gebhart/patrepeval huggingface dataset:
Receptor Tyrosine Kinases as Therapeutic Targets the Model of the MET Oncogene (2001)

Control of cell growth and differentiation occurs via extracellular signals known as growth factors. Growth factors are high affinity ligands for transmembrane receptors belonging to the family of receptor tyrosine kinases (RTKs). A number of genetic evidences have implicated RTKs in human diseases including developmental disorders and cancer. For instance, germline missense mutations involving the Ret receptor are found in patients affected by multiple endocrine neoplasia types 2A and 2B (MEN2A and MEN2B) or familial medullary thyroid carcinomas. Somatic mutations in the Kit receptor are found in mastocytomas and in gastrointestinal tumors. Germline and sporadic mutations of the Met receptor have been described in kidney and hepatocellular carcinomas. Overexpression of the HER-2/neu receptor in breast cancer has been associated with tumor progression. The enzymatic activity of RTKs is strictly regulated and is usually inhibited under basal conditions. Receptor activation triggers a biochemical signalling cascade inside the cytoplasm, named signal transduction, which is subverted during the malignant transformation of cells. Signal transduction by RTKs is a multistep process which includes: (i) Ligand binding and receptor dimerization, (ii) receptor phosphorylation on tyrosine residues; (iii) recruitment to the receptor and activation of cytoplasmic signaling molecules that transmit signals to the nucleus. Each of the steps involved in this process can potentially be targeted to block the aberrant properties of tyrosine kinase receptors. By using the MET oncogene as a model this review focuses on the strategies that can be applied to therapeutically target RTKs.
Preparation of Ti2SnC by solid—liquid reaction synthesis and simultaneous densification method (2002)

Polycrystalline Ti2SnC was prepared by a novel solid-liquid reaction synthesis and simultaneous densification method using elemental Ti, Sn and graphite as starting materials. The method is a one-step process and it provides the advantages of simultaneous synthesis and densification. The microstructure evolution during the high temperature processing was described and the reaction route was described. The reaction path for the formation of Ti2SnC can be described in the following steps. Sn melted at 230 °C, which provided a favorable liquid circumstance for the reactions between Ti and Sn to form Ti-Sn intermetallic compounds. At high temperatures, TiCx formed and reacted with Ti-Sn intermetallics at ~1100 °C to yield ternary carbide Ti2SnC. The material prepared by this method was dense and showed a layered anisotropic microstructure. The electrical conductivity of polycrystalline Ti2SnC was metallic and anisotropic due to the anisotropic microstructure. The Vickers hardness was 3.7 GPa and the flexural strength was 313 MPa. Under compression, Ti2SnC was damage tolerant at room temperature and deformed plastically at above 1000 °C.
Coding in 2D: Using Intentional Dispersity to Enhance the Information Capacity of Sequence‐Coded Polymer Barcodes (2016)

Abstract A 2D approach was studied for the design of polymer‐based molecular barcodes. Uniform oligo(alkoxyamine amide)s, containing a monomer‐coded binary message, were synthesized by orthogonal solid‐phase chemistry. Sets of oligomers with different chain‐lengths were prepared. The physical mixture of these uniform oligomers leads to an intentional dispersity (1st dimension fingerprint), which is measured by electrospray mass spectrometry. Furthermore, the monomer sequence of each component of the mass distribution can be analyzed by tandem mass spectrometry (2nd dimension sequencing). By summing the sequence information of all components, a binary message can be read. A 4‐bytes extended ASCII‐coded message was written on a set of six uniform oligomers. Alternatively, a 3‐bytes sequence was written on a set of five oligomers. In both cases, the coded binary information was recovered.
P2X Receptor Trafficking in Neurons Is Subunit Specific (2002)

P2X receptors within the CNS mediate excitatory synaptic transmission and also act presynaptically to modulate neurotransmitter release. We have studied the targeting and trafficking of P2X4 and P2X2 receptors heterologously expressed in cultured olfactory bulb neurons. Homomeric P2X4 receptors had a punctate distribution, and many of the puncta colocalized with early endosomes. In contrast, P2X2 receptors were primarily localized at the plasma membrane. By antibody-labeling of surface receptors in living neurons, we showed that P2X4 receptors undergo rapid constitutive internalization and subsequent reinsertion into the plasma membrane, whereas P2X2 receptors were not regulated in such a way. The internalization of P2X4 receptors was dynamin-dependent, and the binding of ATP enhanced the basal rate of retrieval in a Ca2+-independent manner. The presence of the P2X4 subunit in a P2X4/6 heteromer governed the trafficking properties of the receptor. P2X receptors acted presynaptically to enhance the release of glutamate, suggesting that the regulated cycling of P2X4-containing receptors might provide a mechanism for modulation of synaptic transmission.
Concise Drug Review: Azacitidine and Decitabine (2013)

The introduction of the hypomethylating agents azacitidine and decitabine has been a major advancement in the treatment of patients with higher-risk myelodysplastic syndromes, chronic myelomonocytic leukemia, and acute myeloid leukemia who are ineligible for more intensive treatments. This concise drug review summarizes the current state of treatment with azacitidine and decitabine.
Potential bioreductive alkylating agents. 7. Antitumor effects of phenyl-substituted 2-chloromethyl-3-phenyl-1,4-naphthoquinones (1976)

Functional groups such as nitro, chloro, bromo, and methoxy were introduced in the meta and para positions of the phenyl ring of the antineoplastic agent 2-chloromethyl-3-phenyl-1,4-naphthoquinone. Tests for tumor-inhibitory potency of these derivatives against Sarcoma 180 ascites cells in mice indicated that the para-substituted methoxyphenyl, chlorophenyl, and bromophenyl derivatives possessed antitumor activity comparable to that of the parent compound 2-chloromethyl-3-phenyl-1,4-naphthoquinone, whereas meta-substituted nitro and bromo derivatives were either inactive or only weakly active anticancer agents in this system.
Metastable capillary filaments in rectangular cross-section open microchannels (2014)

Spontaneous capillary flow (SCF) in microchannels occurs for specific geometrical and wetting conditions. When the channel walls form corner angles with the channel bottom, liquid filaments may form in the corners. These capillary filaments are often called Concus-Finn (CF) filaments, and they can theoretically spread infinitely.In this work we consider rectangular open U-grooves of varying cross-section width, and we theoretically determine the flow conditions as a function of the aspect ratio of the channel and the liquid-solid contact angle. These flow conditions are numerically checked. Especially, we analyze the configurations where precursor capillary filaments form. We show that these filaments can be metastable, i.e. disappear into a bulk capillary flow if the proper conditions are met. A diagram of the flow regimes is deduced from theoretical developments and checked using numerical modeling.
Invariant chain induces B cell maturation in a process that is independent of its chaperonic activity (2002)

Early stages of B cell development take place in the bone marrow, resulting in formation of immature B cells, which migrate to the spleen for their final differentiation into mature cells. This final maturation step is essential for B cells to become responsive to antigens and to participate in the immune response. Previously, we showed that the MHC class II chaperone, invariant chain (Ii), controls the differentiation of B cells from the immature to the mature stage. In this study, by generating transgenic mice expressing truncated Ii lacking its luminal domain, we could dissect the chaperonin activity of Ii from its role in B cell maturation. We demonstrate in vivo that Ii N-terminal domain is directly involved in the maturation of B cells and is sufficient to promote B cell differentiation.
The HIV-1 Surface Protein gp120 Has No Effect on Transmembrane Signal Transduction in T Cells (1992)

The ability of HIV-1 envelope glycoprotein gp120 to induce transmembrane signaling processes in human T cells and tumor T-cell lines was investigated. Differently glycosylated gp120 preparations were characterized with respect to their purity, the fraction of native gp120, and the affinity of the gp120-CD4 interaction. These data were used to establish experimental conditions that allow a substantial fraction of the CD4 receptor to be complexed with gp120 in the course of the experiments. The results are in contrast to several previous studies since no effect of gp120 on the intracellular Ca2+ concentration, the metabolism of inositol phosphates and arachidonic acid, protein kinase C translocation, and tyrosine phosphorylation was found. Cross-linking of the gp120:CD4 complex by anti-gp120 antibodies did not elicit additional effects.
Hyperspectral image data analysis (2002)

The fundamental basis for space-based remote sensing is that information is potentially available from the electromagnetic energy field arising from the Earth's surface and, in particular, from the spatial, spectral, and temporal variations in that field. Rather than focusing on the spatial variations, which imagery perhaps best conveys, why not move on to look at how the spectral variations might be used. The idea was to enlarge the size of a pixel until it includes an area that is characteristic from a spectral response standpoint for the surface cover to be discriminated. The article includes an example of an image space representation, using three bands to simulate a color IR photograph of an airborne hyperspectral data set over the Washington, DC, mall.
Plasmid-Encoded Phthalate Catabolic Pathway in Arthrobacter keyseri 12B (2001)

Several 2-substituted benzoates (including 2-trifluoromethyl-, 2-chloro-, 2-bromo-, 2-iodo-, 2-nitro-, 2-methoxy-, and 2-acetyl-benzoates) were converted by phthalate-grown Arthrobacter keyseri (formerly Micrococcus sp.) 12B to the corresponding 2-substituted 3,4-dihydroxybenzoates (protocatechuates). Because these products lack a carboxyl group at the 2 position, they were not substrates for the next enzyme of the phthalate catabolic pathway, 3,4-dihydroxyphthalate 2-decarboxylase, and accumulated. When these incubations were carried out in iron-containing minimal medium, the products formed colored chelates. This chromogenic response was subsequently used to identify recombinant Escherichia coli strains carrying genes encoding the responsible enzymes, phthalate 3,4-dioxygenase and 3,4-dihydroxy-3,4-dihydrophthalate dehydrogenase, from the 130-kbp plasmid pRE1 of strain 12B. Beginning with the initially cloned 8.14-kbp PstI fragment of pRE824 as a probe to identify recombinant plasmids carrying overlapping fragments, a DNA segment of 33.5 kbp was cloned from pRE1 on several plasmids and mapped using restriction endonucleases. From these plasmids, the sequence of 26,274 contiguous bp was determined. Sequenced DNA included several genetic units: tnpR, pcm operon, ptr genes, pehA, norA fragment, and pht operon, encoding a transposon resolvase, catabolism of protocatechuate (3,4-dihydroxybenzoate), a putative ATP-binding cassette transporter, a possible phthalate ester hydrolase, a fragment of a norfloxacin resistance-like transporter, and the conversion of phthalate to protocatechuate, respectively. Activities of the eight enzymes involved in the catabolism of phthalate through protocatechuate to pyruvate and oxaloacetate were demonstrated in cells or cell extracts of recombinant E. coli strains.
Innate immunity in plants and animals: striking similarities and obvious differences (2004)

Innate immunity constitutes the first line of defense against attempted microbial invasion, and it is a well-described phenomenon in vertebrates and insects. Recent pioneering work has revealed striking similarities between the molecular organization of animal and plant systems for nonself recognition and anti-microbial defense. Like animals, plants have acquired the ability to recognize invariant pathogen-associated molecular patterns (PAMPs) that are characteristic of microbial organisms but which are not found in potential host plants. Such structures, also termed general elicitors of plant defense, are often indispensable for the microbial lifestyle and, upon receptor-mediated perception, inevitably betray the invader to the plant's surveillance system. Remarkable similarities have been uncovered in the molecular mode of PAMP perception in animals and plants, including the discovery of plant receptors resembling mammalian Toll-like receptors or cytoplasmic nucleotide-binding oligomerization domain leucine-rich repeat proteins. Moreover, molecular building blocks of PAMP-induced signaling cascades leading to the transcriptional activation of immune response genes are shared among the two kingdoms. In particular, nitric oxide as well as mitogen-activated protein kinase cascades have been implicated in triggering innate immune responses, part of which is the production of antimicrobial compounds. In addition to PAMP-mediated pathogen defense, disease resistance programs are often initiated upon plant-cultivar-specific recognition of microbial race-specific virulence factors, a recognition specificity that is not known from animals.
Guidelines for Using the QuantiFERON-TB Gold Test for Detecting Mycobacterium tuberculosis Infection, United States (2005)

On May 2, 2005, a new in vitro test, QuantiFERON-TB Gold (QFT-G, Cellestis Limited, Carnegie, Victoria, Australia), received final approval from the U.S. Food and Drug Administration as an aid for diagnosing Mycobacterium tuberculosis infection. This test detects the release of interferon-gamma (IFN-g) in fresh heparinized whole blood from sensitized persons when it is incubated with mixtures of synthetic peptides representing two proteins present in M. tuberculosis: early secretory antigenic target-6 (ESAT-6) and culture filtrate protein-10 (CFP-10). These antigens impart greater specificity than is possible with tests using purified protein derivative as the tuberculosis (TB) antigen. In direct comparisons, the sensitivity of QFT-G was statistically similar to that of the tuberculin skin test (TST) for detecting infection in persons with untreated culture-confirmed tuberculosis (TB). The performance of QFT-G in certain populations targeted by TB control programs in the United States for finding latent TB infection is under study. Its ability to predict who eventually will have TB disease has not been determined, and years of observational study of substantial populations would be needed to acquire this information. In July 2005, CDC convened a meeting of consultants and researchers with expertise in the field to review scientific evidence and clinical experience with QFT-G. On the basis of this review and discussion, CDC recommends that QFT-G may be used in all circumstances in which the TST is currently used, including contact investigations, evaluation of recent immigrants, and sequential-testing surveillance programs for infection control (e.g., those for health-care workers). This report provides specific cautions for interpreting negative QFT-G results in persons from selected populations. This report is aimed at public health officials, health-care providers, and laboratory workers with responsibility for TB control activities in the United States.
Photophysics of Pt-porphyrin electrophosphorescent devices emitting in the near infrared (2007)

The triplet annihilation dynamics of near infrared organic light-emitting devices are studied with peak electrophosphorescence at a wavelength of 772nm using a platinum-porphyrin derivative Pt(II)-tetraphenyltetrabenzoporphyrin as dopant. Both the photoluminescent decay transients of the thin films and the quantum efficiency versus current density characteristics of devices using tris(8-hydroxyquinoline) aluminum or 4,4′-bis(N-carbazolyl)biphenyl (CBP) as hosts are fitted by a model based on triplet-triplet annihilation. When the phosphor is codoped with Ir(III) bis(2-phenyl quinolyl-N,C2′) acetylacetonate in CBP, the quantum efficiency is enhanced, and the observed decrease of efficiency at high current densities is explained by field-induced charge pair dissociation. The external quantum efficiency has a maximum of (8.5±0.3)%, decreasing to (5.0±0.3)% at 1mA∕cm2.
Acute Effects of High Frequency Vagal Nerve Stimulation on Balance and Cognitive Motor Performance in Epilepsy: Three Case Study Reports (1992)

Quantitative measures of area of sway, total sway, and cognitive function failed to show significant differences in acute (50 minute) "ON-OFF-ON-OFF" studies of high frequency left vagal stimulation in three epileptic patients undergoing treatment for chronic complex partial seizures. Fluctuation in blood levels of anticonvulsants may have been associated with some clinical effects. There were no significant adverse effects of acute left vagal stimulation in these three subjects.
Stereotaxic computed tomography (1976)

A method for stereotaxic computed tomography is described. A head fixation system has been devised enabling the exact transfer of information fromthe diagnostic coordinate system of the scanner to other therapeutic or diagnostic coordinate systems.
T (Brachyury) is a direct target of Wnt3a during paraxial mesoderm specification (1999)

Wnt3a encodes a signal that is expressed in the primitive streak of the gastrulating mouse embryo and is required for paraxial mesoderm development. In its absence cells adopt ectopic neural fates. Embryos lacking the T-box-containing transcription factors, Brachyury or Tbx6, also lack paraxial mesoderm. Here we show that Brachyury is specifically down-regulated in Wnt3a mutants in cells fated to form paraxial mesoderm. Transgenic analysis of the T promoter identifies T (Brachyury) as a direct transcriptional target of the Wnt signaling pathway. Our results suggest that Wnt3a, signaling via Brachyury, modulates a balance between mesodermal and neural cell fates during gastrulation.
The Corneal Epithelial Stem Cell (2002)

The aim of this paper was to develop a GFP-expressing transgenic mouse model for the keratoepithelioplasty and to use this to follow the outcome of this form of graft, when placed on an inflamed corneal surface. Further aims were to characterize both the graft and the epithelial surface of the mouse and rat cornea using putative stem cell markers (P63 and Telomerase) and marker of cell differentiation (14-3-3 sigma). Keratepithelioplasty was carried out using a GFP transgenic mouse cornea as donor tissue. Fluorescent epithelial outgrowth from each keratepithelioplasty was scored and quantified. Donor corneal graft tissue was obtained from the paracentral region or the anatomical limbal region of murine corneas. Paracentral donor grafts (n = 20) consistently demonstrated a significant increase in proliferative potential compared to grafts obtained from the anatomical limbal region of the mouse cornea (n = 25) (P = 0.000, Mann-Whitney U). Correspondingly, P63 expression was maximal in the paracentral region of the mouse cornea, in keeping with the demonstrated increased proliferative potential of donor grafts harvested from this region of the cornea. The murine corneal epithelium demonstrated decreased rather than increased cellular layers at the limbal region, in contrast to that of the rat or human epithelium. In addition, as a general finding in all species tested, there was an apparent increase noted in P63 expression in basal corneal epithelial cells in regions that had increased cellular layers (limbus in humans and rats and the paracentral corneal region in the mouse). Epithelium, which had migrated from donor grafts onto recipient corneas, retained P63 expression for the period of time examined (up to 3 days postengraftment). In addition, the conjunctival surface of an injured conjunctivalized displayed an abnormal pattern of P63 expression. Telomerase expression was widespread throughout many layers of both the murine and rat corneal epithelium. In the mouse and rat corneal epithelium P63 expression was maximal in areas of increased proliferative potential. Its expression, however, was not confined to stem cells alone. Migrating cells from transplanted keratoepithelial grafts retained P63 expression at least in the early stages post-transplantation. Finally, damaged conjunctivalized corneas displayed an abnormal P63 expression pattern when compared to either normal conjunctiva or normal cornea.
Channel‐forming, self‐assembling, bishelical amphiphilic peptides: design, synthesis and crystal structure of Py(Aibn)2, n = 2, 3, 4 (2000)

The design, synthesis, characterization and self-assembling properties of a new class of amphiphilic peptides, constructed from a bifunctional polar core attached to totally hydrophobic arms, are presented. The first series of this class, represented by the general structure Py(Aibn)2 (Py=2,6-pyridine dicarbonyl unit; Aib=alpha, alpha'-dimethyl glycine; n=1-4), is prepared in a single step by the condensation of commercially available 2,6-pyridine dicarbonyl dichloride with the methyl ester of homo oligoAib peptide (Aibn-OMe) in the presence of triethyl amine. 1H NMR VT and ROESY studies indicated the presence of a common structural feature of 2-fold symmetry and an NH...N hydrogen bond for all the members. Whereas the Aib3 segment in Py(Aib3)2 showed only the onset of a 3(10)-helical structure, the presence of a well-formed 3(10)-helix in both Aib4 arms of Py(Aib4)2 was evident in the 1H NMR of the bispeptide. X-ray crystallographic studies have shown that in the solid state, whereas Py(Aib2)2 molecules organize into a sheet-like structure and Py(Aib3)2 molecules form a double-stranded string assembly, the tetra Aib bispeptide, Py(Aib4)2, is organized to form a tetrameric assembly which in turn extends into a continuous channel-like structure. The channel is totally hydrophobic in the interior and can selectively encapsulate lipophilic ester (CH3COOR, R=C2H5, C5H11) molecules, as shown by the crystal structures of the encapsulating channel. The crystal structure parameters are: 1b, Py(Aib2)2, C25H37N5O8, sp. gr. P2(1)2(1)2(1), a=9.170(1) A, b=16.215(2) A, c=20.091(3) A, R=4.80; 1c, Py(Aib3)2, C33H51N7O10H2O, sp. gr. P1, a=11.040(1) A, b=12.367(1) A, c=16.959(1) A, alpha =102.41 degrees, beta =97.29 degrees, gamma =110.83 degrees, R1=6.94; 1 da, Py(Aib4)2.et ac, C41H65N9O12.1.5H2O.C4H8O2, sp. gr. P1, a=16.064(4) A, b=16.156 A, c=21.655(5) A, alpha =90.14(1)degrees, beta=101.38(2) degrees, gamma=97.07(1)degrees, Z=4, R1=9.03; 1db, Py(Aib4)2.amylac, C41H65N9O12.H2O.C7H14O2, P2(1)/c, a=16.890(1) A, b=17.523(1)A, c=20.411(1) A, beta=98.18 degrees, Z=4, R=11.1 (with disorder).