Miracle-dz/UniFAR-FTUs huggingface dataset:
Observability in hybrid multi agent recurrent nets for natural language processing

Reading a sequence of lexical items in a sentence is equivalent to providing progressively more data at the input to a Kalman observer. The observer architecture includes a model of the lexical/syntactical sequence generator, with state and output variables, driven by the error between the observed sequence and its evolving 'mirror' within the observer. The theoretical foundations for this observer are put forward and the conditions for observability and controllability of hybrid recurrent nets are explained. Knowledge mining architectures are proposed which consist of an extensible recurrent hybrid net hierarchy of multi-agents where the composite behaviour of agents at any one level is determined by those of the level immediately below.
Study of the Protein Complex, Pore Diameter, and Pore-forming Activity of the Borrelia burgdorferi P13 Porin*

Background: B. burgdorferi P13 has unique characteristics compared with other porins. Results: P13 is a homo-oligomer with a 0.6 nS conductance in 1 m KCl and a substrate cut-off of 400 Da. Conclusion: P13 represents a general diffusion pathway for small solutes into Borrelia. Significance: Understanding the molecular transport through P13 may play a role in designing more efficient antibiotic treatments against Borrelia infections. P13 is one of the major outer membrane proteins of Borrelia burgdorferi. Previous studies described P13 as a porin. In the present study some structure and function aspects of P13 were studied. P13 showed according to lipid bilayer studies a channel-forming activity of 0.6 nanosiemens in 1 m KCl. Single channel and selectivity measurements demonstrated that P13 had no preference for either cations or anions and showed no voltage-gating up to ±100 mV. Blue native polyacrylamide gel electrophoresis was used to isolate and characterize the P13 protein complex in its native state. The complex had a high molecular mass of about 300 kDa and was only composed of P13 monomers. The channel size was investigated using non-electrolytes revealing an apparent diameter of about 1.4 nm with a 400-Da molecular mass cut-off. Multichannel titrations with different substrates reinforced the idea that P13 forms a general diffusion channel. The identity of P13 within the complex was confirmed by second dimension SDS-PAGE, Western blotting, mass spectrometry, and the use of a p13 deletion mutant strain. The results suggested that P13 is the protein responsible for the 0.6-nanosiemens pore-forming activity in the outer membrane of B. burgdorferi.
Discovering Motifs in Ranked Lists of DNA Sequences

Computational methods for discovery of sequence elements that are enriched in a target set compared with a background set are fundamental in molecular biology research. One example is the discovery of transcription factor binding motifs that are inferred from ChIP–chip (chromatin immuno-precipitation on a microarray) measurements. Several major challenges in sequence motif discovery still require consideration: (i) the need for a principled approach to partitioning the data into target and background sets; (ii) the lack of rigorous models and of an exact p-value for measuring motif enrichment; (iii) the need for an appropriate framework for accounting for motif multiplicity; (iv) the tendency, in many of the existing methods, to report presumably significant motifs even when applied to randomly generated data. In this paper we present a statistical framework for discovering enriched sequence elements in ranked lists that resolves these four issues. We demonstrate the implementation of this framework in a software application, termed DRIM (discovery of rank imbalanced motifs), which identifies sequence motifs in lists of ranked DNA sequences. We applied DRIM to ChIP–chip and CpG methylation data and obtained the following results. (i) Identification of 50 novel putative transcription factor (TF) binding sites in yeast ChIP–chip data. The biological function of some of them was further investigated to gain new insights on transcription regulation networks in yeast. For example, our discoveries enable the elucidation of the network of the TF ARO80. Another finding concerns a systematic TF binding enhancement to sequences containing CA repeats. (ii) Discovery of novel motifs in human cancer CpG methylation data. Remarkably, most of these motifs are similar to DNA sequence elements bound by the Polycomb complex that promotes histone methylation. Our findings thus support a model in which histone methylation and CpG methylation are mechanistically linked. Overall, we demonstrate that the statistical framework embodied in the DRIM software tool is highly effective for identifying regulatory sequence elements in a variety of applications ranging from expression and ChIP–chip to CpG methylation data. DRIM is publicly available at http://bioinfo.cs. technion.ac. il/drim.
Sex-specific differences in the association of a common aldehyde dehydrogenase 2 gene polymorphism and alcohol consumption with stroke risk in a Korean population: a prospective cohort study

BACKGROUND/OBJECTIVES It is well-known that alcohol consumption is associated with stroke risk as well as with aldehyde dehydrogenase 2 gene (ALDH2) polymorphisms. However, it is unclear whether ALDH2 polymorphisms are associated with stroke risk independent of alcohol consumption and whether such association is modified by sex. We evaluated sex-specific associations of a common ALDH2 polymorphism and alcohol consumption with stroke risk in a Korean population. SUBJECTS/METHODS We conducted a prospective cohort study involving 8,465 men and women, aged 40-69 years and free of stroke between June, 2001 and January, 2003, and followed for the development of stroke. We identified new cases of stroke, which were self-reported or ascertained from vital registration data. Based on genome-wide association data, we selected a single-nucleotide polymorphism (rs2074356), which shows high linkage disequilibrium with the functional polymorphism of ALDH2. We conducted Cox proportional hazards regression analysis considering potential risk factors collected from a baseline questionnaire. RESULTS Over the median follow-up of 8 years, 121 cases of stroke were identified. Carrying the wild-type allele of the ALDH2 polymorphism increased stroke risk among men. The multivariate hazard ratio [95% confidence interval] of stroke was 2.02 [1.03-3.99] for the wild-type allele compared with the mutant alleles, but the association was attenuated after controlling for alcohol consumption. Combinations of the wild-type allele and other risk factors of stroke, such as old age, diabetes mellitus, and habitual snoring, synergistically increased the risk among men. Among women, however, the ALDH2 polymorphism was not associated with stroke risk. CONCLUSIONS The prospective cohort study showed a significant association between a common ALDH2 polymorphism and stroke risk in Korean men, but not in Korean women, and also demonstrated that men with genetic disadvantages gain more risk when having risk factors of stroke. Thus, these men may need to make more concerted efforts to control modifiable risk factors of stroke.
MavHome: an agent-based smart home

The goal of the MavHome (Managing An Intelligent Versatile Home) project is to create a home that acts as an intelligent agent. In this paper we introduce the MavHome architecture. The role of prediction algorithms within the architecture is discussed, and a meta-predictor is presented which combines the strengths of multiple approaches to inhabitant action prediction. We demonstrate the effectiveness of these algorithms on smart home data.
The CSP Dichotomy Holds for Digraphs with No Sources and No Sinks (A Positive Answer to a Conjecture of Bang-Jensen and Hell)

Bang-Jensen and Hell conjectured in 1990 (using the language of graph homomorphisms) a constraint satisfaction problem (CSP) dichotomy for digraphs with no sources or sinks. The conjecture states that the CSP for such a digraph is tractable if each component of its core is a cycle and is $NP$-complete otherwise. In this paper we prove this conjecture and, as a consequence, a conjecture of Bang-Jensen, Hell, and MacGillivray from 1995 classifying hereditarily hard digraphs. Further, we show that the CSP dichotomy for digraphs with no sources or sinks agrees with the algebraic characterization conjectured by Bulatov, Jeavons, and Krokhin in 2005.
Estradiol Increases Dendritic Spine Density by Reducing GABA Neurotransmission in Hippocampal Neurons

We have previously shown that estradiol causes a twofold rise in dendritic spine density in cultured rat hippocampal neurons, as it doesin vivo. More recently, estrogen receptors have been localized to aspiny inhibitory hippocampal interneurons, indicating that their effect on spiny pyramidal neurons may be indirect. We therefore examined the possibility that estradiol affects spine density by regulating inhibition in cultured hippocampal interneurons. Immunocytochemically, estrogen receptors were found to be co-localized with glutamate decarboxylase (GAD)-positive neurons (∼21% of total neurons in the culture). Exposure of cultures to estradiol for 1 d caused a marked decrease (up to 80%) in the GAD content of the interneurons, measured both by immunohistochemistry and Western blotting. Also, the number of GAD-positive neurons in the cultures decreased to 12% of the total cell population. Moreover, GABAergic miniature IPSCs were reduced in both size and frequency by estradiol, whereas miniature EPSCs increased in frequency. We then mimicked the proposed effects of estradiol by blocking GABA synthesis with mercaptopropionic acid (MA). Cultures treated with MA expressed a dose-dependent decrease in GABA immunostaining that mimicked that seen with estradiol. MA-treated cultures displayed a significant 50% increase in dendritic spine density over controls, similar to that produced by estradiol. These results indicate that estradiol decreases GABAergic inhibition in the hippocampus, which appears to effectively increase the excitatory drive on pyramidal cells, and thus may provide a mechanism for formation of new dendritic spines.
Test generation for global delay faults

This paper describes test generation for delay faults caused by global process disturbances. The correlations between path delays is used to reduce the number of paths that must be tested. We build macro models of path delays as a function of process parameters to reduce test generation time. The test generation problem is formulated as a nonlinear optimization using a set of candidate paths supplied by a path generator. Results are given for the ISCAS85 benchmarks.
Music in the exercise domain: a review and synthesis (Part II)

Since a 1997 review by Karageorghis and Terry, which highlighted the state of knowledge and methodological weaknesses, the number of studies investigating musical reactivity in relation to exercise has swelled considerably. In this two-part review paper, the development of conceptual approaches and mechanisms underlying the effects of music are explicated (Part I), followed by a critical review and synthesis of empirical work (spread over Parts I and II). Pre-task music has been shown to optimise arousal, facilitate task-relevant imagery and improve performance in simple motoric tasks. During repetitive, endurance-type activities, self-selected, motivational and stimulative music has been shown to enhance affect, reduce ratings of perceived exertion, improve energy efficiency and lead to increased work output. There is evidence to suggest that carefully selected music can promote ergogenic and psychological benefits during high-intensity exercise, although it appears to be ineffective in reducing perceptions of exertion beyond the anaerobic threshold. The effects of music appear to be at their most potent when it is used to accompany self-paced exercise or in externally valid conditions. When selected according to its motivational qualities, the positive impact of music on both psychological state and performance is magnified. Guidelines are provided for future research and exercise practitioners.
Climate variability and Ross River virus transmission

Objectives: (1) To examine the feasibility to link climate data with monthly incidence of Ross River virus (RRv). (2) To assess the impact of climate variability on the RRv transmission. Design: An ecological time series analysis was performed on the data collected between 1985 to 1996 in Queensland, Australia. Methods: Information on the notified RRv cases was obtained from the Queensland Department of Health. Climate and population data were supplied by the Australian Bureau of Meteorology and the Australian Bureau of Statistics, respectively. Spearman's rank correlation analyses were performed to examine the relation between climate variability and the monthly incidence of notified RRv infections. The autoregressive integrated moving average (ARIMA) model was used to perform a time series analysis. As maximum and minimum temperatures were highly correlated with each other (rs=0.75), two separate models were developed. Results: For the eight major cities in Queensland, the climate-RRv correlation coefficients were in the range of 0.12 to 0.52 for maximum and minimum temperatures, -0.10 to 0.46 for rainfall, and 0.11 to 0.52 for relative humidity and high tide. For the whole State, rainfall (partial regression coefficient: 0.017 (95% confidence intervals 0.009 to 0.025) in Model I and 0.018 (0.010 to 0.026) in Model II), and high tidal level (0.030 (0.006 to 0.054) in Model I and 0.029 (0.005 to 0.053) in Model II) seemed to have played significant parts in the transmission of RRv in Queensland. Maximum temperature was also marginally significantly associated with the incidence of RRv infection. Conclusion: Rainfall, temperature, and tidal levels may be important environmental determinants in the transmission cycles of RRv disease.
Magnetic resonance spectroscopy in intracranial tumours of glial origin.

BACKGROUND AND PURPOSE To determine in vivo magnetic resonance spectroscopy (MRS) characteristics of intracranial glial tumours and to assess MRS reliability in glioma grading and discrimination between different histopathological types of tumours. MATERIAL AND METHODS Analysis of spectra of 26 patients with glioblastomas, 6 with fibrillary astrocytomas, 4 with anaplastic astrocytomas, 2 with pilocytic astrocytoma, 3 with oligodendrogliomas, 3 with anaplastic oligodendrogliomas and 17 control spectra taken from healthy hemispheres. RESULTS All tumours' metabolite ratios, except for Cho/Cr in fibrillary astrocytomas (p = 0.06), were statistically significantly different from the control. The tumours showed decreased Naa and Cr contents and a high Cho signal. The Lac-Lip signal was high in grade III astrocytomas and glioblastomas. Reports that Cho/Cr ratio increases with glioma's grade whereas Naa/Cr decreases were not confirmed. Anaplastic astrocytomas compared to grade II astrocytomas had a statistically significantly greater mI/Cr ratio (p = 0.02). In pilocytic astrocytomas the Naa/Cr value (2.58 ± 0.39) was greater, whilst the Cho/Naa ratio was lower (2.14 ± 0.64) than in the other astrocytomas. The specific feature of oligodendrogliomas was the presence of glutamate/glutamine peak Glx. However, this peak was absent in two out of three anaplastic oligodendrogliomas. Characteristically, the latter tumours had a high Lac-Lip signal. CONCLUSIONS MRS in vivo cannot be used as a reliable method for glioma grading. The method is useful in discrimination between WHO grade I and WHO grade II astrocytomas as well as oligodendrogliomas from other gliomas.
Catatonia in Down syndrome; a treatable cause of regression

Objective: The main aim of this case series report is to alert physicians to the occurrence of catatonia in Down syndrome (DS). A second aim is to stimulate the study of regression in DS and of catatonia. A subset of individuals with DS is noted to experience unexplained regression in behavior, mood, activities of daily living, motor activities, and intellectual functioning during adolescence or young adulthood. Depression, early onset Alzheimer’s, or just “the Down syndrome” are often blamed after general medical causes have been ruled out. Clinicians are generally unaware that catatonia, which can cause these symptoms, may occur in DS. Study design: Four DS adolescents who experienced regression are reported. Laboratory tests intended to rule out causes of motor and cognitive regression were within normal limits. Based on the presence of multiple motor disturbances (slowing and/or increased motor activity, grimacing, posturing), the individuals were diagnosed with unspecified catatonia and treated with anti-catatonic treatments (benzodiazepines and electroconvulsive therapy [ECT]). Results: All four cases were treated with a benzodiazepine combined with ECT and recovered their baseline functioning. Conclusion: We suspect catatonia is a common cause of unexplained deterioration in adolescents and young adults with DS. Moreover, pediatricians and others who care for individuals with DS are generally unfamiliar with the catatonia diagnosis outside schizophrenia, resulting in misdiagnosis and years of morbidity. Alerting physicians to catatonia in DS is essential to prompt diagnosis, appropriate treatment, and identification of the frequency and course of this disorder.
Atorvastatin reduction of intravascular thrombosis, increase in cerebral microvascular patency and integrity, and enhancement of spatial learning in rats subjected to traumatic brain injury.

OBJECT Atorvastatin, a beta-hydroxy-beta-methylglutaryl coenzyme A reductase inhibitor, has pleiotropic effects, such as promoting angiogenesis, increasing fibrinolysis, and reducing inflammatory responses, and has shown promise in enhancing recovery in animals with traumatic brain injury (TBI) and stroke. The authors tested the effect of atorvastatin on vascular changes after TBI. METHODS Male Wistar rats subjected to controlled cortical impact injury were perfused at different time points with fluorescein isothiocyanate (FITC)--conjugated dextran 1 minute before being killed. Spatial memory function had been measured using a Morris Water Maze test at various points before and after TBI. The temporal profile of intravascular thrombosis and vascular changes was measured on brain tissue sections by using a microcomputer imaging device and a laser confocal microscopy. The study revealed the following results. 1) Vessels in the lesion boundary zone and hippocampal CA3 region showed a variety of damage, morphological alterations, reduced perfusion, and intraluminal microthrombin formation. 2) Atorvastatin enhanced FITC-dextran perfusion of vessels and reduced intravascular coagulation. 3) Atorvastatin promoted the restoration of spatial memory function. CONCLUSIONS These results indicated that atorvastatin warrants investigation as a potential therapeutic drug for TBI.
A Sequential Dual Method for Structural SVMs

In many real world prediction problems the output is a structured object like a sequence or a tree or a graph. Such problems range from natural language processing to compu- tational biology or computer vision and have been tackled using algorithms, referred to as structured output learning algorithms. We consider the problem of structured classifi- cation. In the last few years, large margin classifiers like sup-port vector machines (SVMs) have shown much promise for structured output learning. The related optimization prob -lem is a convex quadratic program (QP) with a large num-ber of constraints, which makes the problem intractable for large data sets. This paper proposes a fast sequential dual method (SDM) for structural SVMs. The method makes re-peated passes over the training set and optimizes the dual variables associated with one example at a time. The use of additional heuristics makes the proposed method more efficient. We present an extensive empirical evaluation of the proposed method on several sequence learning problems.Our experiments on large data sets demonstrate that the proposed method is an order of magnitude faster than state of the art methods like cutting-plane method and stochastic gradient descent method (SGD). Further, SDM reaches steady state generalization performance faster than the SGD method. The proposed SDM is thus a useful alternative for large scale structured output learning.
Four-Neutrino Oscillations at SNO

We discuss the potential of SNO to constraint the four-neutrino mixing schemes favoured by the results of all neutrino oscillations experiments. These schemes allow simultaneous transitions of solar $\nu_e's$ into active $\nu_\mu$'s, $\nu_\tau$'s and sterile $\nu_s$ controlled by the additional parameter $\cos^2(\vartheta_{23}) \cos^2(\vartheta_{24})$ and they contain as limiting cases the pure $\nu_e$-active and $\nu_e$-sterile neutrino oscillations. We first obtain the solutions allowed by the existing data in the framework of the BP00 standard solar model and quantify the corresponding predictions for the CC and the NC/CC event ratios at SNO for the different allowed regions as a function of the active-sterile admixture. Our results show that some information on the value of $\cos^2(\vartheta_{23}) \cos^2(\vartheta_{24})$ can be obtained by the first SNO measurement of the CC ratio, while considerable improvement on the knowledge of this mixing will be achievable after the measurement of the NC/CC ratio.
Association Study between Cervical Lesions and Single or Multiple Vaccine-Target and Non-Vaccine Target Human Papillomavirus (HPV) Types in Women from Northeastern Brazil

We performed an association between high-grade squamous intraepithelial lesions (HSIL), low-grade squamous intraepithelial lesions (LSIL) and single or multiple vaccine-target as well as non-vaccine target Human papillomavirus (HPV) types. Using bead-based HPV genotyping, 594 gynecological samples were genotyped. An association between squamous intraepithelial lesion (SIL) and presence of HPV16, 18, 31, 58 and 56 types were calculated. The risk was estimated by using odds ratio (OR) and 95% of confidence intervals (CI). A total of 370 (62.3%) women were HPV positive. Among these, 157 (42.7%) presented a single HPV infection, and 212 (57.3%) were infected by more than one HPV type. HPV31 was the most prevalent genotype, regardless single and multiple HPV infections. Single infection with HPV31 was associated with LSIL (OR=2.32; 95%CI: 1.01 to 5.32; p=0.04); HPV31 was also associated with LSIL (OR=3.28; 95%CI: 1.74 to 6.19; p= 0.0002) and HSIL (OR=3.82; 95%CI: 2.10 to 6.97; p<0.001) in multiple HPV infections. Risk to harbor cervical lesions was observed in multiple HPV infections with regard to the HPV56 (OR=5.39; 95%CI: 2.44 to 11.90; p<0.001for LSIL; OR=5.37; 95%CI: 2.71 to 10.69; p<0.001) and HPV58 (OR=3.29; 95%CI: 1.34 to 8.09; p=0.0091 for LSIL; OR=3.55; 95%CI: 1.56 to 8.11; p=0.0026) genotypes. In addition, women coinfected with HPV16/31/56 types had 6 and 5-fold increased risk of HSIL (OR=6.46; 95%CI: 1.89 to 22.09; p=0.002) and LSIL (OR=5.22; 95%CI: 1.10 to 24.70; p=0.03), respectively. Multiple HPV infections without HPV16/18 has 2-fold increased risk of HSIL (OR=2.57; 95%CI: 1.41 to 4.70; p=0.002) and LSIL OR=2.03; 95%CI: 1.08 to 3.79; p=0.02). The results of this study suggest that single and multiple vaccine target as well as non-vaccine target HPV types are associated with LSIL and HSIL. These finding should be taken into consideration in the design of HPV vaccination strategies.