gebhart/patrepeval huggingface dataset:
Human Immunodeficiency Virus Type 1 (HIV-l)-Seronegative Injection Drug Users at Risk for HIV Exposure Have Antibodies to HLA Class I Antigens and T Cells Specific for HIV Envelope (1996)

The question of whether persistently seronegative persons at high risk for human immunodeficiency virus type 1 (HIV-1) infection exhibit HIV-1-specific T cell responses and antibodies to HIV-1 envelope epitopes shared with selected HLAs was assessed. These antibodies are not detectable by conventional serologic methods. Envelope-specific helper T (Env-Th) cell responses and antibodies specific for the HIV/HLA epitopes were studied in 21 HIV-1-negative injection drug users (IDUs). HIV/HLA antibodies were detected in 7 (33.3%) of 21 IDUs and 4 (4.3%) of 94 low-risk controls. Env-Th cell responses were detected in 16 (76.2%) of 21 IDUs and in 2 (3.1%) of 65 low-risk controls. All HIV/HLA antibody-positive IDUs also had Env-Th cell responses. These findings confirm the presence of HIV-1-specific immunity in conventionally seronegative individuals. Further characterization of these responses could provide the basis for new preventive strategies.
Electrophoresis and Blotting of DNA (2004)

Abstract DNA electrophoresis and blotting are techniques commonly used to visualize DNA. Electrophoresis uses gels to separate DNA molecules on the basis of size; whereas blotting allows researchers to identify specific DNA fragments on the basis of their sequences.
Flicker, motion artifacts, and depth distortions in stereo 3D displays (2012)

Most stereoscopic displays rely on field-sequential presentation to present different images to the left and right eyes. With sequential presentation, images are delivered to each eye in alternation with dark intervals, and each eye receives its images in counter phase with the other eye. This type of presentation can exacerbate image artifacts including flicker, and the appearance of unsmooth motion. To address the flicker problem, some methods repeat images multiple times before updating to new ones. This greatly reduces flicker visibility, but makes motion appear less smooth. I describe an investigation of how different presentation methods affect the visibility of flicker, motion artifacts, and distortions in perceived depth. It begins with an examination of these methods in the spatio-temporal frequency domain. From this examination, it describes a series of predictions for how presentation rate, object speed, simultaneity of image delivery to the two eyes, and other properties ought to affect flicker, motion artifacts, and depth distortions. I then report a series of experiments that tested these predictions. The results confirmed essentially all of the predictions. I conclude with a summary and series of recommendations for the best approach to minimize these undesirable effects. Meeting abstract presented at OSA Fall Vision 2012
Intrinsic Activation of β-catenin Signaling by CRISPR/Cas9-mediated Exon Skipping Contributes to Immune Evasion in Hepatocellular Carcinoma (2021)

Abstract Comprehensive analysis of clinical samples has recently identified molecular and immunological classification of hepatocellular carcinoma (HCC), and the CTNNB1 (β-catenin)-mutated subtype exhibits distinctive characteristics of immunosuppressive tumor microenvironment. For clarifying the molecular mechanisms, we first established human and mouse HCC cells with exon 3 skipping of β-catenin, which promoted nuclear translocation and activated the Wnt/β-catenin signaling pathway, by using newly developed multiplex CRISPR/Cas9-based genome engineering system. Gene set enrichment analysis indicated downregulation of immune-associated gene sets in the HCC cells with activated β-catenin signaling. T cell killing assays demonstrated that the mouse Ctnnb1 Δex3 HCC cells evaded immune surveillance. Comparative analysis of gene expression profiles between HCC cells harboring wild-type and exon 3 skipping β-catenin elucidated that the expression levels of eight cytokines were commonly decreased in human and mouse β-catenin-mutated HCC cells. Public exome and transcriptome data of 373 human HCC samples showed significant downregulation of five candidate cytokine genes, CCL20 , CXCL1 , CXCL2 , NAMPT and VEGFA , in HCC tumors with β-catenin hotspot mutations. Taken together, this study discovered that cytokine controlled by β-catenin signaling activation could contribute to immune evasion, and provided novel insights into cancer immunotherapy for the β-catenin-mutated HCC subtype.
Evaluation of the relative Lewis acidities of lanthanoid(III) compounds by tandem mass spectrometry (1999)

H. Tsuruta, T. Imamoto and K. Yamaguchi, Chem. Commun., 1999, 1703 DOI: 10.1039/A905569J
Hybrid positron emission tomography-magnetic resonance imaging for assessing different stages of cardiac impairment in patients with Anderson–Fabry disease: AFFINITY study group (2019)

In females with AFD, focal 18F-FDG uptake with a trend towards a pseudo-normalization of abnormal T1 mapping values, may represent an intermediate stage before the development of myocardial fibrosis. These findings suggest a potential relationship between progressive myocyte sphingolipid accumulation and inflammation.
Recent Progress in the Field of β-(1,3)-Glucans and New Applications (2006)

International audience
Abstract 12112: Clinical Outcomes of Percutaneous Epicardial Ablation (2015)

Introduction: Percutaneous epicardial access (EAc) is increasingly performed as part of VT/PVC ablation, especially in those that have failed prior ablation. We aimed to delineate the outcomes of EAc. Methods: We retrospectively analyzed individuals undergoing EAc for arrhythmia ablation between June 2004 and July 2014. Acute procedural success was defined as elimination/non-inducibility of the clinical arrhythmia after ablation; clinical success was defined as absence of symptoms/arrhythmia. Results: Of 175 patients, 126 (72%) were male with a mean age of 52.8±15.7 years. Eighty-three (47.4%) patients had NICM, 25 (14.3%) had ICM and 34 (19.4%) had normal hearts. Baseline EF was 44±16%. Patients had failed an average of 1.7±1.2 antiarrhythmic drugs; 139 patients (79%) had failed prior endocardial (endo) ablation (average 1.3±1.1). Six (3.4%) had prior EAc and 18 (10.3%) prior cardiac surgery. The indication for ablation was VT or PVC in 113 (64.6%) and 60 (34.3%) patients, respectively. Successful access was obtained in 168 (98%) patients. Anterior access, inferior access, or both, was utilized in 89 (52.7%), 77 (45.6%) and 2 (1.2%) patients, respectively. There were an average of 2.7±2.2 VT/PVCs identified, and 1.6±1.1 ablated. Endo, epicardial (epi) or combined ablation was performed in 58 (33.1%), 14 (8%), and 100 (57.1%) patients, respectively; 3 did not undergo ablation. Procedural success was obtained in 158 of 173 (91.3%) patients for whom data was available. At 12 months, clinical success was maintained in 62% with no difference between endo, epi or combined ablation (figure). Cardiac tamponade requiring repeat EAc occurred in 12 (6.9%) patients. There were no procedural related deaths. Conclusion: Epicardial access is feasible in almost all patients with no prior cardiac surgery, and permits acute procedural success in 91.3% of patients, most of whom had failed previous ablation. Furthermore, complications are relatively infrequent in this complex cohort.
Development of New Placental and Fetal Expressed Sequence Tags (EST) for Gene Discovery in Pig Reproduction (2001)

One major problem that has high economic impact on pig reproduction is the unexplained loss of potential porcine conceptuses during the first month of gestation. To better understand when and how these losses occur, it is imperative to investigate the underlying genetic regulatory mechanisms. We have recently initiated a large-scale cDNA sequencing project to provide molecular information regarding the genes expressed in female reproductive tissues. cDNA libraries are planned for ovary, hypothalamus, pituitary, placenta, uterus, and several stages of embryonic development. Sequence information will also be highly useful in developing sequence-tagged sites for physical mapping and developing comparative links between the human, mouse, and pig genome maps. We have previously reported the creation of two cDNA libraries, porcine fetal (day 20), and conceptus (day 17). Sequencing of these libraries produced 220 Expressed Sequence Tags (ESTs), with 180 sequences analyzed by clustering algorithms, and 139 clusters identified within these sequences. We now report the creation of two more libraries from porcine fetal (day 45) and placental tissues. The day 45 fetal library has 971,150 independent clones (average insert: 1.4 kb), whereas the placental library has 1,320,000 independent clones. Initial sequencing of the fetal library has produced 119 ESTs (81 clusters), whereas we have obtained 1411 ESTs (1056 clusters) from the placental library. After clustering all sequences thus far obtained, we have identified 1,233 unique clusters. Sequences obtained in this project will be deposited into Genbank dbEST, and all comparative homology
Transcranial ultrasound neuromodulation of the contralateral visual field in awake monkey (2013)

In this work, we investigated the effect of low intensity pulsed focused ultrasound in the brain of two awake Maccaca Mulatta monkeys using the antisaccade (AS) paradigm. The objective of the study was to determine if transcranial ultrasound has an effect on behavioural tasks in awake animal involving a specific brain structure. Two Maccaca Mulatta monkeys (Y and L) were trained to perform antisaccade (AS) movements where they initially have to fix a central stimulus on a screen and then refrain from looking at an appearing peripheral target but instead initiate as soon as possible a saccade towards the opposite direction. In order to investigate the effect of low intensity focused ultrasound, a continuous 100 ms sonication pulse (derated pressure estimated at 0.35 ± 0.05 MPa) was focused at the frontal eye field using a 320 kHz transducer (H115, Sonic Concept, Bothell, WA, USA). Ipsilateral mean AS latencies with ultrasound stimulation were significantly (t-test;monkey Y: p=.0345, monkey L: p= .0311) increased compared to the non-stimulation condition (monkey Y: +14ms; monkey L: +15 ms). The study demonstrates the feasibility of using focused ultrasound to causally modulate behaviour in awake non-human primate brain.
Modeling and Experimental Validation of DNA Motion in Uniform and Nonuniform DC Electric Fields (2010)

We are developing a new technique to insert foreign DNA into a living cell using a microelectromechanical system. This new technique relies on electrical forces to move DNA in a nonuniform electric field. To better understand this phenomenon, we perform integrated modeling and experiments of DNA electrophoresis. This paper describes the protocol and presents the results for DNA motion experiments using fabricated gel electrophoresis devices. We show that DNA motion is strongly correlated with ion transport (current flow) in the system. A better understanding of electrophoretic fundamentals allows for the creation of a mathematical model to predict the motion of DNA during electrophoresis in both uniform and nonuniform electric fields. The mathematical model is validated within 4% through comparison with the experimental results.
Modeling the intonation of discourse segments for improved online dialog ACT tagging (2008)

Prosody is an important cue for identifying dialog acts. In this paper, we show that modeling the sequence of acoustic-prosodic values as n-gram features with a maximum entropy model for dialog act (DA) tagging can perform better than conventional approaches that use coarse representation of the prosodic contour through acoustic correlates of prosody. We also propose a discriminative framework that exploits preceding context in the form of lexical and prosodic cues from previous discourse segments. Such a scheme facilitates online DA tagging and offers robustness in the decoding process, unlike greedy decoding schemes that can potentially propagate errors. Using only lexical and prosodic cues from 3 previous utterances, we achieve a DA tagging accuracy of 72% compared to the best case scenario with accurate knowledge of previous DA tag, which results in 74% accuracy.
CHARACTERIZATION OF TMPRSS2-ETS GENE ABERRATIONS IN ANDROGEN INDEPENDENT METASTATIC PROSTATE CANCER (2008)

You have accessJournal of Urology1 Apr 2008CHARACTERIZATION OF TMPRSS2-ETS GENE ABERRATIONS IN ANDROGEN INDEPENDENT METASTATIC PROSTATE CANCER Rohit Mehra, Scott A Tomlins, Lei Wang, Anjana Menon, Kenneth Pienta, Rajal B Shah, and Arul M Chinnaiyan Rohit MehraRohit Mehra More articles by this author , Scott A TomlinsScott A Tomlins More articles by this author , Lei WangLei Wang More articles by this author , Anjana MenonAnjana Menon More articles by this author , Kenneth PientaKenneth Pienta More articles by this author , Rajal B ShahRajal B Shah More articles by this author , and Arul M ChinnaiyanArul M Chinnaiyan More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(08)60735-1AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "CHARACTERIZATION OF TMPRSS2-ETS GENE ABERRATIONS IN ANDROGEN INDEPENDENT METASTATIC PROSTATE CANCER." The Journal of Urology, 179(4S), p. 254 © 2008 by American Urological AssociationFiguresReferencesRelatedDetails Volume 179Issue 4SApril 2008Page: 254 Advertisement Copyright & Permissions© 2008 by American Urological AssociationMetricsAuthor Information Rohit Mehra More articles by this author Scott A Tomlins More articles by this author Lei Wang More articles by this author Anjana Menon More articles by this author Kenneth Pienta More articles by this author Rajal B Shah More articles by this author Arul M Chinnaiyan More articles by this author Expand All Advertisement PDF downloadLoading ...
Pulse response of multimode interference devices (2006)

Multimode interference (MMI) devices operating at high data rates are important in optical interconnects and optical networks. Their 1timesN splitting provides a fundamental functionality in these and other applications. To determine the speed limitations of MMI devices, the ultrashort pulse response of these devices is modeled. For example, for 50-fs Gaussian input pulses into a 1 times 16 splitter, the output pulses are severely degraded in coupling efficiency (48%) and completely broken up in time primarily due to intermodal and intramodal (waveguide) dispersion. Material dispersion is found to play only a minor role in the pulse response of MMI devices. However, for 1-ps input pulses into the same 1 times 16 splitter, the output pulses are only moderately degraded in coupling efficiency (86%) and only slightly degraded in shape
Markov model based noise modeling and its application to noisy speech recognition using dynamical features of speech (2002)

In this paper, some algorithms to recognize speech in time varying noise are proposed. In the proposed methods, spectral subtraction and Markov model based noise models are successfully utilized in the framework of spectral decomposition of noisy speech. Firstly, we considered the problem of the mis-subtraction noise which is caused in the subtraction based decomposition procedure. Then, the precise use of dynamical feature of speech such as delta cepstrum is discussed. Using the methods proposed here, recognition performance are improved more than 60% compared to no compensation method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immobilized Metal Complex Catalysts and Heterogeneous Precious Metal Catalysts on Polysiloxane Supports and Their Application in Organic Synthesis (2017)

The synthesis of immobilized metal complex catalysts 1 via the polycondensation of ligand functionalized metal complexes and the preparation of heterogeneous metal catalysts 2 via the adsorption/precipitation of metal salts on suitably functionalized polysiloxane supports are reported. https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9781315138855/34060206-aad8-4ad9-be2f-7d1369816bee/content/fig383_1.tif"/> https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9781315138855/34060206-aad8-4ad9-be2f-7d1369816bee/content/fig383_2.tif"/> Applications of these catalysts in organic synthesis, which are described, include the selective hydrogenation of steroids, α,β-unsaturated aldehydes, fatty acids, high molecular weight olefins, nitroaromatics, etc. and the hydroformylation of 1-octene. The outstanding behavior of these unique catalysts is explained by their particle- and pore-size distribution and their structural composition.
Developing visual interfaces for mobile devices (2011)

The popularity of mobile interfaces and application development is increasing along with the rapid expansion of the mobile electronics market and its migration from text-based applications to various multimedia applications. Real-time graphics and web applications are becoming one of the most attractive applications in mobile terminals due to their benefits for enterprise, gaming, and social media. This hands-on course will cover a comprehensive set of topics for developing mobile visual interfaces, including an overview of the mobile market, a comparison of mobile and desktop applications, and a survey of mobile development environments. We will also undertake a detailed discussion of UI development for mobiles, and graphics development for mobiles. During the course, various smartphones will be loaned to attendees for trying out several in-class exercises.
Two Generations of Insulinotropic Imidazoline Compounds (2002)

The imidazoline RX871024 increased basal- and glucose-stimulated insulin release in vitro and in vivo. The compound inhibited activity of ATP-sensitive K(+) channels as well as voltage-gated K(+) channels, which led to membrane depolarization, an increase in the cytosolic Ca(2+) concentration ([Ca(2+)](i)), and insulin release. Importantly, RX871024 also enhanced the insulinotropic effect of glucose in cells with clamped [Ca(2+)](i) but in the presence of high ATP and Ca(2+)concentration inside the cell. We believe that the latter effect on insulin exocytosis was at least in part mediated by a rise in diacylglycerol, which then activated protein kinase C (PKC) and increased the generation of arachidonic acid (AA) metabolites. Activation of both the PKC and AA pathways resulted in potentiation of glucose effects on insulin secretion. Unlike RX871024, the novel imidazoline BL11282 did not block ATP-dependent K(+) channels, but similarly to RX871024, it stimulated insulin secretion in depolarized or permeabilized islets. Accordingly, BL11282 did not influence glucose and insulin levels under basal conditions either in vitro or in vivo, but it markedly enhanced the insulinotropic effects of glucose. BL11282 restored the impaired insulin response to glucose in islets from spontaneously diabetic GK rats. We conclude that BL11282 belongs to a new class of insulinotropic compounds that demonstrate a strong glucose-dependent effect on insulin exocytosis.
Stability Analysis of Electrostatically Actuated Resonators With Delayed Feedback Controller (2010)

In this work we investigate the stability of parallel-plate electrostatic MEMS resonators using a delayed feedback controller. Two case studies are investigated: a capacitive sensor made of cantilever beams with a proof mass at their tip and a clamped-clamped microbeam. Dover-cliff integrity curves and basin-of-attraction analysis are used for the stability assessment of the frequency response of the resonators for several scenarios of positive and negative gain in the controller. It is found that, in the case of a positive gain, a velocity or a displacement feedback controller can be used to effectively enhance the stability of the resonators. This is confirmed by an increase in the area of the safe basin of attraction and in shifting the Dover-cliff curve upward. On the other hand, it is shown that a negative gain can significantly weaken the stability of the resonators. This can be of useful use in MEMS for actuation applications, such as in the case of capacitive switches, to lower the activation voltage of these devices and to ensure their trigger under all initial conditions.
Identification of Chromatophore Membrane Protein Complexes Formed under Different Nitrogen Availability Conditions in Rhodospirillum rubrum (2011)

The chromatophore membrane of the photosynthetic diazotroph Rhodospirillum rubrum is of vital importance for a number of central processes, including nitrogen fixation. Using a novel amphiphile, we have identified protein complexes present under different nitrogen availability conditions by the use of two-dimensional Blue Native/SDS-PAGE and NSI-LC-LTQ-Orbitrap mass spectrometry. We have identified several membrane protein complexes, including components of the ATP synthase, reaction center, light harvesting, and NADH dehydrogenase complexes. Additionally, we have identified differentially expressed proteins, such as subunits of the succinate dehydrogenase complex and other TCA cycle enzymes that are usually found in the cytosol, thus hinting at a possible association to the membrane in response to nitrogen deficiency. We propose a redox sensing mechanism that can influence the membrane subproteome in response to nitrogen availability.
A microengineered Brain-Chip to model neuroinflammation in humans (2022)

Species differences in brain and blood-brain barrier (BBB) biology hamper the translation of findings from animal models to humans, impeding the development of therapeutics for brain diseases. Here, we present a human organotypic microphysiological system (MPS) that includes endothelial-like cells, pericytes, glia, and cortical neurons and maintains BBB permeability at <i>in vivo</i> relevant levels. This human Brain-Chip engineered to recapitulate critical aspects of the complex interactions that mediate neuroinflammation and demonstrates significant improvements in clinical mimicry compared to previously reported similar MPS. In comparison to Transwell culture, the transcriptomic profiling of the Brain-Chip displayed significantly advanced similarity to the human adult cortex and enrichment in key neurobiological pathways. Exposure to TNF-α recreated the anticipated inflammatory environment shown by glia activation, increased release of proinflammatory cytokines, and compromised barrier permeability. We report the development of a robust brain MPS for mechanistic understanding of cell-cell interactions and BBB function during neuroinflammation.