gebhart/patrepeval huggingface dataset:
Morphological Transitions Governed by Density Dependence and Lipoxygenase Activity inAspergillus flavus (2008)

Aspergillus flavus differentiates to produce asexual dispersing spores (conidia) or overwintering survival structures called sclerotia. Results described here show that these two processes are oppositely regulated by density-dependent mechanisms and that increasing the cell density (from 10(1) to 10(7) cells/plate) results in the lowest numbers of sclerotial and the highest numbers of conidial. Extract from spent medium of low-cell-density cultures induced a high-sclerotium-number phenotype, whereas high-cell-density extract increased conidiation. Density-dependent development is also modified by changes in lipid availability. Exogenous linoleic acid increased sclerotial production at intermediate cell densities (10(4) and 10(5) cells/plate), whereas oleic and linolenic acids inhibited sclerotium formation. Deletion of Aflox encoding a lipoxygenase (LOX) greatly diminished density-dependent development of both sclerotia and conidia, resulting in an overall increase in the number of sclerotia and a decrease in the number of conidia at high cell densities (>10(5) cells/plate). Aflox mutants showed decreased linoleic acid LOX activity. Taken together, these results suggest that there is a quorum-sensing mechanism in which a factor(s) produced in dense cultures, perhaps a LOX-derived metabolite, activates conidium formation, while a factor(s) produced in low-density cultures stimulates sclerotium formation.
Oligonucleotide Synthesis Using Solution Photogenerated Acids (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTOligonucleotide Synthesis Using Solution Photogenerated AcidsXiaolian Gao, Peilin Yu, Eric LeProust, Laëtitia Sonigo, Jean Philippe Pellois, and Hua ZhangView Author Information Department of Chemistry University of Houston Houston, Texas 77204-5641 Cite this: J. Am. Chem. Soc. 1998, 120, 48, 12698–12699Publication Date (Web):November 20, 1998Publication History Received31 July 1998Published online20 November 1998Published inissue 1 December 1998https://pubs.acs.org/doi/10.1021/ja9827191https://doi.org/10.1021/ja9827191rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views588Altmetric-Citations37LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Biopolymers,Chemical reactions,High-performance liquid chromatography,Light,Reagents Get e-Alerts
Near‐Infrared Spectroscopy of Cereals (2001)

Abstract This chapter introduces cereal grains and their role in the industry, and in life. Their basic composition is reviewed together with their functionality (the capability of a commodity to produce consumer‐acceptable end‐products). By far the most important sphere of vibrational spectroscopy as it applies to cereals is near‐infrared spectroscopy (NIRS). The particular characteristics associated with composition and functionality of individual cereals and other grains for which analysis by NIRS is applicable are outlined. Application of NIRS to industrial aspects of cereals is summarized, including grading and pricing of grains, together with the degree of success achieved in application of NIRS to factors pertinent to the grading and the plant‐breeding selection process. Features of NIR spectroscopy that are peculiar to cereals and other grains are described. The application of NIRS to these materials is complicated by interactions among constituents, which strongly influence wavelength selection and instrument calibration. Spectra of select commodities are used to illustrate some of the anomalies that can occur in the application of NIRS to grains. These include apparent suppression of absorption bands in the natural or “raw” spectra of whole grains, although the bands are distinct when the grains are ground to a meal. Steps in the development of calibration models, and the approaches to their interpretation by statistical processes are explained.
Cytokines and cytokine inhibitors or antagonists in rheumatoid arthritis (1990)

This review has summarized some of the evidence suggesting that cytokines may play an important role in mediating pathophysiologic events in RA. However, these proteins are capable of mediating both stimulatory (agonist) and inhibitory (antagonist) effects in the rheumatoid synovium. GM-CSF, IL-1, TNF alpha, and PDGF are all produced in the rheumatoid synovium and may function to induce inflammation, enzyme release, fibroblast proliferation, and tissue destruction. Local release of IL-6 may alter the effects of IL-1 and TNF alpha, as well as induce Ig production and hepatic synthesis of acute-phase proteins. However, specific inhibitors of IL-1 and TNF alpha exist, which, if also released into the synovium, may antagonize the proinflammatory effects of these cytokines. In addition, IL-1 may have antiinflammatory effects, such as the induction of the synthesis of collagen and enzyme inhibitors by chondrocytes and synovial fibroblasts. Stimulation of these latter cells by TGF beta also may result in decreased matrix degradation and increased formation of scar tissue. The developing scenario is one of cell-cell interactions that are influenced in positive and negative manners by the local release of various mediators. A further understanding of cytokines and cytokine inhibitors in the rheumatoid synovium may lead to the development of more specific and effective therapeutic agents.
Retrovirus-Mediated Gene Transfer into Rhesus Monkey Hematopoietic Stem Cells: The Effect of Viral Titers on Transduction Efficiency (1993)

We have generated a cell line, designated POAM-P1, shedding amphotropic recombinant retroviruses carrying the human adenosine deaminase (hADA) gene. It exhibits a 1 log increased retrovirus titer on NIH-3T3 cells and a five-fold more efficient transduction of human ADA-deficient T lymphocytes, as compared to the previously generated cell line POC-1 which produces the same recombinant hADA retrovirus. To study whether the titer of retrovirus-producing cell lines influences the transduction efficiency of hematopoietic stem cells in a co-culture setting, we compared the POAM-P1 and POC-1 cell lines with respect to their gene transfer efficiency on rhesus monkey bone marrow. Following co-cultivation of rhesus monkey bone marrow with POAM-P1 cells, successful transduction could be demonstrated in approximately 10% of myeloid progenitor colonies (CFU-C) and 0.1% of peripheral blood mononuclear cells (PBMC) and granulocytes in vivo until > 1 year after autologous transplantation. In addition, the presence of functional hADA enzyme was detected in red blood cells, PBMC, and granulocytes. Monkeys receiving POC-1 co-cultured bone marrow carried transduced blood cells for > 2 years after transplantation. Despite the higher retrovirus titer of POAM-P1 cells as compared to POC-1 cells, no difference was observed in gene transfer efficiency into CFU-C and long-term repopulating stem cells. This shows that in our co-cultivation procedure the retrovirus titer was not limiting the transduction efficiency of primate hematopoietic stem cells.
An optical infrastructure for future telecommunications networks (1995)

For the transport of the increasing traffic volume caused by existing and new narrowband services and evolving broadband services, the enhancement of the existing public telecommunication transport network is necessary. For this purpose an optical network layer with cross-connect and add/drop functionalities will be added to the existing transport network. A comparative analysis of space, time, and optical frequency division multiplexing has shown that for the time being optical frequency multiplexing is best suited for the realization of that new network layer. This multiplexing scheme offers the greatest advantages such as very high bandwidth utilization in the fiber and simple and efficient cross-connecting of high bitrate streams. In the near future, technology will be mature enough for the realization of a demonstrator network based on optical frequency division multiplexing. The functionalities of the optical network are evaluated and the results clearly show that optical frequency conversion and regeneration should be provided by the optical network. The article also deals with the realization aspects (cross-connecting, supervision, and operation and maintenance) of an optical node.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Models of the Posterior Parietal Cortex Which Perform Multimodal Integration and Represent Space in Several Coordinate Frames (2000)

Many neurons in the posterior-parietal cortex (PPC) have saccadic responses to visual and auditory targets. The responses are modulated by eye position and head position. These findings suggest that PPC integrates multisensory inputs and may provide information about saccadic targets represented in different coordinate frames. In addition to an eyecentered output representation, PPC may also project to brain areas which contain head-centered and body-centered representations of the space. In this report, possible coordinate transformations in PPC were examined by comparing several sets of models of PPC, each having different representations in the output layer: (i) an eye-centered map only; (ii) a head-centered map only; (iii) an eye-centered map and a head-centered map; and (iv) an eye-centered map, a head-centered map, and a body-centered map. These output maps correctly encoded saccades to visual and auditory targets through training. The units in the hidden layers of the models exhibited the following properties: (1) The units had gain fields (GFs) for eye position, and also for head position if the model had a body-centered output representation; (2) As the result of the GF and the nonlinear activation function of the units, the hidden layers often employed "intermediate" coding, e.g., the hidden units coded targets partially in eye-centered coordinates and, partially, in head-centered coordinates; (3) Different types of coordinate transformations in these models were carried out by different relationships between the receptive fields (RFs) and the GFs of the hidden units; and (4) The properties of PPC neurons are in better accordance with the hidden units of the models that had multiple-output representations than the models that had only one single-output representation. In conclusion, the results show that the GF is an effective mechanism for performing coordinate transformations. The models also suggest that neurons with intermediate coding are to be expected in the process of coordinate transformations.
High-performance InAs quantum-dot lasers near 1.3 μm (2001)

High-performance quantum dot (QD) lasers near 1.3 μm were fabricated using four stacks of InAs QDs embedded within strained InGaAs quantum wells as an active region and a reactive-ion-etched 5-μm-ridge waveguide design. For a 1.5-mm-long cavity QD laser, ground-state continuous-wave (cw) lasing has been achieved with a single facet output power of 15 mW at temperatures as high as 100 °C, while at room temperature having a differential quantum efficiency of 55% and a single facet output power of 50 mW. The characteristic temperature T0 for ground-state cw lasing is 78 K up to our temperature measurement limit of 100 °C.
Side Population Is Enriched in Tumorigenic, Stem-Like Cancer Cells, whereas ABCG2+ and ABCG2− Cancer Cells Are Similarly Tumorigenic (2005)

Recently, several human cancers including leukemia and breast and brain tumors were found to contain stem-like cancer cells called cancer stem cells (CSC). Most of these CSCs were identified using markers that identify putative normal stem cells. In some cases, stem-like cancer cells were identified using the flow cytometry-based side population technique. In this study, we first show that approximately 30% of cultured human cancer cells and xenograft tumors examined ( approximately 30 in total) possess a detectable side population. Purified side population cells from two cell lines (U373 glioma and MCF7 breast cancer) and a xenograft prostate tumor (LAPC-9) are more tumorigenic than the corresponding non-side population cells. These side population cells also possess some intrinsic stem cell properties as they generate non-side population cells in vivo, can be further transplanted, and preferentially express some "stemness" genes, including Notch-1 and beta-catenin. Because the side population phenotype is mainly mediated by ABCG2, an ATP-binding cassette half-transporter associated with multidrug resistance, we subsequently studied ABCG2+ and ABCG2- cancer cells with respect to their tumorigenicity in vivo. Although side population cells show increased ABCG2 mRNA expression relative to the non-side population cells and all cancer cells and xenograft tumors examined express ABCG2 in a small fraction (0.5-3%) of the cells, highly purified ABCG2+ cancer cells, surprisingly, have very similar tumorigenicity to the ABCG2- cancer cells. Mechanistic studies indicate that ABCG2 expression is associated with proliferation and ABCG2+ cancer cells can generate ABCG2- cells. However, ABCG2- cancer cells can also generate ABCG2+ cells. Furthermore, the ABCG2- cancer cells form more and larger clones in the long-term clonal analyses and the ABCG2- population preferentially expresses several "stemness" genes. Taken together, our results suggest that (a) the side population is enriched with tumorigenic stem-like cancer cells, (b) ABCG2 expression identifies mainly fast-cycling tumor progenitors, and (c) the ABCG2- population contains primitive stem-like cancer cells.
Repetitive structure in the long-terminal-repeat element of a type II human T-cell leukemia virus. (1984)

The majority of human T-cell leukemia virus isolates (HTLV-I) are associated with clinically aggressive adult T-cell leukemia/lymphomas. By contrast, HTLV-II has been isolated from a patient with a relatively benign hairy T-cell leukemia. To characterize differences in the viral genomes that might contribute to these different pathologies, we determined the nucleotide sequence of the long terminal repeat (LTR) of a HTLV-II provirus. Comparison with the type I HTLV LTR reveals that, whereas the overall structural features are similar, the two sequences differ markedly throughout most of the length of the LTR. Despite the overall differences, the sequences of several functional regions of the two LTRs are conserved. These include the 5' boundary of U3, the RNA cap site, and the tRNAPro-binding site immediately 3' to the LTR. Another point of similarity is a 21-base sequence that is repeated four times in the U3 region of HTLV-II and three times in the U3 region of HTLV-I. This sequence has a formal analogy to, but no common sequence with, viral transcriptional enhancers. The U3 region of HTLV-II possesses a series of imperfect tandem direct repeats, 42 bases long, 21 bases long, 19 bases long, and 7 bases long. These structures differ from those of HTLV-I except for the 21-base repeat sequence. Thus, the structure of HTLV-II differs substantially from that of HTLV-I in the region that governs transcriptional initiation and tissue specificity. Such differences may account for some of the differences in clinical presentation of HTLV-associated adult T-cell leukemia/lymphomas and hairy T-cell leukemia.
Transthyretin Protects against A-Beta Peptide Toxicity by Proteolytic Cleavage of the Peptide: A Mechanism Sensitive to the Kunitz Protease Inhibitor (2008)

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the deposition of amyloid beta-peptide (A-Beta) in the brain. Transthyretin (TTR) is a tetrameric protein of about 55 kDa mainly produced in the liver and choroid plexus of the brain. The known physiological functions of TTR are the transport of thyroid hormone T(4) and retinol, through binding to the retinol binding protein. TTR has also been established as a cryptic protease able to cleave ApoA-I in vitro. It has been described that TTR is involved in preventing A-Beta fibrilization, both by inhibiting and disrupting A-Beta fibrils, with consequent abrogation of toxicity. We further characterized the nature of the TTR/A-Beta interaction and found that TTR, both recombinant or isolated from human sera, was able to proteolytically process A-Beta, cleaving the peptide after aminoacid residues 1, 2, 3, 10, 13, 14,16, 19 and 27, as determined by mass spectrometry, and reversed phase chromatography followed by N-terminal sequencing. A-Beta peptides (1-14) and (15-42) showed lower amyloidogenic potential than the full length counterpart, as assessed by thioflavin binding assay and ultrastructural analysis by transmission electron microscopy. A-Beta cleavage by TTR was inhibited in the presence of an alphaAPP peptide containing the Kunitz Protease Inhibitor (KPI) domain but not in the presence of the secreted alphaAPP derived from the APP isoform 695 without the KPI domain. TTR was also able to degrade aggregated forms of A-Beta peptide. Our results confirmed TTR as a protective molecule in AD, and prompted A-Beta proteolysis by TTR as a protective mechanism in this disease. TTR may prove to be a useful therapeutic agent for preventing or retarding the cerebral amyloid plaque formation implicated in AD pathology.
Antisense strategies for glycosylation engineering of Chinese hamster ovary (CHO) cells (1998)

Novel glycoproteins, inaccessible by other techniques, can be obtained by metabolic engineering of the oligosaccharide biosynthesis pathway. Furthermore, alteration of cell-surface oligosaccharides can change the properties of receptors involved in cell–cell adhesion. Sialyl Lewis X (sLex) is a cell-surface oligosaccharide determinant which is specifically expressed on granulocytes and monocytes and which interacts with selectins to influence leukocyte trafficking, thrombosis, inflammation, and cancer. Antisense technology targeting fucosyltransferase VI (Fuc-TVI), an enzyme necessary for the synthesis of the sLex in engineered Chinese hamster ovary (CHO) cells, has reduced Fuc-TVI activity, sLex synthesis, and adhesion to endothelial cells. Antisense methodology to reduce targeted activity in oligosaccharide biosynthesis or other pathways is an important addition to CHO cell metabolic engineering capabilities. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:445–450, 1998.
Asymmetric Thermal Transformation, a New Way to Enantiopure Biphenyl-Bridged Titanocene and Zirconocene Complexes:  Efficient Catalysts for Asymmetric Imine Hydrogenation1 (1999)

Enantiopure biphenyl-bridged titanocene and zirconocene complexes were obtained, by an asymmetric thermal transformation of the binaphthol complexes formed from the metallocene racemates and subsequent transformation to the corresponding dichlorides, in practically quantitative yields. Increased rates of this transformation in the presence of O2 gas or TEMPO indicate a radical reaction mechanism. The biphenyl-bridged titanocene enantiomers give rise to an efficient asymmetric catalysis for the hydrogenation of cyclic and noncyclic imines.
Runtime power monitoring in high-end processors: methodology and empirical data (2003)

With power dissipation becoming an increasingly vexing problem across many classes of computer systems, measuring power dissipation of real, running systems has become crucial for hardware and software system research and design. Live power measurements are imperative for studies requiring execution times too long for simulation, such as thermal analysis. Furthermore, as processors become more complex and include a host of aggressive dynamic power management techniques, per-component estimates of power dissipation have become both more challenging as well as more important. In this paper we describe our technique for a coordinated measurement approach that combines real total power measurement with performance-counter-based, per-unit power estimation. The resulting tool offers live total power measurements for Intel Pentium 4 processors, and also provides power breakdowns for 22 of the major CPU subunits over minutes of SPEC2000 and desktop workload execution. As an example application, we use the generated component power breakdowns to identify program power phase behaviour. Overall, this paper demonstrates a processor power measurement and estimation methodology and also gives experiences and empirical application results that can provide a basis for future power-aware research.
Turnabout is fair play (2012)

Pathogen attachment to host tissues is one of the initial and most crucial events during the establishment of bacterial infections and thus interference with this step could be an efficient strategy to fight bacterial colonization. Our recent work has identified one of the factors involved in initial binding of host cells by a wide range of Gram-negative pathogens, Multivalent Adhesion Molecule (MAM) 7. Interference with MAM7-mediated attachment, for example by pre-incubation of host cells with recombinant MAM7, significantly delays the onset of hallmarks of infection, such as pathogen-mediated cytotoxicity or the development of other adhesive structures such as actin pedestals. Thus, we are trying to develop tools based on MAM7 that can be used to prevent or diminish certain Gram-negative bacterial infections. Herein, we describe the use of bead-coupled MAM7 as an inhibitor of infection with the clinically relevant pathogen Pseudomonas aeruginosa.
Understanding software systems using reverse engineering technology perspectives from the Rigi project (1993)

Software engineering research has focused mainly on software construction and has neglected software maintenance and evolution. Proposed is a shift in research from synthesis to analysis. Reverse engineering is introduced as a possible solution to program understanding and software analysis. Presented is reverse engineering technology developed as part of the Rigi project. The Rigi approach involves the identification of software artifacts in the subject system and the aggregation of these artifacts to form more abstract architectural models. Reported are some analyses on the source code of SQL/DS, performed by the authors while visiting the Program Understanding project at the IBM Centre for Advanced Studies in Toronto.