gebhart/patrepeval huggingface dataset:
Mast cells as potent inflammatory cells. (1996)

In the last decade, new information was achieved on mast cells (MC). Their origin is assumed to be different from that of the basophils. There are two types of MC with differences in structure, distribution and function: conjunctival and mucosal. MCs are among the most important cells in the development of allergic inflammation through the cytokines and mediators released on the activation of the surface receptors (high-affinity receptors for IgE: Fc epsilon R1). The cytokines released by MCs, e.g., interleukin 5 (IL5), IL8, are chemoattractants for eosinophils and neutrophils, respectively. The two types of mediators released by MC-those preformed, such as histamine, tryptase, serotonin, and the newly-synthetized ones, such as prostaglandin D2 (PGD2), leukotrienes C4 (LTD4), D4 (LTD4), E4 (LTE4), induce vasodilatation, bronchoconstriction, cellular chemotaxis, increase vascular permeability. The involvement of MC in many human diseases was shown within in vivo and in vitro studies (in allergy, lung fibrosis, atherosclerosis, carcinogenesis, etc.).
A rough set approach to knowledge reduction based on inclusion degree and evidence reasoning theory (2003)

Abstract: The theory of rough sets is an extension of set theory for studying intelligent systems characterized by insufficient and incomplete information. We discuss the basic concept and properties of knowledge reduction based on inclusion degree and evidence reasoning theory, and propose a knowledge discovery approach based on inclusion degree and evidence reasoning theory.
AAV8-mediated Gene Therapy Prevents Induced Biochemical Attacks of Acute Intermittent Porphyria and Improves Neuromotor Function (2009)

Acute intermittent porphyria (AIP), an autosomal dominant hepatic porphyria due to half-normal hydroxymethylbilane synthase (HMB-synthase) activity, is manifested by life-threatening acute neurological attacks that are precipitated by factors that induce heme biosynthesis. The acute attacks are currently treated with intravenous hemin, but a more continuous therapy is needed, particularly for patients experiencing frequent attacks. Thus, a recombinant AAV8-based serotype vector expressing murine HMB-synthase driven by liver-specific regulatory elements was generated and its effectiveness to prevent the biochemical induction of an acute attack was evaluated in an AIP mouse model. Intraperitoneal administration of the adeno-associated viral (AAV) vector resulted in a rapid and dose-dependent increase of HMB-synthase activity that was restricted to the liver. Stable expression of hepatic HMB-synthase was achieved and wild-type or greater levels were sustained for 36 weeks. When heme synthesis was periodically induced by a series of phenobarbital injections, the treated mice did not accumulate urinary delta-aminolevulinic acid (ALA) or porphobilinogen (PBG), indicating that the expressed enzyme was functional in vivo and prevented induction of the acute attack. Further, rotarod performance and footprint analyses improved significantly. Thus, liver-directed gene therapy provided successful long-term correction of the hepatic metabolic abnormalities and improved neuromotor function in the murine model of human AIP.
Localization of cofactor binding sites with monoclonal anti-idiotype antibodies: phenylalanine hydroxylase. (1991)

A monoclonal anti-idiotype antibody, NS7, previously shown to mimic the binding of the pterin cofactor of phenylalanine hydroxylase (phenylalanine 4-monooxygenase, EC 1.14.16.1) has been used to localize the cofactor binding site within the phenylalanine hydroxylase catalytic domain to a 27-amino-acid sequence that is highly conserved among the three aromatic amino acid hydroxylases. The binding of NS7 to a synthetic peptide corresponding to the phenylalanine hydroxylase sequence from residue 263 to residue 289 was blocked by the competitive inhibitor of phenylalanine hydroxylase enzyme activity, 7,8-dihydro-6,7-dimethylpterin. In addition this peptide competed with native phenylalanine hydroxylase for binding to 6,7-dimethyl-5,6,7,8-tetrahydropterin conjugated to a polyglutamate carrier. Application of this simple and direct approach to other enzymes is likely to greatly facilitate the identification of ligand binding sites on enzymes, which will significantly contribute to the understanding of enzyme structure-function relationships.
Direct, Highly Enantioselective Pyrrolidine Sulfonamide Catalyzed Michael Addition of Aldehydes to Nitrostyrenes (2005)

Just can't get enough: The highly versatile pyrrolidine sulfonamide organocatalyst 1, which has been used in α-aminoxylation and Mannich-type reactions, also mediates diastereo- and enantioselective Michael addition reactions of aldehydes and ketones to nitroolefins (see scheme).
Weighted coloring based channel assignment for WLANs (2005)

We propose techniques to improve the usage of wireless spectrum in the context of wireless local area networks (WLANs) using new channel assignment methods among interfering Access Points (APs). We identify new ways of channel re-use that are based on realistic interference scenarios in WLAN environments. We formulate a weighted variant of the graph coloring problem that takes into account realistic channel interference observed in wireless environments, as well as the impact of such interference on wireless users. We prove that the weighted graph coloring problem is NP-hard and propose scalable distributed algorithms that achieve significantly better performance than existing techniques for channel assignment. We evaluate our algorithms through extensive simulations and experiments over an in-building wireless testbed.
The mRNA Cap Structure Stimulates Rate of Poly(A) Removal and Amplifies Processivity of Degradation (2001)

Poly(A)-specific ribonuclease (PARN) is an oligomeric, processive, and cap-interacting 3' exonuclease. We have studied how the m7G(5')ppp(5')G cap structure affects the activity of PARN. It is shown that the cap has four distinct effects: (i) It stimulates the rate of deadenylation if provided in cis; (ii) it inhibits deadenylation if provided at high concentration in trans; (iii) it stimulates deadenylation if provided at low concentration in trans; and (iv) it increases the processivity of PARN when provided in cis. It is shown that the catalytic and cap binding sites on PARN are separate. The important roles of the 7-methyl group and the inverted guanosine residue of the cap are demonstrated. An active deadenylation complex, consisting of the poly(A)-tailed RNA substrate and PARN, has been identified. Complex formation does not require a cap structure on the RNA substrate. The multiple effects of cap are all accounted for by a simple, kinetic model that takes the processivity of PARN into account.
Inertial and Magnetic Tracking of Limb Segment Orientation for Inserting Humans into Synthetic Environments (2000)

Current motion tracking technologies fail to provide accurate wide area tracking of multiple users without interference and occlusion problems. This research proposes to overcome current limitations using nine-axis magnetic/angular/rate/gravity (MARG) sensors combined with a quaternion-based complementary filter algorithm capable of continuously correcting for drift and following angular motion through all orientations without singularities. Primarily, this research involves the development of a prototype tracking system to demonstrate the feasibility of MARG sensor body motion tracking Mathematical analysis and computer simulation are used to validate the correctness of the complementary filter algorithm The implemented human body model utilizes the world-coordinate reference frame orientation data provided in quaternion form by the complementary filter and orients each limb segment independently. Calibration of the model and the inertial sensors is accomplished using simple but effective algorithms. Physical experiments demonstrate the utility of the proposed system by tracking of human limbs in real-time using multiple MARG sensors. The system is "sourceless" and does not suffer from range restrictions and interference problems. This new technology overcomes the limitations of motion tracking technologies currently in use. It has the potential to provide wide area tracking of multiple users in virtual environment and augmented reality applications.
In vitro priming of cytotoxic T lymphocytes against poorly immunogenic epitopes by engineered antigen‐presenting cells (1994)

Cytotoxic T lymphocytes (CTL) recognize antigenic peptides presented by major histocompatibility complex class I (MHC-I) molecules on the surface of target cells. Optimal induction of CD8+ CTL depends on the amount of relevant peptide/MHC-I complexes and the presence of co-stimulatory molecules on antigen-presenting cells (APC). The antigen-processing defective mutant cell line RMA-S, when cultured at low temperature, expresses high amounts of MHC-I molecules that do not contain endogenously derived peptides. These "empty" MHC-I molecules can be stabilized by addition of MHC-binding peptides. RMA-S cultured at low temperatures with selected peptides have been used for in vitro CTL induction with conflicting results. RMA-S cells do not express detectable amounts of B7 co-stimulatory molecule. This could explain their unpredictable efficiency as APC. We have evaluated whether RMA-S cells, stably transfected with cDNA encoding for the human B7.1 molecule could provide effective co-stimulation for CD8+ T lymphocytes. RMA-S/B7 cells, loaded with different synthetic peptides, demonstrated a high and sometimes unique efficiency for in vitro primary CTL induction, even when "sub-optimal" antigen peptides were used. Most importantly, RMA-S/B7 cells pulsed with naturally processed peptides extracted from the poorly immunogenic B16 melanoma cells were able to prime CD8+ cells against B16 melanoma. We conclude that the use of RMA-S/B7 cells as APC represents an ideal strategy for in vitro CTL immunization without prior in vivo priming. This system may also help to address the issue of the different contributions of co-stimulation and relative occupancy of MHC-I by single peptide epitopes in CTL priming.
GH Releasing Peptides - Structure and Kinetics (1993)

A new class of small synthetic peptides has been developed which specifically release GH. They consist of 6-7 amino acids and release GH in animals as well as humans. So far 3 of these peptides have been administered to humans, i.e., GHRP-6, GHRP-1 and GHRP-2. As in rats, these 3 peptides have been found to be increasingly more effective in releasing GH in humans. All 3 GHRPs release GH more efficaciously than GHRH 1-44 NH2 in humans. Particularly note-worthy is that GHRP-6, GHRP-1 AND GHRP-2 all release GH after oral administration. Near maximal amounts of GH can be released after GHRP-1 and GHRP-2 oral administration. In the present studies, the GH responses and serum irGHRP levels after i.v., s.c. and oral administration have been determined in normal younger men and/or women. By each route of administration GH was very effectively released. Additionally, GH release was induced by oral GHRP-6 in children with various degrees of GH deficiency. Noteworthy is the synergistic release of GH induced by the combined i.v. bolus administration of 1 microgram/kg of GHRP-1 + GHRH 1-44NH2. Thus, these results demonstrate GHRPs' potential importance at the theoretical as well as pharmaceutical level.
Analysis of random halftone dithering using second order statistics (1991)

An analytical approach is proposed to explain the appearance of unwanted low frequency artifacts during the random dithering halftoning process. The solution uses a theorem which relates the correlation of the input gray level (continuous) signal to the correlation of the output (halftone) binary signal. The numerical solution of the above relationship suggests that: 1. Introduction of low frequency artifacts is inevitable. 2. The effect is enhanced for mean gray levels farther from mid-gray. 3. High frequency information in the input signal is attenuated more than low frequency information.
Synthesis and Application of Quantum Dots FRET-Based Protease Sensors (2006)

Preparation of FRET-based quantum dots as protease sensors-RGDC peptide molecules are bound to the surface of CdSe/ZnS quantum dots. The peptide molecules are then labeled with rhodamine dye molecules. The emission color of the quantum dots change from green to orange due to fluorescence resonance energy transfer (FRET) between the quantum dots and the bound rhodamine molecules. Cleavage of the peptide by selective proteases releases the rhodamine molecules from the quantum dots surface, which results in decreasing FRET efficiency between the quantum dots and the rhodamine molecules. The emission color of the quantum dots changes back to green.
Mutation in the splicing factor Hprp3p linked to retinitis pigmentosa impairs interactions within the U4/U6 snRNP complex (2007)

Mutations in PRPF3, a gene encoding the essential pre-mRNA splicing factor Hprp3p, have been identified in patients with autosomal dominant retinitis pigmentosa type 18 (RP18). Patients with RP18 have one of two single amino acid substitutions, Pro493Ser or Thr494Met, at the highly conserved Hprp3p C-terminal region. Pro493Ser occurs sporadically, whereas Thr494Met is observed in several unlinked RP families worldwide. The latter mutation also alters a potential recognition motif for phosphorylation by casein kinase II (CKII). To understand the molecular basis of RP18, we examined the consequences of Thr494Met mutation on Hprp3p molecular interactions with components of the U4/U6.U5 small nuclear ribonucleoprotein particles (snRNPs) complex. Since numerous mutations causing human diseases change pre-mRNA splice sites, we investigated whether Thr494Met substitution affects the processing of PRPF3 mRNA. We found that Thr494Met does not affect PRPF3 mRNA processing, indicating that the mutation may exert its effect primarily at the protein level. We used small hairpin RNAs to specifically silence the endogenous PRPF3 while simultaneously expressing HA-tagged Thr494Met. We demonstrated that the C- but not N-terminal region of Hprp3p is indeed phosphorylated by CKII in vitro and in cells. CKII-mediated Hprp3p phosphorylation was significantly reduced by Thr494Met mutation. Consequently, the Hprp3p C-terminal region is rendered partially defective in its association with itself, Hprp4p, and U4/U6 snRNA. Our findings provide new insights into the biology of Hprp3p and suggest that the loss of Hprp3p phosphorylation at Thr494 is a key step for initiating Thr494Met aberrant interactions within U4/U6 snRNP complex and that these are likely linked to the RP18 phenotype.
Regulatory T Cells and Systemic Lupus Erythematosus (2006)

CD4+CD25+ regulatory T cells (Treg) constitute an important mechanism of peripheral immune tolerance. Organ-specific autoimmune conditions, such as thyroiditis and insulin-dependent diabetes mellitus have been attributed to a breakdown of this tolerance mechanism. However, this T-cell subset has not been well studied in patients and mice with systemic lupus erythematosus (SLE; lupus). The information that has been gathered so far using new tools that discriminate Treg from activated T cells indicates that reduced numbers of Treg may exist in patients with lupus. In addition, potential defects in SLE Treg function have been documented in humans and mice. Our group has demonstrated equivalent proportions of thymic Treg in lupus prone and normal mice. We therefore propose that Treg function in SLE is the more important factor to address in future studies of murine lupus. Recent studies have shown that Toll-like receptor (TLR) ligation can result in an abrogation of Treg-mediated suppression; specifically ligation of TLR-2, -4, -8 and -9. We address this new information about TLRs and Treg and propose a model for Treg tolerance breakdown to nucleic acid-binding SLE autoantigens.
Preparatory Study for the Synthesis of the Starfish Alkaloid Imbricatine. Syntheses of 5-Arylthio-3-methyl-L-histidines. (1994)

Chiral syntheses of 3-methyl-5-(phenylthio)-L-histidine (8a) and 3-methyl-5-(1-naphthalenylthio)-L-histidine (8b), selected as models for the asteroid alkaloid imbricatine (7), have been accomplished through a 10-step route starting from 4(5)-bromoimidazole (9). The key steps involved were methylation of 9, hydroxymethylation of 4-bromo-1-methyl-1H-imidazole (11), replacement of the 4-bromo group by an arylthio group in the aldehyde 14, and introduction of a chiral α-amino acid moiety into the chlorides 17a and 17b by the 'bis-lactim ether' method. The synthesis of the 4-(4-methoxybenzyl)thio analogue 17c, carried out in a similar manner, concluded formal syntheses of ovothiols A and C (1 and 3).
Nitric oxide blocks the cell cycle of mouse macrophage‐like cells in the early G2+M phase (1994)

The effects of nitric oxide produced by macrophage-like cells (Mm1) on the cell cycle were investigated. Mm1 cells lost proliferative activity in the presence of interleukin-6 (IL-6) and a subpopulation accumulated in the G2+M phase. This level increased in proportion to the incubation time. The DNA content of the cells was slightly lower than that of Mm1 cells treated with vinblastine or demecolcine, drugs which block the cell cycle in the M phase. The peak of the early G2+M phase was reduced by treatment with NG-mono-methyl-L-arginine. However, after treatment with exogenous nitric oxide or sodium nitroprusside, the G0/G1 phase increased, but the early-G2+M and the S phase decreased. The flow cytometry pattern in IL-6-treated Mm1 was the same as that of cytochalasin B-treated Mm1. These data suggest that endogenous nitric oxide affects the microfilament system of IL-6-treated Mm1 cells and blocks the cell cycle in the early G2+M phase.
Influence of Dysphagia on Short-Term Outcome in Patients with Acute Stroke (2011)

Although it is necessary to indicate other factors, such as the physical status to establish better rehabilitation networks, clinical assessment of swallowing in acute stroke is very important to determine whether the patients can go home directly.
Molecular Epidemiology of Infectious Bursal Disease Viruses: Distribution and Genetic Analysis of Newly Emerging Viruses in the United States (2005)

Genetic mutations in the genome of infectious bursal disease virus (IBDV) have resulted in antigenic and pathogenic variants that continue to cause disease in commercially reared chickens. The extent of the genetic diversity among IBDV strains circulating in the United States is unknown. This study was designed to identify newly emerging viruses infecting chickens on poultry farms experiencing immune suppression-related problems. Fifty IBDV-positive samples were identified from 273 bursa samples using a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. Mutation probes were designed to the hydrophilic B coding region of the VP2 gene. Six mutation probes used in this study were based on the nucleotide sequences of the Del-E, Bursine 2, D-78, STC, G6, and T1 IBDV strains. Following real-time RT-PCR, these mutation probes identified 11 of the 50 viruses in the melting temperature (Tm) analysis. The results indicated that the remaining 39 viruses had one or more nucleotide mutations compared with the six mutation probes in this region of the VP2 gene. Thirty-eight viruses were chosen for nucleotide sequence analysis across the hypervariable region of the VP2 gene. Within this group of 38 viruses, four were identified by the mutation probes and their nucleotide sequences confirmed that real-time RT-PCR data. In the remaining 34 viruses, nucleotide mutations were observed in as many as 8 of 23 nucleotides across the hydrophilic B epitope coding region. Furthermore, every amino acid position except one between 316 and 324 had at least one substitution mutation. Phylogenic analysis placed two of the 38 viruses sequenced on branches with classic viruses and the remaining 36 viruses were placed on four distinct branches. Branches 1 and 2 contained a majority of the viruses, which were distributed across most of the major poultry-producing states in the United States. These branches contained previously characterized variant IBDV strains. Viruses in branches 3 and 4 were confined to three states and did not contain any previously characterized IBDV strains.
Critically ill patients have high basal growth hormone levels with attenuated oscillatory activity associated with low levels of insulin–like growth factor‐I (1991)

We have demonstrated that critically ill patients have low IGF-I levels associated with augmented baseline GH levels which show reduced oscillatory activity. The results would be compatible with the hypothesis that there is an adaptive change in critically ill patients away from the indirect effects of GH (stimulation of IGF-I production and anabolism) and toward the direct effects (lipolysis and insulin antagonism) which increase the availability of energy substrates. The pattern of GH levels seen in our patients may be important in this adaptation.
Synthesis of X-Tolerant Convolutional Compactors (2005)

The paper presents a very efficient method for synthesis of convolutional compactors capable of tolerating a number of unknown states in a single time frame while providing very high compaction ratios.
Glycosylation and high‐level secretion of human tumour necrosis factor‐beta in recombinant baculovirus‐infected insect cells (1993)

Human tumour necrosis factor-beta (TNF-beta) was produced in eukaryotic cells using the insect baculovirus cloning and expression system. A novel insect signal sequence, the honey-bee (Apis mellifera) prepromelittin secretory sequence, was used to aid in the post-translational modifications, glycosylation and secretion of recombinant human TNF-beta. Human TNF-beta cDNA was cloned using the insect baculovirus vector pAcC4s. Expression of the human TNF-beta was regulated by the insect Autographa californica nuclear-polyhedrosis-virus polyhedrin promoter. The 5' end of the TNF-beta cDNA was fused to the honey-bee prepromelittin signal sequence on the baculovirus vector. Insect [Spodoptera frugiperda (Sf9)] cells infected with the recombinant baculovirus secreted high levels of recombinant human TNF-beta into the culture medium. The amount of TNF-beta secreted by the Sf9 cells was estimated to be 28 micrograms of TNF-beta/ml of culture medium at 60-72 h post infection. The secreted human TNF-beta was a 22.5 kDa polypeptide which was glycosylated. Amino acid sequencing of the N-terminus of the recombinant human TNF-beta purified from the infected Sf9-cell culture confirmed that the secreted product was indeed human TNF-beta. This demonstrates that the honey-bee prepromelittin signal sequence was efficiently recognized and accurately cleaved in the Sf9 insect cells. The insect-derived TNF-beta exhibited a high cytotoxic activity similar to that of the native human TNF-beta when assessed by cytotoxic assays using murine L929 cells. Thus the insect baculovirus expression vector can be used for the production of abundant quantities of biologically active, glycosylated human TNF-beta protein.