gebhart/patrepeval huggingface dataset:
Generation of Induced Pluripotent Stem Cells by Reprogramming Human Fibroblasts with the Stemgent Human TF Lentivirus Set (2009)

In 2006, Yamanaka and colleagues first demonstrated that retrovirus-mediated delivery and expression of Oct4, Sox2, c-Myc and Klf4 is capable of inducing the pluripotent state in mouse fibroblasts.(1) The same group also reported the successful reprogramming of human somatic cells into induced pluripotent stem (iPS) cells using human versions of the same transcription factors delivered by retroviral vectors.(2) Additionally, James Thomson et al. reported that the lentivirus-mediated co-expression of another set of factors (Oct4, Sox2, Nanog and Lin28) was capable of reprogramming human somatic cells into iPS cells.(3) iPS cells are similar to ES cells in morphology, proliferation and the ability to differentiate into all tissue types of the body. Human iPS cells have a distinct advantage over ES cells as they exhibit key properties of ES cells without the ethical dilemma of embryo destruction. The generation of patient-specific iPS cells circumvents an important roadblock to personalized regenerative medicine therapies by eliminating the potential for immune rejection of non-autologous transplanted cells. Here we demonstrate the protocol for reprogramming human fibroblast cells using the Stemgent Human TF Lentivirus Set. We also show that cells reprogrammed with this set begin to show iPS morphology four days post-transduction. Using the Stemolecule Y27632, we selected for iPS cells and observed correct morphology after three sequential rounds of colony picking and passaging. We also demonstrate that after reprogramming cells displayed the pluripotency marker AP, surface markers TRA-1-81, TRA-1-60, SSEA-4, and SSEA-3, and nuclear markers Oct4, Sox2 and Nanog.
Detection of β‐lactamase reporter gene expression by flow cytometry (2003)

The ratiometric fluorescence readout of the beta-lactamase system based on fluorescence resonance energy transfer allowed more sensitive and accurate detection of gene expression than the currently available beta-galactosidase substrates. Further, the cell-permeant nature of the substrate improved experimental convenience. These properties facilitated cell engineering and enabled a variety of applications including selection of rare cells from large populations and measurement of low-expressing or downregulated genes.
Modeling the Effects of Memory Hierarchy Performance on Throughput of Multithreaded Processors (2005)

Understanding the relationship between the performance of the on-chip processor caches and the overall performance of the processor is critical for both hardware design and software program optimization. While this relationship is well understood for conventional processors, it is not understood for new multithreaded processors that hide a workload's memory latency by executing instructions from several threads in parallel. In this paper we present a model for estimating processor throughput as a function of the cache hierarchy performance. Our model has a closed-form solution, is robust against a range of workloads and input parameters, and gives estimates of processor throughput that are within 13% of measured values for heterogeneous workloads. We demonstrate how this model can be used in an operating system scheduler tailored for multithreaded processor systems.
Brain Imaging: Applications in Psychiatry (1988)

Various brain imaging techniques have become available in the past decade. These include techniques to evaluate brain structure, such as computed tomography and magnetic resonance imaging, and techniques to assess functional activity, such as measurement of regional cerebral blood flow, single photon emission computed tomography, and positron emission tomography. These techniques can be used to map brain structure and function in normal human beings, and they have enlarged our knowledge of the pathophysiology of mental illnesses by demonstrating structural, metabolic, and neurochemical abnormalities in a wide range of mental disorders.
Rheumatoid synovium is enriched in mature antigen-presenting dendritic cells. (1994)

Monocytes and dendritic cells (DC) can be purified from fresh peripheral blood (PB) based on their expression of CD33, CD13, and CD14. Whereas DC can be identified as CD33+ CD14dim or CD13+CD14dim cells, monocytes can be identified as CD33+CD14bright or CD13+CD14bright cells. Rheumatoid synovial fluid (SF) and synovial tissue (ST) non-T cells were found to be enriched in CD33+CD14dim cells compared with PB. Whereas 4 to 14% of normal or rheumatoid PB non-T cells were CD33+ and CD14dim, in rheumatoid SF or ST these cells comprised 20 to 45% of non-T mononuclear cells. Synovial CD33+CD14dim cells assumed a typical dendritic morphology on in vitro culture. Freshly isolated CD33+CD14dim PB DC precursors express low levels of HLA-DQ, CD40, and B7, which increase after in vitro incubation. In contrast, freshly isolated SF DC constitutively expressed these markers, and increased densities of HLA-DR and MHC class I molecules. Rheumatoid SF DC showed a specifically enhanced ability to stimulate autologous PB T cells compared with PB DC, or PB or SF monocytes. PB DC or monocytes preincubated in granulocyte-macrophage-CSF, TNF-alpha, or both cytokines exhibited enhanced expression of HLA-DR. Furthermore, DC preincubated in both granulocyte-macrophage-CSF and TNF-alpha were better stimulators of the autologous MLR than DC preincubated in medium, or in either cytokine alone. The data indicate that DC are enriched in rheumatoid SF and ST, and display a more differentiated phenotype than PB DC. These results suggest that PB DC accumulate in the synovium where they undergo phenotypic and functional differentiation in situ, which may be mediated by local cytokines. DC may play an important role in the ongoing presentation of antigen to autoreactive T cells in RA synovium.
Positive regulation of the beta-galactosidase gene from Kluyveromyces lactis is mediated by an upstream activation site that shows homology to the GAL upstream activation site of Saccharomyces cerevisiae. (1987)

In contrast to the Escherichia coli lac operon, the yeast beta-galactosidase gene is positively regulated. In the 5'-noncoding region of the Kluyveromyces lactis LAC4 gene, we mapped an upstream activation site (UAS) that is required for induction. This sequence, located between positions -435 and -326 from the start of translation, functions irrespective of its orientation and can confer lactose regulation to the heterologous CYC1 promoter. It is composed of at least two subsequences that must act in concert. One of these subsequences showed a strong homology to the UAS consensus sequence of the Saccharomyces cerevisiae GAL genes (E. Giniger, S. M. Varnum, and M. Ptashne, Cell 40:767-774, 1985). We propose that this region of homology located at about position -426 is a binding site for the product of the regulatory gene LAC9 which probably induces transcription of the LAC4 gene in a manner analogous to that of the GAL4 protein.
Cardiotrophic Effects of Protein Kinase C ε (2000)

Protein kinase C (PKC) is a key mediator of many diverse physiological and pathological responses. Although little is known about the specific in vivo roles of the various cardiac PKC isozymes, activation-induced translocation of PKC is believed to be the primary determinant of isozyme-specific functions. Recently, we have identified a catalytically inactive peptide translocation inhibitor (epsilonV1) and translocation activator (psiepsilonRACK [receptors for activated C kinase]) specifically targeting PKCepsilon. Using cardiomyocyte-specific transgenic expression of these peptides, we combined loss- and gain-of-function approaches to elucidate the in vivo consequences of myocardial PKCepsilon signaling. As expected for a PKCepsilon RACK binding peptide, confocal microscopy showed that epsilonV1 decorated cross-striated elements and intercalated disks of cardiac myocytes. Inhibition of cardiomyocyte PKCepsilon by epsilonV1 at lower expression levels upregulated alpha-skeletal actin gene expression, increased cardiomyocyte cell size, and modestly impaired left ventricular fractional shortening. At high expression levels, epsilonV1 caused a lethal dilated cardiomyopathy. In contrast, enhancement of PKCepsilon translocation with psiepsilonRACK resulted in selectively increased beta myosin heavy chain gene expression and normally functioning concentric ventricular remodeling with decreased cardiomyocyte size. These results identify for the first time a role for PKCepsilon signaling in normal postnatal maturational myocardial development and suggest the potential for PKCepsilon activators to stimulate "physiological" cardiomyocyte growth.
Evaluation of Off-State Current Characteristics of Transistor Using Oxide Semiconductor Material, Indium–Gallium–Zinc Oxide (2012)

We measured a significantly low off-state current (135 yA/µm at 85 °C) of a metal oxide semiconductor (MOS) transistor using indium–gallium–zinc oxide (IGZO), which is an oxide semiconductor material. Note that "y" is 10-24. A transistor in which the hydrogen concentration in an IGZO film is lowered (5×1019 cm-3 or lower) was used. To estimate the minute current accurately, we established a measurement method in which changes in the amount of electrical charge are measured for a long time. Such extremely low off-state current characteristics show promise for new applications of IGZO transistors in memories.
Strong constraint on ever-presentΛ (2007)

We show that the causal-set approach to creating an ever-present cosmological ``constant'' in the expanding universe is strongly constrained by the isotropy of the microwave background. Fluctuations generated by stochastic lambda generation which are consistent with COBE and WMAP observations are far too small to dominate the expansion dynamics at $z&lt;1000$ and so cannot explain the observed late-time acceleration of the universe. We also discuss other observational constraints from the power spectrum of galaxy clustering and show that the theoretical possibility of ever-present lambda arises only in $3+1$ dimensional space-times.
Trial of Different Intensities of Anticoagulation in Patients with Prosthetic Heart Valves (1990)

We compared the efficacy and complications of anticoagulation with warfarin in 258 patients with prosthetic heart valves treated with regimens of "moderate intensity" (prothrombin-time ratio, 1.5; international normalized ratio, 2.65) or "high intensity" (prothrombin-time ratio, 2.5; international normalized ratio, 9) in a prospective, randomized study. The two patient groups were followed up for 421 patient-years and 436 patient-years, respectively. Eleven patients were lost to follow-up. Thromboembolism occurred with similar frequency in the two groups (4.0 and 3.7 episodes per 100 patient-years, respectively), but there was a total of 6.2 bleeding episodes per 100 patient-years in the moderate-intensity group, as compared with 12.1 episodes in the high-intensity group (P less than 0.002). There were 5.2 episodes of minor bleeding per 100 patient-years in the moderate-intensity group, as compared with 10.1 episodes in the high-intensity group (P less than 0.01). Major bleeding was also more common in the high-intensity group (2.1 episodes per 100 patient-years--including the only two fatal hemorrhages--as compared with 0.95 episode in the moderate-intensity group), but the difference was not statistically significant. We conclude that a moderate anticoagulant effect (prothrombin-time ratio, about 1.5) in patients with a mechanical prosthetic heart valve offers protection equivalent to that of more intensive therapy, but at a significantly lower risk.
A novel p53‐inducible apoptogenic gene, PRG3, encodes a homologue of the apoptosis‐inducing factor (AIF) (2002)

The p53 tumor suppressor protein induces cell cycle arrest or apoptosis in response to cellular stresses. We have identified PRG3 (p53-responsive gene 3), which is induced specifically under p53-dependent apoptotic conditions in human colon cancer cells, and encodes a novel polypeptide of 373 amino acids with a predicted molecular mass of 40.5 kDa. PRG3 has significant homology to bacterial oxidoreductases and the apoptosis-inducing factor, AIF, and the gene was assigned to chromosome 10q21.3-q22.1. Expression of PRG3 was induced by the activation of endogenous p53 and it contains a p53-responsive element. Unlike AIF, PRG3 localizes in the cytoplasm and its ectopic expression induces apoptosis. An amino-terminal deletion mutant of PRG3 that lacks a putative oxidoreductase activity retains its apoptotic activity, suggesting that the oxidoreductase activity is dispensable for the apoptotic function of PRG3. The PRG3 gene is thus a novel p53 target gene in a p53-dependent apoptosis pathway.
Biologically Active Transcripts of Beet Necrotic Yellow Vein Virus RNA-3 and RNA-4 (1988)

Summary Synthetic transcripts of beet necrotic yellow vein virus (BNYVV) RNA-3 and RNA-4 were prepared from cloned cDNA in a bacteriophage T7 in vitro run-off transcription system. The RNA-3 transcripts tested had 5′ non-viral extensions of 1, 23 or 64 nucleotides and identical 3′ non-viral extensions of 12 nucleotides. An RNA-4 transcript with a 12 nucleotide 5′ non-viral extension and a 28 nucleotide 3′ non-viral extension was also synthesized. All of the transcripts were biologically active when coinoculated to Chenopodium quinoa with BNYVV isolates deficient in RNA-3 and/or RNA-4 but the presence of a long 5′ non-viral sequence on the RNA-3 transcripts was found to diminish their specific activities considerably.
Solid-State, Dye-Labeled DNA Detects Volatile Compounds in the Vapor Phase (2008)

This paper demonstrates a previously unreported property of deoxyribonucleic acid-the ability of dye-labeled, solid-state DNA dried onto a surface to detect odors delivered in the vapor phase by changes in fluorescence. This property is useful for engineering systems to detect volatiles and provides a way for artificial sensors to emulate the way cross-reactive olfactory receptors respond to and encode single odorous compounds and mixtures. Recent studies show that the vertebrate olfactory receptor repertoire arises from an unusually large gene family and that the receptor types that have been tested so far show variable breadths of response. In designing biomimetic artificial noses, the challenge has been to generate a similarly large sensor repertoire that can be manufactured with exact chemical precision and reproducibility and that has the requisite combinatorial complexity to detect odors in the real world. Here we describe an approach for generating and screening large, diverse libraries of defined sensors using single-stranded, fluorescent dye-labeled DNA that has been dried onto a substrate and pulsed with brief exposures to different odors. These new solid-state DNA-based sensors are sensitive and show differential, sequence-dependent responses. Furthermore, we show that large DNA-based sensor libraries can be rapidly screened for odor response diversity using standard high-throughput microarray methods. These observations describe new properties of DNA and provide a generalized approach for producing explicitly tailored sensor arrays that can be rationally chosen for the detection of target volatiles with different chemical structures that include biologically derived odors, toxic chemicals, and explosives.
Quantitative myocardial infarction on delayed enhancement MRI. Part II: Clinical application of an automated feature analysis and combined thresholding infarct sizing algorithm (2006)

Abstract Purpose To compare global and regional myocardial infarction (MI) measurements on clinical gadolinium‐enhanced magnetic resonance (MR) images using human manual contouring and a computer algorithm previously validated by histopathology, and to study the degree to which visual assessment and human contouring of infarct extent agreed with the computer algorithm. Materials and Methods Infarct size in 20 patients was measured by human manual contouring and with an automated feature analysis and combined thresholding (FACT) computer algorithm. Short‐axis slices were divided into myocardial sectors for regional analysis. Extent of infarction was also graded visually by consensus of expert readers and compared to human and computer contouring. Results Despite good correlations (R = 0.93–0.95) between human contouring and the FACT algorithm, human contouring overestimated infarct size by 3.8% of the left ventricle (23.8% of the MI) area ( P &lt; 0.001). Human contouring also overestimated the circumferential extent, transmural extent, and extent of infarction within a sector by 7.1%, 18.2%, and 27.9%, respectively (all P &lt; 0.001). Both consensus reading and human contouring overestimated infarct grades compared with the FACT algorithm ( P = 0.002 and P &lt; 0.001). Conclusion Clinically relevant overestimation of MI can occur in visual interpretation and in human manual contouring, particularly with respect to extent of infarction on a regional basis. J. Magn. Reson. Imaging 2006. Published 2006 Wiley‐Liss, Inc.
Outcome Analysis of Helmet Therapy for Positional Plagiocephaly Using a Three-Dimensional Surface Scanning Laser (2009)

Use of the three-dimensional scanning laser and objective scoring system shows significant improvement in patients who were compliant with helmet therapy.
Lidocaine Attenuates Cytokine-Induced Cell Injury in Endothelial and Vascular Smooth Muscle Cells (2003)

This study demonstrates that lidocaine attenuates cytokine-induced injury of endothelial and vascular smooth muscle cells via mechanisms involving adenosine triphosphate-sensitive potassium channels. Protection of the vasculature from cytokine-induced inflammation may preserve important physiological endothelial and vascular smooth muscle functions.
Patent Literature on Mosquito Repellent Inventions which Contain Plant Essential Oils - A Review (2011)

Bites Bites of mosquitoes belonging to the genera Anopheles Meigen, Aedes Meigen, Culex L. and Haemagogus L. are a general nuisance and are responsible for the transmission of important tropical diseases such as malaria, hemorrhagic dengue and yellow fevers and filariasis (elephantiasis). Plants are traditional sources of mosquito repelling essential oils (EOs), glyceridic oils and repellent and synergistic chemicals. A Chemical Abstracts search on mosquito repellent inventions containing plant-derived EOs revealed 144 active patents mostly from Asia. Chinese, Japanese and Korean language patents and those of India (in English) accounted for roughly 3/4 of all patents. Since 1998 patents on EO-containing mosquito repellent inventions have almost doubled about every 4 years. In general, these patents describe repellent compositions for use in topical agents, cosmetic products, incense, fumigants, indoor and outdoor sprays, fibers, textiles among other applications. 67 EOs and 9 glyceridic oils were individually cited in at least 2 patents. Over 1/2 of all patents named just one EO. Citronella [Cymbopogon nardus (L.) Rendle, C.winterianus Jowitt ex Bor] and eucalyptus (Eucalyptus LʼHér. spp.) EOs were each cited in approximately 1/3 of all patents. Camphor [Cinnamomum camphora (L.) J. Presl], cinnamon (Cinnamomum zeylanicum Blume), clove [Syzygium aromaticum (L.) Merr. & L.M. Perry], geranium (Pelargonium graveolens LʼHér.), lavender (Lavandula angustifolia Mill.), lemon [Citrus × limon (L.) Osbeck], lemongrass [Cymbopogon citratus (DC.) Stapf] and peppermint (Mentha × piperita L.) EOs were each cited in > 10% of patents. Repellent chemicals present in EO compositions or added as pure “natural” ingredients such as geraniol, limonene, p-menthane-3,8-diol, nepetalactone and vanillin were described in approximately 40% of all patents. About 25% of EO-containing inventions included or were made to be used with synthetic insect control agents having mosquito repellent properties such as pyrethroids, N,N-diethyl-m-toluamide (DEET), (±)-p-menthane-3,8-diol (PMD) and dialkyl phthalates. Synergistic effects involving one or more EOs and synthetic and/or natural components were claimed in about 10% of all patents. Scientific literature sources provide evidence for the mosquito repellency of many of the EOs and individual chemical components found in EOs used in patented repellent inventions.
Eotaxin is a natural antagonist for CCR2 and an agonist for CCR5 (2001)

Eotaxin is a potent inducer of eosinophil chemotaxis and was considered as a selective ligand of the CC chemokine receptor 3 (CCR3), which is expressed on eosinophils, basophils, and Th2 lymphocytes. This study shows that eotaxin also interacts with CCR2 and CCR5 and can, thus, affect the responses of monocytes, which express both receptors. In human monocytes pretreatment with eotaxin decreased responsiveness to MCP-1, a selective ligand for CCR2, as well as to RANTES and MIP-1 beta, which bind to CCR5. Similar effects were obtained with transfected cells expressing CCR2 or CCR5, but here a difference became apparent: Eotaxin triggered CCR5 at a concentration of 100 nM but not CCR2 even at 1 microM, suggesting an antagonistic effect on this receptor. In agreement with this observation, eotaxin induced internalization of CCR5 but not of CCR2 in human monocytes and transfected cells. Binding studies showed that eotaxin displaces (125) I-MCP-1 from monocytes in a concentration-dependent manner, and functional experiments showed that eotaxin inhibits MCP-1-induced chemotaxis and enzyme release. The results demonstrate that eotaxin is a CCR5 agonist and a CCR2 antagonist. The present findings suggest a role of eotaxin in the fine-tuning of cellular responses occurring at sites of allergic inflammation, in which both MCP-1 and eotaxin are produced. (Blood. 2001;97:1920-1924)
Microfluidic Selection and Retention of a Single Cardiac Myocyte, On-Chip Dye Loading, Cell Contraction by Chemical Stimulation, and Quantitative Fluorescent Analysis of Intracellular Calcium (2005)

A microfluidic method to study the contraction of a single cardiac myocyte (heart muscle cell) has been developed. This method integrates various single-cell operations as well as on-chip dye loading, and quantitative analysis of intracellular calcium concentration, [Ca2+]i. After the channel enlargement by on-chip etching to accommodate large-sized cardiac myocytes, a single cell is selected and retained at a V-shaped cell retention structure within the microchip. Owing to the fragile property of the cardiac myocytes that could easily be damaged by centrifugation, the calcium-sensitive fluorescent dye was loaded in the cell by on-chip dye loading. This on-chip method minimized the damage to the cells from the use of a centrifuge in the conventional method and provided a way of cellular analysis of fragile cells. Subsequently, quantitative analysis of [Ca2+]i of a single cardiac myocyte by fluorescence measurement was achieved for the first time in a microfluidic chip, thanks to the intracellular calcium stimulant of ionomycin. The resting [Ca2+]i of the cardiomyocyte determined was consistent with the literature value. From the spontaneous contraction study, it was found that fluorescence intensity cannot represent the [Ca2+]i variation accurately, which implied the importance of the quantitative analysis of [Ca2+]i.