gebhart/patrepeval huggingface dataset:
Heterocyclic syntheses from o-halogeno-acids. Part II. Thienopyridinones and thienopyranones from 3-bromothiophen-2- and 4-bromothiophen-3-carboxylic acids (1975)

The sodium salt of 3-bromothiophen-2- and 4-bromothiophen-3-carboxylic acids react with carbanions in the presence of copper or copper(II) acetate to give condensation products by displacement of bromide ion (often with simultaneous deacylation). Thus ethyl acetoacetate gives the mono-ethyl esters of the homophthalic acid analogues, 2- and 4-carboxythiophen-3-acetic acids. Cyclisation reactions of the condensation products provide convenient routes to thienopyranones and thienopyridinones. 4-Phenacylthiophen-3-carboxylic acid is reduced to the 4-phenethyl-acid, which is cyclised by polyphosphoric acid at 100 °C to give 9,10-dihydrobenzo[4,5]-cyclohepta[1,2-c]thiophen-4-one. At 160 °C, however, this ketone, or the acid, yields the isomeric 4,5-dihydrobenzo[5,6]cyclohepta[1,2-b]thiophen-10-one, apparently by acidic cleavage to form an acylium ion which recyclises by attack on the α-position of the thiophen ring.
Dendrogenin A arises from cholesterol and histamine metabolism and shows cell differentiation and anti-tumour properties (2013)

We previously synthesized dendrogenin A and hypothesized that it could be a natural metabolite occurring in mammals. Here we explore this hypothesis and report the discovery of dendrogenin A in mammalian tissues and normal cells as an enzymatic product of the conjugation of 5,6α-epoxy-cholesterol and histamine. Dendrogenin A was not detected in cancer cell lines and was fivefold lower in human breast tumours compared with normal tissues, suggesting a deregulation of dendrogenin A metabolism during carcinogenesis. We established that dendrogenin A is a selective inhibitor of cholesterol epoxide hydrolase and it triggered tumour re-differentiation and growth control in mice and improved animal survival. The properties of dendrogenin A and its decreased level in tumours suggest a physiological function in maintaining cell integrity and differentiation. The discovery of dendrogenin A reveals a new metabolic pathway at the crossroads of cholesterol and histamine metabolism and the existence of steroidal alkaloids in mammals.
Development of Energy-efficient Cryogenic Optical (ECO) data link (2013)

We develop an energy efficient digital data link connecting cryogenic superconducting single flux quantum (SFQ) circuits to room-temperature electronics. The design is based on low-temperature (4 K) superconductor ERSFQ SFQ/dc drivers, high-temperature superconductor data cables spanning 4 K to 70 K temperature stages, mid-temperature (70 K) polarization modulation vertical cavity surface emitting lasers (PM VCSELs), and fiber optic links to room temperature electronics. The Energy-efficient Cryogenic Optical (ECO) data link design is based on balancing power dissipation and signal gain at each temperature stage to maximize overall energy efficiency following the recently introduced Thermo-Gain Rule. To achieve VCSEL light emission with two switchable distinct polarization modes, a cruciform-shaped anisotropic optical cavity is formed by fabrication of a photonic crystal with etched periodic air holes surrounding the unetched cruciform region. In this report, we present the results of design, fabrication, and preliminary testing of the ECO data link components.
Amyloid-β assessed by florbetapir F 18 PET and 18-month cognitive decline (2012)

Florbetapir PET may help identify individuals at increased risk for progressive cognitive decline.
Crystal Structure of the Human Cytomegalovirus Glycoprotein B (2015)

Human cytomegalovirus (HCMV), a dsDNA, enveloped virus, is a ubiquitous pathogen that establishes lifelong latent infections and caused disease in persons with compromised immune systems, e.g., organ transplant recipients or AIDS patients. HCMV is also a leading cause of congenital viral infections in newborns. Entry of HCMV into cells requires the conserved glycoprotein B (gB), thought to function as a fusogen and reported to bind signaling receptors. gB also elicits a strong immune response in humans and induces the production of neutralizing antibodies although most anti-gB Abs are non-neutralizing. Here, we report the crystal structure of the HCMV gB ectodomain determined to 3.6-Å resolution, which is the first atomic-level structure of any betaherpesvirus glycoprotein. The structure of HCMV gB resembles the postfusion structures of HSV-1 and EBV homologs, establishing it as a new member of the class III viral fusogens. Despite structural similarities, each gB has a unique domain arrangement, demonstrating structural plasticity of gB that may accommodate virus-specific functional requirements. The structure illustrates how extensive glycosylation of the gB ectodomain influences antibody recognition. Antigenic sites that elicit neutralizing antibodies are more heavily glycosylated than those that elicit non-neutralizing antibodies, which suggest that HCMV gB uses glycans to shield neutralizing epitopes while exposing non-neutralizing epitopes. This glycosylation pattern may have evolved to direct the immune response towards generation of non-neutralizing antibodies thus helping HCMV to avoid clearance. HCMV gB structure provides a starting point for elucidation of its antigenic and immunogenic properties and aid in the design of recombinant vaccines and monoclonal antibody therapies.
Prevention of ischemic brain injury by treatment with the membrane penetrating apoptosis inhibitor, TAT-BH4 (2009)

In acute thromboembolic stroke, neurological damage is due to ischemia-induced apoptotic death of neuronal cells and the surrounding vascular network. Here, we demonstrate that the BH4 domain of the anti-apoptotic protein, Bcl-x(L), attached to the membrane transport peptide, TAT, reduces stroke injury after intracerebroventricular infusion into immature rats subjected to carotid artery ligation and additional exposure to hypoxia. The injected TAT-BH4 entered neuron bodies, maintained brain architecture, protected neuronal and endothelial cells from apoptosis and promoted neuronal stem cell recruitment. In vitro, TAT-BH4 enhanced the survival of endothelial cells exposed to H(2)O(2), increased neuronal differentiation, and induced axonal remodelling of adult neuronal stem cells. These findings indicate that TAT-BH4 administration protects against acute hypoxia/ischemia injury in the brain by preventing endothelial and neuron cell apoptosis and by inducing neuronal plasticity.
Centrally active modulators of glutamate receptors facilitate the induction of long-term potentiation in vivo. (1994)

An experimental drug, 1-(1,3-benzodioxol-5-ylcarbonyl)piperidine, that facilitates glutamatergic transmission in brain after systemic administration was tested for its effects on the induction of long-term potentiation in the hippocampus of rats. Intraperitoneal injections of the drug markedly increased the degree and duration of long-term potentiation; similar results were obtained with an analogue of 1-(1,3-benzodioxol-5-ylcarbonyl)piperidine that was also found to improve retention of memory in a radial maze task and in an odor-matching problem. These results define tools for enhancing long-term potentiation in vivo and confirm an important prediction from the hypothesis that long-term potentiation is a substrate of memory.
Analysis of Restriction Fragment Length Polymorphisms of the Major Histocompatibility Complex of 15I5-B-Congenic Chicken Lines (1990)

Eight 15I5 B-congenic White Leghorn chicken lines, containing haplotypes B2, B5, B12, B13, B15, B19, and B21, were subjected to molecular genotyping with chicken B-F (Class I) and B-L (Class II) major histocompatibility complex (MHC) probes. Genomic DNA was digested with restriction enzymes, hybridized with a Class I or Class II probe, and analyzed for restriction fragment length polymorphisms. Digestion with HindIII or EcoRI yielded no B-L polymorphisms. Digestion with PvuII or BglII and hybridization with a B-L or B-F probe produced polymorphisms that were shared between several haplotypes, although the haplotypes with similar patterns were clustered differently between Class I and Class II probes. The genetic variation seen for B-L and B-F probe hybridization of PvuII digests was much less than that previously demonstrated for B-G probing of PvuII digests of the same lines. Description of MHC Class I and II restriction patterns of the well-characterized 15I5 B-congenic lines will aid in identification of genes important in disease resistance.
Fault Diagnosis for the Virtualized Network in the Cloud Environment using Reinforcement Learning (2019)

In the cloud environment, the virtualized network provides the connectivity to a massive of virtual machines through various virtual network devices. In such a complicated networking system, network faults are not occasional. It is urging for the system administrators to have the ability to investigate a fault and recover from it. However, the complexity of the virtualized network and the similarity among the symptom of faults makes the accurate diagnosis challenging. In this paper, we leverage the method of reinforcement learning to facilitate the fault diagnosis in the cloud environment, where it diagnoses the faults through an “exploration and exploitation” manner. Further, we investigate the key factors that influence the network performance and may cause the network faults. Based on this investigation, we present how to train the network diagnosis module with the Q-learning algorithm. Experimental results show that the diagnosis accuracy of our reinforcement learning based method is around 8% higher than traditional methods, and incurs very slight system overhead.
The Jindalee operational radar network: its architecture and surveillance capability (2002)

The expansive surveillance capability of the Jindalee over-the-horizon operational radar network (JORN) stems in part from the ability to centralise control and co-ordination of remote sensors. The two radar sensors are located at Laverton, Western Australia and at Longreach, Queensland, while the surveillance co-ordination centre is situated in Adelaide, South Australia. An extensive communications network will be developed to support the radars and their associated frequency management systems. The principle of operation, configuration and the key architectural components of the Jindalee project are briefly outlined to provide the context of the surveillance capability.
Study of mitochondrial membrane potential, reactive oxygen species, DNA fragmentation and cell viability by flow cytometry in human sperm (2002)

Analysis of mitochondrial membrane potential is the most sensitive test by which to determine sperm quality. These findings promise development of a test that may help to predict successful IVF.
Histomorphologic correlation with routine histology and optical coherence tomography (2004)

Due to the deformation by histological processing and slightly different sectioning levels, the comparison of histological pictures and OCT images seems difficult. Nevertheless, in two cases it was possible to demonstrate the same morphological structures with OCT imaging and histological investigation. Our method could play an important role for further evaluation of OCT images. We estimate better evaluation of OCT imaging using a 3D reconstruction method.
Synthesis of a Novel Poly(MePEG cyanoacrylate-co-alkyl cyanoacrylate) Amphiphilic Copolymer for Nanoparticle Technology (1997)

In order to develop “stealth” injectable PEG-coated poly(alkyl cyanoacrylate) (PACA) nanoparticles, a novel poly(MePEG cyanoacrylate-co-alkyl cyanoacrylate) copolymer has been synthetized in a simple way by condensing MePEG cyanoacetate esters with formaldehyde in the presence of dimethylamine. This approach allowed the covalent linkage of PEG moieties to the cyanoacrylate polymer, thus avoiding the risk of desorption of PEG, as in the case of a PEG coating obtained by simple adsorption onto preformed nanoparticles. In addition, the condensation procedure allowed a better control of the polymerization process than in the case of anionic polymerization of alkyl cyanoacrylates. Finally, we have shown that the hydrophobicity of the copolymer can be perfectly modulated by adjusting the MePEG cyanoacetate/alkyl cyanoacetate ratio. Characterization of the copolymer has been performed by NMR, GPC, and FTIR analysis. Monodispersed nanoparticles were easily prepared by nanoprecipitation of this amphiphilic copolymer.
Thiophene-2-aryl-2H-benzotriazole-thiophene Oligomers with Adjustable Electronic Properties (2011)

The synthesis and the optical and electrochemical properties of 2-aryl-2H-benzotriazole based thiophene oligomers with chemical modifications either on the phenyl side group or on the backbone are presented. All data, supported by DFT calculations, show that modification on the backbone has a major impact on the electronic properties while the side groups can fine-tune the electronic properties. In addition, one compound exhibits a thermotropic mesophase.
Cross‐shore sediment transport and the equilibrium morphology of mudflats under tidal currents (2003)

We describe a mathematical model of suspended sediment transport under cross‐shore tidal currents on an intertidal mudflat. We employ a Lagrangian formulation to obtain periodic solutions for the sediment transport over idealized bathymetries and use these to investigate the process of settling lag. In deep water away from the shoreline the concentration of suspended sediment tends to a constant value, and we may invert the relation between bathymetry and offshore concentration to estimate how the gradient of a flat in a state of equilibrium varies with the sediment properties and supply. These analytical estimates are compared successfully with the numerical experiments of previous studies. We discuss the robustness of our modeling framework and demonstrate its application to different descriptions of sediment transport and tidal regimes.
Comparative analysis of the ability of leucocytes, endothelial cells and platelets to degrade the subendothelial basement membrane: Evidence for cytokine dependence and detection of a novel sulfatase (1995)

The subendothelial basement membrane (BM) is regarded as an important barrier to the entry of leucocytes into inflammatory sites. This study compares the ability of leucocytes, platelets and endothelial cells (EC) to degrade a [35SO4]-labelled subendothelial extracellular matrix (ECM) and assesses the effect of PMA and various pro-inflammatory cytokines on this degradative activity. The different products of degradation, identified by fast protein liquid chromatography (FPLC) gel filtration chromatography, were indicative of protease, endoglycosidase (heparanase) and exoglycosidase and/or sulfatase activity. In terms of ECM degradation, EC and platelets were the most active, with PMA stimulation further enhancing the degradative activity of these two cell types. Platelets exhibited predominantly heparanase activity whereas the EC degradation products suggested a range of enzymic activities, namely proteases, heparanases and sulfatases. Interestingly, EC in suspension expressed these three enzymic activities whereas confluent EC monolayers only exhibited sulfatase activity, suggesting that the former situation might represent an angiogenic response. In the case of leucocytes, neutrophils and lymphocytes degraded the ECM to a much greater extent than monocytes. Each cell type also differed in the predominant enzymic activities it expressed, for example, heparanase activity by lymphocytes, protease activity by neutrophils and sulfatase activity by monocytes. Furthermore, PMA stimulation was shown to have differential effects on these enzymic activities. Some pro-inflammatory cytokines were found to be cell-type specific in their effects on ECM degradation. Thus, IL-1 + TNF enhanced neutrophil and EC degradation of the ECM but inhibited lymphocyte ECM degradation. In contrast, the chemokine IL-8 enhanced ECM degradation by neutrophils, lymphocytes and EC. Of particular interest was the unique sulfatase activity expressed by EC and monocytes which was induced in EC by TNF + IL-1 and IL-8, whereas in monocytes the sulfatase activity was exclusively induced by the chemokine monocyte chemotactic and activating factor (MCAF). Collectively, the results of this study show that leucocytes differ markedly in the enzymes they express to degrade the BM during extravasation and that PMA and cytokines are cell-type specific in their induction of hydrolytic enzyme activity. These results also indicate that EC may play an important role, not only in the recruitment of leucocytes, but also via sulfatase activity in the preparation of vascular BM for leucocyte extravasion.
A 10 bit 80 MHz glitchless CMOS D/A converter (2002)

A high-accuracy (10-b) and high-speed (80-MHz) glitchless D/A (digital-to-analog) converter has been realized. The device is based on the following circuit techniques: 1023 new cells with a clocked AND-NOR gate for data-latch function; a new current source circuit for reduction of switching noise; and a current source arrangement independent of current variation. The LSI has been fabricated by a 1.0- mu m double-metal CMOS process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An endocrine-specific element is an integral component of an exocrine-specific pancreatic enhancer. (1993)

We have analyzed the function of individual elements of the elastase I transcriptional enhancer in transgenic animals. This pancreas-specific enhancer comprises three functional elements, one of which (the B element) plays a dual role. Within the context of the enhancer, the B element contributes to appropriate acinar cell expression. However, when separated from the other enhancer components, the B element selectively directs transcription in islet cells of transgenic animals. This islet-specific activity is normally suppressed by an upstream repressor domain. The B element binds a novel islet-specific factor, and similar B-like elements are present in other pancreatic genes, both exocrine and endocrine specific. We suggest that a principal role of this transcriptional element and its associated factors is to activate many pancreatic genes as part of the program of pancreatic determination prior to the divergence of the acinar and islet cell lineages.
The Henry Coefficient of CO2 in the MEA-CO2-H2O System (2017)

The Henry Coefficient of CO2 is a fundamental property and crucial for the accurate simulation of the absorption and desorption of CO2 in MEA solutions related to post combustion capture (PCC). The free CO2 concentration in amine solutions is very small and is difficult to be measured since it reacts with the solution. The “N2O analogy” is traditionally applied to estimate the physical solubility of CO2 based on the assumption that the two gases behave similarly in amine solutions. We propose a direct way to determine Henry Coefficient of CO2 in MEA solutions as an alternative to N2O analogy. The method only requires vapor liquid equilibrium measurements of the MEA-CO2-H2O system. Based on the total MEA concentration, loading and known equilibrium constants the free CO2 can be computed which allows the determination of the Henry Coefficient. A 6-parameter polynomial is used to approximate the Henry Coefficient as a function of the total MEA concentration and total CO2 concentration at 40 oC.
Cache-oblivious shortest paths in graphs using buffer heap (2004)

We present the Buffer Heap (BH), a cache-oblivious priority queue that supports Delete-Min, Delete, and Decrease-Key operations in O(1overB log2 NoverB) amortized block transfers from external memory, where B is the (unknown) block-size and N is the maximum number of elements in the queue. As is common in cache-oblivious algorithms, we assume a 'tall cache' (i.e., M = Ω(B1 + ε), where M is the size of the main memory). We also assume the Decrease-Key operation only verifies that the element does not exist in the priority queue with a smaller key value, hence it also supports the insert operation in the same amortized bound. The amortized time bound for each operation is O(log N). We also present a Cache-Oblivious Tournament Tree (COTT), which is simpler than the Buffer Heap, but has weaker bounds.Using the Buffer Heap we present cache-oblivious algorithms for undirected and directed single-source shortest path (SSSP) problems for graphs with non-negative edge-weights. On a graph with V vertices and E edges, our algorithm for the undirected case performs O(V + EoverB log2 VoverB) block transfers and for the directed case performs O((V + EoverB) . log2 VoverB) block transfers. The running time of both algorithms is O((V + E). log V).For both priority queues with Decrease-Key operation, and for shortest path problems on general graphs, our results appear to give the first non-trivial cache-oblivious bounds.
Toward the Development of an Injectable Dosage Form of Propofol: Preparation and Evaluation of Propofol–Sulfobutyl Ether 7‐β‐Cyclodextrin Complex (2004)

The objectives of the present study were to undertake activities toward the development of an aqueous-based formulation of propofol (2,6-diisopropyl phenol), using sulfobutylether 7-beta-cyclodextrin (SBECD). Preformulation studies, including high performance liquid chromatography (HPLC) method development and phase-solubility evaluation in the presence of SBECD were conducted. It was determined that equilibrium solubility has been reached by 4-day and 7-day phase-solubility analysis at 30 degrees C and 37 degrees C. The apparent binding constants and various thermodynamic parameters were calculated from this data. These results suggest that "nonclassical hydrophobic effects" are the driving forces for inclusion complex formation. Compounding and lyophilization of the formulation with 20% SBECD yielded a product with propofol concentration of 10 mg/mL. The formulation properties were probed by using techniques that included modulated differential scanning calorimetry (MDSC) and Karl Fischer analysis. MDSC showed that propofol, SBECD, and the Propofol-SBECD complex displayed thermal properties at widely varying temperatures, suggesting the formation of a new solid form. The active pharmaceutical ingredient in the liquid formulation and lyophilized product was determined by the newly developed and qualified HPLC method. Short-term stability studies of the liquid formulation showed that they were stable for a month at 4 degrees C. Short-term stability studies of the freeze-dried cakes showed that the product was stable for over a month at 4 degrees C, 37 degrees C, and 50 degrees C. Based on these preliminary results, we believe that an aqueous based injectable formulation of propofol with sulfobutylether 7-beta-cyclodextrin can be successfully developed.
Genome-wide analysis reveals a cell cycle–dependent mechanism controlling centromere propagation (2008)

Centromeres are the structural and functional foundation for kinetochore formation, spindle attachment, and chromosome segregation. In this study, we isolated factors required for centromere propagation using genome-wide RNA interference screening for defects in centromere protein A (CENP-A; centromere identifier [CID]) localization in Drosophila melanogaster. We identified the proteins CAL1 and CENP-C as essential factors for CID assembly at the centromere. CID, CAL1, and CENP-C coimmunoprecipitate and are mutually dependent for centromere localization and function. We also identified the mitotic cyclin A (CYCA) and the anaphase-promoting complex (APC) inhibitor RCA1/Emi1 as regulators of centromere propagation. We show that CYCA is centromere localized and that CYCA and RCA1/Emi1 couple centromere assembly to the cell cycle through regulation of the fizzy-related/CDH1 subunit of the APC. Our findings identify essential components of the epigenetic machinery that ensures proper specification and propagation of the centromere and suggest a mechanism for coordinating centromere inheritance with cell division.