bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent Developments in Clinical Terminologies — SNOMED CT, LOINC, and RxNorm
Authors: Bodenreider Oliver , Cornet Ronald , Vreeman Daniel 
Published: August 2018

Objective: To discuss recent developments in clinical terminologies. SNOMED CT (Systematized Nomenclature of Medicine Clinical Terms) is the world's largest clinical terminology, developed by an international consortium. LOINC (Logical Observation Identifiers, Names, and Codes) is an international terminology widely used for clinical and laboratory observations. RxNorm is the standard drug terminology in the U.S.
Methods and results: We present a brief review of the history, current state, and future development of SNOMED CT, LOINC and RxNorm. We also analyze their similarities and differences, and outline areas for greater interoperability among them.
Conclusions: With different starting points, representation formalisms, funding sources, and evolutionary paths, SNOMED CT, LOINC, and RxNorm have evolved over the past few decades into three major clinical terminologies supporting key use cases in clinical practice. Despite their differences, partnerships have been created among their development teams to facilitate interoperability and minimize duplication of effort.
Algorithmen und Leitlinien zur Behandlung der akuten Depression
Authors: Adli M. , Bschor T. , Seemüller F. 
Published: August 2018

ZusammenfassungTherapiealgorithmen stellen explizite und systematische Behandlungsprotokolle dar, welche standardisierte Handlungsanweisungen für therapeutische Entscheidungen beinhalten. Die wichtigsten nationalen und internationalen Leitlinien werden im Hinblick auf die Empfehlungen zur medikamentösen Akuttherapie der unipolaren depressiven Episode verglichen und Unterschiede sowie Gemeinsamkeiten herausgearbeitet. Von den meisten Leitlinien wird für die mittelschwere Depression eine Monotherapie mit einem Antidepressivum und bei einer psychotischen Depression die Kombination aus einem Antipsychotikum und einem Antidepressivum empfohlen. Bei initialer Non-Response empfiehlt die S3-Leitlinie, therapeutisches Drugmonitoring, Dosiserhöhung, Augmentation mit Lithium und Quetiapin oder eine Kombinationstherapie von TZA, SSRI und SNRI mit entweder Mianserin oder Mirtazapin. Bei den internationalen Leitlinien zeigt sich in diesem Fall die größte Übereinstimmung für eine Augmentation des initialen Antidepressivums mit einem Antipsychotikum der zweiten Generation.
Ketamin in der Behandlung depressiver Episoden
Authors: Deuschle M. , Gilles M. 
Published: August 2018

ZusammenfassungKetamin, ein hochaffiner nicht kompetitiver Antagonist am glutamatergen N-Methyl-D-Aspartat (NMDA-)Rezeptor zeigt potente und schnell wirksame antidepressive Effekte bei Patienten mit therapieresistenter unipolarer und bipolarer Depression. Dieser rasch einsetzende antidepressive Effekt konnte seit 2000 in vielen, wenn auch meist mit kleiner Fallzahl, randomisiert kontrollierten Studien gezeigt werden. Bis heute ist die Ketamingabe zur Behandlung depressiver Störungen eine Off-label-Behandlung. Behandlungsrichtlinien und -algorithmen im klinischen Umfeld sind ebenso wie mehr Forschung bezüglich der Beobachtung möglicher (nachteiliger) klinischer Langzeitwirkungen und Sicherheitsdaten von wiederholten Ketamingaben und -erhaltungstherapie nötig.
Mineralocorticoid Receptor and Cardiovascular Disease
Authors: Buonafine Mathieu , Bonnard Benjamin , Jaisser Frédéric 
Published: August 2018

AbstractActivation of the mineralocorticoid receptor (MR) in the distal nephron by its ligand, aldosterone, plays an important role in sodium reabsorption and blood pressure regulation. However, expression of the MR goes beyond the kidney. It is expressed in a variety of other tissues in which its activation could lead to tissue injury. Indeed, MR activation in the cardiovascular (CV) system has been shown to promote hypertension, fibrosis, and inflammation. Pharmacological blockade of the MR has protective effects in several animal models of CV disease. Furthermore, the use of MR antagonists is beneficial for heart failure patients, preventing mortality and morbidity. A better understanding of the implications of the MR in the setting of CV diseases is critical for refining treatments and improving patient care. The mechanisms involved in the deleterious effects of MR activation are complex and include oxidative stress, inflammation, and fibrosis. This review will discuss the pathological role of the MR in the CV system and the major mechanisms underlying it.
Synergizing CRISPR/Cas9 off-target predictions for ensemble insights and practical applications
Authors: Zhang Shixiong , Li Xiangtao , Lin Qiuzhen , Wong Ka-Chun 
Published: August 2018

AbstractMotivationThe RNA-guided CRISPR/Cas9 system has been widely applied to genome editing. CRISPR/Cas9 system can effectively edit the on-target genes. Nonetheless, it has recently been demonstrated that many homologous off-target genomic sequences could be mutated, leading to unexpected gene-editing outcomes. Therefore, a plethora of tools were proposed for the prediction of off-target activities of CRISPR/Cas9. Nonetheless, each computational tool has its own advantages and drawbacks under diverse conditions. It is hardly believed that a single tool is optimal for all conditions. Hence, we would like to explore the ensemble learning potential on synergizing multiple tools with genomic annotations together to enhance its predictive abilities.ResultsWe proposed an ensemble learning framework which synergizes multiple tools together to predict the off-target activities of CRISPR/Cas9 in different combinations. Interestingly, the ensemble learning using AdaBoost outperformed other individual off-target predictive tools. We also investigated the effect of evolutionary conservation (PhyloP and PhastCons) and chromatin annotations (ChromHMM and Segway) and found that only PhyloP can enhance the predictive capabilities further. Case studies are conducted to reveal ensemble insights into the off-target predictions, demonstrating how the current study can be applied in different genomic contexts. The best prediction predicted by AdaBoost is up to 0.9383 (AUC) and 0.2998 (PRC) that outperforms other classifiers. This is ascribable to the fact that AdaBoost introduces a new weak classifier (i.e. decision stump) in each iteration to learn the DNA sequences that were misclassified as off-targets until a small error rate is reached iteratively.Availability and implementationThe source codes are freely available on GitHub at https://github.com/Alexzsx/CRISPR.Supplementary informationSupplementary data are available at Bioinformatics online.
HitPickV2: a web server to predict targets of chemical compounds
Authors: Hamad Sabri , Adornetto Gianluca , Naveja J Jesús , Chavan Ravindranath Aakash , Raffler Johannes , Campillos Mónica 
Published: August 2018

Abstract

Motivation
The identification of protein targets of novel compounds is essential to understand compounds’ mechanisms of action leading to biological effects. Experimental methods to determine these protein targets are usually slow, costly and time consuming. Computational tools have recently emerged as cheaper and faster alternatives that allow the prediction of targets for a large number of compounds.

Results
Here, we present HitPickV2, a novel ligand-based approach for the prediction of human druggable protein targets of multiple compounds. For each query compound, HitPickV2 predicts up to 10 targets out of 2739 human druggable proteins. To that aim, HitPickV2 identifies the closest, structurally similar compounds in a restricted space within a vast chemical–protein interaction area, until 10 distinct protein targets are found. Then, HitPickV2 scores these 10 targets based on three parameters of the targets in such space: the Tanimoto coefficient (Tc) between the query and the most similar compound interacting with the target, a target rank that considers Tc and Laplacian-modified naïve Bayesian target models scores and a novel parameter introduced in HitPickV2, the number of compounds interacting with each target (occur). We present the performance results of HitPickV2 in cross-validation as well as in an external dataset.

Availability and implementation
HitPickV2 is available in www.hitpickv2.com.

Supplementary information
Supplementary data are available at Bioinformatics online.
NanoShaper–VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems
Authors: Decherchi Sergio , Spitaleri Andrea , Stone John , Rocchia Walter 
Published: August 2018

Abstract

Summary
NanoShaper is a program specifically aiming the construction and analysis of the molecular surface of nanoscopic systems. It uses ray-casting for parallelism and it performs analytical computations whenever possible to maximize robustness and accuracy of the approach. Among the other features, NanoShaper provides volume, surface area, including that of internal cavities, for any considered molecular system. It identifies pockets via a very intuitive definition based on the concept of probe radius, intrinsic to the definition of the solvent excluded surface. We show here that, with a suitable choice of the parameters, the same approach can also permit the visualisation of molecular channels. NanoShaper has now been interfaced with the widely used molecular visualization software VMD, further enriching its already well furnished toolset.

Availability and implementation
VMD is available at http://www.ks.uiuc.edu/Research/vmd/. NanoShaper, its documentation, tutorials and supporting programs are available at http://concept.iit.it/downloads.

Supplementary information
Supplementary data are available at Bioinformatics online.
RNAdetect: efficient computational detection of novel non-coding RNAs
Authors: Chen Chun-Chi , Qian Xiaoning , Yoon Byung-Jun 
Published: August 2018

Abstract

Motivation
Non-coding RNAs (ncRNAs) are known to play crucial roles in various biological processes, and there is a pressing need for accurate computational detection methods that could be used to efficiently scan genomes to detect novel ncRNAs. However, unlike coding genes, ncRNAs often lack distinctive sequence features that could be used for recognizing them. Although many ncRNAs are known to have a well conserved secondary structure, which provides useful cues for computational prediction, it has been also shown that a structure-based approach alone may not be sufficient for detecting ncRNAs in a single sequence. Currently, the most effective ncRNA detection methods combine structure-based techniques with a comparative genome analysis approach to improve the prediction performance.

Results
In this paper, we propose RNAdetect, a computational method incorporating novel features for accurate detection of ncRNAs in combination with comparative genome analysis. Given a sequence alignment, RNAdetect can accurately detect the presence of functional ncRNAs by incorporating novel predictive features based on the concept of generalized ensemble defect (GED), which assesses the degree of structure conservation across multiple related sequences and the conformation of the individual folding structures to a common consensus structure. Furthermore, n-gram models (NGMs) are used to extract features that can effectively capture sequence homology to known ncRNA families. Utilization of NGMs can enhance the detection of ncRNAs that have sparse folding structures with many unpaired bases. Extensive performance evaluation based on the Rfam database and bacterial genomes demonstrate that RNAdetect can accurately and reliably detect novel ncRNAs, outperforming the current state-of-the-art methods.

Availability and implementation
The source code for RNAdetect and the benchmark data used in this paper can be downloaded at https://github.com/bjyoontamu/RNAdetect.
The challenges and contradictions of state-funded community organizing
Authors: Grimshaw Lucy , Mates Lewis , Reynolds Andie 
Published: August 2018

AbstractThe UK coalition government introduced the Community Organisers Programme in 2010, providing state funding to train community organizers in England for the first time. This article presents a case study in the north of England, exploring the implementation of the programme. It illustrates the challenges and contradictions faced by trainee community organizers and suggests lessons for community practitioners and policymakers of all political complexions in the United Kingdom and other countries.
Centrality and Partial Correlation Coefficient-Based Assortativity Analysis of Real-World Networks
Authors: Meghanathan Natarajan 
Published: August 2018

AbstractThe assortativity index (A. Index) of a complex network has been hitherto computed as the Pearson’s correlation coefficient of the remaining degree centrality (R-DEG) of the first-order neighbors (i.e. end vertices of the edges) in the network. In this paper, we seek to evaluate the assortativity of real-world networks with respect to prototypical centrality metrics (in addition to R-DEG) such as eigenvector centrality (EVC), betweenness centrality (BWC) and closeness centrality (CLC). Unlike R-DEG, the centrality values of the vertices with respect to these three metrics are influenced by the centrality values of the vertices in the neighborhood. We propose to use the notion of ‘Partial Correlation Coefficient’ to nullify the influence of the second-order neighbors (i.e. vertices that are two hops away) and quantify the assortativity of the first-order neighbors with respect to a particular centrality metric (such as EVC, BWC and CLC). We conduct an exhaustive assortativity analysis on a suite of 70 real-world networks of diverse degree distributions. We observe real-world networks to be more assortative (A. Index &gt; 0) with respect to CLC and EVC and relatively more dissortative (A. Index &lt; 0) with respect to BWC and R-DEG.
On the Question of Genericity of Hyperbolic Knots
Authors: V Malyutin Andrei 
Published: August 2018

AbstractA well-known conjecture in knot theory says that the proportion of hyperbolic knots among all of the prime knots of $n$ or fewer crossings approaches $1$ as $n$ approaches infinity. In this article, it is proved that this conjecture contradicts several other plausible conjectures, including the 120-year-old conjecture on additivity of the crossing number of knots under connected sum and the conjecture that the crossing number of a satellite knot is not less than that of its companion.
Deformations of Lie Groupoids
Authors: Crainic Marius , Mestre João Nuno , Struchiner Ivan 
Published: August 2018

AbstractWe study deformations of Lie groupoids by means of the cohomology which controls them. This cohomology turns out to provide an intrinsic model for the cohomology of a Lie groupoid with values in its adjoint representation. We prove several fundamental properties of the deformation cohomology including Morita invariance, a van Est theorem, and a vanishing result in the proper case. Combined with Moser’s deformation arguments for groupoids, we obtain several rigidity and normal form results.
Resource-based view on safety culture’s influence on hospital performance: The moderating role of electronic health record implementation
Authors: Upadhyay Soumya , Weech-Maldonado Robert , Lemak Christy H. , Stephenson Amber , Mehta Tapan , Smith Dean G. 
Published: August 2018

Background:
Patient safety and safety culture have received increasing attention from agencies such as the Agency of Healthcare Research and Quality and the Institute of Medicine. Safety culture refers to the fundamental values, attitudes, and perceptions that provide a unique source of competitive advantage to improve performance. This study contributes to the literature and expands understanding of safety culture and hospital performance outcomes when considering electronic health record (EHR) usage.

Purpose:
Based on the resource-based view of the firm, this study examined the association between safety culture and hospital quality and financial performance in the presence of EHR.

Methodology/Approach:
Data consist of the 2016 Hospital Survey on Patient Safety, Hospital Compare, American Hospital Association’s annual survey, and the American Hospital Association’s Information Technology supplement. Our final analytic sample consisted of 154 hospitals. We used a two-part nested regression model approach.

Results/Conclusion:
Safety culture has a direct positive relationship with financial performance (operating margin). Furthermore, having basic EHR as compared to not having EHR further enhances this positive relationship. On the other hand, safety culture does not have a direct association with quality performance (readmissions) in most cases. However, safety culture coupled with basic EHR functionalities, compared to not having EHR, is associated with lower readmissions.

Practice Implications:
Hospitals should strive to improve patient safety culture as part of their strategic plan for quality improvement. In addition, hospital managers should consider implementing EHR as a resource that can support safety culture’s effect on outcomes such as financial and quality performance indicators. Future studies can examine the differences between basic and advanced EHR presence in relation to safety culture.
Cognitive Performance of Severely Hearing-impaired Older Adults Before and After Cochlear Implantation: Preliminary Results of a Prospective, Longitudinal Cohort Study Using the RBANS-H
Authors: Claes Annes J. , Van de Heyning Paul , Gilles Annick , Van Rompaey Vincent , Mertens Griet 
Published: August 2018

Objective:
To evaluate cognitive change in severely hearing-impaired older adults after cochlear implantation.

Study Design:
Prospective, longitudinal cohort study with assessments before, and at 6 and 12 months after implantation.

Patients:
Twenty older adults (median age: 71.5 yr).

Main Outcome Measures:
Change in the Repeatable Battery for the Assessment of Neuropsychological Status for Hearing-impaired individuals (RBANS-H) total score and subdomain scores were used to assess cognitive evolution. In addition, change in best-aided speech audiometry in quiet (monosyllabic words) and in noise (Leuven Intelligibility Sentences Test [LIST]) was examined, as well as patient-reported measures of health-related quality of life (Nijmegen Cochlear Implant Questionnaire [NCIQ]), self-perceived hearing disability (Speech, Spatial, and Qualities of hearing Scale—12 [SSQ12]), sound quality (Hearing Implant Sound Quality Index—19 [HISQUI19]), and states of anxiety and depression (Hospital Anxiety and Depression Scale [HADS]).

Results:
The RBANS-H total scores improved significantly after 12 months cochlear implant (CI) usage (p < 0.001). At subdomain level, significant improvements were observed in the immediate and delayed memory domain (p = 0.005 and p = 0.002, respectively), and to a lesser extent also in the attention domain (p = 0.047). Furthermore, speech perception in quiet and in noise improved significantly after 6 months and remained stable after 12 months. Similarly, a significant improvement was observed on all patient-reported measures after 6 months of CI usage. These results remained stable after 12 months, except for the HADS.

Conclusions:
A significant improvement in overall cognition after 12 months of CI usage was established. However, future research is imperative to further disentangle possible practice effects from the effects of the cochlear implantation. The significant, positive effect of cochlear implantation on speech perception and patient-reported measures was confirmed.
Pediatric headache: overview
Authors: Kelly Meaghan , Strelzik Jeffrey , Langdon Raquel , DiSabella Marc 
Published: August 2018

Purpose of review
Headache is a common medical complaint in children and adolescents with the majority having experienced some type of headache by their teenage years. Pediatric headache presentations often differ compared to adults, and children may have difficulty describing their symptoms. Thus, a thorough understanding of the approach to the pediatric headache patient is essential to ensure appropriate diagnosis, evaluation, and management.

Recent findings
In the following article we will review the components of a comprehensive pediatric headache assessment, as well as discuss primary and secondary headache types seen in children with focus on clinical pearls and ‘red flags’ necessitating diagnostic testing.

Summary
Headaches in children may be due to primary or secondary etiologies. Common primary headache types include migraine or tension-type headache. Secondary headache causes are broad and include infections, trauma, vascular disorders, substance use/withdrawal, and psychiatric conditions. Current American Academy of Neurology (AAN) guidelines recommend against routine lab studies, lumbar puncture, electro-encephalogram (EEG), or neuroimaging in patients with no headache red flags by history and a normal neurologic examination.
Factors Influencing Patient Satisfaction in Plastic Surgery: A Nationwide Analysis
Authors: Chen Kevin , Congiusta Susan , Nash Ira S. , Coppa Gene F. , Smith Mark L. , Kasabian Armen K. , Thorne Charles , Tanna Neil 
Published: August 2018

Background:
Patient satisfaction surveys are an increasingly important part of health care, influencing the practice of physicians. Press Ganey has developed tools to assess physician and department performance that are used by 50 percent of hospitals in the United States and over 10,000 health care organizations. The authors sought to evaluate the factors that influence patient satisfaction in plastic surgery patients both locally and nationally.

Methods:
A 24-item Press Ganey survey was distributed to patients of 686 participating plastic surgeons nationwide, including those at the authors’ home institution. The responses from January to December of 2016 were analyzed retrospectively with Pearson correlation coefficients. The items “likelihood to recommend provider” and “likelihood to recommend practice” were correlated to all other items of the survey, as these items have been shown to be surrogates for overall satisfaction.

Results:
There were 411 survey responses from patients in the Northwell Health System and 36,836 responses from patients nationally. Items that were not well correlated (r < 0.5) with “likelihood to recommend practice” or “provider” were items such as wait time and courtesy of registration staff. The items that were best correlated (r > 0.8) with “likelihood to recommend practice” or “provider” were the patient’s confidence in the care provider and the provider’s concern for questions. All correlations were statistically significant (p < 0.001).

Conclusion:
In an evolving patient centric culture, the patient’s confidence and trust of the provider is more important than perception of the provider’s office environment to maintaining patient loyalty and market share.
Increased Skeletal Muscle FDG Uptake Due to Sexual Activity on PET/CT in a Middle Age Woman
Authors: Wang Wei , Kan Ying , Liu Jie , Yuan Leilei , Yang Jigang 
Published: August 2018

Abstract
A 48-year-old woman with gradually growing left lung nodule underwent FDG PET/CT scan, which demonstrated mild 18F-FDG uptake in the nodule of the left lobe, suggestive of malignancy. Unexpectedly, increased FDG uptake in bilateral gluteus medius, gluteus minimus, and piriformis was shown. She described having sexual activity in missionary position the night prior. The case emphasizes the importance of avoiding sexual activity before the FDG PET/CT study.