gebhart/patrepeval huggingface dataset:
Single cell behavior in metastatic primary mammary tumors correlated with gene expression patterns revealed by molecular profiling. (2002)

We have developed animal models of breast cancer that allow the direct examination of the behavior of individual green fluorescent protein-expressing carcinoma cells in live nonmetastatic and metastatic primary tumors in situ. We have combined this model with multiphoton microscopy to image differences in cell behavior within the primary tumor. Differences in cell behavior between nonmetastatic and metastatic cells in culture and within live primary tumors were correlated with results from cDNA microarray analyses to identify potentially important genetic determinants for breast cancer invasion and metastasis. Using multiphoton microscopy, we found five major differences in carcinoma cell behavior between the nonmetastatic and metastatic primary breast tumors involving extracellular matrix, cell motility, and chemotaxis. Behavioral differences were correlated with seven categories of molecules that were differentially expressed and related to these behaviors. We have found that extracellular matrix composition, actin nucleation factors, molecules involved in mechanical stability and survival, and cell polarity and chemotaxis showed large and consistent differences in gene expression. We conclude that aligning cell behavior in vivo with patterns of gene expression can lead to new insights into the microenvironment of carcinoma cells in the primary tumor and the molecular mechanisms behind cell behavior.
Femtosecond laser-assisted microstructuring of silicon for novel detector, sensing and display technologies (2004)

In this talk we present the unique optical and electronic properties of microstructured silicon photodiode, discuss the formation process of conical microstructures, and review the chemical and structural make-up of the surface that are responsible for the novel optoelectronic microstructures. We also discuss future directions for this technique including structuring of new materials, incorporation of new ambient gases, and better control over the position and density of the microstructures themselves.
Assignments of Lowest Triplet State in Ir Complexes by Observation of Phosphorescence Excitation Spectra at 6 K (2006)

We tried the assignment of the origin of phosphorescent bands in Ir complexes. It is important to elucidate the luminescent mechanism in order to design organic light-emitting devices (OLEDs) besed on new materials. The Stokes shift between the phosphorescence and phosphorescence excitation spectra of Ir complexes such as fac-tris(2-phenylpyridine) iridium(III) [Ir(ppy)3], fac-tris(2-(2-thienyl)pyridine) iridium(III) [Ir(thpy)3], bis(2-phenylpyridine) iridium(III)benzo[h]quinoline [Ir(ppy)2bzq], fac-tris(benzo[h]quinoline) iridium(III) [Ir(bzq)3] and bis[(4,6-difluorophenyl)pyridinato](picolinato) iridium(III) [FIrpic] was measured in a solution and (phenyl)4Sn at 6 K. The amount of Stokes shift corresponds to the nature of the lowest triplet state. We discovered that the amount of Stokes shift clearly differs depending on whether the lowest triplet state of each Ir complex is triplet metal-to-ligand charge transfer (3MLCT) or 3π–π*. Namely, the case of 3MLCT shows a large shift, while the case of 3π–π* shows a small shift. We also present the resolved phosphorescence and phosphorescence excitation spectra of Ir complexes in (phenyl)4Sn. The sharp bands were assigned to the 3π–π* transition, and the broad bands were assigned to the 3MLCT state. The nature of the lowest triplet state is also discussed on the basis of resolved spectra.
Rpe65 Leu450Met variant is associated with reduced levels of the retinal pigment epithelium lipofuscin fluorophores A2E and iso-A2E (2004)

There is a growing body of evidence that the nondegradable fluorophores that accumulate as the lipofuscin of retinal pigment epithelium (RPE) are involved in mechanisms leading to the degeneration of RPE in macular degeneration. Most of the constituents of RPE lipofuscin are inadvertent products of the retinoid visual cycle, the enzymatic pathway by which the 11-cis-retinal chromophore of rhodopsin is generated. Indeed, a major constituent of RPE lipofuscin, the pyridinium bisretinoid A2E, is a diretinal conjugate that forms in photoreceptor cells and is deposited in RPE cells as a consequence of the phagocytosis of the outer segment membrane by RPE cells. Given the adverse effects of A2E, there is considerable interest in combating its deposition so as to protect against vision loss. These efforts, however, necessitate an understanding of factors that modulate its formation. Here we show that an amino acid variant in murine Rpe65, a visual-cycle protein required for the regeneration of 11-cis-retinal, is associated with reduced A2E accumulation.
Ligand exchange leads to efficient triplet energy transfer to CdSe/ZnS Q-dots in a poly(N-vinylcarbazole) matrix nanocomposite (2013)

Upon exchanging long chain alkylamine ligands with a carbazole terminated fatty acid as 6-(N-carbazolyl)-hexanoic acid (C6) and 11-(N-carbazolyl) undecanoic acid (C11), efficient photoluminescence (PL) of CdSe/ZnS colloidal quantum dots (QDs) was observed upon excitation in the absorption band of the carbazole moiety at 330 nm. This effect, which occurred both in solution and in a poly(N-vinylcarbazole) (PVK) matrix doped with the QDs, is attributed to sensitization of the QDs by PVK and the ligands. More efficient energy transfer was observed in solution for the shorter ligand (C6) capped QDs, due to a shorter average distance between the donor (carbazole) and the acceptor (QD). The binding of C6 and C11 to the QDs was confirmed by 1H solution nuclear magnetic resonance, which showed line broadening of the carbazole signal due to a decrease of the mobility of the carbazoles upon binding to the QDs compared with the sharp lines observed for the free molecules in solution. In doped PVK films, the significant enhancement of the energy transfer to the QD core could also be related to a better miscibility between the QDs and the PVK as confirmed by optical transmission and confocal microscopy images. In contrast to the experiment in solution, the overall energy transfer in the doped films was found more efficient for QDs capped with C11. To study in more detail the energy transfer between the carbazole moieties and the QDs, time-resolved fluorescence measurements were performed for solutions of C6 and C11, capped QDs and PVK films doped with the QDs. In contrast to the large enhancement of the QD emission indicated by steady-state PL spectra, the latter experiments suggested only a relatively low efficiency (19.6% and 10.8%) for singlet transfer from the carbazole ligands to the QDs. This suggests that the enhancement of the QD emission must be largely due to triplet transfer.
Anti-apoptosis gene, survivin, and prognosis of neuroblastoma (1998)

Neuroblastoma may be aggressive with a dismal outcome or regress spontaneously. Prognostic factors including age, stage, and ploidy, N-myc amplification, and histology are necessary to direct treatment. Gene products controlling apoptosis may modulate neuroblastoma's variable course. 1 Pritchard J Hickman JA Why does stage 4s neuroblastoma regress spontaneously?. Lancet. 1994; 344: 869-870 Abstract PubMed Scopus (104) Google Scholar Although expression of anti-apoptotic bcl-2 has been linked to a more aggressive disease, 2 Castle VP Heidelberger KP Bromberg J Ou X Dole M Nunez G Expression of the apoptosis-suppressing protein bcl-2, in neuroblastoma is associated with unfavourable histology and N-myc amplification. Am J Pathol. 1993; 143: 1543-1550 PubMed Google Scholar and inversely correlated with morphological features of apoptosis, it is unclear whether inhibition or apoptosis is a predictive factor in neuroblastoma or whether it reflects the degree of cell differentiation. 3 Hoehner JC Hedborg F Wiklund HJ Olsen L Pahlman S Cellular death in neuroblastoma: In situ correlation of apoptosis and bcl-2 expression. Int J Cancer. 1995; 62: 19-24 Crossref PubMed Scopus (59) Google Scholar An apoptosis inhibitor, survivin, 4 Ambrosini G Adida C Altieri DC A novel anti-apoptosis gene, survivin, expressed in cancer and lymphoma. Nat Med. 1997; 3: 917-921 Crossref PubMed Scopus (3000) Google Scholar has recently been identified. Unlike other members of the bcl-2 and IAP gene families, survivin is selectively expressed in all the most common human cancers but not in normal adult tissues. 4 Ambrosini G Adida C Altieri DC A novel anti-apoptosis gene, survivin, expressed in cancer and lymphoma. Nat Med. 1997; 3: 917-921 Crossref PubMed Scopus (3000) Google Scholar We determined the expression of survivin in neuroblastoma and its relation to disease progression.
Advances in the Inhibitors of Janus Kinase (2014)

The janus kinases (JAKs) comprise an important class of non-receptor protein tyrosine kinases. Cytokine and receptor binding can cause the activation of JAKs, and then activate the "signal transcripts and transcriptional activator", making JAK enter the nucleus to induce target gene expression. JAKs regulate inflammatory diseases, bone marrow hyperplasia and a variety of malignant tumours. Using JAKs inhibitors as the therapy for organ transplantation and immune disease has a very important significance. In recent years, many of the JAKs inhibitors have been developed one after another. Pan JAKs inhibitor and selective JAK2 or JAK3 inhibitor research progress are reviewed in this article.
Distinct binding sites of Ala48-hirudin1-47 and Ala48-hirudin48-65 on alpha-thrombin. (1990)

The interaction of alpha-thrombin with Ala48-hirudin, Ala48-hirudin1-47, and Ala48-hirudin48-65 was analyzed. Mutations at Pro48 were found to cause only slight changes in the kon (human: 3.1 +/- 0.3 x 10(8) M-1 s-1; bovine: 1.03 +/- 0.3 x 10(8) M-1 s-1) and koff (human: 0.4 +/- 0.2 x 10(-3) s-1; bovine: 2.9 +/- 0.4 x 10(-3) s-1) rate constants for the formation of the thrombin-hirudin complex. The amino-terminal fragment Ala48-hirudin1-47 containing the three disulfide bridges and the carboxyl-terminal fragment Ala48-hirudin48-65 were derived from the Ala48 mutant by proteolysis with endoproteinase Lys-C. These fragments inhibit bovine alpha-thrombin clotting activity with IC50 values of 0.6 and 4.9 microM, respectively (2.4 nM for r-hirudin). By mapping the interaction of Ala48-hirudin-derived fragments with bovine alpha-thrombin by limited proteolysis with trypsin and pancreatic elastase distinct binding sites for each fragment were determined. The carboxyl-terminal fragment was found to bind to the proposed anion-binding exosite in the region B62-74, whereas the amino-terminal fragment binds to a region around the elastase cleavage site at residues 150-151 of the alpha-thrombin B-chain.
Breeding for drought and nitrogen stress tolerance in maize: From theory to practice (2000)

Breeding for drought and nitrogen stress tolerance in maize :from theory to practice , Breeding for drought and nitrogen stress tolerance in maize :from theory to practice , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
IP Payload Compression Using ITU-T V.44 Packet Method (2001)

This document describes a compression method based on the data compression algorithm described in International Telecommunication Union (ITU-T) Recommendation V.44. Recommendation V.44 is a modem standard but Annex B, Clause B.1, of the recommendation describes the implementation of V.44 in packet networks (e.g., V.44 Packet Method). This document defines the application of V.44 Packet Method to the Internet Protocol (IP) Payload Compression Protocol (RFC 2393). RFC 2393 defines a method for applying lossless compression to the payload portion of IP datagrams.
Local heparin delivery prior to coronary stent implantation: Acute and six-month clinical and angiographic results (1997)

Stents increase smooth muscle cell proliferation, which may also lead to in-stent restenosis. A local delivery strategy provides higher drug concentration at the angioplasty site and may limit the proliferative response following stenting. Local heparin delivery was attempted in 35 patients following balloon angioplasty using an "over-the-balloon" style catheter (infusion sleeve). The infusion sleeve was successfully tracked and heparin was delivered in 33 (94%) patients. Heparin (1,000 IU/ml) was delivered under low (45 psi, 2 ml, n = 4), intermediate (75 psi, 4 ml, n = 11), and high (100 psi, 4 ml, n = 18) proximal infusion pressures. Stent placement was successful in all cases. Acute and in-hospital complications were a severe arterial spasm after heparin delivery, a non Q-wave myocardial infarction, and two vascular complications. Ten dissections were observed after PTCA and prior to heparin delivery. Of these dissections, 7 remained unchanged, 2 worsened, and 1 improved with local delivery. When heparin was delivered in the absence of dissection, no new dissections were observed. Of the 33 patients who received heparin, 30 (91%) had no symptoms and a negative exercise test at clinical follow-up. QCA analysis of 6-month follow-up angiograms, performed in 32 of 33 (97%) patients, demonstrated an acute gain of 1.98 +/- 0.67 mm, a late loss of 0.94 +/- 0.78 mm, a net gain of 1.04 +/- 0.78 mm, and a loss index of 0.48 +/- 0.32. Restenosis (> or = 50% stenosis) was observed in 4 of 32 (12%) patients. Local delivery of heparin via the infusion sleeve following PTCA and prior to stent deployment is feasible with an acceptable safety profile and a low clinical and angiographic restenosis rate at 6 months.
Control of biochemical reactions through supramolecular RING domain self-assembly (2002)

RING domains act in a variety of unrelated biochemical reactions, with many of these domains forming key parts of supramolecular assemblies in cells. Here, we observe that purified RINGs from a variety of functionally unrelated proteins, including promyelocytic leukemia protein, KAP-1TIF1beta, Z, Mel18, breast cancer susceptibility gene product 1 (BRCA1), and BRCA1-associated RING domain (BARD1), self-assemble into supramolecular structures in vitro that resemble those they form in cells. RING bodies form polyvalent binding surfaces and scaffold multiple partner proteins. Separation of RING bodies from monomers reveals that self-assembly controls and amplifies their specific activities in two unrelated biochemistries: reduction of 5' mRNA cap affinity of eIF4E by promyelocytic leukemia protein and Z, and E3 ubiquitin conjugation activity of BARD1:BRCA1. Functional significance of self-assembly is underscored by partial restoration of assembly and E3 activity of cancer predisposing BRCA1 mutant by forced oligomerization. RING self-assembly creates bodies that act structurally as polyvalent scaffolds, thermodynamically by amplifying activities of partner proteins, and catalytically by spatiotemporal coupling of enzymatic reactions. These studies reveal a general paradigm of how supramolecular structures may function in cells.
Onset of Catalytic Activity of Gold Clusters on Titania with the Appearance of Nonmetallic Properties (1998)

Gold clusters ranging in diameter from 1 to 6 nanometers have been prepared on single crystalline surfaces of titania in ultrahigh vacuum to investigate the unusual size dependence of the low-temperature catalytic oxidation of carbon monoxide. Scanning tunneling microscopy/spectroscopy (STM/STS) and elevated pressure reaction kinetics measurements show that the structure sensitivity of this reaction on gold clusters supported on titania is related to a quantum size effect with respect to the thickness of the gold islands; islands with two layers of gold are most effective for catalyzing the oxidation of carbon monoxide. These results suggest that supported clusters, in general, may have unusual catalytic properties as one dimension of the cluster becomes smaller than three atomic spacings.
SURFTrac: Efficient tracking and continuous object recognition using local feature descriptors (2009)

We present an efficient algorithm for continuous image recognition and feature descriptor tracking in video which operates by reducing the search space of possible interest points inside of the scale space image pyramid. Instead of performing tracking in 2D images, we search and match candidate features in local neighborhoods inside the 3D image pyramid without computing their feature descriptors. The candidates are further validated by fitting to a motion model. The resulting tracked interest points are more repeatable and resilient to noise, and descriptor computation becomes much more efficient because only those areas of the image pyramid that contain features are searched. We demonstrate our method on real-time object recognition and label augmentation running on a mobile device.
Modelling Hydrogen Induced Crack Growth: Validation by Comparison with Experiment (1995)

Abstract A finite difference hydrogen induced crack (HIC) growth model has been developed, enabling for the first time an accurate simulation of the growth of HIC cracks in the wall of pipelines and/or pressure vessels. In the model, parameters such as defect size, location, fracture toughness and hydrogen concentration, can be varied. The predictions of the HIC model are compared with experimental HIC crack growth curves, which were generated in a unique hydrogen permeation-ultrasonic scanning experiment. Both the observed time until initiation for HIC cracks and the crack growth rate show excellent agreement with the model calculations. The experiment in combination with the HIC model shows that defects initiate and propagate through segregation zones with a low fracture toughness. As soon as the defects reach the end of the segregation zone the HIC growth stops. The fracture toughness of the segregation zone as well as the bulk fracture toughness were determined by fitting the HIC model to the experimental data.
Modification of the tandem reactive centres of human inter-α-trypsin inhibitor with butanedione and cis-dichlorodiammineplatinum(II) (1988)

Human inter-alpha-trypsin inhibitor (I alpha I) is a plasma proteinase inhibitor active against cathepsin G, leucocyte elastase, trypsin and chymotrypsin. It owes its broad inhibitory specificity to tandem Kunitz-type inhibitory domains within an N-terminal region. Sequence studies suggest that the reactive-centre residues critical for inhibition are methionine and arginine. Reaction of I alpha I with the arginine-modifying reagent butane-2,3-dione afforded partial loss of inhibitory activity against both cathepsin G and elastase but complete loss of activity against trypsin and chymotrypsin. Reaction of I alpha I with the methionine-modifying reagent cis-dichlorodiammineplatinum(II) resulted in partial loss of activity against cathepsin G and elastase but did not affect inhibition of either trypsin or chymotrypsin. Employment of both reagents eliminated inhibition of cathepsin G and elastase. These findings suggest that both cathepsin G and elastase are inhibited at either of the reactive centres of I alpha I. Trypsin and chymotrypsin, however, appear to be inhibited exclusively at the arginine reactive centre.
Neolacto-series gangliosides induce granulocytic differentiation of human promyelocytic leukemia cell line HL-60. (1988)

Neolacto-series gangliosides having linear poly-N-acetyl-lactosaminyl oligosaccharide structure have been demonstrated to be increased characteristically during granulocytic differentiation of human promyelocytic leukemia cell line HL-60 cells induced by dimethyl sulfoxide or retinoic acid (Nojiri, H., Takaku, F., Tetsuka, T., Motoyoshi, K., Miura, Y., and Saito, M. (1984) Blood 64, 534-541). When HL-60 cells were cultured in the presence of neolacto-series gangliosides prepared from mature granulocytes, the cells were found to be differentiated into mature granulocytes on the basis of the changes of morphology, surface membrane antigens, nonspecific esterase activity, and the activity of phagocytosis and respiratory burst. The differentiation of cells was dependent on the concentration of gangliosides and accompanied with inhibition of cell growth. These findings suggest that the particular ganglioside molecules play an important role in regulation of cell differentiation and that the appearance of neolacto-series gangliosides on cell surface membrane not only triggers the differentiation but also determines the direction of differentiation in HL-60 cells.
Structural study of long arm fragments of laminin (1988)

The outer segments of the long arm of laminin have recently been shown to mediate attachment of many cell types and to stimulate neurite outgrowth. For a structural characterization of this part of the molecule we prepared, by limited elastase digestion of laminin, fragments E3 and E8, previously identified as a globular heparin-binding domain and as a 35-nm-long rod with a terminal globule, respectively. Fragment E3 is a domain adjacent to fragment E8. Both structures together comprise the complete terminal half of the long arm. Our data confirm current models, which predict that the C-terminal segments from all three chains contribute to its structure. The B chains terminate at the end of the rod like domain, while the large terminal globule is formed by A-chain structures only. In addition to fragment E3, two new fragments T1 and T2 obtained by tryptic cleavage of fragment E8 were characterized as substructures of the globular domain. Screening of a mouse cDNA library with synthetic oligonucleotides allowed isolation of an 1.8-kb cDNA clone encoding 547 C-terminal amino acids of the A chain and some 196 nucleotides of the 3'-untranslated region including a single polyadenylation site. The clone contained portions of domain T2 and the complete heparin binding domain E3 which was thus identified as the most C-terminal domain of the A chain. Sequence alignment indicated that the terminal globule is formed by homologous repeats of some 140 residues having no counterpart in the B chains.
Real-Time PCR Assay of Individual Human Immunodeficiency Virus Type 1 Variants in Coinfected Human Lymphoid Tissues (2003)

In the course of infection, human immunodeficiency virus type 1 (HIV-1) mutates, diverging into a "swarm" of viral quasispecies, and the predominance of CCR5- or CXCR4-utilizing quasispecies is strongly associated with the pattern of disease progression. Quantification of CCR5- and CXCR4-utilizing viruses in viral swarms is important in the investigation of the mechanisms of this phenomenon. Here, we report on a new real-time PCR-based methodology for the evaluation of replication of individual CCR5- and CXCR4-utilizing variants. The assay is highly reproducible, with a coefficient of variation of <3%, and it accurately estimates the numbers of virus-specific RNA copies even when their difference in the mixture is 2 orders of magnitude. We demonstrate that replications of CCR5- and CXCR4-utilizing variants can be evaluated and distinguished in experimentally coinfected human lymphoid tissue. The assay we developed may facilitate study of the mechanisms of the R5-to-X4 switch in viral swarms in human tissues infected with HIV-1.