bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective Comprehensive Genomic Profiling of Advanced Gastric Carcinoma Cases Reveals Frequent Clinically Relevant Genomic Alterations and New Routes for Targeted Therapies
Authors: Ali Siraj M. , Sanford Eric M. , Klempner Samuel J. , Rubinson Douglas A. , Wang Kai , Palma Norma A. , Chmielecki Juliann , Yelensky Roman , Palmer Gary A. , Morosini Deborah , Lipson Doron , Catenacci Daniel V. , Braiteh Fadi , Erlich Rachel , Stephens Philip J. , Ross Jeffrey S. , Ou Sai-Hong Ignatius , Miller Vincent A. 
Published: April 2015

Abstract

Background.
Gastric cancer (GC) is a major global cancer burden and the second most common cause of global cancer-related deaths. The addition of anti-ERBB2 (HER2) targeted therapy to chemotherapy improves survival for ERBB2-amplified advanced GC patients; however, the majority of GC patients do not harbor this alteration and thus cannot benefit from targeted therapy under current practice paradigms.

Materials and Methods.
Prospective comprehensive genomic profiling of 116 predominantly locally advanced or metastatic (90.0%) gastric cancer cases was performed to identify genomic alterations (GAs) associated with a potential response to targeted therapies approved by the U.S. Food and Drug Administration or targeted therapy-based clinical trials.

Results.
Overall, 78% of GC cases harbored one clinically relevant GA or more, with the most frequent alterations being found in TP53 (50%), ARID1A (24%), KRAS (16%), CDH1 (15%), CDKN2A (14%), CCND1 (9.5%), ERBB2 (8.5%), PIK3CA (8.6%), MLL2 (6.9%), FGFR2 (6.0%), and MET (6.0%). Receptor tyrosine kinase genomic alterations were detected in 20.6% of cases, primarily ERBB2, FGFR2, and MET amplification, with ERBB2 alterations evenly split between amplifications and base substitutions. Rare BRAF mutations (2.6%) were also observed. One MET-amplified GC patient responded for 5 months to crizotinib, a multitargeted ALK/ROS1/MET inhibitor.

Conclusion.
Comprehensive genomic profiling of GC identifies clinically relevant GAs that suggest benefit from targeted therapy including MET-amplified GC and ERBB2 base substitutions.
Advanced Torque and Drag Considerations in Extended-Reach Wells
Authors: Payne M. L. , Abbassian F. 
Published: April 2015

Abstract
Excessive torque and drag can be critical limitations in Extended-Reach Drilling (ERD). This paper details issues related to torque and drag prediction, monitoring, and management in ERD wells. Results are presented from sensitivity analyses of extreme ERD trajectories such as 7 to 8 km departures at 1600 m TVD. Several such wells have now been successfully drilled at BP's Wytch Farm oil-field using results from these studies. In such high-angle ERD wells, compression generated in the drillpipe during tripping and sliding operations can exceed the critical buckling load and cause the drillpipe to buckle. As a result, buckling initiation and post-buckling analyses are used to quantify the extent and severity of buckling and the associated increases in drag forces and pipe stresses. The paper addresses the importance of drilling data in calibrating torque/drag models in order to capture the continual changes in drilling parameters and operating conditions. The paper presents a number of field case studies where analyses have been conducted to directly assist drilling operations. This paper should be of high interest to engineers executing, planning, or evaluating ERD operations.
Comparative Evaluation of BacT/ALERT 3D Culture Medium and Nested PCR in the Diagnosis of Tuberculous Meningitis
Authors: Rahaman H Sk , Kumar G , Meena VK , Agarwal A , Nath G , Kumar K 
Published: April 2015

Introduction: We evaluated the efficacy of BacT/ALERT 3D culture medium in comparison with nested polymerase chain reaction (PCR) for early diagnosis of Mycobacterium tuberculosis (MTb) in cerebrospinal fluid (CSF). Methodology: A total of 50 clinically suspected patients with CSF findings suggestive of TBM (Tuberculous meningitis) and 20 healthy controls were included in the present study.CSF from each of the patient was inoculated in BacT/ALERT-MP culture media along with the culture on convention Lowenstein in Jensen’s medium. Simultaneously nested PCR was carried out both in CSF and growth positive above culture media targeting heat shock protein gene (hsp65), a conserved gene of MTb. Results: The culture showed 76% (38/50) positivity in TBM; however, 15% (3/20) of controls also showed false positivity by BacT/ALERT-MP system. By nested CSF-PCR, TBM could be detected in 92% (46/50)cases and 5% (1/20) in the controls. The other interesting observation was that when DNA isolated from broth of BacT/ALERT MP culture were subjected for PCR amplification, 15 (39.5%) of them yielded the desired amp icon for MTb while the broths subjected to conventional LJ media yielded for M. tuberculosis in 12 of the 38 bottles (31.5%). None of culture negative medium was positive by PCR. Sensitivity and specificity of BacT/ALERT MP culture considering all of them as real positive were 76% and 85% while for nested PCR the corresponding values were 92% and 95% respectively. Conclusions: BacT/ALERT 3D culture medium seems to be unsatisfactory as isolation sensitivity rate is very poor. Moreover, growth indicated in the medium must be confirmed for being Myco bacteria as other contaminants can also grow.DOI: http://dx.doi.org/10.3126/saarctb.v11i2.12429SAARC J TUBER LUNG DIS HIV/AIDS, 2014;XI(2),Page: 15-20
Impairment of preoperative language mapping by lesion location: a functional magnetic resonance imaging, navigated transcranial magnetic stimulation, and direct cortical stimulation study
Authors: Ille Sebastian , Sollmann Nico , Hauck Theresa , Maurer Stefanie , Tanigawa Noriko , Obermueller Thomas , Negwer Chiara , Droese Doris , Boeckh-Behrens Tobias , Meyer Bernhard , Ringel Florian , Krieg Sandro M. 
Published: April 2015

OBJECT
Language mapping by repetitive navigated transcranial magnetic stimulation (rTMS) is increasingly used and has already replaced functional MRI (fMRI) in some institutions for preoperative mapping of neurosurgical patients. Yet some factors affect the concordance of both methods with direct cortical stimulation (DCS), most likely by lesions affecting cortical oxygenation levels. Therefore, the impairment of the accuracy of rTMS and fMRI was analyzed and compared with DCS during awake surgery in patients with intraparenchymal lesions.

METHODS
Language mapping was performed by DCS, rTMS, and fMRI using an object-naming task in 27 patients with left-sided perisylvian lesions, and the induced language errors of each method were assigned to the cortical parcellation system. Subsequently, the receiver operating characteristics were calculated for rTMS and fMRI and compared with DCS as ground truth for regions with (w/) and without (w/o) the lesion in the mapped regions.

RESULTS
The w/ subgroup revealed a sensitivity of 100% (w/o 100%), a specificity of 8% (w/o 5%), a positive predictive value of 34% (w/o: 53%), and a negative predictive value (NPV) of 100% (w/o: 100%) for the comparison of rTMS versus DCS. Findings for the comparison of fMRI versus DCS within the w/ subgroup revealed a sensitivity of 32% (w/o: 62%), a specificity of 88% (w/o: 60%), a positive predictive value of 56% (w/o: 62%), and a NPV of 73% (w/o: 60%).

CONCLUSIONS
Although strengths and weaknesses exist for both rTMS and fMRI, the results show that rTMS is less affected by a brain lesion than fMRI, especially when performing mapping of language-negative cortical regions based on sensitivity and NPV.
Association of intracranial aneurysms and meningiomas: a case-control study
Authors: Kim Young-Hoon , Lee Young Jin , Han Jung Ho , Ahn Soyeon , Lee Jaebong , Kim Jae Hyoung , Choi Byung Se , Bang Jae Seung , Kim Chae-Yong , Hwang Gyojun , Kwon O-Ki , Oh Chang Wan 
Published: April 2015

OBJECT
The authors aimed to assess whether the prevalence of intracranial aneurysms in patients with intracranial meningiomas was higher than that in a healthy population.

METHODS
The authors performed a hospital-based case-control study of 300 patients with newly diagnosed intracranial meningiomas and 900 age- and sex-matched controls without a history of brain tumors to evaluate any associations between intracranial aneurysms and intracranial meningiomas. Unconditional multivariate logistic regression models were used for case-control comparisons.

RESULTS
Intracranial aneurysms were identified in 23 patients (7.7%) and 24 controls (2.7%; p < 0.001). There was a significant association between intracranial aneurysms and intracranial meningiomas (OR 2.913, 95% CI 1.613–5.261) and hypertension (OR 1.905, 95% CI 1.053–3.446). In a subgroup analysis of the patients with newly diagnosed intracranial meningiomas, there was a significant association between intracranial aneurysms and hypertension (OR 2.876, 95% CI 1.125–7.352) and tumor volume (OR 1.012, 95% CI 1.001–1.024). These patients were also more likely than controls to have other intracranial vascular diseases (p < 0.001), such as isolated occlusion of the intracranial vessels, excluding intracranial aneurysms.

CONCLUSIONS
The prevalence of intracranial aneurysms was higher in patients with intracranial meningiomas. Hypertension and tumor volume appear to be associated with the formation of intracranial aneurysms in these patients.
Comparison of sinonasal quality of life and health status in patients undergoing microscopic and endoscopic transsphenoidal surgery for pituitary lesions: a prospective cohort study
Authors: Little Andrew S. , Kelly Daniel F. , Milligan John , Griffiths Chester , Prevedello Daniel M. , Carrau Ricardo L. , Rosseau Gail , Barkhoudarian Garni , Jahnke Heidi , Chaloner Charlene , Jelinek Kathryn L. , Chapple Kristina , White William L. 
Published: April 2015

OBJECT
Despite the widespread adoption of endoscopic transsphenoidal surgery for pituitary adenomas, the sinonasal quality of life (QOL) and health status in patients who have undergone this technique have not been compared with these findings in patients who have undergone the traditional direct uninostril microsurgical technique. In this study, the authors compared the sinonasal QOL and patient-reported health status after use of these 2 surgical techniques.

METHODS
The study design was a nonblinded prospective cohort study. Adult patients with sellar pathology and planned transsphenoidal surgery were screened at 4 pituitary centers in the US between October 2011 and August 2013. The primary end point of the study was postoperative patient-reported sinonasal QOL as measured by the Anterior Skull Base Nasal Inventory–12 (ASK Nasal-12). Supplementary end points included patient-reported health status estimated by the 8-Item Short Form Health Survey (SF-8) and EuroQol (EQ)-5D-5L instruments, and sinonasal complications. Patients were followed for 6 months after surgery.

RESULTS
A total of 301 patients were screened and 235 were enrolled in the study. Of these, 218 were analyzed (111 microsurgery patients, 107 endoscopic surgery patients). Demographic and tumor characteristics were similar between groups (p ≥ 0.12 for all comparisons). The most common complication in both groups was sinusitis (7% in the microsurgery group, 13% in the endoscopic surgery group; p = 0.15). Patients treated with the endoscopic technique were more likely to have postoperative nasal debridements (p < 0.001). The ASK Nasal-12 and SF-8 scores worsened substantially for both groups at 2 weeks after surgery, but then returned to baseline at 3 months. At 3 months after surgery, patients treated with endoscopy reported statistically better sinonasal QOL compared with patients treated using the microscopic technique (p = 0.02), but there were no significant differences at any of the other postoperative time points.

CONCLUSIONS
This is the first multicenter study to examine the effect of the transsphenoidal surgical technique on sinonasal QOL and health status. The study showed that surgical technique did not significantly impact these patient-reported measures when performed at high-volume centers.
Clinical trial registration no.: NCT01504399 (clinicaltrials.gov).
Long-term follow-up study of osteoporotic vertebral compression fracture treated using balloon kyphoplasty and vertebroplasty
Authors: Liu Jung-Tung , Li Cho-shun , Chang Cheng-Siu , Liao Wen-Jui 
Published: April 2015

OBJECT
Long-term follow-up study is required for verifying whether the clinical outcomes of kyphoplasty and vertebroplasty are altered. The authors' findings showed only subtle differences between these operations within a 5-year period. However, they still suggest the use of vertebroplasty over kyphoplasty in view of the treatment costs. In their previous study, the authors performed a short-term prospective comparison between vertebroplasty and kyphoplasty. Vertebroplasty was recommended instead of kyphoplasty for the treatment of vertebral compression fractures (VCFs) because of the subtle differences between this procedure and kyphoplasty and the treatment costs. To determine whether these clinical outcomes persist in the long term, they continued to observe the patients from their short-term study over a longer-term period.

METHODS
One hundred cases of VCF were assigned randomly to either the kyphoplasty or the vertebroplasty group. In cement augmentation, the authors used polymethylmethacrylate as bone filler. Pain was assessed by using a visual analog scale (VAS). For each patient, vertebral body height and wedge angle were measured from reconstructed CT images.

RESULTS
The duration of the follow-up period was 5 years. Vertebral body height, kyphotic wedge angle, and VAS score were not evidently altered. Eight patients in the kyphoplasty group had an adjacent fracture after the procedure, whereas 7 patients in the vertebroplasty group had an adjacent fracture after the procedure. These adjacent fractures occurred within 1 year of surgery in both treatment groups except in 1 kyphoplasty-treated patient in whom the adjacent fracture was noted 16 months after treatment. Three patients in the vertebroplasty group had a nonadjacent fracture, and 4 patients in the kyphoplasty group had a nonadjacent fracture. The link between angular correction and the occurrence of adjacent fracture was statistically significant in the vertebroplasty group.

CONCLUSIONS
Excessive angular correction is a critical concern in the risk of adjacent fracture after vertebroplasty. Given the subtle differences between vertebroplasty and kyphoplasty observed over the course of 5 years, vertebroplasty remains the preferred option in view of the costs.
Long-term quality of life after endonasal endoscopic resection of adult craniopharyngiomas
Authors: Patel Kunal S. , Raza Shaan M. , McCoul Edward D. , Patrona Aikaterini , Greenfield Jeffrey P. , Souweidane Mark M. , Anand Vijay K. , Schwartz Theodore H. 
Published: April 2015

OBJECT
Craniopharyngiomas are benign parasellar tumors for which surgical removal, although potentially curative, often leads to morbidity with resulting decreases in quality of life (QOL). The endonasal endoscopic approach is a minimal-access technique for removing these tumors and may reduce postoperative morbidity. The QOL following this method for resection of craniopharyngiomas has not been documented.

METHODS
The authors reviewed a database of consecutive endonasal endoscopic surgeries done at Weill Cornell Medical College. Adult patients with histologically proven craniopharyngiomas were included who had completed either only postoperative (> 9 months) or both pre- and postoperative QOL forms, the Anterior Skull Base Quality of Life (ASBQ) questionnaire, and the 22-Item Sinonasal Outcome Test (SNOT-22). Rates of gross-total resection (GTR), complications, and visual and endocrine function were collected. Retrospective independence (Wen score) was also assigned. A contemporaneous group of patients undergoing endonasal endoscopic pituitary macroadenoma resection was used as a control.

RESULTS
This study included 33 procedures performed in 31 patients. The average postoperative ASBQ score was 3.35 and the SNOT-22 score was 19.6. Better QOL was associated with GTR and postoperative radiation. Worse QOL was associated with persistent visual defects, hypopituitarism, tumor recurrence, increase in body mass index, and worsening Wen score. In a subset of 10 patients, both pre- and postoperative (> 9 months) QOL scores were obtained. Both ASBQ and SNOT-22 scores showed stability and a trend toward improvement, from 2.93 ± 0.51 to 2.96 ± 0.47 (ASBQ) and 23.7 ± 10.8 to 18.4 ± 11.6 (SNOT-22). Compared with 62 patients undergoing endoscopic pituitary macroadenoma resection, patients with craniopharyngiomas had worse postoperative QOL on the ASBQ (3.35 vs 3.80; p = 0.023) and SNOT-22 (19.6 vs 13.4; p = 0.12).

CONCLUSIONS
This report of validated site-specific QOL following endoscopic surgery for craniopharyngiomas shows an overall maintenance of postoperative compared with preoperative QOL. Better QOL could be seen in patients with GTR and radiation therapy, and worse QOL was found in patients with visual or endocrine deficits. Nevertheless, patients with craniopharyngiomas still had worse QOL than those undergoing similar surgery for pituitary macroadenomas, confirming the worse prognosis of craniopharyngiomas even when removed via a minimally invasive approach. These measures should serve as benchmarks for comparison with open transcranial approaches to similar tumors.
A Combined Quantum Mechanics and Molecular Mechanics Study on Nitrogen Oxide Adsorption/Dissociation on a Tungsten Oxide Surface
Authors: Izadyar Mohammad , Balgerdi Rahim , Pourayoubi Mehrdad 
Published: April 2015

The kinetics and mechanism of the adsorption and dissociation of nitrogen monoxide (NO) into N2 and O2 molecules on a tungsten oxide nanocrystalline surface have been studied. Calculations were carried out using the framework of density functional theory (DFT) with the ONIOM method at the (B3LYP/LANL2DZ:UFF) level. In this study, four models of the dissociation have been proposed and investigated theoretically. Density of states (DOS) spectral analysis showed that the Fermi level is shifted to higher values and confirmed the effective interaction between the nanocrystal and adsorbate. The band gap is also reduced after adsorption. Quantum reactivity indices showed that the chemical hardness was reduced after adsorption, which corresponds to the reduction in band gap. The electronic chemical potential has been shifted to more positive values while the electrophilicity of the surface has been reduced, both after adsorption. These parameters predict that charge transfers to the surface. Considering the activation energy, the first and second proposed models provide the most probable route of NO decomposition. Finally, from a comparison between the decomposition and oxidation processes, it is confirmed that NO oxidation is preferred.
Linking surface hydrology to flow regimes and patterns of velocity variability on Devon Ice Cap, Nunavut
Authors: Wyatt Faye R. , Sharp Martin J. 
Published: April 2015

AbstractSupraglacial meltwater reaching a glacier bed can increase ice surface velocities via hydraulic jacking and enhanced basal sliding. However, the relationships between the structure of supraglacial drainage systems, sink-point distributions, glacier flow processes and the magnitude of interannual velocity variability are poorly understood. To explore the hypothesis that spatial variations in the rate and mechanisms of glacier flow are linked to variations in supraglacial drainage system structure and sink-point distribution across an ice cap, we mapped supraglacial drainage systems on Devon Ice Cap from Landsat-7 ETM+ imagery. Spatial patterns of surface velocity and interannual velocity variability were determined using gradient correlation applied to Landsat-7 ETM+ images. Velocity variability is greater in areas close to sink-point locations, presumably because hydrologically forced basal sliding and/or bed deformation are enhanced in such areas. The distribution and characteristics of supraglacial drainage systems may play an important role in determining the distribution of regions of basal sliding, highlighting the need for knowledge of the supraglacial drainage system structure and sink-point distribution to inform efforts to model the dynamic response of Arctic ice caps to future climate warming.
Assessment of current methods of positive degree-day calculation using in situ observations from glaciated regions
Authors: Wake L.M. , Marshall S.J. 
Published: April 2015

AbstractThe continued use of the positive degree-day (PDD) method to predict ice-sheet melt is generally favoured over surface energy-balance methods partly due to the computational efficiency of the algorithm and the requirement of only one input variable (temperature). In this paper, we revisit some of the assumptions governing the application of the PDD method. Using hourly temperature data from the GC-Net network we test the assumption that monthly PDD total (PDDM) can be represented by a Gaussian distribution with fixed standard deviation of monthly temperature (σM). The results presented here show that the common assumption of fixed σM does not hold, and that σM may be represented more accurately as a quadratic function of average monthly temperature. For Greenland, the mean absolute error in predicting PDDM using our methodology is 3.9°C d, representing a significant improvement on current methods (7.8°C d, when σM = 4.5°C). Over a range of glaciated settings, our method reproduces PDDM, on average, to within 1.5–8.5°C d, compared to 4.4–15.7°C d when σM = 4.5°C. The improvement arises because we capture the systematic reduction in temperature variance that is observed over melting snow and ice, when surface temperatures cannot warm above 0°C.
The second Chinese glacier inventory: data, methods and results
Authors: Guo Wanqin , Liu Shiyin , Xu Junli , Wu Lizong , Shangguan Donghui , Yao Xiaojun , Wei Junfeng , Bao Weijia , Yu Pengchun , Liu Qiao , Jiang Zongli 
Published: April 2015

AbstractThe second Chinese glacier inventory was compiled based on 218 Landsat TM/ETM+ scenes acquired mainly during 2006–10. The widely used band ratio segmentation method was applied as the first step in delineating glacier outlines, and then intensive manual improvements were performed. The Shuttle Radar Topography Mission digital elevation model was used to derive altitudinal attributes of glaciers. The boundaries of some glaciers measured by real-time kinematic differential GPS or digitized from high-resolution images were used as references to validate the accuracy of the methods used to delineate glaciers, which resulted in positioning errors of ±10 m for manually improved clean-ice outlines and ±30 m for manually digitized outlines of debris-covered parts. The glacier area error of the compiled inventory, evaluated using these two positioning accuracies, was ±3.2%. The compiled parts of the new inventory have a total area of 43 087 km2, in which 1723 glaciers were covered by debris, with a total debris-covered area of 1494 km2. The area of uncompiled glaciers from the digitized first Chinese glacier inventory is ∼8753 km2, mainly distributed in the southeastern Tibetan Plateau, where no images of acceptable quality for glacier outline delineation can be found during 2006–10.