bluuebunny/crossref_metadata_2025_split huggingface dataset:
U.S. High-Level Isolation Unit Clinical Laboratory Capabilities Update
Authors: Herstein Jocelyn J. , Iwen Peter C. , Jelden Katelyn C. , Biddinger Paul D. , Gibbs Shawn G. , Le Aurora B. , Hewlett Angela L. , Lowe John J. 
Published: November 2017

ABSTRACT
In late 2014, 56 hospitals in the United States were designated by state and federal public health authorities as specially designed high-level isolation units (HLIUs) equipped with advanced infrastructure, laboratory capabilities, and trained staff to care for patients with highly hazardous communicable diseases (HHCDs), such as Ebola virus disease. This survey describes the clinical laboratory support capabilities of U.S. HLIUs, including the specific test menus that HLIUs have identified to safely manage HHCD patients and the locations where such testing would be performed. In spring 2016, a survey was electronically distributed, as a fillable pdf file, to the 56 U.S. HLIUs. Site representatives completed the surveys, and data were coded and analyzed in an electronic spreadsheet, using descriptive statistics. Thirty-six HLIUs (64%) responded, and 33 completed the laboratory capabilities section. Thirty-one HLIUs (94%) had performed risk analyses for all laboratory procedures and equipment. Twenty-nine (88%) had decontamination procedures specified for all laboratory equipment used for patients with suspected or confirmed HHCDs. On-site laboratories in 27 HLIUs (81%) had the capacity to inventory and to securely store HHCD patient specimens. Ten HLIUs (31%) had at least one test they would conduct within the patient isolation room. The high-risk nature of HHCDs and the occupational exposures that may occur in clinical laboratories demand advanced preparation and risk assessment of work practices, laboratory equipment, and instrumentation by HLIU laboratories. Although risk analyses of clinical laboratory testing and equipment that HLIUs have conducted have likely focused on those for Ebola virus, HLIUs must be prepared to revise their current procedures for other HHCDs.
Human Adenovirus Core Protein V Is Targeted by the Host SUMOylation Machinery To Limit Essential Viral Functions
Authors: Freudenberger Nora , Meyer Tina , Groitl Peter , Dobner Thomas , Schreiner Sabrina 
Published: November 2017

ABSTRACT
Human adenoviruses (HAdV) are nonenveloped viruses containing a linear, double-stranded DNA genome surrounded by an icosahedral capsid. To allow proper viral replication, the genome is imported through the nuclear pore complex associated with viral core proteins. Until now, the role of these incoming virion proteins during the early phase of infection was poorly understood. The core protein V is speculated to bridge the core and the surrounding capsid. It binds the genome in a sequence-independent manner and localizes in the nucleus of infected cells, accumulating at nucleoli. Here, we show that protein V contains conserved SUMO conjugation motifs (SCMs). Mutation of these consensus motifs resulted in reduced SUMOylation of the protein; thus, protein V represents a novel target of the host SUMOylation machinery. To understand the role of protein V SUMO posttranslational modification during productive HAdV infection, we generated a replication-competent HAdV with SCM mutations within the protein V coding sequence. Phenotypic analyses revealed that these SCM mutations are beneficial for adenoviral replication. Blocking protein V SUMOylation at specific sites shifts the onset of viral DNA replication to earlier time points during infection and promotes viral gene expression. Simultaneously, the altered kinetics within the viral life cycle are accompanied by more efficient proteasomal degradation of host determinants and increased virus progeny production than that observed during wild-type infection. Taken together, our studies show that protein V SUMOylation reduces virus growth; hence, protein V SUMOylation represents an important novel aspect of the host antiviral strategy to limit virus replication and thereby points to potential intervention strategies.

IMPORTANCE
Many decades of research have revealed that HAdV structural proteins promote viral entry and mainly physical stability of the viral genome in the capsid. Our work over the last years showed that this concept needs expansion as the functions are more diverse. We showed that capsid protein VI regulates the antiviral response by modulation of the transcription factor Daxx during infection. Moreover, core protein VII interacts with SPOC1 restriction factor, which is beneficial for efficient viral gene expression. Here, we were able to show that core protein V also represents a novel substrate of the host SUMOylation machinery and contains several conserved SCMs; mutation of these consensus motifs reduced SUMOylation of the protein. Unexpectedly, we observed that introducing these mutations into HAdV promotes adenoviral replication. In conclusion, we offer novel insights into adenovirus core proteins and provide evidence that SUMOylation of HAdV factors regulates replication efficiency.
Vaccine Effects on Heterogeneity in Susceptibility and Implications for Population Health Management
Authors: Langwig Kate E. , Wargo Andrew R. , Jones Darbi R. , Viss Jessie R. , Rutan Barbara J. , Egan Nicholas A. , Sá-Guimarães Pedro , Kim Min Sun , Kurath Gael , Gomes M. Gabriela M. , Lipsitch Marc 
Published: November 2017

ABSTRACTHeterogeneity in host susceptibility is a key determinant of infectious disease dynamics but is rarely accounted for in assessment of disease control measures. Understanding how susceptibility is distributed in populations, and how control measures change this distribution, is integral to predicting the course of epidemics with and without interventions. Using multiple experimental and modeling approaches, we show that rainbow trout have relatively homogeneous susceptibility to infection with infectious hematopoietic necrosis virus and that vaccination increases heterogeneity in susceptibility in a nearly all-or-nothing fashion. In a simple transmission model with anR0of 2, the highly heterogeneous vaccine protection would cause a 35 percentage-point reduction in outbreak size over an intervention inducing homogenous protection at the same mean level. More broadly, these findings provide validation of methodology that can help to reduce biases in predictions of vaccine impact in natural settings and provide insight into how vaccination shapes population susceptibility.IMPORTANCEDifferences among individuals influence transmission and spread of infectious diseases as well as the effectiveness of control measures. Control measures, such as vaccines, may provide leaky protection, protecting all hosts to an identical degree, or all-or-nothing protection, protecting some hosts completely while leaving others completely unprotected. This distinction can have a dramatic influence on disease dynamics, yet this distribution of protection is frequently unaccounted for in epidemiological models and estimates of vaccine efficacy. Here, we apply new methodology to experimentally examine host heterogeneity in susceptibility and mode of vaccine action as distinct components influencing disease outcome. Through multiple experiments and new modeling approaches, we show that the distribution of vaccine effects can be robustly estimated. These results offer new experimental and inferential methodology that can improve predictions of vaccine effectiveness and have broad applicability to human, wildlife, and ecosystem health.
Capsular Polysaccharide Interferes with Biofilm Formation byPasteurella multocidaSerogroup A
Authors: Petruzzi Briana , Briggs Robert E. , Swords W. Edward , De Castro Cristina , Molinaro Antonio , Inzana Thomas J. 
Published: November 2017

ABSTRACTPasteurella multocidais an important multihost animal and zoonotic pathogen that is capable of causing respiratory and multisystemic diseases, bacteremia, and bite wound infections. The glycosaminoglycan capsule ofP. multocidais an essential virulence factor that protects the bacterium from host defenses. However, chronic infections (such as swine atrophic rhinitis and the carrier state in birds and other animals) may be associated with biofilm formation, which has not been characterized inP. multocida. Biofilm formation by clinical isolates was inversely related to capsule production and was confirmed with capsule-deficient mutants of highly encapsulated strains. Capsule-deficient mutants formed biofilms with a larger biomass that was thicker and smoother than the biofilm of encapsulated strains. Passage of a highly encapsulated, poor-biofilm-forming strain under conditions that favored biofilm formation resulted in the production of less capsular polysaccharide and a more robust biofilm, as did addition of hyaluronidase to the growth medium of all of the strains tested. The matrix material of the biofilm was composed predominately of a glycogen exopolysaccharide (EPS), as determined by gas chromatography-mass spectrometry, nuclear magnetic resonance, and enzymatic digestion. However, a putative glycogen synthesis locus was not differentially regulated when the bacteria were grown as a biofilm or planktonically, as determined by quantitative reverse transcriptase PCR. Therefore, the negatively charged capsule may interfere with biofilm formation by blocking adherence to a surface or by preventing the EPS matrix from encasing large numbers of bacterial cells. This is the first detailed description of biofilm formation and a glycogen EPS byP. multocida.IMPORTANCEPasteurella multocidais an important pathogen responsible for severe infections in food animals, domestic and wild birds, pet animals, and humans.P. multocidawas first isolated by Louis Pasteur in 1880 and has been studied for over 130 years. However, aspects of its lifecycle have remained unknown. Although formation of a biofilm byP. multocidahas been proposed, this report is the first to characterize biofilm formation byP. multocida. Of particular interest is that the biofilm matrix material contained a newly reported amylose-like glycogen as the exopolysaccharide component and that production of capsular polysaccharide (CPS) was inversely related to biofilm formation. However, even highly mucoid, poor-biofilm-forming strains could form abundant biofilms by loss of CPS or followingin vitropassage under biofilm growth conditions. Therefore, the carrier state or subclinical chronic infections withP. multocidamay result from CPS downregulation with concomitant enhanced biofilm formation.
First-principles calculations of electronic, magnetic and optical properties of HoN doped with TM (Ti, V, Cr, Mn, Co and Ni)
Authors: Rouchdi M. , Salmani E. , Dehmani M. , Ez-Zahraouy H. , Hassanain N. , Benyoussef A. , Mzerd A. 
Published: November 2017

Using the first-principles calculations within the Korringa–Kohn–Rostoker (KKR) method combined with the coherent potential approximation (CPA), the structural, optical and magnetic properties of rare-earth nitride Ho[Formula: see text]TM[Formula: see text]N doped with transition metal (TM) atoms (Ti, V, Cr, Mn, Co and Ni) are investigated as a function the generalized gradient approximation and self-interaction correction (GGA–SIC) approximation. The optical properties are studied in detail by using ab-initio calculations. Using GGA–SIC we have showed that the bandgap value is in good agreement with the experimental value. Using GGA–SIC approximation for HoN, we have obtained a bandgap of 0.9 eV. Some of the dilute magnetic semiconductors (DMS) like Ho[Formula: see text]TM[Formula: see text]N under study exhibit a half-metallic behavior, which makes them suitable for spintronic applications. Moreover, the optical absorption spectra confirm the ferromagnetic stability based on the charge state of magnetic impurities.
Near-eye light field holographic rendering with spherical waves for wide field of view interactive 3D computer graphics
Authors: Shi Liang , Huang Fu-Chung , Lopes Ward , Matusik Wojciech , Luebke David 
Published: November 2017

Holograms display a 3D image in high resolution and allow viewers to focus freely as if looking through a virtual window, yet computer generated holography (CGH) hasn't delivered the same visual quality under plane wave illumination and due to heavy computational cost. Light field displays have been popular due to their capability to provide continuous focus cues. However, light field displays must trade off between spatial and angular resolution, and do not model diffraction.
We present a light field-based CGH rendering pipeline allowing for reproduction of high-definition 3D scenes with continuous depth and support of intra-pupil view-dependent occlusion. Our rendering accurately accounts for diffraction and supports various types of reference illuminations for hologram. We avoid under- and over-sampling and geometric clipping effects seen in previous work. We also demonstrate an implementation of light field rendering plus the Fresnel diffraction integral based CGH calculation which is orders of magnitude faster than the state of the art [Zhang et al. 2015], achieving interactive volumetric 3D graphics.
To verify our computational results, we build a see-through, near-eye, color CGH display prototype which enables co-modulation of both amplitude and phase. We show that our rendering accurately models the spherical illumination introduced by the eye piece and produces the desired 3D imagery at the designated depth. We also analyze aliasing, theoretical resolution limits, depth of field, and other design trade-offs for near-eye CGH.
Mix-and-match holography
Authors: Peng Yifan , Dun Xiong , Sun Qilin , Heidrich Wolfgang 
Published: November 2017

Computational caustics and light steering displays offer a wide range of interesting applications, ranging from art works and architectural installations to energy efficient HDR projection. In this work we expand on this concept by encoding several target images into pairs of front and rear phase-distorting surfaces. Different target holograms can be decoded by mixing and matching different front and rear surfaces under specific geometric alignments. Our approach, which we call mix-and-match holography, is made possible by moving from a refractive caustic image formation process to a diffractive, holographic one. This provides the extra bandwidth that is required to multiplex several images into pairing surfaces.
We derive a detailed image formation model for the setting of holographic projection displays, as well as a multiplexing method based on a combination of phase retrieval methods and complex matrix factorization. We demonstrate several application scenarios in both simulation and physical prototypes.
Residual Convolutional Neural Network for the Determination of IDH Status in Low- and High-Grade Gliomas from MR Imaging
Authors: Chang Ken , Bai Harrison X. , Zhou Hao , Su Chang , Bi Wenya Linda , Agbodza Ena , Kavouridis Vasileios K. , Senders Joeky T. , Boaro Alessandro , Beers Andrew , Zhang Biqi , Capellini Alexandra , Liao Weihua , Shen Qin , Li Xuejun , Xiao Bo , Cryan Jane , Ramkissoon Shakti , Ramkissoon Lori , Ligon Keith , Wen Patrick Y. , Bindra Ranjit S. , Woo John , Arnaout Omar , Gerstner Elizabeth R. , Zhang Paul J. , Rosen Bruce R. , Yang Li , Huang Raymond Y. , Kalpathy-Cramer Jayashree 
Published: November 2017

Abstract
Purpose: Isocitrate dehydrogenase (IDH) mutations in glioma patients confer longer survival and may guide treatment decision making. We aimed to predict the IDH status of gliomas from MR imaging by applying a residual convolutional neural network to preoperative radiographic data.
Experimental Design: Preoperative imaging was acquired for 201 patients from the Hospital of University of Pennsylvania (HUP), 157 patients from Brigham and Women's Hospital (BWH), and 138 patients from The Cancer Imaging Archive (TCIA) and divided into training, validation, and testing sets. We trained a residual convolutional neural network for each MR sequence (FLAIR, T2, T1 precontrast, and T1 postcontrast) and built a predictive model from the outputs. To increase the size of the training set and prevent overfitting, we augmented the training set images by introducing random rotations, translations, flips, shearing, and zooming.
Results: With our neural network model, we achieved IDH prediction accuracies of 82.8% (AUC = 0.90), 83.0% (AUC = 0.93), and 85.7% (AUC = 0.94) within training, validation, and testing sets, respectively. When age at diagnosis was incorporated into the model, the training, validation, and testing accuracies increased to 87.3% (AUC = 0.93), 87.6% (AUC = 0.95), and 89.1% (AUC = 0.95), respectively.
Conclusions: We developed a deep learning technique to noninvasively predict IDH genotype in grade II–IV glioma using conventional MR imaging using a multi-institutional data set. Clin Cancer Res; 24(5); 1073–81. ©2017 AACR.
Import Dependence and Food and Nutrition Security Implications
Authors: Bhattacharjya Souvik , Chaudhury Saswata , Nanda Nitya 
Published: November 2017

Pulses are the staple sources of protein for Indians and contribute significantly to their nutritional security. However, limited growth in domestic production, has led to India’s increased import dependence. India’s import of pulses almost doubled in the last ten years and is currently estimated to be more than 3 million tonnes. Imports account for 15–20 per cent of total domestic production. The article presents the factors behind stagnating pulses production, India’s vulnerability to pulses import shortage and thereby food security implications. It also suggests strategies to promote sustainable supply of pulses to ensure food security. JEL: Q130, Q180, Q170, Q020, F680
The Role of Focal Laser in the Anti–Vascular Endothelial Growth Factor Era
Authors: Crosson Jason N , Mason Lauren , Mason John O 
Published: November 2017

Introduction: To review important studies examining focal laser for diabetic macular edema (DME), to examine real-world data regarding actual treatments patients are receiving, to present long-term visual outcomes in real-world practice, and to suggest an evidence-based approach for the use of focal laser. Methods: This study is a review of landmark studies evaluating focal laser and pharmacologic therapy for DME. In addition, the authors include a retrospective review of 102 consecutive eyes of 53 patients in our practice setting in rural Alabama. A chart review was performed, and patients were included if they were diagnosed with DME and were treated with both focal laser and bevacizumab. Bevacizumab and focal laser were given on a “as needed basis” at the discretion of one treating physician (J.O.M.). Worse visual acuity or worsening macular edema were indications for additional treatment. Statistical analysis was performed using frequencies and percentages. Best-corrected visual acuity (BCVA) was recorded at baseline and at the end of treatment (mean of 5 years) in the medical record. Primary outcome measures were BCVA, patients with better than 20/40 BCVA, patients with worse than 20/200 BCVA, and patients with stable BCVA. Results: Anti–vascular endothelial growth factor (VEGF) therapies are the first-line treatment for DME, but real-world claims data suggest that diabetic patients cannot come in for monthly injections as in large clinical trials. In our series, after a mean of 5 lasers and 5.5 injections, 90% of eyes had stable or better BCVA, 65% were ≥20/40, and only 13% were ≤20/200. Conclusions: Laser treatment for DME remains an important adjunctive therapy
Study on Defense Mechanisms to Cope With Stress Due to Stigma Among People Living With HIV/AIDS Reported in Eastern India: A Single Center Experience
Authors: Mukherjee Ayan , Lahiry Sandeep , Mukherjee Anindya , Choudhury Shouvik , Sinha Rajasree 
Published: November 2017

Aim: To explore the stigmatizing pattern in people living with HIV/AIDS (PLWHA) and assess coping strategies adopted for quality of life (QOL) appraisal. Methods: In the background of a descriptive, cross-sectional research design, PLWHA attending HIV (human immunodeficiency virus) outpatient clinic at Medical College, Kolkata (n = 120) were enrolled through “snowball sampling.” A brief semistructured interview schedule was used to elicit data on socio-demographics. Stigma was assessed using a 4-point scale (40-item). Quality of life was assessed using WHOQOL-BREF (World Health Organization Quality-of-Life) scale (26-item). Results: About 96.7% reported being stressed. Stigma was mostly confronted in socio-familial context. Fear of being stigmatized was much higher compared with those who actually faced stigma (69.2% vs 27.5%; P < .01). Quality of life negatively correlated with internalizing of stigma in the psychological domain ( P < .01). Proportion experiencing actual stigma (women vs men: 79% vs 74%) experienced an above moderate QOL. Multiple defense mechanisms were identified. “Altruism,” “Anticipation,” and “Humor” were the most preferred defense strategies. However, such coping strategies appeared to be self-taught and only modestly helpful in managing perceived stigma. Conclusions: People living with HIV/AIDS should avoid internalizing stigmatized feeling and engage in social activities to work toward a better QOL.
Nonenhanced MRI Planning for Endovascular Repair of Abdominal Aortic Aneurysms: Comparison With Contrast-Enhanced CT Angiography
Authors: Piacentino Filippo , Fontana Federico , Micieli Camilla , Angeretti Maria G. , Cardim Larissa Nocchi , Coppola Andrea , Molinelli Valeria , Piffaretti Gabriele , Novario Raffaele , Fugazzola Carlo 
Published: November 2017

Background: To assess whether noncontrast-enhanced magnetic resonance imaging (NC-MRI) is an alternative to contrast-enhanced computed tomography angiography (CTA) for aortoiliac measurements before endovascular abdominal aortic aneurysm repair (EVAR). Methods: This study encompasses 30 patients admitted for elective EVAR (27 men and 3 women). Two expert readers (vascular radiologist and vascular surgeon) reviewed CTA images in consensus and chose the proper endograft for each patient. Subsequently, a vascular radiologist and a resident radiologist (observer 1 and 2) reviewed CTA and NC-MRI examinations in a double-blind way and completed standard measurements. The interobserver and intermodality agreement was calculated by intraclass correlation coefficients (ICCs). Furthermore, the correlation between the endograft size chosen by the first pair and the second pair of observers was evaluated. Results: Concerning all measurements, no significant difference was found. Both CTA and NC-MRI angiographic measurements showed strong correlation. Interobserver ICCs for CTA and NC-MRI showed ranges of 0.62 to 0.99 (mean: 0.92) and 0.56 to 0.99 (mean: 0.91); intermodality ICCs for observer 1 and 2 showed ranges of 0.64 to 0.99 (mean: 0.92) and 0.56 to 0.99 (mean: 0.92). The CTA and NC-MRI vascular measurements correlated strongly, except for both external iliac artery diameters. The choice of stent size was always the same between the 2 observers; furthermore, graft size was always in agreement with that selected prospectively. Conclusion: Computed tomography angiography remains the standard of reference for EVAR planning; NC-MRI can be an option for patients with contraindications for CTA, in particular those with renal impairment.