gebhart/patrepeval huggingface dataset:
Caveolin-3 regulates the activity of Ca2+/calmodulin-dependent protein kinase II in C2C12 cells (2022)

Caveolins, encoded by the <i>Cav</i> gene family, are the main components of caveolae. Caveolin-3 (<i>Cav3</i>) is specifically expressed in muscle cells. Mutations in <i>Cav3</i> are responsible for a group of muscle diseases called caveolinopathies, and <i>Cav3</i> deficiency is associated with sarcolemmal membrane alterations, disorganization of T-tubules, and disruption of specific cell-signaling pathways. However, Cav3 overexpression increases the number of sarcolemmal caveolae and muscular dystrophy-like regenerating muscle fibers with central nuclei, suggesting that the alteration of Cav3 expression levels or localization influences muscle cell functions. Here, we used mouse C2C12 myoblasts in which <i>Cav3</i> expression was suppressed with short hairpin RNA and found that <i>Cav3</i> suppression impaired myotube differentiation without affecting the expression of <i>MyoD</i> and <i>Myog</i>. We also observed an increase of intracellular Ca<sup>2+</sup> levels, total calpain activity, and Ca<sup>2+</sup>-dependent calmodulin kinase II (CaMKII) levels in <i>Cav3</i>-depleted myoblasts. Importantly, those phenotypes due to <i>Cav3</i> suppression were caused by the ryanodine receptor activation. Furthermore, pharmacological inhibition of CaMKII rescued the impairment of myoblast differentiation due to <i>Cav3</i> knockdown. Our results suggest that <i>Cav3</i> regulates intracellular Ca<sup>2+</sup> concentrations by modulating ryanodine receptor activity in muscle cells and that CaMKII suppression in muscle could be a novel therapy for caveolinopathies.
An Iterative Cellular YNSN Method for Color Printer Characterization (1998)

We propose an iterative method for color printer characterization. We employ a parametric spectral model for color printers based on cellular YNSN (Yule-Nielsen modified spectral Neugebauer) equations. We find the Yule-Nielsen parameter from least squares regression over a training set of spectral measurements using the Euclidean distance in spectral distributions space as the error criterion. We iteratively divide the cells in the colorant space until the average prediction error &#x394;E in every cell is less than a given value.
Response to “Comment on ‘In situ imaging of ultra-fast loss of nanostructure in nanoparticle aggregates’” [J. Appl. Phys. 119, 066103 (2016)] (2016)

First Page
Frege's judgement stroke (2000)

This paper brings to light a new puzzle for Frege interpretation, and offers a solution to that puzzle. The puzzle concerns Frege's judgement-stroke ('r), and consists in a tension between three of Frege's claims. First, Frege vehemently maintains that psychological considerations should have no place in logic. Second, Frege regards the judgementstroke---and the associated dissociation of assertoric force from content, of the act of judgement from the subject matter about which judgement is made---as a crucial part of his logic. Third, Frege holds that judging is an inner mental process, and that the distinction marked by the judgement-stroke, between entertaining a thought and judging that it is true, is a psychological distinction. I argue that what initially looks like confusion here on Frege's part appears quite reasonable when we remind ourselves of the differences between Frege's conception of logic and our own.
Cooling Rate Effects on the Structure of 45S5 Bioglass: Computational and Experimental Evidence of Si--P Avoidance (2019)

Due to its ability to bond with living tissues upon dissolution, 45S5 bioglass and related compositions are promising materials for the replacement, regeneration, and repair of hard tissues in the human body. However, the details of their atomic structure remain unclear. This is partially due to the non-equilibrium nature of glasses, as their non-crystalline structure is highly dependent on their thermal history, namely, the cooling rate used during quenching. Herein, using molecular dynamics (MD) simulations and magic angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy experiments, we investigate the structure of the nominal 45S5 bioglass composition prepared using cooling rates ranging over several orders of magnitude. We show that the simulations results are in very good agreement with experimental data, provided that they are extrapolated toward lower cooling rates achieved in experiments. These results highlight that previously reported inconsistencies between simulations and experiments stem from the difference in cooling rate, thereby addressing one of the longstanding questions on the structure of bioglass. Based on these results, we demonstrate the existence of a Si--P avoidance behavior, which may be key in controlling the bioactivity of 45S5 bioglass.
Pro-inflammatory properties of stromal cell-derived factor-1 (CXCL12) in collagen-induced arthritis (2005)

CXCL12 (stromal cell-derived factor 1) is a unique biological ligand for the chemokine receptor CXCR4. We previously reported that treatment with a specific CXCR4 antagonist, AMD3100, exerts a beneficial effect on the development of collagen-induced arthritis (CIA) in the highly susceptible IFN-gamma receptor-deficient (IFN-gammaR KO) mouse. We concluded that CXCL12 plays a central role in the pathogenesis of CIA in IFN-gammaR KO mice by promoting delayed type hypersensitivity against the auto-antigen and by interfering with chemotaxis of CXCR4+ cells to the inflamed joints. Here, we investigated whether AMD3100 can likewise inhibit CIA in wild-type mice and analysed the underlying mechanism. Parenteral treatment with the drug at the time of onset of arthritis reduced disease incidence and modestly inhibited severity in affected mice. This beneficial effect was associated with reduced serum concentrations of IL-6. AMD3100 did not affect anti-collagen type II antibodies and, in contrast with its action in IFN-gammaR KO mice, did not inhibit the delayed type hypersensitivity response against collagen type II, suggesting that the beneficial effect cannot be explained by inhibition of humoral or cellular autoimmune responses. AMD3100 inhibited the in vitro chemotactic effect of CXCL12 on splenocytes, as well as in vivo leukocyte infiltration in CXCL12-containing subcutaneous air pouches. We also demonstrate that, in addition to its effect on cell infiltration, CXCL12 potentiates receptor activator of NF-kappaB ligand-induced osteoclast differentiation from splenocytes and increases the calcium phosphate-resorbing capacity of these osteoclasts, both processes being potently counteracted by AMD3100. Our observations indicate that CXCL12 acts as a pro-inflammatory factor in the pathogenesis of autoimmune arthritis by attracting inflammatory cells to joints and by stimulating the differentiation and activation of osteoclasts.
A physically-based lumped-charge SCR model (2002)

A physical silicon-controlled rectifier (SCR) model is developed by using the lumped-charge modeling technique to simplify device physics. The model is based on fundamental semiconductor equations and includes most important SCR characteristics; yet it is simple enough to use in circuit simulators. This SCR model is the first to provide correct turn-on and turn-off waveforms for simulation of power switching circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Reliability of 1310 nm Wafer Fused VCSELs (2013)

Wafer fusion vertical cavity surface emitting laser (VCSEL) technology has produced devices that successfully passed all mechanical and electrical Telcordia qualification tests. Accelerated lifetime tests result in times to 1% failure at 70 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^{\circ}{\rm C}$</tex></formula> of 18 years and 30 years at VCSEL driving currents of 9 and 8 mA, respectively. These lifetimes meet the telecom industry reliability requirements for applications in fiber-optic communications networks.
A Practical Preparation of 2-Carboxyphenylboronic Acid and its Application for the Preparation of Biaryl-2-carboxylic Acids using Suzuki Coupling Reactions (2002)

A practical synthesis of 2-carboxyphenylboronic from 2-tolylboronic acid and aqueous potassium permanganate under mild conditions is reported. The title compound couples with aryl bromides containing electron-withdrawing groups to give biaryl-2-carboxylic acids.
Aza-nickelacycle key intermediate in nickel(0)-catalyzed transformation reactions (2015)

This Perspective provides an overview of the oxidative cyclization reactions of alkynes and imines with nickel(0) to give five-membered aza-nickelacycles. These reactions could be a key step in multicomponent coupling and cycloaddition reactions to afford nitrogen-containing organic compounds.
Progressive bridge identification (2004)

We present an efficient algorithm for identification of two-line bridges in combinational CMOS logic that narrows down the two-line bridge candidates based on tester responses for voltage tests. Due to the implicit enumeration of bridge sites, no layout extraction or precomputed stuck-at fault dictionaries are required. The bridge identification is easily refined using additional test pattern results when necessary. We present results for benchmark circuits and four common fault models (wiredAND, wired-OR, dominant, and composite), evaluate the diagnosis against other possible fault types, and summarize the quality of our results.
Interfering with UDP-GlcNAc Metabolism and Heparan Sulfate Expression Using a Sugar Analogue Reduces Angiogenesis (2013)

Heparan sulfate (HS), a long linear polysaccharide, is implicated in various steps of tumorigenesis, including angiogenesis. We successfully interfered with HS biosynthesis using a peracetylated 4-deoxy analogue of the HS constituent GlcNAc and studied the compound's metabolic fate and its effect on angiogenesis. The 4-deoxy analogue was activated intracellularly into UDP-4-deoxy-GlcNAc, and HS expression was inhibited up to ∼96% (IC50 = 16 μM). HS chain size was reduced, without detectable incorporation of the 4-deoxy analogue, likely due to reduced levels of UDP-GlcNAc and/or inhibition of glycosyltransferase activity. Comprehensive gene expression analysis revealed reduced expression of genes regulated by HS binding growth factors such as FGF-2 and VEGF. Cellular binding and signaling of these angiogenic factors was inhibited. Microinjection in zebrafish embryos strongly reduced HS biosynthesis, and angiogenesis was inhibited in both zebrafish and chicken model systems. All of these data identify 4-deoxy-GlcNAc as a potent inhibitor of HS synthesis, which hampers pro-angiogenic signaling and neo-vessel formation.
Atorvastatin Donor Pretreatment Prevents Ischemia/Reperfusion Injury in Renal Transplantation in Rats: Possible Role for Aldose-Reductase Inhibition (2007)

Our data suggest that downregulation of aldose reductase in renal tissue might underlie the protective effect of donor atorvastatin treatment. Donor pretreatment with a statin or an aldose reductase inhibitor could offer a new treatment strategy to prevent transplantation associated tissue injury.
Lack of association between cholesterol blood levels and platelet serotonin uptake (1995)

It has been suggested that low serum cholesterol interferes with brain serotonergic functioning, which results in increased suicidal and aggressive tendencies. To test this hypothesis we investigated the relationship between serum cholesterol, high-density lipoprotein (HDL), low-density lipoprotein (LDL) and triglyceride levels, and serotonin uptake by blood platelets in 17 healthy men aged 39.5 +/- 10.2 years. Platelet serotonin uptake and serum lipids were assayed concomitantly for each individual. Serum cholesterol levels and other serum lipid levels did not correlate with serotonin uptake by platelets at the concentration of 2 x 10(-5) M (a concentration within the maximal uptake capacity range). The results indicate no influence of cholesterol on serotonin uptake, as opposed to some investigators who suggested that high risk of suicide and aggressiveness in hypocholesterolemic individuals is related to impaired serotonin transport.
Thyroid Hormone Replacement Therapy in Patients with Various Types of Cancer (2019)

Primary hypothyroidism is a common endocrine disorder that is effectively treated with l-thyroxine (T4) replacement. Preclinical and limited clinical evidence, however, indicates that T4 is a growth factor for a variety of cancers, acting at the thyroid hormone receptor on plasma membrane integrin αvβ3. T4 is the primary ligand for this receptor, whereas 3,5,3′-triiodo-l-thyronine (T3) is the principal intracellular thyroid hormone analogue. The evidence is reviewed here that T4 is a proliferative for breast, lung, kidney and prostate cancers and for glioblastoma, regulates cancer cell respiration and is a pro-angiogenic factor in established tumors. The recommendation is made that T3 be considered alternative replacement treatment for patients with primary hypothyroidism who also have cancer.
A low dose simulation tool for CT systems with energy integrating detectors (2013)

The proposed method can accurately simulate low-dose CT data starting from high-dose data, including effects from photon starvation and detector noise. This is potentially a very useful tool in helping to determine minimum dose requirements for a wide range of clinical protocols and advanced reconstruction algorithms.
Long-Term Follow-up of Syme Amputations for Peripheral Vascular Disease Associated with Diabetes Mellitus (1988)

Ten patients underwent Syme amputation for diabetic peripheral vascular disease between 1980 and 1986 and were observed postoperatively for an average of 5 years. Surgical wounds healed in only five of the 10 patients; they were then fitted for a permanent Syme's prosthesis. All failures resulted from the inability to heal the surgical incisions primarily. The clinical records of these patients were retrospectively analyzed for predictors of successful clinical outcome. The ischemic index, grade of the lesion, initial wound treatment, and presence of the infection at the time of amputation were not found to be reliable predictors of a successful level of amputation. Clinical assessment of both the vascular and nutritional status of the patient was necessary to predict a successful result at this level of amputation.
Improvement of smooth surface of RuO2 bottom electrode on Al2O3 buffer layer and characteristics of RuO2/TiO2/Al2O3/TiO2/RuO2 capacitors (2017)

Ruthenium oxide (RuO2) thin films, which are deposited by plasma-enhanced atomic layer deposition (PE-ALD) with a Ru(EtCp)2 precursor and oxygen plasma, exhibit a smoother surface [root mean square (RMS) roughness &amp;lt;1 nm] on ionic Al2O3 and TiO2 buffer layers than on a covalent SiO2 buffer layer (RMS roughness of RuO2: 2.5 nm). The Al2O3 and TiO2 buffer layers which have some charges enable us to prolong the duration time of the Ru(EtCp)2 precursor on the buffer layer and cause the nucleation of RuO2 to occur uniformly. The RuO2 film deposited on the Al2O3 buffer layer by PE-ALD (hereafter “PE-ALD-RuO2”) was used as the bottom electrode for a metal-insulator-metal with a TiO2/Al2O3/TiO2 (TAT) insulator. RuO2/TAT/RuO2 capacitors on the Al2O3 and TiO2 buffer layers had a low enough leakage current density (J) (on the order of ∼10−8 A/cm2), unlike RuO2/TAT/RuO2 capacitors on the SiO2 buffer layer and TiN/TAT/TiN capacitors. These results suggest that the different J properties must be related to the surface roughness of the bottom electrode rather than the work function of RuO2 and TiN. Furthermore, the overall dielectric constant of TAT in RuO2/TAT/RuO2 capacitors reasonably ranged from 50 to 30 as the Al2O3 interlayer thickness increased from 0 to 5 nm. During conductive-atomic force microscopy measurements, the TAT/TiN stack structure exhibited several leakage points, while no such leakage points were observed in the case of TAT/RuO2 on the Al2O3 buffer layer. Thus, PE-ALD-RuO2 on the Al2O3 buffer layer is a candidate bottom electrode material for future dynamic random access memory.
A simple model for NMR relaxation in the presence of internal motions with dynamical coupling (2004)

In this paper some effects of dynamical coupling between two interaction-carrying vectors on the internal auto- and cross-correlation functions are investigated in the limit of small amplitude motions. A linearized Langevin approach allows the derivation of explicit expressions for these correlation functions and for the corresponding order parameters.
Informed coding for color hardcopy watermarking (2013)

We investigate informed coding and multi-bit spread spectrum modulation framework for watermarking color images intended to be deployed as printed media. We propose improvements on the embedding and the detection watermarking techniques, aiming for improved color hardcopy watermarking using inkjet printers. The modulation approach allows to increase the watermarking robustness to achieve high payload with good transparency. At the encoding phase the impact of the color background on the detection metric is evaluated based on the estimated ink color correlation between the watermark and the document. This correlation is used to estimate and compare the robustness of sets of patterns which would be otherwise considered equivalent for modulating the same message. This approach allows a proper selection of a set of sequences to be embedded for improved robustness. The detection is further improved by using a proposed whitening filter and a color rejection algorithm. Examples using real life images illustrate the performance enhancement achievable by employing the proposed approaches in color hardcopy watermarking systems.
DTM-based Filtrations (2018)

Despite strong stability properties, the persistent homology of filtrations classically used in Topological Data Analysis, such as, e.g. the Cech or Vietoris-Rips filtrations, are very sensitive to the presence of outliers in the data from which they are computed. In this paper, we introduce and study a new family of filtrations, the DTM-filtrations, built on top of point clouds in the Euclidean space which are more robust to noise and outliers. The approach adopted in this work relies on the notion of distance-to-measure functions, and extends some previous work on the approximation of such functions.
Abstract 4585: Breaking metastatic dormancy during surgical resection of a primary tumor and implications for treatment strategies. (2013)

Abstract At the time of a cancer diagnosis, most patients have localized tumors. Despite elaborate staging schemas for each cancer type in an attempt to stratify patients, the vast majority of patients that die will do so from metastatic disease. We hypothesized that surgery augments the already ongoing activation and mobilization of bone marrow-derived progenitor cells that are critical to colonizing tumor cells at distant sites. These bone marrow-derived cells, by inducing a local inflamed tumor microenvironment, provide survival signals to these seeding tumor cells. Our data show increased metastatic burden in the lung after surgical resection of the primary tumor using two murine cancer models, B16 melanoma and E0771 breast carcinoma. In these models, we also show a surge in hematopoietic and endothelial progenitor cells in the hours and days immediately following resection of the primary tumor, which is not similarly observed in control mice, where surgery was performed in the absence of the primary tumor. We also confirmed that a factor specific to the plasma of the tumor-bearing mice is responsible for this mobilization by using in vitro migration assays, whereby plasma from tumor-bearing mice and surgically resected mice induced an increased migration of lineage negative bone marrow cells compared to the plasma of wild type mice. We confirmed increased levels of MCP-1 and MCSF, both known to mobilize progenitor cells, in the plasma of mice with surgical resection. Additionally, targeting these bone marrow derived hematopoietic and endothelial progenitor cells with Pazopanib prevents the surge in bone marrow-derived cells into the circulation, abolishes the enhanced metastatic spread in mice undergoing surgical resection of the primary tumor, and provides a significant prolongation of survival. Finally, we correlated these data to a cohort of breast cancer patients where circulating levels of progenitor cells were analyzed at time points before and after surgery, which confirmed the mobilization of progenitor cells with surgery. Together, these results provide evidence for the increased risk of metastatic spread after surgical resection of the primary tumor and suggest that blocking progenitor cell mobilization by adjuvant treatment during or immediately following surgery, the incidence of metastatic recurrence may be reduced. Citation Format: Selena R. Granitto, Amber Giles, Simon Lavotshkin, Daniel Rutigliano, David Lyden, Rosandra N. Kaplan. Breaking metastatic dormancy during surgical resection of a primary tumor and implications for treatment strategies. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4585. doi:10.1158/1538-7445.AM2013-4585
Rational Cooperation in the Finitely Repeated Prisoners' Dilemma (2010)

The purpose of this note is to demonstrate how reputation effects due to informational asymmetries can generate cooperative behavior in finitely-repeated versions of the classic prisoners' dilemma. The methods employed are those developed in our work on the chain-store paradox (Kreps and Wilson 1981, Milgrom and Roberts 1981). We refer the reader to those papers for motivation, formal definitions, and interpretation. (Author)
Manipulating the Electronic Excited State Energies of Pyrimidine-Based Thermally Activated Delayed Fluorescence Emitters To Realize Efficient Deep-Blue Emission (2017)

The development of efficient and robust deep-blue emitters is one of the key issues in organic light-emitting devices (OLEDs) for environmentally friendly, large-area displays or general lighting. As a promising technology that realizes 100% conversion from electrons to photons, thermally activated delayed fluorescence (TADF) emitters have attracted considerable attention. However, only a handful of examples of deep-blue TADF emitters have been reported to date, and the emitters generally show large efficiency roll-off at practical luminance over several hundreds to thousands of cd m<sup>-2</sup>, most likely because of the long delayed fluorescent lifetime (τ<sub>d</sub>). To overcome this problem, we molecularly manipulated the electronic excited state energies of pyrimidine-based TADF emitters to realize deep-blue emission and reduced τ<sub>d</sub>. We then systematically investigated the relationships among the chemical structure, properties, and device performances. The resultant novel pyrimidine emitters, called Ac-XMHPMs (X = 1, 2, and 3), contain different numbers of bulky methyl substituents at acceptor moieties, increasing the excited singlet (E<sub>S</sub>) and triplet state (E<sub>T</sub>) energies. Among them, Ac-3MHPM, with a high E<sub>T</sub> of 2.95 eV, exhibited a high external quantum efficiency (η<sub>ext,max</sub>) of 18% and an η<sub>ext</sub> of 10% at 100 cd m<sup>-2</sup> with Commission Internationale de l'Eclairage chromaticity coordinates of (0.16, 0.15). These efficiencies are among the highest values to date for deep-blue TADF OLEDs. Our molecular design strategy provides fundamental guidance to design novel deep-blue TADF emitters.