bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nef Secretion into Extracellular Vesicles or Exosomes Is Conserved across Human and Simian Immunodeficiency Viruses
Authors: McNamara Ryan P. , Costantini Lindsey M. , Myers T. Alix , Schouest Blake , Maness Nicholas J. , Griffith Jack D. , Damania Blossom A. , MacLean Andrew G. , Dittmer Dirk P. 
Published: February 2018

ABSTRACT
Extracellular vesicles (EVs) or exosomes have been implicated in the pathophysiology of infections and cancer. The negative regulatory factor (Nef) encoded by simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV) plays a critical role in the progression to AIDS and impairs endosomal trafficking. Whether HIV-1 Nef can be loaded into EVs has been the subject of controversy, and nothing is known about the connection between SIV Nef and EVs. We find that both SIV and HIV-1 Nef proteins are present in affinity-purified EVs derived from cultured cells, as well as in EVs from SIV-infected macaques. Nef-positive EVs were functional, i.e., capable of membrane fusion and depositing their content into recipient cells. The EVs were able to transfer Nef into recipient cells. This suggests that Nef readily enters the exosome biogenesis pathway, whereas HIV virions are assembled at the plasma membrane. It suggests a novel mechanism by which lentiviruses can influence uninfected and uninfectable, i.e., CD4-negative, cells.

IMPORTANCE
Extracellular vesicles (EVs) transfer biologically active materials from one cell to another, either within the adjacent microenvironment or further removed. EVs also package viral RNAs, microRNAs, and proteins, which contributes to the pathophysiology of infection. In this report, we show that both human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) incorporate the virus-encoded Nef protein into EVs, including EVs circulating in the blood of SIV-infected macaques and that this presents a novel mechanism of Nef transfer to naive and even otherwise non-infectable cells. Nef is dispensable for viral replication but essential for AIDS progression
in vivo
. Demonstrating that Nef incorporation into EVs is conserved across species implicates EVs as novel mediators of the pathophysiology of HIV. It could help explain the biological effects that HIV has on CD4-negative cells and EVs could become biomarkers of disease progression.
Boosted neural networks scoring functions for accurate ligand docking and ranking
Authors: Ashtawy Hossam M. , Mahapatra Nihar R. 
Published: February 2018

Predicting the native poses of ligands correctly is one of the most important steps towards successful structure-based drug design. Binding affinities (BAs) estimated by traditional scoring functions (SFs) are typically used to score and rank-order poses to select the most promising conformation. This BA-based approach is widely applied and some success has been reported, but it is inconsistent and still far from perfect. The main reason for this is that SFs are trained on experimental BA values of only native poses found in co-crystallized structures of protein-ligand complexes (PLCs). However, during docking, they are needed to discriminate between native and decoy poses, a task for which they have not been specifically designed. To overcome this limitation, we propose to build task-specific SFs that model binding affinities (scoring task) as well as conformations (docking task) using the root mean square deviation (RMSD) of a ligand pose from the native pose. Our models are based on boosted ensembles of neural networks and other state-of-the-art machine learning (ML) algorithms in conjunction with multi-perspective interaction modeling techniques for accurate characterization of PLCs.We assess the docking and scoring/ranking accuracies of the proposed ML SFs as well as three conventional SFs in the context of the 2014 CSAR benchmark exercise that encompasses three high-quality protein systems and a diverse set of drug-like molecules. Our proposed docking-specific SFs provide a substantial improvement in the docking task. We find that RMSD-based SFs for BsN, an ensemble neural networks (NN) model based on boosting, and six other ML models provide more than 120% improvement, on average, over their BA-based counterparts. In terms of scoring/ranking accuracy, we find that the approach of using RMSD-based BsN to select the top ligand pose followed by applying BA-based BsN to rank ligands using predicted BA scores leads to consistent and correctly ranked ligands for the two protein targets Spleen Tyrosine Kinase (SYK) and tRNA (m1G37) methyltransferase (TrmD). In addition, the ensemble NN SF BsN is at least 250% more accurate than a single neural network (SNN) model. We further find that ensemble models based on NNs surpass SFs based on other state-of-the-art ML algorithms such as BRT, RF, SVM, and [Formula: see text]NN. Finally, our RF model fitted to PLCs characterized by multiple sets of descriptors from four different sources (X-Score, AffiScore, RF-Score, and GOLD) substantially outperforms the SF RF-Score that uses only one set of features, underlining the value of multi-perspective modeling.
A genetic classification of caves and its application in eastern Austria
Authors: Oberender P. , Plan L. 
Published: February 2018

Abstract
Based on existing classifications of caves that often involve descriptive terms, a classification is presented that is based purely on genetic processes. An attribute key is developed that allows the classification of caves by means of cave maps, photographs and reports. This method is applied to a dataset of 6007 caves in a study area in eastern Austria. The area comprises diverse geological units of the Eastern Alps and the southern Bohemian Massif. A total of 94% of the caves could be classified with the surprising result that mechanical weathering and erosion caves are almost as common as solution caves even though the vast majority of caves are developed in carbonate rocks. Field checks confirmed the result and showed that the error is acceptable. The classified caves can also be used as indicator of natural phenomena like gravitational mass movements or vulnerable karst areas by decision-makers non-specialized in cave genesis.
New insights into salt tectonics in the northern Dutch offshore: a framework for hydrocarbon exploration
Authors: van Winden Matthijs , de Jager Jan , Jaarsma Bastiaan , Bouroullec Renaud 
Published: February 2018

Abstract
The northern Dutch offshore is an area that has seen less hydrocarbon exploration activity than other areas of The Netherlands. Acquisition of a new regional 3D seismic dataset allowed further testing and re-evaluation of established geological concepts in this area. It is recognized that the presence and movement of Upper Permian Zechstein evaporites had a major impact on depositional patterns in Mesozoic sediments, structural development and hydrocarbon migration. As such, this study looks specifically at the role of salt tectonics in tectonosedimentary development. To assess this salt tectonic evolution within its structural context, a restoration of the Step Graben and Dutch Central Graben was performed. It follows that depositional patterns are closely linked to the nature of salt structure movement and the timing of regional tectonism. For example, during Late Triassic rifting, salt pillows developed and sedimentation focused away from salt structures into depocentres along regional fault trends. Restoration results show that this interplay between salt movement and tectonism is needed to accommodate the sedimentation patterns associated with the formation of the Step Graben and Central Graben during the Triassic and Jurassic, and later during Late Cretaceous and Cenozoic inversion tectonics.
Advancing Clean Technology Entrepreneurship in the Middle East and North African (mena) Region: Law, Education and Policy Imperatives
Authors: Tok Mohammed Evren , Olawuyi Damilola S. , D’Alessandro Cristina 
Published: February 2018

Two of the key priorities of the Arab world in the coming years are to develop and deploy clean technologies (cleantech) needed to combat the adverse effects of climate change in the region; and to diversify domestic economies to become low carbon economies with greater prospects for green jobs. However, despite broad political discussions of these policy goals, several countries in the Middle East and North African (mena) region continue to lag in terms of the level and adequacy of entrepreneurial cleantech start-up activities. For mena countries to bridge current gaps in entrepreneurial cleantech capital, entrepreneurship education and training is critical.
This article investigates the ethical and contextual basis of cleantech entrepreneurship in the mena region. Focusing on clean technology businesses, given their national and global economic and environmental role in future low-carbon societies and economies, the article then investigates the principal causes of the limited development of cleantech entrepreneurship in the mena region. The Qatari example offers original insights on clean technology joint ventures, startups, and projects. The results indicate the need for mena countries to mainstream and integrate entrepreneurial education and training into national action plans and policies on low carbon development, in order to promote local capacity and awareness on cleantech entrepreneurship.
Optimizing thermal comfort considerations with electrical demand response program implementation
Authors: Aghniaey Sama , Lawrence Thomas M , Mohammadpour Javad , Song WenZhan , Watson Richard T , Boudreau Marie C 
Published: February 2018

Maintaining thermal comfort within an occupied building requires energy; thus, optimized solution methods for balancing energy use with indoor environmental quality (adequate thermal comfort, lighting, etc.) are needed. Current building temperature control systems do not adequately take in account the adaptive capability of the occupants, but this concept can be used advantageously during implementation of demand response. Demand response programs can affect both the occupants’ thermal comfort from temporary adjustments to space temperature settings. This paper describes ongoing research and field testing of methods to optimize building energy consumption for heating, ventilation and air conditioning applications accounting for human factors such as the thermal comfort by the occupants. Model predictive controllers could serve as powerful tools to optimize the operation of smart buildings and improve human comfort perceptions while helping to better integrate renewable energy systems with increased grid stability. Practical application: This work outlines how the operation of cooling systems can be optimized with respect to reducing peak demand while still maintaining thermal comfort within acceptable ranges.
The impact of wrist fracture, surgical repair and immobilization on patients: a qualitative study
Authors: Watson Narelle J , Martin Sally A , Keating Jennifer L 
Published: February 2018

Objective: To investigate patients’ experience following wrist fracture, surgical repair and immobilization. Design: A qualitative investigation involving individual participant interviews. Setting: A metropolitan trauma service. Subjects: In all, 31 participants were consecutively recruited from three groups within a randomized controlled trial comparing immobilization for one ( n = 11), three ( n = 10) or six weeks ( n = 10) following surgical treatment for wrist fracture. Intervention: Individual interviews were conducted within three months of cast removal. Questions prompted discussion of the experience of fracture, surgery and immobilization. Interviews were audio-recorded, transcribed verbatim. At least two independent researchers performed coding and theming following principles of thematic analysis. Results: Two themes were identified: (1) impact of the injury varies widely and (2) health care consumers want trustworthy dialogue. Participant reports indicated that recovery from wrist fracture, surgery and immobilization is challenging with significant changes to social role and increased dependence. For many, lack of empathy from health professionals and limited acknowledgement of the personal impact of injury led to dissatisfaction. Health professionals did not consistently tailor communication or adopt strategies to address specific needs for pain management, education and support requirements. There was no evidence that processes were implemented to enhance participant recall and comprehension. Most participants experienced their cast as a barrier to function. However, within the group of participants immobilized for one week, a number felt the cast was removed too soon. Conclusion: Participant reports indicate that recovery from surgically repaired wrist fracture is challenging. Opportunities exist to refine care in pain management, education and active engagement of patients in their care.
Circumstances of hospital admissions in palliative care: A cross-sectional survey of patients admitted to hospital with palliative care needs
Authors: Robinson Jackie , Gott Merryn , Frey Rosemary , Ingleton Christine 
Published: February 2018

Background: On average, people will experience 2.28 hospital admissions in the last year of life with the likelihood of a hospital admission increasing in the last 2 weeks of life. Reducing hospital admissions has become a focus for high-income countries as they work to manage the financial implications of an ageing population. However, the circumstances by which patients with palliative care needs are admitted to hospital remain poorly understood. Aim: To explore the circumstances of hospital admissions for patients with palliative care needs. Design: Cross-sectional survey design using face-to-face questionnaires. Setting/participants: In total, 116 patients aged >18 years admitted to a tertiary hospital with palliative care needs. Results: Those with a non-cancer diagnosis and those aged over 75 years were less likely to have hospice involved prior to the admission ( x2 (1, n = 116) = 10.19, p = 0.00). Few patients recognised community services as having a role in enabling them to remain at home. Those with cancer placed a significantly higher priority on receiving information about their illness ( t(114) = 2.03, p = 0.04) and receiving tests and investigations ( t(114) = 2.37, p = 0.02) in hospital. Conclusion: This study has demonstrated the complexity of hospital admissions in palliative care. Further research is needed to explore patient perceptions of care at home and the role of community services to enable them to remain at home. Understanding the motivation to come to hospital in the context of an incurable illness and limited treatment options may help to inform the development of services that can enable better care at home.
Integrated palliative care networks from the perspectives of patients: A cross-sectional explorative study in five European countries
Authors: den Herder-van der Eerden Marlieke , Ebenau Anne , Payne Sheila , Preston Nancy , Radbruch Lukas , Linge-Dahl Lisa , Csikos Agnes , Busa Csilla , Van Beek Karen , Groot Marieke , Vissers Kris , Hasselaar Jeroen 
Published: February 2018

Background: Although examining perspectives of patients on integrated palliative care organisation is essential, available literature is largely based on administrative data or healthcare professionals’ perspectives. Aim: (1) Providing insight into the composition and quality of care networks of patients receiving palliative care and (2) describing perceived integration between healthcare professionals within these networks and its association with overall satisfaction. Design: Cross-sectional explorative design. Setting/participants: We recruited 157 patients (62% cancer, 25% chronic obstructive pulmonary disease, 13% chronic heart failure, mean age 68 years, 55% female) from 23 integrated palliative care initiatives in Belgium, Germany, the United Kingdom, Hungary and the Netherlands. Results: About 33% reported contact with a palliative care specialist and 48% with a palliative care nurse. Relationships with palliative care specialists were rated significantly higher than other physicians ( p < 0.001). Compared to patients with cancer, patients with chronic obstructive pulmonary disease (odds ratio = 0.16, confidence interval (0.04; 0.57)) and chronic heart failure (odds ratio = 0.11, confidence interval (0.01; 0.93)) had significantly lower odds of reporting contact with palliative care specialists and patients with chronic obstructive pulmonary disease (odds ratio = 0.23, confidence interval (0.08; 0.71)) had significantly lower odds of reporting contact with palliative care nurses. Perceptions of main responsible healthcare professionals or caregivers in patient’s care networks varied across countries. Perceived integration was significantly associated with overall satisfaction. Conclusion: Palliative care professionals are not always present or recognised as such in patients’ care networks. Expert palliative care involvement needs to be explicated especially for non-cancer patients. One healthcare professional should support patients in understanding and navigating their palliative care network. Patients seem satisfied with care provision as long as continuity of care is provided.
Family carers’ experiences of coping with the deaths of adults in home settings: A narrative analysis of carers’ relevant background worries
Authors: Thomas Carol , Turner Mary , Payne Sheila , Milligan Christine , Brearley Sarah , Seamark David , Wang Xu , Blake Susan 
Published: February 2018

Background: Internationally, evidence on the support needs of family carers who look after a terminally ill adult in home settings is incomplete. Aim: To illustrate the relevance of ‘relevant background worries’ in family carers’ accounts of caring at home for a dying adult. Design: A qualitative cross-sectional observational study was conducted in England, United Kingdom, in 2011–2013 on the experiences of adult family carers ( n = 59) of older dying adults (aged 50+ years) with malignant and/or non-malignant conditions. Interviews occurred post-bereavement. This article reports on a subset of participants’ interview transcripts ( n = 30) where narrative analysis was undertaken. Setting/participants: Carers were interviewed in their home setting, having been purposively recruited via general practitioner practices in two study sites in England. The subset of participants ( n = 30) was purposively selected from the parent sample with reference to carers’ age, relationship to the patient, family circumstances and study sites. Results: Evidence is provided on the importance of what we conceptualise as carers’ ‘relevant background worries’; these varied in nature, significance and impact. Four case studies are presented where these worries constituted psychosocial factors that impacted on caregivers’ actions and emotional well-being. Two themes are discussed: (1) whether relevant background worries are important enough to be identified and responded to and (2) how such worries could be picked up and managed by professionals. Conclusion: It is argued that the quality of clinical practice could be improved if specialist palliative care teams in community contexts both identified and responded to significant support needs associated with family carers’ relevant background worries.
Lateral Augmentation Procedures in Anterior Cruciate Ligament Reconstruction: Anatomic, Biomechanical, Imaging, and Clinical Evidence
Authors: Weber Alexander E. , Zuke William , Mayer Erik N. , Forsythe Brian , Getgood Alan , Verma Nikhil N. , Bach Bernard R. , Bedi Asheesh , Cole Brian J. 
Published: February 2018

Background: There has been an increasing interest in lateral-based soft tissue reconstructive techniques as augments to anterior cruciate ligament reconstruction (ACLR). The objective of these procedures is to minimize anterolateral rotational instability of the knee after surgery. Despite the relatively rapid increase in surgical application of these techniques, many clinical questions remain. Purpose: To provide a comprehensive update on the current state of these lateral-based augmentation procedures by reviewing the origins of the surgical techniques, the biomechanical data to support their use, and the clinical results to date. Study Design: Systematic review. Methods: A systematic search of the literature was conducted via the Medline, EMBASE, Scopus, SportDiscus, and CINAHL databases. The search was designed to encompass the literature on lateral extra-articular tenodesis (LET) procedures and the anterolateral ligament (ALL) reconstruction. Titles and abstracts were reviewed for relevance and sorted into the following categories: anatomy, biomechanics, imaging/diagnostics, surgical techniques, and clinical outcomes. Results: The search identified 4016 articles. After review for relevance, 31, 53, 27, 35, 45, and 78 articles described the anatomy, biomechanics, imaging/diagnostics, surgical techniques, and clinical outcomes of either LET procedures or the ALL reconstruction, respectively. A multitude of investigations were available, revealing controversy in addition to consensus in several categories. The level of evidence obtained from this search was not adequate for systematic review or meta-analysis; thus, a current concepts review of the anatomy, biomechanics, imaging, surgical techniques, and clinical outcomes was performed. Conclusion: Histologically, the ALL appears to be a distinct structure that can be identified with advanced imaging techniques. Biomechanical evidence suggests that the anterolateral structures of the knee, including the ALL, contribute to minimizing anterolateral rotational instability. Cadaveric studies of combined ACLR-LET procedures demonstrated overconstraint of the knee; however, these findings have yet to be reproduced in the clinical literature. The current indications for LET augmentation in the setting of ACLR and the effect on knee kinematic and joint preservation should be the subject of future research.
Monitoring and addressing global poverty: A new approach and implications for Australia
Authors: Saunders Peter 
Published: February 2018

AbstractTony Atkinson’s death at the beginning of 2017 deprived economics of one of its leading contributors to research on public economics, inequality, poverty and the welfare state. This article focuses on his last official role, as Chair of the World Bank Commission on Global Poverty. The report of the Commission – already referred to as the Atkinson Commission – proposes a new approach to measuring and monitoring the global poverty reduction targets established as part of the Sustainable Development Goals agreed by the United Nations in 2015. Atkinson developed the framework and provided the academic impetus to the work of the Commission and wrote much of its report, assisted by comments provided by an Advisory Board of eminent experts in the field and a smaller working group of selected members. The article describes some of the main features of the report’s 21 recommendations, focusing on the measurement of poverty in both monetary and non-monetary dimensions and its attempt to draw together national and global efforts to measure and reduce poverty in all its forms. It concludes with a discussion of the implications of the new approach for Australia, which like many other developed countries has so far failed to engage actively with the debate over addressing extreme global poverty.