gebhart/patrepeval huggingface dataset:
Catalyzing Bacterial Speciation: Correlating Lateral Transfer with Genetic Headroom (2001)

Unlike crown eukaryotic species, microbial species are created by continual processes of gene loss and acquisition promoted by horizontal genetic transfer. The amounts of foreign DNA in bacterial genomes, and the rate at which this is acquired, are consistent with gene transfer as the primary catalyst for microbial differentiation. However, the rate of successful gene transfer varies among bacterial lineages. The heterogeneity in foreign DNA content is directly correlated with amount of genetic headroom intrinsic to a bacterial species. Genetic headroom reflects the amount of potentially dispensable information—reflected in codon usage bias and codon context bias—that can be transiently sacrificed to allow experimentation with functions introduced by gene transfer. In this way, genetic headroom offers a potential metric for assessing the propensity of a lineage to speciate.
Influence of Organ Extracts of Triatoma infestans on Differentiation of Trypanosoma cruzi (1981)

The influence that extracts of different T. infestans organs possess to induce Trypanosoma cruzi differentiation from epimastigotes to metacyclic forms in Grace's and modified Grace's media was analyzed. Growth of epimastigotes was adequate in Grace's medium when homogenates of stomach, testes, and ovaries from recently fed insects were added. Growth of epimastigotes was adequate when testes or ovaries obtained from recently fed triatomes were added to modified Grace's medium. Similar results were obtained in Grace's or modified Grace's media supplemented with stomach or intestinal homogenates obtained from "starved" triatomes. None of the above culture conditions induced differentiation of epimastigotes to the metacyclic stage. When extracts of intestine or stomach obtained from triatomes fed 24 to 48 hr previously were used to supplement the modified Grace's medium, growth and differentiation to the metacyclic stage was induced in a high percentage of the population. When extracts of intestine obtained from recently fed insects were used to supplement Grace's medium, differentiation and growth was an in modified Grace's medium. No important differences were observed if cultures were prepared at pH 6.4 or 7.0. The triatome food source did not seem to be important for the differentiation. The parasite population after differentiation to metacyclic type forms showed a higher degree of infectivity than the original population constituted mostly by epimastigotes. These studies suggest the importance of factors from the insect vector in differentiation of T. cruzi.
A Gas‐Phase Flow Reactor for Ethylene Carbonate Synthesis from Waste Carbon Dioxide (2009)

Go with the flow: A gas-phase flow reactor that contains a silica-supported catalyst for the conversion of ethylene oxide and CO2 into ethylene carbonate has been developed (see scheme). Since the reactor operates at atmospheric pressure and at temperatures accessible utilising “waste heat”, the process is suitable for retro-fitting to the exhaust stream of a fossil fuel power station or any other major fixed-site CO2 producer. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
68Ga-labelled exendin-3, a new agent for the detection of insulinomas with PET (2010)

[Lys(40)((68)Ga-DOTA)]Exendin-3 specifically accumulates in insulinomas, although the uptake is lower than that of [Lys(40)((111)In-DTPA)]exendin-3. Therefore, [Lys(40)((68)Ga-DOTA)]exendin-3 is a promising tracer to visualize insulinomas with PET.
Search of antimicrobial activity of selected non-antibiotic drugs. (2003)

A variety of pharmaceutical preparations, which are applied in the management of non-infectious diseases, have shown in vitro some antimicrobial activity. These drugs are called "non-antibiotics". The aim of this study was to detect and characterise the antimicrobial activity of non-antibiotic drugs. selected from the preparations analysed during state control performed at the Drug Institute in Poland. Over 160 pharmaceutical preparations were randomly chosen from different groups of drugs. The surveillance study was performed on standard ATCC microbial strains used for drug control: S aureus, E. coil, P. aeruginosa and C. albicans. It was shown that the drugs listed below inhibited growth of at least one of the examined strains:acyclovir (Awirol 5%, cream), alendronate (Alenato 5 mg, tabl.), alverine (Meteospasmyl 20 mg, caps.), butorphanole (Butamidor 10 mg/ml, amp.), clodronate (Sindronat 400 mg, caps), diclofenac (Olfen 75 mg, amp.), emadastine (Emadine 0.05%, eye dr.), etodolac (Febret 200 mg, caps.), fluvastatine (Lescol 40 mg, tabl.), ketamine (Ketamidor 10%, amp.), levocabastine (Histimet 0.5 mg/ml, eye dr.), losartan (Lorista 50 mg, tabl.), matipranolol (Betaman 0.3% eye dr.), mesalazine (Pentasa 1%, susp.), naproxen (Nalgesin 550 mg, tabl.), oxaprosine (Reumax 600 mg, tabl.), oxymethazoline (Nasivin 0.025%, nose dr.), proxymetacaine (Alcaine 0.5%, eye dr.), ribavirin (Rebetol 200 mg, caps.), rutoside with ascorbic acid (Cerutin 20+200 mg, tabl.), sulodexide (Vessel due F, 250 LSU, caps.), tegaserole (Zelmac 50 mg, tabl.), telmisartan (Pritor 20 mg, tabl.), temosolomide (Temodal 100 mg, caps.), ticlopidine (Ticlid 250 mg, tabl.), tolfenamic acid (Migea rapid 200 mg, tabl.), tramadole (Tramundin 100 mg, tabl.), tropicamide (Tropicamidum 1%, eye dr.). Staphylococcus aureus was susceptible to most of the drugs listed above. Ticlopidine showed activity against S. aureus, E. coli and C. albicans (MICs equal to: 0.45; 0.45 and 0.65 mg/ml, respectively). Oxymetazoline showed activity against S. aureus and E. coli (MICs: 0.005 and 0.025 mg/ml, respectively). Pseudomonas aeruginosa was sensitive to alendronate, clondronate, oxaprozine, ribavirin and tramadole (MICs: 10, 63, 60, 3 and 43 mg/ml, respectively).
Lattice-Based Memory Allocation (2005)

We investigate the problem of memory reuse in order to reduce the memory needed to store an array variable. We develop techniques that can lead to smaller memory requirements in the synthesis of dedicated processors or to more effective use by compiled code of software-controlled scratchpad memory. Memory reuse is well-understood for allocating registers to hold scalar variables. Its extension to arrays has been studied recently for multimedia applications, for loop parallelization, and for circuit synthesis from recurrence equations. In all such studies, the introduction of modulo operations to an otherwise affine mapping (of loop or array indices to memory locations) achieves the desired reuse. We develop here a new mathematical framework, based on critical lattices, that subsumes the previous approaches and provides new insight. We first consider the set of indices that conflict, those that cannot be mapped to the same memory cell. Next, we construct the set of differences of conflicting indices. We establish a correspondence between a valid modular mapping and a strictly-admissible integer lattice-one having no nonzero element in common with the set of conflicting index differences. The memory required by an optimal modular mapping is equal to the determinant of the corresponding lattice. The memory reuse problem is thus reduced to the (still interesting and nontrivial) problem of finding a strictly admissible integer lattice-of least determinant. We then propose and analyze several practical strategies for finding strictly admissible integer lattices, either optimal or optimal up to a multiplicative factor, and, hence, memory-saving modular mappings. We explain and analyze previous approaches in terms of our new framework.
Absolute Neutrophil Counts From Automated Hematology Instruments Are Accurate and Precise Even at Very Low Levels (2012)

Using 106 samples from patients with an absolute neutrophil count (ANC) less than 2.0 × 10(9)/L, two 5-part differential hematology instruments (Sysmex XE-2100, Sysmex, Kobe, Japan, and Advia 2120i, Siemens Healthcare Diagnostics, Deerfield, IL), two 3-part differential hematology instruments (Sysmex K4500, Sysmex, and Advia 60, Siemens Healthcare Diagnostics), and an automated system for examination of microscopic slides (CellaVision DM96, CellaVision, Lund, Sweden) were compared with a flow cytometric (FCM) neutrophil count using monoclonal antibodies for cell classification. The precision and accuracy of the 5-part differential instrument ANC was very good at more than 0.1 × 10(9)/L, although a small systematic difference (10.3%) was found between the 2 instruments. The ANC of the 3-part differential instruments was less reliable, but the WBC count correlated very well with the WBC count from the 5-part differential instruments. Also, the neutrophil count from the CellaVision DM96 compared very well with FCM. When used in the correct laboratory setting, all of the evaluated instruments provide ANCs and WBCs with adequate accuracy and precision.
Chemically deglycosylated human chorionic gonadotropin subunits: characterization and biological properties (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemically deglycosylated human chorionic gonadotropin subunits: characterization and biological propertiesHenry T. Keutmann, Patrick J. McIlroy, Elizabeth R. Bergert, and Robert J. RyanCite this: Biochemistry 1983, 22, 13, 3067–3072Publication Date (Print):June 21, 1983Publication History Published online1 May 2002Published inissue 21 June 1983https://pubs.acs.org/doi/10.1021/bi00282a007https://doi.org/10.1021/bi00282a007research-articleACS PublicationsRequest reuse permissionsArticle Views72Altmetric-Citations73LEARN 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 Get e-Alerts
Crystal versus solution structure of enzymes: NMR spectroscopy of a peptide boronic acid-serine protease complex in the crystalline state. (1989)

The effectiveness of boronic acids as inhibitors of serine proteases has been widely ascribed to the ability of the boronyl group to form a tetrahedral adduct with the active-site serine that closely mimics the putative tetrahedral intermediate or transition state formed with substrates. However, recent 15N NMR studies of alpha-lytic protease (EC 3.4.21.12) in solution have shown that some boronic acids and peptide boronic acids form adducts with the active-site histidine instead of with the serine. Such histidine-boron adducts have not thus far been reported in x-ray diffraction studies of boronic acid-serine protease complexes. Here, we report an 15N NMR study of the MeOSuc-Ala-Ala-Pro-boroPhe complex of alpha-lytic protease in the crystalline state using magic-angle spinning. Previous 15N NMR studies have shown this complex involves the formation of a histidine-boron bond in solution. The 15N NMR spectra of the crystalline complex are essentially identical to those of the complex in solution, thereby showing that the structure of this complex is the same in solution and in the crystal and that both involve formation of a histidine-boron adduct.
NK cells provide helper signal for CD8+ T cells by inducing the expression of membrane-bound IL-15 on DCs (2009)

NK cell recognition of cells that do not express or express low amounts of MHC class I molecules results not only in direct killing of target cells but also in the generation of specific T cell responses consequent to the induction of dendritic cell (DC) activation. While IL-12 production by NK cell-activated DCs is generally thought to play a critical role, a similar DC-mediated NK cell help has been reported also in IL-12-knockout mice. Here, we show that human NK cells can induce on DC surface membrane, via IFN-gamma secretion, the expression of high levels of IL-15. Remarkably, we show that DC expression of this membrane-bound form of IL-15, which is only partially associated with IL-15R molecules, is essential to promote specific CD8(+) T lymphocyte response in the absence of DC-derived IL-12.
Restoring the Phenotype of Fragile X Syndrome: Insight from the Mouse Model (2001)

A mouse model for the fragile X syndrome, the most common form of inherited mental retardation, was generated a number of years ago. It shows characteristics compatible with the clinical symptoms of human patients. These include pathological changes such as macroorchidism, behavioral problems, and diminished visuo-spatial abilities. To investigate whether the fragile X syndrome is a potentially correctable disorder, several groups attempted to 'rescue' the knockout mutation by introduction of an intact copy of the FMR1 gene in the knockout mouse. Two different types of rescue mice have been created by injection of constructs based on FMR1 cDNA or on FMR1 genomic DNA. Several pathological, behavioral and cognitive function tests were performed on these two different rescue mouse lines to compare their characteristics with those of the knockout and control littermates. Each rescue line resembled the control in some aspects though neither of the 2 lines was a full 'rescue', e.g. resemble the control in all aspects investigated. Thus, rescue of some aspects of the phenotype has been achieved by introduction of FMR1 constructs in the fragile X knockout mice. The results implicate that, even if FMR1 production is cell type specific, the quantity of the FMRP expression is highly critical as overproduction may have a harmful effect.
Reactive Astrocytes Protect Tissue and Preserve Function after Spinal Cord Injury (2004)

Reactive astrocytes are prominent in the cellular response to spinal cord injury (SCI), but their roles are not well understood. We used a transgenic mouse model to study the consequences of selective and conditional ablation of reactive astrocytes after stab or crush SCI. Mice expressing a glial fibrillary acid protein-herpes simplex virus-thymidine kinase transgene were given mild or moderate SCI and treated with the antiviral agent ganciclovir (GCV) to ablate dividing, reactive, transgene-expressing astrocytes in the immediate vicinity of the SCI. Small stab injuries in control mice caused little tissue disruption, little demyelination, no obvious neuronal death, and mild, reversible functional impairments. Equivalent small stab injuries in transgenic mice given GCV to ablate reactive astrocytes caused failure of blood-brain barrier repair, leukocyte infiltration, local tissue disruption, severe demyelination, neuronal and oligodendrocyte death, and pronounced motor deficits. Moderate crush injuries in control mice caused focal tissue disruption and cellular degeneration, with moderate, primarily reversible motor impairments. Equivalent moderate crush injuries combined with ablation of reactive astrocytes caused widespread tissue disruption, pronounced cellular degeneration, and failure of wound contraction, with severe persisting motor deficits. These findings show that reactive astrocytes provide essential activities that protect tissue and preserve function after mild or moderate SCI. In nontransgenic animals, crush or contusion SCIs routinely exhibit regions of degenerated tissue that are devoid of astrocytes. Our findings suggest that identifying ways to preserve reactive astrocytes, to augment their protective functions, or both, may lead to novel approaches to reducing secondary tissue degeneration and improving functional outcome after SCI.
Distribution of shufflon among IncI plasmids (1987)

A shufflon or clustered inversion is a novel type of DNA rearrangement originally discovered in the IncI1 plasmid R64 (T. Komano, A. Kubo, and T. Nisioka, Nucleic Acids Res. 15:1165-1172, 1987). In a 1.95-kilobase region of R64 DNA, four DNA segments inverted independently or in groups, resulting in a complex DNA rearrangement. We found similar types of shufflon in other IncI1 plasmids, including delta, pIP111, pIP565, pIP112, pIP186, R144, R163, R483, and R621a. A variant type of shufflon occurs in the IncI1 plasmid ColIb.
The IBM 3090 system: An overview (1986)

The first part of this paper places the IBM 3090 system in historical perspective with respect to its predecessors. Treated briefly are the technology and the design process, both of which were critical to the development of the 3090. Presented in detail is the 3090 system itself, with emphasis on its features that differ from those of prior systems.
The structure and function of fluorescent proteins (2009)

The current complement of fluorescent proteins (FPs) contains color variants whose emission spectra span most of the visible spectrum, providing researchers with a versatile toolset of fluorescent probes for live cell imaging applications. FP family members generate their chromophores autocatalytically through a series of posttranslational modifications. The fluorescence characteristics of GFP-family members are influenced in important ways by the local microenvironment surrounding the chromophore. In this tutorial review, we first examine the molecular factors that influence the photophysical properties of FP family members and then briefly discuss some of the ways in which these fascinating proteins have been applied to the field of live cell imaging.
Efficiency of embryoid body formation and hematopoietic development from embryonic stem cells in different culture systems (2002)

Embryonic stem (ES) cells have tremendous potential as a cell source for cell-based therapies. Realization of that potential will depend on our ability to understand and manipulate the factors that influence cell fate decisions and to develop scalable methods of cell production. We compared four standard ES cell differentiation culture systems by measuring aspects of embryoid body (EB) formation efficiency and cell proliferation, and by tracking development of a specific differentiated tissue type-blood-using functional (colony-forming cell) and phenotypic (Flk-1 and CD34 expression) assays. We report that individual murine ES cells form EBs with an efficiency of 42 +/- 9%, but this value is rarely obtained because of EB aggregation-a process whereby two or more individual ES cells or EBs fuse to form a single, larger cell aggregate. Regardless of whether EBs were generated from a single ES cell in methylcellulose or liquid suspension culture, or aggregates of ES cells in hanging drop culture, they grew to a similar maximum cell number of 28,000 +/- 9,000 cells per EB. Among the three methods for EB generation in suspension culture there were no differences in the kinetics or frequency of hematopoietic development. Thus, initiating EBs with a single ES cell and preventing EB aggregation should allow for maximum yield of differentiated cells in the EB system. EB differentiation cultures were also compared to attached differentiation culture using the same outputs. Attached colonies were not similarly limited in cell number; however, hematopoietic development in attached culture was impaired. The percentage of early Flk-1 and CD34 expressing cells was dramatically lower than in EBs cultured in suspension, whereas hematopoietic colony formation was almost completely inhibited. These results provide a foundation for development of efficient, scalable bioprocesses for ES cell differentiation, and inform novel methods for the production of hematopoietic tissues.
Hurler and Hunter Syndromes: Mutual Correction of the Defect in Cultured Fibroblasts (1968)

The biochemical defect of cultuired skin fibroblasts from Hurler or Hunter patients (faulty degradation of sulfated mucopolysaccharide, resulting in excessive intracellular accumulation) may be corrected if cells of these two genotypes are mixed with each other or with normal cells. The effect is mediated by substances released into the medium.
Uniformly dispersed deposition of colloidal nanoparticles and nanowires by boiling (2007)

Uniformly dispersed deposition of various nanoparticles (gold and silver of 20–50nm) and nanowires (ZnO and VOx) on different surfaces (Si, GaAs, mica, and steel) was obtained by boiling colloid drops on preheated substrates. Our results suggest a deposition mechanism based on the formation of microdrops induced by boiling. Indeed, microdrops produced by an ink-jet printing system resulted in uniformly dispersed deposits when the substrate was heated to high temperatures. We demonstrate that boil-deposited gold nanoparticles could be used for the catalytic growth of ZnO nanowires as well as for the manipulation of individual particles by means of an atomic force microscope.
Experimental and numerical investigation of the electrical characteristics of vertical n-p junction diodes created by Si implantation into p-GaN (2008)

Vertical n-p junction diodes were fabricated by Si <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> ion implantation into Mg doped p/p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> GaN, followed by rapid thermal annealing at 1260degC in NH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> for 30 s. Implantations were performed at 40, 60 and 80 keV and circular contacts on the n-region were fabricated with various diameters between 100 and 600 mum. Light emission from the periphery of the contact under forward bias conditions confirmed the existence of an n-p junction. Current-voltage characteristics revealed rectifying behaviour associated with n-p junction. 2-Dimensional Sentaurus Devicetrade was used to simulate the device. Current density distribution indicates high current near the peripheral region and it appears that the performance of the device is not determined by the implantation conditions. Further optimisation of the vertical structure is required to improve the device performance.