gebhart/patrepeval huggingface dataset:
Prolonged Dominance of Clonally Restricted CD4+T Cells in Macaques Infected with Simian Immunodeficiency Viruses (2000)

The repertoire of functional CD4(+) T lymphocytes in human immunodeficiency virus type 1-infected individuals remains poorly understood. To explore this issue, we have examined the clonality of CD4(+) T cells in simian immunodeficiency virus (SIV)-infected macaques by assessing T-cell receptor complementarity-determining region 3 (CDR3) profiles and sequences. A dominance of CD4(+) T cells expressing particular CDR3 sequences was identified within certain Vbeta-expressing peripheral blood lymphocyte subpopulations in the infected monkeys. Studies were then done to explore whether these dominant CD4(+) T cells represented expanded antigen-specific cell subpopulations or residual cells remaining in the course of virus-induced CD4(+) T-cell depletion. Sequence analysis revealed that these selected CDR3-bearing CD4(+) T-cell clones emerged soon after infection and dominated the CD4(+) T-cell repertoire for up to 14 months. Moreover, inoculation of chronically infected macaques with autologous SIV-infected cell lines to transiently increase plasma viral loads in the monkeys resulted in the dominance of these selected CDR3-bearing CD4(+) T cells. Both the temporal association of the detection of these clonal cell populations with infection and the dominance of these cell populations following superinfection with SIV suggest that these cells may be SIV specific. Finally, the inoculation of staphylococcal enterotoxin B superantigen into SIV-infected macaques uncovered a polyclonal background underlying the few dominant CDR3-bearing CD4(+) T cells, demonstrating that expandable polyclonal CD4(+) T-cell subpopulations persist in these animals. These results support the notions that a chronic AIDS virus infection can induce clonal expansion, in addition to depletion of CD4(+) T cells, and that some of these clones may be SIV specific.
The Use of isometric transformations and bayesian estimation in compressive sensing for fMRI classification (2010)

Compressive sensing (CS) is a popular technique used to reconstruct a signal from few training examples, a problem which arises in many machine learning applications. In this paper, we introduce a technique to guarantee that our data obeys certain isometric properties. In addition, we introduce a bayesian approach to compressive sensing, which we call ABCS, allowing us to obtain complete statistics for estimated parameters. We apply these ideas to fMRI classification and find that by isometrically transforming our data, significant improvements in classification accuracy can be achieved using the LASSO and Dantzig selector methods, two standard techniques used in CS. In addition, applying the ABCS method offers improvements in classification accuracy over both LASSO and Dantzig. Finally, we find that applying both the ABCS method together with isometric transformations, we are able to achieve an error rate of 0.0%.
Majorana fermion codes (2010)

We initiate the study of Majorana fermion codes. These codes can be viewed as extensions of Kitaev's 1D model of unpaired Majorana fermions in quantum wires to higher spatial dimensions and interacting fermions. The purpose of Majorana fermion codes (MFCs) is to protect quantum information against low-weight fermionic errors, that is, operators acting on sufficiently small subsets of fermionic modes. We examine to what extent MFCs can surpass qubit stabilizer codes in terms of their stability properties. A general construction of 2D MFCs is proposed which combines topological protection based on a macroscopic code distance with protection based on fermionic parity conservation. Finally, we use MFCs to show how to transform any qubit stabilizer code to a weakly self-dual CSS code.
Verified three-way program merge (2018)

Even though many programmers rely on 3-way merge tools to integrate changes from different branches, such tools can introduce subtle bugs in the integration process. This paper aims to mitigate this problem by defining a semantic notion of conflict-freedom, which ensures that the merged program does not introduce new unwanted behaviors. We also show how to verify this property using a novel, compositional algorithm that combines lightweight summarization for shared program fragments with precise relational reasoning for the modifications. Towards this goal, our method uses a 4-way differencing algorithm on abstract syntax trees to represent different program versions as edits applied to a shared program with holes. This representation allows our verification algorithm to reason about different edits in isolation and compose them to obtain an overall proof of conflict freedom. We have implemented the proposed technique in a new tool called SafeMerge for Java and evaluate it on 52 real-world merge scenarios obtained from Github. The experimental results demonstrate the benefits of our approach over syntactic conflict-freedom and indicate that SafeMerge is both precise and practical.
Supplemental Figure S3 from MGD011, A CD19 x CD3 Dual-Affinity Retargeting Bi-specific Molecule Incorporating Extended Circulating Half-life for the Treatment of B-Cell Malignancies (2023)

&lt;p&gt;MGD011 mediated concentration-dependent cytotoxicity against CD19+ HBL-2 and Jeko-1 lymphoma cell lines&lt;/p&gt;
ITS Band Roadside to Vehicle Communications in a Highway Setting: Interim Summary (2007)

Dedicated Short Range Communications (DSRC) between automobiles and the road side stations can be accomplished in a special 75 MHz band at 5.9 GHz frequency that has been set aside for transportation use by the Federal Communications Commission (FCC). The Intelligent Transportation Society of America and the United States Department of Transportation are promoting the development of the Wireless Access in a Vehicular Environment (WAVE) IEEE 1609 protocols, which have been adopted for trial use, and the IEEE 802.11p WAVE amendment, which is being considered by the IEEE 802.11 Working Group. In the first part of an on-going California Partners for Advanced Transit and Highways (PATH) project, UCLA and UC Berkeley researchers collaborated under Task Order 5214 to develop a DSRC/WAVE test bed for testing and evaluation of the radio and communication protocol standards in the context of high-value Intelligent Transportation Systems (ITS) applications
Excimer laser photoresist stripping (1996)

A new method for stripping the most challenging photoresists on deep sub-micron technology semiconductor wafers has been developed. The method uses a combination of UV excimer laser ablation and reactive chemistry to strip the photoresist in a single dry process, eliminating the wet acids or solvents often used following ashing of high dose implantation (HDI) and reactive ion etching (RIE). The stripping process combines new removal mechanisms: chemical assisted UV excimer laser ablation/etching, laser induced chemical etching of side walls and residues, and enhanced combustion. During the laser pulses photolysis of the process gas occurs, UV laser radiation breaks the photoresist polymer chain bonds, and the photoresist (including foreign materials imbedded in it) is ablated. The combustion is ignited by the ablative impact of laser radiation and enhanced by the radicals formed during photo-thermal decomposition of the process gases. Following this process, the volatilized products and gases are evacuated. The optimum laser stripping conditions were developed to provide a wide process window for the most challenging stripping conditions, such as after HDI and RIE (metal, polysilicon), without causing damage to the wafer devices. A photoresist stripping system based on the described technology was designed and built. The system has been designated as the L-Stripper<SUP>TM</SUP> and provides stripping time of 0.15 s/(micrometer cm<SUP>2</SUP>).
Coherent Detector for Near-Angle Scattering and Polarization Characterization of Telescope Mirror Coatings (2012)

A report discusses the difficulty of measuring scattering properties of coated mirrors extremely close to the specular reflection peak. A prototype Optical Hetero dyne Near-angle Scatterometer (OHNS) was developed. Light from a long-coherence-length (&gt;150 m) 532-nm laser is split into two arms. Acousto-optic modulators frequency shift the sample and reference beams, establishing a fixed beat frequency between the beams. The sample beam is directed at very high f/# onto a mirror sample, and the point spread function (PSF) formed after the mirror sample is scanned with a pinhole. This light is recombined by a non-polarizing beam splitter and measured through heterodyne detection with a spectrum analyzer. Polarizers control the illuminated and analyzed polarization states, allowing the polarization dependent scatter to be measured. The bidirectional reflective or scattering distribution function is normally measured through use of a scattering goniometer instrument. The instrumental beam width (collection angle span) over which the scatterometer responds is typically many degrees. The OHNS enables measurement at angles as small as the first Airy disk diameter.
The Hydropathy Index of the HCDR3 Region of the B-Cell Receptor Identifies Two Subgroups of IGHV-Mutated Chronic Lymphocytic Leukemia Patients With Distinct Outcome (2021)

The HCDR3 sequences of the B-cell receptor (BCR) undergo constraints in length, amino acid use, and charge during maturation of B-cell precursors and after antigen encounter, leading to BCR and antibodies with high affinity to specific antigens. Chronic lymphocytic leukemia consists of an expansion of B-cells with a mixed immature and "antigen-experienced" phenotype, with either a mutated (M-CLL) or unmutated (U-CLL) tumor BCR, associated with distinct patient outcomes. Here, we investigated the hydropathy index of the BCR of 138 CLL patients and its association with the IGHV mutational status and patient outcome. Overall, two clearly distinct subgroups of M-CLL patients emerged, based on a neutral (mean hydropathy index of -0.1) vs. negatively charged BCR (mean hydropathy index of -1.1) with molecular features closer to those of B-cell precursors and peripheral/mature B-cells, respectively. Despite that M-CLL with neutral HCDR3 did not show traits associated with a mature B-cell repertoire, important differences in IGHV gene usage of tumor cells and patient outcome were observed in this subgroup of patients once compared to both U-CLL and M-CLL with negatively charged HCDR3 sequences. Compared to M-CLL with negatively charged HCDR3 sequences, M-CLL with neutral HCDR3 sequences showed predominance of men, more advanced stages of the disease, and a greater frequency of genetic alterations-e.g., del(17p)-together with a higher rate of disease progression and shorter time to therapy (TTT), independently of other prognostic factors. Our data suggest that the hydropathy index of the HCDR3 sequences of CLL cells allows the identification of a subgroup of M-CLL with intermediate prognostic features between U-CLL and the more favorable subgroup of M-CLL with a negatively charged BCR.
Acoustic Scattering in Dispersions * (2019)

Acoustic propagation in dispersions has interested scientists and mathematicians for very many years and sound has always fascinated human beings. As an incidental consequence of this work on acoustics, Rayleigh derived the famous long wavelength limit result, which explains the blue colour of the sky. P. Lloyd and M. V. Berry were really interested in the density of electron states in disordered materials and their result for acoustic scattering appears almost incidentally. The chapter shows that R. E. Kleinman’s iterative solution to the Helmholtz equation can easily be generalised to the case of two coupled fields and two Helmholtz equations in the more complex problem of thermo-acoustic scattering. Very many solid systems, especially soft solids, can be viewed as systems of particles interacting through forces of the same order as those present in acoustic fields. Thus acoustic, electromagnetic, neutron and electron scattering all have a common mathematical basis.
A 13 kV 4H-SiC n-Channel IGBT with Low R<sub>diff,on </sub>and Fast Switching (2008)

For the first time, high power 4H-SiC n-IGBTs have been demonstrated with 13 kV blocking and a low Rdiff,on of 22 mWcm2 which surpasses the 4H-SiC material limit for unipolar devices. Normally-off operation and &gt;10 kV blocking is maintained up to 200oC base plate temperature. The on-state resistance has a slight positive temperature coefficient which makes the n-IGBT attractive for parallel configurations. MOS characterization reveals a low net positive fixed charge density in the oxide and a low interface trap density near the conduction band which produces a 3 V threshold and a peak channel mobility of 18 cm2/Vs in the lateral MOSFET test structure. Finally, encouraging device yields of 64% in the on-state and 27% in the blocking indicate that the 4H-SiC n-IGBT may eventually become a viable power device technology.
Harmonic Performance Analysis of an OPWM-Controlled STATCOM in Network Applications (2005)

The method of selective harmonic elimination is often used as an efficient means for obtaining harmonic-reduced waveforms from voltage sourced converters (VSC). However, the switching angles required for its implementation are usually pre-calculated on the basis of a fixed dc bus voltage. In practice, there are harmonics present in the dc source because of the finite dc bus capacitance and other realistic operating conditions, which can potentially introduce additional noncharacteristic harmonics. This paper examines the harmonic performance of a VSC-based static synchronous compensator as a function of design and operating parameters. These include the value of dc capacitor, the strength of the connected ac network and ac system unbalance. The results are generated using theoretical analysis for special cases and numerical simulation using electromagnetic transients simulation for the more general case.
A system for contact free energy expenditure assessment under free-living conditions: monitoring metabolism for weight loss using carbon dioxide emission (2020)

Weight disorders are strikingly prevalent globally and can contribute to a wide array of potentially fatal diseases spanning from type II diabetes to coronary heart disease. These disorders have a common cause: poor calorie balance. Since energy expenditure (EE) (kcal d<sup>-1</sup>) constitutes one half of the calorie balance equation (the other half being food intake), its measurement could be of great value to those suffering from weight disorders. A technique for contact free assessment of EE is presented, which only relies on CO<sub>2</sub>concentration monitoring within a sealed office space, and assessment of carbon dioxide production rate (VCO<sub>2</sub>). Twenty healthy subjects were tested in a cross-sectional study to evaluate the performance of the aforementioned technique in measuring both resting EE (REE) and exercise EE using the proposed system (the 'SmartPad') and a U.S. Food and Drug Administration (FDA) cleared gold standard reference instrument for EE measurement. For VCO<sub>2</sub>and EE measurements, the method showed a correlation slope of 1.00 and 1.03 with regression coefficients of 0.99 and 0.99, respectively, and Bland-Altman plots with a mean bias = -0.232% with respect to the reference instrument. Furthermore, two subjects were also tested as part of a proof-of-concept longitudinal study where EE patterns were simultaneously tracked with body weight, sleep, stress, and step counts using a smartwatch over the course of a month, to determine correlation between the aforementioned parameters and EE. Analysis revealed moderately high correlation coefficients (Pearson's<i>r</i>) for stress (<i>r</i><sub>average</sub>= 0.609) and body weight (<i>r</i><sub>average</sub>= 0.597) for the two subjects. The new SmartPad method was demonstrated to be a promising technique for EE measurement under free-living conditions.
Ultrasensitive, visible tunable diode laser detection of NO_2 (1996)

Recent advances in room-temperature visible diode lasers and ultrasensitive detection techniques have been exploited to create a highly sensitive tunable diode laser absorption technique for in situ monitoring of NO(2) in the lower troposphere. High sensitivity to NO(2) is achieved by probing the visible absorption band of NO(2) with an AlGalnP diode laser at 640 or 670 nm combined with a balanced ratiometric electronic detection technique. We have demonstrated a sensitivity of 3.5 × 10(10) cm(-3) for neat NO(2) in a 1-m path at 640 nm and have estimated a sensitivity for ambient operation of 5 ppbv m (l0 ppbv m at 670 nm), where ppbvm is parts in 10(9) by volume per meter of absorption path length, from measured pressure-broadening coefficients.
The mechanisms of inhibition of human IL 2 production. II. PGE2 induction of suppressor T lymphocytes. (1984)

In vitro and in vivo experiments indicate that the production of interleukin 2 (IL 2) by T lymphocytes is critical for the development of the effector phase of immunity. Complex cellular interactions are involved for the induction of IL 2 production. We have shown in a previous study that in humans monocytes can transmit opposite signals to the IL 2-producing cells. In addition to the positive signal delivered through the release of interleukin 1, human monocytes can deliver a negative signal through the release of prostaglandin E2 (PGE2). This monokine, known to activate suppressor mechanisms in several systems, was shown to inhibit IL 2 production. The data presented in this paper show that this PGE2-dependent inhibition is strictly dependent upon the presence of radiosensitive T cells in the culture, suggesting that PGE2 induces the activation of suppressor T cells modulating IL 2 production. Kinetics experiments indicate that these suppressor cells are radiosensitive during their induction phase but become radioresistant after 18 hr of incubation in the presence of PGE2. Successful in vitro induction of suppressor cells by incubation of enriched T cells with PGE2 was decisive for the analysis of the phenomenon. The induced suppressors were capable of inhibiting IL 2 production by fresh autologous T cells as well as inhibiting PHA proliferative response by these cells. A quantitative evaluation of IL 2 receptors on PGE2-treated cells has indicated that this absorption capacity was similar to the capacity of PBL known to express a low number of IL 2 receptors, thus excluding a suppression via absorption or competition for IL 2. No detectable killing of IL 2-producing cells by PGE2-induced suppressors was observed. The OKT4 and OKT8 phenotype of suppressor cells was examined. T cells were purified at two stages of differentiation before or after induction by PGE2 in vitro treatment. We conclude from these experiments that PGE2 activates suppressor cells among precursors segregating predominantly with the OKT8 subset and fewer cells with the OKT4 subset. After differentiation, however, the suppressor cells segregate with the OKT8 subset only. Such results were obtained by using positive selection (cellular affinity columns) and negative selection (monoclonal antibodies plus complement).
Supplementary Figure 4 from Low Levels of Circulating Estrogen Sensitize PTEN-Null Endometrial Tumors to PARP Inhibition <i>In Vivo</i> (2023)

&lt;p&gt;PDF file - 139K, Figure S4. Three-dimensional in vitro model for growth and treatment of PTEN-null epithelia co-cultured with WT endometrial stroma.&lt;/p&gt;
07291 Abstracts Collection – Scientific Visualization (2008)

From 06-14-2009 to 06-19-2009, the Dagstuhl Seminar 09251 ``Scientific Visualization '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, over 50 international participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general.
Multichannel SQUID Magnetoneurograph System for Functional Imaging of Spinal Cords and Peripheral Nerves (2021)

We developed a superconducting quantum interference device (SQUID)-based biomagnetometer system for magnetoneurograms. The system was improved from a previously reported prototype magnetospinograph (MSG)/neurograph (MNG) system to satisfy the additional requirements that arose when we investigated practical clinical applications of the MSG/MNG in a hospital. The dimensions of the vector-type SQUID flux sensor array were increased to 150 mm × 188 mm, and the shape of the cryostat was modified so that the peripheral nerves at different body parts of a subject who assumed various postures, including positions provoking neurological symptoms, could be examined. In this paper, the improved MNG system is described in detail. Functional imaging of the brachial plexuses of subjects whose arms were in the abduction and external rotation position, which is one of the typical symptom-provocative positions for the shoulder, was achieved using the improved MNG system.
Origin of the resonant dependence of the instability current in a magnetic field (1985)

The instability current in the case of Sn--I--Sn tunnel junctions in weak magnetic fields is investigated in detail. (AIP)
Deep nulling of visible laser light (1999)

Nulling interferometry, a proposed technique for dimming a star relative to its surroundings by destructively interfering the light collected by two individual telescopes [Bracewell, Nature 274, 780-781 (1978); Shao and Colavita, Ann. Rev. Astron. Astrophys. 30, 457-498 (1992)], has the potential to permit the direct detection of nearby extrasolar planets. However, because of the extremely high degree of symmetry required for useful levels of starlight nulling, the technique remains in its infancy. We present results of laboratory experiments with a rotational shearing interferometer that are aimed at demonstrating the feasibility of deep nulling at the levels needed for direct planet detection. Our first results include the successful nulling of red laser light to a part in 10(5) and the stabilization of the null leakage to a part in 10(4).
Visco-Elastic Settling Rate Models to Determine Sag Potential of Non-Aqueous Drilling Fluids (2013)

One of less-understood phenomena in invert-emulsion non-aqueous drilling fluids (NAF) is sag that leads to unwanted density variations. Sag is considered to be a static as well as dynamic phenomenon and can become severe for highly deviated/complex wells. To understand and tackle this issue, there has been need for experimental techniques and empirical methods to predict sag for different well environments and fluid compositions. A method for quantitatively determining the solids settling rate in a NAF under shear is presented in this paper. The method is based on empirical equation which is a modified form of Stoke’s Law that considers effects of viscous as well as elastic properties of NAF on solids settling rate. For building and validating the empirical equation, viscosity is measured using conventional oilfield viscometers while the elastic properties of fluid under shear in form of the first normal stress difference N1 are measured using an advanced rheometer. This is combined with experimental data on solids settling rate U(mm/hr) in NAF obtained from using the Dynamic High Angle Sag Tester (DHAST TM ) instrument at specified conditions of temperature, pressure and shear rate. A method to make an accurate determination of sag in the field has been an unresolved need for a long time. This method may be used readily for accurate solids settling rate predictions using the rheology data under relevant conditions of temperature, pressure and shear. The model could serve as a handy tool to mud engineers to evaluate the sag behavior at given well conditions and to make speedy decisions at the rig site to optimize fluid formulations for sag management.