Miracle-dz/UniFAR-FTUs huggingface dataset:
Semi-supervised visual clustering for spherical coordinates systems

In this paper we propose a method that combines the advanced data analysis of the automatic statistical methods and the flexibility and manual parameter tuning of interactive visual clustering. We present the Semi-Supervised Visual Clustering (SSVC) interface; its main contribution is the learning of the optimal projection distance metric for the star and spherical coordinate visualization systems. Beyond the conventional manual setting, it couples the visual clustering with the automatic setting where the projection distance metric is learned from the available set of user feedbacks in the form of either item similarities or direct item annotations. Moreover, SSVC interface allows for the hybrid setting where some parameters are manually set by the user while the remaining parameters are determined by the optimal distance algorithm.
Deconstructing Bentham’s Panopticon: The New Metaphors of Surveillance in the Web 2.0 Environment

This article reflects on the meaning of the words “control” and “privacy” in light of the intensive diffusion of user generated content on the web. It presents some results of an empirical research based on 145 essays written by Italian students. The data were analysed from a qualitative point of view to understand how young people frame the topic of control on web 2.0. The attention is focused on the metaphors used to describe online platforms and on the social environments they mention when they speak about the impacts of online diffusion of personal content on offline life. The results show that the new control practices cannot be adequately described within the classical framework of vertical control. The traditional panoptic principle of observation has to a certain extent been transformed and the Panopticon itself is no more an effective metaphor to describe the control dynamics on web 2.0.
Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana

Every plant cell has a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple environmental signals that vary across the plant. How does the plant integrate clock rhythms, both within and between organs, to ensure coordinated timing? To address this question, we examined the clock at the sub-tissue level across Arabidopsis thaliana seedlings under multiple environmental conditions and genetic backgrounds. Our results show that the clock runs at different speeds (periods) in each organ, which causes the clock to peak at different times across the plant in both constant environmental conditions and light-dark cycles. Closer examination reveals that spatial waves of clock gene expression propagate both within and between organs. Using a combination of modeling and experiment, we reveal that these spatial waves are the result of the period differences between organs and local coupling, rather than long distance signaling. With further experiments we show that the endogenous period differences, and thus the spatial waves, are caused by the organ specificity of inputs into the clock. We demonstrate this by modulating periods using light and metabolic signals, as well as with genetic perturbations. Our results reveal that plant clocks are set locally by organ specific inputs, but coordinated globally via spatial waves of clock gene expression.
Tracking via Robust Multi-task Multi-view Joint Sparse Representation

Combining multiple observation views has proven beneficial for tracking. In this paper, we cast tracking as a novel multi-task multi-view sparse learning problem and exploit the cues from multiple views including various types of visual features, such as intensity, color, and edge, where each feature observation can be sparsely represented by a linear combination of atoms from an adaptive feature dictionary. The proposed method is integrated in a particle filter framework where every view in each particle is regarded as an individual task. We jointly consider the underlying relationship between tasks across different views and different particles, and tackle it in a unified robust multi-task formulation. In addition, to capture the frequently emerging outlier tasks, we decompose the representation matrix to two collaborative components which enable a more robust and accurate approximation. We show that the proposed formulation can be efficiently solved using the Accelerated Proximal Gradient method with a small number of closed-form updates. The presented tracker is implemented using four types of features and is tested on numerous benchmark video sequences. Both the qualitative and quantitative results demonstrate the superior performance of the proposed approach compared to several state-of-the-art trackers.
Mitochondrial OPA1, apoptosis, and heart failure.

AIMS Mitochondrial fusion and fission are essential processes for preservation of normal mitochondrial function. We hypothesized that fusion proteins would be decreased in heart failure (HF), as the mitochondria in HF have been reported to be small and dysfunctional. METHODS AND RESULTS Expression of optic atrophy 1 (OPA1), a mitochondrial fusion protein, was decreased in both human and rat HF, as observed by western blotting. OPA1 is important for maintaining normal cristae structure and function, for preserving the inner membrane structure and for protecting cells from apoptosis. Confocal and electron microscopy studies demonstrated that the mitochondria in the failing hearts were small and fragmented, consistent with decreased fusion. OPA1 mRNA levels did not differ between failing and normal hearts, suggesting post-transcriptional control. Simulated ischaemia in the cardiac myogenic cell line H9c2 cells reduced OPA protein levels. Reduction of OPA1 expression with shRNA resulted in increased apoptosis and fragmentation of the mitochondria. Overexpression of OPA1 increased mitochondrial tubularity, but did not protect against simulated ischaemia-induced apoptosis. Cytochrome c release from the mitochondria was increased both with reduction in OPA1 and with overexpression of OPA1. CONCLUSION This is the first report, to our knowledge, of changes in mitochondrial fusion/fission proteins in cardiovascular disease. These changes have implications for mitochondrial function and apoptosis, contributing to the cell loss which is part of the downward progression of the failing heart.
Translational control of nicotine-evoked synaptic potentiation in mice and neuronal responses in human smokers by eIF2α

Adolescents are particularly vulnerable to nicotine, the principal addictive component driving tobacco smoking. In a companion study, we found that reduced activity of the translation initiation factor eIF2α underlies the hypersensitivity of adolescent mice to the effects of cocaine. Here we report that nicotine potentiates excitatory synaptic transmission in ventral tegmental area dopaminergic neurons more readily in adolescent mice compared to adults. Adult mice with genetic or pharmacological reduction in p-eIF2α-mediated translation are more susceptible to nicotine’s synaptic effects, like adolescents. When we investigated the influence of allelic variability of the Eif2s1 gene (encoding eIF2α) on reward-related neuronal responses in human smokers, we found that a single nucleotide polymorphism in the Eif2s1 gene modulates mesolimbic neuronal reward responses in human smokers. These findings suggest that p-eIF2α regulates synaptic actions of nicotine in both mice and humans, and that reduced p-eIF2α may enhance susceptibility to nicotine (and other drugs of abuse) during adolescence. DOI: http://dx.doi. org/10.7554/eLife.12056. 001
Cloning , expression and functional study of translation elongation factor 2 ( EF2 ) in zebrafish

We have identified translation elongation factor 2 (EF-2) in zebrafish (GenBank Accession No. AAQ91234). Analysis of the DNA sequence of zebrafish EF-2 shows that the 2826 bp cDNA spans an open reading frame between nucleotide 55 to 2631 and encodes a protein of 858 amino acids. Zebrafish EF-2 protein shares 92%, 93%, 93% and 92% identity with the corresponding amino acid sequence in human, mouse, Chinese hamster and Gallus EF-2, respectively. Whole-mount in situ hybridization showed that zebrafish EF-2 was a developmentally regulated gene and might play important roles during the early development of zebrafish embryos. Therefore, we further studied the function of EF-2 during early embryogenesis. Using morpholino antisense oligo knockdown assays, anti-MO injected embryos were found to display abnormal development. The yolk balls were larger than normal and the melanophores spreading on their bodies became fewer. Furthermore, their tails were incurvate and their lenses were much smaller than those of the normal embryos. However the EF-2 overexpression data showed that extra EF-2 protein had no obvious effect on zebrafish embryonic development.
Tracheal Aspirate Levels of the Matricellular Protein SPARC Predict Development of Bronchopulmonary Dysplasia

Background Isolation of tracheal aspirate mesenchymal stromal cells (MSCs) from premature infants has been associated with increased risk of bronchopulmonary dysplasia (BPD). MSCs show high levels of mRNAs encoding matricellular proteins, non-structural extracellular proteins that regulate cell-matrix interactions and participate in tissue remodeling. We hypothesized that lung matricellular protein expression predicts BPD development. Methods We collected tracheal aspirates and MSCs from mechanically-ventilated premature infants during the first week of life. Tracheal aspirate and MSC-conditioned media were analyzed for seven matricellular proteins including SPARC (for Secreted Protein, Acidic, Rich in Cysteine, also called osteonectin) and normalized to secretory component of IgA. A multiple logistic regression model was used to determine whether tracheal aspirate matricellular protein levels were independent predictors of BPD or death, controlling for gestational age (GA) and birth weight (BW). Results We collected aspirates from 89 babies (38 developed BPD, 16 died before 36 wks post-conceptual age). MSC-conditioned media showed no differences in matricellular protein abundance between cells from patients developing BPD and cells from patients who did not. However, SPARC levels were higher in tracheal aspirates from babies with an outcome of BPD or death (p<0.01). Further, our logistic model showed that tracheal aspirate SPARC (p<0.02) was an independent predictor of BPD/death. SPARC deposition was increased in the lungs of patients with BPD. Conclusions In mechanically-ventilated premature infants, tracheal aspirate SPARC levels predicted development of BPD or death. Further study is needed to determine the value of SPARC as a biomarker or therapeutic target in BPD.
CLAMS: Cross-layer Multi-cloud Application Monitoring-as-a-Service Framework

Cloud computing provides on-demand access to affordable hardware (e.g., multi-core CPUs, GPUs, disks, and networking equipment) and software (e.g., databases, application servers, data processing frameworks, etc.) platforms. Application services hosted on single/multiple cloud provider platforms have diverse characteristics that require extensive monitoring mechanisms to aid in controlling run-time quality of service (e.g., access latency and number of requests being served per second, etc.). To provide essential real-time information for effective and efficient cloud application quality of service (QoS) monitoring, in this paper we propose, develop and validate CLAMS-Cross-Layer Multi-Cloud Application Monitoring-as-a-Service Framework. The proposed framework is capable of: (a) performing QoS monitoring of application components (e.g., database, web server, application server, etc.) that may be deployed across multiple cloud platforms (e.g., Amazon and Azure), and (b) giving visibility into the QoS of individual application component, which is something not supported by current monitoring services and techniques. We conduct experiments on real-world multi-cloud platforms such as Amazon and Azure to empirically evaluate our framework and the results validate that CLAMS efficiently monitors applications running across multiple clouds.
A robust real-time tracking system based on an adaptive selection mechanism for mobile robots

Extensive research has been conducted in the domain of object tracking. Among the existing tracking methods, most of them mainly focus on using various cues such as color, texture, contour, features, motion as well as depth information to achieve a robust tracking performance. The tracking methods themselves are highly emphasized while properties of the objects to be tracked are usually not exploited enough. In this paper, we first propose a novel adaptive tracking selection mechanism dependent on the properties of the objects. The system will automatically choose the optimal tracking algorithm after examining the textureness of the object. In addition, we propose a robust tracking algorithm for uniform objects based on color information which can cope with real world constraints. In the mean time, we deployed a textured object tracking algorithm which combines the Lucas-Kanade tracker and a model based tracker using the Random Forests classifier. The whole system was tested and the experimental results on a variety of objects show the effectiveness of the adaptive tracking selection mechanism. Moreover, the promising tracking performance shows the robustness of the proposed tracking algorithm. The computation cost of the algorithm is very low, which proves that it can be further used in various real-time robotics applications.
Heritability estimation of osteoarthritis in the pig-tailed macaque (Macaca nemestrina) with a look toward future data collection

We examine heritability estimation of an ordinal trait for osteoarthritis, using a population of pig-tailed macaques from the Washington National Primate Research Center (WaNPRC). This estimation is non-trivial, as the data consist of ordinal measurements on 16 intervertebral spaces throughout each macaque’s spinal cord, with many missing values. We examine the resulting heritability estimates from different model choices, and also perform a simulation study to compare the performance of heritability estimation with these different models under specific known parameter values. Under both the real data analysis and the simulation study, we find that heritability estimates from an assumption of normality of the trait differ greatly from those of ordered probit regression, which considers the ordinality of the trait. This finding indicates that some caution should be observed regarding model selection when estimating heritability of an ordinal quantity. Furthermore, we find evidence that our real data have little information for valid heritability estimation under ordered probit regression. We thus conclude with an exploration of sample size requirements for heritability estimation under this model. For an ordinal trait, an incorrect assumption of normality can lead to severely biased heritability estimation. Sample size requirements for heritability estimation of an ordinal trait under the threshold model depends on the pedigree structure, trait distribution and the degree of relatedness between each phenotyped individual. Our sample of 173 monkeys did not have enough information from which to estimate heritability, but estimable heritability can be obtained with as few as 180 related individuals under certain scenarios examined here.
Threshold ring signature without random oracles

In this paper, we present the notion and construction of threshold ring signature without random oracles. This is the first scheme in the literature that is proven secure in the standard model. Our scheme extends the Shacham-Waters signature from PKC 2007 in a non-trivial way. We note that our technique is specifically designed to achieve a threshold ring signature in the standard model. Interestingly, we can still maintain the signature size to be the same as the Shacham-Waters signature, while only a tiny computation cost is added.
Lung and kidney cancer mortality associated with arsenic in drinking water in Córdoba, Argentina.

BACKGROUND Studies in Taiwan have found dose-response relations between arsenic ingestion from drinking water and cancers of the skin, bladder, lung, kidney and liver. To investigate these associations in another population, we conducted a study in Córdoba, Argentina, which has a well-documented history of arsenic exposure from drinking water. METHODS Mortality from lung, kidney, liver and skin cancers during the period 1986-1991 in Córdoba's 26 counties was investigated, expanding the authors' previous analysis of bladder cancer in the province. Counties were grouped a priori into low, medium and high arsenic exposure categories based on available data. Standardized mortality ratios (SMR) were calculated using all of Argentina as the reference population. RESULTS We found increasing trends for kidney and lung cancer mortality with arsenic exposure, with the following SMR, for men and women respectively: kidney cancer, 0.87, 1.33, 1.57 and 1.00, 1.36, 1.81; lung cancer, 0.92, 1.54, 1.77 and 1.24, 1.34, 2.16 (in all cases, P < 0.001 in trend test), similar to the previously reported bladder cancer results (0.80, 1.28, 2.14 for men, 1.22, 1.39, 1.81 for women). There was a small positive trend for liver cancer but mortality was increased in all three exposure groups. Skin cancer mortality was elevated for women only in the high exposure group, while men showed a puzzling increase in mortality in the low exposure group. CONCLUSIONS The results add to the evidence that arsenic ingestion increases the risk of lung and kidney cancers. In this study, the association between arsenic and mortality from liver and skin cancers was not clear.
Kinematics and H{2} morphology of the multipolar post-AGB star IRAS 16594-4656

Context. The spectrum of IRAS 16594-4656 shows shock-excited H 2 emission and collisionally excited emission lines such as [O i], [C i], and [Fe ii]. Aims. The goal is to determine the location of the H 2 and [Fe ii] shock emission, to determine the shock velocities, and to constrain the physical properties in the shock. Methods. High resolution spectra of the H 2 1–0 S(1), H 2 2–1 S(1), [Fe ii], and Pa β emission lines were obtained with the near infrared spectrograph Phoenix on Gemini South. Results. The position-velocity diagrams of H 2 1–0 S(1), H 2 2–1 S(1), and [Fe ii] are presented. The H 2 and [Fe ii] emission is spatially extended. The collisionally excited [O i] and [C i] optical emission lines have a similar double-peaked profile compared to the extracted H 2 profile and appear to be produced in the same shock. They all indicate an expansion velocity of ~8 km s -1 and the presence of a neutral, very high-density region with n e about $3\,\times\,10^6$ to $5\,\times\,10^7$ cm -3 . However, the [Fe ii] emission is single-peaked. It has a Gaussian FWHM of 30 km s -1 and a total width of 62 km s -1 at 1% of the peak. The Pa β profile is even wider with a Gaussian FWHM of 48 km s -1 and a total width of 75 km s -1 at 1% of the peak. Conclusions. The H 2 emission is excited in a slow 5 to 20 km s -1 shock into dense material at the edge of the lobes, caused by the interaction of the AGB ejecta and the post-AGB wind. The 3D representation of the H 2 data shows a hollow structure with less H 2 emission in the equatorial region. The [Fe ii] emission is not present in the lobes, but originates close to the central star in fast shocks in the post-AGB wind or in a disk. The Pa β emission also appears to originate close to the star.
The Nuclear Transcription Factor CREB: Involvement in Addiction, Deletion Models and Looking Forward

Addiction involves complex physiological processes, and is characterised not only by broad phenotypic and behavioural traits, but also by ongoing molecular and cellular adaptations. In recent years, increasingly effective and novel techniques have been developed to unravel the molecular implications of addiction. Increasing evidence has supported a contribution of the nuclear transcription factor CREB in the development of addiction, both in contribution to phenotype and expression in brain regions critical to various aspects of drug-seeking behaviour and drug reward. Abstracting from this, models have exploited these data by removing the CREB gene from the developing or developed mouse, to crucially determine its impact upon addiction-related processes. More recent models, however, hold greater promise in unveiling the contribution of CREB to disorders such as addiction.
Phylogenetic characterization of bovine parainfluenza 3 from contaminated cell cultures and field isolates from Brazil

Genomic fragments of the HN and L genes from Brazilian bovine parainfluenza 3 virus (bPIV-3) isolated as contaminants from cell cultures and clinical specimens were amplified by reverse transcription-polymerase chain reaction (RT-PCR), sequenced using specific degenerate primers and analyzed by phylogenetic comparison with reference strains of bPI3V. The Brazilian isolates revealed a high degree of genomic when compared to SF4/32 prototype strain, within the recently proposed genotype A of bPIV-3.
A dynamic two-phase commit protocol for self-adapting services

Next-generation applications based on Web services impose additional requirements on the use of coordination protocols with various optimizations, such as the two-phase commit protocol (2PC). We analyse the well-known 2PC optimizations presumed commit and presumed abort, and present an improved 2PC that is suitable for Web services based applications. More specifically, the protocol allows every individual service provider to choose dynamically the most appropriate presumption for any distributed transaction. The protocol does not introduce extra overhead to the previous 2PC variants in terms of number of messages and log records, and it is easy to understand and realize.