Yoo Jae-Doo , Huh Min-Hwan , Lee Chan-Woo , Roh Young-Hak , D’Lima Darryl D. , Shin Young-Soo 
Published: September 2023

Background:
The purpose of this study was to compare the functional outcomes and re-dislocation rates of medial patellofemoral ligament (MPFL) reconstruction, MPFL repair, combined proximal realignment (CPR), and conservative management for primary patellar dislocation by conducting a systematic literature search of the available studies. The hypothesis was that MPFL repair and MPFL reconstruction would be better options for treating primary patellar dislocation.

Methods:
Randomized controlled trials or prospective studies of primary patellar dislocation treated with MPFL reconstruction, MPFL repair, CPR, or conservative management were identified from the MEDLINE, EMBASE, and the Cochrane Library databases through December 31, 2021. A total of 626 patients met the prespecified inclusion criteria. The methodological quality of each study was assessed using a risk of bias table, Detsky quality index, and Newcastle-Ottawa Scale. The end-point data collected included comparisons of the mean in functional scores on knee outcomes scales and the number of patients who experienced re-dislocation. A network meta-analysis of the relevant literature was performed to investigate which treatment showed better outcomes.

Results:
In total, 10 trials were included in this study. There was no statistically significant difference in the subgroup analysis in terms of the functional outcomes among MPFL reconstruction, MPFL repair, CPR, and conservative management. However, MPFL reconstruction showed statistically significantly better outcomes than MPFL repair, CPR, or conservative management in terms of the re-dislocation rate. Additionally, surface under the cumulative ranking curve percentage showed that MPFL reconstruction had a lower probability of re-dislocation than MPFL repair even though there was no significant difference (0.24, 95% confidence interval: 0.02–2.91).

Conclusion:
Using a network meta-analysis, this meta-analysis showed that there was no significant difference in functional outcomes in a subgroup analysis. In re-dislocation subgroup analysis, MPFL repair and MPFL reconstruction produced significantly better results than other treatments. Also, surface under the cumulative ranking curve percentage showed that MPFL reconstruction had a lower probability of re-dislocation than MPFL repair.
Causes and Outcome of Central Venous Catheter Repair in Children with Intestinal Failure on Home Parenteral Nutrition
Authors: Zaidi Zafar , Littlechild Hannah , Hill Susan , Köglmeier Jutta 
Published: September 2023

Objectives:
Children requiring a central venous catheter (CVC) for long-term parenteral nutrition (PN) are at risk of CVC breakage. Modern intestinal failure (IF) management aims to preserve vascular access sites. CVC repair rather than removal is hence attempted for broken catheters. The aim of this study was to describe causes and outcomes of CVC repairs in home PN dependent children.

Methods:
All patients (ages 0–17 years) with CVC dependency enrolled in the IF rehabilitation program of a pediatric referral center were identified, and those who underwent a CVC repair between January 2019 and November 2020 included. Data on associated cause for breakage and incidence of central line-associated bloodstream infections (CLABSIs) post repair were documented retrospectively. Descriptive statistics including medians, percentages, and frequencies were used.

Results:
Forty children, 15 males (37%) and 25 females (63%), were identified. Fifteen of 40 (37.5%) patients underwent a total of 29 CVC repairs (0.1 repairs per 1000 catheter days); 8 of 15 (53%; 33% females) were <5 years of age. The most common reason for repair was CVC fracture by biting (41%) followed by catheter occlusion with intraluminal PN deposition (13.2%). Repair was successful in 100% cases. Only 1 patient had a confirmed CLABSI post repair (1/29 repairs; 3%) who presented 3 days late after the initial catheter breakage. Catheter salvage was successful with antibiotics.

Conclusion:
CVC repair in our cohort was very successful and infection rate after repair minimal. CVC repair rather than removal is recommended to preserve central venous access.
Women Who Give Birth Preterm Do Not Meet Dietary Guidelines During Pregnancy
Authors: Filatava Evgenia Jen , Overton Nicolette E. , El Habbal Noura , Capotosto Melissa Perez , Gregas Matt , Gregory Katherine E. 
Published: September 2023

Abstract

Purpose:
To evaluate maternal dietary intake during pregnancy compared with the 2015-2020 and 2020-2025 Dietary Guidelines for Americans (DGA).

Study Design and Methods:
A retrospective observational study design was used. The cohort included women who gave birth to preterm infants between 25 1/7 weeks and 33 6/7 weeks of gestation. Within 2 weeks of birth, participants were asked to recall their diet in the last month of pregnancy using the Dietary Screener Questionnaire. Participants' dietary intakes were compared to current 2020-2025 DGA that include specific recommendations for pregnant women and prior 2015-2020 DGA that were in place during the study period but were not pregnancy-specific.

Results:
Forty-five women participated in the study. None met the 2015-2020 or 2020-2025 DGA recommended intake of all seven dietary components. When compared to both DGAs, 2.2% of participants met the recommended dairy intake, 26.7% met the calcium intake, 15.6% were below the threshold for added sugar, and none met the vegetable or whole grain intake. When compared to the 2015-2020 DGA, 28.9% met the fruit intake and 2.2% met the fiber intake. However, when compared to the 2020-2025 DGA, only 2.2% met the fruit intake and none met the fiber intake.

Clinical Implication:
Women who gave birth preterm did not adhere to the 2015-2020 or 2020-2025 DGA recommendations in the last month of pregnancy. Nurses are uniquely positioned to provide pregnant women with nutritional screening and counseling as part of routine prenatal care.
The concomitant use of sodium-glucose co-transporter 2 inhibitors improved the renal outcome of Japanese patients with type 2 diabetes treated with glucagon-like peptide 1 receptor agonists
Authors: Kobayashi Kazuo , Toyoda Masao , Hatori Nobuo , Tsukamoto Shunichiro , Kimura Moritsugu , Sakai Hiroyuki , Furuki Takayuki , Chin Keiichi , Kanaoka Tomohiko , Aoyama Togo , Umezono Tomoya , Ito Shun , Suzuki Daisuke , Takeda Hiroshi , Degawa Hisakazu , Hishiki Toshimasa , Shimura Hidetoshi , Nakajima Shinichi , Miyauchi Masaaki , Yamamoto Hareaki , Hatori Yutaka , Hayashi Masahiro , Sato Kazuyoshi , Miyakawa Masaaki , Terauchi Yasuo , Tamura Kouichi , Kanamori Akira 
Published: September 2023

Aims
This study aimed to clarify the renal influence of glucagon-like peptide 1 receptor agonists (GLP1Ras) with or without sodium-glucose co-transporter 2 inhibitors (SGLT2is) on Japanese patients with type 2 diabetes mellitus (T2DM).

Methods
We retrospectively extracted 547 patients with T2DM who visited the clinics of members of Kanagawa Physicians Association. The progression of albuminuria status and/or a ≥ 15% decrease in the estimated glomerular filtration rate (eGFR) per year was set as the renal composite outcome. Propensity score matching was performed to compare GLP1Ra-treated patients with and without SGLT2i.

Results
After matching, 186 patients in each group were compared. There was no significant difference of the incidence of the renal composite outcomes (17% vs. 20%, P = 0.50); however, the annual decrease in the eGFR was significantly smaller and the decrease in the urine albumin-to-creatinine ratio was larger in GLP1Ra-treated patients with the concomitant use of SGLT2is than in those without it (−1.1 ± 5.0 vs. −2.8 ± 5.1 mL/min/1.73 m2, P = 0.001; and −0.08 ± 0.61 vs. 0.05 ± 0.52, P = 0.03, respectively).

Conclusion
The concomitant use of SGLT2i with GLP1Ra improved the annual decrease in the eGFR and the urine albumin-to-creatinine ratio in Japanese patients with T2DM.
Prevalence of Symptomatic Bacteriuria and Associated Risk Factors among Patients Attending Major Hospitals in Calabar, Nigeria
Authors: Bassey Emmanuel E. , Mbah Maurice , Akpan Samuel S. , Ikpi Edet E. , Alaribe Ambrose A. A. 
Published: September 2023

ABSTRACTIntroductionUrinary tract infections (UTIs) are among the most encountered bacterial infection of humans and affect both male and female of all age groups, resulting in high mortality of infected patients if not properly managed.Hypothesis/Gap statementSeveral studies in different sub-Saharan Africa locations show variations in incidence of UTI as well as it’s causative organisms.AimThis study aimed to assess the prevalence, etiological agents, and factors associated with urinary tract infections among patients attending selected hospitals in Calabar metropolis, Nigeria.MethodologyThis was a cross-sectional study. Mid-stream urine samples collected from 240 patients with UTI were cultured using Cystine Lactose Electrolyte Deficient Agar (CLED). Data on socio-demographic, clinical symptoms and risk factors were obtained using structured questionnaire. Uropathogens were characterized using microbiological and biochemical tests and confirmed with API®20E and 20NE (Biomérieux) identification system. Pearson Chi-square was employed to check associations between categorical variables.P-value of <.05 was considered statistically significant.ResultsOut of the 240 urine samples collected, 13 were contaminated during collection, and 227 analyzed. Sixty-five (28.6%) patients had significant bacteriuria. Previous history of UTI (P=.000, CI=1.582-5.180), use of drugs without prescription (P=.000, CI=0.040-0.220), pregnancy (P=.001, CI=1.858-12.575) and history of urinary catheter (P=.031, CI=1.024-19.053) showed significant association with the occurrence of UTI.Klebsiella pneumoniae(23.1%) was the most predominant isolate, followed by Coagulase-negative Staphylococci (16.9%) andEscherichia coli(12.3%).ConclusionThe study shows that routine UTI screening is beneficial for pregnant women, patients with difficult or painful urination, patients with previous episodes of UTI, catheterized patients and appropriate drugs administered for positive cases. In addition, self-administration of antibiotics should be avoided.
Addressing preferred orientation in single-particle cryo-EM through AI-generated auxiliary particles
Authors: Zhang Hui , Zheng Dihan , Wu Qiurong , Yan Nieng , Shi Zuoqiang , Hu Mingxu , Bao Chenglong 
Published: September 2023

AbstractThe single-particle cryo-EM field faces the persistent challenge of preferred orientation, lacking general computational solutions. We introduce cryoPROS, an AI-based approach designed to address the above issue. By generating the auxiliary particles with a conditional deep generative model, cryoPROS addresses the intrinsic bias in orientation estimation for the observed particles. We effectively employed cryoPROS in the cryo-EM single particle analysis of the hemagglutinin trimer, showing the ability to restore the near-atomic resolution structure on non-tilt data. Moreover, the enhanced version named cryoPROS-MP significantly improves the resolution of the membrane protein NaXusing the no-tilted data that contains the effects of micelles. Compared to the classical approaches, cryoPROS does not need special experimental or image acquisition techniques, providing a purely computational yet effective solution for the preferred orientation problem. Finally, we conduct extensive experiments that establish the low risk of model bias and the high robustness of cryoPROS.
Fungal Pathogen Gene Selection for Predicting the Onset of Infection Using a Multi-Stage Machine Learning Approach
Authors: Thomas Graham , Stoner Oliver , Costa Fabrizio , Ames Ryan M 
Published: September 2023

Phytopathogenic fungi pose a serious threat to global food security. Next-generation sequencing technologies, such as transcriptomics, are increasingly used to profile infection, assess environmental adaptation and gauge host-responses. The accumulation of these large-scale data has created the opportunity to employ new computational methods to gain greater biological insights. Machine learning approaches, that learn to identify patterns in complex data sets, have recently been applied to the field of plant-pathogen interactions. Here, we apply a machine learning approach to transcriptomics data for the fungal pathogenZymoseptoria tritici, to predict the onset of infection as measured by timing of the appearance of necrosis. We present a method for identifying the most important genes that predict infection timings, accurately classify isolates as early and late infectors and predict the timing of infection of ‘novel’ isolates using only a subset of the data. These methods and the genes identified further demonstrate the use of these tools in the field of plant-pathogen interactions and have implications for the identification of biomarkers for disease monitoring and forecasting.Fungi that infect plants pose a serious threat to global food security. Methods to study these pathogens generate vast amounts of data that create new opportunities for computational tools to analyse them. Machine learning methods can learn patterns in complex data such as when genes are turned on or off in fungal plant pathogens. In this study we use machine learning approaches to predict the onset of infection in several isolates of an important fungal pathogen. We show that these methods can identify a small group of genes that are predictive of the infection onset. We can even use these methods on ‘novel’ isolates to infer the likely timing of disease development. Our work has implications for plant disease diagnosis, monitoring and forecasting.
TEM Experiment and Complete Genome Sequencing with Comparative Genomic Analysis to Uncover Potential Probiotic Features of IsolatedLactobacillus delbrueckiisubsp.indicusTY-11
Authors: Jakaria Al-Mujahidy Sk. Md. , Kryukov Kirill , Ikeo Kazuho , Saito Kei , Uddin Md. Ekhlas , Ibn Sina Abu Ali 
Published: September 2023

AbstractBackgroundProbiotics refer to living microorganisms that exerts a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis to uncover the probiotic potential ofLactobacillus delbrueckiisubsp.indicusTY-11 isolated from native yogurt in Bangladesh. We also performed Transmission Electron Microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. These experiments on subspeciesindicuswere not studied previously.ResultsThe strain TY-11 was identified asLactobacillus delbrueckiisubsp.indicus,whose genome (1916674bp) contained genes to adapt to diverse and stressful environments of the human gut, and no gene was identified for either antibiotic resistance or toxic metabolites. It embraced genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance in the gut, and acidic pH tolerance in the stomach. Genes were annotated for inhibiting pathogenic bacteria in the gut by inhibitory substances, (bacteriocin: Helveticin-J (331bp) and Enterolysin-A (275bp), hydrogen peroxide, and acid); blockage of adhesion sites; and competition for nutrients. Its metabolic pathway helped the human gut to recover the digestive disorders and digest indigestible nutrients. The TY-11 genome possessed additional 37 core genes of subspeciesindicuswhich were deficient in the core genome of the most popular subspeciesbularicus.ConclusionsThis is the first study to explore the molecular insights into intestinal residence and probiotic roles including antimicrobial activities of a representative strain (TY-11) ofLactobacillus delbrueckiisubsp.indicus.
MARCO in alveolar macrophages negatively regulates Ace expression and aldosterone production
Authors: O’Brien Conan J O , Ratti Giorgio , Haberman Emma , Sweeney Charles , Gordon Siamon , Domingos Ana I 
Published: September 2023

AbstractAldosterone is a potent cholesterol-derived steroid hormone that plays a major role in controlling blood pressure via regulation of blood volume. The release of aldosterone is typically controlled by the renin-angiotensin aldosterone system, situated in the adrenal glands, kidneys, and lungs. Here, we reveal that the class A scavenger receptor MARCO, expressed on alveolar macrophages, negatively regulates aldosterone production and suppresses angiotensin converting enzyme (Ace) expression in the lung. Collectively, our findings point to alveolar macrophages as additional players in the renin-angiotensin-aldosterone system and introduce a novel example of interplay between the immune and endocrine systems.
TransGeneSelector: A Transformer-based Approach Tailored for Key Gene Mining with Small Plant Transcriptomic Datasets
Authors: Huang Kerui , Tian Jianhong , Sun Lei , Xie Peng , Zhou Shiqi , Deng Aihua , Mo Ping , Zhou Zhibo , Jiang Ming , Li Guiwu , Wang Yun , Jiang Xiaocheng 
Published: September 2023

AbstractGene mining, particularly from small sample sizes such as in plants, remains a challenge in life sciences. Traditional methods often omit significant genes, while deep learning techniques are hindered by small sample constraints and lack specialized gene mining approaches. This paper presents TransGeneSelector, the first deep learning method tailored for key gene mining in small transcriptomic datasets, ingeniously integrating data augmentation, sample filtering, and a Transformer-based classifier. Tested onArabidopsis thalianaseeds’ germination classification using just 79 samples, it not only achieves classification performance on par with, if not superior to, Random Forest and SVM but also excels in identifying upstream regulatory genes that Random Forest might miss, and these pinpointed genes more accurately reflect the metabolic processes inherent in seed germination. TransGeneSelector’s ability to mine vital genes from limited datasets signifies its potential as the current state-of-the-art in gene mining in small sample scenarios, providing an efficient and versatile solution for this critical research area.