gebhart/patrepeval huggingface dataset:
Phenotype Switching: Tumor Cell Plasticity as a Resistance Mechanism and Target for Therapy (2014)

Mutations in BRAF are present in the majority of patients with melanoma, rendering these tumors sensitive to targeted therapy with BRAF and MEK inhibitors. Unfortunately, resistance almost invariably develops. Recently, a phenomenon called "phenotype switching" has been identified as an escape route. By switching from a proliferative to an invasive state, melanoma cells can acquire resistance to these targeted therapeutics. Interestingly, phenotype switching bears a striking resemblance to the epithelial-to-mesenchymal-like transition that has been described to occur in cancer stem cells in other tumor types. We propose that these changes are manifestations of one and the same underlying feature, namely a dynamic and reversible phenotypic tumor cell plasticity that renders a proportion of cells both more invasive and resistant to therapy. At the same time, the specific characteristics of these tumor cell populations offer potential for being explored as target for therapeutic intervention.
Analysis of chemokine and chemokine receptor expression in squamous cell carcinoma of the head and neck (SCCHN) cell lines (2010)

The purpose of this work was to analyze chemokine and chemokine receptor expression in untreated and in irradiated squamous cell carcinoma of the head and neck (SCCHN) tumor cell lines, aiming at the establishment of assays to test for the relevance of chemokine and chemokine receptor expression in the response of SCCHN to radiotherapy and radiochemotherapy. Five low passage and 10 established SCCHN lines, as well as two normal cell lines, were irradiated at 2 Gy or sham-irradiated, and harvested between 1 and 48 h after treatment. For chemokines with CC and CXC structural motifs and their receptors, transcript levels of target and reference genes were quantified relatively by real-time PCR. In addition, CXCL1 and CXCL12 protein expression was analyzed by ELISA. A substantial variation in chemokine and chemokine receptor expression between SCCHN was detected. Practically, all cell lines expressed CCL5 and CCL20, while CCL2 was expressed in normal cells and in some of the tumor cell lines. CXCL1, CXCL2, CXCL3, CXCL10, and CXCL11 were expressed in the vast majority of the cell lines, while the expression of CXCL9 and CXCL12 was restricted to fibroblasts and few tumor cell lines. None of the analyzed cell lines expressed the chemokines CCL3, CCL4, or CCL19. Of the receptors, transcript expression of CCR1, CCR2, CCR3, CCR5, CCR7, CCXR2, and CCXR3 was not detected, and CCR6, CXCR1, and CXCR4 expression was restricted to few tumor cells. Radiation caused up- and down-regulation with respect to chemokine expressions, while for chemokine receptor expressions down-regulations were prevailing. CXCL1 and CXCL12 protein expression corresponded well with the mRNA expression. We conclude that the substantial variation in chemokine and chemokine receptor expression between SCCHN offer opportunities for the establishment of assays to test for the relevance of chemokine and chemokine receptor expression in the response of SCCHN to radiotherapy and radiochemotherapy.
Field study of moving bed biofilm reactor technology for post-treatment of wastewater lagoon effluent at 1°C (2014)

The goal of this study was to investigate the potential use ofmoving bed biofilm reactor (MBBR) systems as ammonia removal post-treatment units for wastewater (WW) treatment lagoons that demonstrate large temperature changes throughout their operational year (1 - 20 degrees C). The study was carried out over a six-month period using laboratory-scale MBBR reactors fed with incoming effluent from a full-scale lagoon. The study shows that significant average ammonia removal rates of 0.26 and 0.11 kgN/m . d were achieved at 20 degrees C and 1C. The increase in the ammonia removal rates with increasing temperature from 1 degrees C to 20 degrees C showed a strong correlation to an applied temperature correction coefficient model. No significant accumulation of effluent nitrite was observed at 1 degrees C or after being fed with synthetic wastewater (SWW); indicating that cold temperatures and transitions from real WW to SWW did not stress the nitrifiers. Furthermore, the study demonstrates that changes in temperature or changes from real WW to SWW do not affect the mass of biofilm attached per MBBR carrier. Hence, based on the results of this study, it is concluded that MBBR is a promising technology for post-treatment ammonia removal of WW lagoon effluent.
The Methods of Correcting NMR Data from Dry Gas Wells Drilled with Formate Based Muds by Advanced NMR Techniques (2017)

Abstract Formate-based drilling mud is used to improve the performance of drilling and completions of high pressure and high temperature (HPHT) wells due to its properties such as high density (up to 19 lbs/gal), non-corrosiveness, eco-friendliness, high stability, and miscibility with brine and other fluids in the drilling muds. However, these strengths of formate muds pose challenges for formation evaluation due to their unusual properties such as high density, low Hydrogen Index (HI), miscibility with connate brines, and high conductivity. The current work addresses challenges of Nuclear Magnetic Resonance (NMR) logging, which is known to provide capillary bound fluid for producibility evaluation and accurate porosity for reserve estimation, in deep dry gas wells drilled with formate mud. With a carefully designed workflow composed of a suit of laboratory NMR techniques, the needs for the correction of T2cutoff and HI by Formate Mud Filtrate (FMF) invasion have been investigated. To quantify the accurate amount of correction required, FMF invasion has been monitored under reservoir conditions. The experimentally determined NMR T2 cutoff values for FMF saturated samples are always slightly longer than those for brine saturated ones. The difference of bulk volume movable (BVM), however, is less than 5% when T2 cutoff value from brine saturated sample is applied to FMF saturated sample. Thus, T2 cutoff determined by conventional NMR laboratory measurement with brine can be applied to NMR log with the formation invaded by FMF. The HI correction factors for BVM and bulk volume irreducible (BVI) are dependent on pore structures. For brine saturated bi-modal sandstones, all pores are displaced by FMF which corresponds to an HI correction factor of 0.74 for both BVM and BVI. For brine saturated carbonate with tri-modal pore system, however, 100% BVM and 70% of BVI have been displaced with FMF which correspond to HI correction factor of 0.78 and 0.80 for the FMF used in the current study, respectively. The outcome of the current study will help to enhance the usage of NMR logging as powerful formation evaluation tool for gas wells drilled with formate based drilling muds.
The language of colloid and interface science: a dictionary of terms (1994)

Covering theory, experiment and application, this volume provides the user with a handy reference to all the terminology found in colloid and interface science literature. Focusing on terminology rather than on symbols and units, the book provides comprehensive coverage, including both current and older terms. Complete cross-references for important synonyms, abbreviations and acronyms are included. Specific literature citations are given where the sources for further information are unique or difficult to find.
Data of the quantification of the influence of DMSO concentration on the kinetic of interaction between TNFα and SPD304 (2021)

The data presented here are related to the article entitled "New contributions to the drug profile of TNFα inhibitor SPD304: affinity, selectivity ADMET considerations" published in the European Journal of pharmacology. As DMSO is usually used as a co-solvent to dissolve low aqueous soluble small molecules, such as SPD304, we have investigated the influence of its concentration on the kinetic of interaction between tumor necrosis factor α (TNF-α) and its inhibitor, SPD304. The presented data, acquired using a surface acoustic wave sensor, can be used in further biological studies to compare the kinetic of interaction between proteins/small molecules in general and TNFα/inhibitors in particular. The estimated dissociation constant can be compared to other ones to statute on the degree of affinity between a protein and a given molecule.
Super<em>B</em> Progress Report for Physics (2010)

SuperB is a high luminosity e{sup +}e{sup -} collider that will be able to indirectly probe new physics at energy scales far beyond the reach of any man made accelerator planned or in existence. Just as detailed understanding of the Standard Model of particle physics was developed from stringent constraints imposed by flavour changing processes between quarks, the detailed structure of any new physics is severely constrained by flavour processes. In order to elucidate this structure it is necessary to perform a number of complementary studies of a set of golden channels. With these measurements in hand, the pattern of deviations from the Standard Model behavior can be used as a test of the structure of new physics. If new physics is found at the LHC, then the many golden measurements from SuperB will help decode the subtle nature of the new physics. However if no new particles are found at the LHC, SuperB will be able to search for new physics at energy scales up to 10-100 TeV. In either scenario, flavour physics measurements that can be made at SuperB play a pivotal role in understanding the nature of physics beyond the Standard Model. Examples for using the interplay between measurements to discriminate New Physics models are discussed in this document. SuperB is a Super Flavour Factory, in addition to studying large samples of B{sub u,d,s}, D and {tau} decays, SuperB has a broad physics programme that includes spectroscopy both in terms of the Standard Model and exotica, and precision measurements of sin{sup 2} {theta}{sub W}. In addition to performing CP violation measurements at the {Upsilon}(4S) and {phi}(3770), SuperB will test CPT in these systems, and lepton universality in a number of different processes. The multitude of rare decay measurements possible at SuperB can be used to constrain scenarios of physics beyond the Standard Model. In terms of other precision tests of the Standard Model, this experiment will be able to perform precision over-constraints of the unitarity triangle through multiple measurements of all angles and sides. This report extends and updates the studies presented in both the SuperB Conceptual Design Report in 2007 and the Proceedings of SuperB Workshop VI in Valencia in 2008. Together, these three documents detail the Physics case of the SuperB Project.
Expression of liver X receptor α and lipid metabolism in granulocyte–macrophage colony‐stimulating factor‐induced human monocyte‐derived macrophage (2009)

Liver X receptor (LXR) is a nuclear receptor that acts as a sterol sensor and metabolic regulator of cholesterol and lipid homeostasis. The foam cell transformation of macrophages (Mϕ) is considered a critical process in atherosclerotic lesions. The relationship, however, of the foam cell transformation of Mϕ and LXR is not fully understood. The purpose of the present study was to examine the expression of LXRα, retinoid X receptor (RXR)α, ATP‐binding cassette transporter (ABCA1), and macrophage scavenger receptor A (MSR‐A), and lipid accumulation in human monocyte‐derived Mϕ. The expression of LXRα, ABCA1, MSR‐A in 7 day cultured granulocyte–macrophage colony‐stimulating factor (GM‐CSF)‐induced Mϕ (GM‐Mϕ) was significantly higher than that in 7 day cultured M‐CSF‐induced Mϕ (M‐Mϕ). The expression levels of LXRα, ABCA1 and MSR‐A protein decreased from 48 h to 5 days after the addition of lipopolysaccharide (LPS) in GM‐Mϕ, but only MSR‐A protein decreased at 5 days after the addition of LPS in M‐Mϕ. Intracellular lipid accumulation was clearly observed when GM‐Mϕ was pre‐stimulated with LPS for 48 h and incubated with oxidized LDL for an additional 5 days. These findings suggest that the inhibitory activity of LXRα, ABCA1 and MSR‐A by LPS may be related to the transformation of Mϕs, especially GM‐Mϕ into foam cells.
From Template to Image: Reconstructing Fingerprints from Minutiae Points (2007)

Most fingerprint-based biometric systems store the minutiae template of a user in the database. It has been traditionally assumed that the minutiae template of a user does not reveal any information about the original fingerprint. In this paper, we challenge this notion and show that three levels of information about the parent fingerprint can be elicited from the minutiae template alone, viz., 1) the orientation field information, 2) the class or type information, and 3) the friction ridge structure. The orientation estimation algorithm determines the direction of local ridges using the evidence of minutiae triplets. The estimated orientation field, along with the given minutiae distribution, is then used to predict the class of the fingerprint. Finally, the ridge structure of the parent fingerprint is generated using streamlines that are based on the estimated orientation field. Line Integral Convolution is used to impart texture to the ensuing ridges, resulting in a ridge map resembling the parent fingerprint. The salient feature of this noniterative method to generate ridges is its ability to preserve the minutiae at specified locations in the reconstructed ridge map. Experiments using a commercial fingerprint matcher suggest that the reconstructed ridge structure bears close resemblance to the parent fingerprint.
OctreoScan Positive Crohn's Disease Mimicking An Ileal Carcinoid Tumor (2008)

Somatostatin receptors have been identified in many tissues throughout the human body. Alterations in the expression of somatostatin receptors have been reported in many disease states including both tumorous and nontumorous conditions. Somatostatin receptor scintigraphy utilizing OctreoScan (Mallinckrodt Medical, Inc., St. Louis, MO), a radiolabled form of octreotide, has been reported to be a highly sensitive imaging technique for identifying pathology, such as neuroendocrine tumors, that are somatostatin receptor dense. Unfortunately, many conditions cause an increase in the quantity of somatostatin receptors and therefore may cause false positive Octreoscans. In this report, we discuss the alterations in somatostatin receptors that occur with Crohn's disease and describe a case of an OctreoScan-positive inflammatory mass mimicking a carcinoid tumor.
Subsurface Characterization at Ground Failure Sites in Adapazari, Turkey (2004)

Ground failure in Adapazari, Turkey during the 1999 Kocaeli earthquake was severe. Hundreds of structures settled, slid, tilted, and collapsed due in part to liquefaction and ground softening. Ground failure was more severe adjacent to and under buildings. The soils that led to severe building damage were generally low plasticity silts. In this paper, the results of a comprehensive investigation of the soils of Adapazari, which included cone penetration test (CPT) profiles followed by borings with standard penetration tests (SPTs) and soil index tests, are presented. The effects of subsurface conditions on the occurrence of ground failure and its resulting effect on building performance are explored through representative case histories. CPT- and SPT-based liquefaction triggering procedures adequately identified soils that liquefied if the clay-size criterion of the Chinese criteria was disregarded. The CPT was able to identify thin seams of loose liquefiable silt, and the SPT (with retrieved samples) allowed for reliable evaluation of the liquefaction susceptibility of fine-grained soils. A well-documented database of in situ and index testing is now available for incorporating in future CPT- and SPT-based liquefaction triggering correlations.
Avoidance of Cross-Phase Modulation in Femtosecond Stimulated Raman Scattering (2019)

The influence of cross-phase modulation on stimulated Raman scattering in the high peak power regime is investigated, resulting in optimized pulse parameters for reduced cross-phase modulation artefacts.
Copper-catalyzed hydride transfer from LiAlH4 for the formation of alkylidenecyclopropane derivatives (2008)

The copper-catalyzed addition of LiAlH(4) to cyclopropenylcarbinol leads to an easy and straightforward preparation of alkylidenecyclopropane derivative.
Advancing and applying Next-Generation DNA-based super-resolution microscopy (2020)

Der Beginn von Superauflösungsmikroskopie hat den räumlichen Auflösungsbereich von Lichtmikroskopie hin zu molekularer Auflösung erweitert. Speziell im Bereich der Biologie ermöglicht diese bemerkenswerte Auflösung Forschern einzelne Moleküle (z.B. Proteine) in Zellen mit Hilfe von Lichtmikroskopie sichtbar zu machen. Verschiedene Techniken zur Umgehung des Beugungslimits wurden unabhängig voneinander entwickelt. Die bekanntesten Techniken sind Stimulated Emission Depletion (STED) Microscopy, Photo Activated Localization Microscopy (PALM), Stochastic Optical Reconstruction Microscopy (STORM), und Point Accumulation In Nanoscale Topography (PAINT). Kürzlich wurden DNA-Moleküle für die PAINT Methode verwendet, was zur Entwicklung von DNA-PAINT geführt hat. Aufgrund der einzigartigen Programmierbarkeit von DNA und der Möglichkeit Interaktionen transient und repetitiv zu gestalten, ermöglicht DNA-PAINT sehr hohe räumliche Auflösung (zur Zeit die höchste Auflösung in Lichtmikroskopie), spektral unlimitiertes Multiplexen und die Fähigkeit, quantitativ Zielmoleküle in dichten Populationen zu zählen, bei denen es schwierig ist, jedes einzelne Molekül aufzulösen. Der Inhalt dieser Arbeit beschreibt die Anwendung und Weiterentwicklung des Konzepts DNA Moleküle als intelligente Proben für Einzelmolekül-basierende Superauflösungsmikroskopie zu verwenden. Im ersten Teil wird DNA-PAINT als Tool verwendet, um die Adressierbarkeit und die Einbaueffizienz von einzelnen DNA Strängen in eine zweidimensionale DNA-Origami Struktur mit molekularer Auflösung zu bestimmen. Im zweiten Teil, wird das Konzept des kürzlich entwickelten Exchange- PAINT für spektral nicht limitiertes Aufnehmen von verschiedenen Zielmolekülen erweitert für andere Superauflösungstechniken wie STORM, STED oder SIM. Ferner wird dieses Konzept auf konventionelle und konfokale Lichtmikroskopie angewandt. Im dritten Teil werden genetisch kodierte Sonden wie SNAP- oder Halo-Tag für DNA-PAINT eingeführt. Zusätzlich werden genetisch kodierte GFP-Proteine verwendet, die dann mit einem Nanokörper markiert werden. Die Kombination dieser „Tags“ mit DNA-PAINT wird dann verwendet, um die molekulare Architektur von Kernporen zu untersuchen. Dies erlaubt, einzelne Kopien von NUP96-Proteinen in einzelnen Kernporen mit einem Abstand von nur ~12 nm aufzulösen. Der vierte Teil kombiniert Spinning-Disk-Konfokalmikroskopie mit DNA-PAINT, um den räumlichen Arbeitsbereich von DNA-PAINT von nah am Deckglas bis hin zu ganzen Zellen und möglicherweise Gewebeproben zu erweitern. Im letzten Teil wird die Abtastgeschwindigkeit und damit der Aufnahmegeschwindigkeit von DNA-PAINT durch die Optimierung der Puffer und der Hybridisationssequenz zwischen der Fluoreszenzprobe und der Bindestelle am Zielmolekül erhöht.
Design and evaluation of a continuous interleaved sampling (CIS) processing strategy for multichannel cochlear implants. (1993)

Two approaches for representing speech information with multichannel cochlear prostheses are being compared in tests with implant patients. Included in these studies are the compressed analog (CA) approach of a standard clinical device and research processors utilizing continuous interleaved sampling (CIS). Initial studies have been completed with nine subjects, seven of whom were selected on the basis of excellent performance with the Ineraid clinical processor, and the remaining two for their relatively poor performance with the same device. The tests include open-set recognition of words and sentences. Every subject has obtained a higher score--or repeated a score of 100% correct--on every test when using a CIS processor. These results are discussed in terms of their implications for processor design.
Integration von Software-Agenten und Soft-Computing-Methoden für die Transportplanung (2006)

Zusammenfassung: Anwendungen in der Transportlogistik zeichnen sich durch eine besonders hohe Komplexitat und Dynamik aus. In diesem Rahmen haben sich Soft-Computing-Ansatze fur die Disposition etabliert, da sie eine effiziente Planung ermoglichen. Daneben werden in der Forschung Ansatze zur Transportplanung mit Hilfe von Multiagentensystemen untersucht, die eine naturliche Reprasentation bieten und hierbei autonomes und robustes Verhalten ermoglichen. Die Integration von Multiagentensystemen und Soft-Computing-Methoden wird in diesem Beitrag als Losungsansatz beschrieben, um robuste und flexibel reagierende selbststeuernde logistische Prozesse in dieser Domane zu realisieren.
Multi-Drug Delivery System Using Streptavidin-Transforming Growth Factor-α Chimeric Protein (1996)

Tissue-specific delivery of a variety of molecules has been a valuable technique for biological and medical research. Therefore, we have constructed a recombinant plasmid containing the coding regions for streptavidin core and mature human transforming growth factor-alpha (TGF-alpha). The recombinant plasmid has been expressed in Escherichia coli to produce a chimeric protein with both streptavidin and TGF-alpha activity. The streptavidin-TGF-alpha chimeric protein (ST-TGF-alpha) could efficiently transfer biotinylated beta-galactosidase into A431 cells via the epidermal growth factor receptor. More than 99% of the cells contained the enzyme transferred. Furthermore, ST-TGF-alpha complexed with biotinylated-glucose oxidase had a significant cytotoxic effect when incubated with A431 cells. These findings suggest that the ST-TGF-alpha chimeric protein could be used to deliver proteins of interest into target cells without the need for chemical linkage or genetic construction. Essentially, ST-TGF-alpha serves as a high-modular "molecular bridge" for the passage of a wide variety of effector molecules into target cells.
A modified RIO algorithm that alleviates the bandwidth skew problem in Internet differentiated service (2002)

The assured service is a service model that can be offered within Internet differentiated services (Diff-Serv) architecture. It provides a statistical bandwidth guarantee to its subscribers, and allows the subscribers to claim a share of the excess network bandwidth in addition to the subscribed bandwidth. It has been observed that assured service does not meet the bandwidth guarantee for high-profile flows in the presence of numerous low-profile flows (such as best-effort). We demonstrate that there is an inadequacy in the packet differentiation algorithm used in the Diff-Serv routers, RIO ("RED with In and Out"), that contributes to the problem. We propose a modified RIO algorithm called RI+O to reduce the effect, and show that it significantly alleviates the problem. Our approach of modifying a router algorithm incurs much less deployment cost than other approaches.