gebhart/patrepeval huggingface dataset:
Controlling complement resistance in cancer by using human monoclonal antibodies that neutralize complement-regulatory proteins CD55 and CD59 (2005)

Expression of the complement-regulatory proteins (CRP) CD46, CD55 and CD59 represents a strategy used by tumor cells to evade complement-dependent cell cytoxicity stimulated by monoclonal antibodies. We have isolated two single-chain variable fragments (scFv) to CD55 and CD59 from a human phage-display library and from these scFv we have produced two miniantibodies (MB), MB-55 (against CD55) and MB-59 (against CD59), containing the human hinge-CH2-CH3 domains of IgG1. The specificity of the two MB for the corresponding CRP was assessed by ELISA using purified CD46, CD55 and CD59. MB-55 and MB-59 neutralized the inhibitory activity of CD55 and CD59, respectively, restoring the complement-mediated lysis of sheep and guinea pig erythrocytes that was otherwise inhibited by the two CRP. FACS analysis revealed binding of MB-55 and MB-59 to the lymphoma cell line Karpas 422. The two MB induced a two-fold increase in the complement-dependent killing of these cells stimulated by Rituximab, a chimeric anti-CD20 monoclonal antibody. Transfection of HEK293T cells with vectors encoding MB-55 or MB-59 markedly reduced the expression of CD55 and CD59. We conclude that the human antibodies MB-55 and MB-59 may represent a therapeutic tool to increase the complement-dependent killing activity of Rituximab in the treatment of non-Hodgkin's lymphoma.
Supplementary Figure from Acetylated HOXB13 Regulated Super Enhancer Genes Define Therapeutic Vulnerabilities of Castration-Resistant Prostate Cancer (2023)

Supplementary Figure from Acetylated HOXB13 Regulated Super Enhancer Genes Define Therapeutic Vulnerabilities of Castration-Resistant Prostate Cancer
Curcumin Disrupts the Mammalian Target of Rapamycin-Raptor Complex (2009)

Curcumin (diferuloylmethane), a polyphenol natural product of the plant Curcuma longa, is undergoing early clinical trials as a novel anticancer agent. However, the anticancer mechanism of curcumin remains to be elucidated. Recently, we have shown that curcumin inhibits phosphorylation of p70 S6 kinase 1 (S6K1) and eukaryotic initiation factor 4E (eIF4E) binding protein 1 (4E-BP1), two downstream effector molecules of the mammalian target of rapamycin complex 1 (mTORC1) in numerous cancer cell lines. This study was designed to elucidate the underlying mechanism. We observed that curcumin inhibited mTORC1 signaling not by inhibition of the upstream kinases, such as insulin-like growth factor 1 receptor (IGF-IR) and phosphoinositide-dependent kinase 1 (PDK1). Further, we found that curcumin inhibited mTORC1 signaling independently of protein phosphatase 2A (PP2A) or AMP-activated protein kinase AMPK-tuberous sclerosis complex (TSC). This is evidenced by the findings that curcumin was able to inhibit phosphorylation of S6K1 and 4E-BP1 in the cells pretreated with PP2A inhibitor (okadaic acid) or AMPK inhibitor (compound C), or in the cells expressing dominant-negative (dn) PP2A, shRNA to PP2A-A subunit, or dn-AMPKalpha. Curcumin did not alter the TSC1/2 interaction. Knockout of TSC2 did not affect curcumin inhibition of mTOR signaling. Finally, we identified that curcumin was able to dissociate raptor from mTOR, leading to inhibition of mTORC1 activity. Therefore, our data indicate that curcumin may represent a new class of mTOR inhibitor.
Self-Assembly of Aβ40, Aβ42 and Aβ43 Peptides in Aqueous Mixtures of Fluorinated Alcohols (2015)

Fluorinated alcohols such as hexafluoroisopropanol (HFIP) and trifluoroethanol (TFE) have the ability to promote α-helix and β-hairpin structure in proteins and peptides. HFIP has been used extensively to dissolve various amyloidogenic proteins and peptides including Aβ, in order to ensure their monomeric status. In this paper, we have investigated the self-assembly of Aβ40, Aβ42, and Aβ43 in aqueous mixtures of fluorinated alcohols from freshly dissolved stock solutions in HFIP. We have observed that formation of fibrillar and non-fibrillar structures are dependent on the solvent composition. Peptides form fibrils with ease when reconstituted in deionized water from freshly dissolved HFIP stocks. In aqueous mixtures of fluorinated alcohols, either predominant fibrillar structures or clustered aggregates were observed. Aqueous mixtures of 20% HFIP are more favourable for Aβ fibril formation as compared to 20% TFE. When Aβ40, Aβ42, and Aβ43 stocks in HFIP are diluted in 50% aqueous mixtures in phosphate buffer or deionized water followed by slow evaporation of HFIP, Aβ peptides form fibrils in phosphate buffer and deionized water. The clustered structures could be off-pathway aggregates. Aβ40, Aβ42, and Aβ43 showed significant α-helical content in freshly dissolved HFIP stocks. The α-helical conformational intermediate in Aβ40, Aβ42, and Aβ43 could favour the formation of both fibrillar and non-fibrillar aggregates depending on solvent conditions and rate of α-helical to β-sheet transition.
Inhibitory Effect of ACTH and Related Peptides on Extinction of Conditioned Avoidance Behavior in Rats (1966)

SummaryACTH, administered during extinction, delays extinction of an avoidance response in rats. To study structure activity relationships, the rate of extinction of an avoidance response performed in a shuttle-box and a pole jumping situation, was investigated in rats treated during the extinction period with ACTH (A3 peptide), synthetic ACTH β 1-24, β-MSH, α-MSH, ACTH 1-10, ACTH 5-10, and ACTH 11-24, administered as long acting zinc phosphate preparations. Zinc phosphate complex and protamine zinc insulin (PZI) were used as placebo control substances. It appeared that ACTH and related peptides significantly delayed the rate of extinction of the avoidance response. Full activity was obtained with ACTH 1-10 peptide while ACTH 5-10 was less active. ACTH 11-24 and PZI were without effect. These results were interpreted to indicate that the active part of ACTH in this respect is located in the N-terminal part of the molecule, presumably in the first 10 amino acids.
Repeated Intracerebroventricular Administration of Glucagon-Like Peptide-1-(7-36) Amide or Exendin-(9-39) Alters Body Weight in the Rat (1999)

Central nervous system glucagon-like peptide-1-(7-36) amide (GLP-1) administration has been reported to acutely reduce food intake in the rat.We here report that repeated intracerebroventricular (icv) injection of GLP-1 or the GLP-1 receptor antagonist, exendin-(9 -39), affects food intake and body weight.Daily icv injection of 3 nmol GLP-1 to schedule-fed rats for 6 days caused a reduction in food intake and a decrease in body weight of 16 5 g (P 0.02 compared with saline-injected controls).Daily icv administration of 30 nmol exendin-(9 -39) to schedule-fed rats for 3 days caused an increase in food intake and increased body weight by 7 2 g (P 0.02 compared with saline-injected controls).Twice daily icv injections of 30 nmol exendin-(9 -39) with 2.4 nmol neuropeptide Y to ad libitumfed rats for 8 days increased food intake and increased body weight by 28 4 g compared with 14 3 g in neuropeptide Y-injected controls (P 0.02).There was no evidence of tachyphylaxis in response to icv GLP-1 or exendin-(9 -39).GLP-1 may thus be involved in the regulation of body weight in the rat.
Clinicopathologic analysis of primary gastroenteropancreatic poorly differentiated neuroendocrine carcinoma; A ten year retrospective study of 68 cases at Moffit Cancer Center (2019)

GEP-PDNECA occurred in many part of the GI tract, most commonly in the colorectal region. Positivity of neuroendocrine markers was variable, which helped to confirm neuro-endocrine differentiation and to avoid under-diagnosis of GEP-PDNECA, especially in metastatic setting. Overall prognosis of GEP-PDNECA patients following platinum and etoposide therapy in our series was relatively favorable but remained poor in the presence of distant metastases.
Defective endoplasmic reticulum-mitochondria contacts and bioenergetics in SEPN1-related myopathy (2020)

SEPN1-related myopathy (SEPN1-RM) is a muscle disorder due to mutations of the SEPN1 gene, which is characterized by muscle weakness and fatigue leading to scoliosis and life-threatening respiratory failure. Core lesions, focal areas of mitochondria depletion in skeletal muscle fibers, are the most common histopathological lesion. SEPN1-RM underlying mechanisms and the precise role of SEPN1 in muscle remained incompletely understood, hindering the development of biomarkers and therapies for this untreatable disease. To investigate the pathophysiological pathways in SEPN1-RM, we performed metabolic studies, calcium and ATP measurements, super-resolution and electron microscopy on in vivo and in vitro models of SEPN1 deficiency as well as muscle biopsies from SEPN1-RM patients. Mouse models of SEPN1 deficiency showed marked alterations in mitochondrial physiology and energy metabolism, suggesting that SEPN1 controls mitochondrial bioenergetics. Moreover, we found that SEPN1 was enriched at the mitochondria-associated membranes (MAM), and was needed for calcium transients between ER and mitochondria, as well as for the integrity of ER-mitochondria contacts. Consistently, loss of SEPN1 in patients was associated with alterations in body composition which correlated with the severity of muscle weakness, and with impaired ER-mitochondria contacts and low ATP levels. Our results indicate a role of SEPN1 as a novel MAM protein involved in mitochondrial bioenergetics. They also identify a systemic bioenergetic component in SEPN1-RM and establish mitochondria as a novel therapeutic target. This role of SEPN1 contributes to explain the fatigue and core lesions in skeletal muscle as well as the body composition abnormalities identified as part of the SEPN1-RM phenotype. Finally, these results point out to an unrecognized interplay between mitochondrial bioenergetics and ER homeostasis in skeletal muscle. They could therefore pave the way to the identification of biomarkers and therapeutic drugs for SEPN1-RM and for other disorders in which muscle ER-mitochondria cross-talk are impaired.
Gel template leaching: An approach to functional nanoporous membranes (1996)

Abstract A novel preparation method for nanoporous structures, denoted “Gel Template Leaching”, is described. The approach is based on the gelation of solutions containing two low molecular weight compounds of which one is crystallizable and the other curable. Gelation of the solute upon cooling followed by curing of the solvent below the gelation temperature lead to the formation of a semi‐IPN consisting of a reversibly and a covalently crosslinked network. After leaching of the solute (the template) a well‐defined nanoporous architecture was formed. Functional pores could be obtained after charging the pore walls with ionic sites.
Signal analysis of NEMS sensors at the output of a chromatography column (2015)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation François Bertholon, Olivier Harant, Christian Jutten, Bertrand Bourlon, Laurent Gerfault, Pierre Grangeat; Signal analysis of NEMS sensors at the output of a chromatography column. AIP Conference Proceedings 13 January 2015; 1641 (1): 329–336. https://doi.org/10.1063/1.4905995 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Chloroperoxidase-catalyzed enantioselective oxidation of methyl phenyl sulfide with dihydroxyfumaric acid/oxygen or ascorbic acid/oxygen as oxidants (1999)

The chloroperoxidase catalyzed oxidation of methyl phenyl sulfide to (R)-methyl phenyl sulfoxide was investigated, both in batch and membrane reactors, using as oxidant H2O2, or O2 in the presence of either dihydroxyfumaric acid or ascorbic acid. The effects of pH and nature and concentration of the oxidants on the selectivity, stability, and productivity of the enzyme were evaluated. The highest selectivity was displayed by ascorbic acid/O2, even though the activity of chloroperoxidase with this system was lower than that obtained with the others. When the reaction was carried out in a membrane reactor, it was possible to reuse the enzyme for several conversion cycles. The results obtained with ascorbic acid/O2 and dihydroxyfumaric acid/O2 as oxidants do not seem to be compatible with either a mechanism involving hydroxyl radicals as the active species or with the hypothesis that oxidation occurs through the initial formation of H2O2. Copyright 1999 John Wiley & Sons, Inc.
Tailoring the group velocity in photonic crystal waveguides (2006)

A silicon-on-insulator photonic crystal waveguide is tailored to obtain a ~20-nm lowloss bandwidth with low group-index dispersion and group velocity around c/20. This is obtained by perturbing the holes adjacent to the waveguide core.
Modeling rater diagnostic skills in binary classification processes (2017)

Many disease diagnoses involve subjective judgments by qualified raters. For example, through the inspection of a mammogram, MRI, or ultrasound image, the clinician himself becomes part of the measuring instrument. To reduce diagnostic errors and improve the quality of diagnoses, it is necessary to assess raters' diagnostic skills and to improve their skills over time. This paper focuses on a subjective binary classification process, proposing a hierarchical model linking data on rater opinions with patient true disease-development outcomes. The model allows for the quantification of the effects of rater diagnostic skills (bias and magnifier) and patient latent disease severity on the rating results. A Bayesian Markov chain Monte Carlo (MCMC) algorithm is developed to estimate these parameters. Linking to patient true disease outcomes, the rater-specific sensitivity and specificity can be estimated using MCMC samples. Cost theory is used to identify poor- and strong-performing raters and to guide adjustment of rater bias and diagnostic magnifier to improve the rating performance. Furthermore, diagnostic magnifier is shown as a key parameter to present a rater's diagnostic ability because a rater with a larger diagnostic magnifier has a uniformly better receiver operating characteristic (ROC) curve when varying the value of diagnostic bias. A simulation study is conducted to evaluate the proposed methods, and the methods are illustrated with a mammography example.
Local method for detecting communities (2005)

We propose a method of community detection that is computationally inexpensive and possesses physical significance to a member of a social network. This method is unlike many divisive and agglomerative techniques and is local in the sense that a community can be detected within a network without requiring knowledge of the entire network. A global application of this method is also introduced. Several artificial and real-world networks, including the famous Zachary karate club, are analyzed.
All-digital VLSI fuzzy inference engine: a case study (1995)

Dedicated fuzzy logic hardware has been developed for several application fields. Both digital and analogue technologies have been adopted. The architecture and VLSI design of a fully digital fuzzy processor are presented. The proposed processor and the related architectural studies form a case study to demonstrate the limits and possibilities of digital technology for fuzzy applications.
Universal Jurisdiction under Attack: An Assessment of African Misgivings towards International Criminal Justice as Administered by Western States (2011)

This article discusses the current criticism, expressed by African states and institutions, of the exercise of universal jurisdiction by Western states, accusing the latter of overstepping their lawful powers, as well as practicing ‘legal colonialism’. In order to gauge whether this criticism is warranted, this article starts by expounding the normative framework. Subsidiary universal jurisdiction derives out of the primary obligations of the territorial state or the state of the perpetrator to initiate criminal investigations and the prosecution of international crimes. These states owe such obligations towards the entire international community (&lt;it&gt;erga omnes&lt;/it&gt;). Inadequate performance by the states bearing prior responsibility therefore triggers the right of other states to exercise universal jurisdiction. An analysis of some cases and legal trends provides this author with the impression that Western courts have made prudent use of universal jurisdiction; that their case law has contributed to the development of international criminal law; and that international criminal tribunals have frequently orchestrated their initiatives. The author therefore concludes that this criticism has, in general, been far-fetched and unfair. Nevertheless, he submits that such indignation might have been triggered by isolated events in which Western judges have overstepped their powers and displayed a remarkable lack of political sensitivity.
Integration schemes for dissipative particle dynamics simulations: From softly interacting systems towards hybrid models (2002)

We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a variety of different conditions often studied in simulations. Specifically, we clarify the performance of integration schemes in hybrid models, which combine microscopic and mesoscale descriptions of different particles using both soft and hard interactions. We find that in all three model systems many commonly used integrators may give rise to surprisingly pronounced artifacts in physical observables such as the radial distribution function, the compressibility, and the tracer diffusion coefficient. The artifacts are found to be strongest in systems, where interparticle interactions are soft and predominated by random and dissipative forces, while in systems governed by conservative interactions the artifacts are weaker. Our results suggest that the quality of any integration scheme employed is crucial in all cases where the role of random and dissipative forces is important, including hybrid models where the solvent is described in terms of soft potentials. Regarding the integration schemes, the best overall performance is found for integrators in which the velocity dependence of dissipative forces is taken into account, and particularly good performance is found for an approach in which velocities and dissipative forces are determined self-consistently. Remaining temperature deviations from the desired limit can be corrected by carrying out the self-consistent integration in conjunction with an auxiliary thermostat, in a manner that is similar in spirit to the well-known Nosé–Hoover thermostat. Further, we show that conservative interactions can play a significant role in describing the transport properties of simple fluids, in contrast to approximations often made in deriving analytical theories. In general, our results illustrate the main problems associated with simulation methods in which dissipative forces are velocity dependent, and point to the need to develop new techniques to resolve these issues.
Azimuthally Varying Guided Mode Resonance Filters (2012)

New and novel sensing schemes require optical functions with unconventional spatial light distributions, as well as complex spectral functionality. Micro-optical elements have shown some flexibility in their ability to spatially encode phase information using surface relief dielectrics. In this paper, we present a novel optical component that exploits the properties of optically resonant structures to make an azimuthally spatially varying spectral filter. The dispersive properties are quite unique with an angular resonance shift of 28 Deg/nm. This device is fabricated using techniques that are compatible with standard micro-electronic fabrication technologies.
Electrical and Chemical Analysis of the In-situ H2 Plasma Cleaned InGaSb-Al2O3 Interface (2017)

No abstract available.
Morphology and Lateral Strain Control of Pt Nanoparticles via Core–Shell Construction Using Alloy AgPd Core Toward Oxygen Reduction Reaction (2012)

Controlling the morphology of Pt-based nanomaterials can be an effective way to improve the catalytic activity on a mass basis. Herein we demonstrate for the first time the synthesis of monodispersed core-shell AgPd@Pt nanoparticles with multiply twinned structures. These multiply twinned particles (MTPs), which possess the icosahedra structure, exhibit superior catalytic activity toward oxygen reduction reaction (ORR) in fuel cells. The Ag component of the alloy AgPd inner core is crucial for the construction of the multiply twinned structure of the core-shell nanoparticles, while the Pd component is used to reduce the tensile strain effect of the Ag on the deposited Pt layers, rendering the Pt binding energy in core-shell AgPd@Pt MTPs to be close to that of commercial Pt nanoparticles. The enhanced ORR activity of AgPd@Pt/C can be explained in terms of a much higher surface fraction of atoms on the (111) facets for icosahedral MTPs. This core-shell structure offers an interesting example to investigate the morphology and lateral strain effect of the substrate on the deposited layers, and their influence on the catalytic activity of metal catalysts.
Single-dose radiosurgical treatment for hepatic metastases - therapeutic outcome of 138 treated lesions from a single institution (2013)

This study confirms safety of SBRT in liver lesions, with 6- and 12 months local control of 87% and 70%. The dataset represents the clinical situation in a large oncology setting, with many competing treatment options and heterogeneous patient characteristics.
Pruned dynamic programming for optimal multiple change-point detection (2010)

Multiple change-point detection models assume that the observed data is a
realization of an independent random process affected by K-1 abrupt changes,
called change-points, at some unknown positions. For off-line detection a
dynamic programming (DP) algorithm retrieves the K-1 change-points minimizing
the quadratic loss and reduces the complexity from \Theta(n^K) to \Theta(Kn^2)
where n is the number of observations. The quadratic complexity in n still
restricts the use of such an algorithm to small or intermediate values of n. We
propose a pruned DP algorithm that recovers the optimal solution. We
demonstrate that at worst the complexity is in O(Kn^2) time and O(Kn) space and
is therefore at worst equivalent to the classical DP algorithm. We show
empirically that the run-time of our proposed algorithm is drastically reduced
compared to the classical DP algorithm. More precisely, our algorithm is able
to process a million points in a matter of minutes compared to several days
with the classical DP algorithm. Moreover, the principle of the proposed
algorithm can be extended to other convex losses (for example the Poisson loss)
and as the algorithm process one observation after the other it could be
adapted for on-line problems.