gebhart/patrepeval huggingface dataset:
Enhanced adsorption efficiency of inorganic chromium (VI) ions by using carbon-encapsulated hematite nanocubes (2020)

In this study, carbon-encapsulated hematite nanocubes with an edge length of ~20 nm (α-Fe2O3@C) were prepared by a two-step hydrothermal method using glucose as a carbon source. The α-Fe2O3@C nanocomposite was found to exhibit enhanced adsorption efficiency for inorganic chromium (VI) ions as compared to bare α-Fe2O3 nanocubes. At optimized conditions, the maximum adsorption capacity and removal efficiency of Cr(VI) using α-Fe2O3@C nanocomposites were 76.92 mg g−1 and 97.6%. The influence of carbon content on the structural features, and on the mechanism of adsorption of the α-Fe2O3@C nanocomposites were investigated and discussed. Adsorption data revealed that the adsorption behavior of the α-Fe2O3@C nanocomposites for chromium (VI) showed good agreement with both Langmuir and pseudo-second-order kinetic models. Moreover, the α-Fe2O3@C nanocomposites still retain high chromium (VI) removal efficiency after three recycles. Carbon-encapsulated hematite nanocubes with high Cr(VI) removal efficiency and excellent regenerability will become a promising absorbent toward the treatment of heavy metals from water solution.
DNA Strand Exchange Stimulated by Spontaneous Complex Formation with Cationic Comb-Type Copolymer (2002)

Cationic comb-type copolymers (CCCs) composed of a polycation backbone and water-soluble side chains accelerate by 4-5 orders the DNA strand exchange reaction (SER) between double helical DNA and its homologous single-strand DNA. The accelerating effect is considered due to alleviation of counterion association during transitional intermediate formation in sequential displacement pathway. CCCs stabilize not only matured hybrids but also the nucleation complex to accelerate hybridization.
The yellow mini-hutch for SAXS experiments at MAX IV Laboratory (2013)

I911-SAXS is the new SAXS (Small-Angle-X-ray-Scattering) beamline at the MAX IV Laboratory in Lund, Sweden. It is one of the 5 stations of the hard X-ray Cassiopeia beamline (I911) at the 1.5 GeV ring MAX II. I911-4 was converted into a multipurpose SAXS station which opened to the scientific community in May 2011. The SAXS users community at this laboratory comes from diverse fields of research with different needs and requirements at the end-station. This results in different set-ups routinely being installed in the easy-accessible experimental mini-hutch. The beam can be focused at sample-to-detector distances between a few hundred millimeters and more than two meters. This versatility permits a selection of q-ranges between 0.006 1/Å and 2 1/Å. The recent acquisition of a fast readout, low noise pixel detector (PILATUS 1M) and the implementation of a high-throughput solution SAXS are the latest beamline upgrades.
Building a fast, virtualized data plane with programmable hardware (2010)

Network virtualization allows many networks to share the same underlying physical topology; this technology has offered promise both for experimentation and for hosting multiple networks on a single shared physical infrastructure. Much attention has focused on virtualizing the network control plane, but, ultimately, a limiting factor in the deployment of these virtual networks is data-plane performance: Virtual networks must ultimately forward packets at rates that are comparable to native, hardware-based approaches. Aside from proprietary solutions from vendors, hardware support for virtualized data planes is limited. The advent of open, programmable network hardware promises flexibility, speed, and resource isolation, but, unfortunately, hardware does not naturally lend itself to virtualization. We leverage emerging trends in programmable hardware to design a flexible, hardware-based data plane for virtual networks. We present the design, implementation, and preliminary evaluation of this hardware-based data plane and show how the proposed design can support many virtual networks without compromising performance or isolation.
Performance of Coupled-Cluster Singles and Doubles on Modern Stream Processing Architectures (2020)

We develop a new implementation of coupled-cluster singles and doubles (CCSD) optimized for the most recent graphical processing unit (GPU) hardware. We find that a single node with 8 NVIDIA V100 GPUs is capable of performing CCSD computations on roughly 100 atoms and 1300 basis functions in less than 1 day. Comparisons against massively parallel implementations of CCSD suggest that more than 64 CPU-based nodes (each with 16 cores) are required to match this performance.
Thermal System Design and Simulation for Growth of Large Grain Multi-crystal Silicon Ingot (2011)

In order to grow large grain multi-crystalline silicon in DSS silicon casting,the key process is to control the thermal system for bulk growth.In this study a moving partition block between the side heater and the heat exchanger block is added.By lifting the partition block and adding a jet cooling on the bottom block,casting process is controlled optimally.Through the numerical simulation,effects of different cooling flux on growth environment are discussed,and then growth interface,isotherm in the melt and crystal,axial temperature distribution in melt and in crystal are modeled.The results indicate: the optimal value of cooling flux is between 5 W/m2 and 15 W/m2;for the new design,the isotherms in the melt and crystal become more flat,and the axial temperature gradient in crystal increases about 1.72 K/cm,which are helpful for avoiding nucleation on the crucible wall,obtaining large grain multi-crystal,and also increasing the growth rate.
Imaging and elasticity measurements of the sarcolemma of fully differentiated skeletal muscle fibres (2005)

This study aimed to describe the three-dimensional structure and the elastic properties of the sarcolemma of adult, fully differentiated, skeletal muscle fibres combining Atomic Force Microscopy (AFM) and optical microscopy. Single fibres were enzymatically dissociated from Flexor Digitorum Brevis of adult mice and were maintained in culture up to 3 weeks. On the sixth day after dissociation, the upper surface of intact fibres, either alive in solution or fixed and kept in solution or fixed and exposed in air, was analysed with AFM. The most prominent features in AFM images were periodic transversal foldings with an interval that corresponded to the sarcomere length. More detailed analysis of the topography profile showed that the depth in the folding decreased with increasing sarcomere length and that the crests of the foldings corresponded to the Z-lines. Minor periodic structures could be detected in the valleys between the major foldings. AFM images also showed deep depressions on the sarcolemma likely corresponding to openings of T tubules and caveolae. Two-dimensional elasticity maps were obtained using AFM as an indenter and showed that the crests of the transversal foldings correspond to higher stiffness regions. This study provides the first complete three-dimensional topography and mechanical characterization of intact, living skeletal muscle fibres and might form the basis for further investigations aimed to compare healthy and dystrophic muscles.
β-Arrestin Promotes Wnt-induced Low Density Lipoprotein Receptor-related Protein 6 (Lrp6) Phosphorylation via Increased Membrane Recruitment of Amer1 Protein (2013)

β-Arrestin is a scaffold protein that regulates signal transduction by seven transmembrane-spanning receptors. Among other functions it is also critically required for Wnt/β-catenin signal transduction. In the present study we provide for the first time a mechanistic basis for the β-arrestin function in Wnt/β-catenin signaling. We demonstrate that β-arrestin is required for efficient Wnt3a-induced Lrp6 phosphorylation, a key event in downstream signaling. β-Arrestin regulates Lrp6 phosphorylation via a novel interaction with phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2)-binding protein Amer1/WTX/Fam123b. Amer1 has been shown very recently to bridge Wnt-induced and Dishevelled-associated PtdIns(4,5)P2 production to the phosphorylation of Lrp6. Using fluorescence recovery after photobleaching we show here that β-arrestin is required for the Wnt3a-induced Amer1 membrane dynamics and downstream signaling. Finally, we show that β-arrestin interacts with PtdIns kinases PI4KIIα and PIP5KIβ. Importantly, cells lacking β-arrestin showed higher steady-state levels of the relevant PtdInsP and were unable to increase levels of these PtdInsP in response to Wnt3a. In summary, our data show that β-arrestins regulate Wnt3a-induced Lrp6 phosphorylation by the regulation of the membrane dynamics of Amer1. We propose that β-arrestins via their scaffolding function facilitate Amer1 interaction with PtdIns(4,5)P2, which is produced locally upon Wnt3a stimulation by β-arrestin- and Dishevelled-associated kinases.
Synthesis Gas Conversion over Rh-Mn-WxC/SiO2 Catalysts Prepared by Atomic Layer Deposition (2018)

The catalytic conversion of synthesis gas to value-added oxygenates and light hydrocarbons was studied on Rh and Rh–Mn clusters on tungsten carbide-overcoated silica (WxC/SiO2) at 523 K, 580 psi, and CO/H2 = 1/1. The WxC-modified SiO2 support was prepared by the overcoating of WOx on SiO2 using atomic layer deposition (ALD) followed by carburization. The reactivities of Rh/WxC/SiO2 catalysts with varying number of ALD cycles (number of cycles = 2, 5, 10, 20, and 30) were measured and showed that 5 ALD cycles of WxC suppressed the formation of methane. All WxC-modified catalysts showed enhancement in selectivity toward methanol and ethanol through CO hydrogenation and acetaldehyde hydrogenation, respectively. These catalysts also improved the overall turnover frequency (TOF). The addition of Mn species further promoted the activity and the selectivity toward ethanol and C2+ hydrocarbons, especially light alkenes. The best performing Rh-2Mn/5cycle-WxC/SiO2 catalyst (Rh:Mn molar ratio = 1:2) achieved 84.7% selectivity toward valuable oxygenates and C2+ hydrocarbons with a ratio of alkenes to alkanes equal to 1.7, compared to Rh/SiO2 which exhibited 80.4% selectivity toward the products aforementioned with a ratio of 0.5. The overall TOF was 20 times higher than that over Rh/SiO2 (i.e., 5.6 × 10–2 s–1 vs 2.9 × 10–3 s–1). X-ray diffraction revealed that the existence of W2C, which was the dominant phase in Rh/5cycle-WxC/SiO2, favored the suppression of methane and enhanced the production of alcohols and C2+ hydrocarbons compared to the WC support. Density functional theory calculations for Rh19, Rh31, and Rh37 clusters on various WC surfaces suggested that the shape of Rh clusters is condition dependent and subject to H2 pressure. The C- and O- binding energies on various sites for the clusters were used with scaling relations to probe their catalytic activity. With the use of this approach, the increase in the O binding energy when moving from the SiO2-supported Rh37 cluster to the WC-supported cluster leads to an increase in the activity of Rh/WxC/SiO2 at the expense of the reduction in the number of sites that are selective toward C2 oxygenates.
Pharmacological study of original 3-alkylamino-2-methyl-2H-pyrido[4,3-e]-1,2,4-thiadiazine 1,1-dioxides (1998)

peer reviewed
Pilot-scale application of an online VFA sensor for monitoring and control of a manure digester (2012)

A volatile fatty acids (VFA) sensor based on headspace chromatography was tested for online monitoring and control of a pilot-scale manure digester. The sensor showed satisfying results in terms of sensitivity and reliability for monitoring of the digester. The online VFA and biogas production data were used for automatic control of the digester based on feed flow manipulation. The control approach was based on optimization of biogas production while using VFA concentration as the alarm threshold. A rule-based supervisory system with a cascade controller was used to optimize the biogas production from the digester. The alarm state was set at 40 mM total VFA and 10 mM propionate concentration. The control algorithms could successfully maximize the biogas production without overloading the process. However, as the algorithm was based on a fixed biogas yield parameter and only used the biogas parameter for optimization, it could not distinguish between the decreases of biogas production from inhibition and from lower organic content in the substrate, which resulted in undesired decreasing of the control gas setpoint when the substrate was diluted. It was necessary to adjust the yield parameter in order to get this control approach to function properly, which is not suitable for the full-scale biogas plant where the organic content of waste streams can vary. An alternative approach could be a modified rule-based algorithm that includes VFA parameters to help distinguish between different process scenarios.
Scalable wavelength-selective crossconnect switch based on MEMS and planar waveguides (2005)

A 72/spl times/72 wavelength-selective crossconnect switch, that is scalable to 1296/spl times/1296 with current technology, is presented. Silica-on-silicon wavelength multiplexers with integrated monitoring taps and a MEMS micromirror array were assembled in a hybrid 3D beam steering crossconnect having 20 dB insertion loss, 100 GHz channel spacing and 30 GHz passbands.
Natural Frequencies and Critical Buckling Loads of Marine Risers (1988)

Natural frequencies, mode shapes and critical buckling loads of marine risers simply supported at both ends are given in closed form by using the WKB method. These solutions allow variable cross section, bending rigidity, tension and mass distribution along the riser length. Furthermore, a simple procedure to predict natural frequencies for other boundary conditions is described. Some special forms of these closed-form solutions are compared with existing solutions in the literature.
Functional analysis of the lysis genes of Staphylococcus aureus phage P68 in Escherichia coli (2005)

Double-stranded DNA phages of both Gram-positive and Gram-negative bacteria typically use a holin-endolysin system to achieve lysis of their host. In this study, the lysis genes of Staphylococcus aureus phage P68 were characterized. P68 gene lys16 was shown to encode a cell-wall-degrading enzyme, which causes cell lysis when externally added to clinical isolates of S. aureus. Another gene, hol15, was identified embedded in the -1 reading frame at the 3' end of lys16. The deduced Hol15 protein has three putative transmembrane domains, and thus resembles class I holins. An additional candidate holin gene, hol12, was found downstream of the endolysin gene lys16 based on two predicted transmembrane domains of the encoded protein, which is a typical trait of class II holins. The synthesis of either Hol12 or Hol15 resulted in growth retardation of Escherichia coli, and both hol15 and hol12 were able to complement a phage lambda Sam mutation. The hol15 gene has a dual start motif beginning with the codons Met1-Lys2-Met3.... Evidence is presented that the hol15 gene encodes a lysis inhibitor (anti-holin) and a lysis effector (actual holin). As depolarization of the membrane converted the anti-holin to a functional holin, these studies suggested that hol15 functions as a typical dual start motif class I holin. The unusual arrangement of the P68 lysis genes is discussed.
Factors and molecules that could impact cell differentiation in the embryo generated by nuclear transfer (2017)

Somatic cell nuclear transfer is a technique to create an embryo using an enucleated oocyte and a donor nucleus. Nucleus of somatic cells must be reprogrammed in order to participate in normal development within an enucleated egg. Reprogramming refers to the erasing and remodeling of cellular epigenetic marks to a lower differentiation state. Somatic nuclei must be reprogrammed by factors in the oocyte cytoplasm to a rather totipotent state since the reconstructed embryo must initiate embryo development from the one cell stage to term. In embryos reconstructed by nuclear transfer, the donor genetic material must respond to the cytoplasmic environment of the cytoplast and recapitulate this normal developmental process. Enucleation is critically important for cloning efficiency because may affect the ultrastructure of the remaining cytoplast, thus resulting in a decline or destruction of its cellular compartments. Nonetheless, the effects of in vitro culturing are yet to be fully understood. In vitro oocyte maturation can affect the abundance of specific transcripts and are likely to deplete the developmental competence. The epigenetic modifications established during cellular differentiation are a major factor determining this low efficiency as they act as epigenetic barriers restricting reprogramming of somatic nuclei. In this review we discuss some factors that could impact cell differentiation in embryo generated by nuclear transfer.
Learning New Facts From Knowledge Bases With Neural Tensor Networks and Semantic Word Vectors (2013)

Knowledge bases provide applications with the benefit of easily accessible, systematic relational knowledge but often suffer in practice from their incompleteness and lack of knowledge of new entities and relations. Much work has focused on building or extending them by finding patterns in large unannotated text corpora. In contrast, here we mainly aim to complete a knowledge base by predicting additional true relationships between entities, based on generalizations that can be discerned in the given knowledgebase. We introduce a neural tensor network (NTN) model which predicts new relationship entries that can be added to the database. This model can be improved by initializing entity representations with word vectors learned in an unsupervised fashion from text, and when doing this, existing relations can even be queried for entities that were not present in the database. Our model generalizes and outperforms existing models for this problem, and can classify unseen relationships in WordNet with an accuracy of 75.8%.
Mutagenicity and tumorigenicity of the four enantiopure bay-region 3,4-diol-1,2-epoxide isomers of dibenz[a,h]anthracene (2013)

Each enantiomer of the diastereomeric pair of bay-region dibenz[a,h]anthracene 3,4-diol-1,2-epoxides in which the benzylic 4-hydroxyl group and epoxide oxygen are either cis (isomer 1) or trans (isomer 2) were evaluated for mutagenic activity. In strains TA 98 and TA 100 of Salmonella typhimurium, the diol epoxide with (1S,2R,3S,4R) absolute configuration [(-)-diol epoxide-1] had the highest mutagenic activity. In Chinese hamster V-79 cells, the diol epoxide with (1R,2S,3S,4R) absolute configuration [(+)-diol epoxide-2] had the highest mutagenic activity. The (1R,2S,3R,4S) diol epoxide [(+)-diol epoxide-1] also had appreciable activity, whereas the other two bay-region diol epoxide enantiomers had very low activity. In tumor studies, the (1R,2S,3S,4R) enantiomer was the only diol epoxide isomer tested that had strong activity as a tumor initiator on mouse skin and in causing lung and liver tumors when injected into newborn mice. This stereoisomer was about one-third as active as the parent hydrocarbon, dibenz[a,h]anthracene as a tumor initiator on mouse skin; it was several-fold more active than dibenz[a,h]anthracene as a lung and liver carcinogen when injected into newborn mice. (-)-(3R,4R)-3β,4α-dihydroxy-3,4-dihydro-dibenz[a,h]anthracene [(-)-3,4-dihydrodiol] was slightly more active than dibenz[a,h]anthracene as a tumor initiator on mouse skin, whereas (+)-(3S,4S)-3α,4β-dihydroxy-3,4-dihydro-dibenz[a,h]anthracene [(+)-3,4-dihydrodiol] had only very weak activity. The present investigation and previous studies with the corresponding four possible enantiopure bay-region diol epoxide enantiomers/diastereomers of benzo[a]pyrene, benz[a]anthracene, chrysene, benzo[c]phenanthrene, dibenz[c,h]acridine, dibenz[a,h]acridine and dibenz[a,h]anthracene indicate that the bay-region diol epoxide enantiomer with [R,S,S,R] absolute stereochemistry has high tumorigenic activity on mouse skin and in newborn mice.
Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome (2009)

Membrane proteomics is challenging because the desirable strong detergents are incompatible with downstream analysis. Recently, we demonstrated efficient removal of SDS by the filter aided sample preparation method (FASP). Here we combine FASP with our previously described small-scale membrane enrichment protocol. Analysis of a single mouse hippocampus enables identification of more than 1000 membrane proteins in a single LC-MS/MS run without protein or peptide prefractionation. To extend proteome coverage, we developed a simple anion exchange fractionation method in a StageTip format. When separating peptides into six fractions, a duplicate analysis resulted in identification of 4206 proteins of which 64% were membrane proteins. This data set covers 83% of glutamate and GABA receptor subunits identified in hippocampus in the Allen Brain Atlas and adds further isoforms. The combined method provides a streamlined protocol for rapid and sensitive membrane proteome mapping. We also provide a generic protocol for combining FASP with StageTip-based ion exchange fractionation, which is generally applicable to proteome analysis.
Adenosine induces fibronectin expression in lung epithelial cells: implications for airway remodeling (2005)

Adenosine is an extracellular nucleoside that is elevated in tissues during hypoxia and ischemia reperfusion and has been implicated in asthma and other lung disorders. There, adenosine is considered an important modulator of physiological functions and inflammation, but its effects on matrix expression and turnover during tissue remodeling are unknown. We examined the effects of adenosine on lung epithelial cells with particular attention to the expression of fibronectin, a matrix glycoprotein highly expressed in injured tissues that has been implicated in wound healing. In A549 lung epithelial cells, we found that adenosine induced expression of fibronectin mRNA and protein in a dose- and time-dependent manner and found that the stimulatory effect of adenosine was inhibited by specific adenosine receptor antagonists. Adenosine stimulation was associated with increased levels of intracellular cAMP and with phosphorylation and DNA binding of the cAMP response element binding protein (CREB), known for its ability to stimulate fibronectin gene transcription. To confirm the latter, A549 cells were transfected with a DNA construct containing the human fibronectin promoter connected to a luciferase reporter gene. Adenosine stimulated transcription of the gene, and this effect was blocked by inhibitors of protein kinase activation. Finally, we tested primary lung fibroblasts and primary alveolar epithelial type II cells and found increased fibronectin expression in response to adenosine. Overall, our observations suggest that adenosine might modulate tissue remodeling by stimulating fibronectin expression in lung epithelial cells through induction of purinergic receptor-mediated signals that target CREB phosphorylation and stimulate fibronectin gene transcription.
All-optical token technique for distributed contention resolution in AWGR-based optical interconnects (2012)

This paper studies the networking performance of a 10Gb/s 64-port AWGR-based optical switch with distributed all-optical contention resolution based on saturation effect in R-SOAs. Significant reduction in latency compared to FBF architecture is observed.