gebhart/patrepeval huggingface dataset:
Conversion of Some Siloxane Polymers to Silicon Oxide by UV/Ozone Photochemical Processes (2000)

A variety of linear and cross-linked polysiloxanes are transformed into silicon oxide (SiOx) through the application of a recently developed room-temperature UV/ozone conversion process. Ozone and atomic oxygen, produced by exposure of atmospheric oxygen to ultraviolet radiation, remove organic portions of the polymers as volatile products and leave a thin silicon oxide surface film. The conversion rates differ for each polysiloxane studied and are related to differences in their chemical structures. X-ray photoelectron spectroscopy (XPS) measurements of atomic ratios indicate that UV/ozone treatment removes up to 89% of the carbon from the resultant surface film, leading to an overall stoichiometry close to that of SiO2. The binding energy of Si(2p) core level photoelectrons shifts from 101.5 eV for the polymer precursors to about 103.5 eV after UV exposure, consistent with the formation of silicon that is coordinated to four oxygen atoms. Ellipsometry measurements of apparent thickness changes during conversion indicate that the SiOx film formed is limited to a thickness on the order of 20−30 nm for poly(dimethylsiloxane) substrates. The results demonstrate that a thin silicon oxide layer can be prepared at room temperature on the surface of polysiloxane films by UV/ozone-induced photochemical reactions.
Alanine Scanning Mutagenesis of Insulin (1997)

Alanine scanning mutagenesis has been used to identify specific side chains of insulin which strongly influence binding to the insulin receptor. A total of 21 new insulin analog constructs were made, and in addition 7 high pressure liquid chromatography-purified analogs were tested, covering alanine substitutions in positions B1, B2, B3, B4, B8, B9, B10, B11, B12, B13, B16, B17, B18, B20, B21, B22, B26, A4, A8, A9, A12, A13, A14, A15, A16, A17, A19, and A21. Binding data on the analogs revealed that the alanine mutations that were most disruptive for binding were at positions TyrA19, GlyB8, LeuB11, and GluB13, resulting in decreases in affinity of 1,000-, 33-, 14-, and 8-fold, respectively, relative to wild-type insulin. In contrast, alanine substitutions at positions GlyB20, ArgB22, and SerA9 resulted in an increase in affinity for the insulin receptor. The most striking finding is that B20Ala insulin retains high affinity binding to the receptor. GlyB20 is conserved in insulins from different species, and in the structure of the B-chain it appears to be essential for the shift from the alpha-helix B8-B19 to the beta-turn B20-B22. Thus, replacing GlyB20 with alanine most likely modifies the structure of the B-chain in this region, but this structural change appears to enhance binding to the insulin receptor.
Warm Temperature-sensitive Transient Receptor Potential Vanilloid 4 (TRPV4) Plays an Essential Role in Thermal Hyperalgesia (2004)

Animals sense various ranges of temperatures by cutaneous thermal stimuli. Transient receptor potential vanilloid 4 (TRPV4) is a cation channel activated at a warm temperature (over 30 degrees C) in exogenously expressed cells. We found in the present study that TRPV4 is essential in thermal hyperalgesia at a warm temperature in vivo. TRPV4-/- and TRPV4+/+ mice exhibited the same latency of escape from 35-50 degrees C hotplates. Neuronal activity in the femoral nerve, however, revealed that the number and activity level of neurons decreased in response to a warm temperature in TRPV4-/- mice. TRPV4-/- mice displayed a significantly longer latency to escape from the plates at 35- 45 degrees C when hyperalgesia was induced by carrageenan without changes in foot volumes. TRPV4 therefore determines the sensitivity rather than the threshold of painful heat detection and plays an essential role in thermal hyperalgesia.
Reduction of the number of iterations in turbo decoding using extrinsic information (2003)

Turbo decoding can be done in an iterative manner. This requires the delay and computational complexity for decoding an input data. We propose an efficient algorithm of decoding turbo codes that can greatly reduce the delay and computation. It uses extrinsic information as the reliability measure of each decoded bit. When the variance of the extrinsic information exceeds a threshold the iteration for decoding stops with negligible performance loss to conventional decoding algorithm.
Identification of insulin-like growth factor-binding protein-3 (IGFBP- 3) fragments and IGFBP-5 proteolytic activity in human seminal plasma: a comparison of normal and vasectomized patients (1994)

10.1210/jc.79.5.1367
Incremental recognition of pedestrians from image sequences (2002)

An approach that uses a volume model consisting of cylinders for model-based recognition of pedestrians in real-world images is presented. The human body is represented by a volume model, and medical motion data are used for simulating the movement of walking. This knowledge is exploited to determine the 3-D position, as well as the posture of an observed person. By applying a Kalman filter, the model parameters in consecutive images are incrementally estimated. The approach is tested on real image data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Human B-cell interleukin-10: B-cell lines derived from patients with acquired immunodeficiency syndrome and Burkitt's lymphoma constitutively secrete large quantities of interleukin-10 [see comments] (1992)

A recent addition to the lymphokine network is human IL-10 (hIL-10). This novel lymphokine has striking homology to BCRF1 protein, the product of a previously uncharacterized open-reading frame in the Epstein-Barr virus (EBV) genome. To date, IL-10 expression has been described in several T clones induced with anti-CD3 and phorbol myristate acetate (PMA), in monocytes stimulated with lipopolysaccharide (LPS), and in murine B-cell lymphomas. We sought to determine whether human B cells express hIL-10 and, if so, its relationship to EBV and to other B-cell lymphokines. We studied 21 EBV-positive B-cell lines derived from patients with acquired immunodeficiency syndrome (AIDS) and Burkitt's lymphoma (n = 6), American Burkitt's (n = 3), African Burkitt's (n = 5), and normal lymphoblastoid cell lines (n = 7), in comparison with seven EBV-negative cell lines. All cell lines were activated with the tumor promoters PMA and teleocidin and were studied by Northern blot analysis, reverse transcription-polymerase chain reaction (RT-PCR), and enzyme-linked immunoadsorbent assay (ELISA). We demonstrated that EBV-positive cell lines derived from patients with American Burkitt's lymphoma, and especially those from patients with AIDS, constitutively express large quantities of hIL-10 by Northern blot analysis and ELISA (range, 3,101 to 25,915 pg/mL), and that both teleocidin and PMA induce hIL-10 in these cell lines. In contrast, six of seven EBV-negative cell lines did not express hIL-10 even by RT-PCR, and hIL-10 was not triggered by PMA or teleocidin. To assure that the 350 bp amplified by PCR was hIL-10 and not BCRF1, we used PCR primers, which do not amplify a fragment from plasmid templates containing BCRF1. Cloning and sequencing of the 350 bp product also demonstrated that B-cell IL-10 is identical to hIL-10 from the T-cell clone B21. Correlation of hIL-10 with other B-cell lymphokines secreted by these B-cell lines demonstrated that hIL-10 secretor cell lines also constitutively secrete or can be induced to secrete IL-6, although to a much lesser amount. Since both lymphokines influence B-cell growth and differentiation, we suggest that hIL-10 may contribute to the polyclonal B-cell activation and hyperglobulinemia seen in AIDS patients. Finally, several reports support the hypothesis that EBV is an important cofactor in the development of human immunodeficiency virus type 1 (HIV-1)-related B-cell lymphomas. Detection of large quantities of hIL-10 in B-cell lines derived from AIDS patients, the close association between EBV and hIL-10 shown in this report, and the ability of BCRF1 to capture hIL-10 activities, make hIL-10/BCRF1 an attractive candidate as a factor causing B-cell growth and immortalization in patients with AIDS and B-cell lymphomas.
Design techniques for improving the HF response of a monolithic JFET operational amplifier (1984)

Bandwidth limitations of an operational amplifier are explored in relation to the second-order frequency response caused by the output follower's inductive emitter impedance when driving capacitive loads or by the local AC feedback associated with the Miller integration function. The substrate p-n-p follower is shown to seriously degrade the bandwidth in the sink mode due to its low /spl omega//SUB /spl tau//. New design techniques are discussed which use the integration capacitor to provide local AC feedback around a new all-n-p-n transistor output stage. This reduces both the open-loop distortion and the quiescent output resistance for a given quiescent current. This also maximizes the lower limit of the inductive frequency range in the sink mode to improve the second-order frequency responses when driving capacitive loads. The multipole local AC feedback loop (Miller loop) is analyzed, and a method of compensation is described which uses pole splitting and feedforward techniques within the Miller loop. As a result, a general-purpose monolithic p-channel JFET quad operational amplifier has been fabricated with standard low-cost technology; the amplifier achieves a 10-MHz bandwidth and a 45-V//spl mu/s slew rate, while consuming only 2.1 mA/amplifier.
Shedding of rotavirus in feces of sows before and after farrowing (1982)

The purpose of this study was to determine whether sows shed rotavirus near the time of farrowing. Twelve sows purchased from a common source and seropositive for rotavirus were housed in isolation in farrowing crates from 5 days before to 3 weeks after farrowing. Fecal samples were collected at 3- to 4-day intervals and examined for the presence of rotavirus by direct electron microscopy. Samples were also treated with pancreatin and inoculated onto monkey kidney cells. Rotaviral antigens were detected by a direct immunofluorescence technique, and selected positive cultures were examined by immunoelectron microscopy. Rotavirus was detected in the feces of 5 of 12 sows as early as 5 days before to 2 weeks after farrowing. Diarrhea related to rotavirus developed in 4 of 12 litters. Two of these four litters were farrowed by sows which shed rotavirus at 7 and 10 and 14 days after farrowing. The results of this study indicate that sows immune to rotavirus can shed virus in their feces at a time when piglets are particularly susceptible to infection and that adult swine are of primary importance in the epidemiology of rotavirus as initiators of infection.
Chronic obstructive pulmonary disease: molecular and cellularmechanisms (2003)

Chronic obstructive pulmonary disease is a leading cause of death and disability, but has only recently been extensively explored from a cellular and molecular perspective. There is a chronic inflammation that leads to fixed narrowing of small airways and alveolar wall destruction (emphysema). This is characterised by increased numbers of alveolar macrophages, neutrophils and cytotoxic T-lymphocytes, and the release of multiple inflammatory mediators (lipids, chemokines, cytokines, growth factors). A high level of oxidative stress may amplify this inflammation. There is also increased elastolysis and evidence for involvement of several elastolytic enzymes, including serine proteases, cathepsins and matrix metalloproteinases. The inflammation and proteolysis in chronic obstructive pulmonary disease is an amplification of the normal inflammatory response to cigarette smoke. This inflammation, in marked contrast to asthma, appears to be resistant to corticosteroids, prompting a search for novel anti-inflammatory therapies that may prevent the relentless progression of the disease.
Adenoviral vector delivery of RNA-guided CRISPR/Cas9 nuclease complexes induces targeted mutagenesis in a diverse array of human cells (2014)

CRISPR/Cas9-derived RNA-guided nucleases (RGNs) are DNA targeting systems, which are rapidly being harnessed for gene regulation and gene editing purposes in model organisms and cell lines. As bona fide gene delivery vehicles, viral vectors may be particularly fit to broaden the applicability of RGNs to other cell types including dividing and quiescent primary cells. Here, the suitability of adenoviral vectors (AdVs) for delivering RGN components into various cell types is investigated. We demonstrate that AdVs, namely second-generation fiber-modified AdVs encoding Cas9 or single guide RNA (gRNA) molecules addressing the Cas9 nuclease to the AAVS1 "safe harbor" locus or to a recombinant model allele can be produced to high-titers (up to 20 × 10(10) transducing units/ml). Importantly, AdV-mediated transduction of gRNA:Cas9 ribonucleoprotein complexes into transformed and non-transformed cells yields rates of targeted mutagenesis similar to or approaching those achieved by isogenic AdVs encoding TALENs targeting the same AAVS1 chromosomal region. RGN-induced gene disruption frequencies in the various cell types ranged from 18% to 65%. We conclude that AdVs constitute a valuable platform for introducing RGNs into human somatic cells regardless of their transformation status. This approach should aid investigating the potential and limitations of RGNs in numerous experimental settings.
<title>Photoacoustic blood glucose and skin measurement based on optical scattering effect</title> (2002)

Non-invasive blood glucose determination has been investigated by more than 100 research groups in the world during the past fifteen years. The commonly optical methods are based on the capacity of near-IR light to penetrate a few hundreds micrometers or a few millimeters into human tissue where it interacts with glucose. A change of glucose concentration may modify the optical parameters in tissue, with the result that its glucose concentration can be extracted by analyzing the received optical signals. This paper demonstrates that glucose affects on the scattering coefficient of human blood, by applying the streak camera and pulsed photoacoustic techniques; and drinking water seems also affecting on PA signal from skin surface.
Crystal structure of the coat protein from the GA bacteriophage: Model of the unassembled dimer (1996)

There are four groups of RNA bacteriophages with distinct antigenic and physicochemical properties due to differences in surface residues of the viral coat proteins. Coat proteins also play a role as translational repressor during the viral life cycle, binding an RNA hairpin within the genome. In this study, the first crystal structure of the coat protein from a Group II phage GA is reported and compared to the Group I MS2 coat protein. The structure of the GA dimer was determined at 2.8 A resolution (R-factor = 0.20). The overall folding pattern of the coat protein is similar to the Group I MS2 coat protein in the intact virus (Golmohammadi R, Valegård K, Fridborg K, Liljas L. 1993, J Mol Biol 234:620-639) or as an unassembled dimer (Ni Cz, Syed R, Kodandapani R. Wickersham J, Peabody DS, Ely KR, 1995, Structure 3:255-263). The structures differ in the FG loops and in the first turn of the alpha A helix. GA and MS2 coat proteins differ in sequence at 49 of 129 amino acid residues. Sequence differences that contribute to distinct immunological and physical properties of the proteins are found at the surface of the intact virus in the AB and FG loops. There are six differences in potential RNA contact residues within the RNA-binding site located in an antiparallel beta-sheet across the dimer interface. Three differences involve residues in the center of this concave site: Lys/Arg 83, Ser/Asn 87, and Asp/Glu 89. Residue 87 was shown by molecular genetics to define RNA-binding specificity by GA or MS2 coat protein (Lim F. Spingola M, Peabody DS, 1994, J Biol Chem 269:9006-9010). This sequence difference reflects recognition of the nucleotide at position -5 in the unpaired loop of the translational operators bound by these coat proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine.
HSPPC-96: a personalised cancer vaccine (2001)

HSPPC-96 is a protein peptide complex consisting of a 96 kDa heat shock protein (Hsp), gp96, and an array of gp96-associated cellular peptides. Immunisation with HSPPC-96 induces T-cell specific immunity against these peptides; gp96 is not immunogenic per se. The non-covalent binding of gp96 to peptides is neither selective nor restricted to cell types. Thus, the collection of gp96-associated peptides represents the antigenic peptide pool of a cell; this is the basis of the peptide-specific immunogenicity elicited by HSPPC-96. Since the repertoire of antigenic peptides in the cell is different between normal and tumour cells and is also distinct among tumours of the same histology due to the randomness of tumour-specific mutations, a purified sample of HSPPC-96 can only effectively immunise against the tumour from which it originates. The immunisation effect is, therefore, specific to both the individual patient and the tumour type. This true custom-based vaccine has been shown to induce protective T-cell immunity against a variety of tumours in animal models. The major mechanism of action is thought to be the ability of HSPPC-96 to prime peptide-specific MHC class I-restricted CD8+ T-cells by interacting with antigen-presenting cells in a receptor-dependent manner. HSPPC-96 is now being widely tested against human malignancies for which effective therapies do not exist. The major challenges of the human studies are immunological monitoring and the determination of optimal dosing, scheduling and route of administration. HSPPC-96 has been well tolerated at all dose levels. Clinical applications are being addressed by numerous studies including an international, multi-centre, double-blind Phase III trial for the treatment of stage III renal cell carcinoma in the adjuvant setting.
Comparative molecular field analysis (CoMFA) model using a large diverse set of natural, synthetic and environmental chemicals for binding to the androgen receptor (2003)

A large number of natural, synthetic and environmental chemicals are capable of disrupting the endocrine systems of experimental animals, wildlife and humans. These so-called endocrine disrupting chemicals (EDCs), some mimic the functions of the endogenous androgens, have become a concern to the public health. Androgens play an important role in many physiological processes, including the development and maintenance of male sexual characteristics. A common mechanism for androgen to produce both normal and adverse effects is binding to the androgen receptor (AR). In this study, we used Comparative Molecular Field Analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) technique, to examine AR-ligand binding affinities. A CoMFA model with r2 = 0.902 and q2 = 0.571 was developed using a large training data set containing 146 structurally diverse natural, synthetic, and environmental chemicals with a 10(6)-fold range of relative binding affinity (RBA). By comparing the binding characteristics derived from the CoMFA contour map with these observed in a human AR crystal structure, we found that the steric and electrostatic properties encoded in this training data set are necessary and sufficient to describe the RBA of AR ligands. Finally, the CoMFA model was challenged with an external test data set; the predicted results were close to the actual values with average difference of 0.637 logRBA. This study demonstrates the utility of this CoMFA model for real-world use in predicting the AR binding affinities of structurally diverse chemicals over a wide RBA range.
Interferon beta-1a as an investigational treatment for CIDP (2003)

A prospective, multicenter, open-label study was conducted to determine the safety and efficacy of intramuscular (IM) interferon beta-1a (IFNbeta-1a) (Avonex) for treatment of chronic inflammatory demyelinating polyradiculoneuropathy (CIDP). Eligible patients received IM IFNbeta-1a 30 microg once weekly for 6 months. Safety and tolerability were evaluated by reporting of adverse events, measurement of vital signs, and results of blood chemistry, hematology, and urinalysis. The primary efficacy end points were changed from baseline to month 6 on a quantitative Neurologic Disability Score (NDS), a clinical grading (CG) scale, and grip strength (GS) measures. Electrophysiologic measurements were performed at baseline and month 6. A total of 20 treatment-resistant patients with CIDP were enrolled in the study. The tolerability of IFNbeta-1a in patients with CIDP was similar to that seen with its use in MS. There were no serious adverse events, and no patients discontinued treatment due to adverse events. Seven patients (35%) showed clinical improvement, 10 (50%) had stable disease, and 3 (15%) continued to deteriorate. Significant improvements from baseline were observed in NDS in both the intent-to-treat and per protocol analyses (p=0.0005). For CG, significant improvement from baseline was observed in the per protocol analysis (p<0.05) but not in the intent-to-treat analysis. There was no significant effect of treatment on GS. Clinical improvement was not dependent on age, gender, clinical form of CIDP, or duration of symptoms. Electrophysiologic data showed improvements in mean median, ulnar, and tibial motor nerve potential areas. There was no correlation between clinical improvement and electrophysiologic data. The promising results of this study, especially given the refractory nature of the patient population, suggest that a larger placebo-controlled study should be performed to further evaluate the efficacy of IM IFNbeta-1a for the treatment of CIDP.
Rational development and characterization of humanized anti–EGFR variant III chimeric antigen receptor T cells for glioblastoma (2015)

Chimeric antigen receptors (CARs) are synthetic molecules designed to redirect T cells to specific antigens. CAR-modified T cells can mediate long-term durable remissions in B cell malignancies, but expanding this platform to solid tumors requires the discovery of surface targets with limited expression in normal tissues. The variant III mutation of the epidermal growth factor receptor (EGFRvIII) results from an in-frame deletion of a portion of the extracellular domain, creating a neoepitope. We chose a vector backbone encoding a second-generation CAR based on efficacy of a murine scFv-based CAR in a xenograft model of glioblastoma. Next, we generated a panel of humanized scFvs and tested their specificity and function as soluble proteins and in the form of CAR-transduced T cells; a low-affinity scFv was selected on the basis of its specificity for EGFRvIII over wild-type EGFR. The lead candidate scFv was tested in vitro for its ability to direct CAR-transduced T cells to specifically lyse, proliferate, and secrete cytokines in response to antigen-bearing targets. We further evaluated the specificity of the lead CAR candidate in vitro against EGFR-expressing keratinocytes and in vivo in a model of mice grafted with normal human skin. EGFRvIII-directed CAR T cells were also able to control tumor growth in xenogeneic subcutaneous and orthotopic models of human EGFRvIII(+) glioblastoma. On the basis of these results, we have designed a phase 1 clinical study of CAR T cells transduced with humanized scFv directed to EGFRvIII in patients with either residual or recurrent glioblastoma (NCT02209376).