bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier
Authors: Xia Jiaqi , Peng Zhenling , Qi Dawei , Mu Hongbo , Yang Jianyi 
Published: December 2016

Abstract

Motivation
Protein fold classification is a critical step in protein structure prediction. There are two possible ways to classify protein folds. One is through template-based fold assignment and the other is ab-initio prediction using machine learning algorithms. Combination of both solutions to improve the prediction accuracy was never explored before.

Results
We developed two algorithms, HH-fold and SVM-fold for protein fold classification. HH-fold is a template-based fold assignment algorithm using the HHsearch program. SVM-fold is a support vector machine-based ab-initio classification algorithm, in which a comprehensive set of features are extracted from three complementary sequence profiles. These two algorithms are then combined, resulting to the ensemble approach TA-fold. We performed a comprehensive assessment for the proposed methods by comparing with ab-initio methods and template-based threading methods on six benchmark datasets. An accuracy of 0.799 was achieved by TA-fold on the DD dataset that consists of proteins from 27 folds. This represents improvement of 5.4–11.7% over ab-initio methods. After updating this dataset to include more proteins in the same folds, the accuracy increased to 0.971. In addition, TA-fold achieved &gt;0.9 accuracy on a large dataset consisting of 6451 proteins from 184 folds. Experiments on the LE dataset show that TA-fold consistently outperforms other threading methods at the family, superfamily and fold levels. The success of TA-fold is attributed to the combination of template-based fold assignment and ab-initio classification using features from complementary sequence profiles that contain rich evolution information.

Availability and Implementation
http://yanglab.nankai.edu.cn/TA-fold/

Supplementary information
Supplementary data are available at Bioinformatics online.
LRSSL: predict and interpret drug–disease associations based on data integration using sparse subspace learning
Authors: Liang Xujun , Zhang Pengfei , Yan Lu , Fu Ying , Peng Fang , Qu Lingzhi , Shao Meiying , Chen Yongheng , Chen Zhuchu 
Published: December 2016

Abstract

Motivation
Exploring the potential curative effects of drugs is crucial for effective drug development. Previous studies have indicated that integration of multiple types of information could be conducive to discovering novel indications of drugs. However, how to efficiently identify the mechanism behind drug–disease associations while integrating data from different sources remains a challenging problem.

Results
In this research, we present a novel method for indication prediction of both new drugs and approved drugs. This method is based on Laplacian regularized sparse subspace learning (LRSSL), which integrates drug chemical information, drug target domain information and target annotation information. Experimental results show that the proposed method outperforms several recent approaches for predicting drug–disease associations. Some drug therapeutic effects predicted by the method could be validated by database records or literatures. Moreover, with L1-norm constraint, important drug features have been extracted from multiple drug feature profiles. Case studies suggest that the extracted drug features could be beneficial to interpretation of the predicted results.

Availability and Implementation
https://github.com/LiangXujun/LRSSL

Supplementary information
Supplementary data are available at Bioinformatics online.
GE-mini: a mobile APP for large-scale gene expression visualization
Authors: Tang Zefang , Li Chenwei , Zhang Karena , Yang Mingyu , Hu Xueda 
Published: December 2016

Abstract

Summary
The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) projects produced large-scale RNA sequencing data, which provides an opportunity for performing integrated expression analysis for all genes across tens of thousands of tumor and normal tissue specimens. Rapid access to and easy visualization of such valuable data could facilitate research in a wide biological area. Here, we present the GE-mini APP for smart phones, a mobile visualization tool for integrated gene expression data based on both TCGA and GTEx. This gene-centric expression viewer provides a convenient method for displaying expression profiles of all available tumor and tissue types, while allowing drilling down to detailed views for specific tissue types.

Availability and Implementation
Both the iOS and Android APPs are freely available to all non-commercial users in App Store and Google Play. The QR codes of App store and Google play are also provided for scanning and download. The GE-mini web server is also available at http://gemini.cancer-pku.cn/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Determinants of Patient Satisfaction in Celiac Disease Care
Authors: Faye Adam S. , Mahadev SriHari , Lebwohl Benjamin , Green Peter H.R. 
Published: December 2016

Background and Goals:
There are little data examining patient satisfaction with celiac disease (CD) care. We sought to assess how satisfied patients are with their CD care, and to determine the influencing factors.

Study:
We distributed an online questionnaire to adults receiving programmatic updates from a CD referral center, querying aspects of CD care and using disease-specific validated instruments to measure quality of life and dietary adherence. The univariable and multivariable analyses were performed using satisfaction as a binary outcome comparing grouped “satisfied” and “very satisfied” respondents to “neutral,” “dissatisfied,” and “very dissatisfied” respondents.

Results:
Three hundred eighty-seven (22%) individuals completed the survey, and 229 met the inclusion criteria of biopsy-proven CD. Seventy-nine individuals (34.5%) reported being “very satisfied” with their CD care, 82 (35.8%) “satisfied,” 46 (20.1%) “neutral,” 14 (6.1%) “dissatisfied,” and 8 (3.5%) “very dissatisfied.” On multivariable analysis, reporting that physicians spend ample time managing CD needs (P=0.013), and having CD-antibody levels checked yearly (P=0.003), were positive predictors of patient satisfaction. Factors that were not correlated with patient satisfaction included symptom severity (P=0.268), quality of life (P=0.13), and following with a CD specialist (P=0.139).

Conclusions:
The majority of patients we surveyed were satisfied with their CD care. We found that patients report higher satisfaction when they feel physicians spend time caring for their CD needs and when they receive annual CD-antibody testing. On the basis of our study, these factors are more important than disease severity, seeing a CD specialist, and quality of life in determining patient satisfaction with CD care.
Physician-Patient Communication is Associated With Hepatocellular Carcinoma Screening in Chronic Liver Disease Patients
Authors: Li Deborah J. , Park Yikyung , Vachharajani Neeta , Aung Wint Yan , Garonzik-Wang Jacqueline , Chapman William C. 
Published: December 2016

Background:
Patients with chronic liver disease are at high risk for developing liver cancer. Factors associated with screening awareness and doctor-patient communication regarding liver cancer were examined.

Study:
Four hundred sixty-seven patients with chronic liver disease at a tertiary-care clinic participated in a phone survey regarding awareness of cancer screening, doctor-patient communication, and health behaviors. Medical records were retrospectively reviewed for data on liver disease etiology and dates of liver imaging tests.

Results:
Seventy-nine percent of patients reported awareness of liver cancer screening, and 50% reported talking to their doctor about liver cancer. Patients with higher education, abstinence from alcohol, and liver cirrhosis were more likely to be aware of liver cancer screening (P=0.06, 0.005, <0.0001). Whites, patients with higher education, and those with cirrhosis were more likely to talk to their doctor about liver cancer (P=0.006; P=0.09, <0.0001). Awareness of liver cancer screening (79%) was similar to that of colorectal cancer screening (85%), lower than breast cancer screening (91%), and higher than prostate cancer screening (66%). Patients who were aware of liver cancer screening and reported talking to their doctor about liver cancer were significantly more likely to receive consistent liver surveillance (odds ratio, 4.81; 95% confidence interval, 2.62-8.84 and odds ratio, 1.97; 95% confidence interval, 1.19-3.28, respectively).

Conclusions:
Our study demonstrates the importance of effective physician communication with chronic liver disease patients on the risks of developing liver cancer and the importance of regular screening, especially among nonwhites and patients with lower education.
The Role of Relocation Patterns and Psychosocial Stressors in Posttraumatic Stress Disorder and Depression Among Earthquake Survivors
Authors: Salcioglu Ebru , Ozden Sahin , Ari Furkan 
Published: December 2016

Abstract
The psychological impact of relocation within and outside of a disaster region was examined in 541 survivors of the 2011 Van earthquake in Turkey at 16.5 months postdisaster. Relocation out of the region was determined by disaster-related property/financial losses and fear during the earthquake. Anticipatory fear of future earthquakes and less sense of control over life were the strongest predictors of posttraumatic stress disorder (PTSD) and depression symptoms. Relocation within the disaster region predicted PTSD but not depression. Dissatisfaction with emotional support received from close ones was significantly associated with depression, but it was associated with PTSD at a marginally significant level. Survivors who experienced more intense fear during the earthquake displayed higher levels of anticipatory fear in the long term, whereas avoidance of trauma reminders and fear-evoking situations sustained anticipatory fear of future earthquakes. These findings suggest that interventions that reduce fear and avoidance behaviors would help survivors overcome traumatic stress and depressive symptoms.
Germ granules prevent accumulation of somatic transcripts in the adultC. elegansgermline
Authors: Kekūpa’a Knutson Andrew , Egelhofer Thea , Rechtsteiner Andreas , Strome Susan 
Published: December 2016

ABSTRACTThe germ cells of multicellular organisms protect their developmental potential through specialized mechanisms. A shared feature of germ cells from worms to humans is the presence of non-membrane-bound ribonucleoprotein organelles called germ granules. Depletion of germ granules inCaenorhabditis elegans(i.e., P granules) leads to sterility and in some germlines expression of the neuronal transgeneunc-119::gfpand the muscle myosin MYO-3. Thus, P granules are hypothesized to maintain germ cell totipotency by preventing somatic development, although the mechanism by which P granules carry out this function is unknown. In this study, we performed transcriptome and single molecule RNA-FISH analyses of dissected P-granule-depleted gonads at different developmental stages. Our results demonstrate that P granules are necessary for adult germ cells to down-regulate spermatogenesis RNAs and to prevent the accumulation of numerous soma-specific RNAs. P-granule-depleted gonads that express theunc-119::gfptransgene also express many other genes involved in neuronal development and concomitantly lose expression of germ cell fate markers. Finally, we show that removal of either of two critical P-granule components, PGL-1 or GLH-1, is sufficient to cause germ cells to express UNC-119::GFP and MYO-3 and to display RNA accumulation defects similar to those observed after depletion of P granules. Our data identify P granules as critical modulators of the germline transcriptome and guardians of germ cell fate.
Tumor Origin Detection with Tissue-Specific miRNA and DNA methylation Markers
Authors: Tang Wei , Wan Shixiang , Zou Quan 
Published: December 2016

AbstractMotivationCancer of unknown primary origin constitutes 3-5% of all human malignancies. Patients with these carcinomas present with metastases without an established primary site, which may not be found even by thorough histological search methods. Patients with cancer of unknown primary origin always have poor prognosis and hardly have efficient treatment since most cancers respond well to specific chemotherapy or hormone drugs. Many studies have proposed classifiers based on miRNAs or mRNAs to predict the tumor origins, but few study focus on high-dimensional DNA methylation profiles.ResultsWe introduced three classifiers with novel feature selection algorithm combined with random forest to effectively identify highly tissue-specific epigenetics biomarkers such as microRNAs and CpG sites, which can help us predict the origin site of tumors. This algorithm, incorporating differential analysis and descending dimension algorithm, was applied on 14 histological tissues and over 5000 samples based on miRNA expression and DNA methylation profiles to assign given primary tumor to its origin tissue. Our study shows all of these three classifiers have an overall accuracy of 87.78% (72.55%-97.54%) based on miRNA datasets and an accuracy of 96.43% (MRMD: 87.85%-99.76%) or 97.06% (PCA: 92.44%-100%) based on DNA methylation datasets on predicting the origin of tumors and suggests that the biomarkers we selected can efficiently predict the origin of tumors and allow the clinicians to avoid adjuvant systemic therapy or to choose less aggressive therapeutic options. We also developed a user-friendly webserver which enables users to predict the origin site of tumors by uploading the miRNAs expression or DNA methylation profiles of those cancers.AvailabilityThe webserver, data, and code are accessible free of charge athttp://server.malab.cn/MMCOP/Contactzouquan@nclab.netSupplementary informationSupplementary data are available atBioinformaticsonline.
Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment
Authors: Burns Michael B. , Montassier Emmanuel , Abrahante Juan , Priya Sambhawa , Niccum David E. , Khoruts Alexander , Starr Timothy K. , Knights Dan , Blekhman Ran 
Published: December 2016

AbstractVariation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues. We found statistically significant associations between loss-of-function mutations in tumor genes and shifts in the abundances of specific sets of bacterial taxa, suggestive of potential functional interaction. This correlation allows us to statistically predict interactions between loss-of-function tumor mutations in cancer-related genes and pathways, including MAPK and Wnt signaling, solely based on the composition of the microbiome. These results can serve as a starting point for fine-grained exploration of the functional interactions between discrete alterations in tumor DNA and proximal microbial communities in CRC. In addition, these findings can lead to the development of improved microbiome-based CRC screening methods, as well as individualized microbiota-targeting therapies.Author summaryAlthough the gut microbiome - the collection of microorganisms that inhabit our gastrointestinal tract - has been implicated in colorectal cancer, colorectal tumors are caused by genetic mutations in host DNA. Here, we explored whether various mutations in colorectal tumors are correlated with specific changes in the bacterial communities that live in and on these tumors. We find that the genes and biological pathways that are mutated in tumors are correlated with variation in the composition of the microbiome. In fact, these changes in the microbiome are consistent enough that we can use them to statistically predict tumor mutations solely based on the microbiome. Our results may be used to understand the roles of specific microbes in CRC biology, and could also be the starting point of microbiome-based diagnostics for not only detection of CRC, but characterization of tumor mutational profiles.
The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation
Authors: Dao Duc Khanh , Song Yun S. 
Published: December 2016

ABSTRACTPrevious studies have shown that translation elongation is regulated by multiple factors, but the observed heterogeneity remains only partially explained. To dissect quantitatively the different determinants of elongation speed, we use probabilistic modeling to estimate initiation and local elongation rates from ribosome profiling data. This model-based approach allows us to quantify the extent of interference between ribosomes on the same transcript. We show that neither interference nor the distribution of slow codons is sufficient to explain the observed heterogeneity. Instead, we find that electrostatic interactions between the ribosomal exit tunnel and specific parts of the nascent polypeptide govern the elongation rate variation as the polypeptide makes its initial pass through the tunnel. Once the N-terminus has escaped the tunnel, the hydropathy of the nascent polypeptide within the ribosome plays a major role in modulating the speed. We show that our results are consistent with the biophysical properties of the tunnel.
Forgotten classics: The Business Guide by James L. Nichols (1894)
Authors: Miller Darryl W. 
Published: December 2016

Purpose
The purpose of this paper is to review a popular business handbook – The Business Guide – by James L. Nichols, first published around the turn of the twentieth century. The analysis is geared toward determining how it fits within the development of marketing thought and education.

Design/methodology/approach
A review of the marketing history literature focusing on marketing thought, education and practice around the turn of the twentieth century is conducted. The content of The Business Guide is analyzed and compared with the themes reflected in the literature review.

Findings
Most editions appeared in the era just proceeding the emergence of marketing as distinct discipline. It is unlikely that it had any appreciable influence on the development of marketing thought. However, it was used as a textbook at North-Western College in Naperville, IL, and may have been at other early business education programs in the USA and Canada. Nichols’ treatment of marketing topics was consistent with the era. It reflected commodities and functional views. For him, marketing was primarily distribution along with advertising, pricing, product management and credit. Consistent with modern marketing philosophy, Nichols placed heavy emphasis on ethics.

Originality/value
Despite the fact that this book was published in multiple editions over several decades, it seems to have been largely forgotten. As far as is known, this paper is the only recent treatment of this historical artifact.
Forgotten classics: Motivation in Advertising, by Pierre Martineau (1957)
Authors: Beard Fred 
Published: December 2016

Purpose
The purpose of this paper is to review and summarize Pierre Martineau’s Motivation in Advertising and to assess its status as a valid forgotten classic of the marketing literature.

Design/methodology/approach
Motivation in Advertising is reviewed and summarized, and its contributions to marketing and advertising history, thought and practice are assessed.

Findings
Martineau was among a handful of figures behind the “motivation research” movement among marketers and advertisers during the late 1940s to the 1960s. His “new philosophy” regarding communication theory, persuasion and advertising message strategy and tactics remains highly influential and relevant. Written during a period of tremendous growth in consumption in the USA and a revolution in the use of qualitative research in marketing and advertising, Martineau’s book represents much more than a work about his experiences with motivation research, but a significant contribution to advertising communication theory as well.

Originality/value
Pierre Martineau was the subject of a historical biography (Martin, 1985), which also focused substantially on the principal themes and contributions of Motivation in Advertising. The book was also widely reviewed shortly after its publication. This more recent review and assessment, however, reveals the work’s valuable historical insights into how postmodern consumption evolved and many present-day perspectives of consumer behavior and advertising effects coalesced during the Consumer Revolution and at the outset of modern advertising’s “Golden Age”.
Advertising in a regulated economy: Swedish advertisements 1760-1800
Authors: Murhem Sofia 
Published: December 2016

PurposeThe aim of this paper is to examine the nature of newspaper advertisements for goods in Stockholm newspapers in the 18th century by studying what goods were advertised, how frequently they were advertised and what marketing strategies were used. The findings are discussed in relation to results from other countries and the institutional context.Design/methodology/approachThe primary sources used are three Swedish papers published in Stockholm, one national, Inrikes tidningar, and two local. Stockholms Weckobladh and Dagligt Allehanda. In all, more than 1300 advertisements were examined. In addition, a number of secondary sources were used.FindingsIn contrast to most other countries, the guilds held a firm grip on Sweden’s (and Stockholm’s) business life throughout the 18th century, and enforced strict restrictions on market entry. Thereby, competition was reduced, the number of tradesmen was more or less constant and the need for marketing was low. The guilds also restricted advertising. This led to marketing strategies being underdeveloped in comparison to other countries, which affected Swedish marketing and Swedish advertisements all through the 19th century. Marketing was a viable option in 18th century Sweden, but only for those not restricted by guilds and societies.Originality/valueThere has been very little research on 18th century Swedish marketing. The paper also illustrates the need for including the institutional context when discussing historical marketing, which often has been neglected for this period in the international literature.