gebhart/patrepeval huggingface dataset:
Extended abstract: The butterfly PUF protecting IP on every FPGA (2008)

IP protection of hardware designs is the most important requirement for many FPGA IP vendors. To this end, various solutions have been proposed by FPGA manufacturers based on the idea of bitstream encryption. An alternative solution was advocated in (E. Simpson and P. Schaumont, 2006). Simpson and Schaumont proposed a new approach based on physical unclonable functions (PUFs) for IP protection on FPGAs. PUFs are a unique class of physical systems that extract secrets from complex physical characteristics of the integrated circuits which along with the properties of unclonability provide a highly secure means of generating volatile secret keys for cryptographic operations. However, the first practical PUF on an FPGA was proposed only later in (J. Guajardo et al., 2007) based on the startup values of embedded SRAM memories which are intrinsic in some of the current FPGAs. The disadvantage of these intrinsic SRAM PUFs is that not all FPGAs support uninitialized SRAM memory. In this paper, we propose a new PUF structure called the butterfly PUF that can be used on all types of FPGAs. We also present experimental results showing their identification and key generation capabilities.
Chemical Manipulation of Hsp70 ATPase Activity Regulates Tau Stability (2009)

Alzheimer's disease and other tauopathies have recently been clustered with a group of nervous system disorders termed protein misfolding diseases. The common element established between these disorders is their requirement for processing by the chaperone complex. It is now clear that the individual components of the chaperone system, such as Hsp70 and Hsp90, exist in an intricate signaling network that exerts pleiotropic effects on a host of substrates. Therefore, we have endeavored to identify new compounds that can specifically regulate individual components of the chaperone family. Here, we hypothesized that chemical manipulation of Hsp70 ATPase activity, a target that has not previously been pursued, could illuminate a new pathway toward chaperone-based therapies. Using a newly developed high-throughput screening system, we identified inhibitors and activators of Hsp70 enzymatic activity. Inhibitors led to rapid proteasome-dependent tau degradation in a cell-based model. Conversely, Hsp70 activators preserved tau levels in the same system. Hsp70 inhibition did not result in general protein degradation, nor did it induce a heat shock response. We also found that inhibiting Hsp70 ATPase activity after increasing its expression levels facilitated tau degradation at lower doses, suggesting that we can combine genetic and pharmacologic manipulation of Hsp70 to control the fate of bound substrates. Disease relevance of this strategy was further established when tau levels were rapidly and substantially reduced in brain tissue from tau transgenic mice. These findings reveal an entirely novel path toward therapeutic intervention of tauopathies by inhibition of the previously untargeted ATPase activity of Hsp70.
Polymerization of cyclic monomers, 4. Synthesis and radical polymerization of bi‐ and trifunctional 2‐vinylcyclopropanes (1997)

Abstract Multifunctional 2‐vinylcyclopropanes were synthesized by esterification of the 1‐methoxycarbonyl‐2‐vinylcyclopropane‐1‐carboxylic acid with ethylene glycol, 1,1,1‐trimethylolpropane or 1,4‐cyclohexanediol in the presence of 1,3‐dicyclohexylcarbodiimide (DCC). The structure of the new vinylcyclopropanes was confirmed by elemental analysis, IR, 1 H NMR and 13 C NMR spectroscopy. The radical polymerization of the 2‐vinylcyclopropanes in bulk with 2,2′‐azoisobutyronitrile (AIBN) results in transparent crosslinked polymers. The polymerization of the liquid monomers is accompanied by a low shrinkage in volume.
Expression of bone morphogenetic protein 2 in breast cancer cells inhibits hypoxic cell death (2005)

BMP-2 is involved in the fetal and postnatal development of the mammary gland but has also been detected in breast cancer cells. To clarify the biological role of BMP-2 in breast cancer, we used the human breast cancer cell line MCF-7. Incubation with BMP-2 under serum-free conditions induced activation of the mitogen activated protein kinases (MAPKs) ERK1/2 and the basic helix-loop-helix transcription factors Id-1, proteins that can protect from apoptosis. Stably transfected MCF-7 cells overexpressing BMP-2 revealed significantly increased resistance to hypoxia-induced apoptosis compared to empty vector controls. Cytoplasmic BMP-2/4 protein expression was detected in carcinoma cells of 81 samples of invasive breast cancer in contrast to adjacent normal mammary epithelial cells. BMP-2/4 expression did not correlate with common prognostic parameters and was not associated with relapse-free or overall survival. We conclude that BMP-2/4 expression is reactivated in invasive breast cancer and part of an autocrine/paracrine mechanism rescuing malignant cells from hypoxic cell death via activation of the MAPK and Id-1 pathway.
Novel ceramic bone replacement material CeraBall® seeded with human mesenchymal stem cells (2009)

CeraBall scaffolds show good biocompatibility in vitro for hMSCs. This opens the way for in vivo applications.
Mutations in the mariner transposase: The D,D(35)E consensus sequence is nonfunctional (1997)

Genetic analysis of eukaryote transposases and comparison with their prokaryote counterparts have been greatly hindered by difficulty in isolating mutations. We describe a simple eye-color screen that facilitates isolation and analysis of mutations in the mariner transposase in Drosophila melanogaster. Use of ethyl methanesulfonate and site-directed mutagenesis has identified 18 residues that are critical for in vivo excision of a target mariner element. When the mutations were examined in heterozygous mutant/nonmutant genotypes, more than half of the mutant transposase proteins were found to reduce the activity of the wild-type transposase, as assayed by the frequency of germline excision of a target element. Remarkably, transposase function is obliterated when the D,D(34)D acidic, ion-binding domain is replaced with the consensus sequence D,D(34)E found in the nematode Tc1 transposase and in many other transposases in the superfamily. A number of mutations strongly complement wild-type transposase in a dominant-negative manner, suggestive of subunit interactions in the excision reaction; these mutations are located in a small region that includes part of the D,D(34)D motif. Transposase function also is eliminated by a mutation in the inferred initiation codon and by a mutation in a putative nuclear localization signal.
Computational nanotechnology with carbon nanotubes and fullerenes (2001)

The authors envision computational nanotechnology's role in developing the next generation of multifunctional materials and molecular-scale electronic and computing devices, sensors, actuators, and machines. They briefly review computational techniques and provide a few recent examples derived from computer simulations of carbon nanotube-based molecular nanotechnology. The four core areas are: molecular-scale, ultralightweight, extremely strong, functional or smart materials; molecular-scale or nanoscale electronics with possibilities for quantum computing; molecular-scale sensors or actuators; and molecular machines or motors with synthetic materials. The underlying molecular-scale building blocks in all four areas are fullerenes and carbon nanotube-based molecular materials. Only the different aspects of their physical, chemical, mechanical, and electronic properties create the many applications possible with these materials in vastly different areas.
Redirected touching: The effect of warping space on task performance (2012)

Passive haptic feedback in virtual environments is compelling, but changes to virtual objects require changes to associated real objects. Recent work suggests that by leveraging visual dominance, virtual space can be warped to map a variety of virtual objects onto a single real object. However, it is unknown whether users can interact with a warped virtual space as effectively as with an unwarped one. We present a study in which we measured task performance using the Fitts'-law-based ISO 9241-9 multidirectional tapping task. With a few caveats, results suggest that for certain tasks, warped virtual objects are no worse than unwarped virtual objects. We also present preliminary exploratory data on how well people can detect discrepancies due to space-warping.
Molecular Transport Junctions: Clearing Mists (2007)

Abstract Recent progress in the measurement and modeling of transport in molecular junctions has been very significant. Tunnel transport in the Landauer–Imry regime is now broadly understood for several systems, although a detailed understanding of the role of contact geometry is still required. We overview some clear indications from recent research and note the quite reasonable agreement between measured and calculated conductance in metal–molecule–metal junctions. The next challenge lies in obtaining a microscopic understanding of charge transport that involves reduction or oxidation of molecules.
Higher harmonics imaging in tapping-mode atomic-force microscopy (2003)

In tapping-mode atomic-force microscopy usually amplitude and phase of the cantilever motion are acquired. These signals are related to the fundamental oscillation frequency neglecting information at higher frequencies. However, the nonlinear contact between tip and sample induces higher frequency vibrations that are harmonics of the fundamental. In order to recover the available information the full tip motion has to be analyzed. The higher harmonics can be employed for image formation. A setup that consists of two independently operated lock-in amplifiers is used to detect higher harmonics in the dynamic atomic-force microscopy signal. Higher harmonic imaging proves to be useful to monitor the imaging conditions in tapping mode and can be applied for nanoscale imaging with a material contrast.
Dual-band high-linearity variable-gain low-noise amplifiers for wireless applications (2003)

A typical dual-band RF receiver front-end architecture is shown. The low-noise amplifiers (LNA) should have low noise figures to increase sensitivity of the receivers, and high linearity to prevent interference from undesired adjacent-channel signals. To increase the dynamic range of the receivers and to reduce linearity required of the downconversion mixers, the LNAs are required to provide variable gain. When the RF input power is large, the gain of the LNA should be reduced.
Comparative Efficiency and Safety of Pharmacological Approaches to the Management of Obesity (2011)

Obesity and overweight are reaching global epidemic proportions affecting more than 1.1 billion individuals worldwide. Excess weight is associated with an increased mortality, chronic morbidity (including type 2 diabetes, arterial hypertension, cardiovascular diseases, and certain cancers), decreased quality of life, and considerable health care costs (1).

Antiobesity drugs work through different mechanisms either in the central nervous system (CNS) or in the peripheral tissues. These mechanisms include: 1 ) suppression of food intake in the CNS, 2 ) decreased gut absorption of nutrients, and 3 ) increased energy expenditure or oxidation of nutrients. The efficacy of antiobesity drugs should be evaluated by their ability to reduce fat stores (preferentially visceral adipose tissue), maintain weight loss, diminish obesity-related health risks, and thus decrease morbidity and mortality, and improve quality of life. An ideal antiobesity drug should be administered orally, devoid of major side effects, and distributed at affordable price. Treatment with antiobesity drugs can be considered in obese patients who failed to achieve a sufficient weight loss to a program of lifestyle change, diet, and physical activity. However, the drug treatment of obesity should be an integral part of the comprehensive obesity treatment program that includes diet, exercise, and cognitive behavioral intervention (2,3). Treatment of obesity should be individually tailored taking into account the degree and character of obesity, age, sex, and the presence of comorbidities (4). Drugs used for the treatment of obesity in the past were associated with serious side effects (psycho-stimulatory, depression, addiction, cardio-excitatory effects, pulmonary hypertension, and valve disease). Antiobesity agents that possess cardio-excitatory and psycho-stimulatory effects (e.g., phentermine, ephedrine, and caffeine mixture) have still been available for the short-term use in some countries (<3 months).

Currently, only two drugs, sibutramine and orlistat, are prescribed for long-term administration. The most important trial evaluating the long-term efficacy of …
Lys63-Linked Polyubiquitination of IRAK-1 Is Required for Interleukin-1 Receptor- and Toll-Like Receptor-Mediated NF-κB Activation (2008)

Stimulation through the interleukin-1 receptor (IL-1R) and some Toll-like receptors (TLRs) induces ubiquitination of TRAF6 and IRAK-1, signaling components required for NF-kappaB and mitogen-activated protein kinase activation. Here we show that although TRAF6 and IRAK-1 acquired Lys63 (K63)-linked polyubiquitin chains upon IL-1 stimulation, only ubiquitinated IRAK-1 bound NEMO, the regulatory subunit of IkappaB kinase (IKK). The sites of IRAK-1 ubiquitination were mapped to Lys134 and Lys180, and arginine substitution of these residues impaired IL-1R/TLR-mediated IRAK-1 ubiquitination, NEMO binding, and NF-kappaB activation. K63-linked ubiquitination of IRAK-1 required enzymatically active TRAF6, indicating that it is the physiologically relevant E3. Thus, K63-linked polyubiquitination of proximal signaling proteins is a common mechanism used by diverse innate immune receptors for recruiting IKK and activating NF-kappaB.
Distribution of Neutral Endopeptidase Activity in Human Blood Leukocytes (1991)

We investigated the distribution of neutral endopeptidase (NEP; EC 3.4.24.11) activity, a possible regulatory enzyme for neuropeptide-induced leukocyte activations, in each cell type of human blood leukocytes. The NEP activity assessed by an NEP inhibitor phosphoramidon-sensitive Met5-enkephalin degrading activity was present in neutrophils and the common acute lymphoblastic leukemia antigen (CALLA)-positive leukemic cells (59 pmol/min/10(6) cells and 62 pmol/min/10(6) cells, respectively); however, the NEP activity was virtually absent in lymphocytes, monocytes, eosinophils, basophils, CALLA-negative leukemic cells, or a promyelocytic cell line HL-60. The enzymatic activity was characterized as NEP on the basis of the values of kinetic parameters (Km = 61 microM, Kcat = 1,692 min-1, and Kcat/Km = 28 min-1 microM-1) and the values of IC50 of two NEP inhibitors phosphoramidon and thiorphan (7.4 nM and 8.4 nM, respectively). The distribution of NEP detected immunocytochemically using anti-NEP monoclonal antibodies was also found to be parallel with the distribution of NEP activity among peripheral blood leukocytes.
3-D transformations of images in scanline order (1980)

Currerntly texture mapping onto projections of 3-D surfaces is time consuming and subject to considerable aliasing errors. Usually the procedure is to perform some inverse mapping from the area of the pixel onto the surface texture. It is difficult to do this correctly. There is an alternate approach where the texture surface is transformed as a 2-D image until it conforms to a projection of a polygon placed arbitrarily in 3-space. The great advantage of this approach is that the 2-D transformation can be decomposed into two simple transforms, one in horizontal and the other in vertical scanline order. horizontal scanline order, Sophisticated light calculation is also time consuming and difficult to calculate correctly on projected polygons. Instead of calculating the lighting based on the position of the polygon, lights, and eye, the lights and eye can be transformed to a corresponding position for a unit square which we can consider to be a canonical polygon. After this canonical polygon is correctly textured and shaded it can be easily conformed to the projection of the 3-D surface.
Endo-F3 Glycosynthase Mutants Enable Chemoenzymatic Synthesis of Core-fucosylated Triantennary Complex Type Glycopeptides and Glycoproteins (2016)

Chemoenzymatic synthesis is emerging as a promising approach to the synthesis of homogeneous glycopeptides and glycoproteins highly demanded for functional glycomics studies, but its generality relies on the availability of a range of enzymes with high catalytic efficiency and well defined substrate specificity. We describe in this paper the discovery of glycosynthase mutants derived from Elizabethkingia meningoseptica endoglycosidase F3 (Endo-F3) of the GH18 family, which are devoid of the inherent hydrolytic activity but are able to take glycan oxazolines for transglycosylation. Notably, the Endo-F3 D165A and D165Q mutants demonstrated high acceptorsubstrate specificity toward α1,6-fucosyl-GlcNAc-Asn or α1,6-fucosyl-GlcNAc-polypeptide in transglycosylation, enabling a highly convergent synthesis of core-fucosylated, complex CD52 glycopeptide antigen. The Endo-F3 mutants were able to use both bi- and triantennary glycan oxazolines as substrates for transglycosylation, in contrast to previously reported endoglycosidases derived from Endo-S, Endo-M, Endo-D, and Endo-A mutants that could not recognize triantennary N-glycans. Using rituximab as a model system, we have further demonstrated that the Endo-F3 mutants are highly efficient for glycosylation remodeling of monoclonal antibodies to produce homogeneous intact antibody glycoforms. Interestingly, the new triantennary glycan glycoform of antibody showed much higher affinity for galectin-3 than that of the commercial antibody. The Endo-F3 mutants represent the first endoglycosidase-based glycosynthases capable of transferring triantennary complex N-glycans, which would be very useful for glycoprotein synthesis and glycosylation remodeling of antibodies.
A Prospective Study of Plasma C-Peptide and Colorectal Cancer Risk in Men (2004)

Elevated insulin production, as reflected by elevated concentrations of plasma C-peptide, may predict the risk of developing colorectal cancer, independently of BMI, factors related to insulin resistance, or levels of IGF-I and IGFBP-3.
Antirenin immunization versus angiotensin converting enzyme inhibition in rats. (1990)

The effects of specific active immunization against renin were compared with those of chronic angiotensin converting enzyme (ACE) inhibition. Male spontaneously hypertensive rats (SHR) were immunized (SHR-I) (n = 10) against pure murine renin (four injections of 30 micrograms/kg s.c.) or received (SHR-P) (n = 11) a converting enzyme inhibitor (perindopril, 2 mg/kg/day per os for 4 weeks). Sham-immunized SHR (SHR-S) (n = 12) and normotensive Wistar-Kyoto (WKY-S) (n = 12) rats served as controls. At 15 weeks of age, 24-hour average blood pressure was obtained in freely moving rats using intra-aortic pressure recording with computer analysis. Antirenin immunization induced high circulating titers of antibodies, a fall in plasma renin activity (-95%), and urinary excretion of mineralocorticoids. Perindopril abolished the pressor response to angiotensin I, whereas plasma ACE was only partly (-56%) decreased. It also increased plasma renin activity and did not alter the urinary excretion of steroids. Both immunization and perindopril allowed the blood pressure of SHR to return to the level of WKY-S rats and reduced the left ventricular weight. These decreases were associated with an elevated sympathetic nervous system activity as indicated by increases in the urinary excretion of catecholamines and their metabolites. It is conclude that, apart from an unaltered steroid synthesis, most of the cardiovascular effects of chronic ACE inhibition are similar to those of antirenin immunization, thus indicating that blockade of the circulating and renal renin-angiotensin system accounts for most of the effects of ACE inhibitors.
Allogeneic hematopoietic stem cell transplantation for multiple myeloma (2012)

High rates of acute and chronic graft-versus-host disease currently limit the implementation of nonmyeloablative allo HSCT. Novel approaches are required so that patients with myeloma can undergo allo HSCT before resistance develops to standard drug combinations.
Asymptotische Darstellungen der hypergeometrischen Funktionen für grosse Werte eines Parameters (1982)

Asymptotic expansions of the hypergeometric function F(a, b, c; z) for |b| \to \infty where a, c, z are fixed complex numbers given in well-known tables (e.g. Bateman/Erdélyi: Higher transcendental functions I. New York 1953) are incorrect. In the present paper asymptotic representations of the hypergeomctric function F for a (complex) \to \infty are derived where b, c (c \neq 0, -1, -2,\dots) and z (z \neq 0 , |Arg (1- z) | &lt; \pi are fixed complex numbers. By change of a and b appropriate asymptotic representations of F for |b| \to \infty are obtained.
Translational control of oskar generates Short OSK, the isoform that induces pole plasm assembly (1995)

At the posterior pole of the Drosophila oocyte, oskar induces a tightly localized assembly of pole plasm. This spatial restriction of oskar activity has been thought to be achieved by the localization of oskar mRNA, since mislocalization of the RNA to the anterior induces anterior pole plasm. However, ectopic pole plasm does not form in mutant ovaries where oskar mRNA is not localized, suggesting that the unlocalized mRNA is inactive. As a first step towards understanding how oskar activity is restricted to the posterior pole, we analyzed oskar translation in wild type and mutants. We show that the targeting of oskar activity to the posterior pole involves two steps of spatial restriction, cytoskeleton-dependent localization of the mRNA and localization-dependent translation. Furthermore, our experiments demonstrate that two isoforms of Oskar protein are produced by alternative start codon usage. The short isoform, which is translated from the second in-frame AUG of the mRNA, has full oskar activity. Finally, we show that when oskar RNA is localized, accumulation of Oskar protein requires the functions of vasa and tudor, as well as oskar itself, suggesting a positive feedback mechanism in the induction of pole plasm by oskar.
Prediction of fetal D status from maternal plasma: introduction of a new noninvasive fetalRHDgenotyping service (2002)

Combination of the sensitivity of real-time PCR with an improved RHD typing assay to distinguish RHD from RHDpsi enables highly accurate prediction of fetal D status from maternal plasma. This has resulted in the implementation of a clinical noninvasive fetal RHD genotyping service.