gebhart/patrepeval huggingface dataset:
Adenosine 2B Receptor Expression on Cancer Cells Promotes Metastasis (2016)

Adenosine plays an important role in inflammation and tumor development, progression, and responses to therapy. We show that an adenosine 2B receptor inhibitor (A2BRi) decreases both experimental and spontaneous metastasis and combines with chemotherapy or immune checkpoint inhibitors in mouse models of melanoma and triple-negative breast cancer (TNBC) metastasis. Decreased metastasis upon A2BR inhibition is independent of host A2BR and lymphocytes and myeloid cells. Knockdown of A2BR on mouse and human cancer cells reduces their metastasis in vivo and decreases their viability and colony-forming ability, while transiently delaying cell-cycle arrest in vitro The prometastatic activity of adenosine is partly tumor A2BR dependent and independent of host A2BR expression. In humans, TNBC cell lines express higher A2BR than luminal and Her2(+) breast cancer cell lines, and high expression of A2BR is associated with worse prognosis in TNBC. Collectively, high A2BR on mouse and human tumors promotes cancer metastasis and is an ideal candidate for therapeutic intervention. Cancer Res; 76(15); 4372-82. ©2016 AACR.
Novel Polyaminolipids Enhance the Cellular Uptake of Oligonucleotides (1995)

Two new polyaminolipids have been synthesized for the purpose of improving cellular uptake of oligonucleotides. The amphipathic compounds are conjugates of spermidine or spermine linked through a carbamate bond to cholesterol. The polyaminolipids are relatively nontoxic to mammalian cells. In tissue culture assays, using fluorescent-tagged or radiolabeled triple helix-forming oligonucleotides, spermine-cholesterol and spermidine-cholesterol significantly enhance cellular uptake of the oligomers in the presence of serum. Spermine-cholesterol is comparable with DOTMA/DOPE (a 1:1 (w/w) formulation of the cationic lipid N-[1-(2,3-dioleyloxy)-propyl]-N,N,N-trimethylammonium chloride (DOTMA) and the neutral lipid dioleylphosphatidylethanolamine (DOPE)) in increasing cellular uptake of oligonucleotides, while spermidine-cholesterol is more efficient. The internalized oligonucleotides are routed to the nucleus as early as 20 min after treatment, suggesting that the polyaminolipids increase the permeability of cellular membranes to oligonucleotides. At later times, much of the incoming oligonucleotides are sequestered within punctate cytoplasmic granules, presumably compartments of endosomal origin. Coadministration with polyaminolipids markedly improves the cellular stability of the oligonucleotides; more than 80% of the material can be recovered intact up to 24 h after addition to cells. In the absence of the polyaminolipids, nearly all of the material is degraded within 6 h. These data suggest that the new polyaminolipids may be useful for the delivery of nucleic acid-based therapeutics into cells.
Native Oxide Removal on Si Surfaces by NF3-Added Hydrogen and Water Vapor Plasma Downstream Treatment (1994)

NF 3 was injected into the downstream of hydrogen and water vapor plasma to produce etching species without generating fluorine atoms, and native oxides on Si(111) surfaces formed in H 2 SO 4 /H 2 O 2 solution were removed. The absence of fluorine atoms in the plasma and the downstream was confirmed by monitoring with a monochromator and an ESR spectrometer, respectively. Thus, etching of the quartz surface of a chamber which led to particle generation was not observed. The Si surfaces after the downstream treatment were investigated and compared with that after HF wet cleaning using attenuated total reflection Fourier transform infrared (FT-IR ATR) spectroscopy and X-ray photoelectron spectroscopy (XPS).
A single point mutation in the pore region of the epithelial Na + channel changes ion selectivity by modifying molecular sieving (1999)

The epithelial Na+ channel (ENaC) belongs to a new class of channel proteins called the ENaC/DEG superfamily involved in epithelial Na+ transport, mechanotransduction, and neurotransmission. The role of ENaC in Na+ homeostasis and in the control of blood pressure has been demonstrated recently by the identification of mutations in ENaC beta and gamma subunits causing hypertension. The function of ENaC in Na+ reabsorption depends critically on its ability to discriminate between Na+ and other ions like K+ or Ca2+. ENaC is virtually impermeant to K+ ions, and the molecular basis for its high ionic selectivity is largely unknown. We have identified a conserved Ser residue in the second transmembrane domain of the ENaC alpha subunit (alphaS589), which when mutated allows larger ions such as K+, Rb+, Cs+, and divalent cations to pass through the channel. The relative ion permeability of each of the alphaS589 mutants is related inversely to the ionic radius of the permeant ion, indicating that alphaS589 mutations increase the molecular cutoff of the channel by modifying the pore geometry at the selectivity filter. Proper geometry of the pore is required to tightly accommodate Na+ and Li+ ions and to exclude larger cations. We provide evidence that ENaC discriminates between cations mainly on the basis of their size and the energy of dehydration.
Wave Chemistry: 2-(4′-Azido 3′,5′,6′-trifluoro 2′-Pyridyl)- Amino Ethylamine as a Key Photoactivatable Building Block with Wide Biological Applications (1996)

Abstract The synthesis of the title compound is described as well as a series of derivatives with wide biological applications
Light field microscopy (2006)

By inserting a microlens array into the optical train of a conventional microscope, one can capture light fields of biological specimens in a single photograph. Although diffraction places a limit on the product of spatial and angular resolution in these light fields, we can nevertheless produce useful perspective views and focal stacks from them. Since microscopes are inherently orthographic devices, perspective views represent a new way to look at microscopic specimens. The ability to create focal stacks from a single photograph allows moving or light-sensitive specimens to be recorded. Applying 3D deconvolution to these focal stacks, we can produce a set of cross sections, which can be visualized using volume rendering. In this paper, we demonstrate a prototype light field microscope (LFM), analyze its optical performance, and show perspective views, focal stacks, and reconstructed volumes for a variety of biological specimens. We also show that synthetic focusing followed by 3D deconvolution is equivalent to applying limited-angle tomography directly to the 4D light field.
Tailoringin vitroevolution for protein affinity or stability (2000)

We describe a rapid and general technology working entirely in vitro to evolve either the affinity or the stability of ligand-binding proteins, depending on the chosen selection pressure. Tailored in vitro selection strategies based on ribosome display were combined with in vitro diversification by DNA shuffling to evolve either the off-rate or thermodynamic stability of single-chain Fv antibody fragments (scFvs). To demonstrate the potential of this method, we chose to optimize two proteins already possessing favorable properties. A scFv with an initial affinity of 1.1 nM (k(off) at 4 degrees C of 10(-4) s(-1)) was improved 30-fold by the use of off-rate selections over a period of several days. As a second example, a generic selection strategy for improved stability exploited the property of ribosome display that the conditions can be altered under which the folding of the displayed protein occurs. We used decreasing redox potentials in the selection step to select for molecules stable in the absence of disulfide bonds. They could be functionally expressed in the reducing cytoplasm, and, when allowed to form disulfides again, their stability had increased to 54 kJ/mol from an initial value of 24 kJ/mol. Sequencing revealed that the evolved mutant proteins had used different strategies of residue changes to adapt to the selection pressure. Therefore, by a combination of randomization and appropriate selection strategies, an in vitro evolution of protein properties in a predictable direction is possible.
In Vitro Effects of Preservatives in Nasal Sprays on Human Nasal Epithelial Cells (2008)

Potassium sorbate appears to be a relatively safer preservative than benzalkonium chloride for use in nasal sprays and drops in vitro study.
Malaria control in humanitarian emergencies (2015)

Malaria control in humanitarian emergencies , Malaria control in humanitarian emergencies , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
BAFF and MyD88 signals promote a lupuslike disease independent of T cells (2007)

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by the production of autoantibodies. However, the underlying cause of disease appears to relate to defects in T cell tolerance or T cell help to B cells. Transgenic (Tg) mice overexpressing the cytokine B cell-activating factor of the tumor necrosis factor family (BAFF) develop an autoimmune disorder similar to SLE and show impaired B cell tolerance and altered T cell differentiation. We generated BAFF Tg mice that were completely deficient in T cells, and, surprisingly, these mice developed an SLE-like disease indistinguishable from that of BAFF Tg mice. Autoimmunity in BAFF Tg mice did, however, require B cell-intrinsic signals through the Toll-like receptor (TLR)-associated signaling adaptor MyD88, which controlled the production of proinflammatory autoantibody isotypes. TLR7/9 activation strongly up-regulated expression of transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI), which is a receptor for BAFF involved in B cell responses to T cell-independent antigens. Moreover, BAFF enhanced TLR7/9 expression on B cells and TLR-mediated production of autoantibodies. Therefore, autoimmunity in BAFF Tg mice results from altered B cell tolerance, but requires TLR signaling and is independent of T cell help. It is possible that SLE patients with elevated levels of BAFF show a similar basis for disease.
Enhancement-Mode N-Polar GaN MOS-HFET With 5-nm GaN Channel, 510-mS/mm $g_{m}$, and 0.66-$\Omega\cdot \hbox{mm}$$R_{\rm on}$ (2011)

We report enhanced dc and small-signal RF performance of enhancement-mode (E-mode) metal-oxide-semiconductor heterojunction field-effect transistors (MOS-HFETs) in N-polar GaN technology with an ultrathin 5-nm GaN channel and graded AlGaN back-barrier structure with a record on-resistance ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> ) of 0.66 Ω·mm. The device has a maximum drain current ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Id</i> ) of 1.15 A/mm, a peak transconductance ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">gm</i> ) of 510 mS/mm, and a peak current-gain cutoff frequency ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ft</i> ) of 122 GHz, with a positive threshold voltage ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) of 1.6 V. The device shows improved saturation and pinchoff characteristics compared to the previously reported N-polar E-mode HFETs with a maximum <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> / <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> ratio of 2.2 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> .
Single‐Molecule Detection of Proteins Using Aptamer‐Functionalized Molecular Electronic Devices (2011)

Filling in the gap: Label-free, real-time electrical detection of proteins is achieved with high selectivity and real single-molecule sensitivity by using aptamer-functionalized molecular electronic devices with single-walled carbon nanotubes as point contacts. 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.
Mass Vaccination of Children with Pertussis Toxoid—Decreased Incidence in Both Vaccinated and Nonvaccinated Persons (2001)

During 1979-1995, there was no vaccination against pertussis in Sweden. With the aim of studying the epidemiology and transmission of pertussis, mass vaccination with pertussis toxoid of children born during the 1990s was instituted in the Göteborg area (population, 778,597) in 1995. Infants were offered 3 doses of pertussis toxoid combined with diphtheria and tetanus toxoids. Children aged > or =1 year were offered 3 doses of pertussis toxoid alone. From June 1995 through February 1999, 167,810 doses of pertussis toxoid were given to 61,219 children born during the 1990s (56% received 3 doses). The number of Bordetella pertussis isolates per year declined from 1214 (1993-1995) to 64 (January 1997 through June 1999; P<.0001), and hospitalizations due to pertussis declined from 62 to 5 (P<.0001). Significant decreases in B. pertussis isolates and hospitalizations occurred in all age groups, including adults and nonvaccinated infants. Thus, mass vaccination of children with pertussis toxoid decreases spread of B. pertussis in the population.
Cellular Distribution of Phosphorothioate Oligonucleotide Following Intravenous Administration in Mice (1998)

Oligonucleotides are promising therapeutic agents for the prevention or treatment of a variety of diseases. The therapeutic potential of oligonucleotide therapy depends greatly on the bioavailability of oligonucleotides to their target cells and organs. We previously reported the pharmacokinetics and distribution of phosphorothioate oligonucleotide in mice using [35S]-labeled oligonucleotide ([35S]-oligo). To extend this study, we administered 30 mg/kg of fluorescent-labeled oligonucleotide (FITC-oligo) to mice and examined oligonucleotide distribution by measuring the fluorescence intensity in various cells and tissues using flow cytometry. Following FITC-oligo administration, fluorescence was detected in all the tissues examined. In terms of the fluorescent intensity, accumulation was greatest in liver and kidney, intermediate in spleen and bone marrow, and very low in peripheral blood mononuclear cells (PBMC). At 4 hours after administration, the level of oligonucleotide uptake in PBMC, spleen lymphocytes, and bone marrow cells revealed the following pattern: monocytes/macrophages > B cells > T cells. Confocal microscopy detected intracellular fluorescence in PBMC prepared under the same conditions as those for flow cytometry. These studies provide a rationale for designing cell targets for antisense therapeutics.
Identification of (Z)-3:(E)-2-Hexenal Isomerases Essential to the Production of the Leaf Aldehyde in Plants (2016)

The green odor of plants is characterized by green leaf volatiles (GLVs) composed of C6 compounds. GLVs are biosynthesized from polyunsaturated fatty acids in thylakoid membranes by a series of enzymes. A representative member of GLVs (E)-2-hexenal, known as the leaf aldehyde, has been assumed to be produced by isomerization from (Z)-3-hexenal in the biosynthesis pathway; however, the enzyme has not yet been identified. In this study, we purified the (Z)-3:(E)-2-hexenal isomerase (HI) from paprika fruits and showed that various plant species have homologous HIs. Purified HI is a homotrimeric protein of 110 kDa composed of 35-kDa subunits and shows high activity at acidic and neutral pH values. Phylogenetic analysis showed that HIs belong to the cupin superfamily, and at least three catalytic amino acids (His, Lys, Tyr) are conserved in HIs of various plant species. Enzymatic isomerization of (Z)-3-hexenal in the presence of deuterium oxide resulted in the introduction of deuterium at the C4 position of (E)-2-hexenal, and a suicide substrate 3-hexyn-1-al inhibited HI irreversibly, suggesting that the catalytic mode of HI is a keto-enol tautomerism reaction mode mediated by a catalytic His residue. The gene expression of HIs in Solanaceae plants was enhanced in specific developmental stages and by wounding treatment. Transgenic tomato plants overexpressing paprika HI accumulated (E)-2-hexenal in contrast to wild-type tomato plants mainly accumulating (Z)-3-hexenal, suggesting that HI plays a key role in the production of (E)-2-hexenal in planta.
Cationic Liposomes Containing Noncytotoxic Phospholipid and Cholesterol Derivatives (1993)

Cationic phospholipid and cholesterol derivatives were synthesized by coupling basic amino acids, e.g. lysine, in an amide linkage to phosphatidylethanolamine or β-alanine in an ester linkage to cholesterol. Small liposomes were prepared from these cationic lipids in combination with other phospholipids or cholesterol and were shown to be noncytotoxic in vitro using a cell growth inhibition assay. The biological application of these cationic liposomes was tested in two different areas. In one approach the mucosal adhesion of the liposomes was tested in unanesthetized rabbit eyes. In this study, we showed an improvement in the extent of ocular retention of these liposomes with an increase in the charge density of the cationic lipid included in the liposomes. Prolonged ocular adhesion was observed with liposomes comprising fluid lipids with cholesterol or saturated lipids alone indicating a better display of the surface charge due to rigidifying membrane structure. Furthermore, the charged amino groups need to extend from the surface of the lipid bilayers for better adhesion. In another approach, the efficiency of cellular transfection of CV-1 cells was evaluated utilizing lysinyl phosphatidylethanolamine (LPE) and cholesteryl ester β-alanine (CEBA) liposomes. These noncytotoxic liposomes were shown to be at least as effective in transiently transfecting cells as the liposomes prepared from dioctadecyldimethylammonium bromide (DDAB) and dioleoyl phosphatidylethanolamine (DOPE).
Piecewise Image Registration in the Presence of Multiple Large Motions (2006)

We present a technique for computing a dense pixel correspondence between two images of a scene containing multiple large, rigid motions. We model each motion with either a homography (for planar objects) or a fundamental matrix. The various motions in the scene are first extracted by clustering an initial sparse set of correspondences between feature points; we then perform a multi-label graph cut optimization which assigns each pixel to an independent motion and computes its disparity with respect to that motion. We demonstrate our technique on several example scenes and compare our results with previous approaches.
Anachronism, Context and Progress in Nineteenth-Century American Communitarianism (1984)

The Presidential Address to the Canadian Association for American Studies, Banff, Alberta, October 28,1983. "He that commiteth sin is of the devil." When John Humphrey Noyes, a twenty- two year old theology student preached that text to his Yale Divinity School colleagues one afternoon in 1834, he knew full well the religious and personal implications. That night he "received the baptism" of freedom from sin in this life forbidden to neoCalvinists. Thus armed, he could face the inevitable onslaught which began the very next day. A fellow student came by and asked Noyes, "Don't you commit sin?" "I knew that my answer would plunge me into the depths of contempt, but I answered deliberately and firmly—NO !" The other man stared at Noyes as if struck by lightning, made Noyes repeat his blasphemy and then bolted, spreading the word that Noyes had said he was perfect, and then that Noyes was crazy. "Thus my confession was made, and I began to suffer the consequences."
A chimera of the cytoplasmic tail of the mannose 6-phosphate/igf-ii receptor and lysozyme localizes to the tgn rather than prelysosomes where the bulk of the endogenous receptor is found (1994)

We fused the cytoplasmic and transmembrane domains of the bovine mannose 6-phosphate/IGF-II receptor (MPR) to lysozyme, a monomeric secretory protein thought to be devoid of sorting information. When the resulting chimera (lys/MPR) was transiently expressed in COS cells or stably expressed in CV1 cells, it had a predominantly intracellular distribution in the trans-Golgi region, with less than 10% present on the surface. In contrast, a similar chimera containing the transmembrane and cytoplasmic domains of the low density lipoprotein receptor (lys/LDLR) was localized to the plasma membrane, even though it endocytoses efficiently. Exchanging domains between the lys/MPR and lys/LDLR chimeras indicated that the MPR cytoplasmic domain contains the information necessary to specify the intracellular localization of the chimeric molecule. This signal must be located in the membrane-proximal third of the tail, as deletion of the last 120 residues of the 163 residue tail has no obvious effect on the distribution of lys/MPR. However, the recycling of the lys/MPR does not completely mimic that of the intact endogenous MPR, as immunofluorescence labelling shows that they are predominantly in different locations, indicating a role for the lumenal domain of the MPR in determining the steady-state distribution of the MPR itself.
Retroviral vector targeting for gene therapy. (1996)

The majority of gene therapy protocols have used or plan to use retroviral vectors based upon murine leukaemia virus. These vectors are able to infect many different cell types, and the retroviral promoter, which is often used to control the expression of a therapeutic gene, is active in a wide range of different cell types. Safe and efficient gene transfer systems, whether based upon retroviruses or other agents, should deliver beneficial genes only to cells that require their therapeutic action, and these genes ideally should be expressed exclusively in such cells. In this paper, strategies for redirecting the infection spectrum of retroviral vectors in order to obtain cell-targeted gene delivery are discussed. These strategies include the engineering of the retroviral envelope protein, which, together with the availability of its cognate receptor, determines infectivity, and the use of proteins from other enveloped viruses of both retroviral and nonretroviral origin in the cell lines used to produce retroviral vector virus particles. Expression targeting can be achieved by limiting the expression of therapeutic genes to the cell type(s) of interest using promoters from genes that are normally active in these cells. This approach to targeting is illustrated using promoters from genes expressed in either the liver, the pancreas or the mammary gland as a means to limit gene expression specifically to the cell types that make up these organs. The successful utilization of new generations of targeted retroviral vectors in the clinic may well pave the way for superior gene delivery systems of the future that seek out their target cell, delivering a therapeutic gene to and expressing it only in such cells.
Major depression: the importance of clinical characteristics and treatment response to prognosis (2009)

Patients with higher levels of depression severity had worse clinical outcomes despite receiving greater intensity of treatment. A new classification of depression is proposed based on clinical severity, course of illness and treatment experience.