Miracle-dz/UniFAR-FTUs huggingface dataset:
Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment.

A new algorithm, WABA, was developed for doing large-scale alignments between genomic DNA of different species. WABA was used to align 8 million bases of Caenorhabditis briggsae genomic DNA against the entire 97-million-base Caenorhabditis elegans genome. The alignment, including C. briggsae homologs of 154 genetically characterized C. elegans genes and many times this number of largely uncharacterized ORFs, can be browsed and searched on the Web (http://www.cse.ucsc.edu/ approximately kent/intronerator). The alignment confirms that patterns of conservation can be useful in identifying regulatory regions and rarely expressed coding regions. Conserved regulatory elements can be identified inside coding exons by examining the level of divergence at the wobble position of codons. The alignment reveals a bimodal size distribution of syntenic regions. Over 250 introns are present in one species but not the other. The 3' and 5' intron splice sites have more similarity to each other in introns unique to one species than in C. elegans introns as a whole, suggesting a possible mechanism for intron removal.
Conjunctive Query Answering in EL using a Database System

We study conjunctive query answering in the description logic EL, the core of the designated OWL2-EL profile of OWL2. In particular, we present an approach that allows the use of conventional relational database technology for conjunctive query answering in EL. This approach is inspired by the OWL support in Oracle Database 11g, semantic technologies.
Practical taint-based protection using demand emulation

Many software attacks are based on injecting malicious code into a target host. This paper demonstrates the use of a well-known technique, data tainting, to track data received from the network as it propagates through a system and to prevent its execution. Unlike past approaches to taint tracking, which track tainted data by running the system completely in an emulator or simulator, resulting in considerable execution overhead, our work demonstrates the ability to dynamically switch a running system between virtualized and emulated execution. Using this technique, we are able to explore hardware support for taint-based protection that is deployable in real-world situations, as emulation is only used when tainted data is being processed by the CPU. By modifying the CPU, memory, and I/O devices to support taint tracking and protection, we guarantee that data received from the network may not be executed, even if it is written to, and later read from disk. We demonstrate near native speeds for workloads where little taint data is present.
Misfolding diverts CFTR from recycling to degradation

To investigate the degradation mechanism of misfolded membrane proteins from the cell surface, we used mutant cystic fibrosis transmembrane conductance regulators (CFTRs) exhibiting conformational defects in post-Golgi compartments. Here, we show that the folding state of CFTR determines the post-endocytic trafficking of the channel. Although native CFTR recycled from early endosomes back to the cell surface, misfolding prevented recycling and facilitated lysosomal targeting by promoting the ubiquitination of the channel. Rescuing the folding defect or down-regulating the E1 ubiquitin (Ub)-activating enzyme stabilized the mutant CFTR without interfering with its internalization. These observations with the preferential association of mutant CFTRs with Hrs, STAM-2, TSG101, hVps25, and hVps32, components of the Ub-dependent endosomal sorting machinery, establish a functional link between Ub modification and lysosomal degradation of misfolded CFTR from the cell surface. Our data provide evidence for a novel cellular mechanism of CF pathogenesis and suggest a paradigm for the quality control of plasma membrane proteins involving the coordinated function of ubiquitination and the Ub-dependent endosomal sorting machinery.
A model-driven approach to develop rich web applications

Many Web applications have among their features the possibility of distributing their data and their business logic between the client and the server, also allowing an asynchronous communication between them. These features, originally associated with the arrival of Rich Internet Applications (RIA), remain particularly relevant and desirable. In the area of RIA, there are few proposals that simultaneously consider these features, adopt MDD (Model-Driven Development), and use implementation technologies based on scripting. In this work, we start from MoWebA, an MDD approach to web application development, and we extend it by defining a specific architecture model with RIA functionalities, supporting the previously mentioned features. We have defined the necessary metamodels and UML profiles, as well as transformation rules that allow you to generate code based on HTML5, Javascript, jQuery, jQuery Datatables and jQuery UI. The preliminary validation of the proposal shows positive evidences regarding the effectiveness, efficiency and satisfaction of the users with respect to the modeling and code generation processes of the proposal.
The Standard Shiftwork Index: a battery of questionnaires for assessing shiftwork-related problems

Abstract The lack of standardization in shiftwork research has been recognized. In response, a battery of selfreport questionnaires has been developed, which might usefully be employed in assessing the impact of different types of shift systems on large groups of individuals. The scales included reflect the most pertinent issues within shiftwork research, and were chosen on the basis of being both relatively short, easy to administer, and having good psychometric properties. The scales fall broadly into three main categories: outcomes, relating to the actual problems experienced by the individuals concerned; modifiers, relating to those differences between individuals which may serve to moderate the impact of shiftwork; and general, including work context and shift system details. Suggestions as to how the questionnaires might usefully be employed are offered. Based on the results of a large sample of nurses and midwives, and a second sample of industrial and service workers, the present paper offers: a s.
Job-embedded Coaching to Implement the Team Analysis of Preschoolers in Routines (TAPIR) Approach: Building Professional Collaboration

iii ACKNOWLEDGEMENTS. iv TABLE OF CONTENTS.v LIST OF TABLES.ix LIST OF FIGURES . x CHAPTER 1: INTRODUCTION.1 Purpose.1 Guiding Questions . 2 CHAPTER 2: REVIEW OF LITERATURE . 4 Policy and Legislation Addressing Functional Practices . 4 Division of Early Childhood (DEC): Recommended Practices . 7 Recommended Practice: Authentic Assessment . 8 Recommended Practice: Interdisciplinary Models . 11 Adult Learning Theory . 15 Professional Development to Support Changes in Practice . 18 Approaches to Support Access and Participation in Early Childhood . 19 Description of the Team Analysis of Preschoolers in Routines . 24 vi Comparison of Approaches to Support Access and Participation . 27 CHAPTER 3: METHODS . 31 Research Methodology.31 Study Design.32 Sampling Procedures . 34 Setting and Participants . 34 Human Subjects Committee Approval and Recruitment . 38 Professional Development Procedures and Components . 38 Data Collection . 41 Data Analysis . 48 Trustworthiness . 50 CHAPTER 4: FINDINGS . 54 Results Part I: Inquiry’s Starting Point . 57 Program Personnel . 58 Existing Program Practices . 59 Relevant Program History . 66 Results Part II: Inquiry Results . 69
Human Movement Modeling to Detect Biosignal Sensor Failures for Myoelectric Assistive Robot Control

In this study, we propose a human movement model both for myoelectric assistive robot control and biosignal-sensor-failure detection. We particularly consider an application to upper extremity exoskeleton robot control. When using electromyography (EMG)-based assistive robot control, EMG electrodes can be easily disconnected or detached from skin surfaces because the human body is always in contact with the robot. If multiple electrodes are used to estimate multiple joint movements, the probability of sensor electrode misplacement increases due to human error. To cope with the aforementioned issues, we propose a novel human movement estimation model that takes anomalies into account as uncertain observations. We estimated human joint torques by automatically modulating the contribution of each sensor channel for the movement estimation based on anomaly scores that were computed according to synergistic muscular coordination. We compared our proposed method with conventional approaches during drinking-movement estimation with five healthy subjects in the three aforementioned anomaly situations and showed the effectiveness of our proposed method. We applied it to a four-DOF upper limb assistive exoskeleton robot and showed proper control in sensor failure situations.
Characterising the Power Consumption of Hadoop Clouds - A Social Media Analysis Case Study

Energy efficiency is often identified as one of the key reasons for migrating to Cloud environments. It is often stated that a data centre hosting the Cloud environment is likely to achieve greater energy efficiency (at a reduced cost) compared to a local deployment. With increasing energy prices, it is also estimated that a large percentage of operational costs within a Cloud environment can be attributed to energy. In this work, we investigate and measure energy consumption of a number of virtual machines running the Hadoop system, over an OpenNebula Cloud. Our workload is based on sentiment analysis undertaken over Twitter messages. Our objective is to understand the tradeoff between energy efficiency and performance for such a workload. From our results we generalise and speculate on how such an analysis could be used as a basis to establish a Service Level Agreement with a Cloud provider – especially where there is likely to be a high level of variability (both in performance and energy use) over multiple runs of the same application (at different times).
Estimation of Low Power Multi-Supply Voltage Level Shifter

This paper presented, an overview of performance analysis and comparisons between power reduction techniques. Power Gating and MTCMOS assuming static and dynamic power consumption of a low low power voltage level shifter has presented here. Cutting back in power dissipation is one of the most significant challenges in VLSI circuit design. Due to scaling, threshold leakage current plays a dominant part in total power dissipation. The main goal of the work is to minimize power dissipation in the circuit, which is in the view of different supply voltages in the circuit. To achieve minimization in power dissipation, the low power voltage level shifter uses MTCMOS (Multi Threshold Complementary Metal Oxide Semiconductor) technique which is a low power design technique and also got better result as compared to Power Gating technique. The model presents a new level shifter for voltage shifting from one voltage domain to another voltage domain acts as interfacing circuit. Without adding up any extra supply pin, it allows communication between different modules. It is a key circuit component in multi supply circuits. The proposed circuit implemented in Cadence Virtuoso CMOS technology process, which adapts 300mV input signal into 1.2V output signal.
The Changing Face of Social Administration

This article explores the changing nature of the discipline of Social Administration in the post-1945 era. The vigorous challenge to Traditional Social Administration in the 1970s and 1980s did not lead, as some had feared, to the demise of the subject's applied, problem-solving, ethos. Within the broader discipline of Social Policy, the Social Administration perspective adapted and evolved. While retaining some elements of Traditional Social Administration namely, empiricism and a problem focus, the emergence of Contemporary Social Administration represents a significant and distinctive change in this sphere of academic enquiry.
Triumphs and Tears: Young People, Markets, and the Transition from School to Work

Training credits and the transition to work in post-Thatcherite Britain stakeholders and training credits anticipations and forced change - Helen's story victim, fool or rebel? - Laura's story choice, empowerment and unsatisfactory training - Elaine and Alison NVQs and "on and off the job" training - Clive and Becky general satisfaction and untroubled progress - David, Peter, Sam and Frances markets, vouchers and training policy career decision-making and careership in the transition from school to work the problem with endings.
Modelling the evolution of organic carbon during its gas-phase tropospheric oxidation: development of an explicit model based on a self generating approach

Abstract. Organic compounds emitted in the atmosphere are oxidized in complex reaction sequences that produce a myriad of intermediates. Although the cumulative importance of these organic intermediates is widely acknowledged, there is still a critical lack of information concerning the detailed composition of the highly functionalized secondary organics in the gas and condensed phases. The evaluation of their impacts on pollution episodes, climate, and the tropospheric oxidizing capacity requires modelling tools that track the identity and reactivity of organic carbon in the various phases down to the ultimate oxidation products, CO and CO2. However, a fully detailed representation of the atmospheric transformations of organic compounds involves a very large number of intermediate species, far in excess of the number that can be reasonably written manually. This paper describes (1) the development of a data processing tool to generate the explicit gas-phase oxidation schemes of acyclic hydrocarbons and their oxidation products under tropospheric conditions and (2) the protocol used to select the reaction products and the rate constants. Results are presented using the fully explicit oxidation schemes generated for two test species: n-heptane and isoprene. Comparisons with well-established mechanisms were performed to evaluate these generated schemes. Some preliminary results describing the gradual change of organic carbon during the oxidation of a given parent compound are presented.
Mining the Clinical Narrative: All Text are Not Equal

Over the past decade, the application of data science techniques to clinical data has allowed practitioners and researchers to develop a sundry of analytical models. These models have traditionally relied on structured data drawn from Electronic Medical Records (EMR). Yet, a large portion of EMR data remains unstructured, primarily held within clinical notes. While recent work has produced techniques for extracting structured features from unstructured text, this work generally operates under the untested assumption that all clinical text can be processed in a similar manner. This paper provides what we believe to be the first comprehensive evaluation of the differences between four major sources of clinical text, providing an evaluation of the structural, linguistic, and topical differences among notes of each category. Our conclusions support the premise that tools designed to extract structured data from clinical text must account for the categories of text they process.
Fast Nonconvex Model Predictive Control for Commercial Refrigeration

Abstract We consider the control of a commercial multi-zone refrigeration system, consisting of several cooling units that share a common compressor. The goal is to minimize the total energy cost, using real-time electricity prices, while obeying temperature constraints on the zones. We propose a variation on model predictive control to achieve this goal. When the right variables are used, the dynamics of the system are linear, and the constraints are convex. The cost function, however, is nonconvex. To handle this nonconvexity we propose a sequential convex optimization method, which typically converges in fewer than 5 or so iterations. We employ a fast convex quadratic programming solver to carry out the iterations, which is more than fast enough to run in real-time. We demonstrate our method on a realistic model, with a full year simulation, using real historical data. These simulations show substantial cost savings, and reveal how the method exhibits sophisticated response to real-time variations in electricity prices. This demand response is critical to help balance real-time uncertainties associated with large penetration of intermittent renewable energy sources in a future smart grid.
The social environment of asthma management in early adolescence

For adolescents with asthma, adhering to asthma regimes implies not only taking medications to relieve asthma attacks, but also adjusting their life styles in order to prevent asthma attacks. These life style modifications, such as avoiding allergens or having to limit physical activity, sometimes force adolescents to compromise their social life. On the other hand, the impact of such life style modifications on their social life may in turn force adolescents to give up adhering to asthma regimes. Indeed, adolescents are learning to be more independent while they enjoy a more complicated social life at home and at school than previously, and this rapid social development may thus be a great life challenge to adolescents with asthma. This thesis reports four studies which investigated the relationship between multi-dimensional asthma management (in medication and life style regimes) and the social life of young people with asthma at the transitional age from childhood to adolescence (or early adolescence, age 9-14), which also marks the transition from primary school to secondary school. In line with the literature on other adolescent chronic illnesses, study 1 demonstrated a downward trend of multi-dimensional asthma management in early adolescence. This developmental change was further investigated in study 2, 3 and 4, in which theories in behavioural psychology were followed to emphasise human behaviour influenced by the social activities and social relationships in the living environment, or the social environment. This was supplemented by theories in developmental psychology to identify relevant aspects of the social environment in early adolescence, especially the social relationships with parents, school staff and peers. Using quantitative and qualitative approaches, the studies not only supported the direct influence of asthma-specific social support, but also explored some mechanisms with which social relationships influenced asthma management in a more subtle and context-dependent way. By approaching asthma management behaviour with theories from behavioural and developmental psychology, it is also hoped that this thesis could be an example that shows the importance of recognising and to understanding the social life of young adolescents when adolescent behaviour is concerned.
High-Density Expression of Ca2+-Permeable ASIC1a Channels in NG2 Glia of Rat Hippocampus

NG2 cells, a fourth type of glial cell in the mammalian CNS, undergo reactive changes in response to a wide variety of brain insults. Recent studies have demonstrated that neuronally expressed acid-sensing ion channels (ASICs) are implicated in various neurological disorders including brain ischemia and seizures. Acidosis is a common feature of acute neurological conditions. It is postulated that a drop in pH may be the link between the pathological process and activation of NG2 cells. Such postulate immediately prompts the following questions: Do NG2 cells express ASICs? If so, what are their functional properties and subunit composition? Here, using a combination of electrophysiology, Ca2+ imaging and immunocytochemistry, we present evidence to demonstrate that NG2 cells of the rat hippocampus express high density of Ca2+-permeable ASIC1a channels compared with several types of hippocampal neurons. First, nucleated patch recordings from NG2 cells revealed high density of proton-activated currents. The magnitude of proton-activated current was pH dependent, with a pH for half-maximal activation of 6.3. Second, the current-voltage relationship showed a reversal close to the equilibrium potential for Na+. Third, psalmotoxin 1, a blocker specific for the ASIC1a channel, largely inhibited proton-activated currents. Fourth, Ca2+ imaging showed that activation of proton-activated channels led to an increase of [Ca2+]i. Finally, immunocytochemistry showed co-localization of ASIC1a and NG2 proteins in the hippocampus. Thus the acid chemosensor, the ASIC1a channel, may serve for inducing membrane depolarization and Ca2+ influx, thereby playing a crucial role in the NG2 cell response to injury following ischemia.
On a workflow model based on generalized communicating P systems

This paper introduces a new formal mathematical model for investigating workflows from dynamical and behavioural point of view. The model is designed on the basis of a special variant of the biology-inspired formal computational model called membrane systems, where the jobs or services are represented by membrane objects whose behaviour is defined by communication and generalization rules. The model supports running computations in a massive parallel manner, which makes it ideal to model high throughput workflow interpreters. Among the variants introduced in the literature, we have selected the Generalized Communicating P Systems, as it focuses on the communication among the membranes. Most of the workflow languages, based on different formal models like Petri nets or Communicating Sequential Processes, support several predefined structures – namely workflow patterns – to control the workflow interpretation such as conditions, loops etc. In this paper we show how these patterns are adapted into the membrane environment which, taking into account that membrane systems can be used to study complex dynamic systems’ runtime behaviour, makes this model a relevant alternative for the current models
An inter-AS routing component for software-defined networks

Network management is a challenging problem of wide impact with many enterprises suffering significant monetary losses, that can be of millions per hour, due to network issues, as downtime cost. The Software Defined Networks (SDN) approach is a new paradigm that enables the management of networks with low cost and complexity. The SDN architecture consists of a control plane, a forwarding plane and a protocol that enables communication with both planes. The control plane is composed by an Operating System and applications that run on top of it. The forwarding plane contains the switches, routers, and other network equipment. Nowadays, inter-domain routing system presents some critical problems, mainly due to its fully distributed model. Recent research has showed that it would be beneficial to apply the SDN approach to address some of those problems. But it became necessary to build a new mechanism to allow inter-domain routing using SDN. The aim of this paper is to present an inter-domain routing solution using a NOX-OpenFlow architecture, based on some characteristics of the today largely used inter-domain protocol, keeping the SDN architectural principles. Although NOX-OpenFlow was originally created for routing only in enterprise networks, we propose routing beyond those, lifting this undesirable restriction of the original architecture. Our tests show that the built of this kind of application provides a much less complex, less prone to errors, and scalable solution.