gebhart/patrepeval huggingface dataset:
Metformin increases antitumor activity of MEK inhibitor binimetinib in 2D and 3D models of human metastatic melanoma cells (2018)

Melanoma is one of the most aggressive and treatment-resistant tumors that responsible for majority of skin-cancer related deaths. Here we propose a combination of MEK inhibitor binimetinib with metformin as a promising therapy against human melanoma cells in vitro, including BRAF -mutated A375, Mel Z, and Mel IL cells, and NRAS-mutated Mel MTP and Mel Me cells. Additionally, we obtained two close to clinical practice models of melanoma progression. The first one was vemurafenib-resistant Mel IL/R melanoma cells with acquired resistance to BRAF inhibition-targeted therapy, and the second one was tumor spheroids, which are 3D in vitro model of small-size solid tumors in vivo. The cytotoxicity of binimetinib and metformin was synergistic in both 2D and 3D melanoma culture and mediated through apoptotic pathway. The combination reduced the number of melanoma-formed colonies, inhibited cell invasion and migration, and led to G0/G1 cell cycle arrest through cyclin D/CDK4/CDK6 pathway. The mechanism of metformin and binimetinib synergy in melanoma cells was associated with increased activation of p-AMPKα and decreased p-ERK, but not with alterations in p-mTOR. In summary, the combination of metformin and binimetinib resulted in stronger anti-proliferative effects on melanoma cells compared to binimetinib alone, and therefore could be promising for clinical applications.
TORCH: a TOSCA-Based Orchestrator of Multi-Cloud Containerised Applications (2021)

Abstract The growth in the number and types of cloud-based services offered to IT customers is supported by the constant entry of new actors in the market and the consolidation of disruptive technologies such as AI, Big Data and Micro-services. From the customer’s perspective, in a market landscape where the cloud offer is highly diversified due to the presence of multiple competing service providers, picking the service that best accommodate their specific needs is a critical challenge. Once the choice is made, so called “cloud orchestration tools” (orchestrators) are required to take care of the customer application’s life-cycle. While big players offer their customers proprietary orchestrators, in the literature quite a number of open-source initiatives have launched multi-cloud orchestrators capable of transparently managing applications on top of the most representative cloud platforms. In this paper, we propose TORCH, a TOSCA-based framework for the deployment and orchestration of cloud applications, both classical and containerised, on multiple cloud providers. The framework assists the cloud customer in defining application requirements by using standard specification models. Unlike other multi-cloud orchestrators, adopts a strategy that separates the provisioning workflow from the actual invocation of proprietary cloud services API. The main benefit is the possibility to add support to any cloud platforms at a very low implementation cost. In the paper, we present a prototypal implementation of TORCH and showcase its interaction with two different container-based cluster platforms. Preliminary performance tests conducted on a small-scale test-bed confirm the potential of TORCH.
Regenerative Micro-Fuel Cells and Electrolyzers (1999)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;A novel reversible proton exchange membrane fuel cell system that is based upon micro-sized membrane and electrode assemblies is discussed. The resulting micro-fuel cell has a reduced size and mass due to an improved design of the bipolar plates and current collectors. Bipolar plates often contribute over 75% of the fuel cell stack mass and volume in traditional fuel cell and electrolyzer designs that results in power densities near 0.1 kW/kg and 0.1 kW/liter. The micro-sized membrane and electrodes allow us to minimize the size of the gas-channels that feed reactants to the electrodes. Physical Sciences Inc.’s (PSI) micro-design approach minimizes stack features resulting in power densities greater than 1 kW/liter and specific power densities greater than 1 kW/kg.&lt;/div&gt;&lt;/div&gt;
Temperature dependence of the photoluminescence of self-assembledInAs∕GaAsquantum dots in pulsed magnetic fields (2008)

We have studied the magnetic field $(&lt;50\phantom{\rule{0.3em}{0ex}}\mathrm{T})$ dependence of the photoluminescence (PL) of self-assembled $\mathrm{In}\mathrm{As}∕\mathrm{Ga}\mathrm{As}$ quantum dots as a function of temperature $(T)$. As the temperature is raised from 4.2 up to $80\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, thermal redistribution causes the PL to be increasingly dominated by dots with a lower PL energy. Magneto-PL demonstrates that these low-energy dots are larger in size only in the growth direction and not in the plane of the sample. At high temperatures $(T&gt;100\phantom{\rule{0.3em}{0ex}}\mathrm{K})$, a different physical phenomenon emerges: we see an anomalous decrease of the PL shift in magnetic field, which is attributed to field enhancement of the quantum dot barrier potential. This mechanism strongly favors excitons in small dots with a weak PL shift in magnetic field, hence laterally smaller dots increasingly dominate the PL at high temperatures and high fields.
Antigen receptor-mediated depletion of FOXP3 in induced regulatory T-lymphocytes via PTPN2 and FOXO1 (2015)

Regulatory T-cells induced via IL-2 and TGFβ in vitro (iTreg) suppress immune cells and are potential therapeutics during autoimmunity. However, several reports described their re-differentiation into pathogenic cells in vivo and loss of their key functional transcription factor (TF) FOXP3 after T-cell antigen receptor (TCR)-signalling in vitro. Here, we show that TCR-activation antagonizes two necessary TFs for foxp3 gene transcription, which are themselves regulated by phosphorylation. Although the tyrosine phosphatase PTPN2 is induced to restrain IL-2-mediated phosphorylation of the TF STAT5, expression of the TF FOXO1 is downregulated and miR-182, a suppressor of FOXO1 expression, is upregulated. TGFβ counteracts the FOXP3-depleting TCR-signal by reassuring FOXO1 expression and by re-licensing STAT5 phosphorylation. Overexpressed phosphorylation-independent active versions of FOXO1 and STAT5 or knockdown of PTPN2 restores FOXP3 expression despite TCR-signal and absence of TGFβ. This study suggests novel targets for stabilisation and less dangerous application of iTreg during devastating inflammation.
Data mining MR image features of select structures for lateralization of mesial temporal lobe epilepsy (2018)

The proposed tristructural MR imaging biomarker provides greater lateralization accuracy relative to single- and double-structural biomarkers and thus, may play a more effective role in the surgical decision-making process. Also, lateralization of the patients with insignificant atrophy of hippocampus by the proposed method supports the notion of associated structural changes involving the amygdala and thalamus.
Preparation Techniques of Small Sample Sizes for Sulphur and Indirect Total Glucosinolate Analysis in Brassica Seeds by X‐Ray Fluorescence Spectroscopy (1993)

Abstract Two new preparation techniques for Brassica seeds are introduced, which enable the determination of total sulphur concentrations and indirectly the total glucosinolate concentrations in small sample sizes and single seeds by means of X‐ray fluorescence spectroscopy. Small sample sizes, down to 250 mg, are milled in peppermill type grinders and prepared as thin layers in liquid cuvettes. Single seeds are embedded by means of a sulphur free glue based on acetylated glucose in wax tablets and cut into halves. Measurement and calibration for small sample sizes are in accordance with the rules for the original X‐RF method. In case of single seeds the area of the cut surface need to be estimated and the collected S‐Kα intensities corrected for the active fluorescent area of the standard reference materials.
Corners in soft solids behave as defects in crystals (2018)

All phases of matter, solid, liquid or gas, present some excess energy, compared to their bulk, at their interfaces with other materials. This excess of energy, known as the surface energy, is a fundamental property of matter and is involved in virtually all interface problems in science, from the shape of bubbles, crystals and biological cells to the delicate motion of some insects on water or the fluttering of red blood cells. Because of their high cohesive internal energies, the surface energies of solids differ fundamentally from those of fluids and depend on the solid deformations. This effect, known as the Shuttleworth effect, is well established for metals but is highly debated for amorphous materials such as glasses, elastomers or biological tissues with recent experimental results yielding strictly opposite conclusions with regards to its very existence. Using a combination of analytical results and numerical simulations, we show in this paper that those seemingly opposite results can be reconciled due to the existence of an analog of the Peach-Koehler force acting on the elastocapillary ridge and conclude that: i) there is no large Shuttleworth effect in soft elastomers and ii) the Neumann construction does not hold in elastowetting.
InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms (2016)

Phasing of single nucleotide (SNV), and structural variations into chromosome-wide haplotypes in humans has been challenging, and required either trio sequencing or restricting phasing to population-based haplotypes. Selvaraj et al demonstrated single individual SNV phasing is possible with proximity ligated (HiC) sequencing. Here, we demonstrate HiC can phase structural variants into phased scaffolds of SNVs. Since HiC data is noisy, and SV calling is challenging, we applied a range of supervised classification techniques, including Support Vector Machines and Random Forest, to phase deletions. Our approach was demonstrated on deletion calls and phasings on the NA12878 human genome. We used three NA12878 chromosomes and simulated chromosomes to train model parameters. The remaining NA12878 chromosomes withheld from training were used to evaluate phasing accuracy. Random Forest had the highest accuracy and correctly phased 86% of the deletions with allele-specific read evidence. Allele-specific read evidence was found for 76% of the deletions. HiC provides significant read evidence for accurately phasing 33% of the deletions. Also, eight of eight top ranked deletions phased by only HiC were validated using long range polymerase chain reaction and Sanger. Thus, deletions from a single individual can be accurately phased using a combination of shotgun and proximity ligation sequencing. InPhaDel software is available at: http://l337x911.github.io/inphadel/.
ChemInform Abstract: A Facile Synthesis of N‐Substituted Pyrroles. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Quantifying Spatially Heterogeneous Dynamics in Computer Simulations of\n Glassforming Liquids (1998)

We examine the phenomenon of dynamical heterogeneity in computer simulations\nof an equilibrium, glass-forming liquid. We describe several approaches to\nquantify the spatial correlation of single-particle motion, and show that\nspatial correlations of particle displacements become increasingly long-range\nas the temperature decreases toward the mode coupling critical temperature.\n
Performance of a Lotka-Volterra System for Representing Biofouling Processes (2014)

In order to assess the feasibility and performance of a minimal multiphysics model for representing the spatiotemporal evolution of biofouling process, we selected the coupled diffusive generalization of the Lotka-Volterra PDEs to govern the spatiotemporal evolution of population densities of predator-prey colonies in a computational domain. The implementation of the finite element solution of the system was performed and the associated numerical solution of the system was achieved. An analysis was performed that highlights certain choices of the control parameters of the model and their effect on the spatiotemporal behavior of the system. Potential extensions of the model are presented to incorporate an agent that inhibits antibiofouling and study its effect. An evaluation of the features of the model are concluding the paper.
Explaining sociotechnical change: an unstable equilibrium perspective (2022)

Within the domain of Information Systems, assumptions around sociotechnical change cohesively build on establishing a stable and balanced relationship between the social and technical structures. When these structures become too rigid, revolutionary moments that punctuate the status quo are required for the structures to accommodate to a new situation. Approaching sociotechnical change with “punctuation of equilibrium” is becoming increasingly ineffective. In line with rising instability and rapid digital development, we argue that new sociotechnical change approaches are needed. In this paper we investigate how individual knowledge workers respond to the increasingly complex challenges they face when orchestrating social and technical structures to support efficient and creative knowledge work. We suggest a new perspective that covers an unstable equilibrium emerging from the interplay between individuals and their usage of “the collection of rigid and flexible workplace technologies”. Our study is based on data from interviews made with 40 knowledge professionals over a period of three years, inquiring into individual experiences with sociotechnical change. Our study reveals contradictory patterns of both technological-individualisation and -socialisation. A universal generative mechanism emerges when these patterns complement each other and generates continuous change that seems to diminish inertia from rigid structures while also intensifying agile responses.
Lymphoid V(D)J recombination. Functional analysis of the spacer sequence within the recombination signal. (1993)

The V(D)J recombination reaction is directed by a pair of signal sequences, each consisting of a palindromic heptamer, an A/T-rich nonamer, and an intervening spacer sequence of 12 or 23 base pairs. The spacer sequence previously has not been analyzed for a functional role. In this study, numerous simultaneous sequence changes have been made in the spacer of each signal to test their functional importance. All of the AT base pairs in each signal were changed to GC base pairs. This particular change is of interest because it markedly increases the energy that would be required to melt out the two strands of each signal to permit the intersignal base pairing proposed in a commonly invoked model for signal-signal interaction in V(D)J recombination. We find that changing 6 to 12 AT base pairs in the 12-signal to GC does not affect V(D)J recombination, nor does changing 11 of 23 AT base pairs in the 23-signal. Substrates with all-GC spacer sequences in both the 12- and the 23-signal also recombine at efficiencies that are not significantly reduced. These studies demonstrate that the sequences at these particular positions are not recognized by the recombinase. In addition, the data do not support models invoking signal-signal base pairing.
Memory Reduction using a Ring Abstraction over GPU RDMA for Distributed Quantum Monte Carlo Solver (2021)

Scientific applications that run on leadership computing facilities often face the challenge of being unable to fit leading science cases onto accelerator devices due to memory constraints (memory-bound applications). In this work, the authors studied one such US Department of Energy mission-critical condensed matter physics application, Dynamical Cluster Approximation (DCA++), and this paper discusses how device memory-bound challenges were successfully reduced by proposing an effective "all-to-all" communication method -- a ring communication algorithm. This implementation takes advantage of acceleration on GPUs and remote direct memory access (RDMA) for fast data exchange between GPUs. Additionally, the ring algorithm was optimized with sub-ring communicators and multi-threaded support to further reduce communication overhead and expose more concurrency, respectively. The computation and communication were also analyzed by using the Autonomic Performance Environment for Exascale (APEX) profiling tool, and this paper further discusses the performance trade-off for the ring algorithm implementation. The memory analysis on the ring algorithm shows that the allocation size for the authors' most memory-intensive data structure per GPU is now reduced to 1/p of the original size, where p is the number of GPUs in the ring communicator. The communication analysis suggests that the distributed Quantum Monte Carlo execution time grows linearly as sub-ring size increases, and the cost of messages passing through the network interface connector could be a limiting factor.
Modelling and identification of coupled markov chain model with application (1996)

A parametrized Markov chain model is developed to model the action of a biological ion channel. The proposed model takes the form of a set of identical binary chains which are dependent according to a coupling parameter. The outputs of these chains combine additively to give a record of ion current buried in large amounts of noise versus time. When varied, the coupling parameter realizes a range of behaviours from tight coupling to complete independence. Other model parameters describe the intrinsic characteristics of the binary chains as well as their behaviour when fully coupled. An identification procedure for the model parameters is developed based on hidden Markov modelling ideas but incorporating a gradient descent estimation algorithm. In this way we cope with the non-linear form of the dependence of the model on the parameters. The model and identification methods are tested and verified on simulated data and real biological data
Roadmap: Numerical-Experimental Investigation and Optimization of 3D-Printed Parts Using Response Surface Methodology (2022)

Several process variables can be taken into account to optimize the fused filament fabrication (FFF) process, a promising additive manufacturing technique. To take into account the most important variables, a numerical-experimental roadmap toward the optimization of the FFF process, by taking into account some physico-chemical and mechanical characteristics, has been proposed to implement the findings through the thermal behavior of materials. A response surface methodology (RSM) was used to consider the effect of liquefier temperature, platform temperature, and print speed. RSM gave a confidence domain with a high degree of crystallinity, Young's modulus, maximum tensile stress, and elongation at break. Applying the corresponding data from the extracted zone of optimization to the previously developed code showed that the interaction of parameters plays a vital role in the rheological characteristics, such as temperature profile of filaments during deposition. Favorable adhesion could be achieved through the deposited layers in the FFF process. The obtained findings nurture motivations for working on the challenges and bring us one step closer to the optimization objectives in the FFF process to solve the industrial challenges.
Solid-Phase Synthesis and Crystallization of Monellin, an Intensely Sweet Protein (1990)

Monellin, a sweet protein, consists of two noncovalently associated polypeptide chains, the A chain of 44 amino acid residues and the B chain of 50 residues. Two different primary structures have been reported for each of the A and B chains. The A and B chains corresponding to one of the reported monellin structures were synthesized by the stepwise solid-phase method using the Fmoc strategy in overall yields of 14.1% and 5.6%, respectively. The characterization of the synthetic peptides by HPLC, FAB-MS, amino acid analysis and sequencing fully supported the expected structures. The individual synthetic A and B chains were not sweet. Combination of the two chains, and subsequent HPLC purification gave monellin in a yield of 53.9%. The synthetic monellin had a distinct, lingering sweet taste (4000 times sweeter than sucrose) and was crystallized by a vapor diffusion method. The synthetic product was identical to natural monellin by HPLC, but not by tryptic mapping. These results indicate that the reported structure for monellin differs slightly from that of natural monellin.
Synaptic localization of the glutamate receptor subunit GluR2 in the rat nucleus tractus solitarii (2003)

The GluR2 subunit controls several key features of the alpha amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA)-type glutamate receptor including calcium permeability, rectification and gating. In the present study, electrophysiological recordings and immunocytochemistry were used to document the synaptic localization of GluR2 in the rat nucleus tractus solitarii (NTS). Synaptic responses recorded in NTS neurons exhibited linear current-voltage relationships suggestive of GluR2-containing AMPA receptor responses. Furthermore, after antigen retrieval GluR2 immunolabelling in the NTS mainly consisted of small puncta. Double-labelling experiments showed that these GluR2 puncta were apposed to glutamatergic synaptic terminals identified by type II vesicular glutamate transporter immunoreactivity. These results indicate that NTS glutamatergic synapses are endowed with AMPA receptors which contain the GluR2 subunit and are therefore likely to be both calcium-impermeable and slowly desensitizing.