bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing enrichment analysis and machine learning for identifying gene properties that discriminate between gene classes
Authors: Fabris Fabio , Palmer Daniel , de Magalhães João Pedro , Freitas Alex A 
Published: February 2019

AbstractBiologists very often use enrichment methods based on statistical hypothesis tests to identify gene properties that are significantly over-represented in a given set of genes of interest, by comparison with a ‘background’ set of genes. These enrichment methods, although based on rigorous statistical foundations, are not always the best single option to identify patterns in biological data. In many cases, one can also use classification algorithms from the machine-learning field. Unlike enrichment methods, classification algorithms are designed to maximize measures of predictive performance and are capable of analysing combinations of gene properties, instead of one property at a time. In practice, however, the majority of studies use either enrichment or classification methods (rather than both), and there is a lack of literature discussing the pros and cons of both types of method. The goal of this paper is to compare and contrast enrichment and classification methods, offering two contributions. First, we discuss the (to some extent complementary) advantages and disadvantages of both types of methods for identifying gene properties that discriminate between gene classes. Second, we provide a set of high-level recommendations for using enrichment and classification methods. Overall, by highlighting the strengths and the weaknesses of both types of methods we argue that both should be used in bioinformatics analyses.
Thalamic Inputs to Posterior Parietal Cortical Areas Involved in Skilled Forelimb Movement and Tool Use in the Capuchin Monkey
Authors: Mayer Andrei , Lewenfus Gabriela , Bittencourt-Navarrete Ruben Ernesto , Clasca Francisco , Franca João Guedes da 
Published: February 2019

Abstract
The posterior parietal cortex (PPC) is a central hub for the primate forebrain networks that control skilled manual behavior, including tool use. Here, we quantified and compared the sources of thalamic input to electrophysiologically-identified hand/forearm-related regions of several PPC areas, namely areas 5v, AIP, PFG, and PF, of the capuchin monkey (Sapajus sp). We found that these areas receive most of their thalamic connections from the Anterior Pulvinar (PuA), Lateral Posterior (LP) and Medial Pulvinar (PuM) nuclei. Each PPC area receives a specific combination of projections from these nuclei, and fewer additional projections from other nuclei. Moreover, retrograde labeling of the cells innervating different PPC areas revealed substantial intermingling of these cells within the thalamus. Differences in thalamic input may contribute to the different functional properties displayed by the PPC areas. Furthermore, the observed innervation of functionally-related PPC domains from partly intermingled thalamic cell populations accords with the notion that higher-order thalamic inputs may dynamically regulate functional connectivity between cortical areas.
Close Patient Follow-up Among Patients Receiving Outpatient Parenteral Antimicrobial Therapy
Authors: Palms Danielle L , Jacob Jesse T 
Published: February 2019

Abstract

Background
Outpatient parenteral antimicrobial therapy (OPAT) programs allow patients to receive intravenous treatment in the outpatient setting. We developed a predictive model of 30-day readmission among hospitalized patients discharged on OPAT from 2 academic medical centers with a dedicated OPAT clinic for management.

Methods
A retrospective medical records review was performed and logistic regression was used to assess OPAT and other outpatient clinic follow-up in conjunction with age, sex, pathogen, diagnosis, discharge medication, planned length of therapy, and Charlson comorbidity score. We hypothesized that at least 1 follow-up visit at the Emory OPAT clinic would reduce the risk for hospital readmission within 30 days.

Results
Among 755 patients, 137 (18%) were readmitted within 30 days. Most patients (73%) received outpatient follow-up care at Emory Healthcare within 30 days of discharge or prior to readmission, including 52% of patients visiting the OPAT clinic. The multivariate logistic regression model indicated that a follow-up OPAT clinic visit was associated with lower readmission compared to those who had no follow-up visit (odds ratio, 0.10 [95% confidence interval, .06–.17]) after adjusting for infection with enterococci, Charlson score, discharge location, and county of residence.

Conclusions
These results can inform potential interventions to prevent readmissions through OPAT clinic follow-up and to further assess factors associated with successful care transitions from the inpatient to outpatient setting.
Lincoln’s well-considered political economy (the ‘American System’) trumped the Free Trade British System
Authors: Phillips Emir 
Published: February 2019

AbstractThe Whigs could legitimately emphasise what Hamilton’s Report had not touched upon: urban labourers made unemployed by import competition could not shift to ‘collateral employments’ with the presumptive ease asserted by Free Trader Democrats. More than anything, it was the structural cyclical instability (Minsky moments) that engendered a new party (Republican) to exert political pressures for government involvement in the management of the economy (mercantilism). Economic beliefs played the most fundamental role in Lincoln’s career, and his mercantilist views, in conformity with Hamilton, Clay and the economist Carey, were key determinants in effectuating the Industrial Revolution within the United States through tariffs, government-supported macro-projects and structurally stimulating aggregate demand through a national currency. Permeating Lincoln's political economy was a fierce non-neutral view of money wherein banks created the funds to ignite the American System. Henry Clay, Henry Carey and Abraham Lincoln were seeking to supplant the Ricardo–Malthus long-term model of economic growth (emphasising distribution within a relatively stagnant economy) with one of expanding productive powers and rising wage levels. These interventionist issues are still quite relevant since US economics students are taught modernised versions of the doctrines of Ricardo and Malthus which were controverted more than a century ago by the American School, and more specifically by Abraham Lincoln.
Short-term effects of sevelamer-carbonate on fibroblast growth factor 23 and pulse wave velocity in patients with normophosphataemic chronic kidney disease Stage 3
Authors: Bouma-de Krijger Annet , van Ittersum Frans J , Hoekstra Tiny , ter Wee Pieter M , Vervloet Marc G 
Published: February 2019

Abstract

Background
High concentrations of both phosphate and fibroblast growth factor 23 (FGF23) observed in chronic kidney disease (CKD) are associated with an increased risk of cardiovascular morbidity and mortality. Pulse wave velocity (PWV) is a surrogate marker for cardiovascular events and all-cause mortality. It is not known whether a reduction of FGF23 or phosphate alters cardiovascular risk. Sevelamer has shown to have the ability to reduce both phosphate and FGF23 concentrations. Furthermore, reduction of PWV is reported with sevelamer use as well, but it is unclear if this is mediated by decline of phosphate or FGF23. We investigated if sevelamer induced a decline in PWV and if this was associated with a reduction in FGF23.

Methods
In all, 24 normophosphataemic CKD Stage 3 patients started treatment with a fixed dose of sevelamer-carbonate (Renvela®) 2.4 g twice daily, with their usual diet for 8 weeks in a single-arm study. PWV was measured and blood samples were obtained before, during and after washout of treatment with sevelamer. Vascular calcification was quantified using the Kauppila Index (KI). The primary outcome was the change of PWV from baseline to 8 weeks of treatment and the secondary endpoint was the difference of FGF23 following treatment with sevelamer. One of the linear mixed models was used to analyse the association between treatment and outcome. Mediation analysis was performed as a sensitivity analysis. The study was registered in the Dutch trial register (http://www.trialregister.nl: NTR2383).

Results
A total of 18 patients completed 8 weeks of treatment with sevelamer and were analysed. Overall, treatment with sevelamer did not induce a significant reduction of PWV (β = −0.36, P = 0.12). However, in patients with less vascular calcification (lower KI score), there was a statistically significant reduction of PWV, adjusted for mean arterial pressure, after treatment (β = 0.63, P = 0.02). Addition of FGF23 to the model did not alter this association. Mediation analysis yielded similar results. FGF23 did not decrease during treatment with sevelamer.

Conclusion
In this short-term pilot study in normophosphataemic CKD patients, treatment with sevelamer did not improve PWV. In subgroup analysis, however, PWV improved in patients with no or limited abdominal aorta calcifications. This was not associated with a decline of FGF23.
An Improved Seed Point Selection-Based Unsupervised Color Clustering for Content-Based Image Retrieval Application
Authors: Pavithra L K , Sree Sharmila T 
Published: February 2019

Abstract
The images involved in the content-based image retrieval (CBIR) applications are collectively represented by features such as color, texture and shape. The precision of the CBIR application relies on the key features used in image representation and its similarity measure. In CBIR, dominant color feature extraction is affected by the predefined intervals used in color quantization. The proposed work mainly concentrates on extracting the dominant color information of the image using the clustering process. The clustering process is initiated by the proposed seed point’s selection approach. This approach derives the number of seed points using the first order statistical measure and maximum range of the distributed pixel values. Moreover, this work gives equal priority to dominant color and its occurrence information in calculating the similarity between query and database images. Finally, the standard databases such as SIMPLIcity, Corel-10k, OT-scene, Oxford flower and GHIM are taken to investigate the performance of the proposed dominant color based image retrieval application.
BigFeel—A Distributed Processing Environment for the Integration of Sentiment Analysis Methods
Authors: Ferreira Roger Santos , Pereira Denilson Alves 
Published: February 2019

Abstract
Sentiment analysis has been the main focus of plenty of research efforts, particularly justified by its commercial significance, both for consumers and businesses. Thus, many methods have been proposed so far, and the most prominent have been compared in terms of effectiveness. Nonetheless, the literature is deficient when it comes to assessing the efficiency of these methods for processing large volumes of data. In this study, we performed an experimental assessment of the efficiency of 22 methods in total, whose implementations were available. We also proposed and assessed an environment for distributed processing methods for sentiment analysis, using the Apache Spark platform, named BigFeel. In this environment, the existing methods, outlined to run in a non-distributed way, can be adapted, without altering their source code, to run in a distributed manner. The experimental results reveal that (i) few methods are efficient in their native form, (ii) the methods improve their efficiency after having been integrated into BigFeel, (iii) some of them, which were unfeasible to process a large dataset, became viable when deployed in a computer cluster and (iv) some methods can only handle small datasets, even in a distributed manner.
Five-year Safety Data From OPUS, a European Observational Safety Registry for Adults With Ulcerative Colitis Treated With Originator Infliximab [Remicade®] or Conventional Therapy
Authors: Panés Julián , Lindsay James O , Teich Niels , Lindgren Stefan , Colombel Jean-Frédéric , Cornillie Freddy , Flynn Heather Ann , Huyck Susan , Stryszak Paul , Yao Ruji , Philip George , Reinisch Walter 
Published: February 2019

Abstract

Background and Aims
The Observational Postmarketing Ulcerative colitis Study [OPUS] was conducted to obtain the first long-term [5 years] safety data assessing treatment with originator infliximab versus conventional therapies in patients with ulcerative colitis [UC] in real-world clinical practice.

Methods
The OPUS registry was a prospective, non-randomised, observational study that measured adverse events in nine prespecified categories of interest in UC patients whose treatment with either originator infliximab or conventional therapy [defined as initiation or dose-increase of corticosteroids and/or immunosuppressants] was determined by their treating physician.

Results
Data for 2239 patients were available: N = 1180 enrolled to conventional therapy [including N = 296 who switched to originator infliximab during follow-up] and N = 1059 enrolled to originator infliximab. Patients in the originator infliximab group, compared with the conventional therapy group, had more severe disease at baseline, based on partial Mayo score [PMS]: 46.0% of patients in the originator infliximab group had severe disease (PMS of 7–9 [out of 9]), compared with 30.5% in the conventional therapy group. In adjusted time-to-event analyses, enrolment into the originator infliximab group was associated with a higher risk of serious infection (hazard ratio = 1.98 [95% confidence interval: 1.34, 2.91; p <0.001]) compared with enrolment into the conventional therapy group. No notable risk differences between groups were identified for haematological disorder, autoimmune disorder, malignancy/lymphoproliferative disorder, hepatobiliary disorder or fatality.

Conclusions
UC patients treated with infliximab had higher risk for serious infection, compared with conventional therapies. No new safety concerns were observed with originator infliximab in the OPUS registry. [ClinicalTrials.gov: NCT00705484.]
Gray Matter Volume Covariance Networks, Social Support, and Cognition in Older Adults
Authors: Cotton Kelly , Verghese Joe , Blumen Helena M 
Published: February 2019

Abstract

Objective
We examined the neural substrates of social support in older adults. Social support is associated with better outcomes in many facets of aging—including cognitive and functional health—but the underlying neural substrates remain largely unexplored.

Methods
Voxel-based morphometry and multivariate statistics were used to identify gray matter volume covariance networks associated with social support in 112 older adults without dementia (M age = 74.6 years, 50% female), using the Medical Outcomes Study Social Support Survey.

Results
A gray matter network associated with overall social support was identified and included prefrontal, hippocampal, amygdala, cingulate, and thalamic regions. A gray matter network specifically associated with tangible social support (e.g., someone to help you if you were confined to bed) was also identified, included prefrontal, hippocampal, cingulate, insular, and thalamic regions, and correlated with memory and executive function.

Discussion
Gray matter networks associated with overall and tangible social support in this study were composed of regions previously associated with memory, executive function, aging, and dementia. Longitudinal research of the interrelationships between social support, brain structure, and cognition is needed, but strengthening social support may represent a new path toward improving cognition in aging that should be explored.
Person–Environment Fit Approach to Trajectories of Cognitive Function Among Older Adults Who Live Alone: Intersection of Life-Course SES Disadvantage and Senior Housing
Authors: Park Sojung , Kwon Eunsun , Kim BoRin , Han Yoonsun 
Published: February 2019

AbstractObjectivesDrawing from life course and environmental perspectives, we examined the trajectory of cognitive function and how senior housing moderates the effects of life-course socioeconomic status (SES) disadvantage among older people living alone over time.MethodSix waves of the Health and Retirement Study (HRS) were used with multilevel growth modeling to analyze developmental patterns of cognitive function over time and how various forms of life-course SES disadvantage affect cognitive function depending on senior housing residency status.ResultsAt baseline, we found a positive role of senior housing in four subgroups: SES disadvantage in childhood only, unstable mobility pattern (disadvantage in childhood and old age only), downward mobility (no disadvantage in childhood, but in later two life stages), and cumulative disadvantage (all three life stages). Over time, the positive role of senior housing for the unstable and the most vulnerable group persisted.DiscussionOur findings provide a much-needed practical and theoretical underpinning for environmental policy-making efforts regarding vulnerable elders who live alone.
Endometriosis and nuclear receptors
Authors: Yilmaz Bahar D , Bulun Serdar E 
Published: February 2019

Abstract

BACKGROUND
Endometriosis is recognized as a steroid-dependent disorder; however, the precise roles of nuclear receptors (NRs) in steroid responsiveness and other signaling pathways are not well understood.

OBJECTIVE AND RATIONALE
Over the past several years, a number of paradigm-shifting breakthroughs have occurred in the area of NRs in endometriosis. We review and clarify new information regarding the mechanisms responsible for: (i) excessive estrogen biosynthesis, (ii) estrogen-dependent inflammation, (iii) defective differentiation due to progesterone resistance and (iv) enhanced survival due to deficient retinoid production and action in endometriosis. We emphasize the roles of the relevant NRs critical for these pathological processes in endometriosis.

SEARCH METHODS
We conducted a comprehensive search using PubMed for human, animal and cellular studies published until 2018 in the following areas: endometriosis; the steroid and orphan NRs, estrogen receptors alpha (ESR1) and beta (ESR2), progesterone receptor (PGR), steroidogenic factor-1 (NR5A1) and chicken ovalbumin upstream promoter-transcription factor II (NR2F2); and retinoids.

OUTCOMES
Four distinct abnormalities in the intracavitary endometrium and extra-uterine endometriotic tissue underlie endometriosis progression: dysregulated differentiation of endometrial mesenchymal cells, abnormal epigenetic marks, inflammation activated by excess estrogen and the development of progesterone resistance. Endometriotic stromal cells compose the bulk of the lesions and demonstrate widespread epigenetic abnormalities. Endometriotic stromal cells also display a wide range of abnormal NR expression. The orphan NRs NR5A1 and NR2F2 compete to regulate steroid-synthesizing genes in endometriotic stromal cells; NR5A1 dominance gives rise to excessive estrogen formation. Endometriotic stromal cells show an abnormally low ESR1:ESR2 ratio due to excessive levels of ESR2, which mediates an estrogen-driven inflammatory process and prostaglandin formation. These cells are also deficient in PGR, leading to progesterone resistance and defective retinoid synthesis. The pattern of NR expression, involving low ESR1 and PGR and high ESR2, is reminiscent of uterine leiomyoma stem cells. This led us to speculate that endometriotic stromal cells may display stem cell characteristics found in other uterine tissues. The biologic consequences of these abnormalities in endometriotic tissue include intense inflammation, defective differentiation and enhanced survival.

WIDER IMPLICATIONS
Steroid- and other NR-related abnormalities exert genome-wide biologic effects via interaction with defective epigenetic programming and enhance inflammation in endometriotic stromal cells. New synthetic ligands, targeting PGR, retinoic acid receptors and ESR2, may offer novel treatment options.
The Applicability of Human Rights Law in International Investment Disputes
Authors: Santacroce Fabio Giuseppe 
Published: February 2019

Abstract
Human rights are becoming increasingly relevant in international investment disputes. A question therefore arises as to whether the application of human rights law to those disputes is justified. This article answers that question in the affirmative. In particular, it suggests that there are at least four legal grounds (which may operate separately or cumulatively) warranting the application of human rights norms in the context of international investment disputes: (i) the fact that international human rights law is part of international law, which in turn governs the merits of investment disputes; (ii) the presence of express references to human rights in the investment treaty; (iii) the presence of implied references to human rights in the investment treaty; and (iv) the principle of systemic integration. Each of these grounds can be the basis for applying international human rights law as an interpretative tool. Some of them, however, can play a more substantive role and justify the direct application of international human rights norms to the merits of the dispute. This may lead to normative conflicts. The article thus also provides a framework to determine, in case of clashes between international investment law and international human rights norms, which norm should apply in concreto.
Providing oxygen to children and newborns: a multi-faceted technical and clinical assessment of oxygen access and oxygen use in secondary-level hospitals in southwest Nigeria
Authors: Bakare Ayobami A , Graham Hamish , Ayede Adejumoke I , Peel David , Olatinwo Olatayo , Oyewole Oladapo B , Fowobaje Kayode R , Qazi Shamim , Izadnegahdar Rasa , Duke Trevor , Falade Adegoke G 
Published: February 2019

Abstract

Background
Oxygen is an essential medical therapy that is poorly available globally. We evaluated the quality of oxygen therapy in 12 secondary-level Nigerian hospitals, including access to oxygen equipment, equipment functionality, healthcare worker knowledge and appropriateness of use.

Methods
We conducted a three-part evaluation of oxygen access and use involving: (1) facility assessment (including technical evaluation of oxygen equipment), (2) clinical audit (children and neonates admitted January 2014–December 2015) and (3) survey of healthcare worker training and experience on the clinical use of oxygen (November 2015).

Results
Oxygen access for children and newborns is compromised by faulty equipment, lack of pulse oximetry and inadequate care practices. One hospital used pulse oximetry for paediatric care. Eleven hospitals had some access to oxygen supplies. Testing of 57 oxygen concentrators revealed two (3.5%) that were ‘fit for use’. Overall, 14.4% (3708/25 677) of children and neonates received oxygen some time during their admission; 19.4% (1944/10 000) of hypoxaemic children received oxygen; 38.5% (1217/3161) of children who received oxygen therapy were not hypoxaemic.

Conclusions
Oxygen access for children in Nigerian hospitals is poor, and likely results in substantial excess mortality. To improve oxygen access for children globally we must focus on actual provision of oxygen to patients—not simply the presence of oxygen equipment at the facility level. This requires a systematic approach to improve both oxygen (access [including equipment, maintenance and affordability]) and oxygen use (including pulse oximetry, guidelines and continuing education).