gebhart/patrepeval huggingface dataset:
How Secure Are FPGAs in Cryptographic Applications (2003)

Abstract. The use of FPGAs for cryptographic applications is highly attractive for a variety of reasons but at the same time there are many open issues related to the general security of FPGAs. This contribution attempts to provide a state-of-the-art description of this topic. First, the advantages of reconfigurable hardware for cryptographic applications are listed. Second, potential security problems of FPGAs are described in detail, followed by a proposal of a some countermeasure. Third, a list of open research problems is provided. Even though there have been many contributions dealing with the algorithmic aspects of cryptographic schemes implemented on FPGAs, this contribution appears to be the first comprehensive treatment of system and security aspects.
A Universal File Server (1980)

A file server is a utility provided in a computer connected via a local communications network to a number of other computer. File servers exist to preserve material for the benefit of client machines or systems. It is desirable for a file server to be able to support multiple file directory and access management systems, so that the designer of a client system retains the freedom to design the system that best suits him. For example, he may wish to use the rile server to support a predefimed directory structure or as a swapping disk. The paper explores the dedgn issues associated with such a file server and proposes some solutions.
A systematic approach for comprehensive T-cell epitope discovery using peptide libraries (2005)

Implementations of our algorithms in R or Perl are available at http://bioinf.wehi.edu.au/folders/immunol.
Stochastic System Identification for Operational Modal Analysis: A Review (2001)

This paper reviews stochastic system identification methods that have been used to estimate the modal parameters of vibrating structures in operational conditions. It is found that many classical input-output methods have an output-only counterpart. For instance, the Complex Mode Indication Function (CMIF) can be applied both to Frequency Response Functions and output power and cross spectra. The Polyreference Time Domain (PTD) method applied to impulse responses is similar to the Instrumental Variable (IV) method applied to output covariances. The Eigensystem Realization Algorithm (ERA) is equivalent to stochastic subspace identification.
Air separation, flue gas compression and purification units for oxy-coal combustion systems (2011)

Air Liquide (AL) has been actively involved in the development of oxy-coal technologies for CO2 capture from power plants for almost 10 years. Large systems for oxygen production and flue gas purification are required for this technology. Air Liquide has been a leader in building large Air Separation Units (ASUs) and more developments have been performed to customize the air separation process for coal-fired power plants. Air Liquide is also actively involved in developing processes for purification of flue gas from oxy-coal combustion systems for enhanced oil recovery applications as well as sequestration in saline aquifers. Through optimization of the overall oxy-coal combustion system, it has been possible to identify key advantages of this solution: minimal efficiency loss associated with CO2 capture (less than 6 pts penalty on HHV efficiency compared to no capture), near zero emission, energy storage, high CO2 purity and high CO2 recovery capability.
Comparative Evaluation of a 5-Day Hershberger Assay Utilizing Mature Male Rats and a Pubertal Male Assay for Detection of Flutamide's Antiandrogenic Activity (2000)

A 5-day Hershberger assay utilizing mature male rats and a pubertal male assay were evaluated for the ability to detect antiandrogenic compounds such as flutamide, an androgen receptor antagonist. Six days after the operation, implantation with two silicon capsules containing testosterone (T) (30 mg/capsule) in castrated rats provided the ventral prostate and seminal vesicle weights as well as serum T and luteinizing hormone (LH) levels equivalent to those of the controls (non-castrated, non-implanted rats). Castrated rats implanted with two T-capsules (6 rats/dose) were treated by gavage for 5 days with vehicle (0.5% carboxymethylcellulose) or flutamide (0.15, 0.6, 2.5, or 10 mg/kg/day). Flutamide produced significant decreases in weights of the seminal vesicles and the levator ani plus bulbocavernosus muscles (> or =0.6 mg/kg/day) and ventral prostate (> or =2.5 mg/kg/day), and an increase in serum LH levels (> or =2.5 mg/kg/day), but no changes in serum T levels. When age-matched intact male rats were treated with 10-mg/kg/day flutamide, a significant increase in serum T levels was observed concomitant with a tendency of increased LH. The organ weights were also decreased; however, the changes were less than those in the castrated, T-implanted rats. Immature intact male rats (10 rats/dose) were treated for 20 days with flutamide (0, 0.15, 0.6, 2.5, or 10 mg/kg/day). Flutamide produced significant decreases in weights of the seminal vesicles, ventral prostate, and levator ani plus bulbocavernosus muscles at 2.5 and 10 mg/kg/day. Serum LH levels, but not T levels, were increased at 10 mg/kg/day. Statistical significance of some of these changes was not observed in the 6 animals/dose examined. Our findings support that the Hershberger assay, in the current conditions, is the most sensitive among the assays examined and a useful short-term screening method for the detection of antiandrogenic compounds.
Luminescence of colloidal cadmium sulfide particles in acetonitrile and acetonitrile/water mixtures (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLuminescence of colloidal cadmium sulfide particles in acetonitrile and acetonitrile/water mixturesJeremy J. Ramsden, Stephen E. Webber, and Michael GraetzelCite this: J. Phys. Chem. 1985, 89, 13, 2740–2743Publication Date (Print):June 1, 1985Publication History Published online1 May 2002Published inissue 1 June 1985https://doi.org/10.1021/j100259a007Request reuse permissionsArticle Views404Altmetric-Citations123LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (457 KB) Get e-Alerts
Targeted inhibition of transcription elongation in cells mediated by triplex-forming oligonucleotides (2000)

Triple-helix-forming oligonucleotides (TFOs) bind in the major groove of double-stranded DNA at oligopyrimidine small middle dotoligopurine sequences and therefore are candidate molecules for artificial gene regulation, in vitro and in vivo. We recently have described oligonucleotide analogues containing N3'-P5' phosphoramidate (np) linkages that exhibited efficient inhibition of transcription elongation in vitro. In the present work we provide conclusive evidence that np-modified TFOs targeted to the HIV-1 polypurine tract (PPT) sequence can inhibit transcriptional elongation in cells, either in transient or stable expression systems. The same constructs were used in transient expression assays (target sequence on transfected plasmid) and in the generation of stable cell lines (target sequence integrated into cellular chromosomes). In both cases the only distinguishable feature between the cellular systems is the presence of an insert containing the wild-type PPT/HIV-1 sequence, a mutated version with two mismatches, or the absence of the insert altogether. The inhibitory action induced by np-TFOs was restricted to the cellular systems containing the complementary wild-type PPT/HIV-1 target, and consequently can be attributed only to a triple-helix-mediated mechanism. As a part of this study we also have applied an imaging technique to quantitatively investigate the dynamics of TFO-mediated specific gene silencing in single cells.
The establishment of two paclitaxel‐resistant prostate cancer cell lines and the mechanisms of paclitaxel resistance with two cell lines (2007)

Our data will provide molecular mechanisms of paclitaxel-resistance and be useful for screening target genes to diagnose paclitaxel sensitivity.
ChemInform Abstract: 2‐C‐NITROMETHYL AND 2‐C‐AMINOMETHYL DERIVATIVES OF D‐RIBOSE. PREPARATION OF 2′‐C‐NITROMETHYLURIDINES (1977)

Abstract Das Benzoat (I) wird durch saure Hydro1yse(Amberlite IR‐1 20 in (II) übergeführt, das zur Ribofuranose (IIIa) oxidiert wird.
Synthesis of the Ezomycin Nucleoside Disaccharide (2000)

[equation--see text] A protected ezomycin octosyl nucleoside was glycosylated at O-6' with a protected ezoaminuroic acid donor to afford, following several functional group modifications, the title compound 1 ( identical with 4-desamino-4-oxoezomycin A(2)).
Microtubule Assembly in the Absence of Added Nucleotides (1973)

Microtubule assembly is enhanced by the addition of 1 M sucrose or 4 M glycerol to the reassembly mixture. Tubulin can be purified from guinea pig brain readily and in good yield by two cycles of assembly in glycerol-containing solutions. The tubules assembled in glycerol and sucrose are more stable than tubules formed in the absence of these compounds. Assembly occurs in glycerol or sucrose in the absence of ATP or GTP, but is greatly accelarated by their presence.
Adaptive coding of monochrome and color images (1977)

An efficient adaptive encoding technique using a new implementation of the Fast Discrete Cosine Transform (FDCT) for bandwidth compression of monochrome and color images is described. Practical system application is attained by maintaining a balance between complexity of implementation and performance. FDCT sub-blocks are sorted into four classes according to level of image activity, measured by the total ac energy within each sub-block. Adaptivity is provided by distributing bits between classes, favoring higher levels of activity over lower levels. Excellent performance is demonstrated in terms of mean square error and direct comparison of original and reconstructed images. Results are presented for both noiseless and noisy transmission at a total rate of 1 bit and 0.5 bit per pixel for a monochrome image and for a total rate of 2 bits and 1 bit per pixel for a color image. In every case the total bit rate includes all overhead required for image reconstruction and bit protection.
Exploring the molecular basis for variability among patients with Becker muscular dystrophy: dystrophin gene and protein studies. (1991)

Becker muscular dystrophy (BMD) often results from in-frame mutations of the dystrophin gene that allow production of an altered but partially functional protein. To address potential structure-function relationships for the various domains of dystrophin, we examined both the dystrophin gene and protein in 68 patients with abnormal dystrophin. Eighty-six percent of BMD patients with dystrophin of altered size have deletions or duplications, and the observed sizes of dystrophin fit well with predictions based on DNA data. Deletions within the amino-terminal domain I tended to result in low levels of dystrophin and a more severe phenotype. The phenotypes of patients with deletions or duplications in the central rod domain were more variable. This region can be divided into three portions based on differences in clinical presentations of patients. Deletions around exons 4553 were most common and generally caused typical BMD; however, phenotypic variability among patients with similar mutations suggests that epigenetic and/or environmental factors play an important role in determining the clinical progression. In contrast, deletions or duplications in the proximal portion of this domain tended to cause severe cramps and myalgia. Finally, loss of the middle of this region probably causes a very mild phenotype, as only one such patient was found and his only symptom was elevated serum creatine phosphokinase levels.
Accurate and Automatic Noise Figure Measurements with Standard Equipment (1980)

Noise figure measures the amount of noise a receiver or a component adds to a system. Minimizing such noise, because it obscures low-level signals, is an important concern in most of today's microwave systems. Noise figure measurements are necessary at the device level, the component level and the system level. They are necessary during design, manufacture and maintenance. Yet noise measurements have been fraught with non-repeatability. If, for example, a vendor and his customer are to independently measure noise figure so they agree within 0.2 dB, they each must usually use a specially calibrated noise source and tediously and manually remove several insidious effects that must otherwise be accepted as measurement errors. Even then, they often go through a time-consuming and expensive period of exchanging components and measurement equipment to achieve repeatability from system to system.
Diazotizable arylamine cellulose papers for the coupling and hybridization of nucleic acids (1982)

We describe the synthesis of a family of arylamine-substituted papers which can be diazotized and coupled with nucleic acids. The synthesis is simple and uses readily obtainable starting materials. A partial characterization of the nucleic acid binding activity is reported, as well as a demonstration of the utility of the activated paper for the detection of electrophoretically separated RNA by blot transfer and hybridization.
<title>New compression paradigms in JPEG 2000</title> (2000)

The JPEG2000 still image compression standard has adopted a new compression paradigm: 'Encode once, decode many.' JPEG2000 architecture allows the codestream to be decoded differently for different application needs. The codestream can be decoded to produce lossless and lossy images, specific spatial regions of the image or images with different quality and resolution. The syntax contains pointers and length fields which allow relevant coded data to be identified without the entropy coder or transforms. Consequently, the codestream can be 'parsed' to create different codestreams without transcoding. For example, such parsing operation can create a new codestream which contains a lower resolution image (e.g. thumbnail) of the original codestream. If a codestream is produced appropriately, it can also be converted to codestreams of lower quality images, or images containing only a specific spatial region. This feature is very useful for many applications, especially on the internet.
Relative importance of temporal envelope and fine structure in lexical-tone perception (L) (2003)

The relative importance of temporal envelope and fine structure in speech and music perception was investigated by Smith et al. [Nature (London) 416, 87–90 (2002)] using “auditory chimera” in which the envelope from one sound was paired with the fine structure of another. Smith et al. found that, when 4 to 16 frequency bands were used, recognition of English speech was dominated by the envelope, whereas recognition of melody was dominated by the fine structure. In the present study, Mandarin Chinese monosyllables were divided into 4, 8, or 16 frequency bands and the fine structure and envelope of one tone pattern were exchanged with those of another tone pattern of the same monosyllable. Five normal-hearing native Mandarin Chinese speakers completed a four-alternative forced-choice tone-identification task. In the vast majority of trials, subjects based their identification of the monosyllables on the fine structure rather than the envelope. Thus, the relative importance of envelope and fine structure for lexical-tone perception resembled that for melody recognition rather than that for English speech recognition. Delivering fine-structure information in cochlear implant stimulation could be particularly beneficial for lexical-tone perception.
Mapping replicational sites in the eucaryotic cell nucleus. (1989)

We have used fluorescent microscopy to map DNA replication sites in the interphase cell nucleus after incorporation of biotinylated dUTP into permeabilized PtK-1 kangaroo kidney or 3T3 mouse fibroblast cells. Discrete replication granules were found distributed throughout the nuclear interior and along the periphery. Three distinct patterns of replication sites in relationship to chromatin domains in the cell nucleus and the period of S phase were detected and termed type I (early to mid S), type II (mid to late S) and type III (late S). Similar patterns were seen with in vivo replicated DNA using antibodies to 5-bromodeoxyuridine. Extraction of the permeabilized cells with DNase I and 0.2 M ammonium sulfate revealed a striking maintenance of these replication granules and their distinct intranuclear arrangements with the remaining nuclear matrix structures despite the removal of greater than 90% of the total nuclear DNA. The in situ prepared nuclear matrix structures also incorporated biotinylated dUTP into replication granules that were indistinguishable from those detected within the intact nucleus.
Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor (2008)

Cellular senescence suppresses cancer by arresting cell proliferation, essentially permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the use of antibody arrays to provide a quantitative assessment of factors secreted by senescent cells. We show that human cells induced to senesce by genotoxic stress secrete myriad factors associated with inflammation and malignancy. This senescence-associated secretory phenotype (SASP) developed slowly over several days and only after DNA damage of sufficient magnitude to induce senescence. Remarkably similar SASPs developed in normal fibroblasts, normal epithelial cells, and epithelial tumor cells after genotoxic stress in culture, and in epithelial tumor cells in vivo after treatment of prostate cancer patients with DNA-damaging chemotherapy. In cultured premalignant epithelial cells, SASPs induced an epithelial-mesenchyme transition and invasiveness, hallmarks of malignancy, by a paracrine mechanism that depended largely on the SASP factors interleukin (IL)-6 and IL-8. Strikingly, two manipulations markedly amplified, and accelerated development of, the SASPs: oncogenic RAS expression, which causes genotoxic stress and senescence in normal cells, and functional loss of the p53 tumor suppressor protein. Both loss of p53 and gain of oncogenic RAS also exacerbated the promalignant paracrine activities of the SASPs. Our findings define a central feature of genotoxic stress-induced senescence. Moreover, they suggest a cell-nonautonomous mechanism by which p53 can restrain, and oncogenic RAS can promote, the development of age-related cancer by altering the tissue microenvironment.
Structure, substrate specificity and functional relatedness to other members of a large superfamily of enzymes (2006)

Our knowledge of the structure and function of alkaline phosphatases has increased greatly in recent years. The crystal structure of the human placental isozyme has enabled us to probe salient features of the mammalian enzymes that differ from those of the bacterial enzymes. The availability of knockout mice deficient in each of the murine alkaline phosphatase isozymes has also given deep insights into their in vivo role. This has been particularly true for probing the biological role of bone alkaline phosphatase during skeletal mineralization. Due to space constraints this mini-review focuses exclusively on structural and functional features of mammalian alkaline phosphatases as identified by crystallography and probed by site-directed mutagenesis and kinetic analysis. An emphasis is also placed on the substrate specificity of alkaline phosphatases, their catalytic properties as phosphohydrolases as well as phosphodiesterases and their structural and functional relatedness to a large superfamily of enzymes that includes nucleotide pyrophosphatase/phosphodiesterase. Abbreviations: ADP – adenosine diphosphate; AMP – adenosine monophosphate; AP – alkaline phosphatase; ATP – adenosine triphosphate; cAMP – cyclic AMP; ECAP – Escherichia coli AP; GCAP – germ cell alkaline phosphatase; GPI – glycosylphosphatidylinositol; IAP – intestinal alkaline phosphatase; iPGM – cofactor-independent phosphoglycerate mutase; kcat – catalytic rate constant; Ki – inhibition constant; Km – Michaelis constant; NPP1 – nucleosidetriphosphate pyrophosphohydrolase-1; Pi – inorganic phosphate; PLAP – placental alkaline phosphatase; PLP – pyridoxal-5-phosphate; pNPP – p-nitrophenylphosphate; PPi – inorganic pyrophosphate; TNAP – tissue-nonspecific alkaline phosphatase; Vmax – maximal velocity; Wt – wild-type
Macrophage migration inhibitory factor covalently complexed with phenethyl isothiocyanate (2012)

Macrophage migration inhibitory factor is irreversibly inhibited via covalent modification by phenethyl isothiocyanate, a naturally occurring compound with anti-inflammatory and anticancer properties. The structure of the modified protein obtained from X-ray diffraction data to 1.64 Å resolution is presented. The inhibitor sits within a deep hydrophobic pocket between subunits of the homotrimer and is highly ordered. The secondary structure of macrophage migratory inhibitory factor is unchanged by this modification, but there are significant rearrangements, including of the side-chain position of Tyr37 and the main chain of residues 31-34. These changes may explain the decreased binding of the modified protein to the receptor CD74. Together with the pocket, the areas of conformational change define specific targets for the design of more selective and potent inhibitors as potential therapeutics.
Loss of heterozygosity for chromosomes 16q and 1p in Wilms' tumors predicts an adverse outcome. (1994)

We have prospectively analyzed Wilms' tumors from 232 patients registered on the National Wilms' Tumor Study for loss of heterozygosity (LOH) on chromosomes 11p, 16q, and 1p. These chromosomal aberrations were found in 70 (33%), 35 (17%), and 21 (12%) of the informative cases, respectively. LOH for two of these regions occurred in only 25 cases, and only one tumor harbored LOH at all three sites. There was no statistically significant association between LOH at any of the three regions and either the stage or histological classification of the tumor. Patients with tumor-specific LOH for chromosome 16q had relapse rates 3.3 times higher (P = 0.01) and mortality rates 12 times higher (P < 0.01) than patients without LOH for chromosome 16q. These differences remained when adjusted for histology or for stage. Patients with LOH for chromosome 1p had relapse and mortality rates three times higher than those for patients without LOH for chromosome 1p, but these results were not statistically significant. In contrast, LOH for chromosome 11p had no effect on measures of outcome. These molecular markers may serve to further stratify Wilms' tumor patients into biologically favorable and unfavorable subgroups, allowing continued use of the clinical trial mechanism in the study of Wilms' tumor.