bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families
Authors: Wang Yan , Shi Qiang , Yang Pengshuo , Zhang Chengxin , Mortuza S. M. , Xue Zhidong , Ning Kang , Zhang Yang 
Published: November 2019

Abstract

Introduction
The ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, we explore new applications of oceanic metagenomes for protein structure and function prediction.

Results
By processing 1.3 TB of high-quality reads from the Tara Oceans data, we obtain 97 million non-redundant genes. Of the 5721 Pfam families that lack experimental structures, 2801 have at least one member associated with the oceanic metagenomics dataset. We apply C-QUARK, a deep-learning contact-guided ab initio structure prediction pipeline, to model 27 families, where 20 are predicted to have a reliable fold with estimated template modeling score (TM-score) at least 0.5. Detailed analyses reveal that the abundance of microbial genera in the ocean is highly correlated to the frequency of occurrence in the modeled Pfam families, suggesting the significant role of the Tara Oceans genomes in the contact-map prediction and subsequent ab initio folding simulations. Of interesting note, PF15461, which has a majority of members coming from ocean-related bacteria, is identified as an important photosynthetic protein by structure-based function annotations. The pipeline is extended to a set of 417 Pfam families, built on the combination of Tara with other metagenomics datasets, which results in 235 families with an estimated TM-score over 0.5.

Conclusions
These results demonstrate a new avenue to improve the capacity of protein structure and function modeling through marine metagenomics, especially for difficult proteins with few homologous sequences.
Advanced platelet-rich fibrin plus gold nanoparticles enhanced the osteogenic capacity of human mesenchymal stem cells
Authors: Ghaznavi Dara , Babaloo Amirreza , Shirmohammadi Adileh , Zamani Arezoo Rezaie Nezhad , Azizi Mehdi , Rahbarghazi Reza , Ghaznavi Aisan 
Published: November 2019

Abstract

Objectives
There is still insufficient clinical evidence of platelet-rich fibrin beneficial effects on bone regeneration. Gold nanoparticles have been shown to enhance osteogenic differentiation and bone mineralization. The purpose of this study was to investigate the effect of advanced-platelet-rich fibrin modified by gold nanoparticles on the osteoblastic differentiation of human mesenchymal stem cells.

Results
MTT assay revealed 0.0125 mM gold nanoparticles had no cytotoxic effects on stem cells after 7 days. The addition of 0.0125 mM gold nanoparticle to advanced-platelet-rich fibrin clot increased cell viability compared to the non-treated control group (p < 0.05). 7-day incubation of stem cells with advanced-platelet-rich fibrin modified by gold nanoparticles conditioned media was shown to promote alkaline phosphatase activity compared to the control cells and group treated with advanced-platelet-rich fibrin condition media (p < 0.05). By using Alizarin Red S staining, red-colored calcium deposits were observed in the group treated with advanced-platelet-rich fibrin and gold nanoparticles conditioned media in comparison with non-treated cells (p < 0.05). Advanced-platelet-rich fibrin conditioned medium was unable to promote calcium deposition compared to the combination of advanced-platelet-rich fibrin and gold nanoparticles (p < 0.05). Adding gold nanoparticles to advanced-platelet-rich fibrin and fibrin and platelet byproducts could be an alternative strategy to improve osteogenic capacity of stem cells.
Direct conversion of human fibroblast to hepatocytes using a single inducible polycistronic vector
Authors: Ballester Maria , Bolonio Miguel , Santamaria Ramon , Castell José V. , Ribes-Koninckx Carmen , Bort Roque 
Published: November 2019

Abstract

Background
Human fibroblasts can be reprogrammed into induced hepatocyte-like cells through the expression of a set of transcription factors. Although the generation of induced hepatocyte-like cells by HNF4A, HNF1A, and FOXA3 expression has proven to be a robust experimental strategy, using multiple lentivirus results in a highly variable heterogeneous population.

Methods
We designed and implemented a novel approach based on the delivery of reprogramming factors and green fluorescent protein in a single doxycycline-inducible lentiviral vector using 2A self-cleaving peptides.

Results
Fibroblasts infected with the lentiviral vector can be amplified in basic fibroblast culture media in the absence of doxycycline without induction of hepatic genes. Upon switching to hepatic maturation media containing doxycycline, cells stop proliferating, activate hepatic gene transcription, and perform metabolic functions characteristic of hepatocytes.

Conclusion
Our strategy can generate an unlimited source of homogeneously induced hepatocyte-like cells from different genetic background donors, capable of performing typical hepatic functions suitable for drug research and other in vitro applications.
The impact of hepatocyte nuclear factor-1α on liver malignancies and cell stemness with metabolic consequences
Authors: Wang Xue , Hassan Waseem , Zhao Jing , Bakht Sahar , Nie Yunjuan , Wang Ying , Pang Qingfeng , Huang Zhaohui 
Published: November 2019

AbstractHepatocyte nuclear factor-1 alpha (HNF-1α) is a transcription factor expressed predominantly in the liver among other organs. Structurally, it contains POU-homeodomain that binds to DNA and form proteins that help in maintaining cellular homeostasis, controlling metabolism, and differentiating cell lineages. Scientific research over the period of three decades has reported it as an important player in various liver malignancies such as hepatocellular cancers (HCCs), hepatocellular adenoma (HA), and a more specific HNF-1α-inactivated human hepatocellular adenoma (H-HCAs). Abundant clinical and rodent data have noted the downregulation of HNF-1α in parallel with liver malignancies. It is also interesting to notice that the co-occurrence of mutated HNF-1α expression and hepatic carcinomas transpires typically along with metabolic repercussion. Moreover, scientific data implies that HNF-1α exerts its effects on cell stemness and hence can indirectly impact liver malignancies and metabolic functioning. The effects of HNF-1α on cell stemness present a future opportunity to explore a possible and potential breakthrough. Although the mechanism through which inactivated HNF-1α leads to hepatic malignancies remain largely obscure, several key signal molecules or pathways, including TNF-α, SHP-1, CDH17, SIRT, and MIA-2, have been reported to take part in the regulations of HNF-1α. It can be concluded from the present scientific data that HNF-1α has a great potential to serve as a target for liver malignancies and cell stemness.
Protocol for a systematic review of the use of qualitative comparative analysis for evaluative questions in public health research
Authors: Hanckel Benjamin , Petticrew Mark , Thomas James , Green Judith 
Published: November 2019

Abstract

Background
There is an increasing recognition that health intervention research requires methods and approaches that can engage with the complexity of systems, interventions, and the relations between systems and interventions. One approach which shows promise to this end is qualitative comparative analysis (QCA), which examines casual complexity across a medium to large number of cases (between 10 and 60+), whilst also being able to generalise across those cases. Increasingly, QCA is being adopted in public health intervention research. However, there is a limited understanding of how it is being adopted. This systematic review will address this gap, examining how it is being used to understand complex causation; for what settings, populations and interventions; and with which datasets to describe cases.

Methods
We will include published and peer-reviewed studies of any public health intervention where the effects on population health, health equity, or intervention uptake are being evaluated. Electronic searches of PubMed, Scopus, Web of Science (incorporating Social Sciences Citation Index and Arts & Humanities Citation Index), Microsoft Academic, and Google Scholar will be performed. This will be supplemented with reference citation tracking and personal contact with experts to identify any additional published studies. Search results will be single screened, with machine learning used to check these results, acting as a ‘second screener’. Any disagreement will be resolved through discussion. Data will be extracted from full texts of eligible studies, which will be assessed against inclusion criteria, and synthesised narratively, using thematic synthesis methods.

Discussion
This systematic review will provide an important map of the increasing use of QCA in public health intervention literature. This review will identify the current scope of research in this area, as well as assessing claims about the utility of the method for addressing complex causation in public health research. We will identify implications for better reporting of QCA methods in public health research and for reporting of case studies such that they can be used in future QCA studies.

Systematic review registration
PROSPERO, CRD42019131910
Clinical significance of premature ventricular contraction among adult patients: protocol for a scoping review
Authors: Suba Sukardi , Pelter Michele M. 
Published: November 2019

Abstract

Background
Premature ventricular contractions (PVCs) are one of the most common arrhythmias detected from electrocardiographic (ECG) monitoring. PVCs were thought to cause lethal arrhythmias and thus were closely monitored and treated. However, in current practice, PVCs generally do not required treatment. There is also concern that PVCs contribute to excessive alarms and lead to alarm fatigue. Practice guidelines for in-hospital monitoring state that monitoring for PVCs may be indicated on some patients but do not recommend continuous ECG monitoring. Despite these recommendations, PVC monitoring practices remain part of routine care, especially in the intensive care unit, for worry of missing potentially significant arrhythmia events. A thorough scoping review of the literature regarding the clinical significance of PVC is imperative, precisely to map out the evidence on the diagnostic and prognostic values of PVCs and to identify research gaps on this issue.

Methods
The primary question of this review is “what is the clinical significance of PVCs in adults?” Preparation of this scoping review will use the PRISMA-P statement. A scoping review framework by Arksey and O’Malley will be adopted. In identifying relevant studies, the Population-Concept-Context (PCC) framework by the Joanna Briggs Institute will be used. A search strategy will be developed, and four major electronic databases will be searched: CINAHL, Embase, PubMed, and Web of Science Core Collection. Manual searches will also be conducted. The study selection process will adopt the 2009 PRISMA flow diagram. EndNote X8 will be used to manage citations, as well as for duplicates screening in addition to Microsoft Excel 2016. Two independent reviewers will assess potential studies in detail against inclusion criteria. A standardized data extraction form will be developed. Finally, critical appraisal will be conducted using a tool adapted from the Quality Appraisal Checklist by the National Institute for Health Care Excellence (NICE).

Discussion
We believe this scoping review will provide a general foundation of evidence on the potential significance of PVCs concerning its diagnostic and prognostic value among the adult patient population. The findings will allow us to map out research gaps on this topic that could shape future research and ultimately clinical practice.

Scoping review registration
This scoping review has been registered in the Open Science Framework (OSF), DOI: https://doi.org/10.17605/OSF.IO/GAVT2.
The effects of cell therapy on seizures in animal models of epilepsy: protocol for systematic review and meta-analysis of preclinical studies
Authors: Dvir Naomi , Javaid Muhammad S. , Jones Nigel C. , Powell Kim L. , Kwan Patrick , O’Brien Terence J. , Antonic-Baker Ana 
Published: November 2019

AbstractBackgroundEpilepsy is one of the most common and serious brain conditions, characterised by recurrent unprovoked seizures. It affects about 1% of the population worldwide. Despite a range of antiepileptic drugs being available, one third of the patients do not achieve adequate seizure control. Only a minority of these patients may be suitable to undergo surgical resection of the seizure focus, but this is an invasive and not always successful procedure. There is an urgent need to develop more effective treatment options for uncontrolled seizures. With the recent advances in regenerative and translational medicine, cell therapies could prove to be beneficial. Here we describe the protocol for a proposed systematic review and meta-analysis to assess the effects for cell transplantation in animal models of epilepsy.MethodsWe will include all preclinical animal models of epilepsy that evaluate the effects of cell transplantation compared to the untreated control. The primary outcome will be the change in frequency and duration of seizures from baseline measured by video electroencephalography (EEG). The secondary outcomes will include histological and neurobehavioural assessments. We will perform an electronic search of MEDLINE via PubMed, Web of Science, and EMBASE. Search results will be screened independently by two reviewers and confirmed by a third reviewer. Data from eligible studies will be extracted and pooled, and the summary estimate of effect size will be calculated using DerSimonian and Laird random effects meta-analysis. Heterogeneity will be explored using sub-group meta-analysis, and meta-regression risk of bias will be assessed by using the CAMARADES checklist for study quality tool.DiscussionThe purpose of this systematic review is to assess and summarise the existing literature in the field of cell transplantation as a treatment for epilepsy in animal models. Efficacy will be measured by evaluating the reduction in seizure intervals, number, and duration, within animal models of epilepsy. Analysis of the existing literature will mark the achievement made in the field and locate the existing gaps, a process that will aid in the search for the next needed step.Systematic review registrationCRD42018103628
Health outcomes of iron supplementation and/or food fortification in iron-replete children aged 4–24 months: protocol for a systematic review and meta-analysis
Authors: Hare Dominic J. , Braat Sabine , Cardoso Bárbara R. , Morgan Christopher , Szymlek-Gay Ewa A. , Biggs Beverley-Ann 
Published: November 2019

Abstract

Background
Direct supplementation or food fortification with iron are two public health initiatives intended to reduce the prevalence of iron deficiency (ID) and iron deficiency anaemia (IDA) in 4–24-month-old infants. In most high-income countries where IDA prevalence is < 15%, the recommended daily intake levels of iron from supplements and/or consumption of fortified food products are at odds with World Health Organisation (WHO) guidelines that recommend shorter-term (3 months/year) supplementation only in populations with IDA prevalence > 40%. Emerging concerns about delayed neurological effects of early-life iron overexposure have raised questions as to whether recommended guidelines in high-income countries are unnecessarily excessive. This systematic review will gather evidence from supplementation/fortification trials, comparing health outcomes in studies where iron-replete children did or did not receive additional dietary iron; and determine if replete children at study outset were not receiving additional iron show changes in haematological indices of ID/IDA over the trial duration.

Methods
We will perform a systematic review of the literature, including all studies of iron supplementation and/or fortification, including study arms with confirmed iron-replete infants at the commencement of the trial. This includes both dietary iron intervention or placebo/average dietary intakes. One reviewer will conduct searches in electronic databases of published and ongoing trials (Medline, Web of Science, Scopus, CENTRAL, EBSCO [e.g. CINAHL Complete, Food Science and Technology Abstracts], Embase, ClinicalTrials.gov, ClinicalTrialsRegister.eu and who.it/trialsearch), digital theses and dissertations (WorldCat, Networked Digital Library of Theses and Dissertations, DART-Europe E-theses Portal, Australasian Digital Theses Program, Theses Canada Portal and ProQuest). For eligible studies, one reviewer will use a data extraction form, and a second reviewing entered data for accuracy. Both reviewers will independently perform quality assessments before qualitative and, if appropriate, quantitative synthesis as a meta-analysis. We will resolve any discrepancies through discussion or consult a third author to resolve discrepancies. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement will be used as the basis for reporting.

Discussion
Recommended iron supplementation and food fortification practices in high-income countries have been criticised for being both excessive and based on outdated or underpowered studies. This systematic review will build a case for revisiting iron intake guidelines for infants through the design of new trials where health effects of additional iron intake in iron-replete infants are the primary outcome.

Systematic review registration
PROSPERO CRD42018093744.
Associations between self-reported diabetes mellitus, disordered eating behaviours, weight/shape overvaluation, and health-related quality of life
Authors: Dias Santana Danilo , Mitchison Deborah , Gonzalez-Chica David , Touyz Stephen , Stocks Nigel , Appolinario Jose Carlos , da Veiga Gloria Valeria , Hay Phillipa 
Published: November 2019

Abstract

Background
Eating disorders (ED) and disordered eating behaviours (DEB) have been found to be common in people with diabetes mellitus (DM). However, findings have been inconsistent.

Objective
This study investigated the association between self-reported diabetes (Type 1 or 2) with ED/DEB (binge eating, subjective binge eating or loss of control overeating, severe dieting and purging) weight/shape overvaluation, and health-related quality of life (HRQoL) in a household survey in South Australia.

Method
In 2017 2977 people aged ≥15 years, who were representative of the general population, were interviewed. Participants reported their gender, age, household income, highest educational attainment, area of residence, presence of DM, ED/DEB, level of overvaluation, current HRQoL and height and weight. For the analyses between ED/DEB, self-reported DM and HRQoL, a grouping variable was created: 1) people without ED/DEB or self-reported DM; 2) people without ED/DEB and with self-reported DM; 3) people with ED/DEB and without self-reported DM; and 4) people with ED/DEB and self-reported DM. Analyses were stratified by sex and age group.

Results
Subjective binge eating prevalence was higher in people with self-reported DM (6.6% vs 2.8%, p = 0.016), and overvaluation was lower in those with DM (36% vs 43.8%, p = 0.007). In analyses stratified by sex and age group, subjective binge eating was higher in women and in people over 45 years with self-reported DM and overvaluation was lower in men and in people over 45 years with self-reported DM. However, these differences were not significant on tests of gender and age interaction. People in both DM groups scored significantly lower than people without DM groups on physical HRQoL. In contrast, people in both ED/DEB groups scored lower than people without ED/BEB on mental HRQoL.

Conclusion
People with self-reported DM had a higher prevalence of subjective binge eating, a lower prevalence of overvaluation and there were no significant effects of age or gender. Furthermore, participants with self-reported DM and comorbid ED or DEB had impairments of both mental and physical HRQoL. Assessing an individual’s sense of control over eating along with other DEB is likely important for identification of these mental health problems.
Dynamic single-slice CT estimates whole-lung dual-energy CT variables in pigs with and without experimental lung injury
Authors: Cronin John N. , Borges João Batista , Crockett Douglas C. , Farmery Andrew D. , Hedenstierna Göran , Larsson Anders , Tran Minh C. , Camporota Luigi , Formenti Federico 
Published: November 2019

Abstract

Background
Dynamic single-slice CT (dCT) is increasingly used to examine the intra-tidal, physiological variation in aeration and lung density in experimental lung injury. The ability of dCT to predict whole-lung values is unclear, especially for dual-energy CT (DECT) variables. Additionally, the effect of inspiration-related lung movement on CT variables has not yet been quantified.

Methods
Eight domestic pigs were studied under general anaesthesia, including four following saline-lavage surfactant depletion (lung injury model). DECT, dCT and whole-lung images were collected at 12 ventilatory settings. Whole-lung single energy scans images were collected during expiratory and inspiratory apnoeas at positive end-expiratory pressures from 0 to 20 cmH2O. Means and distributions of CT variables were calculated for both dCT and whole-lung images. The cranio-caudal displacement of the anatomical slice was measured from whole-lung images.

Results
Mean CT density and volume fractions of soft tissue, gas, iodinated blood, atelectasis, poor aeration, normal aeration and overdistension correlated between dCT and the whole lung (r2 0.75–0.94) with agreement between CT density distributions (r 0.89–0.97). Inspiration increased the matching between dCT and whole-lung values and was associated with a movement of 32% (SD 15%) of the imaged slice out of the scanner field-of-view. This effect introduced an artefactual increase in dCT mean CT density during inspiration, opposite to that caused by the underlying physiology.

Conclusions
Overall, dCT closely approximates whole-lung aeration and density. This approximation is improved by inspiration where a decrease in CT density and atelectasis can be interpreted as physiological rather than artefactual.