gebhart/patrepeval huggingface dataset:
Upscaling of Relative Permeability Curves for Reservoir Simulation: An Extension to Areal Simulations Based on Realistic Average Water Saturations (2003)

Abstract Special core analysis laboratories generally obtain relative permeability curves through frontal advance theory developments. The outer face of the sample, where production rates are measured, is usually selected to perform calculations. As a result, relative permeability curves are reported as function of point fluids saturations and not as function of average saturations. In spite of this procedure, numerical simulators perform their calculations using the average water saturation within every cell. Although point and average saturations are expected to be the same at infinitely small grid sizes, this is not the case with real application grids. As previously shown by the authors1, relative permeability curves as a function of average water saturation could be used to overcome numerical dispersion and drastically reduce the number of grid cells needed for linear numerical simulation situations. In this paper a series of experimental tests were performed to extend the methodology to 2D (areal) displacement. On this geometry, an additional issue should be taken into account that does not impact the linear cases. A geometry effect appears as a consequence of flow leaving the grid cells in a direction perpendicular from where it enters. As in the previously studied linear situation, water-cut as a function of produced oil was analyzed. The history was matched using a numerical simulator and relative permeability curves defined as a function of point saturations and average water saturation for different grid sizes. Representative relative permeability curves were previously determined through routine laboratory explicit computation based on linear unsteady state displacement. It is shown that only curves taking into account average saturation values and geometry considerations give reliable data, and a general methodology to obtain the proper relative permeability curve for every cell is examined.
Resource Prediction and Admission Control for Interactive Video (1999)

Highly interactive multimedia applications, like browsing in video databases, generate strongly varying loads on the media server during the presentation of media data. Existing admission control approaches for limiting the number of concurrent users and thus guaranteeing acceptable service quality are only suited for applications with uniform load characteristics like videoon-demand. We propose a session-oriented approach to admission control that is based on the stochastical model of Continuous Time Markov Chains, which allows to describe the different presentation states occurring in the interactive access to the multimedia database. The model is derived from semantic information on the forthcoming browsing session. In particular, it considers the relevance of the videos to the user. In this way a more precise prediction on resource usage can be given for achieving the two goals of Quality of Service (QoS) and good server utilization. The admission control mechanism is part of a multimedia database architecture for supporting efficient browsing in large video collections.
Protease-Resistant Peptide Ligands from a Knottin Scaffold Library (2011)

Peptides within the knottin family have been shown to possess inherent stability, making them attractive scaffolds for the development of therapeutic and diagnostic agents. Given its remarkable stability to proteases, the cyclic peptide kalata B1 was employed as a scaffold to create a large knottin library displayed on the surface of E. coli. A library exceeding 10(9) variants was constructed by randomizing seven amino acids within a loop of the kalata B1 scaffold and screened using fluorescence-activated cell sorting to identify peptide ligands specific for the active site of human thrombin. Refolded thrombin binders exhibited high nanomolar affinities in solution and slow dissociation rates and were able to inhibit thrombin's enzymatic activity. Importantly, 80% of a knottin-based thrombin inhibitor remained intact after a 2 h incubation both with trypsin and with chymotrypsin, demonstrating that modifying the kalata B1 sequence did not compromise its stability properties. In addition, the knottin variant mediated 20-fold enhanced affinity for thrombin, when compared to the same seven residue binding epitope constrained by a single disulfide bond. Our results indicate that peptide libraries derived from the kalata B1 scaffold can yield high-affinity protein ligands that retain the remarkable protease resistance associated with the parent scaffold. More generally, this strategy may prove useful in the development of stable peptide ligands suitable for in vivo applications.
Functional analysis of the ALD gene family of Saccharomyces cerevisiae during anaerobic growth on glucose: the NADP+-dependent Ald6p and Ald5p isoforms play a major role in acetate formation (2004)

In Saccharomyces cerevisiae, acetate is formed by acetaldehyde dehydrogenase (ACDH), a key enzyme of the pyruvate dehydrogenase (PDH) bypass, which fulfils the essential task of generating acetyl-CoA in the cytosol. The role of the five members of the ACDH family (ALD genes) was investigated during anaerobic growth on glucose. Single and multiple ald Delta mutants were generated in the wine-yeast-derived V5 and laboratory CEN.PK strains and analysed under standard (YPD 5 % glucose) and wine (MS 20 % glucose) fermentation conditions. The deletion of ALD6 and ALD5 decreased acetate formation in both strains, demonstrating for the first time that the mitochondrial Ald5p isoform is involved in the biosynthesis of acetate during anaerobic growth on glucose. Acetate production of the ald4 Delta mutant was slightly decreased in the CEN.PK strain during growth on YPD only. In contrast, the deletion of ALD2 or ALD3 had no effect on acetate production. The absence of Ald6p was compensated by the mitochondrial isoforms and this involves the transcriptional activation of ALD4. Consistent with this, growth retardation was observed in ald6 Delta ald4 Delta, and this effect was amplified by the additional deletion of ALD5. A ald Delta null mutant, devoid of ACDH activity, was viable and produced similar levels of acetate to the ald6 Delta ald4 Delta ald5 Delta strain, excluding a role of Ald2p and Ald3p. Thus, acetate is mainly produced by the cytosolic PDH bypass via Ald6p and by a mitochondrial route involving Ald5p. An unknown alternative pathway can compensate for the loss of Ald6p, Ald4p and Ald5p.
Influence of the Surface Properties on Nanoparticle-Mediated Transport of Drugs to the Brain (2004)

Poly(alkyl cyanoacrylate) nanoparticles enable the delivery of a number of drugs, including doxorubicin, loperamide, tubocurarine, the NMDA receptor antagonist MRZ 2/576, and the peptides dalargin and kytorphin across the blood-brain barrier (BBB) after coating with surfactants. However, only the surfactants polysorbate (Tween) 20, 40, 60 and 80, and some poloxamers (Pluronic F 68) can induce this uptake. The mechanism for the delivery across the BBB most likely is endocytosis via the LDL receptor by the endothelial cells lining the brain blood capillaries after injection of the nanoparticles into the blood stream. This endocytotic uptake seems to be mediated by the adsorption of apolipoprotein B and/or E adsorption from the blood. Thus, the nanoparticles could mimic lipoprotein particles and act as "Trojan Horses." The drug, then, may be released either within these cells followed by passive diffusion into the brain or be transported into the brain by transcytosis.
Precision medicine for human cancers with Notch signaling dysregulation (Review) (2019)

NOTCH1, NOTCH2, NOTCH3 and NOTCH4 are transmembrane receptors that transduce juxtacrine signals of the delta‑like canonical Notch ligand (DLL)1, DLL3, DLL4, jagged canonical Notch ligand (JAG)1 and JAG2. Canonical Notch signaling activates the transcription of BMI1 proto‑oncogene polycomb ring finger, cyclin D1, CD44, cyclin dependent kinase inhibitor 1A, hes family bHLH transcription factor 1, hes related family bHLH transcription factor with YRPW motif 1, MYC, NOTCH3, RE1 silencing transcription factor and transcription factor 7 in a cellular context‑dependent manner, while non‑canonical Notch signaling activates NF‑κB and Rac family small GTPase 1. Notch signaling is aberrantly activated in breast cancer, non‑small‑cell lung cancer and hematological malignancies, such as T‑cell acute lymphoblastic leukemia and diffuse large B‑cell lymphoma. However, Notch signaling is inactivated in small‑cell lung cancer and squamous cell carcinomas. Loss‑of‑function NOTCH1 mutations are early events during esophageal tumorigenesis, whereas gain‑of‑function NOTCH1 mutations are late events during T‑cell leukemogenesis and B‑cell lymphomagenesis. Notch signaling cascades crosstalk with fibroblast growth factor and WNT signaling cascades in the tumor microenvironment to maintain cancer stem cells and remodel the tumor microenvironment. The Notch signaling network exerts oncogenic and tumor‑suppressive effects in a cancer stage‑ or (sub)type‑dependent manner. Small‑molecule γ‑secretase inhibitors (AL101, MRK‑560, nirogacestat and others) and antibody‑based biologics targeting Notch ligands or receptors [ABT‑165, AMG 119, rovalpituzumab tesirine (Rova‑T) and others] have been developed as investigational drugs. The DLL3‑targeting antibody‑drug conjugate (ADC) Rova‑T, and DLL3‑targeting chimeric antigen receptor‑modified T cells (CAR‑Ts), AMG 119, are promising anti‑cancer therapeutics, as are other ADCs or CAR‑Ts targeting tumor necrosis factor receptor superfamily member 17, CD19, CD22, CD30, CD79B, CD205, Claudin 18.2, fibroblast growth factor receptor (FGFR)2, FGFR3, receptor‑type tyrosine‑protein kinase FLT3, HER2, hepatocyte growth factor receptor, NECTIN4, inactive tyrosine‑protein kinase 7, inactive tyrosine‑protein kinase transmembrane receptor ROR1 and tumor‑associated calcium signal transducer 2. ADCs and CAR‑Ts could alter the therapeutic framework for refractory cancers, especially diffuse‑type gastric cancer, ovarian cancer and pancreatic cancer with peritoneal dissemination. Phase III clinical trials of Rova‑T for patients with small‑cell lung cancer and a phase III clinical trial of nirogacestat for patients with desmoid tumors are ongoing. Integration of human intelligence, cognitive computing and explainable artificial intelligence is necessary to construct a Notch‑related knowledge‑base and optimize Notch‑targeted therapy for patients with cancer.
Phase I dose escalation pharmacokinetic assessment of intravenous humanized anti-MUC1 antibody AS1402 in patients with advanced breast cancer (2009)

ClinicalTrials.gov Identifier: NCT00096057.
Programmed cell death and the control of cell survival (1994)

We draw the following tentative conclusions from our studies on programmed cell death (PCD): (i) the amount of normal cell death in mammalian development is still underestimated; (ii) most mammalian cells constitutively express the proteins required to undergo PCD; (iii) the death programme operates by default when a mammalian cell is deprived of signals from other cells; (iv) many normal cell deaths may occur because cells fail to obtain the extracellular signals they need to suppress the death programme; and (v) neither the nucleus nor mitochondrial respiration is required for PCD (or Bcl-2 protection from PCD), raising the possibility that the death programme, like mitosis, is orchestrated by a cytosolic regulator that acts on multiple organelles in parallel.
YFCC100M (2016)

This publicly available curated dataset of almost 100 million photos and videos is free and legal for all.
Dynamic interaction between tectonic plates, subducting slabs, and the mantle (1997)

Mantle convection models have been formulated to investigate the relation between plate kinematics and mantle dynamics.The cylindrical geometry models incorporate mobile, faulted plate margins, a phase change at 670 km depth, non-Newtonian rheology, and tectonic plates.Models with a variety of parameters indicate that a relatively stationary trench is more likely to be associated with a subducted slab that penetrates into the lower mantle with a steep dip angle.However, a subducted slab that is deflected above the 670-km phase change with a shallow dip is more likely to be associated with a margin that has undergone rapid retrograde trench migration.This relation between slab morphology and plate kinematics is consistent with seismic tomography and plate reconstruction of western Pacific subduction zones.The efficiency of slab penetration through the 670-km phase change is controlled by both the buoyancy of the subducting plate and the mobility of the overriding plate.While older subducting plates have a greater propensity for slab penetration, trench mobility reduces the propensity for slab penetration.Smaller overriding plates have a greater mobility.When subducted slabs approach the bottom thermal boundary layer, hot fluid is pushed aside, and plumes form on the periphery of slab accumulations.There are sharp temperature contrasts between the subducted slab and the thermal boundary layer
Oral Care with Vancomycin Paste for Reduction in Incidence of α-Hemolytic Streptococcal Sepsis (1995)

This analysis suggests that vanc paste effectively reduces AHS sepsis, does not increase gram-negative bacteremia, and is not associated with vancomycin resistance. A multicentered, placebo-controlled, double-blind study is currently planned.
Can cardiomyocytes divide? (2001)

There is no doubt that research in the field of myocardial regeneration has a remarkably exciting future. This is reflected by a recent statement of the special emphasis panel at the National Heart, Lung, and Blood Institute in the USA, which was assigned to identify areas which should be in the focus of cardiovascular research within the next decades.1 It says that we need to acquire “ . . .fundamental understanding of stem cell biology, cardiogenic differentiation, and cell cycle control”. However, there are certain limitations we face when we want to embark on this field of research:

(1)
: the availability of human tissue necessary to study cardiomyocyte division is limited and the heart consists of a heterogenous cell population;
(2)
: compared to the contractile protein apparatus there is only a low abundance of most cell cycle regulating factors;
(3)
: it may be necessary to convince people that counting cells alone may not give us the right answer about tissue regeneration.



If we wish to make progress in the field of myocardial regeneration in the nearer future, there are a number of issues that need to be addressed:



Cellular division is one of the key features and the basis of life in all metazoa. Therefore, any multicellular organ has to be endowed with a programme allowing cytokinesis. However, because of specific requirements some of these cells withdraw from the cell cycle during the perinatal period and become postmitotic. This is particularly true of cells comprising central organs such as the brain and the heart. For the latter, postnatal growth—which is essential to meet the increasing demand for work to support body growth—is achieved primarily by hypertrophy. This is probably because ongoing cellular division would render the heart mechanically unstable, and thus it would not be able to establish a functional circulatory homeostasis.

In contrast to skeletal muscle cells, where differentiation and cell division …
Numerical model of vagus nerve electrical stimulation (2009)

Purpose The electric stimulation of the vagus nerve is used to obtain therapeutic results in epilepsy, depression and Alzheimer diseases. The purpose of this paper is to show numerical model of stimulation, focusing on the mathematical approach to modeling a phenomenon of neural cells activation and its propagation in the nerve. Design/methodology/approach The paper presents a model based on the bidomain theory. It uses two continuous, averaged domains which depict the intra‐ and extra‐cellular domains and are connected with the membrane ionic currents. The numerical model uses 3D cylindrical model approximating the anatomical shape of the neck. The simulator is based on a time domain finite element method. Findings The presented approach allows to model the discrete behaviour of the membrane potential in the macroscopic, realistic model of the nerve. The validation of the parameters with the velocity of activation propagations suggests the strong disscussion on physical interpretation to the bidomain theory parameters. To obtain realistic results the parameters needed to be unrealistic. Originality/value The paper presents the combination of bidomain model of neural tissue with the time domain finite element method along with the atributes of bidomain model for realistic modeling of the process of propagtion of activation.
Microstructure of lateral epitaxial overgrown InAs on (100) GaAs substrates (2003)

Substantial defect reduction was achieved in InAs/GaAs by lateral epitaxial overgrowth in which InAs was grown on mask-patterned (100) GaAs with stripe-shaped windows of various widths by metalorganic chemical vapor deposition. The InAs growth morphology, crystal quality, and microstructure were evaluated using double-crystal x-ray rocking curves and scanning and transmission electron microscopy. The microstructure of the InAs grown on mask-free control samples was comprised of micron-scale misoriented grains and dislocations at a density of 1011 cm−2. As the width of the mask openings decreased to 0.8 μm, the rocking curves narrowed, grain boundaries disappeared and the dislocation density decreased to &amp;lt;107 cm−2. The distribution of the remaining defects suggests substantial changes in microstructural development when the window width is ≲1 μm.
Surgical treatment of arthritic varus knee by tibial corticotomy and angular distraction with an external fixator. (1992)

The authors report their experience in surgical treatment of the arthritic varus knee. After a comparative study of the most commonly used osteotomy techniques, they describe the results of their first cases of metaphyseal tibial corticotomy and angular distraction using an external fixator (25 cases).
Mathematical simulation and analysis of cellular metabolism and regulation (1999)

gzz78923@ggr.co.uk
Effects of geometry of hydroxyapatite as a cell substratum in BMP‐induced ectopic bone formation (2000)

Three different types of porous hydroxyapatite with pore sizes of 100–200 μm in diameter—porous particles of hydroxyapatite (PPHAP), porous blocks of hydroxyapatite (PBHAP), and honeycomb-shaped hydroxyapatite (HCHAP)—were compared in terms of their abilities to induce osteogenesis when implanted subcutaneously with recombinant human BMP-2 into rats and extracted at 1, 2, 3, and 4 weeks. Histologically, direct bone formation occurred in PPHAP and PBHAP while only endochondral ossification took place in HCHAP. Interestingly, cartilage in the central zones and bone in the orifice zones of the tunnels of the HCHAP were observed at 2 weeks. After 3 weeks, the cartilage disappeared and bone formation occurred throughout the inner surface of the tunnels of the HCHAP, always leaving space for capillaries within the tunnels. Alkaline phosphatase activity and osteocalcin content were the highest in HCHAP among the three hydroxyapatite implants. These results clearly indicate that BMP-induced bone formation is highly dependent on the geometry of the carrier, which provides feasible structural factors for vascularization. © 2000 John Wiley & Sons, Inc. J Biomed Mater Res, 51, 491–499, 2000.
Optical burst switching (OBS) - a new paradigm for an optical Internet (1999)

To support bursty traffic on the Internet (and especially WWW) efficiently, optical burst switching (OBS) is proposed as a way to streamline both protocol and hardware in building the future generation Optical Internet. By leveraging the attractive properties of optical communications and at the same time, taking into account its limitations, OBS combines the best of optical circuitswitching and packet/cell switching. In this paper, the general concept of OBS protocols and in particular, those based on Just-Enough-Time (JET), is described, along with the applicability of OBS protocols to IP over WDM. Specific issues such as the use of fiber delay-lines (FDL) for accommodating processing delay and/or resolving conflicts are also discussed. In addition, the performance of JET-based OBS protocols which use an offset time along with delayed reservation to achieve efficient utilization of both bandwidth and FDLs as well as to support priority-based routing is evaluated. Keywords: bursty tr...
Diverse marrow stromal cells protect CLL cells from spontaneous and drug-induced apoptosis: development of a reliable and reproducible system to assess stromal cell adhesion-mediated drug resistance (2009)

Marrow stromal cells (MSCs) provide important survival and drug resistance signals to chronic lymphocytic leukemia (CLL) cells, but current models to analyze CLL-MSC interactions are heterogeneous. Therefore, we tested different human and murine MSC lines and primary human MSCs for their ability to protect CLL cells from spontaneous and drug-induced apoptosis. Our results show that both human and murine MSCs are equally effective in protecting CLL cells from fludarabine-induced apoptosis. This protective effect was sustained over a wide range of CLL-MSC ratios (5:1 to 100:1), and the levels of protection were reproducible in 4 different laboratories. Human and murine MSCs also protected CLL cells from dexamethasone- and cyclophosphamide-induced apoptosis. This protection required cell-cell contact and was virtually absent when CLL cells were separated from the MSCs by micropore filters. Furthermore, MSCs maintained Mcl-1 and protected CLL cells from spontaneous and fludarabine-induced Mcl-1 and PARP cleavage. Collectively, these studies define common denominators for CLL cocultures with MSCs. They also provide a reliable, validated tool for future investigations into the mechanism of MSC-CLL cross talk and for drug testing in a more relevant fashion than the commonly used suspension cultures.
Application of Wavelet Cross-Correlation Analysis to a Plane Turbulent Jet. (1997)

A new cross-correlation method, which is called wavelet cross-correlation analysis and is used to express the statistical cross-correlation of two arbitrary signals in terms of scale and time delay, is proposed and its main properties are presented. By analyzing two test signals, it is shown that wavelet cross-correlation does not have the limitations of classical cross-correlation. As a practical application to fluid mechanics, wavelet cross-correlation is employed to determine the cross-correlation relationships between the x-components of the fluctuation velocities at two points on opposite sides of the centerline amd along the centerline of a plane turbulent jet in terms of period and time delay. In the distributions of the wavelet cross-correlation coefficients, similar structures with various scales are observed instantaneously, and the period of eddy and apparent flapping motions can be determined easily in terms of period and time delay. It is found that the apparent flapping behavior appears first in region with an intermediate period. It is also revealed that a similar structure with a high period consists of similar structures with a low period, i.e., a large eddy contains small eddies.