Miracle-dz/UniFAR-FTUs huggingface dataset:
The distribution of circulating microRNA and their relation to coronary disease

Background: MicroRNAs (miRNAs) are small RNAs that regulate gene expression by suppressing protein translation and may influence RNA expression. MicroRNAs are detected in extracellular locations such as plasma; however, the extent of miRNA expression in plasma its relation to cardiovascular disease is not clear and many clinical studies have utilized array-based platforms with poor reproducibility. Methods and Results: Initially, to define distribution of miRNA in human blood; whole blood, platelets, mononuclear cells, plasma, and serum from 5 normal individuals were screened for 852 miRNAs using high-throughput micro-fluidic quantitative RT-PCR (qRT-PCR). In total; 609, 448, 658, 147, and 178 miRNAs were found to be expressed in moderate to high levels in whole blood, platelets, mononuclear cells, plasma, and serum, respectively, with some miRNAs uniquely expressed. To determine the cardiovascular relevance of blood miRNA expression, plasma miRNA (n=852) levels were measured in 83 patients presenting for cardiac catheterization. Eight plasma miRNAs were found to have over 2-fold increased expression in patients with significant coronary disease (≥70% stenosis) as compared to those with minimal coronary disease (less than 70% stenosis) or normal coronary arteries. Expression of miR-494, miR-490-3p, and miR-769-3p were found to have significantly different levels of expression. Using a multivariable regression model including cardiovascular risk factors and medications, hsa-miR-769-3p was found to be significantly correlated with the presence of significant coronary atherosclerosis. Conclusions: This study utilized a superior high-throughput qRT-PCR based method and found that miRNAs are found to be widely expressed in human blood with differences expressed between cellular and extracellular fractions. Importantly, specific miRNAs from circulating plasma are associated with the presence of significant coronary disease.
Chasing Hypernyms in Vector Spaces with Entropy

In this paper, we introduce SLQS , a new entropy-based measure for the unsupervised identification of hypernymy and its directionality in Distributional Semantic Models (DSMs). SLQS is assessed through two tasks: (i.) identifying the hypernym in hyponym-hypernym pairs, and (ii.) discriminating hypernymy among various semantic relations. In both tasks, SLQS outperforms other state-of-the-art measures.
Towards Student-Centred Learning: Factors Contributing to the Adoption of E-Learn@USM

In 2009, Universiti Sains Malaysia (USM) launched E-Learn@USM, an electronic system for delivering and sharing learning materials as well as engaging lecturers and students in online discussions. Rather than replacing the traditional face-to-face classroom method, the role of E-Learn@USM is to foster student-centred learning, which is lauded for its effectiveness in the educational setting. The current study aims to examine factors contributing to the adoption of E-Learn@USM among USM students. The factors are categorised into individual factors (personal innovativeness, self-efficacy and attitude), organisational factors (university, administrator and instructor supports), and technological factors (relative advantage, compatibility, complexity, trialability and observability). These factors were selected based on the Diffusion of Innovations Theory and on previous studies on adoption within the innovation-diffusion framework. Using multistage cluster sampling, a survey was conducted on a total of 495 students sampled from a large population of undergraduate students at USM. The results of the hypothesis testing revealed significant relationships between all factors (except for complexity) and the adoption of E-Learn@USM. Five significant predictors – attitude, university support, trialability, relative advantage and self-efficacy – were identified.
Approximate geodesic distances reveal biologically relevant structures in microarray data

MOTIVATION Genome-wide gene expression measurements, as currently determined by the microarray technology, can be represented mathematically as points in a high-dimensional gene expression space. Genes interact with each other in regulatory networks, restricting the cellular gene expression profiles to a certain manifold, or surface, in gene expression space. To obtain knowledge about this manifold, various dimensionality reduction methods and distance metrics are used. For data points distributed on curved manifolds, a sensible distance measure would be the geodesic distance along the manifold. In this work, we examine whether an approximate geodesic distance measure captures biological similarities better than the traditionally used Euclidean distance. RESULTS We computed approximate geodesic distances, determined by the Isomap algorithm, for one set of lymphoma and one set of lung cancer microarray samples. Compared with the ordinary Euclidean distance metric, this distance measure produced more instructive, biologically relevant, visualizations when applying multidimensional scaling. This suggests the Isomap algorithm as a promising tool for the interpretation of microarray data. Furthermore, the results demonstrate the benefit and importance of taking nonlinearities in gene expression data into account.
Oxygen-regulated expression of the RNA-binding proteins RBM3 and CIRP by a HIF-1-independent mechanism

The transcriptional regulation of several dozen genes in response to low oxygen tension is mediated by hypoxia-inducible factor 1 (HIF-1), a heterodimeric protein composed of two subunits, HIF-1α and HIF-1β. In the HIF-1α-deficient human leukemic cell line, Z-33, exposed to mild (8% O2) or severe (1% O2) hypoxia, we found significant upregulation of two related heterogenous nuclear ribonucleoproteins, RNA-binding motif protein 3 (RBM3) and cold inducible RNA-binding protein (CIRP), which are highly conserved cold stress proteins with RNA-binding properties. Hypoxia also induced upregulation of RBM3 and CIRP in the murine HIF-1β-deficient cell line, Hepa-1 c4. In various HIF-1 competent cells, RBM3 and CIRP were induced by moderate hypothermia (32°C) but hypothermia was ineffective in increasing HIF-1α or vascular endothelial growth factor (VEGF), a known HIF-1 target. In contrast, iron chelators induced VEGF but not RBM3 or CIRP. The RBM3 and CIRP mRNA increase after hypoxia was inhibited by actinomycin-D, and in vitro nuclear run-on assays demonstrated specific increases in RBM3 and CIRP mRNA after hypoxia, which suggests that regulation takes place at the level of gene transcription. Hypoxia-induced RBM3 or CIRP transcription was inhibited by the respiratory chain inhibitors NaN3 and cyanide in a dose-dependent fashion. However, cells depleted of mitochondria were still able to upregulate RBM3 and CIRP in response to hypoxia. Thus, RBM3 and CIRP are adaptatively expressed in response to hypoxia by a mechanism that involves neither HIF-1 nor mitochondria.
Analysis of Multi-Cell MIMO Measurements in an Urban Macrocell Environment

In this paper we analyze the properties of Multiple Input Multiple Output (MIMO) channels in urban macro-cell environments based on a narrow-band measurement campaign with simultaneous measurements from two sites in the GSM-1800 band. We focus here on bulk parameters such as shadow-fading, angle-spread, and their variation in space and cross-correlation among different sectors. We also look on the dependence between Direction of Arrival and Direction of Departure, (DoA/DoD). Our analysis result shows virtually no cross-site correlation of the studied parameters, while cross-sector correlation is substantial.
Survey of Temporal Information Retrieval and Related Applications

Temporal information retrieval has been a topic of great interest in recent years. Its purpose is to improve the effectiveness of information retrieval methods by exploiting temporal information in documents and queries. In this article, we present a survey of the existing literature on temporal information retrieval. In addition to giving an overview of the field, we categorize the relevant research, describe the main contributions, and compare different approaches. We organize existing research to provide a coherent view, discuss several open issues, and point out some possible future research directions in this area. Despite significant advances, the area lacks a systematic arrangement of prior efforts and an overview of state-of-the-art approaches. Moreover, an effective end-to-end temporal retrieval system that exploits temporal information to improve the quality of the presented results remains undeveloped.
Insect ectoparasites on wild birds in the Czech Republic during the pre-breeding period

Wild passerine birds (Passeriformes) from the northeastern part of the Czech Republic were examined for ectoparasites during the pre-breeding period in 2007. Two species of fleas of the genera Ceratophyllus and Dasypsyllus (Siphonaptera: Ceratophyllidae), and 23 species of chewing lice belonging to the genera Ricinus, Myrsidea, Menacanthus (Phthiraptera: Menoponidae), Brueelia, Penenirmus, and Philopterus (Phthiraptera: Philopteridae) were found on 108 birds of 16 species. Distribution of insect ectoparasites found on wild birds during pre-breeding was compared with previous data from the post-breeding period. There was no difference in total prevalence of chewing lice in prebreeding and post-breeding periods. Higher prevalence of fleas and slightly higher mean intensity of chewing lice were found on birds during the pre-breeding period. There was a significant difference in total prevalence but equal mean intensity of chewing lice on resident and migrating birds.
Seismic $P$ Phase Picking Using a Kurtosis-Based Criterion in the Stationary Wavelet Domain

The seismic P phase first arrival identification is a fundamental problem in seismology. The accurate identification of the P -wave first arrival is not a trivial process, particularly when the seismograms present a very low signal-to-noise ratio (SNR) or are contaminated with artificial transients that could produce false alarms. In this paper, a new approach based on higher order statistics and the stationary wavelet transform is presented. The P onset is obtained under a statistical criterion applied in the time-frequency domain. The results have been compared to those estimated by another P phase picking algorithm and P onsets picked by expert analysts. The comparison shows that our proposed method efficiently provides a good estimate of the P onset picks that are consistent with analyst picks, particularly in cases of very low SNR.
Occupational Hazards And Safety Practices: A Concern Among Small Scale Sawmilling Industries In Tamale Metropolis, Ghana

Occupational hazards and safety should be paramount for the well-being of any industrial worker. The main aim of this study was to ascertain the prevalent hazards/dangers encountered by workers in the Tamale Metropolis when working on wood/timber species. A survey involving the use of questionnaires, interviews and observations were used as tools for the investigation. The sample size for this study was made up of 60 respondents from the three constituencies within the Metropolis (Tamale North, Tamale South and Tamale Central). The data collected were analyzed using the Statistical Package for Social Scientists, version 16. Per our findings, work hazards are associated with a wide range of injuries and illnesses such as cut-type of injuries, fractures, sprains, catarrh, waist pains, eye problems and dizziness. Also, a significant number of workers in the study area did not use Personal Protective Equipment (PPE) when operating machines or performing jobs that required their use. Hence, the attitude and behavior of workers towards health and safety should be of major concern to employers or management of this industry. Health and safety education as well as training and provision of PPE’s are therefore strongly recommended to prevent or minimize workrelated accidents, injuries and illnesses. Keywords— Accidents, Injuries, Personal protective equipment, Sawmills ————————————————————
Browning of White Adipose Tissue Uncouples Glucose Uptake from Insulin Signaling

Presence of thermogenically active adipose tissue in adult humans has been inversely associated with obesity and type 2 diabetes. While it had been shown that insulin is crucial for the development of classical brown fat, its role in development and function of inducible brown-in-white (brite) adipose tissue is less clear. Here we show that insulin deficiency impaired differentiation of brite adipocytes. However, adrenergic stimulation almost fully induced the thermogenic program under these settings. Although brite differentiation of adipocytes as well as browning of white adipose tissue entailed substantially elevated glucose uptake by adipose tissue, the capacity of insulin to stimulate glucose uptake surprisingly was not higher in the brite state. Notably, in line with the insulin-independent stimulation of glucose uptake, our data revealed that brite recruitment results in induction of solute carrier family 2 (GLUT-1) expression in adipocytes and inguinal WAT. These results for the first time demonstrate that insulin signaling is neither essential for brite recruitment, nor is it improved in cells or tissues upon browning.
Study on the Axis Problem of Rough 3-Valued Algebras

The collection of all the rough sets of an approximation space can be made into a 3-valued Lukasiewicz algebra. Thus, we call the algebra constructed by the collection of rough sets of an approximation space a rough 3-valued Lukasiewicz algebra. In this paper, whether the rough 3-valued Lukasiewicz algebra is an axled 3-valued Lukasiewicz algebra is examined.
Land‐use intensity and the effects of organic farming on biodiversity: a hierarchical meta‐analysis

Summary The benefits of organic farming to biodiversity in agricultural landscapes continue to be hotly debated, emphasizing the importance of precisely quantifying the effect of organic vs. conventional farming. We conducted an updated hierarchical meta‐analysis of studies that compared biodiversity under organic and conventional farming methods, measured as species richness. We calculated effect sizes for 184 observations garnered from 94 studies, and for each study, we obtained three standardized measures reflecting land‐use intensity. We investigated the stability of effect sizes through time, publication bias due to the ‘file drawer’ problem, and consider whether the current literature is representative of global organic farming patterns. On average, organic farming increased species richness by about 30%. This result has been robust over the last 30 years of published studies and shows no sign of diminishing. Organic farming had a greater effect on biodiversity as the percentage of the landscape consisting of arable fields increased, that is, it is higher in intensively farmed regions. The average effect size and the response to agricultural intensification depend on taxonomic group, functional group and crop type. There is some evidence for publication bias in the literature; however, our results are robust to its impact. Current studies are heavily biased towards northern and western Europe and North America, while other regions with large areas of organic farming remain poorly investigated. Synthesis and applications. Our analysis affirms that organic farming has large positive effects on biodiversity compared with conventional farming, but that the effect size varies with the organism group and crop studied, and is greater in landscapes with higher land‐use intensity. Decisions about where to site organic farms to maximize biodiversity will, however, depend on the costs as well as the potential benefits. Current studies have been heavily biased towards agricultural systems in the developed world. We recommend that future studies pay greater attention to other regions, in particular, areas with tropical, subtropical and Mediterranean climates, in which very few studies have been conducted.
Crowding-Out Charitable Contributions in Canada: New Knowledge from the North

Using data from charitable organizations in the US, authors have established that government grants to charities largely crowd out giving from other sources, but that this reduction is due mostly to reduced fundraising activities of the charity itself. We use much more detailed data from over 6000 charities in Canada, measured for up to 15 years, to provide valuable new insights into this phenomenon. In particular, dollars received from individuals is largely unchanged by government grants. Instead, the crowding out is attributable to two other sources of donations not differentiated in US data: giving from other charities and charitable foundations, and donations gained from special fundraising activities, like galas or sponsorships. Only the latter-which is about half of the measured crowding out-represents a potential loss of dollars to the charitable sector as a result of government grants.
A Hierarchical Security Assessment Model for Object-Oriented Programs

We present a hierarchical model for assessing an object-oriented program's security. Security is quantified using structural properties of the program code to identify the ways in which `classified' data values may be transferred between objects. The model begins with a set of low-level security metrics based on traditional design characteristics of object-oriented classes, such as data encapsulation, cohesion and coupling. These metrics are then used to characterise higher-level properties concerning the overall readability and writ ability of classified data throughout the program. In turn, these metrics are then mapped to well-known security design principles such as `assigning the least privilege' and `reducing the size of the attack surface'. Finally, the entire program's security is summarised as a single security index value. These metrics allow different versions of the same program, or different programs intended to perform the same task, to be compared for their relative security at a number of different abstraction levels. The model is validated via an experiment involving five open source Java programs, using a static analysis tool we have developed to automatically extract the security metrics from compiled Java byte code.
DESIGN AND CONVERGENCE OF AFEM IN H(DIV)

We design an adaptive finite element method (AFEM) for mixed boundary value problems associated with the differential operator A-∇div in H(div, Ω). For A being a variable coefficient matrix with possible jump discontinuities, we provide a complete a posteriori error analysis which applies to both Raviart–Thomas ℝ𝕋n and Brezzi–Douglas–Marini 𝔹𝔻𝕄n elements of any order n in dimensions d = 2, 3. We prove a strict reduction of the total error between consecutive iterates, namely a contraction property for the sum of energy error and oscillation, the latter being solution-dependent. We present numerical experiments for ℝ𝕋n with n = 0, 1 and 𝔹𝔻𝕄1 which document the performance of AFEM and corroborate as well as extend the theory.
A self‐consistent mechanism for slow dynamic deformation and tsunami generation for earthquakes in the shallow subduction zone

Dynamic pore pressure changes in the overriding wedge above a shallow‐dipping plate interface significantly affect the rupture dynamics of shallow subduction zone earthquakes and their tsunamigenesis. For a wedge on the verge of Coulomb failure everywhere including the basal fault, the dynamic pore pressure increase due to up‐dip rupture propagation leads to widespread yielding within the wedge, which is greatly enhanced by the shallow dip of the fault. The widespread yielding reduces the stress drop, slip velocity, slip, and rupture velocity, giving rise to prolonged rupture duration, thus explaining many anomalous features of shallow subduction zone earthquakes. Significant inelastic seafloor uplift occurs in the case of a shallow fault dip, with the largest uplift located landward from the trench. Integrating this physical mechanism with existing seismic, geodetic, and tsunami observations can provide new insights into earthquake dynamics and deformation processes in shallow subduction zones.
Similarity Based Control Strategy Reconfiguration by Fuzzy Reasoning and Fuzzy Automata

In case of control partially known complex systems, a kind of control strategy could be built simply by combining some known, partially valid control strategies. These known strategies are covering only a part of the whole state space of the possible control strategies. In some situation, these strategies could be combined in a hierarchical fuzzy way to form a strategy covering at least the same state space as all the attendant strategies. There are two main questions of this kind of strategy reconfiguration. The first is the decision about the level of necessity and the type of the strategy (rulebase in the case of fuzzy control) needed to use by the actual system. The second is the way of generating the actual strategy, as a combination of the different existing known partially valid strategies. One solution for these questions could be the combination of the fuzzy automata based system state approximation and the hierarchical interpolative fuzzy reasoning-the similarity based strategy reconfiguration. As an example for the practical application of the proposed structure, path tracking a collision avoidance strategy of a simulated AGV is introduced in this paper.
Measurement of cytoplasmic streaming in single plant cells by magnetic resonance velocimetry

In the giant cylindrical cells found in Characean algae, multitudes of the molecular motor myosin transport the cytoplasm along opposing spiralling bands covering the inside of the cell wall, generating a helical shear flow in the large central vacuole. It has been suggested that such flows enhance mixing within the vacuole (van de Meent, Tuval & Goldstein, Phys. Rev. Lett., vol. 101, 2008, paper no. 178102) and thereby play a role in regulating metabolism. For this to occur the membrane that encloses the vacuole, namely the tonoplast, must transmit efficiently the hydrodynamic shear generated in the cytoplasm. Existing measurements of streaming flows are of insufficient spatial resolution and extent to provide tests of fluid mechanical theories of such flows and information on the shear transmission. Here, using magnetic resonance velocimetry (MRV), we present the first measurements of cytoplasmic streaming velocities in single living cells. The spatial variation of the longitudinal velocity field in cross-sections of internodal cells of Chara corallina is obtained with spatial resolution of 16 μm and is shown to be in quantitative agreement with a recent theoretical analysis (Goldstein, Tuval & van de Meent, Proc. Natl. Acad. Sci. USA, vol. 105, 2008, p. 3663) of rotational cytoplasmic streaming driven by bidirectional helical forcing in the cytoplasm, with direct shear transmission by the tonoplast. These results highlight the open problem of understanding tonoplast motion induced by streaming. Moreover, this study suggests the suitability of MRV in the characterization of streaming flows in a variety of eukaryotic systems and for microfluidic phenomena in general.