bluuebunny/crossref_metadata_2025_split huggingface dataset:
Devastating Consequences of Sex Trafficking on Women's Health
Authors: McTavish Fr. James 
Published: November 2017

Sex trafficking has devastating consequences on the physical and mental well-being of millions of women around the world. These trafficking victims often come in contact with medical personnel, and these encounters with suitably prepared staff can be a step toward healing of the victims. The Catholic Church, especially through Pope Francis, is making strenuous efforts to curb the spread of sex trafficking. Same-sex feelings and behavior may arise post-trafficking in individuals, although this does not appear to be mentioned thus far in the literature. Here, we are most likely dealing with a type of “pseudo-lesbianism” post-trauma. The trafficking survivor can be helped to understand some of the likely roots of her feelings such as anti-male sentiments following abuse. She needs to be patiently, and expertly, accompanied to process the trauma she has experienced, and learn how to meet her genuine needs for female affection and affirmation in healthy, chaste, and non-erotic ways. Summary Around the world, millions of female victims of human trafficking are forced into sex “work,” often resulting in serious physical and mental-health problems. Healthcare staff should be alert to spot victims of sex trafficking and be ready to assist them. The Catholic Church, especially through Pope Francis, has been vocal in denouncing this form of modern slavery. Some female victims of sex trafficking may experience same-sex feelings afterward. Healing for such young women involves helping them to process their traumatic experiences, as well as patiently accompanying them as they seek to develop healthy, chaste friendships with other females and males.
Investigation on the fiber based approach to estimate the axial load carrying capacity of the circular concrete filled steel tube (CFST)
Authors: Piscesa B , Attard M M , Suprobo P , Samani A K 
Published: November 2017

Abstract
External confining devices are often used to enhance the strength and ductility of reinforced concrete columns. Among the available external confining devices, steel tube is one of the most widely used in construction. However, steel tube has some drawbacks such as local buckling which needs to be considered when estimating the axial load carrying capacity of the concrete-filled-steel-tube (CFST) column. To tackle this problem in design, Eurocode 4 provided guidelines to estimate the effective yield strength of the steel tube material. To study the behavior of CFST column, in this paper, a non-linear analysis using a fiber-based approach was conducted. The use of the fiber-based approach allows the engineers to predict not only the axial load carrying capacity but also the complete load-deformation curve of the CFST columns for a known confining pressure. In the proposed fiber-based approach, an inverse analysis is used to estimate the constant confining pressure similar to design-oriented models. This paper also presents comparisons between the fiber-based approach model with the experimental results and the 3D non-linear finite element analysis.
Do Nutrient Management Plans Actually Manage Nutrients? Evidence from a Nationally‐Representative Survey of Hog Producers
Authors: Sneeringer Stacy , Key Nigel , Pon Shirley 
Published: November 2017

AbstractA nutrient management plan (NMP) specifies recommended practices to match applied nutrients with crops’ uptake capacity. Because monitoring nutrient applications is difficult, regulators instead oversee NMP adoption. In this paper we examine whether having NMPs make hog farms more likely to adopt nutrient management practices. We estimate nutrient application and uptake rates to assess whether operations with NMPs are less likely to over‐apply nutrients. Using an endogenous treatment effects model to control for potential confounding and selection bias, we find that NMPs are positively correlated with the adoption of nutrient management practices, as well as with the reduced application of excess nutrients.
ThetaMater: Bayesian estimation of population size parameter θ from genomic data
Authors: Adams Richard H , Schield Drew R , Card Daren C , Corbin Andrew , Castoe Todd A 
Published: November 2017

Abstract

Summary
We describe ThetaMater, an open source R package comprising a suite of functions for efficient and scalable Bayesian estimation of the population size parameter θ from genomic data.

Availability and implementation
ThetaMater is available at GitHub (https://github.com/radamsRHA/ThetaMater).

Supplementary information
Supplementary data are available at Bioinformatics online.
Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies
Authors: Derkach Andriy , Zhang Haoyu , Chatterjee Nilanjan 
Published: November 2017

Abstract

Motivation
Genome-wide association studies are now shifting focus from analysis of common to rare variants. As power for association testing for individual rare variants may often be low, various aggregate level association tests have been proposed to detect genetic loci. Typically, power calculations for such tests require specification of large number of parameters, including effect sizes and allele frequencies of individual variants, making them difficult to use in practice. We propose to approximate power to a varying degree of accuracy using a smaller number of key parameters, including the total genetic variance explained by multiple variants within a locus.

Results
We perform extensive simulation studies to assess the accuracy of the proposed approximations in realistic settings. Using these simplified power calculations, we develop an analytic framework to obtain bounds on genetic architecture of an underlying trait given results from genome-wide association studies with rare variants. Finally, we provide insights into the required quality of annotation/functional information for identification of likely causal variants to make meaningful improvement in power.

Availability and implementation
A shiny application that allows a variety of Power Analysis of GEnetic AssociatioN Tests (PAGEANT), in R is made publicly available at https://andrewhaoyu.shinyapps.io/PAGEANT/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Capillary rarefaction from the kidney point of view
Authors: Afsar Baris , Afsar Rengin E , Dagel Tuncay , Kaya Ege , Erus Suat , Ortiz Alberto , Covic Adrian , Kanbay Mehmet 
Published: November 2017

ABSTRACTCapillary rarefaction is broadly defined as a reduction in vascular density. Capillary rarefaction in the kidneys is thought to promote hypoxia, impair hemodynamic responses and predispose to chronic kidney disease (CKD) progression and hypertension development. Various mechanisms have been suggested to play a role in the development of capillary rarefaction, including inflammation, an altered endothelial-tubular epithelial cell crosstalk, a relative deficiency in angiogenic growth factors, loss of pericytes, increased activity of Transforming growth factor -β1 and thrombospondin-1, vitamin D deficiency, a link to lymphatic neoangiogenesis and INK4a/ARF (Cylin-dependent kinase inhibitor 2a; CDKN2A). In this review, we summarize the tools available to monitor capillary rarefaction noninvasively in the clinic, the contribution of capillary rarefaction to CKD and hypertension, the known mechanisms of capillary rarefaction, and potential future strategies to attenuate capillary rarefaction and reduce its negative impact. Therapeutic strategies to be explored in more detail include optimization of antihypertensive therapy, vitamin D receptor activators, sirtuin 1 activators, Hypoxia inducible factor prolyl hydroxylase inhibitors and stem cell therapy.
Gender and cardiovascular disease: are sex-biased microRNA networks a driving force behind heart failure with preserved ejection fraction in women?
Authors: Florijn Barend W , Bijkerk Roel , van der Veer Eric P , van Zonneveld Anton Jan 
Published: November 2017

AbstractCardiovascular disease (CVD) is the primary cause of death among men and women worldwide. Nevertheless, our comprehension of how CVD progresses in women and elicits clinical outcomes is lacking, leading CVD to be under-diagnosed and under-treated in women. A clear example of this differential presentation of CVD pathophysiologies in females is the strikingly higher prevalence of heart failure with preserved ejection fraction (HFpEF). Women with a history of pre-eclampsia or those who present with co-morbidities such as obesity, hypertension, and diabetes mellitus are at increased risk of developing HFpEF. Long understood to be a critical CVD risk factor, our understanding of how gender differentially affects the development of CVD has been greatly expanded by extensive genomic and transcriptomic studies. These studies uncovered a pivotal role for differential microRNA (miRNA) expression in response to systemic inflammation, where their co-ordinated expression forms a post-transcriptional regulatory network that instigates microcirculation defects. Importantly, the potential sex-biased expression of the given miRNAs may explain sex-specific cardiovascular pathophysiologies in women, such as HFpEF. Sex-biased miRNAs are regulated by oestrogen (E2) in their transcription and processing or are expressed from loci on the X-chromosome due to incomplete X-chromosome inactivation. Interestingly, while E2-induced miRNAs predominantly appear to serve protective functions, it could be argued that many X-linked miRNAs have been found to challenge microvascular and myocardial integrity. Therefore, menopausal E2 deficiency, resulting in protective miRNA loss, and the augmentation of X-linked miRNA expression, may well contribute to the molecular mechanisms that underlie the female-specific cardiovascular aetiology in HFpEF.
HisgAtlas 1.0: a human immunosuppression gene database
Authors: Liu Yuan , He Mengqi , Wang Dan , Diao Lihong , Liu Jinying , Tang Li , Guo Shuzhen , He Fuchu , Li Dong 
Published: November 2017

Abstract
Immunosuppression is body’s state in which the activation or efficacy of immune system is weakened. It is associated with a wide spectrum of human diseases. In the last two decades, tremendous efforts have been made to elucidate the mechanism of hundreds of immunosuppression genes. Immunosuppression genes could be valuable drug targets or biomarkers for the immunotherapeutic treatment of different diseases. However, the information of all previously identified immunosuppression genes is dispersed in thousands of publications. Here, we provide the HisgAtlas database that collects 995 previously identified human immunosuppression genes using text mining and manual curation. We believe HisgAtlas will be a valuable resource to search human immunosuppression genes as well as to investigate their functions in further research.
Database URL: http://biokb.ncpsb.org/HisgAtlas/
The impact of architectural spaces’ geometric forms and construction materials on the users’ brainwaves and consciousness status
Authors: Elbaiuomy Eslam , Hegazy Ibrahim , Sheta Sherif 
Published: November 2017

Abstract
Biogeometry is the patented science of using the energy of shapes and forms to qualitatively make a balance between the biological energy systems and accommodate their interactions with the environment. Balancing the activities of daily life, attaining harmony with our environment, humanizing modern technology, and incorporating science and spirituality are the work of the science of biogeometry. The research in biogeometry was and still is mainly dedicated to the development of a new form of architecture that would improve the human biological system. In this context, the current study aims to develop a scientific approach to investigate the influence of the geometric forms and construction materials of the architectural spaces on the users’ brainwaves and then on their consciousness status which is considered as the main controlling factor in human bioenergy. Trying to consolidating the theoretical views of this effect to be measurable scientifically, the study is based on using a numerical analysis based on a computerized simulation. The results of this study show different influences based on geometric forms and construction materials. The study is carried out using CST Microwave Studio to identify the resonance frequency occurred inside different geometric forms with different construction materials, and then distinguish the related user’s brainwaves which influence his/her consciousness status. This may assist architects and designers in identifying appropriate geometric forms to suit the required uses and functions that need particular consciousness statuses.
Physiologic Modulators of Neural Injury After Brain and Spinal Cord Injury
Authors: Dietrich W. Dalton 
Published: November 2017

Abstract
Brain and spinal cord injury are leading causes of death and long-term disability, producing diverse burdens for the affected individuals, their families, and society. Such injuries, including traumatic brain injury, stroke, subarachnoid hemorrhage, and spinal cord injury, have common patterns of neuronal cell vulnerability that are associated with a complex cascade of pathologic processes that trigger the propagation of tissue damage beyond the acute injury. Secondary injury mechanisms, including oxidative stress, edema formation, changes in cerebral blood flow and vessel reactivity, metabolic and blood–brain barrier disruption, and neuroinflammation, are therefore important therapeutic targets. Several key physiological parameters require monitoring and intensive management during various phases of treatment to ameliorate secondary injury mechanisms and potentially protect against further neuronal injury. This chapter reviews the core physiological targets in the management of brain and spinal cord injury and relates them to secondary injury mechanisms and outcomes.
Neurophysiologic Monitoring and Neuroprotection
Authors: Alawi Aws , Reznik Michael , Claassen Jan 
Published: November 2017

Abstract
One of the main goals of monitoring neurologically ill patients is detection of secondary brain injury early enough to intervene to prevent permanent damage. In some patients with impaired levels of consciousness and those who require sedation, monitoring various brain physiologic parameters by invasive and noninvasive means has become an essential tool in the care of critically ill patients. Integration of multiple physiological parameters provides a more comprehensive physiological assessment of the injured brain and allows real-time, early detection of secondary cerebral injury and intervention to prevent permanent damage. Importantly, these modalities should be interpreted collectively and not in isolation in order to manage acute brain injuries, which are often complex and dynamic at the same time.
Assessment of Postoperative Cognitive Decline
Authors: Uysal Suzan , Reich David L. 
Published: November 2017

Abstract
Neurocognitive outcome studies are a potentially rich source of information for evidence-based approaches to neuroprotection. This chapter provides a critical examination of assessment methods for studying postoperative cognitive decline (POCD), with regard to definition of the phenomenon, the role of hypotheses regarding mechanisms and localization of neural injury, and psychometric considerations for the design of POCD assessment protocols. It also describes an approach to conducting clinical neuropsychological assessments outside of research contexts for patients who present with signs or symptoms of POCD when there are no preoperative baseline cognitive test data. The authors propose a set of guidelines for designing, conducting, interpreting, and evaluating cognitive outcome studies in surgical patients and performing clinical POCD assessments.
Neuroprotection for Cardiac Arrest
Authors: Pitcher Joseph H. , Seder David B 
Published: November 2017

Abstract
This chapter reviews the pathophysiology of brain injury after resuscitation from cardiac arrest and describes a pragmatic approach to neuroprotection. Common mechanisms of brain injury in the postresuscitation milieu are discussed and strategies for optimizing physiological variables such as blood pressure, oxygen, ventilation, and blood glucose in order to minimize secondary injury are presented. Neuroprotective therapies, such as targeted temperature management and pharmacologic neuroprotective agents, are covered in detail. Finally, the use of raw and processed electroencephalography and other diagnostic tools are described for the purposes of determining severity of brain injury, triaging patients to different treatment pathways, and for prognostic value.
Neuroprotection for Premature Birth and Neonatal Brain Injury
Authors: Chang Eugene 
Published: November 2017

Abstract
Preterm birth is associated with increased risk of perinatal brain injury. Although there has been little headway made in reducing preterm birth rates, survival of infants born prematurely has improved greatly. Because of this, the neurodevelopmental consequences related to prematurity have become significant issues, especially in those infants born at less than 32 weeks gestation. Hypoxic-ischemic encephalopathy commonly leads to neonatal brain injury both before and after delivery. While perinatal birth asphyxia accounts for a proportion of neonatal brain injury in neonates younger than 37 weeks, preterm birth is the more significant risk factor. This chapter explores the neurodevelopmental consequences associated with preterm birth, the pathophysiology of perinatal brain injury, and the imaging modalities used to assess the newborn brain. Finally, various neuroprotective interventions in clinical use and in development will be described.
Neuroprotection for General, Orthopedic, Peripheral Vascular, and ENT Surgery
Authors: Selim Magdy 
Published: November 2017

Abstract
Unlike stroke after cardiac and carotid surgery, stroke after general; orthopedic; peripheral vascular; and ear, nose, and throat surgery has not been investigated extensively. The incidence, predisposing factors, and etiological mechanisms of stroke in patients undergoing these procedures are reviewed. Recommendations to prevent, recognize, and treat stroke following these surgical procedures are provided to minimize postoperative stroke risk and its associated morbidity and disability. Although these recommendations can help to decrease the incidence of perioperative stroke, there is an unmet need to find novel and effective neuroprotective strategies that can be used pre- or intraoperatively to minimize the effects of stroke on brain tissue and resulting disability. Future studies should evaluate the potential usefulness of neuroprotective therapies or interventions, including various anesthetic agents that can be used prophylactically in the perioperative setting.
In-solution Y-chromosome capture-enrichment on ancient DNA libraries
Authors: Cruz-Dávalos Diana I , Nieves-Colón María A , Sockell Alexandra , David Poznik G , Schroeder Hannes , Stone Anne C , Bustamante Carlos D , Malaspinas Anna-Sapfo , Ávila-Arcos María C 
Published: November 2017

AbstractBackgroundAs most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach – in-solution capture-enrichment – retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3,000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC+Y) versus non-enriched (pre-capture) libraries.ResultsWe recovered 17–4,152 times more targeted unique Y-chromosome sequences after capture, where 0.01-6.2% (WGC+Y) and 0.01-23.5% (YCC) of the sequence reads were on-target, compared to 0.0002-0.004% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC+Y) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, WGC+Y yielded greater enrichment than YCC alone. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins.ConclusionsWe present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC+Y enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture for low-complexity libraries, as clonality increases considerably with each round.
deepNF: Deep network fusion for protein function prediction
Authors: Gligorijević Vladimir , Barot Meet , Bonneau Richard 
Published: November 2017

AbstractThe prevalence of high-throughput experimental methods has resulted in an abundance of large-scale molecular and functional interaction networks. The connectivity of these networks provide a rich source of information for inferring functional annotations for genes and proteins. An important challenge has been to develop methods for combining these heterogeneous networks to extract useful protein feature representations for function prediction. Most of the existing approaches for network integration use shallow models that cannot capture complex and highly-nonlinear network structures. Thus, we propose deepNF, a network fusion method based on Multimodal Deep Autoencoders to extract high-level features of proteins from multiple heterogeneous interaction networks. We apply this method to combine STRING networks to construct a common low-dimensional representation containing high-level protein features. We use separate layers for different network types in the early stages of the multimodal autoencoder, later connecting all the layers into a single bottleneck layer from which we extract features to predict protein function. We compare the cross-validation and temporal holdout predictive performance of our method with state-of-the-art methods, including the recently proposed method Mashup. Our results show that our method outperforms previous methods for both human and yeast STRING networks. We also show substantial improvement in the performance of our method in predicting GO terms of varying type and specificity.AvailabilitydeepNF is freely available at: https://github.com/VGligorijevic/deepNF