bluuebunny/crossref_metadata_2025_split huggingface dataset:
Removal of old nest material decreases reuse of artificial burrows by burrowing owls
Authors: Riding Corey S. , Belthoff James R. 
Published: June 2015

ABSTRACTArtificial burrows are considered an important management and conservation tool for burrowing owls (Athene cunicularia). This species regularly adorns natural and artificial burrows with mammal dung and other materials, which remain between years so that previous use of a nest site is often obvious. Moreover, ectoparasites (fleas) potentially overwinter in accumulated material and infest subsequent occupants. How evidence of prior use affects burrowing owl nest‐site decisions is not completely understood. We examined potential effects of the presence of old nest material on reuse of nests by burrowing owls in southwestern Idaho, USA, during 2004 and 2005. We manipulated artificial burrows that owls used for nesting in the prior year by; 1) removing material from the entrance, tunnel, and nesting chamber and replacing it with fresh soil; 2) microwaving old nest material to kill ectoparasites before returning it; or 3) removing and returning material without treatment to serve as a control. Relative to removal burrows, odds of burrowing owl reuse of ‘control’ and “microwave” burrows were 3.5 and 3.8 times greater, respectively. Removing ectoparasites by microwaving did not increase odds of reuse relative to control burrows, and fleas were present on nestlings in all 3 treatment groups. Presence of old material may help owls locate specific burrows when returning from migration or may provide physiological and feeding benefits. Thus, cleaning by removal of nest material from previously used artificial burrows may be counterproductive if maximizing reuse of nest sites by burrowing owls is a management objective. © 2015 The Wildlife Society.
Testing nest deterrents for Chihuahuan ravens on H‐frame transmission structures
Authors: Dwyer James F. , Leiker Diana L. , King Shauna N. D. 
Published: June 2015

ABSTRACTChihuahuan ravens (Corvus cryptoleucus) regularly perch and nest on electric utility structures. Because ravens perch on overhead shield wires, for which no perch discourager exists, management focuses on nests. When nests occur above energized wires (phase wires), risk of line faults, pole fires, and power outages develop. In southeastern Colorado, USA, Chihuahuan ravens nesting on H‐frame transmission structures historically nested exclusively above the center phase. Nest deterrents prevent ravens from nesting over the center phase on short line segments (1.5 km), but effectiveness over longer line segments is unknown. We installed nest deterrents over the center phase on all structures within a 25.7‐km line segment (n = 93 structures), and compared nesting there with nesting on two 0.75‐km untreated segments adjacent to each end of the treated segment (n = 10 adjacent structures) and on a 25.6‐km untreated segment (n = 93 distant structures). Data were collected over 7 surveys in Bent, Kiowa, and Crowley counties in southeastern Colorado, spring 2012. Ravens placed nest material on 25.8% of treated structures, 90.0% of adjacent untreated structures, and 78.5% of distant untreated structures. Used nests (containing eggs or nestlings) occurred on 2.1% of treated structures, 40.0% of adjacent untreated structures, and 17.2% of distant untreated structures. No used nest occurred above the center phase on any treated tangent structure, whereas all used nests occurred above the center phase on untreated structures. Future research should evaluate whether placing deterrents above all phases further reduces nesting. If so, this application could also be used in areas where ravens are potential predators of species of special concern. © 2015 The Wildlife Society.
Multiple X‐ray approaches to discriminate the origin of liquefied sand erupted during the 2012 Emilia Romagna earthquake
Authors: Di Giuseppe Dario , Tessari Umberto , Faccini Barbara , Coltorti Massimo , Vaccaro Carmela , Marin Emanuela 
Published: June 2015

Geochemical, mineralogical and sedimentological analyses were carried out on sands erupted from sand volcanoes and soil cracks during the 2012 Emilia earthquakes with the aim of determining their origin and depth of provenance in a complex stratigraphic plain generated by different fluvial contributions. Geochemical, mineralogical and sedimentological analyses were performed by wavelength dispersive X‐ray fluorescence, X‐ray powder diffraction and Sedigraph and Settling tube, respectively.Distinct textural features, as well as Ni/MgO and Cr/Al2O3ratios, allow discriminating two populations: an A‐area located close to San Carlo village and a B‐area nearby Scortichino village. Sediments from A‐area show chemical and mineralogical characteristics well comparable with those of the sediments derived from the Apennine rivers, whereas sands from B‐area have strong similarities with the sediments from the Po river.In the earthquake crater area most of the liquefaction phenomena were related to superficial sandy deposits (fluvial ridges, paleochannels and crevasse splays) generated by Apennine rivers. The Po river sediments in the B‐area derive from a layer at a depth at which liquefaction phenomena were excluded, because of the greater lithostatic load. These sediments thus shed a new light on the mechanisms that may induce liquefaction during an earthquake or even without a seismic triggering.It is suggested that a gas phase (mainly methane), which is commonly found below the Po plain, could have been dissolved in the water, near to the saturation threshold or already exsolved, increasing the interstitial overpressure and facilitating the liquefaction and the eruption of the sandy sediments. Copyright © 2015 John Wiley & Sons, Ltd.
“Is It Worth Knowing?” Focus Group Participants’ Perceived Utility of Genomic Preconception Carrier Screening
Authors: Schneider Jennifer L. , Goddard Katrina A. B. , Davis James , Wilfond Benjamin , Kauffman Tia L. , Reiss Jacob A. , Gilmore Marian , Himes Patricia , Lynch Frances L. , Leo Michael C. , McMullen Carmit 
Published: June 2015

AbstractAs genome sequencing technology advances, research is needed to guide decision‐making about what results can or should be offered to patients in different clinical settings. We conducted three focus groups with individuals who had prior preconception genetic testing experience to explore perceived advantages and disadvantages of genome sequencing for preconception carrier screening, compared to usual care. Using a discussion guide, a trained qualitative moderator facilitated the audio‐recorded focus groups. Sixteen individuals participated. Thematic analysis of transcripts started with a grounded approach and subsequently focused on participants’ perceptions of the value of genetic information. Analysis uncovered two orientations toward genomic preconception carrier screening: “certain” individuals desiring all possible screening information; and “hesitant” individuals who were more cautious about its value. Participants revealed valuable information about barriers to screening: fear/anxiety about results; concerns about the method of returning results; concerns about screening necessity; and concerns about partner participation. All participants recommended offering choice to patients to enhance the value of screening and reduce barriers. Overall, two groups of likely users of genome sequencing for preconception carrier screening demonstrated different perceptions of the advantages or disadvantages of screening, suggesting tailored approaches to education, consent, and counseling may be warranted with each group.
Determination of Nutritional and Cyclopropenoid Fatty Acids in Cottonseed by a Single GC Analysis
Authors: Mitchell Barb , Rozema Brent , Vennard Thomas , Sabbatini Jane 
Published: June 2015

AbstractHistorically, a complete analysis of cottonseed fatty acids required two separate analyses: gas chromatography (GC) for nutritional fatty acids and a separate analysis for cyclopropenoid fatty acids (CPFA). Using base esterification and optimized GC conditions, the method presented combines both analyses into a single GC procedure that improves analytical processes and streamlines workflow. While there were challenges, the resolution of critical pairs malvalic/stearic and dihydrosterculic/alpha linolenic methyl esters were adequately separated, allowing for accurate quantitation. Single lab reproducibility measurements (RSD) for major nutritional fatty acids ranged from 0.7 to 2.0 %. For CPFA the RSD ranged from 1.1 to 5.4 %, with the higher variability seen in the extracted cottonseed. In oils, the precision was similar between nutritional fatty acids and CPFA at equivalent concentrations, indicating the variation comes from the extraction process. Average spiked recovery results ranged from 93.3 to 106.5 % for selected fatty acids. In addition, complete fatty acid profile results compare favorably with other methodologies and historical data, demonstrating that it is possible to combine two legacy methods into one.
A complete S-shape feed rate scheduling approach for NURBS interpolator
Authors: Du Xu , Huang Jie , Zhu Li-Min 
Published: June 2015

Abstract
This paper presents a complete S-shape feed rate scheduling approach (CSFA) with confined jerk, acceleration and command feed rate for parametric tool path. For a Non-Uniform Rational B-Spline (NURBS) tool path, the critical points of the tool path where the radius of curvature reaches extreme values are found firstly. Then, the NURBS curve is split into several NURBS sub-curves or blocks by the critical points. A bidirectional scanning strategy with the limitations of chord error, normal/tangential acceleration/jerk and command feed rate is employed to make the feed rate at the junctions between different NURBS blocks continuous. To improve the efficiency of the feed rate scheduling, the NURBS block is classified into three types: short block, medium block and long block. The feed rate profile corresponding to each NURBS block is generated according to the start/end feed rates and the arc length of the block and the limitations of tangential acceleration/jerk. In addition, two compensation strategies are proposed to make the feed rate more continuous and the arc increment more precise. Once the feed rate profile is determined, a second-order Taylor׳s expansion interpolation method is applied to generate the position commands. Finally, experiments with two free-form NURBS curves are conducted to verify the applicability and accuracy of the proposed method.
The efficacy of ultrasound‐guided extracorporeal shockwave therapy in patients with cervical spondylosis and nuchal ligament calcification
Authors: Lin Tz‐Yan , Chen Jing‐Ting , Chen Yu‐Yu , Chen Tien‐Wen , Lee Chia‐Ling , Chen Chia‐Hsin , Huang Mao‐Hsiung 
Published: June 2015

AbstractWe investigated the effects of extracorporeal shockwave therapy (ESWT) on the rehabilitation of cervical spondylosis with nuchal ligament (NL) calcification under X‐ray and ultrasound guidance. Sixty patients with cervical spondylosis and calcification of NL were selected and randomly assigned to three groups: A, B, and C. Patients in Group A received rehabilitation with 20 minutes of hot packs and underwent 15 minutes of intermittent cervical traction three times/week for 6 weeks. Patients in Group B received the same rehabilitation as those in Group A and ESWT (2000 impulses, 0.27 mJ/mm2) over the calcified NL guided by X‐ray image. Patients in Group C received the same treatment as those in Group B, but the ESWT was guided by musculoskeletal sonography. The therapeutic effects were evaluated by: changes in range of motion (ROM) of the cervical spine including flexion, extension, lateral bending, and rotation; visual analog pain scale; and Neck Disability Index before and after treatment and at follow up 3 months later. We found a significant reduction in pain in each treated group after treatment and at follow up. However, patients in Groups B and C showed more improvements in ROM and neck pain relief after treatment and a decrease in Neck Disability Index. Furthermore, patients in Group C showed better cervical ROM at follow up than Group B. ESWT is an adjuvant treatment in the management of cervical spondylosis with calcification of NL and ultrasound‐guided ESWT results in more functional improvements.
Incidence and prognostic factor of ethambutol‐related optic neuropathy: 10‐year experience in southern Taiwan
Authors: Chen Shih‐Chou , Lin Muh‐Chiou , Sheu Shwu‐Jiuan 
Published: June 2015

AbstractTo investigate the incidence and prognostic factors of ethambutol‐related optic neuropathy (EON) in one medical center of southern Taiwan, a retrospective chart review study with 4803 newly diagnosed tuberculosis cases from January 2002 to July 2011 at one medical center hospital in southern Taiwan were reviewed. Of these patients, 1004 had ophthalmic records. Sixty‐two cases (1.29%) experienced visual impairment and were diagnosed as EON with mean visual acuity of 0.86 ± 0.69 by logMAR. Sixteen of the 62 patients had a follow‐up time > 6 months. Of these, eight patients (50%) showed visual improvement (an increase in visual acuity of ≥ 2 Snellen lines) after ethambutol was discontinued. Another eight patients (50%) showed no visual improvement. We analyzed multiple factors between the patients with and without visual improvement by logistic regression, including body weight, daily dose of ethambutol, duration of ethambutol use, cumulative dose of ethambutol, renal function, underlying disease of diabetes mellitus, hypertension, and initial visual acuity showed no statistically significant difference. In conclusion, the incidence of EON was 1.29%. Half of the patients showed visual improvement after discontinuation of ethambutol, and no obvious prognostic factors were found to facilitate the vision recovery. Ethambutol should be discontinued as soon as EON is suspected.
5‐Fluorouracil preferentially sensitizes mutant KRAS non‐small cell lung carcinoma cells to TRAIL‐induced apoptosis
Authors: Wang Haizhen , Yang Tao , Wu Xiangwei 
Published: June 2015

Mutations in the KRAS gene are very common in non–small cell lung cancer (NSCLC), but effective therapies targeting KRAS have yet to be developed. Interest in tumor necrosis factor–related apoptosis‐inducing ligand (TRAIL), a potent inducer of cell death, has increased following the observation that TRAIL can selectively kill a wide variety of human cancer cells without killing normal cells both in vitro and in xenograft models. However, results from clinical trials of TRAIL‐based therapy are disappointingly modest at best and many have demonstrated a lack of therapeutic benefit. Current research has focused on selecting a subpopulation of cancer patients who may benefit from TRAIL‐based therapy and identifying best drugs to work with TRAIL. In the current study, we found that NSCLC cells with a KRAS mutation were highly sensitive to treatment with TRAIL and 5‐fluorouracil (5FU). Compared with other chemotherapeutic agents, 5FU displayed the highest synergy with TRAIL in inducing apoptosis in mutant KRAS NSCLC cells. We also found that, on a mechanistic level, 5FU preferentially repressed survivin expression and induced expression of TRAIL death receptor 5 to sensitize NSCLC cells to TRAIL. The combination of low‐dose 5FU and TRAIL strongly inhibited xenograft tumor growth in mice. Our results suggest that the combination of TRAIL and 5FU may be beneficial for patients with mutant KRAS NSCLC.
Genome-wide binding and mechanistic analyses of Smchd1-mediated epigenetic regulation
Authors: Chen Kelan , Hu Jiang , Moore Darcy L. , Liu Ruijie , Kessans Sarah A. , Breslin Kelsey , Lucet Isabelle S. , Keniry Andrew , Leong Huei San , Parish Clare L. , Hilton Douglas J. , Lemmers Richard J. L. F. , van der Maarel Silvère M. , Czabotar Peter E. , Dobson Renwick C. J. , Ritchie Matthew E. , Kay Graham F. , Murphy James M. , Blewitt Marnie E. 
Published: June 2015

SignificanceStructural maintenance of chromosomes flexible hinge domain containing 1 (Smchd1) is a protein that plays an important role in maintaining gene silencing in many biological circumstances, including facioscapulohumeral muscular dystrophy; however, how it brings about gene silencing is unknown. Understanding the molecular mechanism by which Smchd1 contributes to stable transcriptional silencing is critical to appreciate how it functions in normal biology and when it is mutated in facioscapulohumeral muscular dystrophy. This study reveals, for the first time to our knowledge, where Smchd1 binds genome-wide, its hitherto unappreciated functional interaction with chromatin organizer CCCTC-binding factor in gene regulation, and which part of the protein is required for chromatin binding. These data lead to a new model of Smchd1 function, where it directly binds DNA to mediate 3D chromatin architecture.
atSNP: transcription factor binding affinity testing for regulatory SNP detection
Authors: Zuo Chandler , Shin Sunyoung , Keleş Sündüz 
Published: June 2015

Abstract
Motivation: Genome-wide association studies revealed that most disease-associated single nucleotide polymorphisms (SNPs) are located in regulatory regions within introns or in regions between genes. Regulatory SNPs (rSNPs) are such SNPs that affect gene regulation by changing transcription factor (TF) binding affinities to genomic sequences. Identifying potential rSNPs is crucial for understanding disease mechanisms. In silico methods that evaluate the impact of SNPs on TF binding affinities are not scalable for large-scale analysis.
Results: We describe affinity testing for regulatory SNPs (atSNP), a computationally efficient R package for identifying rSNPs in silico. atSNP implements an importance sampling algorithm coupled with a first-order Markov model for the background nucleotide sequences to test the significance of affinity scores and SNP-driven changes in these scores. Application of atSNP with &gt;20 K SNPs indicates that atSNP is the only available tool for such a large-scale task. atSNP provides user-friendly output in the form of both tables and composite logo plots for visualizing SNP-motif interactions. Evaluations of atSNP with known rSNP-TF interactions indicate that SNP is able to prioritize motifs for a given set of SNPs with high accuracy.
Availability and implementation: https://github.com/keleslab/atSNP.
Contact: keles@stat.wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data
Authors: Zou Meng , Liu Zhaoqi , Zhang Xiang-Sun , Wang Yong 
Published: June 2015

AbstractMotivation: In prognosis and survival studies, an important goal is to identify multi-biomarker panels with predictive power using molecular characteristics or clinical observations. Such analysis is often challenged by censored, small-sample-size, but high-dimensional genomic profiles or clinical data. Therefore, sophisticated models and algorithms are in pressing need.Results: In this study, we propose a novel Area Under Curve (AUC) optimization method for multi-biomarker panel identification named Nearest Centroid Classifier for AUC optimization (NCC-AUC). Our method is motived by the connection between AUC score for classification accuracy evaluation and Harrell’s concordance index in survival analysis. This connection allows us to convert the survival time regression problem to a binary classification problem. Then an optimization model is formulated to directly maximize AUC and meanwhile minimize the number of selected features to construct a predictor in the nearest centroid classifier framework. NCC-AUC shows its great performance by validating both in genomic data of breast cancer and clinical data of stage IB Non-Small-Cell Lung Cancer (NSCLC). For the genomic data, NCC-AUC outperforms Support Vector Machine (SVM) and Support Vector Machine-based Recursive Feature Elimination (SVM-RFE) in classification accuracy. It tends to select a multi-biomarker panel with low average redundancy and enriched biological meanings. Also NCC-AUC is more significant in separation of low and high risk cohorts than widely used Cox model (Cox proportional-hazards regression model) and L1-Cox model (L1 penalized in Cox model). These performance gains of NCC-AUC are quite robust across 5 subtypes of breast cancer. Further in an independent clinical data, NCC-AUC outperforms SVM and SVM-RFE in predictive accuracy and is consistently better than Cox model and L1-Cox model in grouping patients into high and low risk categories.Conclusion: In summary, NCC-AUC provides a rigorous optimization framework to systematically reveal multi-biomarker panel from genomic and clinical data. It can serve as a useful tool to identify prognostic biomarkers for survival analysis.Availability and implementation: NCC-AUC is available at http://doc.aporc.org/wiki/NCC-AUC.Contact: ywang@amss.ac.cnSupplementary information: Supplementary data are available at Bioinformatics online.
Prophylactic anticonvulsants for gliomas: a seven-year retrospective analysis
Authors: Lapointe Sarah , Florescu Marie , Nguyen Dang K. , Djeffal Chanez , Bélanger Karl 
Published: June 2015

AbstractBackgroundThe American Academy of Neurology (AAN) does not recommend routine use of prophylactic antiepileptic drugs (pAEDs) in patients with newly diagnosed brain tumors. If used in the perioperative setting, discontinuation is suggested after the first postoperative week. It is unclear whether such recommendations are followed. Our objective was to compare our perioperative and long-term pAED use in glioma patients with AAN practice parameters.MethodsRetrospective chart review was performed on 578 glioma patients from 2006 to 2013. Seizures and AED use were assessed at surgery, 3 months postoperatively and death, last visit or 16 months postoperatively. Patients were divided into three groups at surgery: seizure-free with pAED, seizure-free without pAED, and seizure patients. Long-term pAED use was defined as continued use at 3 months postsurgery without seizures. pAEDs efficacy, factors influencing its use, and survival were examined.ResultsOut of 578 patients identified, 330 (57.1%) were seizure-naïve preoperatively. There were no significant differences in age, histology, tumor location or resection status between seizure-free populations with and without prophylaxis. Of 330 seizure-naïve patients, 205 (62.1%) received pAEDs at surgery. Ninety-six (46.9%) of those patients were still on pAEDs 3 months postsurgery (median use = 58 days). Rate of long-term prophylaxis use decreased by 13.5% over 6 years (70.3% in 2006; 56.8% in 2012). Phenytoin was preferred in 2006 (98.2%) with increasing use of levetiracetam over 6 years (44.6% in 2012). The only predictive factor for pAED use was complete resection (P = .0069). First seizure prevalence was similar in both seizure-free populations (P = .91). The seizure population had more men (P = .007), younger patients (P < .0001), lower-grade gliomas (P = .0003) and survived longer (P = .001) compared with seizure-free populations.ConclusionsIn our center, long-term prophylactic AED use is high, deviating from current AAN Guidelines. Corrective measures are warranted.
What Is the Essence of Spiritual Care? A Danish Hospice Perspective
Authors: Steenfeldt Vibeke Ostergaard 
Published: June 2015

ABSTRACT:
This study explored patients', relatives', and healthcare professionals' experience of life and caring practice in two Danish hospice settings. Using a phenomenological approach, four caring themes emerged from data analysis: recognized as an individual human being; caring as doing and being; caring for the whole body; and spaces of caring. Spiritual care was understood as providing whole-body experiences, respecting the patient, and involving the other person.