gebhart/patrepeval huggingface dataset:
High-throughput, temperature-controlled microchannel acoustophoresis device made with rapid prototyping (2012)

We report a temperature-controlled microfluidic acoustophoresis device capable of separating particles and transferring blood cells from undiluted whole human blood at a volume throughput greater than 1 L h−1. The device is fabricated from glass substrates and polymer sheets in microscope-slide format using low-cost, rapid-prototyping techniques. This high-throughput acoustophoresis chip (HTAC) utilizes a temperature-stabilized, standing ultrasonic wave, which imposes differential acoustic radiation forces that can separate particles according to size, density and compressibility. The device proved capable of separating a mixture of 10- and 2-μm-diameter polystyrene beads with a sorting efficiency of 0.8 at a flow rate of 1 L h−1. As a first step toward biological applications, the HTAC was also tested in processing whole human blood and proved capable of transferring blood cells from undiluted whole human blood with an efficiency of 0.95 at 1 L h−1 and 0.82 at 2 L h−1.
Current and emerging therapies in osteoporosis (2002)

Osteoporosis is a systemic skeletal disorder leading to decreased bone mineralisation and a propensity for fracture. The disease affects millions of people and is a source of significant morbidity and mortality. Fracture-related costs have skyrocketed in recent years and projections suggest an increase as the population ages. Recent advances in the understanding of bone biology have improved the therapeutic options for osteoporosis. This is a review of the osteoporotic therapies that have recently become available and a discussion of emerging options. An overview on current practice guidelines is provided.
Risk of Malignant Disease Among 1525 Adult Male US Veterans With Gaucher Disease (2007)

We found 2- to 3-fold risks of non-Hodgkin lymphoma, malignant melanoma, and pancreatic cancer in patients with Gaucher disease, but no significant association between Gaucher disease and cancer in general or with other specific malignancies such as multiple myeloma.
Cannabidiol enhances cytotoxicity of anti-cancer drugs in human head and neck squamous cell carcinoma (2020)

Cannabidiol (CBD) has anti-tumorigenic activity. However, the anti-cancer effect of CBD on head and neck squamous cell carcinoma (HNSCC) remains unclear. The cytotoxicity of CBD on HNSCC was analyzed using cell survival and colony-forming assays in vitro. RNA-seq was used for determining the mechanism underlying CBD-induced cell death. Xenograft mouse models were used to determine CBD's effects in vivo. CBD treatment significantly reduced migration/invasion and viability of HNSCC cells in a dose- and time-dependent manner. HNSCC mouse xenograft models revealed anti-tumor effects of CBD. Furthermore, combinational treatment with CBD enhanced the efficacy of chemotherapy drugs. Apoptosis and autophagy processes were involved in CBD-induced cytotoxicity of HNSCCs. RNA-seq identified decreased expression of genes associated with DNA repair, cell division, and cell proliferation, which were involved in CBD-mediated cytotoxicity toward HNSCCs. We identified CBD as a new potential anti-cancer compound for single or combination therapy of HNSCC.
Identification of human endogenous retroviruses with complex mRNA expression and particle formation. (1993)

Retroviruses comprise strains with considerable disease potential in animals and humans. In addition to exogenous strains transmitted horizontally, endogenous proviruses are transmitted through the germ line. Some of these endogenous retroviruses can be pathogenic in mice and possibly in other animal species. They may also be considered as mobile genetic elements with the potential to produce mutations. In humans, genomic DNA contains numerous endogenous retroviral sequences detected by their partial relatedness to animal retroviruses. However, all proviruses sequenced so far have been found to be defective. In this communication, we describe the expression of a family of human endogenous retrovirus sequences (HERV-K) in GH cells, a teratocarcinoma cell line producing the human teratocarcinoma-derived retrovirus (HTDV) particles previously described by us. Four viral mRNA species could be identified, including a full-length mRNA. The other three subgenomic mRNAs are generated by single or double splicing events. This expression pattern is reminiscent of the more complex control of virus gene regulation observed, for example, with lenti- or spumavirus strains, although HERV-K shows no sequence homology to human T-lymphotropic virus or human immunodeficiency virus. Sequence analysis of expressed HERV-K genomes revealed non-defective gag genes, a prerequisite for particle formation. Open reading frames were also observed in pol and env. Antisera raised against recombinant gag proteins of HERV-K stained HTDV particles in immunoelectron microscopy, linking them to the HERV-K family.
Family 39 α-l-Iduronidases and β-d-Xylosidases React through Similar Glycosyl−Enzyme Intermediates:  Identification of the Human Iduronidase Nucleophile (2003)

The inclusion of both beta-D-xylosidases and alpha-L-iduronidases within the same sequence-related family (family 39), despite the considerable difference in substrate structures and poor sequence conservation around the putative nucleophile, raises concerns about whether a common mechanism is followed by the two enzymes. A novel anchimeric assistance mechanism for iduronidases involving a lactone intermediate is one possibility. NMR analysis of the methanolysis reaction catalyzed by human alpha-L-iduronidase reveals that, as with the beta-D-xylosidases, alpha-L-iduronidase is a retaining glycosidase. Using two different mechanism-based inactivators, 5-fluoro-alpha-L-iduronyl fluoride and 2-deoxy-2-fluoro-alpha-L-iduronyl fluoride, the active site nucleophile in the human alpha-L-iduronidase was identified as Glu299 within the (295)IYNDEAD(301) sequence. The equivalent, though loosely predicted, glutamic acid was identified as the nucleophile in the family 39 beta-D-xylosidase from Bacillus sp. [Vocadlo, D., et al. (1998) Biochem. J. 335, 449-455]; thus, a common mechanism involving a covalent glycosyl-enzyme intermediate that adopts the rather uncommon (2,5)B conformation is predicted.
Direct multilevel carrier modulation using millimeter-wave balanced vector modulators (1998)

The importance of being able to design affordable, high-performance, millimeter-wave transmitters for digital communications and radar applications is increasing. To this end, two monolithic millimeter-wave vector modulators have been realized at 38 and 60 GHz for use in direct multilevel carrier modulation. It is shown that, by employing balanced biphase amplitude modulator elements, accurate constellations are achieved with broad-band operation from 20 to 40 GHz and 55 to 65 GHz. Modulations of 16- and 256-QAM have been demonstrated, both at 38 and 60 GHz, using this technique. Each balanced biphase amplitude modulator uses a pair of reflection-type attenuators operated in push-pull mode. This study investigates the suitability of this topology for use as a full biphase amplitude modulator for multilevel digital modulation schemes. It is found that the technique is very robust and the resulting analog vector modulator can be a very important component for many future millimeter-wave applications.
MicroRNA-155 Regulates Human Angiotensin II Type 1 Receptor Expression in Fibroblasts (2006)

A large number of studies have demonstrated that the expression of the angiotensin II type 1 receptor (AT(1)R) is regulated predominantly by post-transcriptional mechanisms. Recently, it has been suggested that 10% of human genes may be regulated, in part, by a novel post-transcriptional mechanism involving microRNAs (miRNAs). miRNAs are small RNAs that regulate gene expression primarily through translational repression. The aim of this study was to determine whether miRNAs could regulate human AT(1)R expression. Luciferase reporter assays demonstrated that miR-155 could directly interact with the 3'-untranslated region of the hAT(1)R mRNA. Functional studies demonstrated that transfection of miR-155 into human primary lung fibroblasts (hPFBs) reduced the endogenous expression of the hAT(1)R compared with non-transfected cells. Additionally, miR-155 transfected cells showed a significant reduction in angiotensin II-induced extracellular signal-related kinase 1/2 (ERK1/2) activation. Furthermore, when hPFBs were transfected with an antisense miR-155 inhibitor, anti-miR-155, endogenous hAT(1)R expression and angiotensin II-induced ERK1/2 activation were significantly increased. Finally, transforming growth factor-beta(1) treatment of hPFBs resulted in the decreased expression of miR-155 and the increased expression of the hAT(1)R. In summary, our studies suggest that miR-155 can bind to the 3'-untranslated region (UTR) of hAT(1)R mRNAs and translationally repress the expression of this protein in vivo. Importantly, the translational repression mediated by miR-155 can be regulated by physiological stimuli.
Theano: A CPU and GPU Math Compiler in Python (2010)

Theano is a compiler for mathematical expressions in Python that combines the convenience of NumPy's syntax with the speed of optimized native machine language. The user composes mathematical expressions in a high-level description that mimics NumPy's syntax and semantics, while being statically typed and functional (as opposed to imperative). These expressions allow Theano to provide symbolic differentiation. Before performing computation, Theano optimizes the choice of expressions, translates them into C++ (or CUDA for GPU), compiles them into dynamically loaded Python modules, all automatically. Common machine learning algorithms implemented with Theano are from to faster than competitive alternatives (including those implemented with C/C++, NumPy/SciPy and MATLAB) when compiled for the CPU and between and faster when compiled for the GPU. This paper illustrates how to use Theano, outlines the scope of the compiler, provides benchmarks on both CPU and GPU processors, and explains its overall design.
Activity of the Hsp70 chaperone complex--DnaK, DnaJ, and GrpE--in initiating phage lambda DNA replication by sequestering and releasing lambda P protein. (1992)

Initiation of DNA replication by phage lambda requires the ordered assembly and disassembly of a specialized nucleoprotein structure at the origin of replication. In the disassembly pathway, a set of Escherichia coli heat shock proteins termed the Hsp70 complex--DnaK, DnaJ, and GrpE--act with ATP to release lambda P protein from the nucleo-protein complex, freeing the DnaB helicase for its DNA-unwinding reaction. To investigate the mechanism of the release reaction, we have examined the interaction between P and the three heat shock proteins by glycerol gradient sedimentation and gel electrophoresis. We have discovered an ATP-dependent ternary interaction between P, DnaK, and DnaJ; this P.DnaK.DnaJ complex is dissociated by GrpE. We have concluded that the function of the Hsp70 complex in sequestering and releasing P protein provides for the critical step in the disassembly pathway. Based on our data and other work on protein folding, the formation of the P.DnaK.DnaJ complex might involve a conformational shift to a folding intermediate of P.
Using WordNet and lexical operators to improve Internet searches (2000)

A natural language interface system for an Internet search engine shows substantial increases in the precision of query results and the percentage of queries answered correctly. The system expands queries based on a word-sense-disambiguation method and postprocesses retrieved documents to extract only the parts relevant to a query.
High-throughput single-cell quantification using simple microwell-based cell docking and programmable time-course live-cell imaging (2010)

Extracting single-cell information during cellular responses to external signals in a high-throughput manner is an essential step for quantitative single-cell analyses. Here, we have developed a simple yet robust microfluidic platform for measuring time-course single-cell response on a large scale. Our method combines a simple microwell-based cell docking process inside a patterned microfluidic channel, with programmable time-course live-cell imaging and software-aided fluorescent image processing. The budding yeast, Saccharomyces cerevisiae (S. cerevisiae), cells were individually captured in microwells by multiple sweeping processes, in which a cell-containing solution plug was actively migrating back and forth several times by a finger-pressure induced receding meniscus. To optimize cell docking efficiency while minimizing unnecessary flooding in subsequent steps, circular microwells of various channel dimensions (4-24 µm diameter, 8 µm depth) along with different densities of cell solution (1.5-6.0 × 10(9) cells per mL) were tested. It was found that the microwells of 8 µm diameter and 8 µm depth allowed for an optimal docking efficiency (>90%) without notable flooding issues. For quantitative single-cell analysis, time-course (time interval 15 minute, for 2 hours) fluorescent images of the cells stimulated by mating pheromone were captured using computerized fluorescence microscope and the captured images were processed using a commercially available image processing software. Here, real-time cellular responses of the mating MAPK pathway were monitored at various concentrations (1 nM-100 µM) of mating pheromone at single-cell resolution, revealing that individual cells in the population showed non-uniform signaling response kinetics.
Enhanced Disease and Pulmonary Eosinophilia Associated with Formalin-Inactivated Respiratory Syncytial Virus Vaccination Are Linked to G Glycoprotein CX3C-CX3CR1 Interaction and Expression of Substance P (2003)

Vaccination with formalin-inactivated respiratory syncytial virus (FI-RSV) vaccine or RSV G glycoprotein results in enhanced pulmonary disease after live RSV infection. Enhanced pulmonary disease is characterized by pulmonary eosinophilia and is associated with a substantial inflammatory response. We show that the absence of the G glycoprotein or G glycoprotein CX3C motif during FI-RSV vaccination or RSV challenge of FI-RSV-vaccinated mice, or treatment with anti-substance P or anti-CX3CR1 antibodies, reduces or eliminates enhanced pulmonary disease, modifies T-cell receptor Vbeta usage, and alters CC and CXC chemokine expression. These data suggest that the G glycoprotein, and in particular the G glycoprotein CX3C motif, is key in the enhanced inflammatory response to FI-RSV vaccination, possibly through the induction of substance P.
Vacuum-Assisted Closure Complicated by Erosion and Hemorrhage of the Anterior Tibial Artery (2005)

We report an erosion and hemorrhage of a left anterior tibial artery associated with a vacuum-assisted closure device. To our knowledge, this report represents the first arterial erosion associated with a vacuum-assisted closure device. We estimate our patient lost 6 units of blood. The hemorrhage was complicated by anticoagulation and a traumatic setting. Based on our complication, we believe great care should be taken when placing a vacuum-assisted closure device adjacent to an exposed artery.
Gene expression analysis with the parametric bootstrap (2001)

Recent developments in microarray technology make it possible to capture the gene expression profiles for thousands of genes at once. With this data researchers are tackling problems ranging from the identification of 'cancer genes' to the formidable task of adding functional annotations to our rapidly growing gene databases. Specific research questions suggest patterns of gene expression that are interesting and informative: for instance, genes with large variance or groups of genes that are highly correlated. Cluster analysis and related techniques are proving to be very useful. However, such exploratory methods alone do not provide the opportunity to engage in statistical inference. Given the high dimensionality (thousands of genes) and small sample sizes (often <30) encountered in these datasets, an honest assessment of sampling variability is crucial and can prevent the over-interpretation of spurious results. We describe a statistical framework that encompasses many of the analytical goals in gene expression analysis; our framework is completely compatible with many of the current approaches and, in fact, can increase their utility. We propose the use of a deterministic rule, applied to the parameters of the gene expression distribution, to select a target subset of genes that are of biological interest. In addition to subset membership, the target subset can include information about relationships between genes, such as clustering. This target subset presents an interesting parameter that we can estimate by applying the rule to the sample statistics of microarray data. The parametric bootstrap, based on a multivariate normal model, is used to estimate the distribution of these estimated subsets and relevant summary measures of this sampling distribution are proposed. We focus on rules that operate on the mean and covariance. Using Bernstein's Inequality, we obtain consistency of the subset estimates, under the assumption that the sample size converges faster to infinity than the logarithm of the number of genes. We also provide a conservative sample size formula guaranteeing that the sample mean and sample covariance matrix are uniformly within a distance epsilon > 0 of the population mean and covariance. The practical performance of the method using a cluster-based subset rule is illustrated with a simulation study. The method is illustrated with an analysis of a publicly available leukemia data set.
Expression of 14-3-3sigma, p16 and p53 proteins in anal squamous intraepithelial neoplasm and squamous cell carcinoma. (2008)

14-3-3sigma is a p53-regulated G2/M inhibitor involved in numerous cellular signaling pathways related to cell cycle, DNA repair and apoptosis. Recent studies have showed that 14-3-3sigma was silenced transcriptionally through promoter hypermethylation mainly in HPV-negative vulvar squamous cell carcinoma (SCC). However, the expression of 14-3-3sigma protein has not yet been studied in anal SCC and its precursor, anal intraepithelial neoplasm (AIN). In this study, we evaluated the expression of 14-3-3sigma, p16 and p53 in 34 cases of normal perianal squamous mucosa, 5 cases of squamous hyperplasia and 62 cases of AIN, including 54 bowenoid and 8 differentiated AINs. Fourteen cases of invasive anal SCC were also included in the study, including 8 cases associated with bowenoid AIN and 6 cases associated with differentiated AIN. Expression of p16, p53 and 14-3-3sigma proteins was not seen in normal squamous epithelium. Weak staining for 14-3-3sigma was seen in anal squamous hyperplasia. Strong and diffuse p16 immunoreactivity was seen in 98.1% of bowenoid AIN, but only in 12.5% of differentiated AIN. In contrast, increased basal staining with suprabasal extension of p53 was seen in 100% of differentiated AIN, but in none of the bowenoid AIN. Expression of p16 and p53 was essentially mutually exclusive except in one case. Overexpression of 14-3-3sigma was detected in 97% (60/62) of AIN cases, including 96.3% of bowenoid AIN and 100% of differentiated AIN. Expression of 14-3-3sigma was independent of immunoreactivity status for p16 and p53. In conclusion, two histopathologic types of AIN, bowenoid and differentiated, have distinct immunoprofiles for p16 and p53, which suggests dual molecular pathways during anal carcinogenesis. Increased expression of 14-3-3sigma protein was found in approximately 97% of AIN lesions, regardless of histopathologic type and independent of p16 and p53 expression. Our study indicates that immunohistochemical detection of 14-3-3sigma in conjunction with p16 and p53 may be useful in histopathologic recognization of AIN.
LASERS & OPTICAL FIBERS IN MEDICINE (1991)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text ABRAHAM KATZIR, "LASERS & OPTICAL FIBERS IN MEDICINE," Optics & Photonics News 2(2), 18-22 (1991) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Relaxation times and microstructures (2001)

A discussion is presented of the evaluation of multiple relaxation components from water protons in biological tissue. The principal focus is to draw attention to the way in which limitations in the raw NMR data, such as signal-to-noise ratio, data sampling density and acquisition window width, affect the precision and resolution in the processed multiple component solution of the return to thermal equilibrium. The second issue discussed is the interpretation of these multiple components in terms of microstructural compartments of the biological sample and, thirdly, we outline some of the successes in determining regional and pathological variations in microstructure in the human body in-vivo, using the technique of multiple relaxation components.
Cellular Actions of the Insulin-Like Growth Factor Binding Proteins (2002)

In addition to their roles in IGF transport, the six IGF-binding proteins (IGFBPs) regulate cell activity in various ways. By sequestering IGFs away from the type I IGF receptor, they may inhibit mitogenesis, differentiation, survival, and other IGF-stimulated events. IGFBP proteolysis can reverse this inhibition or generate IGFBP fragments with novel bioactivity. Alternatively, IGFBP interaction with cell or matrix components may concentrate IGFs near their receptor, enhancing IGF activity. IGF receptor-independent IGFBP actions are also increasingly recognized. IGFBP-1 interacts with alpha(5)beta(1) integrin, influencing cell adhesion and migration. IGFBP-2, -3, -5, and -6 have heparin-binding domains and can bind glycosaminoglycans. IGFBP-3 and -5 have carboxyl-terminal basic motifs incorporating heparin-binding and additional basic residues that interact with the cell surface and matrix, the nuclear transporter importin-beta, and other proteins. Serine/threonine kinase receptors are proposed for IGFBP-3 and -5, but their signaling functions are poorly understood. Other cell surface IGFBP-interacting proteins are uncharacterized as functional receptors. However, IGFBP-3 binds and modulates the retinoid X receptor-alpha, interacts with TGFbeta signaling through Smad proteins, and influences other signaling pathways. These interactions can modulate cell cycle and apoptosis. Because IGFBPs regulate cell functions by diverse mechanisms, manipulation of IGFBP-regulated pathways is speculated to offer therapeutic opportunities in cancer and other diseases.