Miracle-dz/UniFAR-FTUs huggingface dataset:
TarBase: A comprehensive database of experimentally supported animal microRNA targets.

MicroRNAs (miRNAs) are approximately 22-nt RNA segments that are involved in the regulation of protein expression primarily by binding to one or more target sites on an mRNA transcript and inhibiting translation. MicroRNAs are likely to factor into multiple developmental pathways, multiple mechanisms of gene regulation, and underlie an array of inherited disease processes and phenotypic determinants. Several computational programs exist to predict miRNA targets in mammals, fruit flies, worms, and plants. However, to date, there is no systematic collection and description of miRNA targets with experimental support. We describe a database, TarBase, which houses a manually curated collection of experimentally tested miRNA targets, in human/mouse, fruit fly, worm, and zebrafish, distinguishing between those that tested positive and those that tested negative. Each positive target site is described by the miRNA that binds it, the gene in which it occurs, the nature of the experiments that were conducted to test it, the sufficiency of the site to induce translational repression and/or cleavage, and the paper from which all these data were extracted. Additionally, the database is functionally linked to several other useful databases such as Gene Ontology (GO) and UCSC Genome Browser. TarBase reveals significantly more experimentally supported targets than even recent reviews claim, thereby providing a comprehensive data set from which to assess features of miRNA targeting that will be useful for the next generation of target prediction programs. TarBase can be accessed at http://www.diana. pcbi.upenn. edu/tarbase.
Effect of the specific proteasome inhibitor bortezomib on cancer‐related muscle wasting

Muscle wasting, a prominent feature of cancer cachexia, is mainly caused by sustained protein hypercatabolism. The enhanced muscle protein degradation rates rely on the activity of different proteolytic systems, although the Adenosine triphosphate (ATP)‐ubiquitin‐proteasome‐dependent pathway and autophagy have been shown to play a pivotal role. Bortezomib is a potent reversible and selective proteasome and NF‐κB inhibitor approved for the clinical use, which has been shown to be effective in preventing muscle wasting in different catabolic conditions. The aim of the present study has been to investigate whether pharmacological inhibition of proteasome by bortezomib may prevent skeletal muscle wasting in experimental cancer cachexia.
Performance of the minimum quantity lubrication technique in turning Inconel 718 at high cutting speed

Conventional cutting fluids used for machining processes are considered a problem for companies because these substances can cause serious damage to workers' health and nature, and are expensive to acquire and maintain, following environmental norms. Economic pressure on industries due to waste disposal is increasing progressively. Today, costs of cutting fluids can reach 20% of production costs. Dry machining with the minimum quantity lubrication (MQL) technique has triggered special interest from researchers and technicians who work in the area of material removal as an alternative to traditional fluids. There are many advantages when compared to conventional cooling. The objective of this study was to investigate the performance of several geometries of ceramic (Al2O3 + SiCw and Al2O3 + TiC) and PCBN (CB7050 with 50% CBN) tools when turning at high cutting speeds, a nickel-based alloy (Inconel 718) hardened by solution and precipitation (44HRc). The experiments were carried out under dry cutting condition using the minimum quantity lubrication technique, to meet environmental requirements. The roughness, temperature and cutting force parameters were analysed. With the results presented in this study, technological and ecological gains can be expected in machining the superalloy using MQL.
Monte Carlo simulations guided by imaging to predict the in vitro ranking of radiosensitizing nanoparticles

This article addresses the in silico–in vitro prediction issue of organometallic nanoparticles (NPs)-based radiosensitization enhancement. The goal was to carry out computational experiments to quickly identify efficient nanostructures and then to preferentially select the most promising ones for the subsequent in vivo studies. To this aim, this interdisciplinary article introduces a new theoretical Monte Carlo computational ranking method and tests it using 3 different organometallic NPs in terms of size and composition. While the ranking predicted in a classical theoretical scenario did not fit the reference results at all, in contrast, we showed for the first time how our accelerated in silico virtual screening method, based on basic in vitro experimental data (which takes into account the NPs cell biodistribution), was able to predict a relevant ranking in accordance with in vitro clonogenic efficiency. This corroborates the pertinence of such a prior ranking method that could speed up the preclinical development of NPs in radiation therapy.
Factors associated with the prevalence of anterior open bite among preschool children: A population-based study in Brazil

INTRODUCTION: The aim of this study was to identify factors associated with the prevalence of anterior open bite among five-year-old Brazilian children. METHODS: A cross-sectional study was undertaken using data from the National Survey of Oral Health (SB Brazil 2010). The outcome variable was anterior open bite classified as present or absent. The independent variables were classified by individual, sociodemographic and clinical factors. Data were analyzed through bivariate and multivariate analysis using SPSS statistical software (version 18.0) with a 95% level of significance. RESULTS: The prevalence of anterior open bite was 12.1%. Multivariate analysis showed that preschool children living in Southern Brazil had an increased chance of 1.8 more times of having anterior open bite (CI 95%: 1.16 - 3.02). Children identified with alterations in overjet had 14.6 times greater chances of having anterior open bite (CI 95%: 8.98 - 24.03). CONCLUSION: There was a significant association between anterior open bite and the region of Brazil where the children lived, the presence of altered overjet and the prevalence of posterior crossbite.
Mechanical properties of asthmatic airway smooth muscle

Airway smooth muscle (ASM) is the major effector of excessive airway narrowing in asthma. Changes in some of the mechanical properties of ASM could contribute to excessive narrowing and have not been systematically studied in human ASM from nonasthmatic and asthmatic subjects. Human ASM strips (eight asthmatic and six nonasthmatic) were studied at in situ length and force was normalised to maximal force induced by electric field stimulation (EFS). Measurements included: passive and active force versus length before and after length adaptation, the force–velocity relationship, maximal shortening and force recovery after length oscillation. Force was converted to stress by dividing by cross-sectional area of muscle. The only functional differences were that the asthmatic tissue was stiffer at longer lengths (p<0.05) and oscillatory strain reduced isometric force in response to EFS by 19% as opposed to 36% in nonasthmatics (p<0.01). The mechanical properties of human ASM from asthmatic and nonasthmatic subjects are comparable except for increased passive stiffness and attenuated decline in force generation after an oscillatory perturbation. These data may relate to reduced bronchodilation induced by a deep inspiration in asthmatic subjects.
Cylindrocarpon didymum — a root pathogen of subterranean clover in the lower south-west of Western Australia

The pathogenicity ofCylindrocarpon didymum towards roots of subterranean clover (Trifolium subterraneum) at four inoculum rates (0.5, 1.0, 2.0, 5.0% w/w) under three temperature regimes (15/10, 18/13, 21/16°C) and the ability ofC. didymum to produce the mycotoxin brefeldin Ain vitro was determined.C. didymum infected and damaged tap and lateral roots of subterranean clover and reduced plant dry weights, particularly when sufficiently high levels of inoculum were present. Most disease occurred at the cooler temperature regime of 15/10°C, a temperature regime that would closely approximate field soil temperatures in the lower south-west of Western Australia during the winter months.C. didymum produced brefeldin Ain vitro and the frequently observed, stunted appearance of affected tap and lateral roots was possibly as a consequence of production of brefeldin A in the root tissue by this pathogen. This is the first published report ofC. didymum as a root pathogen of subterranean clover.
Virulence Gene Pool Detected in Bovine Group C Streptococcus dysgalactiae subsp. dysgalactiae Isolates by Use of a Group A S. pyogenes Virulence Microarray

ABSTRACT A custom-designed microarray containing 220 virulence genes of Streptococcus pyogenes (group A Streptococcus [GAS]) was used to test group C Streptococcus dysgalactiae subsp. dysgalactiae (GCS) field strains causing bovine mastitis and group C or group G Streptococcus dysgalactiae subsp. equisimilis (GCS/GGS) isolates from human infections, with the latter being used for comparative purposes, for the presence of virulence genes. All bovine and all human isolates carried a fraction of the 220 genes (23% and 39%, respectively). The virulence genes encoding streptolysin S, glyceraldehyde-3-phosphate dehydrogenase, the plasminogen-binding M-like protein PAM, and the collagen-like protein SclB were detected in the majority of both bovine and human isolates (94 to 100%). Virulence factors, usually carried by human beta-hemolytic streptococcal pathogens, such as streptokinase, laminin-binding protein, and the C5a peptidase precursor, were detected in all human isolates but not in bovine isolates. Additionally, GAS bacteriophage-associated virulence genes encoding superantigens, DNase, and/or streptodornase were detected in bovine isolates (72%) but not in the human isolates. Determinants located in non-bacteriophage-related mobile elements, such as the gene encoding R28, were detected in all bovine and human isolates. Several virulence genes, including genes of bacteriophage origin, were shown to be expressed by reverse transcriptase PCR (RT-PCR). Phylogenetic analysis of superantigen gene sequences revealed a high level (>98%) of identity among genes of bovine GCS, of the horse pathogen Streptococcus equi subsp. equi, and of the human pathogen GAS. Our findings indicate that alpha-hemolytic bovine GCS, an important mastitis pathogen and considered to be a nonhuman pathogen, carries important virulence factors responsible for virulence and pathogenesis in humans.
Pharmacologic Inhibition of JAK1/JAK2 Signaling Reduces Experimental Murine Acute GVHD While Preserving GVT Effects

Purpose: Immune-mediated graft-versus-tumor (GVT) effects can occur after allogeneic hematopoietic stem cell transplantation (HSCT), but GVT is tightly linked to its main complication, graft-versus-host disease (GVHD). Strategies aimed at modulating GVHD, while maintaining the GVT effect, are needed to improve the cure rate of transplant. Given the emerging role of Janus-activated kinase (JAK) signaling in lymphoproliferative and myeloproliferative diseases and its established function at dictating T-cell differentiation, we postulated that JAKs might be potential therapeutic targets through a pharmacologic approach. Experimental Design: We examined the effect of JAK1/JAK2 modulation by ruxolitinib in a mouse model of fully MHC mismatched bone marrow transplant comprising in vivo tumor inoculation. Results: JAK1/JAK2 inhibition by ruxolitinib improved both overall survival (P = 0.03) and acute GVHD pathologic score at target organs (P ≤ 0.001) of treated mice. In addition, treatment with ruxolitinib was associated with a preserved GVT effect, as evidenced by reduction of tumor burden (P = 0.001) and increase of survival time (P = 0.01). JAK1/JAK2 inhibition did not impair the in vivo acquisition of donor T-cell alloreactivity; this observation may account, at least in part, to the preserved GVT effect. Rather, JAK1/JAK2 inhibition of GVHD was associated with the modulation of chemokine receptor expression, which may have been one factor in the reduced infiltration of donor T cells in GVHD target organs. Conclusions: These data provide further evidence that JAK inhibition represents a new and potentially clinically relevant approach to GVHD prevention. Clin Cancer Res; 21(16); 3740–9. ©2015 AACR.
Influence of respiratory rate on the variability of blood volume pulse characteristics

Photoplethysmogram (PPG) measures have been proven useful for the quantification of sympathetic reactivity and continuous monitoring of vascular reactivity. This study was designed to delineate the influence of respiratory rate on the variability of various PPG characteristics in time and frequency domains. PPG, electrocardiogram (ECG) and respiration were simultaneously recorded for 2 min from eight healthy volunteers during paced respiration of 6, 12 and 18 cycles min−1. The PPG characteristics such as peak-to-peak interval (PPI), systolic peak amplitude, slope, Tcrest, Tdecay and pulse transit time (PTT) were computed for every pulse. In time domain, the mean of amplitude, slope and Tcrest were not significantly different amongst three different respiratory rates. However, the mean of Tdecay, PPI and PTT were significantly increased (p < 0.05, p < 0.05 and p < 0.01, respectively) during respiration of 6 cycles min−1 compared to 12 cycles min−1. The maximal spectral powers of the variability of all PPG measures were centred on the respiratory frequency in frequency domain. In conclusion, the results that the amplitude and slope in time domain are not altered by the respiratory frequency suggest their application in faithful assessment of cardiovascular reactivity. As the variability of PPI, Tdecay and PTT are altered by the slow respiration, the influence of respiration on these time derivatives should not be ignored during interpretation of vascular reactivity.
Scale-aware shape manipulation

A novel representation of a triangular mesh surface using a set of scale-invariant measures is proposed. The measures consist of angles of the triangles (triangle angles) and dihedral angles along the edges (edge angles) which are scale and rigidity independent. The vertex coordinates for a mesh give its scale-invariant measures, unique up to scale, rotation, and translation. Based on the representation of mesh using scale-invariant measures, a two-step iterative deformation algorithm is proposed, which can arbitrarily edit the mesh through simple handles interaction. The algorithm can explicitly preserve the local geometric details as much as possible in different scales even under severe editing operations including rotation, scaling, and shearing. The efficiency and robustness of the proposed algorithm are demonstrated by examples.
Socioeconomic and technical characteristics of pig farming in the urban and peri-urban zone of Dschang-West region of Cameroon.

The study attempts to investigate the socio-economic and technical characteristics of pig producers and their husbandry practices in the urban and peri-urban zones of Dschang –West region of Cameroon. 114 pig farmers were randomly selected from the zone and interviewed. A structural questionnaire was used to interview the pig farmers. Data generated included: socio-economic characteristics of the respondents, housing, breeding, feeding, health care, management practices, and constrains in pig production. The data collected were analysed by descriptive statistics (percentages). The results showed the influence of some socio-economic variable on pig production. The study revealed that most of the respondents (77.19 %) were male and 52 % were between 36 – 55 years old. 88 % of the farmers were married and almost (94 %) all the respondents were Christians. With regards to education, 86 % of the farmers could read and write while 53 % had farming experience of 11 to 15 years. Family labour (75 %) was widely used. Most of the respondents (65 %) were small holders with herd size between 1 - 5 and reared pigs for sales. Majority of the farmers (96 %) rear cross (indigenous x exotic) breed pigs. All the farmers followed stall feeding, about 63 % of the respondents supplied commercial feed associated with kitchen and farm residues to their pigs twice daily, morning and evening. All the farmers reared pigs in confinement while 74 % raised in elevated slated platform constructed with local materials and in most cases (96 %) the floor space was inadequate per adult animal. Most of the respondents (89 %) identified heat from the behavior of the animals while 57 % reported mating their pigs in the second day of heat. The average litter size at birth was 7 and at weaning 6. With regards to health care, worm, diarrhoea, Mange and anaemia were predominant throughout the year. Most of the respondents (89.96 %) identified as one of the major constrains.
Evaluating tracking performance and a new carrier-to-noise estimation method using SNACS

Multipath propagation is still one of the main error sources for many GNSS applications. The introduction of new GNSS signals of Galileo and the modernized GPS, for example, will provide higher signal bandwidths which alleviate the disruptive effects of multipath propagation. To study the influences of highly time-variant channels on GNSS tracking performance, simulations of various environments and signal combinations have to be considered. Many signal studies are based on correlation function simulation techniques. Yet to simulate GNSS signal processing with respect to multipath channels, the time-domain simulation approach serves as the most realistic and accurate but also as the most complex and computationally demanding method. This paper presents the further development of the time-domain GNSS simulation tool SNACS and its extension with additional modulations and GNSS coding schemes. Furthermore, a newly developed loss-of-lock detection method is presented and its performance is evaluated using SNACS.
Germacrene D, A Common Sesquiterpene in the Genus Bursera (Burseraceae)

The volatile components of the leaves of five Bursera species, B. copallifera, B. exselsa, B. mirandae, B. ruticola and B. fagaroides var. purpusii were determined by gas chromatography–mass spectrometry (GC–MS). Germacrene D was one of the predominant components (15.1–56.2%) of all of these species. Germacrene D has also been found in other Bursera species and some species of Commiphora, the sister group of Bursera, suggesting that the production of germacrene D might be an ancient trait in the genus Bursera.
Comprehensive Analysis of Alternative Splicing and Functionality in Neuronal Differentiation of P19 Cells

Background Alternative splicing, which produces multiple mRNAs from a single gene, occurs in most human genes and contributes to protein diversity. Many alternative isoforms are expressed in a spatio-temporal manner, and function in diverse processes, including in the neural system. Methodology/Principal Findings The purpose of the present study was to comprehensively investigate neural-splicing using P19 cells. GeneChip Exon Array analysis was performed using total RNAs purified from cells during neuronal cell differentiation. To efficiently and readily extract the alternative exon candidates, 9 filtering conditions were prepared, yielding 262 candidate exons (236 genes). Semiquantitative RT-PCR results in 30 randomly selected candidates suggested that 87% of the candidates were differentially alternatively spliced in neuronal cells compared to undifferentiated cells. Gene ontology and pathway analyses suggested that many of the candidate genes were associated with neural events. Together with 66 genes whose functions in neural cells or organs were reported previously, 47 candidate genes were found to be linked to 189 events in the gene-level profile of neural differentiation. By text-mining for the alternative isoform, distinct functions of the isoforms of 9 candidate genes indicated by the result of Exon Array were confirmed. Conclusions/Significance Alternative exons were successfully extracted. Results from the informatics analyses suggested that neural events were primarily governed by genes whose expression was increased and whose transcripts were differentially alternatively spliced in the neuronal cells. In addition to known functions in neural cells or organs, the uninvestigated alternative splicing events of 11 genes among 47 candidate genes suggested that cell cycle events are also potentially important. These genes may help researchers to differentiate the roles of alternative splicing in cell differentiation and cell proliferation.
A CRITICAL PLANE APPROACH TO MULTIAXIAL FATIGUE DAMAGE INCLUDING OUT‐OF‐PHASE LOADING

Abstract— A modification to Brown and Miller's critical plane approach is proposed to predict multiaxial fatigue life under both in-phase and out-of-phase loading conditions. The components of this modified parameter consist of the maximum shear strain amplitude and the maximum normal stress on the maximum shear strain amplitude plane. Additional cyclic hardening developed during out-of-phase loading is included in the normal stress term. Also, the mathematical formulation of this new parameter is such that variable amplitude loading can be accommodated. Experimental results from tubular specimens made of 1045 HR steel under in-phase and 90° out-of-phase axial-torsional straining using both sinusoidal and trapezoidal wave forms were correlated within a factor of about two employing this approach. Available Inconel 718 axial-torsional data including mean strain histories were also satisfactorily correlated using the aforementioned parameter.
Human capital and innovation in Sub-Saharan countries: a firm-level study

AbstractThis paper contributes to the scarce literature on the relationship between human capital and innovation at the firm-level. In this paper we examine whether human capital endowments, such as the general level of schooling within a firm, and practices of firms, such as formal training and employee slack time, have a positive relationship with the innovative output of firms. We contribute by using a more sophisticated approach and analyse how different combinations of human capital elements affect innovation. We study this relationship in Sub-Saharan countries where the general level of human capital is lower compared with developed countries. The results illustrate that internal mechanisms that spur human capital are of particular importance for innovative output in this context. In addition, our results indicate that specific combinations of human capital elements can even have negative effects. In particular, for firms in the manufacturing sector that offer employee slack, the effect of employee .
Properness Without Elementaricity

Abstract We present reasons for developing a theory of forcing notions which satisfy the properness demand for countable models which are not necessarily elementary sub-models of some (H(χ), ∈). This leads to forcing notions which are “reasonably” definable. We present two specific properties materializing this intuition: nep (non-elementary properness) and snep (Souslin non-elementary properness) and also the older Souslin proper. For this we consider candidates (countable models to which the definition applies). A major theme here is “preservation by iteration”, but we also show a dichotomy: if such forcing notions preserve the positiveness of the set of old reals for some naturally defined c.c. c. ideal, then they preserve the positiveness of any old positive set hence preservation by composition of two follows. Last but not least, we prove that (among such forcing notions) the only one commuting with Cohen is Cohen itself; in other words, any other such forcing notion make the set of old reals to a meager set. In the end we present some open problems in this area.