bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous application of oral and intravaginal probiotics for Helicobacter pylori and its antibiotic-therapy-induced vaginal dysbacteriosis
Authors: Wang Yufan , Zhang Zhenyu , Chen Qi , Chen Tingtao 
Published: June 2024

AbstractHelicobacter pylori is a prevalent bacterial pathogen globally, implicated in various gastrointestinal disorders. Current recommended antibiotic therapies for H. pylori infection have been proven to be therapeutically insufficient, with low eradication rates and high recurrence rates. Emerging evidence suggests that antibiotic therapy for H. pylori can lead to gastrointestinal and subsequent vaginal dysbiosis, posing challenges for conventional antibiotic approaches. Thus, this article proposes a novel probiotic therapy involving simultaneous oral and intra-vaginal probiotic administration alongside antibiotics for H. pylori treatment, aiming to enhance eradication rates and mitigate dysbiosis. We begin by providing an overview of gastrointestinal and vaginal microbiota and their interconnectedness through the vagina-gut axis. We then review the efficacy of current antibiotic regimens for H. pylori and discuss how antibiotic treatment impacts the vaginal microenvironment. To explore the feasibility of this approach, we evaluate the effectiveness of oral and intra-vaginal probiotics in restoring normal microbiota in the gastrointestinal and vaginal tracts, respectively. Additionally, we analyze the direct mechanisms by which oral and intra-vaginal probiotics act on their respective tracts and discuss potential cross-tract mechanisms. Considering the potential synergistic therapeutic effects of probiotics in both the gastrointestinal and vaginal tracts, dual-channel probiotic therapy holds promise as a more effective approach for H. pylori eradication and dysbiosis mitigation, presenting a novel concept in the collaborative treatment of gastrointestinal and genital disorders.
Target engagement and immunogenicity of an active immunotherapeutic targeting pathological α-synuclein: a phase 1 placebo-controlled trial
Authors: Eijsvogel Pepijn , Misra Pinaki , Concha-Marambio Luis , Boyd Justin D. , Ding Shuang , Fedor Lauren , Hsieh Yueh-Ting , Sun Yu Shuang , Vroom Madeline M. , Farris Carly M. , Ma Yihua , de Kam Marieke L. , Radanovic Igor , Vissers Maurits F. J. M. , Mirski Dario , Shareghi Ghazal , Shahnawaz Mohammad , Singer Wolfgang , Kremer Philip , Groeneveld Geert Jan , Yu Hui Jing , Dodart Jean-Cosme 
Published: June 2024

AbstractInvestigational therapeutics that target toxic species of α-synuclein (αSyn) aim to slow down or halt disease progression in patients with Parkinson’s disease (PD). Here this 44-week, randomized, placebo-controlled, double-blind, single-center phase 1 study investigated safety, tolerability and immunogenicity of UB-312, an active immunotherapeutic targeting pathological αSyn, in patients with PD. The primary outcome measures were adverse event frequency and change in anti-αSyn antibody titers in blood and cerebrospinal fluid (CSF). Exploratory outcomes were changes in clinical scales and biomarker-based target engagement as measured by seed amplification assays. Twenty patients were randomized 7:3 (UB-312:placebo) into 300/100/100 μg or 300/300/300 μg (weeks 1, 5 and 13) intramuscular prime-boost dose groups. Safety was similar across groups; adverse events were mostly mild and transient. Two patients experienced three serious adverse events in total, one possibly treatment related; all resolved without sequalae. Anti-αSyn antibodies in serum from 12/13 and CSF from 5/13 patients who received three UB-312 doses confirmed immunogenicity. Mean serum titers (in log-dilution factor) increased from baseline by 1.398 and 1.354, and peaked at week 29 at 2.520 and 2.133, for 300/100/100 μg and 300/300/300 μg, respectively. CSF titers were 0 at baseline and were 0.182 and 0.032 at week 21, respectively. Exploratory analyses showed no statistical differences in clinical scales but a significant reduction of αSyn seeds in CSF of a subset of UB-312-treated patients. These data support further UB-312 development. ClinicalTrials.gov:NCT04075318.
A new small-sized predatory pseudosuchian archosaur from the Middle-Late Triassic of Southern Brazil
Authors: Müller Rodrigo T. 
Published: June 2024

AbstractBefore the rise of dinosaurs and pterosaurs, pseudosuchians—reptiles from the crocodilian lineage—dominated the Triassic land ecosystems. This lineage diversified into several less inclusive clades, resulting in a wide ecomorphological diversity during the Middle and Late Triassic. Some giant pseudosuchians occupied the top of the trophic webs, while others developed extensive bony armor as a defense mechanism, which later evolved as a convergence in the avemetatarsalian lineage. On the other hand, there were groups like the Gracilisuchidae, which was composed of carnivorous forms with lightweight build and less than 1 m in length. The fossil record of gracilisuchids is geographically restricted to China and Argentina, with one ambiguous record from Brazil. In the present study, the first unambiguous gracilisuchid from Brazil is described. Parvosuchus aurelioi gen. et sp. nov. comes from the Dinodontosaurus Assemblage Zone of the Santa Maria Formation, which is associated with the Ladinian-Carnian boundary. Composed of a complete cranium, vertebrae, pelvic girdle and hindlimbs, the new species nests with Gracilisuchus stipanicicorum and Maehary bonapartei in a phylogenetic analysis. Its discovery fills a taxonomic gap in Brazilian pseudosuchian fauna and reveals the smallest known member of this clade from the Dinodontosaurus Assemblage Zone, highlighting the diversity of pseudosuchians during the moment that preceded the dawn of dinosaurs.
Hybrid transformer-CNN model for accurate prediction of peptide hemolytic potential
Authors: Almotairi Sultan , Badr Elsayed , Abdelbaky Ibrahim , Elhakeem Mohamed , Abdul Salam Mustafa 
Published: June 2024

AbstractHemolysis is a crucial factor in various biomedical and pharmaceutical contexts, driving our interest in developing advanced computational techniques for precise prediction. Our proposed approach takes advantage of the unique capabilities of convolutional neural networks (CNNs) and transformers to detect complex patterns inherent in the data. The integration of CNN and transformers' attention mechanisms allows for the extraction of relevant information, leading to accurate predictions of hemolytic potential. The proposed method was trained on three distinct data sets of peptide sequences known as recurrent neural network-hemolytic (RNN-Hem), Hlppredfuse, and Combined. Our computational results demonstrated the superior efficacy of our models compared to existing methods. The proposed approach demonstrated impressive Matthews correlation coefficients of 0.5962, 0.9111, and 0.7788 respectively, indicating its effectiveness in predicting hemolytic activity. With its potential to guide experimental efforts in peptide design and drug development, this method holds great promise for practical applications. Integrating CNNs and transformers proves to be a powerful tool in the fields of bioinformatics and therapeutic research, highlighting their potential to drive advancement in this area.
Oscillatory zoning of minerals as a fingerprint of impurity-mediated growth
Authors: Torii Hiroki , Miura Hitoshi 
Published: June 2024

AbstractWe propose a kinetic mathematical model of the oscillatory compositional zoning profile recorded in minerals based on the crystal growth suppression induced by impurities. Notably, the presence of a small amount of impurities significantly inhibits crystal growth, and a growth inhibition mechanism called the pinning effect is widely accepted. Here we show that a model that considers the pinning effect and adsorption/desorption kinetics of impurities on the crystal surface can reproduce the oscillatory compositional zoning. As impurities are common in nature, this model suggests the existence of a universal mechanism that can occur in the growth processes of various crystals.
Performance evaluation of a new sponge-based moving bed biofilm reactor for the removal of pharmaceutical pollutants from real wastewater
Authors: Chalipa Zohreh , Hosseinzadeh Majid , Nikoo Mohammad Reza 
Published: June 2024

AbstractPharmaceutical pollutants, a group of emerging contaminants, have attracted outstanding attention in recent years, and their removal from aquatic environments has been addressed. In the current study, a new sponge-based moving bed biofilm reactor (MBBR) was developed to remove chemical oxygen demand (COD) and the pharmaceutical compound Ibuprofen (IBU). A 30-L pilot scale MBBR was constructed, which was continuously fed from the effluent of the first clarifier of the Southern Tehran wastewater treatment plant. The controlled operational parameters were pH in the natural range, Dissolved Oxygen of 1.5–2 mg/L, average suspended mixed liquor suspended solids (MLSS), and mixed liquor volatile suspended solids (MLVSS) of 1.68 ± 0.1 g/L and 1.48 ± 0.1 g/L, respectively. The effect of hydraulic retention time (HRT) (5 h, 10 h, 15 h), filling ratio (10%, 20%, 30%), and initial IBU concentration (2 mg/L, 5 mg/L, 10 mg/L) on removal efficiencies was assessed. The findings of this study revealed a COD removal efficiency ranging from 48.9 to 96.7%, with the best removal efficiency observed at an HRT of 10 h, a filling ratio of 20%, and an initial IBU concentration of 2 mg/L. Simultaneously, the IBU removal rate ranged from 25 to 92.7%, with the highest removal efficiency observed under the same HRT and filling ratio, albeit with an initial IBU concentration of 5 mg/L. An extension of HRT from 5 to 10 h significantly improved both COD and IBU removal. However, further extension from 10 to 15 h slightly enhanced the removal efficiency of COD and IBU, and even in some cases, removal efficiency decreased. Based on the obtained results, 20% of the filling ratio was chosen as the optimum state. Increasing the initial concentration of IBU from 2 to 5 mg/L generally improved COD and IBU removal, whereas an increase from 5 to 10 mg/L caused a decline in COD and IBU removal. This study also optimized the reactor’s efficiency for COD and IBU removal by using response surface methodology (RSM) with independent variables of HRT, filling ratio, and initial IBU concentration. In this regard, the quadratic model was found to be significant. Utilizing the central composite design (CCD), the optimal operating parameters at an HRT of 10 h, a filling ratio of 21%, and an initial IBU concentration of 3 mg/L were pinpointed, achieving the highest COD and IBU removal efficiencies. The present study demonstrated that sponge-based MBBR stands out as a promising technology for COD and IBU removal.
Cox proportional hazards regression in small studies of predictive biomarkers
Authors: Jóźwiak K. , Nguyen V. H. , Sollfrank L. , Linn S. C. , Hauptmann M. 
Published: June 2024

AbstractPredictive biomarkers are essential for personalized medicine since they select the best treatment for a specific patient. However, of all biomarkers that are evaluated, only few are eventually used in clinical practice. Many promising biomarkers may be erroneously abandoned because they are investigated in small studies using standard statistical techniques which can cause small sample bias or lack of power. The standard technique for failure time endpoints is Cox proportional hazards regression with a multiplicative interaction term between binary variables of biomarker and treatment. Properties of this model in small studies have not been evaluated so far, therefore we performed a simulation study to understand its small sample behavior. As a remedy, we applied a Firth correction to the score function of the Cox model and obtained confidence intervals (CI) using a profile likelihood (PL) approach. These methods are generally recommended for small studies of different design. Our results show that a Cox model estimates the biomarker-treatment interaction term and the treatment effect in one of the biomarker subgroups with bias, and overestimates their standard errors. Bias is however reduced and power is increased with Firth correction and PL CIs. Hence, the modified Cox model and PL CI should be used instead of a standard Cox model with Wald based CI in small studies of predictive biomarkers.
Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane
Authors: González-López Adrián , Larsson Daniel S. D. , Koripella Ravi Kiran , Cain Brett N. , Chavez Martin Garcia , Hergenrother Paul J. , Sanyal Suparna , Selmer Maria 
Published: June 2024

AbstractThe antibiotic fusidic acid (FA) is used to treat Staphylococcus aureus infections. It inhibits protein synthesis by binding to elongation factor G (EF-G) and preventing its release from the ribosome after translocation. While FA, due to permeability issues, is only effective against gram-positive bacteria, the available structures of FA-inhibited complexes are from gram-negative model organisms. To fill this knowledge gap, we solved cryo-EM structures of the S. aureus ribosome in complex with mRNA, tRNA, EF-G and FA to 2.5 Å resolution and the corresponding complex structures with the recently developed FA derivative FA-cyclopentane (FA-CP) to 2.0 Å resolution. With both FA variants, the majority of the ribosomal particles are observed in chimeric state and only a minor population in post-translocational state. As expected, FA binds in a pocket between domains I, II and III of EF-G and the sarcin-ricin loop of 23S rRNA. FA-CP binds in an identical position, but its cyclopentane moiety provides additional contacts to EF-G and 23S rRNA, suggesting that its improved resistance profile towards mutations in EF-G is due to higher-affinity binding. These high-resolution structures reveal new details about the S. aureus ribosome, including confirmation of many rRNA modifications, and provide an optimal starting point for future structure-based drug discovery on an important clinical drug target.
Transcranial electrical stimulation modulates emotional experience and metabolites in the prefrontal cortex in a donation task
Authors: Mugnol-Ugarte Luiza , Bortolini Tiago , Yao Bo , Mikkelsen Mark , Carneiro Monteiro Marina , Andorinho de Freitas Ferreira Ana Carolina , Bramatti Ivanei , Melo Bruno , Hoefle Sebastian , Meireles Fernanda , Moll Jorge , Pobric Gorana 
Published: June 2024

AbstractUnderstanding the neural, metabolic, and psychological mechanisms underlying human altruism and decision-making is a complex and important topic both for science and society. Here, we investigated whether transcranial Direct Current Stimulation (tDCS) applied to two prefrontal cortex regions, the ventromedial prefrontal cortex (vmPFC, anode) and the right dorsolateral prefrontal cortex (DLPFC, cathode) can induce changes in self-reported emotions and to modulate local metabolite concentrations. We employed in vivo quantitative MR Spectroscopy in healthy adult participants and quantified changes in GABA and Glx (glutamate + glutamine) before and after five sessions of tDCS delivered at 2 mA for 20 min (active group) and 1 min (sham group) while participants were engaged in a charitable donation task. In the active group, we observed increased levels of GABA in vmPFC. Glx levels decreased in both prefrontal regions and self-reported happiness increased significantly over time in the active group. Self-reported guiltiness in both active and sham groups tended to decrease. The results indicate that self-reported happiness can be modulated, possibly due to changes in Glx concentrations following repeated stimulation. Therefore, local changes may induce remote changes in the reward network through interactions with other metabolites, previously thought to be unreachable with noninvasive stimulation techniques.
Prognostic scoring system based on indicators reflecting the tumor glandular differentiation and microenvironment for patients with colorectal cancer
Authors: Kobayashi Toshinori , Ishida Mitsuaki , Miki Hisanori , Yamamoto Nobuyuki , Harino Takashi , Yagyu Takuki , Hori Soshi , Hatta Masahiko , Hashimoto Yuki , Kotsuka Masaya , Yamasaki Makoto , Inoue Kentaro , Hirose Yoshinobu , Sekimoto Mitsugu 
Published: June 2024

AbstractPrognostic stratification is an urgent concern for patients with colorectal cancer (CRC). The desmoplastic reaction (DR) is speculated to mirror the tumor microenvironment. DR types are considered independent prognostic indicators in CRC, but have not been incorporated in previous prognostic nomograms. We aimed to assess the prognostic significance of a novel approach incorporating histopathological indicators reflecting tumor glandular differentiation and microenvironment. We evaluated 329 consecutive patients with CRC who underwent surgical resection at Kansai Medical University. Histological glandular differentiation was scored as 2 (0 point), 3 (1 point), or 4 (2 points). Tumor buddings (TBs) were classified as TB1 (0 point), TB2 (1 point), or TB3 (2 points). pT1 or 2 was considered as 0 point, pT3 or 4 + DR non-immature type as 1 point, and pT3 or 4 + DR immature type as 2 points. Lymph node metastasis was classified as pN0 (0 point), pN1 (1 point), or pN2 (2 points). The preoperative carcinoembryonic antigen levels were categorized as < 5.0 ng/mL (0 point) and ≧5.0 (1 point). Considering these factors, the following D&M (tumor differentiation and microenvironment) scoring system was applied: I (0–2 points), II (3–4 points), III (5–6 points), and IV (7–9 points). Kaplan–Meier curves showed significant differences in disease-specific survival and recurrence-free survival among the assigned scores, highlighting their enhanced utility compared with the American Joint Committee on Cancer 8th edition staging system. The D&M scoring system was valuable as the initial prognostic nomogram, including DR.
Sex-related DNA methylation is associated with inflammation and gene expression in the lungs of healthy individuals
Authors: Patel Devki , McElroy Joseph P. , Weng Daniel Y. , Sahar Kamel , Reisinger Sarah A. , Freudenheim Jo L. , Wewers Mark D. , Shields Peter G. , Song Min-Ae 
Published: June 2024

AbstractLung cancer exhibits sex-biased molecular characteristics and epidemiological trends, suggesting a need for sex-specific approaches to understanding its etiology and treatment. DNA methylation alterations play critical roles in lung carcinogenesis and may serve as valuable biomarkers for precision medicine strategies. We employed the Infinium MethylationEPIC array to identify autosomal sex-related differentially methylated CpG sites (DM-CpGs) in lung epithelium of healthy individuals (32 females and 37 males) while controlling for age, BMI, and tobacco use. We correlated DM-CpGs with gene expression in lung epithelium and immune responses in bronchoalveolar lavage. We validated these DM-CpGs in lung tumors and adjacent normal tissue from The Cancer Genome Atlas (TCGA). Among 522 identified DM-CpGs, 61% were hypermethylated in females, predominantly located in promoter regions. These DM genes were implicated in cell-to-cell signaling, cellular function, transport, and lipid metabolism. Correlation analysis revealed sex-specific patterns between DM-CpGs and gene expression. Additionally, several DM-CpGs were correlated significantly with cytokines (IL-1β, IL-4, IL-12p70, and IFN-γ), macrophage, and lymphocyte counts. Also, some DM-CpGs were observed in TCGA lung adenocarcinoma, squamous cell carcinoma, and adjacent normal tissues. Our findings highlight sex-specific DNA methylation patterns in healthy lung epithelium and their associations with lung gene expression and lung immune biomarkers. These findings underscore the potential role of lung sex-related CpGs as epigenetic predispositions influencing sex disparities in lung cancer risk and outcomes, warranting further investigation for personalized lung cancer management strategies.
Mitigation of drought stress in chili plants (Capsicum annuum L.) using mango fruit waste biochar, fulvic acid and cobalt
Authors: Hareem Misbah , Danish Subhan , Obaid Sami Al , Ansari Mohammad Javed , Datta Rahul 
Published: June 2024

AbstractDrought stress can have negative impacts on crop productivity. It triggers the accumulation of reactive oxygen species, which causes oxidative stress. Limited water and nutrient uptake under drought stress also decreases plant growth. Using cobalt and fulvic acid with biochar in such scenarios can effectively promote plant growth. Cobalt (Co) is a component of various enzymes and co-enzymes. It can increase the concentration of flavonoids, total phenols, antioxidant enzymes (peroxidase, catalase, and polyphenol oxidase) and proline. Fulvic acid (FA), a constituent of soil organic matter, increases the accessibility of nutrients to plants. Biochar (BC) can enhance soil moisture retention, nutrient uptake, and plant productivity during drought stress. That’s why the current study explored the influence of Co, FA and BC on chili plants under drought stress. This study involved 8 treatments, i.e., control, 4 g/L fulvic acid (4FA), 20 mg/L cobalt sulfate (20CoSO4), 4FA + 20CoSO4, 0.50%MFWBC (0.50 MFWBC), 4FA + 0.50MFWBC, 20CoSO4 + 0.50MFWBC, 4FA + 20CoSO4 + 0.50MFWBC. Results showed that 4 g/L FA + 20CoSO4 with 0.50MFWBC caused an increase in chili plant height (23.29%), plant dry weight (28.85%), fruit length (20.17%), fruit girth (21.41%) and fruit yield (25.13%) compared to control. The effectiveness of 4 g/L FA + 20CoSO4 with 0.50MFWBC was also confirmed by a significant increase in total chlorophyll contents, as well as nitrogen (N), phosphorus (P), and potassium (K) in leaves over control. In conclusion4g/L, FA + 20CoSO4 with 0.50MFWBC can potentially improve the growth of chili cultivated in drought stress. It is suggested that 4 g/L FA + 20CoSO4 with 0.50MFWBC be used to alleviate drought stress in chili plants.
Regio- and diastereoselective synthesis of thioxothiazolidin-indolin-2-ones, oxoindolin-carbamodithioate hybrids, and their base-catalyzed conversion into dispirocyclopentanebisoxindoles
Authors: Aghamiri Bagher , Moghaddam F. Matloubi , Badpa Sara , Kavoosi Leila 
Published: June 2024

AbstractIn this publication, we reported a regio-, diastereoselective, and kinetically controlled reaction for synthesizing thioxothiazolidin-indolin-2-ones, oxoindolin-carbamodithioate hybrids, and their base-catalyzed conversion into dispirocyclopentanebisoxindoles. Obtaining only the kinetic thioxothiazolidin-indolin-2-one products together with their straightforward conversion to dispirocyclopentanebisoxindoles, excellent regio- and diastereoselectivity, easy reaction workup, and one-pot synthetic operation are considerable advantages of this work.