gebhart/patrepeval huggingface dataset:
Improving mass spectrometer sensitivity using a high-pressure electrodynamic ion funnel interface (2006)

We report on a new electrodynamic ion funnel that operates at a pressure of 30 torr with no loss of ion transmission. The enhanced performance compared with previous ion funnel designs optimized for pressures of <5 torr was achieved by reducing the ion funnel capacitance and increasing the RF drive frequency (1.7 MHz) and amplitude (100–170 V peak-to-peak). No degradation of ion transmission was observed for pressures from 2 to 30 torr. The ability to operate at higher pressure enabled a new tandem ion funnel mass spectrometer interface design that can accommodate a greater gas load (e.g., from an ESI source). When combined with a multicapillary inlet, the interface provided more efficient introduction of ions, resulting in a significant enhancement in mass spectrometer sensitivity and detection limits.
Cupredoxin−Cancer Interrelationship:  Azurin Binding with EphB2, Interference in EphB2 Tyrosine Phosphorylation, and Inhibition of Cancer Growth (2007)

Azurin is a member of a family of metalloproteins called cupredoxins. Although previously thought to be involved in electron transfer, azurin has recently been shown to preferentially enter cancer cells than normal cells and induce apoptosis in such cells. Azurin also demonstrates structural similarity to a ligand known as ephrinB2, which binds its cognate receptor tyrosine kinase EphB2 to initiate cell signaling. Eph/ephrin signaling is known to be involved in cancer progression. We now demonstrate that azurin binds to the EphB2-Fc receptor with high affinity. We have localized a C-terminal domain of azurin (Azu 96-113) that exhibits structural similarity to ephrinB2 at the G-H loop region known to be involved in receptor binding. A synthetic peptide (Azu 96-113) as well as a GST fusion derivative GST-Azu 88-113 interferes with the growth of various human cancer cells. In a prostate cancer cell line DU145 lacking functional EphB2, azurin or its GST-fusion derivatives had little cytotoxic effect. However, in DU145 cells expressing functional EphB2, azurin and GST-Azu 88-113 demonstrated significant cytotoxicity, whereas ephrinB2 promoted cell growth. Azurin inhibited the ephrinB2-mediated autophosphorlyation of the EphB2 tyrosine residue, thus interfering in upstream cell signaling and contributing to cancer cell growth inhibition.
Probing Gene Expression in Live Cells, One Protein Molecule at a Time (2006)

We directly observed real-time production of single protein molecules in individual Escherichia coli cells. A fusion protein of a fast-maturing yellow fluorescent protein (YFP) and a membrane-targeting peptide was expressed under a repressed condition. The membrane-localized YFP can be detected with single-molecule sensitivity. We found that the protein molecules are produced in bursts, with each burst originating from a stochastically transcribed single messenger RNA molecule, and that protein copy numbers in the bursts follow a geometric distribution. The quantitative study of low-level gene expression demonstrates the potential of single-molecule experiments in elucidating the workings of fundamental biological processes in living cells.
Simple Mail Transfer Protocol (1981)

The SMTP design is based on the following model of communication: as the result of a user mail request, the sender-SMTP establishes a full-duplex transmission channel to a receiver-SMTP. The receiver-SMTP may be either the ultimate destination or an intermediate. SMTP commands are generated by the sender-SMTP and sent to the receiver-SMTP. SMTP replies are sent from the receiver-SMTP to the sender-SMTP in response to the commands.
BK Virus-Specific T Cells for Use in Cellular Therapy Show Specificity to Multiple Antigens and Polyfunctional Cytokine Responses (2011)

Possible clinical uses for BKV-specific T cells generated using this method include immune reconstitution posthemopoietic stem-cell transplantation or prophylaxis and treatment of immune deficiency in renal transplant recipients, fulfilling the need for effective therapy for BKV-related hemorrhagic cystitis and renal dysfunction.
HMM-based Passage Models for Document Classification and Ranking (2001)

We present an application of Hidden Markov Models to supervised document classification and ranking. We consider a family of models that take into account the fact that relevant documents may contain irrelevant passages; the originality of the model is that it does not explicitly segment documents but rather considers all possible segmentations in its final score. This model generalizes the multinomial Naive Bayes and it is derived from a more general model for different access tasks. The model is evaluated on the REUTERS test collection and compared to the multinomial Naive Bayes model. It is shown to be more robust with respect to the training set size and to improve the performance both for ranking and classification, specially for classes with few training examples.
Shape-Controlled Synthesis of Ternary Chalcogenide ZnIn2S4 and CuIn(S,Se)2 Nano-/Microstructures via Facile Solution Route (2006)

We demonstrated in this paper the shape-controlled synthesis of ZnIn2S4, CuInS2, and CuInSe2 nano- and microstructures through a facile solution-based route. One-dimensional ZnIn2S4 nanotubes and nanoribbons were synthesized by a solvothermal method with pyridine as the solvent, while ZnIn2S4 solid or hollow microspheres were hydrothermally prepared in the presence of a surfactant such as cetyltrimethylammonium bromide (CTAB) or poly(ethylene glycol) (PEG). The mechanisms related to the phase formation and morphology control of ZnIn2S4 are proposed and discussed. The UV-vis absorption spectra show that the as-prepared nano- and micromaterials have strong absorption in a wide range from UV to visible light and that their band gaps are somewhat relevant to the size and morphology. The photoluminescence measurements of the ZnIn2S4 microspheres at room temperature reveal intense excitation at approximately 575 nm and red emission at approximately 784 nm. Furthermore, CuInS2 and CuInSe2 with different morphologies such as spheres, platelets, rods, and fishbone-like shapes were also obtained by similar hydrothermal and solvothermal synthesis.
Quantum confinement in Si nanocrystals (1993)

The electronic structure of nanocrystalline Si which shows visible photoluminescence is calculated using the density-functional approach for finite structures. Except for geometry this is the same theory as for first-principles band structures of semiconductors and other solids. Our results for clusters ranging up to 706 Si atoms suggest that the band gap scales linearly with ${\mathit{L}}^{\mathrm{\ensuremath{-}}1}$, where L is the cluster diameter. For such clusters it is found that dipole transitions across the gap are symmetry allowed. The finite structures thus show a direct band gap which is considerably larger than the one of bulk silicon. For larger clusters we find a strong decrease of oscillator strength, consistent with the occurrence of the indirect gap in the bulk limit.
The road map to oral bioavailability: an industrial perspective (2006)

Optimisation of oral bioavailability is a continuing challenge for the pharmaceutical and biotechnology industries. The number of potential drug candidates requiring in vivo evaluation has significantly increased with the advent of combinatorial chemistry. In addition, drug discovery programmes are increasingly forced into more lipophilic and lower solubility chemical space. To aid in the use of in vitro and in silico tools as well as reduce the number of in vivo studies required, a team-based discussion tool is proposed that provides a 'road map' to guide the selection of profiling assays that should be considered when optimising oral bioavailability. This road map divides the factors that contribute to poor oral bioavailability into two interrelated categories: absorption and metabolism. This road map provides an interface for cross discipline discussions and a systematic approach to the experimentation that drives the drug discovery process towards a common goal - acceptable oral bioavailability using minimal resources in an acceptable time frame.
Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity (1988)

A complete kinetic scheme describing the polymerization of correct and incorrect dNTPs by the Klenow fragment (KF) of DNA polymerase I has been developed by using short DNA oligomers of defined sequence. The high fidelity arises from a three-stage mechanism. The first stage of discrimination [(1.1 X 10(4-) greater than 1.2 X 10(6]-fold] comes primarily from a dramatically reduced rate of phosphodiester bond formation for incorrect nucleotides, but it also gains a smaller contribution from selective dNTP binding. After phosphodiester bond formation, a conformational change slows dissociation of the incorrect DNA products from KF and, in conjunction with editing by the 3'----5'-exonuclease, increases fidelity 4- greater than 61-fold. Finally, KF polymerizes the next correct dNTP onto a mismatch very slowly, providing a further 6- greater than 340-fold increase in fidelity. Surprisingly, the 3'----5'-exonuclease did not in its hydrolysis reaction differentiate between correctly and incorrectly base-paired nucleotides; rather, an increased lifetime of the enzyme-DNA complex containing the misincorporated base is responsible for discrimination.
In interleukin‐4‐deficient mice, alum not only generates T helper 1 responses equivalent to Freund's complete adjuvant, but continues to induce T helper 2 cytokine production (1996)

The role of interleukin (IL)-4 in the activity of two frequently used vaccine adjuvants, Freund's complete adjuvant (FCA) and the aluminum hydroxide gels (alum), was studied using the standard antigen ovalbumin (OVA) in IL-4 genedisrupted mice (IL-4 -/-). In the absence of adjuvant, there was an overall reduction in antibody production to OVA in IL-4 -/- mice and significantly greater amounts of interferon (IFN)-gamma were produced following restimulation of splenocytes with antigen in vitro compared with immunocompetent controls (IL-4 +/+). FCA and alum boosted the immune response to OVA in both IL-4 -/- and IL-4 +/+ mice. In IL-4 +/+ mice, while FCA stimulated a wide-spectrum immunoglobulin response, including both Th1-associated IgG2a and Th2-associated IgG1, alum enhanced only Th2 antibody production and no OVA-specific IgG2a could be detected. In IL-4-deficient mice, however, not only was IgG2a production increased in all adjuvant-treated groups, but alum was as potent at stimulating this antibody subclass as FCA. Similarly, increased production in vitro by splenocytes of the Th1 cytokine IFN-gamma, equivalent to that produced after inoculation with FCA/OVA, was only detected in IL-4 -/- mice inoculated with alum/OVA. There was no IgE production in IL-4 -/- mice and OVA-specific IgG1 production, although still at significant levels, was reduced compared with wild-type mice irrespective of the adjuvant used. However, although production of the Th2 cytokine IL-5 was totally inhibited in IL-4-deficient mice inoculated with FCA/OVA, there was no significant difference in IL-5 production between the two strains when alum was used as adjuvant.
Fast and Sensitive Pretargeted Labeling of Cancer Cells through a Tetrazine/ trans ‐Cyclooctene Cycloaddition (2009)

A label for six, please! A fluorescent tetrazine derivative was used to image trans-cyclooctene-modified affinity ligands on live cancer cells through a bioorthogonal cycloaddition with a reaction rate of approximately 6000±200 M−1 s−1 in serum at 37 °C (see scheme). To maximize the fluorescence signal, up to six trans-cyclooctene moieties were attached to the antibody used to pretarget cells for labeling.
Understanding the Role of the Essential Asp251 in Cytochrome P450cam Using Site-Directed Mutagenesis, Crystallography, and Kinetic Solvent Isotope Effect (1998)

Proton transfer in cytochromes P450 is a critical step in the activation of molecular oxygen. Extensive study of the P450cam active site has identified several residues that play a central role in dioxygen bond scission. A highly conserved carboxylate, aspartate-251 in P450cam in the distal helix I, participates in a series of hydrogen-bond/ion pairs near the molecular surface and has been implicated in the catalytic mechanism. Mutation of Asp251 is known to lower activity by 2 orders of magnitude and change the rate-limiting step in the catalytic cycle, suggesting a role for an acid functionality in generation of iron-oxygen reactive intermediates. The turnover rates of the Asp251Asn mutant in various protium-deuterium mixtures have been determined and show a significantly larger kinetic solvent isotope effect, with an overall magnitude of 10 compared to 1.8 for the wild-type P450cam. In addition, a much larger number of protons are involved in the rate-limiting step for the Asp251Asn mutant than in the wild-type enzyme. These results indicate that Asp251 is an essential part of the normal proton delivery machinery required for O-O bond scission. The crystal structure of the Aps251Asn mutant obtained from data collected at cryogenic temperatures has been refined to 1.9 A. Key hydrogen bonds required to hold Asp251 in position have been broken which allows the mutant Asn251 side chain to swing out and away from the O2 binding site leading to a more open active site. This change could allow easier access by water and thus contribute to the observed kinetic solvent isotope effects.
Intravenous Pamidronate for Treatment of Reflex Sympathetic Dystrophy During Breast Feeding (2000)

A 39-year-old woman presented in the first month of pregnancy with reflex sympathetic dystrophy involving both lower legs. Symptoms became so severe that she could not walk unassisted, and the pain worsened after delivery. Radiographs showed patchy reduction in apparent density in the tarsal bones and around the ankles and knees. Uptake was increased in these areas on technetium methylene diphosphonate bone scan. Bone density (dual-energy X-ray absorptiometry) was reduced in the spine, hip, and radius. Biochemical tests were normal except for an increase in urinary excretion of the N-telopeptide cross-linking region of type I collagen (NTx). Because the patient wanted to continue breast-feeding, intravenous pamidronate was administered at monthly intervals. Breast milk was collected for 48 h after the infusion. The pain began to decrease soon after drug administration was initiated, and it was virtually gone by 6 months. NTx excretion fell by 78% and bone density increased by as much as 18.9% over the 6-month treatment interval. The baby was healthy and grew normally. Milk expressed after the first treatment was assayed for pamidronate content by high-performance liquid chromatography with fluorescence detection. None was detected (limit of quantitation, 0.4 micromol/liter). This case shows that pamidronate may be considered for treatment of lactating women.
2′-Fluoro-4′-thio-2′,3′-unsaturated Nucleosides: Anti-HIV Activity, Resistance Profile, and Molecular Modeling Studies (2003)

Both D- and L-2'-fluoro-4'-thio-2',3'-unsaturated nucleosides were synthesized and their anti-HIV activity against the drug sensitive virus and lamivudine-resistant mutant (M184V) were evaluated. In vitro antiviral evaluation indicated that the L-isomers are more potent than the D-isomers, but unfortunately all were cross-resistant with 3TC. Molecular modeling studies revealed that the unnatural sugar moiety of the L-nucleosides as well as 4'-sulfur atom of the D-isomer has a steric conflict with the bulky side chain of valine 184, resulting in cross-resistance.
CpG oligodeoxynucleotides inhibit tumor growth and reverse the immunosuppression caused by the therapy with 5-fluorouracil in murine hepatoma (2005)

The present data suggests that CpG ODN used as single therapeutic agent triggers anti-tumor immune response to inhibit the growth of implanted hepatoma and reverses the immunosuppression caused by the chemotherapy with 5-FU.
Simulation of Nitrogen Mineralization in the Below-Ground Food Webs of Two Winter Wheat Fields (1993)

P. C. De Ruiter, J. C. Moore, K. B. Zwart, L. A. Bouwman, J. Hassink, J. Bloem, J. A. De Vos, J. C. Y. Marinissen, W. A. M. Didden, G. Lebrink, L. Brussaard, Simulation of Nitrogen Mineralization in the Below-Ground Food Webs of Two Winter Wheat Fields, Journal of Applied Ecology, Vol. 30, No. 1 (1993), pp. 95-106
Reactive Oxygen Species as Intracellular Messengers During Cell Growth and Differentiation (2001)

Reactive oxygen species (ROS) are generated following ligand-receptor interactions and function as specific second messengers in signaling cascades involved in cell proliferation and differentiation. Although ROS are generated intracellularly by several sources, including mitochondria, the primary sources of ROS involved in receptor-mediated signaling cascades are plasma membrane oxidases, preferentially NADPH oxidases, with a rapid kinetics of activation and inactivation. This allows a tight up- and downregulation of intracellular ROS levels within the short time required for the transduction of signals from the plasma membrane to the cell nucleus. The mode of action of ROS may involve direct interaction with specific receptors, and/or redox-activation of members of signaling pathways such as protein kinases, protein phosphatases, and transcription factors. Furthermore, ROS act in concert with intracellular Ca(2+) in signaling pathways which regulate the balance of cell proliferation versus cell cycle arrest and cell death. The delicate intracellular interplay between oxidizing and reducing equivalents allows ROS to function as second messengers in the control of cell proliferation and differentiation.
Inhibition of Factor XIa as a New Approach to Anticoagulation (2010)

The dose-limiting issue with available anticoagulant therapies is bleeding. Is there an approach that could provide antithrombotic protection with reduced bleeding? One hypothesis is that targeting proteases upstream from the common pathway provides a reduction in thrombin sufficient to impede occlusive thrombosis yet allows enough thrombin generation to support hemostasis. The impairment of intrinsic coagulation by selective inhibition of factor XI (FXI) leaves the extrinsic and common pathways of coagulation intact, making FXI a drug target. This concept is supported by the observation that human deficiency in FXI results in a mild bleeding disorder compared with other coagulation factor deficiencies, and that elevated levels of FXI are a risk factor for thromboembolic disease. Moreover, FXI knockout mice have reduced thrombosis with little effect on hemostasis. The results from genetic models have been supported by studies using neutralizing antibodies, peptide inhibitors, and small-molecule inhibitors. These agents impede thrombosis without affecting bleeding time in a variety of experimental animals, including primates. Together, these data strongly support FXIa inhibition as a viable method to increase the ratio of benefit to risk in an antithrombotic drug.
NF-κB-mediated repression of growth arrest- and DNA-damage-inducible proteins 45α and γ is essential for cancer cell survival (2004)

The NF-kappaB/IkappaB signaling pathway is a critical regulator of cell survival in cancer. Here, we report that combined down-regulation of growth arrest- and DNA-damage-inducible proteins (GADD)45alpha and gamma expression by NF-kappaB is an essential step for various cancer types to escape programmed cell death. We demonstrate that inhibition of NF-kappaB in cancer cells results in GADD45alpha- and gamma-dependent induction of apoptosis and inhibition of tumor growth. Inhibition of GADD45alpha and gamma in cancer cells by small interfering RNA abrogates apoptosis induction by the inhibitor of NF-kappaB and blocks c-Jun N-terminal kinase activation, whereas overexpression of GADD45alpha and gamma activates c-Jun N-terminal kinase and induces apoptosis. These results establish an unambiguous role for the GADD45 family as an essential mediator of cell survival in cancer cells with implications for cancer chemotherapy and novel drug discovery.
A new classic camera calibration method based on coplanar Points (2009)

As a necessary step of 3D reconstruction, and a premise and base for computer vision obtaining the spatial information of 3D objects, research on the camera calibration methods has great important significance of theoretical study and practical value. This paper introduces a new simply, flexible and more accurate classic camera calibration method based on coplanar points. This method only requires a coplanar target and without camera motion. We use step-by-step calibration thinking, and first calibrate the principal point, and then neglect the lens distortion and linearly solve all the parameters, when high accuracy is required, we can include Weng's lens distortion model and solve the distortion coefficient by nonlinear algorithm. The experiment of images proves the proposed method is accurate and effective.
Identification and Analysis of Multivalent Proteolytically Resistant Peptides from Gluten:  Implications for Celiac Sprue (2005)

Dietary gluten proteins from wheat, rye, and barley are the primary triggers for the immuno-pathogenesis of Celiac Sprue, a widespread immune disease of the small intestine. Recent molecular and structural analyses of representative gluten proteins, most notably alpha- and gamma-gliadin proteins from wheat, have improved our understanding of these pathogenic mechanisms. In particular, based on the properties of a 33-mer peptide, generated from alpha-gliadin under physiological conditions, a link between digestive resistance and inflammatory character of gluten has been proposed. Here, we report three lines of investigation in support of this hypothesis. First, biochemical and immunological analysis of deletion mutants of alpha-2 gliadin confirmed that the DQ2 restricted T cell response to the alpha-2 gliadin are directed toward the epitopes clustered within the 33-mer. Second, proteolytic analysis of a representative gamma-gliadin led to the identification of another multivalent 26-mer peptide that was also resistant to further gastric, pancreatic and intestinal brush border degradation, and was a good substrate of human transglutaminase 2 (TG2). Analogous to the 33-mer, the synthetic 26-mer peptide displayed markedly enhanced T cell antigenicity compared to monovalent control peptides. Finally, in silico analysis of the gluten proteome led to the identification of at least 60 putative peptides that share the common characteristics of the 33-mer and the 26-mer peptides. Together, these results highlight the pivotal role of physiologically generated, proteolytically stable, TG2-reactive, multivalent peptides in the immune response to dietary gluten in Celiac Sprue patients. Prolyl endopeptidase treatment was shown to abolish the antigenicity of both the 33-mer and the 26-mer peptides, and was also predicted to have comparable effects on other proline-rich putatively immunotoxic peptides identified from other polypeptides within the gluten proteome.