gebhart/patrepeval huggingface dataset:
RSFQ-based D/A converter for AC voltage standard (1999)

Digital to analog converters based on the Josephson effect are promising for voltage standards, because they produce voltage steps with ultimate precision and stability. In this paper, we describe a project to develop a Josephson D/A converter designed for synthesizing a sinusoidal waveform with metrological accuracy. The D/A converter is based on RSFQ (Rapid Single Flux Quantum) logic circuits, and consists of a frequency multiplier (FM), a pulse distributor (PD), and a number of voltage multipliers (VMs). Each VM circuit, corresponding to the n-th bit digital code, multiplies the number of SFQ pulses by a factor of 2/sup n/. By gating the input SFQ pulses from the FM to the VMs using the PD circuits, a programmable output voltage is obtained. Possible sources of uncertainties in the measurement of the rms value of the synthesized sine wave are discussed.
Conformation of sequential and random copolypeptides of lysine and alanine in sodium dodecyl sulfate solution (1983)

Abstract A series of sequential polypeptides, (Lys i ‐Ala j ) n , and random copolypeptides, (Lys x , Ala y ) n , were synthesized. The competitive effect of Ala, a helix former, and Lys, whose homopolymer has a β‐form in neutral NaDodSO 4 solution, was determined by CD and absorption spectroscopy. All the polypeptides studied were unordered in neutral solution without the surfactant. Of the six sequential polypeptides only (Lys‐Ala) n adopted a stable β‐form in NaDodSO 4 solution. Most striking is the difference between this polypeptide, (Lys 2 ‐Ala 2 ) n and (Lys x , Ala y ) n , even though they all have equimolar Lys and Ala. (Lys 2 ‐Ala 2 ) n was partially helical in 2.5–5 m M NaDodSO 4 but approached the unordered form in 50 m M NaDodSO 4 , whereas (Lys 50 , Ala 50 ) n was completely helical in all NaDodSO 4 concentrations. Even Lysrich (Lys 2 ‐Ala) n and (Lys 3 ‐Ala) n formed a partial helix and a trace of the β‐form, respectively, in low NaDodSO 4 concentrations; both reverted to the unordered form in high NaDodSO 4 concentrations. These results can be explained by Pauling‐Corey's model for β‐pleated sheets. Only (Lys‐Ala) n has all DodSO ‐bound Lys + residues on one side and Ala residues on the other side of the polypeptide chain. They can nestle quiet efficiently in a β‐sheet and between neighboring β‐sheets. Our results further imply that random copolypeptides are not completely random; they comprise varying segments of (Lys k ‐Ala m ), where k and m could vary from zero to a small integer.
Generation of unstructured tetrahedral meshes by advancing front technique (1993)

Abstract An algorithm for generating unstructured tetrahedral meshes by the advancing front technique is presented. Emphasis is placed on the construction of tetrahedral elements. Several measures are employed to prevent difficult situations. A control line/surface scheme is used to specify element size. Numerical examples are provided to show the performance of the algorithm.
Gene amplification of EGFR, HER2, FGFR2 and MET in esophageal squamous cell carcinoma (2013)

Molecular targeted therapy is expected to be a promising therapeutic approach for the treatment of esophageal squamous cell carcinoma (ESCC); however, the gene amplification status of molecular targeted genes in ESCC remains largely unclear. The gene amplification of EGFR, HER2, FGFR2 and MET was examined using a real-time PCR-based copy number assay of 245 ESCC surgical specimens of formalin-fixed, paraffin-embedded samples. Fluorescence in situ hybridization (FISH) and comparative genomic hybridization analyses verified the results of the copy number assay. EGFR mutation was detected using the Scorpions-ARMS method. The EGFR status and drug sensitivity to an EGFR tyrosine kinase inhibitor was then evaluated in vitro. Gene amplification of EGFR and HER2 was observed in 7% (16/244) and 11% (27/245) of the ESCC specimens. A multivariate analysis revealed that HER2 amplification was a significant predictor of a poor prognosis in patients with stage III post-operative ESCC. The L861Q type of EGFR mutation with hypersensitivity to EGFR tyrosine kinase inhibitor was found in one of the eight ESCC cell lines and one del745 type of EGFR mutation was identified in 107 clinical samples. In addition, we demonstrated for the first time that FGFR2 amplification was observed in 4% (8/196) of the ESCC specimens. MET amplification was observed in 1% (2/196). In conclusion, the frequent gene amplification of EGFR, HER2 and FGFR2 and the presence of active EGFR mutations were observed in ESCC specimens. Our results strongly encourage the development of molecular targeted therapy for ESCC.
Secretion of Human Furin into Mouse Milk (1997)

We have previously described the expression of the human proprotein convertase furin or paired basic amino acid-cleaving enzyme, in mice transgenic for paired basic amino acid-cleaving enzyme and human Protein C (HPC). Here we show 100-fold or higher expression of furin in the mammary gland, compared with endogenous furin. Furin and recombinant HPC were detected in the same regions of the mammary gland and regulated similar to the endogenous whey acidic protein. In addition to the expected intracellular localization, furin was secreted into the milk as an 80-kDa form lacking the transmembrane and cytoplasmic domains. Furin present at levels of up to 40,000 units/ml milk cleaved the t-butoxycarbonyl-RVRR-AMC substrate with a Km of 32 microM, and processed the recombinant HPC precursor at the appropriate sites. Surprisingly, the expression of an active protease was not toxic to the mammary gland. This is a rare example of an animal model secreting active truncated forms of a processing endoprotease into a bodily fluid.
F-Cooper: Feature based Cooperative Perception for Autonomous Vehicle Edge Computing System Using 3D Point Clouds (2019)

Autonomous vehicles are heavily reliant upon their sensors to perfect the perception of surrounding environments, however, with the current state of technology, the data which a vehicle uses is confined to that from its own sensors. Data sharing between vehicles and/or edge servers is limited by the available network bandwidth and the stringent real-time constraints of autonomous driving applications. To address these issues, we propose a point cloud feature based cooperative perception framework (F-Cooper) for connected autonomous vehicles to achieve a better object detection precision. Not only will feature based data be sufficient for the training process, we also use the features' intrinsically small size to achieve real-time edge computing, without running the risk of congesting the network. Our experiment results show that by fusing features, we are able to achieve a better object detection result, around 10% improvement for detection within 20 meters and 30% for further distances, as well as achieve faster edge computing with a low communication delay, requiring 71 milliseconds in certain feature selections. To the best of our knowledge, we are the first to introduce feature-level data fusion to connected autonomous vehicles for the purpose of enhancing object detection and making real-time edge computing on inter-vehicle data feasible for autonomous vehicles.
Gordon-Haus jitter suppression using a single phasemodulator (1994)

The authors show that the inclusion of a single phase modulator close to the midpoint of an optical fibre communication system substantially reduces the Gordon-Haus jitter of optical solitons. In a numerical example, a factor of 5 reduction is achieved in the timing variance of a 5 Gbit/s, 9000 km system.
The combined role of P- and E-selectins in atherosclerosis. (1998)

P- and E-selectins are adhesion molecules mediating the first step in leukocyte extravasation. Because their function in leukocyte adhesion is overlapping, we hypothesized that there might be a combined effect of these selectins on the development of atherosclerotic lesions. We bred P- and E-selectin-double-deficient mice onto the low-density lipoprotein receptor (LDLR)-deficient background (LDLR-/- P/E-/-) and compared lesion development in these mice to that in mice wild type for both selectins (LDLR-/- P/E+/+). After 8 wk on atherogenic diet, the LDLR-/- P/E-/- mice developed fatty streaks in the aortic sinus that were five times smaller than those in LDLR-/- P/E+/+ mice. The density of macrophages in the fatty streaks was comparable between LDLR-/- P/E+/+ and LDLR-/- P/E-/- mice. After 22 wk on the diet, the lesions spread throughout the aorta but this process was delayed in LDLR-/- P/E-/- mice. At 37 wk on diet, the lesions progressed to the fibrous plaque stage in both genotypes. However, the lesions in the aortic sinus in LDLR-/- P/E-/- mice were 40% smaller and less calcified than those of LDLR-/- P/E +/+ mice. Our results suggest that P- and E-selectins together play an important role in both early and advanced stages of atherosclerotic lesion development.
Chronic Kidney Disease – How Many Have It? (2002)

A 52-year-old woman with HIV and recent antiretroviral therapy non-adherence presented with a 5-day history of widespread painful vesicular skin lesions. Direct fluorescent antibody testing of the skin lesions was positive for varicella zoster virus (VZV). On day 3, she developed profound right upper extremity weakness. MRI of the brain and cervical spine was suggestive of VZV myelitis. Lumbar puncture was positive for VZV PCR in the cerebrospinal fluid (CSF) and CSF HIV viral load was detected at 1030 copies/mL, indicating ‘secondary’ HIV CSF escape. She was treated with intravenous acyclovir for 4 weeks and subsequent oral therapy with famciclovir then valacyclovir for 6 weeks. She also received dexamethasone. The patient had an almost full recovery at 6 months. Myelitis is a rare complication of reactivated VZV infection that can have atypical presentation in immunocompromised patients. Such ‘secondary’ HIV CSF escape should be considered in immunosuppressed patients with concomitant central nervous system infection.
Interaction of Silane Coupling Agents with Cellulose (2002)

The adsorption of several prehydrolyzed alkoxysilanes onto the surface of cellulosic fibers in ethanol/water mixtures has been studied quantitatively. The corresponding isotherms show the formation of a monolayer followed by further adsorption. The nature of the fourth substituent on the silane plays a specific role on the features of this association. Whereas at room temperature only dispersive and polar attractive interactions occur, heating above 100 °C produces condensation reactions resulting in covalent bonding between the substrate and the silane forming the monolayer. As a result of this investigation, the possibility of calling upon this surface modification in order to compatibilize cellulosic fibers with polyolefinic matrixes for the elaboration of composite materials seems to be a promising strategy.
Evaluation of Hand Micromovement Features for Continuous Authentication of Smartphone Users During Typing (2015)

Biometricka autentizace je způsob ověřeni identity, který spoleha na fyziologicke nebo behavioralni charakteristiky uživatele. V teto praci se zabývame vyhodnocenim Hand Movement, Orientation and Grasp (HMOG), nove behavioralni biometriky pro průběžnou autentizaci uživatelů pisicich na chytrých telefonech. HMOG nevtiravě zachytava male otřesy a změny orientace, ktere vznikaji tim, jak uživatel drži telefon a jak na něm pise. Vyhodnotili jsme schopnost HMOG featur autentizovat uživatele na datech posbiraných od sta pisicich uživatelů za dvou podminek: během sezeni a při chůzi. Kombinace HMOG s featurami běžně použivanými v soucasne době (charakteristiky poklepani a dynamiky klavesových uderů) zlepsila EER pro chodici uživatele (z 10.51% na 6.92%). Pro sedici uživatele se EER zlepsilo v kratsich autentizacnich oknech (např. z 19.11% na 15.44% pro 20 sekund dlouhe autentizacni okno).
National spreadsheet for agricultural distortions in India (2007)

This chapter analyzes the impact on incentives for India's agriculture resulting of price, trade and exchange rate policies, focusing on incentives for agriculture relative to incentives for manufacturing and the rest of the economy. This study updates the earlier estimates to 2005 and incorporates estimates for agriculture going back to 1965. In addition it extends the previous work by taking account of policies affecting incentives for the production of fresh fruit and vegetables and dairying, which between them account for large shares of the rural economy as measured by their contributions to gross domestic product (GDP). In addition, policies affecting food processing are discussed briefly. The chapter is organized as follows. It begins with brief overviews of Indian economic growth and structural changes in the economy and the evolution of India's trade policies since independence, including comments on the effects of India's present agricultural trade policies on agricultural trade with its neighbors in South Asia. This is followed by a discussion of the exchange rate and how exchange rate changes have interacted with trade policies, especially during the massive Rupee devaluation which started in 1985 and ended in 1993. Quantitative evidence on nominal rates of assistance to various agricultural sub-sectors, including via electricity and fertilizer input subsidies, are then provided, followed by estimates of distortions to incentives for farmers relative to producers of non-agricultural tradable. The latter shows that the marked anti-agricultural bias of policies of earlier years gradually disappeared, and in the current decade has been replaced by a slight bias in favor of agriculture. Finally, the authors discuss the political economy forces that are likely to influence the direction of future Indian policies, including the possibility that a strong pro-agricultural bias may emerge along the lines followed by more-advanced densely populated economies in East Asia and elsewhere.
Functional expression and characterization of the envelope glycoprotein E1E2 heterodimer of hepatitis C virus (2019)

Hepatitis C virus (HCV) is a member of Hepacivirus and belongs to the family of Flaviviridae. HCV infects millions of people worldwide and may lead to cirrhosis and hepatocellular carcinoma. HCV envelope proteins, E1 and E2, play critical roles in viral cell entry and act as major epitopes for neutralizing antibodies. However, unlike other known flaviviruses, it has been challenging to study HCV envelope proteins E1E2 in the past decades as the in vitro expressed E1E2 heterodimers are usually of poor quality, making the structural and functional characterization difficult. Here we express the ectodomains of HCV E1E2 heterodimer with either an Fc-tag or a de novo designed heterodimeric tag and are able to isolate soluble E1E2 heterodimer suitable for functional and structural studies. Then we characterize the E1E2 heterodimer by electron microscopy and model the structure by the coevolution based modeling strategy with Rosetta, revealing the potential interactions between E1 and E2. Moreover, the E1E2 heterodimer is applied to examine the interactions with the known HCV receptors, neutralizing antibodies as well as the inhibition of HCV infection, confirming the functionality of the E1E2 heterodimer and the binding profiles of E1E2 with the cellular receptors. Therefore, the expressed E1E2 heterodimer would be a valuable target for both viral studies and vaccination against HCV.
Recombinant Allergens with Reduced Allergenicity but Retaining Immunogenicity of the Natural Allergens: Hybrids of Yellow Jacket and Paper Wasp Venom Allergen Antigen 5s (2001)

The homologous venom allergen Ag 5s from the yellow jacket (Vespula vulgaris) and paper wasp (Polistes annularis) have 59% sequence identity of their respective 204 and 205 amino acid residues, and they have low degrees of antigenic cross-reactivity in insect allergic patients and in animal models. Hybrids containing different segments of these two vespid Ag 5s were expressed in yeast. Circular dichroism spectroscopy suggests the hybrids to have the secondary structure of natural Ag 5. Inhibition ELISA with human and murine Abs suggests the hybrids to have the discontinuous B cell epitopes of the natural Ag 5 but with an altered epitope density. The hybrids were immunogenic in mice for B and T cell responses to both Ag 5s. The N-terminal region of Ag 5 was found to contain its dominant B cell epitope(s). Hybrids containing 10-49 residues of yellow jacket Ag 5 showed 100- to 3000-fold reduction in allergenicity when tested by histamine release assay with basophils of yellow jacket-sensitive patients. Our findings suggest that hybrids represent a useful approach to map the discontinuous B cell epitope-containing regions of proteins. They also suggest that Ag 5 hybrids may be useful immunotherapeutic reagents in man.
Reversible Acyl-Homoserine Lactone Binding to Purified <i>Vibrio fischeri</i> LuxR Protein (2004)

The Vibrio fischeri LuxR protein is the founding member of a family of acyl-homoserine lactone-responsive quorum-sensing transcription factors. Previous genetic evidence indicates that in the presence of its quorum-sensing signal, N-(3-oxohexanoyl) homoserine lactone (3OC6-HSL), LuxR binds to lux box DNA within the promoter region of the luxI gene and activates transcription of the luxICDABEG luminescence operon. We have purified LuxR from recombinant Escherichia coli. Purified LuxR binds specifically and with high affinity to DNA containing a lux box. This binding requires addition of 3OC6-HSL to the assay reactions, presumably forming a LuxR-3OC6-HSL complex. When bound to the lux box at the luxI promoter in vitro, LuxR-3OC6-HSL enables E. coli RNA polymerase to initiate transcription from the luxI promoter. Unlike the well-characterized LuxR homolog TraR in complex with its signal (3-oxo-octanoyl-HSL), the LuxR-30C6-HSL complex can be reversibly inactivated by dilution, suggesting that 3OC6-HSL in the complex is not tightly bound and is in equilibrium with the bulk solvent. Thus, although LuxR and TraR both bind 3-oxoacyl-HSLs, the binding is qualitatively different. The differences have implications for the ways in which these proteins respond to decreases in signal concentrations or rapid drops in population density.
The OPTLS Protocol and TLS 1.3 (2016)

We present the OPTLS key-exchange protocol, its design, rationale and cryptographic analysis. OPTLS design has been motivated by the ongoing work in the TLS working group of the IETF for specifying TLS 1.3, the next-generation TLS protocol. The latter effort is intended to revamp the security of TLS that has been shown inadequate in many instances as well as to add new security and functional features. The main additions that influence the cryptographic design of TLS 1.3 (hence also of OPTLS) are a new "0-RTT requirement" (0-RTT stands for "zero round trip time") to allow clients that have previously retrieved or cached the public key of the server to send protected data already in the first flow of the protocol, making perfect forward secrecy (PFS) a mandatory requirement, and moving to elliptic curves as the main cryptographic basis for the protocol (for performance and security reasons). Accommodating these requirements calls for moving away from the RSA-centric design of TLS in favor of a protocol based on Diffie-Hellman techniques. OPTLS offers a simple design framework that supports all the above requirements from the protocol with a uniform and modular logic that helps in the specification, analysis, performance optimization, and future maintenance of the protocol. The current (draft) specification of TLS 1.3 builds upon the OPTLS framework as a basis for the cryptographic core of the handshake protocol adapting the different modes of OPTLS to the TLS 1.3 context.
Anxiety and the irritable bowel syndrome: psychiatric, medical, or both? (1997)

The association between the irritable bowel syndrome (IBS) and psychiatric disorders is well-known to most clinicians, but the nature of the relationship is far from clear. There is an increased prevalence of psychiatric illness in IBS patients and an increase in IBS in psychiatric patients. Whether this association exists outside of treatment-seeking populations (i.e., in IBS sufferers who do not seek treatment) has not been well investigated. This paper will selectively review the existing literature regarding the association of IBS and psychiatric illness in both patient and nonpatient samples. A model of the brain-gut interaction will be presented, as will practical implications of this model for treatment of individuals with IBS.
Loniceroside C, an Antiinflammatory Saponin from Lonicera japonica. (2003)

A new triterpenoid saponin, loniceroside C was isolated from the aerial parts of Lonicera japonica. Its structure was established to be 3-O-beta-D-glucopyranosyl hederagenin 28-O-alpha-L-rhamnopyranosyl (1-->2)-[beta-D-xylopyranosyl(1-->6)]-beta-D-glucopyranosyl ester by spectroscopic techniques and chemical transformations. Loniceroside C showed in vivo antiinflammatory activity against mouse ear edema provoked by croton oil.
Detection of platelet antibodies by flow cytometric analysis. (1984)

A rapid, sensitive indirect immunofluorescence assay utilizing flow cytometry to detect immune-mediated thrombocytopenia is described. Fluorescein-conjugated F(ab')2 antihuman IgG or IgGAM is reacted with donor platelets after their incubation with test sera and the resulting immune complex is measured using flow cytometric analysis. With this technique excess of Ig on the platelet, expressed as a ratio of fluorescence of test sera/autologous control sera, was noted in 24 of 30 patients (80%) with immune thrombocytopenias caused by auto- or allo-antiplatelet antibodies. Twenty-four sera from nonimmune thrombocytopenic patients were consistently negative. This technique has the advantage of being highly reproducible and avoids the subjective interpretation inherent with manual immunofluorescence assays.
An expanding universe of the non-coding genome in cancer biology (2014)

Neoplastic transformation is caused by accumulation of genetic and epigenetic alterations that ultimately convert normal cells into tumor cells with uncontrolled proliferation and survival, unlimited replicative potential and invasive growth [Hanahan,D. et al. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674]. Although the majority of the cancer studies have focused on the functions of protein-coding genes, emerging evidence has started to reveal the importance of the vast non-coding genome, which constitutes more than 98% of the human genome. A number of non-coding RNAs (ncRNAs) derived from the 'dark matter' of the human genome exhibit cancer-specific differential expression and/or genomic alterations, and it is increasingly clear that ncRNAs, including small ncRNAs and long ncRNAs (lncRNAs), play an important role in cancer development by regulating protein-coding gene expression through diverse mechanisms. In addition to ncRNAs, nearly half of the mammalian genomes consist of transposable elements, particularly retrotransposons. Once depicted as selfish genomic parasites that propagate at the expense of host fitness, retrotransposon elements could also confer regulatory complexity to the host genomes during development and disease. Reactivation of retrotransposons in cancer, while capable of causing insertional mutagenesis and genome rearrangements to promote oncogenesis, could also alter host gene expression networks to favor tumor development. Taken together, the functional significance of non-coding genome in tumorigenesis has been previously underestimated, and diverse transcripts derived from the non-coding genome could act as integral functional components of the oncogene and tumor suppressor network.