bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concurrent abnormal non-acid reflux is associated with additional chronic rejection risk in lung transplant patients with increased acid exposure
Authors: Lo Wai-Kit , Muftah Mayssan , Goldberg Hilary J , Sharma Nirmal , Chan Walter W 
Published: March 2024

Summary
Acid reflux has been associated with allograft injury and rejection in lung transplant patients; however, the pathogenic role of non-acid reflux remains debated. We aimed to evaluate the impact of concurrent abnormal non-acid reflux with acid reflux on chronic rejection in lung transplant patients with acid reflux. This was a retrospective cohort study of lung transplant recipients who underwent pre-transplant combined impedance–pH study off acid suppression. Only subjects with acid exposure &gt;4% were included. Non-acid reflux (pH &gt; 4) episodes &gt;27 was considered abnormal per prior normative studies. Chronic rejection was defined as chronic lung allograft dysfunction (CLAD) per International Society for Heart and Lung Transplantation criteria. Time-to-event analyses were performed using Cox proportional hazards and Kaplan–Maier methods, with censoring at death, anti-reflux surgery, or last follow-up. In total, 68 subjects (28 abnormal/40 normal non-acid reflux) met inclusion criteria for the study. Baseline demographic/clinical characteristics were similar between groups. Among this cohort of patients with increased acid exposure, subjects with concurrent abnormal non-acid reflux had significantly higher risk of CLAD than those without on Kaplan–Meier analysis (log-ranked P = 0.0269). On Cox multivariable regression analysis controlling for body mass index, age at transplantation, and proton pump inhibitor use, concurrent abnormal non-acid reflux remained independently predictive of increased CLAD risk (hazard ratio 2.31, confidence interval: 1.03–5.19, P = 0.04). Presence of concurrent abnormal non-acid reflux in lung transplant subjects with increased acid exposure is associated with additional risk of chronic rejection. Non-acid reflux may also contribute to pathogenicity in lung allograft injury/rejection, supporting a potential role for impedance-based testing in this population.
Fecal microbiota related to postoperative endoscopic recurrence in patients with Crohn's disease
Authors: Wang Haichao , Yan Guorong , Wu Yaling , Zhuoma Deji , Liu Zhanju , Gao Xuefeng , Wang Xiaolei 
Published: March 2024

Abstract

Background
Postoperative recurrence (POR) remains a major challenge for patients with Crohn’s disease (CD). Gut microbial dysbiosis has been reported to be involved in the pathogenesis of POR. This study aims to investigate the relationship between fecal microbiome and endoscopic recurrence in patients with CD after ileocolonic resection.

Methods
This is a cross-sectional study. Fecal samples were collected from 52 patients with CD after surgical intervention from 6 to 12 months before endoscopic examination. Endoscopic recurrence was defined as Rutgeerts score ≥ i2. The microbiome was analyzed by sequencing the V3–V4 hypervariable regions of the 16S rRNA gene.

Results
A total of 52 patients were included and classified into POR (n = 27) and non-POR (n = 25) groups. Compared with the non-POR group, the POR group had a significantly lower community richness (Chao1 index: 106.5 vs 124, P = 0.013) and separated microbial community (P = 0.007 for Adonis, P = 0.032 for Anosim), combined with different distribution of 16 gut microbiotas and decrease of 11 predicted metabolic pathways (P &lt; 0.05). Lactobacillus and Streptococcus were identified to closely correlate to non-POR (P &lt; 0.05) after controlling for confounding factors. Kaplan-Meier analysis indicated that the patients with higher abundance of Streptococcus experienced longer remission periods (P &lt; 0.01), but this was not for Lactobacillus. The predicted ethylmalonyl-coA pathway related to increased amount of succinate was positively correlated with Streptococcus (r &gt; 0.5, P &lt; 0.05).

Conclusions
The characteristic alterations of fecal microbiota are associated with postoperative endoscopic recurrence in patients with CD; particularly, high abundance of Streptococcus may be closely related to endoscopic remission.
DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps
Authors: Liu Huiling , Ma Wenxiu 
Published: March 2024

Abstract
Recent advances in high-throughput chromosome conformation capture (Hi-C) techniques have allowed us to map genome-wide chromatin interactions and uncover higher-order chromatin structures, thereby shedding light on the principles of genome architecture and functions. However, statistical methods for detecting changes in large-scale chromatin organization such as topologically associating domains (TADs) are still lacking. Here, we proposed a new statistical method, DiffGR, for detecting differentially interacting genomic regions at the TAD level between Hi-C contact maps. We utilized the stratum-adjusted correlation coefficient to measure similarity of local TAD regions. We then developed a nonparametric approach to identify statistically significant changes of genomic interacting regions. Through simulation studies, we demonstrated that DiffGR can robustly and effectively discover differential genomic regions under various conditions. Furthermore, we successfully revealed cell type-specific changes in genomic interacting regions in both human and mouse Hi-C datasets, and illustrated that DiffGR yielded consistent and advantageous results compared with state-of-the-art differential TAD detection methods. The DiffGR R package is published under the GNU General Public License (GPL) ≥ 2 license and is publicly available at https://github.com/wmalab/DiffGR.
Inter- and Intraobserver Variability on Endoscopic Scoring Systems in Crohn’s Disease and Ulcerative Colitis: A Systematic Review and Meta-Analysis
Authors: Hashash Jana G , Yu Ci Ng Faye , Farraye Francis A , Wang Yeli , Colucci Daniel R , Baxi Shrujal , Muneer Sadaf , Reddan Mitchell , Shingru Pratik , Melmed Gil Y 
Published: March 2024

Abstract

Background
Endoscopy scoring is a key component in the diagnosis of ulcerative colitis (UC) and Crohn’s disease (CD). Variability in endoscopic scoring can impact patient trial eligibility and treatment effect measurement. In this study, we examine inter- and intraobserver variability of inflammatory bowel disease endoscopic scoring systems in a systematic review and meta-analysis.

Methods
We included observational studies that evaluated the inter- and intraobserver variability using UC (endoscopic Mayo Score [eMS], Ulcerative Colitis Endoscopic Index of Severity [UCEIS]) or CD (Crohn’s Disease Endoscopic Index of Severity [CDEIS], Simple Endoscopic Score for Crohn’s Disease [SES-CD]) systems among adults (≥18 years of age) and were published in English. The strength of agreement was categorized as fair, moderate, good, and very good.

Results
A total of 6003 records were identified. After screening, 13 studies were included in our analysis. The overall interobserver agreement rates were 0.58 for eMS, 0.66 for UCEIS, 0.80 for CDEIS, and 0.78 for SES-CD. The overall heterogeneity (I2) for these systems ranged from 93.2% to 99.2%. A few studies assessed the intraobserver agreement rate. The overall effect sizes were 0.75 for eMS, 0.87 for UCEIS, 0.89 for CDEIS, and 0.91 for SES-CD.

Conclusions
The interobserver agreement rates for eMS, UCEIS, CDEIS, and SES-CD ranged from moderate to good. The intraobserver agreement rates for eMS, UCEIS, CDEIS, and SES-CD ranged from good to very good. Solutions to improve interobserver agreement could allow for more accurate patient assessment, leading to richer, more accurate clinical management and clinical trial data.
Rediversion of the Failing Ileoanal Pouch: First Step in Pouch Salvage?
Authors: Uchino Tairin , Lincango Eddy P , Hernandez Dominguez Oscar , Bhama Anuradha , Gorgun Emre , Kanters Arielle , Kessler Hermann , Lipman Jeremy , Liska David , Sommovilla Joshua , Valente Michael , Steele Scott R , Hull Tracy , Holubar Stefan D 
Published: March 2024

Abstract

Background
Ileal pouch–anal anastomosis is a technically demanding procedure with many potential complications. Rediversion with an ileostomy is often the first step in pouch salvage; however, it may not be clear if an individual patient will undergo subsequent pouch salvage surgery. We aimed to describe the indications and short- and long-term outcomes of rediversion in our pouch registry.

Methods
We queried our institutional pouch registry for patients who underwent index 2- or 3-stage IPAA and subsequent rediversion at our institution between 1985 and 2022. Pouches constructed elsewhere, rediverted elsewhere, or those patients who underwent pouch salvage/excision without prior rediversion were excluded. Patients were selected for pouch salvage according to the surgeon’s discretion.

Results
Overall, 177 patients (3.4% of 5207 index pouches) were rediverted. At index pouch, median patient age was 32 years and 50.8% were women. Diagnoses included ulcerative colitis (86.4%), indeterminate colitis (6.2%), familial adenomatous polyposis (4.0%), and others (3.4%). Median time from prior ileostomy closure to rediversion was 7.2 years. Indications for rediversion were inflammatory in 98 (55.4%) and noninflammatory in 79 (44.6%) patients. After rediversion, 52% underwent pouch salvage, 30% had no further surgery, and 18.1% underwent pouch excision. The 5-year pouch survival rates for inflammatory and noninflammatory indications were 71.5% and 94.5%, respectively (P = .02).

Conclusion
Rediversion of ileoanal pouches is a safe initial strategy to manage failing pouches and is a useful first step in pouch salvage in many patients. Subsequent salvage surgery for noninflammatory indications had a significantly higher pouch salvage rate than those rediverted for inflammatory complications.
Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut
Authors: Tan Yi Han , Arros Patricio , Berríos-Pastén Camilo , Wijaya Indrik , Chu Wilson H W , Chen Yahua , Cheam Guoxiang , Mohamed Naim Ahmad Nazri , Marcoleta Andrés E , Ravikrishnan Aarthi , Nagarajan Niranjan , Lagos Rosalba , Gan Yunn-Hwen 
Published: March 2024

Abstract
The hypervirulent lineages of Klebsiella pneumoniae (HvKp) cause invasive infections such as Klebsiella-liver abscess. Invasive infection often occurs after initial colonization of the host gastrointestinal tract by HvKp. Over 80% of HvKp isolates belong to the clonal group 23 sublineage I that has acquired genomic islands (GIs) GIE492 and ICEKp10. Our analysis of 12 361 K. pneumoniae genomes revealed that GIs GIE492 and ICEKp10 are co-associated with the CG23-I and CG10118 HvKp lineages. GIE492 and ICEKp10 enable HvKp to make a functional bacteriocin microcin E492 (mccE492) and the genotoxin colibactin, respectively. We discovered that GIE492 and ICEKp10 play cooperative roles and enhance gastrointestinal colonization by HvKp. Colibactin is the primary driver of this effect, modifying gut microbiome diversity. Our in vitro assays demonstrate that colibactin and mccE492 kill or inhibit a range of Gram-negative Klebsiella species and Escherichia coli strains, including Gram-positive bacteria, sometimes cooperatively. Moreover, mccE492 and colibactin kill human anaerobic gut commensals that are similar to the taxa found altered by colibactin in the mouse intestines. Our findings suggest that GIs GIE492 and ICEKp10 enable HvKp to kill several commensal bacterial taxa during interspecies interactions in the gut. Thus, acquisition of GIE492 and ICEKp10 could enable better carriage in host populations and explain the dominance of the CG23-I HvKp lineage.
The impact of indole and mucin on sporulation, biofilm formation, and enterotoxin production in foodborne Clostridium perfringens
Authors: Wang Chao , Defoirdt Tom , Rajkovic Andreja 
Published: March 2024

Abstract

Aims
Indole and mucin are compounds found in the host environment as they are produced by the host or by the host-associated microbiota. This study investigated whether indole and mucin impact Clostridium perfringens growth and sporulation, as well as enterotoxin production and biofilm formation.

Methods and results
There was no impact on growth of Cl. perfringens for up to 400 µM indole and 240 mg/l mucin, and neither indole nor mucin affected sporulation. Reverse-transcriptase qPCR showed that mucin strongly upregulated the expression of Cl. perfringens enterotoxin (up to 121-fold increase), whereas indole had a much more modest effect (2-fold). This was also reflected in increased Cl. perfringens enterotoxin levels in mucin-treated Cl. perfringens (as assessed by a reversed passive latex agglutination assay). Finally, mucin and indole significantly increased biofilm formation of Cl. perfringens, although the effect size was relatively small (less than 1.5 fold).

Conclusion
These results indicate that Cl. perfringens can sense its presence in a host environment by responding to mucin, and thereby markedly increased enterotoxin production.
Development of Green and High-Throughput Microwell Spectrophotometric Methods for Determination of Galidesivir in Bulk Drug and Dosage Forms Based on Simple Oxidimetric Reactions With Inorganic Agents
Authors: Darwish Ibrahim A , Alzoman Nourah Z , Abuhejail Reem M 
Published: March 2024

Abstract

Background
Galidesivir hydrochloride (GDV) is a new potent and safe antiviral drug used for the treatment of a broad spectrum of viral diseases, including COVID-19. In the literature, no analytical method exists for the determination of GDV in bulk or dosage form.

Objective
The objective of this study was the investigation of oxidation reactions of GDV with five inorganic oxidizing reagents and the employment of the reactions in the development of five green microwell spectrophotometric methods (MW-SPMs) with simple procedure and high throughputs for determination of GDV in its bulk and dosage forms (capsules).

Methods
The reactions were carried out in 96-well plates, and the absorbances of reaction solutions were measured by an absorbance microplate reader. Variables influencing the reactions were carefully investigated and optimized.

Results
Under the refined optimum conditions, Beer’s law with excellent correlation coefficients (0.9992–0.9997) was followed in GDV concentrations in a general range of 5–700 µg/mL, and the limits of detection were ≥1.8 µg/mL. All validation parameters of all methods were acceptable. The methods were successfully applied to the analysis of GDV in bulk drug and capsules with high accuracy and precision; the recovery percentages were 98.6–101.2 ± 0.58–1.14%. The greenness of MW-SPMs was evaluated by three comprehensive metric tools, which demonstrated the adherence of MW-SPMs to the principles of the green analytical chemistry (GAC) approach.

Conclusions
The proposed MW-SPMs combined the advantages of microwell-based practice and the use of common laboratory reagents for the analysis. The advantages of microwell analysis were the high throughput, readily available for semi-automation, reduced samples/reagents volume, precise measurements, and versatility. The advantages of using common laboratory reagents were the availability, consistency, compatibility, safety, and cost-effectiveness.

Highlights
Overall, the proposed MW-SPMs are versatile, valuable tools for the quantitation of GDV during its pharmaceutical manufacturing.
Genomic regions and biological pathways associated with sex-limited reproductive traits in bovine species
Authors: Olasege Babatunde S , Oh Zhen Yin , Tahir Muhammad S , Porto-Neto Laercio R , Hayes Ben J , Fortes Marina R S 
Published: March 2024

Abstract
Many animal species exhibit sex-limited traits, where certain phenotypes are exclusively expressed in one sex. Yet, the genomic regions that contribute to these sex-limited traits in males and females remain a subject of debate. Reproductive traits are ideal phenotypes to study sexual differences since they are mostly expressed in a sex-limited way. Therefore, this study aims to use local correlation analyses to identify genomic regions and biological pathways significantly associated with male and female sex-limited traits in two distinct cattle breeds (Brahman [BB] and Tropical Composite [TC]). We used the Correlation Scan method to perform local correlation analysis on 42 trait pairs consisting of six female and seven male reproductive traits recorded on ~1,000 animals for each sex in each breed. To pinpoint a specific region associated with these sex-limited reproductive traits, we investigated the genomic region(s) consistently identified as significant across the 42 trait pairs in each breed. The genes found in the identified regions were subjected to Quantitative Trait Loci (QTL) colocalization, QTL enrichment analyses, and functional analyses to gain biological insight into sexual differences. We found that the genomic regions associated with the sex-limited reproductive phenotypes are widely distributed across all the chromosomes. However, no single region across the genome was associated with all the 42 reproductive trait pairs in the two breeds. Nevertheless, we found a region on the X-chromosome to be most significant for 80% to 90% (BB: 33 and TC: 38) of the total 42 trait pairs. A considerable number of the genes in this region were regulatory genes. By considering only genomic regions that were significant for at least 50% of the 42 trait pairs, we observed more regions spread across the autosomes and the X-chromosome. All genomic regions identified were highly enriched for trait-specific QTL linked to sex-limited traits (percentage of normal sperm, metabolic weight, average daily gain, carcass weight, age at puberty, etc.). The gene list created from these identified regions was enriched for biological pathways that contribute to the observed differences between sexes. Our results demonstrate that genomic regions associated with male and female sex-limited reproductive traits are distributed across the genome. Yet, chromosome X seems to exert a relatively larger effect on the phenotypic variation observed between the sexes.
Overexpression of cytochrome P450 gene CYP6K1 is associated with pyrethroid resistance in German cockroaches (Blattodea: Ectobiidae) from California
Authors: Tseng Shu-Ping , Lee Shao-Hung , Choe Dong-Hwan , Lee Chow-Yang 
Published: March 2024

Abstract
We investigated the expression of 4 cytochrome P450 genes (CYP4G19, CYP6J1, CYP6K1, and CYP4C21) in 4 field-collected strains (WM, RG386, CDR, and Ryan) of the German cockroach, Blattella germanica (L.), collected from California. The UCR susceptible strain was used as a comparison. Topical assays using a diagnostic dose (3× LD95) of deltamethrin revealed decreased sensitivity in all field-collected strains with mortality ranging from 0% to 58%, and the addition of PBO before deltamethrin treatment increased mortality to 52.5%–87.5%. Using qPCR to investigate the expression levels of CYP4G19, CYP4C21, CYP6J1, and CYP6K1, we found that only CYP6K1 was significantly overexpressed (2.1–5.8× higher) in all field-collected strains when compared to the UCR strain. Next, we investigated the role of the CYP6K1 gene by performing gene knockdown using RNAi. After dsCYP6K1 treatment, the expression levels of CYP6K1 in WM and Ryan strains were significantly reduced (P &lt; 0.01) by 91%–94% vs. those treated with dsEGFP (control) on the third and sixth day posttreatment. RG386, CDR, and Ryan strains were more susceptible compared to their respective controls to topically applied deltamethrin 6 days after treatment with dsCYP6K1. This study provides evidence of the involvement of the P450 CYP6K1 gene in pyrethroid resistance in some populations of German cockroaches.
Adaptive graph Laplacian MTL L1, L2 and LS-SVMs
Authors: Ruiz Carlos , Alaíz Carlos M , Dorronsoro José R 
Published: March 2024

Abstract
Multi-Task Learning tries to improve the learning process of different tasks by solving them simultaneously. A popular Multi-Task Learning formulation for SVM is to combine common and task-specific parts. Other approaches rely on using a Graph Laplacian regularizer. Here we propose a combination of these two approaches that can be applied to L1, L2 and LS-SVMs. We also propose an algorithm to iteratively learn the graph adjacency matrix used in the Laplacian regularization. We test our proposal with synthetic and real problems, both in regression and classification settings. When the task structure is present, we show that our model is able to detect it, which leads to better results, and we also show it to be competitive even when this structure is not present.
A comparison of time series lags and non-lags in Spanish electricity price forecasting using data science models
Authors: Vega-Márquez Belén , Solís-García Javier , Nepomuceno-Chamorro Isabel A , Rubio-Escudero Cristina 
Published: March 2024

Abstract
Electricity is an indicator that shows the progress of a civilization; it is a product that has greatly changed the way we think about the world. Electricity price forecasting became a fundamental task in all countries due to the deregulation of the electricity market in the 1990s. This work examines the effectiveness of using multiple variables for price prediction given the large number of factors that could influence the price of the electricity market. The tests were carried out over four periods using data from Spain and deep learning models. Two different attribute selection methods based on Pearson’s correlation coefficient have been used to improve the efficiency of the training process. The variables used as input to the different prediction models were chosen, considering those most commonly used previously in the literature. This study attempts to test whether using time series lags improves the non-use of lags. The results obtained have shown that lags improve the results compared to a previous work in which no lags were used.
In vitro effect of diazoxon on cell signaling and second messengers in Nile tilapia (Oreochromis niloticus) leukocytes
Authors: Camacho-Pérez Milton Rafael , Díaz-Resendiz Karina Janice Guadalupe , Ortiz-Butrón Rocío , Covantes-Rosales Carlos Eduardo , Benitez-Trinidad Alma Betsaida , Girón-Pérez Daniel Alberto , Toledo-Ibarra Gladys Alejandra , Pavón Lenin , Girón-Pérez Manuel Iván 
Published: March 2024

Abstract
The physiological and molecular responses of leukocytes are altered by organophosphate pesticides. Some reports have shown that diazinon causes immunotoxic effects; diazoxon, the oxon metabolite of diazinon, is attributed to influence the immune response by affecting the leukocyte cholinergic system. In this study, the in vitro effects of diazoxon on molecules involved in cell signaling (cAMP, IP3, DAG, JAK1, and STAT3), which play a crucial role in the activation, differentiation, and survival of leukocytes, were evaluated. Data indicate that diazoxon leads to a decrease in cAMP concentration and an increase in basal IP3 levels. However, diazoxon does not affect basal levels of JAK1 and STAT3 phosphorylation. Instead, diazoxon inhibits leukocyte responsiveness to phorbol myristate acetate and ionomycin, substances that, under normal conditions, enhance JAK/STAT signaling. These findings demonstrate that diazoxon significantly affects key molecular parameters related to cell signaling.