gebhart/patrepeval huggingface dataset:
Osteoactivin regulates head and neck squamous cell carcinoma invasion by modulating matrix metalloproteases (2017)

Nearly 60% of patients with head and neck squamous cell carcinoma (HNSCC) die of metastases or locoregional recurrence. Metastasis is mediated by cancer cell migration and invasion, which are in part dependent on extracellular matrix degradation by matrix metalloproteinases. Osteoactivin (OA) overexpression plays a role in metastases in several malignancies, and has been shown to upregulate matrix metalloproteinase (MMP) expression and activity. To determine how OA modulates MMP expression and activity in HNSCC, and to investigate OA effects on cell invasion, we assessed effects of OA treatment on MMP mRNA and protein expression, as well as gelatinase and caseinolytic activity in HNSCC cell lines. We assessed the effects of OA gene silencing on MMP expression, gelatinase and caseinolytic activity, and cell invasion. OA treatment had differential effects on MMP mRNA expression. OA treatment upregulated MMP-10 expression in UMSCC14a (p = 0.0431) and SCC15 (p < 0.0001) cells, but decreased MMP-9 expression in UMSCC14a cells (p = 0.0002). OA gene silencing decreased MMP-10 expression in UMSCC12 cells (p = 0.0001), and MMP-3 (p = 0.0005) and -9 (p = 0.0036) expression in SCC25 cells. In SCC15 and SCC25 cells, OA treatment increased MMP-2 (p = 0.0408) and MMP-9 gelatinase activity (p < 0.0001), respectively. OA depletion decreased MMP-2 (p = 0.0023) and -9 (p < 0.0001) activity in SCC25 cells. OA treatment increased 70 kDa caseinolytic activity in UMSCC12 cells consistent with tissue type plasminogen activator (p = 0.0078). OA depletion decreased invasive capacity of UMSCC12 cells (p < 0.0001). OA's effects on MMP expression in HNSCC are variable, and may promote cancer cell invasion.
Laser cavitation rheology for measurement of elastic moduli and failure strain within hydrogels (2020)

We introduce laser cavitation rheology (LCR) as a minimally-invasive optical method to characterize mechanical properties within the interior of biological and synthetic aqueous soft materials at high strain-rates. We utilized time-resolved photography to measure cavitation bubble dynamics generated by the delivery of focused 500 ps duration laser radiation at λ = 532 nm within fibrin hydrogels at pulse energies of E<sub>p</sub> = 12, 18 µJ and within polyethylene glycol (600) diacrylate (PEG (600) DA) hydrogels at E<sub>p</sub> = 2, 5, 12 µJ. Elastic moduli and failure strains of fibrin and PEG (600) DA hydrogels were calculated from these measurements by determining parameter values which provide the best fit of the measured data to a theoretical model of cavitation bubble dynamics in a Neo-Hookean viscoelastic medium subject to material failure. We demonstrate the use of this method to retrieve the local, interior elastic modulus of these hydrogels and both the radial and circumferential failure strains.
Clustering of conformational IgE epitopes on the major dog allergen Can f 1 (2017)

Immunoglobulin E (IgE)-associated allergy affects more than 25% of the population. Can f 1 is the major dog allergen associated with respiratory symptoms but the epitopes recognized by allergic patients IgE on Can f 1 are unknown. To characterize IgE epitopes of Can f 1 recognized by dog allergic patients, six overlapping peptides spanning the Can f 1 sequence were synthesized. In direct IgE epitope mapping experiments peptides were analyzed for IgE reactivity by dot blot and Enzyme-linked immunosorbent assay (ELISA) with sera from dog allergic patients. For indirect epitope-mapping, rabbits were immunized with the peptides to generate specific IgG antibodies which were used to inhibit allergic patients' IgE binding to Can f 1. IgE binding sites were visualized on a model of the Can f 1 three-dimensional structure. We found that Can f 1 does not contain any relevant sequential IgE epitopes. However, IgE inhibition experiments with anti-peptide specific IgGs showed that Can f 1 N- and C-terminal portion assembled a major conformational binding site. In conclusion, our study is the first to identify the major IgE epitope-containing area of the dog allergen Can f 1. This finding is important for the development of allergen-specific treatment strategies.
Synthesis and characterization of polycarbonates based on bisphenol S by melt transesterification (1997)

Several sulfone-containing polycarbonates, having inherent viscosity 0.25–0.30 dL g−1 in N,N-dimethylformamide (DMF), were prepared by melt polycondensation of diphenyl carbonate (DPC) with various aromatic and aliphatic diols, in the presence of zinc acetate as transesterification catalyst. The polycarbonates were examined with IR spectra, inherent viscosity, solubility, tensile strength, contact angle, DSC and TGA. Almost all polymers were soluble in DMF, pyridine, N-methyl pyrrolidinone (NMP), THF, phenol and dimethylsulfoxide (DMSO), partially soluble in nitrobenzene, but insoluble in acetone. Polycarbonate with introduced ether linkages leads to enhanced flexibility and elongation strength. The contact angle of the polycarbonate based on bisphenol S was found in the range 42–80°, smaller than that of polycarbonates based on bisphenol AF and bisphenol A. The wettability of polycarbonate films based on bisphenol S remarkably increased with increasing oxyethylene unit in polymer chain. The smaller values of Td of PC-3-PC-7 than of PC-1 is attributed to the flexible ether linkage. The thermal stability of a brominated aromatic polycarbonate (PC-2) is less than that of the unbrominated one (PC-1). The brominated aromatic polycarbonate (PC-2) has good flame retardency, as indicated by the large limiting oxygen index 56. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 2453–2460, 1997
NONDESTRUCTIVE IDENTIFICATION OF CHEMICAL WARFARE AGENTS AND EXPLOSIVES BY NEUTRON GENERATOR-DRIVEN PGNAA (2007)

This is a preprint of a paper intended for publication in a journal or proceedings. Since changes may be made before publication, this preprint should not be cited or reproduced without permission of the author. This document was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, or any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for any third party’s use, or the results of such use, of any information, apparatus, product or process disclosed in this report, or represents that its use by such third party would not infringe privately owned rights. The views expressed in this paper are not necessarily those of the United States Government or the sponsoring agency.
Supplementary Table 1 from Cleaved NOTCH1 Expression Pattern in Head and Neck Squamous Cell Carcinoma Is Associated with NOTCH1 Mutation, HPV Status, and High-Risk Features (2023)

&lt;p&gt;Supplementary Table 1. Clinicopathological characteristics of tumors with NICD1 IHC available compared with unavailable.&lt;/p&gt;
Learn about 3D Printing's Cutting Edge at July's Additive International Summit (2022)

This July, leading researchers from the world of additive manufacturing will gather at Nottingham's Additive International Summit to share insights into the technologies that are shaping the future of the sector. Summit co-chairs - Professors Richard Hague and Chris Tuck - celebrate the welcome return of an event that is key for a sector which thrives on knowledge sharing.
ChemInform Abstract: STEREOCHEMIE CYCLISCHER ORGANOPHOSPHORVERBINDUNGEN 3. MITT. STEREOSPEZIFISCHE SYNTH. VON CIS‐ UND TRANS‐2‐PHENYLAMINO‐2‐OXO‐4‐METHYL‐1,3,2‐DIOXAPHOSPHORINAN (1973)

Abstract Die Reaktion des Phosphits (I) über das Chlor‐dioxaphosphorinan (II) zu der Titelverbindung (III) geht ebenso wie die Reaktion (IV)‐(V) unter Umkehr der Konfiguration am Pbei jedem Schritt vor sich, während bei den Reaktionsfolgen (I)‐(VI)‐(VII) und (VIII)‐(IX)‐(X) die Konfiguration am P gewahrt bleibt.
Session Initiation Protocol (SIP) Extension for Instant Messaging Status of this Memo (2002)

Instant Messaging (IM) refers to the transfer of messages between users in near real-time. These messages are usually, but not required to be, short. IMs are often used in a conversational mode, that is, the transfer of messages back and forth is fast enough for participants to maintain an interactive conversation. This document proposes the MESSAGE method, an extension to the Session Initiation Protocol (SIP) that allows the transfer of Instant Messages. Since the MESSAGE request is an extension to SIP, it inherits all the request routing and security features of that protocol. MESSAGE requests carry the content in the form of MIME body parts. MESSAGE requests do not themselves initiate a SIP dialog; under normal usage each Instant Message stands alone, much like pager messages. MESSAGE requests may be sent in the context of a dialog initiated by some other SIP request.
Nanomechanical characterization of single-walled carbon nanotube reinforced epoxy composites (2004)

Nanomechanical properties of single-walled carbon nanotube (SWNT) reinforced epoxy composites with varying weight percentage (0, 1, 3, and 5 wt%) of nanotubes were measured by nanoindentation and nanoscratch techniques. Hardness and elastic modulus were measured using a nanoindenter. Scratch resistance and scratch damage were studied using the AFM tip sliding against the SWNT reinforced sample surfaces. Nanoindentation/nanoscratch deformation and fracture behaviour was studied by in situ imaging of the indentation impressions/scratch tracks. Viscoelastic properties of the nanocomposites were measured using nanoindentation dynamic mechanical analysis tests. The reinforcing mechanisms are discussed with reference to the nanotube dispersion, interfacial bonding, and load transfer in the SWNT reinforced polymer composites.
Evaluation of the voltage support strategies for the low voltage grid connected PV generators (2010)

Admissible range of grid voltage is one of the strictest constraints for the penetration of distributed photovoltaic (PV) generators especially connection to low voltage (LV) public networks. Voltage limits are usually fulfilled either by network reinforcements or limiting of power injections from PVs. In order to increase PV penetration level further, new voltage support control functions for individual inverters are required. This paper investigates distributed reactive power regulation and active power curtailment strategies regarding the development of PV connection capacity by evaluation of reactive power efforts and requirement of minimum active power curtailment. Furthermore, a small scale experimental setup is built to reflect real grid interaction in the laboratory by achieving critical types of grid (weak and sufficiently stiff).
Learning with a non-exhaustive training dataset (2009)

For a training dataset with a nonexhaustive list of classes, i.e. some classes are not yet known and hence are not represented, the resulting learning problem is ill-defined. In this case a sample from a missing class is incorrectly classified to one of the existing classes. For some applications the cost of misclassifying a sample could be negligible. However, the significance of this problem can better be acknowledged when the potentially undesirable consequences of incorrectly classifying a food pathogen as a nonpathogen are considered. Our research is directed towards the real-time detection of food pathogens using optical-scattering technology. Bacterial colonies consisting of the progeny of a single parent cell scatter light at 635 nm to produce unique forward-scatter signatures. These spectral signatures contain descriptive characteristics of bacterial colonies, which can be used to identify bacteria cultures in real time. One bottleneck that remains to be addressed is the nonexhaustive nature of the training library. It is very difficult if not impractical to collect samples from all possible bacteria colonies and construct a digital library with an exhaustive set of scatter signatures. This study deals with the real-time detection of samples from a missing class and the associated problem of learning with a nonexhaustive training dataset. Our proposed method assumes a common prior for the set of all classes, known and missing. The parameters of the prior are estimated from the samples of the known classes. This prior is then used to generate a large number of samples to simulate the space of missing classes. Finally a Bayesian maximum likelihood classifier is implemented using samples from real as well as simulated classes. Experiments performed with samples collected for 28 bacteria subclasses favor the proposed approach over the state of the art.
HCO3− Secretion by Murine Nasal Submucosal Gland Serous Acinar Cells during Ca2+-stimulated Fluid Secretion (2008)

Airway submucosal glands contribute to airway surface liquid (ASL) composition and volume, both important for lung mucociliary clearance. Serous acini generate most of the fluid secreted by glands, but the molecular mechanisms remain poorly characterized. We previously described cholinergic-regulated fluid secretion driven by Ca(2+)-activated Cl(-) secretion in primary murine serous acinar cells revealed by simultaneous differential interference contrast (DIC) and fluorescence microscopy. Here, we evaluated whether Ca(2+)-activated Cl(-) secretion was accompanied by secretion of HCO(3)(-), possibly a critical ASL component, by simultaneous measurements of intracellular pH (pH(i)) and cell volume. Resting pH(i) was 7.17 +/- 0.01 in physiological medium (5% CO(2)-25 mM HCO(3)(-)). During carbachol (CCh) stimulation, pH(i) fell transiently by 0.08 +/- 0.01 U concomitantly with a fall in Cl(-) content revealed by cell shrinkage, reflecting Cl(-) secretion. A subsequent alkalinization elevated pH(i) to above resting levels until agonist removal, whereupon it returned to prestimulation values. In nominally CO(2)-HCO(3)(-)-free media, the CCh-induced acidification was reduced, whereas the alkalinization remained intact. Elimination of driving forces for conductive HCO(3)(-) efflux by ion substitution or exposure to the Cl(-) channel inhibitor niflumic acid (100 microM) strongly inhibited agonist-induced acidification by >80% and >70%, respectively. The Na(+)/H(+) exchanger (NHE) inhibitor dimethylamiloride (DMA) increased the magnitude (greater than twofold) and duration of the CCh-induced acidification. Gene expression profiling suggested that serous cells express NHE isoforms 1-4 and 6-9, but pharmacological sensitivities demonstrated that alkalinization observed during both CCh stimulation and pH(i) recovery from agonist-induced acidification was primarily due to NHE1, localized to the basolateral membrane. These results suggest that serous acinar cells secrete HCO(3)(-) during Ca(2+)-evoked fluid secretion by a mechanism that involves the apical membrane secretory Cl(-) channel, with HCO(3)(-) secretion sustained by activation of NHE1 in the basolateral membrane. In addition, other Na(+)-dependent pH(i) regulatory mechanisms exist, as evidenced by stronger inhibition of alkalinization in Na(+)-free media.
Classically Stable Nonsingular Cosmological Bounces (2016)

One of the fundamental questions of theoretical cosmology is whether the Universe can undergo a nonsingular bounce, i.e., smoothly transit from a period of contraction to a period of expansion through violation of the null energy condition (NEC) at energies well below the Planck scale and at finite values of the scale factor such that the entire evolution remains classical. A common claim has been that a nonsingular bounce either leads to ghost or gradient instabilities or a cosmological singularity. In this Letter, we consider a well-motivated class of theories based on the cubic Galileon action and present a procedure for explicitly constructing examples of a nonsingular cosmological bounce without encountering any pathologies and maintaining a subluminal sound speed for comoving curvature modes throughout the NEC violating phase. We also discuss the relation between our procedure and earlier work.
[Basic study on relationship between estimated rate constants and noise in FDG kinetic analysis]. (1996)

For accurate estimation of the rate constants in 18F-FDG dynamic study, the shape of the estimation function (phi) is crucial. In this investigation, the relationship between the noise level in tissue time activity curve and the shape of the least squared estimation function which is the sum of squarred error between a function of model parameters and a measured data is calculated in 3 parameter model of 18F-FDG. In the first simulation, by using actual plasma time activity curve, the true tissue curve was generated from known sets of rate constants ranging 0.05 < or = k1 < or = 0.15, 0.1 < or = k2 < or = 0.2 and 0.01 < or = k3 < or = 0.1 in 0.01 step. This procedure was repeated under various noise levels in the tissue time activity curve from 1 to 8% of the maximum value in the tissue activity. In the second simulation, plasma and tissue time activity curves from clinical 18F-FDG dynamic study were used to calculate the phi. Results are: (1) In the noise-free case, because the global minima is separated from neighboring local minimums, it was easy to find out the optimum point. However, with increasing noise level, the optimum point was buried in many neighboring local minima. Making it difficult to find out the optimum point. (2) The optimum point was found within 20% of the convergence point by standard non-linear optimization method. (3) The shape of phi for the clinical data was similar to that with the noise level of 3 or 5% in the first simulation. Therefore direct search within the area extending 20% from the result of usual non-linear curve fitting procedure is recommended for accurate estimation of the constants.
Titelbild: Expanding the Functional Group Compatibility of Small‐Molecule Microarrays: Discovery of Novel Calmodulin Ligands (Angew. Chem. 21/2003) (2003)

Mikroarrays aus kleinen Molekülen ermöglichen die robuste und skalierbare Suche nach Ligand‐Protein‐Wechselwirkungen. Das Titelbild zeigt das Protein Calmodulin im Komplex mit einem kleinen Molekül, das mithilfe der neuartigen “Slide‐Capture”‐Methode auf einer Glasoberfläche immobilisiert wurde. Mehr über diese Technik und ihre Anwendung erfahren Sie in der Zuschrift von S. L. Schreiber et al. auf S. 2478ff.
A Single-Trim CMOS Bandgap Reference With a $3\sigma$ Inaccuracy of $\pm$0.15% From ${-}$40$^{\circ}$C to 125$^{\circ}$C (2011)

A CMOS bandgap reference with an inaccuracy of ±0.15% (3 σ) from -40°C to 125°C is presented. In contrast to prior art, it requires only a single trim to achieve this level of precision. A detailed analysis of the various error sources is provided, and techniques to reduce them are discussed. The prototype bandgap reference draws 55 μA from a 1.8 V supply, and occupies 0.12 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in a 0.16 μm CMOS process. Experimental results from two runs show that, with the use of chopping and higher-order curvature correction to remove non-PTAT errors, the residual error of a bandgap reference is mainly PTAT, and can be removed by a single room temperature trim.
Performance of a packet switch with input and output queueing under unbalanced traffic (1992)

High performance in advanced packet switches can be achieved by providing queuing both at the input and the output ports. The author studies the performance of this class of switches under nonuniform traffic. Two different output queuing arrangements are considered, namely, the case where dedicated queues are provided at each output port, and the case where the output queuing space is shared among all the output ports. An analytical approach is presented for the performance study of these two schemes in the case of operation with fixed-size packets and under various degrees of traffic imbalance at the inputs or the outputs. The measures investigated include the average delay, the maximum throughput of the switch in the case of output traffic imbalance, and the saturation load in the case of input traffic imbalance. Analytical results for these measures are derived for the case of a switch with a large number of input and output ports. Numerical results for the maximum throughput and the saturation load are presented. It is demonstrated that the scheme of output sharing performs better than the scheme of dedicated output queuing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
KOH vs Deionized Water Operation in Anion Exchange Membrane Electrolyzers (2022)

Anion exchange membrane water electrolyzers (AEMELs) have recently received significant attention due to their potential advantages over proton exchange membrane electrolyzers (PEMELs). However, some AEMELs feed an aqueous salt solution to the cell where PEMELs typically feed deionized (DI) water. DI water is preferred to keep the system and maintenance costs low. Because of this, many AEMEL researchers report performance both in the salt solution (typically KOH) and DI water. However, the methodology for switching between KOH and DI water is often poorly defined, and it is unclear what impact the residual salt has on cell performance after switching from salt to DI water. Having a fully deionized environment is important because the presence of salts in the water feed increase the effective electrochemical surface area of the catalyst in the three-dimensional electrode and residual salt remaining after switching to DI water feed can have a misleading transient effect on cell performance. This paper focuses on understanding the transition from KOH to DI water testing in AEMELs. It is shown that when switching from salt to DI water feed, a large volume of DI water must be fed over several hours to achieve true DI-water performance. It is also shown that starting AEMELs from the beginning with DI water feed (without any KOH ever being fed to the cell) results in better cell durability. Lastly, a cell is demonstrated having operated exclusively on DI water at 1.0 A cm −2 for 500 h at an operating voltage of ca. 2 V and a low degradation rate.
Iminosugar inhibitors for treating the lysosomal glycosphingolipidoses (2005)

The inherited metabolic disorders of glycosphingolipid (GSL) metabolism are a relatively rare group of diseases that have diverse and often neurodegenerative phenotypes. Typically, a deficiency in catabolic enzyme activity leads to lysosomal storage of GSL substrates and in many diseases, several other glycoconjugates. A novel generic approach to treating these diseases has been termed substrate reduction therapy (SRT), and the discovery and development of N-alkylated imino sugars as effective and approved drugs is discussed. An understanding of the molecular mechanism for the inhibition of the key enzyme in GSL biosynthesis, ceramide glucosyltransferase (CGT) by N-alkylated imino sugars, has also lead to compound design for improvements to inhibitory potency, bioavailability, enzyme selectivity, and biological safety. Following a successful clinical evaluation of one compound, N-butyl-deoxynojirimycin [(NB-DNJ), miglustat, Zavesca], for treating type I Gaucher disease, issues regarding the significance of side effects and CNS access have been addressed as exposure of drug to patients has increased. An alternative experimental approach to treat specific glycosphingolipid (GSL) lysosomal storage diseases is to use imino sugars as molecular chaperons that assist protein folding and stability of mutant enzymes. The principles of chaperon-mediated therapy (CMT) are described, and the potential efficacy and preclinical status of imino sugars is compared with substrate reduction therapy (SRT). The increasing use of imino sugars for clinical evaluation of a group of storage diseases that are complex and often intractable disorders to treat has considerable benefit. This is particularly so given the ability of small molecules to be orally available, penetrate the central nervous system (CNS), and have well-characterized biological and pharmacological properties.