gebhart/patrepeval huggingface dataset:
Searchable Encryption Revisited: Consistency Properties, Relation to Anonymous IBE, and Extensions. (2005)

We identify and fill some gaps with regard to consistency (the extent to which false positives are produced) for public-key encryption with keyword search (PEKS). We define computational and statistical relaxations of the existing notion of perfect consistency, show that the scheme of [8] is computationally consistent, and provide a new scheme that is statistically consistent. We also provide a transform of an anonymous identity-based encryption (IBE) scheme to a secure PEKS scheme that, unlike the previous one, guarantees consistency. Finally, we suggest three extensions of the basic notions considered here, namely anonymous hierarchical identity-based encryption, public-key encryption with temporary keyword search, and identity-based encryption with keyword search.
Measurement of 25-Hydroxyvitamin D Revisited (2006)

A notable shortcoming of the HPLC method for measuring 25-hydroxyvitamin D described by Lensmeyer et al. (1) is its failure to adequately remove interference by the C3-epimer. Although the authors dismiss this because the interference was less than the lowest limit of quantification, this would not be true in some samples collected from children >1 year old, in which the concentration of this metabolite can be as high as 92 μg/L(2 …
Prenatal Detection of Fetal Triploidy from Cell-Free DNA Testing in Maternal Blood (2013)

cfDNA testing by targeted sequencing and allelic ratio analysis of single nucleotide polymorphisms covering chromosomes 21, 18, 13, X, and Y can detect diandric triploidy and raise the suspicion of digynic triploidy.
On the structure of the ‘synaptosecretosome’ Evidence for a neurexin/synaptotagmin/syntaxin/Ca<sup>2+</sup>channel complex (1993)

Recent experiments have identified interactions between presynaptic and synaptic vesicle membrane proteins, that might be important in organizing the components of the fast neurotransmitter release mechanism to ensure that the process follows a rapid time course. Here we extend previous investigations to show that in addition to the alpha-latrotoxin receptor (neurexin) and synaptotagmin another presynaptic protein, syntaxin, co-purifies on a alpha-latrotoxin affinity column. This implies that syntaxin is associated with these two molecules in a complex; a conclusion supported by the immunoprecipitation of [125I]latrotoxin binding by syntaxin antibodies. In addition, antibodies against syntaxin and the alpha-latrotoxin receptor immunoprecipitate [125I]omega-conotoxin binding sites, indicating that calcium channels are associated with this complex. Thus, neurexin, synaptotagmin, syntaxin, and calcium channels can be found in a structure we propose to call the 'synaptosecretosome'. The components of the synaptosecretosome, in association with additional proteins, are postulated to organize the process of neurotransmitter release.
Preclinical activity of the Hsp90 inhibitor, ganetespib, in ALK- and ROS1-driven cancers. (2012)

3090 Background: Ganetespib is a potent inhibitor of heat shock protein 90 (Hsp90) currently being studied in a broad range of clinical trials. Phase II results with ganetespib demonstrated an encouraging objective response rate of 50% in non-small cell lung carcinoma (NSCLC) patients whose tumors contained ALK translocations and had progressed on previous treatments. To further understand the clinical potential of ganetespib in ALK-driven cancers, we evaluated its activity in (1) crizotinib-sensitive and -resistant cancer cells harboring ALK fusions; (2) cells expressing amplified ALK or ROS1 translocations (a kinase structurally similar to ALK); and (3) in combination with crizotinib. Methods: H3122 NSCLC cells, which express EML4-ALK, were treated with ganetespib, crizotinib or the combination, and cell viability and signaling cascades were assessed. Similar experiments were done in cells with amplified, constitutively active ALK (NB-39-nu) or ROS1 kinase fusions (HCC-78, U118MG). To generate a model of crizotinib resistance, NPM-ALK-expressing BaF3 cells were exposed to various crizotinib concentrations. Fifteen different ALK kinase domain substitutions were identified; clonal NPM-ALK/BaF3 cells were made for each resistance mutation and assayed for sensitivity to ganetespib. Results: Ganetespib was 50-fold more potent than crizotinib in killing H3122 cells, and when combined together at sub-lethal doses, displayed strong synergistic anticancer activity. Ganetespib showed similar potency in other cells driven by constitutively active ALK or ROS1 kinase fusions, due to abrogation of their oncogenic kinase activity. All 15 of the crizotinib-resistant NPM-ALK/BaF3 mutant clones were highly sensitive to ganetespib (IC50 values ranging from 14-23 nM), including the 7 mutations reported to date in patients with ALK-driven tumors. Conclusions: Ganetespib effectively inhibits the activity of ALK and ROS1, kinases associated with several tumor types, resulting in marked single agent anticancer activity in cells driven by them. Importantly, ganetespib retains its potency irrespective of the mutational status of ALK. The strong synergy observed between ganetespib and crizotinib warrants further study.
Coordinated Multi-Agent Imitation Learning (2017)

We study the problem of imitation learning from demonstrations of multiple coordinating agents. One key challenge in this setting is that learning a good model of coordination can be difficult, since coordination is often implicit in the demonstrations and must be inferred as a latent variable. We propose a joint approach that simultaneously learns a latent coordination model along with the individual policies. In particular, our method integrates unsupervised structure learning with conventional imitation learning. We illustrate the power of our approach on a difficult problem of learning multiple policies for fine-grained behavior modeling in team sports, where different players occupy different roles in the coordinated team strategy. We show that having a coordination model to infer the roles of players yields substantially improved imitation loss compared to conventional baselines.
Synthesis and Characterization of Polyimide/Silica Hybrid Composites (1999)

A new class of polyimide/silica composites with chemical bonds between the polyimide and silica network has been synthesized by the sol−gel reaction and characterized. The hybrid composite films were obtained by the hydrolysis and polycondensation of (3-aminopropyl)triethoxysilane (APTES) and tetraethoxysilane (TEOS) in N,N-dimethylacetamide solution (DMAc), followed by heating at 100, 200, and 300 °C. The presence of chemical bonds between polyimide (PI) and silica has great effect on the properties of polyimide films, especially on their mechanical properties. The modulus and ultimate strength of the hybrid composite films increased and elongation at break decreased with increased silica content. These hybrid films showed no apparent decrease in thermal decomposition temperature.
An LED-based multitouch sensor for LCD screens (2010)

In recent years, a large number of multitouch sensor concepts have been presented. Particularly optical sensors are highly popular due to their versatility. However, especially camera-based systems often require a significant amount of space behind the screen and are not well suited to flatscreen-based setups. While integrated sensors for flatscreens have already been presented, they are mostly complex, expensive or both.
miR-200 Expression Regulates Epithelial-to-Mesenchymal Transition in Bladder Cancer Cells and Reverses Resistance to Epidermal Growth Factor Receptor Therapy (2009)

Members of the miR-200 family appear to control the EMT process and sensitivity to EGFR therapy in bladder cancer cells and the expression of miR-200 is sufficient to restore EGFR dependency at least in some of the mesenchymal bladder cancer cells. The targets of miR-200 include ERRFI-1, which is a novel regulator of EGFR-independent growth.
Discovery of a New Class of Anilinoquinazoline Inhibitors with High Affinity and Specificity for the Tyrosine Kinase Domain of c-Src (2004)

Deregulated activity of the nonreceptor tyrosine kinase c-Src is believed to result in signal transduction, cytoskeletal and adhesion changes, ultimately promoting a tumor-invasive phenotype. We report here the discovery of a new class of anilinoquinazoline inhibitors with high affinity and specificity for the tyrosine kinase domain of the c-Src enzyme. Special attention was directed toward finding inhibitors selective against KDR tyrosine kinase in order to ensure that the in vivo profile of a specific Src inhibitor could be determined. The 4-aminobenzodioxole quinazoline series gave compounds with excellent potency and selectivity. The most interesting compounds were evaluated in vivo and displayed good pharmacokinetics following oral dosing. Compounds such as the aminobenzodioxoles were shown to be potent inhibitors of tumor growth in a c-Src-transformed 3T3 xenograft model in vivo, resulting in more than 90% growth inhibition at doses as low as 6 mg/kg po once daily. Src tyrosine kinase inhibitors such as these may provide a novel therapeutic modality for targeting cancer invasion and metastasis.
N-(3,4-Methylenedioxyphenyl)carbamates as Potent Flower-Inducing Compounds in Asparagus Seedlings as Well as Probes for Binding to Cytochrome P-450 (1995)

Abstract N-(3,4-Methylenedioxyphenyl)carbamates and related compounds were prepared to develop flower-inducing compounds in Asparagus seedlings and to assay binding to microsomal P-450 that has been postulated to be a possible triggering site for flowering. Some of the compounds had flower-inducing activity as effective as that of the previous potent com­ pounds. The microsomal P-450 formed a type I spectrum with a representative of the present compounds as well as with previous, structurally different classes of flower-inducing compounds; which are carbamate and amidine derivatives and piperonyl butoxide, a methylene-dioxy compound known as broad-spectrum P-450 inhibitor. Upon addition of NADPH , the spectra of these compounds changed to those with a peak centered at 460 nm, indicating that they all form a reactive, high affinity species to produce a complex with P-450. The target species of the compounds that induce flowering in asparagus seedlings was thought to be cytochrome P-450.
Human factors in waste management (1994)

This article examines the role of human factors in radioactive waste management. Although few problems and ergonomics are special to radioactive waste management, some problems are unique especially with long term storage. The entire sociotechnical system must be looked at in order to see where improvement can take place because operator errors, as seen in Chernobyl and Bhopal, are ultimately the result of management errors.
Bevacizumab in hepatocellular carcinoma in patients without metastasis and without invasion of the portal vein (2004)

4088 Background: Hepatocellular Carcinoma (HCC) is a highly vascular tumor in which angiogenic cytokines (including VEGF) likely contribute to pathogenesis. Bevacizumab (anti-VEGF) has been shown to delay progression in colorectal and renal cancers. VEGF-inhibition has not been previously attempted in cirrhosis and bevacizumab has been associated with bleeding complications in non-HCC patients. Methods: Hence, we enrolled a limited cohort of patients with unresectable HCC to treatment with bevacizumab at 5mg/kg every 14 days to assess safety. Inclusion criteria were BR < 3.0mg/dl, transaminases < 5X upper limit of normal, platelets > 75K and prothrombin time within 4 seconds of normal. Additional criteria included no history of gastrointestinal bleeding, myocardial infarction stroke, or condition requiring ongoing antiplatelet or antithrombotic therapy. Results: An initial safety assessment indicates that 5 of 6 patients treated for at least 8 weeks tolerated bevacizumab with minimal toxicity (grade 1 neutropenia, acneform rash, proteinuria, fatigue and vocal changes; grade 2 thrombocytopenia). One patient had a fatal esophageal variceal bleed which was possibly related to therapy, although concomitant HCC progression likely contributed to this event. The protocol has been modified to more readily identify and treat esophageal varices prior to enrollment. An additional patient died of fulminant peritonitis and sepsis within five days of receiving initial bevacizumab; this has been determined to be unrelated to therapy. For the 5 patients evaluable for efficacy, there has been 1 PR, 3 SD (with eventual progression at 6.4, 7.2 and 7.6 months). Conclusions: Preliminary assessment indicates that bevacizumab is safe and potentially efficacious in localized HCC in patients with adequate liver function. Because of safety concerns, an additional 6 patients will be enrolled at 5mg/kg before safety/efficacy is evaluated at 10mg/kg. Additional data regarding tumor necrosis and treatment related changes in tumor perfusion will be presented at the meeting. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Merck; Pfizer
PASSIVE TRANSFER OF ADJUVANT ARTHRITIS BY LYMPH NODE OR SPLEEN CELLS (1964)

All adjuvant-induced arthritis has been passively transferred in a highly inbred strain of rats by transfer of viable lymph node or spleen cells, but not thymus cells, to normal recipients. After an interval averaging 4.3 days recipients developed arthritis, whereas animals actively sensitized with adjuvant never developed disease before the 9th day (average 11.3 days). The transferred disease had all of the gross and pathological characteristics of primary disease, except for a lesser severity. Control studies using non-viable cells either of lymphoidal or other tissue origin were always negative. It is concluded that adjuvant arthritis is the result of an immunologic reaction which is perhaps similar to delayed hypersensitivity. The antigen in this reaction so far remains obscure.
Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution (2012)

Holliday junction (HJ) resolvases are structure-specific endonucleases that cleave four-way DNA junctions (HJs) generated during DNA recombination and repair. Bacterial RuvC, a prototypical HJ resolvase, functions as homodimer and nicks DNA strands precisely across the junction point. To gain insights into the mechanisms underlying symmetrical strand cleavages by RuvC, we performed crystallographic and biochemical analyses of RuvC from Thermus thermophilus (T.th. RuvC). The crystal structure of T.th. RuvC shows an overall protein fold similar to that of Escherichia coli RuvC, but T.th. RuvC has a more tightly associated dimer interface possibly reflecting its thermostability. The binding mode of a HJ-DNA substrate can be inferred from the shape/charge complementarity between the T.th. RuvC dimer and HJ-DNA, as well as positions of sulfate ions bound on the protein surface. Unexpectedly, the structure of T.th. RuvC homodimer refined at 1.28 Å resolution shows distinct asymmetry near the dimer interface, in the region harboring catalytically important aromatic residues. The observation suggests that the T.th. RuvC homodimer interconverts between two asymmetric conformations, with alternating subunits switched on for DNA strand cleavage. This model provides a structural basis for the 'nick-counter-nick' mechanism in HJ resolution, a mode of HJ processing shared by prokaryotic and eukaryotic HJ resolvases.
Dietary Effect of Silk Protein Sericin or Fibroin on Plasma and Epidermal Amino Acid Concentration of NC/Nga Mice (2006)

Free amino acids in epidermis function as a major component of Natural Moisturizing Factor (NMF), which maintains the optimal level of water in skin even at the low humidity. In fact, the depletion of free amino acids is reported in the epidermis of atopic dermatitis, the skin condition involving dryness. As an effort searching the dietary source for improving the level of water and free amino acid in epidermis, the dietary effects of silk protein, sericin (S) and fibroin (F) on trans epidermal water loss (TEWL), and plasma and epidermal levels of free amino acids were compared in this study. Thirty of male NC/Nga mice, an animal model of atopic dermatitis, were divided into three groups: group CA as an atopic control with control diet, group S: 1% sericin diet and group F: 1% fibroin diet. Ten of male BALB/c mice were served as group C (control group) with control diet. All mice were fed on diet and water ad libitum for 10weeks. Dry skin condition was established in group CA as TEWL was increased (148.7% of group C). In parallel, epidermal level of glutamate, one of major amino acids functioning as NMF, was dramatically decreased and epidermal levels of methionine and alanine were inversely elevated. Dietary supplementation of sericin (group S) reduced TEWL at the similar level with group C and increased epidermal levels of glutamate as well as serine and glycine, the other major amino acids as NMF. Despite a marked decrease of methionine and alanine, the reduction of TEWL and epidermal levels of glutamate, serine and glycine of group F were less than of group S. Furthermore, in contrast to similar levels of other free amino acids in plasma and epidermis of group S and group C, plasma and epidermal levels of other free amino acids, specifically phenylalanine, isoleucine, cysteine and tyrosine in epidermis of group F, were significantly higher than of group C. Together, our data demonstrate that dietary supplementation of sericin is more effective at improving dry skin condition that paralleled with the normalization of free amino acids in plasma and epidermis of NC/Nga mice.
Predicting Controller Capacity in Supervisory Control of Multiple UAVs (2008)

In the future vision of allowing a single operator to remotely control multiple unmanned vehicles, it is not well understood what cognitive constraints limit the number of vehicles and related tasks that a single operator can manage. This paper illustrates that, when predicting the number of unmanned aerial vehicles (UAVs) that a single operator can control, it is important to model the sources of wait times (WTs) caused by human-vehicle interaction, particularly since these times could potentially lead to a system failure. Specifically, these sources of vehicle WTs include cognitive reorientation and interaction WT (WTI), queues for multiple-vehicle interactions, and loss of situation awareness (SA) WTs. When WTs were included, predictions using a multiple homogeneous and independent UAV simulation dropped by up to 67%, with a loss of SA as the primary source of WT delays. Moreover, this paper demonstrated that even in a highly automated management-by-exception system, which should alleviate queuing and WTIs, operator capacity is still affected by the SA WT, causing a 36% decrease over the capacity model with no WT included.
Sampling algorithms in a stream operator (2005)

Complex queries over high speed data streams often need to rely on approximations to keep up with their input. The research community has developed a rich literature on approximate streaming algorithms for this application. Many of these algorithms produce samples of the input stream, providing better properties than conventional random sampling. In this paper, we abstract the stream sampling process and design a new stream sample operator. We show how it can be used to implement a wide variety of algorithms that perform sampling and sampling-based aggregations. Also, we show how to implement the operator in Gigascope - a high speed stream database specialized for IP network monitoring applications. As an example study, we apply the operator within such an enhanced Gigascope to perform subset-sum sampling which is of great interest for IP network management. We evaluate this implemention on a live, high speed internet traffic data stream and find that (a) the operator is a flexible, versatile addition to Gigascope suitable for tuning and algorithm engineering, and (b) the operator imposes only a small evaluation overhead. This is the first operational implementation we know of, for a wide variety of stream sampling algorithms at line speed within a data stream management system.
Functional Interactions of Transforming Growth Factor β-activated Kinase 1 with IκB Kinases to Stimulate NF-κB Activation (1999)

Several mitogen-activated protein kinase kinase kinases play critical roles in nuclear factor-kappaB (NF-kappaB) activation. We recently reported that the overexpression of transforming growth factor-beta-activated kinase 1 (TAK1), a member of the mitogen-activated protein kinase kinase kinase family, together with its activator TAK1-binding protein 1 (TAB1) stimulates NF-kappaB activation. Here we investigated the molecular mechanism of TAK1-induced NF-kappaB activation. Dominant negative mutants of IkappaB kinase (IKK) alpha and IKKbeta inhibited TAK1-induced NF-kappaB activation. TAK1 activated IKKalpha and IKKbeta in the presence of TAB1. IKKalpha and IKKbeta were coimmunoprecipitated with TAK1 in the absence of TAB1. TAB1-induced TAK1 activation promoted the dissociation of active forms of IKKalpha and IKKbeta from active TAK1, whereas the IKK mutants remained to interact with active TAK1. Furthermore, tumor necrosis factor-alpha activated endogenous TAK1, and the kinase-negative TAK1 acted as a dominant negative inhibitor against tumor necrosis factor-alpha-induced NF-kappaB activation. These results demonstrated a novel signaling pathway to NF-kappaB activation through TAK1 in which TAK1 may act as a regulatory kinase of IKKs.
Copolymerization of Ethylene and Propylene with Functionalized Vinyl Monomers by Palladium(II) Catalysts (1996)

Ziegler-Natta and related catalysts based on early transition metal d0 complexes are extensively used for the coordination polymerization of nonpolar olefins such as ethylene and propylene. However, due to their highly oxophilic nature, these catalysts are incompatible with functionalized vinyl monomers. Late transition metal catalysts are less oxophilic, but they most often dimerize or oligomerize olefins rather than form high molar mass polymers. Thus, ethylene-acrylate or ethyleneviny acetate copolymers are still exclusively produced by radical routes, which often require high pressure.
Genomic signatures of honey bee association in an acetic acid symbiont (2018)

Abstract Honey bee queens are central to the success and productivity of their colonies; queens are the only reproductive members of the colony, and therefore queen longevity and fecundity can directly impact overall colony health. Recent declines in the health of the honey bee have startled researchers and lay people alike as honey bees are agriculture’s most important pollinator. Honey bees are important pollinators of many major crops and add billions of dollars annually to the US economy through their services. One factor that may influence queen and colony health is the microbial community. Although honey bee worker guts have a characteristic community of bee-specific microbes, the honey bee queen digestive tracts are colonized by a few bacteria, notably an acetic acid bacterium not seen in worker guts: Bombella apis. This bacterium is related to flower-associated microbes such as Saccharibacter floricola and other species in the genus Saccharibacter, and initial phylogenetic analyses placed it as sister to these environmental bacteria. We used comparative genomics of multiple honey bee-associated strains and the nectar-associated Saccharibacter to identify genomic changes associated with the ecological transition to bee association. We identified several genomic differences in the honey bee-associated strains, including a complete CRISPR/Cas system. Many of the changes we note here are predicted to confer upon them the ability to survive in royal jelly and defend themselves against mobile elements, including phages. Our results are a first step towards identifying potential benefits provided by the honey bee queen microbiota to the colony’s matriarch.