Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatiotemporal regulation of meiotic recombination by Liaisonin

Sexual reproduction involves diversification of genetic information in successive generations. Meiotic recombination, which substantially contributes to the increase in genetic diversity, is initiated by programmed DNA double-strand breaks (DSBs) catalyzed by the evolutionarily conserved Spo11 protein. Spo11 requires additional partner proteins for its DNA cleavage reaction. DSBs are preferentially introduced at defined chromosomal sites called “recombination hotspots. ” Recent studies have revealed that meiotically established higher-order chromosome structures, such as chromosome axes and loops, are also crucial in the control of DSB formation. Most of the DSB sites are located within chromatin loop regions, while many of the proteins involved in DSB formation reside on chromosomal axes. Hence, DSB proteins and DSB sites seem to be distantly located. To resolve this paradox, we conducted comprehensive proteomics and ChIP-chip analyses on Spo11 partners in Schizosaccharomyces pombe, in combination with mutant studies. We identified two distinct DSB complexes, the “DSBC (DSB Catalytic core)“ and “SFT (Seven-Fifteen-Twenty four; Rec7-Rec15-Rec24)” subcomplexes. The DSBC subcomplex contains Spo11 and functions as the catalytic core for the DNA cleavage reaction. The SFT subcomplex is assumed to execute regulatory functions. To activate the DSBC subcomplex, the SFT subcomplex tethers hotspots to axes via its interaction with Mde2, which can interact with proteins in both DSBC and SFT subcomplexes. Thus, Mde2 is likely to bridge these two subcomplexes, forming a “tethered loop-axis complex. ” It should be noted that Mde2 expression is strictly regulated by S phase checkpoint monitoring of the completion of DNA replication. From these observations, we proposed that Mde2 is a central coupler for meiotic recombination initiation to establish a tethered loop-axis complex in liaison with the S phase checkpoint.
Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

1. How do ribozymes work? 241 2. The hammerhead RNA as a prototype ribozyme 242 2.1 RNA enzymes 242 2.2 Satellite self-cleaving RNAs 242 2.3 Hammerhead RNAs and hammerhead ribozymes 244 3. The chemical mechanism of hammerhead RNA self-cleavage 246 3.1 Phosphodiester isomerization via an SN2(P) reaction 247 3.2 The canonical role of divalent metal ions in the hammerhead ribozyme reaction 251 3.3 The hammerhead ribozyme does not actually require metal ions for catalysis 254 3.4 Hammerhead RNA enzyme kinetics 257 4. Sequence requirements for hammerhead RNA self-cleavage 260 4.1 The conserved core, mutagenesis and functional group modifications 260 4.2 Ground-state vs. transition-state effects 261 5. The three-dimensional structure of the hammerhead ribozyme 262 5.1 Enzyme–inhibitor complexes 262 5.2 Enzyme–substrate complex in the initial state 264 5.3 Hammerhead ribozyme self-cleavage in the crystal 264 5.4 The requirement for a conformational change 265 5.5 Capture of conformational intermediates using crystallographic freeze-trapping 266 5.6 The structure of a hammerhead ribozyme ‘early’ conformational intermediate 267 5.7 The structure of a hammerhead ribozyme ‘later’ conformational intermediate 268 5.8 Is the conformational change pH dependent? 269 5.9 Isolating the structure of the cleavage product 271 5.10 Evidence for and against additional large-scale conformation changes 274 5.11 NMR spectroscopic studies of the hammerhead ribozyme 278 6. Concluding remarks 280 7. Acknowledgements 281 8. References 281 1. How do ribozymes work? 241 The discovery that RNA can be an enzyme (Guerrier-Takada et al. 1983; Zaug & Cech, 1986) has created the fundamental question of how RNA enzymes work. Before this discovery, it was generally assumed that proteins were the only biopolymers that had sufficient complexity and chemical heterogeneity to catalyze biochemical reactions. Clearly, RNA can adopt sufficiently complex tertiary structures that make catalysis possible. How does the three- dimensional structure of an RNA endow it with catalytic activity? What structural and functional principles are unique to RNA enzymes (or ribozymes), and what principles are so fundamental that they are shared with protein enzymes?
Chronic Dehydration and Regularly Drinking Water to Mitigate Age-Related Cognitive Impairment

Age-related cognitive impairment undergoes a continuous progression:pre-mild cognitive impairment(preMCI),mild cognitive impairment(MCI)and Alzheimer's disease(AD). So far,chronic dehydration is regarded as a common symptom for the patients with age-related cognitive impairment,in particular of those with AD. Monitored with an infrared-CCD camera,a marked decrease in the drinking frequency(P0.05)and water consumption quantity(P0.01)of 10-month old C57 BL/6 mice was observed in comparison with that of 1-month old counterparts. On the one hand,chronic dehydration for the patients may be resulted from their declined of the perception of"thirsty"and loss of memory. On the other hand,dehydration causes accumulation of cytotoxic metabolic compounds such as endogenous formaldehyde,worsening cognitive impairment worse. The interaction between dehydration and cognitive impairment leads to a vicious circle. Furthermore,chronic impairment of central nervous system due to the disorder of formaldehyde metabolism is believed as one risk factor for age-related impairment because of the increase in endogenous formaldehyde with aging(65 years old)and in the hippocampus of Alzheimer's patients. Regularly drinking water relieves not only chronic dehydration for aging people,but also significantly decreases the concentration of endogenous formaldehyde,which may offer protection of central nervous system. Therefore,building the habit to regularly drink water should be emphasized at the early stage to relieve chronic dehydration and scavenge cytotoxic metabolic products including formaldehyde for aging people,which might be beneficial to mitigate age-related cognitive impairment at its early stage.
Alcohol Use among Chinese Men Who Have Sex with Men: An Epidemiological Survey and Meta-Analysis

The HIV/AIDS epidemic among Chinese men who have sex with men (MSM) has become a significant public health concern. Knowledge of alcohol consumption in this population is limited. In this study, 1,155 Chinese MSM were surveyed to assess alcohol use and its correlates. A meta-analysis was also performed to aggregate pooled prevalence of current alcohol use. MSM who were unmarried (aOR: 1.87; 95% CI: 1.29–2.71) or unemployed/retired (aOR: 2.77; 95% CI: 1.73–4.45) were more likely to drink alcohol more than once per week. MSM who consumed alcohol more than once per week were more likely to use drug (P < 0.01), have sex with women (P < 0.01), have unprotected insertive (P = 0.04) or receptive (P = 0.03) anal sex with men, have more than 10 lifetime male sex partners (P < 0.01), predominantly practice insertive anal sex (P < 0.01), and trade sex for money (P < 0.01). Pooled overall alcohol use prevalence was 32%. Pooled prevalence for MSM who drank alcohol more than once per week and who drank alcohol before sex with male partners was 23%. Our findings provide the basis for further exploring the alcohol-HIV association and developing risk reduction interventions.
HYL1 regulates the balance between adaxial and abaxial identity for leaf flattening via miRNA-mediated pathways

HYPONASTIC LEAVES1 (HYL1) is an important regulator of microRNA (miRNA) biogenesis. Incurvature of rosette leaves in loss-of-function mutants of HYL1 implicates the regulation of leaf flatness by HYL1 via miRNA pathways. Recent studies have identified jba-1D, jaw-1D, and oe-160c, the dominant mutants of MIR166g, MIR319a, and MIR160c genes, respectively, which display three types of leaf curvature. However, it remains unclear whether or how HYL1 controls leaf flatness through the pathways mediated by these miRNAs. To define which miRNAs and target genes are relevant to the hyl1 phenotype in terms of leaf incurvature, the effects of three mutated MIRNA genes and their targets on the direction and extent of leaf curvature in hyl1 mutants were examined. The genetic analysis shows that the hyl1 phenotype is strongly rescued by jba-1D, but not by jaw-1D or oe-160c, whereas the mutant phenotypes of jba-1D, jaw-1D, or oe-160c leaves are compromised by the hyl1 allele. Expression analysis indicates that reduced accumulation of miR166, rather than of miR319a or miR160, causes incurvature of hyl1 leaves, and that miR319a-targeted TCP3 positively regulates the adaxial identity gene PHABULOSA while miR160-targeted ARF16 negatively regulates the abaxial identity gene FILAMENTOUS FLOWER. In these cases, the direction and extent of leaf incurvature are associated with the expression ratio of adaxial to abaxial genes (adaxial to abaxial ratio). HYL1 regulates the balance between adaxial and abaxial identity and modulates leaf flatness by preventing leaf incurvature, wavy margins, and downward curvature. It is concluded that HYL1 monitors the roles of miR165/166, miR319a, and miR160 in leaf flattening through the relative activities of adaxial and abaxial identity genes, thus playing an essential role in leaf development.
Variance based classifier comparison in text catergorization (poster session)

Text categorization is one of the key functions for utilizing vast amount of documents. It can be seen as a classification problem, which has been studied in pattern recognition and machine learning fields for a long time and several classification methods have been developed such as statistical classification, decision tree, support vector machines and so on. Many researchers applied those classification methods to text categorization and reported their performance (e.g., decision tree[3], Bayes classifier[2], support vector machine[l]). Yang conducted comprehensive study of comparison or text categorization and reported that k nearest neighbor and support vector machines works well for text categorization[4]. In the previous studies, classification methods were usually compared using single pair of training and test data However, classification method with more complex family of classifiers requires more training data and small training data may result in deriving unreliable classifier, that is, the performance of the derived classifier varies much depending on training data. Therefore, we need to take the size of training data into account when comparing and selecting a classification method. In this paper, we discuss how to select a classifier from those derived by various classification methods and how the size of training data affects the performance of the derived classifier. In order to evaluate the reliability of classification method, we consider the variance of accuracy of derived classifier. We first construct a statistical model. In the text categorization, each document is usually represented with a feature vector that consists of weighted frequencies of terms. In the vector space model, document is a point in high dimensional feature space and a classifier separates the feature space into subspaces each of which is labeled with a category.
Fast inverse kinematics algorithm for large DOF system with decomposed gradient computation based on recursive formulation of equilibrium

This paper presents a fast inverse kinematics (IK) algorithm. In recent years, the robotics computation theory is often applied for detailed and complex multi-body systems. However, the computational complexity of IK is too high to be implemented in large DOF systems. IK of multi-body system is often formulated as nonlinear optimization to minimize the residuals from the references. It usually requires the computation of the gradient vector of the evaluation function. In the method, the computation of the gradient is decomposed into two parts. First, the residuals are considered as external forces and are distributed to each link. Then, the gradient can be computed from static equilibrium by the recursive Newton-Euler algorithm. In addition with the efficient direction search algorithms of nonlinear programing, the computation complexity of IK can be dramatically reduced. The results of numerical evaluation using a large-DOF manipulator and a human musculoskeletal model are shown.
An iterative improvement algorithm for low power data path synthesis

We address the problem of minimizing power consumption in behavioral synthesis of data-dominated circuits. The complex nature of power as a cost function implies that the effects of several behavioral synthesis tasks like module selection, clock selection, scheduling and resource sharing on supply voltage and switched capacitance need to be considered simultaneously to fully derive the benefits of design space exploration at the behavior level. We present an efficient algorithm for performing scheduling, clock selection, module selection, and resource allocation and assignment simultaneously with an aim of reducing the power consumption in the synthesized data path. The algorithm, which is based on an iterative improvement strategy, is capable of escaping local minima in its search for a low power solution. The algorithm considers diverse module libraries and complex scheduling constructs such as multicycling chaining, and structural pipelining. We describe supply voltage and clock pruning strategies that significantly improve the efficiency of our algorithm by cutting down on the computational effort involved in exploring candidate supply voltages and clock periods that are unlikely to lead to the best solution. Experimental results are reported to demonstrate the effectiveness of the algorithm. Our techniques can be combined with other known methods of behavioral power optimization like data path replication and transformations, to result in a complete data path synthesis system for low power applications.
Updates and view maintenance in soft real-time database systems

A database system contains base data items which record and model a physical, real world environment. For better decision support, base data items are summarized and correlated to derive views. These base data and views are accessed by application transactions to generate the ultimate actions taken by the system. As the environment changes, updates are applied to the base data, which subsequently trigger view recomputations. There are thus three types of activities: base data update, view recomputation, and transaction execution. In a real-time system, two timing constrains need to be enforced. We require transactions meet their deadlines (transaction timeliness) and read fresh data (data timeliness). In this paper we define the concept of absolute and relative temporal consistency from the perspective of transactions. We address the important issue of transaction scheduling among the three types of activities such that the two timing requirements can be met. We also discuss how a real-time database system should be designed to enforce different levels of temporal consistency.
Unimodal contaminations in testing point null hypothesis.

The problem of testing a point null hypothesis from the Bayesian perspective is considered. The uncertainties are modelled through use of "{contamination class with the class of contaminations including: i) All unimodal distributions and ii). All unimodal and symmetric distributions. Over these classes, the in¯mum of the posterior probability of the point null hypothesis is computed and compared with the p{value and a better approach than the one known is obtained. [RESUMEN]Contaminaciones unimodales en el contraste de hip¶otesis nula puntual. Se considera el problema del contraste de hipotesis nula puntual desde el punto de vista Bayesiano. La incertidumbre se modeliza mediante el uso de la clase de las distribuciones "{contaminadas, cuando la clase de las contaminaciones incluye:i) todas las distribuciones unimodales y ii) todas las distribuciones unimodales y sim¶etricas. Se calcula el infimo de las probabilidades a posteriori de la hip¶otesis nula puntual sobre estas clases y se compara con el p{valor, obteniendose una aproxi- macion aceptable entre ambos valores.
An efficient noise-robust automatic speech recognition system using artificial neural networks

The Human Auditory System for speech recognition is highly robust against background noise compared to state-of-the-art Automatic Speech Recognition (ASR) systems. One of the best ways to add robustness to a speech recognition system is to have a compressed and highly robust feature set. In this paper, we present a novel approach for feature compression which makes the proposed noise-robust ASR system simple and very efficient. The other popular approach for feature compression is K-means which is complex and time-consuming. The experiments were performed on the proposed noise-robust ASR system for recognizing 65 different words with very low Signal to Noise Ratio (SNR) of -5 dB. The Mel Frequency Cepstrum Coefficients (MFCCs) were used as features for speech recognition. Back propagation Artificial Neural Network (ANN) was used to design the ASR system. Specialized versions of feedforward neural networks and training algorithms were tested on the speech recognition system and results are presented for each type. Experimental results show that the recognition accuracy of the proposed noise-robust ASR system is very high even with such a low SNR.
Stress and type 2 diabetes : A review of how stress contribute to the development of T 2 D

Current policy and research around type 2 diabetes (T2D) interventions largely invoke a behavioral model. We suggest that activation of the physiologic stress response (PSR) from chronic exposure to stressors, low socioeconomic status (SES), severe mental health problems, or aggressive behavior increases the risk of T2D. This article is a comprehensive review of the literature on the link between T2D and psychosocial factors focusing on prospective studies of the risk for developing diabetes. The review found an increased risk for T2D in people: exposed to stressful working conditions or traumatic events; with depression; with personality traits or mental health problems that put them in conflict with others; of low SES, either currently or in childhood; and in racial/ethnic minority populations, independent of current SES. This review suggests that T2D prevention research would be more effective if (a) the PSR to psychosocial factors (especially social disparities) was recognized and (b) intervention programs evaluated reduction in social disparities as part of a comprehensive approach.
Inflationary scenarios from branes at angles

We describe a simple mechanism that can lead to inflation within string-based brane-world scenarios. The idea is to start from a supersymmetric configuration with two parallel static Dp-branes, and slightly break the supersymmetry conditions to produce a very flat potential for the field that parametrises the distance between the branes, i.e. the inflaton field. This breaking can be achieved in various ways: by slight relative rotations of the branes with small angles, by considering small relative velocities between the branes, etc. If the breaking parameter is sufficiently small, a large number of e-folds can be produced within the D-brane, for small changes of the configuration in the compactified directions. Such a process is local, i.e. it does not depend very strongly on the compactification space nor on the initial conditions. Moreover, the breaking induces a very small velocity and acceleration, which ensures very small slow-roll parameters and thus an almost scale invariant spectrum of metric fluctuations, responsible for the observed temperature anisotropies in the microwave background. Inflation ends as in hybrid inflation, triggered by the negative curvature of the string tachyon potential. In this paper we elaborate on one of the simplest examples: two almost parallel D4-branes in a flat compactified space.
The Role of Salt in the Pathogenesis of Fructose-Induced Hypertension

Metabolic syndrome, as manifested by visceral obesity, hypertension, insulin resistance, and dyslipidemia, is reaching epidemic proportions in the Western World, specifically the United States. Epidemiologic studies suggest that the increased prevalence of metabolic syndrome directly correlates with an increase in the consumption of fructose, mainly in the form of high-fructose corn syrup. This inexpensive alternative to traditional sugar has been increasingly utilized by the food industry as a sweetener since the 1960s. While augmented caloric intake and sedentary lifestyles play important roles in the increasing prevalence of obesity, the pathogenesis of hypertension in metabolic syndrome remains controversial. One intriguing observation points to the role of salt in fructose-induced hypertension. Recent studies in rodents demonstrate that increased dietary fructose intake stimulates salt absorption in the small intestine and kidney tubules, resulting in a state of salt overload, thus setting in motion a cascade of events that will lead to hypertension. These studies point to a novel interaction between the fructose-absorbing transporter, Glut5, and the salt transporters, NHE3 and PAT1, in the intestine and kidney proximal tubule. This paper will focus on synergistic roles of fructose and salt in the pathogenesis of hypertension resulting from salt overload.
A framework for multimedia content abstraction and its application to rushes exploration

Multimedia content abstraction methods such as summarisation, skimming and browsing are of growing importance for the exploration of multimedia collections, complementing search and retrieval approaches. The methods proposed in literature differ in a number of aspects (e.g. form, purpose, presentation), but nonetheless many similarities in the creation of multimedia content abstractions can be identified. Thus we propose a generic multimedia content abstraction process and a software framework that implements it. We demonstrate the practical usability of the framework by using it to build an application for browsing a collection of rushes.
A Secure Content Delivery System Based on a Partially Reconfigurable FPGA

We developed a content delivery system using a partially reconfigurable FPGA to securely distribute digital content on the Internet. With partial reconfigurability of a Xilinx Virtex-II Pro FPGA, the system provides an innovative single-chip solution for protecting digital content. In the system, a partial circuit must be downloaded from a server to the client terminal to play content. Content will be played only when the downloaded circuit is correctly combined (= interlocked) with the circuit built in the terminal. Since each circuit has a unique I/O configuration, the downloaded circuit interlocks with the corresponding built-in circuit designed for a particular terminal. Thus, the interface of the circuit itself provides a novel authentication mechanism. This paper describes the detailed architecture of the system and clarify the feasibility and effectiveness of the system. In addition, we discuss a fail-safe mechanism and future work necessary for the practical application of the system.
Java object look aside buffer for embedded applications

Java has been widely used in embedded systems such as mobile phones. Just-In-Time compilation technique (JIT) is used for PC applications, but many embedded systems have not much memory or processor power. Therefore, JIT method for Java is hardly used in small embedded systems such as mobile phones and PDAs.In this paper, a new optimization method without JIT: Java Object Look Aside Buffer (JOLAB) for Java Virtual Machine and/or Java processor is proposed. JOLAB keeps resolution information for speedup constant pool references of JVM bytecode. Hence, JOLAB will reduce effective object access latency, as well as TLB for virtual addressing.We also present some performance number with benchmarks.