bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers
Authors: Wang Yu , Xu Xiaomeng , Chen Huan , Yang Fang , Xu Bo , Wang Kun , Liu Qianwen , Liang Guixin , Zhang Ruiqi , Jiao Xin’an , Zhang Yunzeng 
Published: September 2023

Abstract
Background
Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a “generalist” species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive.

Results
In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events.

Conclusions
A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers’ gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.
Quantitative trait loci and candidate genes for yield-related traits of upland cotton revealed by genome-wide association analysis under drought conditions
Authors: Sun Fenglei , Yang Yanlong , Wang Penglong , Ma Jun , Du Xiongming 
Published: September 2023

AbstractBackgroundDue to the influence of extreme weather, the environment in China’s main cotton-producing areas is prone to drought stress conditions, which affect the growth and development of cotton and lead to a decrease in cotton yield.ResultsIn this study, 188 upland cotton germplasm resources were phenotyped for data of 8 traits (including 3 major yield traits) under drought conditions in three environments for two consecutive years. Correlation analysis revealed significant positive correlations between the three yield traits. Genetic analysis showed that the estimated heritability of the seed cotton index (SC) under drought conditions was the highest (80.81%), followed by that of boll weight (BW) (80.64%) and the lint cotton index (LC) (70.49%) With genome-wide association study (GWAS) analysis, a total of 75 quantitative trait loci (QTLs) were identified, including two highly credible new QTL hotspots. Three candidate genes (Gh_D09G064400,Gh_D10G261000andGh_D10G254000) located in the two new QTL hotspots, QTL51 and QTL55, were highly expressed in the early stage of fiber development and showed significant correlations with SC, LC and BW. The expression of three candidate genes in two extreme materials after drought stress was analyzed by qRT-PCR, and the expression of these two materials in fibers at 15, 20 and 25 DPA. The expression of these three candidate genes was significantly upregulated after drought stress and was significantly higher in drought-tolerant materials than in drought-sensitive materials. In addition, the expression levels of the three candidate genes were higher in the early stage of fiber development (15 DPA), and the expression levels in drought-tolerant germplasm were higher than those in drought-sensitive germplasm. These three candidate genes may play an important role in determining cotton yield under drought conditions.ConclusionsThis study is helpful for understanding the regulatory genes affecting cotton yield under drought conditions and provides germplasm and candidate gene resources for breeding high-yield cotton varieties under these conditions.
Utilizing hydrothermal time models to assess the effects of temperature and osmotic stress on maize (Zea mays L.) germination and physiological responses
Authors: Khan Waqif , Shah Sumbal , Ullah Abd , Ullah Sami , Amin Fazal , Iqbal Babar , Ahmad Naveed , Abdel-Maksoud Mostafa A. , Okla Mohammed k. , El-Zaidy Mohamed , Al-Qahtani Wahidah H. , Fahad Shah 
Published: September 2023

AbstractThe application of germination models in economic crop management makes them extremely useful for predicting seed germination. Hence, we examined the effect of varying water potentials (Ψs; 0. − 0.3, − 0.6, − 0.9, − 1.2 MPa) and temperatures (Ts; 20, 25, 30, 35, 40 °C) on maize germination and enzymatic antioxidant mechanism. We observed that varying Ts and Ψs significantly influenced germination percentage (GP) and germination rate (GR), and other germination parameters, including germination rate index (GRI), germination index (GI), mean germination index (MGI), mean germination time (MGT), coefficient of the velocity of germination (CVG), and germination energy (GE) (p ≤ 0.01). Maximum (87.60) and minimum (55.20) hydro-time constant (θH) were reported at 35 °C and 20 °C, respectively. In addition, base water potential at 50 percentiles was highest at 30 °C (15.84 MPa) and lowest at 20 °C (15.46 MPa). Furthermore, the optimal, low, and ceiling T (To, Tb and Tc, respectively) were determined as 30 °C, 20 °C and 40 °C, respectively. The highest θT1 and θT2 were reported at 40 °C (0 MPa) and 20 °C (− 0.9 MPa), respectively. HTT has a higher value (R2 = 0.43 at 40 °C) at sub-optimal than supra-optimal temperatures (R2 = 0.41 at 40 °C). Antioxidant enzymes, including peroxidase (POD), catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX), and glutathione peroxidase (GPX), increased with decreasing Ψs. In contrast, CAT and POD were higher at 20 °C and 40 °C but declined at 25, 30, and 35 °C. The APX and GPX remained unchanged at 20, 25, 30, and 40 °C but declined at 35 °C. Thus, maintaining enzymatic activity is a protective mechanism against oxidative stress. A decline in germination characteristics may result from energy diverting to anti-stress tools (antioxidant enzymes) necessary for eliminating reactive oxygen species (ROS) to reduce salinity-induced oxidative damage. The parameters examined in this study are easily applicable to simulation models of Z. mays L. germination under extreme environmental conditions characterized by water deficits and temperature fluctuations.
Correlation of serum complement factor 5a level with inflammatory response and cognitive function in patients with Alzheimer’s disease of different severity
Authors: Li Zhilian , Wu Huifang , Luo Yi , Tan Xianpei 
Published: September 2023

Abstract
Background
Alzheimer’s disease (AD) is a common cause of dementia. Serum complement factor 5a (C5a) is exceedingly implicated in AD. We explored the role of C5a levels in AD patients of different severity.

Methods
Mild, moderate, and severe AD patients, and healthy controls were included. C5a and pro-inflammatory factor (TNF-α, IL-1β, IL-6, CRP) levels were assessed by ELISA, and cognitive function was evaluated by Mini-Mental state examination (MMSE) score. The correlations between C5a, inflammatory factor levels, MMSE score, and plasma Aβ42/Aβ40 ratio were analyzed by Pearson tests. Independent risk factors for AD aggravation were assessed by logistic multivariate regression analysis. According to the cut-off value of receiver operating characteristic (ROC) curve analysis of C5a level, AD patients were assigned into low/high expression groups, and severe AD incidence was compared. Severe AD cumulative incidence was analyzed by Kaplan-Meier curve.

Results
Serum C5a, TNF-α, IL-1β, IL-6 and CRP levels were raised, and MMSE score was lowered in AD. Serum C5a, TNF-α, IL-1β, IL-6 and CRP levels in severe AD patients were higher than those in mild/moderate AD patients, but there were no significant differences in these cytokines between moderate and mild AD groups. The MMSE score of severe AD patients was lower than that of mild/moderate AD patients. Serum C5a level was positively correlated with serum TNF-α, IL-1β, IL-6, and CRP levels, and negatively correlated with MMSE score, with no obvious correlation with plasma Aβ42/Aβ40 ratio. Serum C5a level was one of the independent risk factors for AD aggravation. The occurrence of severe AD might be related to an increase in serum C5a level.

Conclusion
Serum C5a level increased with AD severity, and its expression was positively correlated with serum pro-inflammatory factor levels, and negatively correlated with cognitive function.
Effects of blended learning training for oncology physicians to advise their patients about complementary and integrative therapies: results from the multicenter cluster-randomized KOKON-KTO trial
Authors: Helmer Stefanie M. , Rogge Alizé A. , King Ryan , Canella Claudia , Pach Daniel , Witt Claudia M. 
Published: September 2023

Abstract
Background
Many oncology physicians are confronted with the topic of complementary and integrative medicine (CIM) by cancer patients. This study examined whether a blended learning (e-learning and a workshop) to train oncology physicians in providing advice on CIM therapies to their cancer patients, in addition to distributing an information leaflet about reputable CIM websites, had different effects on physician-reported outcomes in regard to consultations compared with only distributing the leaflet.

Methods
In a multicenter, cluster-randomized trial, 48 oncology physicians were randomly allocated to an intervention group (CIM consultation and an information leaflet) or a control group (information leaflet only). After the training, the oncology physicians conducted 297 consultations with their cancer patients. Measurements were assessed at oncology physician, physician–patient-interaction (measured by external reviewers), and patient levels. This analysis focused on the physician outcomes of stress reaction and perceived consultation skill competency. In addition, qualitative interviews were conducted with a subsample of oncology physicians who experienced both, the intervention and control condition.

Results
The oncology physicians in the intervention group showed a lower stress reaction in all measured dimensions after CIM consultations than those in the control group. There was no significant difference between oncology physicians in the intervention and control groups regarding the perceived consultation skill competency (overburden: intervention 1.4 [95% CI: 0.7;2.1]; control 2.1 [95% CI: 1.4;2.7], tension: 1.3 [95% CI: 0.7;2.0] vs. 1.9 [95% CI: 1.3;2.5], and discomfort with consultation situations: 1.0 [95% CI: 0.4;1.7]; vs. 1.7 [95% CI: 1.2;2.3]). The qualitative data showed that only providing the leaflet seemed impersonal to oncology physicians, while the training made them feel well prepared to conduct a full conversation about CIM and provide the information leaflet.

Conclusions
In our exploratory study providing structured CIM consultations showed positive effects on the perceived stress of oncology physicians, and the training was subjectively experienced as an approach that improved physician preparation for advising cancer patients about CIM, however no effects regarding perceived consultation skill competency were found.

Trial registration
The trial registration number of the KOKON-KTO study is DRKS00012704 in the German Clinical Trials Register (Date of registration: 28.08.2017).
Posterior urethral valve in thai boys
Authors: Ekarat Prakorn , Attawettayanon Worapat , Limratchapong Chompoonut , Sophark Praewa , Vachvanichsanong Prayong 
Published: September 2023

Abstract
Background
Posterior urethral valve (PUV) is the most common congenital bladder outlet obstruction in boys, causing renal damage beginning in utero. There are scarce data from Thailand regarding the long-term outcomes of PUV in boys, thus the aim of this study was to examine the presentation, clinical course, complications, outcomes and renal survival in PUV boys.

Methods
We reviewed the medical records of PUV boys treated at the Pediatric Nephrology Clinic, Prince of Songkla University, Thailand, over a 30-year-period.

Results
Seventy-seven PUV boys were identified, with a median age at diagnosis of 4.8 months. The most common presentations were urinary tract infection (UTI), poor urine stream and urinary dribbling in 26 (33.8%), 19 (24.7%) and 11 (14.3%) boys, respectively. Renal ultrasound results in 70 boys showed 8 (11.4%) unilateral and 56 (80%) bilateral hydronephroses. Of 72 voiding cystourethrograms, 18 (25.0%) showed unilateral and 22 (30.6%) bilateral vesicoureteral refluxes. 99mTc dimercaptosuccinic acid renal scans in 30 boys showed 12 (40%) unilateral and 8 (26.7%) bilateral renal damage. Fifty-nine (76.6%) boys had 149 UTIs; 42 (54.4%) had recurrent UTI. Forty-eight boys had valve ablation at the median age of 30.3 months. 22 boys (28.6%) developed chronic kidney disease (CKD) at a median age of 15.0 years.

Conclusion
Of 77 PUV Thai boys, UTI was the most common presentation. Recurrence of UTI and CKD was the most common consequence. Lifelong follow-up for renal and bladder functions is essential for all PUV patients.
Impulsivity across severe mental disorders: a cross-sectional study of immune markers and psychopharmacotherapy
Authors: Hjell Gabriela , Rokicki Jaroslav , Szabo Attila , Holst René , Tesli Natalia , Bell Christina , Fischer-Vieler Thomas , Werner Maren Caroline Frogner , Lunding Synve Hoffart , Ormerod Monica Bettina Elkjær Greenwood , Johansen Ingrid Torp , Djurovic Srdjan , Ueland Thor , Andreassen Ole Andreas , Melle Ingrid , Lagerberg Trine Vik , Mørch-Johnsen Lynn , Steen Nils Eiel , Haukvik Unn Kristin 
Published: September 2023

Abstract
Background
Impulsivity is a transdiagnostic feature linked to severe clinical expression and a potential target for psychopharmacological strategies. Biological underpinnings are largely unknown, but involvement of immune dysregulation has been indicated, and the effects of psychopharmacological agents vary. We investigated if impulsivity was associated with circulating immune marker levels and with a range of psychopharmacological treatment regimens in severe mental disorders.

Methods
Impulsivity was assessed in a sample (N = 657) of patients with schizophrenia or schizophreniform disorder (SCZ) (N = 116) or bipolar disorder (BD) (N = 159) and healthy participants (N = 382) using the Barratt Impulsiveness Scale (BIS-11) questionnaire. Plasma levels of systemic immune markers (RANTES, IL-1RA, IL-18, IL-18BP, sTNFR-1) were measured by enzyme immunoassays. Patients underwent thorough clinical assessment, including evaluation of psychotropic medication. Associations were assessed using linear regressions.

Results
Impulsivity was positively associated with SCZ (p < 0.001) and BD (p < 0.001) diagnosis and negatively associated with age (p < 0.05), but not significantly associated with any of the circulating immune markers independently of diagnostic status. Among patients, impulsivity was negatively associated with lithium treatment (p = 0.003) and positively associated with antidepressant treatment (p = 0.011) after controlling for diagnosis, psychotropic co-medications, manic symptoms, and depressive symptoms.

Conclusions
We report elevated impulsivity across SCZ and BD but no associations to systemic immune dysregulation based on the current immune marker selection. The present study reveals associations between impulsivity in severe mental disorders and treatment with lithium and antidepressants, with opposite directions. Future studies are warranted to determine the causal directionality of the observed associations with psychopharmacotherapy.
An exploration of suicidal ideation and attempts, and care use and unmet need among suicide-ideators in a Belgian population study
Authors: Rens Eva , Portzky Gwendolyn , Morrens Manuel , Dom Geert , Van den Broeck Kris , Gijzen Mandy 
Published: September 2023

Abstract
Background
Suicidal ideation, or thinking about death and suicide, is common across all layers of society. The aim of this paper is to add to the understanding of suicidal ideation in the general population, as well as help-seeking behaviors and perceived unmet mental health needs among those who report suicidal thoughts.

Methods
The research is part of a representative population-based survey study of mental wellbeing in Antwerp (Flanders, Belgium) carried out in 2021. A total of 1202 participants between 15 and 80 years old answered the Ask Suicide-Screening Questions (ASQ), and an additional question about suicide plans. Participation was by invitation only and possible online or via a postal paper questionnaire. Univariate and multivariate logistic regression analyses were used to explore the association between both current suicidal ideation and self-reported lifetime suicide attempt with the sociodemographic factors age, gender, educational level, origin and financial distress. Moreover, formal care use for mental health was examined among those experiencing suicidal ideation, and logistic regression analyses were used to assess associated sociodemographic factors. Finally, perceived unmet mental health needs were assessed among suicide ideators.

Results
The point-prevalence of suicidal ideation was 8.6% and was higher among younger age groups and individuals reporting financial distress. The lifetime-prevalence of suicide attempts is 6.5% and was higher in younger people and individuals with a primary educational level and with financial distress. About half (45.6%) of those with suicidal ideation consulted a professional for mental health problems in the past twelve months. Men and those with a primary educational level were less likely to seek help. Half of suicide ideators without care use perceived some need for mental health care, and a third of suicide ideators who used care perceived the obtained help as insufficient, resulting in a population prevalence of 3.6% suicide ideators with a fully or partially perceived unmet need.

Conclusions
The prevalence of suicide attempts, suicidal ideation and unmet needs among suicide-ideators is high in this Belgian sample. Mental health care need perception in suicide ideators needs further investigation.
Flexible delivery of opioid agonist treatment during COVID-19 in Norway: qualitative and quantitative findings from an online survey of provider experiences
Authors: McDonald Rebecca , Bech Anne Berit , Clausen Thomas 
Published: September 2023

Abstract
Background
For patients receiving daily opioid agonist treatment (OAT) for opioid dependence, several countries relaxed treatment guidelines at the beginning of the COVID-19 pandemic. This involved longer take-home intervals for methadone and buprenorphine doses as well as a reduction in supervised dosing and drug screening. To date, little is known about the medium or long-term experience of OAT deregulation. Therefore, we conducted a survey to explore how OAT providers perceived greater flexibility in OAT service delivery at the end of the second year of the pandemic.

Methods
Nationwide cross-sectional study of twenty-three OAT units in 19 publicly funded hospital trusts in Norway. OAT units were sent a 29-item online questionnaire comprising closed-format and open-ended questions on treatment provider experiences and changes in OAT service delivery during the past 12 months (January to December 2021).

Results
Twenty-three (of whom female: 14; 60.8%) managers or lead physicians of OAT units completed the questionnaire reporting that, in 2021, most OAT units (91.3%, n = 21) still practiced some adjusted approaches as established in the beginning of the pandemic. The most common adaptions were special protocols for COVID-19 cases (95.7%, n = 22), increased use of telephone- (91.3%, n = 21) and video consultations (87.0%, n = 20), and longer take-home intervals for OAT medications (52.2%, n = 12). The use of depot buprenorphine also increased substantially during the pandemic. According to the OAT providers, most patients handled flexible treatment provision well. In individual cases, patients’ substance use was identified as key factor necessitating a reintroduction of supervised dosing and drug screening. Collaboration with general practitioners and municipal health and social services was generally perceived as crucial for successful treatment delivery.

Conclusions
Overall, the Norwegian OAT system proved resilient in the second year of the COVID-19 pandemic, as its healthcare workforce embraced innovation in technology (telemedicine) and drug development (depot buprenorphine). According to our nationally representative sample of OAT providers, most patients were compliant with longer take-home doses of methadone and buprenorphine. Our findings suggest that telemedicine can be useful as adjunct to face-to-face treatment and provide greater flexibility for patients.
Analysis of the stability of the reference genes GAPDH, SDHA and RPL-19 in sheep from a semi-arid region infected by gastrointestinal nematodes
Authors: Lucas Nascimento Souza Jorge , Cavalcante Silva Fernanda , da Silva Carlikelly Gleicy , Maria Fortaleza Neves Bomfim Isabela , Rocha de Medeiros Henrique , Giotto Zaros Lilian 
Published: September 2023

AbstractAnalyzing the stability of reference genes already described as universal is an important methodology to lead gene expression analysis because different studies have shown that the expression of universal reference genes may vary between experimental treatments. In this sense, the glyceraldehyde 3-phosphate dehydrogenase (GAPDH), Succinate dehydrogenase complex subunit A (SDHA) and Ribosomal Protein L-19 (RPL-19) reference genes (already described in other studies with sheep from different regions, breeds and infectious agents or in organisms evolutionarily close to sheep) were investigated in the abomasum, small and large intestines of resistant and susceptible crossbred sheep groups to gastrointestinal nematode infections in the Semi-arid region in Northeast of Brazil. The animals were naturally infected to determine the resistance or susceptibility status by counting eggs per gram (EPG) of feces from the gastrointestinal tract after 33 weeks of observations of infection evolution. Relative gene expression was performed by RT-qPCR methodology using Sybr green and relative gene expression stability was tested by different software programs such as REST, BestKeeper, geNorm and Normfinder. Our results showed the susceptible animals had increase in egg counts per gram of feces than resistant animals (p < 0.001), and both groups showed a mixed infection by nematodes of the genus Haemonchus, Trichostrongylus, Oesophagostomum and Trichuris. Furthermore, we show the importance of analyzing different genes in different software programs and the importance to choose ideal reference genes. In this sense, GAPDH was the most stable gene in the abomasum, whereas SDHA was the most stable in the small and large intestines. In addition, we discuss about variables which can interfere in relative expression such as breed, species, climate and tissue. However, utilizing other reference genes already described in other studies with the same and different variables should be performed.