gebhart/patrepeval huggingface dataset:
Expression of the quorum-sensing regulatory protein LasR is strongly affected by iron and oxygen concentrations in cultures of Pseudomonas aeruginosa irrespective of cell density (2005)

The expression of the transcriptional regulatory protein LasR, a main component of the quorum-sensing (QS) system in Pseudomonas aeruginosa, was recently found to be sensitive to several environmental factors in addition to its dependency on cell density. However, the inherent effects of the different factors have seldom been separately demonstrated due to concurrent changes of culture conditions in typical experimental settings. Furthermore, the interplays of the different factors are unknown. In this work, the effects and interplay of iron concentration and dissolved oxygen tension (pO(2)) on the expression of lasR in P. aeruginosa were studied in defined growth media with varied iron concentration and pO(2) values in computer-controlled batch and continuous cultures. beta-Galactosidase activity in a recombinant P. aeruginosa PAO1 (NCCB 2452) strain with a lasRp-lacZ fusion was used as a reporter for lasR expression. In batch culture with a constant pO(2) approximately 10 % air saturation, a strong correlation between the exhaustion of iron and the increase of lasR expression was observed. In continuous culture with nearly constant cell density but varied pO(2) values, lasR expression generally increased with increasing oxidative stress with the exception of growth under O(2)-limited conditions (pO(2) approximately equal to 0 %). Under O(2) limitation, the expression of lasR strongly depended on the concentration of iron. It showed a nearly twofold increase in cells grown under iron deprivation in comparison with cells grown in iron-replete conditions and reached the expression level seen at high oxidative stress. A preliminary proteomic analysis was carried out for extracellular proteins in samples from batch cultures grown under different iron concentrations. Several of the extracellular proteins (e.g. AprA, LasB, PrpL) which were up-regulated under iron-limited conditions were found to be QS regulated proteins. Thus, this study clearly shows the links between QS and genes involved in iron and oxygen regulation in P. aeruginosa.
Probing the Cytotoxicity of Semiconductor Quantum Dots (2003)

With their bright, photostable fluorescence, semiconductor quantum dots show promise as alternatives to organic dyes for biological labeling. Questions about their potential cytotoxicity, however, remain unanswered. While cytotoxicity of bulk cadmium selenide (CdSe) is well documented, a number of groups have suggested that CdSe QDs are cytocompatible, at least with some immortalized cell lines. Using primary hepatocytes as a liver model, we found that CdSe-core QDs were indeed acutely toxic under certain conditions. Specifically, we found that the cytotoxicity of QDs was modulated by processing parameters during synthesis, exposure to ultraviolet light, and surface coatings. Our data further suggests that cytotoxicity correlates with the liberation of free Cd<sup>2+</sup> ions due to deterioration of the CdSe lattice. When appropriately coated, CdSe-core QDs can be rendered non-toxic and used to track cell migration and reorganization <i>in vitro</i>. Our results inform design criteria for the use of QDs in vitro and especially in vivo where deterioration over time may occur.
Mixed phosphine/N-heterocyclic carbene palladium complexes: synthesis, characterization and catalytic use in aqueous Suzuki–Miyaura reactions (2013)

A series of N-heterocyclic carbene (NHC)/PR3 palladium(II) and palladium(0) complexes has been synthesized and fully characterized. X-ray crystallographic data have allowed comparison of ligand steric properties. The NHC ligand was found to vary its steric properties as a function of the phosphine co-ligand. These complexes display interesting catalytic properties in the Suzuki-Miyaura reaction performed in aqueous media. The pre-catalyst [PdCl2(IPr)(XPhos)] (IPr = N,N'-bis-(2,6-diisopropylphenyl)imidazol-2-ylidene; XPhos = 2-dicyclohexylphosphino-2',4',6'-triisopropylbiphenyl) was found to be the most efficient system, promoting the coupling of a wide range of aryl chlorides with boronic acids in aqueous media with a typical catalyst loading of 0.03 mol%.
Evolution of the soluble diiron monooxygenases (2003)

Based on structural, biochemical, and genetic data, the soluble diiron monooxygenases can be divided into four groups: the soluble methane monooxygenases, the Amo alkene monooxygenase of Rhodococcus corallinus B-276, the phenol hydroxylases, and the four-component alkene/aromatic monooxygenases. The limited phylogenetic distribution of these enzymes among bacteria, together with available genetic evidence, indicates that they have been spread largely through horizontal gene transfer. Phylogenetic analyses reveal that the alpha- and beta-oxygenase subunits are paralogous proteins and were derived from an ancient gene duplication of a carboxylate-bridged diiron protein, with subsequent divergence yielding a catalytic alpha-oxygenase subunit and a structural beta-oxygenase subunit. The oxidoreductase and ferredoxin components of these enzymes are likely to have been acquired by horizontal transfer from ancestors common to unrelated diiron and Rieske center oxygenases and other enzymes. The cumulative results of phylogenetic reconstructions suggest that the alkene/aromatic monooxygenases diverged first from the last common ancestor for these enzymes, followed by the phenol hydroxylases, Amo alkene monooxygenase, and methane monooxygenases.
Fully Transparent ZnO Thin‐Film Transistor Produced at Room Temperature (2005)

Fully transparent thin-film transistors (TFTs) are produced at room temperature by radiofrequency magnetron sputtering. Measuring the drain current (IDS) as a function of drain voltage (VDS) at different gate voltages (VGS) shows the TFTs possess “hard saturation” with on-currents of about 0.2 mA (see Figure) and saturation mobilities of 20 cm2 V–1 s–1. The optical and electrical properties and the compatibility of the fabrication process with low-cost plastic substrates show promise for invisible and flexible electronic circuits.
Home treatment of obstructive sleep apnoea with continuous positive airway pressure applied through a nose-mask. (1984)

Continuous positive airway pressure (CPAP) applied through the nose completely prevented obstructive apnoea during all night testing in 50 patients with severe obstructive apnoea. In early 1981, we began a home treatment trial of nasal CPAP. Patients were treated in hospital for 3 to 5 nights, a period in which they were trained to fit the custom made nose-mask used to provide nasal CPAP. Patients subsequently continued treatment at home. Daytime somnolence resolved within days of starting therapy, and did not recur while the nasal CPAP unit was used on a regular basis. At present, we have 35 patients who have been on therapy for periods ranging between 3 and 30 months. Although each patient has displayed a reduction of severity of the underlying sleep apnoea when tested without nasal CPAP, the majority continue to require regular nightly nasal CPAP. In a few patients, treatment with nasal CPAP appeared to help in weight control such that obstructive apnoea and snoring have resolved. Nasal CPAP is a safe, fully effective therapy for obstructive apnoea, and can be used indefinitely by the patient at home.
Virologic and Immunologic Characterization of Long-Term Survivors of Human Immunodeficiency Virus Type 1 Infection (1995)

Subjects who remain asymptomatic for many years despite HIV-1 infection have low levels of HIV-1 and a combination of strong virus-specific immune responses with some degree of attenuation of the virus.
A phase I trial of the novel proteasome inhibitor PS341 in advanced solid tumor malignancies. (2002)

Given the results of this trial, it is safe and reasonable to recommend treatment with PS341 on the schedule used in this trial at 1.56 mg/m2/dose in Phase II trials. Particular care should be taken with patients with preexisting neuropathy. Further testing in Phase II trials is warranted.
Impaired long‐term memory and long‐term potentiation in N‐type Ca2+channel‐deficient mice (2006)

Voltage-dependent N-type Ca(2+) channels, along with the P/Q-type, have a crucial role in controlling the release of neurotransmitters or neuromodulators at presynaptic terminals. However, their role in hippocampus-dependent learning and memory has never been examined. Here, we investigated hippocampus-dependent learning and memory and synaptic plasticity at hippocampal CA3-CA1 synapses in mice deficient for the alpha(1B) subunit of N-type Ca(2+) channels. The mutant mice exhibited impaired learning and memory in the Morris water maze and the social transmission of food preference tasks. In particular, long-term memory was impaired in the mutant mice. Interestingly, among activity-dependent long-lasting synaptic changes, theta burst- or 200-Hz-stimulation-induced long-term potentiation (LTP) was decreased in the mutant, compared with the wild-type mice. This type of LTP is known to require brain-derived neurotrophic factor (BDNF). It was found that both BDNF-induced potentiation of field excitatory postsynaptic potentials and facilitation of the frequency of miniature excitatory postsynaptic currents (mEPSCs) were reduced in the mutant. Taken together, these results demonstrate that N-type Ca(2+) channels are required for hippocampus-dependent learning and memory, and certain forms of LTP.
Establishment of a Functional Human Immunodeficiency Virus Type 1 (HIV-1) Reverse Transcription Complex Involves the Cytoskeleton (1998)

After interaction of human immunodeficiency virus type 1 (HIV-1) virions with cell surface receptors, a series of poorly characterized events results in establishment of a viral reverse transcription complex in the host cell cytoplasm. This process is coordinated in such a way that reverse transcription is initiated shortly after formation of the viral reverse transcription complex. However, the mechanism through which virus entry and initiation of reverse transcription are coordinated and how these events are compartmentalized in the infected cell are not known. In this study, we demonstrate that viral reverse transcription complexes associate rapidly with the host cell cytoskeleton during HIV-1 infection and that reverse transcription occurs almost entirely in the cytoskeletal compartment. Interruption of actin polymerization before virus infection reduced association of viral reverse transcription complexes with the cytoskeleton. In addition, efficient reverse transcription was dependent on intact actin microfilaments. The localization of reverse transcription to actin microfilaments was mediated by the interaction of a reverse transcription complex component (gag MA) with actin but not vimentin (intermediate filaments) or tubulin (microtubules). In addition, fusion, but not endocytosis-mediated HIV-1 infectivity, was impaired when actin depolymerizing agents were added to target cells before infection but not when added after infection. These results point to a previously unsuspected role for the host cell cytoskeleton in HIV-1 entry and suggest that components of the cytoskeleton promote establishment of the reverse transcription complex in the host cell and also the process of reverse transcription within this complex.
Personal Adaptive Web agent: a tool for information filtering (2002)

This paper highlights the problem of information overload and recall on the WWW. It briefly mentions four categories of solutions which are: Search Engines, Personal Homepages, Information Management Tools, and Information Retrieval Agents. The paper also presents our own framework of a Personal Adaptive Web (PAW) agent and its current results. Our agent uses a real-time database, automatic text analysis, a competitive learning network, and fuzzy logic to learn the different categories of Web documents that the user is interested in, then finds and suggests new similar documents.
Polymer surfaces structured with random or aligned electrospun nanofibers to promote the adhesion of blood platelets (2008)

Fibrous membranes (nonwoven meshes) prepared via electrospinning technique have great potential in tissue engineering. This work is the first study on the behaviors of blood platelets at the nanostructured surface generated by electrospinning. Poly[acrylonitrile-co-(N-vinyl-2-pyrrolidone)] (PANCNVP) that shows excellent antiplatelet adhesion ability was directly electrospun onto its dense membrane surface. Polyacrylonitrile (PAN) samples were used as controls. The depth as well as the density of the nanofibers can be easily controlled. The results showed that the PANCNVP dense membrane certainly suppressed the activation and adhesion of platelets. However, whether the nanofibers and underlying membranes were composed of PAN or PANCNVP, the nanostructured surfaces promoted the activation, adhesion, and orientation of platelets. It was also found that, if the space between fibers was too large or the depth of fibers was too small, the nanostructured surface did not change the property of antiplatelet adhesion of PANCNVP. The promotion of activation and adhesion of platelets was obviously due to the presence of nanofibers, which induced the changes of surface topography and charge.
Cytotoxic ribonuclease chimeras. Targeted tumoricidal activity in vitro and in vivo. (1992)

Monoclonal antibodies to the transferrin receptor or to the T cell antigen, CD5, were chemically linked to mammalian RNase A and found to specifically inhibit protein synthesis in antigen-positive cells. Antibody-mediated specificity of these cytotoxic ribonuclease chimeras (CRCs) was demonstrated in three ways. 1) Toxicity was due to the chemical linkage of RNase to antibody, as the individual components added separately or in combination did not inhibit protein synthesis; 2) the anti-transferrin receptor CRCs inhibited protein synthesis in those cells expressing the human transferrin receptor (K562, U251, Jurkat cells) but had no detectable toxicity to cells lacking the human transferrin receptor (Vero or NIH 3T3 cells); 3) free antibody to either the human transferrin receptor (454A12 or 5E-9) or to the T cell antigen, CD5 (T101), blocked the cytotoxicity of the respective CRC. Two CRC species, designated P1 and P2, that differed in size and stoichiometry of RNase A to antibody, were purified by size-exclusion high performance liquid chromatography. The higher molecular weight P1 conjugate had an IC50 of 20-30 nM, whereas the P2 conjugate had a higher IC50 of 300-500 nM. Bioactivity could be reversibly increased more than 10-fold by freezing. The cytotoxicity of the CRCs was examined in vivo in a solid tumor animal model. Intratumoral injections of an anti-transferrin receptor CRC into established U251 human glioblastoma tumors grown in the flanks of nude mice prevented tumor growth, whereas RNase A mixed with antibody was ineffective. CRCs, therefore, express cytotoxicity in vitro and in vivo. Mammalian nucleases coupled to antibodies may be utilized as cell type-selective cytotoxins and have potential as pharmacologic reagents. The systemic toxicity and immunogenicity observed with mammalian derived cytotoxins may be significantly less than that of the currently employed plant- and bacterial-derived immunotoxins.
A multiscale stochastic image model for automated inspection (1995)

In this paper, we develop a novel multiscale stochastic image model to describe the appearance of a complex threedimensional object in a two-dimensional monochrome image.This formal image model is used in conjunction with Bayesian estimation techniques to perform automated inspection.The model is based on a stochastic tree structure in which each node is an important subassembly of the three-dimensional object.The data associated with each node or subassembly is modeled in a wavelet domain.We use a fast multiscale search technique to compute the sequential MAP (SMAP) estimate of the unknown position, scale factor, and 2-D rotation for each subassembly.The search is carried out in a manner similar to a sequential likelihood ratio test, where the process advances in scale rather than time.The results of this search determine whether or not the object passes inspection.A similar search is used in conjunction with the EM algorithm to estimate the model parameters for a given object from a set of training images.The performance of the algorithm is demonstrated on two different real assemblies. I. INTRODUCTIONF ORMAL mathematical image models have long been used in the design of image processing algorithms for applications such as compression, restoration, and enhancement [1].Such models are traditionally low level stochastic models of limited complexity.In recent years, however, important theoretical advances and increasingly powerful computers have led to more complex and sophisticated image models.Depending on the application, researchers have proposed both low-level and high-level models.Low-level image models describe the behavior of individual image pixels relative to one another.Markov random fields and other spatial interaction models have proven useful for a variety of applications, including image segmentation and restoration [2]; [3].Bouman and Shapiro [4], along with Willsky, Benveniste, and their associates [5], [6], have developed multiscale stochastic models for image data.High-level models are generally used to describe a more restrictive class of images.These models describe larger struc-
Hereditary Protein S Deficiency: Clinical Manifestations (1987)

To analyze the clinical manifestations of protein S deficiency, we evaluated 136 members of 12 families with the disorder. Seventy-one persons were found to be heterozygous for protein S deficiency, which is inherited as an autosomal dominant trait. Venous thrombotic events occurred in 39 patients (55%) and were recurrent in 77%. Most symptomatic patients had various combinations of deep venous thrombosis (74%), superficial thrombophlebitis (72%), and pulmonary embolism (38%), either in succession or simultaneously. On five occasions thrombosis was found at unusual sites, like the axillary, mesenteric, and cerebral veins. The age at the first thrombotic event ranged from 15 to 68 years (mean, 28 years), and at age 35 the probability to be still free of thrombosis was only 32%. Fifty-six percent of the thrombotic events were not preceded by a precipitating condition. In these respects protein S deficiency is similar to protein C deficiency.
A dynamic transcriptomic atlas of cytokine-induced killer cells (2018)

Several clinical immunotherapy trials with cytokine-induced killer (CIK) cells have been reported. However, molecular evidence of cell expansion, acquisition of tumor cytotoxicity, and safety of CIK cells is required before putting them to clinical use. Here, we performed dynamic transcriptomic analyses of CIKs generated from primary peripheral blood mononuclear cells exposed to interferon-γ, OKT3, and interleukin-2. CIK mRNAs were extracted and sequenced at days 0, 1, 7, and 14 and subjected to bioinformatics analyses. Using weighted correlation network analysis (WGCNA), we identified two major gene modules that mediate immune cell activation and mitosis. We found that activation and cytotoxicity of CIK cells likely rely on cluster of differentiation 8 (CD8) and its protein partner LCK proto-oncogene, Src family tyrosine kinase (LCK). A time-course series analysis revealed that CIK cells have relatively low immunogenicity because of decreased expression of some self-antigens. Importantly, we identified several crucial activating receptors and auxiliary adhesion receptors expressed on CIK cells that may function as tumor sensors. Interestingly, cytotoxicity-associated genes, including those encoding PRF1, GZMB, FASL, and several cytokines, were up-regulated in mature CIK cells. Most immune-checkpoint molecules and inflammatory tumor-promoting factors were down-regulated in the CIK cells, suggesting efficacy and safety in future clinical trials. Notably, insulin-like growth factor 1 (IGF-1) was highly expressed in CIK cells and may promote cytotoxicity, although it also could facilitate tumorigenesis. The transcriptomic atlas of CIK cells presented here may inform efforts to improve CIK-associated tumor cytotoxicity and safety in clinical trials.
The collective stance in modeling expertise in individuals and organizations (1994)

This paper is concerned with modeling the nature of expertise and its role in society in relation to research on expert systems and enterprise models. It argues for the adoption of a collective stance in which the human species is viewed as a single organism recursively partitioned in space and time into sub-organisms that are similar to the whole. These parts include societies, organizations, groups, individuals, roles, and neurological functions. Notions of expertise arise because the organism adapts as a whole through adaptation of its interacting parts. The phenomena of expertise correspond to those leading to distribution of tasks and functional differentiation of the parts. The mechanism is one of positive feedback from parts of the organism allocating resources for action to other parts on the basis of those latter parts past performance of similar activities. Distribution and differentiation follow if performance is rewarded, and low performers of tasks, being excluded by the feedback mechanism from opportunities for performance of those tasks, seek out alternative tasks where there is less competition. The knowledge-level phenomena of expertise, such as meaning and its representation in language and overt knowledge, arise as byproducts of the communication, coordination and modeling processes associated with the basic exchange-theoretic behavioral model. The model is linked to existing analyses of human action and knowledge in biology, psychology, sociology and philosophy, and is used to analyze the role of information technology in supporting activities in the lifeworld.