gebhart/patrepeval huggingface dataset:
Fundamental Concepts of Bioinformatics (2002)

Fundamental Concepts of Bioinformatics is the first book co-authored by a biologist and computer scientist that is specifically designed to make bioinformatics accessible and provide readers for more advanced work. Readers learn what programs are available for analyzing data, how to understand the basic algorithms that underlie these programs, what bioinformatic research is like, and other basic concepts. Information flows easily from one topic to the next, with enough detail to support the major concepts without overwhelming readers. Problems at the end of each chapter use real data to help readers apply what they have learned so they know how to critically evaluate results from both a statistical and biological point of view. Focus on fundamentally important algorithms at the core of bioinformatics. For anyone interested in bioinformatics (in biology or computer science), computational biology, molecular biology, or genomics.
Replication Timing: A Fingerprint for Cell Identity and Pluripotency (2011)

Many types of epigenetic profiling have been used to classify stem cells, stages of cellular differentiation, and cancer subtypes. Existing methods focus on local chromatin features such as DNA methylation and histone modifications that require extensive analysis for genome-wide coverage. Replication timing has emerged as a highly stable cell type-specific epigenetic feature that is regulated at the megabase-level and is easily and comprehensively analyzed genome-wide. Here, we describe a cell classification method using 67 individual replication profiles from 34 mouse and human cell lines and stem cell-derived tissues, including new data for mesendoderm, definitive endoderm, mesoderm and smooth muscle. Using a Monte-Carlo approach for selecting features of replication profiles conserved in each cell type, we identify "replication timing fingerprints" unique to each cell type and apply a k nearest neighbor approach to predict known and unknown cell types. Our method correctly classifies 67/67 independent replication-timing profiles, including those derived from closely related intermediate stages. We also apply this method to derive fingerprints for pluripotency in human and mouse cells. Interestingly, the mouse pluripotency fingerprint overlaps almost completely with previously identified genomic segments that switch from early to late replication as pluripotency is lost. Thereafter, replication timing and transcription within these regions become difficult to reprogram back to pluripotency, suggesting these regions highlight an epigenetic barrier to reprogramming. In addition, the major histone cluster Hist1 consistently becomes later replicating in committed cell types, and several histone H1 genes in this cluster are downregulated during differentiation, suggesting a possible instrument for the chromatin compaction observed during differentiation. Finally, we demonstrate that unknown samples can be classified independently using site-specific PCR against fingerprint regions. In sum, replication fingerprints provide a comprehensive means for cell characterization and are a promising tool for identifying regions with cell type-specific organization.
Role of the retinoblastoma protein in the pathogenesis of human cancer. (1997)

The retinoblastoma gene (RB-1) was originally identified as the gene involved in hereditary retinoblastoma. However, RB-1 mutations are found in a number of common mesenchymal and epithelial malignancies. The retinoblastoma protein (pRB) acts as a transcriptional regulator of genes involved in DNA synthesis and cell-cycle control. In this regard, the functional interaction between pRB and the E2F transcription factor family appears to be critical. The pRB-E2F interaction is, in turn, regulated by a pathway that includes cyclin D1, cdk4, and p16. Mutations that affect this pathway have been documented in nearly every type of adult cancer. Thus, perturbation of pRB function may be required for the development of cancer. Insights into the biochemical functions of pRB, and its upstream regulators, may form the basis for the development of novel antineoplastic agents.
Initial ground-based thermospheric wind measurements using Doppler asymmetric spatial heterodyne spectroscopy (DASH) (2010)

We present the first thermospheric wind measurements using a Doppler Asymmetric Spatial Heterodyne (DASH) spectrometer and the oxygen red-line nightglow emission. The ground-based observations were made from Washington, DC and include simultaneous calibration measurements to track and correct instrument drifts. Even though the measurements were made under challenging thermal and light pollution conditions, they are of good quality with photon statistics uncertainties between about three and twenty-nine meters per second, depending on the nightglow intensity. The wind data are commensurate with a representative set of Millstone Hill Fabry-Perot wind measurements selected for similar geomagnetic and solar cycle conditions.
MicroRNA Screen of Human Embryonic Stem Cell Differentiation Reveals miR‐105 as an Enhancer of Megakaryopoiesis from Adult CD34+ Cells (2014)

MicroRNAs (miRNAs) can control stem cell differentiation by targeting mRNAs. Using 96-well plate electroporation, we screened 466 human miRNA mimics by four-color flow cytometry to explore differentiation of common myeloid progenitors (CMP) derived from human embryonic stem cells (hESCs). The transfected cells were then cultured in a cytokine cocktail that supported multiple hematopoietic lineages. At 4-5 days post-transfection, flow cytometry of erythroid (CD235(+)CD41(-)), megakaryocyte (CD41(+)CD42(+)), and myeloid (CD18(+)CD235(-)) lineages revealed miR-105 as a novel enhancer of megakaryocyte production during in vitro primitive hematopoiesis. In hESC-derived CMPs, miR-105 caused a sixfold enhancement in megakaryocyte production. miR-513a, miR-571, and miR-195 were found to be less potent megakaryocyte enhancers. We confirmed the relevance of miR-105 in adult megakaryopoiesis by demonstrating increased megakaryocyte yield and megakaryocyte colony forming potential in human adult CD34(+) cells derived from peripheral blood. In addition, adult CD34(+) cells express endogenous miR-105 during megakaryocyte differentiation. siRNA knockdown of the hematopoietic transcription factor c-Myb caused a similar enhancement of megakaryocyte production as miR-105. Finally, a luciferase/c-Myb-3'UTR construct and Western blot analysis demonstrated that the hematopoietic transcription factor c-Myb mRNA was a target of miR-105. We report a novel hESC-based miR screening platform and demonstrate that miR-105 is an enhancer of megakaryopoiesis in both primitive and definitive hematopoiesis.
Effects of Levetiracetam on Tardive Dyskinesia (2008)

clinicaltrials.gov Identifier: NCT00291213.
Cloning, sequence, and expression of a chitinase gene from a marine bacterium, Altermonas sp. strain O-7 (1993)

The gene encoding an extracellular chitinase from marine Alteromonas sp. strain O-7 was cloned in Escherichia coli JM109 by using pUC18. The chitinase produced was not secreted into the growth medium but accumulated in the periplasmic space. A chitinase-positive clone of E. coli produced two chitinases with different molecular weights from a single chitinase gene. These proteins showed almost the same enzymatic properties as the native chitinase of Alteromonas sp. strain O-7. The N-terminal sequences of the two enzymes were identical. The nucleotide sequence of the 3,394-bp SphI-HindIII fragment that included the chitinase gene was determined. A single open reading frame was found to encode a protein consisting of 820 amino acids with a molecular weight of 87,341. A putative ribosome-binding site, promoter, and signal sequence were identified. The deduced amino acid sequence of the cloned chitinase showed sequence homology with chitinases A (33.4%) and B (15.3%) from Serratia marcescens. Regardless of origin, the enzymes of the two bacteria isolated from marine and terrestrial environments had high homology, suggesting that these organisms evolved from a common ancestor.
MRP7/ABCC10expression is a predictive biomarker for the resistance to paclitaxel in non-small cell lung cancer (2008)

We used the paclitaxel-resistant human small cell lung cancer subline PC-6/TAX1-1, selected from PC-6 cells by paclitaxel, to test whether MRP7/ABCC10 (ABCC10) confers paclitaxel resistance. We found that gene expression of both ABCB1/MDR1 (ABCB1) and ABCC10 was higher in PC-6/TAX1-1 cells than in PC-6 cells. The expression levels of ABCC10 showed a significant inverse correlation with paclitaxel sensitivity (r = 0.574; P < 0.05) in 17 non-small cell lung cancer (NSCLC) cells unlike the expression levels of ABCB1. Pretreatment with the ABCC10 inhibitor sulfinpyrazone altered the sensitivity to paclitaxel in ABCC10-expressing NSCLC cells, concomitant with increased intracellular paclitaxel accumulation. These findings suggest that expression of the ABCC10 gene is induced by paclitaxel and that ABCC10 confers paclitaxel resistance by enhancing the efflux for paclitaxel. To confirm this hypothesis, we tested the effect on paclitaxel cytotoxicity of decreasing the expression of ABCC10 by small interfering RNA and found that this enhanced paclitaxel cytotoxicity in NCI-H23 cells concomitant with increased intracellular paclitaxel accumulation. These data indicate that ABCC10 may be one of the biomarkers for paclitaxel resistance in NSCLC.
Simple Method for Production of Randomized Human Tenth Fibronectin Domain III Libraries for use in Combinatorial Screening Procedures (2008)

Challenges such as the rapid development of detection reagents for emerging or engineered pathogens, the goal of identifying probes for every protein in the human proteome, and the development of therapeutic molecules require systems for development of epitope binding molecules that are faster and cheaper than conventional antibody development. To be practical and effective, antibody mimics must be small, stable molecules that contain exposed loops or surfaces that can be randomized and screened using selective combinatorial assays. The tenth human fibronectin type III domain (10Fn3) fits these requirements and has recently been developed as an antibody mimic for use in detection and therapeutic platforms. Previously described systems for working with 10Fn3 used PCR-based approaches to anneal multiple oligonucleotides to generate randomized 10Fn3 libraries. Here we describe a simplified approach for creating randomized 10Fn3 libraries and report the first use of a T7-based phage display system for screening these libraries.
IEEE standard 802.16: a technical overview of the WirelessMAN/sup TM/ air interface for broadband wireless access (2002)

The broadband wireless access industry, which provides high-rate network connections to stationary sites, has matured to the point at which it now has a standard for second-generation wireless metropolitan area networks. The IEEE standard 802.16, with its WirelessMAN/sup TM/ air interface, sets the stage for widespread and effective deployments worldwide. This article overviews the technical medium access control and physical layer features of this new standard.
Enhancement of light trapping in thin-film hydrogenated microcrystalline Si solar cells using back reflectors with self-ordered dimple pattern (2008)

In this article, the light-trapping effect of textured back surface reflectors in thin-film Si solar cells is investigated. A unique substrate with a periodic dimple pattern has been developed by utilizing anodic oxidation of Al as a self-ordering process. n-i-p hydrogenated microcrystalline Si (μc-Si:H) cells fabricated on the Al substrate with a period of 0.9 μm show an improved infrared response compared to those fabricated on randomly textured substrates. A high short circuit current density of 24.3 mA/cm2 has been achieved in a 1-μm-thick μc-Si:H cell by adopting the patterned Al substrate.
The Isolation of Biological Rhythm Mutations on the Autosomes of Drosophila melanogaster (1983)

A selection for autosomal circadian rhythm variants in Drosophila melanogaster resulted in the isolation of 3 new mutants, all of which display an abnormal synchronization of daily rhythms to entraining environmental cycles. In populations of phase-angle-2 (psi-2) and phase-angle-3 (psi-3) mutants, daily peaks of adult emergence are hours earlier than normal when the strains are entrained to cycles of either light and dark or high and low temperature. Like an early-emerging strain previously isolated in Drosophila pseudoobscura, the psi strains have slightly lengthened periods for the circadian rhythm in adult emergence. In addition, psi-2 brings about an abnormal synchronization of locomotor activity to light-dark cycles and lengthens periods for the activity rhythm. The emergence of adults in a third mutant strain designated gat is poorly synchronized becoming aperiodic in conditions of continuous darkness and constant temperature.
Antibody response to viral proteins U (vpu) and R (vpr) in HIV-1-infected individuals. (1990)

Antibodies to E. coli-produced HIV-1 vpr and vpu were determined by enzyme immunoassay in serial sets of sera from 72 men seroconverting for antibodies to HIV-1 structural proteins, and from 196 initially symptom-free men who were positive for such antibodies at study entry. First detection of vpr- and vpu-specific antibodies always was within 12 months of seroconversion for antibodies to structural proteins. In the combined cohort of 268 men, vpr- and vpu-specific antibodies were found persistently in 26 and 43% of men, respectively. Vpr- and vpu-specific antibodies were transiently detected in 3 and 7%, respectively, and intermittently detected in 18 and 13% of men, respectively. No association was found between the patterns of vpr- or vpu-specific antibody response and clinical outcome. In subjects with different patterns of vpr- and vpu-specific antibody response, no clear temporal relationship existed between the appearance or disappearance of antibodies and the onset of HIV-1-related disease.
Resolution improvement by nonconfocal theta microscopy (1999)

We present a novel scanning fluorescence microscopy technique, nonconfocal theta microscopy (NCTM), that provides almost isotropic resolution. In NCTM, multiphoton absorption from two orthogonal illumination directions is used to induce fluorescence emission. Therefore the point-spread function of the microscope is described by the product of illumination point-spread functions with reduced spatial overlap, which provides the resolution improvement and the more isotropic observation volume. We discuss the technical details of this new method.
Type-specific stimulation of adenylylcyclase by protein kinase C. (1993)

Ca(2+)-stimulable (type I), Ca(2+)-insensitive (type II), and Ca(2+)-inhibitable adenylylcyclase (type VI) were transiently expressed in the human embryonic kidney 293 cell line. Phorbol 12,13-dibutyrate (PDBu) increased cAMP synthesis by the Ca(2+)-insensitive type II adenylylcyclase more than 9-fold within 10 min, while the treatment had no effect on the other two types of adenylylcyclases. This stimulatory effect of PDBu on type II activity was dose-dependent and synergistic with the effect of forskolin. Another phorbol ester, phorbol 12-myristate 13-acetate (PMA), had a similar stimulatory effect on type II activity, while its inactive isomer, 4 alpha-phorbol 12-myristate 13-acetate (4 alpha-PMA), had no effect. Staurosporine, a potent protein kinase C (PKC) inhibitor, markedly attenuated the action of PDBu on cAMP synthesis by type II adenylylcyclase. These results are particularly significant in that they indicate that a species of adenylylcyclase that is insensitive to regulation by one arm of the phosphatidylinositide pathway, i.e. Ca2+, nevertheless can be regulated by the other arm, i.e. PKC.
Cannabidiol, extracted fromCannabis sativa, selectively inhibits inflammatory hypermotility in mice (2008)

Cannabidiol selectively reduces croton oil-induced hypermotility in mice in vivo and this effect involves cannabinoid CB1 receptors and FAAH. In view of its low toxicity in humans, cannabidiol may represent a good candidate to normalize motility in patients with inflammatory bowel disease.
Treatment results with an aggressive chemotherapeutic regimen (MACOP-B) for intermediate- and some high-grade non-Hodgkin's lymphomas. (1990)

Seventy previously untreated patients with stage II, III, and IV intermediate- or high-grade lymphoma were treated with methotrexate, doxorubicin, cyclophosphamide, vincristine, prednisone, and bleomycin (MACOP-B) between September 1985 and November 1987. Forty-nine of these patients had diffuse large-cell lymphoma (DLCL), and eight of these patients were human immunodeficiency virus (HIV)-positive. Complete responses were achieved in 54% of all patients and 52% of those with DLCL. With follow-up extending to 36 months, 45% of all DLCL patients are alive, and 50% are still living, if the HIV-positive patients are excluded from the analysis. Chemotherapy was quite toxic. Seventy-five percent of patients had severe mucositis, 42% had peripheral neuropathy, 50% required hospitalization, and 54% experienced leukopenia with a WBC count below 1,000/microL. Seven percent (five patients) died of toxicity related to the chemotherapy. Our analysis of prognostic parameters indicated that B symptoms, a performance status below 80, and, to a lesser extent, elevation of serum lactic acid dehydrogenase (LDH) (in HIV-negative DLCL patients) were associated with an inferior survival. Advanced age, sex, and bulky disease were not found to have a statistically significant effect on survival. Our preliminary results indicate that MACOP-B chemotherapy is an effective regimen for high- and intermediate-grade lymphomas. However, the survival for patients with DLCL treated with MACOP-B is no different than that achieved with previous regimens at our institution.
DeLS-3D: Deep Localization and Segmentation with a 3D Semantic Map (2018)

For applications such as autonomous driving, self-localization/camera pose estimation and scene parsing are crucial technologies. In this paper, we propose a unified framework to tackle these two problems simultaneously. The uniqueness of our design is a sensor fusion scheme which integrates camera videos, motion sensors (GPS/IMU), and a 3D semantic map in order to achieve robustness and efficiency of the system. Specifically, we first have an initial coarse camera pose obtained from consumer-grade GPS/IMU, based on which a label map can be rendered from the 3D semantic map. Then, the rendered label map and the RGB image are jointly fed into a pose CNN, yielding a corrected camera pose. In addition, to incorporate temporal information, a multi-layer recurrent neural network (RNN) is further deployed improve the pose accuracy. Finally, based on the pose from RNN, we render a new label map, which is fed together with the RGB image into a segment CNN which produces per-pixel semantic label. In order to validate our approach, we build a dataset with registered 3D point clouds and video camera images. Both the point clouds and the images are semantically-labeled. Each video frame has ground truth pose from highly accurate motion sensors. We show that practically, pose estimation solely relying on images like PoseNet may fail due to street view confusion, and it is important to fuse multiple sensors. Finally, various ablation studies are performed, which demonstrate the effectiveness of the proposed system. In particular, we show that scene parsing and pose estimation are mutually beneficial to achieve a more robust and accurate system.
Compact integrated tunable chromatic dispersion compensator with a 4000 ps/nm tuning range (2002)

A +/-2000 ps/nm continuous tuning range with low group delay ripple was demonstrated for 10 Gb/s NRZ signals using ring resonator allpass filters with diameters of 2 mm in silica-on-silicon planar waveguides.
Trellis precoding for the broadcast channel (2002)

This paper considers the vector Gaussian broadcast channel where a single transmitter with multiple antennas sends independent information to multiple receivers. An achievable rate region is derived by decomposing the broadcast channel into a series of single-user channels with non-causal side information. The side information may be completely pre-subtracted using precoding techniques. A practical trellis precoding method is presented. Trellis precoding can be viewed as a generalization of the Tomlinson-Harashima(1971, 1969) precoder. By taking into account the entire non-causal side-information sequence, a trellis precoder gives an additional shaping gain up to 1.53 dB compared to a Tomlinson precoder.
Antisense Expression of Protein Kinase C?? Inhibits the Growth and Tumorigenicity of Human Glioblastoma Cells (1994)

TO INVESTIGATE THE role of protein kinase C (PKC) in the growth of astrocytic brain tumors, human glioblastoma cell line U-87 was stably transfected with the antisense complementary deoxyribonucleic acid encoding PKCα. The effect of selectively down-regulating the α isoform on other PKC isoforms, as well as serum-dependent proliferation and in vivo tumorigenicity, was determined. U-87 cells expressed high levels of PKCα and lesser amounts of the γ, η, and ζ isoforms, and a similar PKC isoform pattern was observed in two other human glioblastoma cell lines. Expression of the antisense PKCα complementary deoxyribonucleic acid resulted in no detectable PKCα by immunoblotting and a 95% reduction in total Ca2+/phospholipid-dependent PKC activity. U-87 cells expressing antisense PKCα exhibited an increase in doubling time in vitro, less serum-dependent growth, and reduced sensitivity to a selective PKC inhibitor, Ro 31-8220. The transplantation of U-87 cells expressing antisense PKCα into nude mice resulted in no tumor formation. These observations suggest that the inhibition of PKCα may be an important chemotherapeutic target for arresting the growth of glioblastomas.
Lewis-acid catalyzed ene reactions (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleLewis-acid catalyzed ene reactionsBarry B. SniderCite this: Acc. Chem. Res. 1980, 13, 11, 426–432Publication Date (Print):November 1, 1980Publication History Published online1 May 2002Published inissue 1 November 1980https://pubs.acs.org/doi/10.1021/ar50155a007https://doi.org/10.1021/ar50155a007research-articleACS PublicationsRequest reuse permissionsArticle Views4676Altmetric-Citations403LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts