gebhart/patrepeval huggingface dataset:
Carbon Source Dependence and Photostimulation of Conidiation in Hypocrea atroviridis (2007)

Hypocrea atroviridis is frequently used as a photomorphogenetic model due to its ability to conidiate upon exposure to light. Light is thereby believed to be the primary trigger for spore formation. In contrast, we show here that conidiation is primarily carbon source dependent and that illumination plays a catalytic role; of a total of 95 tested carbon sources, only a small set of carbohydrates, polyols, and sugar acids allowed conidiation in darkness, and on most of them, conidiation was significantly more strongly expressed in light. In addition, there are also a number of carbon sources on which H. atroviridis conidiates in darkness, but light does not further stimulate the process. Yet on another small set of carbon sources (L-sorbitol, D-fucose, D- and L-arabinose, and erythritol), H. atroviridis shows better sporulation in darkness than in light. No sporulation was observed on organic acids and amino acids. Mutants with deletions in the two blue-light receptor proteins BLR-1 and BLR-2 generally showed weaker conidiation on a smaller number of carbon sources than did the parental strain, yet they clearly sporulated on 15 and 27 of the 95 carbon sources tested, respectively. Of the carbon sources supporting sporulation, only 11 supported the conidiation of both mutants, suggesting that the BLR-1 and BLR-2 receptors are variously involved in the carbon source-dependent regulation of spore formation. The addition of cyclic AMP, which has been reported to lead to conidiation in darkness, both positively and negatively affected sporulation and resulted in different effects in the parental strain and the two Deltablr mutants. Our data show that the carbon source is the prime determinant for conidiation and that it influences the organism's regulation of conidiation by means of BLR-1 and BLR-2 and their cross talk with cyclic AMP.
Self-stabilizing systems in spite of distributed control (1974)

The synchronization task between loosely coupled cyclic sequential processes (as can be distinguished in, for instance, operating systems) can be viewed as keeping the relation “the system is in a legitimate state” invariant. As a result, each individual process step that could possibly cause violation of that relation has to be preceded by a test deciding whether the process in question is allowed to proceed or has to be delayed. The resulting design is readily—and quite systematically—implemented if the different processes can be granted mutually exclusive access to a common store in which “the current system state” is recorded.
Effect of quality and quantity of dietary protein on free amino acids in plasma and tissues of adult rats. (1981)

The nutritional significance of plasma free amino acids was examined by studying the effects of the quality and quantity of dietary protein on free amino acids in plasma and tissues of adult rats. The animals were given a diet containing 3, 6 or 10% egg protein or 3, 13 or 20% wheat gluten or rice protein for 4 weeks. At the end of the 4-week period, the rats were fasted for 12hr and the samples were prepared for the measurements of free amino acids in plasma and tissues. In rats on lowprotein diets, the plasma levels of essential amino acids (EAAs) decreased significantly, the reduction unexpectedly being greatest in rats on egg protein and least in those on wheat gluten. However, the levels of threonine, leucine and phenylalanine showed significant correlations with the dietary protein level, irrespective of the protein source. Moreover, the plasma lysine levels in rats on rice and wheat gluten diets were maintained at almost the normal levels, irrespective of the protein level, although lysine is a limiting factor in these proteins. Of the nonessential amino acids (NEAAs), serine and glycine in the plasma increased greatly in rats on low-protein diets, and then the ratio of EAAs to NEAAs (E/N) decreased significantly to about half (0.44 to 0.47) the values in rats on the highest protein diets, irrespective of the protein source. Findings in muscle were comparable to those in plasma. In liver, the ingestion of low-protein diets resulted in higher levels of serine and threonine, especially in groups on poor quality protein, while total EAAs were not affected by the dietary protein level. Unlike in the plasma and other tissues, in the small intestine tissue, free amino acids showed no consistent change in response to the dietary protein. It is suggested that this tissue contributes to correcting the amino acid pattern of the ingested protein.
Comparison of Transgene Expression Stability after Agrobacterium-mediated or Biolistic Gene Transfer into Perennial Ryegrass (Lolium perenne L.) (2006)

Perennial ryegrass (Lolium perenne L.) is the most widely distributed grass species in areas with temperate climate. Genetic engineering of perennial ryegrass is complementing traditional breeding in the development of improved germplasm. The generation of large numbers of transgenic perennial ryegrass plants from turf type- or forage type cultivars following biolistic or Agrobacterium-mediated gene transfer was recently reported by us. Transgenic plants generated by the two alternative transformation systems were compared regarding transgene integration pattern, fertility and stability of transgene expression after vegetative and sexual reproduction. Advantages and limitations of the two perennial ryegrass transformation systems are discussed.
mTOR Signalling in Health and Disease (2011)

The TOR (target of rapamycin) proteins are found in all eukaryotes. TOR has a protein kinase domain, as well as other domains through which it interacts with partner proteins to form at least two types of multiprotein complex, TORC1 and TORC2 (TOR complexes 1 and 2). Rapamycin, an antibiotic and immunosuppressant, inhibits functions of TORC1. Use of this drug has revealed roles for TORC1 and its mammalian counterpart, mTORC1, in promoting many anabolic processes. mTORC1 signalling is activated by growth factors and nutrients. It is highly active in many cancers and plays a role in tumorigenesis and in other diseases. Much less is known so far about the functions and regulation of (m)TORC2. The goal of this meeting was to bring together researchers studying the roles of mTORC1/2 in normal cell and animal physiology in diverse systems, as well as scientists exploring the therapeutic value of inhibiting mTOR (mammalian TOR) signalling.
Serum Concentrations of Ubiquitin C-Terminal Hydrolase-L1 and Glial Fibrillary Acidic Protein after Pediatric Traumatic Brain Injury (2016)

Objective reliable markers to assess traumatic brain injury (TBI) and predict outcome soon after injury are a highly needed tool for optimizing management of pediatric TBI. We assessed serum concentrations of Glial Fibrillary Acidic Protein (GFAP) and Ubiquitin C-Terminal Hydrolase-L1 (UCH-L1) in a cohort of 45 children with clinical diagnosis of TBI (Glasgow Coma Scale [GCS] 3-15) and 40 healthy subjects, evaluated their associations with clinical characteristics and outcomes, and compared their performance to previously published data on two well-studied blood biomarkers, S100B and MBP. We observed higher serum levels of GFAP and UCH-L1 in brain-injured children compared with controls and also demonstrated a step-wise increase of biomarker concentrations over the continuum of severity from mild to severe TBI. Furthermore, while we found that only the neuronal biomarker UCH-L1 holds potential to detect acute intracranial lesions as assessed by computed tomography (CT), both markers were substantially increased in TBI patients even with a normal CT suggesting the presence of undetected microstructural injuries. Serum UCH-L1 and GFAP concentrations also strongly predicted poor outcome and performed better than S100B and MBP. Our results point to a role of GFAP and UCH-L1 as candidate biomarkers for pediatric TBI. Further studies are warranted.
A Genome-Wide CRISPR Library for High-Throughput Genetic Screening in Drosophila Cells (2015)

The simplicity of the CRISPR/Cas9 system of genome engineering has opened up the possibility of performing genome-wide targeted mutagenesis in cell lines, enabling screening for cellular phenotypes resulting from genetic aberrations. Drosophila cells have proven to be highly effective in identifying genes involved in cellular processes through similar screens using partial knockdown by RNAi. This is in part due to the lower degree of redundancy between genes in this organism, whilst still maintaining highly conserved gene networks and orthologs of many human disease-causing genes. The ability of CRISPR to generate genetic loss of function mutations not only increases the magnitude of any effect over currently employed RNAi techniques, but allows analysis over longer periods of time which can be critical for certain phenotypes. In this study, we have designed and built a genome-wide CRISPR library covering 13,501 genes, among which 8989 genes are targeted by three or more independent single guide RNAs (sgRNAs). Moreover, we describe strategies to monitor the population of guide RNAs by high throughput sequencing (HTS). We hope that this library will provide an invaluable resource for the community to screen loss of function mutations for cellular phenotypes, and as a source of guide RNA designs for future studies.
Penrith: An Employment Strategy to Generate Increased Employment Positions (2008)

The proposed Glenmore Park Stage II development will add significantly to the stock of housing in Penrith. Peter Brain and Ian Manning examine how the additional resident population fits into Penrith Council's Economic Development Strategy. The established Penrith Economic Development Strategy addresses the problem that, even by the standards of Sydney local government areas, Penrith has a very low ratio of local employment to resident population. The current ratio is approximately 35 per cent: the Council's objective is to increase the ratio to 70 per cent. The strategy requires the developers of new major residential areas to design and implement an Employment Development Strategy (EDS) prior to Council endorsement of a rezoning for the site. The options are on-site and off-site job generation. Developers can contribute to the former by setting aside land for activities that will generate employment, and to the latter by contributing to employment generation in other parts of Penrith emphasised in the Council strategy.
SycE, a chaperone‐like protein of Yersinia enterocolitica involved in the secretion of YopE (1993)

Pathogenic yersiniae secrete a set of 11 anti-host proteins called Yops. The yop genes, scattered around the pYV plasmid, constitute a thermoinduced regulon controlled by the product of virF gene. The secretion of the Yops also requires the presence of the products of the other vir genes and operons, namely virA, virB and virC. The large virC operon and presumably some genes of the virA region encode a new secretion system. Mutations in any of these vir genes impair the production of all the Yops. In contrast, mutations in the yerA locus, located close to yopE, specifically abolish the expression of the cytotoxin YopE. We describe here the counterpart of yerA in Yersinia enterocolitica W22703. We demonstrate that the gene product of yerA regulates the production of YopE at a post-transcriptional level. It specifically binds the YopE protein. We consider that it acts as a specific chaperone and we call it SycE (for specific YopE chaperone). We hypothesize that SycE is a link between translation and the specific Yop export machinery. It is the first representative of a new family of pYV-encoded proteins.
IN SITU SPLITTING OF THE CADAVERIC LIVER FOR TRANSPLANTATION1 (1997)

In situ split liver transplantation can be accomplished without complications and provides results that are superior to those obtained previously with ex vivo methods. It abolishes ex vivo benching and prolonged ischemia times and provides two optimal grafts with hemostasis accomplished. This technique decreases pediatric waiting time and allows adult recipients to receive right-sided grafts safely. In situ splitting is the method of choice for expanding the cadaveric liver donor pool.
Bioengineering T cells to target carbohydrate to treat opportunistic fungal infection (2014)

Clinical-grade T cells are genetically modified ex vivo to express chimeric antigen receptors (CARs) to redirect their specificity to target tumor-associated antigens in vivo. We now have developed this molecular strategy to render cytotoxic T cells specific for fungi. We adapted the pattern-recognition receptor Dectin-1 to activate T cells via chimeric CD28 and CD3-ζ (designated "D-CAR") upon binding with carbohydrate in the cell wall of Aspergillus germlings. T cells genetically modified with the Sleeping Beauty system to express D-CAR stably were propagated selectively on artificial activating and propagating cells using an approach similar to that approved by the Food and Drug Administration for manufacturing CD19-specific CAR(+) T cells for clinical trials. The D-CAR(+) T cells exhibited specificity for β-glucan which led to damage and inhibition of hyphal growth of Aspergillus in vitro and in vivo. Treatment of D-CAR(+) T cells with steroids did not compromise antifungal activity significantly. These data support the targeting of carbohydrate antigens by CAR(+) T cells and provide a clinically appealing strategy to enhance immunity for opportunistic fungal infections using T-cell gene therapy.
Array-based evaluation of multi-dimensional queries in object-relational database systems (2002)

Since multi-dimensional arrays are a natural data structure for supporting multi-dimensional queries, and object-relational (O/R) database systems support multi-dimensional array ADTs (abstract data types), it is natural to ask if a multi-dimensional array-based ADT can be used to improve O/R DBMS performance on multi-dimensional queries. As an initial step toward answering this question, we have implemented a multi-dimensional array in the Paradise O/R DBMS. In this paper, we describe the implementation of this compressed-array ADT and explore its performance for queries including star-join consolidations and selections. We show that, in many cases, the array ADT can provide significantly higher performance than can be obtained by applying techniques such as bitmap indices and star-join algorithms to relational tables.
Electroreduction of O2 to Water on the “Wired” Laccase Cathode (2001)

Oxygen was electrocatalytically reduced to water at a current density of 5 mA/cm2 and at +0.7 V (NHE) in pH 5 citrate buffer at 37.5 °C. The electrocatalyst was a composite of laccase cross-linked with a redox polymer on a hydrophilic cloth of 10 μm diameter carbon fibers. The redox polymer, PVI−Os(tpy)(dme-bpy)2+/3+, [poly-N-vinyl imidazole with 1/5th of the imidazoles complexed with [Os(tpy)(dme-bpy)]2+/3+ (tpy=terpyridine; dme-bpy= 4,4‘-dimethyl-2,2‘-bipyridine)], electrically connected (“wired”) the laccase reaction centers to the fibers.
Production of an Electrolyte Beverage from Milk Permeate (1992)

The objective of this study was to prepare shelf-stable electrolyte beverages from milk permeate. The average composition of permeate was 4.59% total solids and .40% ash. Lactose was hydrolyzed (approximately 80%) with a commercial fungal lactase enzyme. Additional sweetness was provided by sucrose. The pH was reduced to 3.5 to 3.8 by the addition of citric acid. Shelf-stable products were made using four processes: 1) UHT followed by aseptic filling, 2) heating of filled bottles to 85 degrees C for 30 min, 3) addition of .05% benzoate, and 4) nanopore filtration. The mineral composition of the finished product, expressed in parts per million, was calcium, 150; phosphorus, 157; magnesium, 43; potassium, 1166; sodium, 286; iron, 17; copper, 8; and zinc, 3.4. Listeria monocytogenes, Salmonella dublin, Salmonella typhimurium, Escherichia coli, Staphylococcus aureus, and Streptococcus agalactiae grew well when they were inoculated into unacidified, hydrolyzed permeate. None of these organisms were isolated from properly processed products. A shelf-stable electrolyte beverage high in minerals was made from whole milk permeate. This beverage could be used to replace electrolytes lost from the human body. The production of a permeate beverage would help alleviate disposal problems of permeate.
Antigenic Analysis of Group I House Dust Mite Allergens Using Random Fragments of <i>Der p</i> I Expressed by Recombinant DNA Libraries (1990)

Antigenic regions of a major house dust mite allergen, Der p I, were identified by a recombinant DNA strategy employing the technique of random fragmentation. Fragments of cDNA coding for Der p I were produced by sonication and used to construct lambda gt 11 expression libraries. Analyses of recombinant fragments reactive with a rabbit anti-Der p I antiserum showed that the B cell determinants expressed in Escherichia coli were limited, with the majority (86%) of antigenic clones isolated mapping to the region comprising amino acid sequence position 60-80. To define antigenic regions of Der p I more precisely, selected overlapping fragments were subcloned into the expression vector pGEX-1. Dot blot immunoassay and immunoabsorption studies using individual fusion proteins revealed five regions - 34-47, 60-72, 82-99, 112-140, and 166-194 - to contain B cell determinants responsible for the antigenicity of recombinant Der p I. Absorption of the antiserum with Dermatophagoides pteronyssinus extract removed reactivity to all fragments, whereas absorption with an extract from the related mite Dermatophagoides farinae removed reactivity to peptides containing residues 34-47, 60-72, and 166-194, but not 82-99 and 112-140. Similarly, rabbit anti-D.farinae reacted strongly with peptides containing residues 34-47, 60-72, and 166-194, but not residues 82-99 and 112-140 which again showed antigenic differences in these residues between the group I allergens.
Strength of granules based on calcium sulfate crystal solvates (2010)

The effect of urea additives forming calcium sulfate crystalline adduct CaSO4 · 4CO(NH2)2 on the strength of granules prepared from phosphogypsum as industrial waste of phosphoric acid manufacture was studied. The strength of granules based on various crystal hydrates and crystal solvates was compared.
Statistical evaluation of SAGE libraries: consequences for experimental design (2002)

Since the introduction of serial analysis of gene expression (SAGE) as a method to quantitatively analyze the differential expression of genes, several statistical tests have been published for the pairwise comparison of SAGE libraries. Testing the difference between the number of specific tags found in two SAGE libraries is hampered by the fact that each SAGE library is only one measurement: the necessary information on biological variation or experimental precision is not available. In the currently available tests, a measure of this variance is obtained from simulation or based on the properties of the tag distribution. To help the user of SAGE to decide between these tests, five different pairwise tests have been compared by determining the critical values, that is, the lowest number of tags that, given an observed number of tags in one library, needs to be found in the other library to result in a significant P value. The five tests included in this comparison are SAGE300, the tests described by Madden et al. (Oncogene 15: 1079-1085, 1997) and by Audic and Claverie (Genome Res 7: 986-995, 1997), Fisher's Exact test, and the Z test, which is equivalent to the chi-squared test. The comparison showed that, for SAGE libraries of equal as well as different size, SAGE300, Fisher's Exact test, Z test, and the Audic and Claverie test have critical values within 1.5% of each other. This indicates that these four tests will give essentially the same results when applied to SAGE libraries. The Madden test, which can only be used for libraries of similar size, is, with 25% higher critical values, more conservative, probably because the variance measure in its test statistic is not appropriate for hypothesis testing. The consequences for the choice of SAGE library sizes are discussed.
Therapeutic Opportunities for Muscarinic Receptors in the Central Nervous System (2000)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTTherapeutic Opportunities for Muscarinic Receptors in the Central Nervous SystemChristian C. Felder, Frank P. Bymaster, John Ward, and Neil DeLappView Author Information Eli Lilly Research Laboratories, Indianapolis, Indiana 46285 Cite this: J. Med. Chem. 2000, 43, 23, 4333–4353Publication Date (Web):November 16, 2000Publication History Received14 December 1999Published online16 November 2000Published inissue 1 November 2000https://pubs.acs.org/doi/10.1021/jm990607uhttps://doi.org/10.1021/jm990607ureview-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1941Altmetric-Citations181LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Agonists,Amines,Antagonists,Receptors,Selectivity Get e-Alerts
Reaction of hydrogen peroxide with organosilanes under chemical vapour deposition conditions (2000)

When a stream of vapour at low pressure which contained a mixture of H2O2 with an organosilane, RSiH3 (R = alkyl or alkenyl), impinged on a silicon wafer, deposition of oxide films of nominal composition RxSiO(2–0.5x), where x = ≤0.17, was observed. The reactions which accompanied oxide film formation liberated a range of volatile organic compounds consistent with release of R˙ radicals in a novel cleavage of Si–C bonds. No oxidation was detected for silanes containing C3 or higher alkyl groups or C5 or higher alkenyl groups. Possible mechanisms for the Si–C bond cleavage reaction are discussed, with energetic rearrangement of radical intermediates of type Si(H)(R)(OOH)˙ being favoured.
Development of the thin-film longitudinal intra-fascicular electrode (2000)

(LIFE) are implantable fine wire based electrodes designed to provide a relativ y selective interface to the nervous system. In an effort to create LIFEs with smaller, more precise, and more reproducible active sites, we have turned to modern microfabrication techniques. A flexible micromachined polymer structure was designed toreplace the key component of the electrode, the fine wire in contact with the endoneural tissue that forms the neural interface of the electrode. Electrodes were constructed and implanted into the medial gastrocnemius nerve of rabbits to test their in-vivo impedance and recording characteristics. We found that the thin film structures could be implanted without damaging the electrode. Their active sites impedances were very consistent with the inter-site impedance variation less than 15%. Moreover, we were able to record from muscle afferents with a signal to noise ratio of between 2 and 8.