gebhart/patrepeval huggingface dataset:
Self-Antigen Recognition by the B Cell Receptors of Follicular Lymphoma (2010)

Abstract Abstract 4124 There is accumulating evidence that FL is a non-autonomous disease. Firstly, the t(14:18) translocation, which places the bcl-2 proto-oncogene under control of the IgH promotor, is a cytogenetic hallmark of FL, yet it can be detected in B cells from healthy individuals, indicating that this translocation is not sufficient for disease. Phenotypically, follicular lymphoma tumor cells resemble antigen experienced germinal center B cells in that they have highly mutated B cell receptors (BCRs) and are continually undergoing somatic hypermutation (SHM). Despite the high risk of SHM leading to the introduction of nonsense mutations, follicular lymphoma cell continue to express functional BCRs on their surface. These features suggest a selective pressure for the maintenance of BCR expression and indicate the possibility that follicular lymphoma cells may be receiving survival signals through the BCR via antigen recognition. We hypothesize that follicular lymphoma BCRs can recognize self-antigens. To determine the frequency of tumors with self-reactive BCRs, recombinant tumor immunoglobulins were utilized in an indirect immunofluorescence assay with the HEp-2 human cell line. With this assay self-reactivity was detected in 43/99 (43%) of tested tumor immunoglobulins. Within the self-reactive tumor immunoglobulins there was a great diversity of staining patterns, indicating the absence of a unifying antigen that is recognized by all follicular lymphoma BCRs. Autoantigen protein microarrays were utilized to determine the frequency of tumor immunoglobulins reactive for known autoantibody targets associated with autoimmune diseases. Irrespective of HEp-2 reactivity status, none of the tumor immunoglobulins tested (0/50) were reactive against known auto-antigens. These observations indicate that the self-antigens recognized by tumor immunoglobulins might be categorically different from those recognized by the autoantibodies present in patients with autoimmune disease. In an effort to identify specific self-antigens being recognized we utilized the recombinant follicular lymphoma immunoglobulins to immunoprecipitate targets from HEp-2 cell lysates. For one patient's tumor immunoglobulin we identified myoferlin as a recognized self-antigen. The presence of ongoing SHM in follicular lymphoma tumors leads to the existence of multiple tumor clones. To assess how antigen recognition changed as this patient's tumor evolved through SHM we performed a rescue fusion, which immortalizes the tumor cells, halts SHM, and allows for the secretion of the tumor immunoglobulins. Recovered clones differed by a number of silent and replacement mutations, yet all remained HEp-2 reactive. Additionally, all clones maintained their ability to bind myoferlin, though with variable avidity. The observation that ongoing SHM did not break the self-reactivity of the patient's tumor supports the possibility that there is a selective pressure to preserve antigen recognition. Disclosures: No relevant conflicts of interest to declare.
New Method Based on RSSI for Passive UHF RFID Localization System (2012)

International audience
Containerless thermophysical property measurements for liquid metals (1995)

Methods for measuring the thermophysical properties of liquid metals including sample size and density, translational and vibrational modes, surface tension, emissivity and thermodynamic temperature have been developed in the authors laboratory. Sample shape, size and density are measured with a video-imaging and computer processing technique. The translational and vibrational frequencies are monitored through the use of a continuous duo-lateral position sensor, where appropriate analysis of the data provides surface tension information. A two-channel polarization modulation ellipsometer has been developed to measure the optical constants and emissivity of a levitated metal drop. Preliminary results from the use of these techniques have been promising.
Radiomics in Brain Tumor: Image Assessment, Quantitative Feature Descriptors, and Machine-Learning Approaches (2017)

Radiomics describes a broad set of computational methods that extract quantitative features from radiographic images. The resulting features can be used to inform imaging diagnosis, prognosis, and therapy response in oncology. However, major challenges remain for methodologic developments to optimize feature extraction and provide rapid information flow in clinical settings. Equally important, to be clinically useful, predictive radiomic properties must be clearly linked to meaningful biologic characteristics and qualitative imaging properties familiar to radiologists. Here we use a cross-disciplinary approach to highlight studies in radiomics. We review brain tumor radiologic studies (eg, imaging interpretation) through computational models (eg, computer vision and machine learning) that provide novel clinical insights. We outline current quantitative image feature extraction and prediction strategies with different levels of available clinical classes for supporting clinical decision-making. We further discuss machine-learning challenges and data opportunities to advance radiomic studies.
Variable albedo surface reconstruction from stereo and shape from shading (2002)

We present a multiview method for the computation of object shape and reflectance characteristics based on the integration of shape from shading (SFS) and stereo, for nonconstant albedo and non-uniformly Lambertian surfaces. First we perform stereo fitting on the input stereo pairs or image sequences. When the images are uncalibrated, we recover the camera parameters using bundle adjustment. Eased on the stereo result, we can automatically segment the albedo map (which is taken to be piece-wise constant) using a minimum description length (MDL) based metric, to identify areas suitable for SFS (typically smooth textureless areas) and to derive illumination information. The shape and the illumination parameter estimates are refined using a deformable model SFS algorithm, which iterates between computing shape and illumination parameters. Our method takes into account the viewing angle dependent for shortening and specularity effects, and compensates as much as possible by utilizing information from more than one images. We demonstrate that we can extend the applicability of SFS algorithms to real world situations when some of its traditional assumptions are violated. We demonstrate our method by applying it to face shape reconstruction. Experimental results indicate a significant improvement over SFS-only or stereo-only based reconstruction. Model accuracy and detail are improved, especially in areas of low texture detail. Albedo information is retrieved and can be used to accurately re-render the model under different illumination conditions.
Nanostructural evidence of mechanical aging and performance loss in ballistic fibers (2017)

ABSTRACT It is understood that the ballistic resistance of aromatic polyamide fibers is related to the fiber's ultimate tensile strength, strain‐to‐failure, and Young's modulus. Ideal high‐performance ballistic materials maximize these properties while minimizing material density. Equally important is long‐term mechanical and chemical stability: the fibers should not exhibit performance loss over their lifetime. However, less is known quantitatively about their modes of degradation, and experimental methods to quantify the aging and degradation in these fibers are critical. Multiple variations of next generation high‐performance fibers have been investigated under chemical and mechanical accelerated aging conditions. Performance losses have been empirically correlated to chemical degradation of the polymer chain and nanostructural changes in the fiber morphology through X‐ray photoelectron spectroscopy (XPS). Here, we introduce positron annihilation lifetime spectroscopy measurements as a sensitive method to quantify the early onset of damage in the flexed fibers as quantified through changes in the nanoscale void structure in the material. Published 2017. † J. Polym. Sci., Part B: Polym. Phys. 2017 , 55 , 1711–1717
ChemInform Abstract: Cycloaddition Reaction of 3,4‐Dihydro‐6,7‐dimethoxyisoquinoline to Pyrylium Salts. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
IL-1R3 blockade broadly attenuates the functions of six members of the IL-1 family, revealing their contribution to models of disease (2019)

Interleukin (IL)-1R3 is the co-receptor in three signaling pathways that involve six cytokines of the IL-1 family (IL-1α, IL-1β, IL-33, IL-36α, IL-36β and IL-36γ). In many diseases, multiple cytokines contribute to disease pathogenesis. For example, in asthma, both IL-33 and IL-1 are of major importance, as are IL-36 and IL-1 in psoriasis. We developed a blocking monoclonal antibody (mAb) to human IL-1R3 (MAB-hR3) and demonstrate here that this antibody specifically inhibits signaling via IL-1, IL-33 and IL-36 in vitro. Also, in three distinct in vivo models of disease (crystal-induced peritonitis, allergic airway inflammation and psoriasis), we found that targeting IL-1R3 with a single mAb to mouse IL-1R3 (MAB-mR3) significantly attenuated heterogeneous cytokine-driven inflammation and disease severity. We conclude that in diseases driven by multiple cytokines, a single antagonistic agent such as a mAb to IL-1R3 is a therapeutic option with considerable translational benefit.
Unified Real-Time Tracking and Recognition with Rotation-Invariant Fast Features (2010)

We present a method that unifies tracking and video content recognition with applications to Mobile Augmented Reality (MAR). We introduce the Radial Gradient Transform (RGT) and an approximate RGT, yielding the Rotation-Invariant, Fast Feature (RIFF) descriptor. We demonstrate that RIFF is fast enough for real-time tracking, while robust enough for large scale retrieval tasks. At 26× the speed, our tracking-scheme obtains a more accurate global affine motion-model than the Kanade Lucas Tomasi (KLT) tracker. The same descriptors can achieve 94% retrieval accuracy from a database of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> images.
Characterization of Polystyrenes (5 and 40 kDa) Functionalized with a Perfluorinated Endgroup by TOF-SIMS: Effects of Molecular Weight (1996)

TOF-SIMS measurements of 5 and 40 kDa polystyrene functionalized with a perfluoroalkyl endgroup are presented. Fragment signals in the low mass range are observed for both 5 and 40 kDa samples, using monolayer sample preparation on a silver substrate. Additionally for the 5 kDa sample, intact oligomer signals in the high mass range and chain cleavage signals in the intermediate mass range are generated. The successful functionalization of the polystyrene with the perfluoroalkyl endgroup can be confirmed by the masses at which the intact oligomer signals arise.
Polymer-polymer interfacial slip in multilayered films (2009)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Patrick C. Lee, Hee Eon Park, David C. Morse, Christopher W. Macosko; Polymer-polymer interfacial slip in multilayered films. Journal of Rheology 1 July 2009; 53 (4): 893–915. https://doi.org/10.1122/1.3114370 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe Society of RheologyJournal of Rheology Search Advanced Search |Citation Search
A rapid and sensitive method to detect siRNA-mediated mRNA cleavage in vivo using 5′ RACE and a molecular beacon probe (2009)

Specific detection of mRNA cleavage by 5'RACE is the only method to confirm the knockdown of mRNA by RNA interference, but is rarely reported for in vivo studies. We have combined 5'-RNA-linker-mediated RACE (5'-RLM-RACE) with real-time PCR using a molecular beacon to develop a rapid and specific method termed MBRACE, which we have used to detect small-interfering RNA (siRNA)-induced cleavage of ApoB, RRM1 and YBX1 transcripts in vitro, and ApoB in vivo. When RNA from siRNA-transfected cells was used for 5'-RLM-RACE and a cleavage site-specific molecular beacon probe was included in subsequent real-time PCR analysis, the specific mRNA cleavage product was detected. Detection of siRNA-mediated cleavage was also observed when RNA from mouse liver following administration of ApoB-specific siRNA was analysed, even in cases where ApoB knockdown measured by real-time PCR was <10%. With its sensitivity and specificity, this variation on the 5'RACE method should prove a useful tool to detect mRNA cleavage and corroborate knockdown studies following siRNA use in vivo.
Liquid Crystal Aligning Capabilities and EO Characteristics of the TN-LCD with Ion-Beam Exposure on a New Diamond-like Carbon Thin Film Layer (2004)

Liquid crystal (LC) alignment capabilities with ion beam (IB) exposure on a diamond like carbon (DLC) layer were studied. A high pretilt angle of 3.5° with IB exposure on the DLC layer can be obtained. Superior LC alignment with the IB alignment method on the DLC layer was observed until an annealing temperature of 200°C. Also, excellent voltage-transmittance (V-T) curve of the ion beam aligned twisted nematic (TN) cell with oblique ion beam exposure on the DLC surface for 1 min was observed. The fast response time of the ion beam aligned TN cell with oblique ion beam exposure on the DLC surface for 1 min can be achieved. The residual DC property of the ion beam aligned TN cell with ion beam exposure on the DLC layer for 1 min is almost same as that of the rubbing aligned TN cell on a rubbed polyimide (PI) surface.
Green Synthesis of Silver Nanoparticles Using Aerial Part Extract of the Anthemis pseudocotula Boiss. Plant and Their Biological Activity (2022)

Green syntheses of metallic nanoparticles using plant extracts as effective sources of reductants and stabilizers have attracted decent popularity due to their non-toxicity, environmental friendliness and rapid nature. The current study demonstrates the ecofriendly, facile and inexpensive synthesis of silver nanoparticles (AP-AgNPs) using the extract of aerial parts of the <i>Anthemis pseudocotula</i> Boiss. plant (AP). Herein, the aerial parts extract of AP performed a twin role of a reducing as well as a stabilizing agent. The green synthesized AP-AgNPs were characterized by several techniques such as XRD, UV-Vis, FT-IR, TEM, SEM and EDX. Furthermore, the antimicrobial and antibiofilm activity of as-prepared AP-AgNPs were examined by a standard two-fold microbroth dilution method and tissue culture plate methods, respectively, against several Gram-negative and Gram-positive bacterial strains and fungal species such as <i>Escherichia coli</i> (<i>E. coli</i>), <i>Staphylococcus aureus</i> (<i>S. aureus</i>), multidrug-resistant <i>Pseudomonas aeruginosa</i> (MDR-PA) and <i>Acinetobacter baumannii</i> (MDR-AB), methicillin-resistant <i>S. aureus</i> (MRSA) and <i>Candida albicans</i> (<i>C. albicans</i>) strains. The antimicrobial activity results clearly indicated that the Gram-negative bacteria MDR-PA was most affected by AgNPs as compared to other Gram-negative and Gram-positive bacteria and fungi <i>C. albicans</i>. Whereas, in the case of antibiofilm activity, it has been found that AgNPs at 0.039 mg/mL, inhibit biofilms formation of Gram-negative bacteria i.e., MDR-PA, <i>E. coli</i>, and MDR-AB by 78.98 ± 1.12, 65.77 ± 1.05 and 66.94 ± 1.35%, respectively. On the other hand, at the same dose (i.e., 0.039 mg/mL), AP-AgNPs inhibits biofilm formation of Gram-positive bacteria i.e., MRSA, <i>S. aureus</i> and fungi <i>C. albicans</i> by 67.81 ± 0.99, 54.61 ± 1.11 and 56.22 ± 1.06%, respectively. The present work indicates the efficiency of green synthesized AP-AgNPs as good antimicrobial and antibiofilm agents against selected bacterial and fungal species.
Identifying Leprosy and Those at Risk of Developing Leprosy by Detection of Antibodies against LID-1 and LID-NDO (2016)

Leprosy is caused by Mycobacterium leprae infection and remains a major public health problem in many areas of the world. Challenges to its timely diagnosis result in delay in treatment, which is usually associated with severe disability. Although phenolic glycolipid (PGL)-I has been reported as auxiliary diagnostic tool, currently there is no serological assay routinely used in leprosy diagnosis. The aim of this study was to evaluate the effectiveness of two related reagents, LID-1 and LID-NDO, for the detection of M. leprae infection. Sera from 98 leprosy patients, 365 household contacts (HHC) and 98 endemic controls from Rio Grande do Norte, Brazil, were evaluated. A subgroup of the HHC living in a hyperendemic area was followed for 7-10 years. Antigen-specific antibody responses were highest in multibacillary (MB) at the lepromatous pole (LL/BL) and lowest in paucibacillary (PB) at the tuberculoid pole (TT/BT). A positive correlation for both anti-LID-1 and anti-LID-NDO antibodies was found with bacterial burden (LID-1, r = 0.84, p<0.001; LID-NDO, r = 0.82, p<0.001), with higher sensitivity than bacilloscopy. According to Receiver Operating Curve, LID-1 and LID-NDO performed similarly. The sensitivity for MB cases was 89% for LID-1 and 95% for LID-NDO; the specificity was 96% for LID-1 and 88% for LID-NDO. Of the 332 HHC that were followed, 12 (3.6%) were diagnosed with leprosy in a median time of 31 (3-79) months after recruitment. A linear generalized model using LID-1 or LID-NDO as a predictor estimated that 8.3% and 10.4% of the HHC would become a leprosy case, respectively. Together, our findings support a role for the LID-1 and LID-NDO antigens in diagnosing MB leprosy and identifying people at greater risk of developing clinical disease. These assays have the potential to improve the diagnostic capacity at local health centers and aid development of strategies for the eventual control and elimination of leprosy from endemic areas.
Comparing B3LYP and B97 Dispersion‐corrected Functionals for Studying Adsorption and Vibrational Spectra in Nitrogen Reduction (2021)

Electrochemical ammonia synthesis is being actively studied as a low temperature, low pressure alternative to the Haber-Bosch process. This work studied pure iridium as the catalyst for ammonia synthesis, following promising experimental results of Pt-Ir alloys. The characteristics studied include bond energies, bond lengths, spin densities, and free and adsorbed vibrational frequencies for the molecules N<sub>2</sub> , N, NH, NH<sub>2</sub> , and NH<sub>3</sub> . Overall, these descriptive characteristics explore the use of dispersion-corrected density functional theory methods that can model N<sub>2</sub> adsorption - the key reactant for electrochemical ammonia synthesis via transition metal catalysis. Specifically, three methods were tested: hybrid B3LYP, a dispersion-corrected form B3LYP-D3, and semi-empirical B97-D3. The latter semi-empirical method was explored to increase the accuracy obtained in vibrational analysis as well as reduce computational time. Two lattice surfaces, (111) and (100), were compared. The adsorption energies are stronger on (100) and follow the trend E<sub>B3LYP</sub> >E<sub>B3LYP-D3</sub> >E<sub>B97-D3</sub> on both surfaces.
Expanding the range of polyhydroxyalkanoates synthesized by methanotrophic bacteria through the utilization of omega-hydroxyalkanoate co-substrates (2017)

The first methanotrophic syntheses of polyhydroxyalkanoates (PHAs) that contain repeating units beyond 3-hydroxybutyrate and 3-hydroxyvalerate are reported. New PHAs synthesized by methanotrophs include poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB-co-4HB)), poly(3-hydroxybutyrate-co-5-hydroxyvalerate-co-3-hydroxyvalerate) (P(3HB-co-5HV-co-3HV)), and poly(3-hydroxybutyrate-co-6-hydroxyhexanoate-co-4-hydroxybutyrate) (P(3HB-co-6HHx-co-4HB)). This was achieved from a pure culture of Methylocystis parvus OBBP where the primary substrate is methane and the corresponding ω-hydroxyalkanoate monomers are added as a co-substrate after the cells are subjected to nitrogen-limited conditions.
Defect analysis in 157-nm photolithography process (2002)

Reducing defects in the semiconductor photolithography process has become increasingly critical. Many kinds of defects can occur during photolithography, such as missing contact holes or pattern collapses that occur during developing. As the pattern size becomes finer, the exposure wavelength has been shortened from 248-nm to 193-nm, and then to 157-nm. In addition, the resin structure and the chemical characteristics of the resist material have changed greatly. Changing the resist material from I-line to 248-nm created the problem of satellite defects peculiar to chemically amplified resist. Previous studies have suggested that a satellite defect is a complex salt of PAG, quencher, and TMAH, and is soluble in water.1) Because the resist material for 157-nm lithography is highly hydrophobic and is used for making ultra-thin films, defect evaluations of it are necessary. This paper evaluates the defects arising with various kinds of 157-nm lithography resist. Just as with 248-nm resist, a deposition defect peculiar to CAR occurs with 157-nm resist, but it occurs more frequently than with 248-nm resist. Unique defects appear with 157-nm resist, but their appearance and frequency seem to depend on the resist structure. The number of missing contact holes increases when the contact angle to ultra-pure water on the 157-nm resist film raise. It is necessary to elucidate on the mechanism that the unique defect occur in 157-nm resist.
Can ABCF2 protein expression predict the prognosis of uterine cancer? (2008)

Uterine cervical and endometrial cancers are common malignant solid neoplasms for which there are no useful prognostic markers. In this study, we evaluate the relationship between ATP-binding cassette superfamily F2 (ABCF2) expression and clinical factors including clinical stage, histologic type, grade and prognosis in uterine cervical and endometrial cancer. Two hundred and sixty seven cervical and 103 endometrial cancers were studied. ATP-binding cassette superfamily F2 cytoplasmic expression was detected by immunohistochemical staining and scored as positive or negative. Among cervical cancer cases, 149 (55.8%) expressed ABCF2. The overall survival was longer in ABCF2-negative than ABCF2-positive cases (P=0.0069). Statistically significant prognostic factors for survival were ABCF2 positivity (risk ratio (rr)=1.437), old age (rr=1.550) and advanced stage (rr=2.577). ATP-binding cassette superfamily F2 positivity was an independent prognostic factor by multivariate proportional hazard test (P=0.0002). Among endometrial cancer cases, 72 (69.9%) were cytoplasmic ABCF2 positive. However, there was no significant relationship between ABCF2 expression and age, clinical stage, histologic type, histologic grade, oestrogen receptor status or prognosis. ATP-binding cassette superfamily F2 expression may be a useful prognostic marker in cervical but not endometrial cancer. The role of ABCF2 protein may differ depending on the type of cancer.