Miracle-dz/UniFAR-FTUs huggingface dataset:
Lessons learned from moving to one scientific name for fungi

With the changes implemented in the International Code of Nomenclature for algae, fungi and plants, fungi may no longer have more than one scientific name. Although determining which scientific name to use is based on the principle of priority, situations exist in which applying a strict principle of priority does not contribute to the nomenclatural stability of fungi, thus exceptions can be made to this principle. Examples are presented showing how the single scientific name is determined at both the generic and specific level. In addition procedures are outlined for making exceptions to this rule. Considerable progress has been made in determining which genus to use for major groups of fungi. Interested scientists are invited to participate in the process of moving to one scientific name for fungi by contacting members dealing with specific groups of fungi as listed on the website of the International Commission for the Taxonomy of Fungi (http://www.fungaltaxonomy.org/subcommissions). A new combination of Clonostachys is also made.
Domain-specific templates for refinement transformations

Model transformations are a major instrument of model-driven software development. Especially in declarative transformation approaches, the structuring of transformations depends to a large extent on the structure of the source models and the generated artefacts. In many cases, similar code is written for transformations that deal with the same source or target metamodel. Writing such transformations can be simplified significantly if re-occurring parts within the transformation rules can be specified in a reusable way. Current approaches to transformation development include means for transformation reuse as well as inheritance. However, modularisation along the boundaries of different parts of domain metamodels is still lacking. Furthermore, the possibilities to reuse transformation fragments that re-occur in multiple transformations is limited. In this paper, we introduce domain-specific templates for refinement transformations with well-defined variation points. Transformation templates are based on known design patterns and enable a modular specification of refinement transformations and thus yield a simpler definition of transformations that can be grasped more easily and developed more efficiently. In addition, we present a real-world case study of transformation templates in the context of component based software architectures. The case study gives insight into the application of the presented approach.
Sarcoma growth factor (SGF): Specific binding to epidermal growth factor (EGF) membrane receptors

Cells transformed by murine sarcoma viruses (MSV) produce and release into their tissue culture media several polypeptide growth stimulating factors. One of these has been partially purified using Bio‐Gel P‐60 column chromatography followed by DEAE‐cellulose chromatography. This growth factor was assigned the name sarcoma growth factor (SGF), and is here shown to require the epidermal growth factor (EGF) receptor in order to function as a growth factor. DEAE‐cellulose chromatography yielded a product that was several‐fold purer than the material present in the Bio‐Gel P‐60 column pool II. The biologically active material from the DEAE‐cellulose column, when labeled with 125I, showed specific binding to EGF membrane receptors. The specific binding could be prevented with the addition of either unlabeled EGF or SGF. Both radiolabeled SGF and EGF will bind to live or fixed cells. We were able to bind 125I‐SGF as well as 125I‐EGF to fixed cells and elute the bound material from fixed receptors. The eluted SGF showed a greater than 25‐fold increase in specific binding. The biological activities of EGF and SGF could be bound to and eluted from fixed cells. A 3T3 clone lacking EGF receptors was unable to respond to either EGF or SGF, whereas it responded well to serum and several other purified growth factors. The SGF isolated using DEAE‐cellulose chromatography was unable to compete in a radioimmune assay using 125I‐EGF and antibody to purified mouse submaxillary gland EGF; it also was not precipitated by anti‐EGF antibody.
Unduloids and their geometry

In this paper we consider non-compact cylinder-like surfaces called unduloids and study some aspects of their geometry. In particular, making use of a Kenmotsu-type representation of these surfaces, we derive explicit formulas for the lengths and areas of arbitrary segments, along with a formula for the volumes enclosed by them.
A new architecture for transformation-based generators

A challenge of many transformation-based generators is that they are trying to achieve three mutually antagonistic goals simultaneously: 1) deeply factored operators and operands to gain the combinatorial programming leverage provided by composition, 2) high-performance code in the generated program, and 3) small (i.e., practical) generation search spaces. The anticipatory optimization generator (AOG) has been built to explore architectures and strategies that address this challenge. The fundamental principle underlying all of AOG's strategies is to solve separate, narrow, and specialized generation problems by strategies that are narrowly tailored to specific problems rather than a single, universal strategy aimed at all problems. A second fundamental notion is the preservation and use of domain-specific information as a way to gain extra leverage on generation problems. This paper focuses on two specific mechanisms: 1) Localization: the generation and merging of implicit control structures and 2) Tag-directed transformations: a new control structure for transformation-based optimization that allows differing kinds of retained domain knowledge (e.g., optimization knowledge) to be anticipated, affixed to the component parts in the reuse library, and triggered when the time is right for its use.
Datrix#8482; source code model and its interchange format: lessons learned and considerations for future work

The Datrix team within Bell Canada has been offering its source code analysis tools to the research community for a number of years. These tools perform a number of analyses that revolve around a central model (Datrix-ASG) developed by the Datrix team, and use an interchange format similar to TA, which we call Datrix-TA. This paper intends to communicate the modeling choices that were made when creating this information model, and the lessons learned over a few years of usage.
Endothelial Dysfunction and Oxidative Stress During Estrogen Deficiency in Spontaneously Hypertensive Rats

BackgroundPostmenopausal estrogen deficiency is associated with an increased cardiovascular risk, hypertension, and oxidative stress. Angiotensin type 1 (AT1) receptor regulation is involved in the pathogenesis of atherosclerosis. To characterize vascular function, oxidative stress, and AT1 receptor regulation during estrogen deficiency, ovariectomized spontaneously hypertensive rats (SHR) were investigated in comparison with sham-operated animals and with ovariectomized rats receiving estrogen replacement therapy with 17&bgr;-estradiol. Methods and ResultsArterial blood pressure was similar in all 3 groups investigated. Five weeks after ovariectomy, endothelial dysfunction in aortic rings was observed, which was reversed by estrogen replacement therapy. Estrogen deficiency led to an enhanced vasoconstriction by angiotensin II. Vascular superoxide production was significantly increased compared with that in sham-operated rats, as measured by lucigenin chemiluminescence assays. Estrogen substitution normalized the production of free radicals in the vessel wall. Vascular AT1 receptor expression was significantly upregulated by estrogen deficiency, as shown by quantitative reverse transcription–polymerase chain reaction, whereas endothelial NO synthase mRNA expression and NO release were unchanged. Five-week treatment of the animals with the AT1 receptor antagonist irbesartan prevented endothelial dysfunction in ovariectomized rats and normalized the vascular production of free radicals. ConclusionsIn SHR, estrogen deficiency leads to increased vascular free radical production and enhanced angiotensin II–induced vasoconstriction via increased vascular AT1 receptor expression, resulting in endothelial dysfunction. Estrogen replacement therapy and AT1 receptor antagonism prevent these pathological changes. Therefore, estrogen deficiency–induced AT1 receptor overexpression and oxidative stress may play an important role in cardiovascular diseases associated with menopause.
Semantic Context-Aware Service Composition for Building Automation System

Service-oriented architecture (SOA) is realized by independent, standardized, and self-describing units known as services. This architecture has been widely used and verified for automatic, dynamic, and self-configuring distributed systems such as in building automation. This paper presents a building automation system adopting SOA paradigm with devices implemented by device profile for web service (DPWS) in which context information is collected, processed, and sent to a composition engine to coordinate appropriate devices/services based on the context, composition plan, and predefined policy rules. A six-phased composition process is proposed to carry out the task. In addition, two other components are designed to support the composition process: building ontology as a schema for representing semantic data and composition plan description language to describe context-based composite services in form of composition plans. A prototype consisting of a DPWSim simulator and SamBAS is developed to illustrate and test the proposed idea. Comparison analysis and experimental results imply the feasibility and scalability of the system.
Is having quality as an item on the executive board agenda associated with the implementation of quality management systems in European hospitals: a quantitative analysis

Objective To assess whether there is a relationship between having quality as an item on the board's agenda, perceived external pressure (PEP) and the implementation of quality management in European hospitals. Design A quantitative, mixed method, cross-sectional study in seven European countries in 2011 surveying CEOs and quality managers and data from onsite audits. Participants One hundred and fifty-five CEOs and 155 quality managers. Setting One hundred and fifty-five randomly selected acute care hospitals in seven European countries (Czech Republic, France, Germany, Poland, Portugal, Spain and Turkey). Main outcome measure(s) Three constructs reflecting quality management based on questionnaire and audit data: (i) Quality Management System Index, (ii) Quality Management Compliance Index and (iii) Clinical Quality Implementation Index. The main predictor was whether quality performance was on the executive board's agenda. Results Discussing quality performance at executive board meetings more often was associated with a higher quality management system score (regression coefficient b = 2.53; SE = 1.16; P = 0.030). We found a trend in the associations of discussing quality performance with quality compliance and clinical quality implementation. PEP did not modify these relationships. Conclusions Having quality as an item on the executive board's agenda allows them to review and discuss quality performance more often in order to improve their hospital's quality management. Generally, and as this study found, having quality on the executive board's agenda matters.
Signal Pathways Which Promote Invasion and Metastasis: Critical and Distinct Contributions of Extracellular Signal-Regulated Kinase and Ral-Specific Guanine Exchange Factor Pathways

ABSTRACT Approximately 50% of metastatic tumors contain Ras mutations. Ras proteins can activate at least three downstream signaling cascades mediated by the Raf–MEK–extracellular signal-regulated kinase family, phosphatidylinositol-3 (PI3) kinase, and Ral-specific guanine nucleotide exchange factors (RalGEFs). Here we investigated the contribution of RalGEF and ERK activation to the development of experimental metastasis in vivo and associated invasive properties in vitro. Each pathway contributes distinct properties to the metastatic phenotype. Following lateral tail vein injection, 3T3 cells transformed by constitutively active Raf or MEK produced lung metastasis that displayed circumscribed, noninfiltrating borders. In contrast, 3T3 cells transformed by Ras(12V,37G), a Ras effector mutant that activates RalGEF but not Raf or P13 kinase, formed aggressive, infiltrative metastasis. Dominant negative RalB inhibited Ras(12V,37G)-activated invasion and metastasis, demonstrating the necessity of the RalGEF pathway for a fully transformed phenotype. Moreover, 3T3 cells constitutively expressing a membrane-associated form of RalGEF (RalGDS-CAAX) formed invasive tumors as well, demonstrating that activation of a RalGEF pathway is sufficient to initiate the invasive phenotype. Despite the fact that Ras(12V,37G) expression does not elevate ERK activity, inhibition of this kinase by a conditionally expressed ERK phosphatase demonstrated that ERK activity was necessary for Ras(12V,37G)-transformed cells to express matrix-degrading activity in vitro and tissue invasiveness in vivo. Therefore, these experiments have revealed a hitherto-unknown but essential interaction of the RalGEF and ERK pathways to produce a malignant phenotype. The generality of the role of the RalGEF pathway in metastasis is supported by the finding that Ras(12V,37G) increased the invasiveness of epithelial cells as well as fibroblasts.
Impact of IEEE 802.15.7 Standard on Visible Light Communications Usage in Automotive Applications

As the demand for wireless communication technologies is exponentially increasing, using the visible light electromagnetic spectral region is a logical option. This article provides a general analysis of the IEEE 802.15. 7 standard for optical communications using visible light, focusing on the PHY I, intended for outdoor applications. Moreover, the article discusses how the standard's specifications apply to visible light communication use in vehicular networking applications. The article concentrates on the standard's applicability in this domain, and points out the fact that it has not been widely accepted, as most of the VLC developers are focused on decreasing system complexity and implementation costs, rather than complying with the standard's requirements. Furthermore, the article points out the necessity of a novel vehicular applications VLC specific standard, which should focus on the requirements imposed in this specific area.
Langerhans cell histiocytosis in children: does soluble interleukin-2-receptor correlate with both disease extent and activity?

BACKGROUND Langerhans cell histiocytosis (LCH) is characterized by monoclonal proliferation of activated Langerhans cells. Neither etiology nor pathomechanism of this disorder is presently known. However, despite monoclonality LCH might represent a reactive clonal disorder induced by immune dysfunction rather than a malignant process. To investigate a putative cytokine dysregulation in the pathogenesis of this disorder and searching for parameters of both disease activity and prognosis, serum concentrations of proinflammatory and T-cell derived cytokines were evaluated in LCH patients. MATERIALS AND METHODS Serum levels of IL-1 beta, IL-2, sIL-2R and TNF-alpha were determined by ELISA in seven children with different types of LCH: Three children (aged 6, 10 and 14 years, respectively) with single system/single bone disease; one child (11 years) with recurrent single system/multiple bone disease and three children (1, 2 and 2 years, respectively) with multisystem disease. RESULTS sIL-2R was elevated at diagnosis in seven children as compared to healthy adults (mean +/- SEM: 5,256 +/- 3,751 U/ml vs. 73 +/- 5.5 U/ml; P < 0.005) or healthy children (mean +/- SEM: 10,195 +/- 2,798 pg/ml vs. 2,638 +/- 156 pg/ml; P < 0.01). A positive correlation between serum levels of sIL-2R and extent of the disease could be observed. During remission, sIL-2R levels declined. IL-1 beta, IL-2, and TNF-alpha remained within the normal range during the study period. CONCLUSIONS Elevated sIL-2R levels seem to correlate positively with both extent and activity of LCH, thus indicating a pathological T-cell activation as a pathogenetic factor. sIL-2R level is a promising parameter to monitor disease activity in LCH and may also be of prognostic relevance.
Shared System for Ordering Small and Large Numbers in Monkeys and Humans

There is increasing evidence that animals share with adult humans and perhaps human infants a system for representing objective number as psychological magnitudes that are an analogue of the quantities they represent. Here we show that rhesus monkeys can extend a numerical rule learned with the values 1 through 9 to the values 10, 15, 20, and 30, which suggests that there is no upper limit on a monkey's numerical capacity. Instead, throughout the numerical range tested, both accuracy and latency in ordering two numerical values were systematically controlled by the ratio of the values compared. In a second experiment, we directly compared humans' and monkeys' performance in the same ordinal comparison task. The qualitative and quantitative similarity in their performance provides the strongest evidence to date of a single nonverbal, evolutionarily primitive mechanism for representing and comparing numerical values.
On the acceptance tests of aperiodic real-time tasks for FPGAs

Partially runtime-reconfigurable devices allow tasks to be placed and removed dynamically at runtime. For real-time systems, tasks have to complete their work and also to meet their deadlines. It is important to decide at arrival time whether the real-time task could meet its deadline or not. Acceptance tests are concerned with determining whether the incoming task can meet its deadline or not. The utilization bound-based acceptance tests (UBTs) -that accept new tasks till certain utilization limit- were proposed to handle single processor with aperiodic tasks which do not apply to the reconfigurable environment. The rejection ratio was used as a measure for performance of acceptance tests when all the rejected tasks have the same failure cost. However, when acceptance tests are used, the tasks that are not accepted to run are diverted to other system resources and not actually rejected. In this paper, we modify the utilization bound acceptance test to cope with the reconfigurable platform. Although this test requires simple calculations, it may reject tasks that could have been accepted if they wait in the system. Then, we present an exact acceptance test (EAT) for real-time non-preemptive tasks. This test decides exactly whether the incoming task can meet its deadline or not, at its arrival time. The test depends on a look- ahead placement (LAP) strategy. Finally, we propose a new factor, acceptance ratio of workload (AROW), to deal with systems that deploy acceptance tests. The AROW is suitable to measure the performance of acceptance tests as it takes into account sizes and computation times of accepted and diverted tasks. The increase in this ratio means an increase in the work done by the accepted tasks and vice versa. We compare the LAP strategy to the UBT and show its performance regarding the diversion ratio and the AROW measure. Our results show that the LAP strategy outperforms the UBT technique by over 80% using the AROW measure and also enhances the diversion ratio by around 40%.
Whole grains protect against atherosclerotic cardiovascular disease

Atherosclerotic cardiovascular disease (ASCVD) is the most common cause of death in most Western countries. Nutrition factors contribute importantly to this high risk for ASCVD. Favourable alterations in diet can reduce six of the nine major risk factors for ASCVD, i.e. high serum LDL-cholesterol levels, high fasting serum triacylglycerol levels, low HDL-cholesterol levels, hypertension, diabetes and obesity. Wholegrain foods may be one the healthiest choices individuals can make to lower the risk for ASCVD. Epidemiological studies indicate that individuals with higher levels (in the highest quintile) of whole-grain intake have a 29% lower risk for ASCVD than individuals with lower levels (lowest quintile) of whole-grain intake. It is of interest that neither the highest levels of cereal fibre nor the highest levels of refined cereals provide appreciable protection against ASCVD. Generous intake of whole grains also provides protection from development of diabetes and obesity. Diets rich in whole-grain foods tend to decrease serum LDL-cholesterol and triacylglycerol levels as well as blood pressure while increasing serum HDL-cholesterol levels. Whole-grain intake may also favourably alter antioxidant status, serum homocysteine levels, vascular reactivity and the inflammatory state. Whole-grain components that appear to make major contributions to these protective effects are: dietary fibre; vitamins; minerals; antioxidants; phytosterols; other phytochemicals. Three servings of whole grains daily are recommended to provide these health benefits.
Subject Areas : Optics A Viewpoint on : Electrically Driven Nonreciprocity Induced by Interband Photonic Transition on a Silicon Chip

On a traditional computer chip, electric signals travel along metallic wires between various informationprocessing electronic components such as transistors arranged on an integrated circuit. One of the goals of highperformance computing is to move away from electric connections to optical connections. The reason is simple: light travels very fast and potentially without any losses en route. Developing such technologies will require developing sophisticated “optical plumbing” capable of delivering (or, better yet, producing), transporting, and modulating streams of photons on a chip. It is increasingly looking like all these developments are not too far in the future. Recent advances in nanofabrication have already produced an impressive range of ultracompact optical devices that can fit on a single computer chip.
Utilization of Health-Care Resources by Patients With IBD in Manitoba: A Profile of Time Since Diagnosis

OBJECTIVES:We tested the hypothesis of nonlinear longitudinal trends in health-care utilization by individuals with Crohn's disease (CD) and ulcerative colitis (UC) in Manitoba.METHODS:Administrative databases were used to report resource use in 2000/1. A total of 5,485 cases of CD and UC and 45,279 matched controls were separated into incident cases (0–2 yr of disease), cases with longstanding disease (3–10 yr), and cases with very longstanding disease (>10 yr). Relative risk ratios (RRR) indicating the likelihood of resource use, given disease duration, were computed using multinomial logistic regression analysis. Sensitivity analysis was conducted to test the robustness of results to altering the disease duration cutoffs.RESULTS:Independent of disease duration, in general, outpatient utilization was over twice as likely among IBD cases compared with controls whether or not the contact was made for IBD-specific reasons. The likelihood of utilization was greatest among incident cases for outpatient visits with an internist (RRR 6.16, 95% CI 5.11–7.43) and surgical visits (RRR 3.78, 95% CI 3.14–4.55). Inpatient stays for IBD-specific reasons in general were considered dependent on disease duration; in particular, there was a fourfold higher likelihood for the incident cases relative to their controls. For non-IBD-specific reasons, IBD cases were 1.5 times as likely to have inpatient stays, regardless of disease duration.CONCLUSIONS:Our results suggest that within the first 2 yr from disease diagnosis the most costly resources were employed. We can likely measure the greatest proportion of treatment effects on resource use within a relatively short period.