gebhart/patrepeval huggingface dataset:
Synthetic receive aperture imaging with phase correction for motion and for tissue inhomogeneities. II. Effects of and correction for motion (1992)

For Pt.I see ibid., vol.39, p.489 (1992). The effects of tissue/transducer motion and artifacts from adaptive focusing on synthetic receive aperture (SRA) imaging are explored using experiment, simulation, and theory. The impact of these issues on the selection of SRA subaperture geometry is discussed, and a technique to address this problem is demonstrated. The results indicate that SRA with phase correction holds promise in improving ultrasonic image quality.
Both intrathymic and peripheral selection modulate the differential expression of V beta 5 among CD4+ and CD8+ T cells. (1992)

Murine T cells expressing V beta 5 are characterized by (a) intrathymic deletion in the presence of I-E and products of endogenous mouse mammary tumor viruses, and (b) a greater representation in CD8+ relative to CD4+ peripheral T cells, thought to be due to more efficient intrathymic positive selection on class I rather than class II major histocompatibility complex antigens. We have engineered mice that are transgenic for a rearranged gene encoding a V beta 5+ beta chain of the T cell receptor for antigen. Deletion is not predicted in I-E- V beta 5+ transgenic mice, and until the age of 2 wk, the CD4/CD8 ratio of peripheral T cells is > 3:1 and indistinguishable between transgenic and nontransgenic mice. Transgenic mice then show a rapid, age-dependent decline in the ratio of CD4+ to CD8+ T cells in the lymphoid periphery, reaching a low of 1:10 by 7 mo of age. Furthermore, the percent of peripheral CD4+ cells that express the transgene drops with age, reaching a low of about 60% at 7 mo, while the percent of CD8+ cells that express V beta 5 remains greater than 95% at all ages. The lymphoid periphery is implicated in this selection against CD4+ V beta 5+ T cells as it occurs more rapidly in thymectomized transgenic mice, and can be delayed in mice whose peripheral T cells are replaced by recent thymic emigrants after depletion by in vivo treatment with anti-Thy-1 antibodies. These results indicate that the relative expression of V beta 5 in T cell subsets can be influenced not only intrathymically in I-E+ V beta 5+ transgenic mice, but also by events in the periphery, in the absence of I-E expression.
Organization of the SUC Gene Family in Saccharomyces (1983)

The SUC gene family of yeast (Saccharomyces) includes six structural genes for invertase (SUC1 through SUC5 and SUC7) found at unlinked chromosomal loci. A given yeast strain does not usually carry SUC+ alleles at all six loci; the natural negative alleles are called suc0 alleles. Cloned SUC2 DNA probes were used to investigate the physical structure of the SUC gene family in laboratory strains, commercial wine strains, and different Saccharomyces species. The active SUC+ genes are homologous. The suc0 allele at the SUC2 locus (suc2(0) in some strains is a silent gene or pseudogene. Other SUC loci carrying suc0 alleles appear to lack SUC DNA sequences. These findings imply that SUC genes have transposed to different chromosomal locations in closely related Saccharomyces strains.
Comparative tumorigenicity and DNA methylation in F344 rats by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone and N-nitrosodimethylamine. (1986)

The tumorigenic activities and DNA methylating abilities in F344 rats of the tobacco specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and the structurally related nitrosamine N-nitrosodimethylamine (NDMA) were compared. Groups of 30 male rats were given 60 s.c. injections of 0.0055 mmol/kg of either NNK or NDMA over a 20-week period (total dose, 0.33 mmol/kg). The experiment was terminated after 104 weeks. The numbers of rats with tumors were as follows for NNK and NDMA, respectively: liver, 10 and 6; lung 13 and 0; and nasal cavity, 6 and 1. NNK was significantly more tumorigenic than was NDMA toward the lung (P less than 0.01) and nasal cavity (P less than 0.05). Groups of rats were treated with a single s.c. injection of 0.39 mmol/kg or 0.055 mmol/kg of NNK or NDMA and the levels of 7-methylguanine and O6-methylguanine were measured in liver, lung, and nasal mucosa 1-48 h after treatment. In liver and lung, levels of 7-methylguanine and O6-methylguanine in DNA were 3-22 times (P less than 0.001) greater in NDMA treated rats than in NNK treated rats. Levels of methylation induced by NDMA and NNK in the nasal mucosa were similar. The results of this study demonstrate that NNK is a more potent tumorigen than NDMA in the F344 rat and suggest that DNA methylation alone does not account for its strong tumorigenicity in rat lung and nasal mucosa.
Elastography - the movement begins (2000)

The advent of real-time ultrasound in the 1970s, together with a growing interest in tissue characterization, led to a number of investigators using the nature of tissue motion to distinguish healthy from diseased tissue. Our group at the (then) Ultrasonics Institute demonstrated the use of phase methods for detecting very small tissue motions, using natural stimuli. The method could also be applied in the lag (autocorrelation) domain to directly measure the amount of deformation to high accuracy. This method was also applied to measuring the amount of dilatation of blood vessels using both conventional and intravascular ultrasound. A basic limitation of these techniques was the poor spatial resolution, and quasistatic methods soon replaced this method of measuring tissue deformation. However, a new way of assessing the health of tissues had been established.
hrpL activates Erwinia amylovora hrp gene transcription and is a member of the ECF subfamily of sigma factors (1995)

hrpL of Erwinia amylovora Ea321 encodes a 21.7-kDa regulatory protein, similar to members of the ECF (extra cytoplasmic functions) subfamily of eubacterial RNA polymerase sigma factors. hrpL is a single-gene operon in complementation group VI of the E. amylovora hrp gene cluster. Its product is required by Ea321 to elicit the hypersensitive response (HR) and to cause disease. HrpL controls the expression of five independent hrp loci, including hrpN, which encodes harpin, a proteinaceous elicitor of the HR. hrpL is environmentally regulated, and its expression is affected by hrpS, another regulatory gene of the hrp gene cluster of E. amylovora. pCPP1078, a multicopy plasmid carrying hrpL, is able to restore HR-eliciting ability to hrpS mutants. A conserved motif was identified upstream of the hrpI and hrpN operons, which are transcriptionally regulated by hrpL. This conserved motif shares a high degree of similarity with other biochemically defined or putative ECF-dependent promoter sequences, including sequences upstream of Streptomyces coelicolor dagA P2, Pseudomonas aeruginosa algD, Pseudomonas syringae pv. syringae 61 hrpZ, and P. syringae pv. tomato avrD. In spite of the similarity between the hrpL genes of E. amylovora and P. syringae 61, no functional cross-complementation was observed.
The rat T-cell differentiation marker RT6.1 is more polymorphic than its alloantigenic counterpart RT6.2. (1988)

Utilizing allotype-specific antibodies to immunoprecipitate RT6.2 from DA.6B rat lymphocyte lysates, we have shown this antigen recently to be composed of two related, non-glycosylated polypeptides with apparent molecular weights (MW) of 24,000 and 26,000 (reducing conditions), which evidently are anchored in the cell membrane by covalent linkage to phosphatidylinositol. The present report shows that RT6.1 allotype-specific antibodies precipitate a more complex pattern of bands from LEW.6A rat lymphocyte lysates. These consist of an endo-F-resistant RT6.2-like 25/27,000 MW doublet (reducing conditions) as well as at least five additional endo-F-sensitive, endo-H-resistant polypeptides of 30,000, 32,000, 33,000, 34,000, 35,000 MW. Endo-F treatment seems to convert the additional higher to the lower molecular weight forms. In contrast to the endo-F-resistant 25/27,000 MW doublet, the higher MW forms of RT6.1 partly bind to lentil lectin and concanavalin A (Con A). Two-dimensional electrophoretic analyses (NEPHGE/SDS-PAGE) reveal similar patterns of charge heterogeneity of the lower and higher MW forms of RT6.1. Neuraminidase treatment does not affect the pIs of the lower MW forms but shifts the pIs of the higher MW forms to those of the lower ones. All forms of RT6.1 evidently employ the covalent linkage to phosphatidylinositol for membrane anchorage. Identical patterns of molecular forms--the doublet for RT6.2, the polymorphic pattern for RT6.1--are observed upon immunoprecipitation of the alloantigens from the lysates of corresponding series of inbred strains of rats with both allotype-specific antibodies and a polyclonal rabbit serum recognizing a common determinant on both alloantigens.
HIV-induced loss of CD44 expression in monocytic cell lines. (1993)

We have found that HIV-1 infection of monocytic cell lines results in a new adhesion phenotype. Whereas uninfected cells grow as single cell suspensions, HIV-infected cells grow as large aggregates. When the expression of adhesion molecules was investigated, CD44 was almost completely depleted from the surface of HIV-infected cells. Immunoprecipitation with mAb confirmed the loss of CD44 from the surface of infected cells. In addition, loss of surface CD44 was not due to formation of internal complexes or release into the culture supernatant. Soluble CD44 was not detected in culture supernatant from HIV-infected cells. Northern blot analysis showed an altered RNA pattern in HIV-infected cells. The high molecular mass CD44 RNA (7.0 kb) was lost from infected cells, and the low molecular mass CD44 RNA (1.2 kb) remained. We have previously shown that anti-CD44 mAb induces homotypic adhesion in CD44+ cell lines. In this report, we show that homotypic adhesion of the HIV-infected cells occurs through a different mechanism than anti-CD44 mAb-induced aggregation. The homotypic adhesion in infected cells was CD18-mediated, but anti-CD44 mAb-induced homotypic adhesion in uninfected cells was CD18-independent. The change in adhesion phenotype and the loss of CD44 from the surface of HIV-1-infected monocytic cells are discussed in terms of their potential implications in cell-to-cell transmission of HIV.
Pulsed photothermal radiometry of port-wine-stain lesions (1993)

Pulsed photothermal radiometry is used to map the heat deposition in human skin after a short laser pulse. It uses an IR (HgCdTe) detector for a rapid noncontact measurement of the skin surface temperature based on the blackbody emission in the 8-12-microm spectrum. The heat deposited by the laser pulse in the superficial epidermis causes an immediate temperature jump, and the heat deposited in basal epidermal melanin and deep port wine stains diffuses to the surface before detection. The time course of the surface temperature T(z = 0, t), indicates the initial spatial distribution of heat, T(z, t = 0), deposited by the laser.
Analysis of the biological effects of a non-thermal plasma on Saccharomyses cerevisiae (2012)

The cellular and the molecular responses of eukaryotic yeast (Saccharomyces cerevisiae) to a non-thermal plasma at atmospheric pressure are analyzed. A plasma device with a dielectric barrier discharge is used in order to understand the mechanisms of the plasma action on eukaryotic microbes. When the yeast cells are exposed to a plasma (at a 2-mm distance) and then cultured on a YPD (yeast extract, peptone, and dextrose) - agar plate, the number of surviving cells is reduced over exposure time. More than a 50% reduction in number is observed after two exposures of 5 minutes’ duration. In addition, very small whitish colonies appear after the two exposures. The microscopic analysis indicates that the yeast cells treated with this plasma exposure have rough and shrunken shapes in comparison to the oval shapes with smooth surfaces of the control cells. The profile of proteins analyzed by using 2-dimentional electrophoresis demonstrates that the level of proteins with high molecular weights is increased in plasma-treated cells.
Synaptic plasticity in rat subthalamic nucleus induced by high‐frequency stimulation (2003)

The technique of deep brain stimulation (DBS) has become a preferred surgical choice for the treatment of advanced Parkinson's disease. The subthalamic nucleus (STN) is presently the most promising target for such DBS. In this study, whole-cell patch-clamp recordings were made from 46 STN neurons in rat brain slices to examine the effect of high-frequency stimulation (HFS) of the STN on glutamatergic synaptic transmission in STN neurons. HFS, consisting of trains of stimuli at a frequency of 100 Hz for 1 min, produced three types of synaptic plasticity in 17 STN neurons. First, HFS of the STN induced short-term potentiation (STP) of evoked postsynaptic current (EPSC) amplitude in four neurons. STP was associated with a reduction in the EPSC paired-pulse ratio, suggesting a presynaptic site of action. Second, HFS of the STN generated long-term potentiation (LTP) of EPSC amplitude in eight neurons. Although the EPSC paired-pulse ratio was reduced transiently in the first 2 min following HFS, ratios measured 6-20 min after HFS were unchanged from control. This suggests that LTP is maintained by a postsynaptic mechanism. Third, HFS produced long-term depression (LTD) of EPSC amplitude in five STN neurons. LTD was associated with a significant increase in EPSC paired-pulse ratios, indicating a presynaptic site of action. These results suggest that HFS can produce long-term changes in the efficacy of synaptic transmission in the STN. HFS-induced synaptic plasticity might be one mechanism underlying the effectiveness of DBS in the STN as a treatment of advanced Parkinson's disease.
Identification of high-affinity binding sites for the insulin sensitizer rosiglitazone (BRL-49653) in rodent and human adipocytes using a radioiodinated ligand for peroxisomal proliferator-activated receptor gamma. (1998)

A radioiodinated ligand, [125I]SB-236636 [(S)-(-)3-[4-[2-[N-(2-benzoxazolyl)-N-methylamino]ethoxy]3-[125I]i odo phenyl]2-ethoxy propanoic acid], which is specific for the gamma isoform of the peroxisomal proliferator activated receptor (PPARgamma), was developed. [125I]SB-236636 binds with high affinity to full-length human recombinant PPARgamma1 and to a GST (glutathione S-transferase) fusion protein containing the ligand binding domain of human PPARgamma1 (KD = 70 nM). Using this ligand, we characterized binding sites in adipose-derived cells from rat, mouse and humans. In competition experiments, rosiglitazone (BRL-49653), a potent antihyperglycemic agent, binds with high affinity to sites in intact adipocytes (IC50 = 12, 4 and 9 nM for rat, 3T3-L1 and human adipocytes, respectively). Binding affinities (IC50) of other thiazolidinediones for the ligand binding domain of PPARgamma1 were comparable with those determined in adipocytes and reflected the rank order of potencies of these agents as stimulants of glucose transport in 3T3-L1 adipocytes and antihyperglycemic agents in vivo: rosiglitazone > pioglitazone > troglitazone. Competition of [125I]SB-236636 binding was stereoselective in that the IC50 value of SB-219994, the (S)-enantiomer of an alpha-trifluoroethoxy propanoic acid insulin sensitizer, was 770-fold lower than that of SB-219993 [(R)-enantiomer] at recombinant human PPARgamma1. The higher binding affinity of SB-219994 also was evident in intact adipocytes and reflected its 100-fold greater potency as an antidiabetic agent. The results strongly suggest that the high-affinity binding site for [125I]SB-236636 in intact adipocytes is PPARgamma and that the pharmacology of insulin-sensitizer binding in rodent and human adipocytes is very similar and, moreover, predictive of antihyperglycemic activity in vivo.
Rapid Deposition of Triangular Silver Nanoplates on Planar Surfaces:  Application to Metal-Enhanced Fluorescence (2005)

A simple and rapid wet-chemical technique for the deposition of silver triangles on conventional glass substrates, which alleviates the need for lithography, has been developed. The technique is based on the seed-mediated cetyltrimethylammonium-bromide-directed growth of silver triangles on glass surfaces, where smaller spherical silver seeds that were attached to the surface were subsequently converted and grown into silver triangles in the presence of a cationic surfactant and silver ions. The size of the silver triangles was controlled by sequential immersion of silver seed-coated glass substrates into a growth solution and by the duration time of immersion. Atomic force microscopy studies revealed that the size of the silver triangles ranged between 100 and 500 nm. Interestingly, these new surfaces are a significant improvement over traditional silver island films for applications in metal-enhanced fluorescence. A routine 16-fold enhancement in emission intensity was typically observed, for protein-immobilized indocyanine green, with a relatively very low loading density of silver triangles on the glass surface.
Revised Bethesda Guidelines for Hereditary Nonpolyposis Colorectal Cancer (Lynch Syndrome) and Microsatellite Instability (2004)

Hereditary nonpolyposis colorectal cancer (HNPCC), also known as Lynch syndrome, is a common autosomal dominant syndrome characterized by early age at onset, neoplastic lesions, and microsatellite instability (MSI). Because cancers with MSI account for approximately 15% of all colorectal cancers and because of the need for a better understanding of the clinical and histologic manifestations of HNPCC, the National Cancer Institute hosted an international workshop on HNPCC in 1996, which led to the development of the Bethesda Guidelines for the identification of individuals with HNPCC who should be tested for MSI. To consider revision and improvement of the Bethesda Guidelines, another HNPCC workshop was held at the National Cancer Institute in Bethesda, MD, in 2002. In this commentary, we summarize the Workshop presentations on HNPCC and MSI testing; present the issues relating to the performance, sensitivity, and specificity of the Bethesda Guidelines; outline the revised Bethesda Guidelines for identifying individuals at risk for HNPCC; and recommend criteria for MSI testing.
Inferring Protein Function from Structure (2003)

This chapter contains sections titled: The Importance of Predicting Function from Structure Protein Functions What Information Can Be Obtained from Three-Dimensiona Protein Structures? Relationship Between Structure and Function Assigning Function from Structure Structural Genomics at Work-Prediction of Function in Earnest Conclusion References
Light‐Triggered Molecular Devices: Photochemical Switching Of optical and Electrochemical Properties in Molecular Wire Type Diarylethene Species (1995)

Abstract Organic photochromic systems represent a starting point for the elaboration of light‐triggered molecular switching devices. The novel bispyridinium and bispyridine compounds 1 2+ and 6 were synthesized as their uncyclized isomers from 3,5‐dibromo‐2‐methylthiophene in overall yields of 43 and 44%, respectively. The diarylethene photochromes 2 and 10 – 13 , substituted with electron donors and acceptors, were prepared from 5‐methylthiophene‐2‐carboxaldehyde in 21–32% overall yield. All of the compounds were found to exhibit pronounced photochromic properties. Irradiation with UV light resulted in essentially complete photocyclization of the open forms to the intensely coloured closed isomers which could, in turn, be reconverted back to the open state with visible light of γ&gt;600 nm. The absorption maxima of the described compounds in their closed forms are shifted far towards, and even into, the near‐IR region. Whereas no thermochromic properties were observed for the open isomers, the rates of thermal decolouration of the cyclized forms was found to be highly dependent on the nature of the substituents on the thiophene rings. It was demonstrated that reversible photochemical interconversion between the two photochromic states could be used to effectively switch a number of physical properties. Thus, the molecules 1 2+ and 12 represent two kinds of redox switches, the former in reduction and the latter in oxidation, in which electron conduction is switched on in the closed state and off in the open state. Compound 12 may also be considered to be a photoswitchable analogue of tetrathiafulvalene type substances. On the other hand, compound 2 displays a marked increase in nonlinear optical activity on conversion from the open to the closed form. Such systems are prototypes of photoswitchable molecular wires where electron conduction and push‐pull interaction can be reversibly modulated by an external stimulus, namely, irradiation by light.
Apoptosis in ocular disease: a molecular overview (1996)

Apoptosis is a form of genetically programmed cell death that can be induced by a variety of different stimuli. It is often referred to as a form of cellular suicide. Typically, apoptosis is characterized by the condensation and shrinkage of the cellular nucleus and cytoplasm, followed by the complete fragmentation of the cell and subsequent phagocytosis of the debris by surrounding cells. Although important during development, and also for maintaining homeostasis in some adult tissues, apoptosis can also be associated with disease processes. Recent laboratory studies indicate that apoptosis is a mechanism of cell death in several important ocular diseases including glaucoma, retinitis pigmentosa, cataract formation, retinoblastoma, retinal ischemia, and diabetic retinopathy. This review summarizes the results of these studies and provides a brief description of some of the key molecules that are involved in the genetic regulation of apoptosis. It is possible that a complete understanding of how these molecules function may someday lead to new treatment options aimed at blocking the death of cells in a variety of ocular diseases.
Toxicity of Haemophilus pleuropneumoniae for porcine lung macrophages, peripheral blood monocytes, and testicular cells (1981)

Strain CM5 of Haemophilus pleuropneumoniae was toxic for porcine lung macrophages in minimum doses of 10(6) colony-forming units per ml and for peripheral blood monocytes at 10(7) colony-forming units per ml. The organism was not toxic for porcine testicular cells in a concentration of 10(8) colony-forming units per ml. Filtered sterile culture supernatant diluted 10(0), 10(-1), and 10(-2) was toxic for porcine pulmonary lavage cells. In dilutions of 10(0) and 10(-1), culture supernatant was toxic for peripheral blood monocytes, and at 10(0) it was toxic for testicular cells. Toxicity associated with bacterial cells was sensitive to heating (60 degrees, 60 min), whereas that of the culture supernatant was heat stable (100 degrees C, 15 min). Swine convalescent serum neutralized supernatant toxicity in dilutions of greater than or equal to 1:320. The findings promote the understanding of the pathogenesis of pleuropneumonia in swine caused by H. pleuropneumoniae.