gebhart/patrepeval huggingface dataset:
Rapid acquisition of in vivo biological images by use of optical coherence tomography (1996)

The development of techniques for high-speed image acquisition in optical coherence tomography (OCT) systems is essential for suppressing motion artifacts when one is imaging living systems. We describe a new OCT system for performing micrometer-scale, cross-sectional optical imaging at four images/s. To achieve OCT image-acquisition times of less than 1 s, we use a piezoelectric fiber stretcher to vary the reference arm delay. A Kerr-lens mode-locked chromium-doped forsterite laser is employed as the low-coherence source for the highspeed OCT system. Dynamic, motion-artifact-free in vivo imaging of a beating Xenopus laevis (African frog) heart is demonstrated.
cDNA cloning of a dihydropyridine-sensitive calcium channel from rat aorta. Evidence for the existence of alternatively spliced forms. (1990)

Several complementary DNAs have been isolated from rat aorta cDNA libraries that encode the alpha 1 subunit of the L-type dihydropyridine-sensitive voltage-dependent calcium channel (VDCC). The clones were isolated using previously cloned rabbit skeletal and cardiac VDCC cDNAs as well as newly isolated rat aorta cDNA clones as probes. The complete nucleotide sequence of the 8305-base pair aortic alpha 1 cDNA codes for a protein of 2169 amino acids, which corresponds to an Mr of 243,615. The deduced amino acid sequence exhibits 93 and 65% amino acid identity with previously cloned rabbit cardiac and rabbit skeletal muscle dihydropyridine-sensitive VDCCs, respectively. The close identity of the aortic alpha 1 cDNA with cardiac alpha 1 cDNAs suggests that they arise from the same gene. Specific divergent areas of the aortic cDNA suggest that this cDNA represents an alternatively spliced form. We report the existence of two forms of a specific region within this aortic cDNA which also exists in cardiac tissue. This evidence supports the existence of alternative splicing for calcium channel cDNAs, a mechanism which provides diversity and potential tissue-specific isoforms of the L-type VDCC. The rat aorta alpha 1 isoform has a message size of 8.6 kilobases (kb). Rat aorta also contains additional transcripts of 12.0 and 6.5 kb. Northern blot analysis of poly(A)+ RNA from several rat tissues including heart, brain, and several smooth muscles reveals the co-existence of the 8.6- and 12.0-kb mRNA species but not the 6.5-kb species. Southern analysis of rat genomic DNA reveals a low copy number of the gene encoding this type of calcium channel.
Optimization of primer sequences for mouse scFv repertoire display library construction (1994)

In immunoglobulin repertoire library cloning, the homology between a particular primer sequence and that of its target template, and the diversity capacity of a primer pool are the two most important parameters which determine the cloning efficiency and the size of a resulting repertoire library. In this report we present an optimized set of primers, compatible with a commercially available vector, for mouse scFv repertoire phage display library construction.
Mechanoluminescent Composites Towards Autonomous Impact Damage Detection of Aerospace Structures (2015)

This study aims to devise mechanoluminescent (ML) composites and characterize the ML properties when the composites are subjected to various levels of compressive impact loads. First, triboluminescent europium dibenzoylmethide triethylammonium (EuD4TEA) crystals are synthesized. EuD4TEA crystals are embedded into siliconbased elastomer to fabricate ML composites. Second, the mechano-photonic energy conversion capability of the ML composites is validated. Finally, ML properties are characterized using the split Hopkins pressure bar to apply impact energy. High-speed camera captured impact moments, and the recorded images are processed to quantify the light emitted from EuD4TEA. doi: 10.12783/SHM2015/275
Introduction to the Biology and Ecology of Gibraltar Range National Park and Adjacent Areas: Patterns, Processes and Prospects (2006)

Papers on the biology and ecology of Gibraltar Range National Park were sought to reflect the increased research focus on the area over the past decade. The 12 papers, published here, come from a variety of natural history disciplines. This collection of papers reflects the start that has been made, and, hopefully, will stimulate further biological and ecological investigation of Gibraltar Range National Park. Gibraltar Range National Park was first dedicated in the 1960s following the construction of the Gwydir Highway connecting Glen Innes and Grafton in northern NSW. Prior to this the area had been used for grazing, prospecting, forestry and had been surveyed for the potential use of hydroelectricity. However, it remained little explored in terms of its biology and ecology until the 1960s and 70s when John B. Williams began to collate species lists and describe the broad patterns of vegetation (Williams 1970, 1976).
Co-Crystal Structures of PKG Iβ (92–227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding (2011)

Our findings suggest that CNBD-A binds cGMP in the syn conformation through its interaction with Thr193 and an unusual cis-peptide forming residues Leu172 and Cys173. Although these studies provide the first structural insights into cyclic nucleotide binding to PKG, our ITC results show only a two-fold preference for cGMP, indicating that other domains are required for the previously reported cyclic nucleotide selectivity.
Enhancement of the host immune responses in cutaneous T-cell lymphoma by CpG oligodeoxynucleotides and IL-15 (2004)

Patients with advanced cutaneous T-cell lymphoma (CTCL) exhibit profound defects in cell-mediated immunity. Host immune functions appear to play an integral role in mediating disease-controlling responses in CTCL, therefore we investigated the effects of synthetic oligode-oxynucleotides with CpG motifs (CpG ODN), which have been recognized as immune stimulatory by virtue of activation of dendritic cells (DCs) following binding to Toll-like receptor (TLR) 9. Peripheral blood mononuclear cells (PBMCs) from patients with advanced CTCL (erythroderma with circulating malignant T cells) and healthy volunteers were cultured with either CpG-A or CpG-B ODN. Patients' PBMCs exhibited marked induction of interferon-alpha (IFN-alpha) release following culture with CpG-A. Similarly significant activation of NK cells and CD8 T cells occurred as assessed by up-modulation of CD69 expression and by natural killer lytic activity. Nevertheless, the PBMCs of patients exhibited blunted responses to CpG-A compared to healthy volunteers. In such cases, IL-15 was capable of producing levels of NK activation that were superior to CpG-A, while the combined effects of CpG-A plus IL-15 induced maximal activation of NK cells and further enhanced activation of CD8 T cells. These findings have important implications for the potential enhancement of antitumor immunity among patients with advanced CTCL.
Hydrodynamic modulation of embryonic stem cell differentiation by rotary orbital suspension culture (2009)

Embryonic stem cells (ESCs) can differentiate into all somatic cell types, but the development of effective strategies to direct ESC fate is dependent upon defining environmental parameters capable of influencing cell phenotype. ESCs are commonly differentiated via cell aggregates referred to as embryoid bodies (EBs), but current culture methods, such as hanging drop and static suspension, yield relatively few or heterogeneous populations of EBs. Alternatively, rotary orbital suspension culture enhances EB formation efficiency, cell yield, and homogeneity without adversely affecting differentiation. Thus, the objective of this study was to systematically examine the effects of hydrodynamic conditions created by rotary orbital shaking on EB formation, structure, and differentiation. Mouse ESCs introduced to suspension culture at a range of rotary orbital speeds (20-60 rpm) exhibited variable EB formation sizes and yields due to differences in the kinetics of cell aggregation. Computational fluid dynamic analyses indicated that rotary orbital shaking generated relatively uniform and mild shear stresses (< or =2.5 dyn/cm(2)) within the regions EBs occupied in culture dishes, at each of the orbital speeds examined. The hydrodynamic conditions modulated EB structure, indicated by differences in the cellular organization and morphology of the spheroids. Compared to static culture, exposure to hydrodynamic conditions significantly altered the gene expression profile of EBs. Moreover, varying rotary orbital speeds differentially modulated the kinetic profile of gene expression and relative percentages of differentiated cell types. Overall, this study demonstrates that manipulation of hydrodynamic environments modulates ESC differentiation, thus providing a novel, scalable approach to integrate into the development of directed stem cell differentiation strategies.
Localization of metastasis suppressor gene(s) for prostatic cancer to the short arm of human chromosome 11. (1992)

Previous studies using somatic cell hybridization of highly metastatic and nonmetastatic rat prostatic cancer cells demonstrated that the resultant hybrids were nonmetastatic if all of the parental chromosomes were retained. Somatic hybrid segregants which underwent nonrandom chromosomal losses reexpressed high metastatic ability. These results demonstrated that there are gene(s) the expression of which can suppress metastatic ability of prostatic cancer cells. To identify the location of homologous gene(s) in the human, specific human chromosomes were introduced into highly metastatic rat prostatic cancer cells using the microcell-mediated chromosome transfer. Introduction of human chromosome 11 into highly metastatic rat prostate cancer cells results in suppression of metastatic ability without suppression of the in vivo growth rate or tumorigenicity of the hybrid cells. Spontaneous deletion of portions of human chromosome 11 in some of the clones delineated the minimal portion of human chromosome 11 capable of suppressing prostatic cancer metastases as the region between 11p11.2-13 but not including the Wilms' tumor-1 locus.
A 43-kilodalton pneumococcal surface protein, PspA: isolation, protective abilities, and structural analysis of the amino-terminal sequence (1991)

PspA is an antigenically variable surface protein of Streptococcus pneumoniae that appears to be essential for full pneumococcal virulence. In addition, monoclonal antibodies to PspA protect mice against infection with specific strains of pneumococci virulent for mice. In this study, we have isolated the 43-kDa N-terminal half of the native 84-kDa PspA and determined the sequence of the first 45 amino acids. This sequence, the first obtained for a pneumococcal surface protein, is consistent with that of an amphiphatic coiled-coil alpha helix with a 7-residue periodicity common to fibrous proteins such as tropomyosin and streptococcal M protein. The 7-residue periodicity begins with residue 8 and extends throughout the remaining sequence for nearly 11 turns of the helix. Mice immunized with this purified PspA segment were protected from fatal pneumococcal challenge, thus demonstrating that those PspA epitopes eliciting protection were present in the N-terminal half of the molecule.
Protective Immunity against Pulmonary Cryptococcosis Is Associated with STAT1-Mediated Classical Macrophage Activation (2012)

Experimental pulmonary Cryptococcus neoformans infection in BALB/c mice is associated with polarized Th2-type cytokine production, alternative macrophage activation, and severe bronchopneumonia. In contrast, pulmonary infection with a C. neoformans strain that secretes IFN-γ, H99γ, elicits Th1-type cytokine production and classical macrophage activation. Additionally, mice infected with H99γ resolve the acute infection and are subsequently protected against challenge with wild-type C. neoformans. The present study characterizes macrophage activation during the protective response to wild-type C. neoformans in mice previously immunized with H99γ. We observed increased pulmonary Th1-type cytokine production in lung homogenates and classical macrophage activation as evidenced by enhanced expression of inducible NO synthase in the lungs of H99γ-immunized mice compared with mice given a nonprotective immunization with heat-killed C. neoformans (HKCn). Furthermore, macrophages isolated from H99γ-immunized mice on day 7 postchallenge and cultured in vitro were fungistatic against C. neoformans, whereas cryptococcal growth was uncontrolled within macrophages from HKCn-immunized mice. Th2-type cytokine production and induction of alternatively activated macrophages were also observed in lungs of HKCn-immunized mice during rechallenge. Gene expression arrays showed that classical macrophage activation during challenge infection in H99γ-immunized mice was associated with induction of the transcription factor STAT1 and its downstream targets IFN regulatory factor-1, suppressor of cytokine signaling-1, CXCL9, and CXCL10. These studies demonstrate that protective responses to C. neoformans challenge in immunized mice include classical macrophage activation and enhanced macrophage fungistasis of C. neoformans yeasts. Finally, the classical activation phenotype of protective anticryptococcal macrophages is likely mediated via STAT1 signal transduction pathways.
Respiratory and calcium transport functions of mitochondria isolated from normal and transformed human lymphocytes. (1980)

Methods have been developed to isolate mitochondria from small amounts of normal and leukemic human lymphocytes obtained from small volumes of circulating blood. Mitochondrial respiratory functions were measured by polarographic techniques, and active calcium uptake was measured by a spectrophotometric procedure utilizing the calcium-sensitive dye murexide. The results indicate that the rates of active oxygen consumption of normal human lymphocyte mitochondria are very low in comparison to values obtained from a number of animal tissue sources. Mitochondria extracted from the lymphocytes of leukemic patients and from cultured, and phytohemagglutinin-transformed human lymphocytes exhibited higher respiratory rates than did normal controls. Although respiratory rates were relatively low in all preparations, the efficiency of energy coupling (ADP:O, ratio of nmol of adenosine diphosphate phosphorylated to nanoatoms of O2 consumed) was within normal limits. The mitochondria extracted from leukemia, cultured, and phytohemagglutinin-transformed lymphocytes exhibited high rates of respiratory substrate-supported calcium uptake compared to controls.
DNA-dependent targeting of cell nuclei by a lupus autoantibody (2015)

A nuclear-penetrating lupus anti-DNA autoantibody, 3E10, has been found to inhibit DNA repair and selectively kill certain cancer cells that are highly vulnerable to DNA damage. In addition, a 3E10 single chain variable fragment (scFv) has been developed for use as a delivery vehicle to carry therapeutic cargo proteins into cell nuclei. A greater understanding of the mechanism by which 3E10 penetrates cell nuclei is needed to help determine the scope of its potential therapeutic applications. Here we show that the presence of extracellular DNA significantly enhances the nuclear uptake of 3E10 scFv. In addition, we find that 3E10 scFv preferentially localizes into tumor cell nuclei in vivo, likely due to increased DNA in the local environment released from ischemic and necrotic regions of tumor. These data provide insight into the mechanism of nuclear penetration by 3E10 and demonstrate the potential for use of 3E10 in therapeutic approaches to diseases ranging from malignancy to ischemic conditions such as stroke.
Overexpression of Catalytic Subunit p110α of Phosphatidylinositol 3-Kinase Increases Glucose Transport Activity with Translocation of Glucose Transporters in 3T3-L1 Adipocytes (1996)

To elucidate the mechanisms of phosphatidylinositol (PI) 3-kinase involvement in insulin-stimulated glucose transport activity, the epitope-tagged p110alpha subunit of PI 3-kinase was overexpressed in 3T3-L1 adipocytes using an adenovirus-mediated gene transduction system. Overexpression of p110alpha was confirmed by immunoblot using anti-tagged epitope antibody. p110alpha overexpression induced a 2.5-fold increase in PI 3-kinase activity associated with its regulatory subunits in the basal state, an increase exceeding that of the maximally insulin-stimulated control cells, while PI 3-kinase activity associated with phosphotyrosyl protein was only modestly elevated. Overexpression of p110alpha induced an approximately 14-fold increase in the basal glucose transport rate, which was also greater than that observed in the stimulated control. No apparent difference was observed in the cellular expression level of either GLUT1 or GLUT4 proteins between control and p110alpha-overexpressing 3T3-L1 adipocytes. Subcellular fractionation revealed translocation of glucose transporters from intracellular to plasma membranes in basal p110alpha-overexpressing cells. The translocation of GLUT4 protein to the plasma membrane was further confirmed using a membrane sheet assay. These findings indicate that an increment in PI 3-kinase activity induced by overexpression of p110alpha of PI 3-kinase stimulates glucose transport activity with translocation of glucose transporters, i.e., mimics the effect of insulin.
Acoustic centering of sources measured by surrounding spherical microphone arrays (2011)

The radiation patterns of acoustic sources have great significance in a wide range of applications, such as measuring the directivity of loudspeakers and investigating the radiation of musical instruments for auralization. Recently, surrounding spherical microphone arrays have been studied for sound field analysis, facilitating measurement of the pressure around a sphere and the computation of the spherical harmonics spectrum of the sound source. However, the sound radiation pattern may be affected by the location of the source inside the microphone array, which is an undesirable property when aiming to characterize source radiation in a unique manner. This paper presents a theoretical analysis of the spherical harmonics spectrum of spatially translated sources and defines four measures for the misalignment of the acoustic center of a radiating source. Optimization is used to promote optimal alignment based on the proposed measures and the errors caused by numerical and array-order limitations are investigated. This methodology is examined using both simulated and experimental data in order to investigate the performance and limitations of the different alignment methods.
Next generation of adeno-associated virus 2 vectors: Point mutations in tyrosines lead to high-efficiency transduction at lower doses (2008)

Recombinant adeno-associated virus 2 (AAV2) vectors are in use in several Phase I/II clinical trials, but relatively large vector doses are needed to achieve therapeutic benefits. Large vector doses also trigger an immune response as a significant fraction of the vectors fails to traffic efficiently to the nucleus and is targeted for degradation by the host cell proteasome machinery. We have reported that epidermal growth factor receptor protein tyrosine kinase (EGFR-PTK) signaling negatively affects transduction by AAV2 vectors by impairing nuclear transport of the vectors. We have also observed that EGFR-PTK can phosphorylate AAV2 capsids at tyrosine residues. Tyrosine-phosphorylated AAV2 vectors enter cells efficiently but fail to transduce effectively, in part because of ubiquitination of AAV capsids followed by proteasome-mediated degradation. We reasoned that mutations of the surface-exposed tyrosine residues might allow the vectors to evade phosphorylation and subsequent ubiquitination and, thus, prevent proteasome-mediated degradation. Here, we document that site-directed mutagenesis of surface-exposed tyrosine residues leads to production of vectors that transduce HeLa cells approximately 10-fold more efficiently in vitro and murine hepatocytes nearly 30-fold more efficiently in vivo at a log lower vector dose. Therapeutic levels of human Factor IX (F.IX) are also produced at an approximately 10-fold reduced vector dose. The increased transduction efficiency of tyrosine-mutant vectors is due to lack of capsid ubiquitination and improved intracellular trafficking to the nucleus. These studies have led to the development of AAV vectors that are capable of high-efficiency transduction at lower doses, which has important implications in their use in human gene therapy.
High-Brightness Blue & Green LEDs Grown by MBE on ZnSe Substrates (1995)

High-brightness blue and green tight-emitting diodes (LEDs) operating at peak wavelengths in the range 489 -514 nm have been successfully synthesized, processed, and tested. The high-brightness LEDs are Il-VI heterostructures grown by molecular beam epitaxy (MBE) at NCSU using (100) ZnSe substrates produced at Eagle-Picher Laboratory by the Seeded Physical Vapor Transport (SPVT TM) process.
The effect of repellents Ocimum forskolei and deet on the response of Anopheles stephensi to host odours (2006)

The behavioural response of Anopheles stephensi Liston (Diptera: Culicidae) to incubated host odours (from human and goat) and to human odour in combination with a repellent plant, Ocimum forskolei (Labiatae), or deet (N, N, diethyl-toluamide) (20%) was tested in a dual-port olfactometer. An. stephensi was significantly attracted to both host odours compared with air alone, but showed no preference when given a choice between both host odours simultaneously. In choice tests, the addition of deet to human odour did not significantly divert mosquitoes to human odour alone, but did divert them to goat odour. O. forskolei combined with human odour diverted mosquitoes to goat or human odour alone. Combinations of human odour and O. forskolei, and human odour and deet were both as unattractive as air alone, and attracted mosquitoes equally when offered simultaneously. The results indicate that use of O. forskolei as a repellent would be beneficial in reducing vector biting if used in communities in areas with partially zoophilic mosquito species such as An. stephensi, and where animals are present.
ICA-based technique for radiating sources estimation: application to airport surveillance (1993)

As aerial traffic becomes greater, it is more difficult to locate and recognise aircraft in the neighbourhood of civil airports. The technique proposed here resorts to a particular device, monopulse radar, and to a recent tool called the independent component analysis (ICA) to separate messages falling in the same radar beam. The algorithms used to compute the ICA use fourthorder cumulants of the observed signals.
Expression of Functional Recombinant Mussel Adhesive Protein Mgfp-5 in Escherichia coli (2004)

Mussel adhesive proteins have been suggested as a basis for environmentally friendly adhesives for use in aqueous conditions and in medicine. However, attempts to produce functional and economical recombinant mussel adhesive proteins (mainly foot protein type 1) in several systems have failed. Here, the cDNA coding for Mytilus galloprovincialis foot protein type 5 (Mgfp-5) was isolated for the first time. Using this cDNA, we produced a recombinant Mgfp-5 fused with a hexahistidine affinity ligand, which was expressed in a soluble form in Escherichia coli and was highly purified using affinity chromatography. The adhesive properties of purified recombinant Mgfp-5 were compared with the commercial extracted mussel adhesive Cell-Tak by investigating adhesion force using atomic force microscopy, material surface coating, and quartz crystal microbalance. Even though further macroscale assays are needed, these microscale assays showed that recombinant Mgfp-5 has significant adhesive ability and may be useful as a bioadhesive in medical or underwater environments.