Miracle-dz/UniFAR-FTUs huggingface dataset:
MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress

Significance Partner and localiser of BRCA2 (PALB2) is a breast cancer susceptibility gene, and the role of its product in repairing broken chromosomes has been extensively described. However, a fraction of PALB2 is also found on intact chromosomes, and it is unknown how and why PALB2 associates with undamaged chromatin. In this study, we establish that the histone binding protein MRG15 is a major interaction partner of PALB2 and plays a key role in tethering PALB2 to active genes. Failure of PALB2 to interact with MRG15 leads to the accumulation of DNA stress at active genes and chromosome instability in dividing cells. These findings shed light on why patients with PALB2 mutations often develop genome instability syndromes, such as cancer. The partner and localiser of BRCA2 (PALB2) plays important roles in the maintenance of genome integrity and protection against cancer. Although PALB2 is commonly described as a repair factor recruited to sites of DNA breaks, recent studies provide evidence that PALB2 also associates with unperturbed chromatin. Here, we investigated the previously poorly described role of chromatin-associated PALB2 in undamaged cells. We found that PALB2 associates with active genes through its major binding partner, MRG15, which recognizes histone H3 trimethylated at lysine 36 (H3K36me3) by the SETD2 methyltransferase. Missense mutations that ablate PALB2 binding to MRG15 confer elevated sensitivity to the topoisomerase inhibitor camptothecin (CPT) and increased levels of aberrant metaphase chromosomes and DNA stress in gene bodies, which were suppressed by preventing DNA replication. Remarkably, the level of PALB2 at genic regions was frequently decreased, rather than increased, upon CPT treatment. We propose that the steady-state presence of PALB2 at active genes, mediated through the SETD2/H3K36me3/MRG15 axis, ensures an immediate response to DNA stress and therefore effective protection of these regions during DNA replication. This study provides a conceptual advance in demonstrating that the constitutive chromatin association of repair factors plays a key role in the maintenance of genome stability and furthers our understanding of why PALB2 defects lead to human genome instability syndromes.
Factor Structure of Nonverbal Cognition

In order to define the factor structure of nonverbal cognitive processes, 156 twenty to sixty year-old participants were selected in Medellin (Colombia). A neuropsychological test battery for assessing different nonverbal cognitive domains (attention, memory, visuoperceptual and visuoconstructive abilities, executive functions, praxis abilities, and written calculation abilities) was administered. Initially, independent factor analyses were carried out for each domain. Three attention factors (Sustained Attention, Divided Attention, and Processing Speed, 73.1% of the variance); two memory factors (Categorical and Non-Categorical Memory, 59.7% of the variance); two visuoperceptual and visuoconstructive factors (Sequential and Simultaneous, 54.0% of the variance); and two executive function factors (Categorization and Trial/Error, 82.0% of the variance) were found. Further, several sequential factor analyses using Varimax orthogonal rotations for noncorrelated variables were performed. The 32 test variables were included, but progressively some variables were removed. This procedure finally selected 13 variables corresponding to five factors accounting for 72.6% of variance. Factor 1 was an Executive Function factor (30% of variance). Factor 2 corresponded to a Sequential-Constructional factor (14.7%). Factor 3 represented a Processing Speed factor and accounted for 10.6% of the variance. Factor 4 was Visuoperceptual factor (9.5% of the variance). Finally, Factor 5 (7.8% of the variance) was a Nonverbal Memory factor. It was concluded that several, different cognitive dimensions are included in nonverbal cognition.
A robust background modeling and foreground object detection using color component analysis

Background modeling and foreground object detection are crucial techniques for embedded image surveillance systems. The popular and accurate methods are mostly pixel based, taking up more memory and requiring longer execution times. Thus, these techniques are not suitable for embedded platforms. This paper presents a block-based major color background modeling and a foreground detection algorithm that possesses efficient processing and low memory requirement in a complex scene, making them feasible for embedded platforms. Our proposed approach consumes 37% less memory and increases accuracy by at least 2.5% compared to other existing methods. Last, implementing the object detection algorithm on the 2.83GHz CPU, we can achieve 26 frames per second for the benchmark video with image size 768×576.
Architecture of coatomer: molecular characterization of delta-COP and protein interactions within the complex

Coatomer is a cytosolic protein complex that forms the coat of COP I- coated transport vesicles. In our attempt to analyze the physical and functional interactions between its seven subunits (coat proteins, [COPs] alpha-zeta), we engaged in a program to clone and characterize the individual coatomer subunits. We have now cloned, sequenced, and overexpressed bovine alpha-COP, the 135-kD subunit of coatomer as well as delta-COP, the 57-kD subunit and have identified a yeast homolog of delta-COP by cDNA sequence comparison and by NH2-terminal peptide sequencing. delta-COP shows homologies to subunits of the clathrin adaptor complexes AP1 and AP2. We show that in Golgi-enriched membrane fractions, the protein is predominantly found in COP I-coated transport vesicles and in the budding regions of the Golgi membranes. A knock-out of the delta-COP gene in yeast is lethal. Immunoprecipitation, as well as analysis exploiting the two-hybrid system in a complete COP screen, showed physical interactions between alpha- and epsilon-COPs and between beta- and delta-COPs. Moreover, the two-hybrid system indicates interactions between gamma- and zeta-COPs as well as between alpha- and beta' COPs. We propose that these interactions reflect in vivo associations of those subunits and thus play a functional role in the assembly of coatomer and/or serve to maintain the molecular architecture of the complex.
Energy-Efficient Joint Scheduling and Application-Specific Interconnection Design

Energy-efficient and high-performance interconnections are critical for multiprocessor architectures. As technology moves into deep submicrometer level, static and dynamic energy consumptions have become dominant constraint factors in high-performance system design. This paper jointly considers scheduling and interconnection design to minimize the interconnection's energy consumption without performance degradation. The Interconnection Energy Minimization Scheduling algorithm is proposed in this paper to design interconnection with segmented buses and to determine a feasible computation and communication schedule to minimize interconnection's energy consumption while meeting tight-latency and high-volume data transfer needs for applications with large inherited parallelism. Experimental results show that interconnection's dynamic energy consumption can be reduced by about 71% and static energy consumption can be reduced by about 35% on average when the proposed algorithm is compared with existing communication cost-conscious scheduling techniques for the evaluated digital signal processing and media applications.
An architecture for unified dialogue in distributed object systems

In traditional information systems, the user interface is controlled by one single application. In distributed systems, several distributed components may want to influence the appearance and logic of the user interface. This paper describes a unified dialogue architecture which enables several distributed components to control the logic and contents of the user dialogue while keeping the dialogue consistent. This architecture is a practical example of using dialogue agents, CORBA and Java. Details are described in connection with a large domain-specific distributed system. Discussion is also provided as to other manners in which this architecture may be implemented, followed by a discussion concerning other problem areas in which the unified dialogue architecture can be effectively applied.
Transcription factor function and promoter architecture govern the evolution of bacterial regulons

Evolutionary changes in ancestral regulatory circuits can bring about phenotypic differences between related organisms. Studies of regulatory circuits in eukaryotes suggest that these modifications result primarily from changes in cis-regulatory elements (as opposed to alterations in the transcription factors that act upon these sequences). It is presently unclear how the evolution of gene regulatory circuits has proceeded in bacteria, given the rampant effects of horizontal gene transfer, which has significantly altered the composition of bacterial regulons. We now demonstrate that the evolution of the regulons governed by the regulatory protein PhoP in the related human pathogens Salmonella enterica and Yersinia pestis has entailed functional changes in the PhoP protein as well as in the architecture of PhoP-dependent promoters. These changes have resulted in orthologous PhoP proteins that differ both in their ability to promote transcription and in their role as virulence regulators. We posit that these changes allow bacterial transcription factors to incorporate newly acquired genes into ancestral regulatory circuits and yet retain control of the core members of a regulon.
Generalized Linear Models for Identifying Predictors of the Evolutionary Diffusion of Viruses

Bioinformatics and phylogeography models use viral sequence data to analyze spread of epidemics and pandemics. However, few of these models have included analytical methods for testing whether certain predictors such as population density, rates of disease migration, and climate are drivers of spatial spread. Understanding the specific factors that drive spatial diffusion of viruses is critical for targeting public health interventions and curbing spread. In this paper we describe the application and evaluation of a model that integrates demographic and environmental predictors with molecular sequence data. The approach parameterizes evolutionary spread of RNA viruses as a generalized linear model (GLM) within a Bayesian inference framework using Markov chain Monte Carlo (MCMC). We evaluate this approach by reconstructing the spread of H5N1 in Egypt while assessing the impact of individual predictors on evolutionary diffusion of the virus.
Co-training for Handwritten Word Recognition

To cope with the tremendous variations of writing styles encountered between different individuals, unconstrained automatic handwriting recognition systems need to be trained on large sets of labeled data. Traditionally, the training data has to be labeled manually, which is a laborious and costly process. Semi-supervised learning techniques offer methods to utilize unlabeled data, which can be obtained cheaply in large amounts in order, to reduce the need for labeled data. In this paper, we propose the use of Co-Training for improving the recognition accuracy of two weakly trained handwriting recognition systems. The first one is based on Recurrent Neural Networks while the second one is based on Hidden Markov Models. On the IAM off-line handwriting database we demonstrate a significant increase of the recognition accuracy can be achieved with Co-Training for single word recognition.
Robust muscle cell segmentation using region selection with dynamic programming

Morphological characteristics of muscle cells, such as cross-sectional areas (CSAs), are critical factors that determine the health and function of the muscle. Automated cell segmentation is usually a prerequisite to calculate the CSAs. However, it is challenging for many traditional segmentation methods to efficiently and effectively separate muscle cells. In this paper, we proposed a region selection-based algorithm for automatic touching cell segmentation on Hematoxylin and Eosin (H&E) stained muscle images. The algorithm starts with generating a set of segmentation candidates and then assigns these candidates proper scores based on a learnt cell shape model and local features. Next, a subset of region candidates is selected as final segmentation based on an Integer Linear Programming scheme under the constraint that no any pair of selected regions can overlap. The algorithm is extensively tested on 60 H&E stained muscle images with over 10,000 cells. Compared with the recent state-of-the-arts, the algorithm provides the best performance.
Functional Characterization of the Human Mariner Transposon Hsmar2

DNA transposons are mobile elements with the ability to mobilize and transport genetic information between different chromosomal loci. Unfortunately, most transposons copies are currently inactivated, little is known about mariner elements in humans despite their role in the evolution of the human genome, even though the Hsmar2 transposon is associated to hotspots for homologous recombination involved in human genetic disorders as Charcot–Marie–Tooth, Prader-Willi/Angelman, and Williams syndromes. This manuscript describes the functional characterization of the human HSMAR2 transposase generated from fossil sequences and shows that the native HSMAR2 is active in human cells, but also in bacteria, with an efficiency similar to other mariner elements. We observe that the sub-cellular localization of HSMAR2 is dependent on the host cell type, and is cytotoxic when overexpressed in HeLa cells. Finally, we also demonstrate that the binding of HSMAR2 to its own ITRs is specific, and that the excision reaction leaves non-canonical footprints both in bacteria and eukaryotic cells.
Bouillonamide: A Mixed Polyketide–Peptide Cytotoxin from the Marine Cyanobacterium Moorea bouillonii

The tropical marine cyanobacterium, Moorea bouillonii, has gained recent attention as a rich source of bioactive natural products. Continued chemical investigation of this cyanobacterium, collected from New Britain, Papua New Guinea, yielded a novel cytotoxic cyclic depsipeptide, bouillonamide (1), along with previously reported molecules, ulongamide A and apratoxin A. Planar structure of bouillonamide was established by extensive 1D and 2D NMR experiments, including multi-edited HSQC, TOCSY, HBMC, and ROESY experiments. In addition to the presence of α-amino acid residues, compound 1 contained two unique polyketide-derived moieties, namely a 2-methyl-6-methylamino-hex-5-enoic acid (Mmaha) residue and a unit of 3-methyl-5-hydroxy-heptanoic acid (Mhha). Absolute stereochemistry of the α-amino acid units in bouillonamide was determined mainly by Marfey’s analysis. Compound 1 exhibited mild toxicity with IC50’s of 6.0 µM against the neuron 2a mouse neuroblastoma cells.
SelPh: Progressive Learning and Support of Manual Photo Color Enhancement

Color enhancement is a very important aspect of photo editing. Even when photographers have tens of or hundreds of photographs, they must enhance each photo one by one by manually tweaking sliders in software such as brightness and contrast, because automatic color enhancement is not always satisfactory for them. To support this repetitive manual task, we present self-reinforcing color enhancement, where the system implicitly and progressively learns the user's preferences by training on their photo editing history. The more photos the user enhances, the more effectively the system supports the user. We present a working prototype system called SelPh, and then describe the algorithms used to perform the self-reinforcement. We conduct a user study to investigate how photographers would use a self-reinforcing system to enhance a collection of photos. The results indicate that the participants were satisfied with the proposed system and strongly agreed that the self-reinforcing approach is preferable to the traditional workflow.
In Situ Surface‐Modification‐Induced Superhydrophobic Patterns with Reversible Wettability and Adhesion

Herein is described a facile, in situ, ink-regulating approach to rapidly achieve reversible water wettability and adhesion transition, with a large degree of contrast, on superhydrophobic TiO2 nanotube array film. The ink printing and removal process allows the wettability and reversible adhesion transitions to be realized. Experimental results demonstrate the potential application of such site-selective, sticky superhydrophobic patterns for droplet manipulation by in situ surface modification.
Using ants as a genetic crossover operator in GLS to solve STSP

Ant Colony Algorithm (ACA) and Genetic Local Search (GLS) are two optimization algorithms that have been successfully applied to the Traveling Salesman Problem (TSP). In this paper we define new crossover operator then redefine ACA's ants as operate according to defined crossover operator then put forward our GLS that uses these ants to solve Symmetric TSP (STSP) instances.
Haldane's Rule: Genetic Bases and Their Empirical Support.

There are few patterns in evolution that are as rigidly held as Haldane's rule (HR), which states, "When in the first generation between hybrids between 2 species, 1 sex is absent, rare, or sterile, that sex is always the heterogametic sex. " Yet despite considerable attention for almost a century, questions persist as to how many independent examples exist and what is (are) the underlying genetic cause(s). Here, we review recent evidence extending HR to plants, where previously it has only been documented in animals. We also discuss recent comparative analyses that show much more variation in sex-chromosome composition than previously recognized, thus increasing the number of potential independent origins of HR dramatically. Finally, we review the standing of genetic theories proposed to explain HR in light of the new examples and new molecular understanding.
Information Hiding and Visibility in Interface Specifications

Information hiding controls which parts of a class are visible to non-privileged and privileged clients (e.g., subclasses). This affects detailed design specifications in two ways. First, specifications should not expose hidden class members. As noted in previous work, this is important because such hidden members are not meaningful to all clients. But it also allows changes to hidden implementation details without invalidating correctness proofs for client code, which is important for maintaining verified programs. Second, to enable sound modular reasoning, certain specifications must be visible to clients. We present rules for information hiding in specifications for Java-like languages, and demonstrate their application to the specification language JML. These rules restrict proof obligations to only mention visible class members, but retain soundness. This allows maintenance of implementations and their specifications without affecting client reasoning.
Language and Gender Author Cohort Analysis of E-mail for Computer Forensics

We describe an investigation of authorship gender and language background cohort attribution mining from e-mail text documents. We used an extended set of predominantly topic content-free e-mail document features such as style markers, structural characteristics and gender-preferential language features together with a Support Vector Machine learning algorithm. Experiments using a corpus of e-mail documents generated by a large number of authors of both genders gave promising results for both author gender and language background cohort categorisation.
Congestion-Mimesis of traffic flow

Taking heed of the approach of physics towards examining reality, constructing laws, and deducing consequences, here we explore the process of creating an algorithmic work of art, through an iterative approach based on the steps of examining the underlying logic of traffic and traffic networks, constructing rules inspired by this logic, and examining the consequences of those rules. However, where in physics the goal is one of prediction and explanation, here we strive to create rules that are an impression of reality.
Galnet: WordNet 3.0 do galego

Neste artigo presentamos o proxecto Galnet do Grupo TALG da Universidade de Vigo, dirixido a construcion da version galega do WordNet 3.0. Tratase dun proxecto que se atopa na sua fase inicial de desenvolvemento, mais do que xa se obtiveron uns primeiros resultados que estan disponibles para a consulta. Describiremos os trazos xerais do proxecto, a metodoloxia e as ferramentas utilizadas, alguns aspectos linguisticos do traballo e os resultados obtidos nesta primeira etapa.
Estimators for fault tolerance coverage evaluation

The problem of estimating the coverage of a fault tolerance mechanism through statistical processing of observations collected in fault injection experiments is addressed. A formal definition of coverage is given in terms of the fault and activation sets that characterize the input space. Two categories of sampling techniques are considered for coverage estimation: sampling in the whole space and sampling in a space partitioned into classes. The estimators for each technique are compared by means of hypothetical examples. Techniques for early estimations of coverage are then studied. These techniques allow unbiased estimations of coverage to be made before all classes of the sampling space have been tested. Finally, the "no-reply" problem that hampers most practical fault-injection experiments is discussed and an a posteriori stratification technique is proposed that allows the scope of incomplete tests to be widened by accounting for available structural information about the target system.
Optimal and Distributed Protocols for Cross-Layer Design of Physical and Transport Layers in MANETs

We seek distributed protocols that attain the global optimum allocation of link transmitter powers and source rates in a cross-layer design of a mobile ad hoc network. Although the underlying network utility maximization is nonconvex, convexity plays a major role in our development. We provide new convexity results surrounding the Shannon capacity formula, allowing us to abandon suboptimal high-SIR approximations that have almost become entrenched in the literature. More broadly, these new results can be back-substituted into many existing problems for similar benefit. Three protocols are developed. The first is based on a convexification of the underlying problem, relying heavily on our new convexity results. We provide conditions under which it produces a globally optimum resource allocation. We show how it may be distributed through message passing for both rate- and power-allocation. Our second protocol relaxes this requirement and involves a novel sequence of convex approximations, each exploiting existing TCP protocols for source rate allocation. Message passing is only used for power control. Our convexity results again provide sufficient conditions for global optimality. Our last protocol, motivated by a desire of power control devoid of message passing, is a near optimal scheme that makes use of noise measurements and enjoys a convergence rate that is orders of magnitude faster than existing methods.