gebhart/patrepeval huggingface dataset:
Platelets lacking functional CD36 (glycoprotein IV) show reduced adhesion to collagen in flowing whole blood (1993)

A parallel-plate perfusion chamber has been used to evaluate the contribution of the adhesive membrane glycoprotein CD36 (GPIV) to platelet adhesion on type I collagen in flowing whole blood at a shear rate of 800 s-1. In one series of experiments, reconstituted normal blood (hematocrit 0.4; platelet count 1.5 x 10(5)/microL) was prepared from washed red blood cells, plasma, and washed platelets that had been incubated with Fab fragments of a monospecific polyclonal anti-CD36 antibody (50 micrograms/mL, 30 minutes, 37 degrees C). Percent surface coverage of collagen-coated coverslips using reconstituted blood with antibody-blocked platelets, as compared with paired reconstituted controls (100%), was 50% at 2 minutes, 87% at 5 minutes, and 90% at 10 minutes. Further studies were performed by perfusion of whole blood from a healthy donor of the Naka-negative phenotype, whose platelets constitutively lack CD36, over collagen-coated coverslips. In this case, percent surface coverage was 55% of normal controls at 2 minutes, 76% of controls at 5 minutes, and 72% of controls at 10 minutes. In both preparations, platelets lacking functional CD36 had a statistically significant decrease (P &lt; .005) in adhesion after 2 minutes and 10 minutes perfusion but not at 5 minutes. These results show that functional CD36 facilitates the rapid adhesion of platelets to collagen and that this effect is seen at the earliest time points of their interaction.
Neurotrophic Factors - A Tool for Therapeutic Strategies in Neurological,Neuropsychiatric and Neuroimmunological Diseases? (2007)

Nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) belong to the protein family of neurotrophins. They both display profound neuromodulatory functions and are essentially involved in the survival and homeostatic maintenance of central and peripheral neurons during development and adulthood. Moreover, NGF and BDNF are known to modulate immune cell function and thus serve as mediators in the reciprocal cross talk between neurons and immune cells. Neurotrophic factors have been implicated in pathophysiological mechanisms of many diseases of the nervous and the immune system, such as amyotrophic lateral sclerosis (ALS), Alzheimers disease (AD), neuropathy, pain, allergic bronchial asthma (BA) and neurotrophic keratitis. For all these diseases research has reached the point of creating strategies for therapeutic intervention with neurotrophins. In this review, we present an overview of the pathophysiology, therapeutic interventions and strategies concerning NGF and BDNF in the mentioned diseases. Keywords: Neurotrophin receptors, glial-derived neurotrophic factor, streptozotoxin, anti-inflammatory, Asthma, amyloid-precursor protein
eIF4E is a central node of an RNA regulon that governs cellular proliferation (2006)

This study demonstrates that the eukaryotic translation initiation factor eIF4E is a critical node in an RNA regulon that impacts nearly every stage of cell cycle progression. Specifically, eIF4E coordinately promotes the messenger RNA (mRNA) export of several genes involved in the cell cycle. A common feature of these mRNAs is a structurally conserved, approximately 50-nucleotide element in the 3' untranslated region denoted as an eIF4E sensitivity element. This element is sufficient for localization of capped mRNAs to eIF4E nuclear bodies, formation of eIF4E-specific ribonucleoproteins in the nucleus, and eIF4E-dependent mRNA export. The roles of eIF4E in translation and mRNA export are distinct, as they rely on different mRNA elements. Furthermore, eIF4E-dependent mRNA export is independent of ongoing RNA or protein synthesis. Unlike the NXF1-mediated export of bulk mRNAs, eIF4E-dependent mRNA export is CRM1 dependent. Finally, the growth-suppressive promyelocytic leukemia protein (PML) inhibits this RNA regulon. These data provide novel perspectives into the proliferative and oncogenic properties of eIF4E.
Radical Polymerization Initiated from a Solid Substrate. 1. Theoretical Background (1999)

From a survey of the literature on grafting free radical polymerization from solid surfaces we suggest kinetic schemes for the process. The system of differential equations in partial derivatives including the diffusion equation based on the classical theory of free radical polymerization and the assumption that surface-bonded free radicals terminate by (1) reactions with bulk free radicals and (2) chain transfer to solvent or monomer are introduced. Computer simulations performed using the equations have shown good agreement with the characteristic features of the grafting process. The rate of grafting is linearly proportional to the surface concentration of the initiator and decreases as the initiation rate in the bulk increases. It follows from the concentration profiles of the bulk free radicals that free radical concentration in the vicinity of the surface can be several times larger than that in the bulk. The concentration profile depends on the distance between two surfaces. For distances less than a critical distance of about 2 μm, the concentration profile of the bulk free radicals is homogeneous.
Ambient backscatter (2013)

We present the design of a communication system that enables two devices to communicate using ambient RF as the only source of power. Our approach leverages existing TV and cellular transmissions to eliminate the need for wires and batteries, thus enabling ubiquitous communication where devices can communicate among themselves at unprecedented scales and in locations that were previously inaccessible.
Dominant transposition-deficient mutants of maize Activator (Ac) transposase. (1993)

The maize transposable element Activator (Ac) encodes a transposase (TPase) protein, whose DNA-binding domain is located in a basic region around aa 200. The N-terminal 102 aa of the TPase are not required for the transposition reaction. In transfected petunia protoplasts, we analyzed the protein levels of the N-terminally truncated TPase and mutants thereof and the corresponding transposition frequencies. The TPase protein forms large insoluble aggregates at high expression levels. There is no proportionality observed between TPase levels and transposition frequency. Twenty-one mutations (of 26), which are distributed over the whole length of the protein, inactivate the TPase completely. By coexpressing inactive mutant and active truncated TPase, it was found that several mutations have a trans-dominant inhibitory effect. Among those are two DNA-binding-deficient mutants, indicating that inhibition of the active TPase is not caused by competition for the binding sites on the transposon. Accordingly, Ac TPase acts as an oligo- or multimer formed by protein-protein interactions. Peculiarly, two mutants lacking 53 and 98 aa from the C terminus that are themselves transpositionally inactive lead to an increased excision frequency when they are coexpressed with the active truncated TPase.
Evolving technology for thermal therapy of cancer (2005)

This paper is intended as a succinct review of technology used for clinical hyperthermia therapy for cancer, as culled from a presentation at the special workshop on Thermal Medicine, Heat Shock Proteins, and Cancer at the Society for Thermal Medicine conference in Spring 2005. Following a brief overview of thermal therapy treatment options and available mechanisms for heating tissue, the paper focuses on the evolution of equipment from basic single element heating devices of the early 1980s to adjustable multi-element heating devices currently in use or in final stages of development. Representative devices from the past, present and near future are cited for further investigation by the interested reader. The paper concludes with a summary of general trends in the evolution of clinical hyperthermia techniques and a statement of current challenges remaining for the field.
Linkage analysis of schizophrenia to chromosome 15 (2001)

We have mapped a sample of 68 families consisting of one or more affected sibling pairs with schizophrenia or schizoaffective disorder with 20 markers spanning all of chromosome 15 to investigate whether there is a locus on chromosome 15 that confers an increased susceptibility to schizophrenia using parametric and nonparametric linkage analyses. Allele sharing identical by descent and multipoint maximum likelihood score (MLS) statistics were employed. Results show excess allele sharing for multiple markers in 15q11.2-q25, a chromosomal region previously found linked to a decrease in the normal inhibition of the P50 auditory-evoked response to the second of paired stimuli, a decrease associated with schizophrenia. Excess allele sharing was found for markers spanning about 48 cM in 15q11.2-q25 (D15S1002-D15S1023). The greatest single point allele sharing was found at D15S659 (62.6%). The multipoint MLS scores were greater than 1.0 in the 30-52 cM interval delimited by ACTC and D15S150, with a maximum value of 2.0 with GENEHUNTER PLUS near D15S1039.
Molecular Mechanism of Lipopolysaccharide-Induced SOCS-3 Gene Expression in Macrophages and Microglia (2007)

Immunological activation of macrophages/microglia within the CNS leads to the production of cytokines and chemokines that ultimately impact on glial and neuronal function. Suppressor of cytokine signaling (SOCS) proteins are negative regulators of adaptive and innate immune responses. Our previous studies demonstrated that SOCS-3 attenuates macrophage/microglial activation in vitro, suggesting that SOCS-3 may exert beneficial effects for immune-mediated CNS diseases in vivo. In this study, we describe LPS as a potent inducer of SOCS-3 transcription and expression in macrophages/microglia. An analysis of the SOCS-3 promoter indicates that AP-1 and IFN-gamma activation sequence (GAS) elements are involved in LPS-induced SOCS-3 transcription. LPS-induced SOCS-3 expression was diminished in IL-10-deficient macrophages at later time points, indicating the involvement of endogenous IL-10 in this response. Blocking STAT-3 expression and activation using STAT-3 small interfering RNA reduced LPS-induced SOCS-3 gene expression. LPS activated the MAPK-ERK1/2, JNK, and p38 pathways that, in addition to STAT-3, were also involved in LPS-induced SOCS-3 expression. LPS treatment of cells led to the acetylation of histones H3 and H4 on the SOCS-3 promoter and the recruitment of STAT-3, c-Jun, c-Fos, CREB-binding protein, p300, and RNA polymerase II to the endogenous SOCS-3 promoter in a time-dependent manner. These results indicate that LPS-induced MAPK activation, the production of endogenous IL-10, and STAT-3 activation play critical roles in SOCS-3 expression, which provides for feedback attenuation of cytokine-induced immune and inflammatory responses in macrophages and microglia.
Spray-dried doxorubicin-albumin microparticulate systems for treatment of multidrug resistant melanomas (2010)

As multidrug resistance continues to be a problem in cancer treatment, controlled release delivery systems, such as microspheres, may aid to give a slower release of anticancer drugs into drug resistant tumor cells. In this study doxorubicin microspheres microencapsulated in an albumin matrix were prepared via the spray-drying method and characterized for particle size, content analysis, and release studies. They were then evaluated in vitro using drug resistant murine melanoma tumor cells for uptake and efflux studies. Spray-drying produced a dispersed powder with a mean particle size of 4.91 ± 1.2 µm, 60% product yield, and encapsulation efficiency of 85% and a ζ potential range of 37 to -40 mV. Intracellular doxorubicin concentrations were higher in drug resistant tumor cells treated with microspheres as opposed to solution, and efflux of doxorubicin from the tumor cell was inhibited. Greater cytotoxic effects were seen in tumor cells treated with doxorubicin microspheres versus solution up to and after 3 days. In vivo pharmacokinetic studies conducted in male Sprague-Dawley rats, revealed a plasma-level time curve indicative of a two-compartment model, and showed prolonged half-life of doxorubicin, greater area under the plasma concentration time curve, and increased plasma concentrations of doxorubicin in rats at 8 and 24 h after administration of doxorubicin microspheres.
Light source depth estimation in porcine skin using spatially resolved diffuse imaging (2016)

We present an inexpensive imaging system for measuring the diffuse surface radiance profile produced by a light source within a turbid medium. The diffusion model of light propagation in multiple scattering media is used to estimate the optical properties of a sample and subsequently approximate the depth of an optical source. The system is shown to accurately estimate the relative changes in source depth in a homogeneous phantom. The absolute depth estimate may be improved with a better estimate of the optical parameters. Preliminary tests on a porcine skin sample show that the simple model can be used to roughly track the relative changes in the depth of a source in a layered medium. However, a rigorous model of the layered geometry may be required to more accurately localize a source, particularly near interfaces between tissue layers.
Fe(I)-Mediated Reductive Cleavage and Coupling of CO2:  An FeII(μ-O,μ-CO)FeII Core (2006)

THF solutions of a new iron(I) source, [PhBPCH2Cy3]Fe ([PhBPCH2Cy3] = [PhBP(CH2P(CH2Cy)2)3]-), effect the reductive cleavage of CO2 via O-atom transfer at ambient temperature. The dominant reaction pathway is bimetallic and leads to the formation of a structurally unprecedented diiron FeII(μ-O)(μ-CO)FeII core. X-ray data are also available to suggest that bimetallic reductive CO2 coupling to generate oxalate occurs as a minor reaction pathway. These initial observations forecast a diverse reaction landscape between CO2 and iron(I) synthons.
Mass Spectrometry—based Metabolomics, Analysis of Metabolite-Protein Interactions, and imaging (2010)

Our understanding of biology has been greatly improved through recent developments in mass spectrometry, which is providing detailed information on protein and metabolite composition as well as protein-metabolite interactions. The high sensitivity and resolution of mass spectrometry achieved with liquid or gas chromatography allows for detection and quantification of hundreds to thousands of molecules in a single measurement. Where homogenization-based sample preparation and extraction methods result in a loss of spatial information, mass spectrometry imaging technologies provide the in situ distribution profiles of metabolites and proteins within tissues. Mass spectrometry-based analysis of metabolite abundance, protein-metabolite interactions, and spatial distribution of compounds facilitates the high-throughput screening of biochemical reactions, the reconstruction of metabolic networks, biomarker discovery, determination of tissue compositions, and functional annotation of both proteins and metabolites.
IFN-gamma inhibits activation-induced expression of E- and P-selectin on endothelial cells. (1998)

E- and P-selectin are cell surface lectins that mediate leukocyte-endothelial cell adhesion and thereby participate in neutrophil recruitment into inflammatory sites. E-selectin can be induced on endothelial cells by various activators, including TNF-alpha, IL-1beta, and PMA. Induction of E-selectin is blocked by pretreatment of endothelial cells with IL-4 or TGF-beta, both of which have antiinflammatory properties in vivo. In addition to its well-known proinflammatory activities, IFN-gamma also has antiinflammatory effects in vivo, one of which is inhibition of neutrophil recruitment. To determine whether IFN-gamma inhibits neutrophil recruitment by inhibiting adhesion molecule expression, the effect of IFN-gamma on activation-induced cell adhesion molecule expression by cultured HUVEC was evaluated. Pretreatment of endothelial cells with IFN-gamma for 24 to 72 h before 6- to 24-h activation with IL-1beta, TNF-alpha, or PMA resulted in significantly reduced levels of cell surface E-selectin, although levels of ICAM-1 and VCAM-1 were the same or increased. The reduction of cell surface E-selectin levels under these conditions was reflected in reduced levels of E-selectin mRNA, indicating an effect at the transcription level or RNA stability. Interestingly, the increase of cell surface P-selectin expression due to IL-4 treatment of HUVEC was also inhibited by IFN-gamma, while constitutive levels of P-selectin were not. These results suggest that the inhibition of neutrophil recruitment by IFN-gamma in vivo may be due, in part, to the ability of IFN-gamma to inhibit E- and P-selectin up-regulation. Furthermore, these findings emphasize the process of leukocyte recruitment as an important step through which IFN-gamma can direct the character of inflammatory reactions.
Mips R4000 User's Manual (1993)

1. Introduction. 2. CPU Instruction Set Summary. 3. The CPU Pipeline. 4. Memory Management. 5. CPU Exception Processing. 6. Floating-Point Unit. 7. Floating-Point Exceptions. 8. R4000 Processor Signal Descriptions. 9. Initialization Interface. 10. Clock Interface. 11. Cache Organization, Operation, and Coherency. 12. System Interface. 13. Secondary Cache Interface. 14. JTAG Interface. 15. R4000 Processor Interrupts. 16. Error Checking and Correcting. Appendix A: CPU Instruction Set Details. Appendix B: FPU Instruction Set Details. Appendix C: Subblock Ordering. Appendix D: Output Buffer ...Di/...Dt Control Mechanism. Appendix E: PLL Passive Components. Appendix F: R4000 Coprocessor 0 Hazards.
Amino acid substitution matrices from protein blocks. (1992)

Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.
Tissue fusion and cell sorting in embryonic development and disease: biomedical implications (2006)

Throughout embryonic development, segregated epithelial and/or mesenchymal cell populations make contact and fuse to shape new tissue units. This process, known as tissue fusion, is a key event in many essential morphogenetic mechanisms and its disruption can lead to congenital malformations. Another mechanism whereby complex tissues can arise involves a cell sorting process in which originally intermixed cells de-mix to generate distinct phases or layers. Different organisms use a combination of tissue fusion and cell sorting to acquire shape. Although the two processes appear to differ mechanistically, they are intricately linked inasmuch as they both involve the same molecular determinants and contribute to the same body plan. We aim to discuss the role of adhesion molecules and cell dynamics in tissue fusion and cell sorting, providing examples of their impact in embryonic development. Finally, we will advance the concept that malignant invasion may be viewed as cell sorting in reverse. Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html).
ATP Induces a Conformational Change in Lipid-bound Cytochrome c (2001)

Resonance energy transfer studies using a pyrene-labeled phospholipid derivative 1-palmitoyl-2-[10-(pyren-1-yl)decanoyl]-sn-glycero-3-phosphoglycerol (donor) and the heme (acceptor) of cytochrome c (cyt c) have indicated that ATP causes changes in the conformation of the lipid-bound protein (Rytömaa, M., Mustonen, P., and Kinnunen, P. K. J. (1992) J. Biol. Chem. 267, 22243-22248). Accordingly, after binding cyt c via its so called C-site to neat phosphatidylglycerol liposomes (mole fraction of PG = 1.0) has commenced, further quenching of donor fluorescence is caused by ATP, saturating at 2 mm nucleotide. ATP-induced conformational changes in liposome-associated cyt c could be directly demonstrated by CD in the Soret band region (380-460 nm). The latter data were further supported by time-resolved spectroscopy using the fluorescent cyt c analog with a Zn(2+)-substituted heme moiety. A high affinity ATP-binding site has been demonstrated in cyt c (Craig, D. B., and Wallace, C. J. A. (1993) Protein Sci. 2, 966-976) that is compromised by replacing the invariant Arg(91) to norleucine. Although no major effects on conformation and function of cyt c were concluded due to the modification, a significantly reduced effect by ATP on the lipid-bound [Nle(91)]cyt c was evident, implying that this modulation is mediated via the Arg(91)-containing binding site.
Distinct sequences on 11q13.5 and 11q23–24 are frequently coamplified with MLL in complexly organized 11q amplicons in AML/MDS patients (2004)

Amplification within chromosome arm 11q involving the mixed-lineage leukemia gene (MLL) locus is a rare but recurrent aberration in acute myeloid leukemia and myelodysplastic syndrome (AML/MDS). We and others have observed that 11q amplifications in most AML/MDS cases have not been restricted to the chromosomal region surrounding the MLL gene. Therefore, we implemented a strategy to characterize comprehensively 11q amplicons in a series of 13 AML/MDS patients with MLL amplification. Analysis of 4 of the 13 cases by restriction landmark genomic scanning in combination with virtual genome scan and by matrix-based comparative genomic hybridization demonstrated that the 11q amplicon in these four cases consisted of at least three discontinuous sequences derived from different regions of the long arm of chromosome 11. We defined a maximally 700-kb sequence around the MLL gene that was amplified in all cases. Apart from the core MLL amplicon, we detected two additional 11q regions that were coamplified. Using fluorescence in situ hybridization (FISH) analysis, we demonstrated that sequences in 11q13.5 and 11q23-24 were amplified in 8 of 13 and 10 of 12 AML/MDS cases, respectively. Both regions harbor a number of potentially oncogenic genes. In all 13 cases, either one or both of these regions were coamplified with the MLL amplicon. Thus, we demonstrated that 11q amplicons in AML/MDS patients display a complex organization and have provided evidence for coamplification of two additional regions on the long arm of chromosome 11 that may harbor candidate target genes.
Molecular beacon: a multitask probe (2005)

Journal Article Molecular beacon: a multitask probe Get access G. Goel, G. Goel Dairy Microbiology Division Search for other works by this author on: Oxford Academic Google Scholar A. Kumar, A. Kumar Molecular Biology Unit, National Dairy Research Institute, Karnal, India Search for other works by this author on: Oxford Academic Google Scholar A.K. Puniya, A.K. Puniya Dairy Microbiology Division Search for other works by this author on: Oxford Academic Google Scholar W. Chen, W. Chen Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA Search for other works by this author on: Oxford Academic Google Scholar K. Singh K. Singh Dairy Microbiology Division Kishan Singh, Principal Scientist, Dairy Microbiology Division, National Dairy Research Institute, Karnal 132 001, Haryana, India (e‐mail: ksndri@rediffmail.com). Search for other works by this author on: Oxford Academic Google Scholar Journal of Applied Microbiology, Volume 99, Issue 3, 1 September 2005, Pages 435–442, https://doi.org/10.1111/j.1365-2672.2005.02663.x Published: 01 September 2005 Article history Received: 17 August 2004 Revision received: 23 March 2005 Accepted: 23 March 2005 Published: 01 September 2005