gebhart/patrepeval huggingface dataset:
Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning (2019)

Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known as "Splicing Codes". The final goal of these algorithms is to make an in-silico prediction of AS outcome from genomic sequence. Here, we develop a deep learning approach, called Deep Splicing Code (DSC), for categorizing the well-studied classes of AS namely alternatively skipped exons, alternative 5<i>'</i>ss, alternative 3<i>'</i>ss, and constitutively spliced exons based only on the sequence of the exon junctions. The proposed approach significantly improves the prediction and the obtained results reveal that constitutive exons have distinguishable local characteristics from alternatively spliced exons. Using the motif visualization technique, we show that the trained models learned to search for competitive alternative splice sites as well as motifs of important splicing factors with high precision. Thus, the proposed approach greatly expands the opportunities to improve alternative splicing modeling. In addition, a web-server for AS events prediction has been developed based on the proposed method and made available at https://home.jbnu.ac.kr/NSCL/dsc.htm.
Structure of the Bordetella pertussis 1414 endotoxin (2000)

The endotoxin (lipopolysaccharide) of Bordetella pertussis, the agent of whooping cough, consists of a lipid A linked to a highly branched dodecasaccharide containing several acid and amino sugars. The elucidation of the polysaccharide structure was accomplished by first analyzing the structures of fragments obtained by hydrolysis and nitrous deamination and then piecing the fragments together. The fine structure of the antigenic distal pentasaccharide, presented here, was determined by chemical analyses as well as by high-resolution nuclear magnetic resonance and mass spectrometry. The complete structure was reconstituted and confirmed by matrix-assisted laser desorption/ionization mass spectrometry. The following structure was derived from the combined experimental data:The detailed structure combined with previously reported serological data now allows the synthesis of its epitopes for potential vaccines.
Fibrates and statins in the treatment of hyperlipidaemia: an appraisal of their efficacy and safety (1995)

Journal Article Fibrates and statins in the treatment of hyperlipidaemia: an appraisal of their efficacy and safety Get access J. Shepherd J. Shepherd Institute of Biochemistry, Royal Infirmary, Glasgow, G4 0SFU.K. Correspondence: J. Shepherd, Institute of Biochemistry, Royal Infirmary, Glasgow G4 OSF, U.K. Search for other works by this author on: Oxford Academic PubMed Google Scholar European Heart Journal, Volume 16, Issue 1, January 1995, Pages 5–13, https://doi.org/10.1093/eurheartj/16.1.5 Published: 01 January 1995 Article history Received: 15 April 1994 Revision received: 26 September 1994 Published: 01 January 1995
The in vitro DNA-binding properties of purified nuclear lamin proteins and vimentin. (1990)

The ability of purified nuclear lamin A, lamin B, lamin C, and vimentin from Ehrlich ascites tumor cells to bind nucleic acids was investigated in vitro via a quantitative filter binding assay. At low ionic strength, vimentin bound more nucleic acid than the nuclear lamins and showed a preference for G-containing nucleic acids. Nuclear lamins A and C were quite similar in their binding properties and bound G- and C-containing nucleic acids preferentially. The binding of poly(dT) by the lamins A and C was reduced in competition experiments by both poly(dG) and poly(dC), but not by poly(dA). Lamin B bound only oligo and poly(dG); no other nucleic acids tested were bound or could compete with the binding of oligo(dG). Vimentin, lamin A, and lamin C specifically bound a synthetic oligonucleotide human (vertebrate) telomere model. The Ka for vimentin (2.7 X 10(7) M-1) was approximately 10-fold higher than those for lamin A (2.8 X 10(6) M-1) and lamin C (2.9 X 10(6) M-1). Lamin B did not bind detectable amounts of the telomere model. Washing of lamin A- and lamin C-nucleic acid complexes, formed at low ionic strength, with solutions containing 150 mM KCl resulted in the elution of 30% of bound poly(dG)12-18 and 70% of bound synthetic oligonucleotide telomere model. These results, using purified individual proteins, are in good agreement with data from competition experiments with vimentin but are at odds with data obtained previously using a crude preparation of nuclear matrix proteins containing all three nuclear lamin proteins (Comings, D. E., and Wallack, A. S. (1978) J. Cell Sci. 34, 233-246). The nuclear lamins A and C and vimentin possess nucleic acid-binding properties that might permit their binding to specific base sequences and/or unique DNA structure, such as that observed for the binding of the telomere model. The significance of the higher affinity binding of nucleic acids by the cytoplasmic protein vimentin (compared with the nuclear lamins) remains to be elucidated.
Immune response to the carcinoembryonic antigen in patients treated with an anti-idiotype antibody vaccine. (1995)

We have generated an IgG1 murine monoclonal anti-idiotype antibody (Ab2) designated 3H1, which mimics a specific epitope on the carcinoembryonic antigen (CEA). Patients with CEA positive tumors are immunologically "tolerant" to CEA. We used 3H1 as a surrogate for CEA for vaccine therapy of 12 patients with advanced colorectal cancer. Each of the patients received a minimum of four intracutaneous injections of aluminum hydroxide precipitated 3H1 at either 1, 2, or 4 mg dosage per injection. 9 of 12 patients demonstrated anti-anti-idiotypic (Ab3) response to 3H1. All nine patients generated specific anti-CEA antibody demonstrated by reactivity with radiolabeled purified CEA; some cases were confirmed by immunoprecipitation of purified CEA. We also demonstrated Ab3 stained both autologous and allogeneic colonic tumors. 7 of 12 patients demonstrated idiotype specific T cell proliferative responses and four also showed T cell proliferation to CEA. Toxicity was limited to local reaction with mild fever and chills. All 12 patients eventually progressed after finishing 4-13 dosages. This is the first report demonstrating that a vaccine therapy is capable of breaking "immune tolerance" to CEA in patients with CEA positive tumors. Future studies will focus on treating patients with minimal residual disease.
Antenna Diversity Performance in Mitigating the Effects of Portable Radiotelephone Orientation and Multipath Propagation (1983)

Antenna diversity can mitigate signal impairments caused by random angular orientation and multipath radio propagation when using portable radiotelephones. Cumulative distributions of signal-to-noise ratio ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S/N</tex> ) were determined for antenna diversity using realistic orientation and multipath propagation models. In a random orientation and multipath propagation environment with -6 dB average crosspolarization coupling, two-branch selection diversity with two perpendicular antennas yields an <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S/N</tex> distribution with the same slope as two-branch selection diversity in the fixed-oriented mobile radio environment. The distribution for random orientation is about 4.5 dB worse, however, than the mobile radio distribution.
Anthrax as a Biological Weapon (1999)

Specific consensus recommendations are made regarding the diagnosis of anthrax, indications for vaccination, therapy for those exposed, postexposure prophylaxis, decontamination of the environment, and additional research needs.
Study on the scope of tert‐amino effect: new extensions of type 2 reactions to bridged biaryls (2012)

Thermal isomerization of aminomethyl‐ or oxygen‐bridged biphenyl systems possessing dicyanovinyl and sec ‐amino groups in ortho ‐ and ortho ′‐positions was investigated. Both systems underwent cyclization via tert ‐amino effect. Thus, 2‐(2‐{[2‐( sec ‐amino)benzyl]‐ N ‐methylamino}benzylidene)malononitriles gave tetrahydroquinolines, whereas a 2‐[2‐( sec ‐amino)phenoxy]benzylidenemalononitrile isomerized to dibenzoxazonine derivative. The ring closure reaction was studied by differential scanning calorimetry measurements. Copyright © 2012 John Wiley &amp; Sons, Ltd.
RF and Microwave Circuit Design for Wireless Communications (1996)

From the Publisher:
RF and Microwave Circuit Design for Wireless Communications addresses the complicated modulation schemes and higher frequencies required of today's wireless communications circuits. Covering cutting-edge developments in mixer circuits, frequency synthesizers, amplifier design, noise, and the future of wireless communication, it helps you design applications for digital cellular telephony, wireless LANs, PCS, GaAs and high-speed silicon bipolar IC technology, and low-power RF circuit technology.
High speed multi-frequency impedance analysis of single particles in a microfluidic cytometer using maximum length sequences (2007)

A novel impedance spectroscopy technique has been developed for high speed single biological particle analysis. A microfluidic cytometer is used to measure the impedance of single micrometre sized latex particles at high speed across a range of frequencies. The setup uses a technique based on maximum length sequence (MLS) analysis, where the time-dependent response of the system is measured in the time domain and transformed into the impulse response using fast M-sequence transform (FMT). Finally fast Fourier transform (FFT) is applied to the impulse response to give the transfer-function of the system in the frequency domain. It is demonstrated that the MLS technique can give multi-frequency (broad-band) measurement in a short time period (ms). The impedance spectra of polystyrene micro-beads are measured at 512 evenly distributed frequencies over a range from 976.5625 Hz to 500 kHz. The spectral information for each bead is obtained in approximately 1 ms. Good agreement is shown between the MLS data and both circuit simulations and conventional AC single frequency measurements.
Activation of mononuclear cells to be used for hybrid monoclonal antibody‐induced lysis of human ovarian carcinoma cells (1988)

Recently we reported that cytotoxic T-cell clones can be retargeted to unrelated tumor cells by bispecific monoclonal antibodies (MAbs), anti-CD3 and anti-ovarian carcinoma (alpha OC/TR) (Mezzanzanica et al., 1988). In the perspective of in vivo tumor immunotherapy, as an alternative to cytotoxic T lymphocytes (CTL) from T-cell clones, since human peripheral blood mononuclear cells (PBMCs) without stimulation were quite ineffective, a suitable in vitro activation method was developed to render PBMCs lytic for relevant targets in the presence of the bispecific hybrid MAb alpha OC/TR. This activation protocol was applied to PBMCs from 9 healthy donors (HD) and 6 ovarian carcinoma patients (P) and to tumor-associated lymphocytes (TAL) from 4 ovarian carcinoma P. The method consisted of in vitro stimulation with phytohemagglutinin (PHA) for 2 days, followed by culture with a low dose of recombinant human interleukin-2 (rIL-2) for 6 to 10 days. The antibody-mediated lysis of CTL from HD PBMCs was found to be specifically directed against cells expressing the relevant ovarian tumor antigen when different tumor cell lines and short-term cultures of tumor and normal cells were tested. The antibody-mediated lysis of CTL from P PBMCs or TAL was efficient both on autologous and allogeneic ovarian tumor cells, whereas no reactivity with autologous normal cells was observed and LAK activity was only evident in 1 out of 4 cases. The hybrid antibody induced cytotoxic activity of CTL from P was, however, lower than that of CTL from HD.
Raman Spectroscopic Characterization of Human Breast Tissues: Implications for Breast Cancer Diagnosis (1993)

Development and application of laser-based diagnostic and therapeutic procedures have been hindered by the current technical inadequacies in tissue diagnosis and characterization. It is now possible to apply the techniques of Raman spectroscopy to achieve rapid, noninvasive, and nondestructive differentiation of diseased from normal tissues. Normal and diseased breast tissues were examined by Raman spectroscopy. The Raman spectra obtained contain features that are attributable to various amounts of carotenoids and lipids. A small contribution from a heme-type signal was detected in some samples of clinically abnormal yet histopathologically benign breast tissue, while a much stronger heme-type signal was detected in most of the breast cancers. Raman spectra of diseased breast tissue (benign and malignant) also show markedly diminished to absent contributions from lipids and reduced contributions from carotenoids. This laser-based spectroscopic modality is readily adaptable to reflected light microscopy and optical fiber techniques, making it potentially useful as an aid in real-time diagnosis, and may thus find application in the fields of histopathology and interventional radiology.
Dropwise condensation theory and experiment: A review (2002)

The paper reviews progress in dropwise condensation research from 1930 to the present. Particular attention is given to heat transfer measurements, theory, transition and effects of surface material. Although it has been known since the 1930s that heat transfer coefficients for dropwise condensation of steam are much higher than those for film condensation, there were, until the 1960s, wide discrepancies between the results of different investigators. Subsequently, more accurate measurements have shown good consistency and the mechanism and theory of the dropwise condensation have become better understood. There has been considerable controversy over the magnitude of the so-called ‘constriction resistance’ and the effect of the surface thermal conductivity on the heat transfer coefficient. The balance of evidence suggests that this is only significant at very low heat fluxes and for very small condensing surfaces. Measurements have also been made with sufficiently high cooling intensities to cover the range of dropwise to filmwise condensation transition. The detailed mechanism of transition is still not fully understood. Perhaps most importantly, the practical problem of promoting lasting dropwise condensation under industrial conditions remains to be solved despite considerable effort spanning more than 70 years.
A Trabecular Bypass Flow Hypothesis (2005)

It is theoretically demonstrated that a single patent trabecular bypass can enhance the facility of outflow and reduce the IOP to physiological levels.
Synthesis and Physical Properties of Estolide Ester Using Saturated Fatty Acid and Ricinoleic Acid (2011)

A study was conveyed to produce estolide ester using ricinoleic acid as the backbone. The ricinoleic acid reacted with saturated fatty acid from C8-C18. These reactions were conducted under vacuum at 60°C for 24 h without solvent. The reaction used acid catalyst, sulphuric acid. The new saturate ricinoleic estolide esters show superior low-temperature properties (-52 ± 0.08°C) and high flash point (>300°C). The yield of the neat estolide esters ranged from 52% to 96%. The viscosity range was 51 ± 0.08 to 86 ± 0.01 cp. These new saturated estolide esters were also compared with saturated branched estolide esters.
Small handset antenna for FM reception (2008)

Abstract A passive internal handset antenna for FM reception is presented using electromagnetic simulations as well as laboratory experiments. Received signal for the antennas have been demodulated and the quality of the audio signal evaluated. Results have been compared with a long antenna (λ/4) confirming that the proposed solution is a good candidate to migrate to a full wireless FM system that may be integrated into a handset phone. © 2008 Wiley Periodicals, Inc. Microwave Opt Technol Lett 50: 2677–2683, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.23774
Simple One-Flask Method for the Preparation of Hydroxamic Acids (2003)

[reaction: see text] A one-step conversion of carboxylic acids to hydroxamic acids under very mild conditions is described. This simple and efficient method has been applied for the synthesis of enantiopure hydroxamate of alpha-amino acids and peptides.
Effects of atherogenic diet consumption on lipoproteins in mouse strains C57BL/6 and C3H (1991)

Inbred mouse strains C57BL/6J (B6) (susceptible) and C3H/HeJ (C3H) (resistant) differ in atherosclerosis susceptibility due to a single gene, Ath-1. Plasma lipoproteins from female mice fed chow or an atherogenic diet displayed strain differences in lipoprotein particle sizes and apolipoprotein (apo) composition. High density lipoprotein (HDL) particle sizes were 9.5 +/- 0.1 nm for B6 and 10.2 +/- 0.1 nm for C3H. No major HDL particle size subclasses were observed. Plasma HDL level in the B6 strain was reduced by the atherogenic diet consumption while the HDL level in the resistant C3H mice was unaffected. The reduction in HDL in the B6 strain was associated with decreases in HDL apolipoproteins A-I(-34%) and A-II(-60%). The HDL apoC content in mice fed chow was two-fold higher in C3H than B6. Lipoproteins containing apolipoprotein B (VLDL, IDL, LDL) shifted from a preponderance of the B-100 (chow diet) to a preponderance of the B-48 (atherogenic diet). The LDL-particle size distribution was strain-specific with the chow diet but not genetically associated with the Ath-1 gene. In both strains on each diet, apolipoprotein E was largely distributed in the VLDL, LDL, and HDL fractions. The B6 strain became sixfold elevated in total lipoprotein E content which in the C3H strain was not significantly affected by diet. However, the C3H LDL apoE content was reduced. On both diets, the C3H strain exhibited apolipoprotein E levels comparable to the atherogenic diet-induced levels of the B6 mice.
Transport in Nanostructures (1997)

This book reviews the results of experimental research into mesoscopic devices, and develops a detailed theoretical framework for understanding their behaviour. The authors begin by discussing the key observable phenomena in nanostructures, including phase interference and weak localization. They then describe quantum confined systems, transmission in nanostructures, quantum dots and single electron phenomena. Separate chapters are devoted to interference in diffusive transport and temperature decay of fluctuations, and the book concludes with a chapter on non-equilibrium transport and nanodevices. Throughout, the authors interweave experimental results with the appropriate theoretical formalism. The book will be of great interest to graduate students taking courses in mesoscopic physics or nanoelectronics, as well as to anyone working on semiconductor nanostructures or the development of new ultrasmall devices.
Copper(II)‐Catalyzed Monoarylation of Vicinal Diols with Diaryliodonium Salts (2012)

Selective and efficient: The copper(II)-catalyzed selective monoarylation of vicinal diols with diaryliodonium triflates was successfully developed. In this catalytic process high chemoselectivity was achieved, even in the presence of a 1:1 mixture of the 1,2-diol and the mono-ol, and a wide range of substrates was tolerated, giving the monoarylated products in good to excellent yields (see scheme). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Oligodendrocyte progenitor cell proliferation and lineage progression are regulated by glutamate receptor-mediated K+ channel block (1996)

We have analyzed the role of glutamate and its receptors (GluRs) in regulating the development of oligodendrocytes. Activation of AMPA-preferring GluRs with selective agonists inhibited proliferation of purified cortical oligodendrocyte progenitor (O-2A) cells cultured with different mitogens, as measured by [3H]thymidine incorporation or bromodeoxyuridine staining. In contrast, activation of GABA or muscarinic receptors did not affect O-2A proliferation. Cell viability and apoptosis assays demonstrated that the inhibition of O-2A proliferation was not attributable to a cytotoxic action of GluR agonists, and was reversible. Activation of GluRs prevented lineage progression from the O-2A (GD3+/nestin+) stage to the prooligodendroblast (O4+) stage, but did not affect O-2A migration. Additional experiments examined the membrane ionic channels mediating these GluR activation effects. We found that proliferating O-2A cells expressed functional delayed rectifier K+ channels, which were absent in pro-oligodendroblasts. GluR agonists and the K+ channel blocker tetraethylammonium (TEA) strongly inhibited delayed rectifier K+ currents in O-2A cells. TEA reproduced the effects of GluR activation on O-2A proliferation and lineage progression in the same concentration range that blocked delayed rectifier K+ currents. These results indicate that glutamate regulates oligodendrogenesis specifically at the O-2A stage by modulating K+ channel activity.
Inflammatory Markers and Platelet Aggregation Tests as Predictors of Hemoglobin and Endogenous Erythropoietin Levels in Hemodialysis Patients (2002)

Subclinical inflammation is an important determinant of anemia in maintenance HD patients. Increased serum IgM reflecting a microinflammatory effect of HD procedures, enhanced whole blood RIPA as a surrogate of vascular endothelial damage, and Lp(a) as its promoter could be markers of such impaired erythropoiesis.
Self-contained LED-pumped single-crystal Nd: YAG fiber laser (1979)

Abstract Lasers have been made from Nd: YAG single crystals grown directly in the form of fibers. These fibers, 50 to 80 μm in diameter and 0.5 cm long, were pumped at 0.8 μm wavelength by a single AlGaAs LED. One milliwatt output power, plane polarized in a single mode at 1.064 μm wavelength, has been achieved in continuous room-temperature operation, and a self-contained laser-LED package has been demonstrated. Construction and operation of the devices are described. Improvement by a factor of two in operating efficiency using straightforward techniques is predicted to yield 1 mW output at a pump diode current of ∼ 75 mA and laser threshold at ∼ 10 mA pump current.