bluuebunny/crossref_metadata_2025_split huggingface dataset:
VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequence
Authors: Kieft Kristopher , Zhou Zhichao , Anantharaman Karthik 
Published: March 2020

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 viral community function from metagenomic assemblies. VIBRANT uses neural networks of protein signatures and a newly developed 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 viral community 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, VirFinder and MARVEL. When applied to 120,834 metagenomically derived viral sequences representing several human and natural environments, VIBRANT recovered an average of 94% of the viruses, whereas VirFinder, VirSorter and MARVEL achieved less powerful performance, averaging 48%, 87% and 71%, respectively. Similarly, VIBRANT identified more total viral sequence and proteins when applied to real metagenomes. When compared to PHASTER, Prophage Hunter and VirSorter 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.
Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms
Authors: Zhang Xiao-Hua , Zhong Haohui , Lehtovirta-Morley Laura , Liu Jiwen , Zheng Yanfen , Lin Heyu , Song Delei , Todd Jonathan D. , Tian Jiwei 
Published: March 2020

Abstract
Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans - the hadal zone (depth > 6,000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.Results: In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1,000 – 4,000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.Conclusions: Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling.
Generalized Estimating Equation Modeling on Correlated Microbiome Sequencing Data with Longitudinal Measures
Authors: Chen Bo , Xu Wei 
Published: March 2020

Abstract
Background Existing models for assessing microbiome sequencing such as operational taxonomic units (OTUs) can only test predictors' effects on OTUs. There is limited work on how to estimate the correlations between multiple OTUs and incorporate such relationship into models to evaluate longitudinal OTU measures.Results We propose a novel approach to estimate OTU correlations based on their taxonomic structure, and apply such correlation structure in Generalized Estimating Equations (GEE) models to estimate both predictors' effects and OTU correlations. We develop a two-part Microbiome Taxonomic Longitudinal Correlation (MTLC) model for multivariate zero-inflated OTU outcomes based on the GEE framework. In addition, longitudinal and other types of repeated OTU measures are integrated in the MTLC model.Conclusions Extensive simulations have been conducted to evaluate the performance of the MTLC method. Compared with the existing methods, the MTLC method shows robust and consistent estimation, and improved statistical power for testing predictors' effects. Lastly we demonstrate our proposed method by implementing it into a human microbiome study to evaluate the obesity on twins.
Cardiopulmonary resuscitation in obese patients
Authors: Borobov Yu. M. , Samsonova A. A. , Lapushkin D. Yu. , Zaripova Z. , Solovieva M. O. , Astakhova D. Yu. 
Published: March 2020

Objective: an analysis of literature covering the effects of morbid obesity on various aspects of cardiopulmonary resuscitation (CPR) and its outcomes. Currently, there is no speciﬁc standard for CPR in morbidly obese patients (body mass index ≤ 30). Signiﬁcant constitutional, anatomical, and physiological factors can lead to negative treatment outcomes in people with signiﬁcant excess weight. The review presents study results evaluating the effectiveness of the essential components of CPR in obese patients. In particular, it discusses issues of indirect cardiac massage and deﬁbrillation, airway management and ventilation, venous access, and pharmacokinetics of drugs used during CPR. It demonstrates that CPR in obese patients has its own characteristics not mentioned in official recommendations and guidelines.
Effect of Concentration Variation on Optical and Structural Properties of TiO2 Thin Films
Authors: Ezike Sabastine Chinedu 
Published: March 2020

Concentrations in weight percent (5- 25 wt %) of TiO2 films used to optimize the film formation. The TiO2 films on glass substrates successfully obtained by spin-coating process using TiO2 nanopowder as precursor. Ultraviolet-Visible (UV-Vis), Scanning Electron Microscopy (SEM) equipped with Electron Diffraction X-ray (EDX) and X-ray Diffractometer (XRD) techniques used to characterize the films. The result of electron transport material (TiO2) showed that film prepared from 15 wt % of TiO2 solution and annealed at 450 has highest transmittance at visible light region with indirect optical band gap of 3.24 eV which corresponds to wavelength of 382 nm whereas 20 wt % has indirect band gap of 2.99 nm equivalent to 414.7 nm . The chemical analysis from Electron Diffraction Spectroscopy (EDS) of the material shows titanium and oxygen present at L and K-shells, respectively. The sample crystallized with preferred orientation at (101) from XRD analysis.
As Principais Formas de Aquisição de Tecnologia Assistiva: Um Estudo Realizado em Clínicas de Reabilitação na Cidade de Anápolis/GO
Authors: Parreira Samara Lamounier Santana , Silva Flavio Roberto Rosa , Valle Éverton Fleury Victorino , Oliveira Acary Souza Bulle , Campos Francisco Itami , Fernandes Viviane Lemos Silva , Rosseto Lucimar Pinheiro , Santos Vagner Rogério dos 
Published: March 2020

Na Convenção dos Direitos das Pessoas com Deficiência da ONU (2006), o Brasil assumiu o compromisso de promover o conhecimento, o acesso e a disponibilização de recursos de Tecnologia Assistiva (TA). O objetivo deste trabalho é apresentar as principais formas de aquisição de TA, utilizadas por pacientes em reabilitações em três instituições de Anápolis/GO. Trata-se de um estudo descritivo, transversal e quantitativo. Participaram desta pesquisa 108 pacientes com sequelas de lesões neurológicas e pais/responsáveis daqueles menores de 18 anos de idade. Ficou constatado que a maioria dos participantes (66%) adquire os recursos de TA através do Sistema Único de Saúde (SUS), o qual disponibiliza recursos por meio das instituições e associações de apoio à pessoa com deficiência. O acesso aos recursos de TA por meio da dispensação, do financiamento, do apoio à redução ou isenção tributária em produtos de TA e o fomento à produção de TA no Brasil, representam o cumprimento das disposições presentes na Constituição Federal, nos tratados internacionais e na legislação infraconstitucional, o que coloca o nosso país em posição de destaque em relação aos direitos humanos. Porém, é necessário que as políticas e programas voltados ao acesso dos recursos de TA sejam revistos, melhorados e ampliados para que possa cumprir com seu propósito e atingir o maior número de pessoas possíveis.
Urban Occupation Increases Water Toxicity of an Important River in Central Brazil
Authors: Bailão Elisa Flávia Luiz Cardoso , Zago Leciana de Menezes Sousa , Silva Nathan Carvalho , Machado Karine Borges , D'Abadia Patrícia Lima , Oliveira Pedro Henrique Francisco de , Nabout João Carlos , Almeida Luciane Madureira de 
Published: March 2020

Meia Ponte River supplies water for two million people in Goiás State, Brazil. Despite its importance, the Meia Ponte River faces serious environmental problems such as the disposal of domestic and industrial effluents, what could impact the aquatic biota and the health of people who consumes its water. In this sense, here we aimed to evaluate the environmental quality and toxicity of surface water along the course of this river. Physicochemical analyses of water at Goiânia urban perimeter were higher than the limits of Brazil environmental regulations for fresh water. In relation to the diversity of species, phytoplankton classes associated to polluted environments were detected closer to urban perimeter. Allium cepa bioassay suggested that this river may contain substances with mitogenic activity. This result is in accordance with genotoxic analysis, because it was observed a significant increase in chromosomal aberrations. This data reveal the genotoxic potential of Meia Ponte River water. This genotoxicity represents a risk for aquatic biota and humans, once the genotoxic agents in water samples might cause the loss of DNA integrity, inducing damages and DNA breaks. In this context, the water utilization from Meia Ponte River without any treatment should be avoided and public policies need to be formulated and implemented to depollute this important river for Goiás State.
Clinical Pharmacology of Ibuprofen and Indomethacin in Preterm Infants with Patent Ductus Arteriosus
Authors: Pacifici Gian Maria 
Published: March 2020

Background:
Ibuprofen and indomethacin are potent non-selective cyclo-oxygenase inhibitors and inhibit prostaglandin E2 synthesis. The patent ductus arteriosus (PDA) occurs in more than 70% of preterm infants weighing <1500 g. Prostaglandin E2 relaxes smooth muscle, tends to inhibit the closure of PDA, yields vasodilatation of the afferent renal arterioles and maintains glomerular filtration rate (GFR). Ibuprofen and indomethacin inhibiting prostaglandin E2 synthesis close PDA and reduce GFR with consequent decrease of urine output and increase of serum creatinine concentrations.

Aims:
The aims of this study are to give the definitive estimates of PDA closure rate following ibuprofen or indomethacin treatment and to evaluate the extent of renal side effects following the administration of these drugs to preterm infants. Other aims are to review the metabolism and the pharmacokinetics of ibuprofen and indomethacin in preterm infants with PDA.

Methods:
The bibliographic search was performed using PubMed and EMBASE databases as search engines, January 2013 was the cutoff point.

Results:
The %PDA closed by ibuprofen (n=24) and indomethacin (n=24) is 77.7±14.1 and 77.3±11.0, respectively. For ibuprofen, the gestational age of the infants included in the study ranged from 25.0 to 39.0 weeks (mean±SD=29.3±3.1 weeks). The %PDA did not correlate with the gestational age (p=0.2516). For indomethacin, the gestational age of infants included in the study ranged from 25.0 and 39.0 weeks (mean±SD=29.4±2.9 weeks). The %PDA did not correlate with the gestational age (p=0.3742). The treatment with ibuprofen reduces the urine output and increases the serum creatinine concentrations less extensively than indomethacin. The half-life (t1/2) of ibuprofen and indomethacin is lengthened and the clearance is reduced in preterm infants as compared with fullterm infants.

Conclusions.
Ibuprofen and indomethacin are equally effective in closing PDA. Treatment with ibuprofen decreases the risk of renal failure. Ibuprofen has the most favourable risk/benefit ratio. The rate of metabolism is reduced and t1/2 is lengthened in prematures as compared with term infants.
In-vitro Comparative Study of Different Brands of Metoclopramide Hydrochloride Tablets Marketed in Saudi Arabia
Authors: Hani Umme , Alhamhoom Yahya , Alqahtani Ali , Osmani Riyaz Ali , Rahamathulla Mohamed , Mohammed Yasmin Begum , Singh Ekta 
Published: March 2020

Background:
Metoclopramide hydrochloride (MCP), a derivative of para-aminobenzoic
acid, which is a freely soluble drug, gets rapidly absorbed from the gastrointestinal tract and is used
in the management of gastrointestinal disorders such as gastric stasis, gastroesophageal reflux and
for the prevention of cancer chemotherapy induced emesis. Several brands of MCP are available in
Saudi Arabia.

Objectives:
The objective of the present study was to evaluate the quality of different marketed
products of MCP tablets 10mg, which were purchased from the retail pharmacy outlets in Abha, Riyadh
and Jeddah, Saudi Arabia with a view to determine their interchangeability in clinical practice.

Methods:
The study was carried out on branded tablets by quality control tests such as weight
variation, hardness, friability, disintegration and dissolution. The results of all marketed products
complied with the official specifications.

Results:
The results showed that all the parameters for MCP tablets were in accordance with the
USP limits. All the tested four brands were bioequivalent and complying with the official tests for
weight variation, friability, disintegration and dissolution tests. The percent friability was also
within the specified limit. Moreover, all formulations disintegrated within 2-6 min. The percentage
content of the active ingredient of four brands of MCP tablets showed values within the monograph
specifications (95-105%).

Conclusion:
All the four brands evaluated in the present work could be considered bio
pharmaceutically equivalent and therefore, patients can safely switch from one brand to another
when there is the unavailability of a particular brand.
A Simple Protein Evolutionary Classification Method Based on the Mutual Relations Between Protein Sequences
Authors: Wan Xiaogeng , Tan Xinying 
Published: March 2020

Background:
Protein is a kind of important organics in life. It is varied with its
sequences, structures and functions. Protein evolutionary classification is one of the popular
research topics in computational bioinformatics. Many studies have used protein sequence
information to classify the evolutionary relationships of proteins. As the amount of protein
sequence data increases, efficient computational tools are needed to make efficient protein
evolutionary classifications with high accuracies in the big data paradigm.

Methods:
In this study, we propose a new simple and efficient computational approach based on
the normalized mutual information rates to compute the relationship between protein sequences,
we then use the “distances” defined on the relationships to perform the evolutionary classifications
of proteins. The new method is computational efficient, model-free and unsupervised, which does
not require training data when performing classifications.

Result:
Simulation studies on various examples demonstrate the efficiency of the new method.
We use precision-recall curves to compare the efficiency of our new method with traditional
methods, results show that the new method outperforms the traditional methods in most of the
cases when performing evolutionary classifications.

Conclusion:
The new method is simple and proved to be efficient in protein evolutionary
classifications, which is useful in future evolutionary analysis particularly in the big data paradigm.
Improvement of the Efficiency and Completeness of Neuro-Oncology Patient Referrals to a Tertiary Center Through the Implementation of an Electronic Referral System: Retrospective Cohort Study
Authors: Fernández-Méndez Rocío , Wong Mei Yin , Rastall Rebecca J , Rebollo-Díaz Samuel , Oberg Ingela , Price Stephen J , Joannides Alexis J 
Published: March 2020

Background
Quality referrals to specialist care are key for prompt, optimal decisions about the management of patients with brain tumors.

Objective
This study aimed to determine the impact of introducing a Web-based, electronic referral (eReferral) system to a specialized neuro-oncology center, using a service-developed proforma, in terms of waiting times and information completeness.

Methods
We carried out a retrospective cohort study based on the review of medical records of referred adult patients, excluding follow-ups. Primary outcome measures were durations of three key phases within the referral pathway and completion rates of six referral fields.

Results
A total of 248 patients were referred to the specialist center during the study period. Median (IQR) diagnostic imaging to referral intervals were 3 (1-5) days with eReferrals, and 9 (4-19), 19 (14-49), and 8 (4-23) days with paper proforma, paper letter, and internal referrals, respectively (P<.001). Median (IQR) referral to multidisciplinary team decision intervals were 3 (2-7), 2 (1-3), 8 (2-24), and 3 (2-6) days respectively (P=.01). For patients having surgery, median (IQR) diagnostic imaging to surgery intervals were 28 (21-41), 34 (27-51), 104 (69-143), and 32 (15-89) days, respectively (P<.001). Proportions of complete fields differed significantly by referral type in all study fields (all with Ps <.001) except for details of presentation, which were present in all referrals. All study fields were always present in eReferrals, as these are compulsory for referral submission. Depending on the data field, level of completeness in the remaining referral types ranged within 69% (65/94) to 87% (82/94), 15% (3/20) to 65% (13/20), and 22% (8/41) to 63% (26/41) in paper proforma, paper letter, and internal referrals, respectively.

Conclusions
An electronic, Web-based, service-developed specific proforma for neuro-oncology referrals performs significantly better, with shorter waiting times and greater completeness of information than other referral types. A wider application of eReferrals is an important first step to streamlining specialist care pathways and providing excellent care.

International Registered Report Identifier (IRRID)
RR2-10.2196/10.2196/15002
A Deep-Learning Algorithm (ECG12Net) for Detecting Hypokalemia and Hyperkalemia by Electrocardiography: Algorithm Development
Authors: Lin Chin-Sheng , Lin Chin , Fang Wen-Hui , Hsu Chia-Jung , Chen Sy-Jou , Huang Kuo-Hua , Lin Wei-Shiang , Tsai Chien-Sung , Kuo Chih-Chun , Chau Tom , Yang Stephen JH , Lin Shih-Hua 
Published: March 2020

Background
The detection of dyskalemias—hypokalemia and hyperkalemia—currently depends on laboratory tests. Since cardiac tissue is very sensitive to dyskalemia, electrocardiography (ECG) may be able to uncover clinically important dyskalemias before laboratory results.

Objective
Our study aimed to develop a deep-learning model, ECG12Net, to detect dyskalemias based on ECG presentations and to evaluate the logic and performance of this model.

Methods
Spanning from May 2011 to December 2016, 66,321 ECG records with corresponding serum potassium (K+) concentrations were obtained from 40,180 patients admitted to the emergency department. ECG12Net is an 82-layer convolutional neural network that estimates serum K+ concentration. Six clinicians—three emergency physicians and three cardiologists—participated in human-machine competition. Sensitivity, specificity, and balance accuracy were used to evaluate the performance of ECG12Net with that of these physicians.

Results
In a human-machine competition including 300 ECGs of different serum K+ concentrations, the area under the curve for detecting hypokalemia and hyperkalemia with ECG12Net was 0.926 and 0.958, respectively, which was significantly better than that of our best clinicians. Moreover, in detecting hypokalemia and hyperkalemia, the sensitivities were 96.7% and 83.3%, respectively, and the specificities were 93.3% and 97.8%, respectively. In a test set including 13,222 ECGs, ECG12Net had a similar performance in terms of sensitivity for severe hypokalemia (95.6%) and severe hyperkalemia (84.5%), with a mean absolute error of 0.531. The specificities for detecting hypokalemia and hyperkalemia were 81.6% and 96.0%, respectively.

Conclusions
A deep-learning model based on a 12-lead ECG may help physicians promptly recognize severe dyskalemias and thereby potentially reduce cardiac events.