bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting protein–DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver
Authors: Peng Yunhui , Sun Lexuan , Jia Zhe , Li Lin , Alexov Emil 
Published: October 2017

Abstract

Motivation
Protein–DNA interactions are essential for regulating many cellular processes, such as transcription, replication, recombination and translation. Amino acid mutations occurring in DNA-binding proteins have profound effects on protein–DNA binding and are linked with many diseases. Hence, accurate and fast predictions of the effects of mutations on protein–DNA binding affinity are essential for understanding disease-causing mechanisms and guiding plausible treatments.

Results
Here we report a new method Single Amino acid Mutation binding free energy change of Protein–DNA Interaction (SAMPDI). The method utilizes modified Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) approach along with an additional set of knowledge-based terms delivered from investigations of the physicochemical properties of protein–DNA complexes. The method is benchmarked against experimentally determined binding free energy changes caused by 105 mutations in 13 proteins (compiled ProNIT database and data from recent references), and results in correlation coefficient of 0.72.

Availability and implementation
http://compbio.clemson.edu/SAMPDI

Supplementary information
Supplementary data are available at Bioinformatics online.
Composite Knots Obtained by Twisting Torus Knots
Authors: Lee Sangyop 
Published: October 2017

Abstract
A twisted torus knot is obtained from a torus knot by performing full twists on some adjacent strands of the torus knot. Morimoto constructed infinitely many twisted torus knots which are composite knots and he conjectured that his knots are all of composite twisted torus knots. We show that his conjecture is almost true by giving a complete list of such twisted torus knots.
The Prevalence of Burnout Among US Neurosurgery Residents
Authors: Shakir Hakeem J , McPheeters Matthew J , Shallwani Hussain , Pittari Joseph E , Reynolds Renée M 
Published: October 2017

Abstract

BACKGROUND
Burnout is a syndrome of emotional exhaustion, depersonalization, and reduced personal accomplishment. Its prevalence among US physicians exceeds 50% and is higher among residents/fellows. This is important to the practice of neurosurgery, as burnout is associated with adverse physical health, increased risk of substance abuse, and increased medical errors. To date, no study has specifically addressed the prevalence of burnout among neurosurgery residents.

OBJECTIVE
To determine and compare the prevalence of burnout among US neurosurgery residents with published rates for residents/fellows and practicing physicians from other specialties.

METHODS
We surveyed 106 US neurosurgery residency training programs to perform a descriptive analysis of the prevalence of burnout among residents. Data on burnout among control groups were used to perform a cross-sectional analysis. Nonparametric tests assessed differences in burnout scores among neurosurgery residents, and the 2-tailed Fisher's exact test assessed burnout between neurosurgery residents and control populations.

RESULTS
Of approximately 1200 US neurosurgery residents, 255 (21.3%) responded. The prevalence of burnout was 36.5% (95% confidence interval: 30.6%-42.7%). There was no significant difference in median burnout scores between gender (P = .836), age (P = .183), or postgraduate year (P = .963) among neurosurgery residents. Neurosurgery residents had a significantly lower prevalence of burnout (36.5%) than other residents/fellows (60.0%; P < .001), early career physicians (51.3%; P < .001), and practicing physicians (53.5%; P < .001).

CONCLUSION
Neurosurgery residents have a significantly lower prevalence of burnout than other residents/fellows and practicing physicians. The underlying causes for these findings were not assessed and are likely multifactorial. Future studies should address possible causes of these findings.
Diagnosis and Outcome of Biopsies of Indeterminate Lesions of the Cavernous Sinus and Meckel's Cave: A Retrospective Case Series in 85 Patients
Authors: Hughes Joshua D , Kapurch Joseph , Van Gompel Jamie J , Meyer Fredric B , Pollock Bruce E , Atkinson John , Link Michael J 
Published: October 2017

Abstract

BACKGROUND
When clinical presentation, laboratory studies, or imaging cannot diagnose cavernous sinus (CS) and/or Meckel's cave (MC) lesions, biopsy may be necessary.

OBJECTIVE
To review our institutional series of biopsies of indeterminate CS and MC lesions.

METHODS
Records from January 1994 to June 2016 were searched for biopsied indeterminate CS and MC lesions. We defined indeterminate as having an atypical imaging appearance or a broad differential and the need for tissue for definitive diagnosis. We defined primary tumors as originating from cells inherent or near the CS and MC.

RESULTS
Eighty-five patients were included (median age 59 [2-85] yr); 22 (28%) had a cancer history. Approaches included frontotemporal craniotomy (n = 48, 56%), endoscopic endonasal (n = 20, 24%), percutaneous transforamen ovale (n = 12, 14%), or retrosigmoid craniotomy (n = 5, 6%). Final diagnosis was metastatic in 27 (32%), primary in 21 (25%), inflammatory in 13 (15%), hematologic in 11 (13%), fungal in 5 (5%), and nondefinitive or nondiagnostic in 8 (10%) patients. Thirteen (59%) patients with a cancer history (n = 22) had a diagnosis consistent with their prior cancer; the remaining had a second pathology (n = 6, 27%) or nondiagnostic biopsy (n = 3, 14%). Two patients had surgical complications resulting in death.

CONCLUSION
In this patient cohort, metastatic tumors were the most likely pathology. The biopsy threshold should be lower in patients with a cancer history if clinical or radiographic diagnosis is uncertain as 27% had a second disease. However, we consider biopsy as a last resort because the risk of major morbidity/mortality, while low, is not zero.
Radiation-Induced Changes After Stereotactic Radiosurgery for Brain Arteriovenous Malformations: A Systematic Review and Meta-Analysis
Authors: Ilyas Adeel , Chen Ching-Jen , Ding Dale , Buell Thomas J , Raper Daniel M S , Lee Cheng-Chia , Xu Zhiyuan , Sheehan Jason P 
Published: October 2017

Abstract

BACKGROUND
Radiation-induced changes (RICs) are the most common complication of stereotactic radiosurgery (SRS) for brain arteriovenous malformations (AVMs), and they appear as perinidal T2-weighted hyperintensities on magnetic resonance imaging, with or without associated neurological symptoms.

OBJECTIVE
To determine the rates of RIC after AVM SRS and identify risk factors.

METHODS
A literature review was performed using PubMed and MEDLINE to identify studies reporting RIC in AVM patients treated with SRS. RICs were classified as radiologic (any neuroimaging evidence), symptomatic (any associated neurological deterioration, regardless of duration), and permanent (neurological decline without recovery). Baseline, treatment, and outcomes data were extracted for statistical analysis.

RESULTS
Based on pooled data from 51 studies, the overall rates of radiologic, symptomatic, and permanent RIC after AVM SRS were 35.5% (1143/3222 patients, 32 studies), 9.2% (499/5447 patients, 46 studies), and 3.8% (202/5272 patients, 39 studies), respectively. Radiologic RIC was significantly associated with lack of prior AVM rupture (odds ratio [OR] = 0.57; 95% confidence interval [CI]: 0.47-0.69; P < .001) and treatment with repeat SRS (OR = 6.19; 95% CI: 2.42-15.85; P < .001). Symptomatic RIC was significantly associated with deep AVM location (OR = 0.38; 95% CI: 0.21-0.67; P < .001).

CONCLUSION
Approximately 1 in 3 patients with AVMs treated with SRS develop radiologically evident RIC, and of those with radiologic RIC, 1 in 4 develop neurological symptoms. Lack of prior AVM hemorrhage and repeat SRS are risk factors for radiologic RIC, and deep nidus location is a risk factor for symptomatic RIC.
Deep Brain Stimulation-Related Infections: Analysis of Rates, Timing, and Seasonality
Authors: Hardaway Fran A , Raslan Ahmed M , Burchiel Kim J 
Published: October 2017

Abstract

BACKGROUND
Infection is one of the most common complications of deep brain stimulation (DBS). Long-term infection rates beyond the immediate postoperative period are rarely evaluated.

OBJECTIVE
To study short- and long-term DBS-related infection rates; to evaluate any potential seasonality associated with DBS-related infections.

METHODS
We retrospectively reviewed all DBS surgeries performed in a 5-yr period at 1 hospital by a single surgeon. Infection rates and clinical characteristics were analyzed. Postoperative “infections” were defined as occurring within 6 mo of implantation of DBS hardware, while “erosions” were defined as transcutaneous exposure of hardware at ≥6 mo after implantation. Based on the date of surgery preceding an infection, rates of infection were calculated on a monthly and seasonal basis and compared using Chi square and logistic regression analyses.

RESULTS
A total of 443 patients underwent 592 operations; 311 patients underwent primary DBS placement with 632 electrodes. Primary DBS placement infection incidence was 2.6%. DBS procedure infection and infection rate by electrode were 2.9% and 3.2%, respectively. Infectious complications presented later than 6 mo postoperatively in 38% of infected patients Summer (July-September) infection rate was significantly higher than other seasons (P = .002). The odds ratio of an infection related to a surgery performed in August was found to be 4.15 compared to other months (P = .021).

CONCLUSION
There is a persistent risk of DBS infection and erosion beyond the first year of DBS implantation. Start of the academic year was associated with increased infection rate at our institution.
Congress of Neurological Surgeons Systematic Review and Evidence-Based Guidelines on Pathological Methods and Prognostic Factors in Vestibular Schwannomas
Authors: Sughrue Michael E , Fung Kar-Ming , Van Gompel Jamie J , Peterson Jo Elle G , Olson Jeffrey J 
Published: October 2017

Abstract

TARGET POPULATION
Adults diagnosed with vestibular schwannomas.

QUESTION 1
What is the prognostic significance of Antoni A vs B histologic patterns in vestibular schwannomas?

RECOMMENDATION
No recommendations can be made due to a lack of adequate data.

QUESTION 2
What is the prognostic significance of mitotic figures seen in vestibular schwannoma specimens?

RECOMMENDATION
No recommendations can be made due to a lack of adequate data.

QUESTION 3
Are there other light microscopic features that predict clinical behavior of vestibular schwannomas?

RECOMMENDATION
No recommendations can be made due to a lack of adequate data.

QUESTION 4
Does the KI-67 labeling index predict clinical behavior of vestibular schwannomas?

RECOMMENDATION
No recommendations can be made due to a lack of adequate data.

QUESTION 5
Does the proliferating cell nuclear antigen labeling index predict clinical behavior of vestibular schwannomas?

RECOMMENDATION
No recommendations can be made due to a lack of adequate data.

QUESTION 6
Does degree of vascular endothelial growth factor expression predict clinical behavior of vestibular schwannomas?

RECOMMENDATION
No recommendations can be made due to a lack of adequate data.
The full guideline can be found at: https://www.cns.org/guidelines/guidelines-management-patients-vestibular-schwannoma/chapter_6.
Patient-Reported Outcome Measures in Neurosurgery: A Review of the Current Literature
Authors: Ghimire Prajwal , Hasegawa Harutomo , Kalyal Nida , Hurwitz Victoria , Ashkan Keyoumars 
Published: October 2017

Abstract

BACKGROUND
Patient-reported outcome measures (PROMs) play an important role in the evaluation of health outcomes, quality of life, and satisfaction, and have been successfully utilized in many areas of clinical medicine and surgical practice. The prevalence of PROMs in neurosurgery is not known.

OBJECTIVE
To review the PROMs that have been utilized in the published neurosurgery literature to date.

METHODS
Articles were searched in MEDLINE, EMBASE, HMIC Health Management Information Consortium, PsycARTICLES, and PsycINFO using search terms related to neurosurgery and PROMs, published from 1806 to August 2016. A total of 268 articles were identified that were stratified by the inclusion and exclusion criteria leading to a total of 137 articles. Twenty-six PROMs, involving both adult and pediatric populations, were identified.

RESULTS
A large number of generic and disease-specific PROMs are used in the neurosurgical literature. Generic PROMs are usually nonspecific measures of health status. Disease-specific PROMs may not address issues relevant to neurosurgical procedures. There are very few neurosurgery-specific PROMs that take into account the impact of a neurosurgical procedure on a specific condition.

CONCLUSION
PROMs that currently feature in the neurosurgical literature may not address the specific outcomes relevant to neurosurgical practice. There is an emergent need for generic and disease-specific PROMs to be validated in neurosurgical patients and neurosurgery-specific PROMs developed to address unmet needs of patients undergoing neurosurgical procedures.
Limited Midline Myelotomy for Intractable Visceral Pain: Surgical Techniques and Outcomes
Authors: Vedantam Aditya , Koyyalagunta Dhanalakshmi , Bruel Brian Mendoza , Dougherty Patrick M , Viswanathan Ashwin 
Published: October 2017

Abstract

BACKGROUND
Limited midline myelotomy targets the midline nociceptive pathway for intractable visceral pain. Multiple techniques are available for limited midline myelotomy; however, outcome data for each technique are sparse.

OBJECTIVE
To review our experience with open and percutaneous approaches for limited midline myelotomy for intractable visceral pain.

METHODS
Patients who underwent limited midline myelotomy for intractable visceral pain were reviewed. Myelotomy was performed using 3 techniques: open limited myelotomy, percutaneous radiofrequency myelotomy, and percutaneous mechanical myelotomy. Demographic and perioperative clinical data were recorded. In addition to the visual analog scale and Karnofsy performance score, outcomes were categorized as excellent (no pain), good (considerable reduction in pain, not requiring opioids stronger than codeine), fair (minimal reduction in pain, but no change in opioid medication requirement), and poor (no reduction in pain).

RESULTS
Eight patients (median age 56.5 yr, 6 females) underwent limited myelotomy. Four patients underwent open limited thoracic myelotomy with excellent pain outcomes. Three patients underwent percutaneous radiofrequency lesioning with fair (n = 1) and poor outcomes (n = 2). One patient underwent percutaneous mechanical lesioning with a good outcome (n = 1). The median duration of follow-up was 11 wk (2-54 wk). Two patients reported minor sensory complications after the procedure.

CONCLUSION
In our preliminary experience, outcomes for open limited thoracic myelotomy were superior to percutaneous approaches. Given the limited utilization of this technique, multicenter registries are needed to further evaluate the best surgical technique for limited midline myelotomy.
Diffusion Tensor Imaging in a Large Longitudinal Series of Patients With Cervical Spondylotic Myelopathy Correlated With Long-Term Functional Outcome
Authors: Rao Avinash , Soliman Hesham , Kaushal Mayank , Motovylyak Olesya , Vedantam Aditya , Budde Matthew D , Schmit Brian , Wang Marjorie , Kurpad Shekar N 
Published: October 2017

Abstract

BACKGROUND
Fractional anisotropy (FA) of the high cervical cord correlates with upper limb function in acute cervical cord injury. We investigated the correlation between preoperative FA at the level of maximal compression and functional recovery in a group of patients after decompressive surgery for cervical spondylotic myelopathy (CSM).

OBJECTIVE
To determine the usefulness of FA as a biomarker for severity of CSM and as a prognostic biomarker for improvement after surgery.

METHODS
Patients received diffusion tensor imaging (DTI) scans preoperatively. FA values of the whole cord cross-section at the level of maximal compression and upper cervical cord (C1-2) were calculated. Functional status was measured using the modified Japanese Orthopedic Association (mJOA) scale preoperatively and at follow-up up to 2 yr. Regression analysis between FA and mJOA was performed. DTI at C4-7 was obtained in controls.

RESULTS
Forty-four CSM patients enrolled prior to decompression were compared with 24 controls. FA at the level of maximal compression correlated positively with preoperative mJOA score. Preoperative FA correlated inversely with recovery throughout the postoperative period. This was statistically significant at 12 mo postoperation and nearly so at 6 and 24 mo. Patients with preoperative FA <0.55 had a statistically significant difference in outcome compared to FA >0.55.

CONCLUSION
In the largest longitudinal study of this kind, FA promises a valid biomarker for severity of CSM and postoperative improvement. FA is an objective measure of function and could provide a basis for prognosis. FA is particularly useful if preoperative values are less than 0.55.
Hemodynamics Associated With Intracerebral Arteriovenous Malformations: The Effects of Treatment Modalities
Authors: Fennell Vernard S , Martirosyan Nikolay L , Atwal Gursant S , Kalani M Yashar S , Ponce Francisco A , Lemole G Michael , Dumont Travis M , Spetzler Robert F 
Published: October 2017

Abstract
The understanding of the physiology of cerebral arteriovenous malformations (AVMs) continues to expand. Knowledge of the hemodynamics of blood flow associated with AVMs is also progressing as imaging and treatment modalities advance. The authors present a comprehensive literature review that reveals the physical hemodynamics of AVMs, and the effect that various treatment modalities have on AVM hemodynamics and the surrounding cortex and vasculature. The authors discuss feeding arteries, flow through the nidus, venous outflow, and the relative effects of radiosurgical monotherapy, endovascular embolization alone, and combined microsurgical treatments. The hemodynamics associated with intracranial AVMs is complex and likely changes over time with changes in the physical morphology and angioarchitecture of the lesions. Hemodynamic change may be even more of a factor as it pertains to the vast array of single and multimodal treatment options available. An understanding of AVM hemodynamics associated with differing treatment modalities can affect treatment strategies and should be considered for optimal clinical outcomes.
A Systematic Review of Atypical Antipsychotics in Chronic Pain Management
Authors: Jimenez Xavier F. , Sundararajan Tharani , Covington Edward C. 
Published: October 2017

Introduction:
Many psychopharmacologic agents are used as primary or adjuncts in pain management. Atypical antipsychotics (AAs) have also been used as adjuncts in pain management regimens in a variety of manners; however, their efficacy in this capacity is unclear.

Methods:
A systematic review of all studies examining AA use for pain was conducted. Three literature databases were utilized to search for word combinations of “pain” and a variety of commonly prescribed AAs ie, (olanzapine, quetiapine, risperidone, aripiprazole, ziprasidone, clozapine, paliperidone, iloperidone, lurasidone). Articles chosen for review included retrospective analyses, randomized control trials, and case series/reports. A Preferred Reporting Items for Systematic Reviews and Meta-Analyses diagram illustrates the study selection process.

Results:
Olanzapine, quetiapine, risperidone, aripiprazole, and ziprasidone are the only AAs with published studies in pain management. Among these, olanzapine and quetiapine have the most studies (11 and 6, respectively). Olanzapine shows preliminary and consistent efficacy in fibromyalgia and headache/migraine, although only 1 study was a randomized controlled trial with level I evidence of efficacy. Other AAs eg, (quetiapine) fail to demonstrate efficacy in pain syndromes and/or lack robust study designs.

Conclusions:
Few studies have been conducted to evaluate the analgesic effects of AAs. The collective findings of multiple studies evaluating olanzapine in pain syndromes suggest a high, yet preliminary level of evidence of efficacy, warranting prospective studies in various pain syndrome contexts. Pharmacological mechanisms of AA action are elaborated, and the findings of this review are discussed. Risk and benefits of using AAs in chronic pain are described, and investigational implications and future directions are explored.
Urinary Oxygenation as a Surrogate Measure of Medullary Oxygenation During Angiotensin II Therapy in Septic Acute Kidney Injury
Authors: Lankadeva Yugeesh R. , Kosaka Junko , Evans Roger G. , Bellomo Rinaldo , May Clive N. 
Published: October 2017

Objectives:
Angiotensin II is an emerging therapy for septic acute kidney injury, but it is unknown if its vasoconstrictor action induces renal hypoxia. We therefore examined the effects of angiotensin II on intrarenal Po
2 in ovine sepsis. We also assessed the validity of urinary Po
2 as a surrogate measure of medullary Po
2.

Design:
Interventional study.

Setting:
Research Institute.

Subjects:
Sixteen adult Merino ewes (n = 8/group).

Interventions:
Sheep were instrumented with fiber-optic probes in the renal cortex, medulla, and within a bladder catheter to measure Po
2. Conscious sheep were infused with Escherichia coli for 32 hours. At 24–30 hours, angiotensin II (0.5–33.0 ng/kg/min) or saline vehicle was infused.

Measurements and Main Results:
Septic acute kidney injury was characterized by hypotension and a 60% ± 6% decrease in creatinine clearance. During sepsis, medullary Po
2 decreased from 36 ± 1 to 30 ± 3 mm Hg after 1 hour and to 20 ± 2 mm Hg after 24 hours; at these times, urinary Po
2 was 42 ± 2, 34 ± 2, and 23 ± 2 mm Hg. Increases in urinary neutrophil gelatinase-associated lipocalin (12% ± 3%) and serum creatinine (60% ± 23%) were only detected at 8 and 24 hours, respectively. IV infusion of angiotensin II, at 24 hours of sepsis, restored arterial pressure and improved creatinine clearance, while not exacerbating medullary or urinary hypoxia.

Conclusions:
In septic acute kidney injury, renal medullary and urinary hypoxia developed several hours before increases in currently used biomarkers. Angiotensin II transiently improved renal function without worsening medullary hypoxia. In septic acute kidney injury, angiotensin II appears to be a safe, effective therapy, and urinary Po
2 may be used to detect medullary hypoxia.