bluuebunny/crossref_metadata_2025_split huggingface dataset:
Current practices, supports, and challenges in speech-language pathology service provision for autistic preschoolers
Authors: Binns Amanda V , Cunningham Barbara Jane , Andres Allison , Oram Cardy Janis 
Published: August 2022

Background Speech-language pathology services are among the most frequently accessed services for young autistic children. Therefore, understanding the nature of these services, what challenges these clinicians face, and what supports they value is critical for developing appropriate policies and practices that can maximize positive outcomes for children and families. This study had two primary aims. The first was to examine the self-reported assessment and intervention practices of community-based Speech Language Pathologists (SLPs) and communicative disorders assistants (CDAs; who provide services under the supervision of a SLP) in supporting preschool children with suspected and diagnosed autism. The second aim was to identify barriers and supports (facilitators) to providing services in the community using the Consolidated Framework for Implementation Research (CFIR) as a framework. Methods A cross-sectional online survey was used to collect qualitative and quantitative data from clinicians in Ontario Canada who were providing speech and language services to preschool children with suspected or diagnosed autism. Quantitative data were used to describe clinicians” practices, and qualitative data captured their perspectives on barriers and supports to providing services. Results A total of 258 clinicians participated in the survey. On average, clinicians reported almost half of the preschoolers on their caseload had either diagnosed or suspected autism. There was consistency across the skill development areas assessed by SLPs, and targeted during therapy sessions, with the top four areas targeted being: foundational social communication, language, play and pragmatics. However, there was wide variation in speech and language assessment and intervention practices reported by this sample of clinicians (i.e., service delivery models, tools or programs used, length and duration of therapy services, level of collaboration with other professionals). Clinicians identified several barriers to providing services: limited funding and time, lack of inter-professional collaboration, difficulty accessing services, community messaging about autism services, family readiness and clinician knowledge. Supports (facilitators) included: access to autism-focused professional development, inter- and intra-professional collaboration, and access to additional supports in the community.
Auditory processing in rodent models of autism: a systematic review
Authors: Wilde Maya , Constantin Lena , Thorne Peter R. , Montgomery Johanna M. , Scott Ethan K. , Cheyne Juliette E. 
Published: August 2022

AbstractAutism is a complex condition with many traits, including differences in auditory sensitivity. Studies in human autism are plagued by the difficulty of controlling for aetiology, whereas studies in individual rodent models cannot represent the full spectrum of human autism. This systematic review compares results in auditory studies across a wide range of established rodent models of autism to mimic the wide range of aetiologies in the human population. A search was conducted in the PubMed and Web of Science databases to find primary research articles in mouse or rat models of autism which investigate central auditory processing. A total of 88 studies were included. These used non-invasive measures of auditory function, such as auditory brainstem response recordings, cortical event-related potentials, electroencephalography, and behavioural tests, which are translatable to human studies. They also included invasive measures, such as electrophysiology and histology, which shed insight on the origins of the phenotypes found in the non-invasive studies. The most consistent results across these studies were increased latency of the N1 peak of event-related potentials, decreased power and coherence of gamma activity in the auditory cortex, and increased auditory startle responses to high sound levels. Invasive studies indicated loss of subcortical inhibitory neurons, hyperactivity in the lateral superior olive and auditory thalamus, and reduced specificity of responses in the auditory cortex. This review compares the auditory phenotypes across rodent models and highlights those that mimic findings in human studies, providing a framework and avenues for future studies to inform understanding of the auditory system in autism.
Using green biosynthesized kaempferol-coated sliver nanoparticles to inhibit cancer cells growth: an in vitro study using hepatocellular carcinoma (HepG2)
Authors: Alyami Nouf M. , Alyami Hanadi M. , Almeer Rafa 
Published: August 2022

AbstractThe ongoing loss of human life owing to various forms of cancer necessitates the development of a more effective/honorable therapeutic approach. Moreover, finding a novel green-synthesized anti-cancer therapy is vital because of the induced drug resistance against the commonly used drugs. Collecting the advantage of the nanometer size of nanoparticles with the biosafety of plant-based substances might potentiate the anticancer effect with minimal toxic effect. In the current study, we aimed to green-synthesize using kaempferol (flavonoid) as a coating the silver nanoparticles (AgNPs) and investigated their anti-cancer activity in hepatocellular carcinoma (HepG2) cell line. First of all, kaempferol-coated AgNPs characters were well-defined using Fourier transmission infrared (FTIR), X-ray diffraction (XRD), zetasizer, and transmission electron microscopy (TEM). The results showed their 200 nm size, spherical shape, less aggregation with high stability characteristics. Then, the cytotoxic effect of both 1/3 and 1/2 LC50 of AgNPs, and doxorubicin (DOX, anticancer drug) on HepG2 cells was evaluated by dimethylthiazolyltetrazolium bromide (MTT) assay and release of lactate dehydrogenase (LDH) leakage percent. Reactive oxygen species (ROS) and apoptotic markers were also analyzed, along with the migration and invasion of HepG2 cells were recorded. Our findings showed that kaempferol-coated AgNPs could induce cytotoxic effects and reduce the viability of HepG2 cells in a concentration-dependent manner. LDH leakage % was significantly increased in cells treated with kaempferol-coated AgNPs confirming their cytotoxic effect. ROS generation and lipid peroxidation could significantly increase in HepG2 cells treated with kaempferol-coated AgNPs along with the exhaustion of antioxidant Glutathione (GSH) marker revealing the induced oxidative damage. Oxidative damage-mediated apoptosis was confirmed by the elevated levels of the pro-apoptotic markers (Bax, Cyt-c, P53, and caspase-3) and the reduced level of anti-apoptotic marker (Bcl-2) using enzyme-linked immunosorbent assay (ELISA). Furthermore, kaempferol-coated AgNPs could suppress the migrating and invading ability of HepG2 cells showing their antimetastatic effect. To end up, kaempferol-coated AgNPs can induce a potential anti-cancer effect in HepG2 cells via oxidative stress-mediated apoptosis.
A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies
Authors: Shao Zhonghe , Wang Ting , Qiao Jiahao , Zhang Yuchen , Huang Shuiping , Zeng Ping 
Published: August 2022

AbstractBackgroundMultilocus analysis on a set of single nucleotide polymorphisms (SNPs) pre-assigned within a gene constitutes a valuable complement to single-marker analysis by aggregating data on complex traits in a biologically meaningful way. However, despite the existence of a wide variety of SNP-set methods, few comprehensive comparison studies have been previously performed to evaluate the effectiveness of these methods.ResultsWe herein sought to fill this knowledge gap by conducting a comprehensive empirical comparison for 22 commonly-used summary-statistics based SNP-set methods. We showed that only seven methods could effectively control the type I error, and that these well-calibrated approaches had varying power performance under the simulation scenarios. Overall, we confirmed that the burden test was generally underpowered and score-based variance component tests (e.g., sequence kernel association test) were much powerful under the polygenic genetic architecture in both common and rare variant association analyses. We further revealed that two linkage-disequilibrium-freePvalue combination methods (e.g., harmonic meanPvalue method and aggregated Cauchy association test) behaved very well under the sparse genetic architecture in simulations and real-data applications to common and rare variant association analyses as well as in expression quantitative trait loci weighted integrative analysis. We also assessed the scalability of these approaches by recording computational time and found that all these methods can be scalable to biobank-scale data although some might be relatively slow.ConclusionIn conclusion, we hope that our findings can offer an important guidance on how to choose appropriate multilocus association analysis methods in post-GWAS era. All the SNP-set methods are implemented in the R package called MCA, which is freely available athttps://github.com/biostatpzeng/.
Volumetric macromolecule identification in cryo-electron tomograms using capsule networks
Authors: Hajarolasvadi Noushin , Sunkara Vikram , Khavnekar Sagar , Beck Florian , Brandt Robert , Baum Daniel 
Published: August 2022

Abstract
Background
Despite recent advances in cellular cryo-electron tomography (CET), developing automated tools for macromolecule identification in submolecular resolution remains challenging due to the lack of annotated data and high structural complexities. To date, the extent of the deep learning methods constructed for this problem is limited to conventional Convolutional Neural Networks (CNNs). Identifying macromolecules of different types and sizes is a tedious and time-consuming task. In this paper, we employ a capsule-based architecture to automate the task of macromolecule identification, that we refer to as 3D-UCaps. In particular, the architecture is composed of three components: feature extractor, capsule encoder, and CNN decoder. The feature extractor converts voxel intensities of input sub-tomograms to activities of local features. The encoder is a 3D Capsule Network (CapsNet) that takes local features to generate a low-dimensional representation of the input. Then, a 3D CNN decoder reconstructs the sub-tomograms from the given representation by upsampling.

Results
We performed binary and multi-class localization and identification tasks on synthetic and experimental data. We observed that the 3D-UNet and the 3D-UCaps had an $$F_1-$$

F
1

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score mostly above 60% and 70%, respectively, on the test data. In both network architectures, we observed degradation of at least 40% in the $$F_1$$

F
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-score when identifying very small particles (PDB entry 3GL1) compared to a large particle (PDB entry 4D8Q). In the multi-class identification task of experimental data, 3D-UCaps had an $$F_1$$

F
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-score of 91% on the test data in contrast to 64% of the 3D-UNet. The better $$F_1$$

F
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-score of 3D-UCaps compared to 3D-UNet is obtained by a higher precision score. We speculate this to be due to the capsule network employed in the encoder. To study the effect of the CapsNet-based encoder architecture further, we performed an ablation study and perceived that the $$F_1$$

F
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-score is boosted as network depth is increased which is in contrast to the previously reported results for the 3D-UNet. To present a reproducible work, source code, trained models, data as well as visualization results are made publicly available.

Conclusion
Quantitative and qualitative results show that 3D-UCaps successfully perform various downstream tasks including identification and localization of macromolecules and can at least compete with CNN architectures for this task. Given that the capsule layers extract both the existence probability and the orientation of the molecules, this architecture has the potential to lead to representations of the data that are better interpretable than those of 3D-UNet.
Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination
Authors: Onasanya Adepeju E. , El-Hage Charles , Diaz-Méndez Andrés , Vaz Paola K. , Legione Alistair R. , Browning Glenn F. , Devlin Joanne M. , Hartley Carol A. 
Published: August 2022

Abstract
Background
Equid gammaherpesvirus 2 (EHV2) is a gammaherpesvirus with a widespread distribution in horse populations globally. Although its pathogenic significance can be unclear in most cases of infection, EHV2 infection can cause upper respiratory tract disease in foals. Co-infection of different strains of EHV2 in an individual horse is common. Small regions of the EHV2 genome have shown considerable genetic heterogeneity. This could suggest genomic recombination between different strains of EHV2, similar to the extensive recombination networks that have been demonstrated for some alphaherpesviruses. This study examined natural recombination and genome diversity of EHV2 field isolates.

Results
Whole genome sequencing analysis of 18 EHV2 isolates, along with analysis of two publicly available EHV2 genomes, revealed variation in genomes sizes (from 173.7 to 184.8 kbp), guanine plus cytosine content (from 56.7 to 57.8%) and the size of the terminal repeat regions (from 17,196 to 17,551 bp). The nucleotide sequence identity between the genomes ranged from 86.2 to 99.7%. The estimated average inter-strain nucleotide diversity between the 20 EHV2 genomes was 2.9%. Individual gene sequences showed varying levels of nucleotide diversity and ranged between 0 and 38.1%. The ratio of nonsynonymous substitutions, Ka, to synonymous substitutions, Ks, (Ka/Ks) suggests that over 50% of EHV2 genes are undergoing diversifying selection. Recombination analyses of the 20 EHV2 genome sequences using the recombination detection program (RDP4) and SplitsTree revealed evidence of viral recombination.

Conclusions
Analysis of the 18 new EHV2 genomes alongside the 2 previously sequenced genomes revealed a high degree of genetic diversity and extensive recombination networks. Herpesvirus genome diversification and virus evolution can be driven by recombination, and our findings are consistent with recombination being a key mechanism by which EHV2 genomes may vary and evolve.
One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts
Authors: Twort Victoria G. , Blande Daniel , Duplouy Anne 
Published: August 2022

Abstract
Background
Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts’ life-histories. Many symbionts however very often go undetected. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis.

Results
In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here.

Conclusions
Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities.
Intelligent prediction of major adverse cardiovascular events (MACCE) following percutaneous coronary intervention using ANFIS-PSO model
Authors: Dehdar Karsidani Sahar , Farhadian Maryam , Mahjub Hossein , Mozayanimonfared Azadeh 
Published: August 2022

Abstract
Background
This study aimed to use the hybrid method based on an adaptive neuro-fuzzy inference system (ANFIS) and particle swarm optimization (PSO) to predict the long term occurrence of major adverse cardiac and cerebrovascular events (MACCE) of patients underwent percutaneous coronary intervention (PCI) with stent implantation.

Method
This retrospective cohort study included a total of 220 patients (69 women and 151 men) who underwent PCI in Ekbatan medical center in Hamadan city, Iran, from March 2009 to March 2012. The occurrence and non-occurrence of MACCE, (including death, CABG, stroke, repeat revascularization) were considered as a binary outcome. The predictive performance of ANFIS model for predicting MACCE was compared with ANFIS-PSO and logistic regression.

Results
During ten years of follow-up, ninety-six patients (43.6%) experienced the MACCE event. By applying multivariate logistic regression, the traditional predictors such as age (OR = 1.05, 95%CI: 1.02–1.09), smoking (OR = 3.53, 95%CI: 1.61–7.75), diabetes (OR = 2.17, 95%CI: 2.05–16.20) and stent length (OR = 3.12, 95%CI: 1.48–6.57) was significantly predicable to MACCE. The ANFIS-PSO model had higher accuracy (89%) compared to the ANFIS (81%) and logistic regression (72%) in the prediction of MACCE.

Conclusion
The predictive performance of ANFIS-PSO is more efficient than the other models in the prediction of MACCE. It is recommended to use this model for intelligent monitoring, classification of high-risk patients and allocation of necessary medical and health resources based on the needs of these patients. However, the clinical value of these findings should be tested in a larger dataset.
Public trust in physicians: empirical analysis of patient-related factors affecting trust in physicians in China
Authors: Li Changle , Khan M. Mahmud 
Published: August 2022

AbstractBackgroundTrust between the parties is essential for the efficient functioning of the healthcare market. Physician-patient relationship represents an asymmetric information situation and trust in physicians is critical for improving health and wellbeing of patients. In China, trust in physicians appears to be quite low creating conflicts between physicians and patients. This study aims to identify some general factors associated with trust in physicians in general using a nationally representative survey.MethodsA cross-sectional analysis using data from 2018 China Family Panel Study (CFPS). Survey responses of individuals aged 16 years or above were extracted from CFPS and the final sample consisted of 29,192 individuals. An ordered probit model was used to identify factors causing heterogeneity in the levels of trust in physicians.ResultsHigher educational attainment and having medical insurance coverage are associated with higher likelihood of trusting physicians. Older adults (> = 30 years), males, urban residents, wage-earners, and self-employed persons are less likely to trust physicians. People who are diagnosed as chronic diseases or current smokers indicate lower level of trust in physicians. Higher perceived quality of services improves trust.ConclusionSocioeconomically disadvantaged population groups and uninsured individuals are less likely to trust physicians. Health care delivery system needs to address the concerns of these specific population groups to reduce tensions between physicians and patients. Increasing health insurance coverage and offering insurance with low out-of-pocket expenses should reduce the perception that physicians are more guided by their income rather than the wellbeing of patients. The system should also develop a comprehensive bill of rights of patients to improve patient-physician relationship.
Lifestyle intervention in early pregnancy can prevent gestational diabetes in high-risk pregnant women in the UAE: a randomized controlled trial
Authors: Sadiya Amena , Jakapure Vidya , Shaar Ghida , Adnan Rama , Tesfa Yohannes 
Published: August 2022

Abstract
Purpose
A prevalence of gestational diabetes mellitus (GDM) is approximately three times higher than the global rate in the UAE. However, it has not yet been studied whether a 12-week moderate-intensity lifestyle intervention can prevent gestational diabetes among pregnant women at high risk in this region.

Patients and methods
A pragmatic, open-label, randomized clinical trial was conducted.
Sixty-three women aged 18 to 45 years, with ≤12 weeks of gestation, singleton pregnancy, and having ≥ two risk factors for GDM were randomly assigned to the Lifestyle Intervention (LI) group (n = 30) or Usual Care (UC) group (n = 33). The women in the LI group received a 12-week, moderate-intensity lifestyle intervention with individualized counseling on a diet, physical activity, and behavior change by a licensed dietitian. The women in the UC group received usual antenatal care. The primary outcome was the incidence of GDM based on the IADPSG criteria at 24-28 weeks of gestation.

Results
The incidence of GDM was 33.3% in LI group and 57.5% in UC group. The crude relative risk (RR) for GDM was 0.59 (95% CI, 0.32-1.04, p = 0.05). The multivariable logistic regression model without adjustment showed OR = 0.37 (95% CI, 0.13-1.02, p = 0.05) and after adjusting with Age, BMI and family history of diabetes reported OR = 0.26, 95%CI 0.07, 0.92, p = 0.04. in LI vs UC. The daily dietary intake of calories (− 120 kcal, p = < 0.01), carbohydrates (− 19 g, p < 0.01), and fat (− 5 g, p = 0.03) was reduced, and physical activity time (+ 52 min, p = 0.05) increased in the LI group after the intervention. However, the LI had no significant effect on maternal and neonatal outcomes.

Conclusion
A 12-week moderate intensity lifestyle intervention in early pregnancy could reduce the relative risk of GDM by 41% among high-risk pregnant women in the UAE. These findings could impact public health outcomes in the region.

Trial registration
Trial registration Retrospectively registered NCT04273412,18/02/2020.