gebhart/patrepeval huggingface dataset:
Interaction of disintegrins with the αIIbβ3 receptor on resting and activated human platelets (1994)

Viper venom disintegrins contain the RGD/KGD motif. They inhibit platelet aggregation and cell adhesion, but show structural and functional heterogeneity. We investigated the interaction of four prototypic disintegrins with alpha IIb beta 3 expressed on the surface of resting and activated platelets. The binding affinity (Kd) of 125I-albolabrin, 125I-echistatin, 125I-bitistatin and 125I-eristostatin toward resting platelets was 294, 153, 48 and 18 nM respectively. The Kd value for albolabrin decreased 3-fold and 6-fold after ADP- or thrombin-induced activation. The Kd values for bitistatin and echistatin also decreased with ADP, but there was no further decrease with thrombin. In contrast, eristostatin bound with the same high affinity to resting and activated platelets. The pattern of fluorescein isothiocyanate (FITC)-eristostatin and FITC-albolabrin binding to resting and activated platelets was consistent with observations using radiolabelled material. Eristostatin showed faster and more irreversible binding to platelets, and greater potency compared with albolabrin in inducing conformational neo-epitopes in beta 3. The anti-alpha IIb beta 3 monoclonal antibody OP-G2 that is RGD-dependent inhibited disintegrin binding to activated platelets more strongly than binding to resting platelets and it inhibited the binding to platelets of albolabrin more strongly than eristostatin. The specificity of disintegrin interaction with alpha IIb beta 3 was confirmed by demonstrating cross-linking of these peptides to alpha IIb beta 3 on normal platelets, but not to thrombasthenic platelets deficient in alpha IIb beta 3.
Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens (2010)

We conclude that extraction kits that incorporated bead-containing lysing matrix and vigorous shaking produced high quality DNA from human fecal specimens (10 to 50 mg, wet wt) that can be resolved as bacterial community fingerprints using PCR-DGGE technique. Subsequently, PCR-DGGE technique can be applied for studying variations in human intestinal microbial communities.
Nature-Inspired Creation of Protein−Polysaccharide Conjugate and Its Subsequent Assembly onto a Patterned Surface (2003)

A protein's functional properties can be adjusted by conjugating it to other polymers. We used a nature-inspired route to create a protein−polysaccharide conjugate and examined the properties of this conjugate. Specifically, the enzyme tyrosinase was used to oxidize accessible tyrosine residues of the model protein green fluorescent protein (GFP). Oxidation yields quinone residues that are “activated” for the covalent conjugation of GFP to nucleophilic groups of the aminopolysaccharide chitosan. Conjugation to chitosan conferred distinct properties to GFP. The GFP−chitosan conjugate was observed to have pH-responsive, “smart” properties, and GFP could be conjugated onto a gel matrix. Additionally, the GFP−chitosan conjugate can be selectively deposited onto a micropatterned surface in response to an applied voltage. This nature-inspired method provides a simple and safe method to conjugate proteins to chitosan, and these conjugates can be readily assembled onto patterned surfaces.
Separate determination of anticoccidial thiamine analogs by high-performance liquid chromatography. (1984)

The separate determination of anticoccidial thiamine analogs such as chloroethylthiamine and dimethialium, and thiamine was achieved by reversed-phase high-performance liquid chromatography after conversion to the corresponding thiochromes by alkaline oxidation. Using this method, it was demonstrated that chloroethylthiamine is accumulated in nonproliferating cells of Saccharomyces cerevisiae by the same transport mechanism as for thiamine and dimethialium.
Hemodynamic Effects of Intravenous Ephedrine in Infants and Children Anesthetized with Halothane and Nitrous Oxide (1996)

The aim of this study was to evaluate the effect of age on the hemodynamic responses to intravenous (IV) ephedrine in pediatric patients anesthetized with halothane, nitrous oxide, and oxygen. One hundred ten pediatric patients, ranging in age from 0.1 to 15 yr, were assigned to receive 0.1 mg/kg (n = 55) or 0.2 mg/kg (n = 55) IV ephedrine. General anesthesia was maintained with 1.0 minimum alveolar anesthetic concentration (MAC) of halothane and 67% nitrous oxide in oxygen after tracheal intubation. Measurements of arterial blood pressure and heart rate were made at 1-min intervals for 10 min after ephedrine 0.1 or 0.2 mg/kg was injected IV as a bolus. Significant correlations were noted between age and changes in mean blood pressure (r = 0.37, P < 0.01 for the subjects receiving ephedrine 0.1 mg/kg; r = 0.63, P < 0.001 for the subjects receiving ephedrine 0.2 mg/kg), but not between age and changes in heart rate. The present results indicate that age correlates with the pressor but not the chronotropic effects of ephedrine in pediatric patients anesthetized with 1 MAC halothane and nitrous oxide.
Safety, Tolerability, and Pharmacokinetics of SMT C1100, a 2-Arylbenzoxazole Utrophin Modulator, following Single- and Multiple-Dose Administration to Pediatric Patients with Duchenne Muscular Dystrophy (2016)

ClinicalTrials.gov NCT02383511.
Contribution of the Reverse Rate of the Conformational Step to Polymerase β Fidelity (2009)

A complete understanding of the kinetic mechanism of fidelity requires comparison of correct and incorrect dNTP incorporation pathways in both the forward and reverse directions. The studies presented here focus on the dNTP-induced conformational step, which has historically been proposed by many to be the major determinant of fidelity. As it was recently highlighted [Tsai, Y. C., and Johnson, K. A. (2006) Biochemistry 45, 9675-9687], chemistry can be the slowest step in the forward direction of the correct dNTP incorporation pathway, yet the corresponding microscopic rate constant would not contribute toward fidelity in the case when the reverse rate of the conformational step is slower than chemistry. Here we use a stopped-flow technique to directly measure the reverse rate of the conformational step in the DNA polymerase beta (Pol beta) kinetic pathway. Extensive pre-steady-state kinetic studies presented include the utilization of 2-aminopurine-labeled DNA substrates, 2-aminopurine nucleotide triphosphate, a nonhydrolyzable nucleotide analogue dAMPCPP, and a rapid sequential mixing reaction scheme. Additionally, the effect of mismatched dNTPs, various metal ions, and the presence of the 3'-terminal hydroxyl group of the primer on the rate of the reverse "opening" conformational step were analyzed. Our analyses indicate that reverse "opening" is drastically facilitated in the presence of mismatched ternary complexes, which is in agreement with the hypothesis that the ternary complex is destabilized by the presence of incorrect dNTP. By analysis of the relative magnitudes of chemistry and reverse "opening" in the presence of both matched and mismatched matched ternary complexes, this work further validates that, for Pol beta, fidelity is dictated by the differences in free energy required to reach the highest energy transition state of the chemical step.
Results of a two‐year followup study of patients with rheumatoid arthritis who received a combination of abatacept and methotrexate (2008)

The improvements in signs and symptoms, physical function, and HRQOL observed after 1 year of abatacept treatment were maintained through 2 years of treatment. This durability was accompanied by a safety profile consistent with that in the double-blind portion of the study. Radiographic progression was further inhibited in year 2 compared with year 1, suggesting an increasing effect of abatacept on the inhibition of structural damage in year 2.
Size selection of colloidal gold aggregates by filtration: effect on surface‐enhanced Raman scattering intensities (1999)

The effect of colloidal Au particle aggregation on surface-enhanced Raman scattering (SERS) spectra was probed by SERS filtration experiments. In this approach, SERS and optical spectra were recorded for trans-1,2-bis(4-pyridyl)ethylene (BPE)-aggregated solutions of colloidal Au filtered through straight-channel membranes with successively smaller diameters. This allowed the overall SERS intensity to be factored into aggregate size-dependent contributions. Experiments were carried out as a function of adsorbate concentration (0.5–2.5 µM BPE) and initial particle size (12–50 nm diameter colloidal Au). The key findings are as follows: (i) under conditions of minimal aggregation, appreciable SERS intensity derives from aggregates with effective diameters less than 200 nm; (ii) the amount of aggregant clearly controls the average aggregate size; and (iii) similarly aggregated solutions based on different diameter colloidal Au particles give different distributions of aggregates. These studies provide an insight into the dynamics of colloidal Au aggregation, suggest a procedure for signal optimization in colloid SERS experiments, and set the stage for controlled surface confinement of SERS-active particle clusters. Copyright © 1999 John Wiley & Sons, Ltd.
Basic formulae for multifocusing stack (1994)

Multifolding coverage is a basic of modern acquisition systems which record a vast size of seismic information. However existing technique of seismic data processing allows to extract only a small part of this information. Only wave fields, corresponding to the CMP and CS(Rec)P configurations are used in data processing in practice . But multifold systems also record wave fields corresponding to many other types of source receiver pair configurations.
Serum amyloid P component binds to histones and activates the classical complement pathway (1992)

Two members of the pentraxin family of proteins, C-reactive protein (CRP) and serum amyloid P component (SAP), bind to chromatin and may be involved in the solubilization and clearance of nuclear material. Previous studies demonstrated that CRP binding to chromatin is mediated by histones. SAP differs from CRP in being able to bind to DNA, but SAP binding to histones has not been reported. CRP is an activator of the classical C pathway, and C-dependent cleavage of chromatin in the presence of CRP and serum has been shown. Oligomers of SAP have recently been found to bind to C1q and consume total C and C4, indicating that SAP can activate C as well. The present study examined CRP and SAP binding to histones H1 and H2A and C activation after binding. SAP binding to histones H1 and H2A was observed as well as SAP binding to chromatin. In contrast to CRP, SAP binding to chromatin did not require H1. SAP partially inhibited CRP binding to chromatin and to H1. However, neither pentraxin inhibited binding of the other to H2A. Binding of either CRP or SAP to H2A activated C in SAP-depleted serum leading to the deposition of C4 and C3. C activation required C1q and produced C4d indicating that it occurred through the classical pathway. These findings demonstrate that CRP and SAP share histone as well as chromatin binding, and that both pentraxins can activate the classical C pathway after ligand binding.
The Role of Estrogen Receptors and Androgen Receptors in Sex Steroid Regulation of B Lymphopoiesis (1998)

Several observations suggest that sex steroids might participate in steady state regulation of B lymphopoiesis. B cell precursors decline dramatically in bone marrow of pregnant or estrogen-treated mice. Reciprocally, the same cell populations are increased in hypogonadal mice or male castrates. Estrogen treatment of hypogonadal mice reduced precursors to normal. However, questions remain about which hormones and receptors are the most important. Furthermore, these observations need to be reconciled with advances regarding new sex steroid receptors. We have now characterized B lymphopoiesis in androgen receptor-deficient testicular feminization (Tfm) mice. Testicular feminization mice had substantially elevated numbers of B cell precursors in the bone marrow and B cells in the spleen as compared with wild-type mice. The importance of one estrogen receptor (ER alpha) was evaluated in gene-targeted mice, and B cell precursors were found to be within the normal range. Our previous studies indicated that hormone receptors in stromal cells may be important for estrogen-mediated suppression of B lymphopoiesis. We now show that estrogen-mediated inhibition of B cell precursor expansion in culture was blocked by a specific estrogen receptor antagonist (ICI 182,780). Stromal cells derived from ER alpha-targeted bone marrow were fully estrogen responsive. RT-PCR analyses of these stromal cells revealed splice-variant transcripts of ER alpha, as well as message for a recently discovered estrogen-binding receptor, ER beta. Thus, androgens may normally inhibit B lymphopoiesis through the androgen receptor, whereas estrogens might utilize one or more receptors to achieve the same physiologic response.
On the nature of the cell wall constituents of Laminaria spp. Mannuronic acid (1931)

THE nature of the cell wall constituents of the red and brown algae has been the subject of study in
Transcranial magnetic stimulation improves naming in Alzheimer disease patients at different stages of cognitive decline (2008)

Repetitive transcranial magnetic stimulation applied to the dlPFC improves naming performance also in the advanced stages of AD. Moreover, in the severe group the effect is not specific for action naming, as in the case of the mild AD group. These findings suggest that rTMS can affect the intrinsic ability of the brain to restore or compensate for damaged function and may represent an useful new tool for cognitive rehabilitation.
Identification of Restriction Factors by Human Genome-Wide RNA Interference Screening of Viral Host Range Mutants Exemplified by Discovery of SAMD9 and WDR6 as Inhibitors of the Vaccinia Virus K1L − C7L − Mutant (2015)

The coevolution of microbial pathogens with cells has led to an arms race in which the invader and host continuously struggle to gain the advantage. For this reason, traditional siRNA screens may fail to uncover important immune mechanisms if the pathogens have already developed effective responses. However, host-restricted viral mutants have lost one or more defense genes needed for their replication in nonpermissive cells. By screening human genome libraries of short RNAs that inhibit the expression of individual host genes in nonpermissive cells, we identified SAMD9 and WDR6 as major restriction factors that prevented replication of a vaccinia virus mutant and suggest that host range screening can be generally useful for the investigation of host-pathogen interactions.
Accurate thickness measurement of graphene (2016)

Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.
A systematic scheme for power amplifier design using a multi-harmonic loadpull simulation technique (2002)

This paper presents, for the first time, a systematic procedure for narrowband power amplifier design using a multi-harmonic loadpull simulation technique. This scheme explores the effects of each harmonic termination on amplifier performance and finds the optimal load at each harmonic. Following this systematic design procedure we can improve the amplifier performance significantly. The advantages of our method are demonstrated for two power amplifiers. Very promising results are obtained.
Representing and Solving Decision Problems with Limited Information (2001)

We introduce the notion of LImited Memory Influence Diagram (LIMID) to describe multistage decision problems in which the traditional assumption of no forgetting is relaxed. This can be relevant in situations with multiple decision makers or when decisions must be prescribed under memory constraints, such as in partially observed Markov decision processes (POMDPs). We give an algorithm for improving any given strategy by local computation of single policy updates and investigate conditions for the resulting strategy to be optimal.
Identification of T follicular helper (Tfh) cells by flow cytometry (2013)

T follicular helper \(Tfh) cells are the main T helper \(Th) cell subset that provides help to B cells, supporting germinal center induction, a nity maturation, and generation of memory B cells and longlived plasma cells. Recently, Tfh cells and Tfh-like transition states have also been implicated in the generation of other Th cell subsets, including Th1 and memory Th cells. Tfh cells are generally characterized by their expression of the chemokine receptor CXCR5, the transcription factor BCL6, and the inhibitory molecule PD-1. Here we provide a simple and reliable optimized staining protocol for the identi cation of murine Tfh cells by ow cytometry. Stained cells can be analyzed directly by ow cytometry. Tfh cell sorting for use in downstream applications is also possible using CXCR5 and PD-1 staining, but intracellular staining for BCL6 is not compatible with live cell recovery.
RSA-TBOS signcryption with proxy re-encryption (2008)

The recent attack on Apple iTunes Digital Rights Management [17] has brought to light the usefulness of proxy re-encryption schemes for Digital Rights Management. It is known that the use of proxy re-encryption would have prevented the attack in [17]. With this utility in mind and with the added requirement of non-repudiation, we propose the first ever signcryption scheme with proxy re-encryption that does not involve bilinear maps. Our scheme is called RSA-TBOS-PRE and is based on the RSA-TBOS signcryption scheme of Mao and Malone-Lee [7]. We adapt various models available in the literature concerning authenticity, unforgeability and non-repudiation and propose a signature non-repudiation model suitable for signcryption schemes with proxy re-encryption. We show the non-repudiability of our scheme in this model. We also introduce and define a new security notion of Weak-IND-CCA2, a slightly weakened adaptation of the IND-CCA2 security model for signcryption schemes and prove that RSA-TBOS-PRE is secure in this model. Our scheme is Weak-IND-CCA2 secure, unidirectional, extensible to multi-use and does not use bilinear maps. This represents significant progress towards solving the open problem of designing an IND-CCA2 secure, unidirectional, multi-use scheme not using bilinear maps proposed in [15][12].
Improving chemotherapeutic drug penetration in tumors by vascular targeting and barrier alteration (2002)

Drug delivery and penetration into neoplastic cells distant from tumor vessels are critical for the effectiveness of solid-tumor chemotherapy.We have found that targeted delivery to tumor vessels of picogram doses of TNF- (TNF), a cytokine able to alter endothelial barrier function and tumor interstitial pressure, enhances the penetration of doxorubicin in tumors in murine models.Vascular targeting was achieved by coupling TNF with CNGRC, a peptide that targets the tumor neovasculature.This treatment enhanced eight-to tenfold the therapeutic efficacy of doxorubicin, with no evidence of increased toxicity.Similarly, vascular targeting enhanced the efficacy of melphalan, a different chemotherapeutic drug.Synergy with chemotherapy was observed with 3-5 ng/kg of targeted TNF (intraperitoneally), about 10 6 -fold lower than the LD 50 and 10 5 -fold lower than the dose required for nontargeted TNF.In addition, we have also found that targeted delivery of low doses of TNF to tumor vessels does not induce the release of soluble TNF receptors into the circulation.The delivery of minute amounts of TNF to tumor vessels represents a new approach for avoiding negative feedback mechanisms and preserving its ability to alter drug-penetration barriers.Vascular targeting could be a novel strategy for increasing the therapeutic index of chemotherapeutic drugs.
Inducing Tumor Immunity through the Selective Engagement of Activating Fcγ Receptors on Dendritic Cells (2002)

Induction of tumor-specific immunity requires that dendritic cells (DCs) efficiently capture and present tumor antigens to result in the expansion and activation of tumor-specific cytotoxic T cells. The transition from antigen capture to T cell stimulation requires a maturation signal; in its absence tolerance, rather than immunity may develop. While immune complexes (ICs) are able to enhance antigen capture, they can be poor at inducing DC maturation, naive T cell activation and protective immunity. We now demonstrate that interfering with the inhibitory signal delivered by FcgammaRIIB on DCs converts ICs to potent maturation agents and results in T cell activation. Applying this approach to immunization with DCs pulsed ex-vivo with ICs, we have generated antigen-specific CD8+ T cells in vivo and achieved efficient protective immunity in a murine melanoma model. These data imply that ICs may normally function to maintain tolerance through the binding to inhibitory FcgammaRs on DCs, but they can be converted to potent immunogenic stimuli by selective engagement of activating FcgammaRs. This mechanism suggests a novel approach to the development of tumor vaccines.
In VivoPostirradiation Protection by a Vitamin E Analog, α-TMG (2003)

The water-soluble vitamin E derivative alpha-TMG is an excellent radical scavenger. A dose of 600 mg/kg TMG significantly reduced radiation clastogenicity in mouse bone marrow when administered after irradiation. The present study was aimed at investigating the radioprotective effect of postirradiation treatment with alpha-TMG against a range of whole-body lethal (8.5-12 Gy) and sublethal (1-5 Gy) doses of radiation in adult Swiss albino mice. Protection against lethal irradiation was evaluated from 30-day mouse survival and against sublethal doses was assessed from micronuclei and chromosomal aberrations in the bone marrow 24 h after irradiation. An intraperitoneal injection of 600 mg/kg TMG within 10 min of lethal irradiation increased survival, giving a dose modification factor (DMF) of 1.09. TMG at doses of 400 mg/kg and 600 mg/kg significantly reduced the percentage of aberrant metaphases, the different types of aberrations, and the number of micronucleated erythrocytes. DMFs of 1.22 and 1.48 for percentage aberrant metaphases and 1.6 and 1.98 for micronuclei were obtained for 400 mg/kg and 600 mg/kg TMG, respectively. No drug toxicity was observed at these doses. The effectiveness of TMG when administered postirradiation suggests its possible utility for protection against unplanned radiation exposures.