Miracle-dz/UniFAR-FTUs huggingface dataset:
SkyFinder: attribute-based sky image search

In this paper, we present SkyFinder, an interactive search system of over a half million sky images downloaded from the Internet. Using a set of automatically extracted, semantic sky attributes (category, layout, richness, horizon, etc.), the user can find a desired sky image, such as "a landscape with rich clouds at sunset" or "a whole blue sky with white clouds". The system is fully automatic and scalable. It computes all sky attributes offline, then provides an interactive online search engine. Moreover, we build a sky graph based on the sky attributes, so that the user can smoothly explore and find a path within the space of skies. We also show how our system can be used for controllable sky replacement.
A Parallel Communication Infrastructure for STAPL

Communication is an important but difficult aspect of parallel programming. This paper describes a parallel communication infrastructure, based on remote method invocation, to simplify parallel programming by abstracting lowlevel shared-memory or message passing details while maintaining high performance and portability. STAPL, the Standard Template Adaptive Parallel Library, builds upon this infrastructure to make communication transparent to the user. The basic design is discussed, as well as the mechanisms used in the current Pthreads and MPI implementations. Performance comparisons between STAPL and explicit Pthreads or MPI are given on a variety of machines, including an HPV2200, Origin 3800 and a Linux Cluster.
Validation of Rapid Neurodevelopmental Assessment Instrument for Under-Two-Year-Old Children in Bangladesh

OBJECTIVE: The objective of this study was to determine the reliability and validity of a comprehensive assessment procedure for ascertaining neurodevelopmental status of children aged 0 to 24 months for use by multidisciplinary professionals in a developing country. METHODS: We developed the Rapid Neurodevelopmental Assessment (RNDA) to determine functional status in the following domains: primitive reflexes, gross motor, fine motor, vision, hearing, speech, cognition, behavior, and seizures. Reliability was determined for 50 children who were aged <3 months and 30 children who were aged ≥3 to 24 months and were administered the RNDA by 8 different professionals (3 physicians, 4 therapists, and 1 special teacher). Validity was determined on 34 children aged <3 months in hospital and 81 children aged ≥3 to 24 months in urban (n = 47) and rural (n = 34) community-based populations by any 1 of the 8 professionals, with simultaneous administration of the adapted Bayley Scales of Infant Development II by a psychologist as the gold standard. RESULTS: Mean κ coefficients of agreement among professionals in overall and individual domains in the 2 age groups ranged from good to excellent. For both younger and older children, there was good concurrent validity (ie, significantly lower mean Mental Development Index and Psychomotor Development Index scores) for children with ≥1 neurodevelopmental impairment and for children with impairments in most functional domains, compared with children with no impairments. Significantly more impairments were found in children from disadvantaged compared with socioeconomically more advantaged communities, indicating good discriminant validity. CONCLUSIONS: The RNDA can be used by professionals from a range of backgrounds with high reliability and validity for determining functional status of children who are younger than 2 years. The study findings have important practical implications for early identification and intervention to mitigate neurodevelopmental impairments in large populations that live in developing countries where professional expertise is sparse.
Satellite number density profiles of primary galaxies in the 2dFGRS.

We analyse the projected radial distribution of satellites around bright primary galaxies in the 2dFGRS. We have considered several primary-satellite subsamples to search for dependencies of the satellite number density profiles, ρ(r p), on properties of satellites and primaries. We find significant differences in the behaviour of ρ(r p) depending on primary characteristics. In star-forming primaries, the satellite number density profile is consistent with power laws within projected distance 20 100 kpc), the density profiles of all primaries are well described by power laws ρ(r p) ∝ r α , although we notice that for red, early spectral type primaries, the outer slope obtained is steeper (α red ∼ 1.12) than that corresponding to blue, late spectral type primaries (α blue ∼− 0.79). We have tested our results by control samples of galaxies identical to the samples of satellites in apparent magnitude and projected distance to the primary, but with a large relative velocity. This sample of unphysical primary-galaxy pairs shows a flat radial density profile beyond r p = 20 kpc indicating that our results are not biased toward a decrease of the true number of objects due to catalogue selection effects. Our results can be understood in terms of dynamical friction and tidal stripping on satellites in the primary haloes. These processes can effectively transfer energy to the dark matter, flattening the central steep profiles of the satellite distribution in evolved systems. Ke yw ords: galaxies: evolution ‐ galaxies: formation ‐ galaxies: haloes.
Roles for 147 embryonic lethal genes on C.elegans chromosome I identified by RNA interference and video microscopy

Early embryonic development involves complex events such as the regulation of cell division and the establishment of embryonic polarity. To identify genes involved in these events, we collected four‐dimensional time‐lapse video recordings of the first three cell divisions and analysed terminal phenotypes after RNA interference of 147 embryonic lethal genes previously identified in a systematic screen of Caenorhabditis elegans chromosome I. Over half gave defects in early processes such as meiosis, the assembly or position of the first mitotic spindle, cytokinesis, and proper nuclear positioning. For some phenotypic classes, the majority of genes are involved in a shared biochemical process. In addition, we identified loss‐of‐function phenotypes for genes of unknown function, but for which homologues exist in other organisms, shedding light on the function of these uncharacterized genes. When applied to the whole genome, this approach should identify the vast majority of genes required for early cell processes, paving the way for a greatly improved understanding of these processes and their regulation at the molecular level.
Independent evolution of an antiviral TRIMCyp in rhesus macaques

The antiretroviral restriction factor TRIM5 has recently emerged as an important mediator of innate immunity and species-specific inhibition of retroviral replication in mammals. Selection pressure from pathogenic infection has driven rapid evolution of TRIM5 genes, leading to the antiviral specificities we see today. Remarkably, the New World owl monkey (Aotus trivirgatus) encodes a TRIM5 protein in which the antiviral determinants in the B30.2 domain have been replaced by cyclophilin A (CypA) encoded by a retrotransposed cDNA. The owl monkey TRIMCyp protein restricts infection by a subset of lentiviruses that recruit CypA to their capsids, including HIV-1 and feline immunodeficiency virus. Here, we show that the Old World monkey, rhesus macaque (Macaca mulatta), also encodes a TRIMCyp protein that has arisen independently from that in owl monkeys. The rhesus TRIMCyp is encoded by a single, but common, allele (Mamu7) of the rhesus TRIM5 gene, among at least six further alleles that encode full-length TRIM5 proteins with no homology to CypA. The antiviral specificity of the rhesus TRIMCyp is distinct, restricting infection of HIV-2 and feline immunodeficiency virus but not HIV-1. Restriction by rhesus TRIMCyp is before reverse transcription and inhibited by blocking CypA binding, with cyclosporine A, or by mutation of the capsid CypA binding site. These observations suggest a mechanism of restriction that is conserved between TRIMCyp proteins. The lack of activity against HIV-1 suggests that Mamu7 homozygous animals will be null for TRIM5-mediated restriction of HIV-1 and could contribute to improved animal models for HIV/AIDS.
Dictionary based sparse representation for domain adaptation

Machine Learning algorithms are often as good as the data they can learn from. Enormous amount of unlabeled data is readily available and the ability to efficiently use such amount of unlabeled data holds a significant promise in terms of increasing the performance of various learning tasks. We consider the task of supervised Domain Adaptation and present a Self-Taught learning based framework which makes use of the K-SVD algorithm for learning sparse representation of data in an unsupervised manner. To the best of our knowledge this is the first work that integrates K-SVD algorithm into the self-taught learning framework. The K-SVD algorithm iteratively alternates between sparse coding of the instances based on the current dictionary and a process of updating/adapting the dictionary to better fit the data so as to achieve a sparse representation under strict sparsity constraints. Using the learnt dictionary, a rich feature representation of the few labeled instances is obtained which is fed to a classifier along with class labels to build the model. We evaluate our framework on the task of domain adaptation for sentiment classification. Both self-domain (requiring very few domain-specific training instances) and cross-domain classification (requiring 0 labeled instances of target domain and very few labeled instances of source domain) are performed. Empirical comparisons of self-domain and cross-domain results establish the efficacy of the proposed framework.
A First-Order Branching Time Logic of Multi-Agent System

This paper presents a first-order branching time temporal logic that is suitable for describing and reasoning about a wide class of computational multi-agent systems. The logic is novel in that it supports reasoning about the beliefs, actions, goals, abilities and structure of groups of agents. A sound proof system for the logic is presented, and some short examples are given, showing how the logic might be used to specify desirable properties of multi-agent systems.
Discrimination of sea-bird sounds vs. garden-bird songs: Do Scottish and German-Saxon infants show the same preferential looking behaviour as adults?

Birdsong and human speech share some genetic origins (Haesler, Rochefort, Georgi, Licznerski, Osten, & Scharff, 2007; Vargha-Khadem, Gadian, Copp, & Mishkin, 2005). In two studies (N = 67 infants and N = 28 adults) in Scotland (UK) and Saxony (Germany), perceptual discrimination of innate, repetitive, lower frequency sea-bird sounds vs. learned, melodic, higher frequency garden-bird songs was tested in infants in their first year as well as in adults, using the conditioned head-turn procedure (CHTP; e.g., Jusczyk, Friederici, Wessels, Svernkerud, & Jusczyk, 1993). Infants and adults reliably distinguished between the two types of sounds. Independently of environment, infants paid more attention to sea-bird sounds than to garden-bird songs, while adults showed the reverse preference. Further analysis revealed additional insights into the underlying processes.
Flipping the Metabolic Switch: Understanding and Applying Health Benefits of Fasting

Intermittent fasting (IF) is a term used to describe a variety of eating patterns in which no or few calories are consumed for time periods that can range from 12 hours to several days, on a recurring basis. This review is focused on the physiological responses of major organ systems, including the musculoskeletal system, to the onset of the metabolic switch: the point of negative energy balance at which liver glycogen stores are depleted and fatty acids are mobilized (typically beyond 12 hours after cessation of food intake).
Robust adaptive beamforming using partial least squares

The goal of this paper is to present an iterative robust adaptive beamformer using partial least squares (PLS) based on the generalized sidelobe canceller (GSC) parameterization of the minimum variance (MV) beamformer. The proposed method can be implemented simply as an iterative process and does not require the choice of a user parameter. The shrinkage properties and the relations among ridge regression (RR) Capon beamformer, principal component regression (PCR) MV beamformer and our proposed method are discussed. The performance of our approach is illustrated by numerical simulations and compared to other robust adaptive beamformers.
A Document Frequency Constraint for Pseudo-Relevance Feedback Models

We study in this paper the behavior of several PRF models, and display their main characteristics. This will lead us to introduce a new heuristic constraint for PRF models, referred to as the Document Frequency (DF) constraint. We then analyze, from a theoretical point of view, state-of-the-art PRF models according to their relation with this constraint. This analysis reveals that the standard mixture model for PRF in the language modeling family does not satisfy the DF constraint. We then conduct a series of experiments in order to see whether the DF constraint is valid or not. To do so, we performed tests with an oracle and a simple family of tf-idf functions based on a prameter k controlling the convexity/concavity of the function. Both the oracle and the results obtained with this family of functions validate the DF constraint.
Dynamic Markov random fields for stochastic modeling of visual attention

This report proposes a new stochastic model of visual attention to predict the likelihood of where humans typically focus on a video scene. The proposed model is composed of a dynamic Bayesian network that simulates and combines a person¿s visual saliency response and eye movement patterns to estimate the most probable regions of attention. Dynamic Markov random field (MRF) models are newly introduced to include spatiotemporal relationships of visual saliency responses. Experimental results have revealed that the propose model outperforms the previous deterministic model and the stochastic model without dynamic MRF in predicting human visual attention.
Lost expression of ADAMTS5 protein associates with progression and poor prognosis of hepatocellular carcinoma

Altered expression of ADAMTS5 is associated with human carcinogenesis and tumor progression. However, the role of ADAMTS5 in hepatocellular carcinoma (HCC) is unclear. This study analyzed ADAMTS5 expression in HCC tissues and tested for association with clinicopathological and survival data from HCC patients and then explored the role of ADAMTS5 in HCC cells in vitro. Paraffin blocks from 48 HCC patients were used to detect ADAMTS5 and vascular endothelial growth factor (VEGF) expression and microvessel density (MVD). A normal liver cell line and HCC cell lines were used to detect ADAMTS5 expression and for ADAMTS5 manipulation. ADAMTS5 cDNA was stably transfected into HCC cells and ADAMTS5 expression assessed by Western blot analysis. Tumor cell-conditioned growth medium was used to assess human umbilical vein endothelial cell migration and Matrigel tube formation. Xenograft assay was performed to determine the role of ADAMTS5 in vivo. The data showed that the expression of ADAMTS5 was reduced in HCC, which was inversely associated with VEGF expression, MVD, and tumor size and associated with poor overall survival of HCC patients. Lentivirus-mediated ADAMTS5 expression significantly inhibited tumor angiogenesis by downregulating in vitro expression of VEGF and inhibiting migration and tube formations, and also inhibited tumor growth and VEGF expression and reduced MVD in vivo in a mouse xenograft model. Taken together, these results suggest that ADAMTS5 plays a role in suppression of HCC progression, which could be further studied as a promising novel therapeutic target and a potential prognostic marker in HCC.
Iranian Journal of Basic Medical Sciences Molecular Characterization of Aspergillus Infections in an Iranian Educational Hospital Using Rapd-pcr Method

ARTICLEINFO ABSTRACT Article type: Original article Objective(s): The nosocomial infections by Aspergillus species are associated with constructions and increased dust loads in hospital indoors. Our main object was to find the environmental sources of Aspergillus species causing hospital acquired infections. Materials and Methods: The clinical and environmental samplings were performed during 18 months from spring 2010 to summer 2011 in Imam educational hospital, Urmia, Iran. A morphological diagnosis was performed including microscopic characterization of isolated aspergillus from cultured specimens and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for the identification in the level of species. Random amplified polymorphic DNA – PCR RAPD-PCR using random primers for rDNA gene was performed to compare Aspergillus isolates of clinical cases with the relevant environmental sources. Results: Use of RAPD method resulted various differential patterns, so that some Aspergillus isolates from the clinical and hospital indoor were completely matched (matched pairs) and some other Aspergillus isolates were not matched. In the case of matched pairs, Aspergillus niger and A. flavus isolated from broncoalveolar lavage and sinus discharge were relevant to those of air conditioner and walls surfaces, respectively. Conclusion: The hospital sources for the Aspergillus clinical isolates included air condition and walls. RAPD-PCR analysis can play a trivial role to find the hospital sources of Aspergillus clinical isolates.
Structure-aware CNF obfuscation for privacy-preserving SAT solving

In this paper, we study the problem of solving hard propositional satisfiability problem in Cloud or computing grid, which is honest-but-curious. We propose an approach to preserve input and output privacy based on CNF obfuscation, and present obfuscation algorithm and its corresponding solution recovery algorithm. By obfuscation, the CNF formula is transformed into another formula, with different circuit structure and over-approximated solution space. Solution of the original CNF can be extracted from the solution of obfuscated CNF by solution recovery. Theoretical analysis demonstrates that, obfuscation algorithm can significantly change the structure of CNF formula with polynomial time complexity, while solution recovery algorithm can filter out solution with linear time complexity. Experimental results on ISCAS89 benchmark show that obfuscation incurs acceptable negative impact on the performance of SAT solving.
SEQUENTIAL EXPERIMENTAL DESIGN AND EXTREMUM CONTROL

We consider the situation where one wants to maximise a function f(θ,x) with respect to x, with f(θ,x) linear in θ, θ unknown and estimated from observations yk = f(θ,xk) + 2k, where 2k is a random error (linear regression model). Special attention is given to sequences defined by xk+1 = argmaxx f(θ̂ ,x)+αkdk(x), with θ̂ k an estimated value of θ obtained from (x1, y1), . , (xk, yk) and dk(x) a penalty for poor estimation. Asymptotic results are given (strong consistency of θ̂) for a particular penalty function dk and suitable weighting sequences {αk}. Approximately optimal rules are suggested for the finite horizon case where one wants to maximize ∑N i=1wif(θ,xi), with {wi} a given weighting sequence. Various examples are presented.
Interconnect delay aware RTL Verilog bus architecture generation for an SoC

As feature size is scaled down to the submicron level, interconnect delay in the design of a high-speed System-on-a-Chip (SoC) becomes a major concern. This concern is especially acute for on-chip buses. In this paper we describe a methodology to generate a custom bus architecture using accurate estimations of interconnect delay. To improve bus delay accuracy, the bus Verilog register-transfer level (RTL) specification was altered based on interconnect delay estimations. Interconnect delay information is provided from an estimated chip layout. The delay estimates for the on-chip buses are used early in the design phase with a corresponding impact on system correctness and performance. As an example of interconnect delay aware bus generation, we compare three different General Global Bus Architecture (GGBA) configurations, showing that certain system blocks (the memory controllers) need to be modified based on interconnect delay estimation. The three different GGBA configurations are evaluated through the simulation of an orthogonal frequency division multiplexing (OFDM) wireless transmitter application. The impact of accurate interconnect delay estimation is shown through a 35.3% reduction in execution time between a worst-case bus delay configuration (GGBA III) and an accurate interconnect delay aware GGBA configuration (GGBA II).
In silico evidence for sequence-dependent nucleosome sliding

Significance The dynamic compaction of DNA into chromatin is essential for gene expression. Errors during compaction are associated with numerous diseases. Several molecular factors are known to affect chromatin dynamics, but their relative importance and the interplay between them are poorly understood. A detailed molecular model is used here to examine chromatin dynamics at the level of its most fundamental building block, namely the nucleosome. Nucleosome dynamics are demonstrated to be encoded in the DNA sequence itself, and key fundamental factors are uncovered that can significantly alter these dynamics at the molecular level. The results serve to complete a hitherto unavailable description of nucleosome dynamics by introducing previously unappreciated molecular processes, with the potential to influence macroscopic chromatin structure and genetics. Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nucleosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nucleosome repositioning. The mechanism of nucleosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.