Miracle-dz/UniFAR-FTUs huggingface dataset:
Clustering Gene Expression Data Using Graph Separators

Recent work has used graphs to modelize expression data from microarray experiments, in view of partitioning the genes into clusters. In this paper, we introduce the use of a decomposition by clique separators. Our aim is to improve the classical clustering methods in two ways: first we want to allow an overlap between clusters, as this seems biologically sound, and second we want to be guided by the structure of the graph to define the number of clusters. We test this approach with a well-known yeast database (Saccharomyces cerevisiae). Our results are good, as the expression profiles of the clusters we find are very coherent. Moreover, we are able to organize into another graph the clusters we find, and order them in a fashion which turns out to respect the chronological order defined by the the sporulation process.
Serum Amyloid P Is a Sialylated Glycoprotein Inhibitor of Influenza A Viruses

Members of the pentraxin family, including PTX3 and serum amyloid P component (SAP), have been reported to play a role in innate host defence against a range of microbial pathogens, yet little is known regarding their antiviral activities. In this study, we demonstrate that human SAP binds to human influenza A virus (IAV) strains and mediates a range of antiviral activities, including inhibition of IAV-induced hemagglutination (HA), neutralization of virus infectivity and inhibition of the enzymatic activity of the viral neuraminidase (NA). Characterization of the anti-IAV activity of SAP after periodate or bacterial sialidase treatment demonstrated that α(2,6)-linked sialic acid residues on the glycosidic moiety of SAP are critical for recognition by the HA of susceptible IAV strains. Other proteins of the innate immune system, namely human surfactant protein A and porcine surfactant protein D, have been reported to express sialylated glycans which facilitate inhibition of particular IAV strains, yet the specific viral determinants for recognition of these inhibitors have not been defined. Herein, we have selected virus mutants in the presence of human SAP and identified specific residues in the receptor-binding pocket of the viral HA which are critical for recognition and therefore susceptibility to the antiviral activities of SAP. Given the widespread expression of α(2,6)-linked sialic acid in the human respiratory tract, we propose that SAP may act as an effective receptor mimic to limit IAV infection of airway epithelial cells.
Vulnerability of speaker verification systems against voice conversion spoofing attacks: The case of telephone speech

Voice conversion - the methodology of automatically converting one's utterances to sound as if spoken by another speaker - presents a threat for applications relying on speaker verification. We study vulnerability of text-independent speaker verification systems against voice conversion attacks using telephone speech. We implemented a voice conversion systems with two types of features and nonparallel frame alignment methods and five speaker verification systems ranging from simple Gaussian mixture models (GMMs) to state-of-the-art joint factor analysis (JFA) recognizer. Experiments on a subset of NIST 2006 SRE corpus indicate that the JFA method is most resilient against conversion attacks. But even it experiences more than 5-fold increase in the false acceptance rate from 3.24 % to 17.33 %.
Design of Low-Voltage MOSFET-Only Switched-Capacitor Filters

A 1.8-V switched-capacitor (SC) and a 1-V switched-opamp (SO) filter in standard digital CMOS technology is presented. The filters use substrate-biased MOSFETs in depletion region as capacitors linearized by parallel compensation technique. The simulation results confirm the capability of compensated depletion-mode MOS capacitors to fulfill analog circuit requirements at low supply voltages. A novel SO biquadratic structure is also presented to realize high-Q filter specifications. At a 1.8-V supply, the SC filter achieves - 40 dB THD, and at a 1-V the SO filter has -46.3 dB THD in 0.18-μm CMOS process.
Orientation Disparity: A Cue for 3D Orientation?

Abstract Orientation disparity, the difference in orientation that results when a texture element on a slanted surface is projected to the two eyes, has been proposed as a binocular cue for 3D orientation. Since orientation disparity is confounded with position disparity, neither behavioral nor neurophysiological experiments have successfully isolated its contribution to slant estimates or established whether the visual system uses it. Using a modified disparity energy model, we simulated a population of binocular visual cortical neurons tuned to orientation disparity and measured the amount of Fisher information contained in the activity patterns. We evaluated the potential contribution of orientation disparity to 3D orientation estimation and delimited the stimulus conditions under which it is a reliable cue. Our results suggest that orientation disparity is an efficient source of information about 3D orientation and that it is plausible that the visual system could have mechanisms that are sensitive to it. Although orientation disparity is neither necessary nor sufficient for estimating slant, it appears that it could be useful when combined with estimates from position disparity gradients and monocular perspective cues.
Studying the Behaviour of Model of Mirror Neuron System in Case of Autism

Several experiment done by the researchers conducted that autism is caused by the dysfunctional mirror neuron system and the dysfunctions of mirror neuron system is proportional to the symptom severity of autism. In the present work those experiments were studied as well as studying a model of mirror neuron system called MNS2 developed by a research group. This research examined the behavior of the model in case of autism and compared the result with those studies conducting dysfunctions of mirror neuron system in autism. To perform this, a neural network employing the model was developed which recognized the three types of grasping (faster, normal and slower). The network was implemented with back propagation through time learning algorithm. The whole grasping process was divided into 30 time steps and different hand and object states at each time step was used as the input of the network. Normally the network successfully recognized all of the three types of grasps. The network required more times as the number of inactive neurons increased. And in case of maximum inactive neurons of the mirror neuron system the network became unable to recognize the types of grasp. As the time to recognize the types of grasp is proportional to the number of inactive neurons, the experiment result supports the hypothesis that dysfunctions of MNS is proportional to the symptom severity of autism.
Biotic effects of sea level change: The Pleistocene test

Species diversity change, and therefore compositional changes in a biota, may be associated with changes at any of three ecological levels, involving the number of provinces within the biosphere, of communities within provinces, and of species represented within communities. Pleistocene sea level changes did not much affect the marine biosphere at any ecological level. An analysis of an extensive data set of Californian Pleistocene and Recent mollusks indicates a continuity of community and species composition during highstands of the last million years. Extensive latitudinal shifts in species' geographic ranges, associated with climatic change and not with sea level itself, created the most significant biotic changes. Extinctions were minimal, well below predicted species-area effects. Evidently, only “perched” faunas are particularly vulnerable to sea level change. Although sea level falls are commonly associated with a faunal hiatus, changes associated therewith can be referred to sea level change itself only in limited situations, and other paleobiologic explanations should be sought in most cases.
Parsing Below the Segment in a Constraint-Based Framework

Parsing Below the Segment in a Constraint Based Framework by Cheryl Cydney Zoll B.A. Harvard University 1985 M.A. Brandeis University 1992 M.A. University of California, Berkeley 1994 A dissertation submitted in partial satisfaction of the requirements for the degree of D octor o f Philosophy in Linguistics in the GRADUATE DIVISION of the UNIVERSITY of CALIFORNIA, BERKELEY Committee in charge: Professor Sharon Inkelas, Chair Professor Larry Hyman Professor Armin Mcslcr Professor Alan Timberlake Reproduced with permission o f the copyright owner. Further reproduction prohibited without permission.
Rapid pulses of uplift, subsidence, and subduction erosion offshore Central America: Implications for building the rock record of convergent margins

Integrated Ocean Drilling Program (IODP) Expedition 334 to southern Costa Rica, Central America, documented unprecedented subduction erosion in an area of active seismic slip. Widespread subduction erosion of the upper plate initiated when the Cocos Ridge, an overthickened aseismic ridge, arrived at the Middle America Trench. Subduction erosion was coeval with the rapid formation of deposition centers on the forearc of the upper plate. The completely recovered shelf sequence constrains a short (<2 m.y.) interval of extreme subsidence (∼1200 m) with a rapid pulse occurring during the first ∼0.3 m.y. This event removed an estimated 1.2 × 106 km3 of forearc material at a rate of ∼1690 km3/m.y. /km of trench during a time of rapid (∼1035 m/m.y.) shelf sediment accumulation. At this erosive margin, a sediment-starved trench persisted, in spite of abundant sediment supply, because subduction erosion led to the creation of forearc basins. Similar rapid pulses of subduction erosion may punctuate the evolution of many margins, contributing disproportionately to crustal recycling at subduction zones with implications for the evolution of continental crust and mountain belts, and recycling of continental material into the mantle.
Early electromagnetic waves from earthquake rupturing: I. theoretical formulations

Yongxin Gao,1,2 Xiaofei Chen,1,2 Hengshan Hu3 and Jie Zhang1,2 1School of Earth and Space Sciences, University of Science and Technology of China, Hefei, 230026, China. E-mail: gaoyongxin1982@yahoo.com. cn 2Laboratory of Seismology and Physics of Earth’s Interior, University of Science and Technology of China, Hefei, 230026, China. 3Department of Astronautics and Mechanics, Harbin Institute of Technology, Harbin, 150001, China
Chimpanzee genomic diversity reveals ancient admixture with bonobos

Of chimpanzees and bonobos Modern non-African human genomes contain genomic remnants that suggest that there was interbreeding between ancient humans and archaic hominoid lineages. Now, de Manuel et al. show similar ancestral interbreeding between the ancestors of today's chimpanzees and bonobos (see the Perspective by Hoelzel). The study also provides population-specific genetic markers that may be valuable for conservation efforts. Science, this issue p. 477; see also p. 414 Genome sequences reveal ancient interbreeding between chimpanzees and bonobos. Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.
Effects of prenatal alcohol exposure on hippocampal volume, verbal learning, and verbal and spatial recall in late childhood

Abstract Children with prenatal alcohol exposure (PAE) show deficits in verbal learning and spatial memory, as well as abnormal hippocampal development. The relationship between their memory and neuroanatomic impairments, however, has not been directly explored. Given that the hippocampus is integral for the synthesis and retrieval of learned information and is particularly vulnerable to the teratogenic effects of alcohol, we assessed whether reduced learning and recall abilities in children with fetal alcohol spectrum disorders (FASDs) are associated with abnormal hippocampal volumes. Nineteen children with FASDs and 18 typically developing controls aged 9 to 15 years were assessed for verbal learning and verbal and spatial recall and underwent structural magnetic resonance imaging. Images were analyzed for total intracranial volume and for right and left hippocampal volumes. Results revealed smaller left hippocampi and poorer verbal learning and verbal and spatial recall performance in children with FASDs than controls, as well as positive correlations between selective memory indices and hippocampal volumes only in the FASD group. Additionally, hippocampal volumes increased significantly with age in controls only, suggesting that PAE may be associated with long-term abnormalities in hippocampal development that may contribute to impaired verbal learning and verbal and spatial recall. (JINS, 2008, 14, 1022–1033.)
Expression of Mouse MGAT in Arabidopsis Results in Increased Lipid Accumulation in Seeds

Worldwide demand for vegetable oil is projected to double within the next 30 years due to increasing food, fuel, and industrial requirements. There is therefore great interest in metabolic engineering strategies that boost oil accumulation in plant tissues, however, efforts to date have only achieved levels of storage lipid accumulation in plant tissues far below the benchmark to meet demand. Monoacylglycerol acyltransferase (MGAT) is predominantly associated with lipid absorption and resynthesis in the animal intestine where it catalyzes monoacylglycerol (MAG) to form diacylglycerol (DAG), and then triacylglycerol (TAG). In contrast plant lipid biosynthesis routes do not include MGAT. Rather, DAG and TAG are either synthesized from glycerol-3-phosphate by a series of three subsequent acylation reactions, or originated from phospholipids via an acyl editing pathway. Mouse MGATs 1 and 2 have been shown to increase oil content transiently in Nicotiana benthamiana leaf tissue by 2.6 fold. Here we explore the feasibility of this approach to increase TAG in Arabidopsis thaliana seed. The stable MGAT2 expression resulted in a significant increase in seed oil content by 1.32 fold. We also report evidence of the MGAT2 activity based on in vitro assays. Up to 3.9 fold increase of radiolabeled DAG were produced in seed lysate which suggest that the transgenic MGAT activity can result in DAG re-synthesis by salvaging the MAG product of lipid breakdown. The expression of MGAT2 therefore creates an independent and complementary TAG biosynthesis route to the endogenous Kennedy pathway and other glycerolipid synthesis routes.
Integration of lithological, geophysical, and remote sensing information: a basis for remote predictive geological mapping of the Baie Verte Peninsula, Newfoundland

The Baie Verte Peninsula is a geologically complex area on the northwest coast of Newfoundland. The region is composed of multiple geological domains and has undergone extensive tectonic activity, uplift, and deformation, producing multiple unconformity surfaces. In addition, multiple phases of intrusion, some with volcanic cover sequences, add to the complexity of the geological model. This study concentrates on establishing a basic framework of the spatial relationships between individual lithological units and their contained mineral deposits from remotely sensed data. Of primary interest is providing basic lithological discrimination, which could form the basis of future field mapping. Multiple thematic maps were produced from compilations of satellite imagery, aerial photography, high-resolution digital elevation maps (DEMs), airborne radiometrics, and aeromagnetics. Common edge boundaries within the geophysical and spectral data were used to discriminate regions having similar physical and mineralogical signatures. The resulting patterns provide a proxy, or remote predictive method, for recognition of the distinct geological features within the study area. Furthermore, the techniques and methods introduced in this paper can be applied to other areas for producing presurvey geological templates.
Dual Opposing Roles of Metallothionein Overexpression in C57BL/6J Mouse Pancreatic β-Cells

Background Growing evidence indicates that oxidative stress (OS), a persistent state of excess amounts of reactive oxygen species (ROS) along with reactive nitrogen species (RNS), plays an important role in insulin resistance, diabetic complications, and dysfunction of pancreatic β-cells. Pancreatic β-cells contain exceptionally low levels of antioxidant enzymes, rendering them susceptible to ROS-induced damage. Induction of antioxidants has been proposed to be a way for protecting β-cells against oxidative stress. Compared to other antioxidants that act against particular β-cell damages, metallothionein (MT) is the most effective in protecting β-cells from several oxidative stressors including nitric oxide, peroxynitrite, hydrogen peroxide, superoxide and streptozotocin (STZ). We hypothesized that MT overexpression in pancreatic β-cells would preserve β-cell function in C57BL/6J mice, an animal model susceptible to high fat diet-induced obesity and type 2 diabetes. Research Design and Methods The pancreatic β-cell specific MT overexpression was transferred to C57BL/6J background by backcrossing. We studied transgenic MT (MT-tg) mice and wild-type (WT) littermates at 8 weeks and 18 weeks of age. Several tests were performed to evaluate the function of islets, including STZ in vivo treatment, intraperitoneal glucose tolerance tests (IPGTT) and plasma insulin levels during IPGTT, pancreatic and islet insulin content measurement, insulin secretion, and islet morphology assessment. Gene expression in islets was performed by quantitative real-time PCR and PCR array analysis. Protein levels in pancreatic sections were evaluated by using immunohistochemistry. Results The transgenic MT protein was highly expressed in pancreatic islets. MT-tg overexpression significantly protected mice from acute STZ-induced ROS at 8 weeks of age; unexpectedly, however, MT-tg impaired glucose stimulated insulin secretion (GSIS) and promoted the development of diabetes. Pancreatic β-cell function was significantly impaired, and islet morphology was also abnormal in MT-tg mice, and more severe damage was detected in males. The unique gene expression pattern and abnormal protein levels were observed in MT-tg islets. Conclusions MT overexpression protected β-cells from acute STZ-induced ROS damages at young age, whereas it impaired GSIS and promoted the development of diabetes in adult C57BL/6J mice, and more severe damage was found in males.
Output feedback stabilization of wireless networked control system with packet dropout

The problem of modeling and stabilization of a wireless networked control system(NCS) with both packet dropout and time-varying delay is investigated in this paper, and the time-varying delay is more or less than one sampling period. The closed-loop wireless NCS is modeled as an asynchronous dynamic system(ADS) with three subsystems. By using the ADS approach, a sufficient condition for the closed-loop wireless NCS to be stable is presented. An illustrative example is provided to demonstrate the effectiveness of the proposed result.
Fabrication of thin, luminescent, single-crystal diamond membranes

The formation of single-crystal diamond membranes is an important prerequisite for the fabrication of high-quality optical cavities in this material. Diamond membranes fabricated using lift-off processes involving the creation of a damaged layer through ion implantation often suffer from residual ion damage, which severely limits their usefulness for photonic structures. The current work demonstrates that strategic etch removal of the most highly defective material yields thin, single-crystal diamond membranes with strong photoluminescence and a Raman signature approaching that of single-crystal bulk diamond. These optically active membranes can form the starting point for fabrication of high-quality optical resonators.
Health effects of physical activity.

OBJECTIVES This article examines the potential protective effect of leisure-time physical activity on the incidence of heart disease and depression. DATA SOURCE The data are from the household longitudinal component of the 1994/95 and 1996/97 cycles of the National Population Health Survey, conducted by Statistics Canada. Results are based on two subsamples: 7,158 respondents aged 20 or older who were healthy and free of heart disease in 1994/95, and 7,593 respondents aged 12 or older who were healthy and free of depression in 1994/95. ANALYTICAL TECHNIQUES Multiple logistic regression was used to estimate the effects of leisure-time physical activity on the incidence of heart disease and depression, while controlling for selected characteristics. MAIN RESULTS Individuals who were healthy and free of heart disease or depression in 1994/95 and who engaged in regular physical activity at a moderate level of energy expenditure had lower odds of reporting a diagnosis of heart disease or an episode of depression in 1996/97 than those who were less active.
Synchronization Conditions for Multiagent Systems With Intrinsic Nonlinear Dynamics

This brief studies local and global synchronization in multiagent systems with nonlinear dynamics with respect to equilibrium points and periodic orbits. For local synchronization, a method is proposed based on the transformation of the original system into an uncertain polytopic system and on the use of homogeneous polynomial Lyapunov functions. For global synchronization, another method is proposed based on the search for a suitable polynomial Lyapunov function. The proposed methods exploit linear matrix inequalities and have several advantages. In particular, the proposed methods require the solution of convex optimization problems. Also, the proposed methods exploit more complex Lyapunov functions than the quadratic Lyapunov functions typically considered in the literature and included in this brief as a special case.
Control of Death-associated Protein Kinase (DAPK) Activity by Phosphorylation and Proteasomal Degradation*

Activation of death-associated protein kinase (DAPK) occurs via dephosphorylation of Ser-308 and subsequent association of calcium/calmodulin. In this study, we confirmed the existence of the alternatively spliced human DAPK-β, and we examined the levels of DAPK autophosphorylation and DAPK catalytic activity in response to tumor necrosis factor or ceramide. It was found that DAPK is rapidly dephosphorylated in response to tumor necrosis factor or ceramide and then subsequently degraded via proteasome activity. Dephosphorylation and activation of DAPK are shown to temporally precede its subsequent degradation. This results in an initial increase in kinase activity followed by a decrease in DAPK expression and activity. The decline in DAPK expression is paralleled with increased caspase activity and cell apoptosis. These results suggest that the apoptosis regulatory activities mediated by DAPK are controlled both by phosphorylation status and protein stability.