gebhart/patrepeval huggingface dataset:
A novel green synthesis approach for polymer nanocomposites decorated with silver nanoparticles and their antibacterial activity (2014)

A novel, low-cost and direct green synthesis strategy was developed for the preparation of polymer composite spheres composed of silver nanoparticles (AgNPs) decorated on the polymer colloids in a raspberry-like fashion. The polymer colloids were employed as both the reductant and the substrate support. The environmentally benign reaction system consists of AgNO3, polymer spheres and an ethanol solvent, without any additional reducing agents or stabilizers. The obtained composite spheres are surprisingly stable. The size range of the formed AgNPs is from several to tens of nanometers, dependent on the reaction time, AgNO3 concentration, and the amount of polymer spheres. A four-step mechanism was proposed for the formation of AgNPs-coated polymer spheres emphasizing the role of ethanol for saturating the external surface of the polymer spheres first. These composites exhibit excellent antibacterial activity, which is dependent on both the concentration of the composite spheres and the size of coated AgNPs.
β-C-Mannosides as Selectin Inhibitors (2002)

Potential E- and P-selectin inhibitors were synthesized to explore a hydrophobic area on the E-selectin surface and the PSGL-1 protein binding site on the P-selectin surface that was recently defined by crystallography. Three series of mannose-based compounds (libraries A, B, and C) were synthesized using solution phase parallel synthesis. Biological evaluation of these compounds was done using two ELISA-based assays and transferred NOE (trNOE) experiments. Some of the compounds showed better activity than sLe(x) in the P-selectin assay.
Structure and Immunogenicity of a Peptide Vaccine, Including the Complete HIV-1 gp41 2F5 Epitope (2014)

The membrane-proximal external region (MPER) of gp41 harbors the epitope recognized by the broadly neutralizing anti-HIV 2F5 antibody, a research focus in HIV-1 vaccine development. In this work, we analyze the structure and immunogenic properties of MPERp, a peptide vaccine that includes the following: (i) the complete sequence protected from proteolysis by the 2F5 paratope; (ii) downstream residues postulated to establish weak contacts with the CDR-H3 loop of the antibody, which are believed to be crucial for neutralization; and (iii) an aromatic rich anchor to the membrane interface. MPERp structures solved in dodecylphosphocholine micelles and 25% 1,1,1,3,3,3-hexafluoro-2-propanol (v/v) confirmed folding of the complete 2F5 epitope within continuous kinked helices. Infrared spectroscopy (IR) measurements demonstrated the retention of main helical conformations in immunogenic formulations based on alum, Freund's adjuvant, or two different types of liposomes. Binding to membrane-inserted MPERp, IR, molecular dynamics simulations, and characterization of the immune responses further suggested that packed helical bundles partially inserted into the lipid bilayer, rather than monomeric helices adsorbed to the membrane interface, could encompass effective MPER peptide vaccines. Together, our data constitute a proof-of-concept to support MPER-based peptides in combination with liposomes as stand-alone immunogens and suggest new approaches for structure-aided MPER vaccine development.
A Novel Technology Allowing Immunohistochemical Staining of a Tissue Section with 50 Different Antibodies in a Single Experiment (2004)

Immunohistochemical (IHC) examination is frequently necessary for a histological differential diagnosis of tumors. To simplify IHC examination, we have developed a novel device called a "multiplex-immunostain chip (MI chip)." The chip is a panel of antibodies contained in a silicon rubber plate that consists of 50 2-mm-diameter wells. A tissue section slide is placed on the plate and is fastened tightly with a specially designed clamp. The plate with the slide is then turned upside down, which applies the antibodies to the section. This technology allows IHC staining of a tissue section with 50 different antibodies in a single experiment, reducing the time, effort, and expense of IHC analysis. In addition, it enables pathologists to compare expression of multiple antigens on a tissue section simply by changing microscopic fields on a single slide. These features are unique to the MI chip technology. The method requires no expensive instruments. This device can be used in various applications in differential diagnosis of tumors and the field of cell biology.
Structure of a ricin mutant showing rescue of activity by a noncatalytic residue (1992)

Ricin A chain is an N-glycosidase which removes a single adenine base from a conservative loop of 28S rRNA, thereby inactivating eukaryotic ribosomes. The mechanism of action has been proposed to include transition-state stabilization of an oxycarbonium ion on the substrate ribose by interaction with Glu 177. Conversion of Glu 177 to Gln reduces activity nearly 200-fold [Ready, M. P., Kim, Y., & Robertus, J. D. (1991) Proteins: Struct., Funct., Genet. 10, 270-278] while conversion to Ala (E177A) reduces activity only 20-fold [Schlossman, D., Withers, D., Welsh, P., Alexander, A., Robertus, J., & Frankel, A. (1989) Mol. Cell. Biol. 9, 5012-5021]. X-ray analysis of the latter mutant protein shows that a residue at the edge of the active site, Glu 208, rotates into the space left vacant by the mutation. Its rearranged carboxylate partially substitutes for that of Glu 177. This is equivalent to the rescue of enzyme activity by a second-site reversion. Kinetic analysis shows the E177A mutation affects kcat and not Km, consistent with the notion that the carboxylate serves in transition-state stabilization.
Pharmacological modulation of peptide growth factor receptor expression on tumor cells as a basis for cancer therapy (1994)

Membrane receptors for peptide growth factor receptors (PGF-R) play a crucial role in the regulation of cancer cell proliferation and may behave as tumor associated antigens (TAA), which are currently regarded as specific targets for immunodetection and immunotherapy of human cancer. PGF-R are often more expressed by tumor cells than by normal counterparts and, by analogy to TAA, their surface expression may be regulated by cytokines. Moreover, the biological functions and specific ligands of most PGF-R are presently well elucidated as opposed to the great majority of TAA. PGF-R may, therefore, represent ideal cellular targets for at least two different therapeutic approaches: (i) naked or conjugated monoclonal antibodies and (ii) genetically engineered fusion proteins composed of PGF-R physiological ligands linked to genetically modified bacterial toxins. To date, clinical studies based on targeting of receptors for epidermal growth factor and interleukin-2 on tumor cells have been performed. Information from such studies suggests that PGF-R as well as TAA targeting strategies are clinically feasible, but that they still have to be optimized. A variety of host and tumor factors which affect targeting of neoplastic cells have been recently identified. For instance, it has been demonstrated that the antigenic density of the targeted molecule at the tumor cell surface is an important factor. In this view upregulation of PGF-R on cancer cells could be of major clinical advantage in immunotargeting. It has been reported that several cytokines and chemical compounds can induce PGF-R modulation on tumor cells. This paper reviews therapeutic opportunities related to the pharmacologic modulation of PGF-R expression. In addition a mechanistic hypothesis regarding PGF-R upregulation induced by cytostatic drugs and cytokines is proposed.
Histochemically demonstrable enzyme activities and their independence of the hormone receptor content in female breast carcinoma (1982)

Acid phosphatase, leucine aminopeptidase, monoamine oxidase and non specific esterase activities were histochemically demonstrated in specimens derived from 15 infiltrating ductal carcinomas of female breast. The relative areas occupied by the enzyme-positive carcinoma cells were visually estimated and, in the cases of leucine aminopeptidase, assessed morphometrically. All enzyme activities were found to be subject to major variations within a single carcinoma and between individual carcinomas, and the activity of any single enzyme was independent of that of three others. None of the enzyme activities correlated with the estrogen and progesterone receptor values, nor the histological grade of malignancy of the tumour. Thus, histochemically demonstrable enzyme activities seem to be of no use in predicting the hormone receptor content in infiltrating ductal carcinomas of the female breast.
Broadly neutralizing anti-influenza antibodies require Fc receptor engagement for in vivo protection (2016)

In vivo protection by antimicrobial neutralizing Abs can require the contribution of effector functions mediated by Fc-Fcγ receptor (Fc-FcγR) interactions for optimal efficacy. In influenza, broadly neutralizing anti-hemagglutinin (anti-HA) stalk mAbs require Fc-FcγR interactions to mediate in vivo protection, but strain-specific anti-HA head mAbs do not. Whether this rule applies only to anti-stalk Abs or is applicable to any broadly neutralizing Ab (bNAb) against influenza is unknown. Here, we characterized the contribution of Fc-FcγR interactions during in vivo protection for a panel of 13 anti-HA mAbs, including bNAbs and non-neutralizing Abs, against both the stalk and head domains. All classes of broadly binding anti-HA mAbs required Fc-FcγR interactions to provide protection in vivo, including those mAbs that bind the HA head and those that do not neutralize virus in vitro. Further, a broadly neutralizing anti-neuraminidase (anti-NA) mAb also required FcγRs to provide protection in vivo, but a strain-specific anti-NA mAb did not. Thus, these findings suggest that the breadth of reactivity of anti-influenza Abs, regardless of their epitope, necessitates interactions with FcγRs on effector cell populations to mediate in vivo protection. These findings will guide the design of antiviral Ab therapeutics and inform vaccine design to elicit Abs with optimal binding properties and effector functions.
Porcine Reproductive and Respiratory Syndrome (PRRS) with special reference to clinical aspects and diagnosis: A review (2002)

After a short introduction on Porcine Reproductive and Respiratory Syndrome (PRRS) regarding the history, the first occurrence in several countries, and the causal virus, designated Lelystad virus, a description is given of the clinical aspects and several diagnostic methods. After some general remarks on the clinical aspects, the epidemic and the endemic phase of the disease are described. Regarding the diagnosis, special attention is paid to the detection of antibodies and of the PRRS Virus (PRRSV). Regarding the detection of antibodies, a description is given of three tests: the immunoperoxidase monolayer assay, the enzyme-linked immunosorbent assay, and the serum neutralization test. Concerning the detection of PRRSV, attention is paid to the isolation of the virus, the demonstration of PRRSV antigens in frozen or fixed tissue using immunohistochemistry or immunofluorescence, the in situ hybridisation technique and the Polymerase Chain Reaction (PCR).
THE 2.0 ANGSTROMS RESOLUTION STRUCTURE OF ESCHERICHIA COLI HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR: A REDETERMINATION (1993)

The x-ray structure of Escherichia coli HPr has been redetermined at 2.0-A resolution. In contrast to the previous study (El-Kabbani, O. A. L., Waygood, E. B., and Delbaere, L. T. J. (1987) J. Biol. Chem. 262, 12926-12929), the overall structure is, in general, similar to other reported NMR and x-ray HPr structures, although there are some important differences in detail. The overall folding topology of HPr is a classical open-faced beta-sandwich, consisting of four antiparallel beta-strands and three alpha-helices. The least square refinement produced an R index of 0.135 for all measured unique data between 8.0 and 2.0 A resolution. The active center consists of His15 which is hydrogen bonded to a sulfate anion, and Arg17 which has a fully open conformation. This corresponds to the first observed "semi-closed" conformation of the active center of HPr. The Streptococcus faecalis HPr structure (Jia, Z., Vandonselaar, M., Quail, J. W., and Delbaere, L. T. J. (1993) Nature 361, 94-97) has the "open" conformation in which the side chains of His15 and Arg17 are directed as far away from each other as possible. The Bacillus subtilis HPr (Herzberg, O., Reddy, P., Sutrina, S., Saier, M. H., Jr., Reizer, J., and Kapadia, G. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 2499-2503) has the "closed" conformation in which the side chains of His15 and Arg17 are close together with a sulfate anion located in the active center. The open conformation represents the unphosphorylated form of HPr whereas the closed conformation likely resembles the phosphorylated form of HPr. The semi-closed conformation observed in the E. coli HPr structure could represent a structural intermediate on the phosphorylation/dephosphorylation pathway of HPr.
Distinct Domains within PSD-95 Mediate Synaptic Incorporation, Stabilization, and Activity-Dependent Trafficking (2009)

The postsynaptic density (PSD) consists of a lattice-like array of interacting proteins that organizes and stabilizes receptors, ion channels, structural, and signaling proteins necessary for synaptic function. To study the stabilization of proteins within this structure and the contribution of these proteins to the integrity of the PSD, we tagged synaptic proteins with PAGFP (photoactivatable green fluorescent protein) and used combined two-photon laser-scanning microscopy and two-photon laser photoactivation to measure their rate of turnover in individual spines of rat CA1 pyramidal neurons. We find that PSD-95 is highly stable within the spine, more so than other PSD-associated proteins such as CaMKIIalpha, CaMKIIbeta, GluR2, and Stargazin. Analysis of a series of PSD-95 mutants revealed that distinct domains stabilize PSD-95 within the PSD and contribute to PSD formation. Stabilization of PSD-95 within the PSD requires N-terminal palmitoylation and protein interactions mediated by the first and second PDZ domains, whereas formation of a stable lattice of PSD-95 molecules within the PSD additionally requires the C-terminal SH3 domain. Furthermore, in a PDZ domain 1 and 2 dependent manner, activation of NMDA receptors with a chemical long-term depression protocol rapidly destabilizes PSD-95 and causes a subset of the PSD-95 molecules previously anchored in the spine to be released. Thus, through the analysis of rates of exchange of synaptic PSD-95, we determine separate domains of PSD-95 that play specific roles in establishing a stable postsynaptic lattice, in allowing proteins to enter this lattice, and in reorganizing this structure in response to plasticity-inducing stimuli.
In vivo vasculogenic potential of human blood-derived endothelial progenitor cells (2007)

Vascularization of tissues is a major challenge of tissue engineering (TE). We hypothesize that blood-derived endothelial progenitor cells (EPCs) have the required proliferative and vasculogenic activity to create vascular networks in vivo. To test this, EPCs isolated from human umbilical cord blood or from adult peripheral blood, and human saphenous vein smooth muscle cells (HSVSMCs) as a source of perivascular cells, were combined in Matrigel and implanted subcutaneously into immunodeficient mice. Evaluation of implants at one week revealed an extensive network of human-specific lumenal structures containing erythrocytes, indicating formation of functional anastomoses with the host vasculature. Quantitative analyses showed the microvessel density was significantly superior to that generated by human dermal microvascular endothelial cells (HDMECs) but similar to that generated by human umbilical vein endothelial cells (HUVECs). We also found that as EPCs were expanded in culture, their morphology, growth kinetics, and proliferative responses toward angiogenic factors progressively resembled those of HDMECs, indicating a process of in vitro maturation. This maturation correlated with a decrease in the degree of vascularization in vivo, which could be compensated for by increasing the number of EPCs seeded into the implants. Our findings strongly support the use of human EPCs to form vascular networks in engineered organs and tissues.
Expression, purification and biochemical characterization of recombinant murine secretory component: a novel tool in mucosal immunology (1999)

Reconstitution of secretory IgA (S-IgA) by the association in vitro of secretory component (SC) and polymeric IgA (pIgA) obtained from hybridomas is a valuable tool in the study of the structure-function relationship in this particular class of antibody. Although dimeric IgA (dIgA) can be obtained and purified from hybridoma clones, SC remains tedious to isolate in sufficient amounts from colostral milk. Several murine models for the study of mucosal immunity are available, which could potentially benefit from the use of cognate IgA antibodies in various molecular forms, including dIgA and S-IgA. We report here on the establishment of two expression systems allowing the production of milligram amounts of pure recombinant murine SC (rmSC) with preserved murine pIgA-binding capability. The first system relies on the use of recombinant vaccinia virus to prompt infected HeLa cells to express the murine SC protein, whereas the second system is based on a stably transfected cell clone exhibiting murine glycosylation. The second source of rmSC will permit the study of the role of its sugar moieties in pathogen-host interactions, and the evaluation of its function in passive protection without risking adverse immune responses. The extensive biochemical characterization conducted in this study demonstrates that rmSC is a dependable and convenient alternative to the natural product, and indicates that the J chain is dispensable in the recognition of pIgA and SCin vitro, whereas it is required for proper pIgA-polymeric Ig receptor interaction in vivo.
Multi-Agent Tensor Fusion for Contextual Trajectory Prediction (2019)

Accurate prediction of others' trajectories is essential for autonomous driving. Trajectory prediction is challenging because it requires reasoning about agents' past movements, social interactions among varying numbers and kinds of agents, constraints from the scene context, and the stochasticity of human behavior. Our approach models these interactions and constraints jointly within a novel Multi-Agent Tensor Fusion (MATF) network. Specifically, the model encodes multiple agents' past trajectories and the scene context into a Multi-Agent Tensor, then applies convolutional fusion to capture multiagent interactions while retaining the spatial structure of agents and the scene context. The model decodes recurrently to multiple agents' future trajectories, using adversarial loss to learn stochastic predictions. Experiments on both highway driving and pedestrian crowd datasets show that the model achieves state-of-the-art prediction accuracy.
Necl2 regulates epidermal adhesion and wound repair (2009)

Differential expression of cell adhesion molecules regulates stem cell location, self-renewal and lineage selection under steady state conditions and during tissue repair. We show that the intercellular adhesion protein nectin-like molecule 2 (Necl2) is highly expressed in bulge stem cells of adult human and mouse hair follicles. Overexpression of Necl2 in cultured human keratinocytes led to upregulation of calcium/calmodulin-associated Ser/Thr kinase (CASK), increased calcium-independent intercellular adhesion, and inhibition of cell motility and in vitro wound healing. Although the rate of cell proliferation was reduced, terminal differentiation was unaffected. To assess the role of Necl2 in vivo, we examined the epidermis of Necl2-null mice and developed transgenic mice that expressed Necl2 in the basal layer of murine epidermis. Necl2 overexpression led to a reduction in S-phase cells and an increase in quiescent cells retaining DNA label in the bulge. Although epidermal homeostasis appeared normal in both transgenic and knockout mice, wound healing was markedly delayed. Necl2 overexpression resulted in reduced proliferation and increased levels of CASK and E-cadherin at the leading edge of healing wounds, consistent with its effects in culture. Our results demonstrate that Necl2 is involved in regulating epidermal stem cell quiescence and location.
Phosphororganische Verbindungen, XXXII. Enthalogenierung von Phenolen und aromatischen Aminen. Austausch phenolischer hydroxylgruppen gegen Chlor (1962)

Abstract Aromatische o ‐und p ‐Bromamine bilden mit Triphenylphosphin Phosphinimidhydrobromide. Aus o ‐und p ‐Brom‐phenolen und Triphenylphosphin werden Aryloxy‐triphenyl‐phosphoniumsalze erhalten, welche hydrolytisch außerordentlich leicht in Phenole und Triphenylphosphinoxyd aufgespalten werden. Bei ihrer thermischen Spaltung entstehen Arylhalogenide. Arylchloride bilden sich daher auch beim Erhitzen aromatischer hydroxyverbindungen mit Triphenylphosphin‐dichlorid oder Diphenyltrichlorphosphoran.
The impact of the HbA1c level of type 2 diabetics on the structure of haemoglobin (2016)

This study explores the impact of HbA1c levels on the structure of haemoglobin (Hb) in patients with type 2 diabetes. Seventy-four diabetic patients were classified into the following two groups based on their level of HbA1c: group A, patients with good glycaemic control (HbA1c < 7.0%, n = 36); group B, patients with persistent hyperglycaemia (HbA1c ≥ 9.0%, n = 38). Thirty-four healthy people served as controls (group H). Hb structure was examined by Fourier transform infrared spectroscopy (FTIR), and diabetic erythrocytes were modelled to estimate the impact of glucose on these cells and Hb. Increasing glucose concentrations altered both erythrocyte parameters and the Hb secondary structure. Group B differed significantly from group H (p < 0.05): in the former, the ordered Hb secondary structure had a strong tendency to transform into a disordered secondary structure, decreasing structural stability. We presumed here that high HbA1c levels might be a factor contributing to Hb structural modifications in diabetic patients. FTIR spectral analysis can provide a novel way to investigate the pathogenesis of type 2 diabetes mellitus.
Electronically Pure Single-Chirality Semiconducting Single-Walled Carbon Nanotube for Large-Scale Electronic Devices (2016)

Single-walled carbon nanotube (SWCNT) networks deposited from a purple single chirality (6,5) SWCNT aqueous solution were electrically characterized as pure semiconductors based on metal/semiconductor/metal Schottky contacts using both complex instruments and a portable device. Both air-stable PMOS (p-type metal-oxide-semiconductor) and NMOS (n-type metal-oxide-semiconductor, resembling amorphous silicon) thin film transistors were fabricated on (6,5) SWCNT in large scale showing the characteristics of fA off current and ION/IOFF ratio of >1 × 10(8). CMOS (complementary metal-oxide-semiconductor) SWCNT inverter was demonstrated by wire-bonding PMOS (6,5) SWCNT TFT and NMOS (6,5) SWCNT TFT together to achieve the voltage gain as large as 52.
Inhibition of DPP-4: a new therapeutic approach for the treatment of type 2 diabetes (2007)

Islet cell dysfunction is central to the pathogenesis of T2DM. Incretin-based therapies, including GLP 1 analogues and DPP-4 inhibitors, have been shown to restore glucose homeostasis and improve glycemic control. The DPP-4 inhibitors, which can be used as monotherapy or in combination with other antidiabetic drugs, are a promising new treatment option, especially for patients with early-stage T2DM and more severe hyperglycemia.