gebhart/patrepeval huggingface dataset:
NF-κB-Inducing Kinase Establishes Self-Tolerance in a Thymic Stroma-Dependent Manner (2004)

Physical contact between thymocytes and the thymic stroma is essential for T cell maturation and shapes the T cell repertoire in the periphery. Stromal elements that control these processes still remain elusive. We used a mouse strain with mutant NF-kappaB-inducing kinase (NIK) to examine the mechanisms underlying the breakdown of self-tolerance. This NIK-mutant strain manifests autoimmunity and disorganized thymic structure with abnormal expression of Rel proteins in the stroma. Production of immunoregulatory T cells that control autoreactive T cells was impaired in NIK-mutant mice. The autoimmune disease seen in NIK-mutant mice was reproduced in athymic nude mice by grafting embryonic thymus from NIK-mutant mice, and this was rescued by supply of exogenous immunoregulatory T cells. Impaired production of immunoregulatory T cells by thymic stroma without normal NIK was associated with altered expression of peripheral tissue-restricted Ags, suggesting an essential role of NIK in the thymic microenvironment in the establishment of central tolerance.
IN VITRO EVALUATION OF CONJUGATED HYALURONIC ACID WITH ASCORBIC ACID (2010)

Hyaluronic acid (Hyalunan, HA), β-1,4-linked D-glucuronic acid and β-1,3 N-acetyl-D-glucosamine polysaccharide, is a nonsulfated glycosaminoglycan(GAG) conserved in the extracellular matrix (ECM). Due to its biocompatibility, biodegradable properties, HA is widely applied for tissue engineering. However, HA also has defects for tissue engineering such as mechanical properties, difficulty of handling. Thus, it is various modified by chemical reaction to produce HA derivative. HA plays an important role in tissue morphogenesis, proliferation and cell differentiation. Ascorbic acid (AA) has an effect on collagen synthesis and bone mineralization. Ascorbate levels also have a significant effect on osteoblast proliferation and alkaline phosphatase (ALP) expression. However AA is weak to heat and light, thus it is easily degradable. Consequently, we conjugated HA with AA in order to make it more stable and effective. In this study, we prepared HA-AA conjugate and evaluated activity of products in pre-osteoblast. To produce more effective conjugation, we synthesised HA derivative, HA-N-hydroxysuccinimide, an activated ester of the glucuronic acid moiety. This HA-active ester intermediate is a precursor for drug-polymer conjugates. The degree of substitution was calculated by NMR analysis. The modified HA was dialysed and lyophilised. The yield of conjugation is calculated by Gel Permeation Chromatography (GPC). After the process, HA was conjugated with AA once again as previously mentioned. In this study, the resultant HA-AA conjugate was tested on MC3T3-E1, murine pre-osteoblast cells. We examined cellular viability (cytotoxicity), proliferation and gene expression. The expression of Type 1 collagen was examined by RT-PCR and western blot. Osteocalcin (OCN), osteopontin (OPN) and bone sialoprotein (BSP), bone proliferation and differentiation marker were detected by RT-PCR. Alkaline phosphatase assay was also performed. For confirmation on bone mineralization, alizarin red staining and von Kossa staining was performed. In conclusion, the in vitro data demonstrate that HA-AA conjugate has an important role in bone formation, as it can increase proliferation and osteogenic differentiation of MC3T3-E1 cells. These observations further support the use of in vivo system for tissue engineering applications.
Non-uniformly spaced tapped-delay-line equalizers (1993)

A systematic way to design nonuniformly spaced tapped-delay-line (TDL) equalizers is described, and the performance of such equalizers is compared to that of uniformly spaced TDL equalizers with the same number of tap coefficients. It is shown that the signal-to-mean-squared-error ratio at the output of a TDL equalizer can be improved by optimally choosing the positions of the tap weights. An algorithm to find both the tap positions and the corresponding tap weights for a given delay span and a given minimum tap spacing of the equalizer is presented. Typical results are illustrated by using, as an example, the magnetic recording channel. For two target waveforms at different densities of recording, it is shown that there is a potential for saving up to seven equalizer taps.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The covalent linking of two nucleotide analogs to antibodies (1985)

Two anticancer drugs, antagonists of nucleic acids, were covalently linked to antibodies specifically reactive with B leukemia cells and thus with a potential possibility of drug targeting to the tumor site. The drugs cytosine 1-beta-D-arabinoside and 5-fluorouridine, competitive inhibitors of enzymes involved in DNA synthesis, were linked to antibodies via a dextran bridge. Cytosine 1-beta-D-arabinoside was linked to periodate-oxidized dextran and fluorouridine to dextran hydrazide. The dextran derivatives were in turn linked to antibodies that recognized a specific membrane IgM on B leukemia cells. The drug-antibody conjugates maintained most of the original antigen-binding capacity of the antibody and the full pharmacological activity of the drugs.
IRESdb: the Internal Ribosome Entry Site database (2003)

Internal Ribosome Entry Sites (IRES) are cis-acting RNA sequences able to mediate internal entry of the 40S ribosomal subunit on some eukaryotic and viral messenger RNAs upstream of a translation initiation codon. These sequences are very diverse and are present in a growing list of mRNAs. Novel IRES sequences continue to be added to public databases every year and the list of unknown IRESes is certainly still very large. The IRES database is a comprehensive WWW resource for internal ribosome entry sites and presents currently available general information as well as detailed data for each IRES. It is a searchable, periodically updated collection of IRES RNA sequences. Sequences are presented in FASTA form and hotlinked to NCBI GenBank files. Several subsets of data are classified according to the viral taxon (for viral IRESes), to the gene product function (for cellular IRESes), to the possible cellular regulation or to the trans-acting factor that mediates IRES function. This database is accessible at http://ifr31w3.toulouse.inserm.fr/IRESdatabase/.
Scalable concurrent hash tables via relativistic programming (2010)

This paper presents a novel concurrent hash table implementation which supports wait-free, near-linearly scalable lookup, even in the presence of concurrent modifications. In particular, this hash table implementation supports concurrent moves of hash table elements between buckets, for purposes such as renames. Implementation of this algorithm in the Linux kernel demonstrates its performance and scalability. Benchmarks on a 64-way POWER system showed a 6x scalability improvement versus fine-grained locking, and a 1.5x improvement versus the current state of the art in Linux. To achieve these scalability improvements, the hash table implementation uses a new concurrent programming technique known as relativistic programming . This approach uses a copy-based update strategy to allow readers and writers to run concurrently without conflicts, avoiding many of the non-scalable costs of synchronization, inter-processor communication, and cache coherence. New techniques such as the proposed hash-table move algorithm allow readers to tolerate the resulting weak memory-ordering behavior that arises from allowing one version of a structure to be read concurrently with updates to a different version of the same structure. Relativistic programming techniques provide performance and scalability advantages over traditional synchronization, as demonstrated through several benchmarks.
Echistatin is a potent inhibitor of bone resorption in culture. (1990)

The venom protein, s-echistatin, originally derived from the saw-scaled viper Echis carinatus, was found to be a potent inhibitor of bone resorption by isolated osteoclasts. This Arg24-Gly25-Asp26-(RGD)-containing protein inhibited the excavation of bone slices by rat osteoclasts (IC50 = 0.1 nM). It also inhibited the release of [3H]proline from labeled bone particles by chicken osteoclasts (IC50 = 100 nM). By comparison, the tetrapeptide Arg-Gly-Asp-Ser (RGDS) inhibited resorption by rat or chicken osteoclasts with an IC50 of 0.1 mM while ala24-echistatin was inactive. Video microscopy showed that rat osteoclast attachment to substrate was more sensitive to s-echistatin than was the attachment of mononuclear cells or chicken osteoclasts. The difference in sensitivity of rat and chicken osteoclasts to s-echistatin may be due to differences between receptors on rat and chicken osteoclasts for s-echistatin. Antibody localization of echistatin on these cells showed much greater echistatin binding to rat osteoclasts than to chicken osteoclasts. Laser scanning confocal microscopy after immunohistochemical staining showed that s-echistatin binds to osteoclasts, that s-echistatin receptors are most abundant at the osteoclast/glass interface, and that s-echistatin colocalizes with vinculin. Confocal interference reflection microscopy of osteoclasts incubated with s-echistatin, demonstrated colocalization of s-echistatin with the outer edges of clusters of grey contacts at the tips of some lamellipodia. Identification of the echistatin receptor as an integrin was confirmed by colocalization of echistatin fluorescence with staining for an alpha-like subunit. Attachment of bone particles labeled with [3H]proline to chicken osteoclasts confirmed that the mechanism of action of echistatin was to inhibit osteoclast binding to bone presumably by disrupting adhesion structures. These data demonstrate that osteoclasts bind to bone via an RGD-sequence as an obligatory step in bone resorption, that this RGD-binding integrin is at adhesion structures, and that it colocalizes with vinculin and has an alpha-like subunit.
Ammonia Pretreatment of Corn Stover Enables Facile Lignin Extraction (2017)

Thermochemical pretreatment of lignocellulose is often employed to render polysaccharides more digestible by carbohydrate-active enzymes to maximize sugar yields. The fate of lignin during pretreatment, however, is highly dependent on the chemistry employed and must be considered in cases where lignin valorization is targeted alongside sugar conversion—an important feature of future biorefinery development. Here, a two-step process is demonstrated in which anhydrous ammonia (AA) pretreatment is followed by mild NaOH extraction on corn stover to solubilize and fractionate lignin. As known, AA pretreatment simultaneously alters the structure of cellulose with enhanced digestibility while redistributing lignin. The AA-pretreated residue is then extracted with dilute NaOH at mild conditions to maximize lignin separation, resulting in a digestible carbohydrate-rich solid fraction and a solubilized lignin stream. Lignin removal of more than 65% with over 84% carbohydrate retention is achieved after mild NaOH extraction of AA-pretreated corn stover with 0.1 M NaOH at 25 °C. Two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy of the AA-pretreated residue shows that ammonolysis of ester bonds occurs to partially liberate hydroxycinnamic acids, and the AA-pretreated/NaOH-extracted residue exhibits a global reduction of all lignin moieties caused by reduced lignin content. A significant reduction (∼70%) in the weight-average molecular weight (Mw) of extracted lignin is also achieved. Imaging of AA-pretreated/NaOH extracted residues show extensive delamination and disappearance of coalesced lignin globules from within the secondary cell walls. Glycome profiling analyses demonstrates ultrastructural level cell wall modifications induced by AA pretreatment and NaOH extraction, resulting in enhanced extractability of hemicellulosic glycans, indicating enhanced polysaccharide accessibility. The glucose and xylose yields from enzymatic hydrolysis of AA-pretreated/NaOH-extracted corn stover were higher by ∼80% and ∼60%, respectively, compared to untreated corn stover at 1% solids loadings. For digestions at 20% solids, a benefit of NaOH extraction is realized in achieving ∼150 g/L of total monomeric sugars (glucose, xylose, and arabinose) in the enzymatic hydrolysates from AA-pretreated/NaOH-extracted corn stover. Overall, this process enables facile lignin extraction in tandem with a leading thermochemical pretreatment approach, demonstrating excellent retention of highly digestible polysaccharides in the solid phase and a highly depolymerized, soluble lignin-rich stream.
Molecular mimetics of polysaccharide epitopes as vaccine candidates for prevention of Neisseria meningitidis serogroup B disease (1999)

Neisseria meningitidis is a major cause of meningitis and sepsis.Despite nearly 25 years of work, there is no promising vaccine candidate for prevention of disease caused by meningococcal B strains.This review summarizes newer approaches for eliciting protective meningococcal B immune responses, including the use of molecular mimetics of group B polysaccharide and conserved membrane proteins as immunogens.The capsular polysaccharide of this organism is conserved and serum antibody to this capsule confers protection against disease.However, the immunogenicity of meningococcal B polysaccharide-based vaccines is poor.Further, a portion of the antibody elicited has autoantibody activity.Recently, our laboratory produced a panel of murine monoclonal antibodies (Mabs) that react specifically with capsular polysaccharide epitopes on meningococcal B that are distinct from host polysialic acid.These Mabs elicit complement-mediated bactericidal activity and confer passive protection in animal models.The anti-capsular Mabs were used to identify molecular mimetics from phage display peptide libraries.The resulting peptides were antigenic mimetics as defined by binding to the Mabs used to select them but, to date, are poor immunogenic mimetics in failing to elicit anti-capsular antibodies.
Subunit of Bovine Rod Photoreceptor cGMP Phosphodiesterase (1990)

A group of cDNA clones encoding the &subunit of bovine rod photoreceptor cGMP phosphodiesterase were isolated for structural analysis. The encoded polypeptide has 853 residues with a calculated molec- ular mass of 98 kDa. The &subunit is 72% identical to the rod cGMP phosphodiesterase a-subunit. Like the a-subunit and the cone cu’-subunit, the B-subunit be- longs to the family of phosphodiesterase genes. The & and a-subunits are more similar to each other than either is to the cone &-subunit, suggesting either that the /3- and a-subunits diverged more recently or that their divergence was restrained by the rod functional environment. Cyclic GMP phosphodiesterase is a key component in the phototransduction cascade in photoreceptor cells. In rod pho- toreceptor cells, visual signaling is triggered upon the absorp- tion of a photon by rhodopsin. Photoexcited rhodopsin acti- vates a GTP-binding protein (transducin), which in turn relieves an inhibitory constraint on phosphodiesterase. Rapid hydrolysis of cGMP by activated phosphodiesterase results in closure of cGMP-gated cation channels in the plasma mem- brane, leading to hyperpolarization of the cell (1). Rod phos- phodiesterase consists of two large polypeptides, (Y and & and two identical small inhibitory y-subunits (2, 3). The primary structures of the cr- and y-subunits (5-8) as well as that of the related cone photoreceptor cY’-subunit (4) have been elu- cidated by partial protein sequencing and cDNA cloning. Sequence comparison and DNA hybridization have revealed that the large polypeptides of rod and cone phosphodiesterases are clearly related, but are encoded by distinct genes. Here, we report the nucleotide sequence of the cDNA
GADD45 induction of a G 2 /M cell cycle checkpoint (1999)

G1/S and G2/M cell cycle checkpoints maintain genomic stability in eukaryotes in response to genotoxic stress. We report here both genetic and functional evidence of a Gadd45-mediated G2/M checkpoint in human and murine cells. Increased expression of Gadd45 via microinjection of an expression vector into primary human fibroblasts arrests the cells at the G2/M boundary with a phenotype of MPM2 immunopositivity, 4n DNA content and, in 15% of the cells, centrosome separation. The Gadd45-mediated G2/M arrest depends on wild-type p53, because no arrest was observed either in p53-null Li-Fraumeni fibroblasts or in normal fibroblasts coexpressed with p53 mutants. Increased expression of cyclin B1 and Cdc25C inhibited the Gadd45-mediated G2/M arrest in human fibroblasts, indicating that the mechanism of Gadd45-mediated G2/M checkpoint is at least in part through modulation of the activity of the G2-specific kinase, cyclin B1/p34(cdc2). Genetic and physiological evidence of a Gadd45-mediated G2/M checkpoint was obtained by using GADD45-deficient human or murine cells. Human cells with endogenous Gadd45 expression reduced by antisense GADD45 expression have an impaired G2/M checkpoint after exposure to either ultraviolet radiation or methyl methanesulfonate but are still able to undergo G2 arrest after ionizing radiation. Lymphocytes from gadd45-knockout mice (gadd45 -/-) also retained a G2/M checkpoint initiated by ionizing radiation and failed to arrest at G2/M after exposure to ultraviolet radiation. Therefore, the mammalian genome is protected by a multiplicity of G2/M checkpoints in response to specific types of DNA damage.
Plasmids : a practical approach (1987)

Part 1 Plasmid replication and maintenance, K. Nordstroem: single-cell resistance (SCR) to antibiotics determination of plasmid copy numbers partition and other maintenance functions incompatibility basic replicons origins (ori) of replication rep functions identification cis/trans activity replicative intermediates timing intermediates timing of replication invitro replication visualization of plasmids. Part 2 Plasmids from gram-positive bacteria, J.C. Alonso and Manuel Espinosa: classification isolation of plasmid DNA host range and plasmid tranfer plasmid replication modes. Part 3 Lactococcal plasmid vectors, K.J. Leenhouts and G. Venema: Lactococcal vector systems special-purpose vectors. Part 4 Virulence plasmids, Marcelo E. Tomalsky et al: isolation of plasmids curing of plasmids mutagenesis fast and small electrophoresis-sequencing gels comparison of helical stability of DNA fragments identification of plasmid-encoded products RNA extraction and analysis. Part 5 Plasmids in agrobacterium tumefaciens and rhodococcus fascians, Jan Desomer et al: identification of endogenous plasmids by small-scale isolation procedures large-scale purification methods introductioon of recombinant plasmids analysis of plasmid-encoded functions. Part 6 Streptomyces plasmid vectors, W. Wohlleben and G. Muth: autonomously replicating streptomyces vectors integrating vectors gene disruption/replacement techniques using temperature-sensitive and non-replicative plasmids. Part 7 Use of lambda-plasmid composite vectors for expression cDNA cloning, Toru Miki and Stuart A. Aaronson: expression cloning using unidirectional cDNA libraries generation of cDNA libraries by the ADC method analysis of cloned cDNAs applications. Part 8 Phagemids and other hybrid vectors, Michelle A. Alting-Mees et al: early vectors new applications phagemids and lambda-zedAP cloning. Part 9 Extrachromosonal cloning vectors of saccharomyces cerevisiae, Robert S. Sikorski: basic cloning vectors of saccharomyces cerevisiae multifunctional cloning vectors of saccharomyces cerevisiae yeast host strain introduction of DNA into saccharomyces cerevisiae. Appendix: supplies of specialist items.
EHD2 and the Novel EH Domain Binding Protein EHBP1 Couple Endocytosis to the Actin Cytoskeleton (2004)

Here we identified two novel proteins denoted EH domain protein 2 (EHD2) and EHD2-binding protein 1 (EHBP1) that link clathrin-mediated endocytosis to the actin cytoskeleton. EHD2 contains an N-terminal P-loop and a C-terminal EH domain that interacts with NPF repeats in EHBP1. Disruption of EHD2 or EHBP1 function by small interfering RNA-mediated gene silencing inhibits endocytosis of transferrin into EEA1-positive endosomes as well as GLUT4 endocytosis into cultured adipocytes. EHD2 localizes with cortical actin filaments, whereas EHBP1 contains a putative actin-binding calponin homology domain. High expression of EHD2 or EHBP1 in intact cells mediates extensive actin reorganization. Thus EHD2 appears to connect endocytosis to the actin cytoskeleton through interactions of its N-terminal domain with membranes and its C-terminal EH domain with the novel EHBP1 protein.
A TWO-PLAYER GAME OF LIFE (2003)

We present a new extension of Conway's game of life for two players, which we call "p2life". P2life allows one of two types of token, black or white, to inhabit a cell and adds competitive elements into the birth and survival rules of the original game. We solve the mean-field equation for p2life and determine, using simulation, that the asymptotic density of p2life approaches 0.0362.
Reproduction and Growth following Prenatal Methylmercuric Chloride Exposure in Mice (1986)

Reproduction and Growth following Prenatal Methylmercuric Chloride Exposure in Mice. GATES, A.H., DOHERTY, R.A., AND Cox, C. (1986). Fundam. Appl. Toxicol. 7, 486-493. Reproductive effects of the environmental pollutant methylmercuric chloride administered as a single dose per os during pregnancy were studied both in treated mice (Go generation) and in their prenatally exposed offspring (G1). Treatment at 9.5 days postfertilization caused no observed effects at doses as high as 12-18 mgHg+/kg. In contrast, treatment at 12.5 and 15.5 days produced toxicity; results were similar and were combined for analysis. Among Go mice, the percentage capable of delivering one or more viable pups showed an estimated threshold level response at 8.0 mg/kg. The percentage of G, pups that were viable at 1 day post partum was significantly dose-related, with an approximate threshold exposure level of 4.3 mg/kg. Among the surviving G1 offspring, body weight in adulthood (8 months) showed a statistically significant reduction that was also dose-related. Fertility testing of Gi offspring revealed no treatment effects on mating behavior judged by time interval between pairing and parturition. However, there was a trend (statistically nonsignificant) toward a dose effect on sizes of females' litters. Sterility (inability to produce offspring) did not occur either among Gi males at 4 months of age (N = 30; dose 8-12 mg/kg) or among females up to the advanced reproductive age of 14 months (N = 29; dose 5.3-12 mg/kg). We conclude that mice exposed prenatally to methylmercuric chloride revealed no greater susceptibility to sterility than to perinatal mortality.