bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid and powerful detection of subtle allelic imbalance from exome sequencing data with hapLOHseq
Authors: San Lucas F. Anthony , Sivakumar Smruthy , Vattathil Selina , Fowler Jerry , Vilar Eduardo , Scheet Paul 
Published: June 2016

Abstract
Motivation: The detection of subtle genomic allelic imbalance events has many potential applications. For example, identifying cancer-associated allelic imbalanced regions in low tumor-cellularity samples or in low-proportion tumor subclones can be used for early cancer detection, prognostic assessment and therapeutic selection in cancer patients. We developed hapLOHseq for the detection of subtle allelic imbalance events from next-generation sequencing data.
Results: Our method identified events of 10 megabases or greater occurring in as little as 16% of the sample in exome sequencing data (at 80×) and 4% in whole genome sequencing data (at 30×), far exceeding the capabilities of existing software. We also found hapLOHseq to be superior at detecting large chromosomal changes across a series of pancreatic samples from TCGA.
Availability and Implementation: hapLOHseq is available at scheet.org/software, distributed under an open source MIT license.
Contact: pscheet@alum.wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Limited role for transforming growth factor–β pathway activation-mediated escape from VEGF inhibition in murine glioma models
Authors: Mangani Davide , Weller Michael , Seyed Sadr Emad , Willscher Edith , Seystahl Katharina , Reifenberger Guido , Tabatabai Ghazaleh , Binder Hans , Schneider Hannah 
Published: June 2016

AbstractBackgroundThe vascular endothelial growth factor (VEGF) and transforming growth factor (TGF)–β pathways regulate key biological features of glioblastoma. Here we explore whether the TGF-β pathway, which promotes angiogenesis, invasiveness, and immunosuppression, acts as an escape pathway from VEGF inhibition.MethodsThe role of the TGF-β pathway in escape from VEGF inhibition was assessed in vitro and in vivo and by gene expression profiling in syngeneic mouse glioma models.ResultsWe found that TGF-β is an upstream regulator of VEGF, whereas VEGF pathway activity does not alter the TGF-β pathway in vitro. In vivo, single-agent activity was observed for the VEGF antibody B20-4.1.1 in 3 and for the TGF-β receptor 1 antagonist LY2157299 in 2 of 4 models. Reduction of tumor volume and blood vessel density, but not induction of hypoxia, correlated with benefit from B20-4.1.1. Reduction of phosphorylated (p)SMAD2 by LY2157299 was seen in all models but did not predict survival. Resistance to B20 was associated with anti-angiogenesis escape pathway gene expression, whereas resistance to LY2157299 was associated with different immune response gene signatures in SMA-497 and GL-261 on transcriptomic profiling. The combination of B20 with LY2157299 was ineffective in SMA-497 but provided prolongation of survival in GL-261, associated with early suppression of pSMAD2 in tumor and host immune cells, prolonged suppression of angiogenesis, and delayed accumulation of tumor infiltrating microglia/macrophages.ConclusionsOur study highlights the biological heterogeneity of murine glioma models and illustrates that cotargeting of the VEGF and TGF-β pathways might lead to improved tumor control only in subsets of glioblastoma.
Scale heights and equivalent widths of the iron K-shell lines in the Galactic diffuse X-ray emission
Authors: Yamauchi Shigeo , Nobukawa Kumiko K. , Nobukawa Masayoshi , Uchiyama Hideki , Koyama Katsuji 
Published: June 2016

Abstract
This paper reports the analysis of the X-ray spectra of the Galactic diffuse X-ray emission (GDXE) in the Suzaku archive. The fluxes of the Fe i Kα (6.4 keV), Fe xxv Heα (6.7 keV), and Fe xxvi Lyα (6.97 keV) lines are separately determined. From the latitude distributions, we confirm that the GDXE is decomposed into the Galactic center (GCXE), the Galactic bulge (GBXE) and the Galactic ridge (GRXE) X-ray emissions. The scale heights (SHs) of the Fe xxv Heα line of the GCXE, GBXE, and GRXE are determined to be ∼40, ∼310, and ∼140 pc, while those of the Fe i Kα line are ∼30, ∼160, and ∼70 pc, respectively. The mean equivalent widths (EWs) of the sum of the Fe xxv Heα and Fe xxvi Lyα lines are ∼750 eV, ∼600 eV, and ∼550 eV, while those of the Fe i Kα line are ∼150 eV, ∼60 eV, and ∼100 eV for the GCXE, GBXE, and GRXE, respectively. The origin of the GBXE, GRXE, and GCXE is separately discussed based on the new results of the SHs and EWs, in comparison with those of the cataclysmic variables, active binaries and coronal active stars.
Should patients with pollen fruit syndrome be prescribed an automatic epinephrine injector?
Authors: Katelaris Constance H. 
Published: June 2016

Purpose of review
The review outlines recent insights into our understanding of the complex relationships between pollen and plant food sensitization patterns resulting in the pollen fruit syndrome and the possible risk, upon ingestion, of generalized symptoms rather than localized oropharyngeal reactions. Appreciation of this risk will inform management strategies, which include epinephrine prescription.

Recent findings
In recent times, the ability to examine molecular components of foods and pollen has allowed further delineation of reactivity patterns. These reveal complex patterns of IgE reactivity and sensitization pathways. More precise definition of these patterns will allow a more accurate analysis of risk of severe food reactions following ingestion.

Summary
Despite improvement in diagnostic tests, there remains no completely reliable way to determine whether an individual with pollen fruit syndrome is at risk of a systemic reaction. The decision to prescribe an epinephrine autoinjector must be based on a risk assessment for the individual patient.
Daily Spiritual Experiences of Nurse Educators and Relationship to Depression and Health
Authors: Johnson Paige Turner , Cheshire Michelle , Wood Felecia G. , Dunn Linda L. , Ewell Patrick J. 
Published: June 2016

ABSTRACT:
This research describes the first reported assessment of spirituality in nurse educators. Faculty members at a public university in a southern U.S. state participated in a study to investigate the relationship between daily spiritual experiences (DSE), self-reported health, and depression. All participants viewed themselves as spiritual, had a religious affiliation, and recognized a difference between spirituality and religiosity. Many who reported spiritual experiences at least daily rated their health as good or excellent; those reporting less frequent DSE reported more depressive symptoms. Nurse educators' self-awareness of spirituality is important as they prepare future nursing professionals who will integrate spirituality into healthcare.
Surviving (Even Thriving?) in a Toxic Workplace
Authors: White Paul E. , Schoonover-Shoffner Kathy 
Published: June 2016

ABSTRACT:
Anything toxic is poisonous and harmful—including a toxic workplace. Surveys of hundreds of individuals and organizations reveal three primary areas that are common in unhealthy work environments: sick systems, toxic leaders, and dysfunctional colleagues. This article draws from research and offers practical steps on how to survive, if not change and thrive, in toxic workplaces.
A Compassionate Visitation Program for Church Homebound Elders
Authors: Emblen Julia Quiring 
Published: June 2016

ABSTRACT:
Homebound elders are vulnerable to decreased quality of life, related to their social and emotional isolation. This article discusses development of a Compassionate Visitation Program in the faith community, including recruitment and training of visitors, assessment of visitees and their environment, and structure and record-keeping of visits.
Strategies for Improving Nursing Students' Mental Health Clinical Rotation
Authors: Kroning Maureen 
Published: June 2016

ABSTRACT:
Mental illness is a huge problem many people face in the U.S. and around the world. The American Psychiatric Nurses Association indicates there is a shortage of nurses in every level and role in psychiatric-mental health nursing. Raising up a generation of nurses who want to work with the mentally ill is a challenge for nurse educators. The use of role playing and simulation in the learning lab prior to entering the clinical setting and reflective journaling in the clinical rotation can improve undergraduate nursing students' mental health clinical experience.
Role of Asymmetrical Dimethylarginine in Diabetic Microvascular Complications
Authors: Du Mei-Rong , Ju Gui-Xia , Li Nian-Sheng , Jiang Jun-Lin 
Published: June 2016

Abstract:
Microvascular complications are the leading causes of acquired blindness, end-stage renal failure, and varieties of neuropathy associated with diabetes. Asymmetric dimethylarginine (ADMA), an endogenous nitric oxide synthase inhibitor, is involved in endothelial dysfunction, oxidative stress, and inflammation associated with the progression of diabetic microvascular complications. Elevated ADMA has been detected in experimental animals and patients with diabetic microangiopathy like retinopathy, nephropathy, and neuropathy. In the review, we focus on the role of ADMA in the pathobiology of major microvascular complications of diabetes.
Advantages of robotics in benign gynecologic surgery
Authors: Truong Mireille , Kim Jin Hee , Scheib Stacey , Patzkowsky Kristin 
Published: June 2016

Purpose of review
The purpose of this article is to review the literature and discuss the advantages of robotics in benign gynecologic surgery.

Recent findings
Minimally invasive surgery has become the preferred route over abdominal surgery. The laparoscopic or robotic approach is recommended when vaginal surgery is not feasible. Thus far, robotic gynecologic surgery data have demonstrated feasibility, safety, and equivalent clinical outcomes in comparison with laparoscopy and better clinical outcomes compared with laparotomy. Robotics was developed to overcome challenges of laparoscopy and has led to technological advantages such as improved ergonomics, visualization with three-dimensional capabilities, dexterity and range of motion with instrument articulation, and tremor filtration. To date, applications of robotics in benign gynecology include hysterectomy, myomectomy, endometriosis surgery, sacrocolpopexy, adnexal surgery, tubal reanastomosis, and cerclage. Though further data are needed, robotics may provide additional benefits over other approaches in the obese patient population and in higher complexity cases. Challenges that arose in the earlier adoption stage such as the steep learning curve, costs, and operative times are becoming more optimized with greater experience, with implementation of robotics in high-volume centers and with improved training of surgeons and robotic teams. Robotic laparoendoscopic single-site surgery, albeit still in its infancy where technical advantages compared with laparoscopic single-site surgery are still unclear, may provide a cost-reducing option compared with multiport robotics. The cost may even approach that of laparoscopy while still conferring similar perioperative outcomes.

Summary
Advances in robotic technology such as the single-site platform and telesurgery, have the potential to revolutionize the field of minimally invasive gynecologic surgery. Higher quality evidence is needed to determine the advantages and disadvantages of robotic surgery in benign gynecologic surgery. Conclusions on the benefits and risks of robotic surgery should be made with caution given limited data, especially when compared with other routes. Route of surgery selection should take into consideration the surgeons’ skill and comfort level that allows for the highest level of safety and efficiency. Ultimately, the robotic device is an additional minimally invasive surgical tool that can further the goal of minimizing laparotomy in gynecology.
Staging the progression to type 1 diabetes with prediagnostic markers
Authors: Sosenko Jay M. 
Published: June 2016

Purpose of review
There are an increasing number of markers that are used to predict the occurrence of type 1 diabetes (T1D), and to study the progression of pathologic changes prior to diagnosis. This review discusses some of those markers, particularly markers for which data are available that pertain to the progression to T1D.

Recent findings
A study of birth cohorts showed that young children who develop multiple autoantibodies are at a particularly high risk for developing T1D, and that there appears to be a typical sequence for autoantibody development. The measurement of autoantibodies by electrochemiluminescence can increase the prediction accuracy for T1D. A new marker of changes in glucose over 6 months (PS6 M) has potential utility as an endpoint in short-term prevention trials. Markers which combine C-peptide and glucose, such as the Diabetes Prevention Trial-Type 1 Risk Score and the Index60, can increase the accuracy of prediction, and can potentially be utilized as prediagnostic endpoints. β-cell death measurements could have substantial utility in future T1D research.

Summary
Markers are highly useful for studying the prediction of and progression to T1D. Moreover, markers can possibly be utilized to diagnose T1D at an earlier stage of disease.
Blistering diseases in neonates
Authors: Zhao Cathy Y. , Murrell Dedee F. 
Published: June 2016

Purpose of review
Neonatal blistering diseases are rare yet potentially fatal. Therefore, it is crucial for clinicians to know its broad range of differential diagnoses. This review discusses the recent literature on the causes and the most appropriate clinical approach to neonatal blistering diseases.

Recent findings
Neonatal infections are the commonest causes for neonatal blistering. On the other hand, autoimmune blistering diseases are extremely rare with the literature limited to case reports and one systematic review only. Inherited genodermatoses are also rare, with recent developments in epidermolysis bullosa classification.

Summary
In conclusion, as neonatal infections are the commonest cause for blistering, any neonate with blistering should have their blister fluid investigated for infection, while an antimicrobial should be initiated early. Autoimmune blistering diseases should be considered in neonates with a maternal history of autoimmune blistering disease. Although pemphigus and bullous pemphigoid have overall good prognoses, linear IgA bullous dermatoses has a poor prognosis and requires aggressive treatment. Inherited genodermatoses should be suspected when there is a family history of genodermatoses or consanguinity. In this case, the clinician should not hesitate to seek dermatology advice, perform a skin biopsy and consider genetic testing.
The ins and outs of managing avoidance diets for food allergies
Authors: Shaker Marcus , Venter Carina 
Published: June 2016

Purpose of review
Food allergic reactions have become more prevalent and management of food allergies requires dietary avoidance of triggers that may place children at nutritional risk.

Recent findings
Immunoglobulin E and non-immunoglobulin E-mediated food allergies lead to dietary avoidance. Although some children outgrow food allergies or become tolerant to cooked/baked versions of the allergen, many do not. Multiple food avoidance increases the risk for inadequate nutrient intake, including protein, calcium, vitamin D, and others. Multidisciplinary management of patients requires careful attention to growth, particularly height, and nutrition.

Summary
Although attention to accurate diagnosis of food allergy is key, understanding nutritional risks of children with food allergies can lead to opportunities to address potential deficiencies resulting from food allergen avoidance.
A Reexamination of Nonpsychiatric Medication Adherence in Individuals With Bipolar Disorder and Medical Comorbidities
Authors: Levin Jennifer B. , Krivenko Anna , Bukach Ashley , Tatsuoka Curtis , Cassidy Kristin A. , Sajatovic Martha 
Published: June 2016

Abstract
Individuals with bipolar disorder (BD) have high rates of nonadherence, medical illness, and premature mortality. This analysis reexamined correlates of poor adherence to nonpsychiatric medication in 73 patients with BD and medical comorbidities. The majority was female (74%) and African American (77%) with mean age of 48.08 (SD, 8.04) years, mean BD duration of 28.67 (SD, 10.24) years, mean years of education of 12.01 (SD, 1.87), and mean proportion of days with missed doses in past week of 43.25 (SD, 31.14). Sex, age, education, race, and living alone did not correlate with adherence. More BD medications and more severe psychiatric symptoms correlated with worse adherence. Specifically, poor adherence correlated with the retardation and vegetative factors of Montgomery-Åsberg Depression Rating Scale and affect factor of the Brief Psychiatric Rating Scale. Among poorly adherent patients with BD and medical comorbidities, the number of BD medications, tension/anxiety, and somatic symptoms of depression related to worse nonpsychiatric medication adherence.
Learning From Lawsuits: Using Malpractice Claims Data to Develop Care Transitions Planning Tools
Authors: Arbaje Alicia I. , Werner Nicole E. , Kasda Eileen M. , Wu Albert W. , Locke Charles F.S. , Aboumatar Hanan , Paine Lori A. , Leff Bruce , Davis Richard O. , Boonyasai Romsai 
Published: June 2016

Objectives
Our understanding of care transitions from hospital to home is incomplete. Malpractice claims are an important and underused data source to understand such transitions. We used malpractice claims data to (1) evaluate safety risks during care transitions and (2) help develop care transitions planning tools and pilot test their ability to evaluate care transitions from the hospital to home.

Methods
Closed malpractice claims were analyzed for 230 adult patients discharged from 4 hospital sites. Stakeholders participated in 2 structured focus groups to review concerns. This led to the development of 2 care transitions planning tools—one for patients/caregivers and one for frontline care providers. Both were tested for feasibility on 53 patient discharges.

Results
Qualitative analysis yielded 33 risk factors corresponding to hospital work system elements, care transitions processes, and care outcomes. Providers reported that the tool was easy to use and did not adversely affect workflow. Patients reported that the tool was acceptable in terms of length and response burden. Patients were often still waiting for information at the time they applied the tool.

Conclusions
Malpractice claims provided insights that enriched our understanding of suboptimal care transitions and guided the development of care transitions planning tools. Pilot testing suggested that the tools would be feasible for use with minor adjustment. The malpractice data can complement other approaches to characterize systems failures threatening patient safety.
Cobalt–Chromium Metallosis With Normal Electroretinogram
Authors: Grillo Lola M. , Nguyen Huy V. , Tsang Stephen H. , Hood Donald C. , Odel Jeffrey G. 
Published: June 2016

Background:Ocular cobalt toxicity is a rare phenomenon reported with increased frequency due to the rise of cobalt–chromium metal hip implants. We report the case of a 66-year-old previously healthy man who developed decreased vision due to cobalt–chromium toxicity from a metal-on-metal hip arthroplasty. Our objective was to determine whether the origin of his visual loss was due to toxicity of the optic nerve, of the retina, or of both.Methods:Ocular examination, 10-2 SITA-Standard Humphrey Visual Field (VF), standard full-field electroretinogram (ERG) as indicated by the International Society for Clinical Electrophysiology of Vision (ISCEV), multifocal electroretinogram (mfERG), multifocal visual evoked potentials (mfVEP), and optical coherence tomography (OCT) were conducted.Results:Ocular examination revealed decreased visual acuity, poor color vision, normal funduscopy, and cecocentral scotomas on VF testing. Because his right eye was amblyopic since childhood, test results from only the left eye are shown. Electrophysiology studies revealed an ISCEV standard full-field ERG with photopic and scotopic responses within normal limits, mfERG with amplitudes and latencies within normal limits, and mfVEP with latencies within normal limits, but with decreased central amplitudes. Peripapillary and macular OCT showed retinal nerve fiber layer and retinal ganglion cell–inner plexiform layer thickness within normal limits.Conclusion:Because decreased color vision and cecocentral scotoma on 10-2 VF are most consistent with toxic optic neuropathy, and decreased central amplitudes on mfVEP are suggestive of neural dysfunction, we hypothesize that our patient presented with an early stage of optic nerve toxicity that was not yet apparent as a structural abnormality on OCT.
A Brief Measure for Assessing Patient Perceptions of Cognitive Side Effects After Electroconvulsive Therapy
Authors: Kumar Divya Rani , Han Hank Ke , Tiller John , Loo Colleen K. , Martin Donel M. 
Published: June 2016

Objectives
Directly inquiring about patient experiences of memory problems after ECT may alert clinicians to the existence of treatment side effects and provide an impression of their intrusiveness. In this study, we examined use of a novel and brief patient-reported measure to assess perceptions of memory side effects and their functional consequences before and after an acute ECT treatment course. These outcomes were compared with objective cognitive and subjective quality of life measures.

Methods
Data for 75 patients who were prescribed an acute course of ECT were analyzed. Subjective and objective measures were assessed before ECT (pretreatment) and at posttreatment. Patient perceptions were assessed using the Subjective Assessment of Memory Impairment, which consists of two items: The Memory Problems item, and The Impact of Cognitive Adverse Events item. Objective cognitive outcomes were assessed using the Montreal Cognitive Assessment. Quality of life was assessed using the Quality of Life Enjoyment and Satisfaction Questionnaire—Short Form.

Results
Patient perceptions of their memory problems did not change across the ECT course, and their functional impact were considered less intrusive after ECT. Greater functional impact of memory impairment was related to poorer quality of life at posttreatment, but not at pretreatment. Subjectively rated cognitive functioning was not associated with objective cognitive outcomes.

Conclusions
The Subjective Assessment of Memory Impairment is a brief tool for measuring patient-rated memory function. Overall, patients did not report any change in subjective memory problems after ECT. Although perceptions of functional memory impairment and quality of life were related after ECT, there was no association with objectively assessed cognitive outcomes.