gebhart/patrepeval huggingface dataset:
Premixed-Gas Flame Propagation in Hele-Shaw Cells (1999)

It is well known that buoyancy and thermal expansion affect the propagation ra and shapes of premixed gas flames. The understanding of such effects is complicated by the large density ratio between the reactants and products, which induces a baroclinic production of vorticity due to misalignment of density and pressure gradients at the front, which in turn leads to a complicated multi-dimensional flame/flow interaction. The Hele-Shaw cell, i.e., the region between closely-spaced flat parallel plates, is probably the simplest system in which multi-dimensional convection is presents consequently, the behavior of fluids in this system has been studied extensively (Homsy, 1987). Probably the most important characteristic of Hele-Shaw flows is that when the Reynolds number based on gap width is sufficiently small, the Navier-Stokes equations averaged over the gap reduce to a linear relation, namely a Laplace equation for pressure (Darcy's law). In this work, flame propagation in Hele-Shaw cells is studied to obtain a better understanding of buoyancy and thermal expansion effects on premixed flames. This work is also relevant to the study of unburned hydrocarbon emissions produced by internal combustion engines since these emissions are largely a result of the partial burning or complete flame quenching in the narrow, annular gap called the crevice volume between the piston and cylinder walls (Heywood, 1988). A better understanding of how flames propagate in these volumes through experiments using Hele-Shaw cells could lead to identification of means to reduce these emissions.
Combined Processing of Micro Cutters Using a Beam of Fast Argon Atoms in Plasma (2021)

We present a new method for coating deposition on micro cutters without an increase in their cutting edges radii caused by the deposition. For this purpose, the cutting edges are sharpened before the coating deposition with a concentrated beam of fast argon atoms. The sharpening decreases the initial radius and, hence, limits its value after the coating deposition. The concentrated beam of fast argon atoms is generated using an immersed in the gas discharge plasma concave grid under a negative high voltage. Ions accelerated from the plasma by the grid pass through the grid holes and are concentrated in the focal point of the grid. As a result of the charge exchange in the space charge sheaths of the grid, they are transformed into fast atoms. A uniform sputtering by the fast atoms of the micro-cutter surface reduces the radius of its cutting edge.
Modelagem e análise de sistemas de transporte de íons em membranas celulares usando verificação de modelos (2011)

Recentemente ha um interesse crescente na aplicacao da Verificacao Probabilistica de Modelos (PMC) na especificacao formal e analise de sistemas biologicos. PMC e uma tecnica que permite uma exploracao exaustiva do conjunto de estados de um sistema estocastico e pode fornecer visoes valiosas do seu comportamento que sao mais dificeis de se obter usando somente abordagens tradicionais de analise de sistemas, como as simulacoes estocastica e deterministica. Neste trabalho, propoe-se o uso de PMC para modelar e analisar sistemas em membranas celulares responsaveis pelo transporte de ions e cruciais para a vida das celulas. Uma especificacao formal e quantitativa da bomba de sodio e potassio (Na,K-ATPase) e inicialmente apresentada. Essa bomba e um importante sistema de transporte de ions presente em todas celulas animais e responsavel por manter as concentracoes dos ions de sodio e potassio dentro da celula, respectivamente, alta e baixa. O trabalho descreve como modelar o mecanismo da bomba usando PMC, considerando diferentes tecnicas de modelagem com o objetivo de lidar com o problema da explosao de estados, inerente da tecnica de verificacao de modelos, independente do contexto. Importantes propriedades relacionadas a reversibilidade da bomba sao verificadas usando PMC. Adicionalmente, o comportamento da bomba e investigado em termos de tendencias de reacoes que computam se existe uma probabilidade superior de certas reacoes ocorrerem. Essas tendencias permitem identificar os gargalos que levam ao lento funcionamento ou mesmo a interrupcao da bomba com o passar do tempo.O trabalho tambem introduz uma abordagem para detectar comportamento periodico com ruidos em sistemas estocasticos usando uma tecnica de verificacao de modelos estatistica. A abordagem proposta e aplicada para um sistema de oscilacao intracelular de calcio, comumentemente encontrado em um grande numero de tipos celulares em resposta a estimulos de componentes quimicos extracelulares. Finalmente, uma metodologia para lidar com a coexistencia de especies com grandes diferencas em suas concentracoes e tambem introduzida. Os resultados sao ainda preliminares, mas indicam os ganhos em escalabilidade de recursos de memoria com a abordagem proposta.
Novel therapeutic approaches in primary hyperoxaluria (2018)

<b>Introduction</b>: Currently, three types of primary hyperoxaluria (PH I-III) are known, all based on different gene-mutations affecting the glyoxylate metabolism in the liver. Disease hallmark is an increased endogenous oxalate production and thus massively elevated urinary excretion of oxalate and other type-specific metabolites. Hyperoxaluria induces the formation of calcium-oxalate kidney stones and/or nephrocalcinosis. In addition to that, a chronic inflammasome activation by hyperoxaluria per se, often leads to an early deterioration of kidney function, regularly resulting in end-stage renal disease (ESRD) at least in patients with type I PH. Except for vitamin B6 treatment in PH I, therapeutic regimen nowadays consists only of supportive measures, like significantly increased fluid intake and medication increasing the urinary solubility like alkaline citrate. <b>Areas covered</b>: Disease burden can be severe, and both clinicians and scientist are eager in finding new therapeutic approaches. The currently ongoing clinical studies and promising research in this field are reported in this paper. To present a complete overview, we searched electronic databases, like Clinical trial gov, National Center for Biotechnology Information PubMed, congress reports, press releases and personal information acquired at congresses and conventions. Searches were conducted using the following medical headings: (primary) hyperoxaluria, PH, therapy, treatment and research. <b>Expert opinion</b>: There is light on the horizon that new treatment options will be available in due time, as there are several promising therapeutic agents currently under investigation, some being at the first levels of drug development, but some already in ongoing clinical trials (phase I-III).
Spontaneously Regressed Probable Retinoblastoma (1969)

A 5-year-old physician's daughter accidently discovered that the vision in her right eye was reduced over the left. The father did an ophthalmoscopic examination and swiftly brought her to us for consultation. There were no complicating factors during maternal pregnancy; the child was a full-term infant with no obvious serious illnesses occurring during childhood. Presently she is in excellent general health. The visual acuity was OD 20/25, OS 20/20. All the pathologic findings were limited to her right fundus (Figure). The vitreous was completely clear. The optic nerve was of good color and sharply delineated. The foveal reflex was normally developed. About one-half disc diameter above the fovea and above the optic nerve was a large lesion measuring about 4 mm in diameter. In the center was a honeycombed mass with ``cottage cheese'' texture. The lesion was surrounded by some translucent, grayish tissue remnants. Through these and at the edge
Bupivacaine‐induced cellular entry of QX‐314 and its contribution to differential nerve block (2013)

Bupivacaine, combined with QX-314, produced a long-lasting sensory nerve block. This did not require QX-314 permeation through TRPA1, although bupivacaine activated these channels. Regardless of entry pathway, the greatly extended duration of block produced by QX-314 and bupivacaine may be clinically useful.
Taxol Induces Brk-dependent Prosurvival Phenotypes in TNBC Cells through an AhR/GR/HIF–driven Signaling Axis (2018)

The metastatic cascade is a complex process that requires cancer cells to survive despite conditions of high physiologic stress. Previously, cooperation between the glucocorticoid receptor (GR) and hypoxia-inducible factors (HIF) was reported as a point of convergence for host and cellular stress signaling. These studies indicated p38 MAPK-dependent phosphorylation of GR on Ser134 and subsequent p-GR/HIF-dependent induction of breast tumor kinase (PTK6/Brk), as a mediator of aggressive cancer phenotypes. Herein, p-Ser134 GR was quantified in human primary breast tumors (<i>n</i> = 281) and the levels of p-GR were increased in triple-negative breast cancer (TNBC) relative to luminal breast cancer. Brk was robustly induced following exposure of TNBC model systems to chemotherapeutic agents (Taxol or 5-fluorouracil) and growth in suspension [ultra-low attachment (ULA)]. Notably, both Taxol and ULA resulted in upregulation of the Aryl hydrocarbon receptor (AhR), a known mediator of cancer prosurvival phenotypes. Mechanistically, AhR and GR copurified and following chemotherapy and ULA, these factors assembled at the Brk promoter and induced Brk expression in an HIF-dependent manner. Furthermore, Brk expression was upregulated in Taxol-resistant breast cancer (MCF-7) models. Ultimately, Brk was critical for TNBC cell proliferation and survival during Taxol treatment and in the context of ULA as well as for basal cancer cell migration, acquired biological phenotypes that enable cancer cells to successfully complete the metastatic cascade. These studies nominate AhR as a p-GR binding partner and reveal ways to target epigenetic events such as adaptive and stress-induced acquisition of cancer skill sets required for metastatic cancer spread.<b>Implication:</b> Breast cancer cells enlist intracellular stress response pathways that evade chemotherapy by increasing cancer cell survival and promoting migratory phenotypes. <i>Mol Cancer Res; 16(11); 1761-72. ©2018 AACR</i>.
Sickle Cell Adhesion to Laminin: Potential Role for the 5 Chain (1998)

Sickle red blood cell (RBC) adhesion to the endothelium and to exposed, underlying subendothelial proteins is believed to contribute to vascular occlusion in sickle cell disease. Laminin, a major component of the subendothelium, supports significant adhesion of sickle, but not normal RBCs. The purpose of this study was to define the adhesive region for sickle RBCs within a human laminin preparation using a flow adhesion assay designed to mimic physiologic flow through postcapillary venules. Because sickle RBCs did not adhere to the common laminin contaminants entactin or collagen type IV, neither of these proteins are likely to contribute to the observed adhesion to laminin. Known adhesive regions of laminin neither supported nor inhibited sickle RBC adhesion to laminin, suggesting a mechanism of adhesion previously uncharacterized in other laminin adhesion studies. Moreover, sickle RBCs did not adhere to mouse EHS laminin or to human laminin-2 (merosin), eliminating the alpha1, alpha2, beta1, and gamma1 chains as mediators of sickle cell adhesion. The monoclonal antibody 4C7, which binds at or near the G-domain of the laminin alpha5 chain, significantly inhibited sickle RBC adhesion. These results suggest that an adhesive region for sickle RBCs is contained within the laminin alpha5 chain.
Cryogenic transmission electron microscopy study: preparation of vesicular dispersions by quenching microemulsions (2016)

We previously showed that long-lived nanoemulsions, seeming initially vesicular, might be prepared simply by diluting and cooling (quenching) warm microemulsions with n-hexadecane with precooled water. In this paper, we confirm that these systems are vesicular dispersions when fresh, and they can be made with similar structures and compositional dependence using alkanes with chain lengths ranging from octane to hexadecane. The nanostructures of fresh nanoemulsions are imaged with cryogenic transmission electron microscopy (cryo-TEM). We confirm that water-continuous microemulsions give simple dispersions of vesicles (sometimes unilamellar), typically less than 100 nm in diameter; these systems can avoid separation for over 2 months. Selected samples were also prepared using halogenated alkanes to create additional contrast in the cryo-TEM, allowing us to confirm that the oil is located in the observed vesicular structures.
Two rheological methods to approach the gastric behavior of infant formulas (2015)

It is well known that one key parameter for food digestion is the rate of emptying of the stomach. However, during its transfer through the stomach, due to the physico-chemical conditions of this compartment (pH, content in digestive enzymes, rate and intensity of contraction), the structure of foodstuff and their rheological properties are strongly modified. This affects the rate of transfer of food into the intestine. The gastric step is particularly essential for colloidal emulsions such as dairy liquids that will gel or precipitate during that step, with changes on their residence time in the stomach. So, our aim is to understand how the structure and the rheology of dairy colloidal emulsion evolve during their digestion and impact the hydrolysis rates of proteins and lipids and the bioavailability of these macro-nutriments. Taking into account these structural and rheological changes is particularly crucial in neonatal nutrition to develop optimized infant formulas. We performed in vitro dynamic gastrointestinal digestions of different infant formulas1. At some specific steps during the digestion, we determined the structure and the rheology of the bolus, together with the hydrolysis rates of proteins and lipids. Rheological measurement can be performed on aliquoted samples by shearing at a low rate. But, only limited sampling can be practiced because digestion systems are limited in volume and sampling the bolus for rheological measurements can introduce bias by applying additional shearing to the sample. Thus, we proposed performing continuous rheological measurements in parallel to the dynamic digestion study.Two continuous rheological methods were tested on different infant formulas, by shearing or small amplitude oscillation. The changes evidenced with these two methods and the one observed in the digestion system were compared.In conclusion, these two methods gave relevant results and were shown to be much simpler than the digestion system. They could be applied to predict the rheological behavior of formulas. Moreover, the methods allowed discriminating the infant formulas in relation with the technological process applied for their manufacture.
Link adaptation design for ultra-reliable communications (2016)

The fifth generation (5G) of cellular networks is expected to provide connectivity for a wide range of services. This requires the network to encounter novel features. Ultra-reliable communications (URC) is one of the considered features, which provides a certain level of communication service almost all the time. This is essential in order to support mission-critical applications, such as industrial automation, public safety, and vehicular communications. This paper studies link adaptation optimization for URC, considering errors in both data and feedback channels. As the implementation of optimal link adaptation is challenging, particularly, for downlink transmissions due to the limited feedback channel, a simple link adaption scheme is also proposed. Results reveal that the performances of the proposed and optimal link adaptation schemes are close. Hence, the proposed scheme can be utilized to efficiently support URC in cellular networks.
R and Bioconductor Packages in Bioinformatics: Towards Systems Biology (2010)

This chapter contains sections titled: Introduction Brief overview of the Bioconductor Project Experimental Data Annotation Models of Biological Systems Conclusion Acknowledgments References
Discovery of Potent and Selective Non-Nucleotide Small Molecule Inhibitors of CD73 (2020)

CD73 is an extracellular mediator of purinergic signaling. When upregulated in the tumor microenvironment, CD73 has been implicated in the inhibition of immune function through overproduction of adenosine. Traditional efforts to inhibit CD73 have involved antibody therapy or the development of small molecules, the most potent of which mimic the acidic and ionizable structure of the enzyme's natural substrate, adenosine 5'-monophosphate (AMP). Here, we report the systematic discovery of a novel class of non-nucleotide CD73 inhibitors that are more potent than all other nonphosphonate inhibitor classes reported to date. These efforts have culminated in the discovery of 4-({5-[4-fluoro-1-(2<i>H</i>-indazol-6-yl)-1<i>H</i>-1,2,3-benzotriazol-6-yl]-1<i>H</i>-pyrazol-1-yl}methyl)benzonitrile (<b>73</b>, IC<sub>50</sub> = 12 nM) and 4-({5-[4-chloro-1-(2<i>H</i>-indazol-6-yl)-1<i>H</i>-1,2,3-benzotriazol-6-yl]-1<i>H</i>-pyrazol-1-yl}methyl)benzonitrile (<b>74</b>, IC<sub>50</sub> = 19 nM). Cocrystallization of <b>74</b> with human CD73 demonstrates a competitive binding mode. These compounds show promise for the improvement of drug-like character via the attenuation of the acidity and low membrane permeability inherent to known nucleoside inhibitors of CD73.
Describing minimum bow force using Impulse Pattern Formulation (IPF) – an empirical validation (2022)

With bowed string instruments, the minimum bow force necessary to produce stable Helmholtz motion has often been discussed over the last decades. If the bowing force is too small or the bowing velocity too large, no stable tone is produced, and bifurcations or noise occurs. The Impulse Pattern Formulation (IPF) is a top-down method proposed previously (Bader, 2013), which explains such transitions between regular periodicity, bifurcation scenarios, and noise. The recursive equation is based on the idea that impulses, produced at a generator within a musical instrument, travel through the instrument, are reflected, exponentially dampened, and finally trigger or interact with succeeding impulses at the generator. Real bowing is measured on an experimental pendulum for self-organized bowing. Bowing force and velocity are recorded during the transitions from bifurcation to stable tone production. Then the IPF is used under a Simulated Annealing paradigm to reproduce this behavior, using the measured bowing pressure and velocity as input parameters. Compared to previous models, the IPF predicts minimum bow force with much higher precision, which is caused by bowing being a nonlinear dynamical system, including, e.g., hysteresis. In contrast, previous works mainly used analytical equations, therefore not considering the self-organizing nature of the process.
Effect of Envelope Proteins on the Mechanical Properties of Influenza Virus (2012)

The envelope of the influenza virus undergoes extensive structural change during the viral life cycle. However, it is unknown how lipid and protein components of the viral envelope contribute to its mechanical properties. Using atomic force microscopy, here we show that the lipid envelope of spherical influenza virions is ∼10 times softer (∼0.05 nanonewton nm(-1)) than a viral protein-capsid coat and sustains deformations of one-third of the virion's diameter. Compared with phosphatidylcholine liposomes, it is twice as stiff, due to membrane-attached protein components. We found that virus indentation resulted in a biphasic force-indentation response. We propose that the first phase, including a stepwise reduction in stiffness at ∼10-nm indentation and ∼100 piconewtons of force, is due to mobilization of membrane proteins by the indenting atomic force microscope tip, consistent with the glycoprotein ectodomains protruding ∼13 nm from the bilayer surface. This phase was obliterated for bromelain-treated virions with the ectodomains removed. Following pH 5 treatment, virions were as soft as pure liposomes, consistent with reinforcing proteins detaching from the lipid bilayer. We propose that the soft, pH-dependent mechanical properties of the envelope are critical for the pH-regulated life cycle and support the persistence of the virus inside and outside the host.
Persistent photoconductivity study in a high mobility AlGaN/GaN heterostructure (2000)

We have used the Shubnikov–de Haas and the Hall effects to investigate the effect of subband gap illumination on the transport properties of a very high mobility, μ=54 000 cm2/V s at T=1.2 K, Al0.09GaN0.91/GaN heterostructure. We have found that this illumination resulted in a photocurrent that was persistent at low temperatures. This photocurrent, which led to an increase in the carrier density, was used to study the dependence of the mobility and the quantum scattering time on the carrier density. Unlike in previous studies of persistent photoconductivity in GaN and AlGaN/GaN by other researchers, we have found that the mobility did not always increase with the carrier density as a result of illumination. For small duration of illumination, the mobility increased with the carrier density. However additional illumination resulted in a decrease of the mobility despite the increase in the carrier density. We believe that screening is responsible for the initial increase in the mobility, while ionization of defects in GaN, interface charges, and alloy disorder may be responsible for the eventual decrease in the mobility.
ChemInform Abstract: PYRROLOPYRIMIDINE NUCLEOSIDES. 19. A TOTAL SYNTHESIS OF THE NUCLEOSIDE ANTIBIOTIC CADEGUOMYCIN (2‐AMINO‐7‐(β‐D‐RIBOFURANOSYL)PYRROLO(2,3‐D)PYRIMIDIN‐4‐ONE‐5‐CARBOXYLIC ACID) (1984)

Abstract Toyocamycin (I) liefert über eine Hydrolyse zu (II) das Amid (IIIa), das zu (IIIb) aminiert wird.
Adverse events and stroke prevention by interventional left atrial appendage occlusion in patients with low CHA2DS2‐VASc score—results from the multicenter German LAARGE registry (2022)

Low-risk patients had no nonfatal strokes and major bleedings within 1 year after hospital discharge but had unexpectedly high rates of moderate procedural complications. The indication in these patients should be strictly defined based on an individual benefit-risk assessment.