gebhart/patrepeval huggingface dataset:
Secondary and Tertiary Structure Changes of Reconstituted P-glycoprotein (1996)

The structure of purified P-glycoprotein functionally reconstituted into liposomes was investigated by attenuated total reflection Fourier transform infrared spectroscopy. A quantitative evaluation of the secondary structure and a kinetic of 2H/H exchange of the P-glycoprotein were performed both in the presence and in the absence of MgATP, MgATP-verapamil, and MgADP. This approach was previously shown to be a useful tool to detect tertiary structure changes resulting from the interaction between a protein and its specific ligands, as established for the Neurospora crassa H+-ATPase. 2H/H exchange measurements provided evidence that a large fraction of the P-glycoprotein is poorly accessible to the aqueous medium. Addition of MgATP induced an increased accessibility to the solvent of a population of amino acids, while addition of MgATP-verapamil resulted in a subtraction of a part of the protein from access to the aqueous solvent. No significant changes were observed upon addition of MgADP or verapamil alone. The secondary structure of P-glycoprotein was not affected by addition of ligands. The variations observed in the 2H/H exchange rate when P-glycoprotein interacted with the above ligands therefore represented tertiary structure changes. Fluorescence quenching experiments confirmed that MgATP-induced changes are to be found in the tertiary structure of the enzyme.
Meniere's disease might be an autoimmune condition? (2012)

Meniere's disease is characterised by intermittent episodes of vertigo, fluctuating sensorineural hearing loss, tinnitus, and aural pressure. The aetiology and pathogenesis remain unknown. Proposed theories of causation include viral infections and immune system-mediated mechanisms. The immune response in Meniere's disease is focused on inner ear antigens. Approximately one-third of Meniere's disease cases seem to be of an autoimmune origin although the immunological mechanisms involved are not clear. The diagnosis of autoimmune inner ear disease is based either on clinical criteria or on a positive response to steroids. The antiviral approach has virtually eliminated the use of various surgical methods used in the past. Steroid responsiveness is high, and with prompt treatment, inner ear damage may be reversible. The administration of etanercept improves or stabilises symptoms in treated patients. Treatment of antiphospholipid syndrome can be directed toward preventing thromboembolic events by using antithrombotic medications. Only warfarin has been shown to be effective. Gene therapy can be used to transfer genetic material into inner ear cells using viral vectors and to protect, rescue, and even regenerate hair cells of the inner ear.
“Intelligent” Polymers in Medicine and Biotechnology (1995)

One can define "intelligent" polymers as those polymers that respond with large property changes to small physical or chemical stimuli. These polymers may be in various forms, such as in solution, on surfaces, or as solids. One may also combine intelligent aqueous polymer systems with biomolecules to yield a large family of polymers that respond intelligently to physical, chemical, or biological stimuli. This article overviews such interesting and versatile polymer systems.
Xampling: analog to digital at sub-Nyquist rates (2011)

The authors present a sub-Nyquist analog-to-digital converter of wideband inputs. The circuit realises the recently proposed modulated wideband converter, which is a flexible platform for sampling signals according to their actual bandwidth occupation. The theoretical work enables, for example, a sub-Nyquist wideband communication receiver, which has no prior information on the transmitter carrier positions. The present design supports input signals with 2 GHz Nyquist rate and 120 MHz spectrum occupancy, with arbitrary transmission frequencies. The sampling rate is as low as 280 MHz. To the best of the authors&apos; knowledge, this is the first reported hardware that performs sub-Nyquist sampling and reconstruction of wideband signals. The authors describe the various circuit design considerations, with an emphasis on the non-ordinary challenges the converter introduces: mixing a signal with a multiple set of sinusoids, rather than a single local oscillator, and generation of highly transient periodic waveforms, with transient intervals on the order of the Nyquist rate. Hardware experiments validate the design and demonstrate sub-Nyquist sampling and signal reconstruction.
Adaptive Modulation and Error Control Techniques (1966)

This report contains the results of an investigation designed to develop, analyze, and evaluate techniques to improve the quality of digital data transmission by adapting the modulation or error control parameters to varying channel conditions. Specific systems for varying the bit rate and the alphabet size are postulated and evaluated analytically in realistic channel environments. Variable block length and variable redundancy error control techniques are described and analyzed in a computer simulation of real channels. In addition, the operation and performance of a laboratory prototype of an adaptive error correction decoder that does not require feedback is described.
Synthesis and Behavior of the Polymer Covering on a Solid Surface. 3. Morphology and Mechanism of Formation of Grafted Polystyrene Layers on the Glass Surface (1998)

Polystyrene films have been grafted by radical polymerization in situ on the surface of glass slides. The morphology of these films resulting from different grafting temperatures has been investigated by both the contact angle method and scanning probe microscopy with respect to the grafting time. At a grafting density regime where the theory proposes the existence of a homogeneous layer, the formation of island structures of grafted polymer with a size substantially higher than expected by the theory has been observed. Overshot polymer structures of large sizes are created. The amount of grafted polymer is substantially higher than that predicted from the conception of monolayer covering. The grafting layer becomes impermeable for water only at a high amount of grafted polymer, which corresponds to the multilayer structure of the coating. We suggested a mechanism for the grafting process that included at least three stages: (a) first, a brushlike polymer layer is formed; (b) subsequently, a second layer of ungrafted chains is created in the regime when excess chains are forced out from the first layer; (c) big polymer clusters, with an average size of 100−200 nm due to gel polymerization in the clusters, formed in the force out regime.
Reduction of phosphatidylcholine hydroperoxide by apolipoprotein A-I: purification of the hydroperoxide-reducing proteins from human blood plasma (1998)

Plasma glutathione peroxidase (GSHPx) has been suggested to reduce submicromolar levels of free fatty acid hydroperoxides and phosphatidylcholine hydroperoxides (PC-OOH), and therefore these hydroperoxides are undetectable in human blood plasma. The capacity for the reduction should be about 2.5 microM as the level of glutathione in human plasma is about 5 microM. However, 2 h of aerobic incubation of 58 microM PC-OOH in human plasma at 37 degrees C resulted in the formation of 36 microM phosphatidylcholine hydroxide (PC-OH). The presence of PC-OOH-reducing protein other than plasma GSHPx was suggested by the results. a) The same rates of PC-OOH decay and PC-OH formation were observed in both sera from rats with selenium-deficient and selenium-supplemented diet; b) the PC-OOH-reducing activity was observed only in the high molecular weight fraction but not in the low molecular weight fraction; and c) albumin did not work as a reducing substrate of plasma GSHPx. We have isolated two hydroperoxide-reducing protein fractions from human plasma by a sequential purification scheme, comprising an ammonium sulfate precipitation followed by sequential chromatography on anion exchange, hydrophobic interaction, and heparin columns. One of the proteins was identified as apolipoprotein A-I by N-terminal amino acid sequence analysis. Moreover, the hydroperoxide-reducing activity of one of the fractions was inhibited almost completely by the addition of anti-apolipoprotein A-I antibody. These findings demonstrate that apolipoprotein A-I in high density lipoprotein can reduce PC-OOH to PC-OH.
Effect of redox environment on the in vitro and in vivo folding of RTEM-1 beta-lactamase and Escherichia coli alkaline phosphatase. (1994)

The oxidative folding mechanisms of two Escherichia coli periplasmic proteins, alkaline phosphatase and RTEM-1 beta-lactamase, have been examined in vitro and in vivo. In contrast to eukaryotic proteins, which require a relatively reducing environment for optimal folding rates, both alkaline phosphatase and beta-lactamase fold fastest under very oxidizing conditions. For example, bovine pancreatic ribonuclease exhibits an optimal folding rate in a redox buffer consisting of 1 mM GSH and 0.2 mM GSSG (Lyles, M. M., and Gilbert, H. F. (1991) Biochemistry 30, 613-619); however, both E. coli alkaline phosphatase and beta-lactamase exhibit optimal in vitro folding rates at low concentrations of GSH (< 0.4 mM) and very high concentrations of GSSG (4-8 mM). For both bacterial proteins, GSH inhibits oxidative folding. Under optimal redox conditions, the rate-limiting step for the in vitro oxidative folding of alkaline phosphatase depends on the concentration of the protein, consistent with a mechanism involving rapid oxidation followed by slow dimerization. With beta-lactamase, the oxidative folding mechanism involves a competition between disulfide bond formation and folding of the molecule into a catalytically active conformation that buries the 2 reduced cysteines in the core of the enzyme. The effects of including a thiol reductant in the growth medium on the in vivo folding of alkaline phosphatase and beta-lactamase are similar to the effects observed during in vitro folding of these enzymes. The levels of both oxidized proteins are decreased by GSH in the growth medium. However, addition of a disulfide oxidant to the growth medium does not positively affect the production of either enzyme. These observations are consistent with the idea that the oxidative folding mechanisms of E. coli periplasmic proteins and, by inference, proteins of the eukaryotic endoplasmic reticulum have evolved to accommodate constraints placed on the folding reaction by the folding environment. The consequences of differences between the folding mechanisms in eukaryotic and prokaryotic disulfide-containing proteins on the expression of eukaryotic proteins in the bacterial periplasm are discussed.
Reduction of the severity of canine osteoarthritis by prophylactic treatment with oral doxycycline (1992)

Prophylactic administration of doxy markedly reduced the severity of OA in weight-bearing regions of the medial femoral condyle. It remains to be determined whether administration of doxy after OA changes have developed is also effective.
Bispecific Monoclonal Antibodies Produced by Somatic Cell Fusion Increase the Potency of Tissue Plasminogen Activator (1990)

Bispecific monoclonal antibodies that bind simultaneously to human fibrin and tissue plasminogen activator (tPA) enhance the fibrinolytic potency of tPA. Two bispecific antibodies (F36.23 and F32.1) were generated by somatic cell fusion. Antibody F36.23 derives its tPA binding from monoclonal anti-tPA antibody TCL8 and its fibrin binding from monoclonal antifibrin antibody 59D8. After purification from cell supernatants and ascites by two steps of affinity chromatography, hybrid-hybridoma bispecific antibody F36.23 simultaneously bound tPA and fibrin in solution and in solid-phase assays. In an assay for the lysis of human fibrin monomer, F36.23 increased the fibrinolytic potency of tPA by 5 to 10 fold, regardless of whether the bispecific antibody had been combined with the tPA before or during the assay. Bispecific F36.23 F(ab')2 also bound tPA and fibrin simultaneously, and the enhancement in fibrinolysis in the presence of F36.23 F(ab')2 was identical to that in the presence of intact F36.23. The second bispecific antibody, F32.1, was produced by an alternative strategy that has a wider potential for application in other systems. Hybridoma bispecific antibody F32.1 was derived from the fusion of immune splenocytes (in mice immunized with a synthetic oligopeptide representing the amino terminus of the alpha-chain of human fibrin) with the anti-tPA cell line TCL8. The properties of hybridoma bispecific antibody F32.1 and its F(ab')2 were indistinguishable from those of hybrid-hybridoma bispecific antibody F36.23 in solid-phase binding assays and in assays of fibrinolysis. Bispecific antibodies produced by somatic cell fusion, particularly in the form of F(ab')2, may have potential for use in clinical thrombolysis.
The importance of gender on myokinetic deficits before and after microinjury (2000)

Our results reveal that muscle force generating capabilities of physically active men exceed that of women both before and after microinjury. Myokinetic deficits were most pronounced acutely, between 24 and 48 h postinjury, followed by a near complete recovery at day 4 (96 h postinjury). Both genders suffered acute and residual deficits for PFP, whereas only men showed significant acute deficits for PRFP. We recommend that athletes, both male and female, refrain from strenuous exercise at least 48 h postinjury, or until force-generating capabilities normalize. More research needs to be conducted to substantiate these findings.
Identification of a second T-cell antigen receptor in human and mouse by an anti-peptide gamma-chain-specific monoclonal antibody. (1987)

We developed a monoclonal antibody (mAb) (9D7) against a synthetic peptide (P13K) selected from the deduced amino acid sequence of the constant region of the gamma chain of the murine T-cell antigen receptor (TCR) (amino acids 118-130). Using this mAb, we identified a putative second TCR expressed on peripheral blood lymphocytes from a patient with severe combined immunodeficiency (SCID) that were propagated in culture with recombinant interleukin 2 (rIL-2) and Con A. This mAb immunoprecipitated two polypeptide chains of 40 and 58 kDa under nonreducing conditions and of 40 and 56 kDa under reducing conditions from 125I-labeled denatured lysates of T3+ WT31- lymphocytes expanded in culture from a SCID patient. These polypeptide chains were not disulfide linked and were not present on human peripheral blood lymphocytes from normal donors cultured for 5 days with phytohemagglutinin or for 2 weeks with rIL-2 and polyclonal activators or on cells of the Jurkat lymphoblastoid human T-cell line. Chemical crosslinking of 125I-labeled cells followed by immunoprecipitation with anti-Leu-4 mAb under nonreducing or reducing conditions revealed that the 40- and 56-kDa polypeptide chains were associated with the T3 differentiation antigen. These results were confirmed by sequential immunoprecipitation with anti-Leu-4 mAb followed by 9D7 anti-P13K mAb. The 9D7 anti-P13K mAb immunoprecipitated two polypeptide chains of 43 and 64 kDa from denatured lysates of lymphocytes from a patient with severe common variable immunodeficiency (CVI) that were expanded in culture with rIL-2 and Con A. Thus, this second TCR may be composed of two polypeptide chains (gamma gamma'), both of which appear to be the product of the gamma-chain gene. These experiments were done with polyclonal cell populations. Cloned T3+ WT31- cell populations are required to determine whether this TCR contains two gamma polypeptide chains. In contrast, only one polypeptide chain of 56 kDa was immunoprecipitated by the 9D7 anti-P13K mAb from peripheral blood lymphocytes from a patient with mild CVI expanded in culture with rIL-2 and polyclonal activators. Using the same 9D7 anti-P13K mAb and immunoblotting analysis, we identified a 35 kDa gamma-chain polypeptide under reducing conditions expressed on purified L3T4- Lyt2- BALB/c mouse thymocytes. This gamma-chain TCR is disulfide linked and has a molecular mass of 80 kDa under nonreducing conditions.
Normal functional characteristics of cultured human promyelocytic leukemia cells (HL-60) after induction of differentiation by dimethylsulfoxide. (1979)

The HL-60 human promyelocytic leukemia cell line can be induced to terminally differentiate to mature myeloid cells sharing a number of functional characteristics with normal granulocytes including response to chemoattractants, development of complement receptors, phagocytosis, superoxide production, and nitroblue tetrazolium dye reduction. Hence the Me2SO-induced HL-60 cells provide a unique in vitro model for studying various important aspects of human myeloid cell differentiation.
The Effects of a Promoter of Cell Differentiation and Selected Hormones on Human Cytomegalovirus Infection Using an In Vitro Cell System (1990)

The influence of factors that can regulate cellular developmental or metabolic processes in host tissue on cytomegalovirus (CMV) replication in vitro was determined. Hydrocortisone treatment of cells before viral infection resulted in a 12- to 13-fold increase in the expression of immediate early proteins at 4 h after virus inoculation. The addition of a phorbol diester 1.5 h after CMV infection resulted in an 8- to 13-fold increase in production of viral progeny. In contrast, beta-human chorionic gonadotropin treatment generally resulted in a 25%-72% suppression of both CMV-specific proteins and progeny. Effects on CMV infection with either progesterone or estradiol were minor and generally suppressive. The stimulating or suppressive effects of these factors on CMV replication in vitro may be important to CMV reactivation in humans. Further study of regulatory factors may lead to the development of therapeutic approaches to the prevention of CMV reactivation in patients at risk for severe disease.
Misdirection of regenerating axons and functional recovery following sciatic nerve injury in rats (2010)

Poor functional recovery found after peripheral nerve injury has been attributed to the misdirection of regenerating axons to reinnervate functionally inappropriate muscles. We applied brief electrical stimulation (ES) to the common fibular (CF) but not the tibial (Tib) nerve just prior to transection and repair of the entire rat sciatic nerve, to attempt to influence the misdirection of its regenerating axons. The specificity with which regenerating axons reinnervated appropriate targets was evaluated physiologically using compound muscle action potentials (M responses) evoked from stimulation of the two nerve branches above the injury site. Functional recovery was assayed using the timing of electromyography (EMG) activity recorded from the tibialis anterior (TA) and soleus (Sol) muscles during treadmill locomotion and kinematic analysis of hindlimb locomotor movements. Selective ES of the CF nerve resulted in restored M-responses at earlier times than in unstimulated controls in both TA and Sol muscles. Stimulated CF axons reinnervated inappropriate targets to a greater extent than unstimulated Tib axons. During locomotion, functional antagonist muscles, TA and Sol, were coactivated both in stimulated rats and in unstimulated but injured rats. Hindlimb kinematics in stimulated rats were comparable to untreated rats, but significantly different from intact controls. Selective ES promotes enhanced axon regeneration but does so with decreased fidelity of muscle reinnervation. Functional recovery is neither improved nor degraded, suggesting that compensatory changes in the outputs of the spinal circuits driving locomotion may occur irrespective of the extent of misdirection of regenerating axons in the periphery.
Modeling video evolution for action recognition (2015)

In this paper we present a method to capture video-wide temporal information for action recognition. We postulate that a function capable of ordering the frames of a video temporally (based on the appearance) captures well the evolution of the appearance within the video. We learn such ranking functions per video via a ranking machine and use the parameters of these as a new video representation. The proposed method is easy to interpret and implement, fast to compute and effective in recognizing a wide variety of actions. We perform a large number of evaluations on datasets for generic action recognition (Hollywood2 and HMDB51), fine-grained actions (MPII- cooking activities) and gestures (Chalearn). Results show that the proposed method brings an absolute improvement of 7–10%, while being compatible with and complementary to further improvements in appearance and local motion based methods.
Oxygen Permeability of a New Type of High Dk Soft Contact Lens Material (1998)

Lotrafilcon A is a biphasic block-copolymer, comprising a highly permeable siloxane-based polymeric phase, coupled with a water phase (hydrogel phase). The high oxygen permeability of this material, and the fact that it is a hydrogel, places it outside the applicability of both the polarographic ISO standard and coulometric ISO draft standards for contact lens Dk determination. The oxygen permeability (Dk) and transmissibility (Dk/t) of lotrafilcon A lenses were determined by an adaptation of the standard coulometric method. Lenses with a thickness (t) range from 30 microns to over 300 microns were measured in a liquid-to-gas and a gas-to-gas configuration in an effort to combine features of the ISO (draft) standards to yield a valid measurement of the intrinsic material's oxygen transmission characteristics. The following results, for lotrafilcon A, are the mean values and SE for the oxygen permeability coefficient (Dk) determined at 34 degrees C: 140 +/- 2 barrer with water overlay (liquid-to-gas) at 2100 rpm stirring speed, 150 +/- 5 barrer with water overlay (liquid-to-gas) at "infinite" stirring speed, and 170 +/- 2 barrer without water overlay (gas-to-gas), where barrer = 10(-11) (mlO2.cm)/(sec.cm2.mm Hg). Clinical lenses produced from this material are expected to be in the 60 to 90 microns thickness range, with an average center thickness of 80 microns. Given that the Dkmaterial is greater than or equal to 140 barrers, for this material, a parallel sided lens of 80 microns central thickness would exhibit a lens transmissibility (Dk/t) of at least 170 x 10(-9) mlO2/(sec.cm2.mm Hg) at 34 degrees C. This transmissibility is well in excess of the 87 x 10(-9) mlO2/(sec.cm2.mm Hg) value postulated to be sufficient to prevent overnight lens-induced corneal swelling and places it in the hyper-permeable material category.
Lymphoma depletion during CD20 immunotherapy in mice is mediated by macrophage FcγRI, FcγRIII, and FcγRIV (2008)

Despite the demonstrated clinical efficacy of CD20 monoclonal antibody (mAb) for lymphoma therapy, the in vivo mechanisms of tumor depletion remain controversial and variable. To identify the molecular mechanisms responsible for lymphoma killing by CD20 mAb in a homologous system amenable to mechanistic studies and genetic manipulation, a mouse lymphoma model was developed using primary tumor cells from a C57BL/6 Emicro-cMyc transgenic mouse and mouse antimouse CD20 mAbs. CD20 mAb treatment of syngeneic mice with adoptively transferred lymphomas prevented tumor development or significantly prolonged mouse survival depending on tumor volume, mAb dose, and treatment timing. Cooperative FcgammaRIV, FcgammaRIII, and FcgammaRI interactions mediated optimal lymphoma depletion by CD20 mAb in vivo, whereas clodronate-mediated depletion of macrophages eliminated the therapeutic benefit of CD20 mAb. Although CD20 mAbs activated complement in vitro and in vivo, normal and malignant B-cell depletion was induced through C1q- and C3-independent mechanisms. Thus, the ability of CD20 mAbs to deplete malignant B cells in vivo required FcgammaR-dependent use of the innate mononuclear cell immune system. These findings allow for mechanism-based predictions of the biologic outcome of CD20 mAb therapy and treatment optimization.