gebhart/patrepeval huggingface dataset:
Directed Differentiation of Induced Pluripotent Stem Cells towards T Lymphocytes (2012)

Adoptive cell transfer (ACT) of antigen-specific CD8(+) cytotoxic T lymphocytes (CTLs) is a promising treatment for a variety of malignancies (1). CTLs can recognize malignant cells by interacting tumor antigens with the T cell receptors (TCR), and release cytotoxins as well as cytokines to kill malignant cells. It is known that less-differentiated and central-memory-like (termed highly reactive) CTLs are the optimal population for ACT-based immunotherapy, because these CTLs have a high proliferative potential, are less prone to apoptosis than more differentiated cells and have a higher ability to respond to homeostatic cytokines (2-7). However, due to difficulties in obtaining a high number of such CTLs from patients, there is an urgent need to find a new approach to generate highly reactive Ag-specific CTLs for successful ACT-based therapies. TCR transduction of the self-renewable stem cells for immune reconstitution has a therapeutic potential for the treatment of diseases (8-10). However, the approach to obtain embryonic stem cells (ESCs) from patients is not feasible. Although the use of hematopoietic stem cells (HSCs) for therapeutic purposes has been widely applied in clinic (11-13), HSCs have reduced differentiation and proliferative capacities, and HSCs are difficult to expand in in vitro cell culture (14-16). Recent iPS cell technology and the development of an in vitro system for gene delivery are capable of generating iPS cells from patients without any surgical approach. In addition, like ESCs, iPS cells possess indefinite proliferative capacity in vitro, and have been shown to differentiate into hematopoietic cells. Thus, iPS cells have greater potential to be used in ACT-based immunotherapy compared to ESCs or HSCs. Here, we present methods for the generation of T lymphocytes from iPS cells in vitro, and in vivo programming of antigen-specific CTLs from iPS cells for promoting cancer immune surveillance. Stimulation in vitro with a Notch ligand drives T cell differentiation from iPS cells, and TCR gene transduction results in iPS cells differentiating into antigen-specific T cells in vivo, which prevents tumor growth. Thus, we demonstrate antigen-specific T cell differentiation from iPS cells. Our studies provide a potentially more efficient approach for generating antigen-specific CTLs for ACT-based therapies and facilitate the development of therapeutic strategies for diseases.
On the Length of Programs for Computing Finite Binary Sequences (1966)

The use of Turing machines for calculating finite binary sequences is studied from the point of view of information theory and the theory of recursive functions. Various results are obtained concerning the number of instructions in programs. A modified form of Turing machine is studied from the same point of view. An application to the problem of defining a patternless sequence is proposed in terms of the concepts here developed.
Studies on Amino Acids. VIII (1957)

With the mold acylase preparation, optimal pH and relative activity to the various acyl amino acids were investigated. As a result, a difference of optimal pH was observed between acetyl and chioroacetyl derivatives. A comparison of the susceptibility disclosed that mold preparation has either a wider or loose specificity than renal acylase. Namely, besides aliphatic amino acids, the acyl derivatives of basic amino acids and aromatic amino acids were readily hydrolyzed by the mold preparation. These results indicate that the mold acylase preparation can be used for the resolution of a great variety of amino acids. As an example of this, the resolution of acetyl-DL-tryptophan was presented.
Murine T-cell response to native and recombinant protein antigens of Rickettsia tsutsugamushi (1993)

A polyclonal T-cell line with TH1 characteristics was used to assess the murine cellular immune response to native and recombinant Rickettsia tsutsugamushi antigens. Proliferation of this T-cell line was observed in response to numerous native antigen fractions, which indicates that the murine T-helper-cell response is directed at multiple scrub typhus antigens with no apparent antigenic immunodominance. Subsequent analysis of recombinant R. tsutsugamushi antigens made it possible to identify a 47-kDa scrub typhus antigen (Sta47) that was stimulatory for the polyclonal T-cell line. Recombinant clones encoding 56-, 58-, and 110-kDa antigens (Sta56, Sta58, and Sta110, respectively) were unable to induce proliferation of this T-cell line. DNA sequence analysis of the cloned rickettsial insert encoding the Sta47 protein revealed the presence of four open reading frames potentially encoding proteins of 47, 30, 18, and 13 kDa. Analysis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated and eluted fractions of lysates from the recombinant HB101(pRTS47B4.3) demonstrated that the fractions containing the 47-kDa protein as well as those containing proteins less than 18 kDa were stimulatory. Selected synthetic amphipathic peptides derived from the Sta47 antigen sequence identified a 20-amino-acid peptide that gave a 10-fold increase in T-cell proliferation over a control malarial peptide of similar length. Recognition of the 47-kDa antigen by a T-cell line with TH1 characteristics implicates this protein as one of potential importance in protection studies and future vaccine development.
Flow Control with Synthetic and Pulsed Jets: Applications to Virtual Aeroshaping, Thrust-Vectoring, and Control of Separation and Cavity Osciallations (2004)

In recent years, a promising approach to the control of wall bounded as well as free shear flows, using synthetic and pulsed jet actuators, has received a great deal of a ttention. A variety of impressive flow control results have been achieved experimentally by many researchers including the vectoring of conventional propulsive jets, modification of aerodynamic characteristics of bluff bodies, control of lift and drag of a irfoils, reduction of skin friction of a flat plate boundary layer, enhanced mixing in circular jets, and control of external as well as internal flow separation and of cavity oscillations. More recently, attempts have been made to numerically simulate som e of these flowfields. Numerically several of the above mentioned flowfields have been simulated primarily by employing the Reynolds -Averaged Navier Stokes (RANS) equations with a turbulence model and a limited few by Direct Numerical Simulation (DNS). In simulations, both the simplified boundary conditions at the exit of the jet as well as the details of the cavity and lip have been included. In this paper, we describe the results of simulations for five different flowfields dealing with virtual aeroshapin g, thrust -vectoring, interaction of a synthetic jet with a turbulent boundary layer and control of separation and cavity oscillations. These simulations have been performed using the RANS equations in conjunction with either one - or a two -equation turbulen ce model.
Membrane‐cytoskeleton interactions and the regulation of chemotactic peptide‐induced activation of human granulocytes: The effects of dihydrocytochalasin B (1985)

When N-formyl chemotactic peptides bind to granulocyte receptors at 37 degrees C they rapidly form a high-affinity ligand-receptor complex whose coisolation with cytoskeletal residues of Triton X-100-extracted cells is under cellular control [Jesaitis et al: J Cell Biol 98:1378, 1984]. Experiments were performed to investigate the significance of this coisolation. When the granulocytes were preincubated with dihydrocytochalasin B (dhCB) for 10 min at 37 degrees C and then stimulated with 50 nM N-formyl-Met-Leu-[3H]Phe, the rate of uptake of the radioligand by the cells was inhibited. Colocalization of the retained peptide with the Triton X-100 fraction of these cells was also reduced relative to this fraction of the untreated cells. This inhibition was apparent before the onset of FMLP endocytosis. The inhibition was 50% effective at 0.25 microgram dhCB/ml. Maximal inhibition (80-90%) occurred at doses of dhCB greater than 1 microgram/ml. The 90% retention of two plasma membrane markers by the cytoskeleton was marginally affected. These results support the hypothesis that coisolation of the high-affinity receptor-peptide complexes with granulocyte cytoskeletons occurs because of specific association of the complexes with the cytoskeleton at the cell surface. In addition, since these events precede internalization, they suggest that formation of the association between the ligand-receptor complex and cytoskeleton may be necessary for ligand-receptor endocytosis. Experiments were also performed to evaluate other functional consequences of cytoskeletal disruption on chemotactic peptide-stimulated functions. f-Met-Leu-Phe stimulation of O2- production was potentiated due to a prolongation of and an increase in the rate of O2- production. This potentiation had the same dose dependency as the inhibition of receptor modulation. The possible relationship of these various functions is discussed.
Lod heat lJtiicaria/angi'a: Evme for his&ermine r&met uw#Hwwt cmnt activation (1981)

A 42-,vr-old whited wmon wported o)~set in 1976 of locul pruritrrs. burning. cryhrmu. and &mu within minutes NJtcr exposure to heut With rnorP ertcw.G~e cxposurc. she orwsionull~ bud trunsient headuches und nuusen. In order to inwstigutc the etiology of this condition, hcv jbreurm was exposed to wuter at 44” C for 4 min. Within u few minutes. u lesion identicul to her spontaneously induced ones developed onl! ut the urcu exposed to hcot. Sumples of venou.) blood from this extremic demonstruted u trunsicwt rise in plusmm histumine Ie\leIs without an> sign$cunt change in serum hemolytic complement uctir~i~ or in C3, C4, or fuctw R. These ,findings suggest that this rare syndrome involves loctrl activution of mediutnr releuse from mu.\t wlls. without purticipution qf the complement sywrn.
The Fast Fourier and Hilbert-Huang Transforms: A Comparison (2006)

The conversion of time domain data via the fast Fourier (FFT) and Hilbert-Huang (HHT) transforms is compared. The FFT treats amplitude vs. time information globally as it transforms the data to an amplitude vs. frequency description. The HHT is not constrained by the assumptions of stationarity and linearity, required for the FFT, and generates both amplitude and frequency information as a function of time. The behavior and flexibility of these two transforms are examined for a number of different time domain signal types.
PRANK: motion Prediction based on RANKing (2020)

Predicting the motion of agents such as pedestrians or human-driven vehicles is one of the most critical problems in the autonomous driving domain. The overall safety of driving and the comfort of a passenger directly depend on its successful solution. The motion prediction problem also remains one of the most challenging problems in autonomous driving engineering, mainly due to high variance of the possible agent's future behavior given a situation. The two phenomena responsible for the said variance are the multimodality caused by the uncertainty of the agent's intent (e.g., turn right or move forward) and uncertainty in the realization of a given intent (e.g., which lane to turn into). To be useful within a real-time autonomous driving pipeline, a motion prediction system must provide efficient ways to describe and quantify this uncertainty, such as computing posterior modes and their probabilities or estimating density at the point corresponding to a given trajectory. It also should not put substantial density on physically impossible trajectories, as they can confuse the system processing the predictions. In this paper, we introduce the PRANK method, which satisfies these requirements. PRANK takes rasterized bird-eye images of agent's surroundings as an input and extracts features of the scene with a convolutional neural network. It then produces the conditional distribution of agent's trajectories plausible in the given scene. The key contribution of PRANK is a way to represent that distribution using nearest-neighbor methods in latent trajectory space, which allows for efficient inference in real time. We evaluate PRANK on the in-house and Argoverse datasets, where it shows competitive results.
Role of prostaglandins in fibroblast activation and fibrosis (2010)

Fibroblasts release prostaglandins and express a range of prostanoid receptors. However the importance of prostaglandins in fibroblast biology have not been fully explored. Our studies showed that the prostaglandin metabolite PGI(2) blocks the activation of fibroblasts, antagonising the induction of Ras/MEK/ERK signalling by TGFbeta. Endogenous PGI(2) acts so as to limit the activation of fibroblasts following tissue injury. By contrast PGE(2) induced in injured tissues or disease states may promote recruitment of inflammatory cells and lead to secondary activation of fibroblasts. The effects of PGI(2) on cell signaling could be manipulated to inhibit fibrosis in patients.
Hydrogen storage in carbon nanotubes: A neutron scattering investigation (2001)

Samples of closed and opened single-walled carbon nanotubes (SWNT’s) were charged with hydrogen and investigated by neutron time-of-flight spectroscopy. Contributions of H2 adsorbed by SWNT’s are observed and analyzed with respect to their microscopic dynamics for different temperatures.
Mouse conceptuses have a limited capacity to elevate the mRNA level of cellular retinoid binding proteins in response to teratogenic doses of retinoic acid (1992)

In these studies, we wished to determine the effect of teratogenic doses of retinoic acid on the expression of cellular retinoic acid binding protein I (CRABP-I) mRNA, cellular retinoic acid binding protein II (CRABP-II) mRNA, cellular retinol binding protein I (CRBP-I) mRNA, and cellular retinol binding protein II (CRBP-II) mRNA in mouse conceptuses. Levels of CRABP-II mRNA and CRBP-I mRNA were modestly elevated (2.5-fold and 1.5-fold, respectively) in 9-day gestation conceptuses following treatment of dams with 100 mg/kg b.w. of retinoic acid. These levels were elevated by 6 hr following treatment and remained elevated until 48 and 24 hr, respectively. Two other retinoids, etretinate and retinoyl beta-glucuronide, also moderately elevated CRABP-II mRNA and CRBP-I mRNA levels in conceptuses. In contrast, the levels of CRABP-I mRNA in the conceptuses remained unaffected by treatment with any of these three retinoids. These results demonstrate that conceptuses have a limited capacity to elevate the cellular retinoid binding proteins mRNA levels and presumably the synthesis of their respective proteins in response to high, teratogenic doses of retinoic acid. As a result, an excess of free retinoic acid becomes available to the nuclear retinoic acid receptors, which may lead to inappropriate gene expression and eventual maldevelopment.
Accuracy of Two Electromagnetic Soil Water Content Sensors in Saline Soils (2015)

Information on the accuracy of commercially available electromagnetic (EM) soil water content sensors in a variety of soil types and over a range of volumetric water content (VWC) and salinity levels is still limited. A laboratory study was conducted to evaluate the accuracy of the Acclima Digital Time Domain Transmissometry (TDT) and the Toro Turf Guard Frequency Domain Reflectometry (FDR) sensors in a loamy sand and a loam soil at soil salinity levels from 2 to 18 dS m−1. Overall linear association between gravimetric and sensor-determined VWC across all salinity levels revealed coefficients of determination between 0.86 and 0.97. In addition to a good linear model fit, a significant quadratic association was also detectable for the TDT sensor in loamy sand at 12 dS m−1 and in loam at 12 and 18 dS m−1. Overall, both sensors reliably measured VWC in both soil types at all salinity levels, however data suggests that different soil types require separate calibration. Moreover, accuracy of the sensor readings can be further improved if differential calibration is applied for different salinity levels. Regression analysis indicated that with increasing salinity, the Turf Guard sensors showed an upward bias (intercept for higher salinities greater than for 3 dS m−1), whereas the TDT sensor exhibited a downward bias (intercept smaller than for low salinitiy levels).
Antiresonant guiding in a poly(methyl-methacrylate) hollow-core optical fiber (2015)

Strong antiresonant reflecting optical waveguiding is demonstrated in a novel poly (methyl-methacrylate) (PMMA) hollow-core fiber. The transmission spectrum of the fiber was characterized using a supercontinuum source and it revealed distinct resonances with resonant dips as strong as ~20 dB in the wavelength range 480-900 nm, where PMMA has low absorption. The total propagation loss of the fiber was measured to have a minimum of ~45 dB m-1 at around 500 nm. The thermal sensitivity of the fiber is 256 ± 16 pm °C-1, defined as the red-shift of the resonances per °C, which is three times higher than the sensitivity of polymer fiber Bragg gratings.
Polyesters with Mesogenic Elements and Flexible Spacers in the Main Chain: A Further Investigation by Conformational Energy Calculations (1984)

Abstract PCILO conformational calculations have been carried out on several model compounds of thermotropic liquid crystalline polyesters [- OC-R1 -CO-O-R2]- where R1 = biphenyl, terphenyl and R2 = (-CH2-)3, -CH2-C(CH3)2-CH2–CH2-C(C2H5-) CH2-. The calculated structures can be compared to the X-ray crystallographic data. The conformational characteristics of the carboxyl groups are independent of the number of phenyl rings. The introduction of substituents into the flexible spacer results in a sharpening of the potential energy wells and an increase in the energy barriers.
Partial Market Liberalization and the Efficiency of Policy Reform: The Case of the European Dairy Sector (2002)

Abstract This article analyzes the efficiency of partial market liberalization and policy reform with an application to the European dairy sector. In a second best world, partial moves toward market liberalization are not always efficiency improving. We develop a general equilibrium model to investigate the efficiency implications of discrete changes in government policy. The analysis covers price and quantity instruments used in both domestic and trade policy. We derive simple cnditions under which partial market liberalization is efficiency improving. We apply the approach to agricultural policy reform in the European dairy sector and identify market liberalization scenarios that are “not” efficiency improving.
Pulse-echo system for measuring parameters of a tubular test object (1986)

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Serum Pentadecanoic Acid, A Biomarker Of Dairy Fat Intake, Is Associated With Lower Risk Of Incident Cardiovascular Disease And All-Cause Mortality In Swedish Men And Women (2017)

Serum Pentadecanoic Acid, A Biomarker Of Dairy Fat Intake, Is Associated With Lower Risk Of Incident Cardiovascular Disease And All-Cause Mortality In Swedish Men And Women
Some aspects of control loop performance monitoring (1994)

In industries where there are a great number of control loops, it would be convenient to have some tool for monitoring the performance of individual loops. This paper starts from one available approach that evaluates the control performance compared to minimum variance control. The authors show, using an example and also from industrial data, that this technique gives an inadequate measure of the performance if the aim is not stochastic control, but step disturbance rejection. Therefore, some modified criteria are proposed and a monitoring tool utilising all available techniques outlined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Changes of Pulmonary Vein Orifice Size and Location throughout the Cardiac Cycle: Dynamic Analysis Using Magnetic Resonance Cine Imaging (2005)

PV orifice size and location is not as stable as anticipated by three-dimensional mapping systems used for PV encircling left atrial ablation procedures. RF application close to the presumed orifice location should therefore be avoided to minimize the risk of PV stenosis.
Diagnosing Multiple Sclerosis: Analysis of the Output from an Adjudication Panel in the Setting of a MS Diagnostic Assay Clinical Trial (P3.184) (2014)

Objective: The objective of this study was to quantify the variance of diagnostic conclusions when MS faculty at academic centers were presented with identical clinical data about patients. Given the continued use of clinical judgement as the gold standard of diagnoses, quantifying the variability in diagnoses will be important as new diagnostic biomarkers are developed. Background: As part of a clinical trial utilizing a new diagnostic technology in MS, a diagnostic adjudication committee was formed. This committee had three MS experts from Academic MS centers review clinical data to determine if patients met criteria for MS based on the 2010 Revised McDonald Criteria. Design Methods: Patients enrolled in the study were undergoing CSF analysis as part of an evaluation for possible MS. This data was prepared by board-certified neurologists from 13 MS centers around the country. Adjudication reviewer votes were collected on identical case summaries and analyzed to determine the rate of concordance and reasons for discordance. Reviewers were given clinical data, MRI data, CSF data and clinical narratives. This data was prepared by board certified neurologists from 13 centers around the country. Patients enrolled in the study were undergoing CSF analysis as part of an evaluation for possible MS. Results: By October 2013, more than 200 subjects had been enrolled. There was 100% concordance in the diagnosis (ie 3 out of 3 adjudication votes) in only 30% of adjudicated cases. 83% of adjudicated cases had 2 of 3 adjudicators agreeing on the diagnosis and 17% had no consensus. Conclusions: Despite the existence of diagnostic criteria for multiple sclerosis, there is great heterogeneity among MS experts in the application of these criteria. This heterogeneity has significant implications for clinical trials including both therapeutic and diagnostic trials. Study Supported by: DioGenix, Inc
Radial stability of density profiles for obliquely incident light (1980)

Self-consistent steady-state plasma density profiles including the effects of the ponderomotive force for obliquely incident light have been obtained for the case of supersonic upstream flow velocity. The radial stability of these density profiles is studied in one-dimensional spherical geometry. Above a modest threshold laser field, these density profiles are found to be unstable and exhibit unsteady flow. The absorption for unstable profiles is found to vary markedly in time. Radiation and plasma waves can be trapped in density troughs which may be unstable to kink or sausage instabilities in two dimensions.
ChemInform Abstract: Arsaphosphenyl and Diphosphenyl Complexes of Chromium and Molybdenum. (1988)

Abstract The reaction of the pentamethylcyclopentadienyl‐substituted arsaphosphene (I) with the tris(acetonitrile)tricarbonyl complexes (II) affords the arsaphosphenyl complexes (IIIa) and (IIIb) via a transfer of the cyclopentadienyl ligand from As to the metal center.