Miracle-dz/UniFAR-FTUs huggingface dataset:
Convex Formulation for Learning from Positive and Unlabeled Data

We discuss binary classification from only positive and unlabeled data (PU classification), which is conceivable in various real-world machine learning problems. Since unlabeled data consists of both positive and negative data, simply separating positive and unlabeled data yields a biased solution. Recently, it was shown that the bias can be canceled by using a particular non-convex loss such as the ramp loss. However, classifier training with a non-convex loss is not straightforward in practice. In this paper, we discuss a convex formulation for PU classification that can still cancel the bias. The key idea is to use different loss functions for positive and unlabeled samples. However, in this setup, the hinge loss is not permissible. As an alternative, we propose the double hinge loss. Theoretically, we prove that the estimators converge to the optimal solutions at the optimal parametric rate. Experimentally, we demonstrate that PU classification with the double hinge loss performs as accurate as the non-convex method, with a much lower computational cost.
When Physics Meets Biology: Low and High-Velocity Penetration, Blunt Impact, and Blast Injuries to the Brain

The incidence of traumatic brain injuries (TBI) in the US has reached epidemic proportions with well over 2 million new cases reported each year. TBI can occur in both civilians and warfighters, with head injuries occurring in both combat and non-combat situations from a variety of threats, including ballistic penetration, acceleration, blunt impact, and blast. Most generally, TBI is a condition in which physical loads exceed the capacity of brain tissues to absorb without injury. More specifically, TBI results when sufficient external force is applied to the head and is subsequently converted into stresses that must be absorbed or redirected by protective equipment. If the stresses are not sufficiently absorbed or redirected, they will lead to damage of extracranial soft tissue and the skull. Complex interactions and kinematics of the head, neck and jaw cause strains within the brain tissue, resulting in structural, anatomical damage that is characteristic of the inciting insult. This mechanical trauma then initiates a neuro-chemical cascade that leads to the functional consequences of TBI, such as cognitive impairment. To fully understand the mechanisms by which TBI occurs, it is critically important to understand the effects of the loading environments created by these threats. In the following, a review is made of the pertinent complex loading conditions and how these loads cause injury. Also discussed are injury thresholds and gaps in knowledge, both of which are needed to design improved protective systems.
Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding

The tails of histone proteins are central players for all chromatin-mediated processes. Whereas the N-terminal histone tails have been studied extensively, little is known about the function of the H2A C-terminus. Here, we show that the H2A C-terminal tail plays a pivotal role in regulating chromatin structure and dynamics. We find that cells expressing C-terminally truncated H2A show increased stress sensitivity. Moreover, both the complete and the partial deletion of the tail result in increased histone exchange kinetics and nucleosome mobility in vivo and in vitro. Importantly, our experiments reveal that the H2A C-terminus is required for efficient nucleosome translocation by ISWI-type chromatin remodelers and acts as a novel recognition module for linker histone H1. Thus, we suggest that the H2A C-terminal tail has a bipartite function: stabilisation of the nucleosomal core particle, as well as mediation of the protein interactions that control chromatin dynamics and conformation.
Contact with Biological Parents for Children in Residental Care: A Vietnam Study

Children living in residential care have a degree of separation from their parents and other family members. Based on attachment theory, this study was conducted to analyze the contact between these children and their biological parents, and the factors affecting this contact. The sample included 382 children (orphans, abandoned or helpless children, children whose parents are deprived of custody or are unable to raise a child) living in residential centers located in North, Central and South of Vietnam. Data were obtained by semi-structured interviews. The results showed that, on average, children contact their parents and family members once a month. In addition, variables such as family image in children’s mind and joyfulness when meeting parents are the best predictors of contact between children and parents, family members. The contact between children and parents is arguably considered as a form of consolidation and maintenance of emotional relationship.
Quantitative analysis of distributed randomized protocols

A wide range of coordination protocols for distributed systems, internet protocols or systems with unreliable components can formally be modelled by Markov decision processes (MDP). MDPs can be viewed as a variant of state-transition diagrams with discrete probabilities and nondeterminism. While traditional model checking techniques for non-probabilistic systems aim to establish properties stating that all (or some) computations fulfill a certain condition, the verification problem for randomized systems requires reasoning about the quantitative behavior by means of properties that refer to the probabilities for certain computations, for instance, the probability to find a leader within 5 rounds or the probability for not reaching an error state.The paper starts with a brief introduction into modelling randomized systems with MDPs and the modelling language ProbMela which is a guarded command language with features of imperative languages, nondeterminism, parallelism, a probabilistic choice operator and lossy channels. We summarize the main steps for a quantitative analysis of MDPs against linear temporal logical specifications. The last part will report on the main features of the partial order reduction approach for MDPs and its implementation in the model checker LiQuor.
Convolutive blind source separation based on multiple decorrelation

Acoustic signals recorded simultaneously in a reverberant environment can be described as sums of differently convolved sources. The task of source separation is to identify the multiple channels and possibly to invert those in order to obtain estimates of the underlying sources. We tackle the problem by explicitly exploiting the nonstationarity of the acoustic sources. Changing cross-correlations at multiple times give a sufficient set of constraints for the unknown channels. A least squares optimization allows us to estimate a forward model, identifying thus the multipath channel. In the same manner we can find an FIR backward model, which generates well separated model sources. Under certain conditions we obtain up to 14 dB signal enhancement in a real room environment.
Biologic interactions determining geographic range size: a one species response to phylogenetic community structure

Range size variation in closely related species suggests different responses to biotic and abiotic heterogeneity across large geographic regions. Species turnover generates a wide spectrum of species assemblages, resulting in different competition intensities among taxa, creating restrictions as important as environmental constraints. We chose to adopt the widely used phylogenetic relatedness (NRI) measurement to define a metric that depicts competition strength (via phylogenetic similarity), which one focal species confronts in its environment. This new approach (NRIfocal) measures the potential of the community structure effect over performance of a single species. We chose two ecologically similar Peucaea sparrows, which co-occur and have highly dissimilar range size to test whether the population response to competition intensity is different between species. We analyzed the correlation between both Peucaea species population sizes and NRIfocal using data from point counts. Results indicated that the widespread species population size was not associated with NRIfocal, whereas the population of restricted-sized species exhibited a negative relationship with competition intensity. Consequently, a species' sensitivity to competition might be a limiting factor to range expansion, which provides new insights into geographic range analysis and community ecology.
Solving constrained optimization via a modified genetic particle swarm optimization

The genetic particle swarm optimization (GPSO) was derived from the original particle swarm optimization (PSO), which is incorporated with the genetic reproduction mechanisms, namely crossover and mutation. Based on which a modified genetic particle swarm optimization (MGPSO) was introduced to solve constrained optimization problems. In which the differential evolution (DE) was incorporated into GPSO to enhance search performance. At each generation GPSO and DE generated a position for each particle, respectively, and the better one was accepted to be a new position for the particle. To compare and ranking the particles, the lexicographic order ranking was introduced. Moreover, DE was incorporated to the original PSO with the same method, which was used to be compared with MGSPO. MGPSO were experimented with well-known benchmark functions. By comparison with original PSO algorithms and the evolution strategy, the simulation results have shown its robust and consistent effectiveness.
Inverse Optimal Stabilization of an Underactuated Spacecraft Using Two Wheels

The problems of optimal stabilization of an underactuated spacecraft using two wheels are investigated in this paper. Considering this kind of spacecraft cannot be stabilized by time-invariant smooth control laws, an inverse optimal control law is presented which circumvents the task of solving the Hamilton-Jacobi equation and minimizes a meaningful cost function based on the direct Lyapunov method and the backstepping technique. Then several simulation results show the asymptotical stability and the optimality of the proposed control law.
Multipartite table methods

A unified view of most previous table-lookup-and-addition methods (bipartite tables, SBTM, STAM, and multipartite methods) is presented. This unified view allows a more accurate computation of the error entailed by these methods, which enables a wider design space exploration, leading to tables smaller than the best previously published ones by up to 50 percent. The synthesis of these multipartite architectures on Virtex FPGAs is also discussed. Compared to other methods involving multipliers, the multipartite approach offers the best speed/area tradeoff for precisions up to 16 bits. A reference implementation is available at http://www.ens-lyon.fr/LIP/Arenaire/.
Brownian descriptor: A rich meta-feature for appearance matching

This paper introduces an image region descriptor and applies it to the problem of appearance matching. The proposed descriptor can be seen as a natural extension of covariance. Driven by recent studies in mathematical statistics related to Brownian motion, we design the Brownian descriptor. In contrast to the classical covariance descriptor, which measures the degree of linear relationship between features, our novel descriptor measures the degree of all kinds of possible relationships between features. We argue that the proposed covariance is a richer descriptor than the classical covariance, especially when fusing non-linearly dependent features. We evaluate our approach on tracking related applications, demonstrating that the Brownian descriptor outperforms the classical covariance in terms of matching accuracy and efficiency.
Targeting DNGR-1 (CLEC9A) with antibody/MUC1 peptide conjugates as a vaccine for carcinomas

DCs are the most potent APCs and are the focus of many immunotherapeutic approaches for the treatment of cancer, although most of these approaches require the ex vivo generation and pulsing of DCs. We have targeted a subset of DCs in vivo using an Ab to DNGR‐1, a C‐type lectin dedicated to the cross‐presentation of Ag expressed by subsets of DCs. HLA‐A2 epitopes from the tumour‐associated Ag, MUC1, were coupled to the anti‐DNGR‐1 Ab, and their efficacy in generating a Th1‐cell response and inhibiting tumour growth was evaluated in a clinically relevant double transgenic mouse model expressing human MUC1 and A2K/b. Using this strategy, we demonstrate that an effective immune response to MUC1 can be generated, which results in a significant delay in the growth of MUC1‐expressing tumours in both prophylactic and therapeutic settings. In addition, we also show, using PBMCs isolated from healthy volunteer blood, that target an MUC1 HLA‐A2 epitope to human DNGR‐1 in vitro can induce an MUC1‐specific CD8+‐T‐cell response, which confirms the relevance of our in vivo murine results in the human setting.
Analysis of the boundaries of Salmonella pathogenicity island 2 and the corresponding chromosomal region of Escherichia coli K-12

We recently identified a pathogenicity island (SPI2) located at 30.7 centisomes on the Salmonella typhimurium chromosome. SPI2 contains genes encoding a type III secretion system whose function is distinct from that of the type III secretion system encoded by a pathogenicity island (SPI1) at 63 centisomes which is involved in epithelial cell entry. An analysis of the boundaries of SPI2 and comparison with the corresponding region of the Escherichia coli chromosome revealed that SPI2 inserted adjacent to the tRNA(Val) gene. The E. coli chromosome contains 9 kb of DNA at the region corresponding to the SPI2 insertion point which appears to be absent in S. typhimurium. The distribution of SPI1 and SPI2 was examined in various Salmonella isolates. In contrast to type III secretion system genes of SPI1, those of SPI2 are not present in Salmonella bongori, which diverged at the first branch point in the Salmonella lineage. These and other data indicate that SPI2 was acquired by a Salmonella strain already harboring SPI1 by horizontal transfer from an unknown source.
Neighborhood coherence and edge based approaches to film scene extraction

In order to enable high-level semantics-based video annotation and interpretation, we tackle the problem of automatic decomposition of motion pictures into meaningful story units, namely scenes. Since a scene is a complicated and subjective concept, we first propose guidelines from film production to determine when a scene change occurs in film. We examine different rules and conventions followed as part of film grammar to guide and shape our algorithmic solution for determining a scene boundary. Two different techniques are proposed as new solutions in this paper. Our experimental results on 10 full-length movies show that our technique based on shot sequence coherence performs well and reasonably better than the color edges-based approach.
Biopsychosocial Update Mental Health

and Rutherford (2008) conducted a " meta-analytic review of HIV interventions for heterosexual African Americans to determine the[ir] overall efficacy in reducing HIV-risk sex behaviors and incident sexually transmitted diseases [(STDs), i.e., the number of new cases each year,] and identify intervention characteristics associated with efficacy " (p. 1177). The investigators identified 38 randomized controlled trials (RCTs) published between 1988 and 2005 that met selection criteria. To aggregate these data, Darbes and colleagues " tested both fixed-effects and random-effects models, and both models yielded similar findings. [The investigators] base[d] the final presentation on the random-effects model because it provides a more conservative estimate of variance and generates more accurate inferences about a population of trials beyond the set of trials included in this study " (p. 1179). Darbes and colleagues report that " thirty-five RCTs provided data on self-reported HIV risk behavior from 14,682 participants. The aggregated effect size was significant. [and indicated] that the intervention groups had [a] 25% reduction in odds of reporting unprotected sexual behavior compared with comparison groups, at an average of 3 months after intervention " (p. 1180). In addition , " data on incident STDs were available from 10 RCTs that included 10,944 participants. The aggregated effect size was marginally significant. [and indicated] that the intervention group had a 12% reduction in the odds of incident STD compared with comparison groups " (p. 1188). " However, the effect became significant when eliminating the trial of the lowest methodological quality. This evidence suggests that behav-ioral interventions can be not only efficacious in changing unprotected sex behaviors but may also reduce incident STDs in heterosexual African Americans " (p. 1191). " Intervention characteristics associated with efficacy include cultural tailoring, aiming to influence social norms in promoting safe[r] sex behavior, utilizing peer education, providing skills training on correct use of condoms and communication skills needed for negotiating safer sex, and multiple sessions and opportunities to practice learned skills " (p. 1177). Finally, Darbes and colleagues observe that this " meta-analysis was. limited by the fact that. only. individual-level and group-level interventions [were included]. There were only a few randomized community level and structural-level interventions available in the literature. However, given that many risk factors associated with HIV risk-taking in heterosexual African Americans are structural (e.g., poverty, access to care), future research should evaluate community-level and structural level interventions when …
The biology of habitat dominance; can microbes behave as weeds?

Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard‐wired to behave in a vigorous and ecologically aggressive manner. These ‘microbial weeds’ are able to dominate the communities that develop in fertile but uncolonized – or at least partially vacant – habitats via traits enabling them to out‐grow competitors; robust tolerances to habitat‐relevant stress parameters and highly efficient energy‐generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat‐specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp. , Salinibacter ruber and Haloquadratum walsbyi. Some microbes, such as Escherichia coli, Mycobacterium smegmatis and Pseudoxylaria spp. , exhibit characteristics of both weed and non‐weed species. We propose that the concept of nonweeds represents a ‘dustbin’ group that includes species such as Synodropsis spp. , Polypaecilum pisce, Metschnikowia orientalis, Salmonella spp. , and Caulobacter crescentus. We show that microbial weeds are conceptually distinct from plant weeds, microbial copiotrophs, r‐strategists, and other ecophysiological groups of microorganism. Microbial weed species are unlikely to emerge from stationary‐phase or other types of closed communities; it is open habitats that select for weed phenotypes. Specific characteristics that are common to diverse types of open habitat are identified, and implications of weed biology and open‐habitat ecology are discussed in the context of further studies needed in the fields of environmental and applied microbiology.
Drusen-associated degeneration in the retina.

PURPOSE Drusen are variably sized extracellular deposits that form between the retinal pigmented epithelium (RPE) and Bruch's membrane. They are commonly found in aged eyes, however, numerous and/or confluent drusen are a significant risk factor for age-related macular degeneration. The purpose of this study was to investigate the impact of drusen on overlying cells of the retina. METHODS Tissue containing retina and RPE/choroid was dissected from human donor eyes, embedded in agarose, and sectioned at 100 micro m using a vibratome. Sections were immunostained with a panel of antibodies that labeled glial cells, first-, second-, and third-order retinal neurons and processed for confocal microscopy. RESULTS Retinal cells that overlie both soft and hard drusen exhibited numerous structural and molecular abnormalities. Normally detectable only in the outer segments of rod photoreceptors, rod opsin immunolabeling was also observed in the inner segment, cell body, axon, and axon terminal of photoreceptors that overlie drusen. Labeling with this antibody also revealed the deflection and shortening of rod inner and outer segments. Cone photoreceptors displayed similar structural abnormalities, as well as a decrease in cone opsin immunoreactivity. Drusen-associated abnormalities in the synaptic terminals of photoreceptor cells were also observed. In addition, an increase in intermediate filament protein immunoreactivity (vimentin and glial fibrillary acidic protein) was observed within Müller glial cells in areas of retina overlying drusen. Both soft and hard drusen were associated with a similar spectrum of effects in both macular and extramacular regions. Second- and third-order neurons, including bipolar, horizontal, amacrine, and ganglion cells all appeared unaffected. The structural and molecular abnormalities observed in photoreceptors and Müller glial cells were confined to retinal regions directly overlying and immediately adjacent to drusen; more distant retinal regions appeared unperturbed. Remarkably, significant abnormalities were observed over small subclinical drusen. CONCLUSIONS Retinal cells overlying both soft and hard drusen exhibit structural and molecular abnormalities indicative of photoreceptor degeneration and Müller glial activation. These abnormalities resemble the degenerative effects common to many forms of retinal degeneration, but are confined to areas directly overlying drusen. This suggests that photoreceptor cell function is compromised as a consequence of drusen formation.