bluuebunny/crossref_metadata_2025_split huggingface dataset:
BatchQC: interactive software for evaluating sample and batch effects in genomic data
Authors: Manimaran Solaiappan , Selby Heather Marie , Okrah Kwame , Ruberman Claire , Leek Jeffrey T. , Quackenbush John , Haibe-Kains Benjamin , Bravo Hector Corrada , Johnson W. Evan 
Published: August 2016

Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. There are several existing batch adjustment tools for ‘-omics’ data, but they do not indicate a priori whether adjustment needs to be conducted or how correction should be applied. We present a software pipeline, BatchQC, which addresses these issues using interactive visualizations and statistics that evaluate the impact of batch effects in a genomic dataset. BatchQC can also apply existing adjustment tools and allow users to evaluate their benefits interactively. We used the BatchQC pipeline on both simulated and real data to demonstrate the effectiveness of this software toolkit.
Availability and Implementation: BatchQC is available through Bioconductor: http://bioconductor.org/packages/BatchQC and GitHub: https://github.com/mani2012/BatchQC.
Contact: wej@bu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
ReadXplorer 2—detailed read mapping analysis and visualization from one single source
Authors: Hilker Rolf , Stadermann Kai Bernd , Schwengers Oliver , Anisiforov Evgeny , Jaenicke Sebastian , Weisshaar Bernd , Zimmermann Tobias , Goesmann Alexander 
Published: August 2016

Motivation: The vast amount of already available and currently generated read mapping data requires comprehensive visualization, and should benefit from bioinformatics tools offering a wide spectrum of analysis functionality from just one source. Appropriate handling of multiple mapped reads during mapping analyses remains an issue that demands improvement.
Results: The capabilities of the read mapping analysis and visualization tool ReadXplorer were vastly enhanced. Here, we present an even finer granulated read mapping classification, improving the level of detail for analyses and visualizations. The spectrum of automatic analysis functions has been broadened to include genome rearrangement detection as well as correlation analysis between two mapping data sets. Existing functions were refined and enhanced, namely the computation of differentially expressed genes, the read count and normalization analysis and the transcription start site detection. Additionally, ReadXplorer 2 features a highly improved support for large eukaryotic data sets and a command line version, enabling its integration into workflows. Finally, the new version is now able to display any kind of tabular results from other bioinformatics tools.
Availability and Implementation: http://www.readxplorer.org
Contact: readxplorer@computational.bio.uni-giessen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Currents of Neo-Liberalism: British Political Ideologies and the New Right, c.1955–1979
Authors: Jackson Ben 
Published: August 2016

Abstract
This article investigates the emergence of neo-liberalism in Britain and its intellectual relationship with each of the three main British political ideologies. The article distinguishes between different currents of neo-liberalism that have been absorbed into British political thought, and shows that this process to some extent pre-dated the electoral success of Thatcherism in the 1980s. The article further suggests that labelling recent British political discourse as unvarnished ‘neo-liberalism’, while at times analytically useful, simplifies a more complicated picture, in which distinctively neo-liberal ideas have been blended in different ways into the ideologies of British Liberalism, Conservatism and even Labour socialism. The article therefore turns the spotlight on a more obscure aspect of the making of British neo-liberalism by exploring how politicians and intellectuals of varying partisan stripes generated policy discourses that presented neo-liberal ideas as an authentic expression of their own ideological traditions. Perhaps the most surprising finding of this article, then, is that neo-liberalism, although frequently characterised as rigid and dogmatic, has in fact proved itself to be a flexible and adaptable body of ideas, capable of colonising territory right across the political spectrum.
A mixed methods study of clinical information availability in obstetric triage and prenatal offices
Authors: Meyerhoefer Chad D , Sherer Susan A , Deily Mary E , Chou Shin-Yi , Peng Lizhong , Hu Tianyan , Nihen Marion , Sheinberg Michael , Levick Donald 
Published: August 2016

Objective: To determine the effect of availability of clinical information from an integrated electronic health record system on pregnancy outcomes at the point of care.
Materials and methods: We used provider interviews and surveys to evaluate the availability of pregnancy-related clinical information in ambulatory practices and the hospital, and applied multiple regression to determine whether greater clinical information availability is associated with improvements in pregnancy outcomes and changes in care processes. Our regression models are risk adjusted and include physician fixed effects to control for unobservable characteristics of physicians that are constant across patients and time.
Results: Making nonstress test results, blood pressure data, antenatal problem lists, and tubal sterilization requests from office records available to hospital-based providers is significantly associated with reductions in the likelihood of obstetric trauma and other adverse pregnancy outcomes. Better access to prenatal records also increases the probability of labor induction and decreases the probability of Cesarean section (C-section). Availability of lab test results and new diagnoses generated in the hospital at ambulatory offices is associated with fewer preterm births and low-birth-weight babies.
Discussion and conclusions: Increased availability of specific clinical information enables providers to deliver better care and improve outcomes, but some types of clinical data are more important than others. More available information does not always result from automated integration of electronic records, but rather from the availability of the source records. Providers depend upon information that they trust to be reliable, complete, consistent, and easily retrievable, even if this requires multiple interfaces.
A clinical care pathway to improve the acute care of patients with glioma
Authors: Riblet Natalie B.V. , Schlosser Evelyn M. , Snide Jennifer A. , Ronan Lara , Thorley Katherine , Davis Melissa , Hong Jennifer , Mason Linda P. , Cooney Tobi J. , Jalowiec Lanelle , Kennedy Nancy L. , Richie Sabrina , Nalepinski David , Fadul Camilo E. 
Published: August 2016

AbstractBackgroundPatients with glioma are at increased risk for tumor-related and treatment-related complications. Few guidelines exist to manage complications through supportive care. Our prior work suggests that a clinical care pathway can improve the care of patients with glioma.MethodsWe designed a quality improvement (QI) project to address the acute care needs of patients with gliomas. We formed a multidisciplinary team and selected 20 best-practice measures from the literature. Using a plan-do-study-act framework, we brainstormed and implemented various improvement strategies starting in October 2013. Statistical process control charts were used to assess progress.ResultsRetrospective data were available for 12 best practice measures. The baseline population consisted of 98 patients with glioma. Record review suggested wide variation in performance, with compliance ranging from 30% to 100%. The team hypothesized that lack of process standardization may contribute to less-than-ideal performance. After implementing improvement strategies, we reviewed the records of 63 consecutive patients with glioma. The proportion of patients meeting criteria for 12 practice measures modestly improved (65% pre-QI; 76% post-QI, P > .1). Unexpectedly, a higher proportion of patients were readmitted within 30 days of hospital discharge (pre-QI: 10%; post-QI: 17%, P > .1). Barriers to pathway development included difficulties with transforming manual measures into electronic data sets.ConclusionsCreating evidence-based clinical care pathways for addressing the acute care needs of patients with glioma is feasible and important. There are many challenges, however, to developing sustainable systems for measuring and reporting performance outcomes overtime.
Aurora candidates from the chronicle of Qíng dynasty in several degrees of relevance
Authors: Kawamura Akito D. , Hayakawa Hisashi , Tamazawa Harufumi , Miyahara Hiroko , Isobe Hiroaki 
Published: August 2016

Abstract
We present the result of a survey of sunspots and auroras in Qíngshǐgǎo (清史稿), a draft chronicle of Qíng dynasty, for the period of 1559–1912 CE. This is a sequel to a series of works surveying historical sunspot and aurora records, and providing online data to the scientific community regarding the attained results. In total of this Qíngshǐgǎo survey, we found 111 records of night-sky luminous events with such keywords as vapor (氣, qì), cloud (雲, yún), and light (光, guāng), which may indicate auroras as well as some other phenomena. Similarly, a keyword survey for sunspots was conducted, but no sunspot record was found. In comparison with the aurora records in the western world, we found that 14 of the 111 records have a corresponding record of simultaneous observation in the western world, and hence are very likely to be aurora. In order to investigate the likeliness of the remainder of the record being aurora, we calculated the lunar age and the phase of a solar cycle for each record. After these calculations, a notable fraction of these records clustered near the full moon were to be found statistically doubtful in considerations with atmospheric optics; meanwhile, a few records of observations near the new moon could be more likely interpreted as being auroras, including three records during the Maunder minimum.
A Meta-Analysis of the Worldwide Prevalence of Pica during Pregnancy and the Postpartum Period
Authors: Fawcett E.J. , Fawcett J.M. , Mazmanian D. 
Published: August 2016

(Int J Gynaecol Obstet. 2016;133(3):277–283)
Pica, the purposeful consumption of nonfood or non-nutritive substances, is commonly reported in women during the period surrounding childbirth. However, the Diagnostic and Statistical Manual of Mental Disorders-5 does not provide a prevalence estimate for pica, and current prevalence estimates during pregnancy range from 0.007% in Denmark to 92.5% in Nigeria. In this meta-analysis, authors estimated the prevalence of pica in pregnant and postpartum populations and characterized potential contributing factors/moderators.
Prophylactic Intravenous Ephedrine to Minimize Fetal Bradycardia After Combined Spinal-epidural Labour Analgesia: A Randomized Controlled Study
Authors: Gambling D.R. , Bender M. , Faron S. , Glaser D. , Farrell T.R. 
Published: August 2016

(Can J Anaesth. 2015;62(11):1201–1208)
The combined spinal-epidural technique has many benefits, including rapid onset, superior first-stage analgesia, and the need for fewer supplemental doses when compared to a standard epidural. For these reasons, this technique is currently gaining in popularity. However, the combined spinal-epidural technique is also known to be associated with a risk of fetal bradycardia. The authors of this study attempted to determine whether the risk of this adverse outcome could be reduced by administering a prophylactic 10 mg dose of intravenous ephedrine. They also evaluated the rate of urgent cesarean delivery, the need for supplemental doses of ephedrine, maternal blood pressure, uterine hypertonus and tachysystole, as well as fetal heart rate patterns before and after the combined spinal-epidural.
Recent Increases in the U.S. Maternal Mortality Rate
Authors: MacDorman Marian F. , Declercq Eugene , Cabral Howard , Morton Christine 
Published: August 2016

OBJECTIVE:
To develop methods for trend analysis of vital statistics maternal mortality data, taking into account changes in pregnancy question formats over time and between states, and to provide an overview of U.S. maternal mortality trends from 2000 to 2014.

METHODS:
This observational study analyzed vital statistics maternal mortality data from all U.S. states in relation to the format and year of adoption of the pregnancy question. Correction factors were developed to adjust data from before the standard pregnancy question was adopted to promote accurate trend analysis. Joinpoint regression was used to analyze trends for groups of states with similar pregnancy questions.

RESULTS:
The estimated maternal mortality rate (per 100,000 live births) for 48 states and Washington, DC (excluding California and Texas, analyzed separately) increased by 26.6%, from 18.8 in 2000 to 23.8 in 2014. California showed a declining trend, whereas Texas had a sudden increase in 2011–2012. Analysis of the measurement change suggests that U.S. rates in the early 2000s were higher than previously reported.

CONCLUSION:
Despite the United Nations Millennium Development Goal for a 75% reduction in maternal mortality by 2015, the estimated maternal mortality rate for 48 states and Washington, DC, increased from 2000 to 2014; the international trend was in the opposite direction. There is a need to redouble efforts to prevent maternal deaths and improve maternity care for the 4 million U.S. women giving birth each year.
Atypical Endometrial Polyps and Concurrent Endometrial Cancer
Authors: de Rijk Simone R. , Steenbergen Marlie E. , Nieboer Theodoor E. , Coppus Sjors F. 
Published: August 2016

OBJECTIVE:
To estimate the risk of concurrent endometrial cancer in nonpolypoid endometrium when atypia was diagnosed within an endometrial polyp.

DATA SOURCES:
MEDLINE, EMBASE, Web of Science, and ClinicalTrials.gov were searched for studies published between 1990 and January 2015 in which 1) women with atypical hyperplastic endometrial polyps underwent a consecutive hysterectomy; or 2) the natural behavior of endometrium with concurrent atypical endometrial polyps was evaluated.

METHODS OF STUDY SELECTION:
Studies were selected when at least one patient within each study was initially diagnosed with an atypical endometrial polyp for which follow-up pathology was available.

RESULTS:
Broad searches yielded 2,922 authentic citations, 307 met criteria for full-text evaluation, and 10 met inclusion criteria. Two authors independently reviewed articles and consensus was reached. The final selection included eight retrospective studies reporting on concurrent endometrial cancer in case of atypical endometrial polyps and two follow-up studies on patients conserving their uterus after hysteroscopic resection of atypical endometrial polyps. In total, 127 patients were included with an initial diagnosis of atypical endometrial hyperplasia within polyps. Meta-analysis showed a pooled risk estimate of 5.6% (95% confidence interval [CI] 0.2–17.6%) on concurrent endometrial cancer after resection of an atypical endometrial polyp.

CONCLUSION:
The pooled risk estimate of 5.6% (95% CI 0.2–17.6%) on endometrial cancer when atypia is found within an endometrial polyp differs from the well-established risk of nonpolypoid atypical endometrial hyperplasia on endometrial cancer of up to 42%. This risk of endometrial cancer is important in the process of shared decision-making regarding follow-up and further treatment.
Salpingo-oophorectomy at the Time of Benign Hysterectomy
Authors: Evans Elizabeth Casiano , Matteson Kristen A. , Orejuela Francisco J. , Alperin Marianna , Balk Ethan M. , El-Nashar Sherif , Gleason Jonathan L. , Grimes Cara , Jeppson Peter , Mathews Cara , Wheeler Thomas L. , Murphy Miles ,   for the Society of Gynecologic Surgeons Systematic Review Group
Published: August 2016

OBJECTIVE:
To compare the long-term risks associated with salpingo-oophorectomy with ovarian conservation at the time of benign hysterectomy.

DATA SOURCES:
MEDLINE, ClinicalTrials.gov, and the Cochrane Central Register of Controlled Trials were searched from inception to January 30, 2015. We included prospective and retrospective comparative studies of women with benign hysterectomy who had either bilateral salpingo-oophorectomy (BSO) or conservation of one or both ovaries.

METHODS OF STUDY SELECTION:
Reviewers double-screened 5,568 citations and extracted eligible studies into customized forms. Twenty-six comparative studies met inclusion criteria. Studies were assessed for results, quality, and strength of evidence.

TABULATION, INTEGRATION, AND RESULTS:
Studies were extracted for participant, intervention, comparator, and outcomes data. When compared with hysterectomy with BSO, prevalence of reoperation and ovarian cancer was higher in women with ovarian conservation (ovarian cancer risk of 0.14–0.7% compared with 0.02–0.04% among those with BSO). Hysterectomy with BSO was associated with a lower incidence of breast and total cancer, but no difference in the incidence of cancer mortality was found when compared with ovarian conservation. All-cause mortality was higher in women younger than age 45 years at the time of BSO who were not treated with estrogen replacement therapy (hazard ratio [HR] 1.41, 95% confidence interval [CI] 1.04–1.92). Coronary heart disease (HR 1.26, 95% CI 1.04–1.54) and cardiovascular death were higher among women with BSO (HR 1.84, 95% CI 1.27–2.68), especially women younger than 45 years who were not treated with estrogen. Finally, there was an increase in the prevalence of dementia and Parkinson disease among women with BSO compared with conservation, especially in women younger than age 50 years. Clinical practice guidelines were devised based on these results.

CONCLUSION:
Bilateral salpingo-oophorectomy offers the advantage of effectively eliminating the risk of ovarian cancer and reoperation but can be detrimental to other aspects of health, especially among women younger than age 45 years.
Recent advances in dermatomyositis-specific autoantibodies
Authors: Fujimoto Manabu , Watanabe Rei , Ishitsuka Yosuke , Okiyama Naoko 
Published: August 2016

Purpose of review
In dermatomyositis, disease-specific autoantibodies now cover more than 70% of patients. These autoantibodies closely correlate with distinct clinical manifestations. In the past few years, extensive evidence has been accumulated on clinical significance of dermatomyositis-specific autoantibodies including autoantibodies against melanoma differentiation antigen 5 (MDA5), transcriptional intermediary factor 1 (TIF1), nuclear matrix protein 2 (NXP2), and small ubiquitin-like modifier activating enzyme (SAE).

Recent findings
Anti-MDA5 antibodies are found with high specificity in clinically amyopathic dermatomyositis presenting rapidly progressive interstitial lung disease (ILD) especially in Asian population. Similar tendency has been reported in the US/Europe, although the frequency of positivity and the type of ILD may differ. Anti-TIF1 antibodies are present in juvenile and adult dermatomyositis patients with close correlation with malignancy in adult population. Anti-NXP2 antibodies share similar phenotype with anti-TIF1 antibodies, except that anti-NXP2 antibodies are associated with calcinosis and severe muscle disease. Although numbers are still small, patients with anti-SAE antibodies tend to present skin disease first and then progress to muscle weakness with systematic symptoms including dysphagia. Moreover, distinct cutaneous manifestations and muscle histopathology findings for each autoantibody have been reported.

Summary
‘Autoantibody-based classification’ of dermatomyositis subsets is now a useful strategy for comprehending the heterogeneous spectrum of dermatomyositis.
Animal models of scleroderma: recent progress
Authors: Marangoni Roberta G. , Varga John , Tourtellotte Warren G. 
Published: August 2016

Purpose of review
We discuss recent advances in evaluating and optimizing animal models of systemic sclerosis (SSc). Such models could be of value for illuminating etiopathogenesis using hypothesis-testing experimental approaches, for developing effective disease-modifying therapies, and for uncovering clinically relevant biomarkers.

Recent findings
We describe recent advances in previously reported and novel animal models of SSc. The limitations of each animal model and their ability to recapitulate the pathophysiology of recognized molecular subsets of SSc are discussed. We highlight attrition of dermal white adipose tissue as a consistent pathological feature of dermal fibrosis in mouse models, and its relevance to SSc-associated cutaneous fibrosis.

Summary
Several animal models potentially useful for studying SSc pathogenesis have been described. Recent studies highlight particular strengths and weaknesses of selected models in recapitulating distinct features of the human disease. When used in the appropriate experimental setting, and in combination, these models singly and together provide a powerful set of in-vivo tools to define underlying mechanisms of disease and to develop and evaluate effective antifibrotic therapies.
Defining Futile and Potentially Inappropriate Interventions: A Policy Statement From the Society of Critical Care Medicine Ethics Committee
Authors: Kon Alexander A. , Shepard Eric K. , Sederstrom Nneka O. , Swoboda Sandra M. , Marshall Mary Faith , Birriel Barbara , Rincon Fred 
Published: August 2016

Objectives:
The Society of Critical Care Medicine and four other major critical care organizations have endorsed a seven-step process to resolve disagreements about potentially inappropriate treatments. The multiorganization statement (entitled: An official ATS/AACN/ACCP/ESICM/SCCM Policy Statement: Responding to Requests for Potentially Inappropriate Treatments in Intensive Care Units) provides examples of potentially inappropriate treatments; however, no clear definition is provided. This statement was developed to provide a clear definition of inappropriate interventions in the ICU environment.

Design:
A subcommittee of the Society of Critical Care Medicine Ethics Committee performed a systematic review of empirical research published in peer-reviewed journals as well as professional organization position statements to generate recommendations. Recommendations approved by consensus of the full Society of Critical Care Medicine Ethics Committees and the Society of Critical Care Medicine Council were included in the statement.

Measurements and Main Results:
ICU interventions should generally be considered inappropriate when there is no reasonable expectation that the patient will improve sufficiently to survive outside the acute care setting, or when there is no reasonable expectation that the patient’s neurologic function will improve sufficiently to allow the patient to perceive the benefits of treatment. This definition should not be considered exhaustive; there will be cases in which life-prolonging interventions may reasonably be considered inappropriate even when the patient would survive outside the acute care setting with sufficient cognitive ability to perceive the benefits of treatment. When patients or surrogate decision makers demand interventions that the clinician believes are potentially inappropriate, the seven-step process presented in the multiorganization statement should be followed. Clinicians should recognize the limits of prognostication when evaluating potential neurologic outcome and terminal cases. At times, it may be appropriate to provide time-limited ICU interventions to patients if doing so furthers the patient’s reasonable goals of care. If the patient is experiencing pain or suffering, treatment to relieve pain and suffering is always appropriate.

Conclusions:
The Society of Critical Care Medicine supports the seven-step process presented in the multiorganization statement. This statement provides added guidance to clinicians in the ICU environment.