gebhart/patrepeval huggingface dataset:
The identification of aluminium-resistance genes provides opportunities for enhancing crop production on acid soils (2010)

Acid soils restrict plant production around the world. One of the major limitations to plant growth on acid soils is the prevalence of soluble aluminium (Al(3+)) ions which can inhibit root growth at micromolar concentrations. Species that show a natural resistance to Al(3+) toxicity perform better on acid soils. Our understanding of the physiology of Al(3+) resistance in important crop plants has increased greatly over the past 20 years, largely due to the application of genetics and molecular biology. Fourteen genes from seven different species are known to contribute to Al(3+) tolerance and resistance and several additional candidates have been identified. Some of these genes account for genotypic variation within species and others do not. One mechanism of resistance which has now been identified in a range of species relies on the efflux of organic anions such as malate and citrate from roots. The genes controlling this trait are members of the ALMT and MATE families which encode membrane proteins that facilitate organic anion efflux across the plasma membrane. Identification of these and other resistance genes provides opportunities for enhancing the Al(3+) resistance of plants by marker-assisted breeding and through biotechnology. Most attempts to enhance Al(3+) resistance in plants with genetic engineering have targeted genes that are induced by Al(3+) stress or that are likely to increase organic anion efflux. In the latter case, studies have either enhanced organic anion synthesis or increased organic anion transport across the plasma membrane. Recent developments in this area are summarized and the structure-function of the TaALMT1 protein from wheat is discussed.
High levels of expression of the tumor suppressor gene APC during development of the rat central nervous system (1994)

The adenomatous polyposis coli (APC) gene is a tumor suppressor gene that is mutated in human familial adenomatous polyposis, an autosomal dominant condition with predisposition to colorectal carcinoma and brain tumors. Although tumor suppressor genes appear to play a general role in regulating cellular proliferation, the normal biological function of the APC gene product is unknown. In the present study, we cloned fragments of the rat homolog of the APC gene and examined its tissue distribution by Northern blot analysis. These studies demonstrated particularly high levels of APC mRNA in brain. To gain clues to the role of the APC gene in brain function, we examined the neuroanatomical distribution of APC mRNA using in situ hybridization. In the adult, prominent expression of APC mRNA was observed in the olfactory bulb, hippocampus, and cerebellum, with low levels of hybridization in other regions of adult rat brain. In contrast, during embryonic and early postnatal development (1-2 weeks), high levels of APC expression were found throughout the brain and then decreased to adult levels by 6 weeks after birth, except in the olfactory bulb where the high levels of APC mRNA found in development persist in the adult. During development of cortex, cerebellum, and retina, APC mRNA expression was particularly prominent in layers containing newly formed postmitotic neurons, with lower levels observed in the proliferative zones where neurogenesis occurs. The high levels of APC expression from early neurogenesis until late stages of neuronal maturation suggest that APC may contribute to suppressing neuronal proliferation during this period of intense growth.
Soft Robot Arm Inspired by the Octopus (2012)

The octopus is a marine animal whose body has no rigid structures. It has eight arms composed of a peculiar muscular structure, named a muscular hydrostat. The octopus arms provide it with both locomotion and grasping capabilities, thanks to the fact that their stiffness can change over a wide range and can be controlled through combined contractions of the muscles. The muscular hydrostat can better be seen as a modifiable skeleton. Furthermore, the morphology the arms and the mechanical characteristics of their tissues are such that the interaction with the environment (i.e., water) is exploited to simplify control. Thanks to this effective mechanism of embodied intelligence, the octopus can control a very high number of degrees of freedom, with relatively limited computing resources. From these considerations, the octopus emerges as a good model for embodied intelligence and for soft robotics. The prototype of a robot arm has been built based on an artificial muscular hydrostat inspired to the muscular hydrostat of the Octopus vulgaris. The prototype presents the morphology of the biological model and the broad arrangement of longitudinal and transverse muscles. Actuation is obtained with cables (longitudinally) and with shape memory alloy springs (transversally). The robot arm combines contractions and it can show the basic movements of the octopus arm, like elongation, shortening and bending, in water.
Anti-oncogenic activity of signalling-defective epidermal growth factor receptor mutants. (1992)

Overexpression and autocrine activation of the epidermal growth factor receptor (EGF-R) cause transformation of cultured cells and correlate with tumor progression in cancer patients. Dimerization and transphosphorylation are crucial events in the process by which receptors with tyrosine kinase activity generate normal and transforming cellular signals. Interruption of this process by inactive receptor mutants offers the potential to inhibit ligand-induced cellular responses. Using recombinant retroviruses, we have examined the effects of signalling-incompetent EGF-R mutants on the growth-promoting and transforming potential of ligand-activated, overexpressed wild-type EGF-R and the v-erbB oncogene product. Expression of a soluble extracellular EGF-R domain had little if any effect on the growth and transformation of NIH 3T3 cells by either tyrosine kinase. However, both a kinase-negative EGF-R point mutant (HERK721A) and an EGF-R lacking 533 C-terminal amino acids efficiently inhibited wild-type EGF-R-mediated, de novo DNA synthesis and cell transformation in a dose-dependent manner. Furthermore, coexpression with the v-erbBES4 oncogene product in NIH 3T3 cells resulted in transphosphorylation of the HERK721A mutant receptor and reduced soft-agar colony growth but had no effect in a focus formation assay. These results demonstrate that signalling-defective receptor tyrosine kinase mutants differentially interfere with oncogenic signals generated by either overexpressed EGF-R or the retroviral v-erbBES4 oncogene product.
Regulation of Membrane Transport by rab GTPases (2003)

Membrane flow through the cell is a highly dynamic process in which intracellular compartments communicate via tubulo-vesicular structures shuttling cargo molecules to their destinations. Transport carriers are formed at a donor compartment and navigate through the cytoplasm to the target organelle, on which they subsequently dock and fuse. Many of these events are regulated by the cooperative action of monomeric rab GTPases and their effector proteins. Research in recent years resulted in the identification of many rab effectors, providing first glimpses how the GTPase switch of individual rab proteins is utilized in discrete transport steps.
Isolation of immunodominant antigens from sera of patients with systemic candidiasis and characterization of serological response to Candida albicans (1987)

Candidal antigens were isolated by affinity chromatography from the sera of patients with disseminated Candida albicans infections. The immunodominant 47-kilodalton (kDa) antigen appeared to be a heat-stable breakdown product of several larger heat-labile components (84 to 92, 74 to 79, and 66 to 72 kDa). It was undetectable in normal sera and sera from four patients with systemic C. parapsilosis, C. tropicalis, and C. krusei infections. Serum samples from 92 patients with proven systemic C. albicans infections were examined by the immunoblot technique. Seventy-four patients had detectable antibody, and 92% of these produced antibody to the 47-kDa antigen. All survivors had major serological responses to this antigen, whereas patients who died had no, minor, or fading responses. Fifty-five of the patients were neutropenic following cytotoxic chemotherapy for malignancies, usually lymphoproliferative disorders (hematological patients). The remainder were surgical or medical patients (nonhematological). Hematological patients differed from nonhematological patients in the range of antigens that were commonly recognized by their immune systems, although antibodies to the 47- and 60-kDa antigens were frequently present in both groups. They also differed in that they produced mainly an immunoglobulin M (IgM) response, failing to seroconvent to IgG. This did not reduce survival rates, which were similar in both groups. It may be responsible, however, for the lower antigen titers that were observed in hematological patients when measured by reverse passive latex agglutination.
Tile-based texture mapping on graphics hardware (2004)

Texture mapping has been a fundamental feature for commodity graphics hardware. However, a key challenge for texture mapping is how to store and manage large textures on graphics processors. In this paper, we present a tile-based texture mapping algorithm by which we only have to physically store a small set of texture tiles instead of a large texture. Our algorithm generates an arbitrarily large and non-periodic virtual texture map from the small set of stored texture tiles. Because we only have to store a small set of tiles, it minimizes the storage requirement to a small constant, regardless of the size of the virtual texture. In addition, the tiles are generated and packed into a single texture map, so that the hardware filtering of this packed texture map corresponds directly to the filtering of the virtual texture. We implement our algorithm as a fragment program, and demonstrate performance on latest graphics processors.
Effect of Hepatitis G Virus Infection on Progression of HIV Infection in Patients with Hemophilia (2000)

Patients with past or current HGV infection have higher CD4+ lymphocyte counts and better AIDS-free survival rates. The mechanism of this association is unknown.
Extracranial vascular changes and the source of pain in migraine headache (1983)

The extracranial circulation of 66 migrainous patients was assessed during unilateral headache by recording the pulse amplitude of the superficial temporal artery and its main frontal branch, by facial thermography, and by changes in the intensity of headache when temporal or carotid arteries were compressed. Amplitude of pulsation of the superficial temporal artery did not differ between headache and headache-free sides but the amplitude of its frontal branch was increased on the headache side, specifically in a subgroup of patients whose headache was relieved by compressing the superficial temporal artery ("extracranial vascular" group). Facial thermograms demonstrated significant differences in heat loss from the temples and orbits between migrainous patients and controls, frontotemporal changes being more conspicuous in the extracranial vascular group. It was concluded that dilatation of the superficial temporal artery and its branches contributes substantially to migraine headache in only a minority of patients.
Type IV Pili and Twitching Motility (2002)

Twitching motility is a flagella-independent form of bacterial translocation over moist surfaces. It occurs by the extension, tethering, and then retraction of polar type IV pili, which operate in a manner similar to a grappling hook. Twitching motility is equivalent to social gliding motility in Myxococcus xanthus and is important in host colonization by a wide range of plant and animal pathogens, as well as in the formation of biofilms and fruiting bodies. The biogenesis and function of type IV pili is controlled by a large number of genes, almost 40 of which have been identified in Pseudomonas aeruginosa. A number of genes required for pili assembly are homologous to genes involved in type II protein secretion and competence for DNA uptake, suggesting that these systems share a common architecture. Twitching motility is also controlled by a range of signal transduction systems, including two-component sensor-regulators and a complex chemosensory system.
Down-Regulation of Cell Surface Receptors Is Modulated by Polar Residues within the Transmembrane Domain (2000)

How recycling receptors are segregated from down-regulated receptors in the endosome is unknown. In previous studies, we demonstrated that substitutions in the transferrin receptor (TR) transmembrane domain (TM) convert the protein from an efficiently recycling receptor to one that is rapidly down regulated. In this study, we demonstrate that the “signal” within the TM necessary and sufficient for down-regulation is Thr 11 Gln 17 Thr 19 (numbering in TM). Transplantation of these polar residues into the wild-type TR promotes receptor down-regulation that can be demonstrated by changes in protein half-life and in receptor recycling. Surprisingly, this modification dramatically increases the TR internalization rate as well (∼79% increase). Sucrose gradient centrifugation and cross-linking studies reveal that propensity of the receptors to self-associate correlates with down-regulation. Interestingly, a number of cell surface proteins that contain TM polar residues are known to be efficiently down-regulated, whereas recycling receptors for low-density lipoprotein and transferrin conspicuously lack these residues. Our data, therefore, suggest a simple model in which specific residues within the TM sequences dramatically influence the fate of membrane proteins after endocytosis, providing an alternative signal for down-regulation of receptor complexes to the well-characterized cytoplasmic tail targeting signals.
Direct carotid puncture for the endovascular treatment of anterior circulation aneurysms. (2006)

We report the usefulness of Guglielmi detachable coil (GDC) embolization by direct carotid puncture for anterior circulation aneurysms. For all 27 patients, GDC embolization by direct carotid puncture was safely performed by using a 5F sheath introducer 5 cm long and a Tracker-38 catheter. Neurologic deficits and hemorrhage were not found in any patient during the follow-up period. If the transfemoral approach cannot be applied, GDC embolization should be considered as an alternative method.
Bone Regeneration on Macroporous Aqueous‐Derived Silk 3‐D Scaffolds (2007)

Spinner flask culture under osteogenic conditions was used to study osteogenic outcomes from human bone marrow-derived mesenchymal stem cells (hMSCs) seeded on aqueous-derived porous silk scaffolds. Of particular novelty was the use of larger sized scaffolds (15 mm diameter, 5 mm thick) and large pore sizes ( approximately 900-1 000 micron diameter). Cultures were maintained for 84 d in the spinner flasks and compared to static controls under otherwise similar conditions. The spinner flask cultures demonstrated enhanced cell proliferation compared to static cultures and the improved fluid flow promoted significantly improved osteogenic related outcomes based on elevated alkaline phosphatase (ALP) activity and the deposition of mineralized matrix. The expression of osteogenic differentiation associated markers based on real time PCR also demonstrated increased responses under the dynamic spinner flask culture conditions. Histological analysis showed organized bone-like structures in the constructs cultured in the spinner flasks after 56 d of culture. These structures stained intensely with von Kossa. The combination of improved transport due to spinner flask culture and the use of macroporous 3D aqueous-derived silk scaffolds with large pore sizes resulted in enhanced outcomes related to bone tissue engineering, even with the use of large sized scaffolds in the study. These results suggest the importance of the structure of the silk biomaterial substrate (water vs. solvent based preparation) and large pore sizes in improved bone-like outcomes during dynamic cultivation.
Electricity Production from Cellulose in a Microbial Fuel Cell Using a Defined Binary Culture (2007)

Microbial fuel cells (MFCs) convert biodegradable materials into electricity, potentially contributing to an array of renewable energy production strategies tailored for specific applications. Since there are no known microorganisms that can both metabolize cellulose and transfer electrons to solid extracellular substrates, the conversion of cellulosic biomass to electricity requires a syntrophic microbial community that uses an insoluble electron donor (cellulose) and electron acceptor (anode). Electricity was generated from cellulose in an MFC using a defined coculture of the cellulolytic fermenter Clostridium cellulolyticum and the electrochemically active Geobacter sulfurreducens. In fed-batch tests using two-chamber MFCs with ferricyanide as the catholyte, the coculture achieved maximum power densities of 143 mW/ m2 (anode area) and 59.2 mW/m2 from 1 g/L carboxymethyl cellulose (CMC) and MN301 cellulose, respectively. Neither pure culture alone produced electricity from these substrates. The coculture increased CMC degradation from 42% to 64% compared to a pure C. cellulolyticum culture. COD removal using CMC and MN301 was 38 and 27%, respectively, with corresponding Coulombic efficiencies of 47 and 39%. Hydrogen, acetate, and ethanol were the main residual metabolites of the binary culture. Cellulose conversion to electricity was also demonstrated using an uncharacterized mixed culture from activated sludge with an aerobic aqueous cathode.
Use of DNS Aliases for Network Services (1997)

It has become a common practice to use symbolic names (usually CNAMEs) in the Domain Name Service (DNS -[RFC-1034, RFC-1035]) to refer to network services such as anonymous FTP [RFC-959] servers, Gopher [RFC-1436] servers, and most notably World-Wide Web HTTP [RFC-1945] servers. This is desirable for a number of reasons. It provides a way of moving services from one machine to another transparently, and a mechanism by which people or agents may programmatically discover that an organization runs, say, a World-Wide Web server.
Trial of Tocilizumab in Giant-Cell Arteritis (2017)

Tocilizumab, received weekly or every other week, combined with a 26-week prednisone taper was superior to either 26-week or 52-week prednisone tapering plus placebo with regard to sustained glucocorticoid-free remission in patients with giant-cell arteritis. Longer follow-up is necessary to determine the durability of remission and safety of tocilizumab. (Funded by F. Hoffmann-La Roche; ClinicalTrials.gov number, NCT01791153 .).
HTLV-III: the etiologic agent of AIDS. (1984)

A retrovirus belonging to the family of human T-cell leukemia/lymphoma virus (HTLV) was isolated from several patients with acquired immunodeficiency syndrome (AIDS), AIDS-related complex (ARC) and asymptomatic homosexual males at increased risk of developing AIDS. This new virus was designated HTLV-III. A serological screening procedure incorporating an enzyme-linked immunosorbent assay (ELISA) and a radioimmunoassay using a Western blot technique was developed employing disrupted HTLV-III as the antigen source. These assays identified serum antibodies to HTLV-III antigens in almost all patients with AIDS, greater than 90% patients with ARC and about 40% of homosexual males at risk for developing AIDS. In a study of transfusion associated AIDS (TA-AIDS) all 19 of the TA-AIDS cases had antibodies to HTLV-III. Similarly 31 of 35 high risk donors who donated to cases of TA-AIDS had antibodies to HTLV-III. All four of the antibody negative high risk donors donated to cases that received blood from at least one other high risk donor. In contrast only 2 of 255 other donors were antibody positive. The data clearly indicate that TA-AIDS cases developed the disease as a result of transmission of HTLV-III through contaminated blood and that HTLV-III is the primary etiologic agent of AIDS.
Purification and properties of deoxyribonucleic acid polymerase from Bacillus stearothermophilus (1981)

Deoxyribonucleic acid polymerase I was purified from Bacillus stearothermophilus to 50 to 70% homogeneity. Its molecular weight was 76,000. The enzyme was insensitive to sulfhydryl blocking agents and showed maximal activity at 60 degrees C, pH 8 to 9, 0.25 M KCl, and 0.02 M MgSO4. The rate of heat inactivation of the deoxyribonucleic acid polymerase followed first-order kinetics with a half-life of 90 min at 60 degrees C; the addition of 0.05% bovine serum albumin protected the enzyme, which could be heated for 180 min without loss of activity. The ratios of polymerase to nuclease activities were about 20 for 5'-3' exonuclease and more than 500 for 3'-5' exonuclease. The Km for deoxyribonucleoside-5'-triphosphates was 7 microM.
Polynomial Codes Over Certain Finite Fields (1960)

Previous article Next article Polynomial Codes Over Certain Finite FieldsI. S. Reed and G. SolomonI. S. Reed and G. Solomonhttps://doi.org/10.1137/0108018PDFPDF PLUSBibTexSections ToolsAdd to favoritesExport CitationTrack CitationsEmail SectionsAbout[1] R. W. Hamming, Error detecting and error correcting codes, Bell System Tech. J., 29 (1950), 147–160 MR0035935 CrossrefISIGoogle Scholar[2] Irving S. Reed, A class of multiple-error-correcting codes and the decoding scheme, Trans. I.R.E., PGIT-4 (1954), 38–49, Prof. Group on Information Theory MR0089789 Google Scholar[3] Neal Zierler, Linear recurring sequences, J. Soc. Indust. Appl. Math., 7 (1959), 31–48 10.1137/0107003 MR0101979 0096.33804 LinkISIGoogle Scholar Previous article Next article FiguresRelatedReferencesCited ByDetails A General Family of MSRD Codes and PMDS Codes with Smaller Field Sizes from Extended Moore MatricesUmberto MartÍnez-Pen͂asSIAM Journal on Discrete Mathematics, Vol. 36, No. 3 | 16 August 2022AbstractPDF (562 KB)Algorithmic Fault Tolerance Using the Lanczos MethodSIAM Journal on Matrix Analysis and Applications, Vol. 13, No. 1 | 31 July 2006AbstractPDF (1962 KB)A New Class of Cyclic CodesSIAM Journal on Applied Mathematics, Vol. 16, No. 1 | 12 July 2006AbstractPDF (1580 KB)Multiple-Burst Error Correction with the Chinese Remainder TheoremJournal of the Society for Industrial and Applied Mathematics, Vol. 11, No. 1 | 13 July 2006AbstractPDF (758 KB)A Class of Error-Correcting Codes in $p^m $ SymbolsDaniel Gorenstein and Neal ZierlerJournal of the Society for Industrial and Applied Mathematics, Vol. 9, No. 2 | 10 July 2006AbstractPDF (691 KB) Volume 8, Issue 2| 1960Journal of the Society for Industrial and Applied Mathematics225-424 History Submitted:21 January 1959Published online:10 July 2006 InformationCopyright © 1960 Society for Industrial and Applied MathematicsPDF Download Article & Publication DataArticle DOI:10.1137/0108018Article page range:pp. 300-304ISSN (print):0368-4245ISSN (online):2168-3484Publisher:Society for Industrial and Applied Mathematics