gebhart/patrepeval huggingface dataset:
Data from Unique Neoantigens Arise from Somatic Mutations in Patients with Gastrointestinal Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;Immunotherapies can mediate regression of human tumors with high mutation rates, but responses are rarely observed in patients with common epithelial cancers. This raises the question of whether patients with these common cancers harbor T lymphocytes that recognize mutant proteins expressed by autologous tumors that may represent ideal targets for immunotherapy. Using high-throughput immunologic screening of mutant gene products identified via whole-exome sequencing, we identified neoantigen-reactive tumor-infiltrating lymphocytes (TIL) from 62 of 75 (83%) patients with common gastrointestinal cancers. In total, 124 neoantigen-reactive TIL populations were identified, and all but one of the neoantigenic determinants were unique. The results of &lt;i&gt;in vitro&lt;/i&gt; T-cell recognition assays demonstrated that 1.6% of the gene products encoded by somatic nonsynonymous mutations were immunogenic. These findings demonstrate that the majority of common epithelial cancers elicit immune recognition and open possibilities for cell-based immunotherapies for patients bearing these cancers.&lt;/p&gt;Significance:&lt;p&gt;TILs cultured from 62 of 75 (83%) patients with gastrointestinal cancers recognized neoantigens encoded by 1.6% of somatic mutations expressed by autologous tumor cells, and 99% of the neoantigenic determinants appeared to be unique and not shared between patients.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 983&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Planar Atom Trap and Magnetic Resonance 'Lens' Designs (2007)

We present various planar magnetic designs that create points above the plane where the magnitude of the static magnetic field is a local minimum. Structures with these properties are of interest in the disciplines of neutral atom confinement, magnetic levitation, and magnetic resonance imaging. Each planar permanent magnet design is accompanied by the equivalent planar single non-crossing conductor design. Presented designs fall into three categories producing: a) zero value magnetic field magnitude point minima, b) non-zero magnetic field magnitude point minima requiring external bias magnetic field, and c) self-biased non-zero magnetic field magnitude point minima. We also introduce the Principle of Amperean Current Doubling in planar perpendicularly magnetized thin films that can be used to improve the performance of each permanent magnet design we present. Single conductor current-carrying designs are suitable for single layer lithographic fabrication, as we experimentally demonstrate. Finally, we present the case that nanometer scale recording of perpendicular anisotropy thin magnetic films using presently available data storage technology can provide the ultimate miniaturization of the presented designs.
Percutaneous transradial coronary palmaz‐schatz stent implantation, guided by intravascular ultrasound (1995)

Intravascular ultrasound (IVUS) allows accurate assessment of stent deployment, its use being confined to the use of 8 French (F) guiding catheters. We evaluated the feasibility of combining transradial artery Palmaz-Schatz stent implantation through 6F guiding catheters with IVUS for assessment of stent diameter after delivery at moderate inflation pressures (10-12 atmospheres [atm]) with compliant balloons and after high pressure dilatations with balloons of intermediate compliance. In 8 consecutive patients, 12 stents were delivered with Scimed Express balloon catheters at 10-12 atm followed by IVUS (EndoSonics CathScanner; Visions FX 3.5F 20 MHz transducer). An ultrasound study was repeated after high pressure dilatations (16-20 atm) with Schneider Magical Speedy balloon catheters. The balloon diameters were derived from manufacturer provided specifications. In all patients the transducer could easily be advanced through the guiding catheters. Reference diameter of the stented segment was 3.7 +/- 0.5 mm (2.7-4.5) and the diameter of Scimed Express balloons during inflation was 4.0 +/- 0.3 mm (3.6-4.7). Stent diameter was 3.0 +/- 0.1 mm (2.8-3.2) (P < 0.001 compared to the reference and the balloon diameter). The diameter of the Schneider Magical Speedy balloons at secondary dilatations with 16 +/- 3 atm (14-20) was 4.1 +/- 0.4 mm (3.3-4.5) (P = 0.50 compared to the initial balloon diameter). Final stent diameter was 3.3 +/- 0.4 mm (2.9-4.1) (P = 0.02 compared to the initial stent diameter). All stents were symmetrically deployed and well apposed. No damage to vessel or stents was detected after passage of the transducer.(ABSTRACT TRUNCATED AT 250 WORDS)
Newer optics efficiently mix, dim, and color-tune LED light (2013)

Low-cost, plastic-injected optics mix light from different color LED dies without a significant decrease in average brightness, simplifying luminaire design both optically and electronically. In solid-state lighting, high-flux and high-color rendering index (CRI) light engines may be achieved by arraying and mixing the light from different color dies or phosphors, or a combination of the two, in the LED package. However, these nonhomogeneous sources, when combined with luminaire optics, tend to produce patterns with undesirable artifacts such as spatial and angular nonuniformities and color separation.
Heterosis in the freezing tolerance of crosses between two Arabidopsis thaliana accessions (Columbia‐0 and C24) that show differences in non‐acclimated and acclimated freezing tolerance (2004)

Heterosis is broadly defined as the increased vigour of hybrids in comparison to their parents. In the model plant Arabidopsis thaliana, a significant heterosis effect on leaf-freezing tolerance was observed in the F(1) generation of a cross between the accessions Columbia-0 (Col) and C24. Parental Col plants were significantly more freezing-tolerant than C24 plants in both the acclimated and non-acclimated (NA) states. Mid-parent heterosis was observed in the F(1) plants, both in the basic tolerance of non-adapted plants and in freezing tolerance after cold acclimation. Best-parent heterosis, on the other hand, was only found after cold acclimation. The heterosis effect was reduced in the F(2) populations such that only mid-parent heterosis was evident. The leaf content of soluble sugars (fructose (Fru), glucose (Glc), sucrose (Suc) and raffinose (Raf)) increased dramatically in the F(1) plants after cold acclimation as compared to the parental lines. The content of proline (Pro), however, was only moderately increased in the F(1) plants under the same conditions. Correlation analyses showed that only Raf content was consistently related to leaf-freezing tolerance in both the acclimated and NA states. A quantification of mRNA levels in leaves of parental and F(1) lines using quantitative real-time RT-PCR showed no clear indication for an involvement of the investigated genes (CBF (C-repeat binding factor)1, CBF2, (cold-regulated protein (COR) 6.6, COR15a, COR15b, COR47 and COR78) in the heterosis effect.
Application of a bootstrapping procedure to the analysis of the conducted propagation of electromagnetic interferences along the power network (2014)

International audience
Mimicking a negative refractive slab by combining two phase conjugators (2009)

A new route toward a lossless superlens has been proposed recently. It relies on the association of two phase-conjugating sheets. The aim of this study is to show how such a lens can be implemented experimentally at optical frequencies. Because efficient phase conjugation of evanescent waves is illusory with the current technology, only the case of propagating waves is considered here. Four wave mixing in BaTiO3 is shown to provide efficient backward and forward phase conjugation over a major part of the angular spectrum, taking advantage of internal reflections inside the non-linear slab. However, phase distortions arise for high spatial frequencies and limit the resolving power of the device. The addition of a second phase-conjugator automatically compensates for these phase distortions. The wave field is then perfectly translated through the system. Actually, such a device performs even better than a negative refracting lens since the association of two phase-conjugating mirrors behaves like a resonant cavity. An amplification of the wave field by a factor of 102 in intensity is predicted, despite the important absorption in BaTiO3.
Provably Good Max–Min- $m$ -Neighbor-TSP-Based Subfield Scheduling for Electron-Beam Photomask Fabrication (2017)

Electron beam lithography (EBL) has been used for high-resolution photomask fabrication; its successive heating process in a certain region, however, may cause critical dimension (CD) distortion. As a result, subfield scheduling, which reorders a sequence of subfields in the writing process, is desirable to avoid the heating problem and thus CD distortion. To consider longer range heat dissipation, this paper models a subfield scheduling problem with blocked region consideration as a constrained max–min <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$m$ </tex-math></inline-formula> -neighbor traveling salesman problem (called constrained <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$m$ </tex-math></inline-formula> -nTSP). To solve the constrained <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$m$ </tex-math></inline-formula> -nTSP which is NP-complete in general, we decompose a constrained <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$m$ </tex-math></inline-formula> -nTSP into subproblems conforming to a special case with points on two parallel lines, solve each of them with a provably good linear-time approximation algorithm, and merge them into a complete scheduling solution. In particular, our algorithm can also minimize the distances between successive subfields to alleviate the throughput degradation of EBL writing due to moving a writing head, while minimizing the heating problem. Average reductions of 10% in the maximum temperature and 14% in the distances between successive subfields over the state-of-the-art work can be achieved.
Handbook of Magnetism and Advanced Magnetic Materials (2007)

The study of quantum phase transitions has been a major focus of theoretical and experimental work in systems of correlated electrons and in correlated ul-tracold atoms in recent years. However, some of the best characterized and understood examples of quantum phase transitions are found in magnetic
Guanine Nucleotides Regulates Both Agonist and Antagonist Binding to Cod Brain α1‐Adrenoceptors (1986)

The effect of guanine nucleotides on the binding of 3H-prazosin and its displacement by various agonists and antagonists were studied in membranes prepared from the cod brain. When cod brain membranes were maintained in a buffer containing 8 mM Mg2+, GTP (1 mM) was found to increase the specific binding of 3H-prazosin Computer modelling 3H-prazosin saturation curves, suggested that the number of binding sites for 3H-prazosin was increased by 18 +/- 5% by GTP without affecting the affinity for 3H-prazosin (dissociation constant, Kd, 56 +/- 3 pM). Displacement of 3H-prazosin by adrenaline produced shallow displacement curves. Computer modelling these curves suggested that adrenaline bound to two sites - one high and one low affinity site - the Kd's being 0.14 +/- 0.03 (KH) and 7.6 +/- 0.5 microM (KL), respectively. When 1 mM GTP was present the displacement curves were shifted to the right and became steeper. Computer modelling these curves suggested that adrenaline now bound to only one low affinity site with a Kd of 7.6 +/- 0.5 microM. When unlabelled prazosin was used to displace 3H-prazosin the displacement curves were uniphasic and steep, irrespective of whether GTP was present or not. Computer modelling these curves suggested that prazosin bound to only one site with a Kd of 68 +/- 11 pM. In the absence of Mg2+ and in the presence of EDTA (0.8 mM) the displacement curve of adrenaline became steeper and the effect of GTP was almost abolished. During these conditions the ability of GTP to enhance 3H-prazosin binding was also abolished.(ABSTRACT TRUNCATED AT 250 WORDS)
Shear-Driven Motion of Supported Lipid Bilayers in Microfluidic Channels (2009)

In this work, we demonstrate how a lateral motion of a supported lipid bilayer (SLB) and its constituents can be created without relying on self-spreading forces. The force driving the SLB is instead a viscous shear force arising from a pressure-driven bulk flow acting on the SLB that is formed on a glass wall inside a microfluidic channel. In contrast to self-spreading bilayers, this method allows for accurate control of the bilayer motion by altering the bulk flow in the channel. Experiments showed that an egg yolk phosphatidylcholine SLB formed on a glass support moved in a rolling motion under these shear forces, with the lipids in the upper leaflet of the bilayer moving at twice the velocity of the bilayer front. The drift velocity of different lipid probes in the SLB was observed to be sensitive to the interactions between the lipid probe and the surrounding molecules, resulting in drift velocities that varied by up to 1 order of magnitude for the different lipid probes in our experiments. Since the method provides a so far unattainable control of the motion of all molecules in an SLB, we foresee great potential for this technique, alone or in combination with other methods, for studies of lipid bilayers and different membrane-associated molecules.
ChemInform Abstract: X‐RAY ABSORPTION EDGE AND EXAFS SPECTROSCOPIC STUDIES OF MOLYBDENUM IONS IN AQUEOUS SOLUTION (1983)

Abstract Messungen an Mo(II)‐, Mo(III)‐,Mo(IV)‐ und Mo(V)‐haltigen sauren wäßrigen Lösungen zeigen, daß die Energie der Absorptionskanten in der Reihe Mo(II) Mo(III) Mo(IV) Mo(V) zunimmt.
In vitro association between the virulence proteins, YopD and YopE, ofYersinia enterocolitica (1998)

The virulence plasmid (pYV) of Y. enterocolitica encodes a set of anti-host proteins, known as Yops, which contribute to survival of the bacteria in the host. Several Yops directly influence the interaction of pathogenic bacteria with host cells which in the case of at least four Yops, YopE, YopH, YopM and YpkA (YopO), involves translocation of the Yop across the eukaryotic cell membrane into the cytoplasm of target cells. Translocation requires the presence of two other pYV-encoded proteins, YopB and YopD, but it is not clear how these proteins mediate translocation of the effector Yops. We have used an affinity blot technique (overlay) to examine potential binding between YopD and other Yops. The results indicated that under the in vitro conditions used in this study, YopD bound preferentially to YopE and YopB. To investigate the interaction of YopD and YopE in more detail we produced different regions of the YopD protein in Escherichia coli by creating fusions of YopD with glutathione S-transferase. These studies showed that YopE bound the central hydrophobic region of YopD. This is the first demonstration of protein interactions between an effector Yop and a putative Yop translocator.
Multi-Mode 60-GHz Radar Transmitter SoC in 45-nm SOI CMOS (2020)

This article introduces an architecture for a millimeter-wave multi-mode radar transmitter IC, which supports three key radar waveforms: 1) continuous-wave (CW/FMCW); 2) pulse; and 3) phase-modulated continuous-wave (PMCW), all from a single front end. The proposed IC, implemented in a 45-nm CMOS silicon-on-insulator (SOI) process for operation in the 60-GHz band, integrates a broadband frequency tripler, a two-stage pre-amplifier, two power mixers, and mixed-signal baseband waveform generation circuitry. The transmitter radar operation in multiple modes is enabled by configuring the power mixers and the associated waveform baseband circuitry. An important advantage of this approach is that the overall signal bandwidth, a key performance metric in radar, is limited only by the RF output nodes in pulse generation. A novel broadband frequency tripler design technique based on a current-reuse topology is also proposed for LO generation with >59% output fractional bandwidth. On-wafer measurement results for the full TX IC in CW mode show an average output power of 12.8 dBm from 54 to 67 GHz with a peak power of 14.7 dBm and the harmonic rejection ratio >27 dB. The measurement in pulse mode demonstrates programmable pulsewidth from 20 to 140 ps, which translates to >40-GHz radar signal bandwidth. The PMCW mode operation is also demonstrated in this case with 10-Gb/s PRBS modulated radar signal. The IC consumes 0.51 W and occupies $2.3\times 0.85$ mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of die area excluding pads.
Clinical characteristics and treatment patterns of patients with venous thromboembolism (VTE) transitioning from hospital to post-discharge settings (2020)

Many patients treated with anticoagulation therapy during a VTE hospital encounter did not fill a prescription for an anticoagulant within 30 days post-discharge, highlighting an opportunity for improved management of care transitions in this patient population.
Automated highway systems - an intelligent transportation system for the next century (2002)

Summary form only given. The California PATH program was established in 1986 by the California Department of Transportation (Caltrans) and the Institute of Transportation Studies (ITS) at the University of California at Berkeley to conduct research on transportation systems, which include automated highway systems (AHS), to find solutions for California transportation problems such as congestion, mobility and productivity of system, safety, air quality and environment, energy consumption, cost effectiveness and regional and state wide economic health. This paper focuses on recent activities on AHS at the California PATH. AHS will include control problems from the vehicle level to the highway network level. The topics described cover PATH work at all levels, but an emphasis is given to control problems at the vehicle level, which will offer a number of challenging opportunities to control engineers.
Tensile properties of a morphologically split supraspinatus tendon (2013)

The supraspinatus tendon consists morphologically of two sub‐regions, anterior and posterior. The anterior sub‐region is thick and tubular while the posterior is thin and strap‐like. The purpose of this study was to compare the structural and mechanical properties of the anterior and posterior sub‐regions of the supraspinatus tendon. The supraspinatus tendons from seven human cadaveric shoulders were morphologically divided into the anterior and posterior sub‐regions. Length, width, and thickness were measured. A servo‐hydraulic testing machine (MTS Systems Corporation, Minneapolis, MN) was used for tensile testing. The maximal load at failure, modulus of elasticity and ultimate tendon stress were calculated. Repeated measures were used for statistical comparisons. The mean anterior tendon cross‐sectional area was 47.3 mm 2 and the posterior was 32.1 mm 2 . Failure occurred most often at the insertion site: anterior (5/7) and posterior (6/7). All parameters of the anterior sub‐region were significantly greater than those of the posterior sub‐region. The moduli of elasticity at the insertion site were 592.4 MPa in the anterior sub‐region and 217.7 MPa in the posterior ( P = 0.01). The ultimate failure loads were 779.2 N in the anterior sub‐region and 335.6 N in the posterior ( P = 0.003). The ultimate stresses were 22.1 MPa in the anterior sub‐region and 11.6 MPa in the posterior ( P = 0.008). We recognized that the anterior and posterior sub‐regions of the SSP tendon have significantly different mechanical properties. In a future study, we need to evaluate how best to repair an SSP tendon considering these region‐specific properties. Clin. Anat. 27:702–706, 2014. © 2013 Wiley Periodicals, Inc.
IMMS: IoT Management and Monitoring System (2018)

The Internet of Things already comprehends billions of connected smart devices. The related issues are vast as well, ranging from the lack of standardized communication to big data management. This paper presents IoT Management and Monitoring System (IMMS), a solution focused on the management of big environments such as smart cities. The The proposed platform brings a novel database implementation to handle large volumes of data and provide quick responses to queries. Its design allows scalable and distributed deployments, while accepting diverse data types. The system was evaluated both in a real-world testbed, in a university campus, and a simulated environment. Results showed low CPU costs while consuming 1.1GB to store 21.5 million measurements. Besides, its scalability behaved as expected, maintaining its performance adequate as data volume increased.
The application of cationic fixing agents to cotton dyed with direct dyes under different pH conditions (1998)

The effect of application pH on the effectiveness of the conventional cationic fixing agents Matexil FC‐ER and Fixogene CXF in improving the wash fastness of the commercial direct dyes CI Direct Red 89, CI Direct Yellow 106 and CI Direct Blue 85 on cotton has been investigated. While the recommended neutral pH application resulted in improved fastness of the dyeings to the ISOC06/C2 wash fastness test, wash fastness was noticeably better when the fixing agents were applied under alkaline conditions.
The feeding ecology of the larvae of the shore fly Scatella picea (Walker) (Diptera: Ephydridae) (1981)

Larvae of the shore fly, Scatella picea (Walker) (Diptera: Ephydridae), were tested on 14 species of algae to determine the suitability of the algae as food. Survivability depended upon the ability of the larval flies to reach the adult stage. The degree of suitability of the algae varied greatly across algal taxa. R. S. Zack and B. A. Foote researched the trophic ecology of S. stagnalis (Fallén), an ephydrid species that commonly coexists with S. picea. In comparing the two flies, it was found that S. stagnalis could utilize blue–green algae as food, while this class of algae was virtually useless to S. picea. It is possible that this difference in utilization efficiency is a factor in resource partitioning between the two species of ephydrids. This difference also can be applied to the problem of taxonomy present in the genus Scatella.
Single Backside Cleaning on Silicon, Silicon Nitride and Silicon Oxide (2005)

In this study, we used an SEZ single-wafer spin-processor to develop a single backside cleaning solution able to remove any metallic or exotic contaminants by etching a few angstroms of the wafer backside, whatever its coating (no coating, Si3N4 or SiO2). An H2O:H2O2:H2SO4:HF mixture was selected because it allowed independent control of the etch rate on the 3 materials of interest, without roughening to much the silicon surface. Chemistry efficiency was then checked on wafers intentionally contaminated with various metals, and on “production wafers” contaminated during exotic materials deposition or classical copper processes.