gebhart/patrepeval huggingface dataset:
Molecular Imaging of Fibrosis (2021)

Fibrosis is the accumulation of extracellular matrix components that make up scar tissue and is a common result of chronic tissue injury. Fibrotic diseases are responsible for a large burden of human illness, and the development of new methods to image fibrosis and fibrogenesis is a large unmet clinical need. This chapter provides an overview of molecular probes for fibrosis imaging by magnetic resonance imaging positron emission tomography and single-photon emission computed tomography. It starts by introducing the molecular processes involved in the development of fibrosis and identifying corresponding imaging targets. It then describes the application of the targeting molecular probes to image fibrotic processes in different organs or diseases. At the end of the chapter, the role of molecular imaging in answering unmet challenges in fibrosis and the next steps needed to translate molecular imaging into human fibrotic diseases are discussed.
Abstract 2742: Identification of tumor antigens in neu transgenic mice may provide biomarkers useful for the early detection and diagnosis of human breast cancer (2010)

Abstract Early detection of breast cancer is crucial for better prognosis and successful treatment of the patients. Development of novel methods for screening for breast cancer is needed for early detection and diagnosis. The human immune system responds to tumor-specific antigens in the pre-malignant stage of breast cancer and produces specific antibodies, which can be detected as potential breast cancer biomarkers. Due to the limited availability of well-annotated pre-cancer and post-cancer sera from human subjects, we performed serial serum collection in a neu transgenic mouse model from the age of 10 weeks to the terminal stage of disease. Using a technique called serological screening of cDNA expression library (SEREX), a high-throughput method to rapidly screen recombinant proteins expressed in a bacteriophage-based cDNA library, we have previously identified tumor antigens in the late stage of neu breast cancers. The mouse tumors have similar immunogenicity as their human counterparts due to the fact that some of these antigens are also immunogenic in human. Indeed, we have found that one mouse antigen called gelsolin, shares 93% homology with human gelsolin and has the highest response to human serum antibody among other antigens. In an ELISA analysis using the serum samples from 50 breast cancer cases and 50 normal donors, the area-under-curve (AUC) value of the receiver-operating-characteristic (ROC) curve of gelsolin ELISA detects more than 70% of cancer patients. Using the SEREX technique, we sought to further identify the early-stage serum antibody biomarkers by comparing the pre-cancer, early stage, and late stage sera from the same mouse. We have identified three early-stage biomarkers, A20/TNFaip3, Rpl5, and Pdhx, in neu mice. In summary, we conclude that identification of tumor antigens in the neu transgenic animal model is useful for the discovery of serum antibody biomarkers for early detection and diagnosis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2742.
Plug-In Stochastic Gradient Method (2018)

Plug-and-play priors (PnP) is a popular framework for regularized signal reconstruction by using advanced denoisers within an iterative algorithm. In this paper, we discuss our recent online variant of PnP that uses only a subset of measurements at every iteration, which makes it scalable to very large datasets. We additionally present novel convergence results for both batch and online PnP algorithms.
Humulus japonicus rescues autistic‑like behaviours in the BTBR T+ Itpr3tf/J mouse model of autism (2021)

<i>Humulus japonicus</i> (HJ) is a traditional herbal medicine that exhibits anti‑inflammatory, antimicrobial and anti‑tumor effects that is used for the treatment of hypertension, pulmonary disease and leprosy. Recently, it has also been reported that HJ demonstrates neuroprotective properties in animal models of neurodegenerative diseases. The current study hypothesised that the administration of HJ would exhibit therapeutic effects in autism spectrum disorder (ASD), a neurodevelopmental disorder with lifelong consequences. The BTBR T<sup>+</sup> Itpr3tf/J mouse model of ASD was used to investigate the anti‑autistic like behavioural effects of HJ. Chronic oral administration of the ethanolic extract of HJ significantly increased social interaction, attenuated repetitive grooming behaviour and improved novel‑object recognition in BTBR mice. Anti‑inflammatory effects of HJ in the brain were analysed using immunohistochemistry and reverse‑transcription quantitative PCR analysis. Microglia activation was markedly decreased in the striatum and hippocampus, and pro‑inflammatory cytokines, including C‑C Motif Chemokine Ligand 2, interleukin (IL)‑1β and IL‑6, were significantly reduced in the hippocampus following HJ treatment. Moreover, HJ treatment normalised the phosphorylation levels of: N‑methyl‑D‑aspartate receptor subtype 2B and calcium/calmodulin‑dependent protein kinase type II subunit α in the hippocampus of BTBR mice. The results of the present study demonstrated that the administration of HJ may have beneficial potential for ameliorating behavioural deficits and neuroinflammation in ASD.
On Best-Response Dynamics in Potential Games (2018)

The paper studies the convergence properties of (continuous-time) best-response dynamics from game theory. Despite their fundamental role in game theory, best-response dynamics are poorly understood in many games of interest due to the discontinuous, set-valued nature of the best-response map. The paper focuses on elucidating several important properties of best-response dynamics in the class of multiagent games known as potential games---a class of games with fundamental importance in multiagent systems and distributed control. It is shown that in almost every potential game and for almost every initial condition, the best-response dynamics (i) have a unique solution, (ii) converge to pure-strategy Nash equilibria, and (iii) converge at an exponential rate.
Active Stereo Vision for Precise Autonomous Vehicle Control (2020)

This paper describes the development of a low-cost, lowpower, accurate sensor designed for precise, feedback control of an autonomous vehicle to a hitch. The solution that has been developed uses an active stereo vision system, combining classical stereo vision with a low cost, low power laser speckle projection system, which solves the correspondence problem experienced by classic stereo vision sensors. A third camera is added to the sensor for texture mapping. A model test of the hitching problem was developed using an RC car and a target to represent a hitch. A control system is implemented to precisely control the vehicle to the hitch. The system can successfully control the vehicle from within 35&#xB0; of perpendicular to the hitch, to a final position with an overall standard deviation of 3.0 m m of lateral error and 1.5&#xB0; of angular error.
Computational design, construction, and characterization of a set of specificity determining residues in protein–protein interactions (2012)

Proteins interact with different partners to perform different functions and it is important to elucidate the determinants of partner specificity in protein complex formation. Although methods for detecting specificity determining positions have been developed previously, direct experimental evidence for these amino acid residues is scarce, and the lack of information has prevented further computational studies. In this article, we constructed a dataset that is likely to exhibit specificity in protein complex formation, based on available crystal structures and several intuitive ideas about interaction profiles and functional subclasses. We then defined a "structure-based specificity determining position (sbSDP)" as a set of equivalent residues in a protein family showing a large variation in their interaction energy with different partners. We investigated sequence and structural features of sbSDPs and demonstrated that their amino acid propensities significantly differed from those of other interacting residues and that the importance of many of these residues for determining specificity had been verified experimentally.
Charge‐transport physics of high‐mobility molecular semiconductors (2012)

Abstract This review is focused on understanding of the charge‐transport physics of high‐mobility organic semiconductors at a molecular level. We review recent high‐mobility small‐molecule and conjugated polymer materials with a focus on crystalline materials that have been able to exceed mobilities of 0.5–1 cm 2 /V s. We discuss some of the main, competing factors that govern charge transport in these materials and present theoretical approaches that have been developed to describe systems in which moderately strong intermolecular electronic interactions and strong electron–phonon interactions are present. Finally, we review recent experimental results that have aimed to address the important question of whether at room‐temperature charge carriers in these high‐mobility organic semiconductors are in fact simply extended Bloch electrons that undergo occasional scattering processes or are localized on individual molecules and move by hopping.
Figure S7 from The Transcriptional Regulator Sin3A Contributes to the Oncogenic Potential of STAT3 (2023)

&lt;p&gt;Data depict the role of Sirtuin 1 and DNMT, HDAC and PI3K inhibition on Stat3 acetylation and TSG expression.&lt;/p&gt;
Resource Delegation and Rewards to Stimulate Forwarding in Multihop Cellular Networks (2005)

Multihop cellular networks that base the forwarding process on user terminals are challenged by a lack of forwarding incentive. In this paper, we present the novel concept of resource delegation which, applied in combination with pricing based rewards, guarantees both the separation of resources between originating transmitters and relays and the economic compensation of the energy investments of the relays. The results show that this strategy leads to the definition of a broad region of prices in which multihopping solutions can achieve the following advantages over classical single-hop architectures: operator's revenues and provided data rates increase significantly, the users' appreciation of the service is enhanced, and the average interference level of the network is lowered.
An Evidential Fusion N etworl( based Context Reasoning for Smart Media Service (2015)

For effective smart media service, a reliable and confidential context recognition is required to prepare and react properly. However, it is difficult to achieve a higher confidence level for several reasons. First, raw data from multiple sensors have different degrees of uncertainty.
Synthetic Access to Noncanonical Strigolactones: Syntheses of Carlactonic Acid and Methyl Carlactonoate (2017)

Strigolactones are plant hormones regulating essential stages of a plant's development. Their low natural abundance combined with a low chemical stability significantly hampered the detailed investigation of their biological activity. Noncanonical strigolactones lack the fused tricyclic ABC-ring system commonly present in canonical-type strigolactones but feature an open-chain unit linking structurally diverse A-ring moieties to the butenolide D-ring. We herein present an efficient synthetic access to enantiomerically pure noncanonical strigolactones by a Stille cross-coupling approach to forge the central diene moiety and demonstrate this strategy by syntheses of natural products methyl carlactonoate and carlactonic acid. Furthermore, a synthetic access to deuterium-labeled analogues of these natural products has been developed.
An In Vitro Model System Used To Study Adherence and Invasion of Francisella tularensis Live Vaccine Strain in Nonphagocytic Cells (2007)

In observing Francisella tularensis interactions with nonphagocytic cell lines in vitro, we noted significant adherence, invasion, and intracellular growth of the bacteria within these cells. F. tularensis live vaccine strain invasion of nonprofessional phagocytic cells is inhibited by cytochalasin D and nocodazole, suggesting that both the actin and microtubule cytoskeletons are important for invasion.
Generation of cw-THz waves with high frequency accuracy by Mach-Zehnder-modulator-based flat comb generator for phase-locking of THz-QCLs (2015)

Generation of cw-THz waves with high frequency accuracy was demonstrated by using a Mach-Zehnder-modulator-based flat comb generator (MZ-FCG). A combination of the MZ-FCG and a highly nonlinear dispersion shifted fiber generated broadband optical combs, and cw-THz waves in the range of 3 THz were generated by photonic down-conversion of two-tone signals extracted from the broadband combs.
Vapor bubble and streamer initiation in water under long duration impulses (2018)

The generation of vapor bubbles in water under high voltage impulses of long duration (500 μs) is investigated experimentally. In most cases, the appearance of bubbles is followed by the inception of discharges occurring within the vapor, eventually transforming the bubble into a propagating streamer. Time delays to bubble and discharge inception are measured versus conductivity and voltage, using fast visualization and optical detection of bubbles. Before bubble inception, the liquid heating and the onset of an electro-hydro-dynamic (EHD) motion can be observed by Schlieren visualization. Electrical measurements show a decrease of the gap resistance versus time, attributable to the heating of water. When conductivity and voltage are changed, the onset of bubble inception is correlated to a nearly constant resistance drop, suggesting that a constant temperature is present when bubbles appear. At short times, the energy dissipation required to observing bubbles is independent of conductivity and applied voltage. Experiments show that vapor bubble generation results from a competition between liquid heating by Joule dissipation, and forced cooling induced by the EHD motion.
c-Jun Regulates Phosphoinositide-dependent Kinase 1 Transcription (2009)

Mutations in N-RAS and B-RAF, which commonly occur in melanomas, result in constitutive activation of the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated protein kinase (ERK) signaling. Active ERK increases expression and activity of the c-Jun transcription factor, linking ERK and Jun N-terminal kinase (JNK) cascades. Here, we show that c-Jun regulates transcription of phosphoinositide-dependent kinase 1 (PDK1) with a concomitant impact on Akt and protein kinase C (PKC) activity and related substrates. Inhibition of c-Jun reduces PDK1 expression and attenuates Akt and PKC activity, which can be restored by exogenous PDK1. c-Jun regulation of PDK1 in melanoma contributes to growth rate and the ability to form tumors in mice. Correspondingly, increased levels of c-Jun in melanoma cell lines coincide with up-regulation of PDK1 and phosphorylation of PKC and Akt. The identification of c-Jun as a transcriptional regulator of PDK1 expression highlights key mechanisms underlying c-Jun oncogenic activity, and provides new insight into the nature of up-regulated Akt and PKC in melanoma.
Comparison between Linear and Nonlinear Regression in a Laboratory Heat Transfer Experiment. (2013)

In order to interpret laboratory experimental data, undergraduate students are used to perform linear regression through linearized versions of nonlinear models. However, the use of linearized models can lead to statistically biased parameter estimates. Even so, it is not an easy task to introduce nonlinear regression and show for the students that this is the best approach. In this work linear and nonlinear regressions are statistically compared in a simple heat transfer laboratory experiment.
Supplementary Table S2 from AMG 479, a fully human anti–insulin-like growth factor receptor type I monoclonal antibody, inhibits the growth and survival of pancreatic carcinoma cells (2023)

Supplementary Table S2 from AMG 479, a fully human anti–insulin-like growth factor receptor type I monoclonal antibody, inhibits the growth and survival of pancreatic carcinoma cells
Eosinophilia with Aberrant T Cells and Elevated Serum Levels of Interleukin-2 and Interleukin-15 (2000)

The hypereosinophilic syndrome comprises various idiopathic myeloproliferative disorders with sustained eosinophilia and damage to the heart, lungs, skin, and other organs by infiltrating eosinophils.1 A single mechanism for this syndrome has not been identified, and multiple factors are likely to be involved. The serum level of interleukin-5, an eosinophilopoietic cytokine, is increased in some patients with the hypereosinophilic syndrome,2 and a few have been found to have unusual T-cell abnormalities, including CD3–CD4+CD8– T cells3,4 and so-called double-negative CD3+CD4–CD8– T cells.5 CD3, a complex of five proteins associated with the T-cell receptor, is a distinctive feature of all normal T . . .
Interactions of the lanthanide- and hapten-binding sites in the Fv fragment from the myeloma protein MOPC 315 (1976)

1. The interactions of lanthanide metals and dinitrophenyl spin-label haptens with the Fv fragment of the mouse myeloma protein MOPC 315 were investigated by the techniques of fluorescence, e.s.r. (electron spin resonance) and high-resolution n.m.r. (nuclear magnetic resonance). 2. The protein fluorescence of Fv fragment at 340nm is quenched by the haptens (fluorescence enhancement, epsilon=0.15) and enhanced by Gd(III) (epsilon=1.14) and other lanthanides. The binding of the haptens studied here is insensitive to pH in the range 5.5-7.0 (dissociation constant KH=0.3-1.0 muM) and shows 1:1 stoicheiometry. The binding of Gd(III) also shows 1:1 stoicheiometry, but is pH-dependent; the binding constant (KM) varies from 10 muM at pH7.0 to 700 muM at pH4.8. La(III) binding is less sensitive to pH. The pH-dependences of the metal-binding constants imply that a group in the protein with pKa greater than or equal to 6.2 is involved in the binding, and probably also other groups with lower pKa values. 3. The apparent binding of the haptens is weakened about 20-fold by Gd(III), and vice versa. An equilibrium scheme involving a ternary complex with an interaction between the two binding sites is derived in Appendix I to explain the experimental results at two pH values. 4. Time-dependent fluorescence changes are observed in the presence of Gd(III) at pH5.5. A two-state kinetic scheme involving a ‘slow’ conformational change in the Fv fragment is derived in Appendix II to explain this time-dependence. This scheme is consistent with the antagonistic equilibrium behaviour. 5. The e.s.r. changes in the spin-label haptens on binding to Fv fragment and on the subsequent addition of lanthanides are consistent with the binding scheme for haptens and lanthanides proposed from the fluorescence studies. A difference between the limiting quenching of the e.s.r. signal from the bound haptens in the presence of saturating concentrations of Gd(III) and La(III) is attributed to dipolar interactions between bound Gd(III) and the nitroxide moiety of the bound hapten. The residual quenching with Gd(III) allows an estimate of 1.2nm to be made for the distance between the two paramagnetic centres. 6. The 270 MHz proton difference spectrum of the Fv fragment resulting from the addition of La(III) suggests that any metal-induced conformational changes are small and involve relatively few amino acid residues on the Fv fragment.
High‐Intensity Ultrasound and Microwave, Alone or Combined, Promote Pd/C‐Catalyzed Aryl—Aryl Couplings. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Induction of cellulases by disaccharides or their derivatives in Penicillium janthinellum EMS-UV-8 mutant (2016)

Disaccharides or their derivatives were analyzed for the induction of cellulases by Penicillium janthinellum EMS-UV-8 mutant. Among seven (Crocin, Gentiobiose, Cellobiose, α-D-Cellobiose octaacetate, Trehalose, Melibiose, Turanose) different compounds tested, α-D-Cellobiose octaacetate (COA) was found to be promising for induction of cellulases. The maximum of 0.8 IU/mL filter paper units, 4.7 IU/mL β–glucosidase and 1.0 mg/mL protein were produced using 0.1% (weight/volume) COA as an inducer and 1% glucose as a carbon source for growth. Next to COA the gentiobiose, trehalose, melibiose and turanose also induce cellulase but at a low level. The induction of cellulase was also analyzed in the presence and absence of light and it was found that the absence of light supports more growth and less cellulase induction, while in the presence of light mycelial growth was restricted but more cellulases were induced. The knowledge of cellulase induction by COA and light could be beneficial for large-scale cellulase production for conversion of cellulosic biomass to biofuels.
Plasmon enhanced detectors for smart lighting applications (2011)

Engineered smart lighting systems by optically sensing the environment can change the way society uses lighting. In this talk we will present our strategies on plasmon enhanced detectors enabling new applications and technologies.
Effect of Commercial Gas Diffusion Layers on Catalyst Durability of Polymer Electrolyte Fuel Cells in Varied Cathode Gas Environment (2022)

Gas diffusion layers (GDLs) play a crucial role in heat transfer and water management of cathode catalyst layers in polymer electrolyte fuel cells (PEFCs). Thermal and water gradients can accelerate electrocatalyst degradation and therefore the selection of GDLs can have a major influence on PEFC durability. Currently, the role of GDLs in electrocatalyst degradation is poorly studied. In this study, electrocatalyst accelerated stress test studies are performed on membrane electrode assemblies (MEAs) prepared using three most commonly used GDLs. The effect of GDLs on electrocatalyst degradation is evaluated in both nitrogen (non-reactive) and air (reactive) gas environments at 100% relative humidity. In situ electrochemical characterization and extensive physical characterization is performed to understand the subtle differences in electrocatalyst degradation and correlated to the use of different GDLs. Overall, no difference is observed in the electrocatalyst degradation due to GDLs based on polarization curves at the end of life. But interestingly, MEA with a cracked microporous layer (MPL) in the GDL exhibited a higher electrocatalyst loading loss, which resulted in a lower and more heterogeneous increase in the average electrocatalyst nanoparticle size.
Material forming apparatus using a directed droplet stream (2023)

Systems and methods are described for rapidly forming precision metallic and intermetallic alloy net shape parts directly from liquid metal droplets. A directed droplet deposition apparatus includes a crucible with an orifice for producing a jet of material, a jet destabilizer, a charging structure, a deflector system, and an impact zone. The systems and methods provide advantages in that fully dense, microstructurally controlled parts can be fabricated at moderate cost.
Photonic Network Optimization via Resource and LSPs Concurrent Allocation: a PCE+ Concept (2010)

This paper proposes the concept of PCE+:a path computation element that performs a concurrent impairments aware routing and regenerator location for a WSON network using a fast analytical assessment of the optical lightpath feasibility.