Miracle-dz/UniFAR-FTUs huggingface dataset:
isqg: A Binary Framework for in Silico Quantitative Genetics

The dna is the fundamental basis of genetic information, just as bits are for computers. Whenever computers are used to represent genetic data, the computational encoding must be efficient to allow the representation of processes driving the inheritance and variability. This is especially important across simulations in view of the increasing complexity and dimensions brought by genomics. This paper introduces a new binary representation of genetic information. Algorithms as bitwise operations that mimic the inheritance of a wide range of polymorphisms are also presented. Different kinds and mixtures of polymorphisms are discussed and exemplified. Proposed algorithms and data structures were implemented in C++ programming language and is available to end users in the R package “isqg” which is available at the R repository (cran). Supplementary data are available online.
A new real-time retinal tracking system for image-guided laser treatment

A new system is proposed for tracking sensitive areas in the retina for computer-assisted laser treatment of choroidal neovascularization (CNV). The system consists of a fundus camera using red-free illumination mode interfaced to a computer that allows real-time capturing of video input. The first image acquired is used as the reference image and utilized by the treatment physician for treatment planning. A grid of seed contours over the whole image is initiated and allowed to deform by splitting and/or merging according to preset criteria until the whole vessel tree is demarcated. Then, the image is filtered using a one-dimensional Gaussian filter in two perpendicular directions to extract the core areas of such vessels. Faster segmentation can be obtained for subsequent images by automatic registration to compensate for eye movement and saccades. An efficient registration technique is developed whereby some landmarks are detected in the reference frame then tracked in the subsequent frames. Using the relation between these two sets of corresponding points, an optimal transformation can be obtained. The implementation details of proposed strategy are presented and the obtained results indicate that it is suitable for real-time location determination and tracking of treatment positions.
Effects of mobilities on the research output and its multidisciplinarity of academics in Hong Kong and Macau: An exploratory study

This article explores how the past mobilities of academics affect their current research output (and its multidisciplinarity). Five types of mobility are used simultaneously in the analysis. Field mobility and transnational educational mobility are associated with academics’ educational path, whereas transnational job mobility, intrasectoral job mobility and intersectoral job mobility refer to their career path. The analysis is based on a representative sample of academics based in Hong Kong and Macau. Results show that intrasectoral job mobility (up to a threshold) and transnational job mobility positively affect research output and its multidisciplinarity, whereas intersectoral job mobility, field mobility and transnational educational mobility exert slight or no effect. Nested analyses of Science, Technology, Engineering and Mathematics (STEM) and non-STEM academics as well as experienced and junior academics offer further insight into the roles of these mobilities. Impacts of mobile experience were stronger among junior than senior academics, and in STEM fields than non-STEM fields. The article discusses these findings along with the significance of considering mobilities rather than mobility when analysing academic trajectories and the determinants of academic research production.
Analyzing brain signals using decision trees: an approach based on neuroscience

This paper presents a case study of treatment of brain signals using decision trees to classify of these signals, and they are analysed based on neuroscience. We have collected brain signals for 3 subjects during an imagination task and we classify these signals using decision trees, a supervised machine learning method. To analyse the processing data in neuroscience, we defined the matching between the electrodes position and the corresponding functions. The results are promising, because we can better understand the brain e its functionalities.
WNT2 Promotes Cervical Carcinoma Metastasis and Induction of Epithelial-Mesenchymal Transition

Background Previously, we found an 11-gene signature could predict pelvic lymph node metastasis (PLNM), and WNT2 is one of the key genes in the signature. This study explored the expression and underlying mechanism of WNT2 in PLNM of cervical cancer. Methods WNT2 expression level in cervical cancer was detected using western blotting, quantitative PCR, and immunohistochemistry. Two WNT2-specific small interfering RNAs (siRNAs) were used to explore the effects of WNT2 on invasive and metastatic ability of cancer cells, and to reveal the possible mechanism of WNT2 affecting epithelial—mesenchymal transition (EMT). The correlation between WNT2 expression and PLNM was further investigated in clinical cervical specimens. Results Both WNT2 mRNA and protein expression was upregulated in cervical cancer. High WNT2 expression was significantly associated with tumor size, lymphovascular space involvement, positive parametrium, and most importantly, PLNM. PLNM and WNT2 expression were independent prognostic factors for overall survival and disease-free survival. WNT2 knockdown inhibited SiHa cell motility and invasion and reversed EMT by inhibiting the WNT2/β-catenin pathway. WNT2 overexpression in cervical cancer was associated with β-catenin activation and induction of EMT, which further contributed to metastasis in cervical cancer. Conclusion WNT2 might be a novel predictor of PLNM and a promising prognostic indicator in cervical cancer.
Sulfur-Oxidizing Bacteria in Soap Lake (Washington State), a Meromictic, Haloalkaline Lake with an Unprecedented High Sulfide Content

ABSTRACT Culture-dependent and -independent techniques were used to study the diversity of chemolithoautotrophic sulfur-oxidizing bacteria in Soap Lake (Washington State), a meromictic, haloalkaline lake containing an unprecedentedly high sulfide concentration in the anoxic monimolimnion. Both approaches revealed the dominance of bacteria belonging to the genus Thioalkalimicrobium, which are common inhabitants of soda lakes. A dense population of Thioalkalimicrobium (up to 107 cells/ml) was found at the chemocline, which is characterized by a steep oxygen-sulfide gradient. Twelve Thioalkalimicrobium strains exhibiting three different phenotypes were isolated in pure culture from various locations in Soap Lake. The isolates fell into two groups according to 16S rRNA gene sequence analysis. One of the groups was closely related to T. cyclicum, which was isolated from Mono Lake (California), a transiently meromictic, haloalkaline lake. The second group, consisting of four isolates, was phylogenetically and phenotypically distinct from known Thioalkalimicrobium species and unique to Soap Lake. It represented a new species, for which we suggest the name Thioalkalimicrobium microaerophilum sp. nov.
Transformational Leadership and Burnout within the Swedish Construction Industry

This study investigated the relationship between perception of transformational leadership and burnout experience and determined the mediation effect of organizational factors on this specific relationship within a Swedish construction company. Further, differences between blue- and white-collar workers in the perception of transformational leadership and burnout experiences were examined. It was found that the perceived transformational leadership style can predict the burnout dimensions cynicism and professional efficacy, but not the exhaustion dimension. As hypothesized, white-collar workers perceive their leaders as more transformational than their blue-collar colleagues. No significant differences between the workers were identified in terms of burnout experience. Analyzed in separate mediation models, the organizational context factors reward and values were found to fully mediate the relationship between transformational leadership perception and cynicism. The relationship between transformational leadership and professional efficacy was fully mediated by the organizational context factors control, fairness, reward, and values. The study emphasizes the importance of transformational leadership and organizational context factors for burnout prevention in the construction industry and gives several implications for this field of studies. (Less)
A Speech-based Just-in-Time Retrieval System using Semantic Search

The Automatic Content Linking Device is a just-in-time document retrieval system which monitors an ongoing conversation or a monologue and enriches it with potentially related documents, including multimedia ones, from local repositories or from the Internet. The documents are found using keyword-based search or using a semantic similarity measure between documents and the words obtained from automatic speech recognition. Results are displayed in real time to meeting participants, or to users watching a recorded lecture or conversation.
Assessing readiness for business process reengineering

Purpose – The purpose of this paper is to propose how to minimize the risks of implementing business process reengineering (BPR) by measuring readiness. For this purpose, the paper proposes an assessment approach for readiness in BPR efforts based on the critical success and failure factors.Design/methodology/approach – A relevant literature review, which investigates success and failure indicators in BPR efforts is carried out and a new categorized list of indicators are proposed. This is a base for conducting a survey to measure the BPR readiness, which has been run in two companies and compared based on a diamond model.Findings – In this research, readiness indicators are determined based on critical success and failure factors. The readiness indicators include six categories. The first five categories, egalitarian leadership, collaborative working environment, top management commitment, supportive management, and use of information technology are positive indicators. The sixth category, resistance to .
Surgical Histopathology of Benign Ovarian Cysts: A Multicentre Study

Background and Objective: Ovarian tumors are among the most frequent pathologic conditions in gynecologic practice and a frequent cause of hospitalization and surgery. The aim of this study was to determine histologic distribution of benign operated masses especially functional ovarian cysts. Material and Methods: Benign ovarian files of operated patients (2961 cases) in 20 tertiary and secondary hospitals were reviewed regarding age and histopathology from 1998- 2005. Analysis was done by SPSS software (version 13). Results: The most common benign histologies in order of frequency were functional cyst (57%), serous cystadenoma (13%), dermoid cyst (10%), mucinous cystadenoma (7%) and endometrioma (6%). Conclusion: Functional cysts were the most common benign ovarian cyst. Nearly high distribution of functional cysts in the present study may be an index of need to management improvement and less surgical decisions in ovarian tumors.
Telemakus : A Schema-Based Information System to Promote Scientific Discovery

With the rapid expansion of scientific research, the ability to effectively find or integrate new domain knowledge in the sciences is proving increasingly difficult. While development of information systems to promote scientific discovery is being explored on a number of fronts, much of this work is based on traditional search and retrieval approaches and the bibliographic citation format remains unchanged. In the Telemakus system, aggregated citation information and content-based research findings are displayed in a conceptual schema. Dynamic mapping provides graphical displays of research interrelationships from documents across a domain. We describe a working implementation of a system designed to enhance the knowledge discovery process through graphical presentation and interaction tools to mine and map author-reported research findings and their associated methods.
The Tumor-Suppressive Function of UNC5D and Its Repressed Expression in Renal Cell Carcinoma

Purpose: As a newly added member of the UNC5H receptors, the function of UNC5D/H4 in tumorigenesis remains poorly defined. The aim of this study was to examine the expression of UNC5D in primary renal cell carcinomas (RCC), analyze the mechanisms responsible for its downregulation in RCC, and assess its functional relevance to tumor growth and migration. Experimental Design: Forty-four paired primary RCCs and corresponding adjacent noncancerous tissues were collected. The mRNA and protein expression level of UNC5D was assessed by reverse transcriptase-PCR, real-time PCR, or immunohistochemistry. Epigenetic alterations in UNC5D promoter and LOH in the UNC5D locus were also analyzed. Ectopic expression of UNC5D in renal cancer cells with silenced expression of UNC5D was used for analysis of the biologic functions of UNC5D. Results: UNC5D expression was attenuated in multiple carcinoma cell lines including renal cancer cells. Similar reduction was also observed in primary RCC tissues as compared with paired adjacent noncancerous tissues. Methylation-specific PCR showed hypermethylation in UNC5D promoter in a significant proportion (18 of 44) of tumor tissue (40.9%). LOH of UNC5D was observed in 13 of 44 patients with RCCs (29.5%). Restoration of UNC5D expression in renal cancer cells significantly inhibited cell proliferation, anchorage-dependent and -independent growth, as well as migration and invasion, whereas knockdown of UNC5D promoted cell growth. Furthermore, ectopic expression of UNC5D induced G2–M cell-cycle arrest. Conclusions: UNC5D is a functional tumor suppressor that is frequently downregulated in RCCs due to promoter hypermethylation and LOH. Clin Cancer Res; 19(11); 2883–92. ©2013 AACR.
Verbal memory processing and fMRI: syntax versus semantics

This thesis examined semantic and syntactic components of verbal encoding in young adults. Participants were asked to judge phrases based on semantic and syntactic information. Recognition and recall tasks measured retention of words encoded using each strategy. FMRI BOLD signal was evaluated in predicted language regions of interest during verbal encoding and the correlation with behavioral data was examined. Results showed increased activation for semantically encoded words within the left (Brodmann’s Area (BA) 21, BA 37, BA 45, and BA 47) and right hemisphere (BA 46). Significant activation was found within left BA 44 and BA 46 for semantic and syntactically encoded words. Correlations between fMRI activation and behavioral measures were not significant. Semantic processes appear to facilitate memory over syntactic processing in accordance with the levels of processing memory model (Craik & Lockhart, 1972) but no significant changes in fMRI activation correlate with rate of memory recall.
Protective Efficacy of BCG Overexpressing an L,D-Transpeptidase against M. tuberculosis Infection

Background M. bovis Bacille Calmette-Guérin (BCG), currently the only available vaccine against tuberculosis (TB), fails to adequately protect individuals from active and latent TB infection. New vaccines are desperately needed to decrease the worldwide burden of TB. Methods and Findings We created a recombinant strain of BCG that overproduces an L,D-transpeptidase in order to alter the bacterial peptidoglycan layer and consequently increase the ability of this immunogen to protect against virulent M. tuberculosis (Mtb). We demonstrate that this novel recombinant BCG protects mice against virulent Mtb at least as well as control BCG, as measured by its ability to reduce bacterial burden in lungs and spleen, reduce lung histopathology, and prolong survival. A nutrient starved recombinant BCG preparation, while offering comparable protection, elicited a response characterized by elevated levels of select Th1 cytokines. Conclusions Recombinant BCG overexpressing a L,D-transpeptidase that is nutrient starved elicits a stronger Th1 type response and is at least as protective as parent BCG. Results from this study suggest that nutrient starvation treatment of live BCG vaccines should be further investigated as a way to increase host induction of Th-1 related cytokines in the development of experimental anti-TB vaccines.
Quantum Measurement Theory in Gravitational-Wave Detectors

The fast progress in improving the sensitivity of the gravitational-wave detectors, we all have witnessed in the recent years, has propelled the scientific community to the point at which quantum behavior of such immense measurement devices as kilometer-long interferometers starts to matter. The time when their sensitivity will be mainly limited by the quantum noise of light is around the corner, and finding ways to reduce it will become a necessity. Therefore, the primary goal we pursued in this review was to familiarize a broad spectrum of readers with the theory of quantum measurements in the very form it finds application in the area of gravitational-wave detection. We focus on how quantum noise arises in gravitational-wave interferometers and what limitations it imposes on the achievable sensitivity. We start from the very basic concepts and gradually advance to the general linear quantum measurement theory and its application to the calculation of quantum noise in the contemporary and planned interferometric detectors of gravitational radiation of the first and second generation. Special attention is paid to the concept of the Standard Quantum Limit and the methods of its surmounting.
Par-KAP: a Knowledge Acquisition Tool for Building Practical Planning Systems

Recently, attention has been focused on providing Knowledge Acquisition (KA) support for building practical planning systems. Such support is needed to guide a knowledge engineer in selecting planning methods, as well as for building and validating the planning knowledge-base for a given practical domain. Following current practice in knowledge acquisition, developing KA tools for planning requires that a number of planning knowledge components are made explicit. This includes explicating (i) a planning domain ontology, (ii) a library of problem-solving methods (PSMs) used in planning, and (iii) a set of domain requirements that are used to select a suitable PSM. In this paper, we summarize the planning knowledge components which we have identified in previous work, and, based on these, present an implementation (Par-KAP) that can exploit these models to aid knowledge engineers in constructing practical planning systems.
Educating and Supporting Tennis Parents Using Web-Based Delivery Methods: A Novel Online Education Program

This study evaluated the effectiveness of a novel online education program for British tennis parents and their experiences of engaging in the program. Using a convergent parallel mixed-methods design, 13 parents completed pre- and post-program online questionnaires, and a subset of 9 participants shared their experiences via an asynchronous e-mail interview. Quantitative findings revealed positive directional changes for almost all of the variables in relation to emotional experiences, goal orientations, tennis parent efficacy, and general parenting efficacy. The contribution of the combined quantitative and qualitative findings and their practical implications are discussed.
Performance of Ultra-Wideband Transmission over 60GHz WPAN Channel

In this paper we evaluate the system performance and outage probability of impulse radio ultra-wideband (UWB) transmission over the practical 60GHz wireless personal area network (WPAN) channel. The modulation scheme employed is DS-BPSK. A general system capacity and performance evaluation approach based on moment generation function (MGF) is introduced. Based on the current IEEE wireless personal area network (WPAN) standard documents, different transmission scenarios have been explored and the performances with RAKE reception has been obtained. The channel model is based on the recent work of IEEE 802.15 WPAN group. Analysis on symbol error probability (SEP) and outage probabilities are provided and numerical results are given to illustrate the system performance
Discovery Potential for the SM Higgs Boson in the Inclusive Search Channels

This paper gives an overview of the potential to discover a Standard Model Higgs Boson in the inclusive search channels at the ATLAS and CMS experiments at the LHC. The most important decay modes, H ! gg, H ! WW ! llnn and H ! ZZ ! 4l are described and a summary of recently published analyses using realistic detector simulations is presented.
A New MPLS-Based Quality of Service Architecture for Wireless Mesh Networks

In this work we describe and analyze a new Quality of Service (QoS) architecture for wireless mesh networks. Such architecture is mainly composed of two components, i.e. a new admission control criteria for flows and a new link metric. The first allows to only admit flows whose required QoS (specified in terms of bandwidth) can be guaranteed, while the latter allows to maximize the number of accepted flows. In particular, the admission control criteria is designed to precisely evaluate the available bandwidth of the WMN links, which depends not only on the transmission rate of the link but also on the number and the transmission rates of the links in the neighboorhood working on the same channel. The new link metric, instead, is designed to select paths for flows so as to reduce the usage of resources. The proposed architecture relies on the ability of explicitly routing flows. To this purpose, we chose to employ MPLS (Multi Protocol Label Switching), which is able to finely control the path of each single flow. Such possibility further allows to increase the number of accepted flows by exploiting bandwidth where available.
Sexual exploitation of adolescent students in Tanzania: Implication for social services

A considerable empirical research has been conducted on sexual exploitation of children and adolescents; however, limited information is available in developing countries. This study describes and discusses the prevalence, nature and characteristics of sexual exploitation of adolescents using data collected from 1116 secondary school students in Tanzania. Results indicate that 21 percent of the surveyed adolescent students had had at least one experience of sexual exploitation. Being a female, living in rural areas and being aged above 15 years were associated with high risk of sexual exploitation. This study underscores gender- and locality-specific social work interventional requirements, with emphasis on interdisciplinary collaborative efforts.