Miracle-dz/UniFAR-FTUs huggingface dataset:
BIOINFORMATICS ORIGINAL PAPER

Motivation: One of the mutational processes that has been monitored genome-wide is the occurrence of regional DNA copy number alterations (CNAs) , which may lead to deletion or over-expression of tumor suppressors or oncogenes, respectively. Understanding the relationship between CNAs and different cancer types is a fundamental problem in cancer studies. Results: This article develops an efﬁcient method that can accurately model the progression of the cancer markers and reconstruct evolutionary relationship between multiple types of cancers using comparative genomic hybridization (CGH) data. Such modeling can lead to better understanding of the commonalities and differences between multiple cancer types and potential therapies. We have developed an automatic method to infer a graph model for the markers of multiple cancers from a large population of CGH data. Our method identiﬁes highly related markers across different cancer types. It then builds a directed acyclic graph that shows the evolutionary history of these markers based on how common each marker is in different cancer types. We demonstrated the use of this model in determining the importance of markers in cancer evolution. We have also developed a new method to measure the evolutionary distance between different cancers based on their markers. This method employs the graph model we developed for the individual markers to measure the distance between pairs of cancers. We used this measure to create an evolutionary tree for multiple cancers. Our experiments on Progenetix database show
Heterotrimeric G protein signaling via GIV/Girdin: Breaking the rules of engagement, space, and time

Canonical signal transduction via heterotrimeric G proteins is spatially and temporally restricted, that is, triggered exclusively at the plasma membrane (PM), only by agonist activation of G protein‐coupled receptors (GPCRs) via a process that completes within a few hundred milliseconds. Recently, a rapidly emerging paradigm has revealed a non‐canonical pathway for activation of heterotrimeric G proteins by the non‐receptor guanidine‐nucleotide exchange factor (GEF), GIV/Girdin. This pathway has distinctive temporal and spatial features and an unusual profile of receptor engagement: diverse classes of receptors, not just GPCRs can engage with GIV to trigger such activation. Such activation is spatially and temporally unrestricted, that is, can occur both at the PM and on internal membranes discontinuous with the PM, and can continue for prolonged periods of time. Here, we provide the most complete up‐to‐date review of the molecular mechanisms that govern the unique spatiotemporal aspects of non‐canonical G protein activation by GIV and the relevance of this new paradigm in health and disease.
The other half of the whole: teaching patients to communicate with physicians.

BACKGROUND AND OBJECTIVES A wide body of research suggests that the nature of communication between patients and physicians is strongly related to health outcomes. Interventions that involve teaching patients to communicate with physicians are important to assess in this context. METHODS We conducted a review of randomized controlled trials (RCTs) in the outpatient setting from 1975 to 2000. Patient communication interventions were classified as high, medium, or low intensive, depending on the length of the intervention, use of personnel, and estimated cost. Characteristics of 16 studies were examined, including sample populations, types of interventions, and the nature of health outcomes. RESULTS Patient improvement in a variety of outcomes as a result of communication training was demonstrated. Positive change variables included patient communication, medical outcomes, functional status, and adherence to treatment. Studies revealed mixed findings on the outcome of patient satisfaction. All US studies suggested that pre-visit training had no effect on the overall length of the medical visit. CONCLUSIONS Studies indicated improvement in a variety of patient outcomes. However, the wide variation in study design, interventions, and outcomes hinders the ability to draw well-founded conclusions. Future research needs to further address biopsychosocial outcomes, cost-effectiveness, and their relationship.
Guide to Investment Strategy: How to Understand Markets, Risk, Rewards and Behaviour

This book explores the controversies that surround the management of wealth and provides guidance on how to construct investment strategies that are appropriate for each investor. With its detailed analysis, supported by data and anecdotes drawn from investment experiences, it is intended above all to be a practical guide. It shows how the insights of behavioural analysis are widely reflected in investor behaviour. It also emphasises the importance of basing recommendations for investment strategy on the principles of traditional finance. And it takes into account new research into behavioural and traditional finance which has created new understandings of what investors want to achieve and investors' customary mistakes. Part one considers the basics of investor objectives, behaviour, risk and investment allocation in terms of stocks, bonds and cash. Part two considers the things on which investors, their advisers and investment managers spend most of their time - the choice of money manager, bonds, equities, hedge fund strategies, private equity and real estate.
Strengthening Financial Infrastructure

This study provides comparative perspectives on the current and prospective situation of financial market development in ASEAN, the PRC, and India, identifies key priorities for strengthening financial infrastructure to promote financial development and regional integration, and produces policy recommendations at the national, sub-regional and regional levels. The four priority areas covered by the study are: market development, opening, and efficiency; financial inclusion; achievement of financial stability; and financial integration.
Localization of serotonin , cholecystokinin and somatostatin immunoreactivity in the lower respiratory tract of embryonic , foetal and postnatal sheep

The lower respiratory tract of the sheep was studied by light-microscopical immunocytochemistry for serotonin, cholecystokinin, somatostatin, bombesin and calcitonin during different periods of lung development; embryonic, foetal and postnatal. At embryonic period only intraepithelial serotonin-containing cells as solitary neuroendocrine cells (NEC) and neuroepithelial bodies (NEB) were found. At foetal stages, immunoreactive cells to serotonin, cholecystokinin and somatostatin were observed in airway epithelium, as solitary NEC and NEBs, and in autonomic intrapulmonary ganglia as single or clusters of small intensely-fluorescent (SIF) cells. In postnatal sheep, serotoninand cholecystokinincontaining cells were found within airway mucosa as solitary NECs and NEBs. No immunoreactive cells were observed with antiserum to bombesin and calcitonin. Quantitative studies showed that serotonin was the predominant substance, and that solitary neuroendocrine cells were more numerous in dista1 conducting airways and at foetal stages.
Synchronous, asynchronous and grouping asynchronous parallel implementation for N-FINDR algorithms in hyperspectral remote sensing image

N-FINDR is a widely used endmember extraction algorithm in hyperspectral imagery. Nevertheless, its computational complexity is high. Plaza's parallel implementation of NFINDR, namely, P-FINDR, demonstrates an excellent way to improve the computing performance of N-FINDR by incorporating with parallel computing technique. In this paper, three parallel implementation patterns, i.e., synchronous, asynchronous and grouping asynchronous pattern, are presented. Two versions of N-FINDR, i.e. iterative N-FINDR and successive N-FINDR, are considered to be implemented in parallel by these patterns respectively. Thus obtains six parallel N-FINDR algorithms. In experiment, both solution quality and parallel performance of these algorithms are compared and suitable patterns for parallel implementation of N-FINDR are obtained.
Evolution of cortical responsiveness subsequent to multiple forelimb nerve transections: An electrophysiological study in adult cat somatosensory cortex

Multiunit recordings along mediolateral rows in the primary somatosensory cortex of the animals described by C. Avendafio, D. Umbriaco, R. W. Dykes, and L. Descarries (1995, J. Comp. Neurol. 354:321–332) provided information about the functional status of the regions in and near the deafferented cortex. Responses changed along this axis from normally organized receptive fields in the hindlimb representation through a transition zone of unusually small receptive fields into the clearly deafferented forelimb representation, where receptive fields were uncommon and often had unusual characteristics.
Development of a tool within the electronic medical record to facilitate medication reconciliation after hospital discharge

Serious medication errors occur commonly in the period after hospital discharge. Medication reconciliation in the postdischarge ambulatory setting may be one way to reduce the frequency of these errors. The authors describe the design and implementation of a novel tool built into an ambulatory electronic medical record (EMR) to facilitate postdischarge medication reconciliation. The tool compares the preadmission medication list within the ambulatory EMR to the hospital discharge medication list, highlights all changes, and allows the EMR medication list to be easily updated. As might be expected for a novel tool intended for use in a minority of visits, use of the tool was low at first: 20% of applicable patient visits within 30 days of discharge. Clinician outreach, education, and a pop-up reminder succeeded in increasing use to 41% of applicable visits. Review of feedback identified several usability issues that will inform subsequent versions of the tool and provide generalizable lessons for how best to design medication reconciliation tools for this setting.
A novel polar surface polysaccharide from Rhizobium leguminosarum binds host plant lectin

Rhizobium bacteria produce different surface polysaccharides which are either secreted in the growth medium or contribute to a capsule surrounding the cell. Here, we describe isolation and partial characterization of a novel high molecular weight surface polysaccharide from a strain of Rhizobium leguminosarum that nodulates Pisum sativum (pea) and Vicia sativa (vetch) roots. Carbohydrate analysis showed that the polysaccharide consists for 95% of mannose and glucose, with minor amounts of galactose and rhamnose. Lectin precipitation analysis revealed high binding affinity of pea and vetch lectin for this polysaccharide, in contrast to the other known capsular and extracellular polysaccharides of this strain. Expression of the polysaccharide was independent of the presence of a Sym plasmid or the nod gene inducer naringenin. Incubation of R. leguminosarum with labelled pea lectin showed that this polysaccharide is exclusively localized on one of the poles of the bacterial cell. Vetch roots incubated with rhizobia and labelled pea lectin revealed that this bacterial pole is involved in attachment to the root surface. A mutant strain deficient in the production of this polysaccharide was impaired in attachment and root hair infection under slightly acidic conditions, in contrast to the situation at slightly alkaline conditions. Our data are consistent with the hypothesis that rhizobia can use (at least) two mechanisms for docking at the root surface, with use of a lectin–glycan mechanism under slightly acidic conditions.
Implementation and Evaluation of a Multiplayer Pong Game

Mobile gaming is a new frontier of the gaming industry with an ever increasing market share. Augmenting processing capabilities coupled with mobile sensing technology are some key ingredients contributing to a steady growth of innovative gaming solutions. In these settings, players could interact with each other in the context they are immersed in and exploit proximity, local information through wireless communication(s). Pursuing this goal, we discuss Multipong, a multiplayer version of the classic Pong game whereby players, in addition to the infrastructure mode, are offered the possibility to interact through ad-hoc communications. Along with the game description, we present a user-study involving 168 subjects undertaken at the University of Padua coupled with energy measurements of the proposed solution. ACM Classification
The strategic value and transaction effectiveness of HRD: A qualitative study of internal customer perspectives

Purpose – The purpose of this article is to outline the role of human resource development (HRD) in Lean strategy as the context for assessing interactions with internal customers. Identifying the perceived gap in role expectations and fulfillment emphasizes important priorities and offers tangible measures for assessing HRD contributions. A focus on business strategies such as Lean enhances HRD's strategic value. Central to the study is the proposition that HRD value and effectiveness revolves around the perceptions of key internal stakeholders in the organization. Design/methodology/approach – This study explores internal customer perceptions of HRD in a select organization using a qualitative case study method. Key stakeholders responsible for Lean implementation were identified as internal customers. Further, the focus on Lean helped to narrow the scope of the investigation. Interactions between key stakeholders and HRD professionals during Lean implementation were assessed. Findings – The findings fr.
Australian Earthquake Engineering: Achievements, challenges and obstacles

The Australian Earthquake Engineering Society was established in 1990 with its main objective to promote and advance the practice of earthquake engineering and engineering seismology in Australia. In the decade or so since its establishment the Society has had some successes in this regard as well as some disappointments. In this paper, the author will highlight these along with research and other important professional developments during this period. The perceived obstacles to getting a better take-up of earthquake engineering amongst Australian practitioners and the role of the Society in furthering the cause of earthquake engineering in Australia will then be discussed. The paper will conclude with an outline of possible strategies for overcoming these obstacles.
BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum

Background and aims: Mutations in BRAF have been linked with colorectal cancers (CRC) showing high level microsatellite instability (MSI-H). However, the distribution of BRAF mutations in MSI-H cancers remains to be clarified with respect to precursor lesions and the CpG island methylator phenotype (CIMP). Methods: Forty three hyperplastic polyps (HP), nine mixed polyps (MP), five serrated adenomas (SA), 28 conventional adenomas (AD), 18 hereditary non-polyposis colorectal cancers (HNPCC), and 127 sporadic CRC (46 MSI-H and 81 non-MSI-H) were collected from patients undergoing colectomy for either CRC or hyperplastic polyposis. Twenty five of 57 serrated lesions were derived from four patients with hyperplastic polyposis. HP were further subdivided according to recently documented morphological criteria into 27 classical HP and 16 variant lesions described as “sessile serrated adenoma” (SSA). All tumours were screened for BRAF activating mutations. Results: The BRAF mutation was more frequent in SSA (75%) and MP (89%) than in classical HP (19%), SA (20%), and AD (0%) (p<0.0001), and also in sporadic MSI-H cancers (76%) compared with HNPCC (0%) and sporadic non-MSI-H cancers (9%) (p<0.0001). The BRAF mutation was identified more often in CIMP-high serrated polyps (72%) and CIMP-high CRC (77%) than in CIMP-low (30%) and CIMP-negative (13%) polyps (p = 0.002) as well as CIMP-low (18%) and CIMP-negative (0%) CRC (p<0.0001). Conclusions: The BRAF mutation was frequently seen in SSA and in sporadic MSI-H CRC, both of which were associated with DNA methylation. Sporadic MSI-H cancers may originate in SSA and not adenomas, and BRAF mutation and DNA methylation are early events in this “serrated” pathway.
The 2.0-Å Crystal Structure of eqFP611, a Far Red Fluorescent Protein from the Sea Anemone Entacmaea quadricolor*

We have crystallized and subsequently determined to 2.0-Å resolution the crystal structure of eqFP611, a far red fluorescent protein from the sea anemone Entacmaea quadricolor. The structure of the protomer, which adopts a β-can topology, is similar to that of the related monomeric green fluorescent protein (GFP). The quaternary structure of eqFP611, a tetramer exhibiting 222 symmetry, is similar to that observed for the more closely related red fluorescent protein DsRed and the chromoprotein Rtms5. The unique chromophore sequence (Met63-Tyr64-Gly65) of eqFP611, adopts a coplanar and trans conformation within the interior of the β-can fold. Accordingly, the eqFP611 chromophore adopts a significantly different conformation in comparison to the chromophore conformation observed in GFP, DsRed, and Rtms5. The coplanar chromophore conformation and its immediate environment provide a structural basis for the far red, highly fluorescent nature of eqFP611. The eqFP611 structure extends our knowledge on the range of conformations a chromophore can adopt within closely related members of the green fluorescent protein family.
Outward Internationalization and FDI: Motives for Malaysian MNEs Moving into China

Firms are pressured to operate globally to reap the benefits of other locations through foreign investment. This phenomenon occurs not only among multinational enterprises from developed countries but also younger multinational enterprises from developing countries. Various factors induce them to invest in foreign locations. This paper highlights the motives of multinationals from developing countries engaging in foreign locations and capitalizing on location to enhance their competitiveness. This study uses one Malaysian company’s experiences to analyze the situation through a qualitative analysis. The results show that intense competition in the domestic and global market has forced firms to move out of their home country and relocate their production centers in China. China offers various factors that entice Malaysian MNEs to escalate their global expansion.
The Core Dimerization Domains of Histidine Kinases Contain Recognition Specificity for the Cognate Response Regulator

ABSTRACT Histidine kinases DivJ and PleC initiate signal transduction pathways that regulate an early cell division cycle step and the gain of motility later in the Caulobacter crescentus cell cycle, respectively. The essential single-domain response regulator DivK functions downstream of these kinases to catalyze phosphotransfer from DivJ and PleC. We have used a yeast two-hybrid screen to investigate the molecular basis of DivJ and PleC interaction with DivK and to identify other His-Asp signal transduction proteins that interact with DivK. The only His-Asp proteins identified in the two-hybrid screen were five members of the histidine kinase superfamily. The finding that most of the kinase clones isolated correspond to either DivJ or PleC supports the previous conclusion that DivJ and PleC are cognate DivK kinases. A 66-amino-acid sequence common to all cloned DivJ and PleC fragments contains the conserved helix 1, helix 2 sequence that forms a four-helix bundle in histidine kinases required for dimerization, autophosphorylation and phosphotransfer. We present results that indicate that the four-helix bundle subdomain is not only necessary for binding of the response regulator but also sufficient for in vivo recognition specificity between DivK and its cognate histidine kinases. The other three kinases identified in this study correspond to DivL, an essential tyrosine kinase belonging to the same kinase subfamily as DivJ and PleC, and the two previously uncharacterized, soluble histidine kinases CckN and CckO. We discuss the significance of these results as they relate to kinase response regulator recognition specificity and the fidelity of phosphotransfer in signal transduction pathways.
Speech Modulation Features for Robust Nonnative Speech Accent Detection

In this paper, we propose to use speech modulation features for robust nonnative accent detection. Modulation spectrum carries long term temporal information of speech and may discriminate accents of native and nonnative speakers. For each speech segment to be tested, we extract a 10 dimension feature vector from modulation spectrum and use it for model training and testing. The proposed modulation features are compared with other popular features such as pitch and formant on a nonnative French accent detection task. Results show that the modulation features produce good detection performance and are quite robust to channel distortions. In addition, when combine test scores of modulation features and pitch features, performance is further significantly reduced. The best equal error rate is 13.1% by fusing pitch and modulation-based systems.
Multitemporal multidimensional speckle filtering of PolSAR images

The combination of the polarimetric information with time observations represents an extremely valuable tool for the different applications of polarimetric SAR images. One of the most important preprocessing steps in this context is speckle filtering. In this paper, a new method to multitemporal multidimensional (MTMD) speckle filter covariance matrices of polarimetric SAR data is presented. MTMD method is based on a temporal statistical criteria dependent on all elements of covariance matrix. The experimental results on Radarsat-2 fine-quad data show that the proposed method preserves radiometric resolution and reduces speckle. Also, we show that the our method has a better performance than the other filters such as boxcar and conventional multitemporal filter based on the equivalent number of looks.
SDSI - A Simple Distributed Security Infrastructure

We propose a new distributed security infrastructure, called SDSI (pronounced “Sudsy”). SDSI combines a simple public-key infrastructure design with a means of defining groups and issuing group-membership certificates. SDSI’s groups provides simple, clear terminology for defining access-control lists and security policies. SDSI’s design emphasizes linked local name spaces rather than a hierarchical global name space.