Miracle-dz/UniFAR-FTUs huggingface dataset:
SHBG Gene Polymorphism (rs1799941) Associates with Metabolic Syndrome in Children and Adolescents

Background Metabolic syndrome (MetS) is a complex disorder characterized by coexistence of several cardiometabolic (CM) factors, i.e. hyperlipidemia, obesity, high blood pressure and insulin resistance. The presence of MetS is strongly associated with increased risk of cardiovascular disease (CVD). The syndrome was originally defined as an adult disorder, but MetS has become increasingly recognized in children and adolescents. Methods Genetic variants influence biological components common to the CM factors that comprise MetS. We investigated single locus associations between six single nucleotide polymorphisms (SNPs), previously shown to modulate lipid or sex hormone binding globulin (SHBG) levels, with MetS in a Turkish pediatric cohort (37 cases, 323 controls). Results Logistic regression analysis revealed a significant association between rs1799941, located in SHBG, and MetS (OR = 3.09, p-value = 0.006). The association with MetS remained after sequential adjustment for each CM factor included in the syndrome definition, indicating that the identified association is not being driven by any single trait. A relationship between rs1799941 and SHBG levels, was also discovered, but it was dependent on MetS status. In control subjects, the A allele of rs1799941 associated with a significant increase in SHBG levels (p = 0.012), while in cases there was no association between rs1799941 and SHBG levels (p = 0.963). Conclusions The significant association between rs1799941 and MetS in children is not contingent on any single CM trait. Additionally, the presence of MetS may abrogate effect of rs1799941 polymorphism on SHBG levels in children.
Estimation of uncertainty in constrained spherical deconvolution fiber orientations

Constrained spherical deconvolution (CSD) is a new reconstruction technique that extracts white matter fiber orientations from diffusion weighted MRI data of the brain. However, since these orientations are estimated from noisy data, they are subject to errors, which propagate during fiber tractography. Therefore, it is important to estimate the uncertainty associated with the fiber orientations. In this work, we investigate the performance of a statistical method called the bootstrap, when estimating confidence intervals for CSD fiber orientations. The bootstrap is a nonparametric statistical technique based on data resampling. We used Monte Carlo simulations to measure both its accuracy and precision when applied to CSD. Also, we evaluated an alternative method called the bootknife, which aims to increase the precision of the bootstrap.
Linking News across Multiple Streams for Timeliness Analysis

Linking multiple news streams based on the reported events and analyzing the streams' temporal publishing patterns are two very important tasks for information analysis, discovering newsworthy stories, studying the event evolution, and detecting untrustworthy sources of information. In this paper, we propose techniques for cross-linking news streams based on the reported events with the purpose of analyzing the temporal dependencies among streams. Our research tackles two main issues: (1) how news streams are connected as reporting an event or the evolution of the same event and (2) how timely the newswires report related events using different publishing platforms. Our approach is based on dynamic topic modeling for detecting and tracking events over the timeline and on clustering news according to the events. We leverage the event-based clustering to link news across different streams and present two scoring functions for ranking the streams based on their timeliness in publishing news about a specific event.
Distributed Context-Aware Systems

Currently, context-aware applications are defined as applications that react appropriately to information sensed in the environment, as opposed to applications that elaborate only information explicitly provided by users. Context is (implicitly or explicitly) thought of as a collection of features of the (physical or virtual) environment, which can affect the behavior of an application. Though this notion of context is relatively unproblematic in systems with central control, it raises a number of challenging issues when applied to distributed systems-namely, systems in which control is distributed over a group of heterogeneous, autonomous, interacting entities (typically, agents). Indeed, in distributed applications, we cannot assume that autonomous entities share a context, even though each of them uses contextual information for its operations. In this essay, we discuss in detail this claim and present a notion of context that seems to be adequate for distributed systems. For the sake of illustration, we outline how this notion of context can be used to design distributed context-aware systems.
Two Alternatively Spliced Isoforms of the Arabidopsis SR45 Protein Have Distinct Roles during Normal Plant Development1[W][OA]

The serine-arginine-rich (SR) proteins constitute a conserved family of pre-mRNA splicing factors. In Arabidopsis (Arabidopsis thaliana), they are encoded by 19 genes, most of which are themselves alternatively spliced. In the case of SR45, the use of alternative 3′ splice sites 21 nucleotides apart generates two alternatively spliced isoforms. Isoform 1 (SR45.1) has an insertion relative to isoform 2 (SR45.2) that replaces a single arginine with eight amino acids (TSPQRKTG). The biological implications of SR45 alternative splicing have been unclear. A previously described loss-of-function mutant affecting both isoforms, sr45-1, shows several developmental defects, including defects in petal development and root growth. We found that the SR45 promoter is highly active in regions with actively growing and dividing cells. We also tested the ability of each SR45 isoform to complement the sr45-1 mutant by overexpression of isoform-specific green fluorescent protein (GFP) fusion proteins. As expected, transgenic plants overexpressing either isoform displayed both nuclear speckles and GFP fluorescence throughout the nucleoplasm. We found that SR45.1-GFP complements the flower petal phenotype, but not the root growth phenotype. Conversely, SR45.2-GFP complements root growth but not floral morphology. Mutation of a predicted phosphorylation site within the alternatively spliced segment, SR45.1-S219A-GFP, does not affect complementation. However, a double mutation affecting both serine-219 and the adjacent threonine-218 (SR45.1-T218A + S219A-GFP) behaves like isoform 2, complementing the root but not the floral phenotype. In conclusion, our study provides evidence that the two alternatively spliced isoforms of SR45 have distinct biological functions.
Adherence to antiretroviral therapy among HIV-positive children: Examination of the role of caregiver health beliefs

This study examined the association between two components of the Health Belief Model (perceived vulnerability and barriers) and adherence to antiretroviral therapy (ART) among children who are HIV-infected. The parents/caregivers of 30 children (mean age = 5.21, SD = 3.18) who were HIV-infected and who were on active ART were surveyed to assess current methods of adherence assessment and educational efforts within the institution. All participants (except one) were African American and reported low monthly family incomes (M = $869.45, SD = $832.63). Assessment instruments included measures of perceived vulnerability, caregiver-reported adherence and perceived barriers, and objective measures of adherence (clinical pill count; electronic measurement). The results failed to demonstrate a significant relationship between parental perceived vulnerability, perceived barriers and adherence to antiretroviral medications. Methods of assessing adherence provided significantly discrepant estimates of adherence. Results are discussed in terms of implications for patient care and for future research in this area. The addition of behavioural and motivational components to traditional educational approaches may positively impact treatment results.
Nootropic, anxiolytic and CNS-depressant studies on different plant sources of shankhpushpi

Context: Shankhpushpi, a well-known drug in Ayurveda, is extensively used for different central nervous system (CNS) effects especially memory enhancement. Different plants are used under the name shankhpushpi in different regions of India, leading to an uncertainty regarding its true source. Plants commonly used under the name shankhpushpi are: Convolvulus pluricaulis Chois. , Evolvulus alsinoides Linn. , both from Convolvulaceae, and Clitoria ternatea Linn. (Leguminosae). Objective: To find out the true source of shankhpushpi by evaluating and comparing memory-enhancing activity of the three above mentioned plants. Anxiolytic, antidepressant and CNS-depressant activities of these three plants were also compared and evaluated. Materials and methods: The nootropic activity of the aqueous methanol extract of each plant was tested using elevated plus-maze (EPM) and step-down models. Anxiolytic, antidepressant and CNS-depressant studies were evaluated using EPM, Porsolt’s swim despair and actophotometer models, respectively. Results: C. pluricaulis extract (CPE) at a dose of 100 mg/kg, p.o. showed maximum nootropic and anxiolytic activity (p < 0.001). E. alsinoides extract (EAE) and C. ternatea extract (CTE) showed maximum memory-enhancing and anxiolytic activity (p < 0.001) at 200 and 100 mg/kg, respectively. Amongst the three plants, EAE and CTE showed significant (p < 0.05), while CPE did not exhibit any antidepressant activity. All the three plants showed CNS-depressant action at higher dose levels. Discussion and conclusions: The above results showed all the three plants possess nootropic, anxiolytic and CNS-depressant activity. The results of memory-enhancing activity suggest C. pluricaulis to be used as true source of shankhpushpi.
Leftover Hashing Against Quantum Side Information

The Leftover Hash Lemma states that the output of a two-universal hash function applied to an input with sufficiently high entropy is almost uniformly random. In its standard formulation, the lemma refers to a notion of randomness that is (usually implicitly) defined with respect to classical side information. Here, a strictly more general version of the Leftover Hash Lemma that is valid even if side information is represented by the state of a quantum system is shown. Our result applies to almost two-universal families of hash functions. The generalized Leftover Hash Lemma has applications in cryptography, e.g., for key agreement in the presence of an adversary who is not restricted to classical information processing.
CRC-Aided Decoding of Polar Codes

CRC (cyclic redundancy check)-aided decoding schemes are proposed to improve the performance of polar codes. A unified description of successive cancellation decoding and its improved version with list or stack is provided and the CRC-aided successive cancellation list/stack (CA-SCL/SCS) decoding schemes are proposed. Simulation results in binary-input additive white Gaussian noise channel (BI-AWGNC) show that CA-SCL/SCS can provide significant gain of 0.5 dB over the turbo codes used in 3GPP standard with code rate 1/2 and code length 1024 at the block error probability (BLER) of 10-4. Moreover, the time complexity of CA-SCS decoder is much lower than that of turbo decoder and can be close to that of successive cancellation (SC) decoder in the high SNR regime.
Aβ Immunotherapy Protects Morphology and Survival of Adult-Born Neurons in Doubly Transgenic APP/PS1 Mice

The hippocampus is heavily affected by progressive neurodegeneration and β-amyloid pathology in Alzheimer's disease (AD). The hippocampus is also one of the few brain regions that generate new neurons throughout adulthood. Because hippocampal neurogenesis is regulated by both endogenous and environmental factors, we determined whether it benefits from therapeutic reduction of β-amyloid peptide (Aβ)-related toxicity induced by passive Aβ immunotherapy. Aβ immunotherapy of 8–9-month-old mice expressing familial AD-causing mutations in the amyloid precursor protein and presenilin-1 genes with an antibody against Aβ decreased compact β-amyloid plaque burden and promoted survival of newly born neurons in the hippocampal dentate gyrus. As these neurons matured, they exhibited longer dendrites with more complex arborization compared with newly born neurons in control-treated transgenic littermates. The newly born neurons showed signs of functional integration indicated by expression of the immediate-early gene Zif268 in response to exposure to a novel object. Aβ immunotherapy was associated with higher numbers of synaptophysin-positive synaptic boutons. Labeling dividing progenitor cells with a retroviral vector encoding green fluorescent protein (GFP) showed that Aβ immunotherapy restored the impaired dendritic branching, as well as the density of dendritic spines in new mature neurons. The presence of cellular prion protein (PrPc) on the dendrites of the GFP+ newly born neurons is compatible with a putative role of PrPc in mediating Aβ-related toxicity in these cells. In addition, passive Aβ immunotherapy was accompanied by increased angiogenesis. Our data establish that passive Aβ immunotherapy can restore the morphological maturation of the newly formed neurons in the adult hippocampus and promote angiogenesis. These findings provide evidence for a role of Aβ immunotherapy in stimulating neurogenesis and angiogenesis in transgenic mouse models of AD, and they suggest the possibility that Aβ immunotherapy can recover neuronal and vascular functions in brains with β-amyloidosis.
GT: picking up the truth from the ground for internet traffic

Much of Internet traffic modeling, firewall, and intrusion detection research requires traces where some ground truth regarding application and protocol is associated with each packet or flow. This paper presents the design, development and experimental evaluation of gt, an open source software toolset for associating ground truth information with Internet traffic traces. By probing the monitored host's kernel to obtain information on active Internet sessions, gt gathers ground truth at the application level. Preliminary experimental results show that gt's effectiveness comes at little cost in terms of overhead on the hosting machines. Furthermore, when coupled with other packet inspection mechanisms, gt can derive ground truth not only in terms of applications (e.g., e-mail), but also in terms of protocols (e.g., SMTP vs. POP3).
In vitro and in vivo characterization of A‐940894: a potent histamine H4 receptor antagonist with anti‐inflammatory properties

Background and purpose: The histamine H4 receptor is widely expressed in cells of immune origin and has been shown to play a role in a variety of inflammatory processes mediated by histamine. In this report, we describe the in vitro and in vivo anti‐inflammatory properties of a potent histamine H4 receptor antagonist, A‐940894 (4‐piperazin‐1‐yl‐6,7‐dihydro‐5H‐benzo[6,7]cyclohepta[1,2‐d]pyrimidin‐2‐ylamine).
Visual speech synthesis by modelling coarticulation dynamics using a non-parametric switching state-space model

We present a novel approach to speech-driven facial animation using a non-parametric switching state space model based on Gaussian processes. The model is an extension of the shared Gaussian process dynamical model, augmented with switching states. Audio and visual data from a talking head corpus are jointly modelled using the proposed method. The switching states are found using variable length Markov models trained on labelled phonetic data. We also propose a synthesis technique that takes into account both previous and future phonetic context, thus accounting for coarticulatory effects in speech.
Context-Enhanced Personalized Social Summarization

A BSTRACT This work investigates an interesting and challenging task in summarization, i.e., personalized social summarization, which aims to adapt summarization result of a specified document to an intended user based on his interests inferred from social context implicitly. Most existing summarization systems generate a uniform version of summary for different users no matter who is reading or generate personalized summaries employing only the local information in the document and the user profile. This paper proposes a novel unsupervised approach by making use of enhanced social context to aid personalized summary generation. In the proposed method, document expansion, user expansion, and implicit induction of the intended user's interest aspects are achieved simultaneously by adopting a fuzzy tripartite clustering algorithm. And both the informativeness of sentences and the user’s interest aspects are incorporated in a unified ranking process. Preliminary experimental results on a social tagging dataset validate the effectiveness of the proposed approach.
Detecting Opinionated Sentences by Extracting Context Information

In this paper, we briefly describe several experimental methods to solve MOAT at NTCIR-7. In the subtask of opinionated sentence detection, two methods aiming to extract the context information of each sentence are proposed. Maximum Entropy model is used to predict the polarity class. A rule-based pattern matching scheme is devised to find topic-relevant sentence. For the subtask of detecting holders and targets, the CRF model is adopted.
Runtime Analysis of Random Local Search on JUMP function with Reinforcement Based Selection of Auxiliary Objectives

In certain optimization problems, aside from the target objective, auxiliary objectives can be used. These auxiliary objectives may be either helpful or not. Often we can not determine whether an auxiliary objective is helpful. In this work we consider the EA+RL method that dynamically chooses auxiliary objectives in random local search using reinforcement learning. This method's runtime has already been theoretically analysed on different monotonic functions, and it was shown that EA+RL can exclude harmful auxiliary objectives from consideration. EA+RL has also shown good results on different real-world problems. However, it has not been theoretically analysed whether this method can efficiently optimize non-monotonic functions using simple evolutionary algorithms and reinforcement learning agents. In this paper we consider optimization of the non-monotonic JUMP function with the EA+RL method. We use two auxiliary objectives. One of them is helpful during the first phase of optimization and another one is helpful during the last phase. On other stages they are constant, so they neither help nor slow optimization down. We show that EA+RL has at least Ω(ℓ/n) probability of solving this problem in polynomial time using random local search, which is impossible for the conventional random local search without learning. We also propose a modification of EA+RL that is guaranteed to find the optimum.
Crashing waves, awesome explosions, turbulent smoke and beyond: applied mathematics and scientiﬁc computing in the visual effects industry

As computers get faster and architectures evolve, simulation of the dynamics of natural phenomena is becoming an increasingly indispensable tool for creating virtual worlds in movie special effects and video games. For example, nearly all companies involved in effects have a team dedicated to simulation-based dynamics of water, fire, smoke, explosions, rigid body dynamics and deformable/elastic bodies etc. Whether it’s an exploding fireball in Star Wars: Episode 3 or a swirling maelstrom in Pirates of the Caribbean: At World’s End, special effects leveraging numerical simulations can be seen in a wide range of Hollywood blockbusters. Although previously considered too involved and prohibitively expensive for applications like movie special effects, simulation of such phenomena is now much more practical on moderately powerful PCs. Also, the bar has been raised so high for realism in these industries that simulating the physics of such phenomena is necessary to produce effects at the state of the art. The governing equations for such phenomena come by and large from classical physics and are most often in the form of a system of partial differential equations. The development of algorithms for solving such equations with the computer is one of the cornerstones of applied mathematics and scientific computing. In fact, some techniques (most notably, level set methods) have completely revolutionized the industry and have even been honored with Technical Academy Awards. And although this is the geek version of the award, at least awardees get the chance to meet celebrity hosts like Jessica Alba!
New data of three rare belondirid species (Nematoda, Dorylaimida, Belondiridae) from Vietnam, with the first record and description of the male of Oxybelondira paraperplexa Ahmad & Jairajpuri, 1979

Abstract Three rare nematode species of the family Belondiridae, originally described from and only known to occur in India are recorded for the first time in Vietnam: Axonchium thoubalicum, Belondira murtazai and Oxybelondira paraperplexa. It is the first report of these three genera in this country. The three species are described, including new morphological data, morphometrics and light microscope pictures. The male of Oxybelondira paraperplexa is collected and described for the first time. It is characterized by its 1.54 mm long body, ad-cloacal pair of genital papillae situated at 9.0 µm from the cloacal aperture, only one ventromedian supplement located at 15 µm from the ad-cloacal pair within the range of spicules, spicules slightly curved ventrad and 42 µm long (7 times as long as wide and 2 times as long as cloacal body diameter), and tail 100 µm long (c = 15, c’ = 5) and similar to that of the female.
Transposon-mediated genic rearrangements underlie variation in small RNA pathways

Transposable elements (TEs) are parasitic DNA sequences that insert into the host genome and can cause alterations in host gene structure and expression. Host organisms cope with the often detrimental consequences caused by recent transposition and develop mechanisms that repress TE activities. In the nematode Caenorhabditis elegans, a small interfering RNA (siRNA) pathway dependent on the helicase ERI-6/7 primarily silences long terminal repeat retrotransposons and recent genes of likely viral origin. By studying gene expression variation among wild C. elegans strains, we discovered that structural variants and transposon remnants at the eri-6/7 locus alter its expression in cis and underlie a trans-acting expression quantitative trait locus affecting non-conserved genes and pseudogenes. Multiple insertions of the Polinton DNA transposon (also known as Mavericks) reshuffled the eri-6/7 locus in different configurations, separating the eri-6 and eri-7 exons and causing the inversion of eri-6 as seen in the reference N2 genome. In the inverted configuration, gene function was previously shown to be repaired by unusual trans-splicing mediated by direct repeats flanking the inversion. We show that these direct repeats originated from terminal inverted repeats specific to C. elegans Polintons. This trans-splicing event occurs infrequently compared to cis-splicing to novel downstream exons, thus affecting the production of ERI-6/7. Diverse Polinton-induced structural variations display regulatory effects within the locus and on targets of ERI-6/7-dependent siRNA pathways. Our findings highlight the role of host-transposon interactions in driving rapid host genome diversification among natural populations and shed light on evolutionary novelty in genes and splicing mechanisms.