bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks
Authors: Gao Jianzhao , Yang Yuedong , Zhou Yaoqi 
Published: August 2016

Motivation: Backbone structures and solvent accessible surface area of proteins are benefited from continuous real value prediction because it removes the arbitrariness of defining boundary between different secondary-structure and solvent-accessibility states. However, lacking the confidence score for predicted values has limited their applications. Here we investigated whether or not we can make a reasonable prediction of absolute errors for predicted backbone torsion angles, Cα-atom-based angles and torsion angles, solvent accessibility, contact numbers and half-sphere exposures by employing deep neural networks.Results: We found that angle-based errors can be predicted most accurately with Spearman correlation coefficient (SPC) between predicted and actual errors at about 0.6. This is followed by solvent accessibility (SPC∼0.5). The errors on contact-based structural properties are most difficult to predict (SPC between 0.2 and 0.3). We showed that predicted errors are significantly better error indicators than the average errors based on secondary-structure and amino-acid residue types. We further demonstrated the usefulness of predicted errors in model quality assessment. These error or confidence indictors are expected to be useful for prediction, assessment, and refinement of protein structures.Availability and Implementation: The method is available at http://sparks-lab.org as a part of SPIDER2 package.Contact: yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
Response to “On Seed Transmissibility of Soybean vein necrosis-associated virus in Symptomless Soybean Seedlings”
Authors: Smith D. L. 
Published: August 2016

A response to M. R. Hajimorad's letter regarding a recent PLoS One paper, in which Groves et al (2016) claims that Soybean vein necrosis-associated virus (SVNaV) was seed transmissible in symptomless seedlings derived from a seed lot of a field-grown soybean variety with symptoms indicative of virus infection. Accepted for publication 28 July 2016.
100 Most Influential Publications in Scoliosis Surgery
Authors: Zhou James Jun , Koltz Michael T. , Agarwal Nitin , Tempel Zachary J. , Kanter Adam S. , Okonkwo David O. , Hamilton D. Kojo 
Published: August 2016

Study Design.
Bibliometric analysis.

Objective.
To apply the established technique of citation analysis to identify the 100 most influential articles in scoliosis surgery research published between 1900 and 2015.

Summary of Background Data.
Previous studies have applied the technique of citation analysis to other areas of study. This is the first article to apply this technique to the field of scoliosis surgery.

Methods.
A two-step search of the Thomson Reuters Web of Science was conducted to identify all articles relevant to the field of scoliosis surgery. The top 100 articles with the most citations were identified based on analysis of titles and abstracts. Further statistical analysis was conducted to determine whether measures of author reputation and overall publication influence affected the rate at which publications were recognized and incorporated by other researchers in the field.

Results.
Total citations for the final 100 publications included in the list ranged from 82 to 509. The period for publication ranged from 1954 to 2010. Most studies were published in the journal Spine (n = 63). The most frequently published topics of study were surgical techniques (n = 35) and outcomes (n = 35). Measures of author reputation (number of total studies in the top 100, number of first-author studies in the top 100) were found to have no effect on the rate at which studies were adopted by other researchers (number of years until first citation, and number of years until maximum citations). The number of citations/year a publication received was found to be negatively correlated with the rate at which it was adopted by other researchers, indicating that more influential manuscripts attained more rapid recognition by the scientific community at large.

Conclusion.
In assembling this publication, we have strived to identify and recognize the 100 most influential articles in scoliosis surgery research from 1900 to 2015.

Level of Evidence: N/A
Bilateral Vestibulopathy Aggravates Balance and Gait Disturbances in Sensory Ataxic Neuropathy, Dysarthria, and Ophthalmoparesis: A Case Report
Authors: van Leeuwen Roeland B. , Smits Bart W. , Rodenburg Richard J. , van Engelen Baziel G. 
Published: August 2016

Abstract
In patients with a triad of sensory ataxic neuropathy, dysarthria, and ophthalmoparesis (SANDO), the presenting features are mainly ataxia or ptosis. SANDO patients often have impaired balance and gait, which is not surprising considering the combination of sensory ataxic neuropathy, and additional symptoms like cerebellar ataxia and limb girdle weakness. We describe a SANDO patient who noticed an increasingly impaired balance and gait, without any dizziness. Neurological investigation revealed an external ophthalmeplegia and a cerebellar ataxia; the head impulse test was not reliable because of eye movement disorders. The caloric reflex tests showed lack of responses on both sides, compatible with severe bilateral vestibulopathy. Making the diagnosis of bilateral vestibulopathy in SANDO patients may have implications for the management of the patient, because specific vestibular rehabilitation can improve gaze and postural stability.
Ulnar Neuropathy at the Elbow in Chronic Alcohol-Dependent Subjects
Authors: Zambelis T. , Kanelli S. , Tzavellas E. , Paparrigopoulos T. , Karandreas N. 
Published: August 2016

Abstract

Objectives:
To evaluate the occurrence of Ulnar neuropathy at the elbow (UNE) among alcohol dependent subjects.

Method:
The study sample comprised 99 consecutive alcohol dependent subjects treated for detoxification voluntarily in the specialized unit of the Athens University Psychiatric Clinic in an inpatient basis.

Results:
UNE was found in 51 subjects (51.5%): in 40.4% on the right side, in 44.6% on the left and in 20.1% on both. Polyneuropathy was diagnosed in 41.4% of the total sample. Statistical analysis showed UNE significantly associated with age of the subjects, age at alcohol dependence onset and duration of alcohol dependence. Was more frequent in men and the probability of UNE was lower in obese subjects.

Conclusions:
UNE is frequent among alcohol dependent subjects and they must be instructed to avoid abnormal postures and to protect their elbow while working with the elbows flexed and resting on a hard object.
Comparative Long-Term Evaluation of Patients With Juvenile Inflammatory Myopathies
Authors: Elahi Hafiz A. , Bertorini Tulio E. , Igarashi Masanori , Mays William H. , Whitaker John N. 
Published: August 2016

Abstract

Objectives:
We conducted a retrospective study analyzing the clinical features, laboratory findings, demographics, and long-term prognoses of patients with juvenile inflammatory myopathies to determine possible predictors indicating the use of aggressive immunotherapy and the response to and complications of treatment.

Methods:
The medical records of 41 patients with juvenile inflammatory myopathies seen at University of Tennessee–affiliated hospitals in Memphis from 1969 to 2008 were evaluated. Patients' clinical characteristics, laboratory studies, muscle biopsies, and electromyography were reviewed. All patients were treated with prednisone initially; additionally, 14 patients received varying combinations of other immunosuppressant therapies.

Results:
Seventy-three percent of the patients experienced remission. Patients in the group that did not go into remission had specific characteristics at onset: they were comparatively older and had more severe rashes, contractures, arthritis, and systemic involvement. Also, patients with positive autoantibodies (antinuclear antibody, rheumatoid arthritis factor) had better outcomes.

Conclusions:
Juvenile inflammatory myopathies have relatively good prognoses. Initial presentation at advanced age or with severe rash, systemic vasculopathies, anemia, or arthritis portends refractory disease; in these patients, second- and third-line therapies improve outcome.
A Review of Azathioprine-Associated Hepatotoxicity and Myelosuppression in Myasthenia Gravis
Authors: Jack Kristin L. , Koopman Wilma J. , Hulley Denise , Nicolle Michael W. 
Published: August 2016

Abstract

Objectives:
Myasthenia gravis (MG) is an autoimmune disorder in which antibodies interfere with neuromuscular transmission. Azathioprine (AZA) is an immunosuppressant frequently used for treatment of various autoimmune conditions, including MG. The literature suggests that the rates of AZA-associated hepatotoxicity and myelosuppression in MG are highly variable. Published studies have not formally analyzed their pattern, severity, timing, and/or recovery. We assessed the prevalence, pattern and timing of AZA associated toxicity in a large group of MG patients.

Methods:
We identified 113 patients with MG with AZA-associated toxicity among 571 managed with this immunosuppressant. The timing of when toxicities occurred as well as pattern of laboratory abnormalities was assessed.

Results:
The overall prevalence of hepatotoxicity and myelosuppression was 15.2% and 9.1%, respectively. The most common pattern of hepatotoxicity seen was gamma-glutamyl transpeptidase (GGT) enzyme elevation in 67.8% of patients. Of note, 21.2% of patients with myelosuppression had normocytic anemia, 17.3% had pancytopenia, and another 17.3% developed macrocytic anemia.

Conclusions:
AZA-associated hepatotoxicity and myelosuppression in MG are not uncommon and may be underrecognized depending on the timing, frequency, and specific tests ordered for blood work monitoring.
Effects of Polymorphisms in NR1H4, NR1I2, SLCO1B1, and ABCG2 on the Pharmacokinetics of Rosuvastatin in Healthy Chinese Volunteers
Authors: Liu Mei , Wu Xiu-Jun , Zhao Gui-Lian , Zhang Ti , Xu Shan-Sen , Sun Ya-Xin , Qiu Feng , Zhao Li-Mei 
Published: August 2016

Abstract:
The nuclear receptors (NR)—farnesoid X receptor (FXR, NR1H4) and pregnane X receptor (PXR, NR1I2)—have important effects on the expression of genes related to the pharmacokinetics (PKs) of rosuvastatin. This study was designed to investigate whether the genetic variants in drug disposition genes (SLCO1B1 and ABCG2) combined with their upstream regulators (NR1H4 and NR1I2) would affect the PKs of rosuvastatin in a Chinese population. Sixty-one healthy male volunteers were enrolled and the plasma concentrations of rosuvastatin were measured using the liquid chromatographic—tandem mass spectrometry/MS method. All subjects were analyzed and grouped according to the genotypes of NR1H4, NR1I2, SLCO1B1, and ABCG2. The exposure of rosuvastatin was higher in subjects carrying the SLCO1B1 521C or ABCG2 421A allele compared with noncarriers. No association was observed of single-nucleotide polymorphisms in NR1H4 or NR1I2 genes with the PKs of rosuvastatin. After adjusting for the 421C>A and 521T>C variants, the Cmax in subjects with NR1I2 63396TT wild type were about 2-fold of those of NR1I2 mutant type (63396CC and CT) (10.7 vs. 20.4 ng/mL, P = 0.023), whereas no significant differences were observed for other parameters. Polymorphisms investigated in the genes of NR1H4 and NR1I2 seemed to play no significant role in the disposition of rosuvastatin.
ACUTE VISION LOSS AS THE ONLY SIGN OF LEUKEMIA RELAPSE
Authors: Cerdà-Ibáñez Marta , Bayo-Calduch Patricia , Manfreda-Domínguez Laura , Duch-Samper Antonio 
Published: August 2016

Purpose:
To report a case of unilateral exudative retinal detachment as the sole presentation of relapsing B-type lymphoblastic leukemia in a 35-year-old man after 3 years of remission.

Methods:
Case report.

Results:
A 35-year-old man in complete remission of high-risk type B acute lymphoblastic leukemia (ALL-B) presented with acute vision loss in his left eye. Exudative retinal detachment was diagnosed at initial evaluation. Hematological and ocular studies were performed. Although there was no evidence of blood, cerebrospinal fluid, or bone marrow disease relapse, transvitreal retinochoroidal cytology identified the infiltration of lymphoblastic leukemic B cells with t(12:21) translocation as the only sign of relapsing ALL-B.

Conclusion:
At first sign of vision loss or ocular symptoms in a patient with a history of lymphoblastic leukemia, and regardless of the hematological findings, exhaustive ophthalmologic exploration and ocular biopsy should be performed without delay—this being crucial for clinical decision making because a prompt diagnosis improves the chances of survival.
IATROGENIC OCCLUSION OF THE OPHTHALMIC ARTERY AFTER SODIUM TETRADECYL SULFATE INJECTION IN THE FOREHEAD
Authors: Esmaili Daniel D. 
Published: August 2016

Purpose:
To describe a patient with ophthalmic artery occlusion after sodium tetradecyl sulfate foam injection in the forehead.

Methods:
In this case report, a description of the clinical examination and imaging findings, including fundus photography, spectral-domain optical coherence tomography, and fluorescein angiography are reported.

Results:
A 33-year-old white woman presented with severe painless vision loss in the left eye after cosmetic treatment of a forehead vein with sodium tetradecyl sulfate foam. Her visual acuity in the left eye was hand motions, and her fundus revealed diffuse retinal whitening in the macula with the absence of a cherry red spot and disruption of the arteriolar blood supply. Spectral-domain optical coherence tomography revealed intense hyperreflectivity of the inner and outer retina with loss of the foveal contour, and fluorescein angiography revealed delayed filling of the choroidal vasculature and cilioretinal artery with incomplete filling of the retinal arterioles in the late frames consistent with ophthalmic artery occlusion.

Conclusion:
This case represents a devastating ocular complication after the inadvertent injection of sodium tetradecyl sulfate into a forehead artery, resulting in occlusion of the ophthalmic artery and severe vision loss.
OUTER RETINAL FOLDS FOLLOWING PARS PLANA VITRECTOMY WITH MEMBRANE PEEL
Authors: Iafe Nicholas A. , Law Simon , Sarraf David , Tsui Irena 
Published: August 2016

Purpose:
To report a case of outer retinal folds following pars plana vitrectomy with epiretinal membrane peel.

Methods:
Retrospective case report. Spectral-domain and en face optical coherence tomography findings are described.

Results:
A 54-year-old man presented with distorted vision 1 month following pars plana vitrectomy with epiretinal membrane peel and subsequent cataract extraction. Optical coherence tomography of the affected eye revealed ripple-type and taco-type outer retinal folds. En face optical coherence tomography illustrated a curvilinear characteristic pattern of the folds that spontaneously resolved with follow-up.

Conclusion:
The authors report a case of outer retinal folds developing in a patient following pars plana vitrectomy with membrane peel. En face optical coherence tomography findings of outer retinal folds may enhance diagnosis.
BILATERAL OCCIPITAL POLE HYPERTENSIVE STROKE DIAGNOSED WITH MACULAR INTEGRITY ASSESSMENT (MAIA) MICROPERIMETRY
Authors: Kasi Sundeep K. , Shahlaee Abtin , Adam Murtaza K. , Ehmann David S. , Sivalingam Arunan 
Published: August 2016

Purpose:
To describe the utility of microperimetry testing in the diagnosis of a bilateral occipital stroke.

Methods:
Retrospective case report.

Results:
A 57-year-old male with hypertension presented with complaints of bilateral blurred central vision and bilateral hypertensive retinopathy with cotton-wool spots. Automated perimetry demonstrated a central scotoma in both eyes that did not respect the vertical midline; however, microperimetry testing revealed a bilateral homonymous hemianopia that suggested cerebrovascular disease which was subsequently confirmed with magnetic resonance imaging.

Discussion:
In cases of unexplained central visual loss, microperimetry testing may be a useful ancillary test for the diagnosis of cerebrovascular disease.
Puerarin Attenuates N-Methyl-d-aspartic Acid–induced Apoptosis and Retinal Ganglion Cell Damage Through the JNK/p38 MAPK Pathway
Authors: Lv Bochang , Huo Fuquan , Dang Xiaojie , Xu Zhiguo , Chen Tao , Zhang Ting , Yang Xinguang 
Published: August 2016

Purpose:
To explore the protective effect of puerarin on N-methyl-d-aspartic acid (NMDA)-induced retinal ganglion cells (RGCs) injury and its underlying mechanism.

Materials and Methods:
Primary RGCs were isolated from P3-P7 Sprague-Dawley rats and purified by sequential immunopanning using Thy1.1 antibodies. NMDA was used to mimic the glutamate activation, cell apoptosis, reactive oxygen species (ROS), malondialdehyde levels, SOD and NO production, nNOS and iNOS expression, as well as caspase-3 activity, Bcl-2, and Bax expression in the RGCs were analyzed by ELISA, RT-PCR, and Western blotting. A rat model of retinal injury was used to detect the protective effect of puerarin.

Results:
Puerarin protected against NMDA-induced RGCs injury in a dose-dependent manner. Compared with the NMDA-treated group, puerarin pretreatment significantly reduced ROS and malondialdehyde levels, promoted SOD and NO production, and downregulated nNOS and iNOS expression in the RGCs. Mechanism analysis showed that pretreatment with puerarin could effectively offset the increase of Bax expression and caspase-3 activity brought by NMDA, and promote Bcl-2 expression in the RGCs. Puerarin pretreatment also effectively inhibited NMDA-induced JNK and p38 phosphorylation in the RGCs, whereas pretreatment with either JNK agonist anisomycin or p38 agonist P79350 could significantly compensate the effects caused by puerarin. Furthermore, puerarin prevented RGCs loss in the retinal injury induced by intravitreal NMDA in a rat model.

Conclusions:
The present results of this study demonstrated that puerarin protected against NMDA-induced apoptosis and RGCs damage through the JNK/p38 MAPK pathway.
Squeeze Me if You Can: Variability in Force Requirements to Extract a Drop From Common Glaucoma Bottles
Authors: Moore Daniel B. , Hammer Jon D. , Akhtari Roozbeh , Beck Judy , Sanders Sheila , Kryscio Richard J. 
Published: August 2016

Purpose:
To determine the force requirements to dispense a single drop from commonly prescribed brand and generic topical glaucoma medications and correlate these findings with pinch strength in a representative patient population.

Patients and Methods:
Four bottles of each medication were tested: 2 in the vertical and 2 in the horizontal orientation. Bottles were housed in a customized force gauge apparatus designed to mimic ballpoint fingertip contact with a bottle tip. For all bottles, each of the first 10 dispensed drops was tested and then tests were performed in increments of 10 until the bottle was empty. For each tested drop, the maximum force and displacement were electronically measured. Concurrently, maximum pinch strength was measured on consecutive glaucoma patients.

Results:
A total of 84 bottles from 21 bottle designs were tested. There was significant variability across the designs, with roughly a 7-fold (0.67 to 4.49 kgf) and 4-fold (0.81 to 3.00 kgf) difference in force requirements in the vertical and horizontal positions, respectively. Of 53 enrolled patients in the glaucoma clinic, the mean pinch strength was 5.05 (range, 1.23 to 10.4 kgf) and 4.82 (range, 1.47 to 10.67 kgf) kgf for the right and left hands, respectively.

Conclusions:
There is statistically significant variability in the force required to squeeze a drop from common glaucoma medications, and a representative sampling of clinic patients suggests that many likely struggle with the force requirements of several bottle designs. These data further support standardization of topical glaucoma drug delivery and design.
Efficacy of Topically Administered Rho-Kinase Inhibitor AR-12286 in Patients With Exfoliation Syndrome and Ocular Hypertension or Glaucoma
Authors: Skaat Alon , Jasien Jessica V. , Ritch Robert 
Published: August 2016

Purpose:
To evaluate the efficacy of rho-associated protein kinase inhibitor, AR-12286 topical solution, for its effect in eyes with exfoliation syndrome (XFS) and ocular hypertension (OHT) or exfoliative glaucoma (XFG) and examine any lasting effect on intraocular pressure (IOP) after discontinuation.

Methods:
Prospective, double-masked, randomized, interventional study. Patients with XFS and OHT or XFG were enrolled. The study eyes were treated once daily with AR-12286, randomized to 0.5% or 0.7% for 24 weeks. Visits included baseline, 1, 4, and 12 weeks after drug initiation; at 12 weeks AR-12286 was discontinued for 1 week and was resumed at week 13. At the week 24 visit, AR-12286 was discontinued, and a final reexamination was performed at week 25.

Results:
Ten patients were treated. Mean baseline IOP was 25±2.4 mm Hg, mean IOP was reduced to 19.1±2.3 mm Hg at 1 week (P<0.001), 17.5±3.6 mm Hg at 4 weeks (P<0.001), and 17.4±3.6 mm Hg at 12 weeks (P<0.001), yielding an average IOP reduction of 23.6%, 30%, and 30.4%, respectively. At the week 13 visit, 1 week after the drug was discontinued, mean IOP increased to 21.6±5.4 mm Hg (P=0.06 compared with baseline visit). At week 24, the mean IOP was 21.8±7.8 mm Hg (P=0.2, and AR-12286 was discontinued). At week 25, the mean IOP was 21.3±5.3 mm Hg (P=0.06).

Conclusions:
AR-12286 was well tolerated and provided statistically significant reduction in IOP in patients with XFS and OHT or XFG. This drug may represent an additional therapeutic paradigm for the treatment of XFG.
Correlation in Severity Between Glaucoma and Erectile Dysfunction
Authors: Law Geoffrey , Nathoo Nawaaz A. , Reiner Ethan , Berkowitz Jonathan , Warner Simon J. , Mikelberg Frederick S. 
Published: August 2016

Purpose:
To examine the association between open-angle glaucoma and erectile dysfunction (ED), and investigate the correlation in severity between these 2 conditions.

Methods:
Cross-sectional study with patient questionnaire and retrospective chart review. A total of 167 male patients over 40 years of age who attended ophthalmology clinic visits in Vancouver, British Columbia, Canada, participated in the study by providing written consent and responding to the survey. Patients with previous radiation or surgical prostate treatment were excluded, leaving final sample sizes of 61 glaucoma patients and 67 control patients. Presence and severity of ED was determined using a validated patient questionnaire (the International Index of Erectile Function questionnaire). Presence of glaucoma was based on previous clinical diagnosis, and severity was graded based on visual field index using a 30-2 visual field test with the SITA Standard protocol. Bivariate analysis examined the presence of ED in glaucoma patients versus controls. Risk factors including dyslipidemia, diabetes, hypertension, and smoking were adjusted for using multiple logistic regression. The association between glaucoma and ED severity was assessed with correlation and scatterplot analysis.

Results:
Glaucoma was found to be a significant risk factor for ED in our population, with an odds ratio of 2.58 (95% confidence interval, 1.15-5.83). Severity of glaucoma and ED were significantly correlated (r=0.365, P=0.007).

Conclusions:
Our results demonstrate that there is a positive association between the presence of ED and the diagnosis of glaucoma and a positive association between the severity of ED and the severity of glaucoma.