bluuebunny/crossref_metadata_2025_split huggingface dataset:
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
Authors: Danaee Padideh , Rouches Mason , Wiley Michelle , Deng Dezhong , Huang Liang , Hendrix David 
Published: April 2018

Abstract
While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, ‘bpRNA-1m’, of over 100 000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.
Differences in Pressure Within the Sac of Human Ruptured and Nonruptured Cerebral Aneurysms
Authors: Li Yiping , Corriveau Mark , Aagaard-Kienitz Beverly , Ahmed Azam , Niemann David 
Published: April 2018

Abstract

BACKGROUND
Hemodynamics plays a critical role in the development, growth, and rupture of intracranial aneurysms. This data could be vital in determining individual aneurysm rupture risk and could facilitate our understanding of aneurysms.

OBJECTIVE
To present the largest prospective cross-sectional cohort study of intrasaccular pressure recordings of ruptured and nonruptured intracranial aneurysms and describe the hemodynamic differences that exist between ruptured and nonruptured aneurysms.

METHODS
During endovascular treatment, a standard 1.8-Fr 200 m length microcatheter was navigated into the dome of the aneurysm prior to coil embolization. With the microcatheter centralized within the dome of the aneurysm, an arterial pressure transducer was attached to the proximal end of the microcatheter to measure the stump pressure inside the aneurysm dome.

RESULTS
In 68 aneurysms (28 ruptured, 40 nonruptured), we observed that ruptured cerebral aneurysms had a lower systolic and mean arterial pressure compared to nonruptured cohort (P = .0008). Additionally, the pulse pressures within the dome of ruptured aneurysms were significantly more narrow than that of unruptured aneurysms (P = .0001). These findings suggest that there may be an inherent difference between ruptured and nonruptured aneurysms and such recordings obtained during routine digital subtraction angiography could potentially become a widely applied technique to augment risk stratification of aneurysms.

CONCLUSION
Our preliminary data present new evidence distinguishing ruptured from unruptured aneurysms that may have a critical role as a predictive parameter to stratify the natural history of nonruptured intracranial aneurysms and as a new avenue for future investigation.
Are Fetal-Type Posterior Cerebral Arteries Associated With an Increased Risk of Posterior Communicating Artery Aneurysms?
Authors: Thiarawat Peeraphong , Jahromi Behnam Rezai , Kozyrev Danil A , Intarakhao Patcharin , Teo Mario K , Choque-Velasquez Joham , Niemelä Mika , Hernesniemi Juha 
Published: April 2018

Abstract

BACKGROUND
Fetal-type posterior cerebral arteries (F-PCAs) might result in alterations in hemodynamic flow patterns and may predispose an individual to an increased risk of posterior communicating artery aneurysms (PCoAAs).

OBJECTIVE
To determine the association between PCoAAs and the presence of ipsilateral F-PCAs.

METHODS
We retrospectively reviewed the radiographic findings from 185 patients harboring 199 PCoAAs that were treated at our institution between 2005 and 2015. Our study population consisted of 4 cohorts: (A) patients with 171 internal carotid arteries (ICAs) harboring unilateral PCoAAs; (B) 171 unaffected ICAs in the same patients from the first group; (C) 28 ICAs of 14 patients with bilateral PCoAAs; and (D) 180 ICAs of 90 patients with aneurysms in other locations. We then determined the presence of ipsilateral F-PCAs and recorded all aneurysm characteristics.

RESULTS
Group A had the highest prevalence of F-PCAs (42%) compared to 19% in group B, 3% in group C, and 14% in group D (odds ratio A : B = 3.041; A : C = 19.626; and A : D = 4.308; P < .001). PCoAAs were associated with larger diameters of the posterior communicating arteries (median value 1.05 vs 0.86 mm; P = .001). The presence of F-PCAs was associated with larger sizes of the aneurysm necks (median value 3.3 vs 3.0 mm; P = .02).

CONCLUSION
PCoAAs were associated with a higher prevalence of ipsilateral F-PCAs. This variant was associated with larger sizes of the aneurysm necks but was not associated with the sizes of the aneurysm domes or with their rupture statuses.
P-E3 Assessment of internationally-available HIV test kits for their suitability to meet manufacturers' claims
Authors: Constantine Niel , Abouhamda Ahmed , Athwal Bhavneet , Saleh Ahmed , Paulus Samantha 
Published: April 2018

Background:
HIV test kits, particularly rapid HIV tests, are used throughout the world as a primary measure to protect the blood supply and provide diagnosis to save lives. The US government purchases large numbers of HIV tests at considerable expense, and expects them to perform adequately.

Objective:
To assess a large number and variety of HIV test kits to determine if they meet the claims of the manufacturers.

Methods:
From September 2010 through July 2017, a total of 1,123 lots of HIV test kits from 14 manufacturers and representing 11 different tests from 26 countries, were received for evaluation at the INSTITUTE OF HUMAN VIROLOGY. Each test kit was assessed for performance characteristics using panels of sera (n=30 or 160) that included positives for HIV-1 and HIV-2 (n=8 or 80), and negatives (n=22 or 80). Several HIV-1 positive samples were weak positives derived from seroconversion panels (SeraCare). Test kits were also assessed for precision using several HIV-1 weak positive samples tested in replicate.

Results:
Of the HIV test kit lots evaluated, 99.2% successfully passed the evaluation with perfect performance. Of the 9 lots that did not pass, 3 were found to produce high background that interfered with reading, 2 performed inadequately with high-temperature testing, and 4 exhibited greater than one false-positive result. In one assessment, a country had reported poor performance of a test kit, but the test kit passed the evaluation; this resulted in a visit to the country to assess the laboratory's activities.

Conclusion:
In our evaluation of a large number and variety of HIV test kit lots from 14 manufacturers, nearly all performed as expected and met the manufacturers' claims.
B-105 Discovery to first-in-man studies of a multi-peptide-based hepatocellular carcinoma vaccine - HEPAVAC
Authors: Buonaguro Luigi 
Published: April 2018

Hepatocellular (HCC)/normal adjacent tissue matched samples have been collected for HLA immunopeptidome analysis. 17 HCC samples from HLA-A*02+ patients and 15 samples from HLA-A*24+ patients have been analysed by mass spectrometry. RNA-expression profiles have been established for 12 HCC samples. HLA-presentation/expression of peptides on primary HCC samples (as well as mRNA expression) were compared to normal tissue samples from relevant organs (including heart, brain, lung, kidney, liver, nerve, skin etc.) present in the Immatics' database.
A total of 16 peptides have been selected and confirmed for immunogenicity for the HepaVac vaccine and are currently synthesized according to GMP standard. Of these, 7 are restricted to HLA-A*02; 5 to HLA-A*24 and 4 to HLA class II.
A single-arm, first-in-man trial entitled HepaVac-101 is designed to investigate in patients with very early, early and intermediate stage of HCC the off-the-shelf multi-peptide-based HCC vaccine (IMA970) plus the CV8102 adjuvant (RNAdjuvant®) following a single pre-vaccination infusion of low-dose cyclophosphamide acting as an immunomodulator. The study drugs are applied without concomitant anti-tumor therapy with the intention to reduce risk of tumor recurrence/progression in patients who have received all indicated standard treatments. The primary endpoints are safety, tolerability, and immunogenicity. Secondary/exploratory endpoints are additional immunological parameters in blood (eg, regulatory T-cells, myeloid-derived suppressor cells, impact of the standard therapy on the natural immune response), infiltrating T-lymphocytes in tumor tissue, biomarkers in blood and tissue, disease-free survival/progression-free survival and overall survival.
Tract-Specific Volume Loss on 3T MRI in Patients With Cervical Spondylotic Myelopathy
Authors: Hopkins Benjamin S. , Weber Kenneth A. , Cloney Michael Brendan , Paliwal Monica , Parrish Todd B. , Smith Zachary A. 
Published: April 2018

Study Design.
Case-control.

Objective.
The aim of this study was to understand the role of high-resolution magnetic resonance (MR) in identifying regional cord volume loss in cervical spondylotic myelopathy (CSM).

Summary of Background Data.
Preliminary studies suggest that compression of the ventral region of the cord may contribute disproportionately to CSM symptomology; however, tract-specific data are lacking in the CSM population. The current study is the first to use 3T MR imaging (MRI) images of CSM patients to determine specific volume loss at the level of detail of individual descending white matter tracts.

Methods.
Twelve patients with CSM and 14 age-matched were enrolled prospectively and underwent 3-Tesla MRI of the cervical spine. Using the high-resolution images of the spinal cord, straightening and alignment with a template was performed and specific spinal cord tract volumes were measured using Spinal Cord Tool-box version 3.0.7. Modified Japanese orthopedic association (mJOA) and Nurick disability scores were collected in a prospective manner and were analyzed in relation to descending spinal tract volumes.

Results.
Having CSM was predicted by anterior/posterior diameter, eccentricity of the cord [odds ratio (OR) 0.000000621, P = 0.004], ventral reticulospinal tract volume (OR 1.167, P = 0.063), lateral corticospinal tract volume (OR 1.034, P = 0.046), rubrospinal tract volume (OR 1.072, P = 0.011), and ventrolateral reticulospinal tract volume (OR 1.474, P = 0.005) on single variable logistic regression. Single variable linear regression showed decreases in anterior/posterior spinal cord diameter (P = 0.022), ventral reticulospinal tract volumes (P = 0.007), and ventrolateral reticulospinal tract volumes (P = 0.017) to significantly predict worsening mJOA scores. Similarly, decreases in ventral reticulospinal tract volumes significantly predicted increasing Nurick scores (P = 0.039).

Conclusion.
High-resolution 3T MRI can detect tract-specific volume loss in descending spinal cord tracts in CSM patients. Anterior/posterior spinal cord diameter, ventral reticulospinal tract, ventrolateral reticulospinal tract, lateral corticospinal tract, and rubrospinal tract volume loss are associated with CSM symptoms.

Level of Evidence: 2
Prognostic Factors of Patients With Malignant Epithelioid Vascular Tumors in the Spine
Authors: Xu Kehan , Liu Yujie , Li Bo , Li Jialin , Zhang Hao , Zhao Yuechao , Huang Quan , Wei Haifeng , Xiao Jianru 
Published: April 2018

Study Design.
A retrospective study of 46 patients with malignant epithelioid vascular tumors (MEVT) in the spine was performed.

Objective.
The purpose of this study was to illustrate the clinic characteristics of MEVT in the spine and to discuss prognostic factors by survival analysis.

Summary of Background Data.
MEVT in the spine is relatively uncommon, and there is little published information regarding this subject. Therefore, prognostic factors of this disease are still controversial.

Method.
The univariate and multivariate analysis of various clinic characteristics were performed to identify the independent factor that affects prognosis for patients with MEVT in the spine who underwent surgical treatment in Changzheng Hospital Orthopedics Oncological Center (CHOOC) between 2005 and 2015. Disease-free survival (DFS) and overall survival (OS) were estimated by Kaplan–Meier method to identify potential prognostic factors. Factors with P values of 0.1 or less were subjected to multivariate analysis by Cox regression analysis. P values of 0.05 or less was considered statistically significant.

Result.
A total of 46 patients with MEVT in the spine were included in the study. The mean follow-up period was 42.6 months (range, 5–143 mo). Recurrence was detected in 22 patients after initial surgery in our center, whereas death in 18 patients. The univariate analysis suggested that age (<30 yr/≥30 yr), metastasis, preoperative Frankel score, postoperative Frankel score, malignant grade and resection mode were potential prognostic factors for DFS and OS. However, as they were submitted to multivariate analyses, only malignant grade and resection mode were independent prognostic factors.

Conclusion.
Total en bloc spondylectomy can significantly improve DFS for MEVT in the spine and low-grade malignancy was favorable factor for DFS. Total spondylectomy and low-grade malignancy considerably improve OS for patients with MEVT in the spine.

Level of Evidence: 4
The Morphology and Clinical Significance of the Extraforaminal Ligaments at the T1–T12 Levels
Authors: Zhao Qinghao , Zhang Weicong , Su Zhihai , Wang Min , Yang Lianjun , Zhong Enyi , Ding Zihai , Li Qingchu , Lu Hai 
Published: April 2018

Study Design.
A dissection-based study of 10 embalmed human cadavers.

Objective.
The purpose of this study was to describe the extraforaminal ligaments in the exit regions of the T1–T12 intervertebral foramina and to discuss their possible clinical significance.

Summary of Background Data.
The ligaments at the lumbar intervertebral foramina have been well studied. However, detailed descriptions of the extraforaminal ligaments at the T1–T12 levels are lacking.

Methods.
Two hundred forty T1–T12 intervertebral foramina from 10 embalmed cadavers were studied. The presence of the ligament was noted. The quantity, morphology, distributions, proximal attachments, distal attachments, and spatial orientations of the extraforaminal ligaments in the exit regions of the T1–T12 intervertebral foramina were examined. The length, width, diameter, and thickness of the ligaments were measured with digital calipers by three independent investigators.

Results.
A total of 564 extraforaminal ligaments were identified in the 229 intervertebral foramina; no ligaments were found in the other 11 intervertebral foramina, resulting in an occurrence rate of extraforaminal ligaments of 95.42%. One hundred thirty-six (24.11%) of the extraforaminal ligaments were radiating ligaments, and 428 (75.89%) were transforaminal ligaments. Radiating ligaments had a tendency to be abundant at T1 and T9–T12 and sparse at T2–T8. There were 245 (43.44%) ligaments at the anterior aspect of the exit regions of the intervertebral foramina, 225 (39.89%) ligaments at the posterior aspect, 64 (11.35%) ligaments at the inferior aspect, and 30 (5.32%) ligaments at the superior aspect.

Conclusion.
In the exit region of thoracic intervertebral foramina, there are two types of extraforaminal ligaments. They may serve as a protective mechanism against traction and play a role in the positioning of the nerves in the intervertebral foramen. Transforaminal ligaments may be an underlying cause of rib or chest pain after thoracic fracture and may be of clinical importance to surgeons.

Level of Evidence: N/A
Market and organizational factors associated with hospital vertical integration into sub-acute care
Authors: Hogan Tory H. , Lemak Christy Harris , Hearld Larry R. , Sen Bisakha P. , Wheeler Jack R.C. , Menachemi Nir 
Published: April 2018

Background:
Changes in payment models incentivize hospitals to vertically integrate into sub-acute care (SAC) services. Through vertical integration into SAC, hospitals have the potential to reduce the transaction costs associated with moving patients throughout the care continuum and reduce the likelihood that patients will be readmitted.

Purpose:
The purpose of this study is to examine the correlates of hospital vertical integration into SAC.

Methodology/Approach:
Using panel data of U.S. acute care hospitals (2008–2012), we conducted logit regression models to examine environmental and organizational factors associated with hospital vertical integration. Results are reported as average marginal effects.

Findings:
Among 3,775 unique hospitals (16,269 hospital-year observations), 25.7% vertically integrated into skilled nursing facilities during at least 1 year of the study period. One measure of complexity, the availability of skilled nursing facilities in a county (ME = −1.780, p < .001), was negatively associated with hospital vertical integration into SAC. Measures of munificence, percentage of the county population eligible for Medicare (ME = 0.018, p < .001) and rural geographic location (ME = 0.069, p < .001), were positively associated with hospital vertical integration into SAC. Dynamism, when measured as the change county population between 2008 and 2011 (ME = 1.19e−06, p < .001), was positively associated with hospital vertical integration into SAC. Organizational resources, when measured as swing beds (ME = 0.069, p < .001), were positively associated with hospital vertical integration into SAC. Organizational resources, when measured as investor owned (ME = −0.052, p < .1) and system affiliation (ME = −0.041, p < .1), were negatively associated with hospital vertical integration into SAC.

Practice Implications:
Hospital adaption to the changing health care landscape through vertical integration varies across market and organizational conditions. Current Centers for Medicare and Medicaid reimbursement programs do not take these factors into consideration. Vertical integration strategy into SAC may be more appropriate under certain market conditions. Hospital leaders may consider how to best align their organization’s SAC strategy with their operating environment.
Use of the Modified Shuttle Walk Test During Inpatient Pediatric Cystic Fibrosis Pulmonary Exacerbation Treatment
Authors: Paranjape Shruti M. , Carson Kathryn A. , Demissie Seifu M. , Loosen Holly , Vela Kerry , Mogayzel Peter J. 
Published: April 2018

Purpose:
Exercise improves pulmonary function and physical conditioning in cystic fibrosis. Exercise capacity was assessed in the inpatient setting to determine whether pulmonary exacerbation treatment with intravenous antibiotics, airway clearance, and exercise would improve exercise capacity independently of lung function.

Methods:
Exercise capacity was measured at hospital admission and hospital discharge by numbers of completed shuttles using the Modified Shuttle Walk Test (MSWT). Resting heart rate, oxyhemoglobin saturation, and assessments of breathlessness and perceived exertion were measured before and after exercise. Pulmonary function tests were obtained on the day of hospital admission and within 2 weeks of hospital discharge.

Results:
Fifty-four children performed the MSWT at hospital admission and hospital discharge. Exercise capacity increased by 15.9% during hospitalization, and lung function, measured as a percentage of the predicted forced expiratory volume in 1 second, by 15.7% during intravenous antibiotic treatment. Children with higher exercise capacity showed greater lung function (r = 0.42, P < .001) and lower preexercise resting heart rate at both hospital admission (r = −0.25, P = .03) and hospital discharge (r = −0.30, P = .007). No differences in breathlessness or perceived exertion were observed.

Conclusions:
Exercise capacity and physical conditioning improved during early pulmonary exacerbation treatment. The MSWT can be used safely to assess changes in exercise capacity during hospitalization.
Reliability, Internal Consistency, and Minimal Detectable Change of the American Physical Therapy Association Professionalism in Physical Therapy: Core Values Self-Assessment
Authors: Anderson Deborah K. , Hall Kathy D. 
Published: April 2018

Introduction.
The American Physical Therapy Association identified professionalism as a key component of the professions' growth and advancement in the 21st Century. Physical therapist education programs are using the professionalism in Physical Therapy: Core Values Self-Assessment (PCVSA) for the evaluation of their students and for research. The objective of this study was to determine the extent to which the PCVSA provides a reliable measurement of professionalism in physical therapist students.

Methods.
The study sample consisted of 267 previously completed PCVSAs from physical therapist (PT) students and 29 paired PCVSAs from a current cohort of PT students. This quantitative, descriptive study examined the reliability, internal consistency, and minimal detectible change of scores from the PCVSA. Scores from previously completed PCVSAs were used to investigate internal consistency reliability using Cronbach's alpha. Scores of PCVSA from current students were used to examine test–retest reliability using the intraclass correlation coefficient (ICC) and standard error of measurement. Minimal detectable change scores were also calculated.

Results.
The total PCVSA score had excellent score consistency (α = 0.97) and stability (ICC = 0.90; 95% confidence interval [CI] = 0.78–0.95). Standard error of measurement on the total score was 5.4 points. Minimal detectable change score at the 90% CI was 13 points (95% CI was 15 points).

Discussion and Conclusion.
Utility of the total PCVSA score for formative assessment of professionalism of PT students is supported. Minimal detectable change scores can be used to track professionalism change over time. The PCVSA should not be used for high stakes decisions regarding student progression due to items that may not be appropriate for students.