gebhart/patrepeval huggingface dataset:
Oligonucleotide conjugated antibody strategies for cyclic immunostaining (2021)

A number of highly multiplexed immunostaining and imaging methods have advanced spatial proteomics of cancer for improved treatment strategies. While a variety of methods have been developed, the most widely used methods are limited by harmful signal removal techniques, difficulties with reagent production and antigen sensitivity. Multiplexed immunostaining employing oligonucleotide (oligos)-barcoded antibodies is an alternative approach that is growing in popularity. However, challenges remain in consistent conjugation of oligos to antibodies with maintained antigenicity as well as non-destructive, robust and cost-effective signal removal methods. Herein, a variety of oligo conjugation and signal removal methods were evaluated in the development of a robust oligo conjugated antibody cyclic immunofluorescence (Ab-oligo cyCIF) methodology. Both non- and site-specific conjugation strategies were assessed to label antibodies, where site-specific conjugation resulted in higher retained binding affinity and antigen-specific staining. A variety of fluorescence signal removal methods were also evaluated, where incorporation of a photocleavable link (PCL) resulted in full fluorescence signal removal with minimal tissue disruption. In summary, this work resulted in an optimized Ab-oligo cyCIF platform capable of generating high dimensional images to characterize the spatial proteomics of the hallmarks of cancer.
Contributions of Nuclear Magnetic Resonance to Renal Biochemistry (1986)

No AccessJournal of UrologyRadiology, Nuclear Medicine and Sonography1 Jun 1986Contributions of Nuclear Magnetic Resonance to Renal Biochemistry B. Ross, D. Freeman, and L. Chan B. RossB. Ross More articles by this author , D. FreemanD. Freeman More articles by this author , and L. ChanL. Chan More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)46124-6AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Contributions of Nuclear Magnetic Resonance to Renal Biochemistry." The Journal of Urology, 135(6), p. 1346 © 1986 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 135Issue 6June 1986Page: 1346 Advertisement Copyright & Permissions© 1986 by The American Urological Association Education and Research, Inc.MetricsAuthor Information B. Ross More articles by this author D. Freeman More articles by this author L. Chan More articles by this author Expand All Advertisement Loading ...
Understanding Pyrolysis: Operandoand in Situcharacterization of Morphology and Composition Changes during Synthesis of M-N-C Electrocatalysts (2020)

Transition metal-nitrogen-carbon (M-N-C) materials have been continuously reported to be one of most promising platinum group metal-free (PGM-free) catalysts for oxygen reduction reaction (ORR)/cathode in low-temperature polymer electrolyte fuel cells (PEFC) and other emerging areas (such as carbon dioxide reduction reaction and nitrogen reduction reaction). They are usually obtained through pyrolysis of low molecular weight (organic) or polymetric precursors. The pyrolysis consists of heat treatment in inert (or reductive) atmosphere. Through the decades of practice, this pyrolysis process has been optimized intuitively and empirically with little-to-no knowledge of the explicit sequence of transformations. Morphological, structural, interfacial and chemical changes during pyrolysis enable the emergence of the new material with atomically dispersed transition metal ions. These ions are incorporated in the graphene-like carbonaceous matrix, doped with nitrogen and forming various Fe-N x catalytically active sites. Often, a secondary pyrolysis process is being carries out, after the completion of the initial one, resulting in better defined, and in many cases, more active and stable catalysts (a.k.a. “re-pyrolysis”). Our team have investigated both stages of the pyrolytic synthesis via in situ XPS, TEM, EDS, XRD and nano- and micro-XCT methods in two separate studies dedicated to (i) pyrolysis of charge-transfer organic salt (nicarbazin) when mixed with silica template (a.k.a. “sacrificial support method” of M-N-C catalyst synthesis) and (ii) re-pyrolysis (secondary, “purification” pyrolysis) of the M-N-C material as a path to obtain atomically dispersed PGM-free catalyst. During the first pyrolysis we have observed for the first time the explicit melting of the precursor (at exact thermal signature), wetting of the hard template and followed major transformation in morphology: pore structure evolution, initial graphitization, metal and metal carbide phase formation, secondary graphitization templated on the transition metal nanoparticles and secondary micro-pores formation. All these observations have been interpreted through cross-referencing tomography, crystallography, microscopy and spectroscopy in situ data streams. We established that the re-pyrolysis of M-N-C materials could result in the amorphization of carbon, the rearrangement of multitudinous N-containing moieties, and increased content and a more uniform distribution of Fe-N x sites, yet without major morphology changes in carbonaceous framework. In summary, the re-pyrolysis has multiple advantages and is recommended for all M-N-C electrocatalysts, no matter what precursors and parameters are set for their synthesis.
Search for light resonances decaying into pairs of muons as a signal of new physics (2011)

A search for groups of collimated muons is performed using a data sample collected by the CMS experiment at the LHC, at a centre-of-mass energy of 7 TeV, and corresponding to an integrated luminosity of 35 pb -1 . The analysis searches for production of new low-mass states decaying into pairs of muons and is designed to achieve high sensitivity to a broad range of models predicting leptonic jet signatures. With no excess observed over the background expectation, upper limits on the production cross section times branching fraction times acceptance are set, ranging from 0.1 to 0.5 pb at the 95% CL depending on event topology. In addition, the results are interpreted in several benchmark models in the context of supersymmetry with a new light dark sector exploring previously inaccessible parameter space.
Parameters Governing Separation Control with Sweeping Jet Actuators (2011)

Parameters governing separation control by sweeping jet actuators are investigated experimentally on a generic “Multiple Flap Airfoil” (MFA). Neither the flow rate nor the momentum input is found to be a sole parameter governing the lift for varying distance between adjacent actuators. However, the product of the mass flow coefficient and a square root of the momentum coefficient collapses the lift onto a single curve regardless of the actuator spacing. Surface flow visualization on the flap suggests the formation of counterrotating pairs of streamwise vortices caused by the interaction of neighboring jets. The actuation intensity required to attach the flow increases with increasing distance from the flap shoulder and increasing flap deflection. No obvious dependence of the ideal actuation location on flap deflection, angle of attack, or actuation intensity is found within the tested range. Comparisons between experimental and numerical results reveal a strong dependence on the thickness of the last flap segment at its hinge. In absence of this geometrical effect potential flow solution appears to be a suitable predictor for the obtainable lift. The flap size affects the achievable lift, the accompanying drag, the required flap deflection, and actuation intensity. By controlling separation the range of achievable lift coefficients is doubled without significant penalty in drag even when considering a safety margin for the maximum applicable incidence.
New phosphoglucose isomerase mutants of Escherichia coli (1975)

The mutants used to show that phosphoglucose isomerase, and glucose itself, are not essential components of Escherichia coli had not been characterized genetically, other than by mapping. We now describe two new pgi mutants, one amber and the other a Mu-phage insertion, presumably both complete inactivation mutations. The new mutations do not give a phenotype markedly different from those described earlier. However, they might be preferred for certain physiological studies, and we have prepared for this a new double mutant, strain DF214, with a Mu insertion in pgi and a deletion in zwf (flucose 6-phosphate dehydrogenase).
Biosynthesis of vitamin B12: use of specific 13C-labelling for structural studies on factor IV (1994)

[1,10,20-13C3]Uro'gen III is unambiguously synthesised for enzymic conversion into precorrin-4 isolated after aerial oxidation as two epimers of Factor IV, the 13C NMR spectra of which rigorously confirm the presence of a C-1 acetyl group in precorrin-4; attachment of the fourth methyl group at C-17 of precorrin-4 is also confirmed by related 13C-labelling experiments.
Method of fitting hearing prosthesis to a patient having impaired hearing (1986)

First Page
ChemInform Abstract: Nitroxide Radicals: Properties, Synthesis and Applications (2011)

Abstract Review: 482 refs.
Leveraging the Immune System during Chemotherapy: Moving Calreticulin to the Cell Surface Converts Apoptotic Death from “Silent” to Immunogenic (2007)

Abstract In contrast to prior belief, tumor cell apoptosis is not necessarily silent but can be immunogenic. By tracing how anthracyclines and γ-irradiation trigger immunogenic cell deaths, we found that they were causally connected to the exposure of calreticulin on the tumor cell surface, before apoptosis in the tumor cell itself occurred. Furthermore, we showed that calreticulin exposure was necessary and sufficient to increase proimmunogenic killing by other chemotherapies. Our findings suggest that calreticulin could serve as a biomarker to predict therapy-associated immune responses, and that tactics to expose calreticulin might improve the clinical efficacy of many cancer therapies. [Cancer Res 2007;67(17):7941–4]
A test site thermal control system for at-speed manufacturing testing (2002)

As microprocessor speeds and power increase, so too does the need for better thermal control. Today's high performance processors generate enormous amounts of heat at the transistor level due to self heating effects within the die. Higher die temperatures reduce performance and increase failure rates. As a result, better thermal control of the microprocessors during testing has become more important. This paper reports on an analysis of this problem, and the superior thermal control obtained using direct, conductive cooling as opposed to forced convective cooling.
Next Generation Photonics Based on 2D Materials (2018)

Two dimensional materials such as monolayer transition metal dichalcogenides (TMD) are expected to have large changes in their optical sheet conductivity by controlling their carrier densities. We demonstrate a platform for waveguide-integrated phase modulators in the near-infrared regime based on Tungsten disulphide (WS <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) gating.
A high-performance ROM compiler for 0.50 μm and 0.36 μm CMOS technologies (2002)

A ROM compiler has been developed for use in IBM's 0.50 /spl mu/m and 0.36 /spl mu/m CMOS ASIC technologies. Late-personalized mask ROMs are generated for sizes from 512 bits to 256 K bits. The 0.50 /spl mu/m technology has a memory cell area of 6.40 /spl mu/m/sup 2/ with a typical access time of 6.0 ns, while the 0.36 /spl mu/m technology reduces memory cell area to 4.64 /spl mu/m/sup 2/ and has a 4.5 ns typical access time. The ROM includes DC and AC self-test.
The Mechanism of Successive Menschtkin Reaction and Solvent Effect of DMSO (1971)

N, N, N', N'-テトラメチルエチレンジアミン (TED) と二塩化-p-キシリレン (XDC) の逐次メンシュトキン反応における重合速度を考察した。反応の進行につれ速度は小さくなるが, これは官能基濃度の減少, 生長鎖荷電部が末端アミノ基の窒素弧立電子対を部分的に引き寄せその求核攻撃力を弱めることにより二次反応速度定数が漸減するためと考えられる。溶媒効果を次表に示した。DMSO は ε の関連だけでは説明できない促進作用がある。これは分極している DMSOの δ+性イオウと XDC の塩素とが静電相互作用を及ぼし, C-Cl 結合を弛緩する過程が反応に関与するため TED の求核攻撃を容易にするからと考えられる。
Modelagem do Processo de Fragmentação de Catalisadores Suportados Durante a Pré-polimerização de Olefinas (2002)

Uma metodologia é proposta para descrever a morfologia das partículas de polímero que são obtidas durante os momentos iniciais da polimerização de olefinas via catálise heterogênea. O método é baseado na análise matemática da capacidade da partícula em liberar a energia mecânica acumulada no seu interior devido à rápida produção de polímero. O balanço entre as quantidades de energia acumulada e liberada é calculado com o auxílio de um modelo dinâmico da reação de pré-polimerização. A combinação da metodologia proposta com o modelo dinâmico permitiu a análise dos mecanismos de fragmentação, indicando a morfologia da partícula de polímero produzida em função do tamanho da partícula e da temperatura do reator.
Adaptive optics for enhanced signal in CARS microscopy (2007)

We report the use of adaptive optics with coherent anti-Stokes Raman scattering (CARS) microscopy for label-free deep tissue imaging based on molecular vibrational spectroscopy. The setup employs a deformable membrane mirror and a random search optimization algorithm to improve signal intensity and image quality at large sample depths. We demonstrate the ability to correct for both system and sample-induced aberrations in test samples as well as in muscle tissue in order to enhance the CARS signal. The combined system and sample-induced aberration correction increased the signal by an average factor of approximately 3x for the test samples at a depth of 700 microm and approximately 6x for muscle tissue at a depth of 260 microm. The enhanced signal and higher penetration depth offered by adaptive optics will augment CARS microscopy as an in vivo and in situ biomedical imaging modality.
ICCAD Special Session Paper: Quantum-Classical Hybrid Machine Learning for Image Classification (2021)

Image classification is a major application domain for conventional deep learning (DL). Quantum machine learning (QML) has the potential to revolutionize image classification. In any typical DL-based image classification, we use convolutional neural network (CNN) to extract features from the image and multi-layer perceptron network (MLP) to create the actual decision boundaries. On one hand, QML models can be useful in both of these tasks. Convolution with parameterized quantum circuits (Quanvolution) can extract rich features from the images. On the other hand, quantum neural network (QNN) models can create complex decision boundaries. Therefore, Quanvolution and QNN can be used to create an end-to-end QML model for image classification. Alternatively, we can extract image features separately using classical dimension reduction techniques such as, Principal Components Analysis (PCA) or Convolutional Autoencoder (CAE) and use the extracted features to train a QNN. We review two proposals on quantum-classical hybrid ML models for image classification namely, Quanvolutional Neural Network and dimension reduction using a classical algorithm followed by QNN. Particularly, we make a case for trainable filters in Quanvolution and CAE-based feature extraction for image datasets (instead of dimension reduction using linear transformations such as, PCA). We discuss various design choices, potential opportunities, and drawbacks of these models. We also release a Python-based framework to create and explore these hybrid models with a variety of design choices.
Inflammation and NF-κB Signaling in Prostate Cancer: Mechanisms and Clinical Implications (2018)

Prostate cancer is a highly prevalent form of cancer that is usually slow-developing and benign. Due to its high prevalence, it is, however, still the second most common cause of death by cancer in men in the West. The higher prevalence of prostate cancer in the West might be due to elevated inflammation from metabolic syndrome or associated comorbidities. NF-κB activation and many other signals associated with inflammation are known to contribute to prostate cancer malignancy. Inflammatory signals have also been associated with the development of castration resistance and resistance against other androgen depletion strategies, which is a major therapeutic challenge. Here, we review the role of inflammation and its link with androgen signaling in prostate cancer. We further describe the role of NF-κB in prostate cancer cell survival and proliferation, major NF-κB signaling pathways in prostate cancer, and the crosstalk between NF-κB and androgen receptor signaling. Several NF-κB-induced risk factors in prostate cancer and their potential for therapeutic targeting in the clinic are described. A better understanding of the inflammatory mechanisms that control the development of prostate cancer and resistance to androgen-deprivation therapy will eventually lead to novel treatment options for patients.
Electrostatic and hydrophobic contributions to protein : peptide surface interactions (2005)

This thesis describes different aspects of protein interactions. Initially the function of peptides and their conjugates with small molecule inhibitors on the surface of Human Carbonic Anhydrase isoenzyme II (HCAII) is evaluated. The affinities for HCAII of the flexible, synthetic helix-loop-helix motif conjugated with a series of spacered inhibitors were measured by fluorescence spectroscopy and found in the best cases to be in the low nM range. Dissociation constants show considerable dependence on linker length and vary from 3000 nM for the shortest spacer to 40 nM for the longest with a minimum of 5 nM for a spacer with an intermediate length. A rationale for binding differences based on cooperativity is presented and supported by affinities as determined by fluorescence spectroscopy. Heteronuclear Single Quantum Correlation Nuclear Magnetic Resonance (HSQC) spectroscopic experiments with 15N-labeled HCAII were used for the determination of the site of interaction. The influence of peptide charge and hydrophobicity was evaluated by surface plasmon resonance experiments. Hydrophobic sidechain branching and, more pronounced, peptide charge was demonstrated to modulate peptide – HCAII binding interactions in a cooperative manner, with affinities spanning almost two orders of magnitude. Detailed synthesis of small molecule inhibitors in a general lead discovery library as well as a targeted library for inhibition of α-thrombin is described. For the lead discovery library 160 members emanate from two N4-aryl-piperazine-2-carboxylic acid scaffolds derivatized in two dimensions employing a combinatorial approach on solid support. The targeted library was based on peptidomimetics of the D-Phe-Pro-Arg showing the scaffolds cyclopropane-1R,2R-dicarboxylic acid and (4-amino-3-oxo-morpholin-2-yl)- acetic acid as proline isosters. Employing 4-aminomethyl-benzamidine as arginine mimic and different hydrophobic amines and electrophiles as D-phenylalanine mimics resulted in 34 compounds showing IC50 values for α-thrombin ranging more than three orders of magnitude with the best inhibitor showing an IC50 of 130 nM. Interestingly, the best inhibitors showed reversed stereochemistry in comparison with a previously reported series employing a 3-oxo-morpholin-2-yl-acetic acid scaffold.
Linkage between the AMSAA models at higher levels of indenture in reliability analysis (2007)

Purpose The purpose of this article is to determine if there is a linkage between the army material systems analysis activity (AMSAA) reliability growth models at the system and subsystem levels and at the subsystem and functional levels of indenture. If such a linkage exists, how this information can be used when tracking reliability of fielded systems to provide early warning signals to detect unwanted reliability problems at lower levels, where improvements are typically made. Design/methodology/approach Actual performance data from large equipments were analyzed for several groupings of such equipment, where equipment age and generation of design determined the groupings. For each dataset, the system‐level trend was measured using the AMSAA model for three different cases. For each of the three cases, all subsystem trends were measured, in addition to the system‐level trend. This was done to see if any relationship exists, as hypothesized, between system and subsystem trends. Data were analyzed using three different combinations of time periods to facilitate a later investigation of the predictive capabilities of the AMSAA model. Findings Results indicate that, for large complex systems or equipment, there appears to be a linkage at the subsystem and functional levels. However, no such hazard rate trending relationship exists between the system and subsystem levels. Based on these results, it can be cautiously concluded that, in terms of reliability, in subsystems that exhibit an increasing trend in unwanted issues, there is a higher likelihood of a function that is driving such a trend. Practical implications A useful approach in reliability studies to see if the hazard rate trending relationships between levels of hardware indenture exists as one progresses toward the system‐level. For large complex systems or equipments, such as the one represented here, the initial results indicate that the answer is no, at least between the system and subsystem levels of indenture. However, there is strong evidence that such relationships are valid between subsystems and their functions. Originality/value This paper advances existing knowledge in the area of reliability analysis by exploring the use of army material systems analysis activity (AMSAA) reliability growth models to determine linkages between the system and subsystem levels and at the subsystem and functional levels of indenture. If such a linkage exists, it is possible to determine how this information can be used to provide early warning signals when tracking reliability of fielded systems.
ChemInform Abstract: Synthesis of Enantiomerically Pure γ‐Azidoalcohols by Lipase‐Catalyzed Transesterification. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Use of Aerospace Structural Sensor Technology for Soil Physical Characterization (1999)

Tractor hitch pins, instrumented by NASA Langley Research Center, are being used between tractors and cultivating equipment to log the spatial variability in the mechanical resistance or drag force required for cultivation. The INEEL Site-Specific Technologies for Agriculture (SST4Ag) research project, in collaboration with university, other federal agency and industry partners, is correlating soil physical spatial variability, measured as tillage tool drag force, with crop productivity.