gebhart/patrepeval huggingface dataset:
Curcumin (diferuloylmethane) down-regulates the constitutive activation of nuclear factor–κB and IκBα kinase in human multiple myeloma cells, leading to suppression of proliferation and induction of apoptosis (2003)

Because of the central role of the transcription factor nuclear factor-kappaB (NF-kappaB) in cell survival and proliferation in human multiple myeloma (MM), we explored the possibility of using it as a target for MM treatment by using curcumin (diferuloylmethane), an agent known to have very little or no toxicity in humans. We found that NF-kappaB was constitutively active in all human MM cell lines examined and that curcumin, a chemopreventive agent, down-regulated NF-kappaB in all cell lines as indicated by electrophoretic mobility gel shift assay and prevented the nuclear retention of p65 as shown by immunocytochemistry. All MM cell lines showed consitutively active IkappaB kinase (IKK) and IkappaBalpha phosphorylation. Curcumin suppressed the constitutive IkappaBalpha phosphorylation through the inhibition of IKK activity. Curcumin also down-regulated the expression of NF-kappaB-regulated gene products, including IkappaBalpha, Bcl-2, Bcl-x(L), cyclin D1, and interleukin-6. This led to the suppression of proliferation and arrest of cells at the G(1)/S phase of the cell cycle. Suppression of NF-kappaB complex by IKKgamma/NF-kappaB essential modulator-binding domain peptide also suppressed the proliferation of MM cells. Curcumin also activated caspase-7 and caspase-9 and induced polyadenosine-5'-diphosphate-ribose polymerase (PARP) cleavage. Curcumin-induced down-regulation of NF-kappaB, a factor that has been implicated in chemoresistance, also induced chemosensitivity to vincristine and melphalan. Overall, our results indicate that curcumin down-regulates NF-kappaB in human MM cells, leading to the suppression of proliferation and induction of apoptosis, thus providing the molecular basis for the treatment of MM patients with this pharmacologically safe agent.
Interleukin 7 (IL-7) Receptor-Specific Cell Killing by DAB389IL-7:  A Novel Agent for the Elimination of IL-7 Receptor Positive Cells (1998)

Interleukin 7 (IL-7) induces the proliferation of B cell progenitors in long-term bone marrow cultures, promotes the growth of resting fetal and adult thymocytes, and costimulates mature human T cell proliferation. IL-7 also induces cell growth in hematologic malignancies such as acute lymphoblastic leukemia, chronic lymphocytic leukemia, acute myelogenous leukemia, and Sezary syndrome. We have constructed a recombinant fusion protein, DAB389 IL-7, composed of the catalytic and transmembrane domains of diphtheria toxin (DT), fused to IL-7. We demonstrate that DAB389 IL-7 is selectively cytotoxic for only those cells bearing the IL-7 receptor and that entry into target cells is mediated through the receptor. The nontoxic mutant, DA(E149S)B389 IL-7, was constructed and used to demonstrate that the catalytic domain of DT is responsible for the ADP ribosylation of elongation factor 2 that results in cytotoxicity. Finally, we demonstrate that DA(E149S)B389 IL-7 induces the growth of IL-7-dependent cells, verifying the bioactivity of the IL-7 binding domain of DAB389 IL-7. We propose that DAB389 IL-7 may be an important reagent in studying the IL-7--IL-7 receptor complex and may possess potential as a therapeutic agent against IL-7 receptor-bearing hematologic malignancies.
Large Visual Repository Search with Hash Collision Design Optimization (2013)

Visual search over large image repositories in real time is one of the key challenges for applications such as mobile visual query-by-capture, augmented reality, and biometrics-based identification. Search accuracy and response speed are two important performance factors. This article focuses on one of the important elements of this technology that enables large-scale visual search: indexing (or hashing). Indexing is the process of organizing a database of searchable elements into an efficiently searchable configuration. The searchable elements in our case are compact features extracted from images. This article explores a new indexing scheme. The authors optimize the design of a hash-code collision and counting scheme to enable fast search of visual features of MPEG CDVS.
Genetic manipulation in higher organisms. I. Goldfish ova as materials of operation, mRNA mediated alteration of the liver specific isozymes. (1978)

Both crucian and carp egg-mRNAs were found to mediate the transformation of goldfish tail from the double (veil-shaped) to the single (fork-shaped). Livers of these single tailed goldfish were tested for genetic change using lactate dehydrogenase isozymes (LDH) as marker. Electrophoresis of liver extracts on starch gel showed that the liver specific LDH-C4 isozymes of both the egg-mRNA and liver-mRNA injected goldfish resembled the control goldfish except an additional intermediate band. The migration distance of this new band matched the third band of the hybrids (carp X goldfish). These findings lead to the conclusion that carp egg-mRNA contains a fraction partly responsible for liver development. Rat liver was found possessing the cathodally migrating C4 isozymes. Injection of rat liver-mRNA into goldfish eggs resulted in the intensification of the liver specific C4 isozymes. It appears therefore that the input informational molecules (liver-mRNA) and the output molecular products (liver C4 isozymes) are causally related. This causal relationship would pave the way for genetic manipulation in higher organisms.
Overt and latent activities of diacylglycerol acytransferase in rat liver microsomes: possible roles in very-low-density lipoprotein triacylglycerol secretion (1997)

The possibility that triacylglycerol (TAG) synthesis occurs on both aspects of the endoplasmic-reticular membrane during the process of incorporation of TAG into secreted very-low-density lipoprotein (VLDL) [Zammit (1996) Biochem. J. 314, 1-14] was investigated by measuring the latency of diacylglycerol acyltransferase (DGAT) in microsomal fractions obtained from rat liver homogenates. Permeabilization of microsomes with taurocholate resulted in the doubling of the activity, indicating that DGAT activities of approximately equal magnitude occur on either aspect of the microsomal membrane. The taurocholate concentrations required for exposure of the latent activity of DGAT were identical with those that resulted in the exposure of marker enzymes for the lumen of the endoplasmic reticulum. Fractionation of the microsomes into smooth and rough populations indicated that the distribution of overt and latent DGAT activities was the same throughout. The possibility that taurocholate effects may result from non-specific activation of the overt enzyme was excluded by employing the channel-forming peptide alamethicin to effect permeabilization, and by varying the mode of delivery of diacylglycerol substrate to the microsomal membranes. Permeabilization using alamethicin gave a slightly higher latent/overt ratio for DGAT. The possible roles of overt and latent DGAT activities in the synthesis and secretion of TAG by the liver are discussed.
Low-drift fibre gyro using a superluminescent diode (1981)

By using a superluminescent diode as the light source and a depolariser inside the fibre coil, a constant scale factor is achieved without using polarisation control elements. For long-term behaviour an RMS-bias drift of 10 degrees/h is obtained.
A yeast RNA-binding protein shuttles between the nucleus and the cytoplasm. (1994)

RNA-binding proteins have been suggested to move in association with RNA as it leaves the nucleus. The NPL3 gene of the yeast Saccharomyces cerevisiae encodes in nuclear protein with consensus RNA-binding motifs and similarity to heterogeneous nuclear ribonucleoproteins and members of the S/R protein family. We show that although Npl3 is located in the nucleus, it can shuttle between nuclei in yeast heterokaryons. In contrast, other nucleus-targeted proteins do not leave the nucleus under similar conditions. Mutants missing the RNA-binding motifs or the N terminus are still capable of shuttling in and out of the nucleus. Npl3 mutants missing the C terminus fail to localize to the nucleus. Overproduction of Npl3 in wild-type cells shows cell growth. This toxicity depends on the presence of series of unique repeats in the N terminus and localization to the nucleus. We suggest that the properties of Npl3 are consistent with it being involved in export of RNAs from the nucleus.
Rescue of rinderpest virus from cloned cDNA (1997)

Rinderpest virus is a morbillivirus and is the causative agent of a widespread and important disease of cattle. The viral genome is a single strand of RNA in the negative sense. We have constructed plasmids containing cDNA copies of the 5' and 3' termini of the virus separated by a reporter gene and have shown that antigenome-sense RNA transcripts of these model genomes can be replicated, transcribed, and packaged by helper virus, both rinderpest virus and the related measles virus. Further, these genome analogs can be replicated and transcribed by viral proteins expressed from cDNA clones by using a recombinant vaccinia virus expressing T7 RNA polymerase (MVA-T7). Using this latter system, we have rescued live rinderpest virus from a full-length cDNA copy of the genome of the RBOK vaccine strain. The recombinant virus appears to grow in tissue culture identically to the original virus.
Development of a new 550× concentrator module with 3J cells - performance and reliability (2005)

The status of the development of a new concentrator module in Japan is discussed based on three arguments, performance, reliability and cost. The peak uncorrected efficiency for a 7,056 cm/sup 2/ 400/spl times/ module with 36 solar cells connected in series was 26.6 % was measured in house. The peak uncorrected efficiencies of the same type of the module with 6 solar cells connected in series and 1,176 cm/sup 2/ area measured by Fraunhofer ISE and NREL were 27.4 % and 24.8 % respectively. The peak uncorrected efficiency for a 550/spl times/ and 5,445 cm/sup 2/ module with 20 solar cells connected in series was 28.9 %. The temperature corrected efficiency under the best sunshine condition in Japan for the 550/spl times/ module was 31.5/spl plusmn/2%. For reliability, some new degradation modes inherent to high concentration III-V solar cell system are discussed and a 20 year lifetime under concentrated flux exposure proven. The fail-safe issues of the concentrated sunlight are also discussed. For cost, the overall scenario for the reduction of material cost is discussed.
Non-radioactive localization of nucleic acids by direct in situ PCR and in situ RT-PCR in paraffin-embedded sections. (1995)

Technological developments have made possible extension of polymerase chain reaction (PCR) analysis to individual cells to localize DNA/RNA with non-radioactive labels at the light microscopic level. This approach, in situ PCR, is particularly useful in resolving low-frequency message expression in mixed populations of cells and tissues. We have established a working protocol for direct in situ PCR and have utilized several controls to validate our results. In this report we outline the procedures for detecting either DNA or RNA in a rapid and reproducible manner. We evaluate the sequential steps required for this analysis, such as protease hydrolysis, DNAse digestion, "hot start" capabilities, and detection methods. We have applied these methods in several applications, including detection of the p53 gene in human tumor samples, localization of insulin-like growth factor-IA mRNA in cell lines with low levels of expression, and distribution of transferrin mRNA in lung cancer cell lines and tumors. We demonstrate from this study that the in situ PCR technique is an investigative approach capable of detecting specific DNA/RNA sequences at the cellular level and of identifying cells with low levels of mRNA expression.
Enantioselective, Copper(I)‐Catalyzed Three‐Component Reaction for the Preparation of Propargylamines (2003)

The one-pot reaction of alkynes, aldehydes, and secondary amines in the presence of CuBr/quinap as the catalytic system provides various enantiomerically enriched propargylamines in good yields (up to 99 %) and good selectivities (up to 96 % ee) [Eq. (1)].
Antagonist Antibodies to PD-1 and B7-H1 (PD-L1) in the Treatment of Advanced Human Cancer (2013)

The immune suppressive molecule programmed death-1 (PD-1) is upregulated in activated T lymphocytes and inhibits T-cell function upon binding to its ligands B7-H1 (PD-L1, CD274) and B7-DC (PD-L2, CD273). Substantial experimental data from in vitro cell culture systems and animal models, and more recently from clinical trials, indicate that PD-1/PD-1-ligand interactions are a major mechanism of immune suppression within the tumor microenvironment. Initial clinical studies of antibodies directed against PD-1 and B7-H1 showed both an encouraging safety profile and remarkable antitumor activity in subsets of patients with metastatic disease, including malignancies--such as lung cancer--which were previously thought to be unresponsive to immunotherapy. Preliminary data have suggested a correlation between tumor membrane B7-H1 expression and clinical response to anti-PD-1 antibodies. Several key challenges remain to optimize development of PD-1/B7-H1 pathway blockade, including defining the biologic significance of all potential ligand-receptor interactions in the tumor microenvironment, developing more accurate predictive biomarkers of response, determining the breadth of activity in human malignancies, and developing rational combinations of therapy that address key mechanisms involved in positive and negative regulation of antitumor immune responses.
Story segmentation and detection of commercials in broadcast news video (2002)

The Informedia Digital Library Project allows full content indexing and retrieval of text, audio and video material. Segmentation is an integral process in the Informedia digital video library. The success of the Informedia project hinges on two critical assumptions: that we can extract sufficiently accurate speech recognition transcripts from the broadcast audio and that we can segment the broadcast into video paragraphs, or stories, that are useful for information retrieval. In previous papers we have shown that speech recognition is sufficient for information retrieval of pre-segmented video news stories. We now address the issue of segmentation and demonstrate that a fully automatic system can extract story boundaries using available audio, video and closed-captioning cues. The story segmentation step for the Informedia Digital Video Library splits full-length news broadcasts into individual news stories. During this phase the system also labels commercials as separate "stories". We explain how the Informedia system takes advantage of the closed captioning frequently broadcast with the news, how it extracts timing information by aligning the closed-captions with the result of the speech recognition, and how the system integrates closed-caption cues with the results of image and audio processing.
Efficacy and safety of vaginally administered lyophilized Lactobacillus crispatus IP 174178 in the prevention of bacterial vaginosis recurrence (2017)

In women with recurrent BV after antibiotics, treatment with Lc IP 174178 administered over four menstrual cycles, could significantly reduce the rate of recurrence and increase the time to recurrence.
1.4 .ANG. Structure of Photoactive Yellow Protein, a Cytosolic Photoreceptor: Unusual Fold, Active Site, and Chromophore (1995)

A photosensing protein directs light energy captured by its chromophore into a photocycle. The protein's structure must accommodate the photocycle and promote the resulting chemical or conformational changes that lead to signal transduction. The 1.4 A crystallographic structure of photoactive yellow protein, determined by multiple isomorphous replacement methods, provides the first view at atomic resolution of a protein with a photocycle. The alpha/beta fold, which differs from the original chain tracing, shows striking similarity to distinct parts of the signal transduction proteins profilin and the SH2 domain. In the dark state structure of photoactive yellow protein, the novel 4-hydroxycinnamyl chromophore, covalently attached to Cys69, is buried within the major hydrophobic core of the protein and is tethered at both ends by hydrogen bonds. In the active site, the yellow anionic form of the chromophore is stabilized by hydrogen bonds from the side chains of Tyr42 and buried Glu46 to the phenolic oxygen atom and by electrostatic complementarity with the positively charged guanidinium group of Arg52. Thr50 further interlocks Tyr42, Glu46, and Arg52 through a network of active site hydrogen bonds. Arg52, located in a concavity of the protein surface adjacent to the dominant patch of negative electrostatic potential, shields the chromophore from solvent and is positioned to form a gateway for the phototactic signal. Overall, the high-resolution structure of photoactive yellow protein supports a mechanism whereby electrostatic interactions create an active site poised for photon-induced rearrangements and efficient protein-mediated signal transduction.
Structural and functional healing of critical‐size segmental bone defects by transduced muscle‐derived cells expressing BMP4 (2004)

This study demonstrated that primary muscle-derived cells transduced with retroBMP4 can elicit both structural and functional healing of critical-size segmental long bone defects created in rats.
The Energy Spilling Reactions of Bacteria and Other Organisms (2007)

For many years it was assumed that living organisms always utilized ATP in a highly efficient manner, but simple growth studies with bacteria indicated that the efficiency of biomass production was often at least 3-fold lower than the amount that would be predicted from standard biosynthetic pathways. The utilization of energy for maintenance could only explain a small portion of this discrepancy particularly when the growth rate was high. These ideas and thermodynamic arguments indicated that cells might have another avenue of energy utilization. This phenomenon has also been called 'uncoupling', 'spillage' and 'overflow metabolism', but 'energy spilling' is probably the most descriptive term. It appears that many bacteria spill energy, and the few that do not can be killed (large and often rapid decrease in viability), if the growth medium is nitrogen-limited and the energy source is in 'excess'. The lactic acid bacterium, Streptococcus bovis, is an ideal bacterium for the study of energy spilling. Because it only uses substrate level phosphorylation to generate ATP, ATP generation can be calculated with a high degree of certainty. It does not store glucose as glycogen, and its cell membrane can be easily accessed. Comparative analysis of heat production, membrane voltage, ATP production and Ohm's law indicated that the energy spilling reaction of S. bovis is mediated by a futile cycle of protons through the cell membrane. Less is known about Escherichia coli, but in this bacterium energy spilling could be mediated by a futile cycle of potassium or ammonium ions. Energy spilling is not restricted to prokaryotes and appears to occur in yeasts and in higher organisms. In man, energy spilling may be related to cancer, ageing, ischemia and cardiac failure.
Micromagnetic Investigation of Precession Dynamics in Magnetic Nanopillars (2007)

This paper interprets and reproduces, by means of full micromagnetic simulations, the pioneering experimental data on magnetization dynamics driven by spin polarized current of the experiment by Kiselev The effect of the spatial dependence of the polarization function together with either nonuniform magnetostatic coupling from the fixed layer and classical Ampere field are shown to play a fundamental role in the magnetization dynamics. A detailed study of the stable magnetization self-oscillations shows that for high field and high current regimes, the dynamics is localized in the sides of the structure, where the energy dissipated by damping and the energy provided by the spin flow compensate exactly.
Altered microbiota associated with abnormal humoral immune responses to commensal organisms in enthesitis-related arthritis (2014)

The abundance of F. prausnitzii in the stool among patients with ERA is reduced compared to controls, and Bacteroides and A. muciniphila are identified as associative agents in subsets of ERA patients. Differences in the humoral responses to these bacteria may contribute to disease.
Direct Quantification of Single-Molecules of MicroRNA by Total Internal Reflection Fluorescence Microscopy (2010)

MicroRNAs (miRNAs) express differently in normal and cancerous tissues and thus are regarded as potent cancer biomarkers for early diagnosis. However, the short length and low abundance of miRNAs have brought challenges to the established detection assay in terms of sensitivity and selectivity. In this work, we present a novel miRNA detection assay in single-molecule level with total internal reflection fluorescence microscopy (TIRFM). It is a solution-based hybridization detection system that does not require pretreatment steps such as sample enrichment or signal amplification. The hsa-miR-21 (miR-21) is chosen as target miRNA for its significant elevated content in a variety of cancers as reported previously. Herein, probes of complementary single-stranded oligonucleotide were hybridized in solution to miR-21 and labeled with fluorescent dye YOYO-1. The fluorescent hybrids were imaged by an electron-multiplying charge-coupled device (EMCCD) coupled TIRFM system and quantified by single-molecule counting. This single molecule detection (SMD) assay shows a good correlation between the number of molecules detected and the factual concentration of miRNA. The detection assay is applied to quantify the miR-21 in extracted total RNA samples of cancerous MCF-7 cells, HepG2 cells, and normal HUVEC cells, respectively. The results agreed very well with those from the prevalent real-time polymerase chain reaction (qRT-PCR) analysis. This assay is of high potential for applications in miRNA expression profiling and early cancer diagnosis.
PET tracers and radiochemistry. (2004)

This paper provides a brief review of the radiochemistry of radiopharmaceuticals used in positron emission tomography (PET). It includes some history of PET, the basic formation of radionuclides in a cyclotron target, the processing of the precursor molecules into a useful PET radiotracer and the clinical significance and outlook for PET radiotracers. This review is based on a series of recent books and articles outlining the fundamental goals of PET and how radiochemistry plays a part in achieving these goals. It is also drawn from the literature that has been developed in PET over the last 30 years since PET became a research and valuable clinical tool. PET is a growing field and the clinical applications of the chemistry and technology have just begun to be explored. There is a great deal left to do in order to explore the full potential of PET in the clinic.