gebhart/patrepeval huggingface dataset:
On Constructing Universal One-Way Hash Functions from Arbitrary One-Way Functions. (2005)

A fundamental result in cryptography is that a digital signature scheme can be constructed from an arbitrary one-way function. A proof of this somewhat surprising statement follows from two results: first, Naor and Yung defined the notion of universal one-way hash functions and showed that the existence of such hash functions implies the existence of secure digital signature schemes. Subsequently, Rompel showed that universal one-way hash functions could be constructed from arbitrary one-way functions. Unfortunately, despite the importance of the result, a complete proof of the latter claim has never been published. In fact, a careful reading of Rompel’s original conference publication reveals a number of errors in many of his arguments which have (seemingly) never been addressed. We provide here what is — as far as we know — the first complete write-up of Rompel’s proof that universal one-way hash functions can be constructed from arbitrary one-way functions. ∗Dept. of Computer Science, University of Maryland. {jkatz,cykoo}@cs.umd.edu †This research was supported in part by NSF CAREER award #0447075.
Retracted: An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus (2003)

Transient gene expression is a fast, flexible and reproducible approach to high-level expression of useful proteins. In plants, recombinant strains of Agrobacterium tumefaciens can be used for transient expression of genes that have been inserted into the T-DNA region of the bacterial Ti plasmid. A bacterial culture is vacuum-infiltrated into leaves, and upon T-DNA transfer, there is ectopic expression of the gene of interest in the plant cells. However, the utility of the system is limited because the ectopic protein expression ceases after 2-3 days. Here, we show that post-transcriptional gene silencing (PTGS) is a major cause for this lack of efficiency. We describe a system based on co-expression of a viral-encoded suppressor of gene silencing, the p19 protein of tomato bushy stunt virus (TBSV), that prevents the onset of PTGS in the infiltrated tissues and allows high level of transient expression. Expression of a range of proteins was enhanced 50-folds or more in the presence of p19 so that protein purification could be achieved from as little as 100 mg of infiltrated leaf material. The effect of p19 was not saturated in cells that had received up to four individual T-DNAs and persisted until leaf senescence. Because of its simplicity and rapidity, we anticipate that the p19-enhanced expression system will have value in industrial production as well as a research tool for isolation and biochemical characterisation of a broad range of proteins without the need for the time-consuming regeneration of stably transformed plants.
Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein protein interaction (2010)

A structure-based approach is described for predicting the effects of amino acid substitutions on protein function. Structures were predicted using a homology modelling method. Folding and binding energy differences between wild-type and mutant structures were computed to quantitatively assess the effects of amino acid substitutions on protein stability and protein protein interaction, respectively. We demonstrated that pathogenic mutations at the interaction interface could affect binding energy and destabilise protein complex, whereas mutations at the non-interface might reduce folding energy and destabilise monomer structure. The results suggest that the structure-based analysis can provide useful information for understanding the molecular mechanisms of diseases.
Photonic Provisioning Using a Packaged SOI Hybrid All-Optical Wavelength Converter in a Meshed Optical Network Testbed (2012)

We demonstrate path wavelength routing and switching using a packaged and pigtailed hybrid integrated silicon-on-insulator (SOI) photonic circuit. The fabricated device incorporates a 1.25 mm nonlinear semiconductor optical amplifier mounted on the SOI board and two multimode interference-based cascaded delay interferometers monolithically integrated on the same SOI substrate. The photonic chip has a footprint of 384 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and performs all-optical wavelength conversion at ultrafast data rates. The packaged and pigtailed module is inserted and tested as a switching node in a meshed optical network testbed carrying real data traffic and encompassing a wavelength division multiplexing optical link. Optical path wavelength switching and routing is implemented by a generalized multiprotocol label switching control plane. We present 10 GbE video-streaming routing as well as 40 Gb/s wavelength switching employing the system integrated all-optical wavelength converter. Error-free transmission and different kind of end-to-end services (video distribution, audio conference, and video conference) have been successfully evaluated.
IL-17 stimulates the production and expression of proinflammatory cytokines, IL-beta and TNF-alpha, by human macrophages. (1998)

IL-17 is a newly described, T cell-derived cytokine with ill-defined physiologic properties. As such, we examined the release of proinflammatory mediators by human macrophages in response to recombinant human (rh) IL-17. IL-1beta and TNF-alpha expression and synthesis were up-regulated by rhIL-17 in a dose (ED50 was 50 +/- 9 ng/ml)- and time-dependent fashion, with cytokine accumulation reaching a zenith after 9 h. Release of IL-6, PGE2, IL-10, IL-12, IL-1R antagonist, and stromelysin was also stimulated by rhIL-17. IL-1beta and TNF-alpha mRNA expression levels were controlled by rhIL-17 in a complex manner with an initial 30-min inhibitory phase, and then up-regulation beginning at 1 h and reaching a plateau at about 3 h. The latter expression pattern closely mirrored the nuclear accumulation of the transcription factor nuclear factor-kappaB. cAMP mimetics isobutyl-1-methylxanthine (IBMX), forskolin, PGE2, and cholera toxin reversed rhIL-17-induced release of TNF-alpha, but had no consistent effect on induced IL-1beta synthesis. Induced release of TNF-alpha was also inhibited by serine/threonine protein kinase inhibitors KT-5720 (protein kinase A) and Calphostin C (protein kinase C), mitogen-activated protein kinase kinase inhibitor PD098059, and a nonspecific tyrosine kinase inhibitor, genistein. Calphostin C alone abrogated the rhIL-17-induced release of IL-1beta. The antiinflammatory cytokines IL-4 (p < 0.01) and IL-10 (p < 0.02) completely reversed rhIL-17-stimulated IL-1beta release, while IL-13 and TGF-beta2 were partially effective (59 and 43% diminution, respectively). IL-10 exerted a significant suppressive effect on IL-17-induced TNF-alpha release (99%, p < 0.02), while the inhibitory effects of IL-4, IL-13, and TGF-beta2 on TNF-alpha secretion were partial (48, 10, and 23%, respectively). The data suggest a pivotal role for IL-17 in initiating and/or sustaining an inflammatory response.
Real-world stereoscopic performance in multiple-focal-plane displays: How far apart should the image planes be? (2012)

Conventional stereoscopic displays present conflicting stimuli to vergence and accommodation, causing fatigue, discomfort, and poor stereo depth perception. One promising solution is 'depth filtering', in which continuous variations in focal distance are simulated by distributing image intensity across multiple focal planes. The required image-plane spacing is a critical parameter, because there are constraints on the total number that can be used. Depth-filtered images have been shown to support continuous and reasonably accurate accommodation responses with 1.1 dioptre (D) image-plane spacings. However, retinal contrast is increasingly attenuated with increasing image-plane separation. Thus, while such stimuli may eliminate the vergence-accommodation conflict, they may also unacceptably degrade stereoscopic depth perception. Here we measured stereoacuity, and the time needed for stereoscopic fusion, for real targets and depth-filtered approximations to the same stimuli (image-plane spacings of 0.6, 0.9 and 1.2 D). Stereo fusion time was reasonably consistent across conditions. Stereoacuity for depth-filtered stimuli was only slightly poorer than for real targets with 0.6 D image-plane separation, but deteriorated rapidly thereafter. Our results suggest that stereoscopic depth perception, not accommodation and vergence responses, is the limiting factor in determining acceptable image-plane spacing for depth-filtered images. We suggest that image-plane spacing should ideally not exceed ~0.6 D.
Polynucleotides. LVI1. Synthesis and properties of poly(2′-deoxy-2′-fluoroinosinic acid) (1978)

Poly (2'-deoxy-2'-fluoroinosinic acid) [ poly(If)] was synthesized by polymerization of 2'-deoxy-2'-fluoroinosine 5'-diphosphate catalyzed by Escherichia coli polynucleotide phosphorylase. Although the UV absorption properties of poly(If) closely resembled those of poly(I), thermal melting curves at Na+ concentrations of 0.15M and 0.75M suggested two ordered structures for poly(If) neutral form. CD psectra taken at 0.15M Na+ concentration showed rather larger amplitudes in both a peak at 273 nm and a trough at 246 nm, suggesting rather strong vertical stacking of bases. When complexed with poly(C), poly(If) forms a double-stranded complex, poly(If).poly(C) which has Tm's higher by 10-20 degrees than those of poly(If).poly(C) measured under the same conditions. The CD spectrum of this complex resembled that of poly(I).poly(C). The effect of the fluorine atom at the 2'-position on thermal stability of polynucleotides is discussed.
Comparison of IOL powers by corrected method in eyes after PRK and LASIK (2002)

The purpose of this study is to compare, by statistical analysis, intraocular lens (IOL) powers by SRK/T formula using autorefractokeratometer-measured keratometric (K) values (SRK/T-ARK-mK), by SRK/T formula using refraction-derived K values (SRK/T-R-dK), and by refraction corrected method (RCM), in eyes treated with photorefractive keratectomy (PRK) and laser in situ keratomileusis (LASIK) for myopia. Thirty-eight consecutive eyes of 23 patients with PRK for mild to moderate myopia and 35 consecutive eyes of 25 patients with LASIK for high myopia were followed up for more than 1 year. In the two groups, IOL powers by SRK/T-ARK-mK, by SRK/T-R-dK, and by RCM were compared by statistical analysis. In PRK group, the mean value of IOL powers by RCM was statistically higher than that obtained by the other two methods (p < 0.05), while there was no significant statistical difference between the mean values of IOL powers by SRK/T-ARK-mK and by SRK/T-R-dK (p > 0.05). However, in LASIK group, the mean values of IOL powers by RCM and by SRK/T-R-dK, which did not differ statistically (p > 0.05), were both statistically higher than that by SRK/T-ARK-mK (p < 0.05). In conclusion, there is a statistical difference in IOL powers by the methods used for IOL calculation, as there is according to the level of myopia in patients with PRK and LASIK treatment. We suggest that, in IOL power calculation in eyes with previous corneal refractive surgery, correction methods such as RCM and SRK/T-R-dK are more effective at higher levels of myopia.
Synthesis and Application of Imidazole Derivatives. Introduction of Carbogenic Substituents into the 5-Position of 1-Methyl-1H-imidazole. (1992)

The 5-position of 1-methyl-2-phenylthio-1H-imidazole (12a) was lithiated by lithium 2, 2, 6, 6-tetramethylpiperidide, and the produced carbanion was reacted with various electrophiles to give the corresponding 5-substituted derivatives in good yields. The reaction position was confirmed by 1H-NMR spectroscopy and X-ray crystallography. The phenylthio group of the 5-substituted compounds could be easily removed by treatment with Raney-nickel.
Antibodies Developing Against a Single Recombinant Interferon Protein May Neutralize Many Other Interferon-α Subtypes (1993)

Three hepatitis C patients out of 15 who received recombinant interferon-α2a (rIFN-α2a) therapy developed high levels of neutralizing antibody coincident with clinical relapse. On analysis, antibodies in their sera were found to also produce some neutralization of lymphoblastoid IFN. Purified lymphoblastoid IFN was separated chromatographically into 10 fractions, each containing one or two IFN-α subtypes, and these were used individually to examine the subtype specificity of the neutralizing antibodies in the patients' sera. All three sera neutralized all the subtypes present in the 10 lymphoblastoid IFN fractions. These findings may explain why some patients who develop antibody-mediated resistance to treatment with rIFN-α2 preparations are unable to respond again when treated instead with a human cell derived preparation containing many IFN-α subtypes.
Sparse Iterative Closest Point (2013)

Abstract Rigid registration of two geometric data sets is essential in many applications, including robot navigation, surface reconstruction, and shape matching. Most commonly, variants of the Iterative Closest Point (ICP) algorithm are employed for this task. These methods alternate between closest point computations to establish correspondences between two data sets, and solving for the optimal transformation that brings these correspondences into alignment. A major difficulty for this approach is the sensitivity to outliers and missing data often observed in 3D scans. Most practical implementations of the ICP algorithm address this issue with a number of heuristics to prune or reweight correspondences. However, these heuristics can be unreliable and difficult to tune, which often requires substantial manual assistance. We propose a new formulation of the ICP algorithm that avoids these difficulties by formulating the registration optimization using sparsity inducing norms. Our new algorithm retains the simple structure of the ICP algorithm, while achieving superior registration results when dealing with outliers and incomplete data. The complete source code of our implementation is provided at http://lgg.epfl.ch/sparseicp .
One Size Fits All? - Part 2: Benchmarking Results (2007)

Two years ago, some of us wrote a paper predicting the demise of “One Size Fits All (OSFA) ” [Sto05a]. In that paper, we examined the stream processing and data warehouse markets and gave reasons for a substantial performance advantage to specialized architectures in both markets. Herein, we make three additional contributions. First, we present reasons why the same performance advantage is enjoyed by specialized implementations in the text processing market. Second, the major contribution of the paper is to show “apples to apples ” performance numbers between commercial implementations of specialized architectures and relational DBMSs in both stream processing and data warehouses. Finally, we also show comparison numbers between an academic prototype of a specialized architecture for scientific and intelligence applications, a relational DBMS, and a widely used mathematical computation tool. In summary, there appear to be at least four markets where specialized architectures enjoy an overwhelming performance advantage.
Receptor-mediated transport of IgG. (1984)

The intestinal epithelium of the neonatal rat is a model system for the study of receptor-mediated endocytosis in which large amounts of IgG are transferred intact across polarized cells. This review summarizes the ultrastructural pathway followed by IgG during cellular transit and several important properties of the membrane receptor that recognizes the IgG.
Highly Regioselective α-Olefin Dimerization Using Zirconium and Hafnium Amine Bis(phenolate) Complexes (2017)

Five new structural analogues of a previously studied group IV amine bis(phenolate) catalyst, Zr(ONNEt2O)Bn2, have been synthesized and tested for oligomerization activity. These structural variations encompass longer alkyl groups, propyl and butyl, on the pendant amine group and two different group IV metals, zirconium and hafnium. Remarkably, all five precatalysts, combined with tris(pentafluorophenyl)borane, oligomerized 1-hexene with almost exclusive selectivity for vinylidene end-groups with a marked preference for dimer formation. The three zirconium amine bis(phenolate) catalysts produced a Schulz–Flory distribution of oligomer products whereas the product distributions of the three hafnium analogues were seen to deviate from a Schulz–Flory distribution. The possible structures for dimers and trimers have been elucidated based on end-group and active site distribution.
Bcl-2 interrupts the ceramide-mediated pathway of cell death. (1996)

Ceramide, a product of sphingomyelin turn-over, has been proposed as a novel lipid second messenger with specific roles in mediating antiproliferative responses including apoptosis and cell cycle arrest. In this study, we examine the relationship between the ceramide-mediated pathway of growth suppression and the bcl-2 protooncogene. In ALL-697 leukemia cells, the addition of the chemotherapeutic agent vincristine resulted in a time-dependent growth suppression characterized by marked apoptosis. The effects of vincristine on cell death were preceded by a prolonged and sustained accumulation of endogenous ceramide levels reaching -10.4 pmol ceramide/nmol phospholipids at 12 hr following the addition of vincristine--an increase of 220% over vehicle-treated cells. Overexpression of bcl-2 resulted in near total protection of cell death in response to vincristine. However, the ceramide response to vincristine was not modulated by overexpression of bcl-2, indicating that bcl-2 does not interfere with ceramide formation. Overexpression of bcl-2 prevented apoptosis in response to ceramide, suggesting that bcl-2 acts at a point downstream of ceramide. On the other hand, bcl-2 did not interfere with the ability of ceramide to activate the retinoblastoma gene product or to induce cell cycle arrest, suggesting that the effects of ceramide on cell cycle arrest can be dissociated from the effects on apoptosis. These studies suggest that ceramide and bcl-2 partake in a common pathway of cell regulation. The results also cast ceramide as a gauge of cell injury rather than an "executor" of cell death with clearly dissociable biological outcomes of its action depending on downstream factors.
Drawing pictures in the dust: Rajasthani children's landscapes (1994)

Our paper conveys some of the ways children in rural Rajasthan, North India, think about their relationships with the environment, and how these relationships are enacted in their workday lives and expressed in their stories and songs. Due to severe deforestation in the region over the past 50 years, these children inherit a landscape very different from the one that was familiar to their parents and grand- parents. Interviews with children and the oral traditions they perform are our two major sources, supplemented with knowledge gained through participant obser vation and experience. We contrast children who work all day herding their families' livestock with children who attend school, focusing on attitudes toward work and on what daily chores and school books teach children about their natural surroundings. Folktales and folksongs rich in images and morals drawn from nature offer vivid insights into children's imaginative worlds.
Acute Activation of Maxi-K Channels ( hSlo ) by Estradiol Binding to the β Subunit (1999)

Maxi-K channels consist of a pore-forming alpha subunit and a regulatory beta subunit, which confers the channel with a higher Ca(2+) sensitivity. Estradiol bound to the beta subunit and activated the Maxi-K channel (hSlo) only when both alpha and beta subunits were present. This activation was independent of the generation of intracellular signals and could be triggered by estradiol conjugated to a membrane-impenetrable carrier protein. This study documents the direct interaction of a hormone with a voltage-gated channel subunit and provides the molecular mechanism for the modulation of vascular smooth muscle Maxi-K channels by estrogens.
Apoptosis: a mechanism contributing to remodeling of skeletal muscle in response to hindlimb unweighting (1997)

The role of apoptosis in the elimination of myonuclei during hindlimb unloading-induced atrophy and the inhibition of apoptosis in the prevention of muscle atrophy were examined. The number of nuclei demonstrating double-stranded DNA fragmentation seen by terminal deoxynucleotidyl transferase (TDT) histochemical staining, an indicator of apoptosis, was significantly increased after 14 days of suspension. Double staining with TDT and antilaminin immunohistochemistry revealed that some TDT-positive nuclei were within the fiber lamina and were most likely myonuclei. The number of fibers containing morphologically abnormal nuclei was also significantly greater in suspended compared with control rats. Combined treatment with growth hormone and insulin-like growth factor I (GH/ IGF-I) and resistance exercise attenuated the increase in TDT-positive nuclei (approximately 26%, P > 0.05) and significantly decreased the number of fibers with morphologically abnormal nuclei. The data suggest that 1) "programmed nuclear death" contributes to the elimination of myonuclei and/or satellite cells from atrophying fibers, and 2) GH/IGF-I administration plus muscle loading ameliorates the apoptosis associated with hindlimb unloading.
Haptic Feedback to Assist Bus Drivers for Pedestrian Safety at Low Speed (2016)

Buses and coaches are massive Passenger Transportation Systems (PTS), because they represent more than half of land PTS in the European Union. Despite that, bus accident figures are lower than other means of transport, but its size and weight increase the severity of accidents in which buses are involved, even at low speed. In urban scenarios, turnings and maneuvers around bus stops are the main causes of accidents, mostly due to low visibility, blind spots, or driver's distractions. Therefore, there is an increasing interest in developing driving assistance systems to avoid these situations, among others. However, even though there are some solutions on the market, they are not meant to work in urban areas at low speed and with the sole purpose of preventing collisions with pedestrians. In this sense, the paper proposes an active safety system for buses in maneuvers at low speed. The safety system consists of haptic feedback devices together with collision avoidance and risk evaluation systems based on detected people nearby the bus. The performance of the active safety system has been validated in a simulated urban scenario. Our results show that driver's reaction time is reduced and time to collision increased due to the proposed low-speed active safety system. In particular, it is shown that there is a reduction in the number of high risk cases and collisions, which implies a considerable improvement in safety terms. In addition to this, a brief discussion about current regulations for innovative safety systems on real vehicles is carried out.
Pheochromocytoma--a rare cause of hypermagnesemia. (1985)

A case of hypermagnesemia associated with pheochromocytoma is described. A further increase in serum Mg was observed with initiation of beta-blocking therapy. Unilateral adrenalectomy normalized serum Mg levels.