Miracle-dz/UniFAR-FTUs huggingface dataset:
Gut Microbiota in HIV Infection: Implication for Disease Progression and Management

Survival rates among HIV patients have significantly improved since the introduction of antiretroviral therapy (ART) in HIV management. However, persistent disease progression and clinical complications in virally suppressed individuals point to additional contributing factors other than HIV replication; microbial translocation is one such factor. The role of underlying commensal microbes and microbial products that traverse the intestinal lumen into systemic circulation in the absence of overt bacteraemia is under current investigation. This review focuses on current knowledge of the complex microbial communities and microbial markers involved in the disruption of mucosal immune T-cells in the promotion of inflammatory processes in HIV infections. Unanswered questions and aims for future studies are addressed. We provide perspective for discussing potential future therapeutic strategies focused on modulating the gut microbiota to abate HIV disease progression.
Changing the Way We Think About Endothelial Cell Insulin Sensitivity, Nitric Oxide, and the Pathophysiology of Type 2 Diabetes

Recent changes in human lifestyles have led to a global epidemic of insulin-resistant type 2 diabetes (1). Type 2 diabetes is a multisystem disorder characterized by the disruption of insulin signaling pathways critical to the integration of tissue repair and nutrient homeostasis that results in loss of protection against a range of chronic disorders of human health including arterial atherosclerosis (2). As a result, type 2 diabetes is a major cause of myocardial infarction, stroke, and peripheral vascular disease affecting millions of individuals worldwide. Insulin resistance, characterized by an initial compensatory increase in insulin production, is a progressive disorder that can differentially affect organs, tissues, cells, and intracellular signaling pathways at different stages of the disease (3). It has recently emerged that in addition to its classical target tissues including liver, skeletal muscle, and adipose tissue, insulin resistance can occur in the endothelium where insulin has been shown to stimulate the release of the signaling radical nitric oxide (NO) (4). As a result, the endothelium, which was previously thought to be an inert lining of the blood vessel, is now established as a highly active organ that regulates a multitude of processes critical to vascular function (5). NO, a metabolite of L-arginine to L-citrulline conversion by endothelial NO synthase (eNOS), is released by the endothelium in response to cues such as shear stress and growth factors and has …
Joint source-channel turbo decoding of entropy coded sources

A new turbo joint source-channel decoding algorithm is presented. The proposed scheme, derived from a Bayesian network representation of the coding chain, incorporates three types of information: the source memory; the residual redundancy of the source coder; and finally the redundancy introduced by the channel coder. Specifically, we modify an existing algorithm by introducing an equivalent graph, that is shown to hold the same state-space while exhibiting far less undirected cycles. A fully consistent solution for joint turbo decoding within the Bayesian networks framework follows. The proposed algorithm is demonstrated to yield considerably better results along with a drastic reduction in computational complexity when compared to the existing one.
Naive and memory T cells show distinct pathways of lymphocyte recirculation

In this report, we have addressed two questions concerning immunological memory: the way in which naive and memory T cells recirculate through the body, and the intrinsic rate of division within the naive and memory populations. We identified naive and memory T cells in sheep by their cell surface phenotype and their ability to respond to recall antigen. Memory T cells were CD2hi, CD58hi, CD44hi, CD11ahi, and CD45R-, as pertains in man. T cells that crossed from blood to the tissues of the hind leg and accumulated in the popliteal afferent lymph were all of memory phenotype. Conversely, T cells in efferent lymph, 90% of which entered the lymph node (LN) via high endothelial venules (HEV), were mostly of the naive phenotype (CD2lo, CD58lo, CD44lo, CD11alo, and CD45R+). The marked enrichment of these two phenotypes in different recirculatory compartments indicated that memory T cells selectively traffic from blood to peripheral tissues to LN (via afferent lymph), whereas naive T cells selectively traffic from blood to LN (via HEV). We argue that the differential use of these two recirculation pathways probably optimizes lymphocyte interactions with antigen. The nonrandom distribution of T cell subsets in various recirculatory compartments may be related to the relative proportion of memory cells in each subset. In particular, gamma/delta T cells in blood were almost exclusively of memory phenotype, and accumulated preferentially in afferent, but not in efferent, lymph. Finally, using the bromo-deoxyuridine labeling technique, we found that at least a sizeable proportion of memory T cells, whether in blood or afferent lymph, were a dividing population of cells, whereas naive T cells were a nondividing population. This result supports an alternative model of lymphocyte memory that assumes that maintenance of memory requires persistent antigenic stimulation.
A Novel Moving Target Detection Approach for Dual-Channel SAR System

A novel approach to moving target detection is proposed for dual-channel SAR system. This approach is on the basis of eigen- decomposition of the sample covariance matrix and examines the statistic of the second eigenvalue and the Along-Track Interferometric (ATI) phase for ground moving target indication. Based on this statistic, a new Constant False Alarm Rate (CFAR) detector can be designed to solve the problem of GMTI. To detect slow moving targets more accurately, the second eigenvalue and the ATI phase pre- thresholds are implemented before a CFAR detector. Experimental results on measured SAR data are presented to demonstrate that this novel detector has wider range of detection velocity and lower false alarm probability.
On Intermediate Precision Required for Correctly-Rounding Decimal-to-Binary Floating-Point Conversion.

The algorithms developed ten years ago in preparation for IBM’s support of IEEE Floating-Point on its mainframe S/390 processors use an overly conservative intermediate precision to guarantee correctly-rounded results across the entire exponent range. Here we study the minimal requirement for both bounded and unbounded precision on the decimal side (converting to machine precision on the binary side). An interesting new theorem on Continued Fraction expansions is oered, as well as an open problem on the growth of partial quotients for ratios of powers of two and five.
In Silico Modeling: the Human Factor

Technology is playing an increasingly larger role in biological research and investigation. We are building ever more sophisticated experimental systems which can sample data at rates well beyond anything possible using traditional methods. To analyse this data computational systems do the bulk of the work. Mathematical and computational modelling methods are being applied to large scale systems. These methods can perform analysis and derive information from such systems even with only incomplete information and partial pictures of networks, which is beyond the powers of what experimental work, or indeed ordinary unaided human cognition, could itself achieve. While human and economic investments in technology development and adoption are growing fast (supported by pressure from many stakeholders) some observers have begun to ask what will all this mean for biology as a science. Undoubtedly, the future of biology is as a technoscience, in which technical and engineering expertise are as important as biological knowledge and experimental skill. As such many of the practices and cultures that have characterized 20 century biology may be supplanted by more automated and algorithmic machine-driven processes. But what can we really expect from technology? How effective will it be and what impact will it have on biological knowledge? How will the role of scientists as human beings be transformed by this epochal transformation? How autonomous will the role of technology be with respect to human contributions in driving research? In sum, how does this human-technology partnership work? Are there any risks or negative drifts that we can foresee and try to counter?
Geodesic distance-based pose-invariant blind watermarking algorithm for three-dimensional triangular mesh model

Pose editing, changing the poses of three-dimensional (3D) mesh model, frequently results in de-synchronization effect which most 3D watermarking methods are sensitive to and normally regard it as an attack. A novel pose-invariant blind watermarking algorithm for 3D triangular mesh model is proposed in this paper to resist the pose changing attack. In this algorithm, the geodesic distance of each vertex pair on the 3D mesh model to be watermarked is calculated, and then this model is segmented into meaningful pose-invariant components based on the calculation result. Each meaningful component is further divided into non-overlapping cells according to the distribution of geodesic distances from its vertices to the cutting boundary. Finally the defined watermark is embedded into these cells by adjusting the mean value of geodesic distances in order to achieve the invariance of pose changing, and later detection follows the same concept. Our experimental result demonstrates that the proposed algorithm has the ability to resist the attacks of pose changing, similarity transformations, vertex reordering, local deformation, cropping, simplification, additive random noise, and smoothing.
Rapamycin-mediated lifespan increase in mice is dose and sex dependent and metabolically distinct from dietary restriction

Rapamycin, an inhibitor of mTOR kinase, increased median lifespan of genetically heterogeneous mice by 23% (males) to 26% (females) when tested at a dose threefold higher than that used in our previous studies; maximal longevity was also increased in both sexes. Rapamycin increased lifespan more in females than in males at each dose evaluated, perhaps reflecting sexual dimorphism in blood levels of this drug. Some of the endocrine and metabolic changes seen in diet‐restricted mice are not seen in mice exposed to rapamycin, and the pattern of expression of hepatic genes involved in xenobiotic metabolism is also quite distinct in rapamycin‐treated and diet‐restricted mice, suggesting that these two interventions for extending mouse lifespan differ in many respects.
Multi-agent plan reconfiguration under local LTL specifications

We propose a cooperative motion and task planning scheme for multi-agent systems where the agents have independently assigned local tasks, specified as linear temporal logic formulas. These tasks contain hard and soft sub-specifications. A least-violating initial plan is synthesized first for the potentially infeasible task and the partially-known workspace. This discrete plan is then implemented by the potential-field-based navigation controllers. While the system runs, each agent updates its knowledge about the workspace via its sensing capability and shares this knowledge with its neighbouring agents. Based on the knowledge update, each agent verifies and revises its motion plan in real time. It is ensured that the hard specification is always fulfilled for safety and the satisfaction for the soft specification is improved gradually. The design is distributed as only local interactions are assumed. The overall framework is demonstrated by a case study and an experiment.
Dwarf-Class Verbs, Theta-Theory andArgument Linking

This paper investigates a class of English verbs that pose a challenge for theories of the relation between thematic roles and syntactic structure. The search for principles that govern this relation is a central task of linguistic theory, and the problem of formulating these principles—the so-called “linking problem”—provides the background for the present study. Traditional solutions to the linking problem have taken a common form: The grammar is assumed to include a thematic hierarchy (e.g., Agent > Theme > Goal > Oblique [Larson 1988]) and a linking principle (e.g., the UTAH [Baker 1988]) that makes reference to structural positions. (See, inter multa alia, Baker 1997, Dowty 1991, Fillmore 1968, Grimshaw 1990, Jackendoff 1987, Perlmutter and Postal 1984, and Speas 1990.) 1
Design and Development of a Serious Game for Medical Training in Cytopathology

We are designing and developing a serious game for cytopathology medical training. This game has some challenging technical requirement as to be deployable both in PCs and in low-cost Android tablets (e.g., 50$ Kindle Fire 7 tablet) with a limited budget. We reviewed some of the existing games or gamified elearning modules to create a shared understanding between medical experts and developers about possible game mechanics and to identify which of those approaches can be suitable for our case.
Cyclooxygenase-2 Is a Target of MicroRNA-16 in Human Hepatoma Cells

Cyclooxygenase-2 (COX-2) expression has been detected in human hepatoma cell lines and in human hepatocellular carcinoma (HCC); however, the contribution of COX-2 to the development of HCC remains controversial. COX-2 expression is higher in the non-tumoral tissue and inversely correlates with the differentiation grade of the tumor. COX-2 expression depends on the interplay between different cellular pathways involving both transcriptional and post-transcriptional regulation. The aim of this work was to assess whether COX-2 could be regulated by microRNAs in human hepatoma cell lines and in human HCC specimens since these molecules contribute to the regulation of genes implicated in cell growth and differentiation. Our results show that miR-16 silences COX-2 expression in hepatoma cells by two mechanisms: a) by binding directly to the microRNA response element (MRE) in the COX-2 3′-UTR promoting translational suppression of COX-2 mRNA; b) by decreasing the levels of the RNA-binding protein Human Antigen R (HuR). Furthermore, ectopic expression of miR-16 inhibits cell proliferation, promotes cell apoptosis and suppresses the ability of hepatoma cells to develop tumors in nude mice, partially through targeting COX-2. Moreover a reduced miR-16 expression tends to correlate to high levels of COX-2 protein in liver from patients affected by HCC. Our data show an important role for miR-16 as a post-transcriptional regulator of COX-2 in HCC and suggest the potential therapeutic application of miR-16 in those HCC with a high COX-2 expression.
Carotenoids and egg quality in the lesser black-backed gull Larus fuscus: a supplemental feeding study of maternal effects

Egg quality is a phenotype of, and can profoundly influence fitness in, both mother and offspring. However, the physiological mechanisms that underlie this maternal effect are poorly understood. Carotenoids are hypothesized to enhance antioxidant activity and immune function, and are responsible for the pigmentation of egg yolk. The proximate basis and consequences of this maternal investment, however, have not previously been studied in wild birds. In this supplemental feeding study of lesser black–backed gulls, Larus fuscus, carotenoid–fed females are shown to have increased integument pigmentation, higher plasma concentrations of carotenoids and antioxidant activity, and lower plasma concentrations of immunoglobulins (Igs) in comparison with controls. In turn, carotenoid–fed females produced eggs containing high carotenoid but low Ig concentrations (i.e. passive immunity), whereas control females produced eggs containing low carotenoid but high Ig concentrations. Within–clutch patterns of these resources varied over the laying sequence in a similar manner in both carotenoid–fed and control nests. Our results suggest that carotenoids could be one resource responsible for egg quality maternal effects in birds. We discuss the possible implications of carotenoid–mediated effects on phenotype for fitness in mothers and their offspring.
Joint DOA and Polarization Estimation for L-Shaped Polarization Sensitive Array

A blind joint Direction of Arrival (DOA) and polarization estimation method for L-shaped polarization sensitive array has been investigated. Analysis of the received signal for the L-shaped array indicates its characteristics of a trilinear model. We derive a trilinear decomposition-based algorithm for joint DOA and polarization estimation, which can be regarded as a generalization of the ESPRIT method. The proposed algorithm shows better performance for DOA and polarization estimation, and has wider application than ESPRIT. Numerical results verify its useful behavior.
Dynamic Scheduling Model for Realtime Applications in MANET

This paper proposes a dynamic scheduling model for realtime multimedia communication over mobile ad hoc networks. The key idea of the model is to ensure maximizing spatial channel reuse among spatially contending nodes. We describe a distributed algorithm based on instantaneous 1-hop and 2-hop neighboring information through a modified beacon message. The simulation result shows that the dynamic scheduling model can provide higher performance under heavy traffic load for realtime communication over mobile ad hoc networks. The number of the RTS packet retransmission was minimized significantly and the delay and jitter were reduced about 60% and 41% respectively. More packets can be transmitted in minimal time, leading to increase the overall network capacity.
Communicative asymmetry, handedness and language experience

Lateralization of human cognitive and linguistic functioning has important implications for the evolution of our species. Various researchers suggest that a link between communicative and manual development in humans, in both ontogeny and phylogeny, led to a human-specific brain lateralization pattern for language, tool-use and possibly other cognitive domains (Corballis, 2003; Fitch & Braccini, 2013). The human-unique character of these asymmetries (namely, the fact that humans are the only animals demonstrating such strong populationlevel biases in both asymmetries), and their presumed importance for humanspecific traits, such as tool-use and language (e.g. Estalrrich & Rosas, 2013; Chance & Crow, 2007), have long attracted researchers’ attention and became a field of studies in its own right. However, the exact nature of handedness-language relationship, as well as its evolutionary history is far from being understood. Particularly concerning is the fact that studies conducted on human infants and primates bring inconsistent results. Some researchers (e.g. Fagard, 2013) have expressed serious concerns regarding the level of understanding of manual/communicative asymmetries relations in human ontogeny and phylogeny. Although there is evidence suggesting that language and handedness are associated, more research is required to test this hypothesis. There are two important notions regrading such a research. First of all, it is necessary to investigate the association between language asymmetry, handedness and other cognitive parameters (Cochet, 2016). Second of all, it is necessary to conduct studies on more diverse samples. The majority of studies investigating manual and communicative asymmetries have been conducted with either human infants or non-human primates, while the number of studies addressing these aspects in the adults is quite limited. Such situation is problematic for our ability to relate the findings of research in children and primates with the research conducted on adult population. Moreover, the studies 510
Contextual phenomena and thematic relations in database QA dialogues: results from a Wizard-of-Oz Experiment

Considering data obtained from a corpus of database QA dialogues, we address the nature of the discourse structure needed to resolve the several kinds of contextual phenomena found in our corpus. We look at the thematic relations holding between questions and the preceding context and discuss to which extent thematic related-ness plays a role in discourse structure.
Querying Heterogeneous Datasets on the Linked Data Web: Challenges, Approaches, and Trends

The growing number of datasets published on the Web as linked data brings both opportunities for high data availability and challenges inherent to querying data in a semantically heterogeneous and distributed environment. Approaches used for querying siloed databases fail at Web-scale because users don't have an a priori understanding of all the available datasets. This article investigates the main challenges in constructing a query and search solution for linked data and analyzes existing approaches and trends.
Mining Urban Traffic Events and Anomalies DM 751

As huge numbers of sensors relay real-time traffic measurements on city roads, real-time information management systems need to be in place that sieve relevant from irrelevant information. This is particularly important in mission critical applications. For example traffic operators need to be informed about potential anomalies caused by road traffic accidents or similar events in order to deploy timely mitigation strategies. We investigate a new method that elevates anomalies visually to an operator by using a combination of change-detection analytics and auxiliary information from human-sensors (e.g., through Twitter). We identify operational regimes of constant behaviour and change points that bound a regime. This allows us to account for drifts that are not captured in a model. This has the advantage over cumulative sum (CUSUM) algorithms that no threshold parameter needs to be specified upfront and relaxes the assumption of stationarity. Stationarity assumptions do not hold in traffic systems, as network effects take hold and traffic signal control intervenes when local traffic states are deteriorating.
Computing Shortest Violation Traces in Model Checking Based on Petri Net Unfoldings and SAT

Model checking based on the causal partial order semantics of Petri nets is an approach widely applied to cope with the state space explosion problem. One of the ways to exploit such a semantics is to consider (finite prefixes of) net unfoldings — themselves a class of acyclic Petri nets — which contain enough information, albeit implicit, to reason about the reachable markings of the original Petri nets. One of the possibilities for the verification process is to build a finite and complete prefix and use it for constructing a Boolean formula such that any satisfying assignment to its variables yields a trace violating the property being checked. (And if there are no satisfying assignments then the property is not violated.) In this paper a method for computing the shortest violation traces (which can greatly facilitate debugging the system) is proposed. Experimental results demonstrate that it can achieve significant reductions in the size of the Boolean formula as well as in the time required to compute a shortest violation trace, when compared with a näıve approach.