gebhart/patrepeval huggingface dataset:
Evaluation of recombinant transferrin-binding protein B variants from Neisseria meningitidis for their ability to induce cross-reactive and bactericidal antibodies against a genetically diverse collection of serogroup B strains (1997)

Transferrin-binding protein B (TbpB) is a surface-exposed protein, variable among strains of Neisseria meningitidis, that has been considered as a vaccine candidate. To define a TbpB molecule that would give rise to broadly cross-reactive antibodies with TbpB of many strains, specific antisera were produced against three recombinant TbpB variants from strain M982: one corresponding to the full-length TbpB; one in which stretches of amino acids located in the central part of the molecule, described as hypervariable, have been deleted; and one corresponding to the N-terminal half of the molecule, described as the human transferrin binding domain. The reactivity of these antisera against 58 serogroup B strains with a 2.1-kb tbpB gene representing different genotypes, serotypes, and subtypes and different geographic origins was tested on intact meningococcal cells. In parallel, the bactericidal activity of the antisera was evaluated against 15 of the 58 strains studied. Of the 58 strains, 56 (98%) reacted with the antiserum specific for the N-terminal half of TbpB M982; this antiserum was bactericidal against 9 of 15 strains (60%). On the other hand, 43 of 58 strains reacted with the antiserum raised to full-length TbpB while 12 of 15 (80%) were killed with this antiserum. The antiserum specific to TbpB deleted of its central domain gave intermediate results, with 53 of 58 strains (91.3%) recognized and 10 of 15 (66.6%) killed. These results indicate that the N-terminal half of TbpB was sufficient to induce cross-reactive antibodies reacting with the protein on meningococcal cells but that the presence of the C-terminal half of the protein is necessary for the induction of cross-bactericidal antibodies.
Quantum amplitude amplification and estimation (2002)

Consider a Boolean function $\chi: X \to \{0,1\}$ that partitions set $X$ between its good and bad elements, where $x$ is good if $\chi(x)=1$ and bad otherwise. Consider also a quantum algorithm $\mathcal A$ such that $A |0\rangle= \sum_{x\in X} \alpha_x |x\rangle$ is a quantum superposition of the elements of $X$, and let $a$ denote the probability that a good element is produced if $A |0\rangle$ is measured. If we repeat the process of running $A$, measuring the output, and using $\chi$ to check the validity of the result, we shall expect to repeat $1/a$ times on the average before a solution is found. *Amplitude amplification* is a process that allows to find a good $x$ after an expected number of applications of $A$ and its inverse which is proportional to $1/\sqrt{a}$, assuming algorithm $A$ makes no measurements. This is a generalization of Grover's searching algorithm in which $A$ was restricted to producing an equal superposition of all members of $X$ and we had a promise that a single $x$ existed such that $\chi(x)=1$. Our algorithm works whether or not the value of $a$ is known ahead of time. In case the value of $a$ is known, we can find a good $x$ after a number of applications of $A$ and its inverse which is proportional to $1/\sqrt{a}$ even in the worst case. We show that this quadratic speedup can also be obtained for a large family of search problems for which good classical heuristics exist. Finally, as our main result, we combine ideas from Grover's and Shor's quantum algorithms to perform amplitude estimation, a process that allows to estimate the value of $a$. We apply amplitude estimation to the problem of *approximate counting*, in which we wish to estimate the number of $x\in X$ such that $\chi(x)=1$. We obtain optimal quantum algorithms in a variety of settings.
A Phase I study of an intravesically administered immunotoxin targeting EpCAM for the treatment of nonmuscle-invasive bladder cancer in BCG-refractory and BCG-intolerant patients (2010)

VB4-845 dosed on a weekly basis for 6 weeks was very well tolerated at all dose levels. Although an MTD was not determined at the doses administered, VB4-845 showed evidence of an antitumor effect that warrants further clinical investigation for the treatment of NMIBC in this patient population.
An Econometric Model of the United States, 1929-1952. (1956)

Journal Article An Econometric Model of the United States, 1929-1952 Get access An Econometric Model of the United States, 1929-1952. By L. R. Klein and A. S. Goldberger. Contributions to Economic Analysis, IX. (Amsterdam: North Holland Publishing Company, 1955. Pp. xv + 165. 34s.) S. J. Prais S. J. Prais Cambridge Search for other works by this author on: Oxford Academic Google Scholar The Economic Journal, Volume 66, Issue 262, 1 June 1956, Pages 325–327, https://doi.org/10.2307/2227976 Published: 01 June 1956
Hamiltonian plasma-harmonic oscillator theory: Generalized depth profilometry of electronically continuously inhomogeneous semiconductors and the inverse problem (1996)

The Hamilton–Jacobi formalism of the propagation of an electron-hole photoexcited plasma in continuously inhomogeneous semiconductors with arbitrary depth profiles in carrier diffusivity and/or minority-carrier lifetime is presented. The theoretical model is based on the variational formulation of the canonical Hamiltonian for the evolution of carrier plasmas and shows that propagating plasma waves can be formally described by a plasma-harmonic oscillator, thus generalizing existing theoretical treatments of photoexcited carrier diffusion in electronic solids. Simple analytical expressions for the free-carrier diffusion magnitude and phase frequency dependencies in the case of exponential carrier diffusivity and minority carrier lifetime profiles are obtained. The effect of continuously varying electronic properties on the surface plasma density magnitude and phase frequency behavior is demonstrated through computer simulations and very good quantitative agreement is obtained with photothermal radiometric data from an ion-implanted Si wafer allowing the reconstruction of the lifetime depth profile.
Heparin Bonding on Colloidal Graphite Surfaces (1963)

Experiments on clotting, both in vitro and in vivo, showed that a colloidal graphite surface, when rinsed with a cationic, surface-active agent, was capable of bonding heparin. The resistance of this graphite-heparin surface to the formation of clots was far greater than plastic or silicone surfaces in comparable studies.
Anti-viral protection conferred by recombinant adenylate cyclase toxins fromBordetella pertussiscarrying a CD8+T cell epitope from lymphocytic choriomeningitis virus (1997)

The elucidation of the mechanisms of antigen presentation by major histocompatibility complex class I molecules has stimulated the search for nonreplicative vectors that could deliver CD8+ T cell epitopes to the cytosol of antigen-presenting cells to trigger the activation of specific cytotoxic T lymphocytes (CTLs) in vivo. In the present study, we investigated the potential ability of an invasive adenylate cyclase toxin from Bordetella pertussis, carrying a CD8+ T cell epitope from the nucleoprotein of lymphocytic choriomeningitis virus (LCMV), to stimulate protective anti-viral immunity. Mice immunized with this recombinant toxin developed strong CTL responses against LCMV-infected target cells. Moreover, these mice were protected against an intracerebral challenge with a virulent strain of LCMV that killed all nonimmunized mice within 7 days. This protection was abolished after in vivo elimination of CD8+ T cells. A mutant toxin devoid of adenylate cyclase activity (i.e., cAMP synthesizing activity) was constructed by insertion of a dipeptide into the catalytic site of the molecule. This genetically detoxified invasive toxin carrying the LCMV epitope stimulated a strong CTL response against both peptide-coated and virus-infected target cells, and mice immunized with this molecule were fully protected against a lethal intracerebral LCMV challenge. To our knowledge, this study represents the first demonstration that a genetically detoxified bacterial toxin carrying a viral CTL epitope can stimulate efficient protective immunity.
Expression of HER3, HER4 and their ligand heregulin-4 is associated with better survival in bladder cancer patients (2004)

The epidermal growth factor system has been associated to prognosis in patients with bladder cancer based mainly on the expression of the epidermal growth factor (EGF) receptor 1 (EGFR) and HER2 and their activating ligands. Since limited information exists concerning the expression of other parts of the EGF system, we examined the expression of the receptors HER3 and HER4 and their activating ligands, the heregulins (HRGs), in bladder cancer patients. Biopsies from bladder cancer tumours were obtained from 88 patients followed for a median of 23 months (range, 1-97 months). The mRNA content of four ligands and their isoforms (HRG1alpha, HRG1beta, HRG2alpha, HRG2beta, HRG3 and HRG4) and two receptors (HER3 and HER4) was quantified by real-time PCR. A significantly lower mRNA expression level of HER3 (P=0.0003), HRG2alpha (P=0.0159), HRG2beta (P=0.0007) and HRG4 (P<0.0001) was observed in muscle-invasive (T2-T4) tumours as compared to superficial (Ta) tumours. The expression of HER3 mRNA correlated strongly to overall survival (P=0.0042); increased expression of HER4 (P=0.0261) and HRG4 (P=0.0245) was also associated with better prognosis. Interestingly, patients with coexpression of HER3 (P=0.0034) or HER4 (P=0.0080) together with their stimulating ligand HRG4 showed even better survival than for HER3 or HER4 alone. Our results together with previous data suggest a dual face for the EGF system. While it is well established that an increased signalling through HER1 and HER2 is related to a poor prognosis, our data suggest that signalling through HER3 and HER4 is related to a favourable outcome in bladder cancer patients.
Statistical analysis of speech signals (1970)

This is a condensed report of a thesis study carried out at the Department of Speech Communication in 1970, The purpose was to determine, for continuous speech, peakfactor, formfactor, long-time av ...
The Double-Edged Sword of Activation-Induced Cytidine Deaminase (2005)

Activation-induced cytidine deaminase (AID) is required for Ig class switch recombination, a process that introduces DNA double-strand breaks in B cells. We show in this study that AID associates with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) promoting cell survival, presumably by resolving DNA double-strand breaks. Wild-type cells expressing AID mutants that fail to associate with DNA-PKcs or cells deficient in DNA-PKcs or 53BP1 expressing wild-type AID accumulate gammaH2AX foci, indicative of heightened DNA damage response. Thus, AID has two independent functions. AID catalyzes cytidine deamination that originates DNA double-strand breaks needed for recombination, and it promotes DNA damage response and cell survival. Our results thus resolve the paradox of how B cells undergoing DNA cytidine deamination and recombination exhibit heightened survival and suggest a mechanism for hyperIgM type II syndrome associated with AID mutants deficient in DNA-PKcs binding.
GeneID in Drosophila (2000)

GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the log-likelihood ratio of a Markov model for coding DNA. In the last step, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. In this paper we describe the obtention of PWMs for sites, and the Markov model of coding DNA in Drosophila melanogaster . We also compare other models of coding DNA with the Markov model. Finally, we present and discuss the results obtained when GeneID is used to predict genes in the Adh region. These results show that the accuracy of GeneID predictions compares currently with that of other existing tools but that GeneID is likely to be more efficient in terms of speed and memory usage. GeneID is available at http://www1.imim.es/∼eblanco/GeneId .
Detection of Multiple Proteins on One Spot by Laser Ablation Inductively Coupled Plasma Mass Spectrometry and Application to Immuno- Microarray with Element-Tagged Antibodies (2007)

Inductively coupled plasma mass spectrometry (ICPMS) has been successfully used for the detection of element-tagged biomolecules with the advantage of multielement capability. However, this technique cannot be used for microarray detection due to the necessity to dissolve the elemental tags before introducing them to the plasma source. Here, we report the detection of multiple proteins on each spot of the immuno-microarray by laser ablation ICPMS. alpha-Fetoprotein IgG (AFP), carcinoembryonic antigen (CEA), and human IgG, as model proteins, have been detected on the basis of sandwich-type immunoreactions on a microarray with Sm3+-labeled AFP antibody, Eu3+-labeled CEA antibody, and Au-labeled goat-anti-human IgG (GAH) as labeled antibodies. The detection limits were 0.20, 0.14, and 0.012 ng mL-1 (3sigma) with the RSD of 5.7%, 2.6%, and 2.3% at the concentration of 1.0 ng mL-1 for AFP, CEA, and human IgG, respectively. The present detection method permits detecting multiple analytes from each spot of microarray with a spatial resolution at micrometer range, which can alleviate the stress to fabricate high-density arrays. Furthermore, the substrate materials and immobilized proteins do not interfere with the detection. The present technique provides a new strategy for readout of microarray.
Hugl-1 induces apoptosis in esophageal carcinoma cells bothin vitroandin vivo (2013)

These results suggest that Hugl-1 induces growth suppression and apoptosis in a human esophageal squamous cell carcinoma cell line both in vitro and in vivo.
Base‐Induced Formation of Two Magnesium Metal‐Organic Framework Compounds with a Bifunctional Tetratopic Ligand (2008)

Abstract Two coordination polymers constructed from magnesium and the tetratopic organic linker 2,5‐dihydroxyterephthalic acid are reported, denominated CPO‐26‐Mg and CPO‐27‐Mg. The organic component carries two different types of protic functional groups. The degree of deprotonation of the organic component can be regulated by the amount of sodium hydroxide employed in the synthesis, thus determining which of the compounds forms. In CPO‐26‐Mg, only the carboxylic acid groups of the linker are deprotonated and take part in the construction of the three‐dimensional framework. The structure is non‐porous, and its topology is based on the PtS net. In CPO‐27‐Mg, both the carboxylic acid and the hydroxy groups are deprotonated and involved in the construction of a microporous three‐dimensional framework which is based on a honeycomb motif containing large solvent‐filled channels. The metal atoms are arranged in chiral chains along the intersection of the honeycomb and contain one water molecule in their coordination sphere, which allows for the creation of coordinatively unsaturated metal sites upon dehydration. CPO‐27‐Mg is a potentially useful lightweight adsorbent with a pore volume of 60 % of the total volume of the structure and an apparent Langmuir surface area of up to 1030 m 2 g –1 . Its thermal stability was investigated by thermogravimetry and variable‐temperature powder X‐ray diffraction, which shows framework degradation to commence at 160 °C in air, at 235 °C under nitrogen, and at 430 °C in a dynamic vacuum. Thermogravimetric dehydration and re‐hydration experiments at miscellaneous temperatures indicate that it is possible to obtain open metal sites in CPO‐27‐Mg, but the water is more tightly bound in this material than in the previously reported isostructural nickel compound.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)
Epidemiology of Bladder Emptying Symptoms in Elderly Men (1992)

We provide estimates of the prevalence, incidence and remission of difficult bladder emptying symptoms (prostatism) among noninstitutionalized men 60 years old and older living in a community in the United States. The prevalence of 1 or more symptoms of prostatism (hesitancy, straining, weak stream, intermittency or use of a catheter) among men who never had prostatic surgery is 35%. The annual incidence rates during years 1 and 2 of followup were 16.4% and 16.1%, respectively. Remission of symptoms of prostatism also was observed. Of the respondents with severe symptoms at baseline 22.9% were asymptomatic 1 year later. The prevalence of prostatic surgery in this population was 20%. The annual incidence rates during years 1 and 2 of followup were 2.6% and 3.3%, respectively. Urological and nonurological correlates of prostatism are identified. The irritative bladder symptoms are all significantly associated with moderate to severe bladder emptying symptoms (p < 0.0005). Nonurological conditions that also are associated with moderate to severe symptoms of prostatism include use of sedatives or tranquilizers, arthritis, poor health status and transient ischemic attacks. These observations are the initial step in documenting and understanding the various symptoms of prostatism, and its application in clinical practice.
Determinants of Glomerular Filtration Rate (1976)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
Characterization of Functional Hepatitis C Virus Envelope Glycoproteins (2004)

Hepatitis C virus (HCV) encodes two envelope glycoproteins, E1 and E2, that assemble as a noncovalent heterodimer which is mainly retained in the endoplasmic reticulum. Because assembly into particles and secretion from the cell lead to structural changes in viral envelope proteins, characterization of the proteins associated with the virion is necessary in order to better understand how they mature to be functional in virus entry. There is currently no efficient and reliable cell culture system to amplify HCV, and the envelope glycoproteins associated with the virion have therefore not been characterized yet. Recently, infectious pseudotype particles that are assembled by displaying unmodified HCV envelope glycoproteins on retroviral core particles have been successfully generated. Because HCV pseudotype particles contain fully functional envelope glycoproteins, these envelope proteins, or at least a fraction of them, should be in a mature conformation similar to that on the native HCV particles. In this study, we used conformation-dependent monoclonal antibodies to characterize the envelope glycoproteins associated with HCV pseudotype particles. We showed that the functional unit is a noncovalent E1E2 heterodimer containing complex or hybrid type glycans. We did not observe any evidence of maturation by a cellular endoprotease during the transport of these envelope glycoproteins through the secretory pathway. These envelope glycoproteins were recognized by a panel of conformation-dependent monoclonal antibodies as well as by CD81, a molecule involved in HCV entry. The functional envelope glycoproteins associated with HCV pseudotype particles were also shown to be sensitive to low-pH treatment. Such conformational changes are likely necessary to initiate fusion.
Upregulation of P2X(7) receptor currents in Müller glial cells during proliferative vitreoretinopathy. (2001)

Müller glial cells from the human retina express purinergic P2X(7) receptors. Because extracellular adenosine triphosphate (ATP) is assumed to be a mediator of the induction or maintenance of gliosis, this study was undertaken to determine whether the expression of these receptors is different in human Müller cells obtained from retinas of healthy donors and of patients with choroidal melanoma and proliferative vitreoretinopathy (PVR).Human Müller cells were enzymatically isolated from donor retinas, and whole-cell patch-clamp recordings were made to characterize the density of the P2X(7) currents and the activation of currents through Ca2+-activated K+ channels of big conductance (I:(BK)) that reflects the increase of the intracellular Ca2+ concentration.Stimulation by external ATP or by benzoylbenzoyl ATP (BzATP) evoked both release of Ca2+ from thapsigargin-sensitive intracellular stores and opening of Ca2+ -permeable P2X(7) channels. These responses caused transient and sustained increases in I:(BK). In Müller cells from patients with PVR, the mean density of the BzATP-evoked cation currents was significantly greater compared with cells from healthy donors. As a consequence, such cells displayed an enlarged I:(BK) during application of purinergic agonists. ATP and BzATP increased the DNA synthesis rate of cultured cells. This effect could be reversed by blocking the I:(BK).The increased density of P2X(7) receptor channels may permit a higher level of entry of extracellular Ca2+ into cells from patients with PVR. Enhanced Ca2+ entry and the subsequent stronger activation of I:(BK) may contribute to the induction or maintenance of proliferative activity in gliotic Müller cells during PVR.
The RNA-binding Site of Bacteriophage Qβ Coat Protein (1996)

The coat proteins of the RNA bacteriophages Qbeta and MS2 are specific RNA binding proteins. Although they possess common tertiary structures, they bind different RNA stem loops and thus provide useful models of specific protein-RNA recognition. Although the RNA-binding site of MS2 coat protein has been extensively characterized previously, little is known about Qbeta. Here we describe the isolation of mutants that define the RNA-binding site of Qbeta coat protein, showing that, as with MS2, it resides on the surface of a large beta-sheet. Mutations are also described that convert Qbeta coat protein to the RNA binding specificity of MS2. The results of these and other studies indicate that, although they bind different RNAs, the binding sites of the two coat proteins are sufficiently similar that each is easily converted by mutation to the RNA binding specificity of the other.
Components and devices for optical communications based on UV-written-fiber phase gratings (1993)

Several years have passed since the demonstration1 that ultraviolet light could be successfully used to permanently modify the refractive index of optical fibers. This permits, for example, the direct writing of phase gratings into the core of a communications fiber, without first removing the cladding material. In this way one can make a low-loss Bragg reflector with a peak reflection wavelength anywhere in one of the communications windows. Recently a number of workers have exploited this principle to make a variety of fiber-based components and devices.