gebhart/patrepeval huggingface dataset:
Imaging Tissue Engineered Blood Vessel Mimics with Optical Coherence Tomography (2008)

Optical coherence tomography (OCT) is a technology that enables 2D cross-sectional images of tissue microstructure. This interferometric technique provides resolutions of approximately 10-20 um with a penetration depth of 1-2 mm in highly scattering tissues. With the use of fiber optics, OCT systems have been developed for intravascular imaging with a demonstrated improvement in both resolution and dynamic range compared to commercial intravascular ultrasound systems. OCT studies of normal, atherosclerotic, and stented arteries indicate the ability of OCT to visualize arterial structures. These results suggest OCT may be a valuable tool for studying luminal structures in tissue engineered constructs.In the present study, new endoscopic OCT systems and analysis techniques were developed to visualize the growth and response of the cellular lining within a tissue engineered blood vessel mimic (BVM). The BVM consists of two primary components. A biocompatible polymeric scaffold is used to form the tubular structure. Human microvessel cells from adipose tissue are sodded on to the inner surface of the scaffold. These constructs are then developed and imaged within a sterile bioreactor.Three specific aims were defined for the present study. First, an OCT longitudinal scanning endoscope was developed. With this endoscope, a study of 16 BVMs was performed comparing images from OCT and corresponding histological sections. The study demonstrated that endoscopic imaging did not visually damage the mimic cellular lining. OCT images showed excellent correlation with corresponding histologicalsections. Second, a concentric three element endoscope was developed to provide radial cross-sections of the BVM. OCT images using this endoscope monitored lining development on three types of polymeric scaffolds. In the third specific aim, automated algorithms were developed to assess the percent cellular coverage of a stent using volumetric OCT images.The results of the present study suggest that OCT endoscopic systems may be a valuable tool for assessing and optimizing the development of tissue engineered constructs. Conversely, the BVMs modeled the arterial response to deployed stents allowing the development of automated OCT analysis software. These results suggest that blood vessel mimics may be used to advance OCT technology and techniques.
Annexin II/Annexin II receptor axis regulates adhesion, migration, homing, and growth of prostate cancer (2008)

One of the most life-threatening complications of prostate cancer is skeletal metastasis. In order to develop treatment for metastasis, it is important to understand its molecular mechanisms. Our work in this field has drawn parallels between hematopoietic stem cell and prostate cancer homing to the marrow. Our recent work demonstrated that annexin II expressed by osteoblasts and endothelial cells plays a critical role in niche selection. In this study, we demonstrate that annexin II and its receptor play a crucial role in establishing metastasis of prostate cancer. Prostate cancer cell lines migrate toward annexin II and the adhesion of prostate cancer to osteoblasts and endothelial cells was inhibited by annexin II. By blocking annexin II or its receptor in animal models, short-term and long-term localization of prostate cancers are limited. Annexin II may also facilitate the growth of prostate cancer in vitro and in vivo by the MAPK pathway. These data strongly suggest that annexin II and its receptor axis plays a central role in prostate cancer metastasis, and that prostate cancer utilize the hematopoietic stem cell homing mechanisms to gain access to the niche.
Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities (1992)

Seven hydrophobic residues ranging in size from glycine to phenylalanine have been substituted for the wild-type methionine residue at position 13 in a 15-residue truncated version (S15) of S-peptide, the small component of ribonuclease S. Complexes of both S-15 and the seven variants with S-protein yielded isomorphous crystals. The structures of all eight complexes have been refined to final R-factors in the range of 17-19%. [See Kim, E. E. Varadarajan, R., Wyckoff, H. W., and Richards, F. M. (1992) Biochemistry (preceding paper in this issue) for the description of the reference S-15 complex.] Multiple side-chain conformations were seen for six residues in all of the complexes and for two to three additional residues in at least some of the complexes. Three of the complexes, Gly, Ala, and alpha-amino-n-butyric acid (ANB), contained a single water molecule in the cavity near residue 13 that makes three hydrogen bonds to protein atoms. Although space is available, no evidence for additional water in this region, ordered or disordered, was found. The atoms in the cavity wall tend to shrink the cavity by moving in on the small residues and to swell the cavity by moving out for the larger Phe substitution. A swelling seen with leucine was attributed to a shape effect since Leu, Ile, and Met all have the same volume. A slight volume contraction of the collection of interior residues outside of the region of position 13 was also noted. (All changes noted are in the direction to maintain a constant packing density averaged over the whole protein.) Leu51, a surface hydrophobic residue, moved considerably in the G, A, and ANB complexes in directionswhich would tend to decrease the cavity volume. The only other major change in position, 1.5 A, was the 66-69 loop, which is about 25 A from position 13. His12, Phe120, and Asp121 appear to be involved in this movement, but the connection with position 13 is not clear at all. The thermodynamic data on the association reaction for all of these complexes have been previously reported [Connelly, P. R., Varadarajan, R., Sturtevant, J. M., & Richards, F. M. (1990) Biochemistry 29, 6108-6114; Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426]. Some comments are offered on our initial attempts to correlate the structural changes with the changes in the thermodynamic parameters.(ABSTRACT TRUNCATED AT 400 WORDS)
High-Dynamic-Range Still-Image Encoding in JPEG 2000 (2005)

The raw size of a high-dynamic-range (HDR) image brings about problems in storage and transmission. Many bytes are wasted in data redundancy and perceptually unimportant information. To address this problem, researchers have proposed some preliminary algorithms to compress the data, like RGBE/XYZE, OpenEXR, LogLuv, and so on. HDR images can have a dynamic range of more than four orders of magnitude while conventional 8-bit images retain only two orders of magnitude of the dynamic range. This distinction between an HDR image and a conventional image leads to difficulties in using most existing image compressors. JPEG 2000 supports up to 16-bit integer data, so it can already provide image compression for most HDR images. In this article, we propose a JPEG 2000-based lossy image compression scheme for HDR images of all dynamic ranges. We show how to fit HDR encoding into a JPEG 2000 encoder to meet the HDR encoding requirement. To achieve the goal of minimum error in the logarithm domain, we map the logarithm of each pixel value into integer values and then send the results to a JPEG 2000 encoder. Our approach is basically a wavelet-based HDR still-image encoding method.
Fine-structure mapping ofcis-acting control sites in thelysCoperon ofBacillus subtilis (1992)

Mutations at the aecA locus of Bacillus subtilis lead to derepression of the lysC operon, which encodes aspartokinase II, and analysis of three independent aecA mutations has shown them to be nucleotide substitutions in the lysC leader region (Y. Lu, N.Y. Chen and H. Paulus (1991) J. Gen. Microbiol. 137, 1135-1141). DNA sequence analysis of the lysC control region of nine other mutants with derepressed levels of aspartokinase II revealed each of the mutations to be associated with changes in one or a few nucleotide residues. The nucleotide substitutions were clustered at two sites in the lysC leader: in a region of imperfect dyad symmetry about 40 base pairs from the transcription start site, and in the open reading frame for a putative leader peptide, which starts about 40 residues further downstream. The effect of nucleotide substitutions at the two sites differed in that those at the upstream site gave twice the degree of derepression. A mutant with a small deletion in the leader peptide coding region potentially affecting RNA secondary structure also had a higher level of lysC derepression. These results suggest that the lysC leader region contains at least two cis-acting control sites that play important and perhaps independent roles in the repression of the lysC operon by lysine.
Organic Vapor Phase Deposition (1998)

Organic vapor phase deposition (OVPD) opens new opportunities in the control of composition and structure of organic thin films. The use of this recently developed process is examined for the growth of four archetypal organic systems: a crystalline organic salt (the optically nonlinear charge transfer salt DAST, see Figure), amorphous and polymeric organic films, and an optically pumped organic laser (Alq3 doped with Rhodamine 6G).
Exendin-(9-39) Is an Inverse Agonist of the Murine Glucagon-Like Peptide-1 Receptor: Implications for Basal Intracellular Cyclic Adenosine 3',5'-Monophosphate Levels and -Cell Glucose Competence (1998)

The effect of exendin-(9-39), a described antagonist of the glucagon-like peptide-1 (GLP-1) receptor, was evaluated on the formation of cAMP- and glucose-stimulated insulin secretion (GSIS) by the conditionally immortalized murine betaTC-Tet cells. These cells have a basal intracellular cAMP level that can be increased by GLP-1 with an EC50 of approximately 1 nM and can be decreased dose dependently by exendin-(9-39). This latter effect was receptor dependent, as a beta-cell line not expressing the GLP-1 receptor was not affected by exendin-(9-39). It was also not due to the endogenous production of GLP-1, because this effect was observed in the absence of detectable preproglucagon messenger RNA levels and radioimmunoassayable GLP-1. Importantly, GSIS was shown to be sensitive to this basal level of cAMP, as perifusion of betaTC-Tet cells in the presence of exendin-(9-39) strongly reduced insulin secretion. This reduction of GSIS, however, was observed only with growth-arrested, not proliferating, betaTC-Tet cells; it was also seen with nontransformed mouse beta-cells perifused in similar conditions. These data therefore demonstrated that 1) exendin-(9-39) is an inverse agonist of the murine GLP-1 receptor; 2) the decreased basal cAMP levels induced by this peptide inhibit the secretory response of betaTC-Tet cells and mouse pancreatic islets to glucose; 3) as this effect was observed only with growth-arrested cells, this indicates that the mechanism by which cAMP leads to potentiation of insulin secretion is different in proliferating and growth-arrested cells; and 4) the presence of the GLP-1 receptor, even in the absence of bound peptide, is important for maintaining elevated intracellular cAMP levels and, therefore, the glucose competence of the beta-cells.
Identification of Two Genes Required in Tomato for Full Cf-9-Dependent Resistance to Cladosporium fulvum. (1994)

Mutagenesis was used to identify and characterize plant genes required for fungal disease resistance gene function in tomato. Seed of a stock homozygous for the Cf-9 gene for resistance to Cladosporium fulvum were treated with ethyl methanesulfonate, and 568 M2 families were screened for mutations to C. fulvum sensitivity. Eight mutants with reduced resistance were isolated. Four mutations, all of which mapped to the Cf-9 gene, lost both resistance and response to the race-specific AVR9 elicitor. The other four mutations partially lost resistance and response to the AVR9 elicitor. Cytological analysis revealed that a unique host cell staining pattern accompanied the reduced-resistance phenotype in three mutants. Two of the mutants with reduced resistance mapped to Cf-9, and two mapped to two distinct loci designated Rcr-1 and Rcr-2 (Required for Cladosporium resistance) that are unlinked to Cf-9.
Homogeneous solutions of hydrophilic enzymes in nonpolar organic solvents New systems for fundamental studies and biocatalytic transformations (1991)

A typical hydrophilic enzyme, CT, can be dissolved in nonpolar organic solvents (n-octane, cyclohexane and toluene) up to microM concentrations. In the homogeneous solution obtained, the enzyme possesses catalytic activity and enormously high thermostability. It does not lose this activity even after several hours refluxing in octane (126 degrees C) or cyclohexane (81 degrees C).
Sequence analysis of the core gene of 14 hepatitis C virus genotypes. (1994)

We previously sequenced the 5' noncoding region of 44 isolates of hepatitis C virus (HCV), as well as the envelope 1 (E1) gene of 51 HCV isolates, and provided evidence for the existence of at least 6 major genetic groups consisting of at least 12 minor genotypes of HCV (i.e., genotypes I/1a, II/1b, III/2a, IV/2b, 2c, V/3a, 4a-4d, 5a, and 6a). We now report the complete nucleotide sequence of the putative core (C) gene of 52 HCV isolates that represent all of these 12 genotypes as well as two additional genotypes provisionally designated 4e and 4f that we identified in this study. The phylogenetic analysis of the C gene sequences was in agreement with that of the E1 gene sequences. A major division in the genetic distance was observed between HCV isolates of genotype 2 and those of the other genotypes in analysis of both the E1 and C genes. The C gene sequences of 9 genotypes have not been reported previously (i.e., genotypes 2c, 4a-4f, 5a, and 6a). Our analysis indicates that the C gene-based methods currently used to determine the HCV genotype, such as PCR with genotype-specific primers, should be revised in light of these data. We found that the predicted C gene was exactly 573 nt long in all 52 HCV isolates, with an N-terminal start codon and no in-frame stop codons. The nucleotide and predicted amino acid identities of the C gene sequences were in the range of 79.4-99.0% and 85.3-100%, respectively. Furthermore, we mapped universally conserved, as well as genotype-specific, nucleotide and deduced amino acid sequences of the C gene. The predicted C proteins of the different HCV genotypes shared the following features: (i) high content of proline residues, (ii) high content of arginine and lysine residues located primarily in three domains with 10 such residues invariant at positions 39-62, (iii) a cluster of 5 conserved tryptophan residues, (iv) two nuclear localization signals and a DNA-binding motif, (v) a potential phosphorylation site with a serine-proline motif, and (vi) three conserved hydrophilic domains that have been shown by others to contain immunogenic epitopes. Thus, we have extended analysis of the predicted C protein of HCV to all of the recognized genotypes, confirmed the existence of highly conserved regions of this important structural protein, and demonstrated that the genetic relatedness of HCV isolates is equivalent when analyzing the most conserved (i.e., C) and the most variable (i.e., E1) genes of the HCV genome.
SiN-based micro cantilever actuators using NdFeB/Ta permanent magnetic thin film (2009)

SiN-based micro cantilever actuators with lengths of the order of 1mm and NdFeB/Ta thin films for actuation were designed, fabricated and characterized. Multilayered thin films of NdFeB and Ta, with total thicknesses of 13µm and 3µm, were deposited on 3µm-thick SiN cantilevers by magnetron sputtering. The remnant flux density and coercive force of the thin film were as high as those obtained for bulk NdFeB magnets. The SiN based magnetic actuator showed good strength even when undergoing considerable bending. Large bidirectional out-of-plane displacements (up to 700µm) were generated using an air cored coil placed beneath the cantilevers. Static and dynamic evaluations were carried out using a CCD camera and an optical fiber displacement sensor, respectively. The experimentally measured displacements were in agreement with simulated values.
From Genes to Clones: Introduction to Gene Technology (1987)

Isolation, Identification, and Characterisation of DNA Fragments Restriction Endonucleases Preparation and Cloning of Eukaryotic cDNA Chemical Synthesis of DNA DNA Sequencing Ligation of DNA Fragments Ligation with DNA Ligases 'In vivo' Ligation 'E. coli' Vectors Plasmids Bacteriophage as Cloning Vehicle Cloning in Yeasts The Life Cycle of 'Saccharomyces cerevisiae' Genetics of 'Saccharomyces cervisiae' Identification of Yeast Genes Genetic Markers and Selection Systems Vectors Gene Expression in Eukaryotes Yeast Expression Vectors Cloning in Gram-positive Bacteria Cloning in 'B. subtilis' Cloning in Streptomycetes Expression Vectors in Prokaryotes 'E. coli' Promoters Ribosome Binding Sites Codon Selection Construction of Expression Vectors Maturation, Transport, and Stability of Eukaryotic Proteins in Bacteria Conclusions Eukaryotic Vectors Selectable Marker for Eukaryotic Cells Simian Virus SV40 Vectors Stimulating and Inhibiting DNA Sequences Methods for Transfection of Viral DNA Papilloma Viruses as Vectors Retroviruses as Vectors Gene Expression by Gene Amplification Gene Transfer into Drosophila Vaccinia Virus Vectors Genomic Libraries Isolation of Genomic DNA Fragments Vectors Ligation Techniques Selection Techniques Cloning in Plants Fusion of Somatic Cells DNA Transfer Identification of Recombinant DNA Direct Methods Indirect Methods Directed Mutagenesis Deletions Insertions Localised Point Mutations Directed Mutagenesis by Synthetic Oligonucleotides Safety in Recombinant DNA Research Laboratory and Industrial Applications Environmental Applications Reproductive Engineering.
Synthetic Aperture Sequential Beamforming (2008)

A synthetic aperture focusing (SAF) technique denoted synthetic aperture sequential beamforming (SASB) suitable for 2D and 3D imaging is presented. The technique differ from prior art of SAF in the sense that SAF is performed on pre-beamformed data contrary to channel data. The objective is to improve and obtain a more range independent lateral resolution compared to conventional dynamic receive focusing (DRF) without compromising frame rate. SASB is a two-stage procedure using two separate beamformers. First a set of B-mode image lines using a single focal point in both transmit and receive is stored. The second stage applies the focused image lines from the first stage as input data. The SASB method has been investigated using simulations in Field II and by off-line processing of data acquired with a commercial scanner. The performance of SASB with a static image object is compared with DRF. For the lateral resolution the improvement in FWHM equals a factor of 2 and the improvement at -40 dB equals a factor of 3. With SASB the resolution is almost constant throughout the range. The resolution in the near field is slightly better for DRF. A decrease in performance at the transducer edges occur for both DRF and SASB, but is more profound for SASB.
The role of bacterial outer membrane vesicles for intra‐ and interspecies delivery (2012)

An increasing number of Gram-negative bacteria have been observed to secrete outer membrane vesicles (OMVs). Many mysteries remain with respect to OMV formation, the regulation of OMV content and mode of targeting and fusion. Bacterial OMVs appear to serve a variety of purposes in intra- and interspecies microbial extracellular activities. OMVs have been shown to mediate cell-to-cell exchange of DNA, protein and small signalling molecules. The impact of such material exchanges on microbial communities and pathogenic processes, including the delivery of toxins at high concentration through OMVs, is discussed. This rather recent aspect of microbial ecology is likely to remain an important area of research as an in-depth understanding of OMVs may allow new approaches for combating bacterial infections and provide new routes for selective drug delivery.
Ground resistance-revisited (1989)

The nature of ground resistance is examined to explain the high impedance of faults directly to ground as contrasted to conventionally assumed low-impedance ground faults to neutral conductors or to towers with low footing resistance. High-impedance faults are shown to be inherently nonlinear due to the characteristics of soil. This nonlinearity is shown to be different from that of the arcing between conductor and ground. The harmonic content of the resulting current is used to distinguish such faults from normal load variations. Specifically, the magnitudes of the resulting harmonic currents appear sufficiently predictable to be utilized in a high-impedance fault detector.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pilot Clinical Study of an Endoscopic, Removable Duodenal-Jejunal Bypass Liner for the Treatment of Type 2 Diabetes (2009)

The DJBL rapidly normalized glycemic control in obese T2DM subjects, a promising development in the search for novel therapies less invasive than bariatric surgery.
The Carbon-13 NMR Spectra and Electronic Structure of 3H-Phenoxazin-3-ones (1985)

Abstract The 13C NMR chemical shifts of 3H-phenoxazin-3-one (1) and eighteen of its derivatives are reported. The chemical shifts of 1 can be explained in terms of a successive polarization of the π-conjugated framework by an electron-withdrawing carbonyl group and a π-donating ether oxygen. The principal factor solution for the chemical shifts of the 2-substituted 3H-phenoxazin-3-ones suggests that the first and the second factors collectively controlling the 2-substituent effect are electronic and steric effects, respectively. A dual substituent parameter analysis elucidated the transmission modes of the polar and resonance effects of the 2-substituents, and that the first and the fourth factor loadings multiplied by the corresponding standard deviation of the chemical shifts correlate with the CNDO/2 substituent-induced σ and π charge densities.
Tissue-engineered growth of bone by marrow cell transplantation using porous calcium metaphosphate matrices (2000)

In this study we investigated not only osteoblastic cell proliferation and differentiation on the surface of calcium metaphosphate (CMP) matrices in vitro but also bone formation by ectopic implantation of these cell-matrix constructs in athymic mice in vivo. Interconnected porous CMP matrices with pores 200 microm in size were prepared to use as scaffolds for rat-marrow stromal-cell attachment. Cell-matrix constructs were cultured in vitro, and cell proliferation and ALPase activities were monitored for 56 days. In addition to their being cultured in vitro, cell-matrix constructs were implanted into subcutaneous sites of athymic mice. In vitro these porous CMP matrices supported the proliferation of osteoblastic cells as well as their differentiation, as indicated by high ALPase activity. In vivo the transplanted marrow cells gave rise to bone tissues in the pores of the CMP matrices. A small amount of woven bone formation was detected first at 4 weeks; osteogenesis progressed vigorously with time, and thick lamellar bones that had been remodeled were observed at 12 weeks. These findings demonstrate the potential for using a porous CMP matrix as a biodegradable scaffold ex vivo along with attached marrow-derived mesenchymal cells for transplantation into a site for bone regeneration in vivo.