bluuebunny/crossref_metadata_2025_split huggingface dataset:
VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences
Authors: Kieft Kristopher , Zhou Zhichao , Anantharaman Karthik 
Published: December 2019

Abstract
Background Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and assessing their metabolic impacts on microbiomes. Design Here we present VIBRANT, the first method to utilize a hybrid machine learning and protein similarity approach that is not reliant on sequence features for automated recovery and annotation of viruses, determination of genome quality and completeness, and characterization of virome function from metagenomic assemblies. VIBRANT uses neural networks of protein signatures and a novel v-score metric that circumvents traditional boundaries to maximize identification of lytic viral genomes and integrated proviruses, including highly diverse viruses. VIBRANT highlights viral auxiliary metabolic genes and metabolic pathways, thereby serving as a user-friendly platform for evaluating virome function. VIBRANT was trained and validated on reference virus datasets as well as microbiome and virome data. Results VIBRANT showed superior performance in recovering higher quality viruses and concurrently reduced the false identification of non-viral genome fragments in comparison to other virus identification programs, specifically VirSorter and VirFinder. When applied to 120,834 metagenomically derived viral sequences representing several human and natural environments, VIBRANT recovered an average of 94.5% of the viruses, whereas VirFinder and VirSorter achieved less powerful performance, averaging 48.1% and 56.0%, respectively. Similarly, VIBRANT identified more total viral sequence and proteins when applied to real metagenomes. When compared to PHASTER and Prophage Hunter for the ability to extract integrated provirus regions from host scaffolds, VIBRANT performed comparably and even identified proviruses that the other programs did not. To demonstrate applications of VIBRANT, we studied viromes associated with Crohn’s Disease to show that specific viral groups, namely Enterobacteriales-like viruses, as well as putative dysbiosis associated viral proteins are more abundant compared to healthy individuals, providing a possible viral link to maintenance of diseased states. Conclusions The ability to accurately recover viruses and explore viral impacts on microbial community metabolism will greatly advance our understanding of microbiomes, host-microbe interactions and ecosystem dynamics.
Health Facility Capacity to Provide Postabortion Care in Afghanistan: A Cross-Sectional Study
Authors: Maruf Farzana , Tappis Hannah , Lu Enriquito , Yaqubi Ghutai Sadeq , Stekelenburg Jelle , Akker Thomas van den 
Published: December 2019

Abstract
Background: Afghanistan has one of the highest burdens of maternal mortality in the world, estimated at 638 deaths per 100,000 live births, Infections, obstetric hemorrhage, and unsafe abortion are the three leading causes. Contraceptive prevalence rate has fluctuated between 10–20% since 2006. The 2016 Afghanistan National Maternal and Newborn Health Quality of Care Assessment evaluated health facilities’ capacity to provide postabortion care, and skilled birth attendants’ knowledge and perceptions. Methods: Accessible public health facilities with at least five births per day on average (n = 77), a nationally representative sample of public health facilities with fewer than five births per day (n = 149), and 20 purposively selected private health facilities were assessed. Data collection methods for provision included a facility inventory and record review tool to verify drug, supply, equipment, and facility record availability, and an interview tool to collect information on skilled birth attendants’ knowledge and perceptions.Results: Most facilities had supplies, equipment, and drugs to manage postabortion care, including family planning counseling and services provision. At public facilities, 36% of skilled birth attendants asked to name essential actions to address abortion complications mentioned manual vacuum aspiration (23% at private facilities); fewer than one-quarter mentioned counseling. When asked what information should be given to postabortion clients, 73% described family planning counseling need (70% at private facilities). Seventy percent of public facilities expected to provide basic emergency obstetric and newborn care had functional manual vacuum aspiration supplies in the delivery room. More than 80% of public health facilities had male condoms, oral contraceptive pills, intrauterine devices, and injectables. Conclusions: This study provides evidence that there is room for improvement in postabortion care services provision in Afghanistan health facilities. Access to high-quality postabortion care needs additional investments to improve providers’ knowledge and practice, and availability of supplies.
Diabetes&nbsp;and&nbsp;HIV:&nbsp;Protocol&nbsp;for&nbsp;a&nbsp;Systematic&nbsp;Review
Authors: Umar David Mohammed , Naidoo Panjasaram 
Published: December 2019

Abstract
Background: The HIV/AIDS challenge continues to affect millions of people worldwide. Over 77 million cases of people infected have been recorded and over 35 million of these have died. Due to availability of effective anti-retroviral therapy in the recent years, mortality due to AID-related illness has been declining; resulting in PLWH living longer. This increase in longevity, along with the adverse effects of some anti-retroviral medications has led to an increase in developing chronic diseases that are age-related, such as diabetes among PLWHIV. This makes is important to embark on a systematic review of literatures to establish the magnitude and the impact of diabetes in PLWH, hence this study.Method: Guided by the PRISMA-P 2015 checklist, a mapping of evidence from studies that are related in peer-reviewed journals that were published from 2000 to 2019 globally will be done. An electronic keyword search of Pubmed, Medline, PsycInfo and EMBASE databases will be carried out. A title screening will be followed by an independent screening of the abstracts and full texts by two reviewers. Any study that is concerned with the prevalence and/or incidence of diabetes among adults (18 years or older) persons living with HIV (PLWH), risk factors of diabetes among PLWH will also be considered. The data will be analyzed using the meta () command R software version 3.6.1Discussion: This review will chart an evidence in the literature of prevalence and incidence of diabetes among PLWH, risk factors of diabetes among PLWH and compare it with the prevalence, incidence and risk factors of diabetes among the general populace.
MRI Characteristics in Acute Ischemic Stroke Patients with Preceding Direct Oral Anticoagulant Therapy as compared to Vitamin K Antagonists
Authors: Meinel Thomas , Kaesmacher Johannes , Gralla Jan , Seiffge David Julian , Auer Elias , Frey Sebastién , El-Koussy Marwan , Arnold Marcel , Fischer Urs , Göldlin Martina , Jung Simon , Hakim Arsany 
Published: December 2019

Abstract
Background: Despite the utility of neuroimaging in the diagnostic and therapeutic management of patients with acute ischemic stroke (AIS), imaging characteristics in patients with preceding direct oral anticoagulants (DOAC) compared to vitamin K antagonists (VKA) have hardly been described. We aimed to determine presence of large vessel occlusion (LVO), thrombus length, infarction diameter, and occurrence of hemorrhagic transformation in AIS patients with preceding DOAC as compared to VKA therapy. Methods: Using a prospectively collected cohort of AIS patients, we performed univariate and multivariable regression analyses regarding imaging outcomes. Additionally, we provide a sensitivity analysis for the subgroup of patients with confirmed therapeutic anticoagulation. Results: We included AIS in patients with preceding DOAC (N=75) and VKA (N=61) therapy, median age 79 (IQR 70 – 83), 39% female. Presence of any LVO between DOAC and VKA patients (29.3% versus 37.7%, P=0.361), and target LVO for endovascular therapy (26.7% versus 27.9%, P=1.0) was equal with a similar occlusion pattern. DOAC as compared to VKA were associated with a similar rate of target LVO for EVT (aOR 0.835, 95% CI 0.368 – 1.898). The presence of multiple lesions and characteristics of the thrombus were similar in DOAC and VKA patients. Acute ischemic lesion diameter in real world patients was equal in patients taking DOAC as compared to VKA. Lesion diameter in VKA patients (median 13 mm, IQR 6 – 26 versus median 20 mm, IQR 7 – 36, P=0.001), but not DOAC patients was smaller in the setting of confirmed therapeutic VKA. The frequency of radiological hemorrhagic transformation and symptomatic intracranial hemorrhage in OAC patients was low. Sensitivity analysis considering only patients with confirmed therapeutic anticoagulation did not change any of the results. Conclusion: Preceding DOAC treatment showed equal rates of LVO and infarct size as compared to VKA in AIS patients. This study adds to the knowledge of imaging findings in AIS patients with preceding anticoagulation.
The influence of immediately loaded basal implant treatment on patient satisfaction
Authors: Awadalkreem Fadia , Khalifa Nadia , Satti Asim , Suleiman Ahmed Mohamed 
Published: December 2019

Abstract
Background: Improving patient satisfaction and quality of life is of great importance when considering the different prosthetic treatment options for patients with severely resorbed residual alveolar ridges. We aimed to evaluate and compare patients’ satisfaction when changing from fixed, removable, and/or conventional implant prostheses to basal implant-supported prostheses. Methods : Sixty patients with a history of fixed, removable, and/or conventional implant prostheses who received basal implant-supported prostheses (BCS Ò , IHDE Implant System) were included in this study. Direct interviews were conducted using a four-section questionnaire that covered sociodemographic data, clinical examination, information on previous prostheses, and new implant information. The obtained data were statistically analysed using a Wilcoxon signed-rank test and chi-square test. Results: Patients were predominantly female, partially edentulous, and aged between 40 and 59 years. Patients’ general satisfaction with basal implants was very high (7.7 out of 8). Patients’ satisfaction with comfort, mastication, speech, and aesthetics significantly improved with the new basal implants. Males aged between 40 and 59 years and patients who had previously used both fixed and removable prostheses were generally the most satisfied. Although some patients had complaints, they still had high satisfaction and would choose the same treatment modality again. Conclusions: Basal implant-supported prostheses have a positive impact on oral health and highly increase patients’ satisfaction.
Diabetics’ self-care practice and its determinants among Adult diabetic patients in Ethiopia: A systematic review and meta-analysis.
Authors: Yehualashet Fikadu Ambaw , Takele Wuber Worku , Tegegne Eleni Tesfaye , Ayele Amare Demsie 
Published: December 2019

Abstract
Background: Appropriate diabetic self-care is indispensable to prevent and limit diabetic associated short and long term complications including death. Therefore, this comprehensive systematic review and meta-analysis were aimed at exploring and determining the pooled national percentage of diabetic self-care and its determinants among adult diabetic patients in Ethiopian. Methods: Different electronic databases including PubMed/Medline and search engines such as Google scholar were used to retrieve published studies. The Joanna Briggs Institute (JBI) quality appraisal checklists were used to appraise the quality of studies. Data were extracted using excel spreadsheets and analyses were done by STATA 14. Heterogeneity among studies was diagnosed using the I2. The DerSimonian and Laird random-effects model was employed for substantial heterogeneity (I2>50%). Sensitivity and subgroup analyses were carried out. The funnel plot and Egger’s regression test was used to identify publication bias. Moreover, the nonparametric trim and fill analysis was done for findings with significant Egger’s test (p<0.05) and asymmetric distribution of studies in the funnel plot. The pooled estimate of diabetic self-care and odds ratio was reported based on the 95% CI. Results: Well over half of the Ethiopian diabetic patients have good self-care 54.04% (47.07-61.01, I2 =97.3, P<0.001). Subgroup analysis showed that the highest and the lowest pooled estimate of self-care was detected in Southern Nations Nationalities and Peoples and Hareri region with 81.96% and 44.53% respectively. Being knowledgeable about diabetes mellitus 2.69%, having good social support 2.25%, owning private glucometer 3.04%, and being urban residents 3.26% have promoted diabetic victims to apply self-care practice. Conclusions: Despite the life-threatening complications of diabetes mellitus, the percentage of patients applying self-care has remained low in Ethiopia, depicting the high proportion of diabetic patients are prone to develop long and short term life-threatening consequences of diabetes mellitus. Therefore, improving the client’s awareness about the disease and counseling clients about the significance of social support are believed to be possible strategies to improve self-care practice and policymakers are strongly recommended to combat diabetic associated complications to attain sustainable development goal 3.4 aims to reduce premature death.
Social and Economic Variables Related with Paraquat Self-Poisoning: an Ecological Study
Authors: Buendia Jefferson , Chavarriaga Gabriel Jaime Restrepo , Zuluaga Andres F. 
Published: December 2019

Abstract
Background Paraquat self-poisonings constitute a significant contributor to the global burden of suicide.Our aim was to evaluate the relationship between social and economic variables with the incidence of self-poisoning with Paraquat in the northeast of Colombia.Methods Records of 154 cases of self-poisoning with Paraquat and several socio-economic variables of six regions of northeast of Colombia were analyzed. Results Most of the cases were mestizos, farmworkers, between 20 and 29 years, with intentional exposure using the oral route. Multivariate analyses revealed significant associations among the incidence of self-poisoning with PQ with the ecological factors such as poverty greater than 30% (IRR 15.9 IC95% 5.56-44.72), land Gini index <0.7 (IRR 7.11 IC95% 3.58-14.12), private health insurance <40% (IRR 3.39 IC95% 1.30-8.82) and planted area >10% (IRR 2.47 IC95% 1.60-3.80).Conclusion There is a relationship between ecological factors and, as such, this study opens the way to further developments in the field.
Hotspots of unimproved sources of drinking water in Ethiopia: Mapping and Spatial analysis of Ethiopia Demographic and Health Survey Data 2016
Authors: Bogale Getahun Gebre 
Published: December 2019

Abstract
Background: More than 35% of Ethiopian population is using drinking water from unimproved sources. As per the United Nations’ Sustainable Development Goals, Ethiopia is aspiring to achieve universal and equitable access to safe and affordable drinking water for all by 2030. For these goals to be accomplished, it is important to map the country’s hotspot areas of unimproved source of drinking-water so that resource allocation and disease control can be optimized there. Methods: A population based cross-sectional study was conducted in Ethiopia from January 18 to June 27, 2016. Data were collected from 10,064 households using a pretested and structured questionnaire. A stratified two-stage cluster sampling was employed where the enumeration areas were primary sampling units and households were secondary sampling units. Systematic sampling with probability proportional to size was employed to select samples. Data were cleaned in spreadsheet and entered in to SaTScan and ArcGIS soft-wares for mapping and analysis. The Global Moran’s I and spatial scan statistical tests (Bernoulli model) were done to explore the presence of clustering in the study area and local spatial clusters (hotspots) of unimproved sources of drinking water using ArcGIS version 10.3 and Kuldorff’s SaTScan version 9.4 soft-wares, respectively. Moran’s I value closer to +1 declared presence of clustering at national level and Log-Likelihood ratio (LLR) greater than the critical value with p<0.05 declared statistical significant hotspots across the regions. Results: In this study, unimproved sources of drinking water were spatially clustered at the study area (Moran’s I: 0.35, p<0.05). A total of 143 significant clusters were identified. Of which, eight were most likely (primary) clusters and the rest 135 were secondary clusters. The first spatial window which contains primary clusters was located in Amhara and Afar regions (LLR: 78.89, at p<0.001). The rest 33 spatial windows which contain secondary clusters were found in all regions, except Gambela region and Addis Abeba city administration (with a range of LLR: 10.09-78.89, p<0.001). Conclusions: This study identified non-random clusters and hot spots of unimproved sources of drinking water. Therefore, the result helps decision makers for their geographical interventions to combat problems related to hotspots.
Appetite Reducing Herbal Drugs from the Perspective of Avicenna and Aghili in Iranian Traditional Medicine (Persian medicine)
Authors: Parsa Elham , Mokaberinejad Roshanak , Khodadoost Mahmood , Zareiyan Armin , Mojahedi Morteza , Yaghmaei Farideh , Jafari Parisa , Hakimi Fatemeh 
Published: December 2019

:
The increasing prevalence of obesity is one of the major problems of today's society. Man
needs food to continue living, daily activities, and even the metabolism of food; and appetite plays an
important role in receiving foods. Appetite and weight reducing synthetic drugs, which are mostly
costly and have significant side effects, are recommended for some patients, and have limited
effectiveness in the treatment of obesity. Given the epidemic of obesity and the lack of satisfaction
with synthetic drugs these days, people are more likely to use herbal medicines. Complementary
medicine has always been considered for the choice of new treatment. This medicine has a long
history. Persian Medicine is one of the traditional medicine systems.

:
This study was a qualitative study on the Books of Canon and the Makhzan Al-Aladvia.

:
Saffron has been introduced in both modern medicine and in Iranian medicine to reduce appetite.

:
In the case of Purslane seed and Chio nut, Figs, Sesame seeds, Camphor, and Solomon's seal, and
Opium poppy, which have been appetite suppressant in traditional medicine books, in the books and
articles of modern medicine, they have not proved to be appetite reducing. Modern medicine has
known Gourd as a weight reducing food with the effects on fat but there is no talk about its effects on
appetite. According to traditional Iranian medicine, Chio nut causes anorexia due to weakness in the
stomach. Therefore, it is not advisable for weight loss. More clinical studies are conducted to prove
the effects of appetite suppressant and weight loss effects of these herbal medicines seem logical.
Effects of N-acetylcysteine on Pulmonary Functions in Patients with Systemic Sclerosis: A Randomized Double Blind, Placebo Controlled Study
Authors: Mehrabi Samrad , Moradi Maryam M. , Khodamoradi Zohre , Nazarinia Mohammad A. 
Published: December 2019

Background:Systemic sclerosis (SSc) is a systematic and rare autoimmune disease that affects many organs. N-acetylcysteine (NAC), thiol-containing compound, can act both as the precursor of reduced glutathione and direct scavenger of reactive oxygen species.Objective:We assessed the clinical effect of NAC on the pulmonary function test of patients with diffuse scleroderma.Methods:This study is a randomized double-blind clinical trial that was done on 25 patients with diffuse SSc without lung involvement on primary chest high-resolution computed tomography. Placebo was administered for 13 patients and 1200 milligram NAC for 12 patients. Body plethysmography parameters were assessed at the beginning of the study and after 24 weeks.Results:Patients in the two groups were matched in the basic demographic data like age, duration of disease, and modified Rodnan skin score. The analysis showed no significant differences in parameters of plethysmography between the two groups. After importing the data of 2 patients in the placebo-treated group, who developed interstitial lung disease, DLCO in the placebo-treated group was 90.69 ± 21.29 milliliter at the end of the study, which significantly decreased compared with the beginning of the study (102.30 ± 13.83 ml). Also, changes of DLCO between the two groups were significantly different.Conclusions:In this trial, the sensitivity of DLCO as the first marker in the evaluation of pulmonary function in patients with SSc was confirmed. On the other hand, NAC had no effect versus placebo in a period of 24 weeks.
Stability Analysis at Key Positions of EGFR Related to Non-small Cell Lung Cancer
Authors: Ghosh Avirup , Yan Hong 
Published: December 2019

Background:
Mutations in a protein called the Epidermal Growth Factor Receptor
(EGFR) can cause Non-Small Cell Lung Cancer (NSCLC), which is the most common form of
lung cancer. Many NSCLC cases arise from the L858R mutation, where Leucine (L) is replaced by
arginine (R) at the 858th position in the EGFR, and that is also recognized as an exon 21
substitution. Moreover, half of the EKFR-mutated lung cancer patients develop acquired resistance
to the first-generation EGFR-TKIs due to another mutation T790M.

Objective:
In this research work, a novel method is used to investigate the possible reason for the
EGFR mutation to takes place in the specific 858th and 790th position, and also, we evaluated the
hydrogen bonds to measure the overall stability of different structures.

Methods:
We performed the molecular dynamics simulation and used Amber tool to achieve our
primary objectives and later we use CPPTRAJ to analyze other changes in the hydrogen bonds for
different mutational structures of EGFR.

Results:
First, we investigated the hydrogen bonds in different positions in the EGFR kinase
domain and estimated why the first stage mutation (L858R) and resistance mutation
(L858R/T790M) take place in the 858th and 790th position respectively. We found the hydrogen
bond counts in the 858th and 790th position is lesser than the neighborhood positions and that yields
to achieve a least stability in that position.

Conclusion:
Our method represents an important contribution to molecular dynamics analysis for
NSCLC studies. The results obtained from this study provide a useful insight into the NSCLC drug
resistance.