Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying genes and regulatory pathways associated with the scleractinian coral calcification process

Reef building corals precipitate calcium carbonate as an exo-skeleton and provide substratum for prosperous marine life. Biomineralization of the coral’s skeleton is a developmental process that occurs concurrently with other proliferation processes that control the animal extension and growth. The development of the animal body is regulated by large gene regulatory networks, which control the expression of gene sets that progressively generate developmental patterns in the animal body. In this study we have explored the gene expression profile and signaling pathways followed by the calcification process of a basal metazoan, the Red Sea scleractinian (stony) coral, Stylophora pistillata. When treated by seawater with high calcium concentrations (addition of 100 gm/L, added as CaCl2.2H2O), the coral increases its calcification rates and associated genes were up-regulated as a result, which were then identified. Gene expression was compared between corals treated with elevated and normal calcium concentrations. Calcification rate measurements and gene expression analysis by microarray RNA transcriptional profiling at two time-points (midday and night-time) revealed several genes common within mammalian gene regulatory networks. This study indicates that core genes of the Wnt and TGF-β/BMP signaling pathways may also play roles in development, growth, and biomineralization in early-diverging organisms such as corals.
Tessellating Cell Shapes for Geographical Clustering

This paper investigates the energy-saving organization of sensor nodes in large wireless sensor networks. Due to a random deployment used in many application scenarios, much more nodes need to be deployed to achieve a complete sensor coverage than theoretically needed in case of an ideal deployment. Consequently, most of the deployed nodes are redundant and can be switched-off for a long time to save energy. A well-known principle to detect the redundancy of nodes is to divide sensor network into equally sized cells. Assuming a well chosen cell size, depending on transmission range and sensing range, it is possible to switch-off all nodes but one per cell. The idea was applied in the extended geographic adaptive fidelity algorithm (XGAF), which divides the network into virtual square cells. In the current work, we improve the idea of XGAF by using different tessellating cell shapes, namely triangles, pentagons and hexagons. Furthermore, we examine the cell shapes in terms of coverage, connectivity and average hop count.
Mathematical Modeling of the Dynamics of Macroscopic Structural Transformations in Self-Propagating High-Temperature Synthesis

Homogeneous and heterogeneous mathematical models of the formation of the macroscopic structure of products in SHS in the case of spontaneous structural formation and under the action of constant exothermal load were described. Equations, auxiliary relations and conditions for the simplification of models were given. A list of works devoted to the modeling of macrostructural transformations and a summary of the main results was provided. P ossible directions for further development of research on the structural dynamics of a substance in SHS were proposed.
Effects of Self-Efficacy, Satisfaction, and Personal Goals on Swimming Performance

The present study tested the effects of self-efficacy, past performance, personal goal setting, and self-satisfaction on swimming performance. Participants (N = 42) performed four trials of a specific swimming task with 10-min intervals between each trial. During the third and fourth trials they performed trials after setting personal goals and completing self-efficacy and selfsatisfaction scales. Results showed significant improvement in level of performance in these two trials. Past performance, self-efficacy, self-satisfaction, and personal goal setting were predictors of performance at the third and the fourth trial. A LISREL VI path analysis indicated that past performance was the main determinant of future performance. Personal goal setting was affected by level of past performance, as well as by perceived self-efficacy and satisfaction. In a second stage of analysis, past performance was eliminated, and results supported the mediating role of personal goals between self-efficacy and performance.
Truncating the Loop Series Expansion for Belief Propagation

Recently, Chertkov and Chernyak (2006b) derived an exact expression for the partition sum (normalization constant) corresponding to a graphical model, which is an expansion around the belief propagation (BP) solution. By adding correction terms to the BP free energy, one for each "generalized loop" in the factor graph, the exact partition sum is obtained. However, the usually enormous number of generalized loops generally prohibits summation over all correction terms. In this article we introduce truncated loop series BP (TLSBP), a particular way of truncating the loop series of Chertkov & Chernyak by considering generalized loops as compositions of simple loops. We analyze the performance of TLSBP in different scenarios, including the Ising model on square grids and regular random graphs, and on PROMEDAS, a large probabilistic medical diagnostic system. We show that TLSBP often improves upon the accuracy of the BP solution, at the expense of increased computation time. We also show that the performance of TLSBP strongly depends on the degree of interaction between the variables. For weak interactions, truncating the series leads to significant improvements, whereas for strong interactions it can be ineffective, even if a high number of terms is considered.
Listeria monocytogenes LO28: Surface Physicochemical Properties and Ability To Form Biofilms at Different Temperatures and Growth Phases

ABSTRACT The surface physicochemical properties of Listeria monocytogenes LO28 under different conditions (temperature and growth phase) were determined by use of microelectrophoresis and microbial adhesion to solvents. The effect of these parameters on adhesion and biofilm formation by L. monocytogenes LO28 on hydrophilic (stainless steel) and hydrophobic (polytetrafluoroethylene [PTFE]) surfaces was assessed. The bacterial cells were always negatively charged and possessed hydrophilic surface properties, which were negatively correlated with growth temperature. The colonization of the two surfaces, monitored by scanning electron microscopy, epifluorescence microscopy, and cell enumeration, showed that the strain had a great capacity to colonize both surfaces whatever the incubation temperature. However, biofilm formation was faster on the hydrophilic substratum. After 5 days at 37 or 20°C, the biofilm structure was composed of aggregates with a three-dimensional shape, but significant detachment took place on PTFE at 37°C. At 8°C, only a bacterial monolayer was visible on stainless steel, while no growth was observed on PTFE. The growth phase of bacteria used to inoculate surfaces had a significant effect only in some cases during the first steps of biofilm formation. The surface physicochemical properties of the strain are correlated with adhesion and surface colonization.
Bacteria, biofilm and honey: A study of the effects of honey on ‘planktonic’ and biofilm-embedded chronic wound bacteria

Chronically infected wounds are a costly source of suffering. An important factor in the failure of a sore to heal is the presence of multiple species of bacteria, living cooperatively in highly organized biofilms. The biofilm protects the bacteria from antibiotic therapy and the patient's immune response. Honey has been used as a wound treatment for millennia. The components responsible for its antibacterial properties are now being elucidated. The study aimed to determine the effects of different concentrations of ‘Medihoney™’ therapeutic honey and Norwegian Forest Honey 1) on the real-time growth of typical chronic wound bacteria; 2) on biofilm formation; and 3) on the same bacteria already embedded in biofilm. Reference strains of MRSE, MRSA, ESBL Klebsiella pneumoniae and Pseudomonas aeruginosa were incubated with dilution series of the honeys in microtitre plates for 20 h. Growth of the bacteria was assessed by measuring optical density every 10 min. Growth curves, biofilm formation and minimum bactericidal concentrations are presented. Both honeys were bactericidal against all the strains of bacteria. Biofilm was penetrated by biocidal substances in honey. Reintroduction of honey as a conventional wound treatment may help improve individual wound care, prevent invasive infections, eliminate colonization, interrupt outbreaks and thereby preserve current antibiotic stocks.
NASA’s UAS Integration into the NAS

In 2011 the National Aeronautics and Space Administration (NASA) began a five-year Project to address the technical barriers related to routine access of Unmanned Aerial Systems (UAS) in the National Airspace System (NAS). Planned in two phases, the goal of the first phase was to lay the foundations for the Project by identifying those barriers and key issues to be addressed to achieve integration. Phase 1 activities were completed two years into the five-year Project. The purpose of this paper is to review activities within the Human Systems Integration (HSI) subproject in Phase 1 toward its two objectives: 1) develop GCS guidelines for routine UAS access to the NAS, and 2) develop a prototype display suite within an existing Ground Control Station (GCS). The first objective directly addresses a critical barrier for UAS integration into the NAS – a lack of GCS design standards or requirements. First, the paper describes the initial development of a prototype GCS display suite and supporting simulation software capabilities. Then, three simulation experiments utilizing this simulation architecture are summarized. The first experiment sought to determine a baseline performance of UAS pilots operating in civil airspace under current instrument flight rules for manned aircraft. The second experiment examined the effect of currently employed UAS contingency procedures on Air Traffic Control (ATC) participants. The third experiment compared three GCS command and control interfaces on UAS pilot response times in compliance with ATC clearances. The authors discuss how the results of these and future simulation and flight-testing activities contribute to the development of GCS guidelines to support the safe integration of UAS into the NAS. Finally, the planned activities for Phase 2, including an integrated human-in-the-loop simulation and two flight tests are briefly described.
A Positron Emission Tomography Study of the 5-Ht1A Receptor in Schizophrenia and during Clozapine Treatment

Several post-mortem studies have identified increases of 5-HT1A receptor density in frontal cortical areas in schizophrenic patients, and one has found increases in the cerebellar vermis. Clozapine has moderate affinity at the 5-HT1A receptor, and this may be of therapeutic importance. This positron emission tomography (PET) study attempted to replicate the post-mortem findings in vivo and sought an occupancy effect of clozapine at the 5-HT1A receptor. We recruited healthy controls, and patients with schizophrenia who were divided into those receiving clozapine and those receiving neuroleptics lacking 5-HT1A receptoraffinity. Each volunteer received a PET scan, using the 5-HT1A receptor radioligand [carbonyl-11C]WAY-100635, and a magnetic resonanceimaging scan. The cerebellar vermis was examined by comparing time-activity data between groups. For other brain regions (the raphe and subdivisions of the cerebral cortex), binding potential images weregenerated to reflect receptor density, then analysed using ‘region of interest’ and voxel-by-voxel methods. No significant changes of 5-HT1A receptor density were found in schizophrenic patients compared tocontrols. Two other PET studies, containing drug naïve rather thanmedicated schizophrenic patients, have also reported no increase in 5-HT1A receptor density in the frontal cortex. The results obtained in vivo bring into question the importance of the receptor in thepathophysiology of the illness. Clozapine did not occupy the 5-HT1A receptor at clinical doses. This is consistent with recent related PET results: 5-HT1A agonists do not appear to measurably block the binding of antagonist radiotracers in man at doses that are pharmacologically active but which are limited by tolerability.
African American Men in Heterosexual Relationships

AfricanAmericanmeninheterosexualrelationshipsarevirtuallyinvisibleinthetheoret-ical and empirical psychological HIV/AIDS literature. This article posits that two theo-retical frameworks—masculinityideologies (MI)andsociocultural context—are impor-tant for comprehending Black men’s condom use. Qualitative methods, althoughrelativelyrareinU.S. psychology,arecriticaltounderstandingthecontextoflivedexpe-rience, particularly with underresearched populations and topics. This study involvedsemistructured interviews with lower-middle-income African American men (
Regional variation of nonimmunologic contact urticaria. Functional map of the human face.

BACKGROUND AND DESIGN Benzoic acid (BA) was used to induce nonimmunologic contact irritation in 10 younger (23-47 years old) and 5 older (72-90 years old) healthy volunteers. BA 2.5% in petrolatum was applied to 8 locations on the face, neck and volar forearm. Changes in the skin blood flow were monitored using a laser Doppler flowmeter. Also measured at each location were baseline measurements of skin blood flow, transepidermal water loss, stratum corneum hydration, skin surface temperature and skin surface pH. RESULTS The neck area exhibited the greatest reaction in both age groups while the forearm exhibited the least. At each site tested, the younger group consistently demonstrated greater reactivity to BA. A significant correlation was noted between stratum corneum hydration and irritation. CONCLUSIONS This information provides a basis to further study the frequent poorly understood intolerance of the face to topical formulation.
Identification and functional analysis of the essential and regulatory light chains of the only type II myosin Myo 1 p in Saccharomyces cerevisiae

ytokinesis in Saccharomyces ce revisiae involves coordination between actomyosin ring contraction and septum formation and/or targeted membrane deposition. We show that Mlc1p, a light chain for Myo2p (type V myosin) and Iqg1p (IQGAP), is the essential light chain for Myo1p, the only type II myosin in S. cerevisiae . However, disruption or reduction of Mlc1p–Myo1p interaction by deleting the Mlc1p binding site on Myo1p or by a point mutation in MLC1 , mlc1-93 , did not cause any obvious defect in cytokinesis. In contrast, a different point C mutation, mlc1-11 , displayed defects in cytokinesis and in interactions with Myo2p and Iqg1p. These data suggest that the major function of the Mlc1p–Myo1p interaction is not to regulate Myo1p activity but that Mlc1p may interact with Myo1p, Iqg1p, and Myo2p to coordinate actin ring formation and targeted membrane deposition during cytokinesis. We also identify Mlc2p as the regulatory light chain for Myo1p and demonstrate its role in Myo1p ring disassembly, a function likely conserved among eukaryotes.
A resonant compensation method for improving the performance of capacitively coupled power transfer system

Capacitively coupled power transfer (CCPT) has been proposed as an alternative contactless/wireless power transfer solution. Unlike inductively coupled power transfer (ICPT), CCPT transfers power via electric field coupling, which is usually modeled as coupling capacitance. As the coupling capacitance of a CCPT system is normally very small due to practical constraints, its impedance needs to be compensated to increase the power transfer capability of the system. In this paper, a new resonant compensation method using an additional inductor and capacitor is proposed to improve the performance of CCPT system. A state space model of the system is established to analyze the characteristics of the proposed system based on a class E converter, and a practical prototype is built and tested which demonstrates that the new compensation method increases the output power transfer capability and serves as a band pass filter for reducing the switching harmonics propagation from the power converter to the load.
Software Repositories: A Source for Traceability Links

paper analyzes six open source projects in order to assess software repositories, such as those managed by Subversion, as a source for uncovering/discovering traceability links between different types of software artifacts. Our finding suggests that software repositories store a variety of artifacts that are central to open source development and use. Furthermore, a heuristic-based approach that uses sequential-pattern mining is presented. This approach analyzes commits in a version history to mine for highly frequent co-occurring changes to different artifacts (e.g., source code and documentation). The hypothesis is if different types of artifacts are committed together frequently then there is a high probability that they have a traceability link between them. Examples of mined traceability links from our preliminary experimentation on mining KDE (K Desktop Environment) repositories are presented.
Renal nerve ablation after SYMPLICITY HTN-3: confused at the higher level?

In spite of all the medical progress, hypertension remains a highly prevalent chronic disease worldwide, contributing importantly to cardiovascular morbidity and mortality in Europe1 and around the globe. Indeed, it has been estimated that in the not too distant future up to 50% of the adult population will develop high blood pressure according to currently used definitions.2 Since Franklin D. Roosevelt died of a cerebral haemorrhage in 1945 due to uncontrolled high blood pressure with values up to 300/190 mmHg, the management of hypertension has made impressive progress. Indeed, while at that time only Kempner's rice diet was available, after the war diuretics, reserpine, guanethidine, and later beta-blockers, spironolactone, calcium antagonists, and angiotensin-converting enzyme (ACE) inhibitors became available. Today, with the advent of angiotensin receptor blockers, renin inhibitors, eplerenone, and beta-blockers, the pharmacological armamentarium to treat high blood pressure has become quite vast, and most patients can be controlled with 1–3 antihypertensive drugs to levels of ≤140/90 mmHg.3 Thanks to this success, it appeared that antihypertensive management had reached its goals and no further developments would be required. Nevertheless, it has been recognized that a small, but significant portion of patients remains uncontrolled in spite of the many drugs available today.4 The European Society of Cardiology together with the European Society of Hypertension, as well as their American counterparts have defined treatment-resistant hypertension as blood pressure values > 140/90 mmHg in spite of three antihypertensive drugs including a diuretic.2 It has been estimated that between 3% and 5% of the patients would fall into this category.5 As the event rates are staggeringly high in this patient population, additional treatment options are an unmet clinical need.6 It has been argued that many of the patients with so-called treatment-resistant hypertension are in fact just non-compliant …
Vitamin D is significantly associated with total testosterone and sex hormone-binding globulin in Malaysian men

Abstract Objective: Cross-sectional studies in the Caucasian population have shown a significant relationship between vitamin D and testosterone levels, but data in the Asian population are limited. This study aimed to determine the association between vitamin D and testosterone levels in Malaysian men. Methods: Chinese and Malay men (n = 382) aged 20 years or above residing in the Klang Valley, Malaysia were recruited. Their fasting blood was collected for serum testosterone, sex hormone-binding globulin (SHBG) and 25-hydroxyvitamin D (25(OH)D) assays. Relationship between 25(OH)D and testosterone levels was analyzed using multiple regression analysis. Testosterone and SHBG levels among subjects with different vitamin D status were compared using univariate analysis. Confounders such as age, ethnicity and body mass index (BMI) were adjusted. Results: 25(OH)D was significantly and positively associated with total testosterone and SHBG levels before and after adjustment for age and ethnicity (p < 0.05). Only association with SHBG remained significant after further adjustment for BMI (p < 0.05). Total testosterone and SHBG values displayed an increasing trend from subjects with vitamin D deficiency to those with optimal level (p < 0.05). The trend was attenuated after adjustment for BMI (p > 0.05). Conclusion: 25(OH)D is significantly associated with total testosterone and SHBG in Malaysian men but this association is BMI-dependent.
ERP and E-Business Systems Development, Innovation and Business Performance--An Empirical Investigation

There has been extensive theoretical work on the potential of information and communication technologies (ICT) to drive significant innovations, which can dramatically enhance firms' performance. However, this potential has not been sufficiently investigated empirically. This paper investigates empirically and compares i) the effects of the two most widely used types of information systems (IS), the ERP and the e-business ones, on innovation, and also ii) to what extent their effects on business performance are through (i.e. mediated by) the innovation they drive. It is concluded that both ERP and e-business IS have positive impact on innovation, with the former being a stronger driver of innovation than the latter. However, most of their positive impact on business performance is mainly through automation and support of existing processes, and only a smaller part of it (20% for the ERP and 30% for the e-business IS) is through innovation.
RNASEQR—a streamlined and accurate RNA-seq sequence analysis program

Next-generation sequencing (NGS) technologies-based transcriptomic profiling method often called RNA-seq has been widely used to study global gene expression, alternative exon usage, new exon discovery, novel transcriptional isoforms and genomic sequence variations. However, this technique also poses many biological and informatics challenges to extracting meaningful biological information. The RNA-seq data analysis is built on the foundation of high quality initial genome localization and alignment information for RNA-seq sequences. Toward this goal, we have developed RNASEQR to accurately and effectively map millions of RNA-seq sequences. We have systematically compared RNASEQR with four of the most widely used tools using a simulated data set created from the Consensus CDS project and two experimental RNA-seq data sets generated from a human glioblastoma patient. Our results showed that RNASEQR yields more accurate estimates for gene expression, complete gene structures and new transcript isoforms, as well as more accurate detection of single nucleotide variants (SNVs). RNASEQR analyzes raw data from RNA-seq experiments effectively and outputs results in a manner that is compatible with a wide variety of specialized downstream analyses on desktop computers.