gebhart/patrepeval huggingface dataset:
Rationalisation and Validation of an Acrylamide-Free Procedure in Three-Dimensional Histological Imaging (2016)

Three-dimensional visualization of intact tissues is now being achieved by turning tissues transparent. CLARITY is a unique tissue clearing technique, which features the use of detergents to remove lipids from fixed tissues to achieve optical transparency. To preserve tissue integrity, an acrylamide-based hydrogel has been proposed to embed the tissue. In this study, we examined the rationale behind the use of acrylamide in CLARITY, and presented evidence to suggest that the omission of acrylamide-hydrogel embedding in CLARITY does not alter the preservation of tissue morphology and molecular information in fixed tissues. We therefore propose a novel and simplified workflow for formaldehyde-fixed tissue clearing, which will facilitate the laboratory implementation of this technique. Furthermore, we have investigated the basic tissue clearing process in detail and have highlighted some areas for targeted improvement of technologies essential for the emerging subject of three-dimensional histology.
Cloning and characterization of band 3, the human erythrocyte anion-exchange protein (AE1). (1989)

The human erythrocyte anion-exchange protein (band 3 or AE1) was cloned from a fetal liver cDNA library. Three overlapping clones, encompassing 3637 nucleotides, were analyzed in detail. These encode a 911-amino acid protein (Mr 101,791) and detect a single 4.7-kilobase species in human reticulocyte RNA. The corresponding gene is located on chromosome 17. The protein is similar in structure to other anion exchangers and is divided into three regions: a hydrophilic, cytoplasmic domain that interacts with a variety of membrane and cytoplasmic proteins (residues 1-403); a hydrophobic, transmembrane domain that forms the anion antiporter (residues 404-882); and an acidic, C-terminal domain of unknown function (residues 883-911). The N-terminal domain contains several conserved sections (e.g., residues 57-86, 102-164, 219-347, and 375-403), some of which may contribute to binding sites for ankyrin, protein 4.1, or protein 4.2. The membrane domain is highly conserved with the exception of a single segment (residues 543-567) that contains several sites for cleavage of the protein by extracellular proteases. Based on hydropathy analyses and the wealth of available topographical and functional data, a model is proposed in which the protein crosses the membrane 14 times.
Signal Transduction in Human Hematopoietic Cells by Vascular Endothelial Growth Factor Related Protein, a Novel Ligand for the FLT4 Receptor (1997)

We have recently identified a novel ligand of the vascular endothelial growth factor (VEGF) family termed VEGF-related protein (VRP), which specifically binds to the FLT4 receptor. To characterize the signaling events after VRP engagement of its cognate receptor in hematopoietic cells, a population of human erythroleukemia (HEL) cells, termed HEL-JW, expressing high levels of FLT4 receptor was isolated. Stimulation of HEL-JW cells with VRP alone and in combination with the c-kit ligand/stem cell factor increased cell growth. VRP induced tyrosine phosphorylation of various proteins, including the FLT4 receptor. Further characterization of these tyrosine phosphorylated molecules revealed that Shc, Grb2, and SOS form a complex with the activated FLT4 receptor. HEL-JW cells also expressed RAFTK, a recently identified member of the focal adhesion kinase family. RAFTK was phosphorylated and activated upon VRP treatment, and there was an enhanced association of this kinase with the adaptor protein Grb2. Furthermore, the c-Jun NH2-terminal kinase (JNK), involved in growth activation and shown to mediate RAFTK signaling in other cell types, was activated by VRP stimulation. We also observed that VRP treatment of HEL-JW cells resulted in the phosphorylation of the cytoskeletal protein paxillin. This treatment resulted in an increased association of paxillin with RAFTK, which was mediated by the C-terminal region of RAFTK. These studies indicate that VRP stimulation induced the formation of a signaling complex at its activated receptor as well as activation of RAFTK. VRP-mediated activation of RAFTK may facilitate signal transduction to the cytoskeleton and downstream to the JNK pathway in FLT4-expressing blood cells.
Inhibitory Regulation of Dendritic Activity in vivo (2012)

The spatiotemporal control of neuronal excitability is fundamental to the inhibitory process. We now have a wealth of information about the active dendritic properties of cortical neurons including axonally generated sodium action potentials as well as local sodium spikelets generated in the dendrites, calcium plateau spikes, and NMDA spikes. All of these events have been shown to be highly modified by the spatiotemporal pattern of nearby inhibitory input which can drastically change the output firing mode of the neuron. This means that particular populations of interneurons embedded in the neocortical microcircuitry can more precisely control pyramidal cell output than has previously been thought. Furthermore, the output of any given neuron tends to feed back onto inhibitory circuits making the resultant network activity further dependent on inhibition. Network activity is therefore ultimately governed by the subcellular microcircuitry of the cortex and it is impossible to ignore the subcompartmentalization of inhibitory influence at the neuronal level in order to understand its effects at the network level. In this article, we summarize the inhibitory circuits that have been shown so far to act on specific dendritic compartments in vivo.
Expression cloning and signaling properties of the rat glucagon receptor (1993)

Glucagon and the glucagon receptor are a primary source of control over blood glucose concentrations and are especially important to studies of diabetes in which the loss of control over blood glucose concentrations clinically defines the disease. A complementary DNA clone for the glucagon receptor was isolated by an expression cloning strategy, and the receptor protein was expressed in several kidney cell lines. The cloned receptor bound glucagon and caused an increase in the intracellular concentration of adenosine 3', 5'-monophosphate (cAMP). The cloned glucagon receptor also transduced a signal that led to an increased concentration of intracellular calcium. The glucagon receptor is similar to the calcitonin and parathyroid hormone receptors. It can transduce signals leading to the accumulation of two different second messengers, cAMP and calcium.
Biochemical structural and functional properties of oxidized low-density lipoprotein (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBiochemical structural and functional properties of oxidized low-density lipoproteinHermann Esterbauer, Martina Dieber-Rotheneder, Georg Waeg, Georg Striegl, and Guenther JuergensCite this: Chem. Res. Toxicol. 1990, 3, 2, 77–92Publication Date (Print):March 1, 1990Publication History Published online1 May 2002Published inissue 1 March 1990https://pubs.acs.org/doi/10.1021/tx00014a001https://doi.org/10.1021/tx00014a001research-articleACS PublicationsRequest reuse permissionsArticle Views514Altmetric-Citations430LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A dynamically configurable coprocessor for convolutional neural networks (2010)

Convolutional neural networks (CNN) applications range from recognition and reasoning (such as handwriting recognition, facial expression recognition and video surveillance) to intelligent text applications such as semantic text analysis and natural language processing applications. Two key observations drive the design of a new architecture for CNN. First, CNN workloads exhibit a widely varying mix of three types of parallelism: parallelism within a convolution operation, intra-output parallelism where multiple input sources (features) are combined to create a single output, and inter-output parallelism where multiple, independent outputs (features) are computed simultaneously. Workloads differ significantly across different CNN applications, and across different layers of a CNN. Second, the number of processing elements in an architecture continues to scale (as per Moore's law) much faster than off-chip memory bandwidth (or pin-count) of chips. Based on these two observations, we show that for a given number of processing elements and off-chip memory bandwidth, a new CNN hardware architecture that dynamically configures the hardware on-the-fly to match the specific mix of parallelism in a given workload gives the best throughput performance. Our CNN compiler automatically translates high abstraction network specification into a parallel microprogram (a sequence of low-level VLIW instructions) that is mapped, scheduled and executed by the coprocessor. Compared to a 2.3 GHz quad-core, dual socket Intel Xeon, 1.35 GHz C870 GPU, and a 200 MHz FPGA implementation, our 120 MHz dynamically configurable architecture is 4x to 8x faster. This is the first CNN architecture to achieve real-time video stream processing (25 to 30 frames per second) on a wide range of object detection and recognition tasks.
An engineered lipocalin specific for CTLA-4 reveals a combining site with structural and conformational features similar to antibodies (2009)

Biomolecular reagents that enable the specific molecular recognition of proteins play a crucial role in basic research as well as medicine. Up to now, antibodies (immunoglobulins) have been widely used for this purpose. Their predominant feature is the vast repertoire of antigen-binding sites that arise from a set of 6 hypervariable loops. However, antibodies suffer from practical disadvantages because of their complicated architecture, large size, and multiple functions. The lipocalins, on the other hand, have evolved as a protein family that primarily serves for the binding of small molecules. Here, we show that an engineered lipocalin, derived from human Lcn2, can specifically bind the T cell coreceptor CTLA-4 as a prescribed protein target with subnanomolar affinity. Crystallographic analysis reveals that its reshaped cup-like binding site, which is formed by 4 variable loops, provides perfect structural complementarity with this "antigen." Furthermore, comparison with the crystal structure of the uncomplexed engineered lipocalin indicates a pronounced induced-fit mechanism, a phenomenon so far considered typical for antibodies. By recognizing the same epitope on CTLA-4 that interacts with the counterreceptors B7.1/B7.2 on antigen-presenting cells the engineered Lcn2 exhibits strong, cross-species antagonistic activity, as evidenced by biological effects comparable with a CTLA-4-specific antibody. With its proven stimulatory activity on T cells in vivo, the CTLA-4 blocking lipocalin offers potential for immunotherapy of cancer and infectious disease. Beyond that, lipocalins with engineered antigen-binding sites, so-called Anticalins, provide a class of small ( approximately 180 residues), structurally simple, and robust binding proteins with applications in the life sciences in general.
Beautification of Design Sketches Using Trainable Stroke Clustering and Curve Fitting (2011)

We propose a new sketch parsing and beautification method that converts digitally created design sketches into beautified line drawings. Our system uses a trainable, sequential bottom-up and top-down stroke clustering method that learns how to parse input pen strokes into groups of strokes each representing a single curve, followed by point-cloud ordering that facilitates curve fitting and smoothing. This approach enables greater conceptual freedom during visual ideation activities by allowing designers to develop their sketches using multiple, casually drawn strokes without requiring them to indicate the separation between different stroke groups. With the proposed method, raw sketches are seamlessly converted into vectorized geometric models, thus, facilitating downstream assessment and editing activities.
Evaluation procedures for wafer bonding and thinning of interconnect test structures for 3D ICs (2004)

Electrical and mechanical impacts of wafer bonding and thinning processes required for three-dimensional (3D) IC fabrication have been evaluated with interconnect structures. In addition to the bonding and thinning required for a two-level 3D IC stack, an additional bonding and thinning process is used along with dielectric glue ashing to expose the previously tested interconnect structures. This procedure permits evaluation of bonding and thinning integrity without inter-wafer interconnect processing. Promising results on wafers with oxide interlevel dielectric (ILD) have been obtained, while some damages observed with the porous low-k ILD.
Side-mode injection locking of semiconductor lasers (1989)

Longitudinal mode selection in diode lasers by injection locking has been studied using the standard multimode rate equations with an optical injection term, and with the effects of spontaneous emission included. The phenomena of spectral narrowing and power switching between the dominant free-running mode and the injected target mode are illustrated and discussed. In general, injection locking into the long-wavelength side of the spectrum is more effective than into the short-wavelength side because of the gain peak shift. The relaxation oscillation frequency is estimated using a small-signal analysis of the single-mode rate equations, an approach that is valid provided the external injection is strong enough. Our calculations indicate that around the gain peak the relaxation oscillation frequency strongly depends on the wavelength of the injected target mode, because of the changing differential gain. Modes with shorter wavelengths have faster relaxation oscillations due to larger differential gain. This can be helpful in increasing the transmission speed in optical communication applications.
Disc-like 7, 14-dicyano-ovalene-3,4:10,11-bis(dicarboximide) as a solution-processible n-type semiconductor for air stable field-effect transistors (2011)

Large disc-like ovalene diimides (ODI and ODI-CN) were prepared for the first time mainly via Diels–Alder cycloaddition reactions at the bay regions of bisanthene. The CN-substituted ovalene diimide (ODI-CN) exhibited typical n-type semiconducting behaviour in solution processing OFET devices, showing high electron mobility up to 1.0 cm2 V−1 s−1 in nitrogen atmosphere and 0.51 cm2 V−1 s−1 in air together with good device stability.
Potent Production of Capsaicinoids and Capsinoids by Capsicum Peppers (2013)

The fundamental structure of capsinoids is a fatty acid ester with vanillyl alcohol, whereas in capsaicinoids, a fatty acid amide is linked to vanillylamine. To clarify the relationship between their biosynthesis in Capsicum plants, we carried out an in vivo tracer experiment using stable isotopically labeled putative precursors. Liquid chromatography-tandem mass spectrometry was used to measure the uptake of isotopes into metabolites after injection of the labeled precursors into intact fruits of a pungent cultivar, Peru, and a non-pungent cultivar, CH-19 Sweet. Labeled vanillylamine was incorporated into capsaicinoids in both cultivars. While labeled vanillyl alcohol was incorporated into capsinoids in both cultivars, the accumulation of intact capsaicinoids in Peru was suppressed by over 60% after administration of vanillyl alcohol. In Peru, labeled vanillin was converted to both vanillylamine and, in 5-fold excess, vanillyl alcohol. Moreover, labeled vanillin was converted exclusively to vanillyl alcohol in CH-19 Sweet. These data are consistent with the incorporation of labeled vanillin into capsaicinoids and capsinoids in both cultivars. We conclude that pungent cultivars are highly potent producers of vanillyl alcohol that is incorporated into capsinoids and that biosynthesis of capsinoids is catalyzed by capsaicin synthase.
Gastric cytoprotective properties of SCH 32651, a novel antiulcer agent. (1984)

The antisecretory activity of SCH 32651 (3-amino-2-methyl-8-phenylmethoxyimidazo[1,2-a] pyrazine HCl . 1/3 H2O) has been described in a preceding paper. This report describes its gastric cytoprotective properties. SCH 32651 inhibited the gastric lesions due to ethanol in a dose-dependent manner (ID50 = 5 mg/kg p.o.) and exerted its maximal effect when given 30 min before ethanol and had a duration of at least 90 min at 30 mg/kg p.o. The activity of SCH 32651 against ethanol was unaffected by indomethacin pretreatment. Furthermore, SCH 32651 produced significant increases in gastric mucus release (10-100 mg/kg p.o.) and rapidly reversed ethanol-induced (30-100 mg/kg p.o.) fall in gastric potential difference (PD). SCH 32651 displayed significant antiulcer activity in indomethacin-(30-100 mg/kg p.o.), aspirin - (30-100 mg/kg p.o.), "aspirin + acid" - (10-100 mg/kg p.o.), reserpine - (10-100 mg/kg p.o.), stress - (30-100 mg/kg p.o.), and cysteamine (10-100 mg/kg p.o.) ulcers. The present data in conjunction with those reported in a preceding paper indicate that SCH 32651 is an orally effective novel antiulcer drug with both gastric antisecretory and cytoprotective properties.
Factor IXa enhances reconstitution of factor VIIIa from isolated A2 subunit and A1/A3-C1-C2 dimer. (1992)

Heterotrimeric factor VIIIa was reconstituted from isolated A2 subunit and A1/A3-C1-C2 dimer of thrombin-activated human factor VIII in a reaction that was sensitive to pH. Maximal levels of reconstituted factor VIIIa at pH 6.0 were as much as 20-fold greater than were values observed at pH 7.5. The presence of factor IXa and phospholipid resulted in a marked increase in factor VIIIa reconstituted at physiologic pH. However, the resultant factor VIIIa was unstable due to slow proteolysis of the A1 subunit. Factor IXa modified by the active site-specific reagent dansyl-glutamyl-glycyl-arginyl-chloromethyl ketone (DEGR-IXa) increased the level of factor VIIIa reconstituted from subunits to a similar extent as was observed for unmodified factor IXa and yielded stable factor VIIIa. This enhancement was saturated above a 1:1 molar ratio of DEGR-IXa to factor VIIIa subunits and could be blocked by an anti-factor IX antibody, suggesting that the DEGR-IXa-dependent increase in factor VIIIa reconstitution correlated with assembly of the factor X-ase complex. At a saturating amount of DEGR-IXa, the level of factor VIIIa reconstitution at pH 7.5 approached values obtained at pH 6.0. Fluorescence polarization measurements indicated that factor VIIIa altered binding of DEGR-IXa to phospholipid. However, neither the A2 subunit nor the A1/A3-C1-C2 dimer alone produced this effect. This result suggested that both A2 and A1/A3-C1-C2 were necessary for association of the cofactor with factor IXa. These results suggest a model in which assembly of the intrinsic factor X-ase complex stabilizes factor VIIIa through inhibition of subunit dissociation.
Nebivolol and Metoprolol for Treating Migraine: An Advance on β ‐Blocker Treatment? (2007)

Our results suggest that nebivolol is as effective as metoprolol in the prophylaxis of migraine attacks, with the advantages of being better tolerated and not requiring up-titration to achieve therapeutic levels. Further and larger trials should be conducted on nebivolol in the prevention of migraine attacks as it may provide an improvement in current migraine prophylaxis with beta-blockers.
Ivermectin: pharmacology and application in dermatology (2004)

Ivermectin is a synthetic derivative of the antiparasitic class of compounds known as avermectins. It is a macrolide endectocide with activity against both endoparasites with cutaneous tropism (Strongyloides stercoralis, Ancylostoma braziliense, Cochliomyia hominivorax, Dermatobia hominis, Filaria bancrofti, Wucheria malayi, Onchocerca volvulus, Loa-loa) and ectoparasites such as Sarcoptes scabies, Pediculus humanus, Demodex folliculorum, and Cheyletiella sp. Ivermectin is of great interest in the treatment of patients with different forms of scabies, head lice, demodecidosis, cutaneous larva migrans, cutaneous larva currens, myiasis, and filariasis.
ChemInform Abstract: Convenient Synthetis of 4,5‐Dimethyl‐2‐furoic Acid. (1986)

Abstract Der aus dem Ketoester (I) zugängliche Aldehyd (II) wird in den Glycidester (IV) übergeführt, der nach saurer Cyclisierung zu (V) und anschließender Verseifung die Dimethylfurancarbonsäure (VI) ergibt.
Molecular genetics of the retinoblastoma suppressor gene. (1991)

The retinoblastoma gene (RB) is the prototype of a class of genes, called tumor suppressor genes, for which loss-of-function mutations are oncogenic. Such genes would then normally function to suppress or prevent tumor formation. Classical genetic and cytogenetic studies of retinoblastoma, a rare childhood eye cancer, laid a fundamental groundwork for the molecular cloning of this gene. Surprisingly, mutations of RB are found not only in retinoblastomas but also in some osteosarcomas, soft-tissue sarcomas, and carcinomas of breast, lung, prostate or bladder, suggesting a broad role for RB in human oncogenesis. In support of this hypothesis, a wild-type copy of RB is able to suppress the neoplastic properties of several types of tumor cells with mutated endogenous RB alleles. The RB gene product, pp110RB, is a nuclear phosphoprotein with DNA binding activity. RB protein is cyclically phosphorylated and dephosphorylated during the cell division cycle, and may play a significant role in its regulation.
Magnetic Resonance Imaging of Fluorine in Rats Infused with Artificial Blood (1985)

An MRI pulse sequence has been developed that enables the visualization of a perfluorocarbon (PFC) emulsion in the vascular system of rats. Images were made at 0.12T on a clinical imaging system using a small receiver coil, at intervals of approximately 2 hours, two days, two weeks, and two months after replacement of 50% of total blood volume. The most successful technique produced PA projections of the entire torso for both the fluorine and proton components. Direct comparison allowed identification of PFC in heart, lung, liver, spleen, and large vessels both in vivo and postmortem. Potential clinical applications to vascular imaging are discussed.