gebhart/patrepeval huggingface dataset:
Development of an Automated and Sensitive Microfluidic Device for Capturing and Characterizing Circulating Tumor Cells (CTCs) from Clinical Blood Samples (2016)

Current analysis of circulating tumor cells (CTCs) is hindered by sub-optimal sensitivity and specificity of devices or assays as well as lack of capability of characterization of CTCs with clinical biomarkers. Here, we validate a novel technology to enrich and characterize CTCs from blood samples of patients with metastatic breast, prostate and colorectal cancers using a microfluidic chip which is processed by using an automated staining and scanning system from sample preparation to image processing. The Celsee system allowed for the detection of CTCs with apparent high sensitivity and specificity (94% sensitivity and 100% specificity). Moreover, the system facilitated rapid capture of CTCs from blood samples and also allowed for downstream characterization of the captured cells by immunohistochemistry, DNA and mRNA fluorescence in-situ hybridization (FISH). In a subset of patients with prostate cancer we compared the technology with a FDA-approved CTC device, CellSearch and found a higher degree of sensitivity with the Celsee instrument. In conclusion, the integrated Celsee system represents a promising CTC technology for enumeration and molecular characterization.
Using a WWW-based Mail User Agent for Secure Electronic Mail Service for Health Care Users (1998)

WWW-based user interface is presented for secure electronic mail service for healthcare users. Using this method, communications between an electronic mail (WWW) server and users (WWW browsers) can be performed securely using Secure Socket Layer protocol-based Hypertext Transfer Protocol (SSL-HTTP). The mail can be encrypted, signed, and sent to the recipients and vice versa on the remote WWW server. The merit of this method is that many healthcare users can use a secure electronic mail system easily and immediately, because SSL-compatible WWW browsers are widely used and this system can be made available simply by installing a WWW-based mail user agent on a mail server. We implemented a WWW-based mail user agent which is compatible with PEM-based secure mail and made it available to about 16,000 healthcare users. We believe this approach is effective in facilitating secure network-based information exchange among medical professionals.
Geometric effects on blackbody radiation (2013)

Planck's formula for blackbody radiation was formulated subject to the assumption that the radiating body is much larger than the emitted wavelength. We demonstrate that thermal radiation exceeding Planck's law may occur in a narrow spectral range when the local radius of curvature is comparable with the wavelength of the emitted radiation. Although locally the spectral enhancement may be of several orders of magnitude, the deviation from the Stefan-Boltzmann law is less than one order of magnitude. The fluctuation-dissipation theorem needs to be employed for adequate assessment of the spectrum in this regime. Several simple examples are presented as well as experimental results demonstrating the effect. For each configuration a geometric form factor needs to be incorporated into Planck's formula in order to properly describe the emitted radiation.
Phosphatidylinositol 3-kinase functions upstream of Ras and Raf in mediating insulin stimulation of c-fos transcription (1993)

Insulin treatment of Chinese hamster ovary (CHO) cells expressing high levels of the insulin receptor (CHO-IR) was found to markedly activate (10-20-fold) transcription of the luciferase reporter gene (Luc) driven by the serum response element (SRE) of the c-fos promoter. SRE-Luc expression was also strongly activated by co-transfection with expression plasmids encoding for either v-Ras or v-Raf. In contrast, insulin-stimulated SRE-Luc activity was inhibited by expression of a negative-dominant Ras (RasAsn-17)- or a negative-dominant Raf (p301-1)-encoding plasmid. Furthermore, the negative-dominant Raf mutant blocked v-Ras activation whereas the negative-dominant Ras mutant had no significant effect on v-Raf activation. Together, these data demonstrate that insulin utilizes the Ras and Raf signaling pathways and that Ras functions upstream of Raf in terms of transcriptional activation of the serum response element. To assess the role of the phosphatidylinositol (PI) 3-kinase in this insulin signaling pathway, CHO-IR cells were co-transfected with the p85 regulatory subunit of the PI 3-kinase. Expression of the p85 subunit inhibited the insulin stimulation of SRE-Luc activity without affecting v-Ras or v-Raf activation. Thus, these data demonstrate that the PI 3-kinase is necessary for insulin signaling of transcriptional events and that, in a linear model of intracellular signaling, the PI 3-kinase functions upstream of both Ras and Raf.
Asymmetric Stereoscopic Video Encoding Algorithm Based on Joint Compensation Prediction (2009)

Stereoscopic video bring people more actual 3D scene feeling, while it also makes bitrates increase largely. To reduce bitrates is highly emphasized in stereoscopic video encoding. In the current stereo video coding scheme, the two views channels have the same spatial resolution. In order to raise the coding efficiency, an asymmetric stereoscopic video encoding algorithm of based on joint compensation prediction is proposed in this paper, using different spatial resolution of the two view channels. And in encoding the lower images phase, a low complexity prediction mode is proposed. Experimental result indicates that this proposed algorithm is more efficient than JMVM algorithm while the coding complexity is also dropped.
Restriction isotyping of human apolipoprotein A-IV: rapid typing of known isoforms and detection of a new isoform that deletes a conserved repeat. (1991)

Genetic polymorphisms of apolipoprotein A-IV (apoA-IV) have been detected by isoelectric focusing of serum proteins. Because genetic variation in apoA-IV has significant effects on lipid risk factors, we used restriction enzyme isoform genotyping (restriction isotyping) to determine apoA-IV isoform genotypes at the DNA level for a large population (n = 509). In contrast to isoelectric focusing methods, restriction isotyping relies on nucleotide differences, enabling unambiguous typing of known isoforms and detection of new alleles that mimic other isoforms with shared charge properties. To determine genotypes for the common A-IV-1 isoform (Gln at aa position 360) and A-IV-2 isoform (360His), we used a mismatched primer for polymerase chain reaction (PCR) to introduce a restriction site (PvuII) that distinguishes each isoform. Using a portion of the same PCR reaction, we used HinfI to distinguish isoforms with Thr at position 347 (347Thr) versus Ser (347Ser). In surveys for these common genotypes, we detected heterozygotes for an allele with an insertion of 12 bp. Nucleotide sequencing showed that this allele is identical to the A-IV-0 isoform that inserts a hydrophilic repeat (Glu Gln Gln Gln) in a conserved region near the carboxy terminus. In addition, we discovered a new allele with a 12 bp deletion that removes a repeat (Glu Gln Gln Gln) from the same region. Nucleotide sequencing showed that this allele removes an acidic charge relative to A-IV-1, so we have named this isoform A-IV-2*. This isoform has not been discovered at the protein level, perhaps due to shared charge properties with A-IV-2 isoforms.
The fibronectin receptor on mammalian erythroid precursor cells: characterization and developmental regulation. (1986)

The plasma membrane of murine erythro-leukemia (MEL) cells contains a 140-kD protein that binds specifically to fibronectin. A 125I-labeled 140-kD protein from surface-labeled uninduced MEL cells was specifically bound by an affinity matrix that contained the 115-kD cell binding fragment of fibronectin, and specifically eluted by a synthetic peptide that has cell attachment-promoting activity. The loss of this protein during erythroid differentiation was correlated with loss of cellular adhesion to fibronectin. Both MEL cells and reticulocytes attached to the same site on fibronectin as do fibroblasts since adhesion of erythroid cells to fibronectin was specifically blocked by a monoclonal antibody directed against the cell-binding fragment of fibronectin and by a synthetic peptide containing the Arg-Gly-Asp-Ser sequence found in the cell-binding fragment of fibronectin. Erythroid cells attached specifically to surfaces coated either with the 115-kD cell-binding fragment of fibronectin or with the synthetic peptide-albumin complex. Thus, the erythroid 140-kD protein exhibits several properties in common with those described for the fibronectin receptor of fibroblasts. We propose that loss or modification of this protein at the cell surface is responsible for the loss of cellular adhesion to fibronectin during erythroid differentiation.
Antitumor Effects of the Proteasome Inhibitor Bortezomib in Medullary and Anaplastic Thyroid Carcinoma Cells in Vitro (2006)

These data provide both insights into the molecular mechanisms of antitumor activity of proteasome inhibitors and the rationale for future clinical trials of bortezomib, alone or in combination with conventional chemotherapy, to improve patient outcome in medullary and anaplastic thyroid carcinomas.
Splenectomy inactivates the cholinergic antiinflammatory pathway during lethal endotoxemia and polymicrobial sepsis (2006)

The innate immune system protects against infection and tissue injury through the specialized organs of the reticuloendothelial system, including the lungs, liver, and spleen. The central nervous system regulates innate immune responses via the vagus nerve, a mechanism termed the cholinergic antiinflammatory pathway. Vagus nerve stimulation inhibits proinflammatory cytokine production by signaling through the alpha7 nicotinic acetylcholine receptor subunit. Previously, the functional relationship between the cholinergic antiinflammatory pathway and the reticuloendothelial system was unknown. Here we show that vagus nerve stimulation fails to inhibit tumor necrosis factor (TNF) production in splenectomized animals during lethal endotoxemia. Selective lesioning of the common celiac nerve abolishes TNF suppression by vagus nerve stimulation, suggesting that the cholinergic pathway is functionally hard wired to the spleen via this branch of the vagus nerve. Administration of nicotine, an alpha7 agonist that mimics vagus nerve stimulation, increases proinflammatory cytokine production and lethality from polymicrobial sepsis in splenectomized mice, indicating that the spleen is critical to the protective response of the cholinergic pathway. These results reveal a specific, physiological connection between the nervous and innate immune systems that may be exploited through either electrical vagus nerve stimulation or administration of alpha7 agonists to inhibit proinflammatory cytokine production during infection and tissue injury.
Cross modality registration of video and magnetic tracker data for 3D appearance and structure modeling (2010)

The paper reports a fully-automated, cross-modality sensor data registration scheme between video and magnetic
tracker data. This registration scheme is intended for use in computerized imaging systems to model the appearance,
structure, and dimension of human anatomy in three dimensions (3D) from endoscopic videos, particularly
colonoscopic videos, for cancer research and clinical practices. The proposed cross-modality calibration procedure
operates this way: Before a colonoscopic procedure, the surgeon inserts a magnetic tracker into the working
channel of the endoscope or otherwise fixes the tracker's position on the scope. The surgeon then maneuvers
the scope-tracker assembly to view a checkerboard calibration pattern from a few different viewpoints for a few
seconds. The calibration procedure is then completed, and the relative pose (translation and rotation) between
the reference frames of the magnetic tracker and the scope is determined. During the colonoscopic procedure, the
readings from the magnetic tracker are used to automatically deduce the pose (both position and orientation)
of the scope's reference frame over time, without complicated image analysis. Knowing the scope movement
over time then allows us to infer the 3D appearance and structure of the organs and tissues in the scene. While
there are other well-established mechanisms for inferring the movement of the camera (scope) from images, they
are often sensitive to mistakes in image analysis, error accumulation, and structure deformation. The proposed
method using a magnetic tracker to establish the camera motion parameters thus provides a robust and efficient
alternative for 3D model construction. Furthermore, the calibration procedure does not require special training
nor use expensive calibration equipment (except for a camera calibration pattern-a checkerboard pattern-that
can be printed on any laser or inkjet printer).
Human Papillomavirus and Overexpression of P16INK4a in Nonmelanoma Skin Cancer (2004)

BACKGROUND P16INK4a overexpression has been identified as a specific biomarker in high-risk human papillomavirus (HPV)–infected cervical (pre)cancer lesions. OBJECTIVE To evaluate the overexpression of this cyclin-dependent kinase inhibitor in skin tumors depending on HPV infections, we analyzed normal skin, benign skin disease, and skin cancer specimens. METHODS Biopsies of 23 patients with normal histology (3), psoriasis (2), verrucae vulgaris (2), actinic keratoses (5), squamous cell carcinoma (SCC) in situ (3), Bowen's carcinoma (1), and SCC (7) were analyzed. Specimens of 23 patients were immunostained using the monoclonal antibody E6H4 specific for p16INK4a. HPV status was assessed by a polymerase chain reaction (PCR) system to detect all currently known HPV types. MY (MY09/MY11 and MYN9/MYN10)-, CP (CP65/CP70 and CP66/CP69)-nested PCR, and three single PCR methods CN1, CN3, and CN4 were used in a first step, and HPV typing was performed by restriction fragment length polymorphism analysis. Only β-globin–positive patients were included in this study. RESULTS HPV DNA was detected in all actinic keratoses, SCC in situ, Bowen's carcinoma, and SCC, in 50% (one of two) of verrucae vulgaris, in 66% (two of three) of normal skin, and in none of two psoriasis. P16INK4a expression was not detected in normal skin, psoriasis, and verrucae vulgares. Overexpression of p16INK4a was detected in a subset of dysplastic cells (10% to 80%) of all skin (pre)cancer lesions such as actinic keratoses, SCC in situ, Bowen's carcinoma, and SCC infected with HPV independent of sun exposure. CONCLUSION P16INK4a appears to be overexpressed in a portion of dysplastic cells from actinic keratoses and SCC. Further studies to examine the association of HPV infection and the overexpression of p16INK4a are warranted.
Dielectric properties of alginate beads and bound water relaxation studied by electrorotation (1999)

The electrical and dielectric properties of Ba2+ and Ca2+ cross-linked alginate hydrogel beads were studied by means of single-particle electrorotation. The use of microstructured electrodes allowed the measurements to be performed over a wide range of medium conductivity from about 5 mS/m to 1 S/m. Within a conductivity range, the beads exhibited measurable electrorotation response at frequencies above 0.2 MHz with two well-resolved co- and antifield peaks. With increasing medium conductivity, both peaks shifted toward higher frequency and their magnitudes decreased greatly. The results were analyzed using various dielectric models that consider the beads as homogeneous spheres with conductive loss and allow the complex rotational behavior of beads to be explained in terms of conductivity and permittivity of the hydrogel. The rotation spectra could be fitted very accurately by assuming (a) a linear relationship between the internal hydrogel conductivity and the medium conductivity, and (b) a broad internal dispersion of the hydrogel centered between 20 and 40 MHz. We attribute this dispersion to the relaxation of water bound to the polysaccharide matrix of the beads. The dielectric characterization of alginate hydrogels is of enormous interest for biotechnology and medicine, where alginate beads are widely used for immobilization of cells and enzymes, for drug delivery, and as microcarriers for cell cultivation.
Pathology, genetics and cell biology of hemangioblastomas. (1996)

Hemangioblastomas are highly vascularized tumors of not well-defined histological origin which are frequently associated with cysts. They arise preferentially in cerebellum, medulla and spinal cord and are histologically indistinguishable from vascular lesions in the retina (so-called angiomatosis retinae). Hemangioblastomas are the most frequent manifestations of the von Hippel-Lindau (VHL) disease, an autosomal-dominant inherited cancer syndrome but also occur as sporadic non-hereditary tumors. The VHL tumor suppressor gene has recently been cloned and enormous progress has been made towards the understanding of molecular biology and biological function of the VHL gene. Germline mutations in VHL patients, as well as somatic mutations in different tumors, including hemangioblastomas, have been identified, its ability to act as a tumor suppressor in vivo has been confirmed, and interaction with transcription factors Elongin B and C leading to inhibition of transcriptional elongation has been demonstrated. The mechanism underlying neovascularization and cyst formation in hemangioblastomas and how this is linked to inactivation of the VHL tumor suppressor gene is not known. However, the finding of dramatic up-regulation of vascular endothelial growth factor (VEGF), a potent endothelial cell growth factor with vascular permeability-inducing activity, in stromal cells and the corresponding receptors, VEGFR-1 and VEGFR-2, in tumor endothelial cells suggests that angiogenesis and cyst formation in hemangioblastomas may be regulated by this signaling pathway via a paracrine mechanism.
Exhaled Nitric Oxide (2005)

FENO measurements greater than 47 ppb provide a means of predicting steroid response in patients with undiagnosed respiratory symptoms. Assessing airway inflammation is of more practical value than diagnostic labeling when considering the potential usefulness of inhaled antiinflammatory therapy.
Influence of Elevated Plasma Levels of Atrial Natriuretic Factor on Bronchial Reactivity in Asthma (1991)

Recent studies have demonstrated that elevation of plasma atrial natriuretic factor (ANF) levels may produce significant bronchodilation in the constricted asthmatic airway. The current study was designed to examine the effect of both physiologic and pharmacologic plasma levels of ANF on bronchial reactivity to histamine in asthmatic subjects. A total of eight atopic men with well-controlled asthma were studied, mean (SD) FEV1 3.50 (0.73) L, equivalent to 87 (11)% of predicted; bronchial reactivity as measured by histamine PC20 was 0.77 mg/ml (geometric mean). On four separate study days infusions of 1, 3, or 10 pmol/kg/min of ANF or placebo were administered in a double-blind, randomized manner. Once steady-state plasma levels had been achieved, measurement of bronchial reactivity was repeated. Mean (SEM) basal ANF level was 18.5 (3.5) pg/ml and rose to 41 (4.3), 157 (15), and 500 (30) pg/ml with increasing doses of ANF. With placebo infusion geometric mean histamine PC20 was 0.77 mg/ml and rose to 1.15 mg/ml (p less than 0.05), 1.90 mg/ml (p less than 0.001), and 3.38 mg/ml (p less than 0.001), corresponding to a 1.5-, 2.5-, and 4.4-fold protection with respective ANF infusions. There was no significant change in plasma epinephrine. These results show that at both physiologic and pathophysiologic plasma levels ANF may significantly decrease bronchial reactivity to histamine in asthma.
The integrase family of tyrosine recombinases: evolution of a conserved active site domain (1997)

The integrases are a diverse family of tyrosine recombinases which rearrange DNA duplexes by means of conservative site-specific recombination reactions. Members of this family, of which the well-studied lambda Int protein is the prototype, were previously found to share four strongly conserved residues, including an active site tyrosine directly involved in transesterification. However, few additional sequence similarities were found in the original group of 27 proteins. We have now identified a total of 81 members of the integrase family deposited in the databases. Alignment and comparisons of these sequences combined with an evolutionary analysis aided in identifying broader sequence similarities and clarifying the possible functions of these conserved residues. This analysis showed that members of the family aggregate into subfamilies which are consistent with their biological roles; these subfamilies have significant levels of sequence similarity beyond the four residues previously identified. It was also possible to map the location of conserved residues onto the available crystal structures; most of the conserved residues cluster in the predicted active site cleft. In addition, these results offer clues into an apparent discrepancy between the mechanisms of different subfamilies of integrases.
Future prospects for network‐based multimedia information retrieval (1990)

This paper asks the reader to consider future information retrieval services that return multimedia documents containing any combination of text, graphics, still raster images, audio, and motion video in response to user queries. It then argues that the emergence of generally available multimedia information services depends on four things: (1) close to ubiquitous high‐bandwidth networks; (2) inexpensive user appliances capable of handling multimedia; (3) adoption of standards for representation, compression, packaging and transport of multimedia information; and (4) development of a corpus of multimedia information and associated infrastructure for organizing and searching it. After some explanation, it asserts that the first three are already happening and expresses reserved optimism about the fourth.
The Regulated Secretion and Vectorial Targeting of Neurotrophins in Neuroendocrine and Epithelial Cells (1996)

The varied roles that neurotrophins play in the development and activity-dependent plasticity of the nervous system presumably require that the sites and quantity of neurotrophin release be precisely regulated. As a step toward understanding how different neurotrophins are sorted and secreted by neurons, we expressed nerve growth factor (NGF), brain-derived neurotrophic factor, and neurotrophin-3 in cell lines used as models for neuronal protein sorting. All three neurotrophins were secreted by a regulated pathway in transfected AtT-20 and PC12 neuroendocrine cells, with a 3-6-fold increase in neurotrophin release in response to 8-bromo-cAMP or depolarization, respectively. To determine if the propeptide directs the intracellular sorting of mature NGF, we examined mutants in which regions spanning the propeptide were deleted. These mutants underwent regulated release in every case in which expression could be detected. Similarly, NGF sorting was not significantly altered by mutations which specifically abolished N-glycosylation or proteolytic processing sites within the NGF precursor. Finally, we found that all three neurotrophins were secreted 65-75% basolaterally by polarized Madin-Darby canine kidney epithelial cells. These findings suggest that the determinants of regulated neurotrophin secretion lie within the mature neurotrophin moiety and that NGF, brain-derived neurotrophic factor, and neurotrophin-3 are likely to be sorted similarly and released in a regulated manner by neurons.