gebhart/patrepeval huggingface dataset:
Reduction in Viscosity of Cystic Fibrosis Sputum in Vitro by Gelsolin (1994)

Obstruction of airways by viscous sputum causes lung damage in patients with cystic fibrosis (CF). Sputum samples from CF patients were shown to contain filamentous actin. Human plasma gelsolin, a protein that severs actin filaments, rapidly decreased the viscosity of CF sputum samples in vitro. Gc globulin and deoxyribonuclease I, proteins that sequester monomeric actin but do not sever actin filaments, were less efficient than gelsolin in diminishing sputum viscosity. These results suggest that gelsolin may have therapeutic potential as a mucolytic agent in CF patients.
Distinct organ-specific metastatic potential of individual breast cancer cells and primary tumors (2005)

We used bioluminescence imaging to reveal patterns of metastasis formation by human breast cancer cells in immunodeficient mice. Individual cells from a population established in culture from the pleural effusion of a breast cancer patient showed distinct patterns of organ-specific metastasis. Single-cell progenies derived from this population exhibited markedly different abilities to metastasize to the bone, lung, or adrenal medulla, which suggests that metastases to different organs have different requirements. Transcriptomic profiling revealed that these different single-cell progenies similarly express a previously described "poor-prognosis" gene expression signature. Unsupervised classification using the transcriptomic data set supported the hypothesis that organ-specific metastasis by breast cancer cells is controlled by metastasis-specific genes that are separate from a general poor-prognosis gene expression signature. Furthermore, by using a gene expression signature associated with the ability of these cells to metastasize to bone, we were able to distinguish primary breast carcinomas that preferentially metastasized to bone from those that preferentially metastasized elsewhere. These results suggest that the bone-specific metastatic phenotypes and gene expression signature identified in a mouse model may be clinically relevant.
Positive regulation of glutamate biosynthesis in Bacillus subtilis (1989)

Nitrogen source regulation of glutamate synthase activity in Bacillus subtilis occurs at the level of transcription of the gltA and gltB genes, which encode the two subunits of the enzyme. We show here that transcription of gltA requires the product of gltC, a gene whose transcription is divergent from that of gltA and whose transcriptional control sequences overlap those of gltA. gltC mutants had decreased, aberrantly regulated levels of glutamate synthase activity and decreased gltA mRNA. The gltC gene product could act in trans to complement both these defects. In addition, the gltC gene product repressed its own transcription. The DNA sequence of gltC revealed that its putative product is very similar to a number of positive regulatory proteins from gram-negative bacteria (the LysR family).
Asymmetric hydrogenation of .beta.-keto carboxylic esters. A practical, purely chemical access to .beta.-hydroxy esters in high enantiomeric purity (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric hydrogenation of .beta.-keto carboxylic esters. A practical, purely chemical access to .beta.-hydroxy esters in high enantiomeric purityRyoji Noyori, Takeshi Ohkuma, Masato Kitamura, Hidemasa Takaya, Noboru Sayo, Hidenori Kumobayashi, and Susumu AkutagawaCite this: J. Am. Chem. Soc. 1987, 109, 19, 5856–5858Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://doi.org/10.1021/ja00253a051RIGHTS & PERMISSIONSArticle Views9601Altmetric-Citations629LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (399 KB) Get e-Alerts Get e-Alerts
Automated annotation of coral reef survey images (2012)

With the proliferation of digital cameras and automatic acquisition systems, scientists can acquire vast numbers of images for quantitative analysis. However, much image analysis is conducted manually, which is both time consuming and prone to error. As a result, valuable scientific data from many domains sit dormant in image libraries awaiting annotation. This work addresses one such domain: coral reef coverage estimation. In this setting, the goal, as defined by coral reef ecologists, is to determine the percentage of the reef surface covered by rock, sand, algae, and corals; it is often desirable to resolve these taxa at the genus level or below. This is challenging since the data exhibit significant within class variation, the borders between classes are complex, and the viewpoints and image quality vary. We introduce Moorea Labeled Corals, a large multi-year dataset with 400,000 expert annotations, to the computer vision community, and argue that this type of ecological data provides an excellent opportunity for performance benchmarking. We also propose a novel algorithm using texture and color descriptors over multiple scales that outperforms commonly used techniques from the texture classification literature. We show that the proposed algorithm accurately estimates coral coverage across locations and years, thereby taking a significant step towards reliable automated coral reef image annotation.
Effect of site-directed mutagenesis of conserved aspartate and arginine residues upon farnesyl diphosphate synthase activity. (1993)

All polyprenyl synthases catalyze the condensation of the allylic substrate, isopentenyl diphosphate, with a specific homoallylic diphosphate substrate. Polyprenyl synthases from Homo sapiens, Ratus rattus, Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, and Erwinia herbicola contain two conserved "aspartate-rich domains" (Ashby, M.N., and Edwards, P.A. (1992) J. Biol. Chem. 267, 4128-4136). In order to determine the importance of these domains in catalysis, the conserved aspartates or arginines in domains I and II of rat farnesyl diphosphate synthase were individually mutated to glutamate or lysine, respectively. The putative "active site" arginine (Brems, D.N., Breunger, E., and Rilling, H. C. (1981) Biochemistry 20, 3711-3718) was mutated to lysine. Each mutant enzyme was overexpressed in E. coli and purified to apparent homogeneity. Detailed kinetic analyses of the wild type and mutant enzymes indicated that mutagenesis of Asp104, Asp107, Arg112, Arg113, and Asp243 resulted in a decreased Vmax of approximately 1000-fold compared to wild type. However, no significant change in the Km values for either the isopentenyl diphosphate or geranyl diphosphate substrate were observed. The results strongly suggest that these amino acids, and to a lesser extent Asp244, are involved in either the condensation of isopentenyl diphosphate and geranyl diphosphate to form farnesyl diphosphate and/or the release of the farnesyl diphosphate product from farnesyl diphosphate synthase. The conservation of these amino acid residues in different enzymes from several species suggests that these domains play a similar role in other polyprenyl synthases.
Treatment of Leukemic (L-1210) Mice with Double-Stranded Polyribonucleotides (1969)

The BDF1 mice when injected with 106 L-1210 ascites leukemia cells die in 8 days. When treated from days 1 to 7 with 5 mg/kg of polyinosinic acid : polycytidylic acid (1:1) they have a 25-40% increase in life span. The material is effective when given i.p. or s.c., but not by oral route, and the component polyribonucleotides are also inactive. The activity of the double-stranded complex in prolonging survival is not due to in vitro cytotoxic or cytostatic activity. It is proposed that the activity of poly I:poly C is due to the induction in the host on interferon which then slows the multiplication of the L-1210 cells in vivo.
The yeast SNF2/SWI2 protein has DNA-stimulated ATPase activity required for transcriptional activation. (1993)

The yeast SNF2 (SWI2) protein functions with SNF5, SNF6, SWI1, and SWI3 in the transcriptional activation of many differently regulated genes. These proteins appear to facilitate activation by gene-specific regulatory proteins. SNF2 is highly conserved among eukaryotes and defines a family of proteins with similarity to helicases and nucleic acid-dependent NTPases. Here, we present genetic and biochemical evidence that SNF2 has DNA-stimulated ATPase activity. Mutations in the nucleoside triphosphate (NTP)-binding motif and other conserved motifs impair SNF2 function. Swapping experiments with another member of this family indicate that the helicase-related domains are functionally interchangeable. Finally, bacterially expressed SNF2 protein has ATPase activity that is stimulated by double-stranded DNA, and mutation of the NTP-binding site abolishes this activity. Deletion analysis shows that the helicase-like region of SNF2 is necessary, but not sufficient, for transcriptional activation.
Platelet-Vessel Wall Interactions in Hemostasis and Thrombosis (2010)

Abstract Platelets are essential mediators of the physiologic process of hemostasis and pathologic thrombosis. While platelets do not interact with vascular walls under normal conditions, vascular injury or inflammation result in a coordinated series of events including platelet adhesion, aggregation, and promotion of coagulation. In this review, we describe the primary mechanisms involved in these responses in various vascular beds of both macro- and microvessels, and outline key unresolved aspects of these important interactions. Table of Contents: Introduction / General Characteristics of Platelets / Platelet Adhesion to Vascular Walls / Platelet Aggregation / Platelet Recruitment and Blood Coagulation / Arterial, Venous, and Microvascular Hemostasis/Thrombosis / Summary
Superantigens anergize cytokine production but not cytotoxicity in vivo. (1994)

We have investigated the effect of the superantigen staphylococcal enterotoxin A (SEA) on the balance between T-cell response and non-responsiveness in T-cell receptor (TcR) V beta 3 transgenic mice. One injection of SEA resulted in a substantial activation of TcR V beta 3+ cells, whereas T cells from mice injected with repeated doses of SEA displayed a diminished response to a subsequent in vitro challenge. The reduced responsiveness became apparent when SEA was injected multiple times with short intervals. Proliferation and cytokine production in anergized T cells were severely reduced when stimulated with SEA in vitro, whereas cytotoxic T lymphocyte (CTL) activity remained unaffected. The dichotomy between these functions was examined in vitro with respect to different T-cell subsets. The total number of CD4+ T cells was reduced in the hyporesponsive spleens, compatible with cell deletion. The remaining CD4+ TcR V beta 3+ T cells showed anergy of all tested functions and did not respond to exogenous interleukin-2 (IL-2). In contrast, there was an expansion of CD8+ TcR V beta 3+ T cells with an intact cytotoxic activity. The in vitro proliferation and production of cytokines in the CD8+ compartment was impaired, but could be partially restored in the presence of exogenously added IL-2. Analysis of the cytokine response to SEA in vivo showed that IL-2 and tumour necrosis factor (TNF) were mainly produced by CD4+ T cells, while interferon-gamma (IFN-gamma) was predominantly released by CD8+ T cells. Induction of anergy resulted in a reduction of IL-2 and TNF mRNA levels, frequencies of producing cells as well as serum protein content. In contrast, there was only a moderate influence on the IFN-gamma level in vivo. The results suggest that SEA-induced hyporesponsiveness involves CD4+ cell deletion and a failure to produce cytokines in the remaining CD4+ T-cell compartment, while IFN-gamma production and cytotoxicity in the CD8+ T-cell compartment stay relatively intact.
Novel surface tagging technology for selection of complex proliferation‐controlled mammalian cell phenotypes (2001)

Regulated overexpression of the cyclin dependent kinase inhibitor p27 enables biphasic production processes which consist of a nonproducing expansion phase followed by an extended proliferation-arrested production phase. During the growth-arrested production phase proliferation-competent mutants emerge as a consequence of genetic drift and strong counterselection. Here, we evaluate the use of cell surface markers for ex vivo selection of growth-arrested phenotypes by magnetic or FACS-mediated cell sorting. Multigene metabolic engineering resulted in a Chinese hamster ovary- (CHO) derived cell line CHO-SS101(5), which expresses the model product protein SEAP (secreted alkaline phosphatase), the human cyclindependent kinase inhibitor p27, and a membrane-anchored multidomain surface marker Hook in a tricistronic tetracycline-repressible manner. In the absence of tetracycline in the cell culture medium, p27 mediated a G1-phase-specific cell-cycle arrest of CHO-SS101(5) and resulted in a fivefold increase in SEAP production compared to proliferation-competent control cells. Concomitant expression of Hook enabled FACS- or magnetic-based selection of CHO-SS101(5) cells from various mixed populations. Surface selection of engineered cells will likely become important for biopharmaceutical manufacturing and for in vivo maintenance of treated cells in gene therapy and tissue engineering.
Distributed display approach using PHMD with infrared camera (2003)

The aim of this study is to explore the feasibility of multiple display environment technology in the real world. In this paper, the wearable projector, with an infrared camera and light source, is used in combination with retro-reflective screens. The visible image and infrared light are projected to the screen and reflected back to the user's eye and the infrared camera. The screen location and the user's fingertip position are calculated using image processing to enable the interaction. Several examples or demonstrations have been constructed to show the usage of this configuration. The screen functions as both the visible screen and the high-gain infrared marker at the same time. Owing to high-reflection gain of retro-reflective screens, a small, lightweight projector can be used. Also, the high contrast between the screen and the other environmental object in the captured infrared image decreases the difficulty of image processing.
Bioreactors mediate the effectiveness of tissue engineering scaffolds (2002)

We hypothesized that the mechanically active environment present in rotating bioreactors mediates the effectiveness of three-dimensional (3D) scaffolds for cartilage tissue engineering. Cartilaginous constructs were engineered by using bovine calf chondrocytes in conjunction with two scaffold materials (SM) (benzylated hyaluronan and polyglycolic acid); three scaffold structures (SS) (sponge, non-woven mesh, and composite woven/non-woven mesh); and two culture systems (CS) (a bioreactor system and petri dishes). Construct size, composition [cells, glycosaminoglycans (GAG), total collagen, and type-specific collagen mRNA expression and protein levels], and mechanical function (compressive modulus) were assessed, and individual and interactive effects of model system parameters (SM, SS, CS, SM*CS and SS*CS) were demonstrated. The CS affected cell seeding (higher yields of more spatially uniform cells were obtained in bioreactor-grown than dish-grown 3-day constructs) and subsequently affected chondrogenesis (higher cell numbers, wet weights, wet weight GAG fractions, and collagen type II levels were obtained in bioreactor-grown than dish-grown 1-month constructs). In bioreactors, mesh-based scaffolds yielded 1-month constructs with lower type I collagen levels and four-fold higher compressive moduli than corresponding sponge-based scaffolds. The data imply that interactions between bioreactors and 3D tissue engineering scaffolds can be utilized to improve the structure, function, and molecular properties of in vitro-generated cartilage.
The Roles of Intrahepatic Vα14+ Nk1.1+ T Cells for Liver Injury Induced By Salmonella Infection in Mice (1999)

To investigate the roles of intrahepatic T cells in liver injury after Salmonella infection, we examined serum alanine transaminase (ALT), histopathology, and bacterial numbers in liver after infection with Salmonella choleraesuis strain 31N-1 in mice genetically lacking TCRalpha beta+, CD4(+), CD8(+), or NK1.1(+)T cells with C57BL/6 background. In control (+/+) mice, serum ALT reached a peak level by day 7 after an intraperitoneal inoculation of 2 x 10(6) CFU Salmonella choleraesuis 31N-1. In TCR-beta-/- mice, liver injury, as assessed by serum ALT level and histological examination, was significantly suppressed on day 7 after Salmonella infection but the numbers of bacteria in liver did not differ from those in normal mice, suggesting that alpha beta T cells are responsible for liver injury induced by Salmonella infection. To further determine which subsets in alpha beta T cells are important for the liver injury, we compared serum ALT level in mice genetically lacking CD4, CD8, beta2-microglobulin (beta2m, IAbeta, or Jalpha281 after Salmonella infection. In CD4(-/-) mice, serum ALT was significantly lower in comparison with control mice, but there was no difference in serum ALT levels in CD8(-/-) and IAbeta-/- mice from that in control mice. Notably, serum ALT levels and pathological lesions in liver were significantly decreased in beta2m-/- or Jalpha281(-/-) mice, which lacked in NK1.1(+) T cells bearing TCR Valpha14-Jalpha281 specific for beta2m-associated CD1d, following Salmonella infection. Taken together, it is suggested that alpha beta T cells bearing NK1.1 and CD4 may be main effector cells for liver injury after Salmonella infection.
Identification and molecular characterization of Unc-33-like phosphoprotein (Ulip), a putative mammalian homolog of the axonal guidance-associated unc-33 gene product (1996)

The control of neuritic extension and guidance is critical for the development, maturation, and regeneration of functional neuronal circuits. We identified a neuronal 64-85 kDa phosphoprotein, the expression of which in mouse brain is regulated during development, reaching a peak at approximately 5 d postnatal, when maturation of neurons and synaptic connections is highly active. The amino acid sequence of the mouse protein deduced from its cloned cDNA reveals similarities with that of the neuritic outgrowth- and guidance-related product of the unc-33 gene in Caenorhabditis elegans. The regulation of its phosphorylation in response to nerve growth factor, as well as its localization in neurites and growth cones and at the neuromuscular junction, further indicates that Ulip (for Unc-33-like phosphoprotein) is not only a structural but likely is also a functional mammalian homolog of Unc-33, potentially involved in the control of neuritic outgrowth and axonal guidance.
Paediatric hospital at home: the first year (1996)

Susan Peter and Gerry Torr evaluate the first year of a hospital at home service
Laser irradiation of polyethylene oxide (1989)

The temperature profiles in polyethlene oxide (PEO) films on a soda lime glass substrate heated by scanning a continuous wave (cw) CO2 laser beam are calculated by finite element methods. The volumetric heating rate in the irradiated film depends on the total power of the laser, the radius of the illuminated spot and the scan rate, as well as film parameters such as absorption depth, density, heat capacity, and thermal conductivity (Ref. 1). The absorption depth in PEO at a wavelength of 10.6 μm is less than, but comparable to the thickness of the the PEO film (40 μm). Therefore, heat loss from the bottom surface of the polymer film cannot be neglected. The thickness of the glass substrate is much greater than that of the PEO, so that heat loss from the bottom surface of the glass may be neglected. We use a coordinate system fixed in the material. The beam is parallel to the z axis and scans continuously along the x direction with velocity v (Fig. 1). A time dependent temperature profile on the surface, along the trajectory of the beam center, is shown in Fig. 2. Comparison of calculated temperature profiles and the shapes of PEO spherulites in the zone refined polymer enable us to elucidate melting, nucleation, and recrystallization under laser irradiation (Refs. 2 and 3).
Regulation of mammalian translation factors by nutrients (2002)

Protein synthesis requires both amino acids, as precursors, and a substantial amount of metabolic energy. It is well established that starvation or lack of nutrients impairs protein synthesis in mammalian cells and tissues. Branched chain amino acids are particularly effective in promoting protein synthesis. Recent work has revealed important new information about the mechanisms involved in these effects. A number of components of the translational machinery are regulated through signalling events that require the mammalian target of rapamycin, mTOR. These include translational repressor proteins (eukaryotic initiation factor 4E-binding proteins, 4E-BPs) and protein kinases that act upon the small ribosomal subunit (S6 kinases). Amino acids, especially leucine, positively regulate mTOR signalling thereby relieving inhibition of translation by 4E-BPs and activating the S6 kinases, which can also regulate translation elongation. However, the molecular mechanisms by which amino acids modulate mTOR signalling remain unclear. Protein synthesis requires a high proportion of the cell's metabolic energy, and recent work has revealed that metabolic energy, or fuels such as glucose, also regulate targets of the mTOR pathway. Amino acids and glucose modulate a further important regulatory step in translation initiation, the activity of the guanine nucleotide-exchange factor eIF2B. eIF2B controls the recruitment of the initiator methionyl-tRNA to the ribosome and is activated by insulin. However, in the absence of glucose or amino acids, insulin no longer activates eIF2B. Since control of eIF2B is independent of mTOR, these data indicate the operation of additional, and so far unknown, regulatory mechanisms that control eIF2B activity.