bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of codon usage bias of thioredoxin in apicomplexan protozoa
Authors: Wang Dawei , Yang Baoling 
Published: November 2023

Abstract
Background
Apicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals, such as malaria, toxoplasmosis, and cryptosporidiosis. Apicomplexan protozoa possess unique thioredoxins (Trxs) that have been shown to regulate various cellular processes including metabolic redox regulation, parasite survival, and host immune evasion. However, it is still unknown how synonymous codons are used by apicomplexan protozoa Trxs.

Methods
Codon usage bias (CUB) is the unequal usage of synonymous codons during translation which leads to the over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact a variety of cellular processes including protein expression levels and genetic variation. This study analyzed the CUB of 32 Trx coding sequences (CDS) from 11 apicomplexan protozoa.

Results
The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in Cryptosporidium spp. and Plasmodium spp., while the Eimeria spp., Babesia spp., Hammondia hammondi, Neospora caninum, and Toxoplasma gondii tended to end in G/C. The average effective number of codon (ENC) value of these apicomplexan protozoa is 46.59, which is > 35, indicating a weak codon preference among apicomplexan protozoa Trxs. Furthermore, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym), and length of amino acids (L_aa) indicated the influence of base composition and codon usage indices on CUB. Additionally, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis further demonstrated that natural selection plays an important role in apicomplexan protozoa Trxs codon bias.

Conclusions
In conclusion, this study increased the understanding of codon usage characteristics and genetic evolution of apicomplexan protozoa Trxs, which expanded new ideas for vaccine and drug research.

Graphical Abstract
Estimating attrition in mild-to-moderate Alzheimer’s disease and mild cognitive impairment clinical trials
Authors: Ritchie Marina , Gillen Daniel L. , Grill Joshua D. 
Published: November 2023

Abstract
Background
Participant retention is a key factor that affects clinical trial integrity. Trial protocols estimate attrition as a function of sample size calculations. Alzheimer’s disease (AD) is an area of active treatment development. We aimed to quantify the association between trial duration and completion rates and provide guidance for estimating attrition in AD trial protocols.

Methods
Using the Alzforum and ClinicalTrials.gov databases, we analyzed retention data from 125 mild-to-moderate AD and 12 mild cognitive impairment (MCI) clinical trials. We compared the rates of completion between trial arms (active vs. control) and ran regression models to test the hypothesis that trials with longer study duration have lower trial completion using all available data and restricting to placebo data. Our primary outcome was the odds of trial completion for a 6-month increase in trial duration. From the regression model, we estimated the proportion of participants completing 6-, 12-, and 18-month trials.

Results
We found that 21 (17%) mild-to-moderate AD trials and 1 (8%) MCI trial demonstrated greater dropout in treatment compared to placebo arms. For every 6-month increase in trial duration, there was a 27% decrease in the odds of trial completion (OR = 0.73; 95% CI 0.66, 0.81; p < 0.001) among participants in mild-to-moderate AD trials and a 55% decrease (OR = 0.45; 95% CI 0.36, 0.57; p < 0.001) among participants in MCI trials. The proportion of participants in the placebo group completing 6-, 12-, and 18-month trials were estimated to be 85.2%, 80.0%, and 73.3% for mild-to-moderate AD trials and 91.9%, 84.2%, and 71.3% for MCI trials, respectively.

Conclusions
Longer duration trials may be underpowered to demonstrate estimated treatment effects and may suffer from a greater risk of bias than do shorter trials.
Association between quality of governance, antibiotic consumption, and antimicrobial resistance: an analysis of Italian regions
Authors: Maugeri Andrea , Barchitta Martina , Agodi Antonella 
Published: November 2023

Abstract
Background
Emerging research has provided evidence suggesting the potential influence of governance on the development and spread of antimicrobial resistance (AMR), accounting for significant disparities observed both between and within countries. In our study, we conducted an ecological analysis to investigate the relationship between governance quality, antibiotic consumption, and AMR across Italian regions.

Methods
By leveraging data from three distinct sources at the regional level, we compiled a comprehensive dataset comprising: AMR proportions for three specific pathogen-antibiotic combinations in the year 2021, antibiotic consumption data for systemic use in the year 2020, and the 2021 European Quality of Government Index (EQI) and its corresponding pillars. Employing mediation analysis, we investigated the potential mediating role of antibiotic consumption in the association between the EQI and an average measure of AMR.

Results
Our analysis revealed substantial variation in the percentages of AMR across different regions in Italy, demonstrating a discernible North-to-South gradient concerning both antibiotic usage and governance quality. The EQI exhibited a statistically significant negative correlation with both antibiotic consumption and AMR percentages, encompassing both specific combinations and their average value. Regions characterized by higher levels of governance quality consistently displayed lower values of antibiotic consumption and AMR, while regions with lower governance quality tended to exhibit higher levels of antibiotic use and AMR. Furthermore, we observed a significant total effect of the EQI on average AMR (β = − 0.97; CI − 1.51; − 0.43). Notably, this effect was found to be mediated by antibiotic consumption, as evidenced by a significant indirect effect (β = − 0.89; CI − 1.45; − 0.32).

Conclusions
These findings draw attention to the regional disparities observed in AMR levels, antibiotic consumption patterns, and governance quality in Italy. Our study also highlights the mediating role of antibiotic consumption in the relationship between governance quality and AMR. This underscores the significance of implementing focused interventions and policies aimed at improving governance quality and promoting responsible antibiotic use.
Deep learning image segmentation for the reliable porosity measurement of high-capacity Ni-based oxide cathode secondary particles
Authors: Lee Hee-Beom , Jung Min-Hyoung , Kim Young-Hoon , Park Eun-Byeol , Jang Woo-Sung , Kim Seon-Je , Choi Ki-ju , Park Ji-young , Hwang Kee-bum , Shim Jae-Hyun , Yoon Songhun , Kim Young-Min 
Published: November 2023

AbstractThe optimization of geometrical pore control in high-capacity Ni-based cathode materials is required to enhance the cyclic performance of lithium-ion batteries. Enhanced porosity improves lithium-ion mobility by increasing the electrode–electrolyte contact area and reducing the number of ion diffusion pathways. However, excessive porosity can diminish capacity, thus necessitating optimizing pore distribution to compromise the trade-off relation. Accordingly, a statistically meaningful porosity estimation of electrode materials is required to engineer the local pore distribution inside the electrode particles. Conventional scanning electron microscopy (SEM) image-based porosity measurement can be used for this purpose. However, it is labor-intensive and subjected to human bias for low-contrast pore images, thereby potentially lowering measurement accuracy. To mitigate these difficulties, we propose an automated image segmentation method for the reliable porosity measurement of cathode materials using deep convolutional neural networks specifically trained for the analysis of porous cathode materials. Combined with the preprocessed SEM image datasets, the model trained for 100 epochs exhibits an accuracy of > 97% for feature segmentation with regard to pore detection on the input datasets. This automated method considerably reduces manual effort and human bias related to the digitization of pore features in serial section SEM image datasets used in 3D electron tomography.Graphical abstract
Engaging East Harlem, New York youth in action gun violence prevention research and child rights: a preliminary study
Authors: Malla Pallavi , Fray Nakesha , Formica Margaret K. , Goldberg Danielle , Marchesani Robert , Hennessy Patricia , Ervine Moshay , Wallace Jacqueline G. , Larson Elaine , Wridt Pamela , Laraque-Arena Danielle ,   IAACT, Mrozowski Adam , Troung Alexander , Lugo Alina , Hoffman Benjamin , Haughton Brianna , Duran Dibrianys , Goldberg Danielle , Laraque-Arena Danielle , Kener David , Sugrim Dyanand , Larson Elaine L. , Wallace Jacqueline G. , Hari Jasmin , Bogard Kimber , Formica Margaret , Reyes Mariela , Canfora Michael , Shajee Mohammad , Ervine Moshay , Fray Nakesha , Agrawal Nina , Malla Pallavi , Wridt Pamela , Hennessy Patricia , Theerman Paul , Richards-Peelle Reggie , Marchesani Robert , Flores Roseanne L. , Taylor Shaneah , Castro Syanne , Graham Yvonne 
Published: November 2023

Abstract
Background
The aim of the study was to have youth participate in the design and implementation of a research project set within a child rights framework to better understand high schoolers’ perceptions of safety in their school and community.

Results
Between June 2020 and March 2021, a team of East Harlem, New York high school students, participated as co-researchers to modify the United Nations Children's Fund Child Friendly Cities Initiative Survey to suit their needs. Due to the COVID-19 pandemic, the final survey was conducted through an online remote classes system during advisory school classes, accompanied by brief focused group discussions. The novel process of conducting an interactive qualitative and quantitative virtual survey during a pandemic via youth participatory action research is outlined in this paper.

Conclusions
Our results demonstrate that youth participatory action research can be utilized as part of a child rights framework approach to assess the views of youth regarding community safety and violence prevention.
Coaches’ Perceptions of Common Planning Concepts Within Training Theory: An International Survey
Authors: Anyadike-Danes Kechi , Donath Lars , Kiely John 
Published: November 2023

Abstract
Background
The planning of training is a popular yet controversial topic among coaches and sports scientists. Periodisation is often presented in the literature as the most efficacious approach to planning training. While historically surveys of coaches appeared to support this a key failing was that no unified definition of periodisation exists. Recent surveys offering a periodisation definition and an alternative planning methodology found many choosing the alternative therefore questioning periodisation’s wide acceptance. The current survey looked to explore how coaches perceived specific concepts, drawn from the literature, that relate to the planning of training.

Methods
106 coaches [age range: 18–65+ years, 31% 15+ years coaching, 58% individual-events/sports and 32% international level] from across the world completed a novel cross-sectional online survey on the planning of training and the training process. Topics included use of periodisation, division of time into discrete periods, assignment of goals and training to pre-determined periods and the adaptability of pre-established plans.

Results
The majority described their planning approach as training periodisation (71%). Similarly, there was strong agreement with the necessity to determining a goal for the season (85%) and divide the season into distinct manageable periods of time (73%). When examining whether physical adaptations are achievable within specific and fixed timeframes only a minority (33%) agreed, a similar result was found for training physical capacities in a sequential order (37%). Finally, there was limited support for training targets remaining fixed over a training period (10%).

Conclusions
As a tool for the planning of athlete’s training, periodisation is often presented as the best and most popular approach. Recent research however has highlighted possible discrepancies in its usage among practitioners. The results of this survey echo this and question the acceptance of periodisation concepts even among periodisation users. In part this may be due to key tenets of periodisation no longer being supported by research or practice. A lingering question then is whether the beliefs of coaches, developed through experience and supported by research, will continue to be marginalized. If sports scientists wish to aid coaches then they need to be engaged in future research initiatives as co-collaborators.
In vivo mutagenicity assessment of orally treated tert-butyl hydroperoxide in the liver and glandular stomach of MutaMouse
Authors: Murata Yasumasa , Suzuki Kenichiro , Shigeta Yoshiyuki , Iso Takako , Hirose Nozomu , Umano Takaaki , Horibata Katsuyoshi , Sugiyama Kei-ichi , Hirose Akihiko , Masumura Kenichi , Matsumoto Mariko 
Published: November 2023

Abstract
Background
tert-Butyl hydroperoxide (TBHP; CAS 75–91-2), a hydroperoxide, is mainly used as a polymerization initiator to produce polyethylene, polyvinyl chloride, and unsaturated polyester. It is a high-production chemical, widely used in industrial countries, including Japan. TBHP is also used as an additive for the manufacturing of food utensils, containers, and packaging (UCP). Therefore, there could be consumer exposure through oral intake of TBHP eluted from UCPs. TBHP was investigated in various in vitro and in vivo genotoxicity assays. In Ames tests, some positive results were reported with and/or without metabolic activation. As for the mouse lymphoma assay, the positive result was reported, regardless of the presence or absence of metabolic activation enzymes. The results of some chromosomal aberrations test and comet assay in vitro also demonstrated the genotoxic positive results. On the other hand, in in vivo tests, there are negative results in the bone marrow micronucleus test of TBHP-administered mice by single intravenous injection and the bone marrow chromosomal aberration test using rats exposed to TBHP for 5 days by inhalation. Also, about dominant lethal tests, the genotoxic positive results appeared. In contrast, there is little information about in vivo mutagenicity and no information about carcinogenicity by oral exposure.

Results
We conducted in vivo gene mutation assay using MutaMice according to the OECD Guidelines for the Testing of Chemicals No. 488 to investigate in vivo mutagenicity of TBHP through oral exposure. After repeated dosing for 28 days, there were no significant differences in the mutant frequencies (MFs) of the liver and glandular stomach up to 300 mg/kg/day (close to the maximum tolerable dose (MTD)). The positive and negative controls produced the expected responses.

Conclusions
These findings show that orally administrated TBHP is not mutagenic in the mouse liver and glandular stomach under these experimental conditions.
A validated RP-UPLC method for estimation of Samidorphan and Olanzapine in mixed powder and combined tablets
Authors: Ponnekanti Krishnaphanisri , Godela Ramreddy 
Published: November 2023

AbstractBack groundThe key objective of the research study is to develop a new stability-indicating RP-UPLC approach to determine the presence of Samidorphan and Olanzapine simultaneously in bulk and their combination. A successful separation of Samidorphan and Olanzapine was achieved by using HSS column C18 (100 × 2.1 mm), a mobile phase of 0.1% orthophospharic acid: Acetonitrile (70:30 v/v), flow rate of 0.3 mL/min, and detection wavelength of 230 nm. The stability of the analytes in bulk and dosage forms was evaluated using extreme forced conditions, such as hydrolysis with acid and base, peroxide oxidation, and heat degradation, following ICH guidelines.ResultsOlanzapine and Samidorphan had retention times of 0.46 and 0.93 min, respectively. Olanzapine and Samidorphan have linear responses from the proposed method in the concentration ranges of 5–30 µg/mL and 2.5–15 µg/mL, respectively. The computed detection and quantification limits for Olanzapine were 0.22 µg/mL and 0.471 µg/mL, and for Samidorphan were 0.12 µg/mL and 0.36 µg/mL. All method validation parameters have complied with the ICH guidelines' Q2 acceptance limits. The stability representing the feature of the approach has been seen with the excellent resolution among the Olanzapine and Samidorphan and degradation products.ConclusionThe suggested RP-UPLC method was extremely sensitive, precise, and stable-indicating. The technique can potentially be used in the production of Olanzapine and Samidorphan for routine analysis in the quality control department.Graphical abstract
A rare case report of Gorlin-Goltz’s syndrome: a multisystemic disorder of otolaryngological domain
Authors: Richa Richa , Kumar Vivek , Ayushree Ayushree 
Published: November 2023

Abstract
Background
Gorlin-Goltz’s syndrome (GGS) is an extremely rare autosomal dominant disorder showing a high penetrance and variable expressivity. Gorlin-Goltz’s syndrome is an infrequent multisystemic disease, which is usually characterized by numerous basal cell carcinomas, odontogenic keratocysts (OKCs), and musculoskeletal malformations along with neurological, ophthalmic, endocrine, and genital manifestations. There are also multiple manifestations in the domain of ENT and patient may primarily present to an ENT clinician with one of the diverse clinical involvements.

Case presentation
We report one such infrequent case of a 24-year-old male patient who presented with an oroantral fistula at our tertiary health care center and was diagnosed to have Gorlin-Goltz’s syndrome. The diagnosis was made in our patient by the presence of 4 major and 2 minor criteria.

Conclusion
Early diagnosis and management of GGS helps to prevent long-term sequelae including malignancy and oro-maxillofacial deformation. The constellation of symptoms of such rare disorders should be promptly recognized and a high index of suspicion should be maintained. This case report is an appraisal of the diagnosis and management of GGS from an otolaryngological perspective and is being reported here for extreme rarity and clinical interest.
Simplified implicit finite-difference method of spatial derivative using explicit schemes with optimized constant coefficients based on L1 norm
Authors: Miao Zhongzheng , Zhang Jinhai 
Published: November 2023

The explicit finite-difference (EFD) method is widely used in numerical simulation of seismic wave propagation to approximate spatial derivatives. However, the traditional and optimized high-order EFD methods suffer from the saturation effect, which seriously restricts the improvement of numerical accuracy. In contrast, the implicit FD (IFD) method approximates the spatial derivatives in the form of rational functions and thus can obtain much higher numerical accuracy with relatively low orders; however, its computational cost is expensive due to the need to invert a multidiagonal matrix. We derive an explicit strategy for the IFD method to reduce the computational cost by constructing the IFD method with the discrete Fourier matrix; then, we transform the inversion of the multidiagonal matrix into an explicit matrix multiplication; next, we construct an objective function based on the [Formula: see text] norm to reduce approximation error of the IFD method. This explicit strategy of the IFD method can avoid inverting the multidiagonal matrix, thus improving the computational efficiency. This constant coefficient optimization method reduces the approximation error in the medium-wavenumber range at the cost of tolerable deviation (smaller than 0.0001) in the low-wavenumber range. For the 2D Marmousi model, the root-mean-square error of the numerical results obtained by this method is one-fifth that of the traditional IFD method with the same order (i.e., 5/3) and one-third that of the traditional EFD method with much higher orders (i.e., 72). The significant reduction of numerical error makes the developed method promising for numerical simulation in large-scale models, especially for long-time simulations.
Effectiveness of Continuous Glucose Monitoring on Metrics of Glycemic Control in Type 2 Diabetes Mellitus: A Systematic Review and Meta-analysis of Randomized Controlled Trials
Authors: Uhl Stacey , Choure Anuja , Rouse Benjamin , Loblack Aggee , Reaven Peter 
Published: November 2023

Abstract

Purpose
To provide a systematic review and meta-analysis synthesizing the findings of randomized controlled trials (RCTs) of continuous glucose monitors (CGMs) in the management of adults with type 2 diabetes mellitus (T2DM) on glucose control and clinical outcomes.

Methods
MEDLINE, Embase, and Cochrane were searched for RCTs that assessed the effectiveness of real-time CGM (rt-CGM) or flash CGM (FGM) in adults (≥18 years) with T2DM that reported on at least 1 of the following outcomes: hemoglobin A1c (HbA1c), time in range, time in hyperglycemia, or time in hypoglycemia. The GRADE approach was used to assess certainty of evidence for primary outcomes.

Results
Fourteen RCTs assessing CGM were included, with 825 patients in 9 RCTs using rt-CGM and 822 in 5 RCTs using FGM. Moderate certainty of evidence indicated that use of CGM had a modest but statistically significant reduction in HbA1c levels of about 0.32%. Our analyses of each device type separately showed similar reductions in HbA1c (0.34% and 0.33%, respectively, for rt-CGM and FGM), with trends for improvement in other glucose metrics favoring rt-CGM over self-monitored blood glucose.

Conclusion
Both rt-CGM and flash CGM led to modest but statistically significant declines in HbA1c among individuals with T2DM, with little heterogeneity in the results. However, the duration of the included RCTs was relatively short and few studies reported on important clinical outcomes, such as adverse events, emergency department use, or hospitalization. Longer term studies are needed to determine if the short-term improvements in glucose control leads to improvements in clinically important outcomes.