bluuebunny/crossref_metadata_2025_split huggingface dataset:
LnCompare: gene set feature analysis for human long non-coding RNAs
Authors: Carlevaro-Fita Joana , Liu Leibo , Zhou Yuan , Zhang Shan , Chouvardas Panagiotis , Johnson Rory , Li Jianwei 
Published: May 2019

AbstractInterest in the biological roles of long noncoding RNAs (lncRNAs) has resulted in growing numbers of studies that produce large sets of candidate genes, for example, differentially expressed between two conditions. For sets of protein-coding genes, ontology and pathway analyses are powerful tools for generating new insights from statistical enrichment of gene features. Here we present the LnCompare web server, an equivalent resource for studying the properties of lncRNA gene sets. The Gene Set Feature Comparison mode tests for enrichment amongst a panel of quantitative and categorical features, spanning gene structure, evolutionary conservation, expression, subcellular localization, repetitive sequences and disease association. Moreover, in Similar Gene Identification mode, users may identify other lncRNAs by similarity across a defined range of features. Comprehensive results may be downloaded in tabular and graphical formats, in addition to the entire feature resource. LnCompare will empower researchers to extract useful hypotheses and candidates from lncRNA gene sets.
HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
Authors: He Jiahua , Wang Jun , Tao Huanyu , Xiao Yi , Huang Sheng-You 
Published: May 2019

AbstractInteractions between nuclide acids (RNA/DNA) play important roles in many basic cellular activities like transcription regulation, RNA processing, and protein synthesis. Therefore, determining the complex structures between RNAs/DNAs is crucial to understand the molecular mechanism of related RNA/DNA–RNA/DNA interactions. Here, we have presented HNADOCK, a user-friendly web server for nucleic acid (NA)–nucleic acid docking to model the 3D complex structures between two RNAs/DNAs, where both sequence and structure inputs are accepted for RNAs, while only structure inputs are supported for DNAs. HNADOCK server was tested through both unbound structure and sequence inputs on the benchmark of 60 RNA–RNA complexes and compared with the state-of-the-art algorithm SimRNA. For structure input, HNADOCK server achieved a high success rate of 71.7% for top 10 predictions, compared to 58.3% for SimRNA. For sequence input, HNADOCK server also obtained a satisfactory performance and gave a success rate of 83.3% when the bound RNA templates are included or 53.3% when excluding those bound RNA templates. It was also found that inclusion of the inter-RNA base-pairing information from RNA–RNA interaction prediction can significantly improve the docking accuracy, especially for the top prediction. HNADOCK is fast and can normally finish a job in about 10 minutes. The HNADOCK web server is available at http://huanglab.phys.hust.edu.cn/hnadock/.
SEPPA 3.0—enhanced spatial epitope prediction enabling glycoprotein antigens
Authors: Zhou Chen , Chen Zikun , Zhang Lu , Yan Deyu , Mao Tiantian , Tang Kailin , Qiu Tianyi , Cao Zhiwei 
Published: May 2019

Abstract
B-cell epitope information is critical to immune therapy and vaccine design. Protein epitopes can be significantly affected by glycosylation, while no methods have considered this till now. Based on previous versions of Spatial Epitope Prediction of Protein Antigens (SEPPA), we here present an enhanced tool SEPPA 3.0, enabling glycoprotein antigens. Parameters were updated based on the latest and largest dataset. Then, additional micro-environmental features of glycosylation triangles and glycosylation-related amino acid indexes were added as important classifiers, coupled with final calibration based on neighboring antigenicity. Logistic regression model was retained as SEPPA 2.0. The AUC value of 0.794 was obtained through 10-fold cross-validation on internal validation. Independent testing on general protein antigens resulted in AUC of 0.740 with BA (balanced accuracy) of 0.657 as baseline of SEPPA 3.0. Most importantly, when tested on independent glycoprotein antigens only, SEPPA 3.0 gave an AUC of 0.749 and BA of 0.665, leading the top performance among peers. As the first server enabling accurate epitope prediction for glycoproteins, SEPPA 3.0 shows significant advantages over popular peers on both general protein and glycoprotein antigens. It can be accessed at http://bidd2.nus.edu.sg/SEPPA3/ or at http://www.badd-cao.net/seppa3/index.html. Batch query is supported.
MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics
Authors: Damre Mangesh , Marchetto Alessandro , Giorgetti Alejandro 
Published: May 2019

Abstract
Atomistic molecular dynamics simulations of membrane proteins have been shown to be extremely useful for characterizing the molecular features underlying their function, but require high computational power, limiting the understanding of complex events in membrane proteins, e.g. ion channels gating, GPCRs activation. To overcome this issue, it has been shown that coarse-grained approaches, although requiring less computational power, are still capable of correctly describing molecular events underlying big conformational changes in biological systems. Here, we present the Martini coarse-grained membrane protein dynamics (MERMAID), a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations and to analyse the trajectories.
ResponseNet v.3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues
Authors: Basha Omer , Mauer Omry , Simonovsky Eyal , Shpringer Rotem , Yeger-Lotem Esti 
Published: May 2019

AbstractResponseNet v.3 is an enhanced version of ResponseNet, a web server that is designed to highlight signaling and regulatory pathways connecting user-defined proteins and genes by using the ResponseNet network optimization approach (http://netbio.bgu.ac.il/respnet). Users run ResponseNet by defining source and target sets of proteins, genes and/or microRNAs, and by specifying a molecular interaction network (interactome). The output of ResponseNet is a sparse, high-probability interactome subnetwork that connects the two sets, thereby revealing additional molecules and interactions that are involved in the studied condition. In recent years, massive efforts were invested in profiling the transcriptomes of human tissues, enabling the inference of human tissue interactomes. ResponseNet v.3 expands ResponseNet2.0 by harnessing ∼11,600 RNA-sequenced human tissue profiles made available by the Genotype-Tissue Expression consortium, to support context-specific analysis of 44 human tissues. Thus, ResponseNet v.3 allows users to illuminate the signaling and regulatory pathways potentially active in the context of a specific tissue, and to compare them with active pathways in other tissues. In the era of precision medicine, such analyses open the door for tissue- and patient-specific analyses of pathways and diseases.
A Proof of Concept for Applying the Radicchi Index (hf ) to Compare Academic Productivity and Scientific Impact Among Medical Specialties
Authors: Do Truong H , Miller Catherine , Low Walter C , Haines Stephen J 
Published: May 2019

Abstract
Many indices have been developed to assess the impact of scientific publications by investigators, disciplines, and institutions. The h-index has emerged as a leading tool in the assessment of the productivity of authors. Differences in publication and citation opportunity among specialties create inappropriate conclusions when the h-index is used to compare authors across different disciplines. An alternative, the Radicchi index, hf
, has been proposed to assess the impact of publications across disciplines. We curated a database of all articles published from 2002 to 2015 from the 3 highest impact factor medical journals: New England Journal of Medicine (NEJM), the Lancet, and the Journal of American Medical Association (JAMA). With this database, articles were categorized into medical subspecialties. We calculated the respective h-index and Radicchi index of each specialty. We found that the Radicchi index eliminated variability associated with publication and citation opportunity between different specialties when compared to the h-index. The Radicchi index is a useful measure of scientific impact and productivity that advances the h-index by allowing interspecialty comparisons. There remains a need to define a researcher's specialty designation especially if he/she conducts multidisciplinary research.
Effect of reducing dietary advanced glycation end products on obesity-associated complications: a systematic review
Authors: Ribeiro Priscila V M , Tavares Juliana F , Costa Mirian A C , Mattar Jéssica B , Alfenas Rita C G 
Published: May 2019

Abstract

Context
Consumption of dietary advanced glycation end products (AGEs) is associated with oxidative stress, inflammation, and other chronic conditions commonly associated with obesity.

Objective
To analyze the effects of dietary AGEs on complications associated with obesity.

Data sources
This systematic review was conducted and reported according to PRISMA guidelines. The PubMed, Cochrane, and Scopus databases were searched, using the terms “advanced glycation end products,” “overweight,” and “obesity.” The last search was performed in October 2018.

Data extraction
Six studies that evaluated the effects of low-AGE and high-AGE diets were included in the review. The duration of the studies ranged from 1 day to 12 weeks. A comparison of all the compiled data was conducted by the authors.

Data analysis
Circulating and urinary AGE markers, besides soluble receptor for AGEs, were considered as the primary outcomes. The secondary outcomes were cardiometabolic, inflammatory, glycemic, anthropometric, and renal markers.

Conclusions
AGE-RAGE interactions can activate the NF-κB (nuclear factor kappa B) signaling pathway and inhibit the PI3K-AKT pathway in adipocytes, which may explain their association with chronic diseases. This interaction can be considered as a novel explanation for the pathogenesis of obesity. AGEs can also be used as a biomarker for monitoring responses to dietary interventions in overweight and obese people.

Systematic Review Registration
PROSPERO registration no. CRD42018082745.
Effect of vitamin D supplementation on serum lipid profiles: a systematic review and meta-analysis
Authors: Dibaba Daniel T 
Published: May 2019

AbstractContextVitamin D deficiency is highly prevalent across the world. The existing evidence suggests vitamin D may have beneficial effects on serum lipid profiles and thus cardiovascular health.ObjectiveThe objective of this systematic review and meta-analysis was to examine the effect of vitamin D supplementation on serum lipid profiles.Data SourceOriginal randomized controlled trials (RCTs) examining the effect of vitamin D supplementation on serum lipid profiles and published before July 2018 were identified by searching online databases, including PubMed, Google Scholar, and ScienceDirect, using a combination of relevant keywords.Data ExtractionData on study characteristics, effect size, measure of variation, type of vitamin D supplementation, and duration of follow-up were extracted by the author.Data AnalysisPRISMA guidelines for systematic reviews were followed. Random effects (DerSimonian and Laird [D-V)] models were used to pool standardized mean differences in total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and triglycerides between the active and the placebo arms of RCT studies. Between-study heterogeneities were assessed using Cochrane Q and I2, and publication bias was assessed using Begg’s test, Egger’s test, and funnel plot.ResultsA total of 41 RCTs comprising 3434 participants (n = 1699 in the vitamin D supplementation arm and n = 1735 in the placebo arm) were identified and included in the meta-analysis. Approximately 63.4% of study participants were women, with 14 studies conducted entirely among women. Approximately 24% of the trials had follow-up duration >6 months, whereas the remaining 76% had follow-up duration of <6 months. The standardized mean differences (SMDs) and 95% confidence intervals (CIs) for comparing the change from baseline to follow-up between the vitamin D supplementation arm and the placebo (control) arm were as follows: total cholesterol = –0.17 (–0.28 to –0.06); LDL cholesterol = –0.12 (–0.23 to –0.01); triglycerides = –0.12 (–0.25 to 0.01); and HDL cholesterol = –0.19 (–0.44 to 0.06). After removing a trial that was an outlier based on the magnitude of the effect size, the SMD for triglycerides was –0.15 (–0.24 to –0.06) and that for HDL cholesterol was –0.10 (–0.28 to 0.09). The improvements in total cholesterol and triglycerides were more pronounced in participants with baseline vitamin D deficiency.ConclusionsVitamin D supplementation appeared to have a beneficial effect on reducing serum total cholesterol, LDL cholesterol, and triglyceride levels but not HDL cholesterol levels. Vitamin D supplementation may be useful in hypercholesterolemia patients with vitamin D insufficiency who are at high risk of cardiovascular diseases.
Evidence for Magma–Wall Rock Interaction in Carbonatites from the Kaiserstuhl Volcanic Complex (Southwest Germany)
Authors: Giebel R J , Parsapoor A , Walter B F , Braunger S , Marks M A W , Wenzel T , Markl G 
Published: May 2019

AbstractThe mineralogy and mineral chemistry of the four major sövite bodies (Badberg, Degenmatt, Haselschacher Buck and Orberg), calcite foidolite/nosean syenite xenoliths (enclosed in the Badberg sövite only) and rare extrusive carbonatites of the Kaiserstuhl Volcanic Complex in Southern Germany provide evidence for contamination processes in the carbonatitic magma system of the Kaiserstuhl. Based on textures and composition, garnet and clinopyroxene in extrusive carbonatites represent xenocrysts entrained from the associated silicate rocks. In contrast, forsterite, monticellite and mica in sövites from Degenmatt, Haselschacher Buck and Orberg probably crystallized from the carbonatitic magma. Clinopyroxene and abundant mica crystallization in the Badberg sövite, however, was induced by the interaction between calcite foidolite xenoliths and the carbonatite melt. Apatite and micas in the various sövite bodies reveal clear compositional differences: apatite from Badberg is higher in REE, Si and Sr than apatite from the other sövite bodies. Mica from Badberg is biotite- and comparatively Fe2+-rich (Mg# = 72–88). Mica from the other sövites, however, is phlogopite (Mg# up to 97), as is typical of carbonatites in general. The typical enrichment of Ba due to the kinoshitalite substitution is observed in all sövites, although it is subordinate in the Badberg samples. Instead, Badberg biotites are strongly enriched in IVAl (eastonite substitution) which is less important in the other sövites. The compositional variations of apatite and mica within and between the different sövite bodies reflect the combined effects of fractional crystallization and carbonatite-wall rock interaction during emplacement. The latter process is especially important for the Badberg sövites, where metasomatic interaction released significant amounts of K, Fe, Ti, Al and Si from earlier crystallized nosean syenites. This resulted in a number of mineral reactions that transformed these rocks into calcite foidolites. Moreover, this triggered the crystallization of compositionally distinct mica and clinopyroxene crystals around the xenoliths and within the Badberg sövite itself. Thus, the presence and composition of clinopyroxene and mica in carbonatites may be useful indicators for contamination processes during their emplacement. Moreover, the local increase of silica activity during contamination enabled strong REE enrichment in apatite via a coupled substitution involving Si, which demonstrates the influence of contamination on REE mineralization in carbonatites.
Public Health and the Virtues of Responsibility, Compassion and Humility
Authors: Nihlén Fahlquist Jessica 
Published: May 2019

AbstractIn contrast to medical care, which is focused on the individual patient, public health is focused on collective health. This article argues that, in order to better protect the individual, discussions of public health would benefit from incorporating the insights of virtue ethics. There are three reasons to for this. First, the collective focus may cause neglect of the effects of public health policy on the interests and rights of individuals and minorities. Second, whereas the one-on-one encounters in medical care facilitate a compassionate and caring attitude, public health involves a distance between professionals and the public. Therefore, public health professionals must use imagination and care to evaluate the effects of policies on individuals. Third, the relationship between public health professionals and the people who are affected by the policies they design is characterized by power asymmetry, demanding a high level of responsibility from those who wield them.Against this background, it is argued that public health professionals should develop the virtues of responsibility, compassion and humility. The examples provided, i.e. breastfeeding information and vaccination policy, illustrate the importance of these virtues, which needed for normative as well as instrumental reasons, i.e. as a way to restore trust.
A NEW THERMOLUMINESCENCE GENERAL ORDER GLOW CURVE FIT FUNCTION CONSIDERING THERMAL QUENCHING EFFECT
Authors: Harooni S , Zahedifar M , Sadeghi E , Ahmadian Z 
Published: May 2019

Abstract
A new thermoluminescence (TL) general order glow curve fit function in terms of the intensity of peak maximum, Im and the peak temperature, Tm is presented in which thermal quenching (TQ) effect has been taken into account. Also, the conventional general order model and the new presented function were fitted to the glow peak 5 of LiF:Mg,Ti (TLD-100) and the kinetic parameters were obtained for different heating rates as the results of fitting procedure. It was found that increasing the heating rate, which makes the TQ more prominent, causes more divergence between the kinetic parameters extracted by applying two models. Considering that the TL intensity and the glow peak area reduce with shifting the glow peak to higher temperatures as a result of TQ, the new presented function gives more reliable results for the kinetic parameters.
A CRISPR/Cas9 Whole-Genome Screen Identifies Genes Required for Aryl Hydrocarbon Receptor-Dependent Induction of Functional CYP1A1
Authors: Sundberg Christopher D , Hankinson Oliver 
Published: May 2019

Abstract
Environmental pollutants including halogenated aromatic hydrocarbons and polycyclic aromatic hydrocarbons, including benzo[a]pyrene, exert their deleterious effects through the activation of the aryl hydrocarbon receptor (AHR) and by the resulting transcription of genes not yet fully identified. Ligand-bound AHR translocates from cytoplasm to nucleus, where it dimerizes with the aryl hydrocarbon receptor nuclear translocator (ARNT) protein. The AHR/ARNT dimer binds to enhancer regions of responsive genes to activate transcription. AHR also mediates carcinogenesis caused by PAHs, likely via CYP1A1, CYP1A2, and CYP1B1, which are massively induced by activated AHR in many tissues and generate carcinogenic electrophilic derivatives of PAHs. In the current study, we have used the mouse GeCKOv2 genome-wide CRISPR/Cas9 library to identify novel genes in the AHR pathway by taking advantage of a B[a]P selection assay that we previously used to identify core AHR pathway genes in Hepa-1c1c7 murine hepatoma cells. Besides Ahr, Arnt, and Cyp1a1, we report the identification of multiple additional putative AHR pathway genes including several that we validated. These include cytochrome P450 reductase (Por), which mediates redox regeneration of cytochromes P450, and 5 genes of the heme biosynthesis pathway: delta-aminolevulinate synthase 1 (Alas1), porphobilinogen deaminase (Hmbs), uroporphyrinogen decarboxylase (Urod), coproporphyrinogen oxidase (Cpox), and ferrochelatase (Fech): heme being an essential prosthetic group of cytochrome P450 proteins. Notably, several of these genes were identified by GeCKO screening, despite not being identifiable by reverse genetics approaches. This indicates the power of high-sensitivity genome-wide genetic screening for identifying genes in the AHR pathway.
Patient Preferences Post IUD Insertion [1G]
Authors: Abern Lauren , de Guzman Glendell , Kiely Kristen , Packard Adelaide , Maguire Karla 
Published: May 2019

INTRODUCTION:
Although the intrauterine device (IUD) is a safe and highly effective method of contraception, patients have concerns about complications. Our objective is to characterize patient apprehensions with IUD insertion and determine if string checks or closer follow-up will help to alleviate these concerns.

METHODS:
Individuals 18 and older presenting for IUD insertion participated in an online survey about reproductive history, reasons for choosing an IUD and concerns for complications.

RESULTS:
603 surveys were completed. The mean age was 28.6 (SD 6.6). The majority (432, 72%) was Caucasian and graduated from college (507, 84%). All participants had insurance (603, 100%). The most common reasons for choosing an IUD were because it was long-acting (501, 84%) and low maintenance (525, 88%). Participants were most concerned about an embedded IUD (285, 53%), uterine perforation (271, 51%), and expulsion (235, 44%) as potential complications. Although only 334 (57%) were counseled about string checks, 436 (74%) plan on performing monthly string checks to determine if their IUD is in place. 424 (72%) desired to return to the office in 4-6 weeks for an IUD check.

CONCLUSION:
Potential complications such as uterine perforation and embedded IUD are primary concerns for those choosing an IUD. Most participants prefer to perform monthly string checks and an office visit for an IUD check. Based on this data, providers should strongly consider counseling patients about string checks and offering an appointment for an IUD check 4-6 weeks after placement for patient reassurance.
A Prospective Investigation of Inflammation and Uric Acid in Preeclampsia [15G]
Authors: Psoinos Rachel , Leung Katherine , Dumont Tina , Simas Tiffany Moore 
Published: May 2019

INTRODUCTION:
The role of uric acid in preeclampsia (PEC) is controversial. We hypothesize that women with PEC express a pro-inflammatory cytokine profile compared to controls related to uricemia.

METHODS:
In an IRB approved secondary analysis of a two-center prospective cohort study of women with PEC risk factors, maternal serum was collected in second and third trimesters. PEC cases were matched with controls on age, body mass index, fetal number, and chronic hypertension. Women with gestational hypertension (GHTN) were matched to PEC cases. Multiplex technology analyzed inflammatory cytokines at diagnosis and at delivery if delayed. Serum uric acid levels were extracted from the medical record.

RESULTS:
Of 258 subjects, 26 PEC and 15 GHTN cases were identified. Of PEC cases, 53.8% were diagnosed preterm and 30.8% had CHTN. PEC cases delivered earlier than controls (P=.020). Unadjusted linear regression showed significant decrease in interleukin-18 (IL-18) in PEC versus controls (P=.033) and in monocyte chemoattractant protein-1 (MCP-1) in PEC versus GHTN cases (P=.022). By multivariable regression, covariates of gestational age, diabetes, PEC history and parity were not significant confounders. Qualitatively, uric acid demonstrated linear increase over pregnancy in PEC whereas controls had more abrupt increases near term.

CONCLUSION:
PEC cases expressed different levels of MCP-1 and IL-18 compared to controls and GHTN, suggesting a unique inflammatory state of PEC. Contrary to our hypothesis, select pro-inflammatory markers were lower in PEC. A larger population may clarify whether differences in subgroups of PEC or timing of sampling relative to diagnosis could explain findings.