gebhart/patrepeval huggingface dataset:
Autophagy is Involved in Optimal Expression of TL1A (TNFSF15) by Microbes in Primary Human Monocytes (2012)

Inflammatory bowel disease (IBD) is postulated to result from a dysregulated mucosal immune response to host microflora in genetically susceptible individuals. Genetic studies identified several IBD associated genes including autophagy genes (ATG16L1 and IRGM) and tumor necrosis factor superfamily member 15 (TNFSF15). Autophagy describes a biological process that involves trafficking and handling of macro-molecules including bacteria. Studies show that autophagy plays an important role in the clearance of microbial pathogens. Alterations in the autophagic machinery such as in ATG16L1 and IRGM may result in the ineffective elimination of pathogens and the persistent activation of the inflammatory cascade in the intestine, which may contribute to the pathogenesis of IBD. TL1A is a cytokine and its elevation is associated with more aggressive IBD disease course. Induction of TL1A expression occurs through a variety of innate immune pathways including activation of Fcc receptor, TLRs, and enteric microorganisms in primary human monocytes. This study examines the role of bacteria-host interaction, specifically the interaction between autophagy, bacteria, and TL1A expression. Fresh human blood monocytes were cultured with E. coli and starvation media (EBSS) to induce autophagy. Monocytes were transiently transfected with siRNAs targeting ATG16L1 or control. Knock-down of ATG16L1 expression is confirmed by RT-PCR. Activation of autophagy was assessed by Western blot for LC3 and P62 and immunofluorescent staining for LC3. TL1A mRNA was measured by RT-PCR and protein expression was measured by flow cytometry and ELISA. To determine the functional relevance of monocyte TL1A induction, we co-cultured bacteria stimulated monocytes with CD4+ T cells with either neutralizing TL1A antibody or isotype antibody and measured IFN-γ production by ELISA. Knock-down of ATG16L1 expression by 70% of baseline expression led to 48% reduction (P = 0.04) in bacteria induced TL1A expression. Activation of autophagy by starvation (elevated LC3-II conversion, reduced P62, and punctate LC3 staining pattern) enhanced bacteria induction of TL1A (mRNA avg 6 fold increase, P<0.01; membrane bound TL1A avg 5 fold increase, P<0.01; secreted TL1A avg 3 fold increase, P<0.01). In contrast, autophagy did not enhance IC induced TL1A expression. Functional analysis showed that autophagy enhanced microbial dependent TL1A production in monocytes potentiated CD4+ T cell effector function by augmenting IFN-γ production that was reduced up to 50% (P = 0.03) by blocking TL1A antibody. Our data suggest that activation of autophagy is important for optimal expression of TL1A, a critical factor in the modulation of gut mucosal inflammation.
Biomarkers of acute kidney injury: the pathway from discovery to clinical adoption (2017)

Acute kidney injury (AKI) is a common complication of critical illnesses and has a significant impact on outcomes, including mortality and morbidities. Unfortunately, apart from prophylactic measures, no effective treatment for this syndrome is known. Therefore, early recognition of AKI not only can provide better opportunities for preventive interventions, but also opens many gates for research and development of effective therapeutic options. Over the last few years, several new AKI biomarkers have been discovered and validated to improve early detection, differential diagnosis, and differentiation of patients into risk groups for progressive renal failure, need for renal replacement therapy (RRT), or death. These novel AKI biomarkers complement serum creatinine (SCr) and urine output, which are the standard diagnostic tools for AKI detection. In this article, we review the available literature on characteristics of promising AKI biomarkers that are currently the focus of preclinical and clinical investigations. These biomarkers include neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule 1 (KIM-1), liver-type fatty acid-binding protein, interleukin 18 (lL-18), insulin-like growth factor-binding protein 7, tissue inhibitor of metalloproteinase 2 (TIMP-2), calprotectin, urine angiotensinogen (AGT), and urine microRNA. We then describe the clinical performance of these biomarkers for diagnosis and prognostication. We also appraise each AKI biomarker's advantages and limitations as a tool for early AKI recognition and prediction of clinical outcomes after AKI. Finally, we review the current and future states of implementation of biomarkers in the clinical practice.
Putting the physical into the digital: issues in designing hybrid interactive surfaces (2009)

Hybrid surfaces are interactive systems combining techniques of direct-manipulation multi-touch surface interaction with elements of tangible user interfaces (TUIs). The design space for such complex hands-on computing experiences is sufficiently broad that it can be difficult to decide when interface elements should be given either a physical or digital instantiation, and the extent to which different interface functions should be made to model real-world interactions. In this paper we present two case studies of hybrid surface systems we are developing and discuss how we have reasoned through these kinds of design decisions. From this, we derive a set of observations about properties of physical and digital elements, and offer them as a design resource.
Large area 1D CMUT phased arrays for multi-modality ultrasound imaging (2011)

We present the design and fabrication of 1D capacitive micromachined ultrasonic transducer (CMUT) arrays optimized for imaging using multiple modalities. A new variation of the fabrication process based on a thick buried oxide layer is used to build these CMUTs. In our process, the via connections for each cell's electrode with the handle layer are made from the front side. This enables fabricating CMUT cells with smaller sizes, and higher resonant frequencies. Initial characterization results agree well with our design simulations.
Spin Torque Resonant Vortex Core Expulsion For An Efficient Radio-Frequency Detection Scheme (2016)

The files contain all information that enables the user to recalculate the figures present in the publication
An efficient, rapid, and non-centrifugation synthesis of nanosized zeolites by accelerating the nucleation rate (2018)

An efficient, rapid, and non-centrifugation synthesis of nanosized zeolites is developed by accelerating the nucleation rate in the starting gel systems.
Involved Site Radiotherapy Extends Time to Premature Menopause in Infra-Diaphragmatic Female Hodgkin Lymphoma Patients – An Analysis of GHSG HD14- and HD17-Patients (2021)

Infradiaphragmatic IFRT impairs gonadal function to a similar extent as two cycles of BEACOPPesc. In comparison, the use of ISRT target volume definition significantly reduced radiation dose to the ovaries and significantly extends the time interval from treatment to premature menopause.
3D VSP: A mine of information for mining exploration (2013)

AbstractThe 3DVSP technique becomes more popular with the emergence of multilevel 3 component borehole tools.The value of the information derived from VSP is not always well understood.In this paper we will present a case history of a joint surface and borehole seismic acquisition, with the goal to de-risk a shaft sinking location on a platinum mine.TD was about 650 m and the VSP tool was 110 m long. On surface a dense grid of receivers and vibrator source points were laid out in a 1.2 km radius circle centred on the well head. A12 level 3C VSP digital tool was lowered in the borehole, in three successive depth positions.The surface 3D cube was processed and interpreted independently from the 3D VSP data. On a near target reflector, the surface data structural interpretation showed mainly a clear E/W fault, and additional sub-seismic lineaments of differing azimuths, difficult to identify in terms of fault. The 3D VSP image limited to a short radius around the borehole confirmed the fault/dyke nature of these lineaments, separating monocline compartments.As a consequence, the surface data was carefully re- interpreted and on the second structural images derived from two surface seismic reflectors and the near surface fault footprint from 3DVSP residual statics, a series of subtle faults were clearly assessed. Last, the few faults intersecting the borehole can be clearly recognized on the logs and the borehole radar logs.This case study demonstrates the added value of a joint interpretation of surface and borehole data in a decision making process for shaft sinking.KeywordsVSPinterpretationfault lineaments AcknowledgmentsAuthors would like to thank Anglo Platinum and Anglo American for their constant support during the phases of this project and permission to publish the results. Geological exchanges with Jaco Vermeulen of Royal Bafokeng Platinum Ltd (RBPlat) are greatly appreciated as well.Additional geophysicists actively contributed to the pre- processing and processing of the presented VSP and surface datasets, namely Patrice Ricarte, Vincent Clochard, Kazem Kazemi and Josette Bruneau of IFPEN, Eric Gillot and Fabienne Pradalie of CGGV.
1,2-Diacetals:  A New Opportunity for Organic Synthesis (2000)

The use of 1,2-diacetals for a number of synthetic applications to provide diol protection and reactivity control was studied. The chiral versions of these systems were used to desymmetrize the enantiotopic diol pairs and to discriminate diequatorial diols in many carbohydrate derivatives. The fusion of these rigid units to the carbohydrate substrates proved effective for tuning the reactivity during glycosidic coupling reactions. The studies confirmed that the methyl groups acted as useful diagnostic markers to analyze the nuclear magnetic resonance features of the compounds.
Sphinganine‐Like Biogenesis of (E)‐1‐Nitropentadec‐1‐ene in Termite Soldiers of the Genus Prorhinotermes (2014)

In 1974, (E)-1-nitropentadec-1-ene, a strong lipophilic contact poison of soldiers of the termite genus Prorhinotermes, was the first-described insect-produced nitro compound. However, its biosynthesis remained unknown. In the present study, we tested the hypothesis that (E)-1-nitropentadec-1-ene biosynthesis originates with condensation of amino acids with tetradecanoic acid. By using in vivo experiments with radiolabeled and deuterium-labeled putative precursors, we show that (E)-1-nitropentadec-1-ene is synthesized by the soldiers from glycine or L-serine and tetradecanoic acid. We propose and discuss three possible biosynthetic pathways.
Corn Stunt Virus: Transmission by Three Cicadellid Vectors1 (1968)

Journal Article Corn Stunt Virus: Transmission by Three Cicadellid Vectors Get access Robert R. Granados, Robert R. Granados Boyce Thompson Institute for Plant Research, Yonkers, New York Search for other works by this author on: Oxford Academic PubMed Google Scholar Johanna S. Granados, Johanna S. Granados Boyce Thompson Institute for Plant Research, Yonkers, New York Search for other works by this author on: Oxford Academic PubMed Google Scholar Karl Maramorosch, Karl Maramorosch Boyce Thompson Institute for Plant Research, Yonkers, New York Search for other works by this author on: Oxford Academic PubMed Google Scholar Josh Rfinitz Josh Rfinitz Boyce Thompson Institute for Plant Research, Yonkers, New York Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 61, Issue 5, 1 October 1968, Pages 1282–1287, https://doi.org/10.1093/jee/61.5.1282 Published: 01 October 1968 Article history Accepted: 09 April 1968 Published: 01 October 1968
Photochemical activation of TRPA1 channels in neurons and animals (2020)

Optogenetics is a powerful research tool because it enables high-resolution optical control of neuronal activity. However, current optogenetic approaches are limited to transgenic systems expressing microbial opsins and other exogenous photoreceptors. Here, we identify optovin, a small molecule that enables repeated photoactivation of motor behaviors in wild type animals. Surprisingly, optovin's behavioral effects are not visually mediated. Rather, photodetection is performed by sensory neurons expressing the cation channel TRPA1. TRPA1 is both necessary and sufficient for the optovin response. Optovin activates human TRPA1 via structure-dependent photochemical reactions with redox-sensitive cysteine residues. In animals with severed spinal cords, optovin treatment enables control of motor activity in the paralyzed extremities by localized illumination. These studies identify a light-based strategy for controlling endogenous TRPA1 receptors in vivo, with potential clinical and research applications in non-transgenic animals, including humans.
Infrared readout electronics; Proceedings of the Meeting, Orlando, FL, Apr. 21, 22, 1992 (1992)

The present volume on IR readout electronics discusses cryogenic readout using silicon devices, cryogenic readout using III-V and LTS devices, multiplexers for higher temperatures, and focal-plane signal processing electronics. Attention is given to the optimization of cryogenic CMOS processes for sub-10-K applications, cryogenic measurements of aerojet GaAs n-JFETs, inP-based heterostructure device technology for ultracold readout applications, and a three-terminal semiconductor-superconductor transimpedance amplifier. Topics addressed include unfulfilled needs in IR astronomy focal-plane readout electronics, IR readout integrated circuit technology for tactical missile systems, and radiation-hardened 10-bit A/D for FPA signal processing. Also discussed are the implementation of a noise reduction circuit for spaceflight IR spectrometers, a real-time processor for staring receivers, and a fiber-optic link design for INMOS transputers.
Non-conventional Trafficking of the Cystic Fibrosis Transmembrane Conductance Regulator through the Early Secretory Pathway (2002)

The mechanism(s) of cystic fibrosis transmembrane conductance regulator (CFTR) trafficking from the endoplasmic reticulum (ER) through the Golgi apparatus, the step impaired in individuals afflicted with the prevalent CFTR-DeltaF508 mutation leading to cystic fibrosis, is largely unknown. Recent morphological observations suggested that CFTR is largely absent from the Golgi in situ (Bannykh, S. I., Bannykh, G. I., Fish, K. N., Moyer, B. D., Riordan, J. R., and Balch, W. E. (2000) Traffic 1, 852-870), raising the possibility of a novel trafficking pathway through the early secretory pathway. We now report that export of CFTR from the ER is regulated by the conventional coat protein complex II (COPII) in all cell types tested. Remarkably, in a cell type-specific manner, processing of CFTR from the core-glycosylated (band B) ER form to the complex-glycosylated (band C) isoform followed a non-conventional pathway that was insensitive to dominant negative Arf1, Rab1a/Rab2 GTPases, or the SNAp REceptor (SNARE) component syntaxin 5, all of which block the conventional trafficking pathway from the ER to the Golgi. Moreover, CFTR transport through the non-conventional pathway was potently blocked by overexpression of the late endosomal target-SNARE syntaxin 13, suggesting that recycling through a late Golgi/endosomal system was a prerequisite for CFTR maturation. We conclude that CFTR transport in the early secretory pathway can involve a novel pathway between the ER and late Golgi/endosomal compartments that may influence developmental expression of CFTR on the cell surface in polarized epithelial cells.
Map matching with inverse reinforcement learning (2013)

We study map-matching, the problem of estimating the route that is traveled by a vehicle, where the points observed with the Global Positioning System are available. A state-of-the-art approach for this problem is a Hidden Markov Model (HMM). We propose a particular transition probability between latent road segments by the use of the number of turns in addition to the travel distance between the latent road segments. We use inverse reinforcement learning to estimate the importance of the number of turns relative to the travel distance. This estimated importance is incorporated in the transition probability of the HMM. We show, through numerical experiments, that the error of map-matching can be reduced substantially with the proposed transition probability.
Conformational Changes of gp120 in Epitopes near the CCR5 Binding Site Are Induced by CD4 and a CD4 Miniprotein Mimetic (1999)

Binding of the T-cell antigen CD4 to human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 has been reported to induce conformational rearrangements in the envelope complex that facilitate recognition of the CCR5 coreceptor and consequent viral entry into cells. To better understand the mechanism of virus docking and cell fusion, we developed a three-component gp120-CD4-17b optical biosensor assay to visualize the CD4-induced conformational change of gp120 as seen through envelope binding to a neutralizing human antibody, 17b, which binds to epitopes overlapping the CCR5 binding site. The 17b Fab fragment was immobilized on a dextran sensor surface, and kinetics of gp120 binding were evaluated by both global and linear transformation analyses. Adding soluble CD4 (sCD4) increased the association rate of full-length JR-FL gp120 by 25-fold. This change is consistent with greater exposure of the 17b binding epitope on gp120 when CD4 is bound and correlates with CD4-induced conformational changes in gp120 leading to higher affinity binding to coreceptor. A smaller enhancement of 17b binding by sCD4 was observed with a mutant of gp120, DeltaJR-FL protein, which lacks V1 and V2 variable loops and N- and C-termini. Biosensor results for JR-FL and DeltaJR-FL argue that CD4-induced conformational changes in the equilibrium state of gp120 lead both to movement of V1/V2 loops and to conformational rearrangement in the gp120 core structure and that both of these lead to greater exposure of the coreceptor-binding epitope in gp120. A 17b binding enhancement effect on JR-FL also was observed with a 32-amino acid charybdotoxin miniprotein construct that contains an epitope predicted to mimic the Phe 43/Arg 59 region of CD4 and that competes with CD4 for gp120 binding. Results with this construct argue that CD4-mimicking molecules with surrogate structural elements for the Phe 43/Arg 59 components of CD4 are sufficient to elicit a similar gp120 conformational isomerization as expressed by CD4 itself.
Lateral leakage in TM-like whispering gallery mode of thin-ridge silicon-on-insulator disk resonators (2009)

The leakage loss due to TM-TE mode coupling of TM-like whispering gallery mode in silicon-on-insulator (SOI) thin-ridge disk resonators is investigated for the first time to the best of our knowledge. We show that the propagation losses of TM-like mode in thin-ridge SOI disk resonators are significantly impacted by the radius of the disk. This behavior is predicted by a simple phenomenological model as well as a rigorous mode matching simulation.
Inheritance of Resistance to Cry1A.105 in Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) (2022)

Cry1A.105 is a bioengineered <i>Bacillus thuringiensis</i> (Bt) insecticidal protein consisting of three domains derived from Cry1Ac, Cry1Ab, and Cry1F. It is one of the two pyramided Bt toxins expressed in the MON 89034 event, a commonly planted Bt maize trait in the Americas. Recent studies have documented that field resistance of the corn earworm, <i>Helicoverpa zea</i> (Boddie), to the Cry1A.105 toxin in maize plants has become widespread in the United States. To investigate the inheritance of resistance to Cry1A.105 in <i>H. zea</i>, two independent tests, each with various genetic crosses among susceptible and Cry1A.105-resistant populations, were performed. The responses of these susceptible, resistant, F<sub>1</sub>, F<sub>2</sub>, and backcrossed insect populations to Cry1A.105 were assayed using a diet overlay method. The bioassays showed that the resistance to Cry1A.105 in <i>H. zea</i> was inherited as a single, autosomal, nonrecessive gene. The nonrecessive nature of the resistance could be an important factor contributing to the widespread resistance of maize hybrids containing Cry1A.105 in the United States. The results indicate that resistance management strategies for Bt crops need to be refined to ensure that they are effective in delaying resistance evolution for nonrecessive resistance (nonhigh dose).
Etiology of experimental calcium oxalate monohydrate nephrolithiasis in rats. (1994)

In a rat-model system, tubular crystal retention as a possible mechanism for the etiology of nephrolithiasis in man, was studied by conventional transmission electron microscopy. The animals were supplied for nine days with a crystal-inducing diet, with ethylene glycol plus NH4Cl in their drinking-water. After this induction period, a two day regime with fresh drinking-water was included, to allow crystals to be removed by spontaneous crystalluria. After aldehyde fixation of the rat kidneys, large crystals were seen inside the tubular lumen. The crystals were attached to cell surfaces and covered by neighboring epithelial cells. Some crystals were overgrown by several epithelial cells and underwent a process of so-called exotubulosis, resulting in free or cell-surrounded crystals in the interstitium, and possibly in crystals in Giant cells. To investigate the fate of the retained crystals, some animals were additionally exposed to a low-oxalate challenge from drinking water containing 0.1 volume per cent of ethylene glycol for 12 or 30 days, respectively. It was assumed that this would interfere with the retained intratubular or interstitial crystals, and allow the crystals to grow into mini-stones. This was not observed. After the oxalate challenge, no crystals were found to be retained in the tubules (free or covered by cells). Interstitial crystals were observed, but it remains to be demonstrated whether such crystals actually grow into mini-stones or that they are removed by the sterile inflammation process observed.
User-Centered Multidimensional Projection Techniques (2012)

Interactive multidimensional projections can be quite effective as interactive visualization tools. It's also advantageous to use local projection techniques over global ones when facing fully interactive applications.
A Numerical Analysis of Magneto-Acousto Electrical Tomography with a Simplified Breast Model (2017)

In this study, Magneto-Acousto Electrical Tomography with magnetic measurements technique is investigated using two dimensional (2D) simplified numerical breast model. This technique comprises of the electrical current induction and ultrasound in the static magnetic field. 2D numerical simplified breast geometry is modeled with an ultrasonic transducer (linear phased array (LPA)) placed on the top side of the simplified breast model. A rectangular loop coil is encircled the breast. The sensitivity matrix is obtained for this transducer-coil configuration. LPA transducer is steered with eleven angles (−25 ° to 25 ° at intervals of 5 °). The characteristics of this modality is shown by the singular value decomposition (SVD) method. The reconstruction of the images is performed by truncated SVD approach. This study shows that perturbations (5 mm × 5 mm) up to a depth of 3 cm can be detected.