bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana
Authors: Alexandre Cristina M , Urton James R , Jean-Baptiste Ken , Huddleston John , Dorrity Michael W , Cuperus Josh T , Sullivan Alessandra M , Bemm Felix , Jolic Dino , Arsovski Andrej A , Thompson Agnieszka , Nemhauser Jennifer L , Fields Stan , Weigel Detlef , Bubb Kerry L , Queitsch Christin 
Published: December 2017

AbstractVariation in regulatory DNA is thought to drive phenotypic variation, evolution, and disease. Prior studies of regulatory DNA and transcription factors across animal species highlighted a fundamental conundrum: Transcription factor binding domains and cognate binding sites are conserved, while regulatory DNA sequences are not. It remains unclear how conserved transcription factors and dynamic regulatory sites produce conserved expression patterns across species. Here, we explore regulatory DNA variation and its functional consequences within Arabidopsis thaliana, using chromatin accessibility to delineate regulatory DNA genome-wide. Unlike in previous cross-species comparisons, the positional homology of regulatory DNA is maintained among A. thaliana ecotypes and less nucleotide divergence has occurred. Of the ∼50,000 regulatory sites in A. thaliana, we found that 15% varied in accessibility among ecotypes. Some of these accessibility differences were associated with extensive, previously unannotated sequence variation, encompassing many deletions and ancient hypervariable alleles. Unexpectedly, for the majority of such regulatory sites, nearby gene expression was unaffected. Nevertheless, regulatory sites with high levels of sequence variation and differential chromatin accessibility were the most likely to be associated with differential gene expression. Finally, and most surprising, we found that the vast majority of differentially accessible sites show no underlying sequence variation. We argue that these surprising results highlight the necessity to consider higher-order regulatory context in evaluating regulatory variation and predicting its phenotypic consequences.
Luminosity effect of O i 7771–5 triplet and atmospheric microturbulence in evolved A-, F-, and G-type stars
Authors: Takeda Yoichi , Jeong Gwanghui , Han Inwoo 
Published: December 2017

Abstract
It is known that the strength of neutral oxygen triplet lines at 7771–5 Å shows a luminosity effect in evolved A through G stars. However, its general behavior across the HR diagram is not yet well understood, since the applicability limit of the relations proposed by various previous work (tending to be biased toward supergiants) still remains unclear. Besides, our understanding on the nature of atmospheric micro-scale turbulence, which is considered to play a significant role (along with the non-LTE line intensification) for the cause of this effect, is still insufficient. Towards clarifying these problems, we carried out an extensive non-LTE spectrum-fitting analysis of O i 7771–5 lines for unbiased sample of 75 evolved A-, F,- and G-type stars over wide luminosity classes (from subgiants through supergiants) including rapid rotators, from which the total equivalent width (W77) was derived and the microturbulence (ξ) was determined by two different (profile- and abundance-based) methods for each star. While we confirmed that W77 tends to increase in the global sense as a star’s absolute magnitude (MV) becomes more luminous, distinctly different trends were found between lower-gravity (log g ≲ 2.5) and higher-gravity (log g ≳ 2.5) stars, in the sense that the MV vs. W77 formulas proposed by past studies are applicable only to the former supergiant group. In case of using W77 for empirical MV evaluation by such simple formulas, it is recommended to confine only to supergiants of −5 ≳ MV ≳ −10. Regarding the microturbulence significantly controlling W77, it roughly shows an increasing tendency with a decrease in surface gravity. However, the trend is not monotonic but rather intricate (e.g., hump, stagnation, or discontinuously large increase) depending on the stellar type and evolutionary stage.
Repercussions of the Coalition Governments Austerity Policy on Community Safety across Merseyside
Authors: Ojo Adegbola , Evans Richard , Karecha Jay 
Published: December 2017

Abstract
This article explains the depth and breadth of financial cuts endured by community safety organizations across Merseyside. The article provides a robust explanation of how cuts to funding impacted on the delivery of public safety priorities under the coalition government (2010–15). This study implemented a mixed-methods approach which entailed in-depth consultations with the major community safety stakeholders within the region. Results reveal that over the course of the immediate past parliament, Merseyside Local Authorities within the Liverpool City Region Combined Authority (LCRCA) and the police force area had to restructure staffing and service provision extensively in order to deliver efficiency savings of over £650 m. Budget cuts have had severe repercussions not just in terms of stakeholder’s capability to provide key services but also for the morale of their staff. We project a further 33% cutback in funding over the course of the current parliament though subsequent more favourable Government announcements suggest a more modest figure of up to 15%. This undoubtedly will result in the further streamlining of public services with potentially serious ramifications for levels of public safety.
Unlikely activists: building worker power under liberalization
Authors: Rothstein Sidney A 
Published: December 2017

AbstractThis article explains variation in the extent to which high skill, high wage workers are able to defend their job security in services-based production regimes. It compares two cases of downsizing at German multinational technology firms in the early 2000s, and shows how workers can protect their jobs against employer threats by building power in the workplace. I find that tech workers mobilize against downsizing when they creatively redeploy management’s discourse to demonstrate the potential effectiveness of collective action in a discourse that resonates with their occupational identity as technical experts. Highlighting the significance of discursive strategies to worker power in the information technology sector advances research on the comparative political economy of liberalization, which tends to view weak labor as a structural characteristic of the knowledge economy. While the transition from manufacturing- to services-led growth has weakened labor, with union density declining and national institutions becoming less effective, successful resistance to downsizing demonstrates that these historical developments relocate and recast workers’ power resources, rather than destroy them outright. This article focuses on political struggle in the workplace to offer empirical evidence that workers can develop considerable power even when they lack access to labor’s traditional resources.
Mechanisms of vascular comorbidity in autoimmune diseases
Authors: Nagy György , Németh Nóra , Buzás Edit I 
Published: December 2017

Purpose of review
Persuasive statistics support the clinical observation that because of cardiovascular comorbidities patients with inflammatory joint disease die significantly earlier despite anti-inflammatory therapy.

Recent findings
The reason for this earlier death is multifactorial and involves a combination of a complex genetic background, environmental influences, classical cardiovascular risk factors and the impact of anti-inflammatory therapy. We will describe the importance of several new mechanisms, especially the diverse intercellular communication routes including extracellular vesicles and microRNAs that support the development of cardiovascular comorbidities.

Summary
The aim of this review is to give an updated overview about the known risk factors in the development of cardiovascular comorbidities with the latest insights about their mechanism of action. Furthermore, the impact of newly identified risk factors and significance will be discussed.
Propofol Related Infusion Syndrome: Ultrastructural Evidence for a Mitochondrial Disorder
Authors: Vollmer Jörg-Peter , Haen Susanne , Wolburg Hartwig , Lehmann Rainer , Steiner Jochen , Reddersen Silke , Fend Falko , Fallier-Becker Petra 
Published: December 2017

Objective:
The objective of this report of a fatal propofol-related infusion syndrome in a young adult was to present—to our knowledge for the first time—direct ultrastructural evidence for the central role of mitochondrial damage in the pathogenesis of this syndrome.

Data Sources:
Histological and electron microscopical analysis of liver, skeletal, and heart muscle obtained by autopsy and blood obtained from patient.

Study Selection:
Case report.

Data Extraction:
In addition to conventional macroscopical and histological investigations, electron-microscopical analysis of myocardial- and skeletal muscle and liver tissue obtained at autopsy from a young man was performed in order to search for ultrastructural changes of mitochondria. Acylcarnitine concentrations of his blood were determined by ultra-high performance liquid chromatography mass spectrometry.

Data Synthesis:
A 19-year-old male was admitted with acute left-side hemiparesis. The patient was intubated, then propofol infusion started, and a craniotomy was performed to remove an intracerebral hematoma. In the postoperative period, the patient presented with elevated intracranial pressure and brain edema. After repeat surgery, the patient showed impaired systolic left ventricular function, increasing fever, anuria, hyperkalemia, and metabolic acidosis, and he finally expired. Electron microscopy revealed dark, electron dense amorphous structures associated with mitochondria in heart muscle and liver tissue obtained at autopsy. Peripheral blood analysis revealed increased levels of acetyl-, propionyl-, butyryl-, malonyl-, and valeryl-carnitine as an indicator for propofol-related infusion syndrome, as well as for propofol-mediated inhibition of free fatty acid uptake into mitochondria, affecting beta-oxidation.

Conclusions:
Electron dense bodies found in association with mitochondria in muscle and liver cells probably correspond to accumulation of free fatty acid provide direct morphological evidence for the mitochondrial damage in propofol-related infusion syndrome.
Treatment of ALK-positive nonsmall cell lung cancer: recent advances
Authors: Thai Alesha A. , Solomon Benjamin J. 
Published: December 2017

Purpose of review
The review will highlight recent advances in development of ALK-TKIs and management of patients with ALK-positive nonsmall cell lung cancer.

Recent findings
There has been rapid progress in the use of targeted therapies for ALK-positive NSCLC. Since the discovery, development and approval of crizotinib in 2011, three second-generation ALK-TKIs, ceritinib, alectinib and brigatinib have been approved by the FDA. A range of newer generation ALK inhibitors with improved potency against ALK and against mutations that confer resistance to crizotinib are in clinical development.

Summary
Our review will discuss the recent phase III data with ceritinib and alectinib as well as clinical trials with other ALK inhibitors. We will also address two important issues in the management of ALK-positive NSCLC, prevention and treatment of brain metastases and management of emergent ALK-TKI resistance mechanisms.
Factors Influencing Various Aspects of Patients' Knowledge of Oral Anticoagulation
Authors: Pourafkari Leili , Baghbani-Oskouei Aidin , Taban-Sadeghi Mohammadreza , Salamzadeh Vida , Ghaffari Samad , Savadi-Oskouei Safa , Nader Nader D. 
Published: December 2017

Objectives:
To identify and examine individual characteristics and socioeconomic factors that contribute to the knowledge of patients who receive warfarin anticoagulation.

Methods:
All patients treated using warfarin for anticoagulation were enrolled during a 6-month period at a university-affiliated cardiac clinic. All relevant demographic and clinical information were collected and the Anticoagulation Knowledge Assessment (AKA) questionnaire consisting of 29 questions was administered. After completion, the questionnaires were scored and the percent correct answers were analyzed for overall scores, as well as the following categories: drug/food interactions, pharmacological knowledge, recognition of complications, and patient compliance. Multiple linear regression analysis was used to identify the contributing factors to the knowledge level of the patients in each category.

Results:
One hundred fifty patients (79 men and 71 women) with a median age of 61.5 years completed the AKA questionnaire. The average overall score was 29.3%. Living alone (P = 0.008), higher levels of education (P = 0.001), and durations of ≥3 years of warfarin therapy (P = 0.018) positively impacted overall AKA scores.

Conclusions:
Socioeconomic factors and level of general education remain the most important elements determining the patient awareness of therapeutic goals, possible drug/food interaction, recognition of adverse effects, and compliance of warfarin treatment.
Comparison of In Vivo Confocal Microscopy, PCR and Culture of Corneal Scrapes in the Diagnosis of Acanthamoeba Keratitis
Authors: Goh Joanne W. Y. , Harrison Rhys , Hau Scott , Alexander Claire L. , Tole Derek M. , Avadhanam Venkata S. 
Published: December 2017

Purpose:

Acanthamoeba keratitis (AK) is an uncommon but serious corneal infection, in which delayed diagnosis carries a poor prognosis. Conventional culture requires a long incubation period and has low sensitivity. Polymerase chain reaction (PCR) and in vivo confocal microscopy (IVCM) are available alternative diagnostic modalities that have increasing clinical utility. This study compares confocal microscopy, PCR, and corneal scrape culture in the early diagnosis of AK.

Methods:
We reviewed the case notes of patients with a differential diagnosis of AK between June 2016 and February 2017 at the Bristol Eye Hospital, United Kingdom. Clinical features at presentation, and results of IVCM, PCR, and corneal scrape cultures were analyzed.

Results:
A total of 25 case records were reviewed. AK was diagnosed in 14 patients (15 eyes). Based on the definition of “definite AK,” the diagnostic sensitivities of IVCM, PCR, and corneal scrape cultures were 100% [95% confidence interval (CI), 63.1%–100%], 71.4% (95% CI, 41.9%–91.6%) and 33.3% (95% CI, 9.9%–65.1%), respectively. The 3 methods showed a specificity of 100% and a positive predictive value of 100%. Using a reference standard of only positive corneal cultures, IVCM, and PCR had a sensitivity of 100% (95% CI, 29.2%–100%) and 75% (95% CI, 19.4%–99.4%), respectively.

Conclusions:
All 3 diagnostic tests are highly specific, and a positive test result is highly predictive of disease presence. IVCM is both highly sensitive and specific when performed by an experienced operator. PCR is a useful adjunct in the diagnosis of AK because of its wider availability compared with IVCM, and it may be used in combination with IVCM for microbiologic confirmation.
Emergency Department Burden of Gastroparesis in the United States, 2006 to 2013
Authors: Hirsch William , Nee Judy , Ballou Sarah , Petersen Travis , Friedlander Daniel , Lee Ha-Neul , Cheng Vivian , Lembo Anthony 
Published: December 2017

Background and Aims:
Gastroparesis, a chronic gastrointestinal disorder defined by delayed stomach emptying in the absence of obstruction, is often associated with frequent and costly visits to the emergency department (ED). The aim of this study was to analyze trends in gastroparesis-related ED visits from 2006 to 2013.

Materials and Methods:
Patients with a primary diagnosis of gastroparesis were identified from the Nationwide Emergency Department Sample (NEDS), the largest publicly available ED all-payer representative database in the United States. ED visits, admission rates, duration of hospitalizations, and charges were compiled. Patients with a secondary diagnosis of diabetes mellitus were analyzed as a subgroup.

Results:
The number of ED visits for gastroparesis as a primary diagnosis in the United States increased from 15,459 in 2006 to 36,820 in 2013, an increase from 12.9 to 27.3 per 100,000 ED visits. The total charges associated with these ED visits and subsequent admissions increased from $286 million to $592 million. In contrast, admission rates through the ED decreased by 22%, procedure rates decreased by 6.2%, and the mean length of stay was shortened by 0.6 days. ED visits for patients with diabetic gastroparesis increased from 5696 to 14,114, an increase from 4.7 to 10.5 per 100,000 ED visits, with an increase in total associated charges for ED visits and subsequent admissions from $84 million to $182 million.

Conclusions:
The number of ED visits and associated charges for a primary diagnosis of gastroparesis with or without a secondary diagnosis of diabetes mellitus rose significantly from 2006 to 2013.
Changes in the World Health Organization 2016 classification of myeloid neoplasms everyone should know
Authors: Hasserjian Robert P. 
Published: December 2017

Purpose of review
This review highlights the main changes in the revised 2016 WHO classification of myeloid neoplasms (published in 2017) that impact diagnosis and ultimately impact management of patients with these diseases.

Recent findings
The revision was based on data accumulated since the 2008 WHO classification, much of which relate to new molecular genetic information about these neoplasms. This massive recent influx of data concerning the significance of pathogenic mutations has affected all myeloid neoplasm categories. The new information has been incorporated as part of the diagnostic criteria of many diseases and has led to the creation of new provisional entities defined by genetic features. Germline mutations that predispose to myeloid neoplasms are also emerging as important findings that impact disease classification.

Summary
The growing body of genetic data have not only altered the classification of myeloid neoplasms, but are also impacting patient management. Genetically-defined disease categories have characteristic prognoses and predicted clinical behavior. Some mutations are associated with responsiveness to certain therapies, including those that target relevant oncogenes. The disease categories in the new classification facilitate the application of risk-adapted therapy based on the most recently available data.
External Volume Expansion Up-Regulates CXCL12 Expression and Enhances Mesenchymal Stromal Cell Recruitment toward Expanded Prefabricated Adipose Tissue in Rats
Authors: Qin Zijin , Cai Junrong , Zhou Tao , Yuan Yi , Gao Jianhua , Dong Ziqing 
Published: December 2017

Background:
External volume expansion devices are effective for adipose tissue regeneration. However, the detailed mechanisms by which external volume expansion devices induce adipose tissue regeneration remain unclear.

Methods:
An external volume expansion device was used to construct expanded prefabricated adipose tissue in a rat model. CXCL12 levels in local exudate and serum were measured by enzyme-linked immunosorbent assay, and CXCL12 expression in adipose tissue was assessed immunohistochemically. Fluorescent dye (CM-DiI)–labeled bone marrow–derived mesenchymal stromal cells and labeled mesenchymal stromal cells pretreated with the CXCR4 antagonist AMD3100 were transplanted into rats and tracked in vivo by fluorescence imaging.

Results:
CXCL12 levels in local exudate and serum peaked 2 and 7 days, respectively, after external volume expansion device application. CXCL12+ cell counts were significantly higher in the external volume expansion than in the control group. These CXCL12+ cells were mainly columnar or cuboidal and began to express peroxisome proliferator-activated receptor γ on day 9. CM-DiI–labeled mesenchymal stromal cells were successfully recruited to the expanded prefabricated adipose tissue, a process partly inhibited by the CXCR4 antagonist AMD3100. These recruited CM-DiI–labeled mesenchymal stromal cells were found among the CXCL12+ columnar cells.

Conclusions:
External volume expansion devices enhance CXCL12 expression levels, especially in columnar and cuboidal cells. The CXCL12/CXCR4 pathway is involved in recruiting circulating mesenchymal stromal cells to participate in adipose regeneration. These findings may reveal the mechanism underlying external volume expansion and provide insights into the refinement of these devices.
CERAD Neuropsychological Battery–Arabic Version: Regression-Based and Stratified Normative Data and Effects of Demographic Variables on Cognitive Performance in Older Omanis
Authors: Alobaidy Ammar , Al-Sinawi Hamed , Al-Asmi Abdullah , Al-Adawi Samir , Mohamed Essa Musthafa , El-Okl Mohamed , Jeyaseelan Lakshmanan , Alsawafi Lamees , Almawali Malak , Alabri Balqees , Alhamrashdi Hajer 
Published: December 2017

Background and Objectives:
Normative data on cognitive performance for the Omani population are scarce. In this study, we tested a sample of older (≥50 years) community-dwelling Omanis on the Consortium to Establish a Registry for Alzheimer’s Disease neuropsychological battery–Arabic version (CERAD-ArNB). We analyzed the participants’ cognitive performance and how it was affected by their sex, age, and level of education.

Methods:
We enrolled 150 older Arabic-speaking Omanis from March 2014 to June 2015. Most of the participants were visitors to patients admitted to a tertiary referral center in the Sultanate of Oman. All participants underwent screening to ensure normal cognitive function before taking the CERAD-ArNB. We used multiple regression analysis and stratification according to demographic variables to illustrate the normative data.

Results:
A total of 125 participants, 65 men (52%) and 60 women (48%), met the inclusion criteria and completed the testing. Multiple regression and univariate analyses showed that although sex and age significantly affected cognitive performance on some CERAD-ArNB subtests, education level had by far the greatest effect.

Conclusions:
Lower education level was associated with poorer CERAD-ArNB performance in a sample of cognitively normal Omanis aged 50 years and older. The normative data obtained from this study will help clinicians correctly interpret cognitive performance in the Omani elderly population, and probably in other, culturally similar Arabic-speaking communities.