gebhart/patrepeval huggingface dataset:
Optical materials: evaluation methodology and data base utility (1991)

The development of advanced infrared optical materials has necessitated a growing requirement for refined optical and mechanical evaluation methodologies, as well as a need for an accurate, updated, optical and mechanical properties data based. Driving this need are new material fabrication and finishing techniques--often substantially different from past methods-- that can lead to optical and material properties data that is significantly at variance with data contained in the current infrared materials data based. In addition, both new and well established measurement methodologies are being applied to measurement problems that are qualitatively different from that for which they were originally developed. An overview of an optical and mechanical reliability evaluation methodology, along with representative data, is discussed.
Endotoxin Contamination in Commercially Available Pokeweed Mitogen Contributes to the Activation of Murine Macrophages and Human Dendritic Cell Maturation (2006)

Commercially available pokeweed mitogen (PWM) has been reported to activate macrophages, leading to production of proinflammatory cytokines and nitric oxide (NO). However, we found that polymyxin B (PMB), a specific inhibitor of endotoxin activity, inhibited the PWM-induced expression of proinflammatory cytokines and NO and the activation of Toll-like receptor 4 (TLR4). A kinetic-turbidimetric Limulus amebocyte lysate assay demonstrated that commercial PWM contained substantial endotoxin, over 10(4) endotoxin units/mg of the PWM. A PWM repurified by PMB-coupled beads no longer induced the expression of proinflammatory cytokines, TLR4 activation, or dendritic cell maturation. However, the repurified PWM remained able to induce proliferation of human lymphocytes, which is a representative characteristic of PWM. These results suggest that commercial PWM might be contaminated with a large amount of endotoxin, resulting in the attribution of misleading immunological properties to PWM.
Potential of cell retention techniques for large‐scale high‐density perfusion culture of suspended mammalian cells (2003)

This review focuses on cultivation of mammalian cells in a suspended perfusion mode. The major technological limitation in the scaling-up of these systems is the need for robust retention devices to enable perfusion of medium as needed. For this, cell retention techniques available to date are presented, namely, cross-flow filters, hollow fibers, controlled-shear filters, vortex-flow filters, spin-filters, gravity settlers, centrifuges, acoustic settlers, and hydrocyclones. These retention techniques are compared and evaluated for their respective advantages and potential for large-scale utilization in the context of industrial manufacturing processes. This analysis shows certain techniques have a limited range of perfusion rate where they can be implemented (most microfiltration techniques). On the other hand, techniques were identified that have shown high perfusion capacity (centrifuges and spin-filters), or have a good potential for scale-up (acoustic settlers and inclined settlers). The literature clearly shows that reasonable solutions exist to develop large-scale perfusion processes.
Tailoring Kinetics of Antibodies Using Focused Combinatorial Libraries (2003)

Antibodies have been used extensively for diagnostic applications for decades. Antibodies also can be used to target specific cells or specific molecules to produce agonist, antagonist, or neutralizing activity. Antibody therapies have been applied successfully in the treatment of several human diseases (1). The advantages of antibodies over other molecules are that they have high affinity for their targets and they bind to targets with high specificity. Antibodies, with six highly diversified complementaritydetermining regions (CDRs) supported by stable β-sheet framework regions, are capable of binding virtually any molecule including proteins, carbohydrates, nucleic acids, and haptens. The intrinsic features of specificity and affinity when combined offer a great advantage in the discovery of a wide-range of lead drug candidates.
Cytotoxic T Cell Responses to DNA Vaccination: Dependence on Antigen Presentation via Class II MHC (1998)

This study was designed to test whether cytotoxic T cell (CTL) responses to DNA vaccination are dependent upon MHC class II-restricted priming of CD4+ T cells. Because DNA vaccination may directly transfect dendritic cells, and dendritic cells may be capable of directly stimulating CD8+ T cell responses, such priming might be unnecessary. To test this hypothesis, C57BL/6 mice were immunized intramuscularly or intradermally with DNA encoding either whole OVA, a class I (Kb)-restricted peptide epitope of OVA (amino acids 257-264, SIINFEKL), or this class I-restricted epitope plus the adjacent class II (I-Ab)-restricted epitope of OVA (amino acids 265-280, TEWTSSNVMEERKIKV). Very low to negligible CTL responses were observed in mice vaccinated with the SIINFEKL construct, whereas mice vaccinated with the SIINFEKLTEWTSSNVMEERKIKV or with the complete OVA construct made equally robust CTL responses. These responses were sensitive to blocking by anti-CD8 mAb and were shown to be SIINFEKL-specific by using SIINFEKL peptide-pulsed EL-4 cells as targets. To ensure that the generation of these CTL responses was indeed dependent upon CD4+ T cell help, mice were depleted of either CD4+ or CD8+ cells before immunization. Depletion of CD4+ cells completely abrogated the CTL response to OVA DNA, as did depletion of CD8+ cells. Thus, we conclude that the CTL response to both intramuscular and intradermal DNA vaccination is highly dependent upon the generation of CD4+ T cell help via a class II MHC-dependent pathway. These results will be relevant for the construction of minimal-epitope vaccines for DNA immunization.
Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of Squamous Cell Carcinomas (2014)

Mining modern genomics for cancer therapies is predicated on weeding out "bystander" alterations (nonconsequential mutations) and identifying "driver" mutations responsible for tumorigenesis and/or metastasis. We used a direct in vivo RNA interference (RNAi) strategy to screen for genes that upon repression predispose mice to squamous cell carcinomas (SCCs). Seven of our top hits-including Myh9, which encodes nonmuscle myosin IIa-have not been linked to tumor development, yet tissue-specific Myh9 RNAi and Myh9 knockout trigger invasive SCC formation on tumor-susceptible backgrounds. In human and mouse keratinocytes, myosin IIa's function is manifested not only in conventional actin-related processes but also in regulating posttranscriptional p53 stabilization. Myosin IIa is diminished in human SCCs with poor survival, which suggests that in vivo RNAi technology might be useful for identifying potent but low-penetrance tumor suppressors.
Expression of cytolytic mediators by synovial fluid lymphocytes in rheumatoid arthritis. (1992)

To understand the role of cytolytic lymphocytes in the pathogenesis of rheumatoid arthritis, we investigated the expression of lymphocyte cytotoxicity mediators, perforin, and serine esterases, in lymphocytes derived from the synovial fluid of 15 patients with rheumatoid arthritis. Previous work has shown that CD8+ lymphocytes that possess markers of activation appear to be present in rheumatoid arthritis (RA). By means of in situ hybridization techniques and immunohistochemical analysis, the authors show that perforin and two serine esterases (serine esterase 1/Hanukah factor/granzyme A, and serine esterase 2/granzyme B) are expressed by subpopulations of CD8+ and CD56+ lymphocytes obtained from synovial fluid. The presence of these cytotoxic mediators suggests a possible mechanism for tissue damage, and provides evidence implicating cytolytic lymphocytes in the pathogenesis of RA.
Methylenetetrahydrofolate reductase variant and schizophrenia/depression (1997)

Patients with methylenetetrahydrofolate reductase (MTHFR) deficiency often show psychiatric manifestations. Since a common variant of the MTHFR gene, T677(Ala), responsible for the thermolabile MTHFR with less than 50% specific MTHFR activity, has been reported, we examined whether the T677 allele is associated with psychiatric disorders in an unrelated Japanese population consisting of 297 schizophrenics, 32 patients with major depression, 40 patients with bipolar disorder, and 419 controls. The genotype homozygous for the T677 allele was significantly frequently observed in schizophrenics with an odds ratio of 1.9 (P = 0.0006), and in patients with major depression with an odds ratio of 2.8 (P = 0.005). Our data suggest associations of the MTHFR gene variant with schizophrenia and depression in the Japanese.
DNA sequencing with blackbody infrared radiative dissociation of electrosprayed ions (1997)

As shown by Williams for positive multiply-charged ions, negative electrosprayed ions trapped in a Fourier-transform ion cyclotron resonance mass spectrometer can be dissociated efficiently with BIRD. For a 50-mer DNA, an ion cell wall temperature of 90°C gives no dissociation and 120°C gives only uninformative base loss. However, 150°C gives extensive dissociation producing ionic products qualitatively similar to those from laser IR, collisionally activated, and nozzle-skimmer dissociation. Under the conditions used, BIRD produces more fragment ions that have lost an additional base (AH). Structurally informative BIRD spectra are also observed for a 100-mer DNA and a double-strand 64-mer DNA. For both samples, BIRD successfully ‘boiled off’ non-covalent adducts that produced an uninterpretable spectrum, while laser IR was only successful in this for the ds 64-mer.
A method of optimizing source configuration in active control systems using Gram-Schmidt orthogonalization (2002)

A method for optimizing the number and the configuration of control sources in an active control system is proposed. In the optimization process, sources are selected one by one so that the corresponding transfer impedance vector is the most linearly independent. From the results of the simulation, it is shown that the optimized configuration yields not only a small average control error but also a small condition number in the transfer impedance matrix, which contributes to the robustness of the system against environmental change.
Potential impact of the bivalent rLP2086 vaccine onNeisseria meningitidiscarriage and invasive serogroup B disease (2013)

Asymptomatic throat carriage of Neisseria meningitidis is common in healthy individuals. In unusual cases, the bacteria become invasive, resulting in life-threatening disease. Effective meningococcal serogroup B (MnB) vaccines should provide broad protection against disease-causing strains and may confer indirect protection by impacting carriage and subsequent transmission. Factor H binding proteins (fHBPs), components of MnB vaccines in development, are classified into two immunologically distinct subfamilies (A and B). fHBP variants of MnB strains carried by adolescents are similar to those detected in infants with MnB disease. A vaccine containing subfamily A and B fHBP variants elicited bactericidal antibody responses (titers ≥ 1:4) against MnB strains expressing fHBP variants common to carriage strains and strains that cause disease in adolescents and infants in 75-100% of adolescent study subjects. This suggests that the bivalent fHBP vaccine has the potential to provide protection against invasive MnB strains and interrupt meningococcal carriage, which may also reduce infant MnB disease.
A chimeric antibody with dual Fc regions (bisFabFc) prepared by manipulations at the IgG hinge. (1989)

A new chimeric antibody for therapeutic use in human cancer is described. First the derivative FabFc was prepared by linking Fab' gamma from monoclonal antibody to Fc gamma from human normal IgG1. The bismaleimide linking agent forms a thioether bond with an SH group released by reduction of SS bonds in the hinge of each constituent. It follows that one of the original two SS bonds in the Fc hinge still has both its S atoms free, and this bond is reformed by thiol-disulphide interchange. The lone free SH in the Fc hinge can now be used to join two FabFc molecules through a similar bismaleimide linker to yield bisFabFc. As regards antibody activity against target cells, bisFabFc can be univalent, bivalent, or bispecific. Its juxtaposed dual Fc regions are designed to promote cooperative binding of effectors, and bisFabFc is indeed notably more powerful than its parent FabFc molecules in promoting complement lysis and antibody-dependent cellular cytotoxicity. However it is not possible at present to distinguish the separate contributions of Fc architecture, antibody affinity and other factors towards this improvement. In the present state of development a variety of FabFc against a given neoplasm may be prepared in high yield from mouse IgG1 and IgG2a antibodies, and when convenient dimerized to bisFabFc in any combination of specificities.
Use of human prostate-specific antigen in monitoring prostate cancer. (1981)

The newly reported human prostate-specific antigen (PA) is a specific histiotypic product of human prostate. With the use of a sensitive enzyme immunoassay, the circulating PA in prostatic cancer patients has been evaluated clinically. In 96 patients with advanced stage of disease (D2) and receiving chemotherapies, the pretreatment serum PA levels were found to be of prognostic value with regard to the patient survival. Ten patients with metastatic prostate cancer were monitored for more than 32 weeks by 183 serial PA values and were found generally to respond to the treatment. Additionally, in another group of 32 patients who underwent curative therapies for localized prostate cancer, 161 serum samples were evaluated during periods of 12 to 114 weeks (average 56 weeks). Of these patients, five developed metastases during follow-up, and all were shown to exhibit increasingly elevated PA values, either corresponding to or preceding the clinical diagnosis of disease recurrence. These results suggest that PA is a new marker with potential value to merit further clinical study.
The N and C Termini of the Splice Variants of the Human Mitogen-Activated Protein Kinase-Interacting Kinase Mnk2 Determine Activity and Localization (2003)

The cap-binding eukaryotic initiation factor eIF4E is phosphorylated by the mitogen-activated protein (MAP) kinase-interacting kinases (Mnk's). Three forms of the Mnk's exist in human cells: Mnk1, Mnk2a, and Mnk2b. These last two are derived from the same gene by alternative splicing and differ only at their C termini. While Mnk2a contains a MAP kinase-binding site in this region, Mnk2b lacks such a sequence and is much less readily activated by MAP kinases in vitro. Expression of Mnk2b in mammalian cells leads to increased phosphorylation of eIF4E, showing that it acts as an eIF4E kinase in vivo. While Mnk2a is cytoplasmic, a substantial amount of Mnk2b is found in the nucleus. Both enzymes contain a stretch of basic residues in their N termini that plays a role in binding to eIF4G and functions as a nuclear localization signal. Binding of eIF4G or nuclear import appears to be regulated by the C terminus of Mnk2a. Furthermore, the MAP kinase-binding site of Mnk2a regulates nuclear entry. Within the nucleus, Mnk2b and certain variants of Mnk2a that are present in the nucleus colocalize with the promyelocytic leukemia protein PML, which also binds to eIF4E.
Mass and position determination of attached particles on cantilever based mass sensors (2007)

An analytical expression relating mass and position of a particle attached on a cantilever to the resulting change in cantilever resonant frequency is derived. Theoretically, the position and mass of the attached particle can be deduced by combining measured resonant frequencies of several bending modes. This finding is verified experimentally using a microscale cantilever with and without an attached gold bead. The resonant frequencies of several bending modes are measured as a function of the bead position. The bead mass and position calculated from the measured resonant frequencies are in good agreement with the expected mass and the position measured.
Intravenous Administration of Self-complementary AAV9 Enables Transgene Delivery to Adult Motor Neurons (2009)

Therapeutic gene delivery to the whole spinal cord is a major challenge for the treatment of motor neuron (MN) diseases. Systemic administration of viral gene vectors would provide an optimal means for the long-term delivery of therapeutic molecules from blood to the spinal cord but this approach is hindered by the presence of the blood-brain barrier (BBB). Here, we describe the first successful study of MN transduction in adult animals following intravenous (i.v.) delivery of self-complementary (sc) AAV9 vectors (up to 28% in mice). Intravenous MN transduction was achieved in adults without pharmacological disruption of the BBB and transgene expression lasted at least 5 months. Importantly, this finding was successfully translated to large animals, with the demonstration of an efficient systemic scAAV9 gene delivery to the neonate and adult cat spinal cord. This new and noninvasive procedure raises the hope of whole spinal cord correction of MN diseases and may lead to the development of new gene therapy protocols in patients.
Manipulating Surface Plasmon Polaritons in a 2-D T-Shaped Metal–Insulator–Metal Plasmonic Waveguide With a Joint Cavity (2010)

A 2-D T-shaped metal-insulator-metal plasmonic waveguide with a joint cavity is introduced. The field distribution of the structure is investigated by using the finite-difference time-domain (FDTD) method. It is found that the surface plasmon polaritons' splitting ratio changes periodically as the joint cavity is moved. The period and maximum for the splitting ratio increase with increasing the width of the joint cavity. The results of the splitting performance obtained by the FDTD agree well with our semi-analytic model based on the scattering matrix theory.
Algorithms for State Restoration and Trace-Signal Selection for Data Acquisition in Silicon Debug (2009)

To locate and correct design errors that escape pre-silicon verification, silicon debug has become a necessary step in the implementation flow of digital integrated circuits. Embedded logic analysis, which employs on-chip storage units to acquire data in real time from the internal signals of the circuit-under-debug, has emerged as a powerful technique for improving observability during in-system debug. However, as the amount of data that can be acquired is limited by the on-chip storage capacity, the decision on which signals to sample is essential when it is not known <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">priori</i> where the bugs will occur. In this paper, we present accelerated algorithms for restoring circuit state elements from the traces collected during a debug session, by exploiting bitwise parallelism. We also introduce new metrics that guide the automated selection of trace signals, which can enhance the real-time observability during in-system debug.
Evidence that postoperative fibrinolytic shutdown is mediated by plasma factors that stimulate endothelial cell type I plasminogen activator inhibitor biosynthesis (1992)

Postoperative fibrinolytic shutdown has been attributed to an increase in plasma levels of type I plasminogen activator inhibitor (PAI-1) activity and may contribute to postoperative venous thrombosis. The purpose of this study was to determine whether the postoperative increase in PAI-1 is contributed to by a plasma mediator(s) that stimulates PAI-1 synthesis and secretion by vascular endothelium. Plasma samples collected from patients (N = 11) before and after surgery for total hip replacement were (1) assayed for endogenous plasma PAI-1 antigen and activity, and (2) incubated with cultured human umbilical vein endothelial cells (HUVECs) and PAI-1 antigen and activity measured in the conditioned medium (CM). Eighteen hours after surgery, endogenous plasma levels of PAI-1 antigen and activity were increased by 225% (P = .003) and 190% (P = .04), respectively over the preoperative values. In addition, compared with preoperative plasma, postoperative plasma increased HUVEC secretion of PAI-1 antigen and activity by 99% (P = .001) and 66% (P = .002), respectively. This increase in HUVEC PAI-1 secretion reflects an increase in PAI-1 mRNA expression and protein biosynthesis as confirmed by metabolic radiolabeling, immunoprecipitation, and Northern blot analysis. Ultra- filtration experiments indicate that the postoperative plasma mediator(s) that stimulates HUVEC PAI-1 biosynthesis is in a molecular weight (MW) range of approximately 30 to 100 Kd. Heat treatment (56 degrees C; 30 minutes) of postoperative plasma abolished the induction of HUVEC PAI-1 production. Enzyme-linked immunosorbent assay and immunoneutralization experiments indicate that tumor necrosis factor- alpha (TNF alpha) and interleukin-1 alpha (IL-1 alpha) do not contribute to the postoperative plasma effect on HUVEC PAI-1 synthesis. These observations demonstrate that postoperative patient plasma contains a factor(s) that may stimulate endothelial cell PAI-1 biosynthesis in vivo and thus mediate postoperative fibrinolytic shut- down.
Colon Adenocarcinoma-Associated Nuclear Antigens (1985)

Colon adenocarcinoma-associated chromosomal nonhistone proteins were determined in rat colon adenocarcinoma chromatin and in colon chromatin of Sprague-Dawley rats treated with 1,2-dimethylhydrazine (DMH) by the enzyme-linked immunosorbent assay method. The specific nuclear proteins are tissue-specific oncofetal antigens. They were also detected in fetal rat colon chromatin but not in adult rat colon chromatin. The specific tumor-associated nonhistone proteins were identified by immunoblot. The molecular weight ranges of these proteins were 79,000-89,000 and 40,000-56,000 daltons. Administration of DMH to Sprague-Dawley rats induced colon tumor and colon tumor-associated nonhistone proteins in the chromatin. However, DMH failed to induce colon tumor and tumor-associated nonhistone proteins in Lobund-Wistar rats.
Soliton propagation in long fibers with periodically compensated loss (1986)

With computer simulation, we study soliton propagation in an all-optical, long-distance communications system where fiber loss is periodically compensated by Raman gain. We find that distortion of the transmitted pulses from true solitons shows a peak near <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z_{0} = L/8</tex> where <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</tex> and z <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> are the amplification and soliton periods, respectively. We also describe optimal system design based on the exceptional pulse stability and low soliton powers obtained in the region <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">z_{0} \gg L/8</tex> . Typical amplification periods are in the range 30-50 km, pump powers are less than 100 mW, and for bit rates in the 10 GHz range, time average signal powers are at most a few milliwatts. The single-channel rate-length product for error rate less than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> is <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\sim29 000</tex> GHz Km. Finally, we show that in the gain-compensated system with wavelength multiplexing, soliton-soliton collisions produce random modulation of individual pulse velocities. Nevertheless, multiplexing can yield rate-length products greater than 300 000 GHz km.