gebhart/patrepeval huggingface dataset:
The Expression of ST2 Gene in Helper T Cells and the Binding of ST2 Protein to Myeloma-Derived RPMI8226 Cells (1997)

The ST2 gene, which is specifically induced by growth stimulation, encodes interleukin-1 receptor-related proteins. Using the RT-PCR method, we found that the ST2 gene was broadly expressed in hematopoietic cell lines. It was also expressed specifically in helper T cell lines among lymphocytic cell lines. We analyzed the expression of ST2 in mouse helper T cell subsets with Northern blotting analysis. Mouse Th1 cell lines so far studied did not express ST2 mRNAs. On the other hand, one of the Th2 cell lines, D10, expressed ST2L (transmembrane form) without stimulation, while co-stimulation by PMA and A23187 induced ST2 (soluble form) mRNA. These results suggest that the ST2 gene is involved in the regulation of the immune system. IL-1 alpha, IL-1 beta, and receptor antagonist did not bind to ST2L protein, which prompted us to search for the specific ligand of ST2. The recombinant human ST2 protein was purified and labeled with FITC. The labeled human ST2 protein bound with myeloma-derived RPMI8226 cells among the various B-cell lines, indicating possible involvement of ST2 in T-cell/B-cell interaction.
Large-Scale Named Entity Disambiguation Based on Wikipedia Data (2007)

This paper presents a large-scale system for the recognition and semantic disambiguation of named entities based on information extracted from a large encyclopedic collection and Web search results. It describes in detail the disambiguation paradigm employed and the information extraction process from Wikipedia. Through a process of maximizing the agreement between the contextual information extracted from Wikipedia and the context of a document, as well as the agreement among the category tags associated with the candidate entities, the implemented system shows high disambiguation accuracy on both news stories and Wikipedia articles. 1 Introduction and Related Work
A Novel Retrotransposon Inserted in the DominantVrn-B1Allele Confers Spring Growth Habit in Tetraploid Wheat (Triticum turgidumL.) (2011)

Vernalization genes determine winter/spring growth habit in temperate cereals and play important roles in plant development and environmental adaptation. In wheat (Triticum L. sp.), it was previously shown that allelic variation in the vernalization gene VRN1 was due to deletions or insertions either in the promoter or in the first intron. Here, we report a novel Vrn-B1 allele that has a retrotransposon in its promoter conferring spring growth habit. The VRN-B1 gene was mapped in a doubled haploid population that segregated for winter-spring growth habit but was derived from two spring tetraploid wheat genotypes, the durum wheat (T. turgidum subsp. durum) variety 'Lebsock' and T. turgidum subsp. carthlicum accession PI 94749. Genetic analysis revealed that Lebsock carried the dominant Vrn-A1 and recessive vrn-B1 alleles, whereas PI 94749 had the recessive vrn-A1 and dominant Vrn-B1 alleles. The Vrn-A1 allele in Lebsock was the same as the Vrn-A1c allele previously reported in hexaploid wheat. No differences existed between the vrn-B1 and Vrn-B1 alleles, except that a 5463-bp insertion was detected in the 5'-UTR region of the Vrn-B1 allele. This insertion was a novel retrotransposon (designated as retrotrans_VRN), which was flanked by a 5-bp target site duplication and contained primer binding site and polypurine tract motifs, a 325-bp long terminal repeat, and an open reading frame encoding 1231 amino acids. The insertion of retrotrans_VRN resulted in expression of Vrn-B1 without vernalization. Retrotrans_VRN is prevalent among T. turgidum subsp. carthlicum accessions, less prevalent among T. turgidum subsp. dicoccum accessions, and rarely found in other tetraploid wheat subspecies.
Porphyromonas gingivalis DPP-7 Represents a Novel Type of Dipeptidylpeptidase (2001)

A novel dipeptidylpeptidase (DPP-7) was purified from the membrane fraction of Porphyromonas gingivalis. This enzyme, with an apparent molecular mass of 76 kDa, has the specificity for both aliphatic and aromatic residues in the P1 position. Although it belongs to the serine class of peptidases, it does not resemble other known dipeptidylpeptidases. Interestingly, the amino acid sequence around the putative active site serine residue shows significant similarity to the C-terminal region of the Staphylococcus aureus V-8 endopeptidase. The genes encoding homologues of DPP-7 were found in genomes of Xylella fastidiosa, Shewanella putrefaciens, and P. gingivalis. It is likely that at least in P. gingivalis, DPP-7 and its homologue, in concert with other di- and tripeptidases, serve nutritional functions by providing dipeptides to this asaccharolytic bacterium.
Solubility of inert gases in biological fluids and tissues: a review. (1980)

Data have been tabulated from more than 150 references on the solubility of inert gases in fluids and tissues of biological interest. Thirty-two gases have been studied in blood with measured solubility ranging from 0.005 to 16 ml of gas at 37 degrees C per ml of blood per ATA (Ostwald coefficient). For most gases, solubility in other tissues such as muscle or brain is between 60% and 300% of blood solubility. Measured solubilities in biological tissues do not correspond well to solubility in water and oil. Most gases decrease in solubility by 1%-6% for each degree C rise in temperature. The effect of pressure on solubility has not been well studied, and only crude estimates can be obtained by using methods of chemical thermodynamics.
Neu4, a Novel Human Lysosomal Lumen Sialidase, Confers Normal Phenotype to Sialidosis and Galactosialidosis Cells (2004)

Three different mammalian sialidases have been described as follows: lysosomal (Neu1, gene NEU1), cytoplasmic (Neu2, gene NEU2), and plasma membrane (Neu3, gene NEU3). Because of mutations in the NEU1 gene, the inherited deficiency of Neu1 in humans causes the severe multisystemic neurodegenerative disorder sialidosis. Galactosialidosis, a clinically similar disorder, is caused by the secondary Neu1 deficiency because of genetic defects in cathepsin A that form a complex with Neu1 and activate it. In this study we describe a novel lysosomal lumen sialidase encoded by the NEU4 gene on human chromosome 2. We demonstrate that Neu4 is ubiquitously expressed in human tissues and has broad substrate specificity by being active against sialylated oligosaccharides, glycoproteins, and gangliosides. In contrast to Neu1, Neu4 is targeted to lysosomes by the mannose 6-phosphate receptor and does not require association with other proteins for enzymatic activity. Expression of Neu4 in the cells of sialidosis and galactosialidosis patients results in clearance of storage materials from lysosomes suggesting that Neu4 may be useful for developing new therapies for these conditions.
Stimulation of intestinal mucosal adenyl cyclase by cholera enterotoxin and prostaglandins (1971)

The effects of several prostaglandins (PG) and a highly purified preparation of cholera enterotoxin (CT) on intestinal mucosal adenyl cyclase activity and the effect of CT on intestinal mucosal cyclic 3',5'-adenosine monophosphate concentration were determined in guinea pig and rabbit small intestine and were correlated with the effects of the same agents on ion transport. Adenyl cyclase activity, measured in a crude membrane fraction of the mucosa, was found at all levels of the small intestine with the highest activity per milligram protein in the duodenum. The prostaglandins, when added directly to the assay, increased adenyl cyclase activity; the greatest effect (2-fold increase) was obtained with PGE(1) (maximal effect at 0.03 mM) and PGE(2). The prostaglandins also increased short-circuit current (SCC) in isolated guinea pig ileal mucosa, with PGE(1) and PGE(2) again giving the greatest effects. The prior addition of theophylline (10 mM) reduced the subsequent SCC response to PGE(1) and vice versa. It was concluded, therefore, that the SCC response to PGE(1), like the response to theophylline, represented active Cl secretion. CT increased adenyl cyclase activity in guinea pig and rabbit ileal mucosa when preincubated with the mucosa from 1 to 2.5 hr in vitro or for 2.5 hr in vivo but not when added directly to the assay. The increments in activity caused by PGE(1) and NaF were the same in CT-treated and control mucosa. Cyclic 3',5'-AMP concentration in rabbit ileal mucosa was increased 3.5-fold after a 2 hr preincubation with CT in vitro. Phosphodiesterase activity in the crude membrane fraction of the mucosa was unaffected by either CT or PGE(1). A variety of other agents including insulin, glucagon, parathormone, thyroid-stimulating hormone, L-thyroxine, thyrocalcitonin, vasopressin, and epinephrine all failed to change adenyl cyclase activity. It is concluded that CT and certain prostaglandins produce small intestinal fluid secretion by increasing mucosal adenyl cyclase activity, thereby stimulating an active secretory process.
Studies on Some Possible Biochemical Treatments of Primary Hyperoxaluria (1979)

The effects of some putative inhibitors of oxalate production or urinary oxalate excretion have been investigated in the Cynamolgus monkey and in patients with Type I primary hyperoxaluria (hyperoxaluria with glycollic aciduria). Sodium-1-hydroxybutan-sulphonate, D,L-phenyllactate, succinimide and isocarboxazide did not reduce the urinary oxalate excretion in the monkeys. Pyridoxine reduced the excretion of oxalate and glycollate in some patients, and its therapeutic use has been documented over a five-year period. Succinimide, which has been used by other workers for the treatment of non-hyperoxaluric stone formers, did not decrease the excretion of either oxalate or glycollate in three patients in whom it was tried. It did not change the inhibitory activity of the urine with respect to the growth and aggregation of calcium oxalate crystals in any of the three patients, and it did not have any consistent effect on the excretion of calcium oxalate crystals in the one patient who had detectable crystaluria before treatment. We have identified several metabolites of succinimide in the urine of patients taking the drug. These include 2,3-dehydrosuccinamic, 2-hydroxysuccinamic and 3-hydroxysuccinamic acids. Isocarboxazide, cholestyramine and thiamine did not affect the urinary oxalate excretion in the patients. The significance of these observations from the viewpoint of the treatment of primary hyperoxaluria is discussed.
A multi-mode variable rate CELP coder based on frame classification (2002)

The authors present a modular CELP (code-excited linear prediction) coder which can switch bit-rates in response to local speech characteristics (source-controlled mode) or external network conditions (network-controlled mode). The coder is capable of operating at several bit-rates and is optimized for 16 kb/s, 8 kb/s, and 4 kb/s. A 925-b/s configuration is included for silent frames. The authors present the results of informal MOS tests which show that the variable-rate system running at an average rate of 8 kb/s achieves subjective speech quality close to that of the 16-kb/s fixed-rate system (a difference of less than 0.1 on the MOS scale).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Age-dependent variations of antibody avidity. (1978)

Age-dependent variations of antibody avidity were studied in the C3HeB/FeJ mouse. Spleen cells from donors of different ages (10--720 days) were transferred and stimulated with TNP-HRBC in lethally irradiated syngenic recipients. The anti-TNP antibody response of the donor cells was estimated from the number of direct PFC per recipient spleen by the Jerne technique with TNP-SRBC. Avidity of the antibodies secreted by PFC was evaluated from the amount of added TNP-BSA that inhibited 50% of the anti-TNP PFC. Under these experimental conditions allowing the exclusion of any influence of the donor milieu during the immune response, age-dependent variations of the antibody response and avidity could be attributed to changes in the donor spleen cell population. Avidity was found to increase with the response and to vary parabolically with age. After appropriate correction of the number of PFC to make it independent from age, avidity values were fitted by a multiple curvilinear regression in which the independent variables playing a significant role were the corrected number of PFC in its linear term and the age in its linear and quadratic terms. From comparison of the standard coefficients of this regression, the observed variations of avidity could be attributed in part (82%) to the response and in part (18%) to the age. For any value of response, avidity increased 15-fold from day 10 to reach a maximum at day 110 and then declined 5-fold at the age of 720 days. Heterogeneity of avidity also changed parabolically with age as high avidity classes were present in adulthood and absent at 10 and 720 days.
Analysis of the Genome Structure of the Nonpathogenic Probiotic Escherichia coli Strain Nissle 1917 (2004)

Nonpathogenic Escherichia coli strain Nissle 1917 (O6:K5:H1) is used as a probiotic agent in medicine, mainly for the treatment of various gastroenterological diseases. To gain insight on the genetic level into its properties of colonization and commensalism, this strain's genome structure has been analyzed by three approaches: (i) sequence context screening of tRNA genes as a potential indication of chromosomal integration of horizontally acquired DNA, (ii) sequence analysis of 280 kb of genomic islands (GEIs) coding for important fitness factors, and (iii) comparison of Nissle 1917 genome content with that of other E. coli strains by DNA-DNA hybridization. PCR-based screening of 324 nonpathogenic and pathogenic E. coli isolates of different origins revealed that some chromosomal regions are frequently detectable in nonpathogenic E. coli and also among extraintestinal and intestinal pathogenic strains. Many known fitness factor determinants of strain Nissle 1917 are localized on four GEIs which have been partially sequenced and analyzed. Comparison of these data with the available knowledge of the genome structure of E. coli K-12 strain MG1655 and of uropathogenic E. coli O6 strains CFT073 and 536 revealed structural similarities on the genomic level, especially between the E. coli O6 strains. The lack of defined virulence factors (i.e., alpha-hemolysin, P-fimbrial adhesins, and the semirough lipopolysaccharide phenotype) combined with the expression of fitness factors such as microcins, different iron uptake systems, adhesins, and proteases, which may support its survival and successful colonization of the human gut, most likely contributes to the probiotic character of E. coli strain Nissle 1917.
Mutated PPP1R3B Is Recognized by T Cells Used To Treat a Melanoma Patient Who Experienced a Durable Complete Tumor Regression (2013)

Adoptive cell therapy with tumor-infiltrating lymphocytes (TILs) represents an effective treatment for patients with metastatic melanoma. However, most of the Ag targets recognized by effective melanoma-reactive TILs remain elusive. In this study, patient 2369 experienced a complete response, including regressions of bulky liver tumor masses, ongoing beyond 7 y following adoptive TIL transfer. The screening of a cDNA library generated from the autologous melanoma cell line resulted in the isolation of a mutated protein phosphatase 1, regulatory (inhibitor) subunit 3B (PPP1R3B) gene product. The mutated PPP1R3B peptide represents the immunodominant epitope recognized by tumor-reactive T cells in TIL 2369. Five years following adoptive transfer, peripheral blood T lymphocytes obtained from patient 2369 recognized the mutated PPP1R3B epitope. These results demonstrate that adoptive T cell therapy targeting a tumor-specific Ag can mediate long-term survival for a patient with metastatic melanoma. This study also provides an impetus to develop personalized immunotherapy targeting tumor-specific, mutated Ags.
A Coagulation Factor IX-Deficient Mouse Model for Human Hemophilia B (1997)

Coagulation factor IX deficiency causes hemophilia B in humans. We have used gene targeting to develop a coagulation factor IX-deficient (factor IX-knockout) mouse strain. Mouse embryonic stem (ES) cells were targeted by a socket-containing vector that replaces the promoter through exon 3 of the factor IX gene by neoDeltaHPRT, which is a functional neo gene plus a partially deleted hypoxanthine phosphoribosyl transferase minigene. Chimeric mice generated using these socket-containing ES cells transmitted the targeted factor IX gene to their female offspring. Male offspring from these females were characterized and shown to exhibit a phenotype similar to hemophilia B. This factor IX-deficient mouse strain will be useful for studying gene therapy methods and structure-function relationships of recombinant factor IX proteins in vivo.
Mutations in the amino‐terminal domain of λ‐integrase have differential effects on integrative and excisive recombination (2005)

Lambda integrase (Int) forms higher-order protein-DNA complexes necessary for site-specific recombination. The carboxy-terminal domain of Int (75-356) is responsible for catalysis at specific core-type binding sites whereas the amino-terminal domain (1-70) is responsible for cooperative arm-type DNA binding. Alanine scanning mutagenesis of residues 64-70, within full-length integrase, has revealed differential effects on cooperative arm binding interactions that are required for integrative and excisive recombination. Interestingly, while these residues are required for cooperative arm-type binding on both P'1,2 and P'2,3 substrates, cooperative binding at the arm-type sites P'2,3 was more severely compromised than binding at arm-type sites P'1,2 for L64A. Concomitantly, L64A had a much stronger effect on integrative than on excisive recombination. The arm-binding properties of Int appear to be intrinsic to the amino-terminal domain because the phenotype of L64A was the same in an amino-terminal fragment (Int 1-75) as it was in the full-length protein.
The Catalytic Role of N-Heterocyclic Carbene in a Metal-Free Conversion of Carbon Dioxide into Methanol: A Computational Mechanism Study (2010)

A density functional theory study at the M05-2X(IEFPCM, THF)/6-311+G**//M05-2X/6-31G* level has been conducted to gain insight into the catalytic mechanism of the first metal-free N-heterocyclic carbene (NHC)-catalyzed conversion of carbon dioxide into methanol. Among the various examined reaction pathways, we found that the most favorable leads to the experimentally detected intermediates, including formoxysilane (FOS), bis(silyl)acetal (BSA), silylmethoxide (SMO), and disiloxane (DSO). However, our study also revealed that formaldehyde (CH(2)O), generated from the dissociation of BSA into DSO and CH(2)O via a mechanism somewhat similar to the Brook rearrangement, should be an inevitable intermediate, although it was not reported by the experimentalists. When NHC catalyzes the reactions of CO(2)/FOS/CH(2)O with silane, there are two activation modes. It was found that NHC prefers to activate Si-H bonds of silane and push electron density to the H atoms of the Si-H bonds in favor of transferring a hydridic atom of silane to the electrophilic C center of CO(2)/FOS/CH(2)O. This holds true in particular for the NHC-catalyzed reactions of silane with FOS/CH(2)O to produce BSA/SMO. The preferred activation mode can operate by first passing an energetically unfavorable NHC-silane local minimum via pi-pi interactions or by directly crossing a transition state involving three components simultaneously. The activation mode involving initial coordination of NHC with the electrophilic C atom of CO(2)/FOS/CH(2)O is less favorable or inoperable. The predicted catalytic mechanism provides a successful interpretation of the experimental observation that phenylsilane is more efficient than diphenylsilane in performing the conversion.
A randomized trial of oral versus intravenous acyclovir for treatment of herpes zoster in bone marrow transplant recipients. Nordic Bone Marrow Transplant Group. (1989)

Twenty-seven bone marrow transplant patients who developed localized herpes zoster were treated with acyclovir in a randomized study comparing oral and intravenous drug administration. Fourteen patients received oral and 13 patients received intravenous treatment. None of the patients developed disseminated disease. No differences were found between the treatment groups in the number of days that new lesions continued to develop, in number of days with pain, or in the number of days from start of treatment until all lesions were crusted over. We suggest that oral acyclovir may be as effective as intravenous acyclovir in the treatment of localized herpes zoster after bone marrow transplantation.
Intact cell transformation of Saccharomyces cerevisiae by polyethylene glycol. (1985)

A new yeast transformation method using intact cells instead ofprotoplasts has recently been developed.1>2) This transformation methodis based on the treatment of intact cells with alkali cations such as lithium acetate or thiol compounds. It has several advantages compared with the current protoplast method3); for example, since lytic enzyme digestion of yeast cell walls can be avoided, re-
The final nail in WEP's coffin (2006)

The 802.11 encryption standard Wired Equivalent Privacy (WEP) is still widely used today despite the numerous discussions on its insecurity. In this paper, we present a novel vulnerability which allows an attacker to send arbitrary data on a WEP network after having eavesdropped a single data packet. Furthermore, we present techniques for real-time decryption of data packets, which may be used under common circumstances. Vendor produced mitigation techniques which cause frequent WEP re-keying prevent traditional attacks, whereas our attack remains effective even in such scenarios. We implemented a fully automatic version of this attack which demonstrates its practicality and feasibility in real networks. As even rapidly re-keyed networks can be quickly compromised, we believe WEP must now be abandoned rather than patched yet again.
An evaluation of garlic lectin as an alternative carrier domain for insecticidal fusion proteins (2008)

Abstract The mannose‐binding lectin GNA (snowdrop lectin) is used as a “carrier” domain in insecticidal fusion proteins which cross the insect gut after oral ingestion. A similar lectin from garlic bulb, ASAII, has been evaluated as an alternative “carrier”. Recombinant ASAII delivered orally to larvae of cabbage moth ( Mamestra brassica ; Lepidoptera) was subsequently detected in haemolymph, demonstrating transport. Fusion proteins comprising an insect neurotoxin, ButaIT ( Buthus tamulus insecticidal toxin ; red scorpion toxin) linked to the C‐terminal region of ASAII or GNA were produced as recombinant proteins (GNA/ButaIT and ASA/ButaIT) by expression in Pichia pastoris. In both cases the C‐terminal sequence of the lectin was truncated to avoid post‐translational proteolysis. The GNA‐containing fusion protein was toxic by injection to cabbage moth larvae (LD 50 ≈ 250 μg/g), and when fed had a negative effect on survival and growth. It also decreased the survival of cereal aphids ( Sitobion avenae ; Homoptera) from neonate to adult by &gt;70% when fed. In contrast, the ASA‐ButaIT fusion protein was non‐toxic to aphids, and had no effect on lepidopteran larvae, either when injected or when fed. However, intact ASA‐ButaIT fusion protein was present in the haemolymph of cabbage moth larvae following ingestion, showing that transport of the fusion had occurred. The stabilities of GNA/ButaIT and ASA/ButaIT to proteolysis in vivo after injection or ingestion differed, and this may be a factor in determining insecticidal activities.