gebhart/patrepeval huggingface dataset:
Differential Expression of Leukocyte Receptor Complex-Encoded Ig-Like Receptors Correlates with the Transition from Effector to Memory CTL (2001)

The human leukocyte receptor complex (LRC) on chromosome 19q13.4 encodes Ig superfamily receptors expressed on hemopoietic cells. Killer Ig-like receptors (KIR) are expressed in cytotoxic lymphocytes but other LRC molecules (Ig-like transcript(ILT)/leukocyte Ig-like receptor (LIR)) are more ubiquitous. We investigated expression of the ILT2/LIR1 inhibitory receptor compared with the related KIR. Both ILT2/LIR1 and KIR were expressed by peripheral CD8(+) T cells with a memory/effector phenotype. ILT2/LIR1(+) T cells demonstrated diverse TCRBV repertoires in contrast to KIR(+) T cells, while numbers of peripheral ILT2/LIR1(+) T cells were greater than KIR(+) T cells and the majority of ILT2/LIR1(+) T cells did not coexpress KIR. Analysis of CD8(+) T cells with specific HLA class I tetramers confirmed this pattern of expression, indicating differential regulation of LRC gene expression in T lymphocytes. Only a minor proportion of ILT2/LIR1(+) KIR(-) clones survived in vitro cloning, were more susceptible to anti-CD3 or cognate peptide induced cell death than KIR(+) T cells and exhibited lower levels of the Bcl-2 survival molecule. Our results indicate a sequential program of LRC-encoded receptor expression with initial ILT2/LIR1 expression in effector T cells and KIR gene transcription in the minor proportion of expanded clones which survives activation-induced cell death to become long term memory T cells.
Transient-grating frequency-resolved optical gating (1997)

We introduce a transient-grating beam geometry for frequency-resolved optical-gating measurements of ultrashort laser pulses and show that it offers significant advantages over currently used geometries. Background free and phase matched over a long interaction length, it is the most sensitive third-order pulse-measurement geometry. In addition, for pulses greater than ~300 fs in length and ~1 microJ in energy, the nonlinear medium can be removed and the nonlinearity of air can be used to measure the pulse.
Gene-knockdown in the honey bee mite Varroa destructor by a non-invasive approach: studies on a glutathione S-transferase (2010)

Our findings on V. destructor are the first report of gene knockdown in any mite species and demonstrate that the small size of such organisms is not a major impediment to applying gene knockdown approaches to the study of such parasitic pests. The immersion in dsRNA solution method provides an easy, inexpensive, relatively high throughput method of gene silencing suitable for studies in V. destructor, other small mites and immature stages of ticks.
Market-based Proportional Resource Sharing for Clusters (2000)

Enabling technologies in high speed communication and global process scheduling have pushed clusters of computers into the mainstream as general-purpose high-performance computing systems. More generality, however, implies more sharing and this raises new questions in the area of cluster resource management. In particular, in systems where the aggregate demand for computing resources can exceed the aggregate supply, how to allocate resources amongst competing applications is an important problem. Traditional solutions to this problem have focused mainly on global optimization with respect to system-centric performance metrics, metrics which ignore higher level user intent. In this paper, we propose an alternative market-based approach based on the notion of a computational economy which optimizes for user value. Starting with fundamental requirements, we describe an abstract architecture for market-based cluster resource management based on the idea of proportional resource sharing of basic computing resources. Using this architecture, we have implemented a 32-node (64 processors) prototype system that provides a market for time-shared CPU usage for sequential and parallel programs. To begin evaluating our ideas, we are currently in the process of studying how users respond to the system by collecting data on real day-to-day usage of the cluster
Acellular Normal and Fibrotic Human Lung Matrices as a Culture System for In Vitro Investigation (2012)

This methodology is expected to allow investigation of important ECM-based hypotheses in human tissues and permits future scientific exploration in an organ- and disease-specific manner.
Biochemical properties of subsarcolemmal and interfibrillar mitochondria isolated from rat cardiac muscle (1977)

Two populations of mitochondria were observed upon ultrastructural examination of cardiac muscle tissue, one located directly beneath the sarcolemma (subsarcolemmal mitochondria) and another between the myofibrils (interfibrillar mitochondria). Subsarcolemmal mitochondria were released by treatment of heart muscle with a Polytron tissue processor, while interfibrillar mitochondria were released by nagarse digestion of the remaining tissue. These results were supported by electron microscopy of Polytron-treated heart tissue showing rupture and loss of sarcolemma with release of the underlying mitochondria but with retention of intact mitochondria between the myofibrils. Electron microscopy of the isolated mitochondria indicated that both mitochondrial types maintained their structural integrity throughout the isolation procedure. Specific activities of succinate dehydrogenase and citrate synthase were higher in the interfibrillar mitochondria as compared to the subsarcolemmal mitochondria, while those of carnitine palmitoyltransferase and alpha-glycerophosphate dehydrogenase were nearly the same in both. Interfibrillar mitochondria oxidized all substrates tested approximately 1.5 times faster than did the subsarcolemmal mitochondria. Thus the two mitochondrial types differed not only in their respective locations in the cell, but also in certain biochemical properties.
Microbiota of De-Novo Pediatric IBD: Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis (2012)

Our results offer a comprehensive examination of the IBD mucosal microbiota at diagnosis, unaffected by therapeutic confounders or changes over time. Our results challenge the current model of a protective role for F. prausnitzii in CD, suggesting a more dynamic role for this organism than previously described.
Induction of psoriasiform inflammation by a bacterial superantigen in the SCID‐hu xenogeneic transplantation model (1997)

Psoriasis is a chronic skin disease affecting about 2% of the Caucasian population, characterized by co-existing inflammation and epidermal hyperproliferation. A T-lymphocyte-mediated autoimmune reaction induced by bacterial superantigens might be central in its pathogenesis. To model psoriasiform inflammation, we transplanted clinically uninvolved skin from psoriatic patients onto SCID mice. Repetitive intradermal injections with a bacterial superantigen and simultaneous intraperitoneal injections with the patients superantigen-stimulated peripheral mononuclear blood cells resulted in an inflammatory reaction exhibiting some of the hallmarks of psoriasis, e.g. epidermal hyperproliferation, papillomatosis, focal neo-expression of ICAMI, and an exocytotic T-lymphocytic infiltrate characterized by the expression of the cutaneous lymphocyte-associated antigen. These observations document the potential of superantigens to trigger psoriasiform dermatitis and provide a model to study lymphocyte homing.
High throughput non-contact SiP testing (2007)

A non-contact method for parallel testing of system-in-package (SiP) assemblies is presented. This technology allows for JTAG testing of partially or fully populated SiPs in wafer form, in advance of final packaging. The technology utilizes non-contact GHz short-range, near field communications to transfer bi-directional data to SiP substrates; creating a wireless test access port or WTAP. The system is integrated with a standard probe card to deliver power and wireless signals. The wireless probes convert high frequency RF (GHz) transceiver signals to standard tester ATE logic levels and allow the use of standard probers and JTAG testers. In addition, all transceivers (DUTand probe) use antenna structures and electronics that are fully CMOS compliant. Enhancing the economics of SiP manufacture by enabling parallel non-contact testing of SiPs before packaging is a key benefit of this technology.
<title>Effects of applied load on bone tissue as observed by Raman spectroscopy</title> (2002)

The skeleton is certainly essential to our physiology. Yet, surprisingly little is understood about how bone responds when a load is applied. This is particularly true at the ultrastructural level, where neither the behavior under stress of the collagenous matrix nor that of the calcium phosphate mineral has been explored. Most standard techniques used in the investigation of the biomechanical properties of bone tissue are unable to obtain information at this level. Raman spectroscopy, however, is capable of probing biological specimens at the molecular level, without interference from water or common histological stains. Using this technique, we are able to observe changes in both the mineral and the matrix of bone during and after the application of load. These changes manifest themselves as band shifts in the bone Raman spectrum. We utilize this ability in this study. Two-dimensional Raman imaging is used to investigate the effect of macroscopic fracture on the mineral in sections of femora from 4-month-old and 18-month-old mice. Changes are seen in the mineral around fractured areas that indicate the fracture process may be causing a phase transformation in the bone mineral, similar to the 'transformation toughening' process that is observed in many ceramics. We discuss the physiological implications of these results.
Antineoplastic agents. 113. Synthesis of natural (-)-combretastatin (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntineoplastic agents. 113. Synthesis of natural (-)-combretastatinGeorge R. Pettit, Sheo Bux Singh, and Gordon M. CraggCite this: J. Org. Chem. 1985, 50, 18, 3404–3406Publication Date (Print):September 1, 1985Publication History Published online1 May 2002Published inissue 1 September 1985https://pubs.acs.org/doi/10.1021/jo00218a032https://doi.org/10.1021/jo00218a032research-articleACS PublicationsRequest reuse permissionsArticle Views548Altmetric-Citations50LEARN 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
Analysis of Homologous Recombination in Cultured Mammalian Cells (1984)

Direct microinjection of DNA into cultured mammalian cells by glass micropipettes provides a number of advantages as a method for studying recombination in somatic cells. We can choose where in the cell the DNA is introduced, the nucleus, cytoplasm, or even cellular organelles such as a mitochondrion. By injecting the DNA directly into the nucleus, we obviate the need for exogenous DNA to transit the cytoplasm. During the transit from cytoplasm to the nucleus, newly introduced DNA may suffer considerable damage (Calos et al. 1983; Razzaque et al. 1983; Wake et al. 1984). The number of plasmid DNA molecules introduced into a cell by microinjection can be controlled within a range of ± 20%. Even with a very low input of plasmid DNA per cell (i.e., 3–5 copies/cell), a high DNA-mediated transformation efficiency of 20–30% is still achieved (Capecchi 1980; Folger et al. 1982). Finally, the form of DNA introduced...
Non-Integrative Lentivirus Drives High-Frequency cre-Mediated Cassette Exchange in Human Cells (2011)

Recombinase mediated cassette exchange (RMCE) is a two-step process leading to genetic modification in a specific genomic target sequence. The process involves insertion of a docking genetic cassette in the genome followed by DNA transfer of a second cassette flanked by compatible recombination signals and expression of the recombinase. Major technical drawbacks are cell viability upon transfection, toxicity of the enzyme, and the ability to target efficiently cell types of different origins. To overcome such drawbacks, we developed an RMCE assay that uses an integrase-deficient lentivirus (IDLV) vector in the second step combined with promoterless trapping of double selectable markers. Additionally, recombinase expression is self-limiting as a result of the exchangeable reaction, thus avoiding toxicity. Our approach provides proof-of-principle of a simple and novel strategy with expected wide applicability modelled on a human cell line with randomly integrated copies of a genetic landing pad. This strategy does not present foreseeable limitations for application to other cell systems modified by homologous recombination. Safety, efficiency, and simplicity are the major advantages of our system, which can be applied in low-to-medium throughput strategies for screening of cDNAs, non-coding RNAs during functional genomic studies, and drug screening.
Decreased Response of Rat Knee Joint Blood Vessels to Phenylephrine in Chronic Inflammation: Involvement of Nitric Oxide (2000)

The effect of chronic inflammation induced by Freund's Complete Adjuvant (FCA) on rat articular blood vessels and knee joint diameter was investigated. Blood flow changes in response to phenylephrine (an 1-adrenoceptor agonist) in FCA-treated and contralateral knee joints were studied over a 40 day period, using the laser Doppler flowmetery (LDF) technique. Unilateral injection of FCA (0.2 ml) increased the injected knee diameter on all days examined post-injection (P < 0.001) and its maximum increase (53 +/- 2 %) was reached on day 3. After this, the diameter decreased gradually but did not return to its initial value. In control animals, topical application of 10-13-10- 7 mol phenylephrine onto the exposed joint capsule decreased blood flow dose dependently (11. 1 +/- 4.4 to 58.2 +/- 4.5 %, respectively, P < 0.001). Unilateral injection with FCA attenuated the phenylephrine response in both ipsilateral and contralateral knees compared with the response of control animals (5.2 +/- 1.6 to 48.3 +/- 6.1 % and 1.9 +/- 2.2 to 45. 3 +/- 5.6 %, respectively, P < 0.05). The reduction persisted for 3 weeks after FCA injection (ipsilateral for 21 days; contralateral for 30 days, P < 0.001). Subsequently the response returned towards normal. To avoid the influence of 2-adrenoceptors, yohimbine (an 2-adrenoceptor antagonist) was injected (0.5 mg kg-1, I.P.) 30 min before phenylephrine application. Yohimbine blocked the vasoconstrictor effect of 10-10-10-7 mol clonidine (an 2-adrenoceptor agonist, topical application) by 44-67.7 % inhibition, respectively (P < 0.001). Prazosin (an 1-adrenoceptor antagonist, 0.1 mg kg-1, I.P.) blocked the vasoconstrictor effect of phenylephrine (10-10-10-7 mol, topical application) effectively (42 to 69.8 % inhibition, respectively, P < 0.001). To assess the role of nitric oxide (NO) on the observed responses, N G-nitro-L-arginine methyl ester (L-NAME, NO synthase inhibitor) was applied topically (0.2 micromol) 5 min before phenylephrine application. L-NAME application at 7 and 14 days after FCA injection potentiated the vasoconstrictor response in the FCA-treated knee (P < 0.001) but had no significant effect on the contralateral knee. Blood pressure monitoring during phenylephrine, clonidine and L-NAME administration indicated that topical application of the drugs had no significant effect on the systemic blood pressure. These findings indicate that the vasoconstrictor response to phenylephrine was decreased in chronic inflammation and increased NO production could be involved.
Oral Microbial Communities: Biofilms, Interactions, and Genetic Systems (2000)

Oral microbial-plaque communities are biofilms composed of numerous genetically distinct types of bacteria that live in close juxtaposition on host surfaces. These bacteria communicate through physical interactions called coaggregation and coadhesion, as well as other physiological and metabolic interactions. Streptococci and actinomyces are the major initial colonizers of the tooth surface, and the interactions between them and their substrata help establish the early biofilm community. Fusobacteria play a central role as physical bridges that mediate coaggregation of cells and as physiological bridges that promote anaerobic microenvironments which protect coaggregating strict anaerobes in an aerobic atmosphere. New technologies for investigating bacterial populations with 16S rDNA probes have uncovered previously uncultured bacteria and have offered an approach to in situ examination of the spatial arrangement of the participant cells in oral-plaque biofilms. Flow cells with saliva-coated surfaces are particularly useful for studies of biofilm formation and observation. The predicted sequential nature of colonization of the tooth surface by members of different genera can be investigated by using these new technologies and imaging the cells in situ with confocal scanning laser microscopy. Members of at least seven genera now can be subjected to genetic studies owing to the discovery of gene-transfer systems in these genera. Identification of contact-inducible genes in streptococci offers an avenue to explore bacterial responses to their environment and leads the way toward understanding communication among inhabitants of a multispecies biofilm.
High UV/visible contrast photodiodes based on epitaxiallateral overgrown GaN layers (1999)

Schottky photodiodes have been fabricated on epitaxial lateral overgrown GaN layers, showing a responsivity of 130 mA/W. An improvement of one order of magnitude in the UV/visible contrast has been observed, in comparison with devices on standard GaN on sapphire. The significantly lower residual doping concentration reduces markedly the leakage current, and increases the detector bandwidth (&gt; 30 MHz in devices with a diameter phis = 200 µm). Detectivities as high as 5 × 109 Hz1/2mW–1 were obtained in photodiodes with phis = 400 µm, working at –3.4 V bias.
A potent and Kv1.3-selective analogue of the scorpion toxin HsTX1 as a potential therapeutic for autoimmune diseases (2014)

HsTX1 toxin, from the scorpion Heterometrus spinnifer, is a 34-residue, C-terminally amidated peptide cross-linked by four disulfide bridges. Here we describe new HsTX1 analogues with an Ala, Phe, Val or Abu substitution at position 14. Complexes of HsTX1 with the voltage-gated potassium channels Kv1.3 and Kv1.1 were created using docking and molecular dynamics simulations, then umbrella sampling simulations were performed to construct the potential of mean force (PMF) of the ligand and calculate the corresponding binding free energy for the most stable configuration. The PMF method predicted that the R14A mutation in HsTX1 would yield a > 2 kcal/mol gain for the Kv1.3/Kv1.1 selectivity free energy relative to the wild-type peptide. Functional assays confirmed the predicted selectivity gain for HsTX1[R14A] and HsTX1[R14Abu], with an affinity for Kv1.3 in the low picomolar range and a selectivity of more than 2,000-fold for Kv1.3 over Kv1.1. This remarkable potency and selectivity for Kv1.3, which is significantly up-regulated in activated effector memory cells in humans, suggest that these analogues represent valuable leads in the development of therapeutics for autoimmune diseases.
Laser Light Scattering in Biomedical Diagnostics and Therapy (1993)

The description of special features of laser light interaction with biotissues, such as the skin, eye and dental tissues etc., with respect to laser diagnostics and therapy methods development is done. Optical models of transparent and turbid biotissues are analyzed. The role of static and dynamic light scattering in the light dosimetry, tissue heating, and receiving information of biotissue optical parameters, its structure, movements, and vibrations is considered.
Intravenous recombinant tissue-type plasminogen activator in patients with acute myocardial infarction: a report from the NHLBI thrombolysis in myocardial infarction trial. (1986)

The efficacy and safety of a 3 hr, 80 mg intravenous infusion of recombinant tissue-type plasminogen activator (rt-PA) were investigated in 47 patients with acute myocardial infarction. Coronary angiography, performed before the administration of rt-PA and for 90 min thereafter, demonstrated that 37 patients had total coronary occlusion before therapy. After 90 min of rt-PA (50 mg), reperfusion of the infarct-related artery was observed in 25 patients (68%). Continuous infusions of heparin for anticoagulation were administered for 8 to 10 days. Of 36 patients who underwent follow-up coronary cineangiography, 21 had initially presented with total occlusion and had experienced reperfusion at 90 min. Sustained perfusion of the infarct-related artery was observed in 14 (67%) of these 21 initially reperfused patients. Late angiography was performed in nine patients who initially demonstrated subtotal occlusion of the infarct-related artery; sustained perfusion was observed in eight (89%). Significant bleeding was observed in 15 patients (32%). A hematoma at the site of the acute catheterization accounted for most instances of significant bleeding (11/15, 73%). Administration of rt-PA resulted in a significant decline in fibrinogen and plasminogen while amounts of fibrin(ogen) degradation products rose. In no patient, however, did fibrinogen levels decline to less than 140 mg/dl. Thus, rt-PA, administered as a brief 80 mg intravenous infusion, is capable of restoring blood flow in a high proportion of patients with acute myocardial infarction due to total coronary obstruction. Declines in plasma fibrinogen and plasminogen are observed. If combined with heparin anticoagulation and invasive vascular procedures, significant bleeding is a common complication.(ABSTRACT TRUNCATED AT 250 WORDS)