bluuebunny/crossref_metadata_2025_split huggingface dataset:
BayMAP: a Bayesian hierarchical model for the analysis of PAR-CLIP data
Authors: Huessler Eva-Maria , Schäfer Martin , Schwender Holger , Landgraf Pablo 
Published: November 2018

Abstract

Motivation
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method for detecting interaction sites of proteins with mRNA. This method introduces T-to-C substitutions at sequenced cDNA that help to detect binding sites on mRNA. However, T-to-C substitutions can also occur due to other reasons such as mismatches or SNPs. Only few statistical procedures exist for detecting binding sites in PAR-CLIP data. Most of these methods do not account for other types of substitutions than those induced by PAR-CLIP, and therefore, also report positions with high T-to-C substitution rates, e.g. SNPs, as binding sites. Moreover, none of these procedures allow to include additional information, e.g. the type of mRNA region, relevant for the biology of microRNA-binding sites.

Results
We have developed BayMAP, a procedure based on a fully Bayesian hierarchical model that takes other sources of substitutions into account. Furthermore, this model enables the incorporation of additional information into the analysis of PAR-CLIP data. This incorporation does not only permit a better detection of binding sites, but also a better understanding of the data and the biology of binding sites. In applications to simulated PAR-CLIP data, BayMAP distinguishes binding sites from noise better than existing methods. Additionally, it yields good estimates of the influence of the additional information. We here demonstrate BayMAP’s usability for real datasets even when noisy data is present.

Availability and implementation
BayMAP is freely available as an R package at http://stat.math.uni-duesseldorf.de/baymap.

Supplementary information
Supplementary data are available at Bioinformatics online.
Hippocampal Wdr1 Deficit Impairs Learning and Memory by Perturbing F-actin Depolymerization in Mice
Authors: Wang Jie , Kou Xiao-Lin , Chen Cheng , Wang Mei , Qi Cui , Wang Jing , You Wei-Yan , Hu Gang , Chen Jiong , Gao Jun 
Published: November 2018

AbstractWD repeat protein 1 (Wdr1), known as a cofactor of actin-depolymerizing factor (ADF)/cofilin, is conserved among eukaryotes, and it plays a critical role in the dynamic reorganization of the actin cytoskeleton. However, the function of Wdr1 in the central nervous system remains elusive. Using Wdr1 conditional knockout mice, we demonstrated that Wdr1 plays a significant role in regulating synaptic plasticity and memory. The knockout mice exhibited altered reversal spatial learning and fear responses. Moreover, the Wdr1 CKO mice showed significant abnormalities in spine morphology and synaptic function, including enhanced hippocampal long-term potentiation and impaired long-term depression. Furthermore, we observed that Wdr1 deficiency perturbed actin rearrangement through regulation of the ADF/cofilin activity. Taken together, these results indicate that Wdr1 in the hippocampal CA1 area plays a critical role in actin dynamics in associative learning and postsynaptic receptor availability.
Measles Immunity at 4.5 Years of Age Following Vaccination at 9 and 15–18 Months of Age Among Human Immunodeficiency Virus (HIV)–infected, HIV-exposed–uninfected, and HIV-unexposed Children
Authors: Mutsaerts Eleonora A M L , Nunes Marta C , van Rijswijk Martijn N , Klipstein-Grobusch Kerstin , Otwombe Kennedy , Cotton Mark F , Violari Avy , Madhi Shabir A 
Published: November 2018

AbstractBackgroundHuman immunodeficiency virus (HIV)–infected and HIV-exposed–uninfected (HEU) children may be at increased risk of measles infection due to waning of immunity following vaccination. We evaluated persistence of antibodies to measles vaccination at 4.5 years of age in HIV-unexposed, HEU, and HIV-infected children with CD4+ ≥25% previously randomized to immediate antiretroviral therapy (ART) interrupted at 12 months (HIV/Immed-ART-12), 24 months (HIV/Immed-ART-24), or when clinically/immunologically indicated (HIV/Def-ART). The HIV/Def-ART group initiated ART by median 5.8 (interquartile range, 4.4–10.3) months of age.MethodsIn this study, HIV-unexposed (n = 95), HEU (n = 84), HIV/Immed-ART-12 (n = 70), HIV/Immed-ART-24 (n = 70), and HIV/Def-ART (n = 62) children were scheduled to receive measles vaccination at age 9 and 15–18 months. Antimeasles serum immunoglobulin G titers were quantified using enzyme-linked immunosorbent assay at 4.5 years.ResultsCompared with HIV-unexposed children (2860 mIU/mL), measles antibody geometric mean titers (GMTs) were significantly lower in both HIV/Immed-ART-12 (571; P < .001) and HIV/Immed-ART-24 (1136; P < .001) but similar in the HIV/Def-ART (2777) and HEU (3242) groups. Furthermore, compared with HIV-unexposed, antibody titers ≥330 mIU/mL (ie, presumed serocorrelate for protection; 99%) were also significantly lower in HIV/Immed-ART-12 (70%; P < .001) and HIV/Immed-ART-24 (83%; P < .001) but similar in the HIV/Def-ART (90%) and HEU (98%) groups.ConclusionsHIV-infected children in whom ART was interrupted at either 12 or 24 months had lower GMTs and lower proportions with seroprotective titers than HIV-unexposed children, indicating a potential downside of ART treatment interruption.Clinical Trials RegistrationNCT00099658 and NCT00102960.
Testosterone in Men With Chronic Hepatitis C Infection and After Hepatitis C Viral Clearance
Authors: Chaudhury Chloe S , Mee Thomas , Chairez Cheryl , McLaughlin Mary , Silk Rachel , Gross Chloe , Kattakuzhy Sarah , Rosenthal Elana , Kottilil Shyam , Stanley Takara L , Hadigan Colleen 
Published: November 2018

Abstract

Background
Hepatitis C virus (HCV) and hepatic dysfunction are associated with low total and free testosterone (TT and FT) and high sex hormone-binding globulin (SHBG). However, little is known about changes in testosterone following successful HCV treatment.

Methods
We evaluated testosterone levels and the prevalence of low testosterone in a cohort of 327 men with chronic HCV infection (human immunodeficiency virus [HIV] coinfection = 150) and in a subset of 85 men with testosterone levels obtained pre-HCV treatment and after sustained virologic response (SVR). Median follow-up was 36 months.

Results
Participants with active HCV at baseline had higher TT (P < .0001) and SHBG (P < .0001) compared with participants who had achieved SVR, whereas FT did not differ. Low TT (<10.4 nmol/L) was more prevalent in participants with SVR compared with active HCV (P = .002); however, low FT (<0.1735 nmol/L) was common (50% active HCV, 43% SVR) and did not different between groups. For participants with longitudinal determinations, TT and SHBG decreased significantly (P < .0001) while FT remained unchanged post-SVR. Low FT persisted after SVR (pre-treatment 58%, post-SVR 54%, P = .72). HIV status and change in aspartate aminotrasferase-to-platelet ratio were significant independent predictors of change in FT following SVR.

Conclusions
During active HCV infection, testosterone deficiency may be masked due to elevated SHBG. Despite improvements in SHBG following SVR, low FT was common and persisted after HCV clearance, indicating the need for enhanced awareness and screening using estimates of FT following successful treatment of chronic HCV.

Clinical Trials Registration
NCT01350648.
Development and Validation of a Deep Learning–based Automatic Detection Algorithm for Active Pulmonary Tuberculosis on Chest Radiographs
Authors: Hwang Eui Jin , Park Sunggyun , Jin Kwang-Nam , Kim Jung Im , Choi So Young , Lee Jong Hyuk , Goo Jin Mo , Aum Jaehong , Yim Jae-Joon , Park Chang Min ,   Deep Learning-Based Automatic Detection Algorithm Development and Evaluation Group, Kim Dong Hyeon , Woo Woo , Choi Choi , Hwang In Pyung , Song Yong Sub , Lim Lim , Kim Kim , Wi Jae Yeon , Oh Su Suk , Kang Mi-Jin 
Published: November 2018

Abstract

Background
Detection of active pulmonary tuberculosis on chest radiographs (CRs) is critical for the diagnosis and screening of tuberculosis. An automated system may help streamline the tuberculosis screening process and improve diagnostic performance.

Methods
We developed a deep learning–based automatic detection (DLAD) algorithm using 54c221 normal CRs and 6768 CRs with active pulmonary tuberculosis that were labeled and annotated by 13 board-certified radiologists. The performance of DLAD was validated using 6 external multicenter, multinational datasets. To compare the performances of DLAD with physicians, an observer performance test was conducted by 15 physicians including nonradiology physicians, board-certified radiologists, and thoracic radiologists. Image-wise classification and lesion-wise localization performances were measured using area under the receiver operating characteristic (ROC) curves and area under the alternative free-response ROC curves, respectively. Sensitivities and specificities of DLAD were calculated using 2 cutoffs (high sensitivity [98%] and high specificity [98%]) obtained through in-house validation.

Results
DLAD demonstrated classification performance of 0.977–1.000 and localization performance of 0.973–1.000. Sensitivities and specificities for classification were 94.3%–100% and 91.1%–100% using the high-sensitivity cutoff and 84.1%–99.0% and 99.1%–100% using the high-specificity cutoff. DLAD showed significantly higher performance in both classification (0.993 vs 0.746–0.971) and localization (0.993 vs 0.664–0.925) compared to all groups of physicians.

Conclusions
Our DLAD demonstrated excellent and consistent performance in the detection of active pulmonary tuberculosis on CR, outperforming physicians, including thoracic radiologists.
Calciphylaxis in a dialysis patient treated by intralesional and systemic sodium thiosulphate on top of multifactorial intervention
Authors: Galassi Andrea , Perna Francesco , De Nicola Enrico , Moneghini Laura , Sganzaroli Adriana B , Cozzolino Mario 
Published: November 2018

Abstract
Calciphylaxis, or calcific uraemic arteriolopathy (CUA), represents a life-threatening disease. Dialysis patients and those receiving warfarin are seen as populations at higher risk for CUA. Treatments for CUA are still uncertain despite the poor survival of the disease. Administration of intravenous sodium thiosulphate (STS) has been purposed to treat CUA in dialysis patients. Due to the poor tolerability of STS, characterized by nausea, hypocalcaemia, metabolic acidosis and QT-interval prolongation, its intralesional administration has been reported. We herein present the improvement of wounds in a haemodialysis patient affected by CUA, treated by multipronged intervention including both intravenous and intralesional STS.
Towards Automatic Data Format Transformations: Data Wrangling at Scale
Authors: Bogatu Alex , Paton Norman W , Fernandes Alvaro A A , Koehler Martin 
Published: November 2018

Abstract
Data wrangling is the process whereby data are cleaned and integrated for analysis. Data wrangling, even with tool support, is typically a labour intensive process. One aspect of data wrangling involves carrying out format transformations on attribute values, for example so that names or phone numbers are represented consistently. Recent research has developed techniques for synthesizing format transformation programs from examples of the source and target representations. This is valuable, but still requires a user to provide suitable examples, something that may be challenging in applications in which there are huge datasets or numerous data sources. In this paper, we investigate the automatic discovery of examples that can be used to synthesize format transformation programs. In particular, we propose two approaches to identifying candidate data examples and validating the transformations that are synthesized from them. The approaches are evaluated empirically using datasets from open government data.
Health concepts among socially disadvantaged children in France, Germany and Switzerland
Authors: Grimminger-Seidensticker Elke , Aceti Monica , Knobé Sandrine , Vieille Marchiset Gilles 
Published: November 2018

Summary
As health concepts develop through exposure to, and experience with particular contexts, and as health concepts influence health behaviour, it is important for actors in health promotion programmes to understand an individual’s health concepts. This study focussed on health concepts among socially disadvantaged children in France, Germany, Italy and Switzerland—a hitherto less researched population group. We conducted focus groups with a total of 167 children aged 7–11 years (mean=8.76 years, SD=0.68). The aim of this study was to explore if the life situation across four different countries leads to similar health concepts, and how the particular, national health discourses are reflected in the children’s health concepts. The data were analysed through a structured qualitative content analysis and revealed four categories: ‘Symbols/symptoms of health/illness’, ‘Emotionality’, ‘Healthy/unhealthy practices’, and ‘Consequences of health problems’. The children’s health concepts are linked to concrete events and objects, and they are able to think in logical sequences. However, the children’s causal argumentation is uni-dimensional; they do not cover the complexity of the development of health problems. In particular, overweight stands for illness and is exclusively the result of unhealthy practices. In their concepts, the children reflect the national health promotion programme discourses about overweight. They seem to understand the messages of health education as ‘behaving well means being healthy’; however, such a health education message initiates accusations of ‘unhealthy persons’. In consequence, challenges for sensitive health education programmes (at school) are discussed.
Hierarchical B-spline complexes of discrete differential forms
Authors: Evans John A , Scott Michael A , Shepherd Kendrick M , Thomas Derek C , Vázquez Hernández Rafael 
Published: November 2018

AbstractIn this paper we introduce the hierarchical B-spline complex of discrete differential forms for arbitrary spatial dimension. This complex may be applied to the adaptive isogeometric solution of problems arising in electromagnetics and fluid mechanics. We derive a sufficient and necessary condition guaranteeing exactness of the hierarchical B-spline complex for arbitrary spatial dimension, and we derive a set of local, easy-to-compute and sufficient exactness conditions for the two-dimensional setting. We examine the stability properties of the hierarchical B-spline complex, and we find that it yields stable approximations of both the Maxwell eigenproblem and Stokes problem provided that the local exactness conditions are satisfied. We conclude by providing numerical results showing the promise of the hierarchical B-spline complex in an adaptive isogeometric solution framework.
Survivorship Science at the NIH: Lessons Learned From Grants Funded in Fiscal Year 2016
Authors: Rowland Julia H , Gallicchio Lisa , Mollica Michelle , Saiontz Nicole , Falisi Angela L , Tesauro Gina 
Published: November 2018

Abstract
Federal investment in survivorship science has grown markedly since the National Cancer Institute’s creation of the Office of Cancer Survivorship in 1996. To describe the nature of this research, provide a benchmark, and map new directions for the future, a portfolio analysis of National Institutes of Health-wide survivorship grants was undertaken for fiscal year 2016. Applying survivorship-relevant terms, a search was conducted using the National Institutes of Health Information for Management, Planning, Analysis and Coordination grants database. Grants identified were reviewed for inclusion and categorized by grant mechanism used, funding agency, and principal investigator characteristics. Trained pairs of coders classified each grant by focus and design (observational vs interventional), population studied, and outcomes examined. A total of 215 survivorship grants were identified; 7 were excluded for lack of fit and 2 for nonresearch focus. Forty-one (19.7%) representing training grants (n = 38) or conference grants (n = 3) were not coded. Of the remaining 165 grants, most (88.5%) were funded by the National Cancer Institute; used the large, investigator-initiated (R01) mechanism (66.7%); focused on adult survivors alone (84.2%), often breast cancer survivors (47.3%); were observational in nature (57.3%); and addressed a broad array of topics, including psychosocial and physiologic outcomes, health behaviors, patterns of care, and economic/employment outcomes. Grants were led by investigators from diverse backgrounds, 28.4% of whom were early in their career. Present funding patterns, many stable since 2006, point to the need to expand research to include different cancer sites, greater ethnoculturally diverse samples, and older (>65 years) as well as longer-term (>5 years) survivors and address effects of newer therapies.
Context dependency of insect and mammalian herbivore effects on tall thistle (Cirsium altissimum) populations
Authors: Russell F Leland , Houseman Gregory R 
Published: November 2018

Abstract

Aims
Identifying factors that drive variation in herbivore effects on plant populations can provide insight for explaining plant distributions and for limiting weeds. Abiotic resource availability to plants is a key explanation for variation in herbivore effects on individual plants, but the role of resources in determining herbivore effects on plant populations is largely unexplored. We tested the hypothesis that soil nutrient availability drives variation in insect and mammal herbivore effects on tall thistle (Cirsium altissimum) population growth.

Methods
In a Kansas USA restored tallgrass grassland that experienced prescribed fires, we manipulated soil nutrients, through fertilizer addition, and presence of insect and mammal herbivores, using combinations of insecticide and fencing, in experimental plots. Over 7 years, we quantified herbivore damage to reproductive tall thistles, tall thistle seed production and population growth rates.

Important Findings
Seed production was reduced by insect herbivores and increased by fertilizer addition, but treatment effects were independent. Herbivore effects on tall thistle population growth depended upon soil nutrients in only one of seven annual transitions. Herbivores reduced thistle population growth in two of three annual transitions that included prescribed fire, whereas they reduced population growth in only one of four transitions without fire. Soil nutrient availability does not provide a general explanation for variation in herbivore effects on tall thistle population growth rates. Disturbance regime may be a more important aspect of ecological context for influencing herbivore effects on tall thistle populations in mesic grasslands.
Canary in the Coal Mine? Transmitted Mutations Conferring Resistance to All Integrase Strand Transfer Inhibitors in a Treatment-Naive Patient
Authors: McGee Kara S , Okeke Nwora Lance , Hurt Christopher B , McKellar Mehri S 
Published: November 2018

Abstract
Transmitted drug resistance to the integrase strand transfer inhibitor (INSTI) class of antiretrovirals is very rare. We present a case of a treatment-naive female patient with human immunodeficiency virus harboring resistance to all INSTIs, including bictegravir and dolutegravir.
Microsurgical Clipping of a Ruptured Basilar Apex Aneurysm: 3-Dimensional Operative Video
Authors: Cheng Chun-Yu , Qazi Zeeshan , Hallam Danial K , Ghodke Basavaraj V , Sekhar Laligam N 
Published: November 2018

Abstract
A 59-yr-old woman presented with a sudden onset of headache with neck pain and stiffness, Hunt and Hess grade 2. Brain computed tomography (CT) showed subarachnoid hemorrhage, Fisher Grade 2. Intra-arterial digital subtraction angiography (IADSA) showed a basilar artery apex aneurysm, dome size 9 mm and neck 3 mm, leaning towards the right, and a dominant right artery of Percheron. Endovascular treatment and microsurgical clipping were both explained to the patient, but she decided to undergo microsurgery due to the durability of treatment.
She underwent a right frontotemporal craniotomy and orbital osteotomy. We performed optic nerve decompression and intradural anterior clinoidectomy to enhance the exposure. Working through the carotid-oculomotor space, the posterior communicating artery was traced back to the posterior cerebral artery. The basilar artery was temporarily occluded for aneurysm dissection after burst suppression to protect the brain. The aneurysm was irregular, multilobulated, and projecting upward. The dominant thalamoperforate artery (artery of Percheron) was arising from the right P1, and densely adherent to the sac of the aneurysm. After dissection of the artery of Percheron away from the aneurysm, it was completely occluded by a side-curved titanium clip. The patient had right oculomotor nerve paresis and headache postoperatively, but at discharge 2 wk later the headache and paresis had completely resolved. The postoperative IADSA showed total occlusion of the aneurysm with patency of the artery of Percheron.
This 3-dimensional video shows the technical nuances of microsurgical clipping of a ruptured basilar apex aneurysm and intraoperative dissection of the artery of Percheron.
Informed consent was obtained from the patient prior to the surgery that included videotaping of the procedure and its distribution for educational purposes. All relevant patient identifiers have also been removed from the video and accompanying radiology slides.
Posterior Cervical Decompression and Instrumented Fusion for Cervical Spondylotic Myelopathy: 2-Dimensional Operative Video
Authors: Khalsa Siri Sahib S , Saadeh Yamaan S , Smith Brandon W , Joseph Jacob R , Oppenlander Mark E 
Published: November 2018

Abstract
Cervical spondylotic myelopathy is a common cause of progressive quadriparesis in adults. It is characterized by compression of the cervical spinal cord due to degenerative changes including intervertebral disc protrusion, ligamentum flavum hypertrophy, and osteophyte formation. Clinically, patients can present with declining motor control in the extremities, gait imbalance, spasticity, hyperreflexia, or possibly frank weakness. Surgical treatment options include ventral and dorsal approaches, whose indications vary depending on spinal alignment, number of levels requiring decompression, the dorsal/ventral/circumferential location of compression, and patient-specific anatomic constraints. Posterior cervical decompression and instrumented fusion is a mainstay of treatment for cervical spondylotic myelopathy when a dorsal approach is indicated. In this video, we present a case of a 60-yr-old female who presented with signs and symptoms of cervical myelopathy, with MRI findings of C3 on C4 anterolisthesis and circumferential central stenosis worst at C4-5 and C5-6. We demonstrate the operative steps to complete a C3 to C6 decompression and instrumented fusion with lateral mass screws. Appropriate patient consent was obtained.
A History of Clinical Child and Adolescent Psychology
Authors: Routh Donald K. 
Published: November 2018

Abstract
The roots of the broader field of clinical child psychology date to the founding of the first psychology clinic by Lightner Witmer at the University of Pennsylvania in 1896. The first professional society dedicated to this discipline, the Section on Clinical Child Psychology, was founded in 1962 by Alan Ross. It became a member of the Society of Clinical Psychology (Division 12) of the American Psychological Association (APA). In 1998, clinical child psychology was recognized as a specialty by the APA. The Section on Clinical Child Psychology evolved into the Society of Clinical Child and Adolescent Psychology (Division 53, APA), and the American Board of Clinical Child and Adolescent Psychology was founded. The emphasis of this field is on evidence-based assessment and treatment of children as individuals, family members, and students in school. The evidence includes controlled randomized trials of clinical procedures, which are increasingly made available to the public.