Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach.

UNLABELLED Copy number alterations (CNAs) are thought to account for 85% of the variation in gene expression observed among breast tumours. The expression of cis-associated genes is impacted by CNAs occurring at proximal loci of these genes, whereas the expression of trans-associated genes is impacted by CNAs occurring at distal loci. While a majority of these CNA-driven genes responsible for breast tumourigenesis are cis-associated, trans-associated genes are thought to further abet the development of cancer and influence disease outcomes in patients. Here we present a network-based approach that integrates copy-number and expression profiles to identify putative cis- and trans-associated genes in breast cancer pathogenesis. We validate these cis- and trans-associated genes by employing them to subtype a large cohort of breast tumours obtained from the METABRIC consortium, and demonstrate that these genes accurately reconstruct the ten subtypes of breast cancer. We observe that individual breast cancer subtypes are driven by distinct sets of cis- and trans-associated genes. Among the cis-associated genes, we recover several known drivers of breast cancer (e.g. CCND1, ERRB2, MDM2 and ZNF703) and some novel putative drivers (e.g. BRF2 and SF3B3). siRNA-mediated knockdown of BRF2 across a panel of breast cancer cell lines showed significant reduction in cell viability for ER-/HER2+ (MDA-MB-453) cells, but not in normal (MCF10A) cells thereby indicating that BRF2 could be a viable therapeutic target for estrogen receptor-negative/HER2-enriched (ER-/HER2+) cancers. Among the trans-associated genes, we identify modules of immune response (CD2, CD19, CD38 and CD79B), mitotic/cell-cycle kinases (e.g. AURKB, MELK, PLK1 and TTK), and DNA-damage response genes (e.g. RFC4 and FEN1). siRNA-mediated knockdown of RFC4 significantly reduced cell proliferation in ER-negative normal breast and cancer lines, thereby indicating that RFC4 is essential for both normal and cancer cell survival but could be a useful biomarker for aggressive (ER-negative) breast tumours. AVAILABILITY under NetStrat.
Reclaiming of ground rubber tire by a novel reclaiming agent. I. virgin natural rubber/reclaimed GRT vulcanizates

Mechanochemically devulcanized ground rubber tire (GRT) was (re)vulcanized in compositions with virgin natural rubber (NR). The NR/GRT (re)vulcanizates with GRT content from 20 to 60 wt% have been prepared and studied. Reclaiming of GRT was successfully carried out by tetra methyl thiuram disulfide (TMTD) in presence of spindle oil at around ambient temperature. The cure characteristics and mechanical properties of the virgin NR/reclaim GRT blend were studied. The optimum cure time decreases but scorch time remain unaltered with increasing reclaim rubber content in the blend. Effect of carbon black was studied in NR/RR (80/20) blend. Ageing characteristics of different NR/RR blends were evaluated. Scanning electron microscopy (SEM) studies further indicate the coherency and homogeneity in the NR/RR vulcanizate. The dynamic mechanical properties and swelling behavior of NR/RR blend vulcanizates were examined. The elastic and storage modulus of the NR/RR vulcanizates become improve with increasing reclaim rubber content. Electrical properties of NR/RR vulcanizates were also studied. POLYM. ENG. SCI., 47:1091–1100, 2007. © 2007 Society of Plastics Engineers
Holographic Renormalization of Asymptotically Lifshitz Spacetimes

A variational formulation is given for a theory of gravity coupled to a massive vector in four dimensions, with Asymptotically Lifshitz boundary conditions on the fields. For theories with critical exponent z = 2 we obtain a well-defined variational principle by explicitly constructing two actions with local boundary counterterms. As part of our analysis we obtain solutions of these theories on a neighborhood of spatial infinity, study the asymptotic symmetries, and consider different definitions of the boundary stress tensor and associated charges. A constraint on the boundary data for the fields figures prominently in one of our formulations, and in that case the only suitable definition of the boundary stress tensor is due to Hollands, Ishibashi, and Marolf. Their definition naturally emerges from our requirement of finiteness of the action under Hamilton-Jacobi variations of the fields. A second, more general variational principle also allows the Brown-York definition of a boundary stress tensor.
Mechanical and rheological behavior of unvulcanized and dynamically vulcanized i-PP/EPDM blends

The mechanical and rheological behavior of dynamically vulcanized PP/ EPDM blends is examined and compared with those of unvulcanized blends. The effect of blend ratio and dynamic vulcanization of EPDM rubber on tensile properties and flow are investigated. The mechanical properties of the blends are strongly influenced by the blend ratio. With the increasing of EPDM content the value of yield stress in a solid state decreases with the elastomer volume fractions less than 0.45 for the unvulcanized blends. For the dynamically vulcanized blends the interval of EPDM content, at which the yield peak is seen, is rather limited below 0.25 elastomer volume fractions. It is shown that dynamic vulcanization changes the deformational behavior of PP/EPDM blends. The rheological properties of dynamically vulcanized blends depending on the ratio of the components may be similar to the properties of polymer composites containing the highly disperse structuring filler. The distinction between the rheological behavior of unvulcanized and dynamically vulcanized blends is related to differences of their structures and viscoelastic characteristics of unvulcanized and vulcanized EPDM phase.
The quality evaluation of image recovery attack for visible watermarking algorithms

Image quality evaluation is an important technique to judge the image fidelity of the image applications. In this study, it not only analyzes and evaluates the entire watermarked image before and after attacks, but also helps the encoder to design the superior watermarking algorithms. In order to get the best practice of transmission power on watermark intensity and perceptual efficiency, this study investigates new visible watermarking algorithms based on human vision system (HVS) model and noise visibility function to provide adequate flexibility during the watermark energy embedding. Since it is not possible for all digital images to go through detailed subjective evaluation, 12 image quality metrics are utilized here to automatically predict the subjective judgments of watermarked image since image quality assessments are influenced by the transparency and robustness of watermarked images. In addition, malicious attack like image recovery is implemented to verify the consistency of image quality metrics. From the experimental results, the algorithm of the perceptual model of contrast-sensitive function (CSF) with noise reduction of the visibility thresholds for HVS in DWT domain outperforms the CSF only based algorithm. On the other hand, the image quality metric evaluation values before and after the malicious attack demonstrate the similar trend of judgment which prove the evaluation consistency. Therefore, such study could help the algorithm design for better image fidelity preservation and secure robustness of practical visual communication.
Calpain-3 Impairs Cell Proliferation and Stimulates Oxidative Stress-Mediated Cell Death in Melanoma Cells

Calpain-3 is an intracellular cysteine protease, belonging to Calpain superfamily and predominantly expressed in skeletal muscle. In human melanoma cell lines and biopsies, we previously identified two novel splicing variants (hMp78 and hMp84) of Calpain-3 gene (CAPN3), which have a significant lower expression in vertical growth phase melanomas and, even lower, in metastases, compared to benign nevi. In the present study, in order to investigate the pathophysiological role played by the longer Calpain-3 variant, hMp84, in melanoma cells, we over-expressed it in A375 and HT-144 cells. In A375 cells, the enforced expression of hMp84 induces p53 stabilization, and modulates the expression of a few p53- and oxidative stress-related genes. Consistently, hMp84 increases the intracellular production of ROS (Reactive Oxygen Species), which lead to oxidative modification of phospholipids (formation of F2-isoprostanes) and DNA damage. Such events culminate in an adverse cell fate, as indicated by the decrease of cell proliferation and by cell death. To a different extent, either the antioxidant N-acetyl-cysteine or the p53 inhibitor, Pifithrin-α, recover cell viability and decrease ROS formation. Similarly to A375 cells, hMp84 over-expression causes inhibition of cell proliferation, cell death, and increase of both ROS levels and F2-isoprostanes also in HT-144 cells. However, in these cells no p53 accumulation occurs. In both cell lines, no significant change of cell proliferation and cell damage is observed in cells over-expressing the mutant hMp84C42S devoid of its enzymatic activity, suggesting that the catalytic activity of hMp84 is required for its detrimental effects. Since a more aggressive phenotype is expected to benefit from down-regulation of mechanisms impairing cell growth and survival, we envisage that Calpain-3 down-regulation can be regarded as a novel mechanism contributing to melanoma progression.
On the incorporating of learning in open multi-agent systems: a systematic approach

The development of large scale multi-agent systems (MASs) requires the introduction and structuring of the learning property throughout the design and implementation stages. In open systems and complex environments, agents have to reason and adapt through machine learning techniques in order to perform their goals. In this paper, we present a methodology to introduce learning techniques into software agents. To assist the design phase, we present a design pattern that guides the design of the learning property. The methodology and pattern are used in the construction of an open MAS for the Trading Agent Competition environment in order to illustrate the suitability of our approach.
Two-level HARQ for turbo coded cooperation: System retransmission gain and optimal time allocation

Hybrid automatic repeat request (HARQ) is a well-known technique for improving system throughput and link performance of wireless communication systems, including cooperative communication systems. In this paper, we exploit the limited feedback applied to the two-source turbo coded cooperation scheme to define a particular cooperative HARQ protocol, called two-level HARQ, where the decision on retransmission at each node is conditioned by two levels: first by the feedback from the destination and second by the feedback from the partner node. To evaluate the performance improvement of this cooperative HARQ system over the original turbo coded cooperation system in terms of frame error probability, we define the system retransmission gain. This gain serves as a decision parameter to determine the conditions under which the cooperative HARQ protocol is useful. Finally, optimal time resource allocation is explored, offering sizable performance improvements.
Role of the Kinesin Neck Region in Processive Microtubule-based Motility

Kinesin is a dimeric motor protein that can move along a microtubule for several microns without releasing (termed processive movement). The two motor domains of the dimer are thought to move in a coordinated, hand-over-hand manner. A region adjacent to kinesin's motor catalytic domain (the neck) contains a coiled coil that is sufficient for motor dimerization and has been proposed to play an essential role in processive movement. Recent models have suggested that the neck enables head-to-head communication by creating a stiff connection between the two motor domains, but also may unwind during the mechanochemical cycle to allow movement to new tubulin binding sites. To test these ideas, we mutated the neck coiled coil in a 560-amino acid (aa) dimeric kinesin construct fused to green fluorescent protein (GFP), and then assayed processivity using a fluorescence microscope that can visualize single kinesin–GFP molecules moving along a microtubule. Our results show that replacing the kinesin neck coiled coil with a 28-aa residue peptide sequence that forms a highly stable coiled coil does not greatly reduce the processivity of the motor. This result argues against models in which extensive unwinding of the coiled coil is essential for movement. Furthermore, we show that deleting the neck coiled coil decreases processivity 10-fold, but surprisingly does not abolish it. We also demonstrate that processivity is increased by threefold when the neck helix is elongated by seven residues. These results indicate that structural features of the neck coiled coil, although not essential for processivity, can tune the efficiency of single molecule motility.
N-Butanoyl-N-(3-chloro-1,4-dioxonaphthalen-2-yl)butanamide

In the title compound, C18H18ClNO4, the imide group with its two alkyl substituents is approximately perpendicular to the plane of the naphthoquinone ring system [dihedral angle = 78.5 (1)°]. Further, the imide carbonyl groups are oriented in an anti sense. In the crystal, the substituted naphthoquinone rings form π–π stacks in the a-axis direction [perpendicular centroid–centroid distance = 3.209 (2) Å and slippage = 4.401 Å].
Coronary Heart Disease Risks Associated with High Levels of HDL Cholesterol

Background The association between high‐density lipoprotein cholesterol (HDL‐C) and coronary heart disease (CHD) events is not well described in individuals with very high levels of HDL‐C (>80 mg/dL). Methods and Results Using pooled data from 6 community‐based cohorts we examined CHD and total mortality risks across a broad range of HDL‐C, including values in excess of 80 mg/dL. We used Cox proportional hazards models with penalized splines to assess multivariable, adjusted, sex‐stratified associations of HDL‐C with the hazard for CHD events and total mortality, using HDL‐C 45 mg/dL and 55 mg/dL as the referent in men and women, respectively. Analyses included 11 515 men and 12 925 women yielding 307 245 person‐years of follow‐up. In men, the association between HDL‐C and CHD events was inverse and linear across most HDL‐C values; however at HDL‐C values >90 mg/dL there was a plateau effect in the pattern of association. In women, the association between HDL‐C and CHD events was inverse and linear across lower values of HDL‐C, however at HDL‐C values >75 mg/dL there were no further reductions in the hazard ratio point estimates for CHD. In unadjusted models there were increased total mortality risks in men with very high HDL‐C, however mortality risks observed in participants with very high HDL‐C were attenuated after adjustment for traditional risk factors. Conclusions We did not observe further reductions in CHD risk with HDL‐C values higher than 90 mg/dL in men and 75 mg/dL in women.
High-resolution measurements of AOA and time-delay for characterizing indoor propagation environments

Presents high resolution results obtained with a large digital beamforming array. Both, angle-of-arrival (AOA) and time delay results are presented, in which it is shown that it is possible to measure the characteristics of all of the modes propagating in a hallway, Based on the techniques it is felt that very comprehensive measurements can be made to fully understand propagation in complex environments. These results will then be used for designing smart antennas to be deployed with PCS systems.
An intelligent information retrieval algorithm based on knowledge discovery and self-organizing feature map neural network

Information retrieval is usually referring to the text information retrieval, including information storage, organization, performance, many aspects, such as query, access and its core is the text indexing and retrieval of information. Under the trend of intelligent data analysis and mining, in this paper, we propose a novel information retrieval algorithm based on knowledge discovery and self-organizing feature map neural network. Knowledge discovery is one of the major intellectual activities of human, the current knowledge discovery activities are increasingly based on network data resources and environment. Enhance semantic correlation method, that is, on the basis of the existing association, found the correlation between the data source, a new connection between different sources of data, or further connection, this process is the process of knowledge discovery activities. For enhancement, we introduce the self-organizing feature map neural network into the method to integrate the semantic information. Since Kohonen self-organizing neural network is put forward, the self-organizing feature map algorithm as a kind of very effective clustering method, in the vector quantization and pattern recognition has been widely research and application. With the reasonable of the mentioned techniques, we propose the enhanced retrieval algorithm. The experimental simulation proves that our method obtains higher robustness and accuracy compared with the other state-of-the-art algorithms.
Are impairments in emotion recognition a core feature of callous–unemotional traits? Testing the primary versus secondary variants model in children

Abstract The role of environmental adversity in the development of high callous–unemotional (CU) traits in children is controversial. Evidence speaks to the traits being largely independent of adversity; however, recent data shows that those with high CU traits and high adversity and/or high anxiety might differ in important ways from those with no such history. We tested this using emotion recognition (ER) skills. We tested whether maltreatment history and anxiety levels moderated the relationship between level of CU traits and ER skills in N = 364 children with behavioral problems who were 3 to 16 years old. As hypothesised, in the full sample, the relationship between CU traits and ER differed according to maltreatment history, such that CU traits were associated with poorer recognition for those with zero or negligible history of maltreatment. This moderation of the CU-ER relationship by maltreatment was inconsistent across subgroups, however, and for the cohort utilizing youth self-report of maltreatment, high CU traits were associated with poor ER in those with lower anxiety levels. Maltreatment history and/or anxiety levels can identify different emotional impairments associated with high CU traits, and the impairments might be characteristic of “primary” high CU traits defined as occurring independently of maltreatment and/or high anxiety.
Social Support, Distress, and Well‐Being in Older Men Living With HIV Infection

Summary: Older men with HIV infection/AIDS, having often lived with the condition longer, are more likely to confront the stress of managing more advanced HIV disease than their younger counterparts. Meanwhile, they also are more likely to have less social support and experience more distress than younger persons with HIV infection. The moderating effect of social support on health functioning and distress is unknown for persons with HIV infection, particularly those who are older. Study objectives were to assess whether the association between perceived health functioning and psychological distress and well‐being is moderated (or influenced) by social support and age and if the impact of social support on distress and well‐being is more pronounced for older than for younger men living with HIV infection/AIDS. In this cross‐sectional study of HIV‐positive adult men (n = 199) who have sex with men, participants completed self‐report assessments of perceived health functioning, social support, and psychological distress and well‐being. Measures of health functioning and overall social support were significantly associated with outcome measures of distress and positive affect (all p < .05). However, the main effect for social support was qualified by a significant age‐by‐social support interaction for both outcomes (&bgr; = ‐.190, p < .01 for distress; &bgr; = .172, p < .05 for positive affect), indicating that the impact of social support on decreasing distress and increasing well‐being was more pronounced in older men. The relationships between perceived health functioning and distress and well‐being were not moderated by social support or age. The influence of social support on negative and positive moods in this population of HIV‐infected men who have sex with men was significantly greater among older than among younger participants. With an increasing number of older people with HIV infection/AIDS, special efforts to create effective and sustainable social support interventions may be particularly beneficial to older persons living with HIV infection.
A Knowledge Growth and Consolidation Framework for Lifelong Machine Learning Systems

A more effective vision of machine learning systems entails tools that are able to improve task after task and to reuse the patterns and knowledge that are acquired previously for future tasks. This incremental, long-life view of machine learning goes beyond most of state-of-the-art machine learning techniques that learn throw-away models. In this paper we present a long-life knowledge acquisition, evaluation and consolidation framework that is designed to work with any rule-based machine learning or inductive inference engine and integrate it into a long-life learner. In order to do that we work over the graph of working memory rules and introduce several topological metrics over it from which we derive an oblivion criterion to drop useless rules from working memory and a consolidation process to promote the rules to the knowledge base. We evaluate the framework on a series of tasks in a chess rule learning domain.
Prevalence, Metabolic Features, and Prognosis of Metabolically Healthy Obese Italian Individuals

OBJECTIVE Some obese individuals have normal insulin sensitivity. It is controversial whether this phenotype is associated with increased all-cause mortality risk. RESEARCH DESIGN AND METHODS Fifteen-year all-cause mortality data were obtained through the Regional Health Registry for 2,011 of 2,074 Caucasian middle-aged individuals of the Cremona Study, a population study on the prevalence of diabetes in Italy. Individuals were divided in four categories according to BMI (nonobese: <30 kg/m2; obese: ≥30 kg/m2) and estimated insulin resistance (insulin sensitive: homeostasis model assessment of insulin resistance <2.5; insulin resistant ≥2.5). RESULTS Obese insulin-sensitive subjects represented 11% (95% CI 8.1–14.5) of the obese population. This phenotype had similar BMI but lower waist circumference, blood pressure, fasting glucose, triglycerides, and fibrinogen and higher HDL cholesterol than obese insulin-resistant subjects. In the 15-year follow-up, 495 deaths (cardiovascular disease [CVD]: n = 221; cancer: n = 180) occurred. All-cause mortality adjusted for age and sex was higher in the obese insulin-resistant subjects (hazard ratio 1.40 [95% CI 1.08–1.81], P = 0.01) but not in the obese insulin-sensitive subjects (0.99 [0.46–2.11], P = 0.97) when compared with nonobese insulin-sensitive subjects. Also, mortality for CVD and cancer was higher in the obese insulin-resistant subjects but not in the obese insulin-sensitive subjects when compared with nonobese insulin-sensitive subjects. CONCLUSIONS In contrast to obese insulin-resistant subjects, metabolically healthy obese individuals are less common than previously thought and do not show increased all-cause, cancer, and CVD mortality risks in a 15-year follow-up study.