gebhart/patrepeval huggingface dataset:
Comparison of hardware and software implementations of selected lightweight block ciphers (2017)

Lightweight block ciphers are an important topic of research in the context of the Internet of Things (IoT). Current cryptographic contests and standardization efforts seek to benchmark lightweight ciphers in both hardware and software. Although there have been several benchmarking studies of both hardware and software implementations of lightweight ciphers, direct comparison of hardware and software implementations is difficult due to differences in metrics, measures of effectiveness, and implementation platforms. In this research, we facilitate this comparison by use of a custom lightweight reconfigurable processor. We implement six ciphers, AES, SIMON, SPECK, PRESENT, LED and TWINE, in hardware using register transfer level (RTL) design, and in software using the custom reconfigurable processor. Both hardware and software implementations are instantiated in identical Xilinx Kintex-7 FPGAs, which enables direct comparison of throughput, area, throughput-to-area (TP/A) ratio, power, and energy. Results show that TWINE and AES have the highest TP/A ratios for hardware and software implementations, respectively, assuming an area target of 300–450 LUTs. In terms of direct comparison, software implementations on tailored reconfigurable processers generally use less power — especially where reconfigurable instruction set extensions are permitted. However, custom hardware implementations have higher throughput and energy-efficiency than software implementations on the same platform.
Effect of caffeinated drinks on substrate metabolism, caffeine excretion, and performance (1998)

The effect of addition of different dosages of caffeine (Caf) to a carbohydrate-electrolyte solution (CES) on metabolism, Caf excretion, and performance was examined. Subjects (n = 15) ingested 8 ml/kg of water placebo (Pla-W), 7% CES (Pla-CES), or 7% CES with 150, 225, and 320 mg/l Caf (CES-150, CES-225, and CES-320, respectively) during a warm-up protocol (20 min) and 3 ml/kg at one-third and two-thirds of a 1-h time trial. Performance was improved with Caf supplementation: 62.5 +/- 1.3, 61.5 +/- 1.1, 60.4 +/- 1.0, 58.9 +/- 1.0, and 58.9 +/- 1.2 min for Pla-W, Pla-CES, CES-150, CES-225, and CES-320, respectively. The postexercise urinary Caf concentration (range 1.3-2.5 microg/ml) was dose dependent and always far below the doping level of the International Olympic Committee (12 microg/ml) in all subjects. Sweat Caf excretion during exercise exceeded postexercise early-void urinary Caf excretion. Caffeinated CES did not enhance free fatty acid availability, ruling out the fact that performance improvement resulted from enhanced fat oxidation. It is concluded that addition of relatively low amounts of Caf to CES improves performance and that postexercise urinary Caf concentration remained low.
Plasminogen interacts with human platelets through two distinct mechanisms. (1986)

Glu-plasminogen, the native form of plasminogen, interacts in a specific and saturable manner with unstimulated human platelets, and the binding is enhanced fivefold by thrombin stimulation (Miles and Plow, 1985. J. Biol. Chem. 260:4303). This study characterizes the nature of the Glu-plasminogen binding sites by analyzing platelets deficient in selected proteins and functions. Platelets from patients with afibrinogenemia, Gray platelet syndrome, and the Cam Variant of thrombasthenia, a form of thrombasthenia with near normal levels of glycoprotein IIb/IIIa (GPIIb/IIIa), showed minimal augmentation of plasminogen binding to thrombin-stimulated platelets but normal binding to unstimulated platelets. This selective deficiency indicates that two distinct mechanisms are involved in the interaction of plasminogen with platelets. These abnormal platelets share a deficiency in fibrinogen. Surface expression of platelet fibrinogen, however, was not sufficient for enhanced plasminogen binding to stimulated platelets, and experiments with alpha-thrombin and gamma-thrombin indicated that fibrin formation on the platelet surface is necessary for the augmented plasminogen binding. Unstimulated and stimulated thrombasthenic platelets deficient in GPIIb/IIIa bound markedly reduced levels of plasminogen, which suggests a role for GPIIb/IIIa in plasminogen binding to unstimulated platelets. Treatment of platelets to dissociate the heterodimeric complex of GPIIb/IIIa did not significantly perturb plasminogen binding to unstimulated platelets, but the complex may be necessary for thrombin-stimulated plasminogen binding via its interaction with platelet fibrin.
An Ebola whole-virus vaccine is protective in nonhuman primates (2015)

Zaire ebolavirus is the causative agent of the current outbreak of hemorrhagic fever disease in West Africa. Previously, we showed that a whole Ebola virus (EBOV) vaccine based on a replication-defective EBOV (EBOVΔVP30) protects immunized mice and guinea pigs against lethal challenge with rodent-adapted EBOV. Here, we demonstrate that EBOVΔVP30 protects nonhuman primates against lethal infection with EBOV. Although EBOVΔVP30 is replication-incompetent, we additionally inactivated the vaccine with hydrogen peroxide; the chemically inactivated vaccine remained antigenic and protective in nonhuman primates. EBOVΔVP30 thus represents a safe, efficacious, whole-EBOV vaccine candidate that differs from other EBOV vaccine platforms in that it presents all viral proteins and the viral RNA to the host immune system, which might contribute to protective immune responses.
Transcriptional activation by Arabidopsis GT‐1 may be through interaction with TFIIA–TBP–TATA complex (1999)

GT-1 belongs to the class of trihelix DNA-binding proteins and binds to a promoter sequence found in many different genes. Data presented in this report show that GT-1 contains a trans-activation function in yeast and in plant cells. However, in tobacco BY-2 protoplasts, this activity functions only when an internal region containing the DNA-binding domain is deleted. Gel-shift and co-immunoprecipitation assays have revealed that GT-1 can interact with and stabilize the TFIIA-TBP-TATA complex. These results suggest that GT-1 may activate transcription through direct inter- action with the transcriptional pre-initiation complex.
Electrical measurements of a dithiolated electronic molecule via conducting atomic force microscopy (2002)

We describe a method of measuring the electrical properties of a molecule via conducting atomic force microscopy (AFM). A dithiolated molecule is chemically inserted into defect sites in an insulating self-assembled monolayer formed on an epitaxial Au substrate and the top thiol terminus of the molecule is reacted with a Au nanoparticle. A Au-coated AFM probe is used to contact the molecule through the nanoparticle, thus electrical data can be obtained. We report preliminary transport measurements of two test molecules. Our data shows qualitative agreement with previously published results for similar molecules deposited in a nanopore containing approximately a thousand molecules. This work indicates that the measured negative differential resistance is not an intermolecular phenomenon.
Efficient and scalable computations with sparse tensors (2012)

For applications that deal with large amounts of high dimensional multi-aspect data, it becomes natural to represent such data as tensors or multi-way arrays. Multi-linear algebraic computations such as tensor decompositions are performed for summarization and analysis of such data. Their use in real-world applications can span across domains such as signal processing, data mining, computer vision, and graph analysis. The major challenges with applying tensor decompositions in real-world applications are (1) dealing with large-scale high dimensional data and (2) dealing with sparse data. In this paper, we address these challenges in applying tensor decompositions in real data analytic applications. We describe new sparse tensor storage formats that provide storage benefits and are flexible and efficient for performing tensor computations. Further, we propose an optimization that improves data reuse and reduces redundant or unnecessary computations in tensor decomposition algorithms. Furthermore, we couple our data reuse optimization and the benefits of our sparse tensor storage formats to provide a memory-efficient scalable solution for handling large-scale sparse tensor computations. We demonstrate improved performance and address memory scalability using our techniques on both synthetic small data sets and large-scale sparse real data sets.
Cellular Senescence in Livers from Children with End Stage Liver Disease (2010)

Cellular senescence in livers of children with end stage disease is associated with damage rather than corresponding to an age dependent phenomenon. Further studies are needed to support the hypothesis that these senescence markers correlate with disease progression.
Heat Capacity Measurements on Small Samples at Low Temperatures (1972)

We describe a new calorimeter for measuring heat capacity in the range 1–35 K, using a silicon chip bolometer as sample holder, temperature sensor, and sample heater. The apparatus is capable of measuring very small samples (1–500 mg), and may be used with a number of different experimental methods.
H2azapa: a Versatile Acyclic Multifunctional Chelator for 67Ga, 64Cu, 111In, and 177Lu (2012)

Preliminary experiments with the novel acyclic triazole-containing bifunctional chelator H2azapa and the radiometals (64)Cu, (67)Ga, (111)In, and (177)Lu have established its significant versatile potential as an alternative to 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) for metal-based radiopharmaceuticals. Unlike DOTA, H2azapa radiolabels quantitatively with (64)Cu, (67)Ga, (111)In, and (177)Lu in 10 min at room temperature. In vitro competition experiments with human blood serum show that (64)Cu remained predominantly chelate-bound, with only 2% transchelated to serum proteins after 20 h. Biodistribution experiments with [(64)Cu(azapa)] in mice reveal uptake in various organs, particularly in the liver, lungs, heart, intestines, and kidneys. When compared to [(64)Cu(DOTA)](2-), the lipophilic neutral [(64)Cu(azapa)] was cleared through the gastrointestinal tract and accumulated in the liver, which is common for lipophilic compounds or free (64)Cu. The chelator H2azapa is a model complex for a click-based bifunctional chelating agent, and the lipophilic benzyl "place-holders" will be replaced by hydrophilic peptides to modulate the pharmacokinetics and direct activity away from the liver and gut. The solid-state molecular structure of [In(azapa)(H2O)][ClO4] reveals a very rare eight-coordinate distorted square antiprismatic geometry with one triazole arm bound, and the structure of [(64)Cu(azapa)] shows a distorted octahedral geometry. The present study demonstrates significant potential for bioconjugates of H2azapa as alternatives to DOTA in copper-based radiopharmaceuticals, with the highly modular and "clickable" molecular scaffold of H2azapa easily modified into a variety of bioconjugates. H2azapa is a versatile addition to the "pa" family, joining the previously published H2dedpa ((67/68)Ga and (64)Cu), H4octapa ((111)In, (177)Lu, and (90)Y), and H5decapa ((225)Ac) to cover a wide range of important nuclides.
Genomic and Expression Analysis of the 12p11-p12 Amplicon Using EST Arrays Identifies Two Novel Amplified and Overexpressed Genes (2002)

We performed parallel array comparative genomic hybridization and array expression analysis of the 12p11-p12 amplicon in human testicular seminomas and an ovarian carcinoma cell line using an expressed sequence tags (ESTs) array spotted with 8254 ESTs. The data were normalized using a robust statistical modeling and the significance inferred from the local SD. We identified two ESTs within the chromosomal amplicon that were amplified and overexpressed in > or =75-100 percent of analyzed tumors with the 12p11-p12 amplicon. These sequences, belonging to coding regions of two novel genes designated here as GCT1 and GCT2, were broadly expressed in a panel of human tissues, including testis and ovary. GCT1 and GCT2 were overexpressed in 92 and 71 percent, respectively, of a panel of seminomas tested. Combined array comparative genomic hybridization and array expression analysis is a valid approach for gene discovery in large chromosomal amplicons.
Effects of Preparation Conditions in Aqueous Solution on Properties of Hydroxyapatites (1990)

Hydroxyapatite powders (HAP: Ca10(PO4)6(OH)2) were prepared from calcium nitrate and di-ammonium hydrogen phosphate at various temperatures in aqueous solution in the absence and presence of carbon dioxide. In the absence of carbon dioxide, the crystallinities as well as the calcium to phosphate ratio (Ca/P ratio) of HAP powders increased with an increase in the preparation temperature. Calcium ion deficiency caused low Ca/P ratios of HAP powders. Such HAP powders decomposed thermally to beta-tricalcium phosphate (beta-TCP: Ca3(PO4)2) at 800 degrees C in 3 hours whereas HAP powders with sufficient calcium were stable at 1200 degrees C for 3 hours. In the presence of carbon dioxide as well the crystallinities of HAP powders increased with an increase in the preparation temperature, but carbonate-bearing HAPs were obtained instead of pure HAP. In addition, calcium carbonate was obtained along with carbonate-bearing HAP prepared below 60 degrees C.
Electrowetting-based valve for the control of the capillary flow (2008)

The behavior of a microfluidic device based on transport by capillary action and control by direct electrowetting was examined by changing the device parameters. The device was constructed with a polydimethylsiloxane (PDMS) substrate with a flow channel and a glass substrate with electrodes to control electrowetting. The microfluidic transport and valve action could be explained by Washburn’s model, which suggests that the model can be used for designing such a device. The device could be used for the timely delivery of a solution into many flow channels as well as for the mixing of solutions.
Effect of IL-6 receptor antisense oligodeoxynucleotide on in vitro proliferation of myeloma cells. (1995)

IL-6 stimulates proliferation of various tumors, including lymphoma and myeloma; thus, inhibiting IL-6 may decrease the growth of these tumors. Accordingly, we examined the effect of IL-6 and IL-6R antisense phosphorothioated oligodeoxynucleotides (ODNs) on proliferation of IL-6 responsive (U266) and nonresponsive (RPMI 8226) myeloma cell lines. Cells were grown in the presence or absence of IL-6, with added antisense to either IL-6 or IL-6R. Cells were evaluated for proliferation ([3H]thymidine uptake) and steady state levels of both IL-6 and IL-6R mRNA by competitive PCR (C-PCR). Proliferation of U266 cells was decreased markedly by IL-6 antisense ODN in the absence of IL-6, but not in its presence. In contrast, IL-6R antisense ODN inhibited proliferation of U266 cells in both the presence and absence of IL-6. As anticipated, neither IL-6 nor IL-6R antisense ODN had an effect on RPMI 8226 proliferation. C-PCR demonstrated a marked and specific decrease of IL-6 and IL-6R mRNA in cells exposed to IL-6 ODN and IL-6R ODN, respectively. These results suggest that IL-6R antisense ODN may be a more effective inhibitor of IL-6-stimulated cells than IL-6 antisense in a therapeutic setting.
Empowering Cross-Domain Internet Media with Real-Time Topic Learning from Social Streams (2012)

This paper aims to connect social media from disparate sources on the Internet by building a common topic space in-between, using which cross domain media recommendations can be realized on the web. The topic space is built and updated in real time by extending the Latent Dirichlet Allocation (LDA) model to cater to streaming online data. Our topical model, named Online Streaming LDA (OSLDA), is able to extract, learn, populate, and update the topic space in real time, scaling with streaming tweets. Based on the proposed topic space learned in real time, we present media recommendation applications that cannot be achieved by conventional media analysis techniques: (1) tweet enrichment by recommending related videos, and (2) popular video recommendation for featuring socially trending topical videos. We conduct experiments over a collection of 3.6 million tweets and 1.2 million click-through data from a video search engine. Our results show that the learned topic model plays a natural role connecting cross-domain social media, leading to a better user experience consuming social media.
Inhibition of human hair follicle growth by endo‐and exocannabinoids (2007)

Recent studies strongly suggest that the cannabinoid system is a key player in cell growth control. Since the organ-culture of human hair follicles (HF) offers an excellent, clinically relevant model for complex tissue interaction systems, we have asked whether the cannabinoid system plays a role in hair growth control. Here, we show that human scalp HF, intriguingly, are both targets and sources of endocannabinoids. Namely, the endocannabinoid N-arachidonoylethanolamide (anandamide, AEA) as well as the exocannabinnoid delta (9) -tetrahydrocannabinol dose-dependently inhibited hair shaft elongation and the proliferation of hair matrix keratinocytes, and induced intraepithelial apoptosis and premature HF regression (catagen). These effects were inhibited by a selective antagonist of cannabinoid receptor-1 (CB1). In contrast to CB2, CB1 was expressed in a hair cycle-dependent manner in the human HF epithelium. Since we successfully identified the presence of endocannabinoids in human HF, our data strongly suggest that human HF exploit a CB1-mediated endocannabinoid signaling system for negatively regulating their own growth. Clinically, CB1 agonists may therefore help to manage unwanted hair growth, while CB1 antagonists might counteract hair loss. Finally, human HF organ culture offers an instructive, physiologically relevant new research tool for dissecting "nonclassical" effects of endocannabinoids and their receptor-mediated signaling in general.
Blockade of Programmed Death 1 Augments the Ability of Human T Cells Engineered to Target NY-ESO-1 to Control Tumor Growth after Adoptive Transfer (2015)

This model offers a platform for preclinical testing of adjuvant immunotherapeutics targeted to human T cells prior to transition to the bedside. Because the model employs engineering of human T cells with a TCR clone instead of a CAR, it allows for study of the biology of tumor-reactive TILs that signal through an endogenous TCR. The lessons learned from TCR-engineered TILs can thus be applied to tumor-reactive TILs.
Are All Cell Volume Changes the Same? (1994)

Little is known about how cells sense volume and convert size signals into regulatory responses. Recent evidence suggests cells can detect more than just swelling or shrinkage. Cells may possess multiple volume detectors and volume regulatory effector pathways that respond specifically to the mechanism and magnitude of volume change.
Structure-Function Relationships in Human Interleukin-11 (1995)

Chemical modification approaches combined with site-directed and deletion mutagenesis have been used to identify functionally critical regions/residues of recombinant human IL-11 (rhIL-11). Incubation of rhIL-11 with iodoacetic acid results in specific alkylation of a single methionine residue, Met58, and a 25-fold reduction of in vitro biological activity on mouse plasmacytoma cells. A similar decrease in activity is observed when Met58 is substituted with Ala, Leu, Gln, Glu, or Lys by site-directed mutagenesis. Treatment of rhIL-11 with succinic anhydride leads to modification of the amino-terminal amino group and partial labeling of 2 lysines, Lys41 and Lys98, and to a 3-fold decrease in activity. The activity losses can be attributed to modification of the lysine residues, since the succinyl derivative of the amino terminus is fully active. In addition, carboxyl-terminal deletion mutagenesis studies have demonstrated that removal of the last 4 residues reduces rhIL-11 activity 25-fold, whereas removal of 8 or more amino acids results in an inactive molecule. Based on secondary structure predictions and the location of exon/intron boundaries in the IL-11 genomic structure, we propose a four-helix bundle topology as a structural model for rhIL-11. This model has been tested by limited proteolysis using three side chain-specific endoproteinases. A limited number of protease-sensitive cleavage sites are present in rhIL-11, and all but two are located in the postulated helix interconnecting loops or at helix termini. alpha-Helices, which in the proposed structure form a compact core of the molecule, are inaccessible to digestion under limiting conditions. According to the model, Met58, Lys41 and Lys98 are located on the surface of the molecule, in agreement with their preferential accessibility to chemical modifications. By analogy with human growth hormone, we postulate that Met58 and the carboxyl terminus of rhIL-11 are involved in the primary receptor binding site (site I), whereas Lys41 and Lys98 may be a part of binding site II.
DIVER: A Distributed Virtual Environment Research platform (1993)

DIVER is the Virtual Environment software architecture library developed at the University of Virginia. It is similar to SGI's Inventor, but was developed specifically as a toolkit for creating Virtual Environments rather than for mouse-based applications. Like Inventor, DIVER was implemented on top of the SGI's GL library and provides a powerful hierarchical graphics database. Unlike Inventor, DIVER is distributed, divorcing the application computations from the rendering computations. DIVER runs the application on a remote CPU and transparently spawns asynchronous rendering processes onto one or more SGIs. DIVER extends the graphics database hierarchy by allowing programmers to perform graphics transformations in any other object's nested coordinate system, and by allowing the programmer to nest the virtual camera (viewpoint) anywhere in the hierarchy. DIVER has been active use for over a year by more than twenty researchers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure, function and regulation of Ca2+‐sensitive cytosolic phospholipase A2 (cPLA2) (1997)

The 85-kDa cytosolic PLA2 (cPLA2) is present in many cells and tissues and its unusual functional properties and catalytic mechanism are being elucidated. Notably, cPLA2 becomes catalytically active in the presence of free Ca2+ concentrations as present in stimulated cells and preferentially cleaves arachidonic acid-containing phospholipids. A variety of agonists, growth factors and cytokines, as well as stressful stimuli activate cPLA2 to hydrolyze cellular phospholipids thereby liberating fatty acids and lysophospholipids and providing the precursor substrates for the biosynthesis of eicosanoids and platelet-activating factor. These products of cPLA2 contribute to inflammatory and degenerative disease states and cPLA2 is therefore an attractive target for the development of novel therapies.