gebhart/patrepeval huggingface dataset:
Impairment of the proapoptotic activity of Bax by missense mutations found in gastrointestinal cancers. (1999)

We have reported previously that codon 169 of the proapoptotic gene BAX is a mutational hot spot in gastrointestinal cancer. Two different mutations were found in this codon, replacing the wild-type threonine by alanine or methionine. To compare the proapoptotic activity of these Bax mutants with wild-type Bax, we established an ecdysone (muristerone A)-inducible system in cultured human embryonal kidney 293 cells. Addition of muristerone A induced a dose-dependent decrease in the viability of cells transfected with wild-type BAX, but this loss of viability was inhibited in cells transfected with BAX mutants. Furthermore, muristerone A induced morphological changes characteristic of apoptosis, including cell shrinkage, rounding, formation of apoptotic bodies, detachment and nuclear condensation and fragmentation, in cells transfected with wild-type BAX. These hallmarks of apoptosis were clearly diminished in cells transfected with BAX mutants. Mutation of threonine 169 did not affect the binding of Bax to Bax, Bcl-2, or Bcl-X(L). These results demonstrate that missense mutations at codon 169 of BAX are functional because they inhibit its apoptotic activity. This is the first report of the functional significance of missense mutations in BAX, or any other proapoptotic member of the Bcl-2 family, in primary human tumors.
Identification of cyclic and anisotropic behaviour of ODS steels tubes (2011)

In this paper, an elastic plastic behaviour model based on internal state variables is investigated. The final aim is to describe the mechanical stress-strain cyclic response of oxide dispersion strengthened (ODS) steels during the cold pilgering process. In this tube forming operation, a material element undergoes a series of small incremental deformations, alternatively under tensile and compressive stresses. The cyclic model considers isotropic hardening and kinematic hardening which can be related to the typical continuous cyclic softening of the ODS steels. Moreover, the identification process of the cyclic model parameters involves experimental data from only one sample. ODS steels tubes usually reveal an anisotropic strength in the radial, ortho-radial and longitudinal directions due to a crystallographic and strongly elongated grain morphology in the rolling direction. Identification of 3 Hill's parameters is done using compression tests of cylindrical specimens cut in three different directions (longitudinal, radial and ortho-radial) combined with an inverse analysis. Â© 2011 Published by Elsevier Ltd.
Pillars article: T-cell antigen CD28 mediates adhesion with B cells by interacting with activation antigen B7/BB-1. 1990. Proc. Natl. Acad. Sci. USA 87: 5031-5035. (2009)

Studies using monoclonal antibodies (mAbs) have implicated the homodimeric glycoprotein CD28 as an important regulator of human T-cell activation, in part by posttranscriptional control of cytokine mRNA levels. Although the CD28 antigen has functional and structural characteristics of a receptor, a natural ligand for this molecule has not been identified. Here we show that the CD28 antigen, expressed in Chinese hamster ovary (CHO) cells, mediated specific intercellular adhesion with human lymphoblastoid and leukemic B-cell lines and with activated primary murine B cells. CD28-mediated adhesion was not dependant upon divalent cations. Several mAbs were identified that inhibited CD28-mediated adhesion, including mAb BB-1 against the B-cell activation antigen B7/BB-1 and some mAbs against major histocompatibility complex class I antigens. B7/BB-1 expression correlated closely with CD28-mediated adhesion, but class I expression did not. Transfected COS cells expressing the B7/BB-1 antigen adhered to CD28 + CHO cells; this adhesion was blocked by mAbs to CD28 and B7/BB-1. The specific recognition by CD28 of the B-cell activation antigen B7/BB-1 represents a heterophillc interaction between members of the immunoglobulin superfamily that may serve to regulate T-cell cytokine levels at sites of B-cell activation.
Membrane Traffic in Sphingolipid Storage Diseases (2000)

In this review, we summarize our studies of membrane lipid transport in sphingolipid storage disease (SLSD) fibroblasts. We recently showed that several fluorescent SL analogs were internalized from the plasma membrane predominantly to the Golgi complex of normal cells, while in ten different SLSD cell types, these lipids accumulated in endosomes and lysosomes (The Lancet 1999;354: 901-905). Additional studies showed that cholesterol homeostasis is perturbed in multiple SLSDs secondary to SL accumulation and that mistargeting of SL analogs was regulated by cholesterol (Nature Cell Biol 1999;1: 386-388). Based on these findings, we hypothesize that endogenous sphingolipids, which accumulate in SLSD cells due to primary defects in lipid catabolism, result in an altered intracellular distribution of cholesterol, and that this alteration in membrane composition then results in defective sorting and transport of SLs. The importance of SL/cholesterol interactions and potential mechanisms underlying the regulation of lipid transport and targeting are also discussed. These studies suggest a new paradigm for regulation of membrane lipid traffic along the endocytic pathway and could have important implications for future studies of protein trafficking as well as lipid transport. This work may also lead to important future clinical developments (e.g. screening tests for SLSD, new methodology for screening drugs which abrogate lipid storage, and possible therapeutic approaches to SLSD).
Sputtering of Metal Oxide Semiconductor n-p Stacks (2019)

P-type Metal Oxide Semiconductors (MOS) are promising sensor array elements, as their surface properties and charge transport mechanism differ from those of their ubiquitous n-type counterparts. As such, the magnitude and temporal evolution of their response can provide supplemental, independent information on the nature of target gases, thus allowing for improved discrimination in electronic nose systems. Moreover, the formation of a heterojunction between n- and p-type MOS can be leveraged to enhance or tune sensing performance. Here, we report on the processing and characterization of stacked SnO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /NiO thin films of varying thickness. Bilayer heterojunction films are deposited via magnetron sputtering, with or without an intermediate thermal anneal. We show that the addition of a p-type NiO layer dramatically alters the behavior of the n-type SnO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> underlayer, reversing the response pattern to Volatile Organic Compounds (VOCs) and causing a shift in the optimal operational temperature of the device. Plausible physical mechanisms leading to the emergence of such behavior are discussed.
Demonstration of 10-40-Gbaud Baud-Rate-Tunable Optical Generation of 16-QAM from a QPSK Signal Using a Variable DGD Element (2011)

We experimentally demonstrate a tunable optical generation of up to 40-Gbaud 16-QAM from a QPSK signal using a variable DGD element based on vector addition between two polarization states. We also show the baud rate tunability and investigate the tolerance of 16-QAM generation to the DGD offset.
Efficient Access History for Race Detection (2021)

While there has been extensive research on race-detection algorithms for task-parallel programs, most of this research has focused on optimizing a particular component, namely, reachability analysis, which checks whether two instructions are logically in parallel. Little attention has been paid to the other important component, the access history, which stores all memory locations previous instructions have accessed. In theory, the access-history component adds no asymptotic overhead; however, in practice, it is often the most expensive component of race detection since it is queried and (possibly) updated at each memory access. We optimize this component based on the observation that, typically, strands within parallel programs access contiguous blocks of memory. Therefore, instead of maintaining the access history at the granularity of individual memory locations, we maintain it at the granularity of these (varying size) intervals. To enable this access history, we propose (1) compiler and runtime mechanisms that allow us to efficiently collect these intervals and (2) a tree-based access-history data structure that allows updates and queries at interval granularity. The resulting tool can race-detect fork-join code with amortized constant overhead, assuming the number of intervals is small compared to the total work of the computation.
Two-photon-resonant difference-frequency mixing with an ArF excimer laser: vacuum-ultraviolet generation and multiphoton spectroscopy (2000)

Two-photon-resonant difference-frequency generation using an ArF excimer laser provides widely tunable vacuum-ultraviolet (VUV) radiation at high pulse energies. Two-photon resonances in H2, Kr, and Hd are within the tuning range of the ArF laser. With this technique we have directly measured &gt;65µJ at 133 nm. H2 has a significantly smaller phase mismatch than Kr, leading to more efficient VUV generation, particularly at shorter VUV wavelengths. However, mixing in H2 also produces additional VUV lines from two-photon excited amplified spontaneous emission. We have observed new amplified spontaneous-emission lines produced in this manner. H2 is ineffective at generation of Lyman-α radiation owing to the production of H atoms. With a phase-matched mixture of Kr and Ar, we have directly measured 7 µJ at Lyman-α. A physical basis for the asymmetric tuning profile in this gas mixture is presented. With light from this VUV source we have performed 1+1 resonantly enhanced multiphoton ionization in Xe at 147 nm and two-photon-excited fluorescence in Ne at 133 nm.
Synthesis of novel hydroxytyrosol analogues as potential anti-amyloidogenic agents (2014)

The antiamyloidogenic properties of the natural derived antioxidant oleuropein (OE) for Alzheimer's disease have been already cited. Our group has previously reported the noncovalent complex between amyloid beta peptide (Aβ) or its oxidized form and oleuropein (OE) by electrospray ionization mass spectrometry (ESI MS) and nuclear magnetic resonance (NMR) spectroscopy. Additionally, hydroxytyrosol, the main phenolic compound of olive oil and one of the major metabolites of OE has been reported as neuroprotective agent against Aβ-induced toxicity. Prompted by these observations we decided to synthesize simple hydroxytyrosol esters, by substitution of the OE aglycon moiety with simple lipophilic groups, in order to further investigate the effect on Aβ complexation and identify new lead compound(s) with improved properties, which will be the scaffold for further optimization and development of novel anti-amyloidogenic agents. We synthesized a series of novel compounds bearing various aliphatic substitutes in the ester moiety (i.e. methyl, heptyl, cyclohexyl, etc). Additionally, we synthesized some aromatic esters of hydroxytyrosol in order to study the impact of the aromatic group on the Aβ complexation. The interaction of the new compounds with the amyloid peptide Aβ was evaluated in vitro with electrospray ionization mass spectrometry (ESI MS) and circular dichroism (CD). The preliminary result suggests that their activity is lower than Oleuropeins. Furthermore, from a direct comparison of the activity with hydroxytyrosol, it is evident that the interaction of the new derivatives with the amyloid peptide Aβ via non covalent complex, is higher. In general, it seems that the compounds bearing the aromatic ester group posses the best activity among the new derivatives, a finding that would require further studies in the future.
Complete regression of cutaneous metastases with systemic immune response in a patient with triple negative breast cancer receiving p53MVA vaccine with pembrolizumab (2017)

A heavily pretreated patient with triple negative breast cancer distinguished by cutaneous metastases received p53MVA vaccine in combination with pembrolizumab. Her cutaneous metastases regressed and after 2 cycles of therapy, a skin biopsy showed a complete pathological response. Systemic response was confirmed with restaging CT and bone scans. Activation of p53-specific T cell responses and elevation of multiple immune response genes in peripheral blood correlated with the rapid clinical response which lasted for 6 months after the initiation of combined therapy.
Supplementary Figure 2 from Route of Administration Modulates the Induction of Dendritic Cell Vaccine–Induced Antigen-Specific T Cells in Advanced Melanoma Patients (2023)

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<title>Interactive system for registering adjacent tissue sections</title> (1998)

The molecular and structural analysis of cells within their tissue context helps us understand disease mechanisms, such as carcinogenesis. Standard analysis of cutting specimens into thin (4 micrometer) sections, followed by labeling and visual microscopic analysis, has the limitation that tissue properties can only be studied within the section plane, and not perpendicular to the plane. We solved these limitations by building a system for registering images of adjacent sections. In addition, the system enables analysis of many molecular markers in a specific tissue volume, by labeling different sections with different markers, followed by using the system to locate the relevant tissue volume in each section. The system has three stages. First, it automatically images each entire section and two fiducial markers per slide. After this stage, the slides can be removed from the microscope. In stage two, pairs of images of adjacent sections are registered. This is done by interactively marking several points that are common to both images, which are used to calculate the translation and rotation of the images relative to each other. Different registrations can be performed on different parts of the images to account for differential stretching, tearing and folding of sections. In stage three, a slide is placed on the microscope stage and the analyst can bring a specific location into the field of view by referring to it in the previously acquired image. Accuracy is approximately equal to 10 micrometers.
Iodine inhibits antiadhesive effect of PEG: Implications for tissue engineering (2007)

Iodine incorporation into the polymer resulted in increased protein adsorption thus counteracting the effect of PEG.
Motexafin gadolinium generates reactive oxygen species and induces apoptosis in sensitive and highly resistant multiple myeloma cells (2004)

Motexafin gadolinium (MGd), an expanded porphyrin, is a tumor-selective redox-mediator that reacts with many intracellular reducing metabolites. Because redox mechanisms mediate apoptosis in multiple myeloma, we hypothesized that disruption of redox balance by MGd would result in cellular cytotoxicity in myeloma. We examined the effects of MGd on cellular cytotoxicity, apoptosis, reactive oxygen species (ROS) production, and intracellular drug uptake in dexamethasone-sensitive (C2E3), dexamethasone-resistant (1-310 and 1-414) chemotherapy-sensitive (8226-RPMI) and highly chemotherapy-resistant (DOX-10V) myeloma cells. We found complete inhibition of proliferation and cytotoxicity in each sensitive and resistant cell line with 24-hour exposure to clinically relevant concentrations of 50 muM MGd and 50 to 100 microM ascorbate, which was required for the effect. The mechanism of cytotoxicity was related to induction of apoptosis as demonstrated by alteration in mitochondrial membrane potential and elevated annexin V expression. This was accompanied by depletion of intracellular glutathione and increased ROS production. Moreover, catalase substantially abrogated MGd-induced cell death. Using fluorescence microscopy and flow cytometry, we found intracellular uptake of MGd and intracellular ROS production. MGd also induced apoptosis in fresh malignant cells from patients with multiple myeloma. These studies provide a rationale for clinical investigation of this novel redox-mediating agent in patients with multiple myeloma and related disorders.
Imaging in radio interferometry by iterative subset scanning using a modified AMP algorithm (2016)

Imaging techniques in radio interferometry often face a significant challenge posed by the large number of antenna signals received, from which the image information needs to be extracted. Beamforming is envisaged to reduce the rate required for transporting data from groups of antennas to a central site for further processing. We propose a novel method for image reconstruction based on the iterative scanning of a region of interest, combined with randomized beamforming. A modified approximate message-passing algorithm is adopted to extract relevant image information from beamformed signals received at the antenna stations. The method is illustrated by simulations, with reference to the LOFAR radio interferometer, and compared with the CLEAN algorithm.
Healthcare supply chain risk management in Rio de Janeiro, Brazil: What is the current situation? (2022)

The healthcare organizations studied by this paper do not apply SCRM. They only apply local isolated solutions not considering a supply chain scope. This can become hazardous since isolated risk mitigation initiatives are often innocuous and have the potential to generate other risks.
AAA and SynDEx-Ic: A Methodology and a Software Framework for the Implementation of Real-Time Applications onto Reconfigurable Circuits (2007)

International audience
Tuning Surface Properties of Poly(butylene terephthalate) Melt Blown Fibers by Alkaline Hydrolysis and Fluorination (2014)

The wetting properties of poly(butylene terephthalate) (PBT) melt blown fibers were tuned by alkaline hydrolysis and subsequent fluorination. Fiber mats were exposed to a NaOH methanol solution for controlled periods of time at several temperatures, resulting in surface hydrolysis (h-PBT). Subsequent simple solution chemistry was applied to the h-PBT fibers, leading to fluorination of the surface (f-PBT) and the transformation of the wetting properties of the material. Electron microscopy revealed that hydrolysis leads to a textured surface that is retained in the fluorinated product. Sessile drop wetting measurements demonstrated superhydrophilicity for the h-PBT fiber mats and sticky superhydrophobicity with the f-PBT fiber mat.
Equine Viral Arteritis: Essential Facts About the Disease (1997)

Although outbreaks are uncommon, equine viral arteritis is an important disease because of the potential risk of abortion in mares and establishment of the carrier state in a relatively high percentage of infected stallions. Equine arteritis virus carrier stallions constitute an important reservoir of infection, and appropriate precautions have to be taken when nonimmunized mares are inseminated with virus-infective semen. Equine viral arteritis is a manageable infection and prevention programs have been developed that have proven successful in controlling this disease. Authors’ address: Maxwell H. Gluck Equine Research Center, Dept. of Veterinary Science, University of Kentucky, Lexington, KY 40546-0099. r 1997 AAEP.
Contextual and Sequential User Embeddings for Large-Scale Music Recommendation (2020)

Recommender systems play an important role in providing an engaging experience on online music streaming services. However, the musical domain presents distinctive challenges to recommender systems: tracks are short, listened to multiple times, typically consumed in sessions with other tracks, and relevance is highly context-dependent. In this paper, we argue that modeling users’ preferences at the beginning of a session is a practical and effective way to address these challenges. Using a dataset from Spotify, a popular music streaming service, we observe that a) consumption from the recent past and b) session-level contextual variables (such as the time of the day or the type of device used) are indeed predictive of the tracks a user will stream—much more so than static, average preferences. Driven by these findings, we propose CoSeRNN, a neural network architecture that models users’ preferences as a sequence of embeddings, one for each session. CoSeRNN predicts, at the beginning of a session, a preference vector, based on past consumption history and current context. This preference vector can then be used in downstream tasks to generate contextually relevant just-in-time recommendations efficiently, by using approximate nearest-neighbour search algorithms. We evaluate CoSeRNN on session and track ranking tasks, and find that it outperforms the current state of the art by upwards of 10% on different ranking metrics. Dissecting the performance of our approach, we find that sequential and contextual information are both crucial.
Compositional programming abstractions for mobile computing (1998)

Recent advances in wireless networking technology and the increasing demand for ubiquitous, mobile connectivity demonstrate the importance of providing reliable systems for managing the reconfiguration and disconnection of components. The design of such systems requires tools and techniques appropriate to the task. Many formal models of computation, including UNITY, are not adequate for expressing reconfiguration and disconnection and are, therefore, inappropriate vehicles for investigating the impact of mobility on the construction of modular and composable systems. Algebraic formalisms such as the /spl pi/-calculus have been proposed for modeling mobility. This paper addresses the question of whether UNITY, a state-based formalism with a foundation in temporal logic, can be extended to address concurrent, mobile systems. In the process, we examine some new abstractions for communication among mobile components that express reconfiguration and disconnection and which can be composed in a modular fashion.