Miracle-dz/UniFAR-FTUs huggingface dataset:
Architectural Extensions for Elliptic Curve Cryptography over GF ( 2 m )

We describe data path extensions for general-purpose microprocessors to accelerate the emerging public-key cryptosystem Elliptic Curve Cryptography (ECC). ECC is computationally more efficient than the popular RSA cryptosystem and, thus, is an enabling security technology for light-weight devices that are limited in compute power, memory capacity, and battery power. Elliptic curves have been standardized by NIST and SECG for fields GF (p) and GF (2m). Though both types of fields offer similar security strengths, the standards offer a choice to accommodate different implementation platforms. While arithmetic operations over fields GF (p) directly map to integer operations found in standard processors, operations over fields GF (2m) are supported rather inefficiently. We show that simple extensions of the data path suffice to efficiently support ECC over GF (2m) and to outperform ECC over GF (p). These extensions include an extended integer multiplier that also generates multiplication results for fields GF (2m) and a multiplyaccumulate instruction for efficient multiple-precision multiplications. On the 8-bit ATmega128 microprocessor running at 8 MHz we measured an execution time for a 163-bit ECC point multiplication over GF (2m) of 0.4 s with the extended multiplier and 0.29 s if, in addition, a multiply-accumulate instruction is provided. In comparison, a 1024-bit RSA private-key operation providing equivalent security strength takes 11 s.
Dual-layered file cache on cc-NUMA system

CC-NUMA is a widely adopted and deployed architecture of high performance computers. These machines are attractive for their transparent access to local and remote memory. However, the prohibitive latency gap between local and remote access deteriorates applications' performance seriously due to memory access stalls. File system cache, especially, being shared by all processes, inevitably triggers many remote accesses. To address this problem, we suggest and implement a mechanism that uses local memory to cache remote file cache, of which the main purpose is to improve data locality. Using realistic workload on a two-node cc-NUMA machine, we show that the cost of such a mechanism is as low as 0.5%, the performance can be increased 14.3% at most, and the local hit ratio can be improved as much as 40%
A Simple Permission Checking for Structural Parallel Programs

This paper presents a simplified "fractional permission'" type system for an imperative language with structured parallelism and synchronization. A permission is a linear value associated with some piece of state in a program and "fractions'' are used to distinguish reads from writes, with which we are able to check interference among parallel threads. In order to detect race conditions and deadlocks in a multithreaded program, we transform expressions and statements into action traces, then permission check all possible interleavings among traces in parallel. We show the operational semantics as well as some selected permission type rules.
The natural history of HIV infection

Purpose of reviewTo review recent published literature around three areas: long-term nonprogression/viral control; predictors of viral load set point/disease progression; and the potential impact of antiretroviral therapy (ART) in early HIV infection. Recent findingsThe natural course of untreated HIV infection varies widely with some HIV-positive individuals able to maintain high CD4 cell counts and/or suppressed viral load in the absence of ART. Although similar, the underlying mechanistic processes leading to long-term nonprogression and viral control are likely to differ. Concerted ongoing research efforts will hopefully identify host factors that are causally related to these phenotypes, thus providing opportunities for the development of novel treatment or preventive strategies. Although there is increasing evidence that initiation of ART during primary infection may prevent the immunological deterioration which would otherwise be seen in untreated HIV infection, recent studies do not address the longer term clinical benefits of ART at this very early stage. SummaryA better understanding of the relative influences of viral, host, and environmental factors on the natural course of HIV infection has the potential to identify novel targets for intervention to prevent and treat HIV-infected persons.
Fast Conditional Independence-based Bayesian Classifier

Machine Learning (ML) has become very popular within Data Mining (KDD) and Artificial Intelligence (AI) research and their applications. In the ML and KDD contexts, two main approaches can be used for inducing a Bayesian Network (BN) from data, namely, Conditional Independence (CI) and the Heuristic Search (HS). When a BN is induced for classification purposes (Bayesian Classifier - BC), it is possible to impose some specific constraints aiming at increasing the computational efficiency. In this paper a new CI based approach to induce BCs from data is proposed and two algorithms are presented. Such approach is based on the Markov Blanket concept in order to impose some constraints and optimize the traditional PC learning algorithm. Experiments performed with the ALARM, as well as other six UCI and three artificial domains revealed that the proposed approach tends to execute fewer comparison tests than the traditional PC. The experiments also show that the proposed algorithms produce competitive classification rates when compared with both, PC and Naive Bayes.
Rethinking Full-Text Search for Multi-lingual Databases

Textual fields are commonly used in databases and applications to capture details that are difficult to formalize—comments, notes, and product descriptions. With the rise of the web, users expect that databases be capable of searching these fields quickly and accurately in their native language. Fortunately, most modern database systems provide some form of full-text indexing of free text fields. However, these capabilities have yet to be combined with the simultaneous demand that databases provide support for world languages. In this paper we introduce several of the challenges for handling multilingual data and introduce a solution based on an architecture that enables flexible processing of texts based upon the properties of each text’s source language. Extending the indexing architecture, and standardizing the query capabilities, are important steps to creating the applications that will serve world markets.
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

BioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.
A Novel Predictive Technique for the MHC Class II Peptide-Binding Interaction

Antigenic peptide is presented to a T-cell receptor through the formation of a stable complex with a Major Histocompatibility Complex (MHC) molecule. Various predictive algorithms have been developed to estimate a peptide’s capacity to form a stable complex with a given MHC Class II allele, a technique integral to the strategy of vaccine design. These have previously incorporated such computational techniques as quantitative matrices and neural networks. We have developed a novel predictive technique that uses molecular modeling of predetermined crystal structures to estimate the stability of an MHC Class II peptide complex. This is the 1st structure-based technique, as previous methods have been based on binding data. ROC curves are used to quantify the accuracy of the molecular modeling technique. The novel predictive technique is found to be comparable with the best predictive software currently available.
Alcohol Gel Ingestion Among Homeless Eastern and Central Europeans in London: Assessing the Effects on Cognitive Functioning and Psychological Health

ABSTRACT Background: Intentional consumption of alcohol-based hand gels has been reported especially amongst non-UK national, alcohol dependent, homeless individuals in London. Whilst alcohol misuse is known to be associated with impaired cognitive functioning and mental health problems, the effects of additional ingestion of alcohol gel are unknown. Objectives: To explore cognitive and psychological functioning in users who intentionally ingest alcohol gel compared with ethyl-alcohol only misusers and controls. Methods: Male, Central and Eastern European alcohol only misusers, (n = 14; mean age 39 years), alcohol gel users (n = 14; mean age 43 years) and controls (n = 12; mean age 31 years) were recruited from a London Homeless Service during 2013/14. Alcohol misusers, alcohol gel users and controls were compared on the Forwards and Backwards Digit Span Test; Block Design test; Retrospective and Prospective Memory Questionnaire (PRMQ) and the Hospital and Anxiety Depression Scale (HADS). Results: Alcohol gel users performed significantly worse on the Block Design task (p < .01) and PRMQ (p < .01) relative to both alcohol only and control groups, and significantly worse on the digit span relative to controls (p = .01). Both alcohol misusing groups scored comparatively on digit span backwards (p < .01), with both groups performing significantly worse than controls. The alcohol gel group reported significantly higher levels of anxiety relative to controls (p = .02). Conclusions: Whilst there could be constitutional differences between alcohol misusers who additionally abuse alcohol gel, the findings suggest that alcohol gel ingestion may have a greater impact on psychological functioning than traditional alcohol misuse.
Creative Compartments: A Design for Future Organization

Foreword Preface Introduction Openness and Trust, Empowerment and Commitment The Blankets of Hierarchy The Size of the Clan Compartments and Communication The Creative Compartment Power and Conflict Markets and Hierarchies, Clans and Fiefs Islands and Bridges The Practice of Critique Redesigning Large Organizations Families of Compartments Widespread Change Bibliography and Further Reading Index
Identification of gene markers associated with metastasis in clear cell renal cell carcinoma

The present study aimed to screen potential target genes for the early diagnosis and treatment of early metastatic clear cell renal cell carcinoma (ccRCC) using the microarray data of early metastatic and non-metastatic ccRCC samples. The DNA microarray dataset GSE47352 was downloaded from Gene Expression Omnibus and included 4 early metastatic and 5 non-metastatic ccRCC samples. Differentially expressed genes (DEGs) were screened using the limma package. Then, pheatmap package was used to conduct two-way clustering for the DEGs. Subsequently, MAPPFinder and GenMAPP were employed separately to perform functional and pathway enrichment analysis for the DEGs. Additionally, a protein-protein interaction (PPI) network was constructed using Cytoscape, and small drug molecules were searched using Connectivity map (cmap). In total, 196 upregulated and 163 downregulated genes were identified. DEGs, including JUN, tumor necrosis factor (TNF), Ras homolog family member B (RHOB) and transforming growth factor β2 (TGFβ2) were significantly enriched in the signaling pathway of renal cell carcinoma. Furthermore, nuclear receptor subfamily 4 group A member 1 (NR4A1) was significantly enriched in the mitogen-activated protein kinase signaling pathway; in addition, laminin subunit α (LAMA) 1, LAMA2 and LAMA4 were significantly enriched in extracellular matrix-receptor interaction. JUN (degree=6) had the highest degree in the PPI network. Thapsigargin (score=−0.913) possessed the highest performance in terms of the treatment of early metastatic ccRCC. In the present study, it was discovered that certain DEGs, including JUN, TNF, RHOB, NR4A1, TGFβ2, LAMA1, LAMA2 and LAMA4 were potential target genes associated with early metastatic ccRCC. In addition, thapsigargin could be used as an efficient small drug molecule for the treatment of early metastatic ccRCC.
Relationship between male head size and mating opportunity in the harem-defence, polygynous tree weta Hemideina maori (Orthoptera: Anostostomatidae)

The most distinguishing feature of the tree weta genus Hemideina (Orthoptera: Anostostomatidae) is their cephalic weaponry, which is thought to be the result of sexual selection on males to aggressively defend groups of reproductive females. Mountain stone weta H. maori is a tree weta that shelters in cavities under flat rocks on rocky outcrops in the alpine region of the South Island. The main objectives of this study were to determine whether males with larger heads have access to greater numbers of females, and whether head size has an effect on male survival and longevity. Males with larger heads associated with larger groups of females than males with smaller heads. Male head size only accounted for 11% of the variation in mating opportunity when all rocks with females were considered, but explained 36% of the variation when only a few specific rocks that had large numbers of females were taken into account. The lower recapture rates of males in general and of small- headed males in particular, further suggested that small males intermittently retreat to small cracks or cavities within tor columns, where there are unlikely to be large female groups. Thus, larger males had access to more females than smaller males. Moreover, larger males had no detectable disadvantage in terms of daily survival and longevity. This study provides strong evidence that larger male tree weta do associate with larger harems in the wild, however, questions relating to male weaponry size and mating success will become clearer only through paternity testing of weta under natural conditions.
The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

Viral immune evasion by sequence variation is a major hindrance to HIV-1 vaccine design. To address this challenge, our group has developed a computational model, rooted in physics, that aims to predict the fitness landscape of HIV-1 proteins in order to design vaccine immunogens that lead to impaired viral fitness, thus blocking viable escape routes. Here, we advance the computational models to address previous limitations, and directly test model predictions against in vitro fitness measurements of HIV-1 strains containing multiple Gag mutations. We incorporated regularization into the model fitting procedure to address finite sampling. Further, we developed a model that accounts for the specific identity of mutant amino acids (Potts model), generalizing our previous approach (Ising model) that is unable to distinguish between different mutant amino acids. Gag mutation combinations (17 pairs, 1 triple and 25 single mutations within these) predicted to be either harmful to HIV-1 viability or fitness-neutral were introduced into HIV-1 NL4-3 by site-directed mutagenesis and replication capacities of these mutants were assayed in vitro. The predicted and measured fitness of the corresponding mutants for the original Ising model (r = −0.74, p = 3.6×10−6) are strongly correlated, and this was further strengthened in the regularized Ising model (r = −0.83, p = 3.7×10−12). Performance of the Potts model (r = −0.73, p = 9.7×10−9) was similar to that of the Ising model, indicating that the binary approximation is sufficient for capturing fitness effects of common mutants at sites of low amino acid diversity. However, we show that the Potts model is expected to improve predictive power for more variable proteins. Overall, our results support the ability of the computational models to robustly predict the relative fitness of mutant viral strains, and indicate the potential value of this approach for understanding viral immune evasion, and harnessing this knowledge for immunogen design.
Questions of Travel: Postmodern Discourses of Displacement

Contemporary theory is replete with metaphors of travel - displacement, diaspora, borders, exile, migration, nomadism, homelessness, and tourism to name a few. In Questions of Travel, Caren Kaplan explores the various metaphoric uses of travel and displacement in literary and feminist theory, traces the political implications of this "travelling theory," and shows how various discourses of displacement link, rather than separate, modernism and postmodernism. Addressing a wide range of writers, including Paul Fussell, Edward Said, James Clifford, Gilles Deleuze, Jean Baudrillard, Gayatri Spivak, Edward Soja, Doreen Massey, Chandra Mohanty, and Adrienne Rich, Kaplan demonstrates that symbols and metaphors of travel are used in ways that obscure key differences of power between nationalities, classes, races, and genders. Neither rejecting nor dismissing the powerful testimony of individual experiences of modern exile or displacement, Kaplan asks how mystified metaphors of travel might be avoided. With a focus on theory's colonial discourses, she reveals how these metaphors continue to operate in the seemingly liberatory critical zones of poststructuralism and feminist theory. The book concludes with a critique of the politics of location as a form of essentialist identity politics and calls for new feminist geographies of place and displacement. An important and timely intervention into contemporary theoretical debates, Questions of Travel will be of interest to scholars in a wide variety of disciplines, including literary criticism, cultural studies, feminist theory, colonial and postcolonial studies, geography, anthropology, and sociology.
Decreased Plasma Tissue Factor Pathway Inhibitor Levels in Patients with Thrombotic Thrombocytopenic Purpura

Summary We measured plasma levels of tissue factor (TF) and tissue factor pathway inhibitor (TFPI) in patients with thrombotic thrombocytopenic purpura (TTP) and disseminated intravascular coagulation (DIC) to examine the relationship between TFPI and vascular endothelial cell injury. TF antigen was detected in the plasma of healthy volunteers, and the levels were significantly increased in the patients with DIC, but decreased slightly in those with TTP. Plasma TFPI levels were significantly decreased in patients with TTP compared with those in healthy volunteers. The concentration of plasma thrombomodulin (TM) antigen was significantly higher in those with TTP than in normal volunteers. One month after treatment, TTP patients showed a significant decrease in plasma TM levels, and a significant increase, in plasma TFPI levels, but plasma levels of TF antigen were not significantly increased. As plasma TFPI/TF ratio was significantly increased after treatment, the hypercoagulable state was therefore improved after treatment. There was no significant difference in plasma TF and TFPI levels between those who achieved complete remission (CR) and those who died. However, plasma TM levels were significantly higher in those who died than in those who achieved CR. Plasma TFPI levels might reflect injury of vascular endothelial cells as do plasma TM levels, and decreased plasma TFPI/TF ratio and vascular endothelial cell injuries might play causative roles in TTP.
Scalable sampling methodology for logic simulation: Reduced-Ordered Monte Carlo

Monte Carlo (MC) simulation plays a key role in EDA as the gold standard against which heuristics are measured. It is also an important stand-alone technique for statistics-based tasks like power estimation and reliability analysis. Accurate simulation requires large sample sets and long runtimes, which can be hard to achieve with conventional MC. We propose an approach called Reduced-Ordered Monte Carlo (ROMC), which improves simulation efficiency, while still producing accurate results. ROMC takes advantage of the (partial) redundancy inherent in digital signals. It prioritizes input signals based on their observability at the outputs, and combines inputs based on a compatibility property that enables them to share samples. Experimental results are presented which demonstrate that the ROMC methodology can decrease simulation runtime by several orders of magnitude.
Separating hippocampal mapsA

The place elds of hippocampal cells in old animals sometimes change when an animal is removed from and then returned to an environment Barnes et al., 1997]. The ensemble correlation between two sequential visits to the same environment shows a strong bimodality for old animals (near 0, indicative of remapping, and greater than 0.7, indicative of a similar representation between experiences), but a strong unimodality for young animals (greater than 0.7, indicative of a similar representation between experiences). One explanation for this is the multi-map hypothesis in which multiple maps are encoded in the hippocampus: old animals may sometimes be returning to the wrong map. A theory proposed by Samsonovich and McNaughton (1997) suggests that the Barnes et al. experiment implies that the maps are pre-wired in the CA3 region of hippocampus. Here, we ooer an alternative explanation in which orthogonalization properties in the dentate gyrus (DG) region of hippocampus interact with errors in self-localization (reset of the path integrator on re-entry into the environment) to produce the bimodality.
Farthest-point optimized point sets with maximized minimum distance

Efficient sampling often relies on irregular point sets that uniformly cover the sample space. We present a flexible and simple optimization strategy for such point sets. It is based on the idea of increasing the mutual distances by successively moving each point to the "farthest point," i.e., the location that has the maximum distance from the rest of the point set. We present two iterative algorithms based on this strategy. The first is our main algorithm which distributes points in the plane. Our experimental results show that the resulting distributions have almost optimal blue noise properties and are highly suitable for image plane sampling. The second is a variant of the main algorithm that partitions any point set into equally sized subsets, each with large mutual distances; the resulting partitionings yield improved results in more general integration problems such as those occurring in physically based rendering.