gebhart/patrepeval huggingface dataset:
Comparison of transcriptional differences between IL-4Ra and IL-5 blockade in a mouse model of asthma (2021)

<b>Rationale:</b> Biologics directed against effectors of type 2 inflammation improve signs and symptoms of asthma by different mechanisms that have not been fully elucidated.&nbsp; <b>Aim:</b> Determine the complete extent of transcription differences and similarities&nbsp;downstream of IL-4Rα&nbsp;and IL-5 blockade in a disease relevant model of asthma. <b>Methods:</b> Mice were exposed to house dust mite for 4 weeks and received twice‐weekly subcutaneous injections of anti-IL-4Rα (dupilumab) or anti‐IL‐5. Gene expression changes in the lung were analyzed by bulk RNA-sequencing.&nbsp; <b>Results:</b> HDM alone significantly perturbed over 700 genes, 208 of which were&nbsp;affected by&nbsp;anti-IL-4Rα (inversely perturbed). There&nbsp;were&nbsp;8&nbsp;HDM responsive&nbsp;genes in common between the two antibody treatments. Interestingly, these genes were&nbsp;related to eosinophilia. Lastly, this study only found 1&nbsp;HDM responsive&nbsp;gene that overlapped with anti-IL-5 treatment. <b>Conclusion:</b> The results&nbsp;show that&nbsp;IL-5 blockade has highly specific effects on eosinophil function, whereas IL-4Rα blockade impacts&nbsp;genes associated with eosinophils, but also has a much broader effect, impacting&nbsp;genes involved in mucus production and secretion, airway remodeling, bronchoconstriction and hyperresponsiveness.
Carbon and Carbon/Silicon Composites Templated in Rugate Filters for the Adsorption and Detection of Organic Vapors (2011)

Undulated carbon nanofiber arrays displaying a reflectance peak due to the periodic structure are prepared by thermolysis of a poly(furfuryl alcohol) precursor in a porous silicon photonic crystal template. The carbon/silicon composites act as optical sensors for organic vapors and are up to ten times more sensitive than the template alone.
N-chlorotaurine Inactivates Acanthamoeba and Candida albicans in the Porcine Ex Vivo Corneal Infection Model (2019)

NCT inactivates A. castellanii and C. albicans in corneal tissue.
Highly reliable fitting for gas delivery systems (1998)

After confirming the basic characteristics of two types of metal gasket fittings, which are used in construction of ultrapure gas delivery systems for semiconductor manufacturing, it is noticed that the pipe usually twists at the time the fitting is tightened. This may be the possible cause of an external leak, therefore a twist leak test was undertaken to confirm the reliability of the seal during assembly. As a result, it was found that one type of fitting leaked and another type of fitting did not leak. This later type did not leak (leak rate is less than 2.98×10−16 Pa m3/s) even after 70° of twisting.
758: Detection and Follow-Up of Kidney Cancer in Urine DNA Using a Tumor Suppressor Gene Hypermethylation Panel (2004)

You have accessJournal of UrologyDiscussed Poster, Monday, May 10, 2004, 8:00 am - 12:00 pm1 Apr 2004758: Detection and Follow-Up of Kidney Cancer in Urine DNA Using a Tumor Suppressor Gene Hypermethylation Panel Robert G. Uzzo, Essel Dulaimi, Tahseen Al-Saleem, Richard E. Greenberg, and Paul Cairns Robert G. UzzoRobert G. Uzzo More articles by this author , Essel DulaimiEssel Dulaimi More articles by this author , Tahseen Al-SaleemTahseen Al-Saleem More articles by this author , Richard E. GreenbergRichard E. Greenberg More articles by this author , and Paul CairnsPaul Cairns More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)38007-8AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "758: Detection and Follow-Up of Kidney Cancer in Urine DNA Using a Tumor Suppressor Gene Hypermethylation Panel." The Journal of Urology, 171(4S), p. 201 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 201 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Robert G. Uzzo More articles by this author Essel Dulaimi More articles by this author Tahseen Al-Saleem More articles by this author Richard E. Greenberg More articles by this author Paul Cairns More articles by this author Expand All Advertisement PDF DownloadLoading ...
The Drunkard's Odometry: Estimating Camera Motion in Deforming Scenes (2023)

Estimating camera motion in deformable scenes poses a complex and open research challenge. Most existing non-rigid structure from motion techniques assume to observe also static scene parts besides deforming scene parts in order to establish an anchoring reference. However, this assumption does not hold true in certain relevant application cases such as endoscopies. Deformable odometry and SLAM pipelines, which tackle the most challenging scenario of exploratory trajectories, suffer from a lack of robustness and proper quantitative evaluation methodologies. To tackle this issue with a common benchmark, we introduce the Drunkard's Dataset, a challenging collection of synthetic data targeting visual navigation and reconstruction in deformable environments. This dataset is the first large set of exploratory camera trajectories with ground truth inside 3D scenes where every surface exhibits non-rigid deformations over time. Simulations in realistic 3D buildings lets us obtain a vast amount of data and ground truth labels, including camera poses, RGB images and depth, optical flow and normal maps at high resolution and quality. We further present a novel deformable odometry method, dubbed the Drunkard's Odometry, which decomposes optical flow estimates into rigid-body camera motion and non-rigid scene deformations. In order to validate our data, our work contains an evaluation of several baselines as well as a novel tracking error metric which does not require ground truth data. Dataset and code: https://davidrecasens.github.io/TheDrunkard'sOdometry/
Laser-sintered thin films of doped SiGe nanoparticles (2012)

We present a study of the morphology and the thermoelectric properties of short-pulse laser-sintered (LS) nanoparticle (NP) thin films, consisting of SiGe alloy NPs or composites of Si and Ge NPs. Laser-sintering of spin-coated NP films in vacuum results in a macroporous percolating network with a typical thickness of 300 nm. The Seebeck coefficient for LS samples is the same as for bulk samples prepared by current-assisted sintering and is typical for degenerate doping. The electrical conductivity of LS films is influenced by two-dimensional percolation effects and rises with increasing temperature, approximately following a power-law.
The PredictAD project: development of novel biomarkers and analysis software for early diagnosis of the Alzheimer's disease (2013)

Alzheimer's disease (AD) is the most common cause of dementia affecting 36 million people worldwide. As the demographic transition in the developed countries progresses towards older population, the worsening ratio of workers per retirees and the growing number of patients with age-related illnesses such as AD will challenge the current healthcare systems and national economies. For these reasons AD has been identified as a health priority, and various methods for diagnosis and many candidates for therapies are under intense research. Even though there is currently no cure for AD, its effects can be managed. Today the significance of early and precise diagnosis of AD is emphasized in order to minimize its irreversible effects on the nervous system. When new drugs and therapies enter the market it is also vital to effectively identify the right candidates to benefit from these. The main objective of the PredictAD project was to find and integrate efficient biomarkers from heterogeneous patient data to make early diagnosis and to monitor the progress of AD in a more efficient, reliable and objective manner. The project focused on discovering biomarkers from biomolecular data, electrophysiological measurements of the brain and structural, functional and molecular brain images. We also designed and built a statistical model and a framework for exploiting these biomarkers with other available patient history and background data. We were able to discover several potential novel biomarker candidates and implement the framework in software. The results are currently used in several research projects, licensed to commercial use and being tested for clinical use in several trials.
1H NMR Investigation of Solvent Effects in Aromatic Stacking Interactions (2001)

One of the marquis challenges in modern Organic Chemistry concerns the design and synthesis of abiotic compounds that emulate the exquisite complex structures and/or functions of biological macromolecules. Oligomers possessing the propensity to adopt well-defined compact conformations, or foldamers, have been attained utilizing hydrogen bonding, torsional restriction, and solvophobic interactions.(1) In this laboratory, aromatic electron donor--acceptor interactions have been exploited in the design of aedamers--foldamers that adopt a novel, pleated secondary structure in aqueous solution. Herein is reported detailed (1)H NMR binding studies of aedamer monomers that were carried out in solvents and solvent mixtures covering a broad polarity range. Curve-fitting analysis of the binding data using a model that incorporated the formation of higher order and self-associated complexes yielded a linear free energy relationship between the free energy of complexation and the empirical solvent polarity parameter, E(T)(30). From these studies, the association of electron-rich and electron-deficient aedamer monomers was seen to be driven primarily by hydrophobic interactions in polar solvents. However, the magnitude of these interactions is modulated to a significant extent by the geometry of the donor--acceptor complex, which, in turn, is dictated by the electrostatic complementarity between the electron-deficient and electron-rich aromatic faces of the monomers.
Effects of rapid thermal annealing (RTA) process on pysical and electrical properties of Bi4La4-xTi3O12 (BLT) thin film (2001)

Abstract Bi3.35La0.75Ti3O12 (BLT) thin (90 nm) film was prepared on a Pt/TiOx/SiO2/Si substrate by metalorganic decomposition (MOD) method, and its microstructure was controlled by rapid thermal annealing (RTA) conditions of temperature and sequence under a fixed furnace annealing (FA) at 650°C. For the conventional RTA before the deposition of Pt top electrode, a random oriented porous film composed of small grains was formed at 500°C, while a strongly c-axis oriented dense film with large grain size was produced at 700°C. The switching polarization (P*−Pˆ) was dependent on both crystalline orientation and grain size, and its highest value of 12 μC/cm2 was obtained at 600°C from the optimized BLT film with weak c-axis orientation and medium grain size. On the other hand, for the modified RTA after top Pt deposition, a random oriented film was formed to have high P*−Pˆ of 12 μC/cm2 irrespective of RTA temperatures of 600 and 700°C. Key Words: Thin filmLa-substituted bismuth titanate (BLT)MODRTAcrystalline orientationgrain sizeswitching polarization
Error propagation from prime variables into specific rates and metabolic fluxes for mammalian cells in perfusion culture (2009)

Error propagation from prime variables into specific rates and metabolic fluxes was quantified for high-concentration CHO cell perfusion cultivation. Prime variable errors were first determined from repeated measurements and ranged from 4.8 to 12.2%. Errors in nutrient uptake and metabolite/product formation rates for 5-15% error in prime variables ranged from 8-22%. The specific growth rate, however, was characterized by higher uncertainty as 15% errors in the bioreactor and harvest cell concentration resulted in 37.8% error. Metabolic fluxes were estimated for 12 experimental conditions, each of 10 day duration, during 120-day perfusion cultivation and were used to determine error propagation from specific rates into metabolic fluxes. Errors of the greater metabolic fluxes (those related to glycolysis, lactate production, TCA cycle and oxidative phosphorylation) were similar in magnitude to those of the related greater specific rates (glucose, lactate, oxygen and CO(2) rates) and were insensitive to errors of the lesser specific rates (amino acid catabolism and biosynthesis rates). Errors of the lesser metabolic fluxes (those related to amino acid metabolism), however, were extremely sensitive to errors of the greater specific rates to the extent that they were no longer representative of cellular metabolism and were much less affected by errors in the lesser specific rates. We show that the relationship between specific rate and metabolic flux error could be accurately described by normalized sensitivity coefficients, which were readily calculated once metabolic fluxes were estimated. Their ease of calculation, along with their ability to accurately describe the specific rate-metabolic flux error relationship, makes them a necessary component of metabolic flux analysis.
of insulin receptors in rat adipocyt (down-regulation/receptor degradation/chloroquine) (2016)

We have investigated the theory that the insulin- induced loss of insulin binding from adipocytes is due to internal- ization of insulin receptors. Cell-surface receptors were assessed by the binding capacity of intact cells at 160C. Total (i.e., cell-sur- face plus intracellular) receptors were assessed by solubilizing the cells in 1% Triton X-100 and then measuring binding by the sol- ubilized extract. Intracellular receptors were measured by treat- ing the cells with trypsin before solubilizing them. The trypsin treatment removed >90% of the cell-surface binding, so that any significant binding by soluble extracts of these cells must represent intracellular receptors. Adipocytes were incubated with insulin (100 ng/ml) with or without chloroquine (0.2 mM) for 4 hr. Insulin alone resulted in a 62% loss of cell-surface receptors, but only a 46% loss of total receptors, and a 170% increase in intracellular receptors, suggesting that the lost cell-surface receptors were in- ternalized, where some were degraded. Insulin in the presence of chloroquine resulted in a 34% loss of cell-surface receptors, but no loss of total receptors, and a 300% increase in intracellular re- ceptors. Thus, in the presence of chloroquine receptors were in- ternalized but not degraded. The loss of cell-surface receptors and appearance of intracellular receptors were time and dose depen- dent and were linearly related. These results demonstrate that insulin causes translocation of insulin receptors from the cell sur- face to the cell interior, where they can be degraded (or inacti- vated) by a chloroquine-sensitive process.
Crosslinkable‐Chitosan‐Enabled Moisture‐Resistant Multilayer Gas Barrier Thin Film (2019)

Front Cover: In article number 1800853 by Michael Cunningham, Jaime Grunlan, and co-workers, the covalent network provided by crosslinkable chitosan reduces the moisture sensitivity of a chitosan-based oxygen barrier film, using fewer bilayers and without needing to introduce an additional crosslinker into the system.
Amplitude and Phase Modulation of Light Using Fano-Resonant Meta-Surfaces Integrated with Graphene (2015)

We experimentally demonstrate amplitude and phase modulation in graphene-integrated Fano-resonant plasmonic metasurfaces. Order of magnitude modulation depth is achieved in mid-IR. Strong coupling between trapped graphene and metallic plasmons is predicted in high-mobility graphene.
Implementation of the IMEC-Clean in advanced CMOS manufacturing (2003)

We present data measured using the wet bench in the prototyping line of IMEC. This wet bench has been running for 3 years an IMEC Clean for prediffusion cleans including the most critical one: the pre-gate oxidation clean. The clean was introduced at IMEC for the 0.35 /spl mu/m CMOS process and its use has been succesfully extended to the 180 nm and 130 nm CMOS modules presently developed at IMEC.
Antitumor Vaccination Using a Major Histocompatibility Complex (MHC) Class I-Restricted Pseudopeptide With Reduced Peptide Bond (2000)

Synthetic peptides have raised a considerable interest in the fields of vaccines and immunotherapy. The authors previously introduced modifications into the peptide backbone of the H-2Kd-restricted epitope CW3. One of these pseudopeptides, C7, bound to Kd with an affinity identical to the parent peptide and was recognized by T cells specific for the parent peptide. The authors now show that this analog has an increased resistance to trypsin and displays an extended half-life in serum. The authors further tested its immunogenicity both in vitro and in vivo and found that cytotoxic T lymphocytes (CTL) induced against the peptide analog recognize the parent peptide. Moreover, analysis of T-cell receptor rearrangements by Immunoscope software revealed that C7-induced CTL display the hallmarks of the response against the parental epitope CW3. Administration of the pseudopeptide into DBA/2 mice induces a protective immune response against a lethal challenge with tumor cells expressing the parent peptide. Therefore, modifications in the backbone of antigenic peptides can decrease protease susceptibility while preserving immunogenicity. Such peptide analogues may therefore prove useful for the development of new therapeutic tools aimed at eradicating pathogens or tumors.
Reliable 4 million micro bumps at 7.6-um pitch interconnection technology for 3D stacked 16 million pixel image sensor (2016)

Our 3D stacked CMOS image sensor (CIS) has an ideal global shutter function with 16 million pixels and 4 million micro-bump interconnections placed at a 7.6-εm pitch between two silicon substrates, achieving interconnections with very low resistance. We confirmed the reliability of our 3D stacked interconnection technology by conducting reliability tests, which included heat cycle tests and high temperature and high humidity tests. The interconnections in our image sensor are comprised of 4 million micro bumps per chip. No increase in the number of failed interconnections or in micro-bump interconnection resistance was observed. For the heat cycle tests, our CIS is designed to have two test modes to detect failed interconnections by scanning all 4 million micro-bump interconnections in a short period. In the high temperature and high humidity tests, we tested the reliability of the interconnections by using test element group (TEG) chips to monitor the resistance precisely. We evaluated the effects of wafer bonding and the micro bumps on a MOS transistor with the TEGs, comparing two types of structures, one with micro bumps and one without, located under an nMOS transistor, and no difference in Vth among them was observed. These results prove that our 3D technology is reliable enough to be applied to our products.
Formation of reversible disulfide bonds with the protein matrix of the endoplasmic reticulum correlates with the retention of unassembled Ig light chains. (1996)

Exposed thiols act as intracellular retention elements for unassembled secretory molecules. Yet, some free Ig lambda light chains are secreted despite the presence of an unpaired cysteine (Cys214). This is due largely to the presence of a flanking acidic residue: substitution of Asp213 for Gly or Lys increases pre-Golgi retention and degradation of free lambda. Secretion is restored by exogenous reducing agents or by assembly with heavy chains. In the endoplasmic reticulum (ER), lambda chains form covalent complexes with many proteins through Cys214. These complexes are absent from the Golgi. They are more abundant in transfectants expressing the lambdaGly2I3 and lambdaLys213 mutants that are poorly secreted. Radioactive N-ethylmaleimide labels some monomeric lambda chains isolated from the ER, but not from the Golgi or from the medium, indicating that the Cys214 thiol is masked during ER-Golgi transport. Mass spectrometry reveals the presence of a free cysteine residue disulfide-linked to Cys214. We suggest that thiol-mediated retention involves the formation of reversible disulfide bonds with the protein matrix of the ER. The presence of an acidic residue next to the critical cysteine may allow the masking of the thiol and transport to the Golgi.
Essentiality, Expression, and Characterization of the Class II 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase of Staphylococcus aureus (2000)

Sequence comparisons have implied the presence of genes encoding enzymes of the mevalonate pathway for isopentenyl diphosphate biosynthesis in the gram-positive pathogen Staphylococcus aureus. In this study we showed through genetic disruption experiments that mvaA, which encodes a putative class II 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, is essential for in vitro growth of S. aureus. Supplementation of media with mevalonate permitted isolation of an auxotrophic mvaA null mutant that was attenuated for virulence in a murine hematogenous pyelonephritis infection model. The mvaA gene was cloned from S. aureus DNA and expressed with an N-terminal His tag in Escherichia coli. The encoded protein was affinity purified to apparent homogeneity and was shown to be a class II HMG-CoA reductase, the first class II eubacterial biosynthetic enzyme isolated. Unlike most other HMG-CoA reductases, the S. aureus enzyme exhibits dual coenzyme specificity for NADP(H) and NAD(H), but NADP(H) was the preferred coenzyme. Kinetic parameters were determined for all substrates for all four catalyzed reactions using either NADP(H) or NAD(H). In all instances optimal activity using NAD(H) occurred at a pH one to two units more acidic than that using NADP(H). pH profiles suggested that His378 and Lys263, the apparent cognates of the active-site histidine and lysine of Pseudomonas mevalonii HMG-CoA reductase, function in catalysis and that the general catalytic mechanism is valid for the S. aureus enzyme. Fluvastatin inhibited competitively with HMG-CoA, with a K(i) of 320 microM, over 10(4) higher than that for a class I HMG-CoA reductase. Bacterial class II HMG-CoA reductases thus are potential targets for antibacterial agents directed against multidrug-resistant gram-positive cocci.
Local segmental relaxation in bidisperse polystyrenes (2004)

Abstract Dynamic mechanical results are reported for segmental relaxation of monodisperse polystyrenes (PSs) with molecular weights of 0.7, 3, 18, and 104 kg/mol and bidisperse PSs created from blending pairs of these materials. The data for the monodisperse polymers confirm previous findings; namely, there is an increase in the glass‐transition temperature normalized temperature dependence of the segmental relaxation times (fragility) with increasing molecular weight, along with a breakdown of the correlation between the fragility and the breadth of the relaxation function. For both the monodisperse and bidisperse PSs, the glass‐transition temperature is a single function of the average number of chain ends, independent of the nature of the molecular weight distribution. It is also found that these materials exhibit fragilities that uniquely depend on the number‐average molecular weight, that is, on the concentration of chain ends. In blends with linear PS, cyclic PS with a low molecular weight behaves as a high polymer, similar to its neat behavior, reflecting the overriding importance of chain ends. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2604–2611, 2004