Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Analysis of Conserved Non-Coding Regions Around the Short Stature hox Gene (shox) in Whole Zebrafish Embryos

Background Mutations in the SHOX gene are responsible for Leri-Weill Dyschondrosteosis, a disorder characterised by mesomelic limb shortening. Recent investigations into regulatory elements surrounding SHOX have shown that deletions of conserved non-coding elements (CNEs) downstream of the SHOX gene produce a phenotype indistinguishable from Leri-Weill Dyschondrosteosis. As this gene is not found in rodents, we used zebrafish as a model to characterise the expression pattern of the shox gene across the whole embryo and characterise the enhancer domains of different CNEs associated with this gene. Methodology/Principal Findings Expression of the shox gene in zebrafish was identified using in situ hybridization, with embryos showing expression in the blood, putative heart, hatching gland, brain pharyngeal arch, olfactory epithelium, and fin bud apical ectodermal ridge. By identifying sequences showing 65% identity over at least 40 nucleotides between Fugu, human, dog and opossum we uncovered 35 CNEs around the shox gene. These CNEs were compared with CNEs previously discovered by Sabherwal et al., resulting in the identification of smaller more deeply conserved sub-sequence. Sabherwal et al.'s CNEs were assayed for regulatory function in whole zebrafish embryos resulting in the identification of additional tissues under the regulatory control of these CNEs. Conclusion/Significance Our results using whole zebrafish embryos have provided a more comprehensive picture of the expression pattern of the shox gene, and a better understanding of its regulation via deeply conserved noncoding elements. In particular, we identify additional tissues under the regulatory control of previously identified SHOX CNEs. We also demonstrate the importance of these CNEs in evolution by identifying duplicated shox CNEs and more deeply conserved sub-sequences within already identified CNEs.
Oscillatory Behavior on a Three-Node Neural Network Model with Discrete and Distributed Delays

This paper investigates the oscillatory behavior of the solutions for a three-node neural network with discrete and distributed delays. Two theorems are provided to determine the conditions for oscillating solutions of the model. The criteria for selecting the parameters in this network are derived. Some simulation examples are presented to illustrate the effectiveness of the results.
Diphone synthesis using unit selection

This paper describes an experimental AT&T concatenative synthesis system using unit selection, for which the basic synthesis units are diphones. The synthesizer may use any of the data from a large database of utterances. Since there are in general multiple instances of each concatenative unit, the system performs dynamic unit selection. Selection among candidates is done dynamically at synthesis, in a manner that is based on and extends unit selection implemented in the CHATR synthesis system [1][4]. Selected units may be either phones or diphones, and they can be synthesized by a variety of methods, including PSOLA [5], HNM [11], and simple unit concatenation. The AT&T system, with CHATR unit selection, was implemented within the framework of the Festival Speech Synthesis System [2]. The voice database amounted to approximately one and one-half hours of speech and was constructed from read text taken from three sources. The rst source was a portion of the 1989 Wall Street Journal material from the Penn Treebank Project, so that the most frequent diphones were well represented. Complete diphone converage was assured by the second text, which was designed for diphone databases [12]. A third set of data consisted of recorded prompts for telephone service applications. Subjective formal listening tests were conducted to compare speech quality for several options that exist in the AT&T synthesizer, including synthesis methods and choices of fundamental units. These tests showed that unit selection techniques can be successfully applied to diphone synthesis.
23 Neuropeptide Y in Brain Function

Neuropeptide Y (NPY), a 36‐amino‐acid peptide is abundantly expressed throughout the mammalian nervous system including: neocortex, hippocampus, striatum, amygdala, hypothalamus, thalamus, and brain stem. NPY has been implicated in the regulation of a number of different behaviors and neurophysiological functions, many of them part of the complex system(s) involved in maintaining and regulating homeostasis. These include, among others, anxiety and stress related responses, feeding, learning and memory, endocrine function, and circadian rhythms. The functions are mediated via different receptor subtype populations (Y1–y6), all belonging to the G‐protein‐coupled receptor super‐family. The Y1 subtype has been shown to mediate the anxiolytic effects of NPY, while the Y2 subtype is involved in regulation of circadian rhythms and neuronal excitability in the hippocampus, and may thus be the receptor subtype involved in the peptide’s effects on memory function. Stimulation of food intake by NPY has been proposed to be mediated by Y5 and/or Y1 receptors within the hypothalamus. Here, we present a summary of current findings concerning the central nervous system (CNS) functions of NPY in the context of homeostasis and reaction to the environment. List of Abbreviations: AA, amino acids; bp, base pair; CNS, central nervous system; CPON, C‐flanking peptide of NPY; CRF, corticotropin‐releasing factor; CSF, cerebrospinal fluid; GABA, gamma‐aminobutyric acid; HPA, hypothalamic–pituitary–adrenal (axis); ICV, intracerebroventricular; IV, intravenously; NPY, neuropeptide Y; NPY‐LI, NPY‐like immunoreactivity; PCR, polymerase chain reaction; PP, pancreatic polypeptide; PVN, paraventricular nucleus; PYY, peptide YY; SCN, suprachiasmatic nucleus; SNP, single nucleotide polymorphism
Organizational Factors Affecting E-commerce Adoption in Small and Medium-sized Enterprises

The use of e-commerce in SMEs has become an important topic in information systems research. Despite the enormous attention given to encourage SMEs to adopt e-commerce by governments, research undertaken to identify strategies of e-commerce adoption for SMEs in developing countries, especially in Sri Lanka is minimal. The primary objective of this study was to examine the relationship between organizational factors and ecommerce adoption to understand the factors that contribute to e-commerce adoption. Quantitative approaches were considered in this research. The study draws on the data obtained from a sample of 200 SMEs in Colombo District using a postal survey. The sample was chosen using a stratified random sampling technique based on business type of the SMEs. Based on correlation, regression and cluster analysis, the findings of this research were revealing and facilitated the understanding of certain organizational factors that influence the level of e-commerce adoption. The main factor identified was organizational culture. The results of this study show empirical evidence that there is a positive correlation between the adhocracy cultural characteristics among the SMEs and the level of e-commerce adoption. Also, hierarchy cultural characteristic showed a negative correlation with the level of e-commerce adoption in SMEs. An argument can be made out that a culture promoting innovation and risk acceptance would provide the needed support for higher levels of adoption of new technologies. Top managers’ opinion towards innovation also influences the way of doing business by the firm. Key words: e-commerce; e-commerce adoption; internet; organizational culture; Small and Medium-sized Enterprises (SMEs) DOI: 10.4038/tar.v22i2. 2829 Tropical Agricultural Research Vol. 22 (2): 204-210 (2011)
A Quirk Review of Translation Models Prepared in Connection with the 2010 Acl/sigir Summer School 1. Smt and Generative Translation Models

The goal of machine translation (MT) is to use a computer system to translate a text written in a source language (e.g., Chinese) into a target language (e.g., English). In this section, we will give an overview of translation models that are widely used in state-of-the-art statistical machine translation (SMT) systems. A nice textbook that provides a comprehensive review is Koehn (2010). Although these models are designed for translating regular natural language sentences, they can also be adapted to the task of search query translation for cross-lingual information retrieval (CLIR). The query translation task differs from the regular text translation mainly in its treatment of word order. In text translation word order is crucial to the readability of the translated sentences, which are present to the end users directly. In CLIR, query translation is an intermediate step that provides a set of translated query terms for the search engine to retrieve documents in the target language. Therefore, word order has little impact on the search quality as long as the translation preservers the underlying search intent, not the appearance, of the original query. This section focuses only on statistical translation models for regular text. Readers who are interested in statistical models for query translation may refer to Gao and Nie (2006) and Gao et al. SMT is typically formulated under the framework of the noisy channel model. Given a source sentence (in Chinese) , we want to find the best English translation among all possible translations: (2.1) where the argmax operation denotes the decoder, i.e., the search algorithm used to find among all possible target sentences the one with the highest probability. Applying Bayes' decision rule and dropping the constant denominator, we have (2.2) where is the language model, assessing the overall well-formedness of the target sentence, and is the translation model, modeling the transformation probability from E to C. In this section, we focus our discussion on the translation model only. Notice that, mathematically, the translation direction has changed from in Equation (2.1) to in Equation (2.2). This could cause a lot of confusion since the concept of what constitutes the source language differs between the mathematical model and the actually application. Following Koehn (2010), we try to avoid confusion by sticking to the notation when describing a translation model. As a significant generalization of the noisy channel model, a log-linear model that models directly has been proposed by …
Scaling of structure functions in homogeneous shear-flow turbulence.

We apply spectral dynamics and non-Gaussian statistical model of velocity difference to study the scaling of structure functions in homogeneous shear-flow turbulence. Let L(S) be the shear length scale and eta the viscous scale. It is found that, when L(S)/eta is finite, due to a combined effect of viscosity and mean shear, the scaling deviates from normal scaling, and the deviation increases as L(S)/eta decreases. In the presence of a strong shear (L(S)/eta<100), the deviation is substantially larger than the prediction of typical intermittency models, in agreement with recent experiments. As L(S)/eta-->infinity, the normal scaling is valid in the inertial range where viscous and shear effects are negligible.
The Use of Stories in User Experience Design

Stories capture the characteristics of the design space and audience that designers and engineers need to understand to build a complete and useful software experience. A story is a design communication tool that transcends the cultural divides of multidisciplinary teams and intertwines a technology with its user's goals. This article describes how stories are powerful tools in software design, defines the elements that make a compelling story, and presents the use of stories at IBM from the authors' experience. It also explores the benefits at each phase of the design process and how stories evolve throughout the design process.
General nonasymptotic and asymptotic formulas in channel resolvability and identification capacity and their application to the wiretap channel

Several nonasymptotic formulas are established in channel resolvability and identification capacity, and they are applied to the wiretap channel. By using these formulas, the epsi capacities of the above three problems are considered in the most general setting, where no structural assumptions such as the stationary memoryless property are made on a channel. As a result, we solve an open problem proposed by Han and Verduacute. Moreover, we obtain lower bounds of the exponents of error probability and the wiretapper's information in the wiretap channel
Dietary effects of faba-bean (Vicia faba L.) tannins on the morphology and function of the small-intestinal mucosa of weaned pigs

The objective of the present study was to evaluate effects of condensed tannins in faba beans (Vicia faba L.) on morphological and functional variables of the small-intestinal mucosa of piglets. In an experiment with young piglets (8–17 kg body weight), fed on either a control diet or a diet containing 200 g/kg of low- or high-tannin faba bean hulls (with < 0·10 and 3·3% catechin equivalents of condensed tannins respectively), morphological and functional characteristics of the jejunal mucosa were determined. Results of the study showed that the morphological variables of the mucosa of the three groups of piglets were similar. Also, no changes due to dietary tannins were observed in sucrase (EC 3.2.1.48)–isomaltase (EC 3.2.1.10) activity in homogenates of mucosa plus submucosa. However, aminopeptidase (EC 3.4.11.2) activity in these homogenates in the proximal part of the small intestine of the animals of the group fed on the high-tannin diet was significantly lower than that in the animals fed on the control diet or the diet with low-tannin hulls (P < 0·05).
Integrating Semantic and Syntactic Descriptions to Chain Geographic Services

Integrating multiple geographic services from different information communities and spatiolinguistic regions is challenging because of its inherent complexity and heterogeneity. A geographic information systems workflow approach can use semantic and syntactic service descriptions to form service chains that can integrate service discovery, composition, and reuse. Service chaining links remote geographic services to help expert users form complex geoprocessing services and perform timely analysis of geodata. This method facilitates the use of XML-based service description languages to build a geoservice-reuse architecture based on common ontologies and shared service descriptions
Functional Studies of Five Toxin-Antitoxin Modules in Mycobacterium tuberculosis H37Rv

Toxin–antitoxin (TA) systems, which consist of an intracellular toxin and its antidote (antitoxin), are encoded by ubiquitous genetic modules in prokaryotes. Commonly, the activity of a toxin is inhibited by its antitoxin under normal growth conditions. However, antitoxins are degraded in response to environmental stress, and toxins liberated from antitoxins consequently induce cell death or growth arrest. In free-living prokaryotes, TA systems are often present in large numbers and are considered to be associated with the adaptation of pathogenic bacteria or extremophiles to various unfavorable environments by shifting cells to a slow growth rate. Genomic analysis of the human pathogen Mycobacterium tuberculosis H37Rv (Mtb) revealed the presence of a large number of TA systems. Accordingly, we investigated five uncharacterized TA systems (Rv2019-Rv2018, Rv3697c-Rv3697A, Rv3180c-Rv3181c, Rv0299-Rv0298, and Rv3749c-Rv3750c) of Mtb. Among these, the expression of the Rv2019 toxin inhibited the growth of Escherichia coli, and M. smegmatis and this growth defect was recovered by the expression of the Rv2018 antitoxin. Interestingly, Rv3180c was toxic only in M. smegmatis, whose toxicity was neutralized by Rv3181c antitoxin. In vivo and in vitro assays revealed the ribosomal RNA (rRNA) cleavage activity of the Rv2019 toxin. Moreover, mRNAs appeared to be substrates of Rv2019. Therefore, we concluded that the ribonuclease activity of the Rv2019 toxin triggers the growth defect in E. coli and that the Rv2018 antitoxin inhibits the ribonuclease activity of the Rv2019 toxin.
Hypermedia on the Web: what will it take?

Introduction Researchers in the hypermedia field often lament that the World Wide Web doesn't support many of hypermedia's rich structuring, navigation and annotation features [BVA97] developed over the last 40 years since Engelbart's NLS system [EE68]. Structuring features include semantically typed anchors, links and nodes; attributes and keywords on these; links to and from content spans within any medium; bidirectional links; links recursively to links and to other hypermedia constructs; transclusions—inclusions providing access to all uses of the same span of content; versioning of hypermedia constructs; landmarks; automatic link propogation; trails and guided tours; and local and global overviews. Navigation features include link traversal; visual feedback upon link arrival; search based on the hypermedia structure (as opposed to content); process enactment through link traversal; backtracking strategies; backjumping; and history mechanisms. Annotation features include comments, bookmarks and reader-authored links with private, workgroup and public access. People can annotate any hypermedia construct, including other annotations recursively.
Simulation of air pollution due to marine engines

This paperwork tried to simulate the combustion inside the marine engines using the newest computer methods and technologies with the result of a diverse and rich palette of solutions, extremely useful for the study and prediction of complex phenomena of the fuel combustion. The paperwork is contributing to the theoretical systematization of the area of interest bringing into attention a thoroughly inventory of the thermodynamic description of the phenomena which take place in the combustion process into the marine diesel engines; to the in depth multidimensional combustion models description along with the interdisciplinary phenomenology taking place in the combustion models; to the FEA (Finite Elements Method) modelling for the combustion chemistry in the nonpremixed mixtures approach considered too; the CFD (Computational Fluid Dynamics) model was issued for the combustion area and a rich palette of results interesting for any researcher of the process.
Automated tracing of microglia using multilevel thresholding and minimum spanning trees

Microglia are immune cells of the central nervous system. Good knowledge about their morphology leads us to a better understanding of their functionality. In this article we propose an automated method to trace microglia in microscopy images. Our approach is powered by two main algorithms: multilevel thresholding (MT) and minimum spanning tree (MST). MT quantizes intensities of image pixels to several levels, then we sample each level with different rates to produce seed points. Each seed point belongs to a level and has a specific value, therefore they can be prioritized. The tree structure of microglia is known a priori, so we apply the MST to the prioritized seed points to preserve this feature. Results show that our proposed method is fast and accurate in reconstruction of large images.
Music reduces pain and increases resting state fMRI BOLD signal amplitude in the left angular gyrus in fibromyalgia patients

Music reduces pain in fibromyalgia (FM), a chronic pain disease, but the functional neural correlates of music-induced analgesia (MIA) are still largely unknown. We recruited FM patients (n = 22) who listened to their preferred relaxing music and an auditory control (pink noise) for 5 min without external noise from fMRI image acquisition. Resting state fMRI was then acquired before and after the music and control conditions. A significant increase in the amplitude of low frequency fluctuations of the BOLD signal was evident in the left angular gyrus (lAnG) after listening to music, which in turn, correlated to the analgesia reports. The post-hoc seed-based functional connectivity analysis of the lAnG showed found higher connectivity after listening to music with right dorsolateral prefrontal cortex (rdlPFC), the left caudate (lCau), and decreased connectivity with right anterior cingulate cortex (rACC), right supplementary motor area (rSMA), precuneus and right precentral gyrus (rPreG). Pain intensity (PI) analgesia was correlated (r = 0.61) to the connectivity of the lAnG with the rPreG. Our results show that MIA in FM is related to top-down regulation of the pain modulatory network by the default mode network (DMN).
SAX : A Tool for Studying Congestion-induced Surfer Behavior

User reaction to traffic congestion can have severe impact on network stability and significant implication for traffic engineering. For example, users who persist in large peer-to-peer transfers despite congestion can drive the network into congestion collapse. On the other hand, users who abort large transfers can smoothen self-similar traffic. We present a tool, called SAX, for studying congestion-induced behavior of web surfers. SAX extracts information from HTTP packet traces and infers clicks, abortions and sessions. Measurements with SAX show how users back-off when congestion occurs.
Automating string processing in spreadsheets using input-output examples

We describe the design of a string programming/expression language that supports restricted forms of regular expressions, conditionals and loops. The language is expressive enough to represent a wide variety of string manipulation tasks that end-users struggle with. We describe an algorithm based on several novel concepts for synthesizing a desired program in this language from input-output examples. The synthesis algorithm is very efficient taking a fraction of a second for various benchmark examples. The synthesis algorithm is interactive and has several desirable features: it can rank multiple solutions and has fast convergence, it can detect noise in the user input, and it supports an active interaction model wherein the user is prompted to provide outputs on inputs that may have multiple computational interpretations. The algorithm has been implemented as an interactive add-in for Microsoft Excel spreadsheet system. The prototype tool has met the golden test - it has synthesized part of itself, and has been used to solve problems beyond author's imagination.
Off-Shore and out of Reach: Student Voice in Pre-Departure EAP pedagogies

This paper explores the complexities of developing and delivering English for Academic Purposes (EAP) pre-departure programs. We reflect on experiences of co-teaching in a Lao PDR based program for students planning to undertake tertiary studies in New Zealand or Australia. Taking a sociocultural perspective, we examine the way that the Lao pre-departure program aims to attend to the particularities of both local and target contexts and to facilitate student adaptation to the chosen institution and discipline. The program takes a participatory approach to EAP and the broader acculturation processes, making space for individual student voice as part of the modeling and scaffolding of academic English. Based on this experience of transnational collaboration in development and delivery, we discuss critical issues of relevance to the planning and delivery of EAP pre-departure courses and productive international study experiences.