bluuebunny/crossref_metadata_2025_split huggingface dataset:
TOPAS: network-based structural alignment of RNA sequences
Authors: Chen Chun-Chi , Jeong Hyundoo , Qian Xiaoning , Yoon Byung-Jun 
Published: January 2019

Abstract

Motivation
For many RNA families, the secondary structure is known to be better conserved among the member RNAs compared to the primary sequence. For this reason, it is important to consider the underlying folding structures when aligning RNA sequences, especially for those with relatively low sequence identity. Given a set of RNAs with unknown structures, simultaneous RNA alignment and folding algorithms aim to accurately align the RNAs by jointly predicting their consensus secondary structure and the optimal sequence alignment. Despite the improved accuracy of the resulting alignment, the computational complexity of simultaneous alignment and folding for a pair of RNAs is O(N6), which is too costly to be used for large-scale analysis.

Results
In order to address this shortcoming, in this work, we propose a novel network-based scheme for pairwise structural alignment of RNAs. The proposed algorithm, TOPAS, builds on the concept of topological networks that provide structural maps of the RNAs to be aligned. For each RNA sequence, TOPAS first constructs a topological network based on the predicted folding structure, which consists of sequential edges and structural edges weighted by the base-pairing probabilities. The obtained networks can then be efficiently aligned by using probabilistic network alignment techniques, thereby yielding the structural alignment of the RNAs. The computational complexity of our proposed method is significantly lower than that of the Sankoff-style dynamic programming approach, while yielding favorable alignment results. Furthermore, another important advantage of the proposed algorithm is its capability of handling RNAs with pseudoknots while predicting the RNA structural alignment. We demonstrate that TOPAS generally outperforms previous RNA structural alignment methods on RNA benchmarks in terms of both speed and accuracy.

Availability and implementation
Source code of TOPAS and the benchmark data used in this paper are available at https://github.com/bjyoontamu/TOPAS.
Streamlined analysis of LINCS L1000 data with the slinky package for R
Authors: Kort Eric J , Jovinge Stefan 
Published: January 2019

Abstract

Summary
The L1000 dataset from the NIH LINCS program holds the promise to deconvolute a wide range of biological questions in transcriptional space. However, using this large and decentralized dataset presents its own challenges. The slinky package was created to streamline the process of identifying samples of interest and their corresponding control samples, and loading their associated expression data and metadata. The package can integrate with workflows leveraging the BioConductor collection of tools by encapsulating the L1000 data as a SummarizedExperiment object.

Availability and implementation
Slinky is freely available as an R package at http://bioconductor.org/packages/slinky
Sstack: an R package for stacking with applications to scenarios involving sequential addition of samples and features
Authors: Matlock Kevin , Rahman Raziur , Ghosh Souparno , Pal Ranadip 
Published: January 2019

Abstract

Summary
Biological processes are characterized by a variety of different genomic feature sets. However, often times when building models, portions of these features are missing for a subset of the dataset. We provide a modeling framework to effectively integrate this type of heterogeneous data to improve prediction accuracy. To test our methodology, we have stacked data from the Cancer Cell Line Encyclopedia to increase the accuracy of drug sensitivity prediction. The package addresses the dynamic regime of information integration involving sequential addition of features and samples.

Availability and implementation
The framework has been implemented as a R package Sstack, which can be downloaded from https://cran.r-project.org/web/packages/Sstack/index.html, where further explanation of the package is available.

Supplementary information
Supplementary data are available at Bioinformatics online.
TopoLink: evaluation of structural models using chemical crosslinking distance constraints
Authors: Ferrari Allan J R , Clasen Milan A , Kurt Louise , Carvalho Paulo C , Gozzo Fabio C , Martínez Leandro 
Published: January 2019

Abstract

Summary
A software was developed to evaluate structural models using chemical crosslinking experiments. The user provides the types of linkers used and their reactivity, and the observed crosslinks and dead-ends. The software computes the minimum length of a physically inspired linker that connects the reactive atoms of interest, and reports the consistency of each distance with the experimental observation. Statistics on model consistency with the links are provided. Tools to evaluate the correlation of crosslinks in ensembles of models were developed. TopoLink was used to evaluate the potential crosslinks of all structures of the CATH database. The number of crosslinks expected as a function of protein size and linker length can be used as guide for experimental design.

Availability and implementation
TopoLink is available as free software at http://m3g.iqm.unicamp.br/topolink, and distributed as source code with a user-friendly graphical interface for Windows. A web server is also provided.

Supplementary information
Supplementary data are available at Bioinformatics online.
PopCluster: an algorithm to identify genetic variants with ethnicity-dependent effects
Authors: Gurinovich Anastasia , Bae Harold , Farrell John J , Andersen Stacy L , Monti Stefano , Puca Annibale , Atzmon Gil , Barzilai Nir , Perls Thomas T , Sebastiani Paola 
Published: January 2019

Abstract

Motivation
Over the last decade, more diverse populations have been included in genome-wide association studies. If a genetic variant has a varying effect on a phenotype in different populations, genome-wide association studies applied to a dataset as a whole may not pinpoint such differences. It is especially important to be able to identify population-specific effects of genetic variants in studies that would eventually lead to development of diagnostic tests or drug discovery.

Results
In this paper, we propose PopCluster: an algorithm to automatically discover subsets of individuals in which the genetic effects of a variant are statistically different. PopCluster provides a simple framework to directly analyze genotype data without prior knowledge of subjects’ ethnicities. PopCluster combines logistic regression modeling, principal component analysis, hierarchical clustering and a recursive bottom-up tree parsing procedure. The evaluation of PopCluster suggests that the algorithm has a stable low false positive rate (∼4%) and high true positive rate (&gt;80%) in simulations with large differences in allele frequencies between cases and controls. Application of PopCluster to data from genetic studies of longevity discovers ethnicity-dependent heterogeneity in the association of rs3764814 (USP42) with the phenotype.

Availability and implementation
PopCluster was implemented using the R programming language, PLINK and Eigensoft software, and can be found at the following GitHub repository: https://github.com/gurinovich/PopCluster with instructions on its installation and usage.

Supplementary information
Supplementary data are available at Bioinformatics online.
The intestine responds to heart failure by enhanced mitochondrial fusion through glucagon-like peptide-1 signalling
Authors: Naruse Genki , Kanamori Hiromitsu , Yoshida Akihiro , Minatoguchi Shingo , Kawaguchi Tomonori , Iwasa Masamitsu , Yamada Yoshihisa , Mikami Atsushi , Kawasaki Masanori , Nishigaki Kazuhiko , Minatoguchi Shinya 
Published: January 2019

AbstractAimsGlucagon-like peptide-1 (GLP-1) is a neuroendocrine hormone secreted by the intestine. Its receptor (GLP-1R) is expressed in various organs, including the heart. However, the dynamics and function of the GLP-1 signal in heart failure remains unclear. We investigated the impact of the cardio-intestinal association on hypertensive heart failure using miglitol, an α-glucosidase inhibitor known to stimulate intestinal GLP-1 production.Methods and resultsDahl salt-sensitive (DS) rats fed a high-salt diet were assigned to miglitol, exendin (9-39) (GLP-1R blocker) and untreated control groups and treated for 11 weeks. Control DS rats showed marked hypertension and cardiac dysfunction with left ventricular dilatation accompanied by elevated plasma GLP-1 levels and increased cardiac GLP-1R expression as compared with age-matched Dahl salt-resistant (DR) rats. Miglitol further increased plasma GLP-1 levels, suppressed adverse cardiac remodelling, and mitigated cardiac dysfunction. In cardiomyocytes from miglitol-treated DS hearts, mitochondrial size was significantly larger with denser cristae than in cardiomyocytes from control DS hearts. The change in mitochondrial morphology reflected enhanced mitochondrial fusion mediated by protein kinase A activation leading to phosphorylation of dynamin-related protein 1, expression of mitofusin-1 and OPA-1, and increased myocardial adenosine triphosphate (ATP) content. GLP-1R blockade with exendin (9-39) exacerbated cardiac dysfunction and led to fragmented mitochondria with disarrayed cristae in cardiomyocytes and reduction of myocardial ATP content. In cultured cardiomyocytes, GLP-1 increased expression of mitochondrial fusion-related proteins and ATP content. When GLP-1 and exendin (9-39) were administered together, their effects cancelled out.ConclusionsIncreased intestinal GLP-1 secretion is an adaptive response to heart failure that is enhanced by miglitol. This could be an effective strategy for treating heart failure through regulation of mitochondrial dynamics.
The incidence and distribution of mediastinal lymph node metastasis and its impact on survival in patients with non-small-cell lung cancers 3 cm or less: data from 2292 cases
Authors: Yang Mu-Zi , Hou Xue , Liang Run-Bin , Lai Ren-Chun , Yang Jie , Li Shuo , Long Hao , Fu Jian-Hua , Lin Peng , Wang Xin , Rong Tie-Hua , Yang Hao-Xian 
Published: January 2019

Abstract

OBJECTIVES
Our goal was to investigate the incidence and distribution of mediastinal lymph node metastases (MLNM) in non-small-cell lung cancers (NSCLC) 3 cm or less, with the purpose of guiding mediastinal lymph node dissection.

METHODS
A total of 2292 cases seen between January 2001 and December 2014 were included. These patients were grouped according to the lobes with the primary tumours. The incidence and distribution of pathological MLNM were compared among the groups. The impact of MLNM on overall survival was also compared.

RESULTS
The most common mediastinal metastatic sites for different primary tumour lobes were as follows: right upper lobe, 17.7% (87/492) for level 4R; right middle lobe, 14.9% (28/188) for level 7; right lower lobe, 19.8% (82/414) for level 7; left upper lobe, 18.2% (96/528) for level 5; and left lower lobe, 16.6% (42/253) for level 7. For patients with tumours in the upper lobe, the median survival time was 32 months for those with MLNM in the subcarinal zone or lower zone compared with 83 months for those with MLNM only in the upper zone (P < 0.01). When the tumours were 1 cm or less, the incidence of MLNM to the lower zone for upper lobe tumours and of MLNM to the upper zone for lower lobe tumours was zero.

CONCLUSIONS
Different primary NSCLC lobe locations have a different propensity to be sites of MLNM for those tumours that are 3 cm or less. For tumours no larger than 1 cm, a lower zone mediastinal lymph node dissection might be unnecessary for upper lobe tumours and an upper zone mediastinal lymph node dissection might be unnecessary for lower lobe tumours.
Domesticated escapees on the run: the second-generation monitoring programme reports the numbers and proportions of farmed Atlantic salmon in &gt;200 Norwegian rivers annually
Authors: Glover K A , Urdal K , Næsje T , Skoglund H , Florø-Larsen B , Otterå H , Fiske P , Heino M , Aronsen T , Sægrov H , Diserud O , Barlaup B T , Hindar K , Bakke G , Solberg I , Lo H , Solberg M F , Karlsson S , Skaala Ø , Lamberg A , Kanstad-Hanssen Ø , Muladal R , Skilbrei O T , Wennevik V 
Published: January 2019

Abstract
Norway is the world’s largest producer of farmed Atlantic salmon and is home to ∼400 rivers containing wild salmon populations. Farmed escapees, a reoccurring challenge of all cage-based marine aquaculture, pose a threat to the genetic integrity, productivity, and evolutionary trajectories of wild populations. Escapees have been monitored in Norwegian rivers since 1989, and, a second-generation programme was established in 2014. The new programme includes data from summer angling, autumn angling, broodstock sampling, and snorkelling surveys in &gt;200 rivers, and &gt;25 000 scale samples are analysed annually. In 2014–2017, escapees were observed in two-thirds of rivers surveyed each year, and between 15 and 30 of the rivers had &gt;10% recorded escapees annually. In the period 1989–2017, a reduction in the proportion of escapees in rivers was observed, despite a &gt;6-fold increase in aquaculture production. This reflected improved escape prevention, and possibly changes in production methods that influence post-escape behaviour. On average, populations estimated to experience the greatest genetic introgression from farmed salmon up to 2014 also had the largest proportions of escapees in 2014–2017. Thus, populations already most affected are those at greatest risk of further impacts. These data feed into the annual risk-assessment of Norwegian aquaculture and form the basis for directing mitigation efforts.
Incidental seabird mortality and discarded catches from trawling off far southern Chile (39–57°S)
Authors: Adasme Luis M , Canales Cristian M , Adasme Nicolás A 
Published: January 2019

AbstractIn world fisheries, incidental non target species mortality have turned in a permanent debate issue. Although many studies have dealt with these interactions from a descriptive overview, there is little information based on fishing operations data. One of the most important species that have awakened scientific concern are seabird, being southern Chile one of the areas with the highest levels in this kind of interactions. In order to improve our understanding on these relationships, we analyze records of fishing hauls of industrial trawlers off the coast of Chile between 39 and 57°S. The results showed that incidental seabird mortality appears to be affected mainly by the collisions with net monitoring systems (net-sonde cable), the duration of fishing hauls, the year period, and the fishing zones, these last related to the breeding period and areas of albatross colonies. We indirectly address a probable relationship between seabird mortality and fishing discards, and some hypothesis are proposed to explain the results. Finally, we demonstrated that longer fishing hauls are less efficient for fishing, beside to a high seabird mortality. Our findings suggest mitigation actions that would harmonize fishing activity with the ecosystem, in particular, for trawl fishing management and operations off far southern Chile.
Weakly supervised natural language processing for assessing patient-centered outcome following prostate cancer treatment
Authors: Banerjee Imon , Li Kevin , Seneviratne Martin , Ferrari Michelle , Seto Tina , Brooks James D , Rubin Daniel L , Hernandez-Boussard Tina 
Published: January 2019

Abstract

Background
The population-based assessment of patient-centered outcomes (PCOs) has been limited by the efficient and accurate collection of these data. Natural language processing (NLP) pipelines can determine whether a clinical note within an electronic medical record contains evidence on these data. We present and demonstrate the accuracy of an NLP pipeline that targets to assess the presence, absence, or risk discussion of two important PCOs following prostate cancer treatment: urinary incontinence (UI) and bowel dysfunction (BD).

Methods
We propose a weakly supervised NLP approach which annotates electronic medical record clinical notes without requiring manual chart review. A weighted function of neural word embedding was used to create a sentence-level vector representation of relevant expressions extracted from the clinical notes. Sentence vectors were used as input for a multinomial logistic model, with output being either presence, absence or risk discussion of UI/BD. The classifier was trained based on automated sentence annotation depending only on domain-specific dictionaries (weak supervision).

Results
The model achieved an average F1 score of 0.86 for the sentence-level, three-tier classification task (presence/absence/risk) in both UI and BD. The model also outperformed a pre-existing rule-based model for note-level annotation of UI with significant margin.

Conclusions
We demonstrate a machine learning method to categorize clinical notes based on important PCOs that trains a classifier on sentence vector representations labeled with a domain-specific dictionary, which eliminates the need for manual engineering of linguistic rules or manual chart review for extracting the PCOs. The weakly supervised NLP pipeline showed promising sensitivity and specificity for identifying important PCOs in unstructured clinical text notes compared to rule-based algorithms.

Trial registration
This is a chart review study and approved by Institutional Review Board (IRB).
ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data
Authors: Glicksberg Benjamin S , Oskotsky Boris , Giangreco Nicholas , Thangaraj Phyllis M , Rudrapatna Vivek , Datta Debajyoti , Frazier Remi , Lee Nelson , Larsen Rick , Tatonetti Nicholas P , Butte Atul J 
Published: January 2019

Abstract

Objectives
Electronic health record (EHR) data are increasingly used for biomedical discoveries. The nature of the data, however, requires expertise in both data science and EHR structure. The Observational Medical Outcomes Partnership (OMOP) common data model (CDM) standardizes the language and structure of EHR data to promote interoperability of EHR data for research. While the OMOP CDM is valuable and more attuned to research purposes, it still requires extensive domain knowledge to utilize effectively, potentially limiting more widespread adoption of EHR data for research and quality improvement.

Materials and methods
We have created ROMOP: an R package for direct interfacing with EHR data in the OMOP CDM format.

Results
ROMOP streamlines typical EHR-related data processes. Its functions include exploration of data types, extraction and summarization of patient clinical and demographic data, and patient searches using any CDM vocabulary concept.

Conclusion
ROMOP is freely available under the Massachusetts Institute of Technology (MIT) license and can be obtained from GitHub (http://github.com/BenGlicksberg/ROMOP). We detail instructions for setup and use in the Supplementary Materials. Additionally, we provide a public sandbox server containing synthesized clinical data for users to explore OMOP data and ROMOP (http://romop.ucsf.edu).
Being Hopeful: Exploring the Dynamics of Post-traumatic Growth and Hope in Refugees
Authors: UMER MADEHA , Elliot Dely Lazarte 
Published: January 2019

AbstractWith more than 60 million people across the world displaced from their homes, the refugee crisis has been in the political limelight and prominent in academic conversations. With a focus on the salutogenic rather than the pathological effects of trauma, this research probed beyond refugees’ distressed psychological wellbeing by exploring contributory factors to refugees’ effective resettlement during the post-migration phase. In this small-scale study, participants were purposively selected. The mixed-methods approach led to the assessment of refugees’ post-traumatic growth and a qualitative investigation of their narrative writings on hope. Adopting a psychological lens, the article critically considers Charles Snyder’s theoretical framework on ‘hope’ and its tenets, namely ‘Goals’, ‘Pathways’, ‘Agency’, ‘Barriers’ and ‘Thoughts & Feelings’, by employing it freshly in a new context and extending the framework in light of refugees’ successful adaptation and integration into society. The research findings endorse the value of developing a hopeful disposition as key to refugees’ acculturation, empowerment and post-traumatic growth.
Expression of STAT3-regulated genes in circulating CD4+ T cells discriminates rheumatoid arthritis independently of clinical parameters in early arthritis
Authors: Anderson Amy E , Maney Nicola J , Nair Nisha , Lendrem Dennis W , Skelton Andrew J , Diboll Julie , Brown Philip M , Smith Graham R , Carmody Ruaidhrí J , Barton Anne , Isaacs John D , Pratt Arthur G 
Published: January 2019

Abstract

Objectives
Dysregulated signal transduction and activator of transcription-3 (STAT3) signalling in CD4+ T cells has been proposed as an early pathophysiological event in RA. We sought further evidence for this observation, and to determine its clinical relevance.

Methods
Microarray technology was used to measure gene expression in purified peripheral blood CD4+ T cells from treatment-naïve RA patients and disease controls newly recruited from an early arthritis clinic. Analysis focused on 12 previously proposed transcripts, and concurrent STAT3 pathway activation was determined in the same cells by flow cytometry. A pooled analysis of previous and current gene expression findings incorporated detailed clinical parameters and employed multivariate analysis.

Results
In an independent cohort of 161 patients, expression of 11 of 12 proposed signature genes differed significantly between RA patients and controls, robustly validating the earlier findings. Differential regulation was most pronounced for the STAT3 target genes PIM1, BCL3 and SOCS3 (&gt;1.3-fold difference; P &lt; 0.005), each of whose expression correlated strongly with paired intracellular phospho-STAT3. In a meta-analysis of 279 patients the same three genes accounted for the majority of the signature’s ability to discriminate RA patients, which was found to be independent of age, joint involvement or acute phase response.

Conclusion
The STAT3-mediated dysregulation of BCL3, SOCS3 and PIM1 in circulating CD4+ T cells is a discriminatory feature of early RA that occurs independently of acute phase response. The mechanistic and functional implications of this observation at a cellular level warrant clarification.
When international mobility meets local connections: Evidence from China
Authors: Li Feng , Tang Li 
Published: January 2019

AbstractTransnational academic mobility has long been championed as positive and worthy of supporting. Yet, little attention has been paid to its joint impact with local connections on the career advancement of established scholars. Utilizing novel curriculum vitae data of 1447 Chang Jiang Scholars, we examine the relationship between academic mobility and the speed of obtaining prestigious academic titles. Our results suggest that local connections accelerate the career development of Chinese scholars, while international academic mobility has a negligible effect or even slows down the speed of late-phase career advancement. Returnee scholars tend to obtain national academic titles within a longer time period compared with their local counterparts. This penalty of international academic mobility also holds for returnees with only overseas PhD training experience and international research visits. Local scientists are more likely than their returnee peers with equivalent ties to have a quicker career trajectory. Policy implications are also discussed.