gebhart/patrepeval huggingface dataset:
Fatty acid biosynthesis in eukaryotic photosynthetic microalgae: Identification of a microsomal delta 12 desaturase in Chlamydomonas reinhardtii (2008)

Polyunsaturated fatty acids (PUFAs) are important components of infant and adult nutrition because they serve as structural elements of cell membranes. Fatty acid desaturases are responsible for the insertion of double bonds into pre-formed fatty acid chains in reactions that require oxygen and reducing equivalents. In this study, the genome-wide characterization of the fatty acid desaturases from seven eukaryotic photosynthetic microalgae was undertaken according to the conserved histidine-rich motifs and phylogenetic profiles. Analysis of these genomes provided insight into the origin and evolution of the pathway of fatty acid biosynthesis in eukaryotic plants. In addition, the candidate enzyme from Chlamydomonas reinhardtii with the highest similarity to the microsomal delta 12 desaturase of Chlorella vulgaris was isolated, and its function was verified by heterologous expression in yeast (Saccharomyces cerevisiae).
Automated response using system-call delays (2000)

Automated intrusion response is an important unsolved problem in computer security. A system called pH (for process homeostasis) is described which can successfully detect and stop intrusions before the target system is compromised. In its current form, pH monitors every executing process on a computer at the system-call level, and responds to anomalies by either delaying or aborting system calls. The paper presents the rationale for pH, its design and implementation, and a set of initial experimental results. 1 Introduction This paper addresses a largely ignored aspect of computer security---the automated response problem. Previously, computer security research has focused almost entirely on prevention (e.g., cryptography, firewalls and protocol design) and detection (e.g., virus and intrusion detection). Response has been an afterthought, generally restricted to increased logging and administrator email. Commercial intrusion detection systems (IDSs) are capable of terminating conne...
Development of a Noise Prediction Model for a Cruise Friendly Circulation Control Wing (2010)

New aircraft concepts that are to meet challenging cruise efficiency, short field takeoff, and noise goals will have to rely on innovative high lift technology. One such technology is the Circulation Control Wing (CCW) which leverages a thin high aspect ratio jet flowing over a curved flap surface to generate tremendous lift coefficients. Of concern is the impact that this technology will have on the overall noise of the aircraft. Some acoustic studies have reported noise characterization of such a CCW with extremely thick airfoils and trailing edges. More practical CCWs must be “cruise friendly”. It is the objective of the current paper to address the noise character of such a CCW configuration and to begin to develop a noise prediction model to assess new aircraft configurations using this technology. A current NASA Fundamental Aeronautics Subsonic Fixed Wing project being conducted by Georgia Tech Research Institute (GTRI) and teammate California Polytechnic State University involves the development of a CCW integrated with engines located over the wing (OTW) to improve the powered high-lift and cruise performance of Cruise Efficient STOL (CESTOL) aircraft. As part of this program, a series of aeroacoustic tests on a 2D model scale CCW are conducted. Far field acoustic data was acquired to quantify the far field noise as a function of aft flyover angles, free stream velocity, and slot jet velocity. It is found that an asymmetrical directivity pattern emerges where higher frequency noise is shielded to observers below the bottom of the flap chord. A 5 order velocity scaling collapses spectra very well for high frequencies and a 6 order works well for lower frequencies. Finally, these data are used as a basis for predicting the community noise of a CESTOL aircraft relative to a conventional take-off and landing aircraft. It was found that using a CCW in conjunction with a STOL trajectory has the potential for reducing overall aircraft noise, however a more complete set of acoustic data on a highly fidelity test article is needed to reduce the uncertainty of the prediction.
High Performance Chemically Amplified Positive Electron-Beam Resist: Optimization of Base Additives for Environmental Stabilization. (1996)

The effects of base additives in chemically amplified positive electron-beam (EB) resist are discussed. The amine additives can improve the resolution of the resist by preventing diffusion of acids outside the exposed area. As a result, 0.1-μm L/S patterns can be obtained, successfully. Additionally, the amine additives can also improve the environmental stability. However, it was demonstrated that the influence on environmental stability differs depending on the chemical structure of amine. The phenomenon is attributable to the process of a proton-base reaction which is investigated by semi-empirical molecular orbital calculation.
Insulators: many functions, many mechanisms (2002)

Eukaryotic genomes are organized into domains containing individual genes and gene clusters that have distinct patterns of expression both during development and in differentiated cells. These genomes contain regulatory elements such as enhancers that are able to activate target genes in cis over considerable distances. They may also contain extended regions of condensed chromatin capable of encroaching on adjacent domains to perturb gene expression. There are a number of ways in which individual domains could be maintained independent of their surroundings through the establishment of boundaries. These boundaries might be variable in position, and established through a balance between countervail
Long-survival in responding patients with metastatic breast cancer treated with doxorubicin-docetaxel combination. A multicentre phase II trial. (2004)

This study confirmed the combination doxorubicin-docetaxel as a very active regimen for metastatic breast cancer. Remarkably long survival times were observed not only in complete responders, but also in those patients who responded partially. This might be equally attributed to first-line treatment and sequential maintenance hormonal therapy.
Highly Successful Therapeutic Vaccinations Combining Dendritic Cells and Tumor Cells Secreting Granulocyte Macrophage Colony-stimulating Factor (2004)

In an attempt to induce potent immune antitumor activities, we investigated, within the rat 9L gliosarcoma model, distal therapeutic vaccinations associating three therapies: dendritic cell vaccination, intratumoral granulocyte macrophage colony-stimulating factor (GM-CSF) gene transfer, and tumor apoptosis induction. Vaccines of dendritic cells coinjected with processed GM-CSF secreting 9L cells induced systemic responses, resulting in the complete regression of distant preimplanted 9L tumor masses in, with the best strategy, 94% of male rats. All of the cured rats developed a long-term resistance to a rechallenge with parental cells. The curative responses were correlated with the detection of elevated specific cytotoxic activities and a CD4+, CD8+ T cell-, and natural killer (NK) cell-mediated IFN-gamma production. The survival rate of the rat seemed more directly linked to the amount of GM-CSF secreted by the transduced tumor cells, which in turn depended on the toxicity of the apoptosis-inducing treatment, than to the level of apoptosis induced. Unexpectedly, alive GM-CSF secreting 9L cells became apoptotic when injected in vivo. Thus we documented the positive role of apoptosis in the induction of therapeutic antitumor responses by comparing, at equal GM-CSF exogenous supply, the effects of dendritic cells coinjected with apoptotic or necrotic 9L cells. The data showed the superior therapeutic efficiency of combined vaccines containing apoptotic tumor cells. In conclusion, vaccinations with dendritic cells associated with apoptotic tumor cells secreting GM-CSF show a very high therapeutic potency that should show promise for the treatment of human cancer.
Phase Space Tweezers for Tailoring Cavity Fields by Quantum Zeno Dynamics (2010)

We discuss an implementation of quantum Zeno dynamics in a cavity quantum electrodynamics experiment. By performing repeated unitary operations on atoms coupled to the field, we restrict the field evolution in chosen subspaces of the total Hilbert space. This procedure leads to promising methods for tailoring nonclassical states. We propose to realize "tweezers" picking a coherent field at a point in phase space and moving it towards an arbitrary final position without affecting other nonoverlapping coherent components. These effects could be observed with a state-of-the-art apparatus.
Identification of Listeria monocytogenes In Vivo-Induced Genes by Fluorescence-Activated Cell Sorting (2001)

Listeria monocytogenes is a gram-positive, intracellular, food-borne pathogen capable of causing severe infections in immunocompromised or pregnant individuals, as well as numerous animal species. Genetic analysis of Listeria pathogenesis has identified several genes which are crucial for virulence. The transcription of most of these genes has been shown to be induced upon entry of Listeria into the host cell. To identify additional genes that are induced in vivo and may be required for L. monocytogenes pathogenesis, a fluorescence-activated cell-sorting technique was initiated. Random fragments of the L. monocytogenes chromosome were cloned into a plasmid carrying a promoterless green fluorescent protein (GFP) gene, and the plasmids were transformed into the L. monocytogenes actA mutant DP-L1942. Fluorescence-activated cell sorting (FACS) was used to isolate L. monocytogenes clones that exhibited increased GFP expression within macrophage-like J774 cells but had relatively low levels of GFP expression when the bacteria were extracellular. Using this strategy, several genes were identified, including actA, that exhibited such an expression profile. In-frame deletions of two of these genes, one encoding the putative L. monocytogenes uracil DNA glycosylase (ung) and one encoding a protein with homology to the Bacillus subtilis YhdP hemolysin-like protein, were constructed and introduced into the chromosome of wild-type L. monocytogenes 10403s. The L. monocytogenes 10403s ung deletion mutant was not attenuated for virulence in mice, while the yhdP mutant exhibited a three- to sevenfold reduction in virulence.
Human Papillomavirus Can Escape Immune Recognition through Langerhans Cell Phosphoinositide 3-Kinase Activation (2005)

Human papillomavirus (HPV) infection of cervical epithelium is linked to the generation of cervical cancer. Although most women infected with HPV clear their lesions, the long latency period from infection to resolution indicates that HPV evolved immune escape mechanisms. Dendritic cells, which are targeted by vaccination procedures, incubated with HPV virus-like particles induce an HPV-specific immune response. Langerhans cells (LC), which are located at the sites of primary infection, do not induce a response implicating the targeting of LC as an immune escape mechanism used by HPV. LC incubated with HPV virus-like particles up-regulate the phosphoinositide 3-kinase (PI3-K) pathway and down-regulate MAPK pathways. With the inhibition of PI3-K and incubation with HPV virus-like particles, LC initiate a potent HPV-specific response. PI3-K activation in LC defines a novel escape mechanism used by HPV, and PI3-K inhibition may serve as an effective clinical target to enhance HPV immunity.
The zinc-finger protein CNBP is required for forebrain formation in the mouse (2003)

Mouse mutants have allowed us to gain significant insight into axis development. However, much remains to be learned about the cellular and molecular basis of early forebrain patterning. We describe a lethal mutation mouse strain generated using promoter-trap mutagenesis. The mutants exhibit severe forebrain truncation in homozygous mouse embryos and various craniofacial defects in heterozygotes. We show that the defects are caused by disruption of the gene encoding cellular nucleic acid binding protein (CNBP); Cnbp transgenic mice were able to rescue fully the mutant phenotype. Cnbp is first expressed in the anterior visceral endoderm (AVE) and, subsequently, in the anterior definitive endoderm (ADE), anterior neuroectoderm (ANE), anterior mesendoderm (AME), headfolds and forebrain. In Cnbp(-/-) embryos, the visceral endoderm remains in the distal tip of the conceptus and the ADE fails to form, whereas the node and notochord form normally. A substantial reduction in cell proliferation was observed in the anterior regions of Cnbp(-/-) embryos at gastrulation and neural-fold stages. In these regions, Myc expression was absent, indicating CNBP targets Myc in rostral head formation. Our findings demonstrate that Cnbp is essential for the forebrain induction and specification.
In vivocloning of PCR products inE.coli (1993)

This report describes an efficient method to clone PCR products exploiting endogenous Escherichia coli enzymatic activities. PCR products are engineered to contain terminal sequences identical to sequences at the two ends of a linearized vector. PCR products and vector DNA are then simply co-transfected into E. coli strain JC8679, obviating the requirement for enzymatic treatment of the PCR product or in vitro ligation. The high rate of homologous recombination in this strain results in efficient incorporation of the insert into the vector, a process we refer to as in vivo cloning (IVC).
Natural Killer Cell-Mediated Killing of Freshly Isolated Neuroblastoma Cells (2004)

In the present study, we assessed the susceptibility of freshly isolated neuroblastoma cells to killing mediated by normal human natural killer (NK) cells and analyzed the receptor-ligand interactions that regulate this event. We show that killing of freshly isolated neuroblasts, similar to neuroblastoma cell lines, involves NKp46 and NKp30 (natural cytotoxicity receptors). However, freshly isolated neuroblasts were generally more resistant to NK-mediated lysis than conventional neuroblastoma cell lines. Moreover, a significant heterogeneity in susceptibility to lysis existed among neuroblastomas derived from different patients. Remarkably, susceptibility to lysis directly correlated with the surface expression, on neuroblasts, of poliovirus receptor [PVR (CD155)], a ligand for the DNAX accessory molecule-1 [DNAM-1 (CD226)] triggering receptor expressed by NK cells. Indeed, PVR-expressing neuroblastomas were efficiently killed by NK cells. Moreover, monoclonal antibody-mediated masking of either DNAM-1 (on NK cells) or PVR (on neuroblasts) resulted in strong inhibition of tumor cell lysis. Thus, assessment of the PVR surface levels may represent a novel useful criterion to predict the susceptibility/resistance of neuroblastomas to NK-mediated killing.
Cyclooxygenase Inhibitors and the Antiplatelet Effects of Aspirin (2001)

The concomitant administration of ibuprofen but not rofecoxib, acetaminophen, or diclofenac antagonizes the irreversible platelet inhibition induced by aspirin. Treatment with ibuprofen in patients with increased cardiovascular risk may limit the cardioprotective effects of aspirin.
Analysis of cross-species IgG binding to human and mouse Fcgamma receptors (FcγRs) (138.29) (2010)

Abstract Monoclonal antibodies from various species are in therapeutic and diagnostic use and are used extensively in cell depletion studies in rodents. Therefore, in the present investigation the cross-species IgG binding to FcγRs were performed using recombinant dimeric soluble form of human and mouse FcγRs. We observed that human CD16A was able to bind to rabbit IgG better than human CD32AH and CD32AR. The binding specificity is hCD16&amp;gt;hCD32AH&amp;gt;&amp;gt;hCD32R. Both hCD32A alleles were able to bind mouse and rat IgG subtypes, whereas hCD16 binds weakly. hCD32AR binds mouse IgG1, IgG2a and IgG2b but not IgG3 (IgG1&amp;gt;&amp;gt;IgG2a≥IgG2b) whereas CD32AH binds IgG2a and IgG2b (IgG2a≥IgG2b) only not IgG1 and IgG3. With rat IgG subtypes, hCD32AR binds IgG1&amp;gt;IgG2a&amp;gt;&amp;gt;IgG2b and hCD32AH binds IgG1&amp;gt;IgG2b&amp;gt;IgG2a whereas neither hCD32A alleles bound to IgG2c. We observed that hCD32AR allele binds stronger than hCD32AH to rat IgG. With human IgG subtypes, both hCD16A and hCD32AR binds IgG3&amp;gt;IgG1&amp;gt;&amp;gt;&amp;gt;IgG2≥IgG4, whereas hCD32AH binds IgG3&amp;gt;IgG1&amp;gt;IgG2&amp;gt;&amp;gt;&amp;gt;IgG4. We have also characterized binding specificity of mouse FcγRs (mCD16A, mCD32B and mFcRIV) to rabbit and mouse IgGs. All three mFcγRs binds to rabbit IgG. For mouse IgG subtypes, mCD16A binds IgG2b&amp;gt;IgG2a≥IgG1, mCD32B binds IgG1≥IgG2b&amp;gt;IgG2a, whereas FcRIV binds IgG2a≥IgG2b only, none of the mFcγR bound to mIgG3. In conclusion, cross-species FcγR binding to different IgGs must be taken into consideration when IgG based therapeutics and diagnostics are evaluated in rodents.
Decision tree classification of proteins identified by mass spectrometry of blood serum samples from people with and without lung cancer (2003)

A classification and regression tree (CART) model was trained to classify 41 clinical specimens as disease/nondisease based on 26 variables computed from the mass-to-charge ratio (m/z) and peak heights of proteins identified by mass spectroscopy. The CART model built on all of the specimens (no cross-validation) had an error rate of 4/41 = 10%. The CART model suggests that mass spectra peaks in the 8000-10,000, 20,000-30,000, 45,000-60, 000, and >125,000 m/z ranges may be valuable in distinguishing between the disease/nondisease specimens. The area under the receiver operating characteristics curve was 0.80 +/- 0.07 for leave-one-out cross-validation.
Tumour-associated macrophages are related to progression in patients with metastatic melanoma following interleukin-2 based immunotherapy (2006)

The aim of the present study was to analyze whether leukocyte subsets in peripheral blood and tumour biopsies obtained before treatment were able to predict response or survival in patients with metastatic melanoma following Interleukin-2 (IL-2) based immunotherapy. Flow cytometry was performed on peripheral blood for CD4(+) T cells, CD8(+) T cells and CD56(+) natural killer (NK) cells. Immunohistochemical analyses were used to identify CD4(+) T cells, CD8(+) T cells, CD57(+) NK cells and CD64(+) (macrophages) cells in tumour biopsies. High numbers of tumour-associated CD64(+) macrophages in tumour biopsies were statistically significantly associated with poor response to treatment. Our data suggest that tumour-associated macrophages may correlate negatively with response, which may be of biological importance for IL-2 based immunotherapy of malignant melanoma.
Quantitative approach to biochemical structure-activity relationships (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantitative approach to biochemical structure-activity relationshipsCorwin HanschCite this: Acc. Chem. Res. 1969, 2, 8, 232–239Publication Date (Print):August 1, 1969Publication History Published online1 May 2002Published inissue 1 August 1969https://pubs.acs.org/doi/10.1021/ar50020a002https://doi.org/10.1021/ar50020a002research-articleACS PublicationsRequest reuse permissionsArticle Views1844Altmetric-Citations765LEARN 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
Decomposition Pathways and in Vitro HIV Inhibitory Effects of IsoddA Pronucleotides:  Toward a Rational Approach for Intracellular Delivery of Nucleoside 5‘-Monophosphates (1996)

The decomposition pathways and kinetics in various biological media and the in vitro anti-HIV-1 and anti-HIV-2 activities of four derivatives of the 5'-mononucleotide of isoddA incorporating carboxylate esterase-labile transient phosphate protecting groups are reported and compared: namely, two mononucleoside aryl phosphoramidate derivatives 1a,b and two mononucleoside phosphotriester derivatives incorporating two S-acyl-2-thioethyl groups 2a,b. All four compounds show better antiviral activity, compared to the parent nucleoside analog isoddA. The results highlight that both types of compounds act as pronucleotides, i.e. they exert their antiviral effect via intracellular delivery of the 5'-mononucleotide of isoddA. The results may give insights for the design of new more efficient pronucleotides.
Spectral Profiling for the Simultaneous Observation of Four Distinct Fluorescent Proteins and Detection of Protein-Protein Interaction via Fluorescence Resonance Energy Transfer in Tobacco Leaf Nuclei (2002)

The control of subcellular localization of proteins and their interaction with other partners in vivo are important parameters that provide clues to their function and regulation. The ability to simultaneously track multiple protein species with high resolution should provide a valuable assay system to study and characterize various types of posttranslational control pathways. In this work, we established the system and a method involving "spectral profiling" for the resolution of four different fluorescent protein tags in the same viewing field using digital imaging technology. With these techniques, we have (a) developed new derivatives of mGFP5, which is commonly used in the plant field, that are about three times brighter; (b) demonstrated that four spectrally distinct fluorescent proteins (cyan, green, yellow, and red) that are fused to a transcription factor could be stably expressed in nuclei and distinguished in tobacco (Nicotiana tabacum) mesophyll cells; and (c) shown that interaction between partners of a dimeric transcription factor can be detected by measuring fluorescence resonance energy transfer. These technologies should help one to study protein-protein interactions efficiently, especially for nuclear proteins under in vivo conditions.
Stereocontrolled Photoinduced Glycosylation Using an Aryl Thiourea as an Organo photoacid (2016)

Photoinduced glycosylation of alcohols with α-glucosyl trichloroacetimidates, using aryl urea and thioureas as organo photoacids, was examined under long wavelength UV (ultraviolet) irradiation. The results show, for the first time, that such glycosylations proceed effectively to give the corresponding glycosides in high yields. In addition, high β-stereoselectivity was obtained under high concentration conditions, whereas high α-stereoselectivity was realized under low concentration conditions.
The small GTP-binding protein Rac is a regulator of cell death in plants (1999)

Cell death plays important roles in the development and defense of plants as in other multicellular organisms. Rapid production of reactive oxygen species often is associated with plant defense against pathogens, but their molecular mechanisms are not known. We introduced the constitutively active and the dominant negative forms of the small GTP-binding protein OsRac1, a rice homolog of human Rac, into the wild type and a lesion mimic mutant of rice and analyzed H(2)O(2) production and cell death in transformed cell cultures and plants. The results indicate that Rac is a regulator of reactive oxygen species production as well as cell death in rice.