gebhart/patrepeval huggingface dataset:
Hypoxia-enhanced Blood-Brain Barrier Chip recapitulates human barrier function and shuttling of drugs and antibodies (2019)

The high selectivity of the human blood-brain barrier (BBB) restricts delivery of many pharmaceuticals and therapeutic antibodies to the central nervous system. Here, we describe an in vitro microfluidic organ-on-a-chip BBB model lined by induced pluripotent stem cell-derived human brain microvascular endothelium interfaced with primary human brain astrocytes and pericytes that recapitulates the high level of barrier function of the in vivo human BBB for at least one week in culture. The endothelium expresses high levels of tight junction proteins and functional efflux pumps, and it displays selective transcytosis of peptides and antibodies previously observed in vivo. Increased barrier functionality was accomplished using a developmentally-inspired induction protocol that includes a period of differentiation under hypoxic conditions. This enhanced BBB Chip may therefore represent a new in vitro tool for development and validation of delivery systems that transport drugs and therapeutic antibodies across the human BBB.
Estimation of blood pressure levels from reflective Photoplethysmograph using smart phones (2013)

As part of preventive healthcare, there is a need to regularly monitor blood pressure (BP) of cardiac patients and elderly people. Mobile Healthcare, measuring human vitals like heart rate, Spo2 and blood pressure with smart phones using the Photoplethysmography technique is becoming widely popular. But, for estimating the BP, multiple smart phone sensors or additional hardware is required, which causes uneasiness for patients to use it, individually. In this paper, we present a methodology to estimate the systolic and diastolic BP levels by only using PPG signals captured with smart phones, which adds to the affordability, usability and portability of the system. Initially, a training model (Linear Regression Model or SVM Model) for various known levels of BP is created using a set of PPG features. This model is later used to estimate the BP levels from the features of the newly captured PPG signals. Experiments are performed on benchmark hospital dataset and data captured from smart phones in our lab. Results indicate that by additionally adding information of height, weight and age play a vital role in increasing the accuracy of the estimation of BP levels.
A Simple and Effective Strategy To Increase the Sensitivity of Fluorescence Probes in Living Cells (2009)

Noninvasive visualization and investigation of interactions among proteins, biomolecules, and enzymes in living cells is an important goal for biologists, and fluorescence probes are powerful tools for this purpose. Because many target molecules are present in only trace amounts, high sensitivity is very important, and it is common to improve the sensitivity of fluorescence probes by focusing on high reaction velocity, K(d). (Gee, K. R.; Archer, E. A.; Lapham, L. A.; Leonard, M. E.; Zhou, Z.; Bingham, J.; Diwu, Z. Bioorg. Med. Chem. Lett. 2000, 10, 1515-1518.) So far, we have designed and synthesized various highly sensitive fluorescence probes based on the above concepts. (Gabe, Y.; Urano, Y.; Kikuchi, K.; Kojima, H.; Nagano, T. J. Am. Chem. Soc. 2004, 126, 3357-3367. Komatsu, K.; Urano, Y.; Kojima, H.; Nagano, T. J. Am. Chem. Soc. 2007, 129, 13447-13454.) Nevertheless, they were sometimes insufficiently sensitive to detect biomolecules in living cells, despite high chemical sensitivity in cuvette. In this report, we suggest a new approach to increase the sensitivity of fluorescence probes, focusing on their intracellular retention. Since calcein is well-retained, we investigated its structural, chemical, and optical characteristics and found that the iminodiacetic acid group (IAG) is a key structure for the intracellular retention. We next designed and synthesized novel fluorescence probes containing IAGs. They showed superior intracellular retention, making it possible to visualize low concentrations of target molecules that would be difficult to observe with conventional probes and permitting long-term observation in living cells. Improvement of intracellular retention of fluorescence probes holds great promise as a strategy for developing a wide range of highly sensitive probes for studies on various biological phenomena.
Programmed Death Ligand-1 expression on the cell surface is regulated by costimulatory molecule CD80 expressed by cancer vaccines (101.4) (2010)

Abstract Programmed Death Ligand 1 (PDL1) is a major obstacle in the development of cancer immunotherapies. PDL1 is constitutively expressed or induced by IFNγ on many tumor cells, resulting in the prevention of T cell activation or the apoptotic cell death of activated T cells. Cell-based vaccines previously developed in our lab were made by modifying tumor cells to express Major Histocompatibility Complex Class II (MHCII) and costimulatory B7-1 (CD80) molecules. These cell-based vaccines do not express PDL1, even after IFNγ stimulation. As determined by flow cytometry using three anti-PDL1 monoclonal antibodies that detect distinct PDL1 epitopes, and human lung, uveal and cutaneous melanoma, and breast cancer cells, the over-expression of CD80 blocks constitutive and IFNγ-induced cell surface expression of PDL1. Quantitative analysis of CD80 and PDL1 expression indicates an inverse relationship between PDL1 and CD80. CD80+ tumor cells contain intracellular PDL1, as assessed by flow cytometry, suggesting that CD80 regulates PDL1 at the protein level. Tumor cells transfected with CD80 constructs lacking a cytoplasmic domain or with an irrelevant non-signaling cytoplasmic domain, retain the ability to block PDL1 expression at the cell surface indicating that CD80 does not modulate PDL1 transcription. These results suggest that in addition to serving as a costimulatory molecule, CD80 facilitates T cell activation by blocking coinhibitory signals and preventing T cell apoptosis.
<title>Automated feature extraction and classification of breast lesions in magnetic resonance images</title> (1998)

We are developing computerized methods to distinguish between malignant and benign lesions in contrast-enhanced magnetic resonance images of the breast. In this study, we compare 2D spatial analysis of lesions with 3D spatial analysis. Our database consists of 28 lesions: 15 malignant and 13 benign. At 90 s intervals, 4 to 6 scans are obtained, and the spatial uptake of contrast agent is analyzed. Computer-extracted features quantify the inhomogeneity of uptake, sharpness of the margins, and shape of the lesion. Stepwise multiple regression is employed to obtain a subset of features, followed by linear discriminant analysis to estimate the likelihood of malignancy. Cross-validation and ROC analysis are used to evaluate the performance of the method in distinguishing between benign and malignant lesions. The procedures are performed in 3D, and in 2D from single and multiple slices. Shape and sharpness of the lesion were the most effective features. ROC analysis yielded an A<SUB>z</SUB> value of 0.96 for 3D features, between 0.67 and 0.92 for single slices, and 0.88 for 2D features from multiple slices. The performance of 2D analysis on single slices depends strongly on the selected plane and may be significantly lower than the accuracy of full 3D analysis.
Speaker verification using mixture decomposition discrimination (2000)

A new approach for speaker verification is presented. Mixture decomposition discrimination (MDD) is based on the idea that, when modeling speech using speaker independent continuous density hidden Markov models (HMM), different speakers speaking the same word would cause different HMM mixture components to dominate. When the mixture information is considered, one can construct a "mixture profile" of a speaker speaking a given word or phrase. This mixture profile is incorporated into a discriminative training procedure to discriminate between a true speaker and all other speakers (or imposters). The effectiveness of MDD is seen when it is incorporated into a hybrid verification system that also includes speaker dependent HMM modeling with cohort normalization. Experimental results show that the hybrid system reduces the average equal error rate (EER) by 46% when compared with the EER of the speaker-dependent HMM verifier. It is also shown that the computational and model storage requirements needed to incorporate MDD into the hybrid system are relatively small.
Optimizing Camera Placements for Overlapped Coverage with 3D Camera Projections (2022)

This paper proposes a method to compute camera 6 DoF poses to achieve a user defined coverage. The camera placement problem is modeled as a combinatorial optimization where given the maximum number of cameras, a camera set is selected from a larger pool of possible camera poses. We propose to minimize the squared error between the desired and the achieved coverage, and formulate the non-linear cost function as a mixed integer linear programming problem. A camera lens model is utilized to project the camera's view on a 3D voxel map to compute a coverage score which makes the optimization problem in real environments tractable. Experimental results in two real retail store environments demonstrate the better performance of the proposed formulation in terms of coverage and overlap for triangulation compared to existing methods.
Separation of seed by‐products by an AC electric field (1984)

Abstract A method for separating constituents of the by‐products derived from agricultural processes offers the possibility of recovering their valuable components. Partial sorting by a unique electric field enriches the protein concentration in sunflower‐seed meal and cottonseed meal by removing objectionable components such as hulls or gossypol. Enrichment is accomplished by the dynamic forces from an electric field that is created by a set of parallel electrodes encased in a plastic panel and connected to an AC power supply. When the panel is activated, particles on its surface become charged, levitated and transported. When a mixture of particles contacts the panel, a difference in the charge is imparted to the components, opposite directions of transportation occur, and, then, the particles separate. The separation, or sorting, offers an additional possibility for upgrading agricultural products. Properties measured for these products and their separated components are charge, charge‐to‐mass ratio, size, size distribution, shape, moisture, nitrogen and gossypol. This new and direct method of separating components seems independent of their size and shape, yet it is probably dependent on the charge‐to‐mass ratio. The single‐stage separation is an analytical tool that might become an engineering process. The electric panel of the contact type contains, transports and refines materials—all without a cup, conveyor or filter touching the sample. Its promise and versatility warrant considering the panel by itself and in conjunction with other processes.
Anisotropic Synthesis of Armchair Graphene Nanoribbon Arrays from Sub-5 nm Seeds at Variable Pitches on Germanium (2019)

At widths below 10 nm, armchair graphene nanoribbons become semiconductors. One promising route to synthesize nanoribbons is chemical vapor deposition (CVD) of hydrocarbons on Ge(001), and synthesis from seeds reduces nanoribbon polydispersity. In this contribution, we advance the seed-initiated synthesis of nanoribbons and explore the impact of seed size and nanoribbon spacing on growth kinetics. Periodic arrays of graphene seeds are lithographically patterned and etched to reduce their diameter. The viability of initiating synthesis from sub-5 nm seeds is demonstrated, and the pitch between nanoribbons is reduced from 500 to 50 nm to show that crowding effects do not perturb nanoribbon growth kinetics. The invariance of kinetics with pitch in combination with density functional theory (DFT) calculations indicate that (1) the growth species for synthesis has a diffusion length of ≪50 nm and/or (2) the kinetics are strongly attachment-limited. These results demonstrate that seed-initiated synthesis on Ge(001) is a promising route for creating dense arrays of armchair graphene nanoribbons for semiconductor electronics applications.
Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study (2017)

Propionibacterium freudenreichii, a dairy starter, can reach a population of almost 10<sup>9</sup> propionibacteria per gram in Swiss-type cheese at the time of consumption. Also consumed as a probiotic, it displays strain-dependent anti-inflammatory properties mediated by surface proteins that induce IL-10 in leukocytes. We selected 23 strains with varied anti-inflammatory potentials in order to identify the protein(s) involved. After comparative genomic analysis, 12 of these strains were further analysed by surface proteomics, eight of them being further submitted to transcriptomics. The omics data were then correlated to the anti-inflammatory potential evaluated by IL-10 induction. This comparative omics strategy highlighted candidate genes that were further subjected to gene-inactivation validation. This validation confirmed the contribution of surface proteins, including SlpB and SlpE, two proteins with SLH domains known to mediate non-covalent anchorage to the cell-wall. Interestingly, HsdM3, predicted as cytoplasmic and involved in DNA modification, was shown to contribute to anti-inflammatory activity. Finally, we demonstrated that a single protein cannot explain the anti-inflammatory properties of a strain. These properties therefore result from different combinations of surface and cytoplasmic proteins, depending on the strain. Our enhanced understanding of the molecular bases for immunomodulation will enable the relevant screening for bacterial resources with anti-inflammatory properties.
Bismuth Substituted Strontium Cobalt Perovskites for Catalyzing Oxygen Evolution (2019)

In this study, we employ the strategy of substitution with more electronegative/acidic A-site ions in the cobalt perovskites to alter O 2p-band center, surface hydroxide affinity, and oxygen evolution reaction (OER) activity and stability in the basic electrolyte. Galvanostatically charged Bi<sub>0.2</sub>Sr<sub>0.8</sub>CoO<sub>3-δ</sub> (δ close to zero) was shown to exhibit record OER specific activity exceeding not only La<sub>x</sub>Sr<sub>1-x</sub>CoO<sub>3-δ</sub> but also charged SrCoO<sub>3-δ</sub> (δ close to zero), one of the most active oxide OER catalysts reported so far. The enhanced OER activity of charged Bi<sub>0.2</sub>Sr<sub>0.8</sub>CoO<sub>3-δ</sub> can be attributed to greater hydroxide affinity facilitating the deprotonation of surface bound intermediates due to the presence of strong Lewis acidic A-site Bi<sup>3+</sup> ions, while the high stability can result from lowered O 2p-band center relative to the Fermi level. This work provides a novel example in the rational design of highly active oxide catalysts for OER by leveraging the inductive effect.
Stator Inter-Turn Fault Detection of Doubly-Fed Induction Generators Using Rotor Current and Search Coil Voltage Signature Analysis (2007)

A novel technique for detecting stator inter-turn faults in a doubly fed induction generator (DFIG) is proposed by analyzing its rotor current and search coil voltage. So far, fault diagnostic techniques proposed for stator inter-turn fault detection in DFIG are based on analysis of stator current or vibration of generator. Results from these methods are ambiguous because either they fail to account for condition when DFIG is operating under unbalanced load or these methods are based on experimental results alone. Our recent observations suggested that harmonics induced in the rotor circuit are very promising in detecting stator inter-turn faults in DFIGs. Hence, in this study, an in-depth investigation was conducted to determine the origin of various harmonic components in the rotor currents and their feasibility to detect inter-turn stator faults unambiguously. Detailed analysis is presented that explains the induction of stator inter-turn fault related harmonics in the rotor circuit. The theory is verified with simulation and extensive experimental results.
Oral Passive Immunization With Plasma-Derived Polyreactive Secretory-Like IgA/M Partially Protects Mice Against Experimental Salmonellosis (2018)

Secretory immunoglobulins have a critical role in defense of the gastrointestinal tract and are known to act by preventing bacterial acquisition. A stringent murine model of bacterial infection with <i>Salmonella enterica</i> Typhimurium was used to examine protection mediated by oral passive immunization with human plasma-derived polyreactive IgA and IgM antibodies (Abs) reconstituted as secretory-like immunoglobulins (SCIgA/M). This reagent has been shown to trigger <i>Salmonella</i> agglutination and to limit the entry of bacterium into intestinal Peyer's patches via immune exclusion. We now demonstrate that upon administration into ligated intestinal loops, SCIgA/M properly anchors in the mucus and is protected from degradation to a better extent that IgA/M or IgG. Moreover, prophylactic oral administration of SCIgA/M before intragastric infection of mice with a virulent strain of <i>S. enterica</i> Typhimurium allows to protect infected animals, as reflected by reduced colonization of both mucosal and systemic compartments, and conserved integrity of intestinal tissues. In comparison with IgA/M or IgG administration, SCIgA/M provided the highest degree of protection. Moreover, such protective efficacy is also observed after therapeutic oral delivery of SCIgA/M. Either prophylactic or therapeutic treatment with passively delivered SCIgA/M ensured survival of up to 50% of infected mice, while untreated animals all died. Our findings unravel the potential of oral passive immunization with plasma-derived polyreactive SCIgA/M Abs to fight gastrointestinal infections.
Six1 Overexpression in Ovarian Carcinoma Causes Resistance to TRAIL-Mediated Apoptosis and Is Associated with Poor Survival (2007)

Tumorigenesis can arise from inappropriate activation of developmental genes in mature tissues. Here, we show that the developmental regulator Six1 is overexpressed in ovarian carcinoma cell lines (OCC) compared with normal ovarian surface epithelium. As observed in other cancers, Six1 overexpression in OCC leads to increased A-type cyclin expression and increased proliferation. In addition, Six1 overexpression renders OCC resistant to tumor necrosis factor-related apoptosis inducing ligand (TRAIL)-mediated apoptosis, and Six1 knockdown in the TRAIL-resistant SKOV3 ovarian carcinoma line dramatically sensitizes the cells to TRAIL. Because inactivation of the TRAIL response has been linked to metastasis, and because antibodies and recombinant ligand that activate the TRAIL pathway are currently in clinical trials against ovarian carcinoma, we screened normal ovarian and carcinoma specimens for Six1 mRNA. Six1 was overexpressed in 50% of the early-stage (stage I) and 63% of the late-stage (stages II, III, and IV) ovarian carcinomas examined, with late-stage carcinomas expressing approximately 3-fold higher Six1 mRNA levels on average compared with early-stage tumors. Importantly, in patients with late-stage disease, high Six1 expression was associated with significantly shortened survival (P = 0.0015). These data suggest that Six1 may contribute to ovarian epithelial carcinogenesis by simultaneously increasing proliferation and decreasing TRAIL-mediated apoptosis and imply that Six1 may be an important determinant of TRAIL therapy response that should be considered in patient selection for TRAIL-related clinical trials.
Multiscale 3D reference visualization (2009)

Reference grids are commonly used in design software to help users judge distances and understand the orientation of the virtual workspace. Despite their ubiquity in 3D graphics applications, little research has gone into important design considerations of the 3D reference grids themselves, which directly impact their usefulness. We have developed two new techniques; the multiscale reference grid and position pegs that form a consistent foundation for presenting relative scale and position information to the user. Our design of a multiscale reference grid consistently subdivides and coalesces gridlines, based on the computation of a closeness metric, while ensuring that there are neither too many nor too few subdivisions. Position pegs extend the grid so that objects that are lying above or below the ground plane can be brought into a common environmental frame of reference without interfering with the grid or object data. We provide a stable analytic viewpoint-determined result, solving several depth cue problems, that is independent of viewing projection.
Multi-task learning of time series and its application to the travel demand (2017)

We address the problem of modeling and prediction of a set of temporal events in the context of intelligent transportation systems. To leverage the information shared by different events, we propose a multi-task learning framework. We develop a support vector regression model for joint learning of mutually dependent time series. It is the regularization-based multi-task learning previously developed for the classification case and extended to time series. We discuss the relatedness of observed time series and first deploy the dynamic time warping distance measure to identify groups of similar series. Then we take into account both time and scale warping and propose to align multiple time series by inferring their common latent representation. We test the proposed models on the problem of travel demand prediction in Nancy (France) public transport system and analyze the benefits of multi-task learning.
A light and flexible plasma tube array with a film substrate (2005)

Abstract— The plasma tube array is expected to lead to the realization of wall‐sized displays. This method will realize an emissive‐type display with a flexible screen and an expandable screen size. We have investigated a plastic film substrate with display electrodes for use as a flexible screen and successfully developed the world's largest bendable emissive display (1000 × 128 mm). The operating voltage distribution was improved compared to that with a plate substrate, and a sufficient voltage margin was maintained.