gebhart/patrepeval huggingface dataset:
Compressive fluorescence microscopy for biological and hyperspectral imaging (2012)

The mathematical theory of compressed sensing (CS) asserts that one can acquire signals from measurements whose rate is much lower than the total bandwidth. Whereas the CS theory is now well developed, challenges concerning hardware implementations of CS-based acquisition devices--especially in optics--have only started being addressed. This paper presents an implementation of compressive sensing in fluorescence microscopy and its applications to biomedical imaging. Our CS microscope combines a dynamic structured wide-field illumination and a fast and sensitive single-point fluorescence detection to enable reconstructions of images of fluorescent beads, cells, and tissues with undersampling ratios (between the number of pixels and number of measurements) up to 32. We further demonstrate a hyperspectral mode and record images with 128 spectral channels and undersampling ratios up to 64, illustrating the potential benefits of CS acquisition for higher-dimensional signals, which typically exhibits extreme redundancy. Altogether, our results emphasize the interest of CS schemes for acquisition at a significantly reduced rate and point to some remaining challenges for CS fluorescence microscopy.
CRISPR-Cas9 Targeting of PCSK9 in Human Hepatocytes In Vivo—Brief Report (2016)

This work yields important information on the efficacy and safety of CRISPR-Cas9 therapy targeting the human PCSK9 gene in human hepatocytes in vivo, and it establishes humanized mice as a useful platform for the preclinical assessment of applications of somatic in vivo genome editing.
Recombinant Expression of Caveolin-1 in Oncogenically Transformed Cells Abrogates Anchorage-independent Growth (1997)

Caveolae are plasma membrane-attached vesicular organelles. Caveolin-1, a 21-24-kDa integral membrane protein, is a principal component of caveolae membranes in vivo. Both caveolae and caveolin are most abundantly expressed in terminally differentiated cells: adipocytes, endothelial cells, and muscle cells. Conversely, caveolin-1 mRNA and protein expression are lost or reduced during cell transformation by activated oncogenes such as v-abl and H-ras (G12V); caveolae are absent from these cell lines. However, its remains unknown whether down-regulation of caveolin-1 protein and caveolae organelles contributes to their transformed phenotype.
Speculative dynamic vectorization (2002)

Traditional vector architectures have shown to be very effective for regular codes where the compiler can detect data-level parallelism. However, this SIMD parallelism is also present in irregular or pointer-rich codes, for which the compiler is quite limited to discover it. In this paper we propose a microarchitecture extension in order to exploit SIMD parallelism in a speculative way. The idea is to predict when certain operations are likely to be vectorizable, based on some previous history information. In this case, these scalar instructions are executed in a vector mode. These vector instructions operate on several elements (vector operands) that are anticipated to be their input operands and produce a number of outputs that are stored on a vector register in order to be used by further instructions. Verification of the correctness of the applied vectorization eventually changes the status of a given vector element from speculative to non-speculative, or alternatively, generates a recovery action in case of misspeculation.The proposed microarchitecture extension applied to a 4-way issue superscalar processor with one wide bus is 19% faster than the same processor with 4 scalar buses to L1 data cache. This speed up is due basically to 1) the reduction in number of memory accesses, 15% for SpecInt and 20% for SpecFP, 2) the transformation of scalar arithmetic instructions into their vector counterpart, 28% for SpecInt and 23% for SpecFP, and 3) the exploitation of control independence for mispredicted branches.
The Structure of Rat Liver Vault at 3.5 Angstrom Resolution (2009)

Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the cellular function remains unclear. We have determined the x-ray structure of rat liver vault at 3.5 angstrom resolution and show that the cage structure consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain, and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The shoulder domain is structurally similar to a core domain of stomatin, a lipid-raft component in erythrocytes and epithelial cells.
Limitations of the Vickrey Auction in Computational Multiagent Systems (1996)

Auctions provide an efficient distributed mechanism for solving problems such as task and resource allocation in multiagent systems.
Potential Biomarkers of Colorectal Adenoma–Dysplasia–Carcinoma Progression: mRNA Expression Profiling and In Situ Protein Detection on TMAs Reveal 15 Sequentially Upregulated and 2 Downregulated Genes (2009)

Background : As most colorectal cancers (CRC) develop from villous adenomas, studying alterations in gene expression profiles across the colorectal adenoma–dysplasia–carcinoma sequence may yield potential biomarkers of disease progression. Methods : Total RNA was extracted, amplified, and biotinylated from colonic biopsies of 15 patients with CRC, 15 with villous adenoma and 8 normal controls. Gene expression profiles were evaluated using HGU133Plus2.0 microarrays and disease progression associated data were validated with RT-PCR. The potential biomarkers were also tested at the protein level using tissue microarray samples of 103 independent and 16 overlapping patients. Results : 17 genes were validated to show sequentially altered expression at mRNA level through the normal–adenoma–dysplasia–carcinoma progression. Prostaglandin-D2 receptor (PTGDR) and amnionless homolog (AMN) genes revealed gradually decreasing expression while the rest of 15 genes including osteonectin, osteopontin, collagen IV–alpha 1, biglycan, matrix GLAprotein, and von Willebrand factor demonstrated progressively increasing expression. Similar trends of expression were confirmed at protein level for PTGDR, AMN, osteopontin and osteonectin. Conclusion : Downregulated AMN and PTGDR and upregulated osteopontin and osteonectin were found as potential biomarkers of colorectal carcinogenesis and disease progression to be utilized for prospective biopsy screening both at mRNA and protein levels. Gene alterations identified here may also add to our understanding of CRC progression.
Biomagnification of cyanobacterial neurotoxins and neurodegenerative disease among the Chamorro people of Guam (2003)

We here report biomagnification (the increasing accumulation of bioactive, often deleterious molecules through higher trophic levels of a food chain) of the neurotoxic nonprotein amino acid beta-methylamino-l-alanine (BMAA) in the Guam ecosystem. Free-living cyanobacteria produce 0.3 microg/g BMAA, but produce 2-37 microg/g as symbionts in the coralloid roots of cycad trees. BMAA is concentrated in the developing reproductive tissues of the cycad Cycas micronesica, averaging 9 microg/g in the fleshy seed sarcotesta and a mean of 1,161 microg/g BMAA in the outermost seed layer. Flying foxes (Pteropus mariannus), which forage on the seeds, accumulate a mean of 3,556 microg/g BMAA. Flying foxes are a prized food item of the indigenous Chamorro people who boil them in coconut cream and eat them whole. Chamorros who die of amyotrophic lateral sclerosis/parkinsonism-dementia complex (AL-SPDC), a neurodegenerative disease with symptoms similar to amyotrophic lateral sclerosis, Parkinson's disease, and Alzheimer's disease, have an average of 6.6 microg/g BMAA in their brain tissues. The biomagnification of BMAA through the Guam ecosystem fits a classic triangle of increasing concentrations of toxic compounds up the food chain. This may explain why the incidence of ALS-PDC among the Chamorro was 50-100 times the incidence of amyotrophic lateral sclerosis elsewhere. Biomagnification of cyanobacterial BMAA may not be unique to Guam; our discovery of BMAA in the brain tissue from Alzheimer's patients from Canada suggests alternative ecological pathways for the bioaccumulation of BMAA in aquatic or terrestrial ecosystems.
Bone morphogenetic protein-5 (BMP-5) promotes dendritic growth in cultured sympathetic neurons (2001)

These data suggest a role for BMP-5 in regulating dendritic growth in sympathetic neurons. The signaling pathway that mediates the dendrite-promoting activity of BMP-5 may involve binding to BMPR-IA and activation of Smad-1, and relative levels of BMP antagonists such as noggin and follistatin may modulate BMP-5 signaling. Since BMP-5 is expressed at relatively high levels not only in the developing but also the adult nervous system, these findings suggest the possibility that BMP-5 regulates dendritic morphology not only in the developing, but also the adult nervous system.
B-cell precursor acute lymphoblastic leukemia and stromal cells communicate through Galectin-3 (2015)

The molecular interactions between B-cell precursor acute lymphoblastic leukemia (pre-B ALL) cells and stromal cells in the bone marrow that provide microenvironmentally-mediated protection against therapeutic drugs are not well-defined. Galectin-3 (Lgals3) is a multifunctional galactose-binding lectin with reported location in the nucleus, cytoplasm and extracellular space in different cell types. We previously reported that ALL cells co-cultured with stroma contain high levels of Galectin-3. We here establish that, in contrast to more mature B-lineage cancers, Galectin-3 detected in and on the ALL cells originates from stromal cells, which express it on their surface, secrete it as soluble protein and also in exosomes. Soluble and stromal-bound Galectin-3 is internalized by ALL cells, transported to the nucleus and stimulates transcription of endogenous LGALS3 mRNA. When human and mouse ALL cells develop tolerance to different drugs while in contact with protective stromal cells, Galectin-3 protein levels are consistently increased. This correlates with induction of Galectin-3 transcription in the ALL cells. Thus Galectin-3 sourced from stroma becomes supplemented by endogenous Galectin-3 production in the pre-B ALL cells that are under continuous stress from drug treatment. Our data suggest that stromal Galectin-3 may protect ALL cells through auto-induction of Galectin-3 mRNA and tonic NFκB pathway activation. Since endogenously synthesized Galectin-3 protects pre-B ALL cells against drug treatment, we identify Galectin-3 as one possible target to counteract the protective effects of stroma.
The discoidin domain receptor tyrosine kinase DDR1 in arterial wound repair (2001)

Collagens act as important signaling molecules regulating vascular smooth muscle cell responses during arterial wound repair. Discoidin domain receptors (DDRs) are a novel class of receptor tyrosine kinases that bind to several collagens and stimulate matrix metalloproteinase (MMP) production, but little is known about their expression and function in the vasculature. We posited a critical role for the DDRs controlling smooth muscle cell migration and proliferation and thus repair following arterial injury. Smooth muscle cells were isolated from the aortas of mice with a targeted deletion of the DDR1 gene (DDR1-null) and studied in culture using models that mimic critical steps in neointimal thickening. Our studies suggest that DDR1 plays an important role in regulating attachment to collagen, chemotaxis, proliferation, and MMP production in smooth muscle cells. Following mechanical injury to the carotid arteries, cross-sectional area of the neointima was significantly lower in DDR1-null mice than in wild-type mice. There was also a significant decrease in collagen deposition in the injured arteries of the DDR1-null mice. Our results support the hypothesis that DDR1 plays an important role as a collagen receptor, mediating intimal thickening after vascular injury.
Relationships of Abdominal Obesity and Hyperinsulinemia to Angiographically Assessed Coronary Artery Disease in Men With Known Mutations in the LDL Receptor Gene (1998)

Results of the present study provide support for the notion that the hyperinsulinemic-insulin-resistant state of abdominal obesity is a powerful predictor of CAD in men, even in a group of patients with raised LDL cholesterol concentrations due to FH.
Fluorescent Detection of Chemical Warfare Agents:  Functional Group Specific Ratiometric Chemosensors (2003)

Indicators providing highly sensitive and functional group specific fluorescent response to diisopropyl fluorophosphate (DFP, a nerve gas (G-agent) simulant) are reported. Nonemissive indicator 2 reacts with DFP to give a cyclized compound 2+A- that shows a high emission due to its highly planar and rigid structure. Very weak emission was observed by the addition of HCl. Another indicator based on pyridyl naphthalene exhibits a large shift in its emission spectrum after reaction with DFP, which provides for quantitative ratiometric detection.
Targeted disruption of the three Rb-related genes leads to loss of G1 control and immortalization (2000)

The retinoblastoma protein, pRB, and the closely related proteins p107 and p130 are important regulators of the mammalian cell cycle. Biochemical and genetic studies have demonstrated overlapping as well as distinct functions for the three proteins in cell cycle control and mouse development. However, the role of the pRB family as a whole in the regulation of cell proliferation, cell death, or cell differentiation is not known. We generated embryonic stem (ES) cells and other cell types mutant for all three genes. Triple knock-out mouse embryonic fibroblasts (TKO MEFs) had a shorter cell cycle than wild-type, single, or double knock-out control cells. TKO cells were resistant to G(1) arrest following DNA damage, despite retaining functional p53 activity. They were also insensitive to G(1) arrest signals following contact inhibition or serum starvation. Finally, TKO MEFs did not undergo senescence in culture and do possess some characteristics of transformed cells. Our results confirm the essential role of the Rb family in the control of the G(1)/S transition, place the three Rb family members downstream of multiple cell cycle control pathways, and further the link between loss of cell cycle control and tumorigenesis.
Coenzyme A Analogues and Derivatives:  Synthesis and Applications as Mechanistic Probes of Coenzyme A Ester-Utilizing Enzymes (2000)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCoenzyme A Analogues and Derivatives: Synthesis and Applications as Mechanistic Probes of Coenzyme A Ester-Utilizing EnzymesPranab K. Mishra and Dale G. DrueckhammerView Author Information Department of Chemistry, State University at Stony Brook, Stony Brook, New York 11794 Cite this: Chem. Rev. 2000, 100, 9, 3283–3310Publication Date (Web):August 10, 2000Publication History Received19 July 1999Published online10 August 2000Published inissue 1 September 2000https://pubs.acs.org/doi/10.1021/cr990010mhttps://doi.org/10.1021/cr990010mresearch-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views3101Altmetric-Citations73LEARN 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 SUBJECTS:Genetics,Inhibitors,Organic compounds,Peptides and proteins,Reaction products Get e-Alerts
Research on Spraying and Fusing of non-self-fluxing Copper Powdered Alloy on Cast Iron Surface (2006)

A new type additive was added to the non-self-fluxing copper powdered alloy, and the powder showed satisfactory performance of spraying am] fusing, self-protecting, and self-fluxing in the oxygen-acetylene flame spraying and fusing process. The additive was melted and could absorb copper oxide when spraying, then it created a layer of film to cover the copper liquid, which protected the copper liquid from oxidizing efficiently and promoted it wetting on iron surface. Thus it lead to real diffusion between Cu and Fe, which resolved the difficulty of combining Cu with Fe and reduced the limitation of the powder, and it promoted the usage value of general powder. Through analysis of microstructures, it was found that the fastness and compactness of the combining interface was excellent as well as the diffusing of transition area, and the hardness was suitable, which meant that the performance could meet the needs of high quality valves completely.
Enhanced Natural Killer Cell Binding and Activation by Low-Fucose IgG1 Antibody Results in Potent Antibody-Dependent Cellular Cytotoxicity Induction at Lower Antigen Density (2005)

Our data showed that fucose removal from IgG1 could reduce the antigen amount required for ADCC induction via efficient recruitment and activation of NK cells.
Generation of antibodies by cell and gene immortalization (1993)

Studies in Transgenic Mice Antigens and Antibodies in Phages Antibody Engineering Bispecific Antibodies Antibody Reshaping Applications in Medicine Human Monoclonal Antibodies Ig Deficits Educational Perspectives.
Matrix Permeability Measurement of Gas Productive Shales (1993)

Abstract Three laboratory methods were developed to measure matrix gas permeability (Km) of Devonian shale cores and drill cuttings at native water saturations. The first method uses pulse pressure testing of core plugs with helium. The second, new method uses pulse pressure testing of core chips or drill cuttings with helium. These methods gave comparable results on 23 companion shale samples from two wells, with Km = 0.2 to 19 × 10−8 md. The third, new method uses degassibility of core plugs with helium and methane, and yielded Km higher by a factor of 3 to 10. Most of the core plugs tested showed multiple microfractures that remain open at reservoir stress, and these dominate conventional flow tests. These microfractures are parallel to bedding, are coring induced, and are not present in the reservoir. Knowledge of Km is important in computer simulation modeling of long term Devonian shale gas production, and has been a key to understanding the nature of the natural fracture network present in the reservoir.
Mutations in the Carboxyl Terminus of the Agouti Protein Decrease Agouti Inhibition of Ligand Binding to the Melanocortin Receptors (1997)

Several mutations that cause ectopic expression of the agouti gene result in obesity, hyperinsulinemia, and yellow coat color. A candidate pathway for agouti induced obesity and hyperinsulinemia is through altered signaling by melanocortin receptors, as agouti normally regulates coat coloration through antagonism of melanocortin receptor 1. Furthermore, melanocortin peptides mediate functions including steroidogenesis, lipolysis, and thermoregulation. We report apparent inhibition dissociation constants for mouse and human agouti protein inhibition of ligand binding to the melanocortin receptors, to determine which of these receptors might be involved in agouti induced diabetes. The similarity in the apparent K(I) values for agouti inhibition of ligand binding to the brain melanocortin receptors 3 and 4 (mouse: K(I) app = 190 +/- 74 and 54 +/- 18 nM; human: K(I) app = 140 +/- 56 and 70 +/- 18 nM, respectively) suggests that the MC3-R is a potential candidate for a receptor mediating the effects of agouti protein overexpression. Agouti residues important for melanocortin receptor inhibition were identified through the analysis of deletion constructs and site-specific variants. Val83 is important for inhibition of binding to MC1-R (K(I) app for Val83Ala agouti increased 13-fold relative to wild-type protein). Arg85, Pro86, and Pro89 are important for selective inhibition of binding between MC1-R and MC3-R and MC4-R as their apparent K(I) values are essentially unchanged at MC1-R, while they have increased 6-10-fold relative to wild-type protein at MC3-R and MC4-R.
Nitric oxide (NO) reduction by retorted oil shale (1984)

Nitric oxide gas (NO) is effectively reduced by retorted oil shale. At 300/sup 0/C half of the NO in a gas stream is removed when the gas stream contacts a bed of crushed retorted oil shale for 0.4 s. The fraction removed in 0.4 s reaches 90% at a temperature of 375/sup 0/C. As long as the reducing agent, presumed to be char in the retorted shale, is not depleted, the rate of reduction of NO appears to be proportional to the partial pressure of NO, and our results can be expressed in terms of a rate constant (k) which is a function of temperature (T, Kelvin) as follows: k = Ae/sup -//sup E/RT/ (s/sup -1/), where A = 4.0 x 10/sup 5/ (s/sup -1/) and E = 59.7 kJ/mole. This rate is many times faster than the rate of reduction of NO by coal char as measured by Furusawa et al. (1983). The principal reduction reaction is unknown; it does not release CO/sub 2/.
Plasma membrane gp96 enhances invasion and metastatic potential of liver cancer via regulation of uPAR (2015)

Targeted therapy is currently under intensive investigation due to the resistance of liver cancer to cytotoxic chemotherapies. Dissecting the molecular events that drive the progression of liver cancer and defining specific targets are urgently needed to develop efficient tailored therapies. Cell membrane gp96 (mgp96) has been implicated in tumor growth and malignancy. Here, we explored the functional and clinical relevance of mgp96 in liver cancer. We found that elevated mgp96 abundance was associated with tumor metastasis and recurrence in patients with primary liver tumors. Decreased KDELR1 levels in hepatoma cells contribute to cell membrane translocation of the normally ER-resident gp96. Urokinase-type plasminogen activator receptor (uPAR) was identified as a mgp96 client protein, and mgp96 stabilized uPAR protein. Our clinical results proved that elevated mgp96 abundance is positively correlated with uPAR expression levels in liver tumors. We further provided evidence that targeting mgp96 with siRNA or a specific mAb that blocked the mgp96-uPAR interaction led to inhibited cell growth, survival, and invasion in vitro, as well as the suppression of liver tumor growth and metastasis in vivo. mgp96 promotes liver cancer progression through increasing the protein stability and signaling of uPAR, and may be a new promising target for suppressing uPAR-mediated tumor growth and metastasis in liver cancer.
Gene expression profiling in the synovium identifies a predictive signature of absence of response to adalimumab therapy in rheumatoid arthritis (2009)

Gene expression studies of the RA synovium may be useful in the identification of early markers of response to TNF blockade. Genes significantly overexpressed at baseline in poor responders are induced by several cytokines in FLSs, thereby suggesting a role for these cytokines in the resistance to TNF blockade in RA.