bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding phage-host interactions: a machine learning approach to predict strain-specific infections
Authors: Camejo Pamela Yael , Rojas Felipe , Ossa Antonio , Hurtado Rodrigo , Tichy Daniel , Pieringer Christian , Pino Michael , Mora-Uribe Paola , Ulloa Soledad , Norambuena Rodrigo , Tobar-Calfucoy Eduardo , Aguilera Matías , Rojas-Martínez Victoria , Cifuentes Onix , Sabag Andrea , Cifuentes Nicolas , Cifuentes Pablo , Pieringer Hans , León Luis E. 
Published: December 2024

Abstract

The use of bacteriophages for biological control of bacterial infections is a promising approach to combat antimicrobial resistant bacteria. Prediction of phage-bacteria interactions is key to identify sensitive bacterial strains to phage therapy. Since these interactions are governed by multiple biological mechanisms, it is not a simple task to predict the outcome of a phage infection, which varies even among strains from the same species. In this study, machine learning-based models capable of predicting the host range of phages from sequencing data were developed. Models were trained using phage-bacteria protein-protein interactions (PPI), predicted from PPI databases, and a host-range dataset obtained from experimental assays with 10 Salmonella enterica and 3 Escherichia coli bacteriophages. The performance of prediction models differed among bacteriophages, ranging from 78–92% of accuracy in the case of Salmonella and 84–94% in Escherichia phages. Results demonstrated the effectiveness of using PPI as a feature to design ML models for phage-bacteria phenotype prediction.
Interprofessional Perspectives on Non-Invasive Respiratory Support Practices in Extremely Preterm Infants: A Canadian Survey
Authors: Shalish Wissam , Alarcon-Martinez Tugba , Remmer Elissa , Mardakis Stephanie , Leone Marisa , Boyer Johanne , Lv Shasha , Beltempo Marc , Sant'Anna Guiherme 
Published: December 2024

Abstract

Objective
To describe the perspectives of physicians, nurses, and respiratory therapists on the provision of non-invasive respiratory support (NRS) in extremely preterm infants.
Study Design:
A cross-sectional web-based anonymized 19-question survey was sent to healthcare professionals (HCP) across tertiary care NICUs in Canada. The survey inquired about perspectives on devices and management strategies during NRS, monitoring of respiratory events, NRS failure, and possible solutions.
Result
391 responses from 61 physicians, 173 nurses, and 147 respiratory therapists were analyzed. HCP perspectives varied regarding appropriateness of different NRS settings and interfaces, documentation of cardiorespiratory events, and prevention of NRS failure. Obtaining effective results on NRS was deemed challenging by 48% of HCPs. Training on NRS provision was deemed adequate by 89% of RTs and 78% of physicians, but only 56% of nurses.
Conclusion
There remain important uncertainties and variations across disciplines on how to best approach NRS in extremely preterm infants.
Aquifer hydraulic characteristics using D-Z parameters: A case study of Lohaghat block, Champawat district, Uttarakhand
Authors: Singh Somvir , Mondal N.C. 
Published: December 2024

Abstract

This study focused on analyzing the geoelectrical properties of shallow aquifers, and estimating their hydraulic parameters in Lohaghat block of Champawat district, Uttarakhand. We conducted twenty Vertical Electrical Soundings (VESs) with electrode separations (AB) varying between 200 and 940 m. Data were analyzed using 1X1D Interpex software, USA make. The qualitative assessment identified four primary geoelectric layer patterns, mainly HK and KH-curves. The interpreted layer resistivities ranged from 24.06 Ω-m to 170.59 Ω-m, with an average resistivity of 80.64 Ω-m. The principal aquifer was located within the fourth to seventh geoelectric layers, consisting of weathered or fractured phyllites, granite, quartzite, and sand. The aquifer depth varied from 17.24 to 91.15 m, and its thickness ranged from 14.59 to 69.56 m. Hydraulic characteristics derived from the geoelectrical layers indicated a porosity range of 37.81–56.14%, protective capacities from 0.12 to 1.07 mhos (average 0.45 mhos), and transverse resistance between 452.91 and 8272.25 Ωm². Transmissivity values ranged from 67.61 to 548.24 m²/day, transverse resistivities from 6.73 Ω-m to 208.53 Ωm, longitudinal resistivities from 37.88 Ωm to 521.63 Ωm, and anisotropy values from 0.27 to 1.35. These parameters were utilized to determine both hydraulic conductivity and transmissivity. By employing the Dar-Zarrouk (D-Z) parameters, which encompass the aquifer thickness, resistivity, hydraulic conductivity, transmissivity, longitudinal conductance, transverse resistance, and anisotropy, we evaluated the groundwater potential, categorizing the area into moderate and good productivity. This study illustrates the effectiveness of surface geophysical methods in estimating aquifer hydraulic characteristics in the absence of pumping test data.
Dental students’ perspective on the distance education system during COVID-19 pandemic: a cross-sectional study
Authors: karmakar shaswata , Kar Mehuli , Francis Delfin Lovelina , reddy saravanan sampoornam pape , modak baishakhi 
Published: December 2024

Abstract

Background
The COVID-19 pandemic has wreaked havoc on education in a variety of settings, particularly medical and dental teaching institutes. During the pandemic, distance learning has become necessary to ensure that education continues.
Objective
The present study aims to analyze dental students’ perceptions of the transition of education from traditional to distance learning.
Methods
This was a cross-sectional study consisting of a 25-statement online questionnaire that was anonymously administered to students studying dentistry at Manipal Academy of Higher Education, Manipal, India. The data collected were analyzed statistically via chi-square test.
Results
A total of 713 out of 800 undergraduate dental students participated in the survey, resulting in an 89.12% response rate. A total of 73.9% of the students did not feel that it was easier to concentrate in online classes than in offline lectures, and 60.9% of the students felt that they could not learn the theoretical aspects adequately. Almost three-fourths of the students (73.9%) felt that lockdowns and distance education severely affected the quality of their dental education. A total of 86.4% of the students felt that a lack of patient exposure would affect their future dental practice. With respect to learning preferences, the majority of the students preferred a combination of traditional methods and online learning.
Conclusion
Despite these difficulties, dental students were able to adapt to the new distance learning education system. The COVID-19 pandemic taught not only the use of technology in education but also future learning strategies.
Demographics and Clinical Features of Children with Allergic Rhinitis:A Single-Center Study from Western Turkey
Authors: Bakır Damla Baysal , Boyacıoğlu Özge Kangallı , Asilsoy Suna , Yağmur Halime , Kabadayı Gizem , Atay Özge , Uzuner Nevin 
Published: December 2024

Abstract

Background
Allergic rhinitis (AR) is a disease that has significant effects on the quality of life of people and exhibits different phenotypic features with different clinical findings. By analyzing the data of pediatric patients, we aimed to reveal the relationship between demographic and laboratory data and clinical features and to gain awareness about allergic rhinitis phenotypes in children.
Methods
Demographic data, clinical complaints, examination findings, and atopy biomarkers are retrospectively analyzed to assess the impact of aeroallergens on the disease phenotype.
Results
In a study of 301 AR patients (median age 11 years; 66.1% male), sneezing (79.1%) was the most common complaint, and pallor of the nasal mucosa was the primary examination finding (83.1%). Seasonal symptoms were reported by 66.8%, and 60.5% were polysensitized. Notably, 42.5% had asthma, often associated with concurrent sensitization to mold or animal dander (p ≤ 0.05). Pollen was the most prevalent allergen (65.8%), with significant increases in sensitization to pollen (p < 0.001) and animal dander (p = 0.003) with age. Patients with pollen sensitization reported more sneezing (p = 0.026) and seasonal symptoms (p ≤ 0.05). Nasal congestion was predominantly seen in house dust mite-sensitized patients (78.4% with concha hypertrophy, p < 0.001). Overall, 67.1% reported seasonal complaints, with polysensitized patients experiencing more frequent seasonal exacerbations.
Conclusion
This study in Western Turkey involving 301 allergic rhinitis patients revealed a high prevalence of polysensitization to pollen and animal dander. The findings highlight the need for early identification and management of AR to reduce asthma risk and further research on environmental factors affecting sensitization.
Influence of Socioeconomic Status on Children's Reading Abilities: The Mediating Role of Home Learning Environment and the Moderating Role of Grade Level
Authors: Li Yageng , Yu Yingqi , Zhang Siqi , Gao Minqi , Yang Xiujie 
Published: December 2024

Abstract

Family socioeconomic status (SES) has been shown to be associated with children’s academic development. However, how SES influences children’s reading ability across grades still warrants investigation. This study recruited 1st - through 6th -grade children (N = 1,534) and examined the role of Home Learning Environment in the relationship between SES and reading development. The results revealed that the number of books at home and the earliest reading age mediated the impact of SES on children’s reading, whereas family teaching activities did not have the expected mediating effect. Grade level moderated the influence of SES and reading age on reading; that is, as grade level increased, earlier reading age and higher family SES contributed more to children’s reading performance. These findings illustrate how SES affects children’s reading through Home Learning Environment across grades, which offers practical insights for guiding family activities in promoting reading development.
The expression changes endothelial and fibrinolytic biomarkers in acute ischemic stroke patients with OSA
Authors: Huang Zhencan , Zhang Yanan , Sun Qingqing , Wang Zan 
Published: December 2024

Abstract

Objective
To assess the expression changes of serum fibrinogen, E-selectin, and tissue-type plasminogen activator (t-PA) in acute ischemic stroke (AIS) patients with varying degrees of obstructive sleep apnea syndrome (OSA), and evaluate their value in diagnosing AIS with OSA.
Methods
Data were gathered from 80 patients with AIS who were admitted to the First Hospital of Jilin University between January 2023 and December 2023. Out of these, 60 patients completed the NIHSS Scale, ESS Scale, STOP-Bang Scale, and underwent polysomnography within a week of symptom onset. Based on the apnea-hypopnea index (AHI) score, patients were categorized into three groups: 15 in the non-exposed group (AHI < 5), 15 in the mildly exposed group (5 ≤ AHI ≤ 15), and 30 in the moderately to severely exposed group (AHI > 15). Serum levels of fibrinogen, E-selectin, and t-PA were determined using enzyme-linked immunosorbent assay.
Results
Polysomnography results indicated AIS with OSA had an increased arousal index and oxygen desaturation index (P < 0.001). Additionally, serum levels of fibrinogen, E-selectin, and t-PA were markedly elevated in the moderately-severely exposed group compared to the non-exposed group (P < 0.001), and these levels positively correlated with the severity of OSA. ROC curves showed the sensitivities of serum of fibrinogen, E-selection, and t-PA was 84.4%, 80%, and 82.2%, respectively, and the specificities of 60%, 66.7%, and 66.7%, compared with that of PSG respectively.
Conclusion
The expression of serum fibrinogen, E-selectin, and t-PA is elevated in AIS with OSA and correlates with the severity of OSA.
Timing of Umbilical Cord Clamping – Attitudes and Beliefs among Midwives, Obstetricians, and Neonatologists
Authors: Wilander Maria , Ekelöf Katarina , Sæther Elisabeth , Berglund Denice , Patriksson Katarina , Svedenkrans Jenny , Rabe Heike , Andersson Ola , Thies-Lagergren Li 
Published: December 2024

Abstract

Objective
To assess the attitudes and beliefs about cord clamping management among health professionals involved in neonatal resuscitation.
Study design:
A cross-sectional survey was administered electronically, using an adaptation of the questionnaire developed by Jelin et al. The survey was conducted among midwives, nursing staff, obstetricians, and pediatricians/neonatologists from September 2022 to August 2023. Results were analyzed descriptively.
Result
Of 838 respondents analyzed, 94% reported cord clamping timing being “very or moderately important” for neonatal outcomes. Midwives were more likely to use an event-based approach to cord clamping compared to physicians. Among midwives and pediatric physicians, 27% and 10% respectively preferred an event-based approach to cord clamping in resuscitation situations. Obstetricians predominantly selected < 30 s as the preferred timing for cord clamping in resuscitation scenarios.
Conclusion
Timing of cord clamping is considered important among respondents. Midwives and physicians differ in their approach to cord clamping.
Deciphering the rhizosphere microbiota composition of nature farming soybean (Glycine max L.) with different nodulation phenotypes
Authors: Agyekum Dominic V. A. , Dastogeer Khondoker M. G. , Okazaki Shin 
Published: December 2024

Abstract

Background
Nature farming, a sustainable agricultural method which avoids agrochemicals and untreated organic amendments, promotes both agricultural productivity and ecological conservation. This system may foster unique plant-microbiota interactions for growth and fitness; however the microbiota of nature-farmed plants remains largely unexplored. Second, root nodule symbiosis (RNS) is crucial for nitrogen fixation in legumes; however, its broader impact on rhizosphere microbiota assembly is not well understood. This study examined the dynamics between impaired nodule symbiosis, soil management, and the rhizosphere microbiota composition and growth of soybean (Glycine max L.).
Results
We evaluated the growth and characterized the rhizosphere bacterial and fungal communities of soybean by comparing wildtype soybeans (Enrei) with the non-nodulating mutants (En1282) across four soils under conventional and nature farming, including fumigated and unfumigated conditions. We found that the non-nodulating soybean mutants (En1282) exhibited reduced growth compared with wild-type (Enrei) plants, especially in untreated soils. Soil fumigation decreased microbial diversity and reshaped rhizosphere community composition with a significant reduction in plant growth and nodulation in all soils. Restriction in RNS increased bacterial diversity in untreated soils, possibly as a compensatory mechanism for nitrogen acquisition, whereas fungal diversity remained relatively stable. Nature farming promoted beneficial microbes like Rhizobium, Trichoderma, and Chloridium, whereas conventional soil plants favored Bacillus and Aspergillus. Notably, differential enrichment analysis identified distinct associations for each nodulation phenotype, with Enrei predominantly enriched for Pseudomonas, and En1282 associated primarily with oligotrophic microbes.
Conclusion
Our study sheds light on the complex interplay between legume symbiosis and rhizosphere microbiota assembly and highlights the significance of eco-friendly farming methods like nature farming in cultivating a healthy rhizosphere for plant growth. The results paves way for future strategies to manipulate rhizosphere microbiota, ultimately promoting robust and sustainable farming systems that reduce reliance on chemical inputs.
Anti-Ro-52 antibody is a risk factor for recurrence in interstitial lung disease with positive anti-aminoacyl tRNA synthetase antibody: A single-center, retrospective observational study
Authors: Takahashi Hiroshi , Arita Machiko , Sato Ryoju , Amano Akihiko , Tanaka Ayaka , Hamakawa Masamitsu , Ishida Tadashi , Tachibana Hiromasa 
Published: December 2024

Abstract

Purpose
Anti-synthetic syndrome-associated interstitial lung disease (ASS-ILD) recurs in approximately 56% of cases, with recurrence associated with poor long-term prognosis; however, there are few reports on the risk factors for recurrence. While anti-Ro52 antibodies are considered risk factors for rapidly progressing interstitial lung disease in ASS, their role in ASS-ILD recurrence remains unclear. ༷e aimed to evaluate the association between anti-Ro52 antibody and the recurrence of ASS-ILD.
Methods
This single-center, retrospective cohort study included 97 patients diagnosed with ASS-ILD between January 2010 and August 2023 who underwent induction remission therapy with corticosteroids and immunosuppressive agents (tacrolimus, cyclosporine, and cyclophosphamide). Patients were classified into anti-Ro52 antibody-positive and anti-Ro52 antibody-negative groups. A competing risk analysis was conducted, with the primary endpoint being ASS-ILD recurrence or interstitial pneumonia (IP)-related death and death from other causes as the competing risk. Multivariate analysis identified recurrence factors.
Results
Forty-four patients were in the anti-Ro52 antibody-positive group and 53 in the anti-Ro52 antibody-negative group. There were no differences between the groups regarding initial and recurrence steroid doses, type of immunosuppressive drugs, and number of discontinued cases. The anti-Ro52 antibody-positive group had a significantly higher rate of recurrent ASS-ILD or ILD-related death in a competing risk analysis (P = 0.011). In multivariate analysis, the anti-Ro52 antibody was identified as an independent risk factor for ASS-ILD recurrence (hazard ratio = 1.84 [1.01–3.36], P = 0.047).
Conclusion
Anti-Ro52 antibodies are a risk factor for ASS-ILD recurrence.
Pharmacogenomic associations with HIV-1 virologic suppression in TB/HIV patients
Authors: Ridolfi Felipe , Amorim Gustavo , Haas David W. , Arriaga Maria , Staats Cody , Cordeiro-Santos Marcelo , Kritski Afrânio L. , Figueiredo Marina C. , Andrade Bruno B. , Sterling Timothy R. , Rolla Valeria C. , (RePORT-Brazil) Regional Prospective Observational Research in Tuberculosis 
Published: December 2024

Abstract

Background: Human genetic variants can affect TB and HIV drug metabolism, which may lead to toxicity or treatment failure. We evaluated associations between genetic variants of antiretroviral therapy (ART) and HIV-1 outcomes among TB/HIV patients.
Methods: We included RePORT-Brazil participants with TB/HIV who initiated standard TB treatment [2 months of isoniazid/rifampicin (or rifabutin)/pyrazinamide/ethambutol, then 4 months or more of isoniazid/rifampicin (or rifabutin)], and ART. The endpoint was HIV-1 virologic suppression (defined as <1,000 HIV-1 RNA copies/mL, for primary analysis, and <50 HIV-1 RNA copies/mL, for secondary analysis) after at least 2 weeks of ART. We compared non-nucleoside reverse transcriptase inhibitor (NNRTI)-based and integrase strand transfer inhibitor (INSTI)-based ART regimens. We genotyped CYP2B6 (rs3745274, rs28399499, rs4803419; affects efavirenz metabolism) and UGT1A1 (rs887829; affects dolutegravir and raltegravir metabolism); all have defined normal, intermediate, and slow genotypes. Genotyping was performed by MassARRAY iPLEX Gold. We compared outcome proportions (Fisher’s test) and time-to- virologic suppression (survival analysis, Wilcoxon-Gehan test).
Results: Among 194 TB/HIV participants included, efavirenz was the most frequent NNRTI ([n=76], one participant received etravirine), and raltegravir was the most frequent INSTI (n=88). The overall virologic suppression was suboptimal, with 32% (n=62) of participants not achieving HIV-1 virologic suppression. Among them, 36% (n=28) used efavirenz-based ART and were more likely to be CYP2B6 normal metabolizers (n=8, 44%); and 30% (n=30) used INSTI-based ART and the UGT1A1 normal genotype was also the most common (n=13, 50%). The median time to virologic suppression for efavirenz-based ART was 184 days (95% Confidence Interval (CI)160-207), and for INSTI-based ART, 188 days (95% CI 144-231) (p=0.84). No significant associations were found comparing the proportions and time to virologic suppression among CYP2B6 and UGT1A1genotypes.
Conclusions: In this observational cohort of patients treated for TB/HIV, the proportion of participants achieving virologic suppression was low, and genetic variants affecting ART metabolism were not significantly associated with the likelihood of virologic suppression.
White Matter Volume and Microstructural Integrity Are Associated with Fatigue in Relapsing Multiple Sclerosis
Authors: Figueroa-Vargas Alejandra , Navarrete Sebastián , Cárcamo Claudia , Ciampi Ethel , Vásquez Macarena , Soler Bernardita , Montalva Cristian , Iriarte-Carter Matías , Martínez-Molina María Paz , Carvajal-Paredes Patricio , Ayala-Ochoa Mariana , Márquez-Rodríguez Víctor , Figueroa-Taiba Paulo , Díaz-Díaz Marcela , Herrero Joaquín , Henríquez-Ch Rodrigo , Stecher Ximena , Manterola Carla , Zamorano Francisco , Guevara Pamela , Aboitiz Francisco , Billeke Pablo 
Published: December 2024

Abstract

Multiple sclerosis (MS) is a prevalent neurological disorder marked by inflammation and demyelination, with fatigue being one of the most reported and debilitating symptoms. While fatigue occurs across various neurological conditions and even in healthy individuals, the specific mechanisms contributing to fatigue in each context remain unclear. In this study, we conducted a cross-sectional analysis involving 33 people with relapsing MS (PwRMS) and 29 healthy controls who also reported fatigue. Participants underwent MRI scans, including T1-weighted and diffusion-weighted imaging, to evaluate brain structure. Additionally, the Modified Fatigue Impact Scale was utilized. To investigate the hypothesis that fatigue correlates differently with brain structures in PwRMS, we employed Bayesian LASSO and Spike-and-Slab LASSO regression models. Our findings indicated that lower white matter volume and compromised microstructural integrity in specific brain regions—such as the caudate part of cingulate gyrus, inferior frontal gyrus, and the banks of the superior temporal sulcus—were significantly associated with fatigue scores in PwRMS. These results suggest that alterations in specific brain regions may play a critical role in the clinical manifestation of fatigue in MS. Understanding these insights could help differentiate general mechanisms of fatigue from those affecting people with relapsing MS, which may guide future therapeutic strategies.