bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibody interface prediction with 3D Zernike descriptors and SVM
Authors: Daberdaku Sebastian , Ferrari Carlo 
Published: November 2018

Abstract

Motivation
Antibodies are a class of proteins capable of specifically recognizing and binding to a virtually infinite number of antigens. This binding malleability makes them the most valuable category of biopharmaceuticals for both diagnostic and therapeutic applications. The correct identification of the antigen-binding residues in the antibody is crucial for all antibody design and engineering techniques and could also help to understand the complex antigen binding mechanisms. However, the antibody-binding interface prediction field appears to be still rather underdeveloped.

Results
We present a novel method for antibody interface prediction from their experimentally solved structures based on 3D Zernike Descriptors. Roto-translationally invariant descriptors are computed from circular patches of the antibody surface enriched with a chosen subset of physico-chemical properties from the AAindex1 amino acid index set, and are used as samples for a binary classification problem. An SVM classifier is used to distinguish interface surface patches from non-interface ones. The proposed method was shown to outperform other antigen-binding interface prediction software.

Availability and implementation
Linux binaries and Python scripts are available at https://github.com/sebastiandaberdaku/AntibodyInterfacePrediction. The datasets generated and/or analyzed during the current study are available at https://doi.org/10.6084/m9.figshare.5442229.

Supplementary information
Supplementary data are available at Bioinformatics online.
ASSESSMENT OF TERRESTRIAL RADIATION BY DIRECT MEASUREMENT OF AMBIENT DOSE EQUIVALENT RATE OF BACKGROUND RADIATION
Authors: Kardan Mohammad Reza , Sadeghi Nahid , Fathabadi Nasrin , Attarilar Ali 
Published: November 2018

Abstract
Estimation of terrestrial external radiation is essential for assessment of public exposure to natural radiation. During national survey of natural radionuclide in soil in Iran, 979 soil samples were collected from different locations, in the same time ambient dose equivalent rate was measured by a scintillator detector. In this work, terrestrial radiation was estimated by direct measurement of ambient dose equivalent rate of background radiation. The response of dose measuring instrument to cosmic radiation at ground level was measured and other components were discussed and estimated. For verification, terrestrial radiation derived from this method was compared with those calculated from activity concentration of natural radionuclides in soil. The averages of ambient dose equivalent rate derived from activity concentration of by natural radionuclide in soil and from direct measurement are 55.07 and 62.57 nSv/h, respectively. The source of statistical and systematic uncertainties are introduced and discussed.
Effects of Acute Deltamethrin Exposure in Adult and Developing Sprague Dawley Rats on Acoustic Startle Response in Relation to Deltamethrin Brain and Plasma Concentrations
Authors: Williams Michael T , Gutierrez Arnold , Vorhees Charles V 
Published: November 2018

Abstract
Deltamethrin (DLM) is a commonly used pesticide that helps to control crop destruction, disease, and nuisance insects. In rodents DLM can produce choreoathetosis, salivation, and decreased acoustic startle responses (ASR). Herein, adult Sprague Dawley rats were assessed for ASR 2 h after DLM delivered in 5 ml/kg corn oil, however no decrease was observed. Therefore, a test-retest protocol was used to reduce variability, and the effects on ASR on postnatal day 15 (P15) and adult rats were assessed 2, 4, 6, and 8 h after DLM administration (0, 1, 2, or 4 mg/kg for P15 rats and 0, 2, 8, or 25 mg/kg for adults). In a separate set of rats identically treated, DLM levels were determined in blood and brain. DLM (8 or 25 mg/kg) in adult rats decreased ASR up to 4 h, whereas in P15 rats decreases were observed between 2 and 8 h. The adult 25 mg/kg group showed consistent signs of salivation and tremor, whereas in P15 rats salivation was observed in the 2 and 4 mg/kg groups and tremor was observed at all doses over the 8-h period. Mortality was observed in all P15 dose groups but not in adults. Dose-dependent increases of DLM in blood and brain regardless of age were observed. At approximately equivalent whole brain concentrations, effects were more pronounced in P15 rats than in adult rats. Comparable brain levels of DLM do not explain differences in ASR and tremor between the P15 and adult rats. These data indicate age-dependent differences in sensitivity to DLM.
Blood Pressure and End-tidal Carbon Dioxide Ranges during Aneurysm Occlusion and Neurologic Outcome after an Aneurysmal Subarachnoid Hemorrhage
Authors: Akkermans Annemarie , van Waes Judith A. , Peelen Linda M. , Rinkel Gabriel J. , van Klei Wilton A. 
Published: November 2018

Abstract

EDITOR’S PERSPECTIVE

What We Already Know about This Topic
It remains unknown what end-tidal carbon dioxide and mean arterial pressure are optimal for surgical management of patients with an aneurysmal subarachnoid hemorrhage

What This Article Tells Us That Is New
The investigators retrospectively evaluated 1,099 patients who had endovascular coiling or surgical clipping for subarachnoid hemorrhages
There were no clinically important or statistical significant associations between either end-tidal carbon dioxide or mean arterial pressure thresholds and Glasgow Outcome Scale at discharge or three months
Other prognostic factors are more important than carbon dioxide and blood pressure, at least within the observed clinical ranges

Background
Hypocapnia, hypotension, and hypertension during aneurysm occlusion in patients with an aneurysmal subarachnoid hemorrhage may lead to a poor prognosis, but evidence for end-tidal carbon dioxide (ETco
2) and mean arterial pressure (MAP) targets is lacking. Within the ranges of standardized treatment, the authors aimed to study the association between hypocapnia (Paco
2 < 35 mmHg), hypotension (MAP < 80 mmHg), and hypertension (MAP >100 mmHg) during general anesthesia for aneurysm occlusion and neurologic outcome.

Methods
This retrospective observational study included patients who underwent early aneurysm occlusion after an aneurysmal subarachnoid hemorrhage under general anesthesia. ETco
2 and MAP were summarized per patient as the mean and time-weighted average area under the curve for various absolute (ETco
2 < 30, < 35, < 40, < 45 mmHg; and MAP < 60, < 70, < 80, > 90, > 100 mmHg) and relative thresholds (MAP < 70%, < 60%, < 50%). Clinical outcome was assessed with the Glasgow Outcome Scale at discharge and at three months, as primary and secondary outcome measure, respectively.

Results
Endovascular coiling was performed in 578 patients, and 521 underwent neurosurgical clipping. Of these 1,099 patients, 447 (41%) had a poor neurologic outcome at discharge. None of the ETco
2 and MAP ranges found within the current clinical setting were associated with a poor neurologic outcome at discharge, with an adjusted risk ratio for any ETco
2 value less than 30 mmHg of 0.95 (95% CI, 0.81 to 1.10; P < 0.496) and an adjusted risk ratio for any MAP less than 60 mmHg of 0.94 (95% CI, 0.78 to 1.14; P < 0.530). These results were not influenced by preoperative neurologic condition, treatment modality and timing of the intervention. Comparable results were obtained for neurologic outcome at three months.

Conclusions
Within a standardized intraoperative treatment strategy in accordance with current clinical consensus, hypocapnia, hypotension, and hypertension during aneurysm occlusion were not found to be associated with a poor neurologic outcome at discharge in patients with an aneurysmal subarachnoid hemorrhage.
Epidemiology of Spinal Fractures in a Level One Trauma Center in the Netherlands
Authors: den Ouden Lars P. , Smits Arjen J. , Stadhouder Agnita , Feller Ricardo , Deunk Jaap , Bloemers Frank W. 
Published: November 2018

Study Design.
Retrospective epidemiological study.

Objective.
To describe the epidemiology of spinal fractures over a 10 years period in a level one trauma center in the Netherlands.

Summary of Background Data.
Spinal fractures may have large socioeconomic consequences. The prevalence and outcomes likely change over the years owing to improved traffic safety, increasing population age and improved medical treatment. This is the first study to address the epidemiology of spinal fractures over a large period in the Netherlands.

Methods.
All patients with a cervical, thoracic, or lumbar spine fracture admitted to a level one trauma center from 2007 to 2016 were prospective registered and retrospectively analyzed. In addition to patient, accident, and associated injury characteristics, radiological and surgery data were obtained from the hospital's Electronic Patient File system.

Results.
Between 2007 and 2016, 1479 patients with a total of 3029 spinal fractures were admitted. Approximately 40.8% were female and 59.2% were male, with a mean age of 52.0 years; 4.9% of fractures occurred at a juvenile age (0–18 years) and 63.6% at the age of 19 to 64 years. Most fractures occurred in the thoracic spine, followed by the lumbar and cervical spine. The most common cause of injury was a fall from height, followed by traffic accidents. Spinal cord injury occurred in 8.5% and associated injuries were reported in 73% of the patients. Sixteen percent of the admitted patients were treated operatively. Over time, there was a larger increase in amount of spine fractures in elderly (≥ 65 years) compared with younger people.

Conclusion.
The total amount of spine fractures per year increased over time. In addition, there was a larger increase in amount of spine fractures in patients over 65 years of age compared with younger patients. Despite this increase, a considerable amount of spine fractures still occur in the age-group of 19 to 64 years. Most fractures were located in the thoracic spine. This study might stimulate development of policy on precautionary actions to prevent spine fractures.

Level of Evidence: 4
Topical Ganciclovir for Prophylaxis of Cytomegalovirus Endotheliitis in Endothelial Keratoplasty
Authors: Basilious Alfred , Chew Hall F. 
Published: November 2018

Purpose:
To describe the presentation and management of 2 cases of Descemet stripping automated endothelial keratoplasty (DSAEK) with failure secondary to cytomegalovirus (CMV) infection and prophylaxis with topical ganciclovir to prevent repeat failure of Descemet membrane endothelial keratoplasty (DMEK) regrafts.

Methods:
A retrospective chart review was conducted for 2 patients with DSAEK failure secondary to CMV infection.

Results:
A 70-year-old immunocompetent man (case 1) and a 53-year-old immunocompromised man (case 2) received DSAEK for presumed pseudophakic bullous keratopathy and endothelial decompensation secondary to recurrent uveitis, respectively. Case 1 had first graft failure at 10 months and case 2 at 21 months with inferior edema and keratic precipitates. Both failed to respond to topical steroid drops, and case 1 had 3 subsequent failed DSAEKs. Anterior chamber paracentesis confirmed CMV DNA. Neither had a clinical response to 6 weeks of oral valganciclovir. They were then administered topical ganciclovir (0.15% ophthalmic gel), and repeat endothelial transplant (DMEK) was performed for both patients. They were again administered topical ganciclovir 4 times daily after surgery because aqueous samples remained positive for CMV. Both remain free of inflammation or failure on topical ganciclovir for 21 months (case 1) and 29 months (case 2) with uncorrected visual acuities of 20/40 and 20/25, respectively.

Conclusions:
Long-term topical ganciclovir use can prevent recurrence of CMV-associated graft failure even in immunocompromised hosts without side effects of systemic antivirals. DMEK may have advantages over DSEK in eyes with previous CMV infection and in eyes prone to inflammation.
The Dangers of Influenza and Benefits of Vaccination in Adults With Chronic Health Conditions
Authors: Schaffner William , McElhaney Janet , Rizzo Albert A. , Savoy Margot , Taylor Allen J. , Young Melissa 
Published: November 2018

Abstract
Influenza (flu) is a serious health concern in adults with certain chronic health conditions including diabetes, lung disease, and cardiovascular disease. Flu-related inflammation may exacerbate chronic lung diseases and has been shown to increase the risk of myocardial infarction and stroke long after resolution of the acute illness. Data from the 2017–2018 flu season show a disproportionate impact on adults with chronic health conditions. Despite strong evidence to support the benefits of annual flu vaccination in mitigating disease severity, reducing hospitalization rates, and disrupting viral transmission, vaccination rates remain suboptimal. Health care professionals play a key role in communicating the known benefits of flu vaccination and improving patient outcomes in adults with chronic health conditions.
Geographical mapping of advanced practice registered nurses in Louisiana: Leveraging the power of data display
Authors: Becnel Brent J. , Pearce Patricia F. , Eiswirth Emily 
Published: November 2018

ABSTRACT:

Background and purpose:
Identifying the locations of advanced practice registered nurses (APRNs) in the state is challenging without data readily available, which can adversely affect stakeholder initiatives. The purpose of this project was to develop an online interactive map reflecting distribution of APRNs licensed by the Louisiana State Board of Nursing (LSBN), heightening APRN visibility and improving usability of data for policy, education, practice, and research initiatives.

Methods:
A descriptive design with development of a graphical interactive map showing all Louisiana parishes with integrated distribution summaries of APRNs was made. Work proceeded from paper to higher fidelity simulations to the final interactive web page. Compatibility with LSBN's web page and annual data upload were ensured.

Conclusion:
The project was done in collaboration with LSBN, an academic institution, and a privately hired web designer. The principals of Louisiana State Board of Nursing approved the final product. The product meets and exceeds the expectations for mapping. Evaluation of use and usability will be done at the discretion of LSBN.

Implications for practice:
The outcome of this project will serve to heighten visibility of the distribution of APRNs in the state of Louisiana, enhancing opportunities for APRNs and for patients. Furthermore, those interested in leveraging the information in policy, education, or research initiatives will be served.
Opioid Misuse Among HIV-Positive Adults in Medical Care: Results From the Medical Monitoring Project, 2009–2014
Authors: Lemons Ansley , DeGroote Nicholas , Peréz Alejandro , Craw Jason , Nyaku Margaret , Broz Dita , Mattson Christine L. , Beer Linda 
Published: November 2018

Background:
People living with HIV are prescribed opioids more often and at higher doses than people who do not have HIV, and disproportionately experience risk factors for substance use disorder, which suggests they could be at increased risk of the misuse of opioids. Researchers also suggest that opioid misuse negatively affects various HIV clinical outcomes, increasing the risk of transmission to partners with an HIV-negative status.

Methods:
We calculated weighted percentages and 95% confidence intervals to estimate substance use characteristics among a probability sample of 28,162 HIV-positive adults receiving medical care in the United States who misused opioids (n = 975). Then, we used Rao-Scott χ2 tests to assess bivariate associations between opioid misuse and selected characteristics.

Results:
In all, 3.3% misused opioids. Misuse was more common among young adults, males, and non-Hispanic whites. Persons who misused opioids were less likely to: have been prescribed antiretroviral therapy (ART) (88.7%), report being adherent to ART medications in the past 3 days (78.1%), and have durable viral suppression (54.3%) than persons who did not misuse opioids (92.5%, 87.7%, and 64.7%, respectively). Persons who misused opioids were more likely to report condomless sex with partners of negative or unknown HIV status while not durably virally suppressed (11.7% vs 3.4%) than persons who did not misuse opioids.

Conclusions:
Opioid misuse among adults receiving HIV medical care is associated with inadequate ART adherence, insufficient durable viral suppression, and higher risk of HIV transmission to sexual partners.
Preputial Grafts
Authors: Ehrlichman Richard J. , Driscoll Daniel N. , Cornejo Kristine , Upton Joseph 
Published: November 2018

Background
The prepuce is an excellent donor site for skin grafts with minimal donor site morbidity. Full-thickness grafts are often required for correction of congenital syndactyly and in burn contractures.

Methods
Preputial skin was used for grafting in 18 children: 5 with burn contractures and 13 with congenital syndactyly.

Results
Excellent graft take was achieved with appropriate postoperative care. Postoperatively, there were occasional milia (42%) and hyperpigmentation. These grafts were noted to have superior mobility and elasticity. There was no donor site morbidity.

Conclusions
Preputial skin is accessible, easy to harvest, and hairless and has minimal donor site morbidity. It is especially well suited for the hands and fingers when elasticity of the graft is beneficial.
An Evidence-Based Approach to Management of Pectus Excavatum and Carinatum
Authors: Buziashvili David , Gopman Jared M. , Weissler Hope , Bodenstein Lawrence , Kaufman Andrew J. , Taub Peter J. 
Published: November 2018

Abstract
Pectus excavatum (PE) and pectus carinatum (PC) are the most common congenital chest wall anomalies. Current research suggests that PE and PC may result from overgrowth of the sternocostal cartilages. This can produce a deformation that displaces the sternum inward as in PE or outward as in PC. The etiology, clinical presentation, evaluation, and management of PE and PC are reviewed. Varied clinical presentations, cardiopulmonary effects, and psychosocial aspects are described.
Perceiving Hesitation requires both the Motor and Mentalizing systems
Authors: Thioux Marc , Suttrup Judith , Keysers Christian 
Published: November 2018

AbstractThe mentalizing network and the putative mirror neuron system (pMNS) are two important large scale brain networks for social cognition, with very little overlap between them. Evidence suggests however that the two networks can collaborate for understanding the state of mind of others on the basis of their body movements. Here using fMRI we find that when participants view hand actions to detect hesitations they activate both their mentalizing and pMNS networks and information is exchanged across these networks. In a follow-up experiment using repetitive TMS we find that disturbing activity in either network slows hesitation attribution. In contrast, watching the same actions to determine the size of the object being grasped only triggered activity in the pMNS network, and rTMS over the mentalizing network then no longer slowed reactions. When we see others’ actions, we recruit our own motor system. Our results suggest that for detecting a simple mental state like hesitation, this pre-processed motor information becomes a necessary input into a mentalizing network that is essential for associating deviations from a predicted motor program with a specific mental state.
Human bone marrow disorders recapitulated in vitro using organ chip technology
Authors: Chou David B. , Frismantas Viktoras , Milton Yuka , David Rhiannon , Pop-Damkov Petar , Ferguson Douglas , MacDonald Alexander , Bölükbaşı Özge Vargel , Joyce Cailin E. , Teixeira Liliana S. Moreira , Rech Arianna , Jiang Amanda , Calamari Elizabeth , Jalili-Firoozinezhad Sasan , Ng Carlos F. , Choe Youngjae , Clauson Susan , Myers Kasiani , Hasserjian Robert P. , Novak Richard , Levy Oren , Prantil-Baun Rachelle , Novina Carl D. , Shimamura Akiko , Ewart Lorna , Ingber Donald E. 
Published: November 2018

AbstractUnderstanding human bone marrow (BM) pathophysiology in the context of myelotoxic stress induced by drugs, radiation, or genetic mutations is of critical importance in clinical medicine. However, study of these dynamic cellular responses is hampered by the inaccessibility of living BMin vivo. Here, we describe a vascularized human Bone Marrow-on-a-Chip (BM Chip) microfluidic culture device for modeling bone marrow function and disease states. The BM Chip is comprised of a fluidic channel filled with a fibrin gel in which patient-derived CD34+ cells and bone marrow-derived stromal cells (BMSCs) are co-cultured, which is separated by a porous membrane from a parallel fluidic channel lined by human vascular endothelium. When perfused with culture medium through the vascular channel, the BM Chip maintains human CD34+ cells and supports differentiation and maturation of multiple blood cell lineages over 1 month in culture. Moreover, it recapitulates human myeloerythroid injury responses to drugs and gamma radiation exposure, as well as key hematopoietic abnormalities found in patients with the genetic disorder, Shwachman-Diamond Syndrome (SDS). These data establish the BM Chip as a new humanin vitromodel with broad potential utility for studies of BM dysfunction.
Wiring together large single-cell RNA-seq sample collections
Authors: Barkas Nikolas , Petukhov Viktor , Nikolaeva Daria , Lozinsky Yaroslav , Demharter Samuel , Khodosevich Konstantin , Kharchenko Peter V. 
Published: November 2018

AbstractSingle-cell RNA-seq methods are being increasingly applied in complex study designs, which involve measurements of many samples, commonly spanning multiple individuals, conditions, or tissue compartments. Joint analysis of such extensive, and often heterogeneous, sample collections requires a way of identifying and tracking recurrent cell subpopulations across the entire collection. Here we describe a flexible approach, called Conos (Clustering On Network Of Samples), that relies on multiple plausible inter-sample mappings to construct a global graph connecting all measured cells. The graph can then be used to propagate information between samples and to identify cell communities that show consistent grouping across broad subsets of the collected samples. Conos results enable investigators to balance between resolution and breadth of the detected subpopulations. In this way, it is possible to focus on the fine-grained clusters appearing within more similar subsets of samples, or analyze coarser clusters spanning broader sets of samples in the collection. Such multi-resolution joint clustering provides an important basis for downstream analysis and interpretation of sizeable multi-sample single-cell studies and atlas-scale collections.