gebhart/patrepeval huggingface dataset:
A human transmembrane protein-tyrosine-phosphatase, PTP zeta, is expressed in brain and has an N-terminal receptor domain homologous to carbonic anhydrases. (1992)

Protein-tyrosine-phosphatases (PTPases, EC 3.1.3.48) play a crucial role in the regulation of protein tyrosine phosphorylation. Recently, it was found that the PTPase gene family exhibits a large variety of different functional domains associated with the PTPase catalytic domains. In this paper, we report the complete cDNA sequence of a human transmembrane PTPase, PTP zeta, isolated from fetal brain cDNA libraries. The deduced amino acid sequence of human PTP zeta is composed of a putative signal peptide of 19 amino acids, a very large extracellular domain of 1616 amino acids, a transmembrane peptide of 26 amino acids, and a cytoplasmic domain of 653 amino acids. The extracellular portion of human PTP zeta contains two striking structural features: the N-terminal 280-amino acid sequence that is homologous to carbonic anhydrases (carbonate hydro-lyase, EC 4.2.1.1), and a sequence of 1048 amino acids without a cysteine residue. While it is unlikely that the carbonic anhydrase-like domain of PTP zeta has any carbonic anhydrase activity, its three-dimensional structure may be quite similar to that of carbonic anhydrases, a structure that appears ideal for binding a small soluble ligand. The cytoplasmic portion of human PTP zeta contains two repeated PTPase-like domains, which, when expressed in Escherichia coli, had PTPase activity in vitro. Mutational analyses indicate that only the membrane-proximal PTPase domain is catalytically active. Reverse transcription-polymerase chain reaction analyses indicate that human PTP zeta is highly expressed in a glioblastoma cell line.
Vesicle adsorption on SiO2 and TiO2: Dependence on vesicle size (2002)

Kinetics of vesicle adsorption on SiO2 and TiO2 surfaces was investigated for vesicle sizes from 25 to 200 nm. On SiO2, nonruptured vesicles are adsorbed up to a critical coverage, Θc, after which spontaneous rupture and bilayer formation occurs in qualitatively the same manner for all vesicle sizes. On TiO2, adsorption of nonruptured vesicles continues up to saturation. A comparison between the kinetics at low coverages on SiO2 and TiO2, where intact vesicles adsorb on both surfaces, reveals that the vesicles on SiO2 are more flattened than nonruptured vesicles adsorbed on TiO2, indicating a stronger vesicle-surface interaction on SiO2.
Absorption of doxycycline from a controlled release pellet formulation: The influence of food on bioavailability (1990)

A three-way crossover study was performed to compare the bioavailability of a new pelletised doxycycline product administered either with food or without food and a reference product taken without food. Four different methods were used to calculate pharmacokinetic parameters from the data. The sums of squares, Akaike's Information Criterion (AIC), and the ranges for the parameters obtained were used for comparison. Good fits to the data were obtained when all four methods were used, each with a lag time. The two compartment open model was the most efficient method for describing the data. The one compartment open model was the least efficient, particularly with respect to predicting the peak concentration of doxycycline in plasma. All the models gave similar rank order results with respect to bioavailability differences between the three treatments. Analysis of the data by different methods suggests that pelletised doxycycline is bioequivalent to the reference product when taken in the absence of food. A standardized feeding regimen affected the rate, but not extent of absorption of doxycycline from the pelletised formulation.
Interferon-regulatory factor 1 is an immediate-early gene under transcriptional regulation by prolactin in Nb2 T cells. (1990)

The pituitary peptide hormone prolactin (Prl) is a potent inducer of Nb2 T lymphoma cell proliferation. To analyze the early genetic response to the mitogenic signals of Prl, a cDNA library was constructed from Nb2 T cells stimulated for 4 h with Prl and the protein synthesis inhibitor cycloheximide. Of 26 distinct clones isolated by differential screening, one clone, designated c25, exhibited extremely rapid but transient kinetics of induction by Prl and superinduction by Prl plus cycloheximide. Run-on transcription analysis indicated that c25 gene transcription was induced greater than 20-fold within 30 to 60 min of Prl stimulation. Surprisingly, DNA sequence analysis of c25 cDNA revealed that this Prl-inducible early-response gene is the rat homolog of the mouse transcription factor interferon-regulatory factor 1 (IRF-1), sharing 91% coding sequence similarity with mouse IRF-1. At the protein level, rat IRF-1 shares 97% and 92% homology with mouse IRF-1 and human IRF-1, respectively, suggesting that this molecule has been functionally conserved throughout evolution. Our studies show that the gene for IRF-1 is an immediate-early gene in Prl-stimulated T cells, which suggests that IRF-1 is a multifunctional molecule. In addition to its role in regulating growth-inhibitory interferon genes, IRF-1 may, therefore, also play a stimulatory role in cell proliferation. The gene for IRF-1 is one of the earliest genes known to be transcriptionally regulated by Prl.
Cross-track and proposed multi-frequency SAR interferometry: comparisons with optical holographic interferometry (2002)

This article points out that the principles of the synthetic aperture radar (SAR) interferometer operating in the cross-track mode and the proposed multi-frequency SAR interferometer are equivalent respectively to those of multi-source and multi- wavelength optical holographic interferometry. Expressions are derived to describe the loss of coherence by various factors. Including the temporally and spatially random as well as deterministic changes in complex reflectivity; and their relative importance is discussed for both the SAR interferometers. The similarities of the decorrelation effect between the SAR interferometers and laser speckle are mentioned. The authors also show that the extracted phase from the cross-track SAR interferometer data does not faithfully represent the range-varying surface height variation. The effect is due to the fact that the holographic principle is applied only to azimuth direction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Universal optical transmission features in periodic and quasiperiodic hole arrays (2008)

We investigate the influence of array order in the optical transmission properties of subwavelength hole arrays, by comparing the experimental spectral transmittance of periodic and quasiperiodic hole arrays as a function of frequency. We find that periodicity and long-range order are not necessary requirements for obtaining enhanced and suppressed optical transmission, provided short-range order is maintained. Transmission maxima and minima are shown to result, respectively, from constructive and destructive interference at each hole, between the light incident upon and exiting from a given hole, and surface plasmon polaritons (SPPs) arriving from individual neighboring holes. These SPPs are launched along both illuminated and exit surfaces, by diffraction of the incident and emerging light at the neighboring individual subwavelength holes. By characterizing the optical transmission of a pair of subwavelength holes as a function of hole-hole distance, we demonstrate that a subwavelength hole can launch SPPs with an efficiency up to 35%, and with an experimentally determined launch phase phi = pi /2, for both input-side and exit-side SPPs. This characteristic phase has a crucial influence on the shape of the transmission spectra, determining transmission minima in periodic arrays at those frequencies where grating coupling arguments would instead predict maxima.
Plasma Uric Acid and the Risk of Type 2 Diabetes in a Chinese Community (2007)

These findings suggest a modest positive association between plasma uric acid concentration and the incidence of type 2 diabetes in Chinese individuals. The association between hyperuricemia and diabetes was partly mediated through the metabolic syndrome.
Linkage Disequilibria and the Site Frequency Spectra in the su(s) and su(wa) Regions of the Drosophila melanogaster X Chromosome (2000)

Over the last decade, surveys of DNA sequence variation in natural populations of several Drosophila species and other taxa have established that polymorphism is reduced in genomic regions characterized by low rates of crossing over per physical length. Parallel studies have also established that divergence between species is not reduced in these same genomic regions, thus eliminating explanations that rely on a correlation between the rates of mutation and crossing over. Several theoretical models (directional hitchhiking, background selection, and random environment) have been proposed as population genetic explanations. In this study samples from an African population (n = 50) and a European population (n = 51) were surveyed at the su(s) (1955 bp) and su(w(a)) (3213 bp) loci for DNA sequence polymorphism, utilizing a stratified SSCP/DNA sequencing protocol. These loci are located near the telomere of the X chromosome, in a region of reduced crossing over per physical length, and exhibit a significant reduction in DNA sequence polymorphism. Unlike most previously surveyed, these loci reveal substantial skews toward rare site frequencies, consistent with the predictions of directional hitchhiking and random environment models and inconsistent with the general predictions of the background selection model (or neutral theory). No evidence for excess geographic differentiation at these loci is observed. Although linkage disequilibrium is observed between closely linked sites within these loci, many recombination events in the genealogy of the sampled alleles can be inferred and the genomic scale of linkage disequilibrium, measured in base pairs between sites, is the same as that observed for loci in regions of normal crossing over. We conclude that gene conversion must be high in these regions of low crossing over.
Calix[4]arene Ligands with Phosphorus-Containing Groups Tethered at the Upper Rim (1999)

The preparation and coordinative properties of two upper-rim functionalized calixarenes, 5,17-bis(tert-butyl)-11,23-bis(diethoxyphosphinomethoxy)-25,26,27,28-tetrakis(2-ethoxyethoxy)calix [4] arene (4) and 5,17-bis(tert-butyl)-11,23-bis(diphenylphosphinomethyl)-25,26,27,28-tetrakis(2-ethoxyethoxy)calix[4]arene (6) are presented. Diphosphine 6 was oxidized by air to the corresponding di(phosphine oxide) 7. The molecular structure of 7·2CHCl3 was elucidated by X-ray crystallography: C78H94O10P2·2CHCl3, a = 16.313 (5) Å, b = 16.553(5) Å, c = 17.068(6) Å, α = 108.04(2)°, β = 93.13(2)°, γ = 100.27(2)°, Z = 2. The calixarene matrix displays a pinched cone conformation, with the two tBu-phenoxy rings of the macrocycle lying almost perpendicular (interplanar angle 84.7°) and the other two phenoxy rings making an angle of 20.9°. Reaction of 6 with 2 equiv of [AuCl(SC4H8)] (SC4H8 = tetrahydrothiophene) in CH2Cl2 afforded the digold complex 6·(AuCl)2 (8). Reaction of 6 with [RuCl2(p-cymene)]2 resulted in formation of the dinuclear complex 6·[RuCl2(p-cymene)]2 (9) while the rhodium complex 6·[RhCl(norbornadiene)]2 (10) was formed by reaction of 6 with [RhCl(norbornadiene)]2. Complex 10 catalyzes hydroformylation of styrene (CO/H2 = 1, P = 40 bar, 70 °C, styrene/Rh ∼ 585) in the presence of NEt3, from which linear and branched aldehydes were obtained in a 9:91 ratio. Diphosphite 4 was found to be suitable for chelate formation; thus [Pd(η3-MeC3H4)(thf)2]BF4 (thf = tetrahydrofuran) reacts with 4 to yield the mononuclear complex [4·{Pd(η3-MeC3H4)}]BF4 (11), where the metal is located at the mouth of the cavity. All complexes were characterized by elemental analyses and by 1H, 13C, and 31P NMR spectroscopy.
<title>Optical and acoustical monitoring of material processing with Q-switched Nd:YAG and excimer laser radiation</title> (1994)

Characterization of the effects of the interaction between short laser pulses and a material has been made in the conditions of surface cleaning and surface micro-machining. Fast heating of the target surface results in a pressure wave that propagates inside the sample and a shock wave in the surrounding gas medium. By monitoring the energy of the shock wave using a microphone and a piezoelectric transducer, it is possible to relate the ablation rate to the observed signals. Experiments have been made using Nd:YAG and KrF lasers. At high fluences, in particular at 1.06 micrometers , gas breakdown drastically alters the process conditions and disperse the recorded data. By using an additional optical beam deflection technique, we have determined the range of validity for monitoring of the process using simple detection devices.
Ethernet Wrapper: extension of the TCP Wrapper (2002)

One of the popular network security programs supporting host access control is the 'TCP Wrapper' (Venema, 1992). TCP Wrapper is a software-only system and many computers connected to the Internet are using it. However, TCP Wrapper does 'IP address-based' access control. The IP address is not such a reliable source when authenticating a host. We point out two possible attacks against the TCP Wrapper, propose a new way to prevent them, and describe the prototype implementation, Ethernet Wrapper. By adding an Ethernet address check, we augmented the TCP Wrapper. The test results showed that Ethernet Wrapper can prevent such attacks effectively.
A Herpes Simplex Virus Type 1 Variant which Fails to Synthesize Immediate Early Polypeptide VmwIE63 (1987)

We report the isolation of a variant (X2D) of herpes simplex virus type 1 strain 17 which has a deletion of 5 X 10(6) mol. wt. in the long unique and long inverted repeat regions, such that one copy of the immediate early (IE) gene 1 and two unique open reading frames coding for polypeptides of 20K and 22K are deleted. The mutant X2D synthesizes reduced levels of VmwIE110, and also apparently fails to synthesize VmwIE63, at both the protein and RNA levels, despite there being no apparent deletion in the coding or controlling regions of the IE2 gene. X2D also fails to synthesize the thymidine kinase polypeptide but exhibits normal growth characteristics in tissue culture.
[Idiopathic autoimmune hemolytic anemia successfully treated with danazol]. (1990)

A 50 year old female suffered from idiopathic autoimmune hemolytic anemia. She was initially treated with prednisolone, and anemia was improved moderately. However, maintenance of Hb value was difficult with the decreased dosage of prednisolone. She was subsequently administered danazol, and anemia was completely improved. It is worth to use danazol for the treatment of the patient of autoimmune hemolytic anemia who is refractory to prednisolone therapy.
Formation and Structure of Gels and Fibrils from Glucagon (1969)

Glucagon in acid solution aggregates to produce gels and ultimately fibrils of β‐chains. The kinetics of the aggregation have been followed by viscometry, and are found to exhibit a sigmoidal profile with a long lag phase, associated with the formation of nuclei for polymerisation. This has been demonstrated by the elimination of the lag when fresh solutions are seeded with a preformed glucagon gel. The aggregation is promoted by salt, increased pH (within the acid range of solubility) and increased temperature up to 30°. The addition of 5% of dioxan completely inhibits the aggregation. The interaction has evidently a large hydrophobic driving force, and is opposed by coulombic repulsion. The latter effect can be minimised by acetylation of the amino groups, when the polymerisation is greatly accelerated. This also occurs when only the terminal amino group is blocked by carbamylation. By contrast esterification of the carboxyl groups completely prevents aggregation. At the working pH this does not involve a change in charge, and thus appears to be a specific steric effect. Optical rotatory dispersion shows no conformational difference between native glucagon and the derivatives. The transition from a gel to a fibrillar form is promoted by salt and increased temperature. A possible explanation for the appearance of the fibrillar form in the electron microscope is that it contains tubular structures 50–70 Å in diameter, with about 40 extended chains around the circumference lying in antiparallel manner along the axis.
Preparation of the extracellular domain of the rabbit prolactin receptor expressed in Escherichia coli and its interaction with lactogenic hormones. (1994)

The cDNA of the extracellular domain of the rabbit prolactin receptor (rbPRLR-ECD) was cloned in the prokaryotic expression vector pTrc99A to enable its expression in Escherichia coli after induction with isopropyl-1-thio-beta-D-galactopyranoside. The bacterially expressed rbPRLR-ECD protein, contained within the refractile body pellet, was solubilized in 4.5 M urea, refolded, and purified on a Q-Sepharose column by stepwise elution with NaCl. The bioactive monomeric fraction was eluted in 0.05 M NaCl, yielding 15-20 mg/8 liters of induced culture. The purified protein was > 98% homogeneous, as shown by SDS-polyacrylamide gel electrophoresis in the presence or absence of reducing agent and by chromatography on a Superdex column. Its molecular mass was 25 kDa as determined by SDS-polyacrylamide gel electrophoresis in the absence of reducing agent and 22 kDa as determined by gel filtration. Binding experiments revealed remarkable differences between rabbit and porcine prolactins (PRLs) and the other tested lactogenic hormones. Gel filtration was used to determine the stoichiometry of the rbPRLR-ECD interaction with ovine, rabbit, and porcine PRLs, with human growth hormone and its truncated des-7 analogue, and with bovine placental lactogen (bPL) and des-13-bPL. The formation of only 1:1 complexes was indicated, except with bPL, for which a 2:1 complex was detected. Identical stoichiometry was also obtained using excess radiolabeled rbPRLR-ECD in gel filtration experiments. Interaction of 125I-labeled ovine PRL with rbPRLR-ECD secreted into conditioned medium by rbPRLR-ECD cDNA-transfected COS 7 cells also indicated formation of 1:1 molar complexes. Despite the differences in binding potency and stoichiometries of the interaction with rbPRLR-ECD, all seven tested hormones were biologically active in inducing PRL receptor-mediated casein synthesis in explants of rabbit mammary gland. We therefore propose that the formation of the 1:2 complexes with soluble rbPRLR-ECD is not predictive of biological activity of the different lactogenic hormones.
K-ras mutation: early detection in molecular diagnosis and risk assessment of colorectal, pancreas, and lung cancers--a review. (2000)

Multiple genomic alterations are involved in the development of most human cancers. They include alterations in oncogenes, tumor suppressor genes, DNA mismatch repair and excision repair genes. Genetic testing for susceptibility has been a part of the management of patients with well-defined but uncommon hereditary cancers in which certain susceptible gene mutations are determined in the germ line. However, a molecular diagnostic approach to sporadic cancers, which comprise the vast majority of malignant tumors in human beings, is still under development. One of the best characterized tumor-related genes is K-ras, which somatically mutates in several types of sporadic human cancers. Since mutations of this gene occur exclusively in three hot spots (codons 12, 13 and 61), and are frequently detected and well characterized in colorectal, pancreas and lung cancers, molecular diagnosis and susceptibility (risk) assessment targeting K-ras mutations are being developed. For this purpose, sample collection methods that reflect the state of the entire affected organ are important. Clinical samples used for molecular diagnosis and risk assessment include stool and lavage fluid, pancreatic and duodenal juices, and sputum and lavage fluids for colorectal, pancreas and lung cancers, respectively. The reported incidence of K-ras mutations detected in these samples ranges from 7% to 80% for colorectal cancers, 25% to 87% for pancreatic cancers, and 25% to 48% for lung cancers. Incidence of mutations clearly depends on the sensitivity of the method for detecting the mutant K-ras allele, as well as the nature and the quality of the clinical samples. Various methods including plaque hybridization, dot blot hybridization, combined PCR and RFLP or SSCP, and sensitive PCR have been used, and they exhibited high specificity (75 to 100%) in detecting mutations. Molecular analysis is demonstrating promise in assessing susceptibility to, or risk of developing, sporadic cancers.
Transcriptional regulation of a Bacillus subtilis dipeptide transport operon (1991)

The Bacillus subtilis dciA operon, which encodes a dipeptide transport system, was induced rapidly by several conditions that caused the cells to enter stationary phase and initiate sporulation. The in vivo start point of transcription was mapped precisely and shown to correspond to a site of transcription initiation in vitro by the major vegetative form of RNA polymerase. Post-exponential expression was prevented by a mutation in the spo0A gene (whose product is a known regulator of early sporulation genes) but was restored in a spo0A abrB double mutant. This implicated AbrB, another known regulator, as a repressor of dciA. In fact, purified AbrB protein bound to a portion of the dciA promoter region, protecting it against DNase I digestion. Expression of dciA in growing cells was also repressed independently by glucose and by a mixture of amino acids; neither of these effects was mediated by AbrB.
Anti-inflammation: Direct Physical Association and Functional Antagonism Between Transcription Factor NF-KB and the Glucocorticoid Receptor (1995)

Glucocorticoids are widely used clinically as anti-inflammatory and immunosuppressive agents. Of all the pharmaceutical approaches to the treatment of asthma, glucocorticoids are undoubtedly the most potent. These effects of glucocorticoids result, to a great extent, from their ability to inhibit cellular release of inflammatory mediators and cytokines. Despite their widespread use, the molecular mechanisms by which glucocorticoids exert their effects are not clearly defined. Glucocorticoids activate genes by interacting with the glucocorticoid receptor (GR) which binds to glucocorticoid response elements (GREs) in the target genes. However, inhibition of gene expression by glucocorticoids cannot always be adequately explained by binding of GR to regulatory sequences in the target genes. Earlier work with the collagenase gene showed that steroids could inhibit gene transcription by interference with the binding of the transcription factors Fos and Jun to the AP-1 site. However, this mechanism does not appear to be the case for inhibition of expression of the interleukin-6 (IL-6) gene and of additional cytokine genes by steroids. We established that activation of the IL-6 gene expression by IL-1 requires both the NF-IL6 and the NF-κB sites in the IL-6 promoter. Since the transcription factor NF-κB has been implicated in the upregulation of multiple inflammation-associated genes, it seemed conceivable that GR might interact with NF-κB to downregulate cytokine gene expression. Our studies indicate that GR physically interacts with the p65 subunit of NF-κB; this interaction may explain the impaired transactivation potential of both proteins in intact cells. In cotransfection experiments, activation of the IL-6 promoter by p65 and NF-IL6 was annulled by the synthetic glucocorticoid dexamethasone, possibly through interactions of GR with p65. Conversely, activation of the mouse mammary tumor virus promoter by GR was inhibited by coexpression of p65. The reciprocal functional antagonism between p65 and GR provides a framework for the opposing actions of inflammatory mediators and steroids.