Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic Communications of the EASST Volume 47 ( 2012 ) Proceedings of the 11 th International Workshop on Graph Transformation and Visual Modeling Techniques ( GTVMT 2012 ) Algebraic Approach to Timed Petri Nets

One aspect often needed when modelling systems of any kind is time-based analysis, especially for real-time or in general time-critical systems. Algebraic place/transition (P/T) nets do not inherently provide a way to model the passing of time or to restrict the firing behaviour with regards to passing time. In this paper, we present an extension of algebraic P/T nets by adding time durations to transitions and timestamps to tokens. We define categories for different timed net classes and functorial relations between them. Our first result is the definition of morphisms preserving firing behaviour for all timed net classes. As second result, we define structuring techniques for timed P/T nets in a way that our category fulfills the properties of M-adhesive systems, a general categorical framework for structuring and transforming high-level algebraic structures. We demonstrate our approach by applying it to model a real-time communication network.
Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

A frequent step in metagenomic data analysis comprises the assembly of the sequenced reads. Many assembly tools have been published in the last years targeting data coming from next-generation sequencing (NGS) technologies but these assemblers have not been designed for or tested in multi-genome scenarios that characterize metagenomic studies. Here we provide a critical assessment of current de novo short reads assembly tools in multi-genome scenarios using complex simulated metagenomic data. With this approach we tested the fidelity of different assemblers in metagenomic studies demonstrating that even under the simplest compositions the number of chimeric contigs involving different species is noticeable. We further showed that the assembly process reduces the accuracy of the functional classification of the metagenomic data and that these errors can be overcome raising the coverage of the studied metagenome. The results presented here highlight the particular difficulties that de novo genome assemblers face in multi-genome scenarios demonstrating that these difficulties, that often compromise the functional classification of the analyzed data, can be overcome with a high sequencing effort.
Neúplná stochastická dominance

In the presented work we study the almost stochastic dominance and it’s properties. Almost stochastic dominance is a relaxation of stochastic dominance. Almost stochastic dominance also deals with paradox situations occurring in case of stochastic dominance. This is a situation when stochastic dominance determines indifferent relationship between two portfolios, but in fact almost all investors can choose the better one. The original almost stochastic dominance presented by Leshno and Levy (2002) is computationally expensive. Lizyayev and Ruszczyński (2012) suggested an alternative approach. This work introduces both approaches. The most interesting part of this work is a search for efficient portfolio with respect to the almost stochastic dominance by the simple linear programming. Lizyayev and Ruszczyński (2012) approach is applied to Kopa and Chovanec (2008) quantile approach for portfolio efficiency testing with respect to second order stochastic dominance.
The dynamic asymmetric fracture test and determination of the dynamic fracture toughness of large-diameter cracked rock specimens

We propose large-diameter (160 mm) pre-cracked chevron notched Brazilian disc (P-CCNBD) specimens were used to study the asymmetric fracture law and determine the dynamic fracture toughness of rock. Specimens were diametrically impacted by a split Hopkinson pressure bar. The dynamic fracture failure process of each specimen was monitored by crack propagation gauges and strain gauges. Each of the large-diameter P-CCNBD specimens was found to exhibit prominent asymmetric fracture under impact load. The stress equilibrium condition cannot be satisfied. The dynamic fracture toughness values of the rocks were measured using the experimental-numerical method rather than the quasi-static method. The calculation results showed that the dynamic fracture toughness of rocks increases with the dynamic loading rate. In addition, at the 3-D crack front, the dynamic stress intensity factor was found be substantially different at each point. These data suggest that the dynamic fracture toughness of P-CCNBD specimens should be calculated by removing the value affected by an edge arc crack and taking the average value of the remaining points.
Cell Adhesion Molecules and Their Involvement in Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders characterized by abnormalities in social interaction, language development and behavior. Recent genetic studies demonstrate that alterations in synaptic genes including those encoding cell adhesion molecules and their interaction partners play important roles in the pathogenesis of ASD. Systematic analyses of different cell adhesion molecule genes will help elucidate their normal functions and regulatory mechanisms in the establishment and maintenance of normal neural circuits and uncover genetic aberrations contributing to ASD.
Treatment Efficiency and Problems of Local Control in Localized Bladder/Prostate Rhabdomyosarcoma

Objectives: To assess the treatment efficiency, outcome and factors affecting the local control of localized bladder/prostate RMS. Patients and methods: Retrospective analysis of 54 patients with localized bladder/prostate RMS treated at Children Cancer Hospital, Egypt between August 2007 and Jan 2017. All patients were treated according to Intergroup Rhabdomyosarcoma Study (IRS -V) and subsequent Children’s Oncology Group COG guidelines. Results: The median age at diagnosis was 3.28 years (range 0.4–13.6). Fifty-one patients (94%) underwent initial biopsy. Complete surgical resection (primary or delayed) was performed in 7 patients (13%). Local control started before/at week 12 in 29 patients (61.7%). Local control methods were: Radiotherapy in 43 patients (79.2%), radiotherapy with surgery in 4 patients (9%), surgery in 1 patient and four patients did not receive local control. With a median follow up of 38.12 months, the 5-year failure-free survival (FFS) and overall (OS) of the whole patients were 60.4 ± 14.5% and 75.4 ± 14.1% respectively. A better 5-year FFS was experienced by those who had early local control (79.2 ± 17% vs. 43.8 ± 25% p= 0.005). Conclusions: Timing of local control and local radiotherapy is crucial and shouldn’t be delayed waiting for further response to the systemic chemotherapy.
Molecular Characterization of Branchial aquaporin 1aa and Effects of Seawater Acclimation, Emersion or Ammonia Exposure on Its mRNA Expression in the Gills, Gut, Kidney and Skin of the Freshwater Climbing Perch, Anabas testudineus

We obtained a full cDNA coding sequence of aquaporin 1aa (aqp1aa) from the gills of the freshwater climbing perch, Anabas testudineus, which had the highest expression in the gills and skin, suggesting an important role of Aqp1aa in these organs. Since seawater acclimation had no significant effects on the branchial and intestinal aqp1aa mRNA expression, and since the mRNA expression of aqp1aa in the gut was extremely low, it can be deduced that Aqp1aa, despite being a water channel, did not play a significant osmoregulatory role in A. testudineus. However, terrestrial exposure led to significant increases in the mRNA expression of aqp1aa in the gills and skin of A. testudineus. Since terrestrial exposure would lead to evaporative water loss, these results further support the proposition that Aqp1aa did not function predominantly for the permeation of water through the gills and skin. Rather, increased aqp1aa mRNA expression might be necessary to facilitate increased ammonia excretion during emersion, because A. testudineus is known to utilize amino acids as energy sources for locomotor activity with increased ammonia production on land. Furthermore, ammonia exposure resulted in significant decreases in mRNA expression of aqp1aa in the gills and skin of A. testudineus, presumably to reduce ammonia influx during ammonia loading. This corroborates previous reports on AQP1 being able to facilitate ammonia permeation. However, a molecular characterization of Aqp1aa from A. testudineus revealed that its intrinsic aquapore might not facilitate NH3 transport. Hence, ammonia probably permeated the central fifth pore of the Aqp1aa tetramer as suggested previously. Taken together, our results indicate that Aqp1aa might have a greater physiological role in ammonia excretion than in osmoregulation in A. testudineus.
Hypomagnesemia in Type-2 Diabetes Mellitus

Magnesium is an intracellular cation. Insulin favours reabsorption of Magnesium from the loop of henle. In Insulin resistance states like Type 2 Diabetes Mellitus, reabsorption of Magnesium from the loop of henle is reduced. Insulin dependent glucose uptake is decreased in hypomagnesemia. The objective of this study is to asses the serum level of magnesium in Type 2 Diabetic patients attending our hospital. This case- control study was conducted in the department of Diabetology in Rajiv Gandhi Government General Hospital Chennai. 100 patients of Type 2 Diabetes Mellitus, defined by fasting plasma glucose level more than 126 mg per dL were included in the study. The controls were 100 healthy subjects matched for age and sex. Serum magnesium was measured by spectrophotometry. The reference values are 1.8-3mg per dL. Results . The mean serum magnesium level in cases and controls were 1.79 (plus or minus 0.619)and 2.03(plus or minus 0.356) respectively. Student t test was used to calculate statistical significance and significant difference was found in magnesium levels between cases and controls. Conclusion. Serum magnesium maybe a significant risk factor for the Type 2 Diabetes Mellitus
Acute Dose-Related Differential Effects of Methylphenidate on Murine Cystometric Parameters

Purpose Methylphenidate is the most widely used central nervous system stimulant in patients with attention deficit hyperactivity disorder. However, few studies have assessed its effects on voiding. Various doses of methylphenidate were investigated for their effects on cystometric parameters in conscious mice. Methods Ten male C57BL/6 mice, weighing between 20 and 23 g, were used in this study. To compare the acute drug responses before and after the oral medication was administered in the awake condition, we injected the solution through a catheter inserted into the stomach. Methylphenidate (1.25, 2.5, and 5 mg/kg) in an injection volume of 0.05 mL was administered. Results Four mice that received high doses of methylphenidate (2.5 and 5 mg/kg) showed no voiding contraction, with urine leakage. Six mice that received a low dose of methylphenidate (1.25 mg/kg) showed typical micturition cycles before and after administration. The micturition pressure decreased and bladder capacity increased without an increased residual volume after administration. Conclusions Methylphenidate has differential, dose-dependent effects on the function of the lower urinary tract, due to the dependent relationship between the brain and lower urinary tract. Especially at higher doses, this drug may interfere with normal micturition. Therefore, more detailed clinical or experimental studies are warranted in the future.
A Two-stage Single-channel Speaker-dependent Speech Separation Approach for Chime-5 Challenge

In this paper, we design a two-stage single-channel speaker-dependent speech separation approach for the CHiME-5 Challenge, targeting the problem of far-field and multi-talker conversational speech recognition in dinner party scenarios involving background noises, reverberations and overlapping speech. First, we make detailed analysis of the CHiME-5 data and observe problems of inaccurate human annotations and low-resource useable data for target speakers. Motivated by this, we conduct a first-stage speaker-dependent speech separation with a learning target for aggressive segregation to generate more and purer target speech data. Then a second-stage speaker-dependent speech separation with a new learning target is performed to obtain the final speech masks, which can be directly fed to back-end acoustic model. Compared with the official baseline, our proposed approach can yield an absolute word error rate reduction of 5.3%, namely from 81.3% to 76.0% in development test set. To the best of our knowledge, it is the first time to discuss a feasible method of single-channel speaker-dependent speech separation for such a challenging task although we make an assumption of oracle speaker diarization following the challenge rules. By integrating this crucial technique, our submitted systems achieved the first place of all four tasks in the CHiME-5 challenge.
Melatonin as a treatment for gastrointestinal cancer: a review

Gastrointestinal cancer is a disease that affects the population worldwide with high morbidity and mortality. Melatonin, an endogenously produced molecule, may provide a defense against a variety of cancer types. In particular, the ability of melatonin to inhibit gastrointestinal cancer is substantial. In this review, we first clarify the relationship between the disruption of the melatonin rhythm and gastrointestinal cancer (based on epidemiologic surveys and animal and human studies) and summarize the preventive effect of melatonin on carcinogenesis. Thereafter, the mechanisms through which melatonin exerts its anti‐gastrointestinal cancer actions are explained, including inhibition of proliferation, invasion, metastasis, and angiogenesis, and promotion of apoptosis and cancer immunity. Moreover, we discuss the drug synergy effects and the role of melatonin receptors involved in the growth‐inhibitory effects on gastrointestinal cancer. Taken together, the information compiled here serves as a comprehensive reference for the anti‐gastrointestinal cancer actions of melatonin that have been identified to date and will hopefully aid in the design of further experimental and clinical studies and increase the awareness of melatonin as a therapeutic agent in cancers of the gastrointestinal tract.
CS787 Project Proposal

The Computer Aided Engineering center at the College of Engineering of UW-Madison has a fairly complex virtual hosting infrastructure that it provides for the college and other university wide services. The ultimate issue we would like to be able to answer is how best to size our server infrastructure to suit the service’s needs using some variant of bin packing, instead of trial and error. In order to explore how we might do this, we first describe the system as it is currently laid out as follows.
Signaling by distinct classes of phosphoinositide 3-kinases.

Many signaling pathways converge on and regulate phosphoinositide 3-kinase (PI3K) enzymes whose inositol lipid products are key mediators of intracellular signaling. Different PI3K isoforms generate specific lipids that bind to FYVE and pleckstrin homology (PH) domains in a variety of proteins, affecting their localization, conformation, and activities. Here we review the activation mechanisms of the different types of PI3Ks and their downstream actions, with focus on the PI3Ks that are acutely triggered by extracellular stimulation.
Informed Consent on the Semantic Web-Issues for Interaction and Interface Designers

This discussion paper highlights differences between semantic webbased and more traditional web-based applications that raise significant privacy and other ethical issues for users when they provide personal data (about themselves or others) into a semantic web environment. The paper introduces the technologies, highlights some key differences and reviews the concepts behind informed consent. It then argues that a critical challenge for interaction and interface designers of semantic web (and related) applications is to ensure that users are enabled to give their fully informed consent before they provide such data. Finally it explores specific aspects of the challenges and potential approaches to meeting them.
Ju n 20 05 CAMS / 0501 Hermitian Geometry and Complex Space-Time

We consider a complex Hermitian manifold of complex dimensions four with a Hermitian metric and a Chern connection. It is shown that the action that determines the dynamics of the metric is unique, provided that the linearized Einstein action coupled to an antisymmetric tensor is obtained, in the limit when the imaginary coordinates vanish. The unique action is of the Chern-Simons type when expressed in terms of the Kähler form. The antisymmetric tensor field has gauge transformations coming from diffeomorphism invariance in the complex directions. The equations of motion must be supplemented by boundary conditions imposed on the Hermitian metric to give, in the limit of vanishing imaginary coordinates, the low-energy effective action for a curved metric coupled to an antisymmetric tensor. ∗ email: chams@aub.edu. lb
Disentangling Stigma from Functional Neurological Disorders: Conference Report and Roadmap for the Future

A multidisciplinary expert review of key issues and future directions from the conference “Controversial labels and clinical uncertainties: psychogenic disorders, conversion disorder, and functional symptoms. ” On October 9 and 10, 2015, a conference entitled “Controversial labels and clinical uncertainties: psychogenic disorders, conversion disorder, and functional symptoms” was held at the Center for Ethics, Emory University, Atlanta, GA, USA. This conference brought together a select group of 30 distinguished thought leaders and practitioners, including ethicists, researchers, clinicians, humanities scholars, and advocates to discuss the unique challenges and controversies related to the diagnosis, treatment, and stigma for patients with what is currently recognized as functional (“psychogenic”) neurological disorders. Our group of experts explored the conflicts and ethical tensions within health care that must be addressed in order to advance care for these disorders. What follows is a reflection on the conversations between conference attendees outlining key challenges and value conflicts in the diagnosis and treatment of patients with functional disorders. With this report, we aim to provide a roadmap for reducing stigma and improving care for functional neurological disorders (FND). A path forward would involve (1) setting a multifactorial research agenda that equally prioritized access to effective psychotherapy as well as identification of novel biomarkers; (2) empowering patients with FND to be heard and to drive changes in care; and (3) reducing isolation for clinicians by providing formal training and setting up multidisciplinary care teams and support networks.
Are Chinese Stock Markets Increasing Integration With Other Markets in the Greater China Region and Other Major Markets?

This paper investigates the cointegrating and long-term causal relationships between the Shanghai A and B-share market, and between these two markets and the Hong Kong, the Taiwanese, the Japanese and the US market of two sub periods between July 1993 and March 2007. On the basis of a new Granger non-causality test procedure developed by Toda-Yamamoto (1995) and Johansen's (1988) cointegration test, my results suggest that a long-term equilibrium relationship measured by cointegration has been merged between the Chinese A-share market and the other markets in greater China region as well as the US market during the post-crisis period which covers the period since Chinese A-share market was opened to the Qualified Foreign Institutional Investors (QFII) in 2002. I also found that the Shanghai A-share market uni-directionally Granger-causes the other regional markets after the Asian financial crisis, while the A-share market and Hong Kong H-share market have had a significant feedback relationship since then. However, I found no evidence there has been cointegrating relationship between Shanghai B-share market and any other market ever since the B-share market was opened to the local retail investors in 2001.
DNA methylation analysis in plants: review of computational tools and future perspectives

Genome-wide DNA methylation studies have quickly expanded due to advances in next-generation sequencing techniques along with a wealth of computational tools to analyze the data. Most of our knowledge about DNA methylation profiles, epigenetic heritability and the function of DNA methylation in plants derives from the model species Arabidopsis thaliana. There are increasingly many studies on DNA methylation in plants-uncovering methylation profiles and explaining variations in different plant tissues. Additionally, DNA methylation comparisons of different plant tissue types and dynamics during development processes are only slowly emerging but are crucial for understanding developmental and regulatory decisions. Translating this knowledge from plant model species to commercial crops could allow the establishment of new varieties with increased stress resilience and improved yield. In this review, we provide an overview of the most commonly applied bioinformatics tools for the analysis of DNA methylation data (particularly bisulfite sequencing data). The performances of a selection of the tools are analyzed for computational time and agreement in predicted methylated sites for A. thaliana, which has a smaller genome compared to the hexaploid bread wheat. The performance of the tools was benchmarked on five plant genomes. We give examples of applications of DNA methylation data analysis in crops (with a focus on cereals) and an outlook for future developments for DNA methylation status manipulations and data integration.
Multiresolution and Wide-Scope Depth Estimation Using a Dual-PTZ-Camera System

Depth information is a critical cue for scene understanding which is very important for video surveillance. Traditional depth estimation approaches based on stereo vision have been well studied in past decades. However, little research is conducted with active cameras. In this correspondence, we discuss the depth estimation problem by employing dual-PTZ (pan/tilt/zoom)-camera system. The contributions of this correspondence includes the following three aspects: 1) we analyze the effect on depth's precision with different PTZ settings; 2) we propose a coarse-to-fine framework to deal with depth estimation problem for complex region; 3) we offer a method to generate mosaic of depth maps to combine depth information from different visual angles and resolutions for large scope. These contributions will widen the usage of dual-PTZ-camera systems to a greater extent. Real-data experimental results show that the proposed approach works well.
Optimal input design for non-linear dynamic systems: A graph theory approach

In this article a new algorithm for the design of stationary input sequences for system identification is presented. The stationary input signal is generated by optimizing an approximation of a scalar function of the information matrix, based on stationary input sequences generated from prime cycles, which describe the set of finite Markov chains of a given order. This method can be used for solving input design problems for nonlinear systems. In particular it can handle amplitude constraints on the input. Numerical examples show that the new algorithm is computationally attractive and that is consistent with previously reported results.