Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomics of Rac GTPase Signaling Reveals Its Predominant Role in Elicitor-Induced Defense Response of Cultured Rice Cells1[W]

We have previously shown that a human small GTPase Rac homolog, OsRac1, from rice (Oryza sativa) induces cascades of defense responses in rice plants and cultured cells. Sphingolipid elicitors (SEs) have been similarly shown to activate defense responses in rice. Therefore, to systematically analyze proteins whose expression levels are altered by OsRac1 and/or SE treatment, we performed a differential display analysis of proteins by the use of two-dimensional gel electrophoresis and mass spectrometry. A total of 271 proteins whose expression levels were altered by constitutively active (CA)-OsRac1 or SE were identified. Interestingly, of 100 proteins that were up-regulated by a SE, 87 were also induced by CA-OsRac1, suggesting that OsRac1 plays a pivotal role in defense responses induced by SE in cultured rice cells. In addition, CA-OsRac1 induces the expression of 119 proteins. Many proteins, such as pathogenesis-related proteins, SGT1, and prohibitin, which are known to be involved in the defense response, were found among these proteins. Proteins involved in redox regulation, chaperones such as heat shock proteins, BiP, and chaperonin 60, proteases and protease inhibitors, cytoskeletal proteins, subunits of proteasomes, and enzymes involved in the phenylpropanoid and ethylene biosynthesis pathways were found to be induced by CA-OsRac1 or SE. Results of our proteomic analysis revealed that OsRac1 is able to induce many proteins in various signaling and metabolic pathways and plays a predominant role in the defense response in cultured rice cells.
FAME: FAirly MEasuring Multithreaded Architectures

Nowadays, multithreaded architectures are becoming more and more popular. In order to evaluate their behavior, several methodologies and metrics have been proposed. A methodology defines when the measurements of a given workload execution are taken. A metric combines those measurements to obtain a final evaluation result. However, since current evaluation methodologies do not provide representative measurements for these metrics, the analysis and evaluation of novel ideas could be either unfair or misleading. Given the potential impact of multithreaded architectures on current and future processor designs, it is crucial to develop an accurate evaluation methodology for them. This paper presents FAME, a new evaluation methodology aimed to fairly measure the performance of multithreaded processors. FAME re-executes all traces in a multithreaded workload until all of them are fairly represented in the final measurements taken from the workload. We compare FAME with previously used methodologies for both architectural research simulators and real processors. Our results show that FAME provides more accurate measurements than other methodologies, becoming an ideal evaluation methodology to analyze proposals for multithreaded architectures.
GROUNDWATER FLOW MODELS

In general, models are conceptual descriptions or approximations that describe physical systems using mathematical equations; they are not exact descriptions of physical systems or processes. By mathematically representing a simplified version of a hydrogeological system, reasonable alternative scenarios can be predicted, tested, and compared. The applicability or usefulness of a model depends on how closely the mathematical equations approximate the physical system being modeled. In order to evaluate the applicability or usefulness of a model, it is necessary to have a thorough understanding of the physical system and the assumptions embedded in the derivation of the mathematical equations.
Assamese Numeral Corpus for Speech Recognition using Cooperative ANN Architecture

Speech corpus is one of the major components in a Speech Processing System where one of the primary requirements is to recognize an input sample. The quality and details captured in speech corpus directly affects the precision of recognition. The current work proposes a platform for speech corpus generation using an adaptive LMS filter and LPC cepstrum, as a part of an ANN based Speech Recognition System which is exclusively designed to recognize isolated numerals of Assamese languagea major language in the North Eastern part of India. The work focuses on designing an optimal feature extraction block and a few ANN based cooperative architectures so that the performance of the Speech Recognition System can be improved. Keywords—Filter, Feature, LMS, LPC, Cepstrum, ANN.
Cross­generational comparison of stochastic mortality of coupled lives

This paper studies the evolution across generations of dependence among individuals of a couple. We consider a well-known data set of couples of individuals provided by a large Canadian insurer, and select three di¤erent generations of couples. For each of them, we model the marginal survival functions with a doubly stochastic approach and perform a best- t selection of the copula. Since the e¤ect of censoring on the dependence structure of the couple varies across di¤erent generations, in the best- t copula test it is necessary to restrict the attention to the subset of complete data. Despite the small sample available, the remarkable result is that the Kendalls tau varies between 30% for the young generation and 45% for the old one. As a consequence, for every candidate copula the dependence parameter decreases when younger generations are taken into account. This result is intuitive and in accordance with the observed increase in the rate of divorces, the creation of enlarged families and so on. The best t copula is not invariant across generations, but di¤erent Archimedean copulas perform similarly. An actuarial application to pricing and reserving of joint life products and reversionary annuities shows that not only insurance companies should dismiss the simplifying independence assumption, but they should also select di¤erent dependence parameters for di¤erent generations.
Visual function in regenerating teleost retina following cytotoxic lesioning

Teleost fish retinas can regenerate in vivo in adulthood. Retinal and visual function was assessed in adult goldfish following comprehensive retinal destruction by intraocular injection of ouabain. Electroretinograms (ERGs) and the dorsal light reflex (DLR) were used to evaluate the return of visual function. ERGs were detectable in regenerating eyes 50 to 70 days following ouabain injection. Amplitudes of both a- and b-waves increased steadily through day 210 following ouabain treatment, at which time a-wave amplitude was 90% and b-wave amplitude approached 50% of the contralateral control eye. The progressive gain observed in the a-wave was attributed to photoreceptor regeneration. The increase in b-wave amplitude was attributed to an increase in the number of inner nuclear layer cells and the number and efficacy of neuronal connections to or within the inner retina. The photopic spectral sensitivity of the b-wave in regenerating retina closely matched the intrafish control retina, suggesting that the relative numbers of cone photoreceptors was normal in regeneration. The recovery of the DLR (indicated by improved postural balance during regeneration) paralleled electrophysiological gains during retinal regeneration. Fish displayed a marked longitudinal body imbalance toward the control eye following retinal destruction. Improvement in equilibrium was correlated with increasing b-wave amplitudes. When the b-wave reached 50% of control amplitude (30 weeks), normal posture was restored. The return of the ERG indicates that photoreceptors and their synaptic connections must be functional in regenerating retina. Failure of the retina to regenerate produced an abnormal DLR that persisted through 30 weeks and ERGs were not measurable. The return of normal equilibrium indicates that the regenerating retina can establish central connections to the brain, and that the regenerated connections can mediate functional visual behavior.
Structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle

Significance Certain metabolic pathways use a carrier protein to shuttle covalently attached intermediates between the active sites of enzymes. However, the details of the carrier protein–partner interactions have only been elucidated in a few cases. We have used biophysical methods and crystallography to obtain a molecular-level description of the interactions between a carrier protein and an enzyme involved in bacterial sulfur oxidation. Characterization of the contact sites between the two proteins suggests a basis for the promiscuous, but specific, binding interactions of the carrier protein. We also infer that the enzyme discriminates between the substrate- and product-bound forms of the carrier protein based on different interaction kinetics and link this behavior to a structural change at the enzyme active site. The bacterial Sox (sulfur oxidation) pathway is an important route for the oxidation of inorganic sulfur compounds. Intermediates in the Sox pathway are covalently attached to the heterodimeric carrier protein SoxYZ through conjugation to a cysteine on a protein swinging arm. We have investigated how the carrier protein shuttles intermediates between the enzymes of the Sox pathway using the interaction between SoxYZ and the enzyme SoxB as our model. The carrier protein and enzyme interact only weakly, but we have trapped their complex by using a “suicide enzyme” strategy in which an engineered cysteine in the SoxB active site forms a disulfide bond with the incoming carrier arm cysteine. The structure of this trapped complex, together with calorimetric data, identifies sites of protein–protein interaction both at the entrance to the enzyme active site tunnel and at a second, distal, site. We find that the enzyme distinguishes between the substrate and product forms of the carrier protein through differences in their interaction kinetics and deduce that this behavior arises from substrate-specific stabilization of a conformational change in the enzyme active site. Our analysis also suggests how the carrier arm-bound substrate group is able to outcompete the adjacent C-terminal carboxylate of the carrier arm for binding to the active site metal ions. We infer that similar principles underlie carrier protein interactions with other enzymes of the Sox pathway.
1 2 M ar 2 01 8 Gradient flow of the norm squared of a moment map over K ä hler manifolds

Inspired by Wilkin’s work [23, 24] on Morse theory for the moduli space of Higgs bundles, we study the moduli space of gauged holomorphic maps by a heat flow approach in the spirit of Atiyah and Bott in a series of papers. In this paper, applying the method of Hong [9], we establish the global existence of smooth solutions of the gradient flow equations of the vortex functional over a compact Kähler manifold.
A cross sectional study on prevalence and pattern of personality disorders in psychiatric inpatients of a tertiary care hospital

Background: Co-occurrence of personality disorders with other psychiatric disorders has also been well documented by many researchers in the past. Diagnosing co occurring personality disorders in psychiatric patients with is of strong clinical significance, considering their association with the duration, recurrence, and outcome of these disorders. They also can have wide range of other adverse health outcomes. However, most of the existing literature regarding the studies related to personality disorders (PDs) in India is confined to community and mental hospitals. Aim: To study the prevalence and factors affecting personality disorders in a general hospital psychiatry unit. Materials and methods: The study was a cross sectional study conducted in a psychiatric unit of a tertiary care teaching hospital in south India. ICD-10, Mini International Neuropsychiatric Interview (MINI) and Structured Clinical Interview for Diagnostic and Statistical Manual of Mental DisordersIV Personality Disorders (SCID-II) were used. Results: A total of 116 participants were included in the study. Majority of the participants were between 26 to 45 years of age. The prevalence of personality disorder was 21.55% (95%CI 14.07 to 29.03) among the study population. The most common type of personality disorder was avoidance (7.7%), followed Maanasa T J, Sivabackiya C, Srinivasan B, Shajahan Ismail, Sabari Sridhar OT, Kailash S. A cross sectional study on prevalence and pattern of personality disorders in psychiatric inpatients of a tertiary care hospital. IAIM, 2016; 3(5): 94-100. Page 95 by anti social (5.17%) and borderline (3.45%) personality disorders. Highest proportion of PD was seen in people with major depressive disorder (35.7%), followed by people with multiple psychiatric illness (31.6%) and Psychotic disorders/mood disorders with psychosis (18.9%). Conclusion: The proportion of personality disorders was highest in 26 to 35 year age group, was higher in males, compared to females. People who studied up to primary school had higher proportion of PD, compared to other educational categories. The proportion was higher in people belonging to higher socio economic strata, people who are separated and people from nuclear family.
Cloning, Expression and Characterization of NAD Kinase from Staphylococcus aureus Involved in the Formation of NADP (H): A Key Molecule in the Maintaining of Redox Status and Biofilm Formation

Background:Staphylococcus aureus has the ability to form biofilms on any niches, a key pathogenic factor of this organism and this phenomenon is directly related to the concentration of NADPH. The formation of NADP is catalyzed by NAD kinase (NADK) and this gene of S. aureus ATCC 12600 was cloned, sequenced, expressed and characterized. Materials and Methods: The NADK gene was polymerase chain reaction amplified from the chromosomal DNA of S. aureus ATCC 12600 and cloned in pQE 30 vector, sequenced and expressed in Escherichia coli DH5α. The pure protein was obtained by passing through nickel metal chelate agarose column. The enzyme kinetics of the enzyme and biofilm assay of the S. aureus was carried out in both aerobic and anaerobic conditions. The kinetics was further confirmed by the ability of the substrates to dock to the NADK structure. Results: The recombinant NADK exhibited single band with a molecular weight of 31kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the gene sequence (GenBank: JN645814) revealed presence of only one kind of NADK in all S. aureus strains. The enzyme exhibited very high affinity for NAD compared to adenosine triphosphate concurring with the docking results. A root-mean-square deviation value 14. 039Š observed when NADK structure was superimposed with its human counterpart suggesting very low homology. In anaerobic conditions, higher biofilm units were found with decreased NADK activity. Conclusion: The results of this study suggest increased NADPH concentration in S. aureus plays a vital role in the biofilm formation and survival of this pathogen in any environmental conditions.
Greening Public Procurement: a review of the issues

Purchasing in the public sector differs in important ways from private sector procurement. Understanding how these differences affect the ‘greening’ of supply practice is important not just for the public sector itself, but also fir any attempt to develop explanations of how organisations in general make a link between what and how they buy and the impact of such purchasing on the environment. This paper summarises the key ideas in green supply and examines why public procurement has a particular relevance to this issue; analyses the issue of regulation and public accountability in relation to green supply; reviews the use of procurement as a tool for policy and explores the impact of budgeting systems and organisational design. The paper is based on: a review of literature on public procurement, drawn the USA and the UK and case studies of public sector organisations - in local and national government – carried out by the authors as part of a research project on Greening of Supply Chains.
Practice of Epidemiology Methods and Software for Estimating Health Disparities : The Case of Children ’ s Oral Health

The National Center for Health Statistics recently issued a monograph with 11 guidelines for reporting health disparities. However, guidelines on confidence intervals (CIs) cannot be readily implemented with the complex sample surveys often used for disease surveillance. In the United States, dental caries (decay) is the most common chronic childhood disease—5 times more common than asthma. Racial/ethnic minorities, immigrants, and persons of lower socioeconomic position (SEP) have a greater prevalence of caries. The authors provide methods for applying National Center for Health Statistics guidelines to complex sample surveys (health disparity indices and absolute and relative difference measures assessing associations of race/ethnicity and SEP to health outcomes with CIs); illustrate the application of those methods to children’s untreated caries; provide relevant software; and report results from a simulation varying prevalence. They use data on untreated caries from the California Oral Health Needs Assessment of Children 2004–2005 and school percentage of participation in free/reduced-price lunch programs to illustrate the methods. Absolute and relative measures, the Slope Index of Inequality, the Relative Index of Inequality (mean and ratio), and the Health Concentration Index were estimated. Taylor series linearization and rescaling bootstrap methods were used to estimate CIs. Oral health differed significantly betweenWhite children and all non-White children and was significantly related to SEP.
A Discriminative Reranking Approach to Spelling Correction

This paper proposes an approach to spelling correction. It reranks the output of an existing spelling corrector, Aspell. A discriminative model (Ranking SVM) is employed to improve upon the initial ranking, using additional features as evidence. These features are derived from state-of-the-art techniques in spelling correction, including edit distance, letter-based n-gram, phonetic similarity and noisy channel model. This paper also presents a method to automatically extract training samples from the query log chain. The system outperforms the baseline Aspell greatly, as well as the previous models and several off-the-shelf systems (e.g. spelling corrector in Microsoft Word 2003). The experimental results based on query chain pairs are comparable to that based on manually-annotated pairs, with 32.2%/32.6% reduction in error rate, respectively.
Anything goes unless forbidden Notes on synchronization and the operational semantics of a relaxed memory model

A memory model dictates which values may be observed when reading from memory, thereby regulating how concurrent processes communicate through shared memory. In this note, we discuss a weak memory model for a calculus inspired by the Go programming language, focusing on buffered channel communication as the sole synchronization primitive. In contrast to an axiomatic semantics, we present an operational interpretation and discuss its rationale and its design.
The BoC-GEM-Fin: Banking in the Global Economy

This article describes the Bank of Canada’s version of the Global Economy Model structured to incorporate an active banking system that features an interbank market and cross-border lending. After describing the new model, the authors use it to examine the responses of selected U.S. and Canadian macroeconomic variables to a “credit crunch” in the United States and also to study the impact of changes in the regulatory limits to bank leverage in Canada. They also discuss the relative merits of a monetary policy framework based on inflation targeting and one based on price-level targeting in the presence of shocks to the U.S. and Canadian banking sectors.
Benchmarking Agility For Multi-legged Terrestrial Robots

In this paper, we present a novel and practical approach for benchmarking agility. We focus on terrestrial, multi-legged locomotion in the field of bio-inspired robotics. We define agility as the ability to perform a set of different but specific tasks executed in a fast and efficient manner. This definition is inspired by the analysis of natural role models, such as dogs and horses as well as robotic systems. An evaluation of existing benchmarks in robotics is done and taken into account in our proposed benchmark. After the general definition, the actual normalized benchmarking values are defined, and measuring methods, as well as an online database for agility score collection and distribution, are presented. To provide a baseline for agile locomotion, various videos of dog-agility competitions were analyzed and agility scores calculated where applicable. Finally, validation and implementation of the benchmark are done with different robots directly available to the authors. In conclusion, our benchmark will enable researchers not only to compare existing robots and find out strengths and weaknesses in different design approaches, but also give a tool to define new fitness functions for optimization, learning processes and future robots developments, intensifying the links between biology and technology even further.
A CNN-Based Spatial Feature Fusion Algorithm for Hyperspectral Imagery Classification

The shortage of training samples remains one of the main obstacles in applying the neural networks to the hyperspectral images classification. To fuse the spatial and spectral information, pixel patches are often utilized to train a model, which may further aggregate this problem. In the existing works, an artificial neural network (ANN) model supervised by centerloss (ANNC) was introduced. Training merely with spectral information, the ANNC yields discriminative spectral features suitable for the subsequent classification tasks. In this paper, we propose a novel convolutional neural network (CNN)-based spatial feature fusion (CSFF) algorithm, which allows a smart integration of spatial information to the spectral features extracted by ANNC. As a critical part of CSFF, a CNN-based discriminant model is introduced to estimate whether two pixels belong to the same class. At the testing stage, by applying the discriminant model to the pixel pairs generated by a test pixel and each of its neighbors, the local structure is estimated and represented as a customized convolutional kernel. The spectral–spatial feature is generated by a convolutional operation between the estimated kernel and the corresponding spectral features within a local region. The final label is determined by classifying the resulting spectral–spatial feature. Without increasing the number of training samples or involving pixel patches at the training stage, the CSFF framework achieves the state of the art by declining 20%–50% classification failures in experiments on three well-known hyperspectral images.
Parametric inference of hidden discrete-time diffusion processes by deconvolution

We study a new parametric approach for hidden discrete-time diffusion models. This method is based on contrast minimization and deconvolution and leads to estimate a large class of stochastic models with nonlinear drift and nonlinear diffusion. It can be applied, for example, for ecological and financial state space models. After proving consistency and asymptotic normality of the estimation, leading to asymptotic confidence intervals, we provide a thorough numerical study, which compares many classical methods used in practice (Non Linear Least Square estimator, Monte Carlo Expectation Maxi-mization Likelihood estimator and Bayesian estimators) to estimate stochastic volatility model. We prove that our estimator clearly outperforms the Maximum Likelihood Estimator in term of computing time, but also most of the other methods. We also show that this contrast method is the most stable and also does not need any tuning parameter.