gebhart/patrepeval huggingface dataset:
A convenient procedure for the synthesis of oligodeoxyribonucleotide affinity columns for the isolation of mRNA (1988)

Journal Article A convenient procedure for the synthesis of oligodeoxyribonucleotide affinity columns for the isolation of mRNA Get access Tom Atkinson, Tom Atkinson * Department of Biochemistry, Faculty of Medicine, 2146 Health Sciences Mall, University of British ColumbiaVancouver, BC V6T 1W5, Canada *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Shirley Gillam, Shirley Gillam Department of Biochemistry, Faculty of Medicine, 2146 Health Sciences Mall, University of British ColumbiaVancouver, BC V6T 1W5, Canada 1Present address: Department of Pathology, Faculty of Medicine, University of British Columbia, Research Centre, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael Smith Michael Smith Department of Biochemistry, Faculty of Medicine, 2146 Health Sciences Mall, University of British ColumbiaVancouver, BC V6T 1W5, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 13, 11 July 1988, Page 6232, https://doi.org/10.1093/nar/16.13.6232 Published: 11 July 1988 Article history Received: 23 May 1988 Published: 11 July 1988
Friends and relations of the cystatin superfamily—new members and their evolution (1997)

The cystatin "superfamily" encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. In recent years, several new members of the superfamily have characterized, including proteins from insects and plants. Based on partial amino acid homology, new members, such as the invariant chain (Ii), and the transforming growth factor-beta receptor type II (TGF-beta receptor II) may, in fact, represent members of an emerging family within the superfamily that may have used some common building blocks to form functionally diverse proteins. Cystatin super-family members have been found throughout evolution and members of each family of the superfamily are present in mammals today. In this review, the new and older, established members of the family are arranged into a possible evolutionary order, based on sequence homology and functional similarities.
BET Bromodomain Inhibition Triggers Apoptosis of NF1-Associated Malignant Peripheral Nerve Sheath Tumors through Bim Induction (2014)

Malignant peripheral nerve sheath tumors (MPNSTs) are highly aggressive sarcomas that develop sporadically or in neurofibromatosis type 1 (NF1) patients. There is no effective treatment for MPNSTs and they are typically fatal. To gain insights into MPNST pathogenesis, we utilized an MPNST mouse model that allowed us to study the evolution of these tumors at the transcriptome level. Strikingly, in MPNSTs we found upregulation of a chromatin regulator, Brd4, and show that BRD4 inhibition profoundly suppresses both growth and tumorigenesis. Our findings reveal roles for BET bromodomains in MPNST development and report a mechanism by which bromodomain inhibition induces apoptosis through induction of proapoptotic Bim, which may represent a paradigm shift in therapy for MPNST patients. Moreover, these findings indicate epigenetic mechanisms underlying the balance of anti- and proapoptotic molecules and that bromodomain inhibition can shift this balance in favor of cancer cell apoptosis.
IL-9 induces differentiation of T H 17 cells and enhances function of FoxP3 + natural regulatory T cells (2009)

The development of T helper (T(H))17 and regulatory T (T(reg)) cells is reciprocally regulated by cytokines. Transforming growth factor (TGF)-beta alone induces FoxP3(+) T(reg) cells, but together with IL-6 or IL-21 induces T(H)17 cells. Here we demonstrate that IL-9 is a key molecule that affects differentiation of T(H)17 cells and T(reg) function. IL-9 predominantly produced by T(H)17 cells, synergizes with TGF-beta1 to differentiate naïve CD4(+) T cells into T(H)17 cells, while IL-9 secretion by T(H)17 cells is regulated by IL-23. Interestingly, IL-9 enhances the suppressive functions of FoxP3(+) CD4(+) T(reg) cells in vitro, and absence of IL-9 signaling weakens the suppressive activity of nT(regs) in vivo, leading to an increase in effector cells and worsening of experimental autoimmune encephalomyelitis. The mechanism of IL-9 effects on T(H)17 and T(regs) is through activation of STAT3 and STAT5 signaling. Our findings highlight a role of IL-9 as a regulator of pathogenic versus protective mechanisms of immune responses.
Selection of antibody single-chain variable fragments with improved carbohydrate binding by phage display (1994)

A single-chain variable fragment (Fv) version of a murine monoclonal antibody, Se155-4, specific for Salmonella serogroup B O-polysaccharide, was used as a model system for testing monovalent phage display as a route for enhancing the relatively low affinities that typify anti-carbohydrate antibodies. Random single-chain Fv mutant libraries generated by chemical and error-prone polymerase chain reaction methods were panned against the serogroup B lipopolysaccharide. Panning of a randomly mutated heavy chain variable domain library indicated selection for improved serogroup B binders and yielded six mutants, five of which showed wild type activity by enzyme immunoassay. Two of these were apparently selected on the basis of better functional single-chain Fv yield in Escherichia coli. A heavy chain mutation (Ile77-->Thr) in one mutant, 3B1, appeared to have a particularly dramatic effect, resulting in yields of approximately 120 mg/liter of functional periplasmic product. The sixth mutant, 4B2, had complementarity determining region 1 (CDR1) and CDR2 mutations and demonstrated 10-fold improved binding, by enzyme immunoassay, relative to the wild type. Extensive analysis of antigen-antibody interactions indicated that the improved binding properties of 4B2 were attributable to a higher association rate constant and interaction with an epitope that is larger than the trisaccharide recognized by the wild type. None of the mutations involved known trisaccharide contact residues; this was consistent with analysis of wild type and mutant single-chain Fvs by titration microcalorimetry. Examination of the structure indicated that two mutations in the heavy chain CDR2 provided improved surface complementarity between the protein and the extended epitope encompassing 2 additional hexose residues. However, introduction of only the CDR2 mutations into the wild type structure failed to confer the improved binding properties of 4B2, indicating an indirect effect by the more distant mutations. Panning of randomly mutated light chain variable domain and full-length single-chain Fv mutant libraries did not yield mutants with improved assembly or binding properties.
3D Flowerlike Ceria Micro/Nanocomposite Structure and Its Application for Water Treatment and CO Removal (2007)

A simple and economical route based on ethylene glycol mediated process was developed to synthesize three-dimensional (3D) flowerlike ceria micro/nanocomposite structure using cerium chloride as a reactant. Scanning electron microscopy (SEM) and X-ray diffraction (XRD) were adopted to investigate the evolution process of ceria precursor, and a two-stage growth process was identified during the morphology evolution. Ceria with the same flowerlike micro/nanocomposite structure was readily obtained by calcination of the ceria precursor. This novel micro/nanocomposite structure held the advantages of both microstructure and nanostructure. Therefore, the as-obtained ceria can be used as not only an effective sorbent for the removal of pollutants in water treatment but also as an excellent support for gold nanoparticles to remove CO by catalytic oxidation, demonstrating a promising potential in environmental remediation.
Optimally controlling Hybrid Electric Vehicles using path forecasting (2009)

The paper examines path-dependent control of Hybrid Electric Vehicles (HEVs). In this approach we seek to improve HEV fuel economy by optimizing charging and discharging of the vehicle battery depending on the forecasted vehicle route. The route is decomposed into a series connection of route segments with (partially) known properties. The dynamic programming is used as a tool to quantify the benefits offered by route information availability.
Activation of phospholipase C by alpha 1-adrenergic receptors is mediated by the alpha subunits of Gq family. (1992)

High efficiency transient transfection of Cos-7 cells was previously used to establish the functional coupling between G alpha q/G alpha 11 and phospholipase C beta 1 (Wu, D., Lee, C-H., Rhee, S. G., and Simon, M. I. (1992) J. Biol. Chem. 267, 1811-1817). Here the same system was used to study the functional coupling between other guanine nucleotide-binding regulatory protein (G-protein) alpha subunits and phospholipases and to study which G alpha subunits mediate the activation of phospholipase C by the alpha 1-adrenergic receptor subtypes, alpha 1 A, alpha 1 B, and alpha 1 C. We found that G alpha 14 and G alpha 16 behaved like G alpha 11 or G alpha q, i.e. they could activate endogenous phospholipases in Cos-7 cells in the presence of AIFn. The synergistic increase in inositol phosphate release in Cos-7 cells after they were cotransfected with cDNAs encoding G alpha subunits and phospholipase C beta 1 indicates that both G alpha 16 and G alpha 14 can activate phospholipase C beta 1. The activation of phospholipase C beta 1 was restricted to members of the Gq subfamily of alpha subunits. They activated phospholipase C beta 1 but not phospholipase C gamma 1, gamma 2, or phospholipase C delta 3. The cotransfection of Cos-7 cells with cDNAs encoding three different alpha 1-adrenergic receptors and G alpha q or G alpha 11 leads to an increase in norepinephrine-dependent inositol phosphate release. This indicates that G alpha q or G alpha 11 can mediate the activation of phospholipase C by all three subtypes of alpha 1-adrenergic receptors. With the same assay system, G alpha 16 and G alpha 14 appear to be differentially involved in the activation of phospholipase C by the alpha 1-adrenergic receptors. The alpha 1 B subtype receptor gave a ligand-mediated synergistic response in the cells cotransfected with either G alpha 14 or G alpha 16. However, the alpha 1 C receptor responded in cells cotransfected with G alpha 14 but not G alpha 16, and the alpha 1 A receptor showed little synergistic response in cells transfected with either G alpha 14 or G alpha 16. The ability of the alpha 1 A and alpha 1 C receptors to activate phospholipase C through G alpha q and G alpha 11 was also demonstrated in a cell-free system.(ABSTRACT TRUNCATED AT 400 WORDS)
A New Method for Node Fault Detection in Wireless Sensor Networks (2009)

Wireless sensor networks (WSNs) are an important tool for monitoring distributed remote environments. As one of the key technologies involved in WSNs, node fault detection is indispensable in most WSN applications. It is well known that the distributed fault detection (DFD) scheme checks out the failed nodes by exchanging data and mutually testing among neighbor nodes in this network., but the fault detection accuracy of a DFD scheme would decrease rapidly when the number of neighbor nodes to be diagnosed is small and the node’s failure ratio is high. In this paper, an improved DFD scheme is proposed by defining new detection criteria. Simulation results demonstrate that the improved DFD scheme performs well in the above situation and can increase the fault detection accuracy greatly.
Recombinant adeno-associated virus vectors in the treatment of rare diseases (2015)

Currently the scope of clinical trials of AAV gene therapy is concentrated in an array of phase I/II safety trials with less than two dozen rare diseases featured. Pre-clinical, translational studies are expanding in number as developments within the last decade have made generation of improved AAV vectors available to more researchers. Further, one bottleneck that is being overcome is the availability of disease models, which will allow for improved preclinical testing and advancement of AAV to more clinical applications.
SAGE is far more sensitive than EST for detecting low-abundance transcripts (2004)

The SAGE method is more efficient than the EST method in detecting the low-abundance transcripts.
Obesity and overweight : healthy lifestyle (2012)

The World Health Organization (WHO) defines obesity and overweight as excessive fat accumulation that presents a health risk. Body mass index (BMI) is used in the classification of patients as underweight, normal weight, overweight or obese (see Table I). BMIs are calculated in the same way, irrespective of age or sex, and should be used as a rough guide only, as they do not always correspond to the same degree of overweight or obesity in different individuals.
A multiplication-free multialphabet arithmetic code (1989)

A recursion for arithmetic codes used for data compression is described which requires no multiplication or division, even in the case of nonbinary alphabets. For this reason, such a code admits a simple and fast hardware implementation. The inputs to the code are, in addition to the symbols to be encoded, either the symbol probabilities or, more simply, the corresponding occurrence counts. Hence, the code is applicable in conjunction with stationary and nonstationary models alike. The code efficiency is typically in the range of 97-99%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Capillary Electrophoresis of Neutral Carbohydrates (2008)

This chapter reports an overview of the recent advances in the analysis of neutral sugars by capillary electrophoresis (CE); furthermore, some relevant reviews and research articles in the field are tabulated. Comparison of CE with chromatography is also presented, with special attention to separation efficiency and sensitivity. The main routes aimed at pretreatment and CE analysis of uncharged mono-, oligosaccharides, and glycosides are described. Representative examples of such procedures are reported in detail, upon describing robust methodologies for the study of (1) neutral mono- and oligosaccharides derivatized by reductive amination and by formation of glycosylamines; (2) underivatized mono- and di-saccharides analyzed using highly alkaline buffers; and (3) anomeric couples of glycosides separated using borate-based buffers.
Complement-induced vascular leukostasis. Its role in tissue injury. (1980)

The plasma complement system evolved as a beneficial antimicrobial mechanism. However, this system can be activated chaotically in such situations as extracorporeal perfusion, trauma, sepsis, or acute pancreatitis. When so activated, the complement component C5a may aggregate granulocytes and cause leukoembolization; it is suggested that such leukoembolization is an important, previously unsuspected mechanism of tissue damage. In addition, toxic oxygen species, such as superoxide, that are produced by granulocytes that have been triggered by C5a can damage the endothelium, an event that may, if it occurs in the lungs, contribute to the development of the adult respiratory distress syndrome (ARDS). Hence the previously empiric use of high doses of corticosteroids in treating shock states, particularly in cases of the ARDS, may have a physiologic basis since very high concentrations of such drugs have been shown to inhibit both superoxide production and granulocyte aggregation.
Results of systematic screening for serious gastrointestinal bleeding associated with NSAIDs in Rostock hospitals (2002)

Gastrointestinal problems resulting from the use of NSAIDs are clinically important. It is concluded, that individual risk profiles, as a criterion for the prophylactic use of effective protective drugs, would be helpful in patients management.
Rapid electrochemical phenotypic profiling of antibiotic-resistant bacteria (2015)

Rapid phenotyping of bacteria to identify drug-resistant strains is an important capability for the treatment and management of infectious disease. At present, the rapid determination of antibiotic susceptibility is hindered by the requirement that, in existing devices, bacteria must be pre-cultured for 2-3 days to reach detectable levels. Here we report a novel electrochemical approach that achieves rapid readout of the antibiotic susceptibility profile of a bacterial infection within one hour. The electrochemical reduction of a redox-active molecule is monitored that reports on levels of metabolically-active bacteria. Bacteria are captured in miniaturized wells, incubated with antimicrobials and monitored for resistance. This electrochemical phenotyping approach is effective with clinically-relevant levels of bacteria, and provides results comparable to culture-based analysis. Results, however, are delivered on a much faster timescale, with resistance profiles available after a one hour incubation period.
Communication and mobility enhancements to the Scout robot (2003)

Small scale distributed robotic systems are ideal for tasks that larger, more expensive robots may not be able to undertake such as surveillance or inspection in enclosed areas. Small scale robots also have the advantage of being easily portable to an area of interest. However, the advantages related to the small size and portability cause an increase in the complexity of development. In addition, the more pronounced effects of interacting with the environment in terms of mobility and communications lead to robotic systems of limited functionality. In order to address such deficiencies, several novel developments and improvements have been made to the Scout robot, which will be discussed. These improvements include the development of a communication relay system facilitating longer distance operation, an improved actuating wheel system increasing the Scout's mobility and a grappling hook system to elevate the Scout. By enhancing the Scout robotic team in this way, the functional use of the team is expanded, allowing more practical use.
Dense Stereo Matching over the Panum Band (2009)

Stereo matching algorithms conventionally match over a range of disparities sufficient to encompass all visible 3D scene points. Human vision, however, works over a narrow band of disparities-Panum's fusional band-whose typical range may be as little as 1/20 of the full range of disparities for visible points. Only points inside the band are fused visually; the remainder of points are seen diplopically. A probabilistic approach is presented for dense stereo matching under the Panum band restriction. It is shown that existing dense stereo algorithms are inadequate in this problem setting and the main problem is segmentation, marking the image into the areas that fall inside the band. An approximation is derived that makes up for missing out-of-band information with a "proxy" based on image autocorrelation. It is shown that the Panum Proxy algorithm achieves accuracy close to what can be obtained when the full disparity band is available, and with gains of between one and two orders of magnitude in computation time. There are also substantial gains in computation space. Panum band processing is also demonstrated in an active stereopsis framework.
BRCA1Mutations in Women Attending Clinics That Evaluate the Risk of Breast Cancer (1997)

Among women with breast cancer and a family history of the disease, the percentage with BRCA1 coding-region mutations is less than the 45 percent predicted by genetic-linkage analysis. These results suggest that even in a referral clinic specializing in screening women from high-risk families, the majority of tests for BRCA1 mutations will be negative and therefore uninformative.
Targeting the B-Cell Lymphoma/Leukemia 2 Family in Cancer (2012)

The B-cell lymphoma/leukemia 2 (BCL-2) family of proteins has attracted the attention of cancer biologists since the cloning of BCL-2 more than 25 years ago. In the intervening decades, the way the BCL-2 family controls commitment to programmed cell death has been greatly elucidated. Several drugs directed at inhibiting BCL-2 and related antiapoptotic proteins have been tested clinically, with some showing considerable promise, particularly in lymphoid malignancies. A better understanding of the BCL-2 family has also provided insight into how conventional chemotherapy selectively kills cancer cells and why some cancers are more chemosensitive than others. Further exploitation of our understanding of the BCL-2 family promises to offer improved predictive biomarkers for oncologists and improved therapies for patients with cancer.
Counting sunrays: from optics to the thermodynamics of light (2009)

This chapter considers quantum solar energy conversion from a thermodynamic point of view. Starting from geometrical optics, the concept of étendue is used to determine the number of photon states in a beam of light. This naturally leads to the definition of entropy, providing the foundation for the statistical mechanics of light beams. With emphasis on the thermodynamic functions per photon (in particular, the chemical potential), these concepts are illustrated first by comparing the thermodynamic limits of the geometric concentrators with the limits obtained by traditional arguments. The thermodynamic framework is then extended to novel applications. The fluorescent collector is modelled as an open thermodynamic system interacting with a room-temperature heat bath. A detailed thermodynamic description of the operation of a p-n junction solar cell then follows, starting from energy (voltage) rather than from the kinetic argument used by Shockley and Queisser. This provides a novel view of fundamental losses, each identified as a specific form of irreversible entropy generation. The chapter concludes with an analysis of a future photovoltaic device – a hot carrier solar cell where the voltage exceeds the Shockley-Queisser limit. The efficiency of this solar cell, obtained by thermodynamic arguments, is free from specific mechanisms or structures such as selective energy contacts. It is argued that this is the fundamental efficiency limit to the operation of single junction solar cells where thermalization of electron-hole pairs has been reduced or entirely eliminated
Sequence-Selective Binding of DNA by Oligopeptides as a Novel Approach to Drug Design (1994)

Recent interest in the development of sequence-specific DNA binding agents as chemotherapeutic agents, structural probes of DNA, and artificial restriction enzymes has led to the development of minor groove DNA binding agents that recognize selective base sequences. A rational approach to the development of low molecular weight oligoimidazolecarboxamide and polymethylene linked analogs of distamycin targeted for long guanine-cytosine (GC) rich sequences of DNA are described.
Intraventricular vortex flow changes in the infarcted left ventricle: numerical results in an idealised 3D shape (2011)

The cardiac diagnostic process is primarily based on the evaluation of myocardial mechanics whereas little is known about blood dynamics that is rarely considered to this purpose. The intraventricular blood flow is analysed here for akinetic and dyskinetic myocardial motion corresponding to the presence of an ischaemic pathology. This study is performed through a 3D numerical model of the left ventricular flow. Results show that the presence of an anterior-inferior wall infarction leads to the shortening and weakening of the diastolic mitral jet. A region of stagnating flow is found near the apex and close to the ischaemic wall. These results are in agreement with previous clinical findings based on echographic imaging. The described phenomena are also noticed for moderate degrees of the ischaemic pathology and suggest a potential value of the study of the intraventricular flow to develop early diagnostic indicators.