gebhart/patrepeval huggingface dataset:
Data from Characterizing the immune microenvironment and neoantigen landscape of Hürthle cell carcinoma to identify potential immunologic vulnerabilities (2023)

&lt;div&gt;Abstract&lt;p&gt;Hürthle cell carcinoma (HCC) is a rare type of thyroid cancer with high rates of distant metastasis and recurrence. Along with the scarcity of effective systemic therapies for HCC, these factors contribute to poor clinical outcomes. The immunologic features of HCC are poorly defined and response rates with immune checkpoint blockade have not been reported. A more comprehensive understanding of the immune landscape and factors that predict response to checkpoint inhibitors is needed. We performed RNA sequencing on 40 tumors to characterize the neoantigen landscape and immune microenvironment of HCC. We analyzed transcriptomic profiles, tumor-infiltrating immune cell populations, and measures of T-cell activation/dysfunction and correlated these to genetic features such as tumor mutation burden, neoantigen burden, mitochondrial mutations, and loss of heterozygosity from chromosomal uniparental disomy. Lastly, immune profiles of patients with recurrence were compared with those of patients without recurrence. HCC tumors exhibited low levels of immune infiltration, with the more aggressive widely invasive phenotype associated with more immune depletion. There was a negative correlation between tumor mutation burden, neoantigen burden, PD-L1 expression, and the immune infiltration score. HCC tumors that exhibited a global loss of heterozygosity from chromosomal uniparental disomy or haploidization had the lowest level of immune infiltration. HCC tumors that recurred displayed an immune-depleted microenvironment associated with global loss of heterozygosity and aerobic glycolysis. These findings offer new insights into the functional immune landscapes and immune microenvironment of HCC. Our data identify potential immunologic vulnerabilities for these understudied and often fatal cancers.&lt;/p&gt;&lt;/div&gt;
Testing Computer Vision techniques for bedload sediment transport evaluation in sewers (2017)

International audience
Figure S6 from Scaffolding Protein Connector Enhancer of Kinase Suppressor of Ras 1 (CNKSR1) Regulates MAPK Inhibition Responsiveness in Pancreas Cancer via Crosstalk with AKT Signaling (2023)

&lt;p&gt;MEK blockade fails to disrupt protein-protein interactions of CNKSR1, KSR1/2, and MEK in CNKSR1low cancer cells.&lt;/p&gt;
Humanization Strategies (2014)

Humanization of monoclonal antibodies (mAbs) from animal sources comprises strategies for reducing their immunogenicity and for improving their activation of the human immune system. There are now many humanized mAbs in late phase clinical trials and several have been given approval to be used as biopharmaceuticals. Although the mechanics of producing the engineered mAb using the techniques of molecular biology are relatively straightforward, the design of the humanized antibody sequence is critical for reproducing the affinity, specificity, and function of the original molecule while minimizing human anti-mouse antibody (HAMA) responses elicited in patients. There are many strategies leading to the design of the humanized variable regions (Fvs) and thus various choices are open to the antibody designer. These strategies and choices are the subject matter of this chapter.
Isolation of secondary products from Ipomoea digitata – a medicinally important plant (2010)

The paper reports the isolation and characterization of â-sitosterol, t-cinnamic acid [undecyl (E)-3-(4- hydroxyphenyl)-2-propenoate], an unknown coumarin and a lignan type resin glycoside from the tuberous roots of Ipomoea digitata. The structures of the compounds were elucidated on the basis of extensive chemical and spectroscopic data. Importantly, one of the compounds exhibited significant antibacterial activity against Pseudomonas aeruginosa and E coli. The resin glycosides are known as purgative ingredients and hence have medicinal value. However, the exact chemical and biological activity of the resin glycoside isolated in this study is yet to be ascertained.
Analysis of 1,115 Patients Tested for <i>MET</i> Amplification and Therapy Response in the MD Anderson Phase I Clinic (2014)

MET amplification was detected in 2.6% of patients with solid tumors and was associated with adenocarcinomas, high-grade histology, and higher metastatic burden. Concomitant alterations in additional pathways (BRAF mutation and PTEN loss) and variable responses on targeted therapies, including c-MET inhibitors, suggest that further studies are needed to target this population.
The role of the c‐<i>kit</i> receptor in the regenerative differentiation of rat Leydig cells (2003)

To determine the physiological role of the c-kit receptor, which is highly expressed in Leydig cells, the regenerative differentiation of Leydig cells was studied following transient degeneration induced by ethane dimethyl sulphonate (EDS) in c-kit-deficient mutant rats (Ws/Ws). EDS caused the destruction of Leydig cells; their functional recovery was evaluated by the weight change of the target organs of androgens, which occurred at the same rate in Ws/Ws and wild-type rats. These results indicate that the tyrosine kinase activity of the c-kit receptor does not play an essential role in the regenerative differentiation of Leydig cells.
Towards robust teams with many agents (2002)

Agents in deployed multi-agent systems monitor other agents to coordinate and collaborate. However, as the number of agents monitored is scaled up, two key challenges arise: (i) the number of monitoring hypotheses to be considered can grow exponentially in the number of agents; and (ii) agents become physically and logically unconnected (unobservable) to their peers. This paper examines these challenges in teams of cooperating agents, focusing on a monitoring task that is of particular importance to robust teamwork: detecting disagreements among team-members. We present YOYO, a highly scalable disagreement-detection algorithm which guarantees sound detection in time linear in the number of agents despite the exponential number of hypotheses. In addition,we present new upper bounds for the number of agents that must be monitored in a team to guarantee disagreement detection. Both YOYO and the new bounds are explored analytically and empirically in thousands of monitoring problems, scaled to thousands of agents.
Fundamentals of Magnetorheological Fluid Utilization in High Precision Finishing (1999)

Magnetorheological finishing (MRF) is an enabling technology that may produce surface accuracy on the order of 30 nm peak to valley (p-v) and surface micro-roughness less than 10 A rms. In MRF, mechanical energy for material removal over the portion of the workpiece surface is generated by the magnetically controlled hydrodynamic flow of a magnetorheological polishing fluid. A fundamental advantage of MRF over existing technologies is that the polishing tool does not wear, since the recirculated fluid is continuously monitored and maintained. Polishing debris and heat are continuously removed. The technique requires no dedicated tooling or special setup. A unique attribute of the MRF process is its determinism that is attained through the use of a well-defined material removal function to eliminate known surface error. The efficiency of material removal and the removal process stability are the crucial factors in MRF. In turn, they are primarily dependent on MR polishing fluid stability. It is shown that the joint use of physicochemical and rheological factors along with specially developed methods of the slurry handling, pumping, and in-line monitoring and maintaining provides a level of MR slurry stability that is quite adequate for high precision finishing. Attention is given to methods of MR slurry property measurements.
Depletion of endogenous kallistatin exacerbates renal and cardiovascular oxidative stress, inflammation, and organ remodeling (2012)

Kallistatin (KS) levels are reduced in the kidney and blood vessels under oxidative stress conditions. To determine the function of endogenous KS in the renal and cardiovascular systems, KS levels were depleted by daily injection of anti-rat KS antibody into DOCA-salt hypertensive rats for 10 days. Administration of anti-KS antibody resulted in reduced KS levels in the circulation but increased levels of serum thiobarbituric acid reactive substances (an indicator of lipid peroxidation) as well as superoxide formation in the aorta. Moreover, anti-KS antibody injection resulted in increased NADH oxidase activity and superoxide production but decreased nitric oxide levels in the kidney and heart. Endogenous KS blockade aggravated renal dysfunction, damage, hypertrophy, inflammation, and fibrosis as evidenced by decreased creatinine clearance and increased serum creatinine, blood urea nitrogen and urinary protein levels, tubular dilation, protein cast formation, glomerulosclerosis, glomerular enlargement, inflammatory cell accumulation, and collagen deposition. In addition, rats receiving anti-KS antibody had enhanced cardiac injury as indicated by cardiomyocyte hypertrophy, inflammation, myofibroblast accumulation, and fibrosis. Renal and cardiac injury caused by endogenous KS depletion was accompanied by increases in the expression of the proinflammatory genes tumor necrosis factor-α and intercellular adhesion molecule-1 and the profibrotic genes collagen I and III, transforming growth factor-β, and tissue inhibitor of metalloproteinase-1. Taken together, these results implicate an important role for endogenous KS in protection against salt-induced renal and cardiovascular injury in rats by suppressing oxidative stress, inflammation, hypertrophy, and fibrosis.
The Stacking Action in Autoclave Molding and a Process Judgment Analysis of the Worker (2015)

Three-dimensional components which incorporate CFRP are molded by skilled workers manually; this makes quality control difficult. This study discusses how workers’ skill influences the mechanical performance of molded products. This study aims to establish qualification criteria and standardize the manufacturing process. Carbon cloth prepreg was stacked in six layers in a mold in a fiber orientation pattern of 0°, 45°, 0°, 0°, 45°, and 0°. The hand lay-up process was applied and subjects chose their own process and tools. Subject A had 13 years of experience and subject B had 1 year of experience. The process was recorded with a video camera and results compared in an interview format, inspecting footage of the process together with the subject. Subject A's movements were very smooth, his body and face close to the mold, whilst subject B's movements were very awkward. Subjects’ use of tools and hands were analyzed. In the judgment analysis, subjects were interviewed and their responses analyzed. The subjects’ decision-making processes were given numeric values and studied, identifying the critical path. There was a noticeable difference in the subjects’ process and a significant difference in the mechanical properties of the molds. This study will be repeated with more subjects in order to identify the various factors.
Plane Wave Electromagnetic Reflection and Transmission from a Thin Geologic Layer (2016)

Abstract not provided.
Comparison of NO titration and fiber optics catalytic probes for determination of neutral oxygen atom concentration in plasmas and postglows (2003)

A comparative study of two different absolute methods NO titration and fiber optics catalytic probe (FOCP) for determination of neutral oxygen atom density is presented. Both methods were simultaneously applied for measurements of O density in a postglow of an Ar/O2 plasma created by a surfatron microwave generator with the frequency of 2.45 GHz an adjustable output power between 30 and 160 W. It was found that the two methods gave similar results. The advantages of FOCP were found to be as follows: it is a nondestructive method, it enables real time measuring of the O density, it does not require any toxic gas, and it is much faster than NO titration. The advantage of NO titration was found to be the ability to measure O density in a large range of dissociation of oxygen molecules.
Co<sup>III</sup>EDTA<sup>-</sup> Reduction by <i>Desulfovibrio vulgaris</i> and Propagation of Reactions Involving Dissolved Sulfide and Polysulfides (2001)

The migration of 60Co, dominantly via transport of Co-EDTA complexes, into surface water and groundwater is a recognized concern at many nuclear production and storage sites. Reduction of CoIIIEDTA- to CoIIEDTA2- should decrease the mobility of 60Co in natural environments by stimulating ligand displacement with Fe(III) or Al(III) or by precipitation of CoSx in sulfidic environments. In this study, we examine direct (enzymatic) and indirect (metabolite) reduction processes of CoIIIEDTA- by the sulfate-reducing bacterium Desulfovibrio vulgaris. D. vulgaris reduces CoIIIEDTA- to CoIIEDTA2-, but growth using it as a terminal electron acceptor was not demonstrated. Rather than acting as a competing electron acceptor and limiting cobalt reduction, introducing sulfate with D. vulgaris enhances the reduction of CoIIIEDTA- as a result of sulfide production. Sulfide reduces CoIIIEDTA- in a pathway involving polysulfide formation and leads to a CoS precipitate. Thus, both direct and indirect (i.e., through the production of sulfide) microbial reduction pathways of CoIIIEDTA- may help to retard its migration within soils and waters.
Polymer Electrolyte Fuel Cells With Porous Materials as Fluid Distributors and Comparisons With Traditional Channeled Systems (2004)

In this study, a novel concept is investigated, according to which the traditional ribbed flow delivery systems are replaced with permeable porous fluid distributors, which circumvent a number of known performance hindering drawbacks. A thorough single-phase model, including the conservation of mass, momentum, energy, species, and electric current, using Butler-Volmer kinetics, is numerically solved in three dimensions, to investigate the impact of different flow configurations on the performance of hydrogen fuel cells. It is found that cells with porous gas distributors generate substantially higher current densities and therefore are more advantageous with respect to mass transfer. Another advantage of porous flow distributors is the potential for higher power densities and reduced stack weight.
Comments on the Use of Diphenyloxazinone Derivatives as Glycine Anion Templates for Amino Acid Synthesis (1992)

Some observations resulting from the use of optically active diphenyloxazinone derivatives 1 and 4 as glycine anion equivalents are reported. The utility of the method is demonstrated in the synthesis of (S,S)-2,6-diamino-2-hydroxymethylheptanedioic acid (7).
Biophone: Physiology monitoring from peripheral smartphone motions (2015)

The large-scale adoption of smartphones during recent years has created many opportunities to improve health monitoring and care delivery. In this work, we demonstrate that motion sensors available in off-the-shelf smartphones can capture physiological parameters of a person during stationary postures, even while being carried in a bag or a pocket. In particular, we develop methods to extract heart and breathing rates from accelerometer data and compare them with measurements obtained with FDA-cleared sensors. We evaluated their accuracy on 12 people across different still body postures (pre- and post- exercise) and were able to reach mean absolute errors of 1.16 beats per minute (STD: 3) and 0.26 breaths per minute (STD: 0.5) when considering different conditions. Furthermore, we evaluated the same methods during regular phone activities, such as when watching a video or listening to a conversation, yielding increased but still comparable error rates for some conditions.
Supplementary Figure 1 from CRM1 and BRAF Inhibition Synergize and Induce Tumor Regression in BRAF-Mutant Melanoma (2023)

&lt;p&gt;Supplementary Figure 1 - PDF file 29K, CRM1 and BRAF inhibition decrease melanoma cell proliferation and are synergistic in vitro&lt;/p&gt;
Common Host-Derived Chemicals Increase Catches of Disease-Transmitting Mosquitoes and Can Improve Early Warning Systems for Rift Valley Fever Virus (2013)

Rift Valley fever (RVF), a mosquito-borne zoonosis, is a major public health and veterinary problem in sub-Saharan Africa. Surveillance to monitor mosquito populations during the inter-epidemic period (IEP) and viral activity in these vectors is critical to informing public health decisions for early warning and control of the disease. Using a combination of field bioassays, electrophysiological and chemical analyses we demonstrated that skin-derived aldehydes (heptanal, octanal, nonanal, decanal) common to RVF virus (RVFV) hosts including sheep, cow, donkey, goat and human serve as potent attractants for RVFV mosquito vectors. Furthermore, a blend formulated from the four aldehydes and combined with CO(2)-baited CDC trap without a light bulb doubled to tripled trap captures compared to control traps baited with CO(2) alone. Our results reveal that (a) because of the commonality of the host chemical signature required for attraction, the host-vector interaction appears to favor the mosquito vector allowing it to find and opportunistically feed on a wide range of mammalian hosts of the disease, and (b) the sensitivity, specificity and superiority of this trapping system offers the potential for its wider use in surveillance programs for RVFV mosquito vectors especially during the IEP.
Visual detection, recognition, and classification of surface-buried UXO based on soft-computing decision fusion (2007)

In this paper, we have addressed the problem of visual inspection, recognition, and discrimination of UXO based on computer vision techniques and introduced three complimentary color, texture, and shape classifiers. The proposed technique initially enhances an image taken from an UXO site and removes terrain background. Next, it applies a blob detector to detect the salient objects of the environment. The UXO classification begins with a perceptive color classifier that classifies the found salient objects based on their color hues. The color classifier attempts to differentiate and classify the color of salient objects based on the color hue information of some known UXO objects in the database. A color ranking scheme is applied for ranking color hue likelihood of the salient objects in the environment. Next, an intuitive texture classifier is applied to characterize the surface texture of the salient objects. The texture signature is used to disjointedly discriminate objects whose surface texture properties matching the priori known UXO textures. Lasting, an intuitive Object Shape Classifier is applied to independently arbitrate the classification of the UXO. Three soft computing methods were developed for robust decision fusion of three UXO feature classifiers. These soft computing techniques include: a statistical-based genetic algorithm, a hamming neural network, and a fuzzy logic algorithm. In this paper, we present details of the UXO feature classifiers and discuss the performance of three decision fusion methods for fusion of results from the three UXO feature classifiers. The main contributing factor of this work is toward designing an ultimate fully-automated tele-robotic system for UXO classification and decontamination.
Repeatability of Received Signal Level Measurements in GSM Cellular Networks (2007)

Received signal level (RSL) measurements are frequently used to verify coverage and ensure quality of service in cellular communication networks. To accomplish these tasks, it is of the utmost importance that these measurements are reliable and repeatable. This paper presents a repeatability study conducted on a series of RSL measurements in the GSM 1900MHz frequency band. The measurements were collected with three different drive-test systems used in common engineering practice. Data obtained from the tests are analyzed using statistical tools and the extent of the RSL measurement repeatability is determined. The analysis provides a quantitative assessment of the RSL dependence on random changes in the propagation environment. Data analysis demonstrates a significant repeatability difference between the measurement systems
Unpatterned Ferroelectric Thin Film Measurements for Optimization of Perovskite Oxide Thin Film Based Microwave Devices (2006)

Abstract The Army's Future Force (FF) antennas require increased bandwidth for multimission communications; increased antenna gain for robust communications and range extension; increased mobility for high data rate on-the-move (OTM) communications; and undetectable antenna visual signatures for low probably of mission detection and increased survivability. Electronic scanning antennas (ESA's) are the key components for such advanced communication systems. ESA's provide rapid scanning capability, which enables modes such as multiple target tracking, track while scan, and sensor fusion operation. One of the major challenges, which must be overcome before such advanced ESA systems can be realized, is the development of affordable, low loss, high tunability, low power, lightweight, and high performance microwave frequency phase shifters. The enabling technology for such phase shifters is centered on the development of single-phase nanometer-scale constituent perovskite oxide thin films with enhanced dielectric, insulating, and microstructural properties. The Army Research Laboratory (ARL) has successfully designed, fabricated, characterized, and optimized, novel pure and acceptor doped Ba 0.6 Sr 0.4 TiO 3 (BST) based thin films on MgO substrates with excellent microwave material properties. Pure and 1-mol% Mg doped BST thin films were fabricated by the metalorganic solution deposition (MOSD) technique and the film's dielectric properties were characterized at microwave frequency via a tuned coupled-split dielectric resonator technique developed at NIST. Using this measurement technique, for first time ever, has allowed the true “singular” dielectric loss (tan δ) and permittivity (ϵ r ) of the BST-based films to be assessed and optimized without the influence of device design (radiative losses) and electrode metallization (conductor losses). Keywords: OTM antennasferroelectric thin filmsphase shifterunpatterned microwave measurements Acknowledgments The authors gratefully acknowledge C. Hubbard for assistance with x-ray data collection.
Ribosomal RNA cleavage, nuclease activation and 2-5A (ppp(A2′p)<sub>n</sub>A) in interferon-treated cells (1981)

Ribosomal RNA (rRNA) in intact ribosomes is cleaved into discrete products on incubation of reticulocyte lysates or L-cell extracts with ppp(A2'p)3A. Cleavage of rRNA may, therefore, provide a useful assay for 2-5A (ppp)A2'p)nA; n = 2 to 4) or for the presence of a 2-5A-dependent nuclease. The results with reticulocyte lysates differed from those obtained in the L-cell-free system in that (a) a different RNA cleavage pattern was produced (with added L-cell ribosomes) and (b) cleavage was fully activated by the analogue ppp(A2'p)3A3'pCp. As might be expected from the relatively high levels of 2-5A present in interferon-treated, encephalomyocarditis virus (EMC)-infected L-cells, rRNA extracted from these cells was also cleaved. The cleavage pattern observed overlapped with that obtained on incubation of an L-cell-free system with 2-5A. Thus, not only is 2-5A present, but the 2-5A-dependent nuclease also appears to be active, in interferon-treated, EMC-infected L-cells.
Stiffness Perception During Active Ankle and Knee Movement (2017)

Our results provide novel insight into how the sensorimotor system senses joint impedance, information that may improve the design and control of impedance-based wearable robotic technologies.