Miracle-dz/UniFAR-FTUs huggingface dataset:
Local Steerable Pyramid Binary Pattern Sequence LSPBPS for Face Recognition Method

In this paper the problem of face recognition under variable illumination conditions is considered. Most of the works in the literature exhibit good performance under strictly controlled acquisition conditions, but the performance drastically drop when changes in pose and illumination occur, so that recently number of approaches have been proposed to deal with such variability. The aim of this work is to introduce an efficient local appearance feature extraction method based steerable pyramid (SP) for face recognition. Local information is extracted from SP sub-bands using LBP(Local binary Pattern). The underlying statistics allow us to reduce the required amount of data to be stored. The experiments carried out on different face databases confirm the effectiveness of the proposed approach. Keywords—Face recognition (FR), Steerable pyramid (SP), local Binary Pattern (LBP).
A noise equivalent counts approach for optimizing I-124 imaging performance with a small animal PET scanner

Due to its long radiological half life, 124I can be used for investigation of lengthy biological processes. However, it is not an ideal PET isotope because it has poor positron yield and half of the positrons are emitted in cascade with 603 keV gammas. This decay spectrum results in coincidences between gammas and annihilation photons (dirty coincidences) leading to both inaccurate quantitation and overall reduction in the image quality. It has been shown that noise equivalent counts (NEC) have a direct link to signal to noise ratio of the reconstructed images. The purpose of this work was to investigate the effect of varying the energy window of the digitizer on the NEC measured from the non-pure positron emitter 124I and hence, on the image quality. Simulations were performed using the GATE software for a 1.32 cm radius cylinder filled with 300 muCi of 124I placed at the center of field of view. We report that by windowing in on the upper energy window of the data acquisition from a symmetric 50% (255-766 keV) energy window, to an asymmetric 255-600 keV one, it is possible to preferentially reduce the dirty coincidences with minor sensitivity changes. These findings will be verified with experimental data, and will lead to optimizing the data acquisition chain for 124I imaging performance
The missing sinks : Slip localization in faults, damage zones, and the seismic energy budget

The majority of work done during an earthquake may be consumed by dissipative processes that occur within geometrically and mechanically complex fault zones, rather than radiated as seismic waves. Many processes are likely to act as dissipative energy sinks in a three-dimensional faulted volume: slip along the principal slip zone is likely to be accompanied by deformation in the surrounding damage zone volume. Examination of exhumed fault zones in granite, which are meters to tens of kilometers long, shows thin principal slip zones developing on the smallest faults. As slip is accumulated on progressively larger faults, the principal slip zones remain less than 10 cm wide, but there is increasing complexity in the damage zone of the larger faults. By considering the amount of energy required to crush fine-grained gouge in the principal slip zone, and the grain size of gouge reported from other (seismogenic) faults, we conclude that principal slip zones must remain relatively thin for all sizes of rupture. Any energy consumed by dissipative processes in the damage zone will therefore tend to make the principal slip zone thinner, and will reduce the energy available to propagate the rupture.
MissForest - non-parametric missing value imputation for mixed-type data

MOTIVATION Modern data acquisition based on high-throughput technology is often facing the problem of missing data. Algorithms commonly used in the analysis of such large-scale data often depend on a complete set. Missing value imputation offers a solution to this problem. However, the majority of available imputation methods are restricted to one type of variable only: continuous or categorical. For mixed-type data, the different types are usually handled separately. Therefore, these methods ignore possible relations between variable types. We propose a non-parametric method which can cope with different types of variables simultaneously. RESULTS We compare several state of the art methods for the imputation of missing values. We propose and evaluate an iterative imputation method (missForest) based on a random forest. By averaging over many unpruned classification or regression trees, random forest intrinsically constitutes a multiple imputation scheme. Using the built-in out-of-bag error estimates of random forest, we are able to estimate the imputation error without the need of a test set. Evaluation is performed on multiple datasets coming from a diverse selection of biological fields with artificially introduced missing values ranging from 10% to 30%. We show that missForest can successfully handle missing values, particularly in datasets including different types of variables. In our comparative study, missForest outperforms other methods of imputation especially in data settings where complex interactions and non-linear relations are suspected. The out-of-bag imputation error estimates of missForest prove to be adequate in all settings. Additionally, missForest exhibits attractive computational efficiency and can cope with high-dimensional data. AVAILABILITY The package missForest is freely available from http://stat.ethz.ch/CRAN/. CONTACT stekhoven@stat.math.ethz.ch; buhlmann@stat.math.ethz.ch
Functional Expression of Human Heme Oxygenase-1 Gene in Renal Structure of Spontaneously Hypertensive Rats

Heme oxygenase (HO), by catabolizing heme to bile pigments, regulates the levels and activity of cellular hemoprotein and HO activity. We examined the effect of delivery of the human HO-1 gene on cellular heme in renal tissue using a retroviral vector. We used a single intracardiac injection of the concentrated infectious viral particles in 5-day-old spontaneously hypertensive rats; 25 were transduced with empty vector and 25 were transduced with the human HO-1 gene. Functional expression of human and rat HO-1 was measured after 2 and 4 weeks. Reverse transcription polymerase chain reaction showed that human HO-1 mRNA was expressed as early as 2 weeks, with the highest levels in the kidney. Western blot analysis showed distribution of human HO-1 protein in rat kidney structures, predominantly in the thick ascending limb of the loop of Henle as well as in proximal tubules and preglomerular arterioles. These areas also demonstrated higher HO activity as measured by increased conversion of heme to bilirubin and carbon monoxide. Functional expression of the human HO-1 gene was associated with a decrease in blood pressure in 4- and 8-week-old spontaneously hypertensive rats. Compared with nontransduced rats, human HO-1 gene overexpression in transduced rats was associated with a 35% decrease in urinary 20-hydroxyeicosatetraenoic acid, a potent vasoconstrictor and an inhibitor of tubular Na+ transport, which may be related to the decrease in blood pressure.
Analysis of the Computational Methods Available for MicroRNA Target Prediction

Biochemistry 218: Computation Molecular Biology MicroRNAs (miRNAs) are non-coding, endogenous RNAs that make up a vast post-transcriptional regulatory network in cells. Processed from primary transcripts that are translated from miRNA genes, mature miRNAs are usually 19-25 nucleotides long. More than 4000 miRNAs have been identified in the genomes of over 80 species. Mature miRNAs are thought to down-regulate the translation of messenger RNAs after recognizing and binding to partially complementary sites in the 3'-untranslated regions (3'-UTR) of the mRNA. MiRNAs have been found to be involved in the control of wide breadth of cell processes, including cell proliferation, death, and metabolism; therefore, their study is tremendously important for the understanding of cell function in eukaryotic species. 1 The functional analysis of miRNAs relies heavily on the identification of their targeted genes. However, experimental studies alone are too slow and limited in scope to be relied on as the only source of miRNA target identification. In order to facilitate the investigation into miRNA function, numerous bioinformatic methods were developed in order to allow high-throughput prediction of miRNA target genes. In the last 7 years, numerous computational algorithms have been developed for target prediction spanning a wide range of approaches and techniques. and PITA, will be discussed and analyzed in the following paper with a focus on possible areas of improvement (Table 1).
Streamware: programming general-purpose multicore processors using streams

Recently, the number of cores on general-purpose processors has been increasing rapidly. Using conventional programming models, it is challenging to effectively exploit these cores for maximal performance. An interesting alternative candidate for programming multiple cores is the stream programming model, which provides a framework for writing programs in a sequential-style while greatly simplifying the task of automatic parallelization. It has been shown that not only traditional media/image applications but also more general-purpose data-intensive applications can be expressed in the stream programming style. In this paper, we investigate the potential to use the stream programming model to efficiently utilize commodity multicore general-purpose processors (e.g., Intel/AMD). Although several stream languages and stream compilers have recently been developed, they typically target special-purpose stream processors. In contrast, we propose a flexible software system, Streamware, which automatically maps stream programs onto a wide variety of general-purpose multicore processor configurations. We leverage existing compilation framework for stream processors and design a runtime environment which takes as input the output of these stream compilers in the form of machine-independent stream virtual machine code. The runtime environment assigns work to processor cores considering processor/cache configurations and adapts to workload variations. We evaluate this approach for a few general-purpose scientific applications on real hardware and a cycle-level simulator set-up to showcase scaling and contention issues. The results show that the stream programming model is a good choice for efficiently exploiting modern and future multicore CPUs for an important class of applications.
2016 Ieee International Conference on Big Data (big Data) Prediction of Information Diffusion in Social Networks Using Dynamic Carrying Capacity

—Online social networks have become an effective channel for influencing millions of users by facilitating exchange and spread of information. Despite recent works on modeling information diffusion in social networks, the complexity of social interactions makes quantification of any spreading phenomenon in social networks a challenging task. Most of the research in this area rely on empirical or statistical approaches without considering the temporal aspects and the carrying capacity of the networks. In this paper, we capture the temporal evolution of information spread in a social network using linear ordinary differential equations (ODEs). Our proposed model shows the influence of users and their temporal actions on the carrying capacity. We validate the diffusion process across the network using a dataset collected from Digg which is a popular social news sharing website. The results show that our dynamic carrying capacity PDE model is able to predict with high accuracy how the information diffuses in the network during the different phases of the lifetime of a news story. We also propose a model to represent the carrying capacity based on the portion of the influenced users.
Sex-Related Differences in the Effects of the Mediterranean Diet on Glucose and Insulin Homeostasis

Objective. To document sex differences in the impact of the Mediterranean diet (MedDiet) on glucose/insulin homeostasis and to verify whether these sex-related effects were associated with changes in nonesterified fatty acids (NEFA). Methods. All foods were provided to 38 men and 32 premenopausal women (24–53 y) during 4 weeks. Variables were measured during a 180 min OGTT before and after the MedDiet. Results. A sex-by-time interaction for plasma insulin iAUC was found (men: −17.8%, P = 0.02; women: +9.4%, P = 0.63; P for sex-by-time interaction = 0.005). A sex-by-time interaction was also observed for insulin sensitivity (Cederholm index, P = 0.03), for which only men experienced improvements (men: +8.1%, P = 0.047; women: −5.9%, P = 0.94). No sex difference was observed for glucose and C-peptide responses. Trends toward a decrease in NEFA AUC (P = 0.06) and an increase in NEFA suppression rate (P = 0.06) were noted, with no sex difference. Changes in NEFA were not associated with change in insulin sensitivity. Conclusions. Results suggest that the more favorable changes in glucose/insulin homeostasis observed in men compared to women in response to the MedDiet are not explained by sex differences in NEFA response. This clinical trial is registered with clinicaltrials.gov NCT01293344.
A tool for morphologically ambiguous text processing

The main course of preliminary natural texts processing is tagging and disambiguating texts. Hence, most of modern language tools are specified for such purposes. In our projects, we carry out a shallow syntax of untagged texts. For this purpose we developed a new query language based on regular expressions. This language allows write queries according to words' ambiguity.
Spacecraft reorientation in presence of attitude constraints via logarithmic barrier potentials

This paper proposes a methodology-based on convex navigation functions-for three-axis attitude reorientation for a rigid body spacecraft in presence of multiple constraints. In this direction, two types of attitude constrained zones are first defined, namely, the attitude forbidden and mandatory zones. The paper then utilizes a convex parameterization of forbidden and mandatory zones for constructing a logarithmic barrier potential function that is subsequently used for the synthesis of the attitude control laws. The feasible controller which uses the feedback of the unit quaternions in the context of the proposed methodology is then implemented using a modified integrator back stepping method in order to compromise the actuator saturations. The paper concludes with a set of simulation results in order to evaluate the effectiveness, and demonstrate the viability, of the proposed methodology.
Exosomes provide a protective and enriched source of miRNA for biomarker profiling compared to intracellular and cell-free blood

Introduction microRNA (miRNA) are small non-coding RNA species that are transcriptionally processed in the host cell and released extracellularly into the bloodstream. Normally involved in post-transcriptional gene silencing, the deregulation of miRNA has been shown to influence pathogenesis of a number of diseases. Background Next-generation deep sequencing (NGS) has provided the ability to profile miRNA in biological fluids making this approach a viable screening tool to detect miRNA biomarkers. However, collection and handling procedures of blood needs to be greatly improved for miRNA analysis in order to reliably detect differences between healthy and disease patients. Furthermore, ribonucleases present in blood can degrade RNA upon collection rendering extracellular miRNA at risk of degradation. These factors have consequently decreased sensitivity and specificity of miRNA biomarker assays. Methods Here, we use NGS to profile miRNA in various blood components and identify differences in profiles within peripheral blood compared to cell-free plasma or serum and extracellular vesicles known as exosomes. We also analyse and compare the miRNA content in exosomes prepared by ultracentrifugation methods and commercial exosome isolation kits including treating samples with RNaseA. Conclusion This study demonstrates that exosomal RNA is protected by RNaseA treatment and that exosomes provide a consistent source of miRNA for disease biomarker detection.
An Experimental Study of the Effects of Coolant Fluid on Surface Roughness in Turning Operation for Brass Alloy

The effect of different cutting fluids on surface roughness of brass alloy workpiece during turning operation was carried out in this research. This was performed with different cutting speed,while other cutting parameters had been regarded as constants(feeding rate , and depth of cut). Surface roughness of machined parts that will be tested by electronic surface roughness tester . The results show that the standard coolant gives the best values of surface roughness for fixed cutting speed ,followed by sun flower oil that has approximately the same effect, while the air stream as a coolant gave unsatisfied results for the evaluation of surface roughness. In the other hand the best values of surface roughness were recorded for maximum cutting speed with all other types of cutting fluids.
Are Genes Associated with Energy Metabolism Important in Asthma and BMI?

Objective. Increased serum leptin levels have been observed in asthmatic patients. Leptin, via proliferation and activation of Th2 cells, may induce inflammation in asthma. It has also been demonstrated that leptin mRNA expression and protein levels increase in response to inflammatory stimuli. We hypothesized that polymorphisms in the leptin receptor, leptin and ghrelin genes, may affect their expression and, therefore, be responsible for altered response to increased leptin levels observed in asthma. To our knowledge, there were no studies on a potential role of LEPR, LEP, and GHRL polymorphisms in asthma. Subjects and methods. We analyzed 129 pediatric patients with asthma and 114 healthy children from the control group ranging from 6 to 18 years of age. The diagnosis of allergic asthma was based on clinical symptoms, the lung function test, and the positive skin prick test and/or increased immunoglobulin E (IgE) levels. Polymorphisms were genotyped by the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) method. Statistical analyses were performed with Statistica v.7. 1 software (Statistica, StatSoft, Poland; available free at http://www.broad.mit.edu/mpg/haploview/index.php). Linkage disequilibrium analysis was performed with Haploview v.4. 0. Results. We observed a statistically significant association of the 3′UTR A/G and the -2549A/G polymorphisms of the leptin gene with asthma. No association with asthma was observed for the K109R and the Q223R polymorphisms of the LEPR gene and the Met72Leu polymorphism of the ghrelin gene. In the analysis of body mass index (BMI) stratified by genotype, we found an association of the -2549A/G LEP, but not of LEPR and GHRL polymorphisms, with higher BMI values in asthmatic patients. We found suggestive evidence for linkage between the two polymorphisms of the LEPR gene (D′ = 0.84 CI: 0.71–0.92; r2 = 0.29) in linkage disequilibrium analysis: The GG haplotype was more frequent in the control healthy group (p = 0.057). No linkage disequilibrium was detected between LEP polymorphisms. Conclusions. Polymorphisms of the leptin gene may be associated with asthma and higher BMI in asthmatic patients. Polymorphisms of the LEPR and GHRL seem unlikely to be associated with asthma or BMI in our sample. The results of haplotype analysis for the LEPR gene may suggest a protective role of the GG haplotype against asthma; however, studies on larger groups are necessary to confirm the observed trend towards association.
Effects of recombinant human IGF-I on glucose and leucine kinetics in men.

To examine the effects of recombinant human (rh) insulin-like growth factor I (IGF-I), insulin, and saline on metabolic parameters, we studied 20 young nonobese healthy men. Euglycemic clamps with 240-min IGF-I infusions at two doses (49 and 33 pmol.kg-1 x min-1, n = 8 and 12 subjects) were performed and compared with hyperinsulinemic-euglycemic clamps (2.25 pmol.kg-1 x min-1, n = 9). Leucine and glucose kinetics were examined with L-[1-13C]leucine and [3-3H]glucose. Glucose rate of appearance (Ra) declined equivalently in the 49 pmol.kg-1.min-1 IGF-I and insulin clamps but remained at basal levels during the 33 pmol.kg-1 x min-1 IGF-I infusions. In contrast, Rd of glucose was increased by 176% in the 49 pmol.kg-1 x min-1 IGF-I and 78% in the 33 pmol.kg-1 x min-1 IGF-I infusions. Furthermore, to prevent hypoglycemia after the termination of both rhIGF-I infusions, it was necessary to infuse glucose for an additional 2-20 h. Ra of leucine was suppressed significantly by both IGF-I and insulin, whereas leucine oxidation was not affected by either hormone. Therefore, the rate of disappearance of leucine expressed as the difference between Ra and oxidation rates was significantly reduced in all clamps. In addition, IGF-I significantly suppressed beta-cell secretion without affecting the other glucoregulatory hormones. In contrast to insulin, IGF-I had no apparent effect on lipolysis, as measured by changes in nonesterified fatty acids. (ABSTRACT TRUNCATED AT 250 WORDS)
Effects of ceramide-1-phosphate on cultured cells: dependence on dodecane in the vehicles⃞ Published, JLR Papers in Press, October 3, 2006.

Ceramide-1-phosphate (C1P), the product of ceramide kinase, is a sphingophospholipid with recently recognized signaling properties. In particular, it was reported to be mitogenic and capable of direct stimulation of cytosolic phospholipase A2α. Much of the present knowledge has relied on the use of C1P of various acyl chain lengths, together with diverse protocols to deliver it to cultured cells. A mixture of ethanol (or methanol) with dodecane, as the vehicle, has become popular. However, the contribution of this solvent to the observed effects of C1P has not been documented. Here, we show that addition of C1P in ethanol-dodecane to culture medium leads to irreversible cytotoxic effects. These culminate in mitochondrial swelling, vacuole formation, and cell death. Not only the toxicity of C1P, but also its ability to trigger prostaglandin E2 release, is fully dependent upon addition of a premade C1P-dodecane mixture. Furthermore, we show that these effects are not restricted to C1P. They result from the capacity of dodecane to interact with phospholipids; hence, they go undetected with a vehicle control. This study should raise awareness about the use of dodecane for phospholipid delivery and, in turn, help in unraveling C1P signaling, which is still poorly understood.
Gel Microrods for 3D Tissue Printing

Large scale 3D ordering of anisotropic gel objects, such as gel microrods, both rigid and soft, is in demand for the engineering of replica tissues but has not yet been achieved. Here, monodisperse gel microrods of gelatin methacrylate (GelMa) or Matrigel are generated by a droplet‐based microfluidics tubing system. The microrods are 50–300 µm wide and 1–3 mm long; the GelMa versions are produced at up to 50 s−1 while the more fragile Matrigel versions are produced at up to 10 s−1 followed by 1 h of gelation. Upon ejection from the tubing, the rods can be printed into robust 3D structures of centimeter dimensions in which the rods are organized into patterns, including various parallel arrangements and tubular structures. Further, mammalian cells contained within the microrods remain viable, and can proliferate and migrate. As well as homogeneous microrods, Janus and ternary rods can be prepared. Gel microrods will be useful for the production of printed tissues, which mimic intricate architectures found in Nature that cannot presently be attained.