gebhart/patrepeval huggingface dataset:
Magnetic Particle Imaging: A Novel in Vivo Imaging Platform for Cancer Detection (2017)

Cancer remains one of the leading causes of death worldwide. Biomedical imaging plays a crucial role in all phases of cancer management. Physicians often need to choose the ideal diagnostic imaging modality for each clinical presentation based on complex trade-offs among spatial resolution, sensitivity, contrast, access, cost, and safety. Magnetic particle imaging (MPI) is an emerging tracer imaging modality that detects superparamagnetic iron oxide (SPIO) nanoparticle tracer with high image contrast (zero tissue background signal), high sensitivity (200 nM Fe) with linear quantitation, and zero signal depth attenuation. MPI is also safe in that it uses safe, in some cases even clinically approved, tracers and no ionizing radiation. The superb contrast, sensitivity, safety, and ability to image anywhere in the body lends MPI great promise for cancer imaging. In this study, we show for the first time the use of MPI for in vivo cancer imaging with systemic tracer administration. Here, long circulating MPI-tailored SPIOs were created and administered intravenously in tumor bearing rats. The tumor was highlighted with tumor-to-background ratio of up to 50. The nanoparticle dynamics in the tumor was also well-appreciated, with initial wash-in on the tumor rim, peak uptake at 6 h, and eventual clearance beyond 48 h. Lastly, we demonstrate the quantitative nature of MPI through compartmental fitting in vivo.
Fluorescent Star-Shaped Polystyrenes: “Core-First” Synthesis from Perylene-Based ATRP Initiators and Dynamic Mechanical Solid-State Properties (2002)

This paper describes the synthesis of two novel tetra 2-bromoisobutyric acid-substituted perylene fluorophores and their use as initiators for the atom transfer radical polymerization of styrene. Different star-shaped polystyrenes covering a wide range of molecular weights were prepared by variations in the initial molar ratio between styrene and the perylene chromophores. Bulk properties of the star polymers were investigated by X-ray scattering, differential scanning calorimetry, and dynamic mechanical measurements. These studies revealed that the polystyrene arms effectively suppress the aggregation of the perylene chromophores and indicated that, especially at low degrees of polymerization, the rigid-core moiety significantly affects the segmental dynamics of the arms. Spin-casting of the polystyrene stars afforded optically transparent films, which displayed high fluorescent quantum yields. Due to the covalent linkage between the polystyrene chains and the perylene chromophore, the dye-contents of such films can be much higher than those achievable by dissolution of the corresponding low-molar-mass perylene dye in a polystyrene matrix. In addition, the polystyrene arms are likely to reduce the mobility of the chromophore within a polystyrene matrix. These features make these fluorescent star-shaped polymers of interest to improve the migration fastness of colored polystyrene samples.
Point Mutagenesis and Cocrystallization of Wild-Type and Mutant Proteins:  A Study of Solid-Phase Coexistence in Two-Dimensional Protein Arrays (2001)

We are studying the molecular organization of protein arrays using two-dimensional streptavidin crystals bound to biotinylated lipid monolayers at the air−water interface. We constructed a mutant form of the streptavidin protein that successfully alters the molecular organization of the streptavidin crystals. Cocrystallization of streptavidin carrying this single targeted point mutation with wild-type streptavidin yields two-dimensional crystals displaying a chiral morphology with molecular coexistence, indicating a solid-phase transition. The phase coexistence and resulting morphologies are reminiscent of two-dimensional crystal behavior of wild-type streptavidin near its isoelectric point, and this analogy is discussed. These results demonstrate the potential to manipulate protein array formation through point mutagenesis and cocrystallization.
A nuclear gene, erd1, encoding a chloroplast‐targeted Clp protease regulatory subunit homolog is not only induced by water stress but also developmentally up‐regulated during senescence in Arabidopsis thaliana (1997)

A cDNA, ERD1, isolated from one-hour-dehydrated plants of Arabidopsis thaliana L. encodes a putative protein that is similar to the regulatory ATPase subunit (ClpA) of the Clp protease and contains a putative chloroplast-targeting transit-peptide at the N-terminus. A chimeric gene with the putative plastid-targeting sequence of the erd1 gene fused to the synthetic green-fluorescent protein (sGFP) gene was constructed and introduced into Arabidopsis protoplasts. The N-terminal region of the ERD1 protein directed the sGFP protein into the plastids of the protoplasts, and functioned as a transit peptide. Northern blot analysis indicated that expression of the erd1 gene was induced not only by water stress, such as dehydration and high salinity, but also by natural senescence and dark-induced etiolation. The erd1 gene was not strongly induced by exogenous abscisic acid. A chimeric gene with the 0.9 kb promoter region of the erd1 gene fused to the beta-glucuronidase (GUS) reporter gene was constructed, and tobacco plants transformed with the construct. The GUS reporter gene driven by the erd1 promoter was induced by dehydration and high salt stress at significant levels in the transgenic plants. The GUS gene was strongly expressed in older leaves without dehydration, and was induced by dark-induced etiolation. Furthermore, GUS activity was reduced by cytokinin treatment during dark-induced etiolation. These results indicate that expression of the erd1 gene is developmentally up-regulated by senescence as well as by water stress.
The role of liquid phase epitaxy during growth of AlGaN by MBE (2011)

Abstract We propose that the growth of III‐Nitride semiconductors by plasma‐assisted MBE under Ga‐rich conditions takes place though the saturation of the liquid Ga covering the surface of the growing film with nitrogen, alloy constituents (aluminum and indium) and impurities. Thus, the proposed growth mode is a liquid phase epitaxy (LPE) rather than physical vapor phase epitaxy. While in traditional LPE growth the driving force is the gradient between the liquid and seed, in the proposed mode of MBE growth of nitrides the driving force is the concentration gradient due to the constant supply of active nitrogen, alloy components and impurities. The proposed LPE growth mechanism explains the relative temperature stability of GaN growth, the efficient doping with silicon and magnesium, and the selective desorption of oxygen and other impurities. Finally, the proposed LPE growth model can also account for the introduction of band structure potential fluctuations in AlGaN alloys, which improves their emission properties and leads to efficient deep UV‐LEDs. (© 2012 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Factors Associated with Quality of Life Among Older Adults with Chronic Disease in Taiwan (2016)

Background: There have been many studies reviewing quality of life (QoL) of older population and found an inverse association between QoL and chronic diseases. However, previous studies have focused only on that of people with specific diseases. In this study, we identified critical quality of life determinants, especially risk for disability, in older adults suffering from chronic diseases. Methods: A cross-sectional, correlational design was used. A purposive sample of 115 older patients, diagnosed with co-morbidity was recruited from an outpatient medical center in Southern Taiwan. Results: Results of a stepwise multiple regression analysis indicated that the overall regression model explained 49% of the variance in QoL. After controlling the sociodemographic factors and health status of older patients, the risk for disabilities in social isolation and depression were negatively correlated with QoL. Alzheimer disease-8 (AD-8) had the strongest association with the total QoL score, and it alone explained 27% of the variance. Conclusion: Understanding the importance of determining factors of poor QoL, such as potential cognitive impairment, potential social isolation and depression, inadequate family income, and diminished ability to perform practical and social activities (IADLs) among older adults with chronic diseases is critical for geriatric health care providers. Awareness of these factors can assist providers in identifying people at risk and guide new intervention programs to improve care for these invaluable members of our communities.
Evaluating Human Embryonic Germ Cells: Concord and Conflict as Pluripotent Stem Cells (2005)

The realization of cell replacement therapy derived from human pluripotent stem cells requires full knowledge of the starting cell types as well as their differentiated progeny. Alongside embryonic stem cells, embryonic germ cells (EGCs) are an alternative source of pluripotent stem cell. Since 1998, four groups have described the derivation of human EGCs. This review analyzes the progress on derivation, culture, and differentiation, drawing comparison with other pluripotent stem cell populations.
Cytokine Response Patterns in Severe Pandemic 2009 H1N1 and Seasonal Influenza among Hospitalized Adults (2011)

A hyperactivated proinflammatory, but suppressed adaptive-immunity (Th1/Th17)-related cytokine response pattern was found in severe pH1N1 pneumonia, different from seasonal influenza. Cytokine/immune-dysregulation may be important in its pathogenesis.
Isolation of Murine Macrophages (1994)

Macrophages isolated from murine peritoneal cavity, bone marrow, and spleen are suitable samples for studying the activation properties of this immunologically important cell type. This unit describes the isolation of murine macrophages from the peritoneal cavity under inflammatory and noninflammatory conditions. To investigate macrophage activation using a more homogeneous population of cells, macrophages derived from immature progenitor cells in bone marrow can be studied. A second protocol describes the isolation of bone marrow-derived progenitor cells and propagation of these immature macrophages by CSFs or IL-3.
Magic-state distillation with the four-qubit code (2012)

The distillation of magic states is an often-cited technique for enabling universal quantum computing once the error probability for a special subset of gates has been made negligible by other means. We present a routine for magic-state distillation that reduces the required overhead for a range of parameters of practical interest. Each iteration of the routine uses a four-qubit error-detecting code to distill the +1 eigenstate of the Hadamard gate at a cost of ten input states per two improved output states. Use of this routine in combination with the 15-to-1 distillation routine described by Bravyi and Kitaev allows for further improvements in overhead.
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 (2003)

We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function.
Neuropilin‐1 expression identifies a subset of regulatory T cells in human lymph nodes that is modulated by preoperative chemoradiation therapy in cervical cancer (2007)

We examined the phenotype and function of CD4+ T cells expressing the semaphorin III receptor neuropilin-1 (Nrp1) in human lymph nodes and peripheral blood. In lymph nodes, Nrp1 identified a small regulatory CD4+ CD25(high) T-cell subpopulation (Nrp1+ Treg) that expressed higher levels of Forkhead box P3 (Foxp3) message and protein than Nrp1- Treg, and various molecular markers of activated Treg, i.e. CD45RO, human leucocyte antigen (HLA)-DR and glucocorticoid-induced tumour necrosis factor receptor (GITR). Similarly to conventional Treg, Nrp1+ Treg proliferated poorly in vitro, and exerted contact-dependent in vitro suppression of T-cell proliferation and cytokine secretion. However, Nrp1+ Treg were more efficient than Nrp1- Treg at inducing suppression. Nrp1 was also expressed on a small subpopulation of CD25(int) and CD25- CD4+ T cells that expressed more Foxp3, CD45RO, HLA-DR and GITR than their Nrp1- counterparts. In contrast, in peripheral blood Nrp1 identified a minor CD4+ T-cell subset that did not display the phenotypic features of Treg lacking Foxp3 expression and marginally expressing CD25. Hence, the function of Nrp1+ CD4+ T cells seemingly depends on their anatomical location. In a previous report, we proposed that Treg may curb the anti-tumour T-cell response in cervical cancer. We show here that Treg and Nrp1+ Treg levels dropped in the tumour-draining lymph nodes of patients with cervical cancer following preoperative chemoradiotherapy in a direct relationship with the reduction of tumour mass, suggesting that suppressor cell elimination facilitated the generation of T cells mediating the destruction of the neoplastic cells left behind after cytotoxic therapy.
Noninvasive prenatal diagnosis of chromosomal aneuploidies by isolation and analysis of fetal cells from maternal blood (2001)

The isolation and analysis of nucleated fetal cells (NFCs) from maternal blood may represent a new approach to noninvasive prenatal diagnosis. Although promising, these techniques require highly accurate separation of NFCs from nucleated cells of maternal origin; the two major problems limiting these techniques are the relative rarity of fetal cells in maternal blood and the need to establish their fetal origin. We now report a novel procedure that has allowed accurate separation of NFCs from maternal cells. The technique reported involves direct micromanipulator isolation of histochemically identified hemoglobin F-positive nucleated cells to obtain fetal nucleated red blood cells (FNRBCs) of high yield and purity. Using this technique, followed by cell-by-cell multicolor fluorescence in situ hybridization (FISH) analysis of purified FNRBCs, we were able to detect some of the most common human aneuploidies (including Down syndrome, Klinefelter syndrome, and trisomy 13) in 33 pregnant women referred for amniocentesis. The procedure used, which can be completed in <72 hrs, produced complete concordance with the results of amniocentesis. We also confirm findings of prior studies suggesting that the number of FNRBCs in maternal circulation is remarkably higher in abnormal pregnancies than in normal pregnancies, especially in women carrying a fetus with trisomy 21.
Ghost Talk: Mitigating EMI Signal Injection Attacks against Analog Sensors (2013)

Electromagnetic interference (EMI) affects circuits by inducing voltages on conductors. Analog sensing of signals on the order of a few millivolts is particularly sensitive to interference. This work (1) measures the susceptibility of analog sensor systems to signal injection attacks by intentional, low-power emission of chosen electromagnetic waveforms, and (2) proposes defense mechanisms to reduce the risks. Our experiments use specially crafted EMI at varying power and distance to measure susceptibility of sensors in implantable medical devices and consumer electronics. Results show that at distances of 1-2m, consumer electronic devices containing microphones are vulnerable to the injection of bogus audio signals. Our measurements show that in free air, intentional EMI under 10 W can inhibit pacing and induce defibrillation shocks at distances up to 1-2m on implantable cardiac electronic devices. However, with the sensing leads and medical devices immersed in a saline bath to better approximate the human body, the same experiment decreases to about 5 cm. Our defenses range from prevention with simple analog shielding to detection with a signal contamination metric based on the root mean square of waveform amplitudes. Our contribution to securing cardiac devices includes a novel defense mechanism that probes for forged pacing pulses inconsistent with the refractory period of cardiac tissue.
A New Calculus for the Treatment of Optical SystemsI Description and Discussion of the Calculus (1941)

The effect of a plate of anisotropic material, such as a crystal, on a collimated beam of polarized light may always be represented mathematically as a linear transformation of the components of the electric vector of the light. The effect of a retardation plate, of an anisotropic absorber (plate of tourmaline; Polaroid sheeting), or of a crystal or solution possessing optical activity, may therefore be represented as a matrix which operates on the electric vector of the incident light. Since a plane wave of light is characterized by the phases and amplitudes of the two transverse components of the electric vector, the matrices involved are two-by-two matrices, with matrix elements which are in general complex. A general theory of optical systems containing plates of the type mentioned is developed from this point of view.
Disruption of Ledgf/Psip1 Results in Perinatal Mortality and Homeotic Skeletal Transformations (2006)

PC4- and SF2-interacting protein 1 (Psip1)-also known as lens epithelium-derived growth factor (Ledgf)-is a chromatin-associated protein that has been implicated in transcriptional regulation, mRNA splicing, and cell survival in vitro, but its biological function in vivo is unknown. We identified an embryonic stem cell clone with disrupted Psip1 in a gene trap screen. The resulting Psip1-betageo fusion protein retains chromatin-binding activity and the PWWP and AT hook domains of the wild-type protein but is missing the highly conserved C terminus. The majority of mice homozygous for the disrupted Psip1 gene died perinatally, but some survived to adulthood and displayed a range of phenotypic abnormalities, including low fertility, an absence of epididymal fat pads, and a tendency to develop blepharitis. However, contrary to expectations, the lens epithelium was normal. The mutant mice also exhibited motor and/or behavioral defects such as hind limb clenching, reduced grip strength, and reduced locomotor activity. Finally, both Psip1(-/-) neonates and surviving adults had craniofacial and skeletal abnormalities. They had brachycephaly, small rib cages, and homeotic skeletal transformations with incomplete penetrance. The latter phenotypes suggest a role for Psip1 in the control of Hox expression and may also explain why PSIP1 (LEDGF) is found as a fusion partner with NUP98 in myeloid leukemias.
Liver X receptor in cholesterol metabolism (2009)

The liver X receptors (LXRs) are nuclear receptors that are activated by endogenous oxysterols, oxidized derivatives of cholesterol. There are two isoforms of LXR, LXRalpha (NR1H3) and LXRbeta (NR1H2). Both LXRalpha and LXRbeta regulate gene expression by binding to DNA sequences associated with target genes as heterodimers with isoforms of the retinoid X receptor (RXR), RXRalpha (NR2B1), RXRbeta (NR2B2), and RXRgamma (NR2B3). LXRs act as cholesterol sensors: when cellular oxysterols accumulate as a result of increasing concentrations of cholesterol, LXR induces the transcription of genes that protect cells from cholesterol overload. In this review, we summarize the roles of LXRs in controlling cholesterol homeostasis, including their roles in bile acid synthesis and metabolism/excretion, reverse cholesterol transport, cholesterol biosynthesis and uptake, and cholesterol absorption/excretion in the intestine. The overlapping and distinct roles of the LXRalpha and LXRbeta isoforms, and the potential use of LXRs as attractive targets for treatment of cardiovascular disease are also discussed.
The product of the ataxia-telangiectasia group D complementing gene, ATDC, interacts with a protein kinase C substrate and inhibitor. (1995)

Ataxia-telangiectasia (AT) is an autosomal recessive human genetic disease characterized by immunological, neurological, and developmental defects and an increased risk of cancer. Cells from individuals with AT show sensitivity to ionizing radiation, elevated recombination, cell cycle abnormalities, and aberrant cytoskeletal organization. The molecular basis of the defect is unknown. A candidate AT gene (ATDC) was isolated on the basis of its ability to complement the ionizing radiation sensitivity of AT group D fibroblasts. Whether ATDC is mutated in any AT patients is not known. We have found that the ATDC protein physically interacts with the intermediate-filament protein vimentin, which is a protein kinase C substrate and colocalizing protein, and with an inhibitor of protein kinase C, hPKCI-1. Indirect immunofluorescence analysis of cultured cells transfected with a plasmid encoding an epitope-tagged ATDC protein localizes the protein to vimentin filaments. We suggest that the ATDC and hPKCI-1 proteins may be components of a signal transduction pathway that is induced by ionizing radiation and mediated by protein kinase C.
Stretchable GaAs Photovoltaics with Designs That Enable High Areal Coverage (2011)

Strategies are presented for achieving, simultaneously, both large areal coverage and high stretchability by using elastomeric substrates with surface relief in geometries that confine strains at the locations of the interconnections, and away from the devices. The studies involve a combination of theory and experiment to reveal the essential mechanics, and include demonstrations of the ideas in stretchable solar modules that use ultrathin, single junction GaAs solar cells.
Ablation of Neuropilin 1 in Myeloid Cells Exacerbates High-Fat Diet–Induced Insulin Resistance Through Nlrp3 Inflammasome In Vivo (2017)

Neuropilin 1 (Nrp1), a coreceptor for class 3 semaphorins and growth factors, is highly expressed in vascular cells and myeloid cells, including macrophages. Unlike well-characterized proangiogenic functions of endothelial cell Nrp1, the contributions of macrophage Nrp1 within the context of metabolic dysfunction remain to be established. The aim of this study was to determine the contributions of macrophage Nrp1 in high-fat diet (HFD)-instigated insulin resistance in vivo. Insulin sensitivity and Nlrp3 inflammasome activation were monitored in wild-type (WT) and myeloid cell-specific Nrp1 knockout (Nrp1<sup>myel-KO</sup>) mice fed an HFD (60% kcal) for 16 weeks. HFD-fed mice exhibited insulin resistance with reduced levels of Nrp1 in macrophages compared with chow-fed mice. Further, HFD-fed Nrp1<sup>myel-KO</sup> mice displayed accentuated insulin resistance, enhanced systemic inflammation, and dramatically increased Nlrp3 inflammasome priming and activation. Importantly, knockout of Nlrp3 ablated HFD-induced insulin resistance and inflammation in Nrp1<sup>myel-KO</sup> mice, indicating that Nrp1 reduction in macrophages instigates insulin resistance by increasing macrophage Nlrp3 inflammasome activation. Mechanistically, Nrp1 deletion activates the nuclear factor-κB pathway, which in turn accentuates the priming of Nlrp3, promotes Nlrp3-ASC inflammasome assembly, and results in the activation of Nlrp3. We conclude that the HFD-instigated Nrp1 reduction in macrophages exacerbates insulin resistance by promoting Nlrp3 inflammasome priming and activation.