bluuebunny/crossref_metadata_2025_split huggingface dataset:
Buddhist Endowments by Śaiva Kings under the Maitrakas of Valabhī in Western India (5th–8th Cent.) and the Yodhāvaka Grant of Dharasena iv, [Valabhī] Year 326
Authors: Schmiedchen Annette 
Published: November 2021

Abstract
The phenomenon of interreligious patronage on the Indian subcontinent in the pre-modern period is best attested in royal inscriptions recording religious endowments. It is striking that most pre-Islamic Indian rulers patronised priests, monks, ascetics, and religious establishments of multiple faiths. The personal religious affiliations of the kings often contrasted remarkably with the patronage patterns followed by them according to the testimony of their epigraphs. The strongest indication for the individual confessions of rulers is given by the religious epithets among their titles. While the ambivalent relationship between the personal beliefs of the kings and their donative practices has been repeatedly described as an expression of Indian religious “tolerance” or of the specific character of Indian religious traditions, this paper emphasises that there were several reasons for the dichotomy. This will be investigated on the basis of the epigraphic material of the Maitraka dynasty, which ruled in Gujarat from the 5th to the 8th centuries. The article also contains an edition and translation of the hitherto unpublished Yodhāvaka Grant of Dharasena iv.
Longitudinal Study of Vocal Development and Language Environments in Infants With Cleft Palate
Authors: Ha Seunghee , Oller Kimbrough D. 
Published: November 2021

Objective This study investigated vocalization and language environment longitudinally in infants with cleft palate (CP) based on day-long audio recordings collected in their natural environments. Design Language Environment Analysis (LENA) data from all-day recordings at home were collected at 3-month intervals for infants from 4-6 to 16-18 months of age. The recordings were analyzed using experimentally blinded human coding as well as LENA automated analysis. Participants Ten infants with CP (± cleft lip) and 10 age-matched infants without CP. Main Outcome Measures Several measurements were obtained from the LENA automated analysis software. In addition, human coded measurements of vocalization and language environment, including the true canonical babbling ratio and the infant-directed speech ratio, were analyzed for each time point of data collection for each infant. Statistical analyses were performed to conduct group and age comparisons for each measure of vocalization and language environment. Results No group differences emerged in number of syllables produced. Infants with CP exhibited late onset and fewer productions of canonical syllables compared to infants without CP. Infants with CP did not show significant differences from infants without CP in measures related to language environment across ages. Conclusion This study provides detailed information through naturalistic all-day home recordings about vocal development and early language environments in infants with CP before and after palatal repair. Clinical implications for early intervention are discussed.
CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens
Authors: Vinceti Alessandro , Karakoc Emre , Pacini Clare , Perron Umberto , De Lucia Riccardo Roberto , Garnett Mathew J. , Iorio Francesco 
Published: November 2021

Abstract
Background
CRISPR-Cas9 genome-wide screens are being increasingly performed, allowing systematic explorations of cancer dependencies at unprecedented accuracy and scale. One of the major computational challenges when analysing data derived from such screens is to identify genes that are essential for cell survival invariantly across tissues, conditions, and genomic-contexts (core-fitness genes), and to distinguish them from context-specific essential genes. This is of paramount importance to assess the safety profile of candidate therapeutic targets and for elucidating mechanisms involved in tissue-specific genetic diseases.

Results
We have developed CoRe: an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens. We demonstrate, through a fully reproducible benchmarking pipeline, that CoRe outperforms state-of-the-art tools, yielding more reliable and biologically relevant sets of core-fitness genes.

Conclusions
CoRe offers a flexible pipeline, compatible with many pre-processing methods for the analysis of CRISPR data, which can be tailored onto different use-cases. The CoRe package can be used for the identification of high-confidence novel core-fitness genes, as well as a means to filter out potentially cytotoxic hits while analysing cancer dependency datasets for identifying and prioritising novel selective therapeutic targets.
Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii
Authors: Chung Dawoon , Kwon Yong Min , Yang Youngik 
Published: November 2021

Abstract
Background
Trichoderma is a genus of fungi in the family Hypocreaceae and includes species known to produce enzymes with commercial use. They are largely found in soil and terrestrial plants. Recently, Trichoderma simmonsii isolated from decaying bark and decorticated wood was newly identified in the Harzianum clade of Trichoderma. Due to a wide range of applications in agriculture and other industries, genomes of at least 12 Trichoderma spp. have been studied. Moreover, antifungal and enzymatic activities have been extensively characterized in Trichoderma spp. However, the genomic information and bioactivities of T. simmonsii from a particular marine-derived isolate remain largely unknown. While we screened for asparaginase-producing fungi, we observed that T. simmonsii GH-Sj1 strain isolated from edible kelp produced asparaginase. In this study, we report a draft genome of T. simmonsii GH-Sj1 using Illumina and Oxford Nanopore technologies. Furthermore, to facilitate biotechnological applications of this species, RNA-sequencing was performed to elucidate the transcriptional profile of T. simmonsii GH-Sj1 in response to asparaginase-rich conditions.

Results
We generated ~ 14 Gb of sequencing data assembled in a ~ 40 Mb genome. The T. simmonsii GH-Sj1 genome consisted of seven telomere-to-telomere scaffolds with no sequencing gaps, where the N50 length was 6.4 Mb. The total number of protein-coding genes was 13,120, constituting ~ 99% of the genome. The genome harbored 176 tRNAs, which encode a full set of 20 amino acids. In addition, it had an rRNA repeat region consisting of seven repeats of the 18S-ITS1–5.8S-ITS2–26S cluster. The T. simmonsii genome also harbored 7 putative asparaginase-encoding genes with potential medical applications. Using RNA-sequencing analysis, we found that 3 genes among the 7 putative genes were significantly upregulated under asparaginase-rich conditions.

Conclusions
The genome and transcriptome of T. simmonsii GH-Sj1 established in the current work represent valuable resources for future comparative studies on fungal genomes and asparaginase production.
Time to death and its determinants among under-five children in Sub-Saharan Africa using the recent (2010–2018) demographic and health survey data: country-based shared frailty analyses
Authors: Tesfa Desalegn , Tiruneh Sofonyas Abebaw , Azanaw Melkalem Mamuye , Gebremariam Alemayehu Digssie , Engdaw Melaku Tadege , Kefale Belayneh , Abebe Bedilu , Dessalegn Tsion 
Published: November 2021

Abstract
Background
Substantial global progress has been made in reducing under-five mortality since 1990, yet progress is insufficient to meet the sustainable development goal of 2030 which calls for ending preventable child deaths. There are disproportional survivals among children in the world. Therefore, the study aimed to assess the Survival status of under-five mortality and determinants in Sub-Saharan African Countries using the recent DHS data.

Methods
The data was retrieved from the birth record file from the standard Demographic and Health Survey dataset of Sub-Saharan Africa countries. Countries that have at least one survey between 2010 and 2018 were retrieved. Parametric shared frailty survival analysis was employed.

Results
A total of 27,221 (7.35%) children were died before celebrating their fifth birthday. Children at an early age were at higher risk of dying and then decrease proportionally with increased age. The risk of death among rich and middle family were lowered by 18 and 8% (AHR =0.82, 95% CI: 0.77-0.87) and (AHR = 0.92, 95% CI: 0.87-0.97) respectively, the hazard of death were 11, 19, 17, 90 and 55% (AHR = 1.06, 95% CI: 1.00-1.12), (AHR = 1.11,95%CI:1.04-1.19), (AHR = 1.17, 95% CI:1.12-1.23), (AHR = 1.90, 95%CI: 1.78-2.04) and (AHR = 1.55, 95% CI:1.47-1.63) higher than among children in rural, use unimproved water, delivered at home, born less than 18 months and between 18 and 23 months birth intervals respectively. The hazard of death was 7% among females and low birth weights (AHR = 0.93, 95%CI: 0.90 – 0.97) and (AHR = 0.93 95%CI: 0.89-0.97) respectively. There was also a significant association between multiple births and birth orders (AHR = 2.11, 95%CI: 2.51 – 2.90), (AHR = 3.01, 95%CI: 2.85-3.19) respectively.

Conclusions
Death rate among under-five children was higher at an early age then decreases as age advanced. Wealth status, residence, water source, place of delivery, sex of the child, plurality, birth size, preceding birth interval, and birth order were the most predictor variables. The health care program should be designed to encourage a healthy family structure. The health care providers should intervene in the community to inspire maternal health services.
Academic motivation among senior students majoring in rehabilitation related professions in China
Authors: Hu Huiling , Luo Hongmei 
Published: November 2021

Abstract
Objective/background
In mainland China, most universities offer general rehabilitation curricula rather than specialized curricula. The purpose of the current study is to investigate senior students’ academic motivation for rehabilitation and examine whether it varies among different curriculum structures, students’ gender, specific interests, and parental average education level.

Methods
This cross-sectional study recruited both senior students in general and those who specialized in rehabilitation curricula using an online survey. The Academic Motivation Scale (AMS) was used to measure academic motivation.

Results
The response rate was 74.68%, and 59 senior students in total (male: 34.48%; female: 65.52%) were analyzed. Twenty-nine (50.00%) students were from a general rehabilitation curriculum at Guangxi Medical University, and the rest (n = 29, 50.00%) were from a specialized curriculum at West China Medical School of Sichuan University. The overall average academic motivation score was 30.96 ± 5.92. Students in the specialized rehabilitation curriculum (32.85 ± 6.26) showed a significantly higher academic motivation score than those in the general rehabilitation curriculum (29.10 ± 5.00, p<0.05). Male (31.13 ± 5.67) and female (30.88 ± 6.12) students had equally high scores (p = 0.88). Students who had specific interests (29.81 ± 4.73) and those who did not (24.69 ± 4.92) shared the same academic motivation (t = 2.00, p = 0.06).

Conclusions
Senior rehabilitation science students in specialized curricula have higher levels of academic motivation than those in general curricula. There was no significant difference in academic motivation scores based on students’ gender, specific interests, or parental average education levels.
An explainable CNN approach for medical codes prediction from clinical text
Authors: Hu Shuyuan , Teng Fei , Huang Lufei , Yan Jun , Zhang Haibo 
Published: November 2021

AbstractBackgroundClinical notes are unstructured text documents generated by clinicians during patient encounters, generally are annotated with International Classification of Diseases (ICD) codes, which give formatted information about the diagnosis and treatment. ICD code has shown its potentials in many fields, but manual coding is labor-intensive and error-prone, lead to researches of automatic coding. Two specific challenges of this task are (1) given an annotated clinical notes, the reasons behind specific diagnoses and treatments are implicit; (2) explainability is important for practical automatic coding method, the method should not only explain its prediction output but also have explainable internal mechanics. This study aims to develop an explainable CNN approach to address these two challenges.MethodOur key idea is that for the automatic ICD coding task, the presence of informative snippets in the clinical text that correlated with each code plays an important role in the prediction of codes, and an informative snippet can be considered as a local and low-level feature. We infer that there exists a correspondence between a convolution filter and a local and low-level feature. Base on the inference, we come up with the Shallow and Wide Attention convolutional Mechanism (SWAM) to improve the CNN-based models’ ability to learn local and low-level features for each label.ResultsWe evaluate our approach on MIMIC-III, an open-access dataset of ICU medical records. Our approach substantially outperforms previous results on top-50 medical code prediction on MIMIC-III dataset, the precision of the worst-performing 10% labels in previous works is increased from 0% to 53% on average. We attribute this improvement to SWAM, by which the wide architecture with attention mechanism gives the model ability to more extensively learn the unique features of different codes, and we prove it by an ablation experiment. Besides, we perform manual analysis of the performance imbalance between different codes, and preliminary conclude the characteristics that determine the difficulty of learning specific codes.ConclusionsOur main contributions can be summarized into the following three: (1) We present local and low-level features, a.k.a. informative snippets play an important role in the automatic ICD coding task, and the informative snippets extracted from the clinical text provide explanations for each code. (2) We propose that there exists a correspondence between a convolution filter and a local and low-level feature. A combination of wide and shallow convolutional layer and attention layer can help the CNN-based models better learn local and low-level features. (3) We improved the precision of the worst-performing 10% labels from 0 to 53% on average.
Construction of the cervical cancer common terminology for promoting semantic interoperability and utilization of Chinese clinical data
Authors: Hong Na , Chang Fengxiang , Ou Zhengjie , Wang Yishang , Yang Yating , Guo Qiang , Ma Jianhui , Zhao Dan 
Published: November 2021

Abstract
Background
We aimed to build a common terminology in the domain of cervical cancer, named Cervical Cancer Common Terminology (CCCT), that will facilitate clinical data exchange, ensure quality of data and support large scale data analysis.

Methods
The standard concepts and relations of CCCT were collected from ICD-10-CM Chinese Version, ICD-9-PC Chinese Version, officially issued commonly used Chinese clinical terms, Chinese guidelines for diagnosis and treatment of cervical cancer and Chinese medical book Lin Qiaozhi Gynecologic Oncology. 2062 cervical cancer electronic medical records (EMRs) from 16 hospitals, belong to different regions and hospital tiers, were collected for terminology enrichment and building common terms and relations. Concepts hierarchies, terms and relationships were built using Protégé. The performance of natural language processing results was evaluated by average precision, recall, and F1-score. The usability of CCCT were evaluated by terminology coverage.

Results
A total of 880 standard concepts, 1182 common terms, 16 relations and 6 attributes were defined in CCCT, which organized in 6 levels and 11 classes. Initial evaluation of the natural language processing results demonstrated average precision, recall, and F1-score percentages of 96%, 72.6%, and 88.5%. The average terminology coverage for three classes of terms, clinical manifestation, treatment, and pathology, were 87.22%, 92.63%, and 89.85%, respectively. Flexible Chinese expressions exist between regions, traditions, cultures, and language habits within the country, linguistic variations in different settings and diverse translation of introduced western language terms are the main reasons of uncovered terms.

Conclusions
Our study demonstrated the initial results of CCCT construction. This study is an ongoing work, with the update of medical knowledge, more standard clinical concepts will be added in, and with more EMRs to be collected and analyzed, the term coverage will be continuing improved. In the future, CCCT will effectively support clinical data analysis in large scale.
Recognition of risk and prevention in safeguarding of children and young people: a mapping review and component analysis of service development interventions aimed at health and social care professionals
Authors: Chambers Duncan , Cantrell Anna , Booth Andrew 
Published: November 2021

Abstract
Background
The term ‘safeguarding’ covers the protection of health, wellbeing and human rights. Effective safeguarding enables people (particularly children, young adults and other vulnerable people) to live free from fear of abuse, harm or neglect. The UK Children Act 2004 required key agencies, including health and social care providers, to consider the need to safeguard children and promote their welfare. Within a larger evidence synthesis project, we sought to identify and map service development interventions (excluding provision of training) aimed at improving awareness of safeguarding and identifying at-risk children and young people in health and social care settings.

Methods
We searched fourteen health and social care databases from 2004 (date of Children Act) to October 2019 and updated the review via a citation search in March 2021.
Studies of any design were eligible if they described or evaluated an intervention (other than training) aimed at health or social care professionals in the United Kingdom and designed to improve recognition of risk in the context of safeguarding children and young people. Studies with no intervention (e.g. qualitative studies) were included to explain why interventions work or fail to work. Included studies were summarised using narrative synthesis. Risk of bias of included studies and overall strength of evidence were assessed using standard methods. We used a 5-item checklist (“TIDieR-Lite”) to map intervention components.

Results
Thirty-nine publications were included, of which 31 dealt with service developments, six with use of data and two with other initiatives. Promising service development initiatives include liaison nurses, assessment clinics, secondment, joint protocols and a ‘hub and spoke’ model. Initiatives involving use of routine data appeared promising and unlikely to generate significant additional costs. However, the quality of the evidence was generally low, with a shortage of controlled and long-term studies.

Conclusions
Health and social care services wishing to improve awareness of child safeguarding issues may benefit from looking beyond high-quality training provision. Future research should focus on service-relevant outcomes and ensure the active involvement of young people and their families/carers.
Prevalence and characteristics of ever regular use of non-combustible nicotine for 1 year or more: a population survey in England
Authors: Cox Sharon , Brown Jamie , Kock Loren , Shahab Lion 
Published: November 2021

Abstract
Introduction
Up-to-date monitoring of non-combustible nicotine products (e.g. e-cigarettes, nicotine replacement therapies (NRT), heated tobacco products (HTP); NNP) is important to assess their impact. To date, there is little evidence on the association between ever regular use (defined here as 1 year or more) of NNP and current smoking status.

Aims/methods
The purpose of this study was to examine the prevalence, and sociodemographic, alcohol and smoking status correlates, of ever regular use of NNP in England in 2020. A cross-sectional survey of adults in England was conducted between February and June 2020.

Results
A total of 8486 adults were surveyed; 94.9% (8055) were complete cases. The weighted prevalence of ever regular NNP use was 5.4% (n = 436; 95% CI 5.0–6.0), of which 82% (n = 360; 95% CI 78.7–85.8) was single and 18% (n = 79; 95% CI 14.8–22) multiple product use. Amongst ever regular NNP users, the prevalence of ever regular NRT, e-cigarette and HTP use was 64.7% (95% CI 60.1–69), 43.4% (95% CI 38.8–48) and 2.5% (95% CI 1.4–4.5), respectively. In adjusted analysis, ever regular NNP use was associated with smoking status, being significantly higher among current (22.3%; adjusted OR (aOR) 34.9, 95% CI 24.0–50.8) and ex-smokers (12.7%, aOR 19.8, 95% CI 11.1–14.4) than among never-smokers (0.6%). More advantaged occupational grade (aOR, 1.27 95% CI 1.02–1.57) and at least hazardous alcohol use (aOR, 1.38 95% CI 1.06–1.78) were associated with greater prevalence of ever regular NNP use.

Conclusions
Ever regularly using NNP was highest among smokers and ex-smokers and rare among never-smokers. Among people who have ever regularly used NNP, NRT is the most popular.
Altered expression of fragile X mental retardation-1 (FMR1) in the thymus in autoimmune myasthenia gravis
Authors: Thomas Scott , Fayet Odessa-Maud , Truffault Frédérique , Fadel Elie , Provost Bastien , Hamza Abderaouf , Berrih-Aknin Sonia , Bonnefont Jean-Paul , Le Panse Rozen 
Published: November 2021

AbstractPredisposition to autoimmunity and inflammatory disorders is observed in patients with fragile X-associated syndromes. These patients have increased numbers of CGG triplets in the 5’ UTR region of FMR1 (Fragile X Mental Retardation 1) gene, that affects its expression. FMR1 is decreased in the thymus of myasthenia gravis (MG) patients, a prototypical autoimmune disease. We thus analyzed the number of CGG triplets in FMR1 in MG, and explored the regulatory mechanisms affecting thymic FMR1 expression. We measured the number of CGGs using thymic DNA from MG and controls, but no abnormalities in CGGs were found in MG that could explain thymic decrease of FMR1. We next analyzed by RT-PCR the expression of FMR1 and its transcription factors in thymic samples, and in thymic epithelial cell cultures in response to inflammatory stimuli. In control thymuses, FMR1 expression was higher in males than females, and correlated with CTCF (CCCTC-binding factor) expression. In MG thymuses, decreased expression of FMR1 was correlated with both CTCF and MAX (Myc-associated factor X) expression. Changes in FMR1 expression were supported by western blot analyses for FMRP. In addition, we demonstrated that FMR1, CTCF and MAX expression in thymic epithelial cells was also sensitive to inflammatory signals. Our results suggest that FMR1 could play a central role in the thymus and autoimmunity. First, in relation with the higher susceptibility of females to autoimmune diseases. Second, due to the modulation of its expression by inflammatory signals that are known to be altered in MG thymuses.