bluuebunny/crossref_metadata_2025_split huggingface dataset:
multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions
Authors: Kang Guangliang , Du Li , Zhang Hong 
Published: June 2016

Abstract
Background
The growing complexity of biological experiment design based on high-throughput RNA sequencing (RNA-seq) is calling for more accommodative statistical tools. We focus on differential expression (DE) analysis using RNA-seq data in the presence of multiple treatment conditions.

Results
We propose a novel method, multiDE, for facilitating DE analysis using RNA-seq read count data with multiple treatment conditions. The read count is assumed to follow a log-linear model incorporating two factors (i.e., condition and gene), where an interaction term is used to quantify the association between gene and condition. The number of the degrees of freedom is reduced to one through the first order decomposition of the interaction, leading to a dramatically power improvement in testing DE genes when the number of conditions is greater than two. In our simulation situations, multiDE outperformed the benchmark methods (i.e. edgeR and DESeq2) even if the underlying model was severely misspecified, and the power gain was increasing in the number of conditions. In the application to two real datasets, multiDE identified more biologically meaningful DE genes than the benchmark methods. An R package implementing multiDE is available publicly at http://homepage.fudan.edu.cn/zhangh/softwares/multiDE.

Conclusions
When the number of conditions is two, multiDE performs comparably with the benchmark methods. When the number of conditions is greater than two, multiDE outperforms the benchmark methods.
Chemical characterisation of archaeological glasses from the Hellenistic site of Jebel Khalid, Syria by electron probe microanalysis
Authors: Reade Wendy J. , Privat Karen L. 
Published: June 2016

Abstract

Background
Jebel Khalid is a single period Hellenistic site on the west bank of the Euphrates River in northern Syria. The occupation of the site dates from the early 3rd century BCE until its abandonment in the late 70s BCE. The so-called Governor’s Palace, an administrative centre on the Acropolis of the site, overlooked this walled Greek garrison city. A considerable quantity of glass, predominantly drinking bowls, was excavated from this building complex. This study concerns the elemental analysis of glass samples from this assemblage by electron probe microanalysis (SEM-WDS).

Results
The preliminary analyses presented in this report reveal that the Jebel Khalid glasses are of the silica-soda-lime type fluxed with mineral soda, typical of late 1st millennium BCE glass composition. Manganese was employed as the chief decolourant. Glass compositions of monochrome bowls, core-formed and mosaic glass vessels are very similar, despite the different forms, colours and manufacturing techniques of the vessels.

Conclusions
While the production centre for the Jebel Khalid glass remains elusive, the similarity to other published Hellenistic glasses from Greek mainland sites, Rhodes, Tel Anafa in Israel, and Gordion in central Turkey, indicates a tightly controlled composition with comparable batch ingredients. Without more comparative material of this date from the Near East and Greece, it is difficult to determine whether production of the vessel glass from this Seleucid site in the Near East occurred in the Aegean region or the Syro-Palestinian Levant, or both. Vessel style and archaeological context lean towards an Aegean connection, but until more comparative glass is analysed, and trace element and isotope data are considered, questions of primary and secondary production remain unresolved.
Platelet activation and platelet–leukocyte interaction in generalized aggressive periodontitis
Authors: Zhan Yalin , Lu Ruifang , Meng Huanxin , Wang Xian’e , Hou Jianxia 
Published: June 2016

Abstract
Generalized aggressive periodontitis (GAgP) is an inflammatory disease of host response to bacterial challenge. To explore the role of platelets in host–microbial interactions in patients with periodontitis, 124 patients with GAgP and 57 healthy subjects were enrolled. Reliable indicators of subclinical platelet functional status, platelet count (PLT), platelet large cell ratio (PLCR), and mean platelet volume (MPV), were significantly lower in the GAgP group than in the control group and were negatively correlated with clinical periodontal parameters. The levels of important cytosolic protein in neutrophils, calprotectin (S100A8/A9) in plasma, and gingival crevicular fluid (GCF) were significantly higher in patients with GAgP compared with healthy subjects. Moreover, the GCF calprotectin level was negatively correlated with PLCR and MPV values. To explore the possible mechanisms of changes in platelet indices in periodontitis, flow cytometry analysis was performed, and patients with GAgP were found to have a higher status of platelet activation compared with healthy controls. Porphyromonas gingivalis (P. gingivalis) and recombinant human S100A8/A9 (rhS100A8/A9) induced platelet activation and facilitated platelet–leukocyte aggregate formation in whole blood of healthy subjects. In response to P. gingivalis and rhS100A8/A9, platelets from patients with GAgP increased activation and increased formation of platelet–leukocyte aggregates compared with those from healthy subjects. Platelet aggregates and platelets attached to leukocytes were found on gingival tissues from patients with GAgP, suggesting that decreased platelet size and count in the circulation might be related to consumption of large, activated platelets at inflamed gingiva. Platelets may have a previously unrecognized role in host response to periodontal infection.
South African Breast Cancer and HIV Outcomes Study: Methods and Baseline Assessment
Authors: Cubasch Herbert , Ruff Paul , Joffe Maureen , Norris Shane , Chirwa Tobias , Nietz Sarah , Sharma Vinay , Duarte Raquel , Buccimazza Ines , Čačala Sharon , Stopforth Laura W. , Tsai Wei-Yann , Stavsky Eliezer , Crew Katherine D. , Jacobson Judith S. , Neugut Alfred I. 
Published: June 2016

PurposeIn low- and middle-income, HIV-endemic regions of sub-Saharan Africa, morbidity and mortality from the common epithelial cancers of the developed world are rising. Even among HIV-infected individuals, access to antiretroviral therapy has enhanced life expectancy, shifting the distribution of cancer diagnoses toward non–AIDS-defining malignancies, including breast cancer. Building on our prior research, we recently initiated the South African Breast Cancer and HIV Outcomes study.MethodsWe will recruit a cohort of 3,000 women newly diagnosed with breast cancer at hospitals in high (average, 20%) HIV prevalence areas, in Johannesburg, Durban, Pietermaritzburg, and Empangeni. At baseline, we will collect information on demographic, behavioral, clinical, and other factors related to access to health care. Every 3 months in year 1 and every 6 months thereafter, we will collect interview and chart data on treatment, symptoms, cancer progression, comorbidities, and other factors.We will compare survival rates of HIV-infected and uninfected women with newly diagnosed breast cancer and their likelihood of receiving suboptimal anticancer therapy. We will identify determinants of suboptimal therapy and context-specific modifiable factors that future interventions can target to improve outcomes. We will explore molecular mechanisms underlying potentially aggressive breast cancer in both HIV-infected and uninfected patients, as well as the roles of pathogens, states of immune activation, and inflammation in disease progression.ConclusionOur goals are to contribute to development of evidence-based guidelines for the management of breast cancer in HIV-positive women and to improve outcomes for all patients with breast cancer in resource-constrained settings.
Fear of Treatments Surpasses Demographic and Socioeconomic Factors in Affecting Patients With Breast Cancer in Urban South Africa
Authors: Rayne Sarah , Schnippel Kathryn , Firnhaber Cynthia , Wright Kathryne , Kruger Deirdre , Benn Carol-Ann 
Published: June 2016

Purpose Breast cancer is the most common cause of cancer in women in South Africa, and often patients present late. There is little understanding of the psychosocial stresses affecting women with breast cancer in Africa. Methods A questionnaire was distributed to 263 patients with breast cancer at two sites (one government and one private facility) in Johannesburg. Self-reported levels of fear were recorded on summative scales and their relationship to demographic variables assessed through univariable and multivariable modified Poisson regression. Results Fears related to treatments and prognosis, particularly radiation, loss of hair, and loss of breast, were far stronger than those related to socioeconomic barriers. Relative risk (RR) of most fears was higher in women younger than age 40 years, including treatment affordability (RR, 1.80; 95% CI, 1.26 to 2.56), hair loss (RR, 1.48; 95% CI, 1.12 to 2.95), and surgery (RR, 1.31; 95% CI, 1.02 to 1.68). Difficulty taking time off work predicted fear of job loss (RR, 2.59; 95% CI, 1.59 to 4.21) and missing appointments because of transport (RR, 2.46; 95% CI, 1.52 to 3.96) or family commitments (RR, 2.46; 95% CI, 1.52 to 3.96). Women with dependents and black women were more afraid of dying (RR, 1.73; 95% CI, 1.03 to 2.90; and RR, 1.79; 95% CI, 1.33 to 2.24, respectively); however, socioeconomic status in this sample was a strong confounder of race and explained most of the racial differences in levels of fear. Conclusion The most significant fears around breast cancer were related to treatment modalities and adverse effects rather than transport, financial, or work concerns. Young age and job insecurity were predictive of increased fears. Education about treatments has a key role to play in improving access to breast cancer care in South Africa.
Low-Cost Simulation to Teach Anesthetists’ Non-Technical Skills in Rwanda
Authors: Skelton Teresa , Nshimyumuremyi Isaac , Mukwesi Christian , Whynot Sara , Zolpys Lauren , Livingston Patricia 
Published: June 2016

BACKGROUND:
Safe anesthesia care is challenging in developing countries where there are shortages of personnel, drugs, equipment, and training. Anesthetists’ Non-technical Skills (ANTS)—task management, team working, situation awareness, and decision making—are difficult to practice well in this context. Cesarean delivery is the most common surgical procedure in sub-Saharan Africa. This pilot study investigates whether a low-cost simulation model, with good psychological fidelity, can be used effectively to teach ANTS during cesarean delivery in Rwanda.

METHODS:
Study participants were anesthesia providers working in a tertiary referral hospital in Rwanda. Baseline observations were conducted for 20 anesthesia providers during cesarean delivery using the established ANTS framework. After the first observation set was complete, participants were randomly assigned to either simulation intervention or control groups. The simulation intervention group underwent ANTS training using low-cost high psychological fidelity simulation with debriefing. No training was offered to the control group. Postintervention observations were then conducted in the same manner as the baseline observations.

RESULTS:
The primary outcome was the overall ANTS score (maximum, 16). The median (range) ANTS score of the simulation group was 13.5 (11–16). The ANTS score of the control group was 8 (8–9), with a statistically significant difference (P = .002). Simulation participants showed statistically significant improvement in subcategories and in the overall ANTS score compared with ANTS score before simulation exposure.

CONCLUSIONS:
Rwandan anesthesia providers show improvement in ANTS practice during cesarean delivery after 1 teaching session using a low-cost high psychological fidelity simulation model with debriefing.
Aurora A kinase regulates proper spindle positioning in C. elegans and in human cells
Authors: Kotak Sachin , Afshar Katayon , Busso Coralie , Gönczy Pierre 
Published: June 2016

ABSTRACT
Accurate spindle positioning is essential for error-free cell division. The one-cell Caenorhabditis elegans embryo has proven instrumental for dissecting mechanisms governing spindle positioning. Despite important progress, how the cortical forces that act on astral microtubules to properly position the spindle are modulated is incompletely understood. Here, we report that the PP6 phosphatase PPH-6 and its associated subunit SAPS-1, which positively regulate pulling forces acting on spindle poles, associate with the Aurora A kinase AIR-1 in C. elegans embryos. We show that acute inactivation of AIR-1 during mitosis results in excess pulling forces on astral microtubules. Furthermore, we uncover that AIR-1 acts downstream of PPH-6–SAPS-1 in modulating spindle positioning, and that PPH-6–SAPS-1 negatively regulates AIR-1 localization at the cell cortex. Moreover, we show that Aurora A and the PP6 phosphatase subunit PPP6C are also necessary for spindle positioning in human cells. There, Aurora A is needed for the cortical localization of NuMA and dynein during mitosis. Overall, our work demonstrates that Aurora A kinases and PP6 phosphatases have an ancient function in modulating spindle positioning, thus contributing to faithful cell division.
Resource Development Opportunities for the Association of Leadership Educators: Phase One
Authors: Noble Donnette J. , Matesi Lyna , Breen Jennifer Moss , Horstmeier Robin Peiter , Anderson Dennis M. , Allen Stuart , Pedigo Leslie 
Published: June 2016

This application brief shares Phase One of an action research project for the Association of Leadership Educators. This project demonstrates how a member-based association can successfully engage its members in terms of identifying needs, defining strategic priorities, and detecting resource development opportunities. This body of work has various implications for leadership and leadership education and provides a model that other associations can replicate to engage in resource development.
A brief history of the association’s first 25 years since its inception is provided in this brief and the work of the Resource Development Committee is presented. The findings from two focus group sessions conducted during the 2014 annual conference are highlighted and the paper closes with a discussion of how the Resource Development Committee can, through specific initiatives, support the association’s wellbeing and strategic direction. By sharing the rationale behind the Association of Leadership Educators board of directors’ decision to invest in a resource development strategy, other association leaders can access and implement a similar action plan to generate additional revenue which, in turn, can be used to enhance association membership services.
Recognition and management of psychological distress in HF
Authors: Irvine Bruce , Mojee Mira , Jury Rebecca , Allan Lesley , Cox Sally , Sharp John , Hawkins Ingrid 
Published: June 2016

Background: Evidence suggests psychological distress is common in people with heart failure (HF) and associated with adverse clinical and quality of life outcomes. Recent national guidelines highlight that there is a need to improve psychological care in HF. Purpose: This retrospective study of 11 917 clinic letters written by specialist heart failure nurses (SHFNs) contained within 2488 patient files aimed to benchmark documented recognition and management of psychological distress in HF patients by SHFNs in 11 NHS Scotland health boards. Conclusions: The study indicated SHFN case note documentation of recognition and management of psychological distress in HF fell dramatically short of clinical guidelines. Few people with HF are recognised as having associated psychological distress and fewer still are accessing evidence-based interventions. Clinical implications: Improvement to the documentation, identification and management of psychological distress in people with HF by SHFNs should be supported by training delivered by accredited psychology practitioners. There is a need for services to have clinical pathways in place to support any increases in identification of psychological distress in HF.
Pedagogy in citizenship education research: A comparative perspective
Authors: Hahn Carole L. 
Published: June 2016

Abstract
The author of this article argues for using a comparative and international perspective to understand the role of pedagogy in civic education. Drawing on her own research in England, Germany and Denmark, the author demonstrates that pedagogical cultures vary. Next, she discusses what international researchers have learned about civic education pedagogy from the large cross-national assessments and what individual researchers have learned from small case studies within diverse countries, such as Canada, the United Kingdom, Australia, the Philippines and Singapore. She then discusses recent research programmes in the United States that have yielded important information related to pedagogy, including the use of discussion, simulations and digital/social media. The author concludes by proposing a list of needed comparative and international research on civic education pedagogy.
Is Student Union a tokenism of student participation in school governance?
Authors: Leung Yan Wing , Yuen Timothy Wai Wa , Cheng Eric Chi Keung , Guo Chunlan 
Published: June 2016

Abstract
This article is a report on part of a larger research on student participation in school governance in the Hong Kong context. It addresses the question ‘Is the Student Union a tokenism of student participation in school governance in the context of Hong Kong?’. The research adopts a mixed methodology comprising both quantitative and qualitative methods. For the quantitative study, 3209 valid student questionnaires from 51 secondary schools of different backgrounds were collected. For the qualitative study, four schools of different levels of student participation were involved in in-depth case studies. Semi-structured interviews and field observations with teachers and students were conducted to collect qualitative data. The study revealed that from the questionnaire, the ‘one student, one vote’ policy was an apparently fair, transparent and democratic procedure for Student Union elections, and gave the Student Union a positive image in relation to student participation. However, the in-depth case studies revealed that these were superficial perceptions. Instead, it was found that schools shared very limited powers with their Student Unions, where the Student Union would have power only in trivial school operational matters. The ultimate, real power was in the hands of school authorities, seriously limiting the influence of student participation. Our studies further revealed that whether students were satisfied with this disempowering situation or not, most of them had become ‘positive and passive’. This was because they had been socialized to accept the status quo, without expressing dissident voices, as they did not want to oppose the caring school ethos that they valued. In summary, Student Unions in Hong Kong are, in general, close to tokenism, a representative mechanism that cannot take meaningful action to bring forth genuine changes in important school matters. This may have negative impacts on students’ citizenship development, and ends up with cultivating students to be non-questioning, non-participatory, cynical, passive and docile citizens.
Late Oligocene macrofloras from fluviatile siliciclastic facies of the Köln Formation at the south-eastern border of the Lower Rhine Embayment (North Rhine-Westphalia, Germany)
Authors: Winterscheid Heinrich , Kvaček Zlatko 
Published: June 2016

Abstract The leaf remains described herein came from the oldest sites of the Cainozoic deposits in the Lower Rhine Embayment, located in the Siebengebirge Volcanic Field at the south-eastern border of this basin, in the area of Siebengebirge and vicinity. These revisited floras are bound to pre-volcanic siliciclastic facies of the Siebengebirge Mts., interpreted as marginal facies of the Köln Formation. Chronostratigraphically they are assigned to the late Oligocene (Chattian). The described leaf remains are partially compressions with preserved epidermal anatomy, and therefore highly useful for systematic determination of leaf impressions recovered from other localities of siliciclastic facies. On account of the epidermal characteristics of leaf compressions varying in gross morphology, the previously determined taxa Quercus goepperti, Laurus phoeboides, and Persea speciosa all fall into the abundantly represented Eotrigonobalanus furcinervis. The siliciclastic deposits originated in coastal and flood plain areas within fluviatile environments of variable deposition energy. Remains of Taxodium dubium, Eotrigonobalanus furcinervis, Populus germanica, and Daphnogene cinnamomifolia dominate among the recovered fossils. The general aspects of this plant assemblage correspond, together with their sedimentary settings, to riparian forest vegetation with mesophytic elements.
Method of estimating the exposure of the natural environment to 50 Hz electric and magnetic fields in power systems with distributed and centralized generations
Authors: Zeńczak Michał 
Published: June 2016

Abstract
The development of a distributed generation will influence the structure of the power transmission and distribution network. Distributed sources have lower power and therefore the lines of lower voltage are used. Therefore, the electric field intensity near such lines is lower. On the other hand magnetic field intensity may prove essential. The main aim of the paper is to present a method estimating the “ballast” of the natural environment at 50 Hz electric and magnetic fields in the power system, with distributed and centralized generation in real operating conditions.
Impact of the sleeve thickness on the armature eccentricity in a solenoid valve
Authors: Goraj Robert 
Published: June 2016

Abstract
Most studies on solenoid valves (SVs) assumed that the armature is concentrically positioned in the sleeve. Under this assumption the transversal component of the magnetic force is equal zero. The article presents an analytical calculation model for the estimation of the armature eccentricity. Using this model the eccentricity was calculated as a function of the sleeve thickness and the hydraulic clearance between the armature and the sleeve. After finding the eccentricity also the permeance of the radial air gap was calculated. This permeance has a direct influence on the drop of the magnetomotive force in the magnetic circuit and finally influences also the axial component of the magnetic force. In the article a calculation of both transversal and axial components of the magnetic force was carried out and presented in the appendix to the article.
Epidemiological trends of hormone-related cancers in Slovenia
Authors: Zadnik Vesna , Krajc Mateja 
Published: June 2016

AbstractThe incidence of hormone-related cancers tends to be higher in the developed world than in other countries. In Slovenia, six hormone-related cancers (breast, ovarian, endometrial, prostate, testicular, and thyroid) account for a quarter of all cancers. Their incidence goes up each year, breast and prostate cancer in particular. The age at diagnosis is not decreasing for any of the analysed cancer types. The risk of breast cancer is higher in the western part of the country, but no differences in geographical distribution have been observed for other hormone-related cancers. Furthermore, areas polluted with endocrine-disrupting chemicals that affect hormone balance such as PCBs, dioxins, heavy metals, and pesticides, do not seem to involve a greater cancer risk. We know little about how many cancers can be associated with endocrine disruptors, as there are too few reliable exposure studies to support an association.