Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial DNA Haplogroups and the Risk of Sporadic Parkinson's Disease in Han Chinese

Background: Mitochondrial dysfunction is linked to the pathogenesis of Parkinson's disease (PD). However, the precise role of mitochondrial DNA (mtDNA) variations is obscure. On the other hand, mtDNA haplogroups have been inconsistently reported to modify the risk of PD among different population. Here, we try to explore the relationship between mtDNA haplogroups and sporadic PD in a Han Chinese population. Methods: Nine single-nucleotide polymorphisms, which define the major Asian mtDNA haplogroups (A, B, C, D, F, G), were detected via polymerase chain reaction-restriction fragment length polymorphism or denaturing polyacrylamide gel electrophoresis in 279 sporadic PD patients and 510 matched controls of Han population. Results: Overall, the distribution of mtDNA haplogroups did not show any significant differences between patients and controls. However, after stratification by age at onset, the frequency of haplogroup B was significantly lower in patients with early-onset PD (EOPD) compared to the controls (odds ratio [OR] =0.225, 95% confidence interval [CI]: 0.082–0.619, P = 0.004), while other haplogroups did not show significant differences. After stratification by age at examination, among subjects younger than 50 years of age: Haplogroup B also showed a lower frequency in PD cases (OR = 0.146, 95% CI: 0.030–0.715, P = 0.018) while haplogroup D presented a higher risk of PD (OR = 3.579, 95% CI: 1.112–11.523, P = 0.033), other haplogroups also did not show significant differences in the group. Conclusions: Our study indicates that haplogroup B might confer a lower risk for EOPD and people younger than 50 years in Han Chinese, while haplogroup D probably lead a higher risk of PD in people younger than 50 years of age. In brief, particular Asian mtDNA haplogroups likely play a role in the pathogenesis of PD among Han Chinese.
Large-Eddy Simulation of Turbulent Dispersion Effects in Direct Injection Diesel and Gasoline Sprays

In most large-eddy simulation (LES) applications to two-phase engine flows, the liquid-air interactions need to be accounted for as source terms in the respective governing equations. Accurate calculation of these source terms requires the relative velocity “seen” by liquid droplets as they move across the flow, which generally needs to be estimated using a turbulent dispersion model. Turbulent dispersion modeling in LES is very scarce in the literature. In most studies on engine spray flows, sub-grid scale (SGS) models for the turbulent dispersion still follow the same stochastic approach originally proposed for Reynolds-averaged Navier-Stokes (RANS). In this study, an SGS dispersion model is formulated in which the instantaneous gas velocity is decomposed into a deterministic part and a stochastic part. The deterministic part is reconstructed using the approximate deconvolution method (ADM), in which the large-scale flow can be readily calculated. The stochastic part, which represents the impact of the SGS flow field, is assumed to be locally homogeneous and isotropic and, therefore, governed by a Langevin-type equation. The model is applied to the spray G and spray H conditions defined by the engine combustion network (ECN) group. Simulation results are compared with the available experimental data for spray characteristics such as penetration rates, mixture fraction profile, and droplet velocity and Sauter mean diameter (SMD) distributions. Simulations with no dispersion and the commonly used RANS-type stochastic model are also performed for comparison purposes. Results show that the turbulent dispersion has a considerable impact on quantitative spray characteristics such as projected liquid volume (PLV) fraction, droplet SMD and velocity, and fuel vapor mixture fractions. On the other hand, the macroscopic spray characteristics such as liquid-and vapor-phase penetrations are not significantly affected by the dispersion modeling. The proposed SGS model also improves the prediction of spray and ignition
Sequential Composition of Walking Motions for a 5-Link Planar Biped Walker

Work by the authors published elsewhere ad- dressed the problem of designing controllers that induce ex- ponentially stable, periodic walking motions at a given xed speed for a 5-link, planar biped robot with one degree of un- deractuation in single support. The key technical tool was the hybrid zero dynamics, a 1-DOF invariant subdynamics of the full robot model. Further exploiting the features of the hybrid zero dynamics, this paper provides an additional con- trol feature: the ability to compose such controllers in order to obtain walking at several discrete speeds with guaranteed stability during the transitions. This feature aords the con- struction of a feedback controller that takes the robot from one exponentially stable walking motion to another while providing local stabilization and disturbance rejection. I. Introduction This work builds on the results in (9,10), which developed the notion of the hybrid zero dynamics for the walking mo- tion of an N-link, planar, biped robot with one less degree of actuation than degree of motion freedom (DOF) during the single support phase. This two dimensional, invariant sub-dynamics of the complete hybrid model of the biped robot was shown to be key to designing exponentially sta- bilizing controllers for walking motions. In particular, ex- ponentially stable orbits of the hybrid zero dynamics can be rendered exponentially stable in the complete hybrid model. The Poincar e map of the hybrid zero dynamics was proven to be dieomorphic to a scalar, LTI system, ren- dering transparent the existence and stability properties of periodic orbits of the hybrid zero dynamics. A special class of output functions based on B ezier polynomials was used to simplify the computation of the hybrid zero dynamics, while at the same time inducing a convenient, nite param- eterization of these dynamics. Parameter optimization was then applied to the hybrid zero dynamics to directly design a provably stable, closed-loop system which satised design
Towards a Context-Aware Photo Recommender System

The main challenge of recommender systems is to be able to identify and recommend items that have a greater chance of meeting the interests of their users, which generally have a very subjective and heterogeneous nature. It is imperative, then, that recommender systems, from the identification of each user's profile, could recommend personalized items. However, the user’s profile is not enough for the system to be able to completely identify the user’s interests. The use of the system in a different context from the usual may cause an unsatisfactory result for the recommendation, requiring it to be adapted to a new context. This paper presents the MMedia2U, a prototype of a mobile photo recommender system that exploits the user’s context and the context when the photo was created as a means to improve the recommendation. Three context dimensions area exploited: spatial, social and temporal. We describe the similarity measures used for each dimension and the results of the system evaluation by 13 users following a Gold Standard approach.
Blocking Linear Algebra Codes for Memory Hierarchies

Because computation speed and memory size are both increasing, the latency of memory, in basic machine cycles, is also increasing. As a result, recent compiler research has focused on reducing the e ective latency by restructuring programs to take more advantage of high-speed intermediate memory (or cache, as it is usually called). The problem is that many real-world programs are non-trivial to restructure, and current methods will often fail. In this paper, we present some encouraging preliminary results of a project to determine how much restructuring is possible with automatic techniques.
Genetic Analysis of a Non-Germinating Mutant of Arabidopsis Thaliana

ii ACKNOWLEDGMENTS . iii TABLE OF CONTENTS . iv LIST OF TABLES . vii LIST OF FIGURES. viii LIST OF ABBREVIATIONS . ix CHAPTER 1: INTRODUCTION. 1 1.1 Overview . 1 1.2 Model Plant Arabidopsis thaliana . 2 1.3 Seed Development . 2 1.4 Seed Dormancy and Germination . 5 1.5 Gibberellin . 9 1.6 Seed Germination Mutants . 10 1.7 The Role of GA Mutants in Genetics and Plant Breeding . 11 1.8 Biosynthetic Pathway of GAs . 12 1.9 Genes Encoding Enzymes for GA Biosynthesis and Signaling . 15 1.10 Positional Mapping Vs. Next Generation Mapping. 17 1.11 Hypothesis and Objectives. 18 CHAPTER 2: MATERIALS AND METHODS. 19 2.1 Plant Materials. 19 2.2 Germination of Seeds and Plant Growth Conditions . 19 2.2.1 Sterilization of Seeds and Preparation of MS Media . 19 2.2.2 Preparation of Gibberellic Acid Supplemented Growth Media . 20 2.2.3 Growth Conditions . 20 v 2.3 Mutant Isolation. 20 2.4 Crossing of Arabidopsis . 21 2.5 Generation of F2 Mapping Population . 24 2.6 Plant Genomic DNA extraction. 24 2.7 Checking the Quality of Isolated DNA. 27 2.8 Bulked DNA Preparation for Bulked-segregant Analysis (BSA) . 27 2.9 Bulked DNA Preparation for Nextgeneration Mapping . 28 2.10 Standard PCR reaction . 29 2.11 DNA Gel Electrophoresis . 29 2.12 Genetic and Physical Mapping of Mutants . 30 2.13 Mapping of Mutant Loci with Next-generation Sequencing . 30 2.14 Sequencing of Candidate Genes . 32 2.15 Screening of Homozygous or Heterozygous T-DNA Mutants . 32 2.16 Confirmation of Candidate Gene (Allelism Test) . 33 2.17 Statistical Analysis . 33 CHAPTER 3: RESULTS . 35 3.1 Screening of F2 Mapping Population. 35 3.2 Bulked-Segregant Analysis (BSA) to Locate the Mutation Site in Chromosome . 35 3.3 Next-generation Mapping by Genome Sequencing . 38 3.4 Mutation is Localized in GA2 Gene . 46 3.4. 1 Identification of Candidate Genes . 46 3.4. 2 Genotyping by DNA Sequencing of the Candidate Gene (ga2) in All 25 F2 Individuals Used for NGM . 47 3.4. 3 sdg8-2 Background is Not Involved in gm11 Phenotype . 51 3.5 Genetic Evidence Confirming that Mutation in ga2 is the Cause of the Germination Mutant Phenotype of gm11. 52 vi 3.5. 1 gm11 is Allelic to ga2. 52 3.5. 2 Allelism Test . 57 3.6 Application of Exogenous GA Rescues Phenotypes of ga2 Mutant. 62 CHAPTER 4: DISCUSSION AND CONCLUSION . 65 REFERENCES. 72 APPENDIX I. License Agreement for Figure One and Two. 82 APPENDIX II. License Agreement for Figure Five . 84 CURRICULUM VITAE. 86
BioCD : An Efficient Algorithm for Self-collision and Distance Computation between Highly Articulated Molecular Models

This paper describes an efficient approach to (self) collision detection and distance computations for complex articulated mechanisms such as molecular chains. The proposed algorithm called BioCD is particularly designed for samplingbased motion planning on molecular models described by long kinematic chains possibly including cycles. The algorithm considers that the kinematic chain is structured into a number of rigid groups articulated by preselected degrees of freedom. This structuring is exploited by a two-level spatially-adapted hierarchy. The proposed algorithm is not limited to particular kinematic topologies and allows good collision detection times. BioCD is also tailored to deal with the particularities imposed by the molecular context on collision detection. Experimental results show the effectiveness of the proposed approach which is able to process thousands of (self) collision tests per second on flexible protein models with up to hundreds of degrees of freedom.
Comparative Analysis of Host Utilization Thresholds in Cloud Datacenters

Computing provides various servicers to its users just over an internet connection. For this the Cloud providers have to set up large datacenters which consists of number of computing nodes. These datacenters consumes a huge amount of energy. This not only leads to higher expenses but it also causes harmful effects on our environments. Thus, the attention is shifting towards energy efficiency in Clouds. This is done by optimizing VM allocation and migrating them to some other hosts. For VM migration various utilization thresholds are required. In this paper, we have done a comparative study of some of these utilization thresholds. The simulation in done on CloudSim toolkit. It has been concluded that for the same configurations of datacenter and for the same workload IQR utilization thresholds gives the best results for energy efficiency as well as lowest SLA violations. Keywordscomputing, Datacenters, Virtual Machines, VM migrations
Amplitude Normalization of Dendritic EPSPs at the Soma of Binaural Coincidence Detector Neurons of the Medial Superior Olive

The principal neurons of the medial superior olive (MSO) encode cues for horizontal sound localization through comparisons of the relative timing of EPSPs. To understand how the timing and amplitude of EPSPs are maintained during propagation in the dendrites, we made dendritic and somatic whole-cell recordings from MSO principal neurons in brain slices from Mongolian gerbils. In somatic recordings, EPSP amplitudes were largely uniform following minimal stimulation of excitatory synapses at visualized locations along the dendrites. Similar results were obtained when excitatory synaptic transmission was eliminated in a low calcium solution and then restored at specific dendritic sites by pairing input stimulation and focal application of a higher calcium solution. We performed dual dendritic and somatic whole-cell recordings to measure spontaneous EPSPs using a dual-channel template-matching algorithm to separate out those events initiated at or distal to the dendritic recording location. Local dendritic spontaneous EPSP amplitudes increased sharply in the dendrite with distance from the soma (length constant, 53.6 μm), but their attenuation during propagation resulted in a uniform amplitude of ∼0.2 mV at the soma. The amplitude gradient of dendritic EPSPs was also apparent in responses to injections of identical simulated excitatory synaptic currents in the dendrites. Compartmental models support the view that these results extensively reflect the influence of dendritic cable properties. With relatively few excitatory axons innervating MSO neurons, the normalization of dendritic EPSPs at the soma would increase the importance of input timing versus location during the processing of interaural time difference cues in vivo. SIGNIFICANCE STATEMENT The neurons of the medial superior olive analyze cues for sound localization by detecting the coincidence of binaural excitatory synaptic inputs distributed along the dendrites. Previous studies have shown that dendritic voltages undergo severe attenuation as they propagate to the soma, potentially reducing the influence of distal inputs. However, using dendritic and somatic patch recordings, we found that dendritic EPSP amplitude increased with distance from the soma, compensating for dendritic attenuation and normalizing EPSP amplitude at the soma. Much of this normalization reflected the influence of dendritic morphology. As different combinations of presynaptic axons may be active during consecutive cycles of sound stimuli, somatic EPSP normalization renders spike initiation more sensitive to synapse timing than dendritic location.
Information Flow Control for Event Handling and the DOM in Web Browsers

Web browsers routinely handle private information. Owing to a lax security model, browsers and JavaScript in particular, are easy targets for leaking sensitive data. Prior work has extensively studied information flow control (IFC) as a mechanism for securing browsers. However, two central aspects of web browsers - the Document Object Model (DOM) and the event handling mechanism - have so far evaded thorough scrutiny in the context of IFC. This paper advances the state-of-the-art in this regard. Based on standard specifications and the code of an actual browser engine, we build formal models of both the DOM (up to Level 3) and the event handling loop of a typical browser, enhance the models with fine-grained taints and checks for IFC, prove our enhancements sound and test our ideas through an instrumentation of WebKit, an in-production browser engine. In doing so, we observe several channels for information leak that arise due to subtleties of the event loop and its interaction with the DOM.
Digital Watermarking using Image Fusion Method

With the growing popularity of digital Medias through the WWW, intellectual property needs copyright protection, prevention of illegal copying and verification of content integrity. The new data hiding techniques need to be developed that satisfy the requirements of imperceptibility, robustness, capacity, or data hiding rate and security of the hidden data in order to keep the distribution of digital multimedia work both profitable for the document owner and reliable for the customer. Previous research (01) indicates that significant portions of the host image, e.g. the low frequency components, have to be modified in order to embed the information in a reliable and robust way. This led to the development of watermarking schemes embedding in the frequency domain. The wavelet transform has the number of advantages over other transforms such as the DCT that can be exploited for both, image compression and watermarking applications. Therefore it is imperative to consider the wavelet transform domain for watermarking applications.
A Model for Structuring and Reusing Security Requirements Sources and Security Requirements

Various security requirements sources need to be incorporated when developing security requirements. A challenge for teams developing security requirements is to identify and structure relevant sources, to satisfy compliancerelated obligations, and to identify and properly address relevant threats, weaknesses and vulnerabilities. In this paper, we present a generic model which can be used for structuring and reusing security requirements sources and security requirements, to improve the efficiency of security requirements engineering and to achieve a desired ‘baseline’ security level and completeness of security requirements. The model supports security requirements engineering in general but can also be applied for continuous security requirements engineering in order to analyze and evaluate the influence of changes in software or the environment on security requirements and the overall software and system security. Elements of the model and their interdependencies are described, and observations on important aspects when applying this model in an organization are provided.
Analog integrated lock-in amplifier for optical sensors

Our work that is described here advances a topology for an analog integrated lock-in amplifier (LIA) for optical sensors. We developed a prototype for application in a plastic optical fiber sensor to measure refractive index in an aqueous medium. The design aims at the integration of all system components in silicon and the generation of a low power and low voltage circuit, to allow its use in portable applications. The amplifier topology features differential inputs and outputs to mitigate problems with noise and interference. The prototype trans-impedance amplifier occupies 0.374 mm2 in a 0.18 μm CMOS process.
Entry on Export Markets and Firm-Level Performance Growth: Intra-Industrial Convergence or Divergence?

This paper investigates theoretically and empirically the endogenous investment decision of firms conditioning on export decision. It shows that theoretically, whatever the form of preferences, firms that start exporting invest more and grow more than the others. However, it is shown that when preferences are CES, within each category of firms (domestic and switchers), initial productivity and investment are strategic complements, inducing intra-industrial divergence. On the contrary, when preferences are quadratic, initial productivity and investment are strategic substitutes: less productive firms invest more and grow more than the others, inducing intra-industrial convergence. Empirical results on French data support the predictions of the quadratic preferences model.
ON METHANE EMISSION IN THE ARCTIC

The problem of modern climate change is still often considered only as a problem of direct anthropogenic influence emission of greenhouse gases from human activity. However, more than half of methane sources are determined by various natural mechanisms. Many of these mechanisms have positive temperature dependence. This fact may be the reason for the increase in emissions in the polar zone, which is caused by the positive feedback between the warming processes and methane emissions. Our analysis of land, sea and satellite measurements of methane fluxes in the Arctic showed that an increase in methane emissions from such buried methane reservoirs as methane gas hydrates, permafrost zones, lakes and northern marshes can significantly exceed the power of anthropogenic sources. At the same time, the contribution of the greenhouse effect from the work of positive feedbacks may turn out to be comparable or even more than anthropogenic contribution in the arctic zone.
Identification of long-term concept-symbols among citations: Can documents be clustered in terms of common intellectual histories?

"Citation classics" are not only highly cited, but also cited during several decades. We test whether the peaks in the spectrograms generated by Reference Publication Years Spectroscopy (RPYS) indicate such long-term impact by comparing across RPYS for subsequent time intervals. Multi-RPYS enables us to distinguish between short-term citation peaks at the research front that decay within ten years versus historically constitutive (long-term) citations that function as concept symbols (Small, 1978). Using these constitutive citations, one is able to cluster document sets (e.g., journals) in terms of intellectually shared histories. We test this premise by clustering 40 journals in the Web of Science Category of Information and Library Science using multi-RPYS. It follows that RPYS can not only be used for retrieving roots of sets under study (cited), but also for algorithmic historiography of the citing sets. Significant references are historically rooted symbols among other citations that function as currency.
Anomaly intrusion detection in dynamic execution environments

We describe an anomaly intrusion-detection system for platforms that incorporate dynamic compilation and profiling. We call this approach "dynamic sandboxing. " By gathering information about applications' behavior usually unavailable to other anomaly intrusion-detection systems, dynamic sandboxing is able to detect anomalies at the application layer. We show our implementation in a Java Virtual Machine is both effective and efficient at stopping a backdoor and a virus, and has a low false positive rate.