gebhart/patrepeval huggingface dataset:
The Downstream Transcriptional Enhancer, Ed, Positively Regulates Mouse Igκ Gene Expression and Somatic Hypermutation (2008)

The mouse Igkappa locus has three known transcriptional enhancers: the matrix association region/intronic enhancer, the 3' enhancer (E3'), and the further downstream enhancer (Ed). Previous studies have shown that both matrix association region/intronic and E3' enhancers are required for maximal gene rearrangement of the locus, and that E3' is also required for maximal expression and somatic hypermutation (SHM). To functionally elucidate Ed in vivo, we generated knockout mice with a targeted germline deletion of Ed. Ed deleted homozygous mice (Ed-/-) have moderately reduced numbers of Igkappa expressing B cells and correspondingly increased numbers of Iglambda expressing B cells in spleen. Ed-/- mice also have decreased Igkappa mRNA expression in resting and T cell-dependent activated splenic B cells and reduced Igkappa chains in sera. However, our analysis indicates that Igkappa gene rearrangement is normal in Ed-/- mice. In addition, our results show that Ed-/- mice exhibit reduced SHM in the Igkappa gene J-C intronic region in germinal center B cells from Peyer's patches. We conclude that Ed positively regulates Igkappa gene expression and SHM, but not gene rearrangement.
Role of MUC20 overexpression as a predictor of recurrence and poor outcome in colorectal cancer (2013)

Cumulatively, MUC20 may serve as an important predictor of recurrence and poor outcome for CRC patients. MUC20 overexpression could enhance migration and invasion abilities of CRC cells. Translation of its roles into clinical practice will need further investigation and additional test validation.
Hyperlink–affiliation network structure of top web sites: Examining affiliates with hyperlink in Korea (2002)

Abstract This article argues that individual Web sites form hyperlink–affiliations with others for the purpose of strengthening their individual trust, expertness, and safety. It describes the hyperlink–affiliation network structure of Korea's top 152 Web sites. The data were obtained from their Web sites for October 2000. The results indicate that financial Web sites, such as credit card and stock Web sites, occupy the most central position in the network. A cluster analysis reveals that the structure of the hyperlink–affiliation network is influenced by the financial Web sites with which others are affiliated. These findings are discussed from the perspective of Web site credibility.
Development of I-123-labeled amines for brain studies: localization of I-123 iodophenylalkyl amines in rat brain. (1980)

Localization in rat brain of forty iodophenylalkyl amines labeled with I-123 was evaluated in an attempt to develop I-123-labeled amines useful for brain studies. For the amines studied, the highest activity in brain and the brain-to-blood activity ratios ranked p > m > o as related to iodine position on the benzene ring: for alkyl groups the rank order was ..cap alpha..-methylethyl > ethyl > methyl > none; for N additions it was single lipophilic group > H > two lipophilic groups. It is suggested that introduction of a halogen into the ring structure of many amines results in greater concentration of the agent in brain than is seen with the nonhalogenated parent compound. The agent N-isopropyl-p-iodoamphetamine was chosen for further study because, in the rat, it showed high brain activity (1.57%/g) and brain-blood ratio (12.6) at 5 min.
Carrageenan Is a Potent Inhibitor of Papillomavirus Infection (2006)

Certain sexually transmitted human papillomavirus (HPV) types are causally associated with the development of cervical cancer. Our recent development of high-titer HPV pseudoviruses has made it possible to perform high-throughput in vitro screens to identify HPV infection inhibitors. Comparison of a variety of compounds revealed that carrageenan, a type of sulfated polysaccharide extracted from red algae, is an extremely potent infection inhibitor for a broad range of sexually transmitted HPVs. Although carrageenan can inhibit herpes simplex viruses and some strains of HIV in vitro, genital HPVs are about a thousand-fold more susceptible, with 50% inhibitory doses in the low ng/ml range. Carrageenan acts primarily by preventing the binding of HPV virions to cells. This finding is consistent with the fact that carrageenan resembles heparan sulfate, an HPV cell-attachment factor. However, carrageenan is three orders of magnitude more potent than heparin, a form of cell-free heparan sulfate that has been regarded as a highly effective model HPV inhibitor. Carrageenan can also block HPV infection through a second, postattachment heparan sulfate-independent effect. Carrageenan is in widespread commercial use as a thickener in a variety of cosmetic and food products, ranging from sexual lubricants to infant feeding formulas. Some of these products block HPV infectivity in vitro, even when diluted a million-fold. Clinical trials are needed to determine whether carrageenan-based products are effective as topical microbicides against genital HPVs.
Reassortment and Insertion-Deletion Are Strategies for the Evolution of Influenza B Viruses in Nature (1999)

The evolution of influenza B viruses is poorly understood. Reassortment of influenza B viruses in nature as a means of genetic variation has not been considered to be a major contributor to their evolution. However, the current practice of assigning evolutionary relationships by antigenic analysis of the hemagglutinin of influenza B viruses would fail to detect reassortants. In this study, influenza B viruses isolated within the past 10 years from sites in the United States and China were studied by nucleotide sequencing of the hemagglutinin and neuraminidase genes and construction of phylogenetic trees to assess evolutionary relationships. A group of viruses represented by B/Houston/1/92 possess a hemagglutinin derived from a B/Yamagata/16/88-like strain and a neuraminidase derived from a B/Victoria/2/87-like strain. A second reassortment event between the hemagglutinin of a B/Yamagata/16/88-like virus closely related to the B/Beijing/184/93 strain and the neuraminidase of a B/Victoria/2/87-like strain is represented by a single virus, B/Memphis/3/93. The neuraminidase of the reassortant viruses is most closely related to that of B/Victoria/2/87-like viruses currently circulating in Nanchang, China. A pattern of insertions and deletions in the hemagglutinin and the neuraminidase of different strains of influenza B viruses is observed. Reassortment plays a role in the evolution of influenza B viruses and may necessitate a change in the methods used to assess and identify new influenza viruses.
Human leukocyte interferon: production, purification to homogeneity, and initial characterization. (1979)

A method of fractionating proteins by high-performance liquid partition chromatography has been developed and used for isolation and purification to homogeneity of one of the species of human leukocyte interferon. The homogeneous interferon exhibited a sharp peak on high-performance liquid chromatography and a single narrow band on sodium dodecyl sulfate/polyacrylamide gel electrophoresis in the presence of 2-mercaptoethanol. Extraction of the gel gave a single sharp peak of antiviral activity coinciding with the protein band. The specific activity of pure interferon was found to be 2--4 X 10(8) units/mg, based on amino acid analysis. The molecular weight is 17,500--18,000.
Double-Blind, Placebo-Controlled Trial of Reformulated Azelastine Nasal Spray in Patients with Seasonal Allergic Rhinitis (2009)

The results of this study showed efficacy both with original azelastine nasal spray and with the reformulated nasal spray and a clear dose-response difference between the 1- and 2-spray dosages.
Escherichia coli formylmethionine tRNA: mutations in GGGCCC sequence conserved in anticodon stem of initiator tRNAs affect initiation of protein synthesis and conformation of anticodon loop. (1987)

We have generated mutants of Escherichia coli formylmethionine initiator tRNA in which one, two, and all three G X C base pairs in the GGGCCC sequence in the anticodon stem are changed to those found in E. coli elongator methionine tRNA. Overproduction of the mutant tRNAs using M13 recombinants as an expression vector and development of a one-step purification scheme allowed us to purify, characterize, and analyze the function of the mutant tRNAs. After aminoacylation and formylation, the function of mutant formylmethionyl tRNAs was analyzed in an MS2 RNA-directed in vitro protein-synthesizing system, in AUG-dependent ribosomal P site binding, and in initiation factor binding. The mutant tRNAs show progressive loss of activity in initiation, the mutant with all three G X C base pairs substituted being the least active. The mutations affect binding to the ribosomal P site. None of the mutations affects binding to initiation factor 2. We also show that there is a progressive increase in accessibility of phosphodiester bonds in the anticodon loop of the three mutants to S1 nuclease, such that the cleavage pattern of the mutant with all three G X C base-pair changes resembles that of elongator tRNAs. These results are consistent with the notion that the contiguous G X C base pairs in the anticodon stem of initiator tRNAs impart on the anticodon loop a unique conformation, which may be important in targeting the initiator tRNA to the ribosomal P site during initiation of protein synthesis.
The Nucleus of the Intervertebral Disc from Development to Degeneration1 (2000)

The nucleus of the intervertebral disc in humans shows the most dramatic changes with age of any cartilaginous tissue. It originates from the notochord. In the foetus and infant, the nucleus contains actively dividing and biosynthetically active notochordal cells. The proteoglycans and other matrix components produced have a high osmotic pressure, imbibe water and maintain a hydrated structure which, though it has little mechanical strength, has a high swelling pressure which maintains disc turgor. In some species, the notochordal cells and the mucoid nucleus pulposus persist throughout adult life. However by about 4 yr of age in humans, the notochordal cells have disappeared to be replaced by those of chondrocytic appearance but of unknown origin. These cells continue to produce proteoglycans but also synthesize significant amounts of collagen. The nucleus becomes firmer and less hydrated and loses its transparent appearance. The cell density of the adult nucleus is very low with cells occupying less than 0.5% of tissue volume; each cell thus has to turn over and maintain a large domain of extracellular matrix. The density of living cells decreases with age, possibly because of problems with nutrient supply to this large avascular tissue. Proteoglycan concentration also falls, and nucleus hydration decreases markedly, the disc discolours and in many cases clefts and fissures form. In most adults, the disc nucleus degenerates eventually to a stage where it can no longer fulfil its mechanical role.
Interaction with the Phosphotyrosine Binding Domain/Phosphotyrosine Interacting Domain of SHC Is Required for the Transforming Activity of the FLT4/VEGFR3 Receptor Tyrosine Kinase (1996)

The FLT4 gene encodes two isoforms of a tyrosine kinase receptor, which belongs to the family of receptors for vascular endothelial growth factor. As the result of an alternative processing of primary mRNA transcripts, the long isoform differs from the short isoform by an additional stretch of 65 amino acid residues located at the C terminus and containing three tyrosine residues, Tyr1333, Tyr1337, and Tyr1363. Only the long isoform is endowed with a transforming capacity in fibroblasts. We show that this activity is related to the capacity of the tyrosine 1337-containing sequence to interact with the phosphotyrosine binding domain of the SHC protein. This demonstrates that a functional property of this newly described domain includes relay of mitogenic signals. In addition, it shows that the same receptor can mediate different functions through the optional binding of the phosphotyrosine binding domain and that the alternative use of this domain is sufficient to direct the signal toward different pathways.
The CTX-M-15-producing Escherichia coli diffusing clone belongs to a highly virulent B2 phylogenetic subgroup (2008)

The CTX-M-15-producing E. coli diffusing clone is associated with a high level of antibiotic resistance and with high virulence, showing that, under certain selective pressures, the previously observed trade-off between resistance and virulence may not apply.
Stereochemical Constraints on the Substrate Specificity of Phosphotriesterase (1998)

A series of achiral, chiral, and racemic mixtures of paraoxon analogues containing various combinations of methyl, ethyl, isopropyl, or phenyl substituents were synthesized as probes of the stereochemical constraints within the active site of phosphotriesterase. The kinetic constants for these paraoxon analogues with the enzyme varied significantly with the size of substituents surrounding the phosphorus center. These results indicate that binding and catalysis depend significantly on the relative size and orientation of the two subsites that must accommodate the coordination of the alkyl or aryl substituents within the enzyme active site. Individual enantiomers of paraoxon analogues were also synthesized and the stereochemical specificity for phosphotriesterase determined. In general, the kinetic constants, kcat and kcat/Km, for the (-)-enantiomers of these phosphotriesters were 1-2 orders of magnitude greater than the (+)-enantiomers. In every case, the preferred isomer is of the SP-configuration. For example, the kcat/Km for SP-(-)-ethyl phenyl p-nitrophenyl phosphate is 1.8 x 10(8) M-1 s-1 but is only 1.8 x 10(6) M-1 s-1 for the RP-(+)-isomer. These results suggest that one enantiomer is positioned for hydrolysis more favorably than the other enantiomer. The inactivation of acetylcholinesterase with the same series of organophosphate nerve agents was also measured. The stereoisomer that more rapidly inactivates human acetylcholinesterase is hydrolyzed more slowly than its enantiomer by the phosphotriesterase.
In Vitro Cytotoxicity Induced by the Bufadienolides 1α,2α-Epoxyscillirosidine and Lanceotoxin B on Rat Myocardial and Mouse Neuroblastoma Cell Lines (2019)

Consumption of bufadienolide-containing plants are responsible for many livestock mortalities annually. Bufadienolides are divided into two groups; non-cumulative bufadienolides and cumulative bufadienolides. Cumulative bufadienolides are referred to as neurotoxic, as the chronic intoxication with this type of bufadienolide results in a paretic/paralytic syndrome known as 'krimpsiekte'. The <i>in vitro</i> cytotoxicity of a non-cumulative bufadienolide, 1α,2α-epoxyscillirosidine, and a cumulative bufadienolide, lanceotoxin B, were compared using the MTT ((3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction) assay after exposing rat myocardial (H9c2) and mouse neuroblastoma (Neuro-2a) cell lines. The effect of these two bufadienolides on cell ultrastructure was also investigated using transmission electron microscopy (TEM). H9c2 cells exhibited greater cytotoxicity when exposed to 1α,2α-epoxyscillirosidine, compared to lanceotoxin B. In contrast, Neuro-2a cells were more susceptible to lanceotoxin B. The EC<sub>50</sub> (half maximal effective concentration) of lanceotoxin B exposure of Neuro-2a cells for 24⁻72 h ranged from 4.4⁻5.5 µM compared to EC<sub>50</sub>s of 35.7⁻37.6 µM for 1α,2α-epoxyscillirosidine exposure of Neuro-2a cells over the same period. 1α,2α-Epoxyscillirosidine induced extensive vacuolization in both cell types, with swollen RER (rough endoplasmic reticulum) and perinuclear spaces. Lanceotoxin B caused swelling of the mitochondria and sequestration of cytoplasmic material within autophagic vesicles. These results corroborate the notion that cumulative bufadienolides are neurotoxic.
CMOS-Based Monolithic Controllers for Smart Sensors Comprising Micromembranes and Microcantilevers (2007)

This paper presents design considerations and implementations of monolithic controllers for smart sensors that make use of micromachined structures such as micromembranes and microcantilevers. Five control techniques are reviewed, and the classic control technique is selected for the design of the controllers. The circuit implementations of an analog proportional controller and a digital proportional-integral-derivative controller are described in detail. The first controller is used for controlling the microhotplate (micromembrane) temperature of a monolithic metal-oxide gas sensor array. The second controller is used for controlling the microcantilever deflection of a monolithic atomic force microscope. The controllers and microsensors are fabricated in standard 0.8-mum CMOS technology combined with post-CMOS micromachining. Chemical measurements and contact-mode imaging are performed to confirm the excellent performance of these monolithic controllers
Organizing Single-Walled Carbon Nanotubes on Gold Using a Wet Chemical Self-Assembling Technique (2000)

We provide a wet chemical approach for organizing randomly tangled single-walled carbon nanotubes (SWCNTs) on gold surfaces. The as-grown nanotubes were first chemically cut into short pipes and thiol-derivatized at the open ends. The ordered assembly of SWCNTs was made by their spontaneous chemical adsorption to gold via Au−S bonds. Tapping mode atomic force microscopy (AFM) images clearly show that the nanotubes have been organized on gold, forming a self-assembled monolayer structure with a perpendicular orientation. The adsorption kinetics of the nanotubes was very slow in comparison to conventional alkanethiols. The adsorption rate varied inversely with tube length. The nanotubes tend to form bundles as the adsorption propagates, following a "nucleation adsorption mechanism". This work demonstrates that "giant" carbon nanotubes can be assembled on Au surfaces using wet chemistry similar to that exploited for "small" organic self-assembling species. We believe that assembled nanotube arrays will provide wide possibilities for applications.
Pulmonary Nodules: Estimation of Malignancy at Thin-Section Helical CT—Effect of Computer-aided Diagnosis on Performance of Radiologists (2006)

Use of the CAD system significantly (P = .009) improved the diagnostic performance of radiology residents for assessment of the malignancy of pulmonary nodules; however, it did not improve that of board-certified radiologists.
Spontaneous and stimulated Raman scattering in long low loss fibers (1978)

This paper considers the problem of forward Raman scattering process in a single transverse mode fiber. Both pump wave depletion and spontaneous scattering are considered in the analysis. Analytic solutions of the governing differential equations are obtained. We examine the conditions under which a nondepleted pump approximation is valid. Expressions are derived for the maximum fiber loss and the minimum fiber length which allow significant pump to Stokes wave conversion. It is shown that for a given fiber length there is an optimal pumping power, or at a given pump power there is an optimal fiber length that yields maximum first-order Stokes power output. Good agreement with published experimental results in the threshold power prediction is obtained.
The Effect of Stress Level, Amino Acid Formula, and Nitrogen Dose on Nitrogen Retention in Traumatic and Septic Stress (1987)

Eighty-seven patients were entered into a randomized, prospective, double-blind, six-center study to evaluate the effect of amino acid loading and a formula that was branched chain enriched (50%) on nitrogen retention in metabolic stress. The patients had varying levels of metabolic stress (0-3) after major surgery, polytrauma, or surgical sepsis. The study was isocaloric and isonitrogenous and lasted for 7 days. The patients received either a standard amino acid formula (SAA) (Travasol) or a 50% branched chain enriched formula that was equimolar, leucine, isoleucine, and valine (MAA) (Travasol + Branchamin concentrate) at a dose of 1.0-2.0 g/kg/day in a fixed ratio with 114 glucose calories per gram of nitrogen administered. The nitrogen retention was proportionate to the nitrogen (and, therefore, caloric) load in both groups. The MAA group, however, had better nitrogen retention, reached nitrogen equilibrium at a lower dose of amino acids, and had less urinary nitrogen excretion per gram of nitrogen administered. Since the groups were isonitrogenous and the calorie to nitrogen ratios were fixed, it appears that nitrogen equilibrium in surgical stress is proportionate to the amino acid load over a range of 0.05-0.4 g/kg/day of nitrogen; and that MAA are more efficient at inducing nitrogen retention and a reduction in urea excretion. These effects on nitrogen retention were more significant at level 2 stress or greater. At these higher stress levels, a dose of 2 +/- 0.2 g/kg/day of MAA seemed most efficient in promoting nitrogen retention.
Stimulatory Autoantibodies to the PDGF Receptor in Systemic Sclerosis (2006)

Stimulatory autoantibodies against PDGFR appear to be a specific hallmark of scleroderma. Their biologic activity on fibroblasts strongly suggests that they have a causal role in the pathogenesis of the disease.
Metabolic Profiling Directly from the Petri Dish Using Nanospray Desorption Electrospray Ionization Imaging Mass Spectrometry (2013)

Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) imaging mass spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1, Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofilm showed a wide range of compounds that this bacterium uses for the dissimilatory reduction of extracellular metal oxides, including riboflavin, iron-bound heme and heme biosynthetic intermediates, and the siderophore putrebactin.
Structural Requirements of Lipid A Responsible for the Functions: A Study with Chemically Synthesized Lipid A and Its Analogues1 (1985)

To confirm the revised lipid A structure of Escherichia coli and to establish the structure responsible for its functions, biological activities of the synthetic compounds based on the presented structure of E. coli lipid A were investigated. Compound 506, 2-deoxy-6-O-(2-deoxy-2-[(R)-3-dodecanoyloxytetradecanoylamino]-3-O [(R)3-tetradecanoyloxytetradecanoyl]-beta-D-glucopyranosyl]-3-O-[(R) -3-hydroxytetradecanoyl]-2-[(R)-3-hydroxytetradecanoylamino]-alpha -D-glucopyranose 1,4'-bis(phosphate), exhibited activities identical to those of natural E. coli lipid A in eliciting Shwartzman reaction and tests on lethality, pyrogenicity, interferon- and tumor necrosis factor-inducing activities as well as in B-cell activating activity and Limulus amebocyte lysate gelating activity. With the exception of the Shwartzman reaction the monophosphorylated synthetic compounds at either the 1 or 4' position showed slightly lower activities than the compound with the bisphosphorylated compound (Compound 506). The compound without the phosphate group showed no or only very weak activities. The structural requirements for each activity (i.e. binding position and composition of fatty acids and presence of phosphate groups) are discussed taking into account the results of previous investigations.