gebhart/patrepeval huggingface dataset:
Image-based computational simulation of flow dynamics in a giant intracranial aneurysm. (2003)

Anatomic realism of lumen geometry and flow pulsatility is essential for elucidating the patient-specific nature of aneurysm hemodynamics. Such image-based CFD analysis may be used to provide key hemodynamic information for prospective studies of aneurysm growth and rupture or to predict the response of an individual aneurysm to therapeutic options.
Surface micromachined metallic microneedles (2003)

A method for fabricating surface micromachined, hollow, metallic microneedles is described. Single microneedle and multiple microneedle arrays with process enabled features such as complex tip geometries, micro barbs, mechanical penetration stops and multiple fluid output ports were fabricated, packaged and characterized. The microneedles were fabricated using electroplated metals including palladium, palladium-cobalt alloys and nickel as structural materials. The microneedles were 200 mm-2.0 cm in length with a cross-section of 70-200 μm in width and 75-120 μm in height, with a wall thickness of 30-35 μm. The microneedle arrays were typically 9.0 mm in width and 3.0 mm in height with between 3 and 17 needles per array. Using water as the fluid medium, the average inlet pressure was found to be 30.0 KPa for a flow rate of 1000 μL/h and 106 KPa for a flow rate 4000 μL/h.
Lanthanide-Binding Tags as Luminescent Probes for Studying Protein Interactions (2006)

Herein, we report a method for studying protein-peptide interactions which exploits the luminescence properties of Tb(III). Lanthanide-binding tags (LBTs) are short peptide sequences comprising 15-20 naturally occurring amino acids that bind Tb(III) with high affinity. These genetically encodable luminescent tags are smaller in size than the Aequorea victoria fluorescent proteins (AFPs) and benefit from the long-lived luminescence lifetime of lanthanides. In this study, luminescence resonance energy transfer (LRET) was used to monitor the interaction between SH2 domains and different phosphopeptides. For the study, the SH2 domains of Src and Crk kinase were each coexpressed with an LBT, and phosphorylated and nonphosphorylated peptides were chemically synthesized with organic fluorophores. The LRET between the protein-bound Tb(III) and the peptide-based organic fluorophore was shown to be specific for the recognition of the SH2 domain and the peptide binding partner. This method can detect differences in binding affinity and can be used to measure the dissociation constant for the protein-peptide interaction. In addition, decay experiments can be used to calculate the distance between a site in the bound peptide and the protein using Förster theory. In all of these experiments, the millisecond luminescence lifetime of Tb(III) can be exploited using time-resolved detection to eliminate background fluorescence from organic fluorophores.
Review: Tissue engineering: Reconstitution of human hematopoiesis ex vivo (1993)

The reconstruction of functioning human tissues ex vivo is becoming an important part of biotechnology. There are compelling scientific, clinical, and biotechnological reasons for fully or partially reconstituting human tissues such as skin, bone marrow, and liver ex vivo. In particular, bone marrow is a tissue of much importance, and there are significant societal and health benefits derived from a successfully constructed ex vivo hematopoietic system. In this article, we review the current status of this effort. The topics covered include the current understanding of the biology of human hematopoiesis, the motivation for reconstructing it ex vivo, the current state of ex vivo human hematopoietic cultures, the development of important metrics to judge culture performance, and an approach based on in vivo mimetics to accomplish this goal. We discuss some applications of functional ex vivo hematopoietic cultures and the biological and engineering challenges that face research in this area.
Synthesis of a Cyclic Peptide Containing Norlanthionine:  Effect of the Thioether Bridge on Peptide Conformation (2003)

Two diastereomeric analogues of ring C of nisin incorporating a novel norlanthionine residue have been synthesized via a triply orthogonal protecting group strategy. A full structural study was carried out by NMR, which elucidated the conformational properties of the two peptides and enabled the identity of each diastereoisomer to be proposed.
The Bisecting GlcNAc on N -Glycans Inhibits Growth Factor Signaling and Retards Mammary Tumor Progression (2010)

The branching of complex N-glycans attached to growth factor receptors promotes tumor progression by prolonging growth factor signaling. The addition of the bisecting GlcNAc to complex N-glycans by Mgat3 has varying effects on cell adhesion, cell migration, and hepatoma formation. Here, we show that Chinese hamster ovary cells expressing Mgat3 and the polyoma middle T (PyMT) antigen have reduced cell proliferation and growth factor signaling dependent on a galectin lattice. The Mgat3 gene is not expressed in virgin mammary gland but is upregulated during lactation and is expressed in mouse mammary tumor virus (MMTV)/PyMT tumors. Mice lacking Mgat3 that cannot transfer the bisecting GlcNAc to N-glycans acquire PyMT-induced mammary tumors more rapidly and have an increased tumor burden, increased migration of tumor cells, and increased early metastasis to lung. Tumors and tumor-derived cells lacking Mgat3 exhibit enhanced signaling through the Ras pathway and reduced amounts of functionally glycosylated alpha-dystroglycan. Constitutive overexpression of an MMTV/Mgat3 transgene inhibits early mammary tumor development and tumor cell migration. Thus, the addition of the bisecting GlcNAc to complex N-glycans of mammary tumor cell glycoprotein receptors is a cell autonomous mechanism serving to retard tumor progression by reducing growth factor signaling.
Chemical Inhibition of Acetyl-CoA Carboxylase Induces Growth Arrest and Cytotoxicity Selectively in Cancer Cells (2007)

Development and progression of cancer is accompanied by marked changes in the expression and activity of enzymes involved in the cellular homeostasis of fatty acids. One class of enzymes that play a particularly important role in this process are the acetyl-CoA carboxylases (ACC). ACCs produce malonyl-CoA, an intermediate metabolite that functions as substrate for fatty acid synthesis and as negative regulator of fatty acid oxidation. Here, using the potent ACC inhibitor soraphen A, a macrocyclic polyketide from myxobacteria, we show that ACC activity in cancer cells is essential for proliferation and survival. Even at nanomolar concentrations, soraphen A can block fatty acid synthesis and stimulate fatty acid oxidation in LNCaP and PC-3M prostate cancer cells. As a result, the phospholipid content of cancer cells decreased, and cells stopped proliferating and ultimately died. LNCaP cells predominantly died through apoptosis, whereas PC-3M cells showed signs of autophagy. Supplementation of the culture medium with exogenous palmitic acid completely abolished the effects of soraphen A and rescued the cells from cell death. Interestingly, when added to cultures of premalignant BPH-1 cells, soraphen A only slightly affected cell proliferation and did not induce cell death. Together, these findings indicate that cancer cells have become dependent on ACC activity to provide the cell with a sufficient supply of fatty acids to permit proliferation and survival, introducing the concept of using small-molecule ACC inhibitors as therapeutic agents for cancer.
Production of Lantipeptides in Escherichia coli (2010)

Lantipeptides are ribosomally synthesized and posttranslationally modified peptides containing thioether cross-links. We describe the preparation of seven different lantipeptides in Escherichia coli and demonstrate that this methodology can be used to incorporate nonproteinogenic amino acids.
Imparting cosmetic effects on textiles (2015)

In recent years, textile materials have found applications in cosmetic field. A new sector of cosmetic textiles is opened up and several commercial cosmetic textile products are currently available in the market. Microencapsulation technology is an effective technique to control the release properties of active ingredients that prolong the functionality of cosmetic textiles. This paper addresses the historical background of microencapsulation technology, its significant advantages and the most commonly used microencapsulation methods. Some typical examples of commercially available microencapsulation based cosmetic textile products are also examined. The recent applications as well as potential development in cosmetic textiles production are also discussed.
The Adenovirus E1B-55K Transforming Polypeptide Modulates Transport or Cytoplasmic Stabilization of Viral and Host Cell mRNAs (1986)

The adenovirus type 5 mutant H5dl338 lacks 524 base pairs within early region 1B. The mutation removed a portion of the region encoding the related E1B-55K and -17K polypeptides but did not disturb the E1B-21K coding region. The virus can be propagated in 293 cells which contain and express the adenovirus type 5 E1A and E1B regions, but it is defective for growth in HeLa cells, in which its final yield is reduced about 100-fold compared with the wild-type virus. The mutant also fails to transform rat cells at normal efficiency. The site of the dl338 defect was studied in HeLa cells. Early gene expression and DNA replication appeared normal. Late after infection, mRNAs coded by the major late transcription unit accumulated to reduced levels. At a time when transcription rates and steady-state nuclear RNA species were normal, the rate at which late mRNA accumulated in the cytoplasm was markedly reduced. Furthermore, in contrast to the case with the wild type, transport and accumulation of cellular mRNAs continued late after infection with dl338. Thus, the E1B product appears to facilitate transport and accumulation of viral mRNAs late after infection while blocking the same processes for cellular mRNAs.
A Proof of Useful Work for Artificial Intelligence on the Blockchain (2020)

Bitcoin mining is a wasteful and resource-intensive process. To add a block of transactions to the blockchain, miners spend a considerable amount of energy. The Bitcoin protocol, named 'proof of work' (PoW), resembles a lottery and the underlying computational work is not useful otherwise. In this paper, we describe a novel 'proof of useful work' (PoUW) protocol based on training a machine learning model on the blockchain. Miners get a chance to create new coins after performing honest ML training work. Clients submit tasks and pay all training contributors. This is an extra incentive to participate in the network because the system does not rely only on the lottery procedure. Using our consensus protocol, interested parties can order, complete, and verify useful work in a distributed environment. We outline mechanisms to reward useful work and punish malicious actors. We aim to build better AI systems using the security of the blockchain.
Advances in Digital Image Processing (1992)

AbstractDue to advances in the semiconductor technology and developments in software, digital image processing is also developing very rapidly. Here an attempt is made to describe/present some of the important applications and some of the recent fast growing fields like pyramid processing, image restoration, texture analysis, fractal analysis and image segmentation.
Cytoplasmic and Nuclear Delivery of a TAT-derived Peptide and a β-Peptide after Endocytic Uptake into HeLa Cells (2003)

Several short, highly cationic peptides are able to enter the cytoplasm and nucleus of cells from the extracellular medium. The mechanism of entry is unknown. A number of fluorescence-based studies suggested that these molecules cross the plasma membrane by an energy-independent process, directly gaining access to the cytoplasm. Recent reports have questioned this conclusion, attributing the prior observations to artifacts resulting from fixation procedures used to prepare cells for fluorescence microscopy. These studies analyzed live cells and showed that the peptides entered through endocytosis and accumulated in endocytic vesicles, without necessarily entering the cytoplasm. To resolve this controversy and to extend the analyses to non-natural beta-peptide sequences, we studied the cytoplasmic and nuclear delivery of a fluorescein-labeled 9-residue sequence derived from the human immunodeficiency virus transactivator of transcription (TAT) peptide, TAT-(47-57), as well as a similarly labeled 12-residue beta-peptide, beta-(VRR)4, in live cells. Using fluorescence confocal microscopy, we show that when added to cells, both peptides are found in endocytic vesicles containing the transferrin receptor as well as in the cytoplasm and nucleus (TAT-(47-57)) or nucleolus (beta-(VRR)4). The cells were verified to be intact through all experimental procedures by demonstrating their ability to exclude propidium iodide. Endocytic entry of the peptides was blocked by the energy poisons sodium azide and 2-deoxyglucose, whereas staining of the nucleus (nucleolus), but not endocytic vesicles, was abrogated by treating the cells with ammonium chloride. Our observations are consistent with the proposal that TAT-(47-57) and beta-(VRR)4 enter cells by endocytosis and then exit an endosomal compartment to enter the cytoplasm by means of a mechanism requiring endosome acidification.
On Edge Detection of X-Ray Images Using Fuzzy Sets (1983)

The effectiveness of the theory of fuzzy sets in detecting different regional boundaries of X-ray images is demonstrated. The algorithm includes a prior enhancement of the contrast among the regions (having small change in gray levels) using the contrast intensification (INT) operation along with smoothing in the fuzzy property plane before detecting its edges. The property plane is extracted from the spatial domain using S, ¿ and (1 ¿) functions and the fuzzifiers. Final edge detection is achieved using max or min operator. The system performance for different parameter conditions is illustrated by application to an image of a radiograph of the wrist.
The activity of the pseudorabies virus latency-associated transcript promoter is dependent on its genomic location in herpes simplex virus recombinants as well as on the type of cell infected (1994)

As do many other alphaherpesviruses, pseudorabies virus (PRV) transcribes a limited portion of its viral genome in latently infected neurons during latency. The sequence of the PRV latency-associated transcript (LAT) is bounded on its 5' end by a putative promoter region which contains sequence elements similar to those characterized for the herpes simplex virus (HSV) LAT promoter. Using the bacterial beta-galactosidase gene as a reporter, we have assayed PRV LAT promoter activity in the genomic environment in recombinant HSVs. The PRV LAT promoter-beta-galactosidase reporter gene was recombined into the terminal and internal long repeat regions (RL regions), replacing the normal HSV LAT promoter, the cap site, and the first 60 bases of the primary transcript. When recombined into the RL region, appreciable reporter gene expression was observed following infection of two cell lines of neuronal origin; little or no activity was seen with these recombinants following infection of rabbit skin or mouse embryo fibroblasts. No significant expression was seen when the promoter was recombined into the gC locus in the long unique region in any of the cell types utilized. Such results suggest that the PRV latency promoter contains neuronal cell-specific elements and that the HSV RL region provides an appropriate genomic environment for the manifestation of that specificity.
Regulation of vitamin D receptor abundance and responsiveness during differentiation of HT-29 human colon cancer cells. (1993)

We have studied the effects of 1,25-dihydroxyvitamin D [1,25-(OH)2D3] on cellular differentiation in the HT-29 human colon cancer cell line. Our aim was to evaluate the regulation of 1,25-dihydroxyvitamin D receptor (VDR) abundance and hormone responsiveness during the transition of rapidly proliferating to differentiated cells. Differentiation was induced by three means: cells were cultured in galactose-supplemented medium without glucose (GAL), grown on Matrigel-coated surfaces (MTG), or treated with 1,25(OH)2D3. Cell proliferation, assessed by [3H]thymidine incorporation, was equivalently inhibited by treatment with 1,25(OH)2D3, GAL or MTG. Differentiation was assessed by the induction of amino-oligo peptidase activity which was low in the proliferating cells. Following treatment with 1,25(OH)2D3, or growth in GAL or on MTG, amino-oligo peptidase activity increased 8- to 9-fold. The abundance of VDR measured by [3H]1,25(OH)2D3 binding, decreased to half without significant change in affinity, in cells differentiated by all three means compared to proliferating cells. Northern blot analyses of differentiated cells showed decreased steady-state levels of VDR messenger RNA (mRNA), indicating that all three treatments similarly decreased the abundance of VDR, at least in part, at the mRNA level. When exposed to 1,25(OH)2D3, the proliferating cells exhibited homologous up-regulation of VDR as well as the induction of 24-hydroxylase mRNA; the differentiated cells failed to exhibit both of these biological responses. Our findings demonstrate that 1,25(OH)2D3, GAL and MTG treatment all inhibit HT-29 cell proliferation and stimulate differentiation. Postproliferative differentiation achieved by the three approaches was associated with decreased VDR abundance, loss of VDR homologous up-regulation, and development of hormone unresponsiveness to 1,25(OH)2D3.
Block Copolymers by Transformation of “Living” Carbocationic into “Living” Radical Polymerization (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorBlock Copolymers by Transformation of "Living" Carbocationic into "Living" Radical PolymerizationSimion Coca and Krzysztof MatyjaszewskiView Author Information Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213 Cite this: Macromolecules 1997, 30, 9, 2808–2810Publication Date (Web):May 5, 1997Publication History Received22 January 1997Revised20 March 1997Published online5 May 1997Published inissue 1 May 1997https://pubs.acs.org/doi/10.1021/ma970073bhttps://doi.org/10.1021/ma970073brapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1171Altmetric-Citations134LEARN 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:Cationic polymerization,Copolymers,Organic compounds,Polymers,Radical polymerization Get e-Alerts
Device-free wireless localization and activity recognition with deep learning (2016)

Recent advance in device-free wireless localization and activity recognition (DFLAR) technique has made it possible to acquire context information of the target without its participation. This novel technique has great potential for lots of applications, e.g., smart space, smart home, and security safeguard. One fundamental question of DFLAR is how to design discriminative features to characterize the raw wireless signal. Existing works manually design handcraft features, e.g., mean and variance of the raw signal, which is not universal for different activities. Inspired by the deep learning theory, we explore to learn universal and discriminative features automatically with a deep learning model. By merging the learned new features into a softmax regression based machine learning framework, we develop a deep learning based DFLAR system. Experimental evaluations with an 8 wireless nodes testbed confirms that compared with traditional handcraft features, DFLAR system with the learned features could achieve better performance.
The chemokine SDF‐1, stromal cell‐derived factor 1, attracts early stage B cell precursors via the chemokine receptor CXCR4 (1997)

In the bone marrow, progenitor (pro-) and precursor (pre-) B cells depend on close contact with stromal cells for growth and maturation. Stromal cell-derived factor 1 (SDF-1), also known as pre-B cell growth-stimulating factor, is produced by bone marrow stromal cells and was reported to act together with interleukin-7 as co-mitogen for pre-B cells. SDF-1 was recently shown to be a chemokine which is chemotactic for different types of leukocytes and acts via the chemokine receptor CXCR4. Using sorted B220+ bone marrow cells and several B cell lines characteristic for different stages of B lymphopoiesis, we now show that SDF-1 is a potent attractant for pro- and pre-B cells, but is inactive on B cells at later stages of development. In early B cell precursors, SDF-1 induced intracellular Ca2+ mobilization and in vitro migration with a potency and efficacy similar to that observed for chemokines acting on blood leukocytes. These responses were mediated via CXCR4 as they could be inhibited by an antireceptor antibody. SDF-1 is the first chemokine shown to act on early-stage B cell precursors. Mice lacking SDF-1 die perinatally and show a severe deficiency in B lymphopoiesis. We propose that SDF-1 released from the stromal cells exerts its critical hematopoietic function by selectively attracting and confining early B cell precursors within the bone marrow microenvironment that provides the necessary factors for growth and differentiation.
Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing (2009)

A single tumor may contain cells with different somatic mutations. By characterizing this genetic heterogeneity within tumors, advances have been made in the prognosis, treatment and understanding of tumorigenesis. In contrast, the extent of epigenetic intra-tumor heterogeneity and how it influences tumor biology is under-explored. We have characterized epigenetic heterogeneity within individual tumors using next-generation sequencing. We used deep single molecule bisulfite sequencing and sample-specific DNA barcodes to determine the spectrum of MLH1 promoter methylation across an average of 1000 molecules in each of 33 individual samples in parallel, including endometrial cancer, matched blood and normal endometrium. This first glimpse, deep into each tumor, revealed unexpectedly heterogeneous patterns of methylation at the MLH1 promoter within a subset of endometrial tumors. This high-resolution analysis allowed us to measure the clonality of methylation in individual tumors and gain insight into the accumulation of aberrant promoter methylation on both alleles during tumorigenesis.