Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient GPU Implementation for Single Block Orthogonal Dictionary Learning

Dictionary training for sparse representations involves dealing with large chunks of data and complex algorithms that determine time consuming implementations. SBO is an iterative dictionary learning algorithm based on constructing unions of orthonormal bases via singular value decomposition, that represents each data item through a single best fit orthobase. In this paper we present a GPGPU approach of implementing SBO in OpenCL. We provide a lock-free solution that ensures full-occupancy of the GPU by following the map-reduce model for the sparse-coding stage and by making use of the Partitioned Global Address Space (PGAS) model for developing parallel dictionary updates. The resulting implementation achieves a favourable trade-off between algorithm complexity and data representation quality compared to PAK-SVD which is the standard overcomplete dictionary learning approach. We present and discuss numerical results showing a significant acceleration of the execution time for the dictionary learning process.
Diabetic kidney disease; review of the current knowledge

Diabetes is the most common cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD) in most parts of the world. 20 to 30% of diabetic patient have diabetic nephropathy in type 1 and type 2. Hyperglycemia is the key of nephropathy creation. Hyperglycemia also by production of toxic materials, advanced glycosylated end product (AGE), increased activity of aldose reductase has some role. Some metabolites of arachidonic acid, hemodynamic derangements and genetic factors have also some role. Although diabetic nephropathy is most common cause of nephropathy in these patients, but diabetic patients are also prone to other urinary tract and renal parenchymal disease and should not be confused with renal failure due to diabetic nephropathy. The principle of treatment of diabetic nephropathy is based on tight control of hyperglycemia, tight control of blood pressure and glomerular pressure, control of dyslipidemia, restriction of protein intake and smoking withdrawal.
The Globular Cluster Systems in the Coma Ellipticals. II. Metallicity Distribution and Radial Structure in NGC 4874 and Implications for Galaxy Formation

Deep Hubble Space Telescope WFPC2 images in V and I are used to investigate the globular cluster system (GCS) in NGC 4874, the central cD galaxy of the Coma cluster. Although the luminosity function of the clusters displays its normal Gaussian-like shape and turnover level, other features of the system are surprising. We find the GCS to be (a) spatially extended, with core radius rc ~ 22 kpc, (b) entirely metal poor (a narrow, unimodal metallicity distribution with ⟨[Fe/H]⟩ ~ -1.5), and (c) modestly populated for a cD-type galaxy, with specific frequency SN = 3.7 ± 0.5. Model interpretations suggest to us that as much as half of this galaxy might have accreted from low-mass satellites, but no single one of the three classic modes of galaxy formation (accretion, disk mergers, in situ formation) can supply a fully satisfactory model for the formation of NGC 4874. Even when they are used in combination, strong challenges to these models remain. We suggest that the principal anomaly in this GCS is essentially the complete lack of metal-rich clusters. If these were present in normal (M87-like) numbers in addition to the metal-poor ones that are already there, then the GCS in total would more closely resemble what we see in many other giant E galaxies. This supergiant galaxy appears to have avoided forming globular clusters during the main metal-rich stage of star formation that built the bulk of the galaxy.
Sensors in Assisted Living: A survey of signal and image processing methods

Our society will face a notable demographic shift in the near future. According to a United Nations report, the ratio of the elderly population (aged 60 years or older) to the overall population increased from 9.2% in 1990 to 11.7% in 2013 and is expected to reach 21.1% by 2050 [1]. According to the same report, 40% of older people live independently in their own homes. This ratio is about 75% in the developed countries. These facts will result in many societal challenges as well as changes in the health-care system, such as an increase in diseases and health-care costs, a shortage of caregivers, and a rise in the number of individuals unable to live independently [2]. Thus, it is imperative to develop ambient intelligence-based assisted living (AL) tools that help elderly people live independently in their homes. The recent developments in sensor technology and decreasing sensor costs have made the deployment of various sensors in various combinations viable, including static setups as well as wearable sensors. This article presents a survey that concentrates on the signal processing methods employed with different types of sensors. The types of sensors covered are pyro-electric infrared (PIR) and vibration sensors, accelerometers, cameras, depth sensors, and microphones.
Staging a recovery from mitotic arrest

Checkpoint controls, the surveillance pathways that impose “an order of execution” on the major cell cycle events, are critical to the maintenance of genome stability. When cells fail to execute a cellular event or do so erroneously due to misregulation or exposure to genotoxic stresses, these evolutionarily conserved regulatory circuits prevent passage to the subsequent event, thus bringing the cell cycle to a halt. Once the checkpoint stimulus is removed, cells recover from the arrest and eventually resume cell cycle progression. While the activation, execution and maintenance, the three major aspects of the checkpoint controls, have been investigated in detail, the recovery process remains underexplored. It is not clear if cells recover passively upon dissipation of the checkpoint signals or require an active participation by specific effectors. A recent study in the yeast Saccharomyces cerevisiae uncovered two previously unsuspected functions of Cdk1 in efficient recovery from the spindle assembly checkpoint (SAC) imposed arrest. An inability to fulfil these requirements in the absence of Cdk1 makes it virtually impossible for cells to recover from the mitotic arrest. Given the conserved nature of the SAC, these findings may have implications for vertebrate cells.
Cross-Sectional and Longitudinal Relationships between Depressive Symptoms and Brain Atrophy in MS Patients

Introduction: Depressive symptoms are a frequent and distressing phenomenon in Multiple Sclerosis (MS) patients. Cross-sectional research links these symptoms to reduced brain gray matter volumes in parts of the prefrontal and temporal lobe as well as subcortical structures like the hippocampus, nucleus caudatus and globus pallidus. Nevertheless, prospective relationships between regional gray matter volume and the course of depressive symptoms are poorly understood. Methods: Forty-four patients with relapsing–remitting or secondary progressive MS participated in a prospective study with two assessments of depressive symptoms and high-resolution MRI with an inter-test-interval of 17 months. Relationships between baseline gray matter volume and baseline depressive symptoms, as well as prospective associations between the development of atrophy and depression were assessed using voxel-based morphometry (VBM). Results: Cross-sectional analyses revealed an association between depressive symptoms and gray matter loss in the left temporal lobe. Prospective analysis showed that gray matter losses in the right middle cingulate and middle frontal gyrus at baseline predicted increasing depressive symptoms during follow-up. Increase in depressive symptoms was related to a concomitant increase in atrophy in the left thalamus and right globus pallidus. Discussion: Our results fit well into the concept of a disturbed cortico–striatal–pallido–thalamic loop in depression. In this framework, progressive gray matter loss in limbic basal ganglia structures including globus pallidus and thalamus may lead to depression-typical deficits in hedonic motivation, whereas atrophy of the prefrontal cortex may contribute to maladaptive coping strategies, promoting an unfavorable development of depressive symptoms.
A multimodal corpus for gesture expressivity analysis

This work presents the design and implementation of corpus recording sessions along with some preliminary processing results. Captured modalities include speech and facial expressions but the focus is on hand gesture expressivity. Thus, this is the primary modality and is recorded using three methods: bare hands, Nintendo Wii remote controls and datagloves. Such a setup allows for multimodal affective analysis and potentially provide quantitative parameters for synthesis of systems affectively aware and able to convey affect, such as Embodied Conversational Agents. Additionally, comparative studies of gesture expressivity based on different recording techniques could be based on the introduced corpus. Cross cultural affective behavior issues are also incorporated since the experiment was performed in three countries i.e. Greece, Germany and Italy.
GmFT2a and GmFT5a Redundantly and Differentially Regulate Flowering through Interaction with and Upregulation of the bZIP Transcription Factor GmFDL19 in Soybean

FLOWERING LOCUS T (FT) is the key flowering integrator in Arabidopsis (Arabidopsis thaliana), and its homologs encode florigens in many plant species regardless of their photoperiodic response. Two FT homologs, GmFT2a and GmFT5a, are involved in photoperiod-regulated flowering and coordinately control flowering in soybean. However, the molecular and genetic understanding of the roles played by GmFT2a and GmFT5a in photoperiod-regulated flowering in soybean is very limited. In this study, we demonstrated that GmFT2a and GmFT5a were able to promote early flowering in soybean by overexpressing these two genes in the soybean cultivar Williams 82 under noninductive long-day (LD) conditions. The soybean homologs of several floral identity genes, such as GmAP1, GmSOC1 and GmLFY, were significantly upregulated by GmFT2a and GmFT5a in a redundant and differential pattern. A bZIP transcription factor, GmFDL19, was identified as interacting with both GmFT2a and GmFT5a, and this interaction was confirmed by yeast two-hybridization and bimolecular fluorescence complementation (BiFC). The overexpression of GmFDL19 in soybean caused early flowering, and the transcription levels of the flowering identity genes were also upregulated by GmFDL19, as was consistent with the upregulation of GmFT2a and GmFT5a. The transcription of GmFDL19 was also induced by GmFT2a. The results of the electrophoretic mobility shift assay (EMSA) indicated that GmFDL19 was able to bind with the cis-elements in the promoter of GmAP1a. Taken together, our results suggest that GmFT2a and GmFT5a redundantly and differentially control photoperiod-regulated flowering in soybean through both physical interaction with and transcriptional upregulation of the bZIP transcription factor GmFDL19, thereby inducing the expression of floral identity genes.
Long-term causal effects of economic mechanisms on agent incentives

Economic mechanisms administer the allocation of resources to interested agents based on their self-reported types. One objective in mechanism design is to design a strategyproof process so that no agent will have an incentive to misreport its type. However, typical analyses of the incentives properties of mechanisms operate under strong, usually untestable assumptions. Empirical, data-oriented approaches are, at best, under-developed. Furthermore, mechanism/policy evaluation methods usually ignore the dynamic nature of a multi-agent system and are thus inappropriate for estimating long-term effects. We introduce the problem of estimating the causal effects of mechanisms on incentives and frame it under the Rubin causal framework \citep{rubin74, rubin78}. This raises unique technical challenges since the outcome of interest (agent truthfulness) is confounded with strategic interactions and, interestingly, is typically never observed under any mechanism. We develop a methodology to estimate such causal effects that using a prior that is based on a strategic equilibrium model. Working on the domain of kidney exchanges, we show how to apply our methodology to estimate causal effects of kidney allocation mechanisms on hospitals' incentives. Our results demonstrate that the use of game-theoretic prior captures the dynamic nature of the kidney exchange multiagent system and shrinks the estimates towards long-term effects, thus improving upon typical methods that completely ignore agents' strategic behavior.
Histones-Mediated Lymphocyte Apoptosis during Sepsis Is Dependent on p38 Phosphorylation and Mitochondrial Permeability Transition

Lymphocyte apoptosis is one reason for immunoparalysis seen in sepsis, although the triggers are unknown. We hypothesized that molecules in plasma, which are up-regulated during sepsis, may be responsible for this. In this study, peripheral lymphocyte apoptosis caused by extracellular histones was confirmed both in mouse and human primary lymphocytes, in which histones induced lymphocyte apoptosis dose-dependently and time-dependently. To identify which intracellular signal pathways were activated, phosphorylation of various mitogen-activated protein kinases (MAPKs) were evaluated during this process, and p38 inhibitor (SB203580) was used to confirm the role of p38 in lymphocyte apoptosis induced by histones. To investigate the mitochondrial injury during these processes, we analyzed Bcl2 degradation and Rhodamine 123 to assess mitochondrial-membrane stability, via cyclosporin A as an inhibitor for mitochondrial permeability transition (MPT). Then, caspase 3 activation was also checked by western-blotting. We found that p38 phosphorylation, mitochondrial injury and caspase 3 activation occurred dose-dependently in histones-mediated lymphocyte apoptosis. We also observed that p38 inhibitor SB203580 decreased lymphocyte apoptotic ratio by 49% (P<0.05), and inhibition of MPT protected lymphocytes from apoptosis. Furthermore, to investigate whether histones are responsible for lymphocyte apoptosis, various concentrations of histone H4 neutralization antibodies were co-cultured with human primary lymphocytes and plasma from cecal ligation and puncture (CLP) mice or sham mice. The results showed that H4 neutralization antibody dose-dependently blocked lymphocyte apoptosis caused by septic plasma in vitro. These data demonstrate for the first time that extracellular histones, especially H4, play a vital role in lymphocyte apoptosis during sepsis which is dependent on p38 phosphorylation and mitochondrial permeability transition. Neutralizing H4 can inhibit lymphocyte apoptosis, indicating that it could be a potential target in clinical interventions for sepsis associated immunoparalysis.
Chandra Detection of XTE J1650–500 in Quiescence and the Minimum Luminosity of Black Hole X-Ray Binaries

The Galactic black hole X-ray binary XTE J1650–500 entered a quiescent regime following the decline from the 2001-2002 outburst that led to its discovery. Here we report on the first detection of its quiescent counterpart in a 36 ks observation taken in 2007 July with the Chandra X-Ray Observatory. The inferred 0.5-10 keV unabsorbed flux is in the range (2.5-5.0) × 10−15 erg s−1 cm−2. Notwithstanding large distance uncertainties, the measured luminosity is comparable to that of the faintest detected black hole X-ray binaries, all having orbital periods close to the expected bifurcation period between j- and n-driven low-mass X-ray binaries. This suggests that a few 1030 erg s−1 might be a limiting luminosity value for quiescent black holes.
Implementing energy efficient technique for defense against Gray-Hole and Black-Hole attacks in wireless sensor networks

In a Wireless Sensor Networks (WSNs), energy consumption is a key challenge due to its dynamic topology, highly decentralized infrastructure and resource constraint sensors. These entities make WSNs easily compromised by various denials of service attacks resulting in disastrous consequences. In the development of various cluster based energy efficient protocols to improve the lifetime of WSNs compromised with some malicious nodes, a challenging problem is how to adopt the most effective energy efficient cluster head selection approach to extend lifetime of WSNs. Gray-Hole and Black-Hole attack are those denial of service attacks that reduces the performance of WSNs. In order to achieve energy efficiency in WSNs, an efficient and trust based secure protocol is proposed to defend against single and cooperative Gray-Hole and Black Hole attacks. A proposed protocol incorporates efficient estimation to determine honest nodes during packets transmission phase. A proposed energy efficient technique is builds to evaluate in detecting and preventing compromised node to become cluster head. Besides, NS2 simulation result compare proposed protocol with LEACH proves that proposed system is efficiently reduces possibility of compromised node to be a part of network communication process and achieves better packet delivery ratio, throughput, less end-to-end delay and extend the lifetime of network significantly.
Single-shot 3D measurement by multi-wavelength parallel phase-shifting digital holography

We proposed the use of multiple wavelengths in parallel phase-shifting digital holography (PPSDH) to widen the measurement range of PPSDH. The technique simultaneously uses multiple laser lines in PPSDH to recording hologram. Processing procedure of the image reconstruction of PPSDH is applied to the single hologram recorded by using the multiple wavelengths, then multiple complex amplitudes of the object corresponding to the multiple wavelengths are obtained. By applying the multi-wavelength phase-unwrapping method to the obtained multiple complex amplitudes for the multiple wavelengths, the height of the object more than either wavelength can be measured. We conducted an experiment of the technique using lasers lines; λ = 473 and 532 nm. Single-shot measurement of the object having a 1.9 μm step was successfully demonstrated.
Spring and Autumn Territoriality in Song Sparrows: Same Behavior, Different Mechanisms?1

Abstract Vertebrates show a diverse array of social behaviors associated with territoriality. Field and laboratory experiments indicate that underlying themes—including mechanisms—may exist. For example in birds, extensive evidence over many decades has implicated a role for testosterone in the activation of territorial aggression in reproductive contexts. Territoriality at other times of the year appeared to be independent of gonadal hormone control. One obvious question is—why this diversity of control mechanisms for an apparently similar behavior? Control of testosterone secretion during the breeding season must balance the need to compete with other males (that tends to increase testosterone secretion), and the need to provide parental care (that requires lower testosterone concentrations). Regulation of aggressive behaviors by testosterone in the non-breeding season may incur substantial costs. A series of experiments on the male song sparrow, Melospiza melodia morphna, of western Washington State have revealed possible mechanisms to avoid these costs. Song sparrows are sedentary and defend territories in both breeding and non-breeding seasons. Dominance interactions, territorial aggression and song during the non-breeding season are essentially identical to those during the breeding season. Although in the non-breeding season plasma testosterone and estradiol levels are very low, treatment with an aromatase inhibitor decreases aggression and simultaneous implantation of estradiol restores territorial behavior. These data suggest that the mechanism by which testosterone regulates territorial behavior at the neural level remains intact throughout the year. How the hormonal message to activate such behavior gets to the brain in different season does, however, appear to be different.
Biological Modeling and Simulation: A Survey of Practical Models, Algorithms, and Numerical Methods

There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix

The spatial organization of an ∼170 kb region of human chromosome 19, including CD22 and GPR40–GPR43 genes, was studied using in situ hybridization of a set of cosmid and PAC probes with nuclear halos prepared from proliferating and differentiated HL60 cells. The whole region under study was found to be looped out into the nuclear halo in proliferating cells. It is likely that the loop observed was attached to the nuclear matrix via MAR elements present at the flanks of the area under study. Upon dimethyl sulfoxide-induced differentiation of the cells the looped fragment became associated with the nuclear matrix. This change in the spatial organization correlated with the activation of transcription of at least two (CD22 and GPR43) genes present within the loop. The data obtained are discussed in the framework of the hypothesis postulating that the spatial organization of chromosomal DNA is maintained via constitutive (basic) and facultative (transcription-related) interactions of the latter with the nuclear matrix.