gebhart/patrepeval huggingface dataset:
Multiple cell surface receptors for the short arms of laminin: alpha 1 beta 1 integrin and RGD-dependent proteins mediate cell attachment only to domains III in murine tumor laminin. (1991)

Cell surface molecules that interact with the cross formed by the three short arms of murine tumor laminin were studied using thermal perturbation, antibody and peptide blocking, and affinity chromatography. Several potential receptors for the laminin short arms were revealed that differed from those mediating cell attachment to the E8 (long arm) fragment. Two cell lines, Rugli and L8 attached well to E1-X (short arm) fragments of laminin. This attachment was blocked by antibodies against alpha 1 integrin chains. Other cells were unable to attach strongly to E1-X, but attached to P1. This attachment was unaffected by anti-beta 1 integrin antibodies, but specifically blocked by the peptide GRGDS. By contrast, binding of Rugli cells was RGD independent and blocked by anti-beta 1 integrin antibodies. G7 and C2C12 myoblasts were very sensitive to GRGDS (ID50 approximately 2 micrograms.ml-1) for attachment to P1 which implied that a non-beta 1 series integrin, possibly alpha v beta 3, was involved. On heat denaturation of P1(3) attachment remained sensitive to RGDS and ID50 was unchanged. On heat denaturation of E1-X, attachment remained sensitive to RGDS but the ID50 increased to approximately 200 micrograms.ml-1. Cellular beta 1 integrins were retained on laminin affinity columns. A beta 1 integrin with an approximately 190 kD alpha-chain could be isolated from Rugli cells whose attachment could be blocked by anti-alpha 1 antibodies and not from cells blocked by RGDS peptides. Anti-alpha 1 antibodies blocked Rugli attachment to native laminin, but only when the E8 cell binding sites on laminin were also blocked. Thus, a receptor related to alpha 1 beta 1 integrin can function simultaneously with a receptor for E8. Anti-alpha 1 also blocked attachment to heated laminin, suggesting that the heat-stable attachment activity in laminin involved the E1-X binding site. Thus, at least two putative receptors mediate attachment to the short arms of laminin. One, related to alpha 1 beta 1 integrin, recognizes RGDS-independent sites in E1-X defined by P1 (within domains III, IIIa, IIIb), and one is an RGD-dependent molecule recognizing sites in P1, and is not a beta 1 integrin.
A comparison of efficacy of Tołpa Torf Preparation (TTP) in the treatment of cervicitis with or without surgery. (1993)

Tołpa Torf Preparation (TTP) is an immunomodulating drug produced by Torf Corporation, Wrocław and registered for human use in Poland. TTP enhances the process of tissue regeneration. Authors evaluate TTP effectiveness in the treatment of inflammatory states of the cervix, especially cervical erosions and the influence of this preparation of the macroscopic, cytological and bacteriological state of the cervix. TTP was used in 31 patients with the diagnosis of cervical erosion. All patients treated as yet were classified into 3 groups, depending on the treatment of cervical erosion used previously. TTP was administered orally in the dose of 5 mg (in 10 ml of water) daily during 10 days and locally in the form of tampons soaked with 1% TTP solution in the volume of 5 ml also during 10 days. TTP administered this way has beneficial therapeutic effects on the healing of cervical erosion accelerating the process of epithelialization and bringing normalization of the cytological picture. Especially beneficial in the treatment of cervical erosion is combined use of TTP and electrocoagulation or curettage--the healing time can be shortened by half.
Comparison of Holsteins Selected for High and Average Milk Production. 2. Health and Reproductive Response to Selection for Milk (1994)

The objective of the experiment was to evaluate direct and correlated responses of secondary (fitness) traits to selection for milk yield. Data consisted of 2768 lactation records from 1078 Holstein cows by 140 sires. Bulls with high PD for milk were mated to daughters of sires with high PD for milk, and bulls with average PD for milk were mated to cows of average genetic merit, creating two genetic lines of cattle. Production, health, and reproductive data were collected. Major health categories were mammary, reproductive, respiratory, digestive, and skin and skeletal disorders. Analyses were per lactation and per lifetime. High PD line cattle averaged 940 kg more milk per lactation than the average line and differed by 500 kg for PTA milk during January 1990. By lactations, the high line cattle averaged 3.8% higher total health costs and 11.2% higher mammary costs than their average herd mates. For most health categories, high line cattle tended to incur higher cost than did average cattle. Selection of sires for high PD milk resulted in daughters that had slightly higher health costs, but total net return was still higher for daughters of high PD bulls.
Cardiac-cardiovascular reflexes induced by hydrogen peroxide in cats (1995)

We have shown previously that reactive oxygen species stimulate abdominal sympathetic afferents to cause reflex cardiovascular activation. Because myocardial ischemia and reperfusion also generate reactive oxygen species, we investigated the possibility that cardiovascular reflexes could be induced by topical application of H2O2 to the anterior or posterior ventricular surface in cats anesthetized with alpha-chloralose. Mean arterial pressure (MAP), heart rate (HR), left ventricular (LV) pressure, aortic flow (AF), and first derivative of LV pressure at 40 mmHg developed pressure (LV dP/dt40) were monitored. H2O2 (44 and 130 mumol) significantly increased MAP but not HR or LV dP/dt40 in intact cats (n = 8). Application of H2O2 (44 mumol) significantly increased MAP (129 +/- 9 to 152 +/- 10 mmHg), HR (240 +/- 11 to 245 +/- 10 beats/min), AF (191 +/- 13 to 212 +/- 17 ml/min), total peripheral resistance (0.68 +/- 0.13 to 0.73 +/- 0.04 peripheral resistance units), and LV dP/dt40 (2,666 +/- 145 to 3,012 +/- 205 mmHg/s) after bilateral cervical vagotomy (n = 6). These H2O2-induced excitatory responses were abolished after bilateral T1-T4 ganglionectomy. In six additional cats, H2O2 (44 mumol) significantly decreased MAP (114 +/- 5 to 102 +/- 5 mmHg), HR (207 +/- 7 to 190 +/- 7 beats/min), and LV dP/dt40 (2,776 +/- 168 to 2,600 +/- 153 mmHg/s) after sympathectomy. These depressor responses were eliminated after vagotomy. The magnitude of the cardiovascular reflexes was increased or decreased in a dose-dependent fashion in vagotomized or sympathectomized cats, respectively, over a range of 440 nmol to 44 mumol H2O2. Application of H2O2 to the anterior or posterior ventricular surface resulted in similar pressor or depressor reflexes. Dimethylthiourea and deferoxamine abolished pressor or depressor responses evoked by H2O2 in both vagotomized (n = 8) and sympathectomized (n = 8) cats. We conclude that reactive oxygen species, particularly the hydroxyl radical, can participate in activating cardiac afferents responsible for reflex cardiovascular responses during myocardial ischemia and reperfusion. An inhibitory reflex is transmitted through vagal afferents, whereas an excitatory reflex is conducted by sympathetic cardiac afferents.
Attenuated Shigella flexneri 2a Δ guaBA Strain CVD 1204 Expressing Enterotoxigenic Escherichia coli (ETEC) CS2 and CS3 Fimbriae as a Live Mucosal Vaccine against Shigella and ETEC Infection (2001)

To construct a prototype hybrid vaccine against Shigella and enterotoxigenic Escherichia coli (ETEC), the genes encoding the production of ETEC CS2 and CS3 fimbriae were isolated and expressed in attenuated Shigella flexneri 2a guaBA strain CVD 1204. The CS2 cotA to -D genes, isolated from ETEC strain C91F, and the CS3 cstA to -H genes, subcloned from plasmid pCS100, were cloned into ~15-copy-number-stabilized pGA1 behind the osmotically regulated ompC promoter, resulting in high expression of both fimbriae. Under nonselective in vitro growth conditions, pGA1-CS2 and pGA1-CS3 were stable in CVD 1204, exhibiting a plasmid loss of only approximately 1% per duplication. Expression of CS2 and CS3 reduced the invasiveness of Shigella for HeLa cells and slowed the intracellular growth rate. Guinea pigs immunized intranasally with CVD 1204(pGA1-CS2) or CVD 1204(pGA1-CS3), or with a mixture of these strains, developed secretory immunoglobulin A (IgA) in tears and serum IgG antibodies against Shigella lipopolysaccharide, CS2, and CS3 antigens. Moreover, the animals were protected against keratoconjunctivitis following conjunctival challenge with virulent S. flexneri 2a strain 2457T. Animals immunized with Shigella expressing CS2 or CS3 developed serum antibodies that agglutinated Shigella as well as an ETEC strain bearing the homologous fimbriae, whereas animals immunized with combined CVD 1204(pGA1-CS2) and CVD 1204(pGA1-CS3) developed antibodies that agglutinated all three test strains. These observations support the feasibility of a multivalent vaccine against shigellosis and ETEC diarrhea consisting of multiple Shigella live vectors expressing relevant ETEC antigens.
Rapid Preparation of Synaptosomes from Mammalian Brain Using Nontoxic Isoosmotic Gradient Material (Percoll) (1984)

A new procedure is described for the isolation of synaptosomes from various parts of mammalian brain. This method utilizes an isoosmotic Percoll/sucrose discontinuous gradient and has some advantages over the traditionally used synaptosomal isolation techniques: (1) it is possible to prepare suitable gradients while retaining isoosmolarity; (2) the time of the preparation is remarkably short (approximately 1 h); (3) if necessary, the gradient material can be easily removed from the samples. Intact synaptosomes were recovered from the 10%/16% (vol/vol) Percoll interphase. The fractions were identified and characterized by electron microscopy and by several biochemical markers for synaptosomes and other subcellular organelles. The homogeneity of the preparations is comparable to or better than that of synaptosomes prepared by the conventional methods. This procedure has been successfully used for the isolation of synaptosomes from very small tissue samples of various experimental animals and human brain.
M13 single-strand purification using a biotinylated probe and streptavidin coated magnetic beads (1992)

A new method for M13 single-strand purification has been developed and tested. The procedure gives sufficient DNA for one set of thermally cycled sequencing reactions when analysed on the Applied Biosystems 373A fluorescent DNA sequencer. For this report, 250 random M13 subclones with 1-2 Kb inserts were grown and prepared using this method.
Structure based molecular inhibition of Caspase-8 for treatment of multi-neurodegenerative diseases using known natural compounds (2014)

Neurodegenerative disorders are often associated with excessive neuronal apoptosis. It is well known that apoptosis is regulated by some intracellular proteases, such as, Caspases (cysteine-dependent, aspartate-specific proteases). In fact, Caspase-8 which is an initiator caspase, has been identified as a key mediator of neuronal apoptosis. In addition, Caspase-8 is found to be coupled with the regulation of various neurodegenerative disorders including Alzheimer׳s disease (AD), Parkinson׳s disease (PD), Huntington׳s Diseases (HD) and Dentatorubral Pallidoluysian Atrophy (DRPLA). Caspase-8 inhibition may provide an effective means of treatment for multiple neurodegenerative disorders. Therefore, the present study describes the molecular interaction of some selected natural compounds with known anti neurodegenerative properties with Caspase-8. Docking between Caspase-8 and each of these compounds (separately) was performed using 'Autodock4.2'. Out of all the selected compounds, rosmarinic acid and curcumin proved to be the most potent inhibitors of Caspase-8 with binding energy (ΔG) of -7.10 Kcal/mol and -7.08 Kcal/mol, respectively. However, further in vitro and in vivo studies are needed to validate the anti-neurodegenerative potential of these compounds.
Structural Insights for Design of Potent Spleen Tyrosine Kinase Inhibitors from Crystallographic Analysis of Three Inhibitor Complexes (2009)

Spleen tyrosine kinase is considered an attractive drug target for the treatment of allergic and antibody mediated autoimmune diseases. We have determined the co-crystal structures of spleen tyrosine kinase complexed with three known inhibitors: YM193306, a 7-azaindole derivative and R406. The cis-cyclohexyldiamino moiety of YM193306 is forming four hydrophobically shielded polar interactions with the spleen tyrosine kinase protein and is therefore crucial for the high potency of this inhibitor. Its primary amino group is inducing a conformational change of the spleen tyrosine kinase DFG Asp side chain. The crystal structure of the 7-azaindole derivative bound to spleen tyrosine kinase is the first demonstration of a 2-substituted 7-azaindole bound to a protein kinase. Its indole-amide substituent is tightly packed between the N- and C-terminal kinase lobes. The co-crystal structure of the spleen tyrosine kinase-R406 complex shows two main differences to the previously reported structure of spleen tyrosine kinase soaked with R406: (i) the side chain of the highly conserved Lys is disordered and not forming a hydrogen bond to R406 and (ii) the DFG Asp side chain is pointing away from and not towards R406. The novel protein-ligand interactions and protein conformational changes revealed in these structures guide the rational design and structure-based optimization of second-generation spleen tyrosine kinase inhibitors.
Nanoparticle vaccines enhance humoral responses to a malaria antigen by expanding Tfh cells and inducing germinal center formation (166.10) (2012)

Abstract Nanoparticles (NP) are promising delivery vehicles for vaccines that promote humoral and cellular immunity in concert. We recently developed a novel lipid-based NP vaccine system, termed interbilayer-crosslinked multilamellar vesicles (ICMVs). ICMVs efficiently entrap and co-deliver antigens and molecular adjuvants to lymphoid tissues, initiating potent cellular and humoral immune responses. ICMVs were synthesized by fusing liposomes containing antigen into multilamellar vesicles, followed by bilayer-to-bilayer crosslinking of lipid bilayers within the vesicle walls to stabilize the particles. ICMVs carrying ovalbumin and the TLR agonist MPLA induced robust cytotoxic T lymphocyte responses in mice, achieving a peak ~30% tetramer+ cells in the CD8+ T-cell population after 3 immunizations. Mice vaccinated with ICMVs containing a candidate Plasmodium vivax antigen raised high-titer, high-avidity antibody responses against the antigen lasting &amp;gt; 1 yr, at 10-fold lower dose of antigen than conventional adjuvants such as alum or Montanide. Compared to vaccination with alum, immunization with ICMVs prolonged antigen accumulation at the draining lymph nodes, enhanced germinal center formation, and increased the expansion of antigen-specific follicular helper T-cells, partially explaining the enhanced antibody response. These results suggest that antigen/adjuvant-carrying ICMVs may serve as a platform to elicit potent cellular and humoral immune responses against infectious pathogens.
Gene transfer into hepatoma cell lines via the serpin enzyme complex receptor (1997)

The serpin enzyme complex receptor (SECR) expressed on hepatocytes binds to a conserved sequence in alpha 1-antitrypain (alpha 1-AT) and other serpins. A molecular conjugate consisting of a synthetic peptide (C1315) based on the SECR binding motif of human alpha 1-AT covalently coupled to poly-L-lysine was used to introduce reporter genes into hepatoma cell lines in culture. This conjugate condensed DNA into spheroidal particles 18-25 nm in diameter. When transfected with the SECR-directed complex containing pGL3, Hep G2 cells that express the receptor, but not Hep G2 cells that do not, expressed a peak luciferase activity of 538,731 +/- 144,346 integrated light units/mg protein 4 days after transfection. Free peptide inhibited uptake and expression in a dose-dependent manner. Complexes of DNA condensed with polylysine or LC-sulfo-N-succinimidyl-3-(2-pyridyldithio)propionate-substituted polylysine were ineffective. Transfection with a plasmid encoding human factor IX produced expression in Hep G2 (high) and HuH7 cells that express SECR but not Hep G2 (low) cells that lack the receptor. Fluorescein-labeled C1315 peptide labeled 9-31% of Hep G2 (high), 10-14% of HuH7, and 0.6-3.4% of Hep G2 (low) cells, and when the lac Z gene was transfected, only these cells expressed beta-galactosidase. SECR-mediated gene transfer gives efficient, specific uptake and high-level expression of three reporter genes, and the system merits further study for gene therapy.
Endotoxin-Induced Gamma Interferon Production: Contributing Cell Types and Key Regulatory Factors (2002)

Gamma interferon (IFN-gamma) is an important mediator of endotoxin (lipopolysaccharide [LPS])-induced immune responses. However, the specific cell types that produce IFN-gamma in response to LPS and the cellular factors that regulate LPS-induced IFN-gamma production have not been fully determined. The present studies were undertaken to characterize the cell populations that produce IFN-gamma after LPS challenge in the spleens of mice and to determine the regulatory factors that modulate LPS-induced production of IFN-gamma. Our studies show that the levels of splenic IFN-gamma mRNA and protein production peak at 6 and 8 h, respectively, after systemic LPS challenge. Approximately 60% of IFN-gamma-producing cells are natural killer (NK) cells (CD3(-)DX5(+)) and 25% are NKT cells (CD3(+)DX5(+)). Most of the remaining IFN-gamma-producing cells are T cells (CD3(+)DX5(-)), macrophages, and dendritic cells. Functionally, interleukin-12 (IL-12) is the major IFN-gamma-stimulating factor after LPS challenge, with costimulation provided by IL-15, IL-18, and B7 proteins. IL-10 is a major inhibitor of LPS-induced IFN-gamma production. Unlike intact heat-killed gram-negative and gram-positive bacteria, the class II major histocompatibility complex did not play a functional role in LPS-induced IFN-gamma production. LPS is a potent stimulus for splenic IL-10, IL-12 p40, and IL-15 mRNA expression, whereas IL-12 p35 and IL-18 mRNAs, as well as B7 proteins, are constitutively expressed in the mouse spleen. Of the factors studied, IL-18 serves as the most potent costimulus with IL-12 for IFN-gamma production, followed by IL-15 and B7 proteins. These data demonstrate that NK cells and NKT cells are the most abundant IFN-gamma-producing cells in the mouse spleen after LPS challenge and that IL-10 and IL-12 are key functional regulators of LPS-induced IFN-gamma production.
A Decade of QTL Mapping for Cyst Nematode Resistance in Soybean (2004)

Soybean cyst nematode (SCN) ( Heterodera glycines Ichinohe), the most destructive pest of soybean [ Glycine max (L.) Merrill], is estimated to be responsible for almost nine million megagrams in annual yield loss worldwide. Host plant resistance is the most cost‐effective and environmentally friendly method of controlling SCN. Resistance is present among soybean plant introductions (PIs) and related wild species, such as Glycine soja Sieb. and Zucc. Molecular marker technology has ushered in a decade devoted to the identification and characterization of quantitative trait loci (QTL) underlying SCN. These genetic mapping efforts uncovered numerous locations of SCN resistance QTL in many PIs. In more than a decade of mapping SCN resistance QTL, there is some consistency in the results. In almost all studies involving various sources of resistance, the QTL conferring the greatest level of resistance mapped to the region containing rhg1 on linkage group (LG) G. In addition, a major resistance QTL was mapped in many sources to the region containing Rhg4 on LG A2. The mapping of QTL to these regions from many sources suggests that these sources may have resistance genes in common, which has caused concern over the possible dependence on a few resistance genes. Recently, two independent research groups reported cloning candidate genes for rhg1 and Rhg4 Despite these advances, there is some degree of trepidation, especially in the public sector, on the use of rhg1 and Rhg4 genetic mapping and cloning information in SCN resistance breeding because of intellectual property issues.
From dense subgraph to graph matching: A label propagation approach (2014)

Graph matching (GM) is a fundamental problem in computer science, and it has been successfully applied to provide solutions to many problems in computer vision. In this paper, we consider GM as a clustering problem in an association graph whose nodes represent candidate correspondences between two graphs to be matched. And we take the dense subgraph as a good prior for correct correspondences, thus we propose a label propagation approach to expand the dense subgraph to resolve the whole cluster. The label propagation approach is achieved by an affinity-preserving manifold ranking algorithm with a dynamic label vector which enforces the matching constraints. And the matching constraints is introduced through a doubly-stochastic normalization procedure. Extensive experiments demonstrate that our algorithm outperforms the state-of-the-art GM algorithms especially in the presence of outliers and deformation.
3D Systems' Technology Overview and New Applications in Manufacturing, Engineering, Science, and Education (2014)

Since the inception of 3D printing, an evolutionary process has taken place in which specific user and customer needs have crossed paths with the capabilities of a growing number of machines to create value-added businesses. Even today, over 30 years later, the growth of 3D printing and its utilization for the good of society is often limited by the various users' understanding of the technology for their specific needs. This article presents an overview of current 3D printing technologies and shows numerous examples from a multitude of fields from manufacturing to education.