bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blood Groups: A Probable Link to Periodontal Diseases
Authors: Jain Aditi , G. Devaraj , Kuckreja Harinder , Kuckreja KBS 
Published: October 2018

AbstractThe presence or absence of blood group antigens has been associated with various diseases, with antigens also acting as receptors for infectious agents. There is paucity of literature available in assessing the relative liability of blood group phenotypes to periodontal diseases. The objective of this study was to determine the association of the ABO blood group and Rhesus factor with periodontal disease to assess whether they can behave as predictors of periodontal diseases. The data was collected from randomly selected 100 individuals who were referred to the Department of Periodontics & Implantology, Mahatma Gandhi Dental College & Hospital, Jaipur for periodontal ailment management or for other reasons related to dental health. The subjects were categorized into three groups according to Russel's Periodontal index: healthy periodontium, gingivitis & periodontitis. Blood samples were collected to identify the ABO blood group and Rh factor by the slide method. The effect of blood subgroups on periodontal health, gingivitis and periodontitis was investigated separately. Results & Conclusion: More number of healthy subjects in blood group A. Gingivitis and periodontitis were found more in blood group O and blood group AB, respectively. Rh positive subjects had higher distribution in all study groups.
Compound and Complex Odontoma Associated with Eruption Disturbances and its Management: Report of two Cases
Authors: Kumar Dinesh , Singh Gurnam , Kapoor Swati , Sethi Shobit , Bajaj Puneet , Mittal Sanjay 
Published: October 2018

AbstractThe most common type of odontogenic tumours is odontomas. Generally, they are benign and asymptomatic in nature. This paper describes two varieties of odontomas in two different cases. In first case a compound odontoma present in maxillary anterior region lead to over retention of primary teeth and non eruption of permanent teeth. Retained deciduous teeth and the lesion were removed and permanent teeth were allowed to erupt and orthodontic treatment was done. In 2nd case a complex odontoma was incidentally found when patient reported for extraction of mandibular third molar which was surgically excised. The results achieved indicate that the early diagnosis of odontomas allows the adoption of a less complex and expensive treatment and ensures better prognosis.
Electronic Registration in Complementary/Homeopathic Medical Practice with Identification of ‘Best Homeopathic Cases’: A Pilot Study
Authors: Klein-Laansma Christien , Rutten Alexander , Fruijtier Paul , Wijtenburg Huib 
Published: October 2018

Background Practice-based registration could identify ‘general’ and ‘homeopathic’ prognostic factors for therapeutic success in patients who seek complementary and alternative medicine (CAM)/homeopathic treatment. Identification of ‘best homeopathic cases’ within a database could inform clinical research and improve homeopathic practice.
Objective To investigate the feasibility of registration in daily CAM/homeopathic practice, evaluate patient-reported outcome measures and tools for identifying ‘best homeopathic cases’ and to make recommendations for an electronic database.
Methods In 2015 and 2016, 25 homeopathic doctors registered details of a maximum of 20 patients each, with 6 months of follow-up (extended follow-up for ‘best homeopathic cases’), in Excel or in the Homeopathic Administration and Registration Program (HARP) database. Informed consent was obtained from each patient. Patient-perceived change of main complaint was measured by a 7-point Likert scale. Best homeopathic cases were defined by treatment with one homeopathic medicine, ≥ 2 months of follow-up, result score +2 to +4 on a 9-point Likert scale by the doctor, and by changes that could be attributed to the homeopathic medicine. Association between scores for change of main complaint and scores for ‘best homeopathic case’ was analysed by the Kruskal gamma test.
Results Three-hundred and ninety-nine patients were included. In 49.1%, the main complaint was present for ≥ 2 years. The most common diagnosis was ‘fatigue’ (N = 56; 14%). Major improvement in the main complaint (score +3) was reported by 22 to 26% at consecutive follow-up visits. One-hundred and ninety-six patients were treated with a single homeopathic medicine, among whom 66 ‘best homeopathic cases’ were identified. The correlation between patient-reported changes of main complaint and assessment by the doctor was significant (gamma = 0.832; p < 0.001).
Conclusions Registration of (co-)diagnoses, chronicity, treatments and outcomes in homeopathic practice with identification of ‘best homeopathic cases’ is feasible, using the tools provided. A user-friendly electronic database for efficient recording is recommended.
Conjugated enynones: preparation, properties and applications in organic synthesis
Authors: Golovanov Alexander A. , Odin Ivan S. , Zlotskii Simon S. 
Published: October 2018

Published data on the preparation methods, properties and chemical transformations of linear- and cross-conjugated enynones are integrated. The molecular and crystal structures, spectral characteristics and non-linear optical properties of these compounds are considered. Data on the reduction of enynones to alcohols and on electrophilic, nucleophilic and pericyclic reactions involving them are described systematically. Primary attention is paid to the regioselectivity and mechanisms of transformations of conjugated enynones. Examples of their application in the targeted organic synthesis of carbo- and heterocyclic compounds are given.
The bibliography includes 250 references.
Verifying Larché–Cahn elasticity, a milestone of 20th-century thermodynamics
Authors: Shi Shan , Markmann Jürgen , Weissmüller Jörg 
Published: October 2018

SignificanceBy concatenating the fields of continuum mechanics and alloy thermodynamics in a unified framework, the theory of open system elasticity by Francis Larché and John W. Cahn achieved one of the key advances in thermodynamics of the 20th century. The theory’s implications for the coupling between stress and composition are generally well acknowledged, yet selected issues are under debate. It is, therefore, dissatisfactory that the predictions for the open system elastic parameters—as the theory’s central materials descriptors—await experimental verification. Here, we report that the variation of the open system Young’s modulus of palladium hydride with composition is in excellent agreement with the prediction. This confirms a cornerstone of materials’ theory.
Multi-unit association measures
Authors: Dunn Jonathan 
Published: October 2018

AbstractThis paper formulates and evaluates a series of multi-unit measures of directional association, building on the pairwiseΔPmeasure, that are able to quantify association in sequences of varying length and type of representation. Multi-unit measures face an additional segmentation problem: once the implicit length constraint of pairwise measures is abandoned, association measures must also identify the borders of meaningful sequences. This paper takes a vector-based approach to the segmentation problem by using 18 unique measures to describe different aspects of multi-unit association. An examination of these measures across eight languages shows that they are stable across languages and that each provides a unique rank of associated sequences. Taken together, these measures expand corpus-based approaches to association by generalizing across varying lengths and types of representation.
QuagmiR: a cloud-based application for isomiR big data analytics
Authors: Bofill-De Ros Xavier , Chen Kevin , Chen Susanna , Tesic Nikola , Randjelovic Dusan , Skundric Nikola , Nesic Svetozar , Varjacic Vojislav , Williams Elizabeth H , Malhotra Raunaq , Jiang Minjie , Gu Shuo 
Published: October 2018

Abstract

Summary
MicroRNAs (miRNAs) function as master regulators of gene expression. Recent studies demonstrate that miRNA isoforms (isomiRs) play a unique role in cancer development. Here, we present QuagmiR, the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designed for the detection and annotation of heterogeneous isomiRs, it permits extensive customization of the query process and reference databases to meet the user 's diverse research needs.

Availability and implementation
QuagmiR is written in Python and can be obtained freely from GitHub (https://github.com/Gu-Lab-RBL-NCI/QuagmiR). QuagmiR can be run from the command line on local machines, as well as on high-performance servers. A web-accessible version of the tool has also been made available for use by academic researchers through the National Cancer Institute-funded Seven Bridges Cancer Genomics Cloud (https://cancergenomicscloud.org).

Supplementary information
Supplementary data are available at Bioinformatics online.
VIRULIGN: fast codon-correct alignment and annotation of viral genomes
Authors: Libin Pieter J K , Deforche Koen , Abecasis Ana B , Theys Kristof 
Published: October 2018

Abstract

Summary
Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit of these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codon-correct alignments of large datasets, with standardized and formalized genome annotation and various alignment export formats.

Availability and implementation
VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project.

Supplementary information
Supplementary data is available at Bioinformatics online.
DIGREM: an integrated web-based platform for detecting effective multi-drug combinations
Authors: Zhang Minzhe , Lee Sangin , Yao Bo , Xiao Guanghua , Xu Lin , Xie Yang 
Published: October 2018

Abstract

Motivation
Synergistic drug combinations are a promising approach to achieve a desirable therapeutic effect in complex diseases through the multi-target mechanism. However, in vivo screening of all possible multi-drug combinations remains cost-prohibitive. An effective and robust computational model to predict drug synergy in silico will greatly facilitate this process.

Results
We developed DIGREM (Drug-Induced Genomic Response models for identification of Effective Multi-drug combinations), an online tool kit that can effectively predict drug synergy. DIGREM integrates DIGRE, IUPUI_CCBB, gene set-based and correlation-based models for users to predict synergistic drug combinations with dose–response information and drug-treated gene expression profiles.

Availability and implementation
http://lce.biohpc.swmed.edu/drugcombination

Supplementary information
Supplementary data are available at Bioinformatics online.
CoMM: a collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information
Authors: Yang Can , Wan Xiang , Lin Xinyi , Chen Mengjie , Zhou Xiang , Liu Jin 
Published: October 2018

Abstract

Motivation
Genome-wide association studies (GWASs) have been successful in identifying many genetic variants associated with complex traits. However, the mechanistic links between these variants and complex traits remain elusive. A scientific hypothesis is that genetic variants influence complex traits at the organismal level via affecting cellular traits, such as regulating gene expression and altering protein abundance. Although earlier works have already presented some scientific insights about this hypothesis and their findings are very promising, statistical methods that effectively harness multilayered data (e.g. genetic variants, cellular traits and organismal traits) on a large scale for functional and mechanistic exploration are highly demanding.

Results
In this study, we propose a collaborative mixed model (CoMM) to investigate the mechanistic role of associated variants in complex traits. The key idea is built upon the emerging scientific evidence that genetic effects at the cellular level are much stronger than those at the organismal level. Briefly, CoMM combines two models: the first model relating gene expression with genotype and the second model relating phenotype with predicted gene expression using the first model. The two models are fitted jointly in CoMM, such that the uncertainty in predicting gene expression has been fully accounted. To demonstrate the advantages of CoMM over existing methods, we conducted extensive simulation studies, and also applied CoMM to analyze 25 traits in NFBC1966 and Genetic Epidemiology Research on Aging (GERA) studies by integrating transcriptome information from the Genetic European in Health and Disease (GEUVADIS) Project. The results indicate that by leveraging regulatory information, CoMM can effectively improve the power of prioritizing risk variants. Regarding the computational efficiency, CoMM can complete the analysis of NFBC1966 dataset and GERA datasets in 2 and 18 min, respectively.

Availability and implementation
The developed R package is available at https://github.com/gordonliu810822/CoMM.

Supplementary information
Supplementary data are available at Bioinformatics online.
Therapeutic Impact of Initial Treatment for Chlamydia trachomatis Among Patients With Pelvic Inflammatory Disease: A Retrospective Cohort Study Using a National Inpatient Database in Japan
Authors: Shigemi Daisuke , Matsui Hiroki , Fushimi Kiyohide , Yasunaga Hideo 
Published: October 2018

Abstract

Background
Pelvic inflammatory disease (PID) is common among women of reproductive age and can be complicated by tuboovarian abscess (TOA), which is a serious and potentially life-threatening disease. However, recent mortality rates from PID on hospital admission and the short-term therapeutic usefulness of initial treatment for Chlamydia trachomatis remain unknown.

Methods
Using the Diagnosis Procedure Combination database, we identified patients who were diagnosed with PID on admission from July 2010 to March 2016 in Japan. We excluded patients who were pregnant, had cancer, or had missing data. Propensity score–adjusted analyses were performed to compare short-term outcomes between patients administered initial treatment for C. trachomatis and those without this treatment. The primary outcome was surgical intervention (laparotomy, laparoscopic surgery, and/or drainage procedure) during hospitalization.

Results
In total, 27841 eligible patients were identified. Of these patients, 2463 (8.8%) had TOA on admission. Mortality during hospitalization was 0.56% and 0.28% in the groups without and with TOA, respectively. Propensity score matching created 6149 pairs. A significant difference was observed in the primary outcome between those receiving initial treatment for C. trachomatis and the control group after propensity score matching (11.5% vs 13.4%; risk difference, −1.9%; 95% confidence interval, −3.1 to −0.7). The group that received initial treatment for C. trachomatis also had a significantly lower mortality rate.

Conclusions
In this retrospective nationwide study, initial treatment for C. trachomatis among hospitalized patients diagnosed with PID had clinical benefits in terms of improved short-term outcomes.
Reconstructing the phylogeny of new world monkeys (platyrrhini): evidence from multiple non-coding loci
Authors: Wang Xiaoping , Lim Burton K , Ting Nelson , Hu Jingyang , Liang Yunpeng , Roos Christian , Yu Li 
Published: October 2018

Abstract
Among mammalian phylogenies, those characterized by rapid radiations are particularly problematic. The New World monkeys (NWMs, Platyrrhini) comprise 3 families and 7 subfamilies, which radiated within a relatively short time period. Accordingly, their phylogenetic relationships are still largely disputed. In the present study, 56 nuclear non-coding loci, including 33 introns (INs) and 23 intergenic regions (IGs), from 20 NWM individuals representing 18 species were used to investigate phylogenetic relationships among families and subfamilies. Of the 56 loci, 43 have not been used in previous NWM phylogenetics. We applied concatenation and coalescence tree-inference methods, and a recently proposed question-specific approach to address NWM phylogeny. Our results indicate incongruence between concatenation and coalescence methods for the IN and IG datasets. However, a consensus was reached with a single tree topology from all analyses of combined INs and IGs as well as all analyses of question-specific loci using both concatenation and coalescence methods, albeit with varying degrees of statistical support. In detail, our results indicated the sister-group relationships between the families Atelidae and Pitheciidae, and between the subfamilies Aotinae and Callithrichinae among Cebidae. Our study provides insights into the disputed phylogenetic relationships among NWM families and subfamilies from the perspective of multiple non-coding loci and various tree-inference approaches. However, the present phylogenetic framework needs further evaluation by adding more independent sequence data and a deeper taxonomic sampling. Overall, our work has important implications for phylogenetic studies dealing with rapid radiations.
Confusion, Seduction, Failure: Emotions as Reflexive Knowledge in Conflict Settings
Authors: Hedström Jenny 
Published: October 2018

Abstract
This article highlights the influence of emotions, affective experiences, and rumors on the construction of knowledge within research on conflict and in international politics, as well as within the research process itself. Drawing from fieldwork undertaken in a conflict zone in Myanmar, it suggests that academic knowledge production practices are informed both by the (violent) context in which research is undertaken and by the demands of the discipline to produce a scientifically accepted piece of research. It proposes that attention to emotions may facilitate strong objectivity (Harding 1992) by foregrounding the relationship between research participants, researchers, and the broader research (institutional and immediate) contexts. It introduces the term “rumors-as-affect” as a means to discuss how affective atmospheres or events in the research environments inform research. Three interview situations are presented, in which different emotional reactions are highlighted, focusing on “confusion and guilt”; “seduction”; and finally, “failure and ignorance.” These events illustrate how, in recognizing the role emotions and affective atmospheres play in research on conflict and in international politics (cf. Crawford 2014; Hutchison and Bleiker 2014; Ross 2013), researchers may begin to do justice to our representations of what is encountered in the field and how knowledge is constructed within the discipline.
Integrated Care Models: Optimizing Adult Ambulatory Care in Inflammatory Bowel Disease
Authors: Schoenfeld Roberta , Nguyen Geoffrey C , Bernstein Charles N 
Published: October 2018

Abstract

Background
Inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, is a chronic, complex and unpredictable disease affecting an increasing number of patients worldwide from a young age. Inflammatory bowel disease is associated with multiple comorbidities and complications, requiring ongoing preventative, acute and chronic care. The purpose of this article is to review the literature on outpatient care models used to treat adults with IBD and to gain insight on how to improve quality of care and reduce costs.

Methods
A comprehensive review of recent literature on PubMed, Scopus and Google Scholar databases about care models used to treat IBD was performed. Key terms included ‘inflammatory bowel disease’, ‘organizational models’, ‘patient care team’ and ‘quality improvement’.

Results
Studies showed that an integrated care model decreases hospital admissions, IBD-related surgeries and comorbidities of IBD, ultimately decreasing direct and indirect costs of IBD compared with a more traditional patient-physician model. A gastroenterologist-led multidisciplinary team (MDT) involving comprehensive care by IBD nurses, a surgeon, psychologist, dietician, pharmacist, and other members as needed is recommended.

Conclusions
A holistic approach to IBD care delivered by a MDT with structured monitoring, active follow-up, patient education and prompt access to care improves outcomes for IBD patients. More research is needed on the cost-effectiveness of integrated care models to demonstrate long-term value and secure funding for implementation. Future research should compare integrated models of care and assess patient and physician satisfaction in these models of delivering IBD care.
Role of Screening History in Clinical Meaning and Optimal Management of Positive Cervical Screening Results
Authors: Castle Philip E , Kinney Walter K , Xue Xiaonan , Cheung Li C , Gage Julia C , Poitras Nancy E , Lorey Thomas S , Katki Hormuzd A , Wentzensen Nicolas , Schiffman Mark 
Published: October 2018

Abstract

Background
Cervical cancer is caused by persistent human papillomavirus (HPV) infection. US consensus management guidelines for a positive cervical screening result typically focus on the current screening result only. A negative testing history may alter risk of the following positive screening results, caused by a new HPV infection, and therefore its optimal management.

Methods
Women ages 30 years and older were screened with triennial HPV and cytology co-testing at Kaiser Permanente Northern California from 2003 to 2014. We estimated the subsequent 5-year risks of cervical intraepithelial neoplasia grade 3 or more severe diagnoses (CIN3+) in a cohort of 1 156 387 women following abnormal (atypical squamous cells of undetermined significance [ASC-US] or worse) cytology and/or positive HPV testing, when the test result followed 0 (n = 990 013), 1 (n = 543 986), 2 (n = 245 974), or 3 (n = 79 946) consecutive negative co-test(s). All statistical tests were two-sided.

Results
Following 0–3 successive negative co-tests, 5-year CIN3+ risks following a positive HPV test decreased progressively from 7.2% (95% CI = 7.0% to 7.4%) to 1.5% (95% CI = 0.7% to 3.4%) (Ptrend < .001). Similarly, risks following an abnormal (ASC-US or worse) cytology result decreased from 6.6% (95% CI = 6.4% to 6.9%) to 1.1% (95% CI = 0.5% to 2.3%) (Ptrend < .001). Risks following low-grade squamous intraepithelial lesion, the risk threshold for referral to colposcopy in the United States, decreased from 5.2% (95% CI = 4.7% to 5.7%) to 0.9% (95% CI = 0.2% to 4.3%). Risks following high-grade squamous intraepithelial lesion or more severe, a specific marker for the presence of precancerous lesions, decreased from 50.0% (95% CI = 47.5% to 52.5%) to 10.0% (95% CI = 2.6% to 34.4%).

Conclusions
Following one or more sequential antecedent, documented negative co-tests or HPV tests, women with HPV-positive ASC-US or low-grade squamous intraepithelial lesion might have sufficiently low CIN3+ risk that they do not need colposcopy referral and might instead undergo 6–12-month surveillance for evidence of higher risk before being referred to colposcopy.