bluuebunny/crossref_metadata_2025_split huggingface dataset:
A virtual simulator designed for collision prevention in proton therapy
Authors: Jung Hyunuk , Kum Oyeon , Han Youngyih , Park Hee Chul , Kim Jin Sung , Choi Doo Ho 
Published: September 2015

Purpose:In proton therapy, collisions between the patient and nozzle potentially occur because of the large nozzle structure and efforts to minimize the air gap. Thus, software was developed to predict such collisions between the nozzle and patient using treatment virtual simulation.Methods:Three‐dimensional (3D) modeling of a gantry inner‐floor, nozzle, and robotic‐couch was performed using SolidWorks based on the manufacturer's machine data. To obtain patient body information, a 3D‐scanner was utilized right before CT scanning. Using the acquired images, a 3D‐image of the patient's body contour was reconstructed. The accuracy of the image was confirmed against the CT image of a humanoid phantom. The machine components and the virtual patient were combined on the treatment‐room coordinate system, resulting in a virtual simulator. The simulator simulated the motion of its components such as rotation and translation of the gantry, nozzle, and couch in real scale. A collision, if any, was examined both in static and dynamic modes. The static mode assessed collisions only at fixed positions of the machine's components, while the dynamic mode operated any time a component was in motion. A collision was identified if any voxels of two components, e.g., the nozzle and the patient or couch, overlapped when calculating volume locations. The event and collision point were visualized, and collision volumes were reported.Results:All components were successfully assembled, and the motions were accurately controlled. The 3D‐shape of the phantom agreed with CT images within a deviation of 2 mm. Collision situations were simulated within minutes, and the results were displayed and reported.Conclusions:The developed software will be useful in improving patient safety and clinical efficiency of proton therapy.
Virome Analysis of Transfusion Recipients Reveals a Novel Human Virus That Shares Genomic Features with Hepaciviruses and Pegiviruses
Authors: Kapoor Amit , Kumar Arvind , Simmonds Peter , Bhuva Nishit , Singh Chauhan Lokendra , Lee Bohyun , Sall Amadou Alpha , Jin Zhezhen , Morse Stephen S. , Shaz Beth , Burbelo Peter D. , Lipkin W. Ian 
Published: September 2015

ABSTRACT

To investigate the transmission of novel infectious agents by blood transfusion, we studied changes in the virome composition of blood transfusion recipients pre- and posttransfusion. Using this approach, we detected and genetically characterized a novel human virus, human hepegivirus 1 (HHpgV-1), that shares features with hepatitis C virus (HCV) and human pegivirus (HPgV; formerly called GB virus C or hepatitis G virus). HCV and HPgV belong to the genera
Hepacivirus
and
Pegivirus
of the family
Flaviviridae
. HHpgV-1 was found in serum samples from two blood transfusion recipients and two hemophilia patients who had received plasma-derived clotting factor concentrates. In the former, the virus was detected only in the posttransfusion samples, indicating blood-borne transmission. Both hemophiliacs were persistently viremic over periods of at least 201 and 1,981 days. The 5′ untranslated region (UTR) of HHpgV-1 contained a type IV internal ribosome entry site (IRES), structurally similar to although highly divergent in sequence from that of HCV and other hepaciviruses. However, phylogenetic analysis of nonstructural genes (NS3 and NS5B) showed that HHpgV-1 forms a branch within the pegivirus clade distinct from HPgV and homologs infecting other mammalian species. In common with some pegivirus variants infecting rodents and bats, the HHpgV-1 genome encodes a short, highly basic protein upstream of E1, potentially possessing a core-like function in packaging RNA during assembly. Identification of this new human virus, HHpgV-1, expands our knowledge of the range of genome configurations of these viruses and may lead to a reevaluation of the original criteria by which the genera
Hepacivirus
and
Pegivirus
are defined.

IMPORTANCE
More than 30 million blood components are transfused annually in the United States alone. Surveillance for infectious agents in the blood supply is key to ensuring the safety of this critical resource for medicine and public health. Here, we report the identification of a new and highly diverse HCV/GB virus (GBV)-like virus from human serum samples. This new virus, human hepegivirus 1 (HHpgV-1), was found in serum samples from blood transfusion recipients, indicating its potential for transmission via transfusion products. We also found persistent long-term HHpgV-1 viremia in two hemophilia patients. HHpgV-1 is unique because it shares genetic similarity with both highly pathogenic HCV and the apparently nonpathogenic HPgV (GBV-C). Our results add to the list of human viruses and provide data to develop reagents to study virus transmission and disease association and for interrupting virus transmission and new human infections.
Dynamics of Wave Setup over a Steeply Sloping Fringing Reef
Authors: Buckley Mark L. , Lowe Ryan J. , Hansen Jeff E. , Van Dongeren Ap R. 
Published: September 2015

AbstractHigh-resolution observations from a 55-m-long wave flume were used to investigate the dynamics of wave setup over a steeply sloping reef profile with a bathymetry representative of many fringing coral reefs. The 16 runs incorporating a wide range of offshore wave conditions and still water levels were conducted using a 1:36 scaled fringing reef, with a 1:5 slope reef leading to a wide and shallow reef flat. Wave setdown and setup observations measured at 17 locations across the fringing reef were compared with a theoretical balance between the local cross-shore pressure and wave radiation stress gradients. This study found that when radiation stress gradients were calculated from observations of the radiation stress derived from linear wave theory, both wave setdown and setup were underpredicted for the majority of wave and water level conditions tested. These underpredictions were most pronounced for cases with larger wave heights and lower still water levels (i.e., cases with the greatest setdown and setup). Inaccuracies in the predicted setdown and setup were improved by including a wave-roller model, which provides a correction to the kinetic energy predicted by linear wave theory for breaking waves and produces a spatial delay in the wave forcing that was consistent with the observations.
Spontaneous pneumomediastinum: Experience in 13 adult patients
Authors: Panigrahi Manoj K , Suresh Kumar Cherlopalli , Jaganathan Venugopal , Vinod Kumar Saka 
Published: September 2015

Background Spontaneous pneumomediastinum is an uncommon disorder. There is a lack of information on spontaneous pneumomediastinum in India. We aimed to understand the clinical profile, hospital course, and long-term outcome of such patients. Methods We retrospectively reviewed all patients (aged ≥15 years) diagnosed with spontaneous pneumomediastinum in the respiratory ward of a tertiary care hospital over a 7-year period from 2005. Results Of the 3326 patients hospitalized during the study period, 13 (10 male) were diagnosed with spontaneous pneumomediastinum, constituting 0.39% of all hospitalizations. The median age was 37 years (interquartile range 20–55 years). The most common presenting symptom was dyspnea in 85% followed by neck swelling (69%), chest pain (69%) and cough (54%). Subcutaneous emphysema and preexisting lung diseases were identified in 11 (85%) patients each. Post-tubercular pulmonary sequelae (5 patients) and asthma (4 patients) were the most common underlying lung diseases. Pneumothorax was identified in 6 (46%) patients; 4 required tube thoracostomy. Chest radiography was diagnostic in 92% of patients. The median length of hospital stay was 9 days (interquartile range 6–12 days). No recurrence was reported in 11 patients followed up for a median of 1550 days (interquartile range 691–1909 days). Conclusions Spontaneous pneumomediastinum is a benign disorder, but underlying lung diseases and concomitant pneumothorax are likely to complicate the disease course. Exacerbation of post-tubercular obstructive airway disease is a common risk factor for spontaneous pneumomediastinum in a tuberculosis endemic country.
Tai Chi for improving cardiopulmonary function and quality of life in patients with chronic obstructive pulmonary disease: a systematic review and meta-analysis
Authors: Guo Jia-Bao , Chen Bing-Lin , Lu Yue-Mei , Zhang Wen-Yi , Zhu Zhao-Jin , Yang Yu-Jie , Zhu Yi 
Published: September 2015

Objective: To examine the effect of Tai Chi on cardiopulmonary function and quality of life in chronic obstructive pulmonary disease. Data sources: Cochrane Library, PUBMED, EMBASE, China Biology Medicine disc, China National Knowledge Infrastructure, and Wanfang database. Methods: Articles on randomized controlled trials comparing Tai Chi with other treatments or no treatment were identified. A random-effects model was used to calculate the pooled mean difference (MD) with 95% confidence interval (CI). Results: Fifteen articles involving 1354 participants were included. Compared with the control group, Tai Chi was more effective in improving exercise capacity on 6-minute walking distance (short term: MD = 16.02, 95% CI 2.86 to 29.17; mid term: MD = 30.90, 95% CI 6.88 to 54.93; long term: MD = 24.63, 95% CI 2.30 to 46.95), as well as pulmonary functions on forced expiratory volume in the first second (mid term: MD = 0.10; 95% CI 0.01 to 0.19), and forced vital capacity (mid term: MD = 0.20; 95% CI 0.04 to 0.36). Concerning quality of life, we found Tai Chi was better than the control group for the Chronic Respiratory Disease Questionnaire dyspnoea score (short term: MD = 0.90; 95% CI 0.51 to 1.29), fatigue score (short term: MD = 0.75; 95% CI 0.42 to 1.09), and total score (short term: MD = 1.92; 95% CI 0.54 to 3.31). Conclusions: Tai Chi may improve exercise capacity in the short, mid, and long terms. However, no significant long term differences in pulmonary function and quality of life were observed for patients with chronic obstructive pulmonary disease.
Alterations of the Deltoid Muscle After Open Versus Arthroscopic Rotator Cuff Repair
Authors: Cho Nam Su , Cha Sang Won , Rhee Yong Girl 
Published: September 2015

Background: Open repair can be more useful than arthroscopic repair for immobile and severely retracted, large to massive rotator cuff tears. However, it is not known whether the deltoid muscle is altered after open repair or to what extent the deltoid origin remains detached after surgery. Purpose: To compare postoperative alterations of the deltoid muscle in open versus arthroscopic repair for severely retracted, large to massive rotator cuff tears. Study Design: Case-control study; Level of evidence, 3. Methods: Enrolled in this study were 135 patients who underwent surgical repair for severely retracted, large to massive rotator cuff tears and who had routine follow-up MRIs at least 6 months after surgery. Open repairs were performed in 56 cases and arthroscopic repairs in 79 cases. The detachment and thickness of the deltoid muscle at its proximal origin were recorded in 5 zones on MRI. The alterations of the deltoid muscle and postoperative integrity of the repaired rotator cuff were evaluated. Results: Partial detachment of the deltoid occurred in 1 patient (1.8%) in the open group and in 2 patients (2.5%) in the arthroscopic group ( P = .80). All the partial detachments occurred in zones 2 and 3. Attenuation of the proximal origin of the deltoid was found in 3 patients (5.4%) in the open group and in 4 patients (5.1%) in the arthroscopic group ( P = .87). Atrophy of the deltoid muscle was shown in 3 patients (5.4%) in the open group and 4 patients (5.1%) in the arthroscopic group ( P = .61). The retear rate of the repaired cuff was 30.4% (17/56) in the open group and 38.0% (30/79) in the arthroscopic group ( P = .74). Conclusion: Between open and arthroscopic repair for severely retracted, large to massive rotator cuff tears, there was no significant difference in detachment of the deltoid origin and alterations of the deltoid muscle after repair. Postoperative alterations of the deltoid occurred in arthroscopic surgery as well as in open surgery. For immobile massive rotator cuff tear, open repair is an acceptable technique as long as the deltoid muscle is meticulously reattached after surgery.
Detection of gamma hydroxybutyrate in emergency department
Authors: Drogies T , Willenberg A , Ramshorn-Zimmer A , Weidhase L , Petros S , Hädrich C , Thiery J , Gries A , Bernhard M 
Published: September 2015

Background: Many patients present to emergency departments (EDs) with an altered state of consciousness. Fast exclusion of gamma hydroxybutyrate (GHB)-associated intoxication in these patients may optimize diagnostic and therapeutic algorithms and decisions in the ED. Methods: Between January and March 2014, a novel enzymatic test system was used to quantify GHB in blood and urine samples of suspected intoxicated patients in the ED of the University Hospital. The underlying causes for suspected intoxication and the diagnostic and therapeutic measures were documented and analysed retrospectively. Results: GHB measurements were performed in 13 patients with suspected ingestion during a 3-month study period. GHB was positive in six patients showing serum levels between 61.8 mg/l and 254.8 mg/l, and GHB was tested negative in seven patients with a range of 0.3–6.2 mg/l (upper reference limit 6.1 mg/l). Additional intoxication was found in five of six GHB positive (83%, alcohol n = 2 and other drugs n = 5) and in six of seven negative-tested patients (86%, alcohol n = 5 and other drugs n = 1). Conclusion: GHB quantification in the ED provides specific additional information for intoxication, which can lead to more precise diagnostic and therapeutic decisions and may also be important for legal aspects. We believe that GHB analysis in unconscious patients with suspected intoxication may improve the efficient treatment of intoxicated patients.
Study designs for determining and comparing sensitivities of disease screening tests
Authors: Prorok Philip C. , Kramer Barnett S. , Miller Anthony B. 
Published: September 2015

Objective To investigate the capability of various study designs to determine the sensitivity of a disease screening test. Methods Quantities that can be calculated from these designs were derived and examined for their relationship to true sensitivity (the ability to detect unrecognized disease that would surface clinically in the absence of screening) and overdiagnosis. Results To examine the sensitivity of one test, the single cohort design, in which all participants receive the test, is particularly weak, providing only an upper bound on the true sensitivity, and yields no information about overdiagnosis. A randomized design, with one control arm and participants tested in the other, that includes sufficient post-screening follow-up, allows calculation of bounds on, and an approximation to, true sensitivity and also determination of overdiagnosis. Without follow-up, bounds on the true sensitivity can be calculated. To compare two tests, the single cohort paired design in which all participants receive both tests is precarious. The three arm randomized design with post screening follow-up is preferred, yielding an approximation to the true sensitivity, bounds on the true sensitivity, and the extent of overdiagnosis of each test. Without post screening follow-up, bounds on the true sensitivities can be calculated. When an unscreened control arm is not possible, the two-arm randomized design is recommended. Individual test sensitivities cannot be determined, but with sufficient post-screening follow-up, an order relationship can be established, as can the difference in overdiagnosis between the two tests.
Overcoming the Challenges Inherent in Conducting Design Research in Mental Health Settings
Authors: Ahern Catherine , McKinnon Margaret C. , Bieling Peter J. , McNeely Heather , Langstaff Karen 
Published: September 2015

Objective: Conducting high-quality design research in a mental health setting presents significant challenges, limiting the availability of high-quality evidence to support design decisions for built environments. Here, we outline key approaches to overcoming these challenges. Background: In conducting a rigorous post-occupancy evaluation of a newly built mental health and addictions facility, St. Joseph’s Healthcare, Hamilton, we identified a number of systematic barriers associated with conducting design research in mental health settings. Methods: Our approach to overcoming these barriers relied heavily upon (i) selecting established measures and methods with demonstrated efficacy in a mental health context, (ii) navigating institutional protocols designed to protect vulnerable members of this population, and (iii) designing innovative data collection strategies to increase participation in research by individuals with mental illness. Each of these approaches drew heavily on the expert knowledge of mental health settings and the experiences with mental health, facilities management, and research of a research team that was well integrated within the parent institution. Conclusions: Engaging multiple stakeholders (e.g., care providers, patients, ethics board, and hospital administrators) contributed their trust and support of the research. Traditionally, post-occupancy evaluation researchers are independent of the facilities they research, yet this is not an effective approach in mental health settings. We found that, in working toward solutions to the three obstacles we described, having team members who were well “networked” within the parent institution was necessary. This approach can turn “gatekeepers” into champions for patients’ engagement in the research, which is essential in generating high-quality evidence.
Translational Research in Kidney Transplantation and the Role of Patient Engagement
Authors: Farragher Janine F. , Elliott Meghan J. , Silver Samuel A. , Lichner Zsuzsanna , Tsampalieros Anne 
Published: September 2015

Background: Translational research is an evolving discipline that is intended to bridge the gaps between basic science research, clinical research, and implementation in clinical practice. It is a fluid, multidirectional process that requires strong interdisciplinary collaboration to produce research that is relevant to end-users. Purpose of this review: This review summarizes current perspectives on translational research and outlines its relevance and importance to kidney transplantation research. Sources of information: Sources of information used for this review include published reports, articles, and research funding websites. Findings: Tissue typing is used as an in-depth example of how translational research has been applied in the field of kidney transplant medicine, and how it has resulted in successful implementation of diagnostic and management options for sensitized individuals undergoing kidney transplantation. The value of actively involving kidney transplant stakeholders (patients, caregivers, and clinicians) in setting research priorities and determining relevant outcomes for future investigation is also discussed. Limitations: This is a narrative review of the literature which has been partly influenced by the perspectives and experiences of its authors. Implications: Translational and patient-oriented research practices should be incorporated into future research endeavours in the field of kidney transplantation in order to create beneficial change in clinical practice and improve patient outcomes. What was known before: Translational research which engages patients in the investigative process can enhance the likelihood that medical discoveries will have a meaningful impact at the bedside. What this adds: This article applies current perspectives on translational research and patient engagement to the field of kidney transplantation, illustrating how these approaches have led to significant advancements in the field. It provides further justification for deliberate, targeted efforts to cross-collaborate and incorporate the patient voice into kidney transplant research.
TCRβ repertoire of CD4+ and CD8+ T cells is distinct in richness, distribution, and CDR3 amino acid composition
Authors: Li Hoi Ming , Hiroi Toyoko , Zhang Yongqing , Shi Alvin , Chen Guobing , De Supriyo , Metter E Jeffrey , Wood William H , Sharov Alexei , Milner Joshua D , Becker Kevin G , Zhan Ming , Weng Nan-ping 
Published: September 2015

Abstract
The TCR repertoire serves as a reservoir of TCRs for recognizing all potential pathogens. Two major types of T cells, CD4+ and CD8+, that use the same genetic elements and process to generate a functional TCR differ in their recognition of peptide bound to MHC class II and I, respectively. However, it is currently unclear to what extent the TCR repertoire of CD4+ and CD8+ T cells is different. Here, we report a comparative analysis of the TCRβ repertoires of CD4+ and CD8+ T cells by use of a 5′ rapid amplification of cDNA ends–PCR–sequencing method. We found that TCRβ richness of CD4+ T cells ranges from 1.2 to 9.8 × 104 and is approximately 5 times greater, on average, than that of CD8+ T cells in each study subject. Furthermore, there was little overlap in TCRβ sequences between CD4+ (0.3%) and CD8+ (1.3%) T cells. Further analysis showed that CD4+ and CD8+ T cells exhibited distinct preferences for certain amino acids in the CDR3, and this was confirmed further by a support vector machine classifier, suggesting that there are distinct and discernible differences between TCRβ CDR3 in CD4+ and CD8+ T cells. Finally, we identified 5–12% of the unique TCRβs that share an identical CDR3 with different variable genes. Together, our findings reveal the distinct features of the TCRβ repertoire between CD4+ and CD8+ T cells and could potentially be used to evaluate the competency of T cell immunity.
A Peripatetic Dialogue in P.Oxy. LIII 3699: A New Edition Based on New Joins
Authors: Verhasselt Gertjan 
Published: September 2015

AbstractThis article presents a new edition with a translation and a commentary of P.Oxy. LIII 3699. By examining the originals I have been able to join the fragments, which were published as separate pieces in the editio princeps. The text is a philosophical dialogue dealing with education and probably belongs to the Aristotelian Peripatos.
Ein medizinischer Papyrus mit Kolumnentitel? Bemerkungen zu einem Exzerpt aus Antyllos’ περὶ βοηθημάτων im Antinoopolis-Papyrus III 128
Authors: Witt Mathias 
Published: September 2015

AbstractP.Ant. III 128, a fragment from a medical compilation, is identified in the present paper to contain a passage from the treatise “On Therapeutic Aids” by Antyllus (2