gebhart/patrepeval huggingface dataset:
Modeling Elastic Walls in Lattice Boltzmann Simulations of Arterial Blood Flow (2013)

Abstract An essential part in the simulation of blood flow in arteries is the incorporation of the arterial elasticity by modeling the vessel wall and its interaction with the fluid inside the vessel. We suggest a simple approach for modeling elastic walls in lattice Boltzmann simulations of arterial blood flow that produces physically correct results. We have developed a simulation software that implements this approach combined with the lattice Boltzmann method and conducted numerical experiments on a generic vessel model. Preliminary results presented in this work are promising and encourage using this method for further simulations with real physiological parameters in medical applications.
Independent effects of Src kinase and podoplanin on anchorage independent cell growth and migration (2022)

The Src tyrosine kinase is a strong tumor promotor. Over a century of research has elucidated fundamental mechanisms that drive its oncogenic potential. Src phosphorylates effector proteins to promote hallmarks of tumor progression. For example, Src associates with the Cas focal adhesion adaptor protein to promote anchorage independent cell growth. In addition, Src phosphorylates Cas to induce Pdpn expression to promote cell migration. Pdpn is a transmembrane receptor that can independently increase cell migration in the absence of oncogenic Src kinase activity. However, to our knowledge, effects of Src kinase activity on anchorage independent cell growth and migration have not been examined in the absence of Pdpn expression. Here, we analyzed the effects of an inducible Src kinase construct in knockout cells with and without exogenous Pdpn expression on cell morphology migration and anchorage independent growth. We report that Src promoted anchorage independent cell growth in the absence of Pdpn expression. In contrast, Src was not able to promote cell migration in the absence of Pdpn expression. In addition, continued Src kinase activity was required for cells to assume a transformed morphology since cells reverted to a nontransformed morphology upon cessation of Src kinase activity. We also used phosphoproteomic analysis to identify 28 proteins that are phosphorylated in Src transformed cells in a Pdpn dependent manner. Taken together, these data indicate that Src utilizes Pdpn to promote transformed cell growth and motility in complementary, but parallel, as opposed to serial, pathways.
Link Stability based Handoff for QoS Provisioning In 4G Network (2014)

Future generation 4G network is considered to bring most seamless data and internet access across different devices and networks. 3G network architecture incorporates several mechanism for continues connectivity. 4G networks abstracts the communication as any form of digital data including but not limited to voice and video calls, media streaming, content sharing, cloud computing and distributed services. 4G network offers a seamless collaboration between core 3G data network, local WiMax networks, GSM networks and so on. Every core network follows it's own architecture and protocols. Therefore switching from one network to another requires techniques that ensures optimum performance and quick switching. However as every switching is performed by set of command exchange between current, bridging and new network, ensuring least frequent switching is as important an issue as determining the best network itself. Once a user opts for a specific network, data exchange within the network and through any other core networks needs QoS provisioning. Most existing protocols focuses on choosing the best network at specific time instance which never ensures either longevity of the connection or quality of it. A Link Quality is an estimation of the nature of all inbound and outbound links of a node that takes into account of power, bandwidth, jitter and latency. Therefore in this work we propose a Link Quality based routing and handoff for 4G network. Considering link quality in routing decisions rather than hops ensures that the obtained routes are optimum in terms of packet delivery and lifetime of the path.
Design and fabrication of a high performance resonant MEMS temperature sensor (2016)

This paper presents a high performance MEMS temperature sensor comprised of a double-ended-tuning-fork (DETF) resonator and strain-amplifying beam structure. The temperature detection is based on the 'thermal strain induced frequency variations' of the DETF resonator. The major source of thermal strain leading to the frequency shifts is the difference in thermal expansion coefficients of the substrate and the device layers of the fabricated structures. By selecting the substrate as glass and the device layers as single crystal silicon, i.e. materials with different thermal expansion coefficients, the tines of the resonators are exposed to axial load with the changing temperature, which causes a change in the resonance frequency of the resonators. This resonance frequency shift can be related with the changing temperature by taking the thermal strain relations into consideration, which enables utilization of the resonator as a highly sensitive temperature sensor. The resonators used in this study have been fabricated by utilizing the advanced MEMS process that incorporates the simple silicon-on-glass process with the wafer level vacuum packaging Torunbalci et al (2015 J. Microelectromech. Syst. 24 556-64). The fabricated resonators have been tested in a temperature-controlled oven between -20 degrees C and 60 degrees C, and the results of two distinct designs are compared to be able to observe the effectiveness of the strain amplifying beam. Measurement results show that the design with the strain amplifying beam increases the temperature coefficient of frequency of the resonators by 33 times when compared to the one-end free DETF resonators. Minimum detectable temperature variations observed by the resonators used in this study is 0.0011 degrees C. This kind of very high resolution temperature sensing can be achieved by integrating this MEMS temperature sensor with any type of physical MEMS sensor where its fabrication process includes different materials for the substrate and sensor structures.
ARE MOLECULAR MARKERS STRENGTHENING PLANT VARIETY REGISTRATION AND PROTECTION? (2001)

In vegetatively propagated ornamentals, new varieties can be obtained from i.) conventional breeding through crossing and selection or ii.) spontaneous or induced variant types of existing (initial) varieties. Indeed, variant types enlarge the assortment to be produced without the need to alter production systems. However, they inherit the breeding effort needed to create a completely new and profitable variety. Under the rules defined by the UPOV convention of 1991 this new variant type should be considered as an “Essentially Derived Variety” (EDV) from the initial variety (IV). Therefore, the breeder of the initial variety might want to claim at least part of the profits acquired by the breeder of the EDV under the form of a royalty. To detect either EDV or fraud, criteria based on plant morphology are insufficient or even not applicable. Here, some case studies are presented to illustrate the possibilities and the limitations of the use of molecular fingerprints in disputes on fraud and essential derivation of ornamental plants. These examples are put in contrast with genetic analysis work that has been performed for the study of phylogenetic relationships, characterization of hybrids and breeders’ gene pools. From this framework, it is discussed what benefits molecular markers could provide to plant variety registration and protection of Plant Breeders’ Rights.
Signal delay in coupled, distributed RC lines in the presence of temporal proximity (2002)

With improvements in technology, accurate delay modeling of interconnects is becoming increasingly important. Due to decreasing feature sizes, the spacing between the signal lines is also decreasing. Consequently, the switching activities on the neighboring lines can have a significant impact on the delay of the line of interest, and can no longer be ignored. Accurate modeling of this phenomenon, which we call the proximity effect, is the subject of this paper. This is similar to the state-dependency of logic gate delays, where signal delay can be affected by the switching activities on the side inputs of a gate. We describe an efficient and accurate delay computation method using precomputed interconnect moments that treats the coupled lines as uniform, distributed RC lines and does not make any lumped approximations. This allows the proposed delay model to be used in a timing analysis tool operating over both gate and interconnect domains while accounting for state-dependency.
Diversity and distribution of coral-associated bacteria (2002)

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 243:1-10 (2002) - doi:10.3354/meps243001 Diversity and distribution of coral-associated bacteria Forest Rohwer1,*, Victor Seguritan2, Farooq Azam3, Nancy Knowlton3,4 1Department of Biology, LS317, and 2Department of Computational Sciences, San Diego State University, San Diego, California 92182-4614, USA 3Marine Biology Research Division, University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California 92093-0202, USA 4Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama *Email: forest@sunstroke.sdsu.edu ABSTRACT: Coral reefs are the most biodiverse of all marine ecosystems; however, very little is known about prokaryotic diversity in these systems. To address this issue, we sequenced over 1000 bacterial 16S rDNAs from 3 massive coral species (Montastraea franksi, Diploria strigosa, and Porites astreoides) in Panama and Bermuda. Analysis of only 14 coral samples yielded 430 distinct bacterial ribotypes. Statistical analyses suggest that additional sequencing would have resulted in a total of 6000 bacterial ribotypes. Half of the sequences shared <93% identity to previously published 16S sequences, and therefore probably represent novel bacterial genera and species; this degree of novelty was substantially higher than that observed for other marine samples. Samples from the Panama corals were more diverse than those from Bermuda, paralleling diversity gradients seen in metazoans. The coral-bacteria associations were non-random. Different coral species had distinct bacterial communities, even when physically adjacent, while bacterial communities from the same coral species separated by time (~1 yr) or space (3000 km) were similar. Analysis of the branching coral Porites furcata showed that bacterial ribotypes can also be structured spatially within colonies. Therefore, corals and reefs represent landscapes of diverse, ecologically structured prokaryotic communities. KEY WORDS: Coral · Bacteria · 16S rDNA · Biodiversity Full text in pdf format NextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 243. Online publication date: November 13, 2002 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2002 Inter-Research.
Reconstructing complex surfaces from multiple stereo views (2002)

We present a framework for 3D surface reconstruction that can be used to model fully 3 dimensional scenes from an arbitrary number of stereo views. Taken from vastly different viewpoints. This is a key step toward producing 3D world descriptions of complex scenes using stereo and is a very challenging problem: real world scenes tend to contain many 3D objects, they do not usually conform to the 2-1/2D assumption made by traditional algorithms, and one cannot take it for granted that the computed 3D points can easily be clustered into separate groups. By combining a particle based representation, robust fitting, and optimization of an image based objective function, we have been able to reconstruct surfaces without any a priori knowledge of their topology and in spite of the noisiness of the stereo data. Our current implementation goes through three steps-initializing a set of particles from the input 3D data, optimizing their location, and finally grouping them into global surfaces. Using several complex scenes containing multiple objects, we demonstrate its competence and ability to merge information and thus to go beyond what can be done with conventional stereo alone.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of iNOS and NF-κB gene silencing on β-cell survival and function (2007)

The gene silencing approach presented here is capable of attenuating the effects of inflammatory cytokines, such as iNOS expression and NO production and it will help to identify new target genes to improve islet transplantation.
Massively parallel identification of causal variants underlying gene expression differences in a yeast cross (2020)

Abstract Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis -regulatory consequences of 5,832 natural DNA variants in the promoters of 2,503 genes in the yeast Saccharomyces cerevisiae . We identified 451 causal variants, which underlie genetic loci known to affect gene expression. Several promoters harbored multiple causal variants. In five promoters, pairs of variants showed non-additive, epistatic interactions. Causal variants were enriched at conserved nucleotides, tended to have low derived allele frequency, and were depleted from promoters of essential genes, which is consistent with the action of negative selection. Causal variants were also enriched for alterations in transcription factor binding sites. Models integrating these features provided modest, but statistically significant, ability to predict causal variants. This work revealed a complex molecular basis for cis -acting regulatory variation.
Glucoraphanin Triggers Rapid Antidepressant Responses in a Rat Model of Beta Amyloid-Induced Depressive-like Behaviour (2022)

Glucoraphanin (GRA) is a natural compound that has shown beneficial effects in chronic diseases and in central nervous system disorders. Moreover, GRA displayed antidepressant activity in preclinical models. We have previously demonstrated that a single intracerebroventricular administration of soluble amyloid-beta 1-42 (sAβ 1-42) in rat evokes a depressive-like phenotype by increasing immobility frequency in the forced swimming test (FST). The aim of this work was to investigate the effect of GRA in naïve and in sAβ-1-42-treated rats by using the FST. Behavioural analyses were accompanied by neurochemical and biochemical measurements in the prefrontal cortex (PFC), such as serotonin (5-HT), noradrenaline (NA), kynurenine (KYN), tryptophan (TRP), reactive oxygen species (ROS) and the transcription nuclear factor kappa B (NF-kB) levels. We reported that GRA administration in naïve rats at the dose of 50 mg/kg reduced the immobility frequency in the FST and increased 5-HT and NA levels in the PFC compared to controls. At the same dose, GRA reverted depressive-like effects of sAβ 1-42 administration, restored the 5-HT levels and reduced NF-kB, KYN and ROS levels in PFC. In conclusion, GRA rapidly reverting depressive-like behaviour, together with biochemical and neurochemical alterations, might represent a safe and natural candidate for the treatment of depression.
Three-component Castagnoli-Cushman reaction with ammonium acetate delivers 2-unsubstituted isoquinol-1-ones as potent inhibitors of poly(ADP-ribose) polymerase (PARP) (2021)

An earlier described three-component variant of the Castagnoli-Cushman reaction employing homophthalic anhydrides, carbonyl compound and ammonium acetate was applied towards the preparation of 1-oxo-3,4-dihydroisoquinoline-4-carboxamides with variable substituent in position 3. These compounds displayed inhibitory activity towards poly(ADP-ribose) polymerase (PARP), a clinically validated cancer target. The most potent compound (PARP1/2 IC<sub>50</sub> = 22/4.0 nM) displayed the highest selectivity towards PARP2 in the series (selectivity index = 5.5), more advantageous ADME prameters compared to the clinically used PARP inhibitor Olaparib.
Designing human-robot interaction via physical world objects (2006)

This paper proposes a new communication model based on physical world objects. In usual human-robot interaction a human looks on the robot's behaviors without responding to them and seldom immerses him/herself in the interaction. The communication model achieves human's immersion in interaction with two types of behaviors. The first draws human's attention to a physical world object or a physical world state. The second stimulates a human's feeling under the attention. The novel idea of the model is to employ the actual physical objects to mediate the human-robot interaction. In particular, since the second behavior relates directly to a sort of human's sensory perception, it is easy for a human to become aware of the referent of the robot's behavior. As a result of the two behaviors, he/she begins to infer robot's intentions and immerses him/herself in the interaction.
Uralkali lifts demand forecast on improving potash outlook (2017)

Russian potash producer Uralkali has revised its 2017 global consumption forecast amid higher sales volume and improving demand outlook.

Increased sales volume lifted Russian potash producer Uralkali OAO's earning in H1, and the improving demand outlook prompted the company to revise its 2017 consumption forecast.

Driven by growth in sales, Uralkali's net revenue rose 23% year-on-year (y-o-y) to $1.095m in the first half of the year, but the company's net profit was halved partly due to the devaluation of the Russian rouble against the US dollar.

Meanwhile, improving global fertiliser demand has also supported higher potash production at Uralkali.

The market environment began to recover gradually. As a consequence, the company has managed to increase the production and sales volume of the main product, said CEO Dmitry Osipov.
Endovascular Clot Retrieval Therapy (2015)

Endovascular acute ischemic stroke therapy is now proven by randomized controlled trials to produce large, clinically meaningful benefits. In response, stroke systems of care must change to increase timely and equitable access to this therapy. In this review, we provide a North American perspective on implications for stroke systems, focusing on the United States and Canada, accompanied by initial recommendations for changes. Most urgently, every community must create access to a hospital that can safely and quickly provide intravenous tissue-type plasminogen activator and immediately transfer appropriate patients onward to a more capable center as required. Safe and effective therapy in the community setting will be ensured by certification programs, performance measurement, and data entry into registries.
Linear response theory for a pair of coupled one-dimensional condensates of interacting atoms (2007)

We use the quantum sine-Gordon model to describe the low-energy dynamics of a pair of coupled one-dimensional condensates of interacting atoms. We show that the nontrivial excitation spectrum of the quantum sine-Gordon model, which includes soliton and breather excitations, can be observed in experiments with time-dependent modulation of the tunneling amplitude, potential difference between condensates, or phase of tunneling amplitude. We use the form-factor approach to compute structure factors corresponding to all three types of perturbations.
Influence of Apigenin on <i>gtf</i> Gene Expression in <i>Streptococcus mutans</i> UA159 (2006)

Apigenin, a potent inhibitor of glucosyltransferase activity, affects the accumulation of Streptococcus mutans biofilms in vitro by reducing the formation of insoluble glucans and enhancing the soluble glucan content of the polysaccharide matrix. In the present study, we investigated the influence of apigenin on gtfB, gtfC, and gtfD expression in S. mutans UA159. Apigenin (0.1 mM) significantly decreased the expression of gtfB and gtfC mRNA (P < 0.05); in contrast, it increased the expression of gtfD in S. mutans growing in the planktonic state. The protein levels of GTF B, GTF C, and GTF D in culture supernatants were also affected; less GTF B and C were detected, whereas the level of GTF D was significantly elevated (P < 0.05). A similar profile of gtf expression was obtained with biofilms, although an elevated concentration (1 mM) of apigenin was required to elicit the effects. The influence of apigenin on gtf gene expression was independent of any effect on GTF activity, did not involve inhibition of growth or effects on pH, and was not affected by addition of sucrose. The data show that apigenin modulates the genetic expression of virulence factors in S. mutans.
Defining and Treating the Spectrum of Intermediate Risk Nonmuscle Invasive Bladder Cancer (2014)

Intermediate risk disease is a heterogeneous category, and there is a paucity of independent studies comparing therapies and outcomes in subgroups of intermediate risk patients. The IBCG has proposed a management algorithm that considers tumor characteristics, timing and frequency of recurrence, and previous treatment. Subgroup analyses of intermediate risk subjects in pivotal EORTC trials and meta-analyses will be important to validate the proposed algorithm and support clear evidence-based recommendations for subgroups of intermediate risk patients.