Miracle-dz/UniFAR-FTUs huggingface dataset:
Muscarinic Suppression of Excitatory Synaptic Responses in Layer II of the Entorhinal Cortex

Entitled: Muscarinic suppression of excitatory synaptic responses in layer II of the entorhinal cortex and submitted in partial fulfillment of the requirements for the degree of Masters of Psychology complies with the regulations of the University and meets the accepted standards with respect to originality and quality. The entorhinal cortex is thought to play a role in mechanisms mediating sensory and mnemonic function, but the effects of acetylcholine on the strength of sensory cortical inputs to the entorhinal cortex are not well understood. We have previously shown that field excitatory postsynaptic potentials (fEPSPs) in the medial entorhinal cortex evoked by stimulation of the piriform cortex are suppressed during theta activity in behaving animals, and that cholinergic agonism suppresses fEPSPs in vivo. In addition, intracellular recordings from neurons in layer II of the entorhinal cortex also show a suppression of EPSPs in response to the cholinergic agonist carbachol. Here, we have used in vitro field potential recordings evoked by stimulation of layer I afferents to investigate the transmitter receptors that mediate the cholinergic suppression of synaptic responses in layer II of the medial entorhinal cortex. Ten-min bath-application of the cholinergic agonist carbachol (10 µM) potently suppressed the amplitude of fEPSPs. Carbachol also enhanced the paired-pulse facilitation ratio for EPSP amplitudes (30 ms interpulse interval), indicating that the cholinergic suppression is likely due to inhibition of transmitter release. Constant bath application of the M 2 receptor blocker methoctramine (5 µM) for 20 min prior to addition of carbachol did not prevent the cholinergic suppression, but application of the M 1 receptor blocker pirenzepine (1 µM) almost completely blocked the carbachol-induced suppression, indicating that the cholinergic suppression of excitatory synaptic responses in the entorhinal cortex is iv dependent primarily on activation of M 1 –like receptors. In addition to enhancements in neuronal excitability that follow cholinergic activation, therefore, cells in the superficial layers of the entorhinal cortex also display a suppression of excitatory synaptic input that is mediated mainly by M 1 muscarinic receptors.
Data cleansing for Web information retrieval using query independent features

We report on a study that was undertaken to better understand what kinds of Web pages are the most useful for web search engine users by exploiting queryindependent features of retrieval target pages. To our knowledge, there has been little research towards query-independent web page cleansing for web information retrieval. Based on more than 30 million web pages obtained both from TREC and from a widely-used Chinese search engine SOGOU (www.sogou.com), we provide analysis on the differences between retrieval target pages and ordinary ones. We also propose a learning-based data cleansing algorithm for reducing Web pages which are not likely to be useful for user request. The results obtained show that retrieval target pages can be separated from low quality pages using queryindependent features and cleansing algorithms. Our algorithm succeeds in reducing 95% web pages with less than 8% loss in retrieval target pages. It makes it possible for web IR tools to meet over 92% users’ needs with only 5% pages on the Web.
Area gestures for a laptop computer enabled by a hover-tracking touchpad

A touchpad has been the most popular pointing device for laptop computers. As large, multi-touch sensing touchpads are now common, we came to think about extending its input vocabulary by adding area gestures. In order to explore this possibility, we constructed a laptop-like mock-up with an optical, proximity sensing touchpad, and implemented a few area gestures that may be useful in such an environment. We conducted a user test and ran a task walkthrough with a realistic scenario in order to verify the feasibility of the area gestures in a laptop environment.
A single determinant for the rate of yeast protein evolution

A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we show that the two most commonly used methods to disentangle the determinants of evolutionary rate, partial correlation analysis and ordinary multivariate regression, produce misleading or spurious results when applied to noisy biological data. To overcome these difficulties, we employ an alternative method, principal component regression, which is a multivariate regression of evolutionary rate against the principal components of the predictor variables. We carry out the first combined analysis of seven predictors (gene expression level, dispensability, protein abundance, codon adaptation index, gene length, number of protein-protein interactions, and the gene's centrality in the interaction network). Strikingly, our analysis reveals a single dominant component which explains 40-fold more variation in evolutionary rate than any other, suggesting that protein evolutionary rate has a single determinant among the seven predictors. The dominant component explains nearly half the variation in the rate of synonymous and protein evolution. Our results support the hypothesis that selection against the cost of translation-error-induced protein misfolding governs the rate of synonymous and protein sequence evolution in yeast.
Calcium signalling during the cleavage period of zebrafish development

Imaging studies, using both luminescent and fluorescent Ca2+-sensitive reporters, have revealed that during the first few meroblastic cleavages of the large embryos of teleosts, localized elevations of intracellular Ca2+ accompany positioning, propagation, deepening and apposition of the cleavage furrows. Here, we will review the Ca2+ transients reported during the cleavage period in these embryos, with reference mainly to that of the zebrafish (Danio rerio). We will also present the latest findings that support the proposal that Ca2+ transients are an essential feature of embryonic cytokinesis. In addition, the potential upstream triggers and downstream targets of the different cytokinetic Ca2+ transients will be discussed. Finally, we will present a hypothetical model that summarizes what has been suggested to be the various roles of Ca2+ signalling during cytokinesis in teleost embryos.
Crystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent roles in catalysis.

The crystal structures of catalytically competent soybean beta-amylase, unliganded and bathed with small substrates (beta-maltose, maltal), were determined at 1.9-2.2-A resolution. Two molecules of beta-maltose substrate bind to the protein in tandem, with some maltotetraose enzymic condensation product sharing the same binding sites. The beta-amylase soaked with maltal shows a similar arrangement of two bound molecules of 2-deoxymaltose, the enzymic hydration product. In each case the nonreducing ends of the saccharide ligands are oriented toward the base of the protein's active site pocket. The catalytic center, located between the bound disaccharides and found deeper in the pocket than where the inhibitor alpha-cyclodextrin binds, is characterized by the presence of oppositely disposed carboxyl groups of two conserved glutamic acid residues. The OE2 carboxyl of Glu 186 is below the plane of the penultimate glucose residue (Glc 2) of bound maltotetraose, 2.6 A from the oxygen atom of that ligand's penultimate alpha-1,4-glucosidic linkage. The OE2 carboxyl of Glu 380 lies above the plane of Glc 2, 2.8 A from the O-1 atom of the more deeply bound beta-maltose. Saccharide binding does not alter the spatial coordinates of these two carboxyl groups or the overall conformation of the 57-kDa protein. However, the saccharide complexes of the active enzyme are associated with a significant (10 A) local conformational change in a peptide segment of a loop (L3) that borders the active site pocket. (ABSTRACT TRUNCATED AT 250 WORDS)
Why people change? The role of cognitive‐control processes in the onset and cessation of substance abuse disorders

Background: The current effectiveness of preventative and therapeutic interventions for substance use disorders (SUDs) is less than satisfying. Progress in understanding the processes related to the onset, course, and cessation of SUDs merits top priority, given the high prevalence and the severe negative consequences. Aims: This position paper, after summarizing major factors related to onset and cessation processes, discusses the possible role of cognitive‐control dysfunctions in the complex interaction between mechanisms of change (mediators) and risk factors (moderators). Findings: In past decades, research has expanded our knowledge about the impact of SUDs on human behaviour. Formal interventions are effective, but there is limited information about the mechanisms responsible for change during the onset and cessation of SUDs and for individual differences related to them. Preliminary results suggest that impairments in higher order control functions play a role in SUDs. Conclusions: Deficiencies in our understanding of behaviour‐change processes during the onset and cessation of SUDs require that research have a different focus. A better understanding of the relevance of impairments in executive‐control functions might help to improve formal preventative and therapeutic interventions and social conditions. Such interventions might reduce the chances that a SUD will develop or increase the likelihood of recovery from it. Copyright © 2008 John Wiley & Sons, Ltd.
Information Extraction for Social Media

The rapid growth in IT in the last two decades has led to a growth in the amount of information available online. A new style for sharing information is social media. Social media is a continuously instantly updated source of information. In this position paper, we propose a framework for Information Extraction (IE) from unstructured user generated contents on social media. The framework proposes solutions to overcome the IE challenges in this domain such as the short context, the noisy sparse contents and the uncertain contents. To overcome the challenges facing IE from social media, State-Of-The-Art approaches need to be adapted to suit the nature of social media posts. The key components and aspects of our proposed framework are noisy text filtering, named entity extraction, named entity disambiguation, feedback loops, and uncertainty handling.
Nonverbal Communication to Support Collaborative Interaction in Collaborative Virtual Environments for Learning

When a group of students, placed around a shared workspace and working on an anticipated task is observed, the teacher or the facilitator intuitively can, to a certain extent, understand how collaboration is taking place within the group, without listening to the students’ discourse. Following this analogy, we propose that some specific nonverbal communication cues should be useful to infer collaborative interaction to such an extent that collaboration can be automatically fostered. Some nonverbal communication cues selected for that purpose and the inferred collaborative learning indicators will be
Supporting multiple accelerators in high-level programming models

Computational accelerators, such as manycore NVIDIA GPUs, Intel Xeon Phi and FPGAs, are becoming common in work-stations, servers and supercomputers for scientific and engineering applications. Efficiently exploiting the massive parallelism these accelerators provide requires the designs and implementations of productive programming models. In this paper, we explore support of multiple accelerators in high-level programming models. We design novel language extensions to OpenMP to support offloading data and computation regions to multiple accelerators (devices). These extensions allow for distributing data and computation among a list of devices via easy-to-use interfaces, including specifying the distribution of multi-dimensional arrays and declaring shared data regions among accelerators. Computation distribution is realized by partitioning a loop iteration space among accelerators. We implement mechanisms to marshal/unmarshal and to move data of non-contiguous array subregions and shared regions between accelerators without involving CPUs. We design reduction techniques that work across multiple accelerators. Combined compiler and runtime support is designed to manage multiple GPUs using asynchronous operations and threading mechanisms. We implement our solutions for NVIDIA GPUs and demonstrate through example OpenMP codes the effectiveness of our solutions for performance improvement.
Virus-specific CD4+ T cells: ready for direct attack

CD4+ T cells are classically thought to orchestrate adaptive immune responses. But recent studies demonstrate that they can also kill infected cells directly. A new paper shows that highly efficient processing of Epstein Barr virus (EBV) glycoproteins for presentation on MHC class II makes virus-transformed B cells susceptible to lysis by CD4+ T cells. Thus, antiviral vaccines should aim to stimulate both helper and cytolytic CD4+ T cells.
Data Issues of the Multilingual Translation Matrix

We describe our experiments with phrase-based machine translation for the WMT 2012 Shared Task. We trained one system for 14 translation directions between English or Czech on one side and English, Czech, German, Spanish or French on the other side. We describe a set of results with different training data sizes and subsets.
The Effect of Multiple Doses of Peginterferon alfa‐2b on the Steady‐State Pharmacokinetics of Methadone in Patients With Chronic Hepatitis C Undergoing Methadone Maintenance Therapy

This multicenter, open‐label study evaluated the effects of multiple doses of peginterferon alfa‐2b on the steady‐state pharmacokinetics of methadone in 20 adults with hepatitis C virus infection who were enrolled in a methadone maintenance program. All subjects received peginterferon alfa‐2b 1.5 μg/kg/wk for 4 weeks and maintained their normal methadone regimen. Serial blood samples were collected immediately before the first and after the fourth peginterferon alfa‐2b dose (day 23). At day 23, exposure to the active methadone R‐enantiomer increased by approximately 15% following administration of peginterferon alfa‐2b, with 90% confidence intervals just outside the bioequivalence criteria (range, 80%–125%). Similar increases in exposure (Cmax, AUC0–24, and AUClast) were observed with S‐methadone and total methadone. Peginterferon alfa‐2b was well tolerated. Peginterferon alfa‐2b is associated with minor increases in exposure to methadone in individuals with hepatitis C virus infection; however, these increases are unlikely to be clinically meaningful and are not associated with any safety concerns.
Testbed on a desktop: strategies and techniques to support multi-hop MANET routing protocol development

The development of multi-hop routing protocols for mobile ad hoc networks (MANETs) typically begins with extensive simulation and then proceeds to implementation and real-world testing. While simulation environments can be carefully controlled, real-world environments present numerous difficulties that hinder efficient protocol implementation and testing. These include uncontrolled radio interference and propagation events, hard-to-reproduce network topologies and node mobility patterns, and experimental setups that are inconveniently large. In this paper we present a method for supporting protocol implementation and experimentation in a small testbed setting where variables can be controlled and experimental conditions can be reproduced. The testbed operation is independent of the operating system of the implementation platforms and works with most modern wireless networking interfaces without modifications. A "testbed on a desktop"constructed using the ideas we discuss allows the developer to create stable testing environments in which real-world conditions can be introduced in a convenient, deterministic and reproducible manner
Control of growth and organ size in Drosophila

Transplantation experiments have shown that developing metazoan organs carry intrinsic information about their size and shape. Organ and body size are also sensitive to extrinsic cues provided by the environment, such as the availability of nutrients. The genetic and molecular pathways that contribute to animal size and shape are numerous, yet how they cooperate to control growth is mysterious. The recent identification and characterization of several mutations affecting growth in Drosophila melanogaster promises to provide insights. Many of these mutations affect the extrinsic control of animal size; others affect the organ‐intrinsic control of pattern and size. In this review, we summarize the characteristics of some of these mutations and their roles in growth and size control. In addition, we speculate about possible connections between the extrinsic and intrinsic pathways controlling growth and pattern. BioEssays 24:54–64, 2002. © 2002 John Wiley & Sons, Inc.
Genetic Characterization of a Streptococcus mutans LraI Family Operon and Role in Virulence

ABSTRACT Proteins belonging to the LraI (for “lipoprotein receptor antigen”) family function as adhesins in several streptococci, as a virulence factor for endocarditis in at least one of these species, and potentially as metal transporters in many bacteria. We have identified and characterized the chromosomal locus containing the LraI family gene (designated sloC) from Streptococcus mutans, an agent of dental caries and endocarditis in humans. Northern blot analysis indicated that sloC is cotranscribed with three other genes. As with other LraI operons, the sloA andsloB genes apparently encode components of an ATP-binding cassette transport system. The product of the fourth gene,sloR, has homology to the metal-dependent regulator fromCorynebacterium diphtheriae, DtxR. A potential binding site for SloR was identified upstream from the sloABCR operon and was conserved upstream from LraI operons in several other streptococci. Potential SloR homologs were identified in the unfinished genomic sequences from two of these, S. pneumoniae andS. pyogenes. Mutagenesis of sloC in S. mutans resulted in apparent loss of expression of the entire operon as assessed by Northern blot analysis. The sloCmutant was indistinguishable from its wild-type parent in a gnotobiotic rat model of caries but was significantly less virulent in a rat model of endocarditis. Virulence for endocarditis was restored by correction of the sloC mutation but not by provision of thesloC gene in trans, suggesting that virulence requires the expression of other genes in the sloC operon.
Super-polynomial lower bounds for depth-4 homogeneous arithmetic formulas

We show that any depth-4 homogeneous arithmetic formula computing the Iterated Matrix Multiplication polynomial IMMn,d -- the (1, 1)-th entry of the product of d generic n × n matrices -- has size nΩ(log n), if d = Ω (log2 n). More-over, any depth-4 homogeneous formula computing the determinant polynomial Detn -- the determinant of a generic n × n matrix -- has size nΩ(log n).
Cytochemical and cytological properties of perineuronal oligodendrocytes in the mouse cortex

Neuronal cell bodies are associated with glial cells collectively referred to as perineuronal satellite cells. One such satellite cell is the perineuronal oligodendrocyte, which is unmyelinating oligodendrocytes attaching to large neurons in various neural regions. However, little is known about their cellular characteristics and function. In this study, we identified perineuronal oligodendrocytes as 2′,3′‐cyclic nucleotide 3′‐phosphodiesterase‐positive cells attaching to neuronal perikarya immunostained for microtubule‐associated protein 2, and examined their cytochemical and cytological properties in the mouse cerebral cortex. 2′,3′‐Cyclic nucleotide 3′‐phosphodiesterase‐positive perineuronal oligodendrocytes were immunonegative to representative glial markers for astrocytes (brain‐type lipid binding protein and glial fibrillary acidic protein), microglia (Iba‐1) and NG2+ glia. However, almost all perineuronal oligodendrocytes expressed glia‐specific or glia‐enriched metabolic enzymes, i.e. the creatine synthetic enzyme S‐adenosylmethionine:guanidinoacetate N‐methyltransferase and l‐serine biosynthetic enzyme 3‐phosphoglycerate dehydrogenase. As to molecules participating in the glutamate–glutamine cycle, none of the perineuronal oligodendrocytes expressed the plasmalemmal glutamate transporters GLAST and GLT‐1, although nearly half of the perineuronal oligodendrocytes were immunopositive for glutamine synthetase. Cytologically, perineuronal oligodendrocytes were mainly distributed in deep cortical layers (layers IV–VI), and attached directly and tightly to neuronal cell bodies, making a long concave impression to the contacting neurons. Interestingly, they attached more to glutamatergic principal neurons than to GABAergic interneurons, and this became evident at postnatal day 14, when the cerebral cortex develops and maturates. These cytochemical and cytological properties suggest that perineuronal oligodendrocytes are so differentiated as to fulfill metabolic support to the associating principal cortical neurons, rather than to regulate their synaptic transmission.
Adult neurogenesis: taking stock in Stockholm

In May this year, Stockholm hosted a Keystone Symposium on Adult Neurogenesis, attracting scientists from around the world despite the lack of customary snow. The symposium offered an extraordinary program, covering diverse topics that ranged from the neural stem cell lineage and regulation of neurogenesis to functional aspects of neurogenesis in homeostasis and disease, and even computational modeling. This Meeting Review describes some of the exciting presentations and emerging themes from the symposium, which reveal how much this young field has matured.
Graffiti: node labeling in heterogeneous networks

We introduce a multi-label classification model and algorithm for labeling heterogeneous networks, where nodes belong to different types and different types have different sets of classification labels. We present a graph-based approach which models the mutual influence between nodes in the network as a random walk. When viewing class labels as "colors", the random surfer is "spraying" different node types with different color palettes; hence the name Graffiti. We demonstrate the performance gains of our method by comparing it to three state-of-the-art techniques for graph-based classification.
Oxidative capacity and fatigability in run‐trained malignant hyperthermia–susceptible mice

Introduction: The purpose of this study was to test the hypothesis that malignant hyperthermia model mice (RyR1Y522S/wt) are more vulnerable to exercise‐induced muscle injury and fatigability and adapt less to run training. Methods: After 6 weeks of voluntary wheel running, we measured anterior crural muscle fatigability, muscle injury, and cytochrome oxidase (COX) and citrate synthase (CS). Results: Although RyR1Y522S/wt mice ran without undergoing MH episodes, they ran 42% less distance than wild‐type (WT) mice. Muscles from WT mice exhibited increased fatigue resistance and COX content after training. Muscles from RyR1Y522S/wt mice demonstrated no significant change in fatigability or COX and CS after training. However, muscles from RyR1Y522S/wt mice displayed less intrinsic fatigability and greater COX/CS content and muscle damage than WT mice. Conclusions: RyR1Y522S/wt mice can run without having rhabdomyolysis, and their inability to adapt to training appears to stem from intrinsic enhancement of mitochondrial enzymes and fatigue resistance. Muscle Nerve, 2012