gebhart/patrepeval huggingface dataset:
Detection and location of amphiregulin and Cripto‐1 expression in the developing postnatal mouse mammary gland (1995)

Amphiregulin (Ar) and Cripto-1 (Cr-1) are growth promoting peptides that share amino acid sequence homology with epidermal growth factor (EGF). The present study examined Ar and Cr-1 mRNA and protein expression during various stages of C57BL/6 mouse mammary morphogenesis. Reverse transcription-polymerase chain reaction (RT-PCR) was used to detect transcripts for Ar and Cr-1 at all stages of mammary development. Immunocytochemical (ICC) localization demonstrated that in virgin 4-week to mature 12-week-old mouse fourth inguinal mammary gland, Ar and Cr-1 are expressed in the stromal cells, luminal epithelial cells, and myoepithelial cells of the branching ducts. Ar, and to lesser extent Cr-1, were also found in the epithelial cap cells and in the luminal epithelial cells of the advancing terminal end bud (TEB) from virgin 4-week and 6-week-old mice. Western blot analysis demonstrated that both Ar (28 and 26 kDa) and Cr-1 (90, 67, 56, and 21 kDa) proteins are expressed in virgin, 13.5 day midpregnant and in the 14 day lactating mammary gland. In addition, Ar and Cr-1 are associated with developing alveolar structures as determined by ICC. These results imply that together with EGF and transforming growth factor alpha (TGF alpha), Ar and Cr-1 may play salient roles as modifiers in the morphogenesis and differentiation of the mammary gland.
Involvement of fatty acid-CoA ligase 4 in hepatocellular carcinoma growth: Roles of cyclic AMP and p38 mitogen-activated protein kinase (2005)

FACL4 is involved in the HCC tumorigenesis and both cAMP and p38 MAPK pathways are associated with the regulation of FACL4 in HCC.
Physics-informed neural networks for myocardial perfusion MRI quantification (2022)

Tracer-kinetic models allow for the quantification of kinetic parameters such as blood flow from dynamic contrast-enhanced magnetic resonance (MR) images. Fitting the observed data with multi-compartment exchange models is desirable, as they are physiologically plausible and resolve directly for blood flow and microvascular function. However, the reliability of model fitting is limited by the low signal-to-noise ratio, temporal resolution, and acquisition length. This may result in inaccurate parameter estimates. This study introduces physics-informed neural networks (PINNs) as a means to perform myocardial perfusion MR quantification, which provides a versatile scheme for the inference of kinetic parameters. These neural networks can be trained to fit the observed perfusion MR data while respecting the underlying physical conservation laws described by a multi-compartment exchange model. Here, we provide a framework for the implementation of PINNs in myocardial perfusion MR. The approach is validated both in silico and in vivo. In the in silico study, an overall decrease in mean-squared error with the ground-truth parameters was observed compared to a standard non-linear least squares fitting approach. The in vivo study demonstrates that the method produces parameter values comparable to those previously found in literature, as well as providing parameter maps which match the clinical diagnosis of patients.
Automatic steering control of vehicle lateral motion with the effect of roll dynamics (1998)

The two dominant motions of automatic vehicle steering control are yaw and lateral motion. A two degree-of-freedom (DOF) model commonly used to describe these motions is called the bicycle model. Experimental results for certain vehicles, however, show the lowered gain characteristics in the lateral acceleration response to the steering input. This is attributed to suspension dynamics. In this paper, a 3 DOF linear model, which incorporate the suspension roll mode, is developed and verified against the experimental data. The H/sub /spl infin// theory is applied to the bicycle model and the 3 DOF model for synthesis of robust steering controllers. The simulation results indicate the importance of the effect of roll dynamics to steering controller design.
Amyloid-β Interactions with Chondroitin Sulfate-derived Monosaccharides and Disaccharides (2001)

In Alzheimer's disease, the major pathological features are diffuse and senile plaques that are primarily composed of the amyloid-beta (A beta) peptide. It has been proposed that proteoglycans and glycosaminoglycans (GAG) facilitate amyloid fibril formation and/or stabilize the plaque aggregates. To develop effective therapeutics based on A beta-GAG interactions, understanding the A beta binding motif on the GAG chain is imperative. Using electron microscopy, fluorescence spectroscopy, and competitive inhibition ELISAs, we have evaluated the ability of chondroitin sulfate-derived monosaccharides and disaccharides to induce the structural changes in A beta that are associated with GAG interactions. Our results demonstrate that the disaccharides GalNAc-4-sulfate(4S), Delta UA-GalNAc-6-sulfate(6S), and Delta UA-GalNAc-4,6-sulfate(4S,6S), the iduronic acid-2-sulfate analogues, and the monosaccharides d-GalNAc-4S, d-GalNAc-6S, and d-GalNAc-4S,6S, but not d-GalNAc, d-GlcNAc, or Delta UA-GalNAc, induce the fibrillar features of A beta-GAG interactions. The binding affinities of all chondroitin sulfate-derived saccharides mimic those of the intact GAG chains. The sulfated monosaccharides and disaccharides compete with the intact chondroitin sulfate and heparin GAGs for A beta binding, as illustrated by competitive inhibition ELISAs. Therefore, the development of therapeutics based on the model of A beta-chondroitin sulfate binding may lead to effective inhibitors of the GAG-induced amyloid formation that is observed in vitro.
Motion Prediction of Human-Driven Vehicles in Mixed Traffic with Connected Autonomous Vehicles (2020)

In this paper, we investigate the motion prediction of human-driven vehicles in traffic flow mixed with connected autonomous vehicles (CAVs). Here, CAVs indicate the self-driving vehicles that can exchange messages with other vehicles through wireless vehicle-to-vehicle (V2V) communication, while human-driven vehicles are not equipped with V2V communication devices. The recursive least square (RLS) method is applied to approximate the dynamic model of the human- driven vehicles immediately ahead of CAVs, and the identified model is further used to predict the future motion of human- driven vehicles. To improve the prediction accuracy, triggering time and physical constraints are included in the predictor. Numerical simulations are utilized to validate the predictor. The effects of uncertain human reaction delays, time-varying parameters of human-driven vehicles, and stochastic packet drops in V2V communication on the accuracy of the RLS prediction are also investigated.
Visualization for the shear modulus anisotropy of 3D and 4D-reinforced composites (2022)

Vectorial surfaces for visualization of the shear modulus is proposed. For example, one can consider anisotropy 3D and 4D-reinforced composites. Proper elastic states are used for describing elastic properties of composites. The effective properties of composites are presented by means the connection between the properties of the composite matrix, fibers and reinforcement parameters. The reinforcement parameters are determined geometric distribution of fibers in the matrix. All relations are analytical. Vectorial surfaces are constructed for analyze the nature of the anisotropy shear modulus depending on the method of reinforcement and volume fraction of fibers.
Molecular Dynamics Simulation of the Kinetic Reaction of Ni and Al Nanoparticles (2008)

Abstract : The U.S. Army has an interest in the use of alloys that produce excessive heat during formation and can be used for structural purposes such as shell casings. Molecular dynamics simulations have been used to provide a more thorough understanding of one of these alloys systems, namely the kinetic reaction of Ni and Al nanoparticles. We have considered the affect of primary particle size on sintering time and sintering temperature for separate nanoparticles and for coated nanoparticles in the form of Ni-coated Al nanoparticles and Al-coated Ni. Simulation results show that the sintering time for coated nanoparticles is linearly dependent upon the number of atoms or volume of the sintering nanoparticles. We have also found that nanoparticle size and surface energy is an important factor in determining the adiabatic reaction temperature.
Molecular engineering of polymer films for amplitude and phase measurements of Ti:sapphire femtosecond pulses (1996)

Using second-harmonic frequency-resolved optical gating and a tricyanovinylaniline polymer thin film, we have measured the amplitude and the phase of mode-locked Ti:sapphire laser pulses as short as 13 fs. These thin films are ideally suited for ultrashort-pulse diagnostics because they eliminate the angle tuning associated with birefringent phase-matched crystals, minimize pulse distortions introduced by group-velocity dispersion, and exhibit excellent photochemical stability.
Rollback-Recovery for Middleboxes (2015)

Network middleboxes must offer high availability, with automatic failover when a device fails. Achieving high availability is challenging because failover must correctly restore lost state (e.g., activity logs, port mappings) but must do so quickly (e.g., in less than typical transport timeout values to minimize disruption to applications) and with little overhead to failure-free operation (e.g., additional per-packet latencies of 10-100s of us). No existing middlebox design provides failover that is correct, fast to recover, and imposes little increased latency on failure-free operations. We present a new design for fault-tolerance in middleboxes that achieves these three goals. Our system, FTMB (for Fault-Tolerant MiddleBox), adopts the classical approach of "rollback recovery" in which a system uses information logged during normal operation to correctly reconstruct state after a failure. However, traditional rollback recovery cannot maintain high throughput given the frequent output rate of middleboxes. Hence, we design a novel solution to record middlebox state which relies on two mechanisms: (1) 'ordered logging', which provides lightweight logging of the information needed after recovery, and (2) a `parallel release' algorithm which, when coupled with ordered logging, ensures that recovery is always correct. We implement ordered logging and parallel release in Click and show that for our test applications our design adds only 30$\mu$s of latency to median per packet latencies. Our system introduces moderate throughput overheads (5-30%) and can reconstruct lost state in 40-275ms for practical systems.
Preclinical assessment of drug–drug interaction of fb‐PMT, a novel anti‐cancer thyrointegrin αvβ3 antagonist (2023)

The objective of the current study was to identify potential drug-drug interactions (DDIs) with the drug candidate fb-PMT, a novel anticancer thyrointegrin αvß3 antagonist. This was accomplished by using several in vitro assays to study interactions of fb-PMT with both cytochrome P450 (CYP) enzymes and drug transporters, two common mechanisms leading to adverse drug effects. In vitro experiments showed that fb-PMT exhibited weak reversible inhibition of CYP2C19 and CYP3A4. In addition, fb-PMT did not show time-dependent inhibition with any of the seven CYP isoforms tested, including 1A2, 2B6, 2C8, 2C9, 2C19, 2D6, and 3A4. Human liver microsomal incubations demonstrated that fb-PMT is stable. Potential transporter-mediated DDIs with fb-PMT were assessed with two ATP binding cassette (ABC) family transporters (P-glycoprotein and breast cancer resistance protein) using Caco2 cells and seven solute carrier family (SLC) transporters (organic cation transporter OCT2, organic anion transporters OAT1 and OAT3, organic anion transporter peptides OATP1B1 and OATP1B3, and the multidrug and toxic extrusion proteins MATE1 and MATE2-K using transfected HEK293 cells). Fb-PMT was not a substrate for any of the nine transporters tested in this study, nor did it inhibit the activity of seven of the transporters tested. However, fb-PMT inhibited the uptake of rosuvastatin by both OATP1B1 and OATP1B3 with half-maximal inhibitory concentrations greater than 3 and less than 10 μM. In summary, data suggest that the systemic administration of fb-PMT is unlikely to lead to DDIs through CYP enzymes or ABC and SLC transporters in humans.
Isotopic labeling investigation of the oxygenation of nickel-bound thiolates by molecular oxygen (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsotopic labeling investigation of the oxygenation of nickel-bound thiolates by molecular oxygenPatrick J. Farmer, Touradj Solouki, Daniel K. Mills, Takako Soma, David H. Russell, Joseph H. Reibenspies, and Marcetta Y. DarensbourgCite this: J. Am. Chem. Soc. 1992, 114, 12, 4601–4605Publication Date (Print):June 1, 1992Publication History Published online1 May 2002Published inissue 1 June 1992https://pubs.acs.org/doi/10.1021/ja00038a023https://doi.org/10.1021/ja00038a023research-articleACS PublicationsRequest reuse permissionsArticle Views480Altmetric-Citations114LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Isolation of Plakinamine I: A New Steroidal Alkaloid from the Marine Sponge Corticium sp. and Synthesis of an Analogue Model Compound (2005)

Abstract A new cytotoxic steroidal alkaloid, plakinamine I, with an unprecedented 3α‐amino‐19‐acetoxy nucleus was isolated from a Corticium sp. sponge. The structure has been elucidated by spectroscopic analysis and secured by the synthesis of the model 19‐acetoxy‐3α‐aminocholestane. The evaluation of the cytotoxic activities of several synthetic derivatives, intermediates of the above synthesis, allowed us to explore the influence of the different functions on the cytotoxicity observed for natural plakinamine I. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Need for Simulation-Based Design Analysis and Optimization (2006)

Recent advances in microfabrication techniques, sensing methods, and miniaturization have enabled automated analysis of samples using microfluidic systems. Each unique application requires successful custom development of integrated lab-on-a-chip devices. This involves design, analysis and characterization of individual components, (pumps, valves, mixers, separators, sensors) and the integrated system. In this regard, first-principle-based simulations of the underlying complex multiphysics phenomena can provide detailed understanding of device function. An overview of modeling and simulation-based analysis for the design and development of microfluidic devices is presented. In particular, we highlight some key factors affecting the performance of lab-on-a-chip systems such as surface tension effects, analyte dispersion, Joule heating, and mass transport limitations, and delineate the parameters that influence them. The limitations of these modeling techniques and future needs are discussed.
Human susceptibility to subtle adversarial image manipulations with unlimited exposure time (2021)

Artificial neural networks (ANNs) have revolutionized multiple fields, and were initially inspired by models of biological neural networks (BNNs). A growing body of work finds similarities between behaviors and representations in ANNs and BNNs. However, despite these similarities and shared foundations, ANNs exhibit surprising properties and failures that are generally believed not to exist in biological networks. One of the most dramatic of these failures is a susceptibility to adversarial perturbations, where a nearly imperceptible perturbation added to an input can cause an ANN to behave in a dramatically different fashion, for instance mislabeling an initially correctly identified school bus as an ostrich. Is human vision also susceptible to adversarial perturbations? Past work has shown that when images with adversarial perturbations of intermediate magnitude (±32 of 256 intensity levels) are shown to humans for a short time (∼70 ms), human object classification judgments are perturbed in the same direction as ANN’s. Other work has found that humans can identify adversarial examples with large magnitude perturbations and extended exposure times. Here, we find that human susceptibility to adversarial examples extends beyond these settings. We display images with small magnitude perturbations (between ±2 and ±32 out of 256 intensity levels) for an unlimited exposure time. We find that even at the smallest ±2 magnitude, these images perturb human judgments of object class in the same direction as an ANN trained to classify images. These results demonstrate that humans exhibit a peculiarity that was once assumed to be specific to machines, and are suggestive that perception in ANNs and BNNs is more similar than commonly believed.
Optimizing Through Learned Errors for Accurate Sports Field Registration (2019)

We propose an optimization-based framework to register sports field templates onto broadcast videos. For accurate registration we go beyond the prevalent feed-forward paradigm. Instead, we propose to train a deep network that regresses the registration error, and then register images by finding the registration parameters that minimize the regressed error. We demonstrate the effectiveness of our method by applying it to real-world sports broadcast videos, outperforming the state of the art. We further apply our method on a synthetic toy example and demonstrate that our method brings significant gains even when the problem is simplified and unlimited training data is available.
Small sized mesoporous silica nanoparticles functionalized with mannose for retinoblastoma cell imaging (2014)

We report the study of the functionalization of small sized MSNs with mannose. Classical procedures which were efficient with 100 nm diameter MSNs led to aggregation of small sized MSNs. Therefore, we grafted long chain amino silane and PEG-silane on the surface of the MSNs and reacted squarate mannose with NH2 groups. Although the MSN suspension was stable in EtOH, immediate aggregation was noticed in PBS which is attributed to remaining amino groups on the surface of the MSNs. We therefore grafted silylated mannose and PEG-silane on the MSN surface. Depending on the conditions, reversible aggregation was observed in PBS when heating to 37 °C and cooling to RT, or stable suspensions were obtained. The stable mannose-functionalized MSN suspensions were used for the imaging of retinoblastoma cells.
Surface Nanopatterning by Organic/Inorganic Self‐Assembly and Selective Local Functionalization (2006)

In the Full Paper by D. Grosso and co-workers published in Issue 4/2006 of Small, the name of one of the authors was spelled incorrectly. Anna Fisher in the author list should have read: Anna Fischer.
Hybrid RANS/LES Turbulence Model Applied to a Transitional Unsteady Boundary Layer on Wind Turbine Airfoil (2019)

A hybrid Reynolds-averaged Navier Stokes/large-eddy simulation (RANS/LES) turbulence model integrated with a transition formulation is developed and tested on a surrogate model problem through a joint experimental and computational fluid dynamic approach. The model problem consists of a circular cylinder for generating coherent unsteadiness and a downstream airfoil in the cylinder wake. The cylinder flow is subcritical, with a Reynolds number of 64,000 based upon the cylinder diameter. The quantitative dynamics of vortex shedding and Reynolds stresses in the cylinder near wake are well captured, owing to the turbulence-resolving large eddy simulation mode that was activated in the wake. The hybrid model switched between RANS and LES modes outside the boundary layers, as expected. According to the experimental and simulation results, the airfoil encountered local flow angle variations up to ±50°. Further analysis through a phase-averaging technique found phase lags in the airfoil boundary layer along the chordwise locations, and both the phase-averaged and mean velocity profiles collapsed into the Law-of-the-wall in the range of 0 &lt; y + &lt; 50 . The features of high blade-loading fluctuations due to unsteadiness and transitional boundary layers are of interest in the aerodynamic studies of full-scale wind turbine blades, making the current model problem a comprehensive benchmark case for future model development and validation.
Wound healing monitoring using near infrared fluorescent fibrinogen (2020)

We demonstrate a method for imaging the wound healing process with near infrared fluorescent fibrinogen. Wound healing studies were performed on a rat punch biopsy model. Fibrinogen was conjugated with a near infrared fluorescent dye and injected into the tail vein. Fibrinogen is a useful protein for tracking wound healing because it is involved in fibrin clot formation and formation of new provisional matrix through transglutaminase’s crosslinking activity. Strong fluorescence specific to the wound was observed and persisted for several days, indicating that the fibrinogen is converted to crosslinked fibrin. Administration of contrast agent simultaneously with wound creation led to primary labeling of the fibrin clot, indicating that the wound was in its early phase of healing. Administration on the following day showed labeling on the wound periphery, indicating location of formation of a new provisional matrix. This method may prove to be useful as a diagnostic for basic studies of the wound healing process, in drug development, or in clinical assessment of chronic wounds.
Expanding lexicons by inducing paradigms and validating attested forms (2002)

One of the bottlenecks in Natural Language Processing for a given language is creating a lexicon that covers the language. The morphological lexicon provides two important pieces of information for NLP applications: 1) the normalization of a word, its lemmatization, which allows the application to recognize two variants of the same word; and 2) the part-of-speech roles that the word can play, which allows the application to parse the text, creating relations between the words in a text. Many NLP applications, e.g. Information Retrieval, Classification, Terminology Extraction, etc., depend upon the normalization and parsing information found in lexicons. When words are not present in these lexicons, it is difficult to predict what their proper lemmatizations and parts-of-speech are. In this paper we present a technique for updating a lexicon given an unknown word via induction of paradigms from an existing, but incomplete, lexicon and validation of the paradigm using corpus evidence. 1.
Distal Biceps Tendon Repair: One- and Two-Incision Techniques (2002)

Ruptures of the distal biceps tendon can be surgically treated with more than one technique. The success of a traditional two-incision technique combined with the evolution of soft tissue fixation options has led to an interest in using a single-incision technique. The following article will describe the indications, surgical techniques, advantages, and disadvantages for each procedure.