bluuebunny/crossref_metadata_2025_split huggingface dataset:
A machine learning framework to determine geolocations from metagenomic profiling
Authors: Huang Lihong , Xu Canqiang , Yang Wenxian , Yu Rongshan 
Published: November 2020

Abstract
Background
Studies on metagenomic data of environmental microbial samples found that microbial communities seem to be geolocation-specific, and the microbiome abundance profile can be a differentiating feature to identify samples’ geolocations. In this paper, we present a machine learning framework to determine the geolocations from metagenomics profiling of microbial samples.

Results
Our method was applied to the multi-source microbiome data from MetaSUB (The Metagenomics and Metadesign of Subways and Urban Biomes) International Consortium for the CAMDA 2019 Metagenomic Forensics Challenge (the Challenge). The goal of the Challenge is to predict the geographical origins of mystery samples by constructing microbiome fingerprints.First, we extracted features from metagenomic abundance profiles. We then randomly split the training data into training and validation sets and trained the prediction models on the training set. Prediction performance was evaluated on the validation set. By using logistic regression with L2 normalization, the prediction accuracy of the model reaches 86%, averaged over 100 random splits of training and validation datasets.The testing data consists of samples from cities that do not occur in the training data. To predict the “mystery” cities that are not sampled before for the testing data, we first defined biological coordinates for sampled cities based on the similarity of microbial samples from them. Then we performed affine transform on the map such that the distance between cities measures their biological difference rather than geographical distance. After that, we derived the probabilities of a given testing sample from unsampled cities based on its predicted probabilities on sampled cities using Kriging interpolation. Results show that this method can successfully assign high probabilities to the true cities-of-origin of testing samples.

Conclusion
Our framework shows good performance in predicting the geographic origin of metagenomic samples for cities where training data are available. Furthermore, we demonstrate the potential of the proposed method to predict metagenomic samples’ geolocations for samples from locations that are not in the training dataset.
The Shamiri group intervention for adolescent anxiety and depression: study protocol for a randomized controlled trial of a lay-provider-delivered, school-based intervention in Kenya
Authors: Osborn Tom L. , Venturo-Conerly Katherine E. , Wasil Akash R. , Rodriguez Micaela , Roe Elizabeth , Alemu Rediet , Arango G. Susana , Gan Jenny , Wasanga Christine , Schleider Jessica L. , Weisz John R. 
Published: November 2020

Abstract
Background
Developing low-cost, socio-culturally appropriate, and scalable interventions for youth depression and anxiety symptoms in low-income regions such as countries in sub-Saharan Africa is a global mental health priority. We developed and intend to evaluate one such intervention for adolescent depression and anxiety in Kenya. The intervention, named Shamiri (a Swahili word for “thrive”), draws upon evidence-based components of brief interventions that involve nonclinical principles rather than treatment of psychopathology (e.g., growth mindset, gratitude, and virtues).

Methods
Four hundred twenty Kenyan adolescents (ages 13–18) with clinically elevated depression and/or anxiety symptoms will be randomized to either the 4-week Shamiri group intervention or a group study-skills control intervention of equal duration and dosage. Participating adolescents will meet in groups of 8–15, led by a high-school graduate trained to deliver Shamiri as a lay-provider. Adolescents will self-report primary outcome measures (depression—measured by the PHQ-8, and anxiety symptoms—measured by the GAD-7) and secondary outcome measures (perceived social support, perceived academic control, self-reported optimism and happiness, loneliness, and academic grades) at the 2-week intervention midpoint, 4-week post-intervention endpoint, and 2-week post-intervention follow-up. We predict that adolescents in the Shamiri group, when compared to the study-skills control group, will show greater improvements in primary outcomes and secondary outcomes.

Discussion
Results may suggest that a brief, lay-provider delivered, school-based intervention may reduce depression and anxiety symptoms, improving academic outcomes and other psychosocial outcomes in adolescents with clinically-elevated symptoms in sub-Saharan Africa.

Trial registration
Pan African Clinical Trials Registry PACTR201906525818462. Registered on 12 June 2019.
An automated structured education intervention based on a smartphone app in Chinese patients with type 1 diabetes: a protocol for a single-blinded randomized controlled trial
Authors: Huang Fansu , Wu Xinyin , Xie Yuting , Liu Fang , Li Juan , Li Xia , Zhou Zhiguang 
Published: November 2020

AbstractBackgroundAlthough evidence had demonstrated the effectiveness of smartphone apps in diabetes care, the majority of apps had been developed for type 2 diabetes mellitus (T2DM) patients and targeted at populations outside of China. The effects of applying a smartphone app with structured education on glycemic control in type 1 diabetes mellitus (T1DM) are unclear. A digital, culturally tailored structured education program was developed in a smartphone app (Yi tang yun qiao) to provide an automated, individualized education program aimed at improving self-management skills in patients with T1DM in China. This trial aims to investigate the effectiveness of this smartphone app among Chinese T1DM patients.Methods and analysisThis single-blinded, 24-week, parallel-group randomized controlled trial of a smartphone app versus routine care will be conducted in Changsha, China. We plan to recruit 138 patients with T1DM who will be randomly allocated into the intervention group (automated, individualized education through an app) or routine care group. The intervention will last for 24 weeks. The primary outcome will be the change in glycated hemoglobin (HbA1c) from baseline to week 24. The secondary outcomes will include time in range, fasting blood glucose, levels of serum triglycerides and cholesterol, blood pressure, body mass index, quality of life, diabetes self-care activities, diabetes self-efficacy, depression, anxiety, and patient satisfaction. Adverse events will be formally documented. Data analysis will be conducted using the intention-to-treat principle with appropriate univariate and multivariate methods. Missing data will be imputed with a multiple imputation method under the “missing at random” assumption.DiscussionThis trial will investigate the effectiveness of an app-based automated structured education intervention for Chinese patients with T1DM. If the intervention is effective, this study will provide a strategy that satisfies the need for effective lifelong diabetes care to reduce the disease burden and related complications resulting from T1DM.Trial registrationClinicalTrials.govNCT04016987. Registered on 29 October 2019.
Effect of targeted vs standard fortification of breast milk on growth and development of preterm infants (≤ 32 weeks): study protocol for a randomized controlled trial
Authors: Seliga-Siwecka Joanna , Chmielewska Anna , Jasińska Katarzyna 
Published: November 2020

Abstract
Background
Human milk is recommended for all very low birth weight infants. Breastmilk is highly variable in nutrient content, failing to meet the nutritional demands of this group. Fortification of human milk is recommended to prevent extrauterine growth retardation and associated poor neurodevelopmental outcome. However, standard fortification with fixed dose multicomponent fortifier does not account for the variability in milk composition. Targeted fortification is a promising alternative and needs further investigation.

Methods
This randomized controlled trial will recruit preterm infants (≤ 32 weeks of gestation) within the first 7 days of life. After reaching 80 ml/kg/day of enteral feeding, patients will be randomized to receive standard fortification (HMF, Nutricia) or targeted fortification (modular components: Bebilon Bialka, Nutricia—protein; Polycal, Nutricia—carbohydrates; Calogen, Nutricia—lipids). The intervention will continue until 37 weeks of post-conception age or hospital discharge. Parents and outcome assessors will be blinded to the intervention. The primary outcome measure is velocity of weight, length, and head growth until 36 weeks post-conceptional age or discharge. Secondary outcomes include neurodevelopment at 12 months assessed with Bayley Scale of Development III, repeated at 36 months; body composition at discharge and at 4 months; and incidence of necrotizing enterocolitis, sepsis, retinopathy of prematurity, and bronchopulmonary dysplasia.

Discussion
Targeted fortification has previously been shown as doable in the neonatal intensive care unit context. If it shows to improve growth and neonatal outcome, choosing the targeted fortification as a first line nutritional approach in very low birth weight infants may become a recommendation.

Trial registration
ClinicalTrials.govNCT03775785, Registered on July 2019.
UVR-sensor wearable device intervention to improve sun behaviors and reduce sunburns in melanoma survivors: study protocol of a parallel-group randomized controlled trial
Authors: Vogel Rachel I. , Nagler Rebekah H. , Ahmed Rehana L. , Brown Katherine , Luo Xianghua , Martinson Brian C. , Lazovich DeAnn 
Published: November 2020

Abstract
Background
Individuals who have been diagnosed with melanoma have more than a 9-fold increased risk of developing another melanoma. Ultraviolet radiation (UVR) exposure following a melanoma diagnosis can be modified to reduce risk of a new melanoma diagnosis. Yet research shows that many melanoma survivors do not report optimal sun protection practices. The objective of this study is to evaluate the effectiveness of a UVR-sensor wearable device to improve sun protection behaviors and reduce sunburns in a randomized controlled trial (RCT) in melanoma survivors.

Methods
We will conduct an RCT among 368 melanoma survivors in two waves (Summer 2020, Summer 2021). This approach allows for adequate recruitment of the required sample and potential improvements to recruitment, compliance, and retention strategies between waves. The intervention includes an informational brochure about sun protection behaviors and a commercially available UVR-sensor wearable device (Shade), which accurately measures UVR. The device, along with its associated mobile application, measures and stores UVR exposure. As UVR exposure accumulates, the device provides notifications to increase sun protection action. Survivors in the control group receive the device and a separate mobile application that does not provide notifications or summary UVR exposure data. Participants will be asked to wear the device for 12 weeks. They will complete surveys about their sun behaviors at study entry, every 4 weeks during the intervention, and 1 year later. At the end of the intervention period, intervention and control groups will be compared for differences in a summary measure of sun protection habits and experience of a sunburn. We will also measure self-reported physical activity, depression, and anxiety to examine potential unintended negative consequences of the intervention.

Discussion
The study intervention will be completed Fall 2021, with anticipated results available in 2022. If this intervention improves sun protection behaviors in melanoma survivors, these findings would support expanding the use of this technology with other populations at high risk for melanoma.

Trial registration
ClinicalTrials.gov NCT03927742. Registered on April 15, 2019.
Planned early delivery versus expectant management to reduce adverse pregnancy outcomes in pre-eclampsia in a low- and middle-income setting: study protocol for a randomised controlled trial (CRADLE-4 Trial)
Authors: Beardmore-Gray Alice , Vousden Nicola , Charantimath Umesh , Katageri Geetanjali , Bellad Mrutyunjaya , Kapembwa Kunda , Chinkoyo Sebastian , Vwalika Bellington , Clark Matthew , Hunter Rachael , Seed Paul , Goudar Shivaprasad , Chappell Lucy C. , Shennan Andrew 
Published: November 2020

Abstract
Background
Pre-eclampsia is a pregnancy complication characterised by high blood pressure and multi-organ dysfunction in the mother. It is a leading contributor to maternal and perinatal mortality, with 99% of these deaths occurring in low- and middle-income countries (LMIC). Whilst clear guidelines exist for management of early-onset (< 34 weeks) and term (≥ 37 weeks) disease, the optimal timing of delivery in pre-eclampsia between 34+ 0 and 36+ 6 weeks is less clear. In a high-income setting, delivery may improve maternal outcomes without detriment to the baby, but this intervention is yet to be evaluated in LMIC.

Methods
The CRADLE-4 Trial is a non-masked, randomised controlled trial comparing planned early delivery (initiation of delivery within 48 h of randomisation) with routine care (expectant management) in women with pre-eclampsia between 34+ 0 and 36+ 6 weeks’ gestation in India and Zambia. The primary objective is to establish whether a policy of planned early delivery can reduce adverse maternal outcomes, without increasing severe neonatal morbidity.

Discussion
The World Health Organization recommends delivery for all women with pre-eclampsia from 37 weeks onwards, based on evidence showing clear maternal benefit without increased neonatal risk. Before 34 weeks, watchful waiting is preferred, with delivery recommended only when there is severe maternal or fetal compromise, due to the neonatal risks associated with early preterm delivery. Currently, there is a lack of guidance for clinicians managing women with pre-eclampsia between 34+ 0 and 36+ 6 weeks. Early delivery benefits the mother but may increase the need for neonatal unit admission in the infant (albeit without serious morbidity at this gestation). On the other hand, waiting to deliver may increase the risk of stillbirth, fetal growth restriction and hypoxic brain injury in the neonate as a result of severe maternal complications. This is especially true for LMIC where there is a higher prevalence of adverse events. The balance of risks and benefits therefore needs to be carefully assessed before making firm recommendations. This is the first trial evaluating the optimal timing of delivery in pre-eclampsia in LMIC, where resources and disease burden are considerably different.

Trial registration
ISRCTN 10672137. Registered on 28 November 2019.
An investigation into the factors affecting investigator-initiated trial start-up in Ireland
Authors: Leddy Lauren , Sukumar Prasanth , O’Sullivan Lydia , Keane Fionnuala , Devane Declan , Doran Peter 
Published: November 2020

Abstract
Background
In common with many countries, Ireland has seen an increasing trend in the number of clinical trials conducted over the past few years. Yet, as elsewhere, trialists in Ireland face several problems and barriers in the starting-up of clinical trials. These barriers impede trial activity significantly, with consequent impacts on patient care. It is critical to understand these issues, to develop approaches to facilitate trial start up. This study identifies the challenges in conducting clinical trials in Ireland and specifically the contractual, ethical, logistical, and regulatory barriers that hinder the start-up of investigator-led trials in Ireland.

Methods
Data for this study were collected in two stages. In the first stage, a survey was conducted among trialists in Ireland. A total of 44 trialists responded to the survey, and information was collected about their experience in conducting clinical trials, the scale and nature of their most recently completed trial, and the details of specific barriers they encountered during the starting-up of the trial. In the second stage, nine semi-structured interviews were conducted with the awardees of 2018 Irish Health Research Board’s Definitive Intervention Feasibility Award. These interviews facilitated a deeper exploration of issues and problems in conducting clinical trials in Ireland.

Results
This study identified several issues and bottlenecks in starting-up clinical trials in Ireland with contracts and ethical approval cited as the major issues. The data shows that site identification and activation was also problematic in some cases. Several respondents reported difficulties in accessing dedicated time for protocol development and believe that support in this area can be greatly beneficial. It was reported that availability of skilled staff members like statisticians and data managers was as an issue, especially for small trials.

Conclusion
This study found that several factors impact trial initiation and progression in Ireland. Delays associated with obtaining contract and ethics approval are perceived as major barriers. Specialist supports in areas such as ethics and regulatory affairs and availability of specialised staff members in areas such as statistics and data management are key actions to enable enhanced clinical trial activity in Ireland.
Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma
Authors: Huang Hechen , Ren Zhigang , Gao Xingxing , Hu Xiaoyi , Zhou Yuan , Jiang Jianwen , Lu Haifeng , Yin Shengyong , Ji Junfang , Zhou Lin , Zheng Shusen 
Published: November 2020

Abstract
Background
The gut-liver axis plays a pivotal role in the pathogenesis of hepatocellular carcinoma (HCC). However, the correlations between the gut microbiome and the liver tumor transcriptome in patients with HCC and the impact of the gut microbiota on clinical outcome are less well-understood.

Methods
Fecal samples collected from HBV-related HCC patients (n = 113) and healthy volunteers (n = 100) were subjected to 16S rRNA sequencing of the microbiome. After a rigorous selection process, 32 paired tumor and adjacent non-tumor liver tissues from the HCC group were subjected to next-generation sequencing (NGS) RNA-seq. The datasets were analyzed individually and integrated with clinical characteristics for combined analysis using bioinformatics approaches. We further verified the potential of the gut microbiota to predict clinical outcome by a random forest model and a support vector machine model.

Results
We found that Bacteroides, Lachnospiracea incertae sedis, and Clostridium XIVa were enriched in HCC patients with a high tumor burden. By integrating the microbiome and transcriptome, we identified 31 robust associations between the above three genera and well-characterized genes, indicating possible mechanistic relationships in tumor immune microenvironment. Clinical characteristics and database analysis suggested that serum bile acids may be important communication mediators between these three genera and the host transcriptome. Finally, among these three genera, six important microbial markers associated with tumor immune microenvironment or bile acid metabolism showed the potential to predict clinical outcome (AUC = 81%).

Conclusions
This study revealed that changes in tumor immune microenvironment caused by the gut microbiota via serum bile acids may be important factors associated with tumor burden and adverse clinical outcome. Gut microbes can be used as biomarkers of clinical features and outcomes, and the microbe-associated transcripts of host tumors can partly explain how gut microbiota promotes HCC pathogenesis.
Associations of dietary inflammatory index, serum levels of MCP-1 and body composition in Iranian overweight and obese women: a cross-sectional study
Authors: Ghodoosi Nasim , Mirzababaei Atieh , Rashidbeygi Elahe , Badrooj Negin , Sajjadi Seyedeh Forough , Setayesh Leila , Yekaninejad Mir Saeed , Keshavarz Seyed Ali , Shiraseb Farideh , Mirzaei Khadijeh 
Published: November 2020

AbstractObjectiveAlthough, several studies have illustrated that there is a relation between dietary inflammatory index (DII) with obesity-related parameters, and inflammation, their results were controversial. This study aimed to investigate this relationship among Iranian women.ResultsMultivariable linear regression showed that fat mass was 0.14 kg lower in the anti-inflammatory diet group, with respect to the pro-inflammatory group, after adjusting covariates such as age, physical activity, economic and job status (β = − 0.142, 95% CI − 4.44, − 1.71,P = 0.03). Fat-free mass (FFM) was 1.5 kg more in the anti-inflammatory diet group, compared to the pro-inflammatory diet group, after adjusting for potentials cofounders (β = 1.50, 95% CI 0, 3.01, p = 0.05). Furthermore, after adjusting for potentials cofounders, it was revealed that the subjects with lower DII had lower monocyte chemoattractant protein-1 (MCP-1) levels in serum (β = − 18.81, 95% CI − 35.84, − 1.79,p = 0.03). These findings suggest an inverse and significant relationship between DII and FFM and also DII is directly related to Fat mass and the level of MCP-1. This finding can be used for developing interventions that aim to promote healthy eating to prevent inflammation and non-communicable disease development among obese females.
Combined frequency-tagging EEG and eye-tracking measures provide no support for the “excess mouth/diminished eye attention” hypothesis in autism
Authors: Vettori Sofie , Van der Donck Stephanie , Nys Jannes , Moors Pieter , Van Wesemael Tim , Steyaert Jean , Rossion Bruno , Dzhelyova Milena , Boets Bart 
Published: November 2020

Abstract
Background
Scanning faces is important for social interactions. Difficulty with the social use of eye contact constitutes one of the clinical symptoms of autism spectrum disorder (ASD). It has been suggested that individuals with ASD look less at the eyes and more at the mouth than typically developing (TD) individuals, possibly due to gaze aversion or gaze indifference. However, eye-tracking evidence for this hypothesis is mixed. While gaze patterns convey information about overt orienting processes, it is unclear how this is manifested at the neural level and how relative covert attention to the eyes and mouth of faces might be affected in ASD.

Methods
We used frequency-tagging EEG in combination with eye tracking, while participants watched fast flickering faces for 1-min stimulation sequences. The upper and lower halves of the faces were presented at 6 Hz and 7.5 Hz or vice versa in different stimulation sequences, allowing to objectively disentangle the neural saliency of the eyes versus mouth region of a perceived face. We tested 21 boys with ASD (8–12 years old) and 21 TD control boys, matched for age and IQ.

Results
Both groups looked longer at the eyes than the mouth, without any group difference in relative fixation duration to these features. TD boys looked significantly more to the nose, while the ASD boys looked more outside the face. EEG neural saliency data partly followed this pattern: neural responses to the upper or lower face half were not different between groups, but in the TD group, neural responses to the lower face halves were larger than responses to the upper part. Face exploration dynamics showed that TD individuals mostly maintained fixations within the same facial region, whereas individuals with ASD switched more often between the face parts.

Limitations
Replication in large and independent samples may be needed to validate exploratory results.

Conclusions
Combined eye-tracking and frequency-tagged neural responses show no support for the excess mouth/diminished eye gaze hypothesis in ASD. The more exploratory face scanning style observed in ASD might be related to their increased feature-based face processing style.