bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of pH alteration on respiratory syncytial virus in human airway epithelial cells
Authors: Saunders Jessica L. , Daniels Ivana A. , Edwards Taiya L. , Relich Ryan F. , Zhao Yi , Smith Laura A. , Gaston Benjamin M. , Davis Michael D. 
Published: April 2023

BackgroundRespiratory syncytial virus (RSV) is a leading cause of respiratory distress and hospitalisation in the paediatric population. Low airway surface pH impairs antimicrobial host defence and worsens airway inflammation. Inhaled Optate safely raises airway surface pH in humans and raises intracellular pH in primary human airway epithelial cells (HAECs)in vitro. We aimed to determine whether raising intracellular pH with Optate would decrease infection and replication of RSV in primary HAECs.MethodsWe cultured HAECs from healthy subjects in both air–liquid interface and submerged conditions. We infected HAECs with green fluorescent protein-labelled RSV (GFP-RSV; multiplicity of infection=1) and treated them with Optate or PBS control. We collected supernatant after a 4-h incubation and then every 24 h. We used fluorescence intensity, fluorescent particle counts, plaque assays, Western blots and ELISA to quantitate infection.ResultsIn submerged culture, fluorescence intensity decreased in Optate-treated cells (48 h p=0.0174, 72 h p≤0.001). Similarly, Optate treatment resulted in decreased fluorescent particle count (48 h p=0.0178, 72 h p=0.0019) and plaque-forming units (48 h p=0.0011, 72 h p=0.0148) from cell culture supernatant. In differentiated HAECs cultured at ALI, Optate treatment decreased fluorescence intensity (p≤0.01), GFPviaWestern blot and ELISA (p<0.0001), and RSV-fusion proteinviaELISA (p=0.001). Additionally, RSV infection decreased as Optate concentration increased in a dose-dependent manner (p<0.001).ConclusionsOptate inhibits RSV infection in primary HAECs in a dose-dependent manner. These findings suggest that Optate may have potential as an inhaled therapeutic for patients with RSV.
Acute health effects of heated tobacco products: comparative analysis with traditional cigarettes and electronic cigarettes in young adults
Authors: Majek Paulina , Jankowski Mateusz , Brożek Grzegorz Marek 
Published: April 2023

BackgroundHeated tobacco products (HTPs) were designed to deliver nicotine by heating the tobacco instead of burning it. This study aimed to examine the acute health effects on the respiratory and cardiovascular systems during the use of HTPs and compare these effects with acute health effects evoked by cigarette smoking or electronic cigarettes (e-cigarettes).MethodsThe study group comprised 160 healthy young adults (age 23 years; quartile 1 (Q1) 21 years; quartile 3 (Q3) 26 years) with both sexes divided into groups according to their smoking status: 40 HTP users (H group), 40 traditional cigarette smokers (T group), 40 e-cigarette users (E group) and 40 non-smokers (C group). Heart rate, blood pressure, oxygen saturation, exhaled nitric oxide fraction (FENO), carbon monoxide concentration, temperature of exhaled air and spirometry were measured three times: initially, immediately after the exposure, and after 30 min. The exposure differed depending on smoking status: heating HTP, smoking a cigarette, using an e-cigarette and simulation of smoking.ResultsAfter 5 min of exposure, a significant decrease inFENOwas observed in the H and E groups, from 12.8±5.5 ppb to 11.2±5.3 ppb in the H group and from 16.9±6.5 ppb to 14.2±6.8 ppb in the E group (p<0.01). A slight but statistically significant increase in the temperature of exhaled air after 30 min was observed in groups T and E, from 34.1°C (Q1 33.6°C; Q3 34.4°C) to 34.4°C (Q1 34.1°C; Q3 34.6°C) (p=0.02) in the T group and from 34.2°C (Q1 33.9°C; Q3 34.5°C) to 34.4°C (Q1 33.8°C; Q3 34.6°C) (p<0.01) in the E group. A significant increase in heart rate and blood pressure was observed in the T, E and H groups. Only cigarette smoking increased carbon monoxide levels (p<0.01).ConclusionsThe use of HTPs elicits acute respiratory and cardiovascular health effects.
Treatment with prophylactic oral anticoagulants and the risk of mortality in COVID-19 patients: a nationwide cohort study
Authors: Altaraihi Sarah , Kamstrup Peter , Eklöf Josefin , Dyrby Johansen Niklas , Biering-Sørensen Tor , Sivapalan Pradeesh , Jensen Jens-Ulrik 
Published: April 2023

Background
Venous thromboembolism has been reported in patients with coronavirus disease 2019 (COVID-19). It remains unclear if premorbid use of prophylactic oral anticoagulation, for reasons other than COVID-19, protects against death in patients with COVID-19. The aim of this study was to estimate if the risk of all-cause mortality, hospital admission or intensive care unit (ICU) admission for individuals with verified SARS-CoV-2 was lower if patients used oral anticoagulant (OAC) therapy prior to a positive COVID-19 status.

Methods
Data were obtained using national health registries. Cohort entry was the day of a positive SARS-CoV-2 test, and individuals were followed for 14 days or until death or hospital admission. Adjusted Cox proportional hazard regressions and competing risk analyses were used to estimate the risk of all-cause mortality, hospital admission and ICU admission in OAC users compared with patients with no use of OAC.

Results

In this nationwide cohort study a total of 244 522 individuals were included (median age 35 years (interquartile range 21–52); 124 095 (51%) female), among whom 3710 (1.5%) were OAC users. In the adjusted Cox regression cohort, there was no difference in risk of all-cause mortality in OAC
versus
non-OAC users. (hazard ratio (HR) 1.13, 95% CI 0.99–1.30). Hospital admission risk (HR 1.11, 95% CI 1.02–1.20) was slightly increased in OAC users, and there was no difference between the groups regarding the risk of ICU admission (HR 0.96, 95% CI 0.74–1.24).

Conclusions
In individuals with confirmed SARS-CoV-2, pre-existing treatment with OAC was not associated with prophylactic benefits in the prevention of hospital admission, ICU admissions or death. Prescription patterns should remain unchanged.
Increased expression of miR146a dysregulates TLR2-induced HBD2 in airway epithelial cells from patients with COPD
Authors: Reddy-Vari Hymavathi , Kim Yerin , Rajput Charu , Sajjan Umadevi S. 
Published: April 2023

BackgroundAirway epithelial cells from patients with COPD show suboptimal innate immune responses to nontypeableHaemophilus influenzae(NTHi) and Toll-like receptor (TLR)2 ligands despite expressing TLR2 similar to normal airway epithelial cells, but the underlying mechanisms are poorly understood.MethodsNormal or COPD mucociliary-differentiated airway epithelial cells were treated with TLR2 agonists or infected with NTHi and expression of β-defensin (HBD)2 was examined. Interleukin-1 receptor-associated kinase (IRAK)-1 and microRNA (miR)146a were genetically inhibited in normal and COPD airway epithelial cell cultures, respectively, and HBD2 responses to TLR2 ligands were determined. IRAK-1 expression in lung sections was determined by immunofluorescence microscopy.ResultsCompared to normal, COPD airway epithelial cell cultures showed impaired expression of HBD2 in response to TLR2 agonists or NTHi infection. Apical secretions from TLR2 agonist-treated normal, but not COPD, airway epithelial cells efficiently killed NTHi. Knockdown of HBD2 significantly reduced NTHi killing by apical secretions of normal airway epithelial cells. Compared to normal, COPD cells showed significantly reduced expression of IRAK-1 and this was associated with increased expression of miR146a. Inhibition of miR146a increased the expression of IRAK-1, improved the expression of HBD2 in response to TLR2 agonists in COPD cells and enhanced the killing of bacteria by apical secretions obtained from TLR2 agonist-treated COPD cells. Bronchial epithelium of COPD patients showed reduced expression of IRAK-1.ConclusionsThese results suggest that reduced levels of IRAK-1 due to increased expression of miR146a may contribute to impaired expression of TLR2-induced HBD2 in COPD airway epithelial cells.
Neuroanatomical restoration of salience network links reduced headache impact to cognitive function improvement in mild traumatic brain injury with posttraumatic headache
Authors: Xu Hui , Xu Cheng , Gu Pengpeng , Hu Yike , Guo Yunyu , Bai Guanghui 
Published: April 2023

Abstract
Background
Neuroanatomical alterations have been associated with cognitive deficits in mild traumatic brain injury (MTBI). However, most studies have focused on the abnormal gray matter volume in widespread brain regions using a cross-sectional design in MTBI. This study investigated the neuroanatomical restoration of key regions in salience network and the outcomes in MTBI.

Methods
Thirty-six MTBI patients with posttraumatic headache (PTH) and 34 matched healthy controls were enrolled in this study. All participants underwent magnetic resonance imaging scans and were assessed with clinical measures during the acute and subacute phases. Surface-based morphometry was conducted to get cortical thickness (CT) and cortical surface area (CSA) of neuroanatomical regions which were defined by the Desikan atlas. Then mixed analysis of variance models were performed to examine CT and CSA restoration in patients from acute to subacute phase related to controls. Finally, mediation effects models were built to explore the relationships between neuroanatomical restoration and symptomatic improvement in patients.

Results
MTBI patients with PTH showed reduced headache impact and improved cognitive function from the acute to subacute phase. Moreover, patients experienced restoration of CT of the left caudal anterior cingulate cortex (ACC) and left insula and cortical surface area of the right superior frontal gyrus from acute to subacute phase. Further mediation analysis found that CT restoration of the ACC and insula mediated the relationship between reduced headache impact and improved cognitive function in patients.

Conclusions
These results showed that neuroanatomical restoration of key regions in salience network correlated reduced headache impact with cognitive function improvement in MTBI with PTH, which further substantiated the vital role of salience network and provided an alternative clinical target for cognitive improvement in MTBI patients with PTH.

Graphical Abstract
Performance optimization of In(Ga)As quantum dot intermediate band solar cells
Authors: Yang Guiqiang , Liu Wen , Bao Yidi , Chen Xiaoling , Ji Chunxue , Wei Bo , Yang Fuhua , Wang Xiaodong 
Published: April 2023

AbstractQuantum dot intermediate band solar cell (QD-IBSC) has high efficiency theoretically. It can absorb photons with energy lower than the bandgap of the semiconductor through the half-filled intermediate band, extending the absorption spectrum of the cell. However, issues in the IBSC, such as the strain around multi-stacking QDs, low thermal excitation energy, and short carrier lifetime, lead to its low conversion efficiency. In recent years, many efforts have been made from different aspects. In this paper, we focus on In(Ga)As QD-IBSC, list the experimental technologies used to improve the performance of the cell and review the recent research progress. By analyzing the effects of different technologies on conversion efficiency, the development direction of the In(Ga)As QD-IBSC in the future is proposed.
Proteomic signature associated with chronic kidney disease (CKD) progression identified by data-independent acquisition mass spectrometry
Authors: Ramírez Medina Carlos R. , Ali Ibrahim , Baricevic-Jones Ivona , Odudu Aghogho , Saleem Moin A. , Whetton Anthony D. , Kalra Philip A. , Geifman Nophar 
Published: April 2023

Abstract
Background
Halting progression of chronic kidney disease (CKD) to established end stage kidney disease is a major goal of global health research. The mechanism of CKD progression involves pro-inflammatory, pro-fibrotic, and vascular pathways, but pathophysiological differentiation is currently lacking.

Methods
Plasma samples of 414 non-dialysis CKD patients, 170 fast progressors (with ∂ eGFR-3 ml/min/1.73 m2/year or worse) and 244 stable patients (∂ eGFR of − 0.5 to + 1 ml/min/1.73 m2/year) with a broad range of kidney disease aetiologies, were obtained and interrogated for proteomic signals with SWATH-MS. We applied a machine learning approach to feature selection of proteins quantifiable in at least 20% of the samples, using the Boruta algorithm. Biological pathways enriched by these proteins were identified using ClueGo pathway analyses.

Results
The resulting digitised proteomic maps inclusive of 626 proteins were investigated in tandem with available clinical data to identify biomarkers of progression. The machine learning model using Boruta Feature Selection identified 25 biomarkers as being important to progression type classification (Area Under the Curve = 0.81, Accuracy = 0.72). Our functional enrichment analysis revealed associations with the complement cascade pathway, which is relevant to CKD as the kidney is particularly vulnerable to complement overactivation. This provides further evidence to target complement inhibition as a potential approach to modulating the progression of diabetic nephropathy. Proteins involved in the ubiquitin–proteasome pathway, a crucial protein degradation system, were also found to be significantly enriched.

Conclusions
The in-depth proteomic characterisation of this large-scale CKD cohort is a step toward generating mechanism-based hypotheses that might lend themselves to future drug targeting. Candidate biomarkers will be validated in samples from selected patients in other large non-dialysis CKD cohorts using a targeted mass spectrometric analysis.
Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
Authors: Cano Marco A. , Tsueng Ginger , Zhou Xinghua , Xin Jiwen , Hughes Laura D. , Mullen Julia L. , Su Andrew I. , Wu Chunlei 
Published: April 2023

Abstract
Background
Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging Schema.org could benefit biomedical research resource providers, but it can be challenging to apply Schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize Schema.org or other biomedical schema projects.

Results
Our browser-based tool includes features which can help address many of the barriers towards Schema.org-compliance such as: The ability to easily browse for relevant Schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schema—a large multi-class schema for harmonizing various COVID-19 related resources.

Conclusions
We have created a browser-based tool to empower biomedical research resource providers to leverage Schema.org classes to make their research outputs more FAIR.
Optimizing the synthesis of yeast Beta-glucan via response surface methodology for nanotechnology application
Authors: Atta-Allah Alshimaa A. , Ahmed Rania F. , Shahin Azza A. M. , Hassan Enas A. , El-Bialy Heba Abd-Alla , El-Fouly Mohie Z. 
Published: April 2023

Abstract
Background
The production of biopolymers from waste resources is a growing trend, especially in high-population countries like Egypt. Beta-glucan (β-glucan) belongs to natural polysaccharides that are derived from plant and microbial origins. In this study, following increasing demands for β-glucan owing to its bioactive properties, a statistical model to enhance microbial β-glucan production was evaluated for its usefulness to the food and pharmaceutical industries. In addition, a trial to convert β-glucan polymer to nanostructure form was done to increase its bioactivity.

Results
Ingredients of low-cost media based on agro-industrial wastes were described using Plackett–Burman and central composite design of response surface methodology for optimizing yeast β-glucan. Minerals and vitamin concentrations significantly influenced β-glucan yield for Kluyveromyces lactis and nitrogen and phosphate sources for Meyerozyma guilliermondii. The maximum predicted yields of β-glucan recovered from K. lactis and M. guilliermondii after optimizing the medium ingredients were 407 and 1188 mg/100 ml; respectively. For the first time, yeast β-glucan nanoparticles (βGN) were synthesized from the β-glucan polymer using N-dimethylformamide as a stabilizer and characterized using UV–vis spectroscopy, transmission electron microscope (TEM), dynamic light scattering (DLS) and Fourier transform infrared spectroscopy (FT-IR). The average size of βGN was about 300 nm as determined by DLS. The quantitative variation of functional groups between β-glucan polymer and βGN was evaluated by FT-IR for explaining the difference in their biological activity against Normal Homo sapiens-Hela contaminant and Hepatic cancer cell lines.

Conclusions
Enriching the low-cost media based on agro-industrial wastes with nutritional ingredients improves the yield of yeast β-glucan. The present study succeeds to form β-glucan nanoparticles by a simple method.
Antibacterial effect of vitamin C against uropathogenic E. coli in vitro and in vivo
Authors: Hassuna Noha Anwar , Rabie E. M. , Mahd W. K. M. , Refaie Marwa M. M. , Yousef Rehab Kamal Mohamed , Abdelraheem Wedad M. 
Published: April 2023

Abstract
Background
Resistance to antibiotics has increased steadily over time, thus there is a pressing need for safer alternatives to antibiotics. Current study aims to evaluate the influence of vitamin C as an antibacterial and anti-biofilm agent against uropathogenic E. coli (UPEC) strains. The expression of beta-lactamases and biofilm encoding genes among E. coli isolates before and after treating the isolates with sub MIC of vitamin C was analyzed by Real-time PCR. The in vivo assessment of the antibacterial and anti-biofilm effects of vitamin C against uropathogenic E. coli strains was done using a urinary tract infection (UTI) rat model.

Results
The effective concentration of vitamin C that could inhibit the growth of most study isolates (70%) was 1.25 mg/ml. Vitamin C showed a synergistic effect with most of the studied antibiotics; no antagonistic effect was detected at all. Vitamin C showed an excellent anti-biofilm effect against studied isolates, where 43 biofilm-producing isolates were converted to non-biofilm at a concentration of 0.312 mg/ml. The expression levels of most studied genes were down-regulated after treatment of E. coli isolates with vitamin C. In vivo assessment of vitamin C in treating UTIs showed that vitamin C has a rapid curative effect as the comparable antibiotic. Administration of both vitamin C and nitrofurantoin at a lower dose for treatment of UTI in rats had a better effect.

Conclusion
Vitamin C as an antibacterial and anti-biofilm agent either alone or in combination with antibiotics could markedly improve UTI in experimental rats.
Prognostic values of modified NUTRIC score to assess outcomes in critically ill patients admitted to the intensive care units: prospective observational study
Authors: Mahmoodpoor Ata , Sanaie Sarvin , Sarfaraz Tohid , Shadvar Kamran , Fattahi Vahid , Hamishekar Hadi , Vahedian-Azimi Amir , Samim Abbas , Rahimi-Bashar Farshid 
Published: April 2023

Abstract
Purpose
Modified Nutrition Risk in the Critically Ill (NUTRIC) score (mNUTRIC score) have been validated as screening tool for quantifying risk of adverse outcome critically ill patients admitted to the intensive care units (ICUs). The aim of this study was to evaluate the prognostic value of mNUTRIC score to assess outcomes in this population.

Materials and methods
This prospective, observational study was conducted on adult patients admitted to the general ICUs of two university affiliated hospital in northwest of Iran. The association between the mNUTRIC score and outcomes was assessed using the univariate and multivariate binary logistic regression. The performance of mNUTRIC score to predict outcomes was assessed using the receiver operating characteristic (ROC)-curve.

Results
In total 445 ICU patients were enrolled. Based on mNUTRIC score, 62 (13.9%) and 383 (86.1%) individuals were identified at high and low nutritional risk, respectively. The area under the curve (AUC) for predicting ICU mortality, using vasopressor, duration of vasopressor, and mechanical ventilation (MV) duration were (AUC: 0.973, 95% CI: 0.954–0.986, P < 0.001), (AUC: 0.807, 95% CI: 0.767–0.843, P < 0.001), (AUC: 0.726, 95% CI: 0.680–0.769, P < 0.001) and (AUC: 0.710, 95% CI: 0.666–0.752, P < 0.001), respectively.

Conclusions
An excellent and good predictive performance of the mNUTRIC score was found regarding ICU mortality and using vasopressor, respectively. However, this predictive was fair for MV and vasopressor duration and poor for ICU and hospital length of stay.
Data source profile reporting by studies that use routinely collected health data to explore the effects of drug treatment
Authors: Wang Wen , Liu Mei , He Qiao , Wang Mingqi , Xu Jiayue , Li Ling , Li Guowei , He Lin , Zou Kang , Sun Xin 
Published: April 2023

Abstract
Background
Routinely collected health data (RCD) are important resource for exploring drug treatment effects. Adequate reporting of data source profiles may increase the credibility of evidence generated from these data. This study conducted a systematic literature review to evaluate the reporting characteristics of databases used by RCD studies to explore the effects of drug treatment.

Methods
Observational studies published in 2018 that used RCD to explore the effects of drug treatment were identified by searching PubMed. We categorized eligible reports into two groups by journal impact factor (IF), including the top 5 general medical journals (NEJM, Lancet, JAMA, BMJ and JAMA Internal Medicine) and the other journals. The reporting characteristics of the databases used were described and compared between the two groups and between studies citing and not citing database references.

Results
A total of 222 studies were included, of which 53 (23.9%) reported that they applied data linkage, 202 (91.0%) reported the type of database, and 211 (95.0%) reported the coverage of the data source. Only 81 (36.5%) studies reported the timeframe of the database. Studies in high-impact journals were more likely to report that they applied data linkage (65.1% vs. 20.2%) and used electronic medical records (EMR) (73.7% vs. 30.0%) and national data sources (77.8% vs. 51.3%) than those published in other medical journals. There were 137/222 (61.7%) cited database references. Studies with database-specific citations had better reporting of the data sources and were more likely to publish in high-impact journals than those without (mean IF, 6.08 vs. 4.09).

Conclusions
Some deficits were found in the reporting quality of databases in studies that used RCD to explore the effects of drug treatment. Studies citing database-specific references may provide detailed information regarding data source characteristics. The adoption of reporting guidelines and education on their use is urgently needed to promote transparency by research groups.