bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic versus targeted next-generation sequencing for detection of microorganisms in bronchoalveolar lavage fluid among renal transplantation recipients
Authors: Huang Zhaoru , Hu Bingxue , Li Jinfeng , Feng Min , Wang Zhigang , Huang Fengxiang , Xu Huan , Liu Lei , Shang Wenjun 
Published: August 2024

BackgroundMetagenomic next-generation sequencing (mNGS), which provides untargeted and unbiased pathogens detection, has been extensively applied to improve diagnosis of pulmonary infection. This study aimed to compare the clinical performance between mNGS and targeted NGS (tNGS) for microbial detection and identification in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs).MethodsBALF samples with microbiological results from mNGS and conventional microbiological test (CMT) were included. For tNGS, samples were extracted, amplified by polymerase chain reaction with pathogen-specific primers, and sequenced on an Illumina Nextseq.ResultsA total of 99 BALF from 99 KTRs, among which 93 were diagnosed as pulmonary infection, were analyzed. Compared with CMT, both mNGS and tNGS showed higher positive rate and sensitivity (p&lt;0.001) for overall, bacterial and fungal detection. Although the positive rate for mNGS and tNGS was comparable, mNGS significantly outperformed tNGS in sensitivity (100% vs. 93.55%, p&lt;0.05), particularly for bacteria and virus (p&lt;0.001). Moreover, the true positive rate for detected microbes of mNGS was superior over that of tNGS (73.97% vs. 63.15%, p&lt;0.05), and the difference was also significant when specific for bacteria (94.59% vs. 64.81%, p&lt;0.001) and fungi (93.85% vs. 72.58%, p&lt;0.01). Additionally, we found that, unlike most microbes such as SARS-CoV-2, Aspergillus, and EBV, which were predominantly detected from recipients who underwent surgery over 3 years, Torque teno virus (TTV) were principally detected from recipients within 1-year post-transplant, and as post-transplantation time increased, the percentage of TTV positivity declined.ConclusionAlthough tNGS was inferior to mNGS owing to lower sensitivity and true positive rate in identifying respiratory pathogens among KTRs, both considerably outperformed CMT.
An exploratory clinical study of β-glucan combined with camrelizumab and SOX chemotherapy as first-line treatment for advanced gastric adenocarcinoma
Authors: Chu Yunqian , He Xuan , Xue Ya , Jiang Hua , Zhu Chan , Qi Chunjian , Zhang Xing , Chen Dongsheng , Dai Hanjue , Xian Qingying , Zhu Wenyu 
Published: August 2024

Backgroundβ-glucan has been reported to be a potential natural immune modulator for tumor growth inhibition. We aimed to evaluate the efficacy and safety of β-glucan plus immunotherapy and chemotherapy in the first-line treatment of advanced gastric adenocarcinoma.MethodsThis is a phase IB, prospective, single-arm, investigator-initiated trail. Advanced gastric adenocarcinoma patients received β-glucan, camrelizumab, oxaliplatin, oral S-1 every 3 weeks. The curative effect was evaluated every 2 cycles. The primary endpoints were objective response rate (ORR) and safety, with secondary endpoints were median progression-free survival (mPFS) and median overall survival (mOS). The exploratory endpoint explored biomarkers of response to treatment efficacy.ResultsA total of 30 patients had been enrolled, including 20 (66.7%) males and all patients with an ECOG PS score of ≥1. The ORR was 60%, the mPFS was 10.4 months (95% confidence interval [CI], 9.52-11.27), the mOS was 14.0 months (95% CI, 11.09-16.91). A total of 19 patients (63.3%) had TRAEs, with 9 patients (30%) with grade ≥ 3. The most common TRAEs were nausea (53.3%). After 2 cycles of treatment, the levels of IL-2, IFN-γ and CD4+ T cells significantly increased (P &lt; 0.05). Furthermore, biomarker analysis indicated that patient with better response and longer OS exhibited lower GZMA expression at baseline serum.ConclusionsThis preliminary study demonstrates that β-glucan plus camrelizumab and SOX chemotherapy offers favorable efficacy and a manageable safety profile in patients with advanced gastric adenocarcinoma, and further studies are needed to verify its efficacy and safety.Clinical Trial RegistrationChinese Clinical Trials Registry, identifier ChiCTR2100044088
Intracellular bactericidal activity and action mechanism of MDP1 antimicrobial peptide against VRSA and MRSA in human endothelial cells
Authors: Dashtbin Shirin , Razavi Shabnam , Ganjali Koli Mokhtar , Barneh Farnoosh , Ekhtiari-Sadegh Sarvenaz , Akbari Reza , Irajian Gholamreza , Pooshang Bagheri Kamran 
Published: August 2024

IntroductionStaphylococcus aureus is a prominent cause of postoperative infections, often persisting within host cells, leading to chronic infections. Conventional antibiotics struggle to eliminate intracellular S. aureus due to poor cell penetration. Antimicrobial peptides are a new hope for tackling intracellular bacteria. Accordingly, this study examines the antimicrobial peptide MDP1, derived from melittin, for its efficacy against intracellular S. aureus.MethodsIn this study, the physiochemical properties (Prediction of three-dimensional structure, circular dichroism and helical wheel projection analysis) were investigated. Extracellular antibacterial activity and cytotoxicity of MDP1 were also assessed. The mechanism of interaction of MDP1 with S. aureus was evaluated by molecular dynamic simulation, atomic force and confocal microscopy. Bacterial internalization into an endothelial cell model was confirmed through culture and transmission electron microscopy. The effect of the peptide on intracellular bacteria was investigated by culture and epi-fluorescence microscopy.Results and discussion3D structural prediction proved the conformation of MDP1 as an α-helix peptide. Helical-wheel projection analysis indicated the proper orientation of hydrophobic amino acid residues for membrane interaction. CD spectroscopy of MDP1 showed that MDP1 in SDS 10 and 30 mM adopted 87 and 91% helical conformation. Atomic force and confocal microscopy assessments as well as molecular dynamics studies revealed the peptide-bacterial membrane interaction. MDP1, at the concentration of 0.32 μg mL−1, demonstrated a fold reduction of 21.7 ± 1.8, 1.7 ± 0.2, and 7.3 ± 0.8 in intracellular bacterial load for ATCC, VRSA, and MRSA, respectively. Molecular dynamics results demonstrate a preferential interaction of MDP1 with POPG/POPE membranes, primarily driven by electrostatic forces and hydrogen bonding. In POPC systems, two out of four MDP1 interacted effectively, while all four MDP1 engaged with POPG/POPE membranes. Gathering all data together, MDP1 is efficacious in the reduction of intracellular VRSA and MRSA proved by culture and epi-fluorescent microscopy although further studies should be performed to increase the intracellular activity of MDP1.
Efficacy and safety of oral sodium bicarbonate in kidney-transplant recipients and non-transplant patients with chronic kidney disease: a systematic review and meta-analysis
Authors: Wu Yun , Wang Ying , Huang Weijun , Guo Xi , Hou Baoluo , Tang Jingyi , Wu Yuqi , Zheng Huijuan , Pan Yanling , Liu Wei Jing 
Published: August 2024

IntroductionWe investigated the efficacy and safety of oral sodium bicarbonate in kidney-transplant recipients and non-transplant patients with chronic kidney disease (CKD), which are currently unclear.MethodsPubMed, Cochrane Library, Embase, and Web of Science were searched for randomized controlled trials investigating the efficacy and safety of sodium bicarbonateversusplacebo or standard treatment in kidney-transplant and non-transplant patients with CKD.ResultsSixteen studies of kidney-transplant recipients (two studies, 280 patients) and non-transplant patients with CKD (14 studies, 1,380 patients) were included. With non-transplant patients, sodium bicarbonate slowed kidney-function declines (standardized mean difference [SMD]: 0.49, 95% confidence interval [CI]: 0.14–0.85,p= 0.006) within ≥12 months (SMD: 0.75 [95% CI: 0.12–1.38],p= 0.02), baseline-serum bicarbonate &lt;22 mmol/L (SMD: 0.41 [95% CI: 0.19–0.64],p= 0.0004) and increased serum-bicarbonate levels (mean difference [MD]: 2.35 [95% CI: 1.40–3.30],p&lt; 0.00001). In kidney-transplant recipients, sodium bicarbonate did not preserve graft function (SMD: -0.07 [95% CI: -0.30–0.16],p= 0.56) but increased blood pH levels (MD: 0.02 [95% CI: 0.00–0.04],p= 0.02). No significant adverse events occurred in the kidney-transplant or non-transplant patients (risk ratio [RR]: 0.89, [95% CI: 0.47–1.67],p= 0.72; and RR 1.30 [95% CI: 0.84–2.00],p= 0.24, respectively). However, oral sodium bicarbonate correlated with increased diastolic pressure and worsened hypertension and edema (MD: 2.21 [95% CI: 0.67–3.75],p= 0.005; RR: 1.44 [95% CI: 1.11–1.88],p= 0.007; and RR: 1.28 [95% CI: 1.00–1.63],p= 0.05, respectively).DiscussionOral sodium bicarbonate may slow kidney-function decline in non-transplant patients with CKD taking sodium bicarbonate supplementation for ≥12 months or a baseline serum bicarbonate level of &lt;22 mmol/L, without preserving graft function in kidney-transplant recipients. Sodium bicarbonate may increase diastolic pressure, and elevate a higher incidence of worsening hypertension and edema.Systematic Review Registration:https://www.crd.york.ac.uk/prospero/, identifier CRD42023413929.
The cell-permeant antioxidant D-thiol ester D-cysteine ethyl ester overcomes physical dependence to morphine in male Sprague Dawley rats
Authors: Getsy Paulina M. , Coffee Gregory A. , Bates James N. , Parran Theodore , Hoffer Lee , Baby Santhosh M. , MacFarlane Peter M. , Knauss Zackery T. , Damron Derek S. , Hsieh Yee-Hsee , Bubier Jason A. , Mueller Devin , Lewis Stephen J. 
Published: August 2024

The ability of morphine to decrease cysteine transport into neurons by inhibition of excitatory amino acid transporter 3 (EAA3) may be a key molecular mechanism underlying the acquisition of physical and psychological dependence to morphine. This study examined whether co-administration of the cell-penetrant antioxidant D-thiol ester, D-cysteine ethyl ester (D-CYSee), with morphine, would diminish the development of physical dependence to morphine in male Sprague Dawley rats. Systemic administration of the opioid receptor antagonist, naloxone (NLX), elicited pronounced withdrawal signs (e.g., wet-dog shakes, jumps, rears, circling) in rats that received a subcutaneous depot of morphine (150 mg/kg, SC) for 36 h and continuous intravenous infusion of vehicle (20 μL/h, IV). The NLX-precipitated withdrawal signs were reduced in rats that received an infusion of D-CYSee, but not D-cysteine, (both at 20.8 μmol/kg/h, IV) for the full 36 h. NLX elicited pronounced withdrawal signs in rats treated for 48 h with morphine (150 mg/kg, SC), plus continuous infusion of vehicle (20 μL/h, IV) that began at the 36 h timepoint of morphine treatment. The NLX-precipitated withdrawal signs were reduced in rats that received a 12 h infusion of D-CYSee, but not D-cysteine, (both at 20.8 μmol/kg/h, IV) that began at the 36 h timepoint of morphine treatment. These findings suggest that D-CYSee may attenuate the development of physical dependence to morphine and reverse established dependence to the opioid in male Sprague Dawley rats. Alternatively, D-CYSee may simply suppress the processes responsible for NLX-precipitated withdrawal. Nonetheless, D-CYSee and analogues may be novel therapeutics for the treatment of opioid use disorders.
Genomic insights and biocontrol potential of ten bacterial strains from the tomato core microbiome
Authors: Nicotra Daniele , Ghadamgahi Farideh , Ghosh Samrat , Anzalone Alice , Dimaria Giulio , Mosca Alexandros , Massimino Maria Elena , Vetukuri Ramesh Raju , Catara Vittoria 
Published: August 2024

IntroductionDespite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health.MethodsWe therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits.ResultsBacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth.DiscussionThis study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera.
Syntactic flexibility and lexical encoding in aging sentence production: an eye tracking study
Authors: Weirick Joshua D. , Lee Jiyeon 
Published: August 2024

PurposeSuccessful sentence production requires lexical encoding and ordering them into a correct syntactic structure. It remains unclear how different processes involved in sentence production are affected by healthy aging. We investigated (a) if and how aging affects lexical encoding and syntactic formulation during sentence production, using auditory lexical priming and eye tracking-while-speaking paradigms and (b) if and how verbal working memory contributes to age-related changes in sentence production.MethodsTwenty older and 20 younger adults described transitive and dative action pictures following auditory lexical primes, by which the relative ease of encoding the agent or theme nouns (for transitive pictures) and the theme and goal nouns (for dative pictures) was manipulated. The effects of lexical priming on off-line syntactic production and real-time eye fixations to the primed character were measured.ResultsIn offline production, older adults showed comparable priming effects to younger adults, using the syntactic structure that allows earlier mention of the primed lexical item in both transitive and dative sentences. However, older adults showed longer lexical priming effects on eye fixations to the primed character during the early stages of sentence planning. Preliminary analysis indicated that reduced verbal working memory may in part account for longer lexical encoding, particularly for older adults.ConclusionThese findings indicate that syntactic flexibility for formulating different grammatical structures remains largely robust with aging. However, lexical encoding processes are more susceptible to age-related changes, possibly due to changes in verbal working memory.
Global hepatitis B and D community advisory board: expectations, challenges, and lessons learned
Authors: Borondy-Jenkins Fiona , Ansah Bright , Chen Jacki , Goldring Amanda , Ibrahim Yasmin , Issa Shaibu , Lesidrenska Silvana , Machado Tanya , Moore Holly , Njouom Richard , Okinedo Prince , Racho Rhea , Scott Lori , Zovich Beatrice , Cohen Chari 
Published: August 2024

IntroductionCommunity Advisory Boards (CABs) play an important role in developing and delivering patient-centered care. However, the impact of participation on CAB members has not been well studied, particularly on the global scale. In 2022, the Hepatitis B Foundation (HBF) convened the first global hepatitis B and hepatitis delta CAB with 23 members from 17 countries, representing six out of the seven World Health Organization (WHO) regions, and countries with the largest hepatitis B and hepatitis delta disease burden.MethodsTo reflect on the process of assembling an effective and motivated CAB and assess the impact on CAB participants, three virtual focus group sessions were held with 16 participants in July and August 2023. Sessions were recorded and transcribed. Questions focused on motivations for joining the CAB, membership experiences, and lessons learned. Grounded theory analysis was used to generate hypotheses about reasons for CAB members’ participation, as well as challenges and suggestions. Qualitative analysis using inductive reasoning identified key themes within responses. Transcripts were independently analyzed by a primary and secondary coder.ResultsMotivations for joining the CAB included participants’ desire to advocate for people living with hepatitis B and hepatitis delta, and other altruistic factors. Participants reflected that through CAB membership, they gained networking and advocacy opportunities and enhanced their hepatitis B- and hepatitis delta-related knowledge. Challenges participants experienced were related to time, physical limitations, and stigma. Finally, participants discussed their limited direct engagement with drug developers and proposed ways the CAB can increase interactions with stakeholders going forward.DiscussionBased on participants’ assessments, establishing a global CAB for stigmatized infectious diseases is worth the effort. Regular internal review of community advisory boards’ structure and performance is critical to ensure the CAB is fulfilling its mission.
The health behaviors differences among male and female school-age adolescents in the Middle East and North Africa region countries: a meta-analysis of the Global School-based Student Health Survey data
Authors: Achak Doha , Azizi Asmaa , El-Ammari Abdelghaffar , Marfak Ibtissam Youlyouz , Saad Elmadani , Nejjari Chakib , Hilali Abderraouf , Peltzer Karl , Marfak Abdelghafour 
Published: August 2024

BackgroundUnderstanding gender disparities in adolescent health behaviors is crucial for developing targeted health promotion strategies. This study uses data from the Global School-based Student Health Survey (GSHS) across 17 MENA countries to analyze gender differences in adolescent health behaviors, aiming to provide a comprehensive overview for both boys and girls.MethodsThis meta-analysis incorporates data from recent years of the GSHS, covering 17 MENA countries. The objective was to assess and compare health behaviors between adolescent girls and boys. A random-effects model was employed to calculate odds ratios for gender comparisons in these behaviors. Statistical analyses and modeling were performed using JAMOVI software.ResultsIn most MENA countries, boys consumed more vegetables compared to girls. Girls were less likely to frequent fast food establishments (OR = 0.82, 95% CI: 0.69–0.98) and generally exhibited better self-care behaviors. Boys reported a higher prevalence of physical altercations (OR = 2.18, 95% CI: 1.88–2.51) and were more involved in fights (OR = 3.00, 95% CI: 2.46–3.67). Girls were more likely to miss school without permission and were consistently described as kinder and more helpful across various income levels. However, in some countries such as Oman and Tunisia, boys missed school more frequently. There were no significant gender differences in parental oversight of homework or knowledge of students’ activities, but girls were reported to have stronger parental relationships and better parental understanding of their problems and free time, with exceptions in Morocco and the Palestinian Territory-Gaza. Boys were more likely to engage in smoking (OR = 3.57, 95% CI: 2.69–4.76) and other substance use. Conversely, girls reported higher levels of physical inactivity and loneliness, but also demonstrated greater kindness and helpfulness in school settings and stronger parental relationships.ConclusionPolicymakers in the MENA region should develop and implement gender-specific interventions targeting key areas such as hygiene practices, physical activity, and substance use. By focusing on these targeted strategies, they can address the distinct health behaviors and needs of both boys and girls. Effective interventions in these areas are crucial for improving overall health outcomes and promoting healthier lifestyles, thereby enhancing adolescent health and well-being across the region.
Aligning extracurricular school activities with physical literacy: pilot evaluation through self-study of practice
Authors: Schmittwilken Louisa , Harding-Kuriger Jodi , Carl Johannes 
Published: August 2024

IntroductionAlthough several important documents of education and health promotion on the international level favor practices geared toward physical literacy (PL), not all countries have yet gained experience with this holistic concept. Therefore, numerous stakeholders and practitioners who intend to align their interventional activities with PL will soon face the situation that there are no recommendations for their specific culture and language for how to design such programs. Given that such recommendations are also lacking for Germany, the goal of the present study within the uncontrolled pilot cycles of the PLACE study was (a) to describe the process of a female pedagogue (27 years old, previously unexperienced with PL) initially familiarizing herself with the PL concept and its implementation opportunities for the school setting, and (b) to retrace the process of developing and refining a PL-driven intervention for extracurricular physical education (60–90 min) of children in grades three and four at primary schools in Bremen.MethodsAdopting a self-study design, this endeavor emphasized continuous reflexivity involving: (a) session protocols; (b) biweekly discussions with another coach; (c) weekly discussions between scientists and stakeholders of youth development (“multi-perspective panel”); (d) weekly observations and impressions during field work; and (e) summative group interviews with children (n = 17, age range: 8–9 years, 17.6% boys). Written documents underwent qualitative content analysis with inductively generated categories.ResultsDespite explicit links between the theoretical PL domains and the intervention content, the character of how PL informed the intervention level was dominated by the stance and atmosphere implemented by the deliverer (e.g., participatory attitude, open mindset). Accordingly, the team revised the intervention primarily on the levels of organization (temporal schedule and sequences), instruction, and materials. After initial stages of didactically “surviving” within classes, the deliverer could increasingly integrate tasks of cognitive engagement and provide choice for students enabling individual autonomy for nurturing a person-centered approach.DiscussionThis study encourages teachers and stakeholders of physical education to seek exchange with scholars or other practitioners while simultaneously demonstrating patience in comprehensively internalizing PL and efficiently translating the concept into routines in line with individual's quality standards.