Miracle-dz/UniFAR-FTUs huggingface dataset:
LER: Least-Error-Rate Replacement Algorithm for Emerging STT-RAM Caches

Spin-transfer-torque RAMs (STT-RAMs) are the most promising technology for replacing Static RAMs (SRAMs) in on-chip caches. One of the major problems in STT-RAMs is the high error rate due to stochastic switching in write operations. Cache replacement algorithms have a major role in the number of write operations into the caches. Due to this fact, it is necessary to redesign cache replacement algorithms to consider the new challenges of STT-RAM caches. This paper proposes a cache replacement algorithm, which is called least error rate (LER), to reduce the error rate in L2 caches. The main idea is to place the incoming block in a line that incurs the minimum error rate in write operation. This is done by comparing the contents of the incoming block with lines in a cache set. Compared with Least Recently Used (LRU) algorithm, LER reduces the error rate by 2× with about 1.4% and 3.6% performance and dynamic energy consumption overheads, respectively. Moreover, LER imposes no area overhead to system.
Application of arithmetic coding for electric power disturbance data compression with wavelet packet enhancement

In this paper, an application of wavelet packet-enhanced arithmetic coding to compress the electric power disturbance data is proposed. In the proposed method, the wavelet packet is first applied in anticipation that the disturbance signal can be optimally decomposed into higher frequency components and lower frequency ones on a best wavelet basis. Then, the arithmetic coding approach is utilized to reduce the redundancy of data encoding, thereby lowering down the cost related with data storage and transmission. This integrated method has been tested on different scenarios and the results are compared with other published techniques.
The 56-kilodalton major protein antigen of Rickettsia tsutsugamushi: molecular cloning and sequence analysis of the sta56 gene and precise identification of a strain-specific epitope

Lasting immunity against Rickettsia tsutsugamushi, the causative agent of scrub typhus fever, has been demonstrated to be strain specific. Two protein antigens of 110 and 56 kilodaltons (kDa) have been shown to exhibit strain-specific epitopes. The 56-kDa scrub typhus antigen (Sta56) is an abundant outer membrane protein of R. tsutsugamushi and is an antigen often recognized by humans infected with this obligate intracellular bacterium. In this study the complete gene encoding Sta56 (strain Karp) was cloned into pBR322 on a 2.3-kilobase genomic HindIII DNA fragment and the complete 56-kDa polypeptide was expressed in Escherichia coli. DNA sequence analysis of the 2.3-kilobase HindIII fragment revealed an open reading frame large enough to encode a 56-kDa polypeptide. A putative signal sequence was identified at the deduced amino terminus of the Sta56 polypeptide, and pulse-chase analysis of maxicells labeled with [35S]methionine demonstrated that a higher-molecular-weight precursor matures into the 56-kDa polypeptide. Epitope scanning analysis with synthetic peptides derived from the deduced amino acid sequence identified an octapeptide (located from amino acid residues 117 to 124) that was reactive with a Karp strain-specific monoclonal antibody (K13F88A). Other epitopes recognized by different monoclonal antibodies, including another Karp strain-specific monoclone (K1E106), were localized to different regions of the protein based on their reactivities with lambda gt11 recombinants expressing various portions of the sta56 gene.
Numerical Algorithms for Polynomial Optimisation Problems with Applications

A tensor is a multi-dimensional array of real (or complex) numbers. It is a natural extension of a matrix with many applications in science and engineering fields. Over the last few years, there have been significant developments on the spectral theory of tensors. Many important characterizations of nonnegative matrices have been extended to some special classes of tensors such as nonnegative tensors. In particular, the Perron-Frobenius theory and the minmax theorem have been extended from nonnegative matrices to the class of nonnegative tensors. Furthermore, the eigenvalue problem for matrices has been generalized to high order tensors. Eigenvalue problems of nonnegative tensors find applications or links with higher order Markov chains, spectral hypergraph theory, and the quantum entanglement. In Chapter 3, we present a fast algorithm for computing the spectral radii of symmetric nonnegative tensors. In particular, by this proposed algorithm we are able to obtain the spectral radii of weakly reducible symmetric nonnegative tensors without requiring the partition of the tensors. As we know, it is very costly to determine the partition for large-size weakly reducible tensors. Numerical results are reported to show that the proposed algorithm in Chapter 3 is efficient and also it is able to compute the spectral radii of large-size tensors. As an application, we present an algorithm for testing the positive definiteness of Ztensors. By this algorithm, it is guaranteed to determine the positive definiteness for any Z-tensor. In Chapter 4, we study homogenous polynomial optimization problems under the unit sphere constraints. These optimization problems have wide applications e.g., in signal and image processing, high order statistics, and computer vision. Since these problems are, in general, NP-hard, we are interested in studying approximation algorithms. In particular, we propose some polynomial-time approximation algorithms with new approximation bounds. In addition, based on these approximation algorithms, some efficient algorithms are presented and numerical results are reported to show the efficiency of our proposed algorithms. In Chapter 5, we study the maximum clique problem (MCP) which is a well-known example of combinatorial optimization. The MCP has been proven to be NP-complete, so it is difficult to determine the global solutions
Emergence of Individual HIV-Specific CD8 T Cell Responses during Primary HIV-1 Infection Can Determine Long-Term Disease Outcome

ABSTRACT Events during primary HIV-1 infection have been shown to be critical for the subsequent rate of disease progression. Early control of viral replication, resolution of clinical symptoms and development of a viral set point have been associated with the emergence of HIV-specific CD8 T cell responses. Here we assessed which particular HIV-specific CD8 T cell responses contribute to long-term control of HIV-1. A total of 620 individuals with primary HIV-1 infection were screened by gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay for HLA class I-restricted, epitope-specific CD8 T cell responses using optimally defined epitopes approximately 2 months after initial presentation. The cohort was predominantly male (97%) and Caucasian (83%) (Fiebig stages II/III [n = 157], IV [n = 64], V [n = 286], and VI [n = 88] and Fiebig stage not determined [n = 25]). Longitudinal viral loads, CD4 count, and time to ART were collected for all patients. We observed strong associations between viral load at baseline (initial viremia) and the established early viral set points (P < 0.0001). Both were significantly associated with HLA class I genotypes (P = 0.0009). While neither the breadth nor the magnitude of HIV-specific CD8 T cell responses showed an influence on the early viral set point, a broader HIV-specific CD8 T cell response targeting epitopes within HIV-1 Gag during primary HIV-1 infection was associated with slower disease progression. Moreover, the induction of certain HIV-specific CD8 T cell responses—but not others—significantly influenced the time to ART initiation. Individual epitope-specific CD8 T cell responses contribute significantly to HIV-1 disease control, demonstrating that the specificity of the initial HIV-specific CD8 T cell response rather than the restricting HLA class I molecule alone is a critical determinant of antiviral function. IMPORTANCE Understanding which factors are involved in the control of HIV-1 infection is critical for the design of therapeutic strategies for patients living with HIV/AIDS. Here, using a cohort of over 600 individuals with acute and early HIV-1 infection, we assessed in unprecedented detail the individual contribution of epitope-specific CD8 T cell responses directed against HIV-1 to control of viremia and their impact on the overall course of disease progression.
Two New Single‐Nucleotide Polymorphisms in the COL1A1 Upstream Regulatory Region and Their Relationship to Bone Mineral Density

Single‐nucleotide polymorphisms (SNPs) in regulatory regions of candidate genes may determine variability in bone mineral density (BMD) because they may be responsible for differences in levels of a gene product in response to external signals. Under this hypothesis, we scanned an 800‐base pair (bp) region within the COL1A1 promoter, known to harbor cis elements important for in vivo expression, and we found two new polymorphisms: −1663indelT and −1997 G/T. The G to T transversion at −1997 was associated with lumbar spine BMD (p = 0.015) when tested in a cohort of 256 postmenopausal women after adjusting by age, body weight, and years since menopause; a lower degree of association was detected also for femoral neck BMD in a subgroup of 146 women in univariate analysis and after adjusting by age (p = 0.044). The polymorphism −1663indelT, which corresponds to a deletion of a T in a tract of eight T residues (−1670 to −1663), did not show significant association with BMD. Interestingly, −1663indelT is in strong linkage disequilibrium (LD) with the previously described Sp1 polymorphism of intron 1, which in this study did not show association with BMD either. Significant interaction between −1997 G/T and −1663indelT (p = 0.019), and between −1997 G/T and Sp1 (p = 0.045) was observed also. Individuals heterozygous for the three polymorphisms showed the highest mean BMD value. Gel retardation assays showed that oligonucleotides containing either the −1663 or the −1997 polymorphic sites specifically bind primary osteoblast nuclear proteins. We named these binding sites as PCOL1 and PCOL2, respectively. In summary, this study describes two new SNPs in the COL1A1 promoter, which may affect bone mass determination.
Microsatellite Markers for Characterization of Native and Introduced Populations of Plasmopara viticola, the Causal Agent of Grapevine Downy Mildew

ABSTRACT We reported 31 microsatellite markers that have been developed from microsatellite-enriched and direct shotgun pyrosequencing libraries of Plasmopara viticola, the causal agent of grapevine downy mildew. These markers were optimized for population genetics applications and used to characterize 96 P. viticola isolates from three European and three North American populations.
RNA Interference Directed against Poly(ADP-Ribose) Polymerase 1 Efficiently Suppresses Human Immunodeficiency Virus Type 1 Replication in Human Cells

ABSTRACT We established small interfering RNA (siRNA) directed against poly(ADP-ribose) polymerase 1 (PARP-1) that effectively reduces the expression of PARP-1 in two human cell lines. Established siRNA against PARP-1 significantly suppressed human immunodeficiency virus type 1 (HIV-1) replication, as well as the activation of the integrated HIV-1 long terminal repeat promoter. These results indicate that PARP-1 is required for efficient HIV-1 replication in human cells. We propose that PARP-1 may serve as a cellular target for RNA interference-mediated gene silencing to inhibit HIV-1 replication.
HISTOSPLINE METHOD IN NONPARAMETRIC REGRESSION MODELS WITH APPLICATION TO CLUSTERED/LONGITUDINAL DATA

Kernel and smoothing methods for nonparametric function and curve estimation have been particularly successful in "standard" settings, where function values are observed subject to independent errors. However, when aspects of the function are known parametrically, or where the sampling scheme has significant structure, it can be quite difficult to adapt standard methods in such a way that they retain good statistical performance and continue to enjoy easy computability and good numerical properties. In particular, when using local linear modeling, it is often awkward to both respect the sampling scheme and produce an estimator with good variance properties without resorting to iterative methods: a good case in point is longitudinal and clustered data. In this paper we suggest a simple approach to overcome these problems. Using a histospline technique we convert a problem in the continuum to one that is governed by only a finite number of parameters, and which is often explicitly solvable. The simple expedient of running a local linear smoother through the histospline produces a function estimator which achieves optimal nonparametric properties, and the "raw" histospline-based estimator of the semiparametric component itself attains optimal semiparametric performance. The function estimator can be used in its own right, or as the starting value for an iterative scheme based on a different approach to inference.
The Ca 2 Homeostasis Defects in a pgm 2 Strain of Saccharomyces cerevisiae Are Caused by Excessive Vacuolar Ca 2 Uptake Mediated by the Ca 2-ATPase Pmc 1 p *

Loss of the major isoform of phosphoglucomutase (PGM) causes an accumulation of glucose 1-phosphate when yeast cells are grown with galactose as the carbon and energy source. Remarkably, the pgm2 strain also exhibits a severe imbalance in intracellular Ca homeostasis when grown under these conditions. In the present study, we examined how the pgm2 mutation alters yeast Ca homeostasis in greater detail. We found that a shift from glucose to galactose as the carbon source resulted in a 2-fold increase in the rate of cellular Ca uptake in wild-type cells, whereas Ca uptake increased 8-fold in the pgm2 mutant. Disruption of the PMC1 gene, which encodes the vacuolar Ca -ATPase Pmc1p, suppressed the Ca -related phenotypes observed in the pgm2 strain. This suggests that excessive vacuolar Ca uptake is tightly coupled to these defects in Ca homeostasis. An in vitro assay designed to measure Ca sequestration into intracellular compartments confirmed that the pgm2 mutant contained a higher level of Pmc1p-dependent Ca transport activity than the wild-type strain. We found that this increased rate of vacuolar Ca uptake also coincided with a large induction of the unfolded protein response in the pgm2 mutant, suggesting that Ca uptake into the endoplasmic reticulum compartment was reduced. These results indicate that the excessive Ca uptake and accumulation previously shown to be associated with the pgm2 mutation are due to a severe imbalance in the distribution of cellular Ca into different intracellular compartments.
Design of a hyper-environment for tracing object-oriented requirements

﻿ Change is inevitable and unending in developing large, complex systems. Changes to requirements arise not only from changes in the social context of the system, but also from improved understanding of constraints and tradeoffs as system development proceeds. How to trace software requirements is the problem addressed by this thesis. We present a solution for requirements tracing in the context of object-oriented software development. Our solution consists of a traceability model and a tool to automate the tracing. TOOR, the tool to implement the model, uses a project specification written in FOOPS, a general purpose object-oriented language with specification capabilities, to set up the environment in which a project is carried out. The project specification defines the trace units and traces as objects and relations, respectively. The evolution of objects from requirements sources to requirements to design to code, and generally to any object taking part in the process is dealt with in a uniform way in TOOR: classes are declared for each kind of object we wish to control, and relations are defined between them. TOOR uses regular expressions to provide a selective tracing mode : the actual configuration of objects and relations is considered as a text and regular expressions are used to retrieve parts of the configuration matching the pattern described by them. TOOR enhances the flexibility of regular expressions by extending the pattern matching procedure by providing different ways of specifying how an object or relation is to be matched. Other modes of tracing in TOOR are the interactive tracing through modules and the non-guided tracing through several browsing mechanisms. TOOR modules are used to structure projects by providing hierarchical scopes for objects used in a project development. The tracing mechanisms of TOOR can use the project structure to order searches or to provide boundaries for searching. Browsing objects provides additional flexibility in situations where little information of what has to be traced is possessed and hyper-media features address the need to re-interpret data usually encoded in different formats. The user-definable features of a project specification provides much of the flexibility necessary for effective use of a software tracing tool. Also, the integration of regular expression tracing with other forms of tracing such as browsing and interactive tracing makes TOOK an extremely versatile tool. The user can select the more appropriate form of tracing depending on context and can switch from one form to another as convenient.
The current status and future of theranostic Copper-64 radiopharmaceuticals

Copper-64 was produced in large scales and high specific activities in late 1990s’ using compact cyclotrons based by 64Ni(p,n)64Cu reaction and many radiopharmaceuticals developed since then by various groups based on interesting physicochemical and nuclear properties of the radionuclide. The unique emission of beta particles as well as positron particles offers a spectacular real therapeutic/diagnostic (“Theranostic”) radionuclide in nuclear medicine. Although the development of copper-64 radiopharmaceuticals continued with a slower rate in 2010s’ due to availability of 68Ga-tracers, however recent advances in application of therapeutic doses of 64Cu has emerged a new trend in the radiopharmaceutical development based on coppe-64. In this review, recent advances in the copper-64 theranostic radiopharmaceuticals including introduction of new chelating groups with enhanced stability as well as radiolabelling conditions as well as application of simple CuCl2 radiopharmaceutical as areal theranostic agent in human subjects are summarized. A proposed strategy for development of peptide based copper-64 radiopharmaceuticals with high and low dose therapeutic applications has been suggested.
A Copula Approach for Detecting Prognostic Genes Associated With Survival Outcome in Microarray Studies

Summary A challenging and crucial issue in clinical studies in cancer involving gene microarray experiments is the discovery, among a large number of genes, of a relatively small panel of genes whose elements are associated with a relevant clinical outcome variable such as time‐to‐death or time‐to‐recurrence of disease. A semiparametric approach, using dependence functions known as copulas, is considered to quantify and estimate the pairwise association between the outcome and each gene expression. These time‐to‐event type endpoints are typically subject to censoring as not all events are realized at the time of the analysis. Furthermore, given that the total number of genes is typically large, it is imperative to control a relevant error rate in any gene discovery procedure. The proposed method addresses the two aforementioned issues by direct incorporation of the censoring mechanism and by appropriate statistical adjustment for multiplicity. The performance of the proposed method is studied through simulation and illustrated with an application using a case study in lung cancer.
Isolation and identification of selenite reducing archaea from Tuz (salt) Lake In Turkey

In this study, Tuz lake brine samples were investigated for isolation and identification of selenite resistant halophilic prokaryotes. Among the 20 strains of extremely halophilic Bacteria and Archaea, a Gram negative rod designated as strain 106, showed high capacity in the resistance to selenite (25 mM) under aerobic conditions. Phenotypic characterizations and phylogenetic analyses based on 16S rDNA sequence comparison indicated that strain 106 was Halorubrum xinjiangense. The ability of strain 106 to deposite selenium‐containing particles were investigated by Transmission Electron Microscopy (TEM). Electron micrographs shows intact cells after selenite reduction and large amounts of selenium‐containing particles are present in the culture medium indicating that strain 106 is able to efficiently transport elemental selenium out of the cell.
DART: Revolutionizing Logistics Planning

For the last two hundred years, the dominant force in international affairs has been the nation state. Most wars have been caused by attempts to create or expand such states. In contrast, over the next twenty years, the risks to international stability seem as likely to come from other factors: ethnic and religious conflict; population and environmental pressures; competition for scarce resources; drugs, terrorism and crime . the consequences of initially local crises may spread dramatically throughout an ever more interdependent world. Planning and implementing an effective military response to a crisis is a highly complex problem. There are a host of interdependent factors to consider from the high-level strategic planning of an evolving crisis situation, to the nuts and bolts of moving people, machinery, and supplies.
Evaluation of DNA barcoding and identification of new haplomorphs in Canadian deerflies and horseflies

This paper reports the first tests of the suitability of the standardized mitochondrial cytochrome c oxidase subunit I (COI) barcoding system for the identification of Canadian deerflies and horseflies. Two additional mitochondrial molecular markers were used to determine whether unambiguous species recognition in tabanids can be achieved. Our 332 Canadian tabanid samples yielded 650 sequences from five genera and 42 species. Standard COI barcodes demonstrated a strong A + T bias (mean 68.1%), especially at third codon positions (mean 93.0%). Our preliminary test of this system showed that the standard COI barcode worked well for Canadian Tabanidae: the target DNA can be easily recovered from small amounts of insect tissue and aligned for all tabanid taxa. Each tabanid species possessed distinctive sets of COI haplotypes which discriminated well among species. Average conspecific Kimura two‐parameter (K2P) divergence (0.49%) was 12 times lower than the average divergence within species. Both the neighbour‐joining and the Bayesian methods produced trees with identical monophyletic species groups. Two species, Chrysops dawsoni Philip and Chrysops montanus Osten Sacken (Diptera: Tabanidae), showed relatively deep intraspecific sequence divergences (∼10 times the average) for all three mitochondrial gene regions analysed. We suggest provisional differentiation of Ch. montanus into two haplotypes, namely, Ch. montanus haplomorph 1 and Ch. montanus haplomorph 2, both defined by their molecular sequences and by newly discovered differences in structural features near their ocelli.