gebhart/patrepeval huggingface dataset:
Comparison of propagation- and grating-based x-ray phase-contrast imaging techniques with a liquid-metal-jet source (2014)

X-ray phase-contrast imaging has been developed as an alternative to conventional absorption imaging, partly for its dose advantage over absorption imaging at high resolution. Grating-based imaging (GBI) and propagation-based imaging (PBI) are two phase-contrast techniques used with polychromatic laboratory sources. We compare the two methods by experiments and simulations with respect to required dose. A simulation method based on the projection approximation is designed and verified with experiments. A comparison based on simulations of the doses required for detection of an object with respect to its diameter is presented, showing that for monochromatic radiation, there is a dose advantage for PBI for small features but an advantage for GBI at larger features. However, GBI suffers more from the introduction of polychromatic radiation, in this case so much that PBI gives lower dose for all investigated feature sizes. Furthermore, we present and compare experimental images of biomedical samples. While those support the dose advantage of PBI, they also highlight the GBI advantage of quantitative reconstruction of multimaterial samples. For all experiments a liquid-metal-jet source was used. Liquid-metal-jet sources are a promising option for laboratory-based phase-contrast imaging due to the relatively high brightness and small spot size.
High-Speed 1-Frame /ms Scanning Confocal Microscope with a Microlens and Nipkow Disks (2002)

We have developed a high-speed confocal laser microscope. A microlens-array disk set in front of a pinhole-array disk improved optical efficiency more than ten times compared with that of conventional Nipkow confocal microscopy. This new microscope achieves a high-speed measurement of 1 frame/ms. We expect that it will be used for measuring biological and industrial active samples.
Laser surface alloying (1985)

AbstractAbstractLaser alloying is a material-processing method which utilizes the high power density available from focused laser sources to melt metal coatings and a portion of the underlying substrate. Since the melting occurs in a very short time and only at the surface, the bulk of the material remains cool, thus serving as an infinite heat sink. Large temperature gradients exist across the boundary between the melted surface region and the underlying solid substrate. This results in rapid self-quenching and resolidification. Quench rates as great as 1011 KS-l and concomitant resolidification velocities of 20m S-l have already been achieved. What makes laser surface alloying both attractive and interesting is the wide variety of chemical and microstructural states that can be retained because of the rapid quench from the liquid phase. These include chemical profiles where the 'alloyed' element is highly concentrated near the atomic surface and decreases in concentration over shallow depths (hundreds of nanometres), and uniform profiles where the concentration is the same throughout the entire melted region. The types of microstructures observed include extended solid solutions, metastable crystalline phases, and metallic glasses.
NR4A Orphan Nuclear Receptor Family in Peripheral Blood Eosinophils from Patients with Atopic Dermatitis and Apoptotic Eosinophils in vitro (2005)

To identify novel genes related to the clinical signs of atopic dermatitis (AD), differentially expressed genes were sought in peripheral blood eosinophils from both AD patients and healthy volunteers. RNA was prepared from eosinophils, expression of various genes was monitored using the Affymetrix GeneChip, and expression was quantified by real-time RT-PCR. Two genes, Nur77 and NOR1, members of NR4A orphan nuclear receptor family, were expressed at a significantly higher level in AD patients than in healthy volunteers. Expression of another gene in the NR4A receptor family, Nurr1, was also higher in AD patients than in healthy volunteers. When peripheral blood leukocytes from healthy volunteers were fractionated, NOR1 expression was highest in eosinophils, but expression of Nur77 and Nurr1 genes was not eosinophil-specific. Extremely intense apoptosis was induced in both eosinophils and an eosinophil cell line, AML14.3D10, by treatment with antibody (Ab) to both CD30 and Fas. Rapid expression of the genes for the NR4A receptor family was observed with anti-CD30 Ab treatment but not with anti-Fas Ab. The NR4A orphan nuclear receptor family gene expression and the subsequent eosinophil apoptosis were downregulated by the MAPK inhibitor, U0126. These results suggest that the expression of the NR4A receptor family genes through CD30 signaling may regulate eosinophil apoptosis in allergic conditions such as AD.
Evaluation of human diacylglycerol kinase(iota), DGKI, a homolog of Drosophila rdgA, in inherited retinopathy mapping to 7q. (2000)

No evidence of disease-associated mutations was found in any of the samples tested. Based on the linkage data and mutation screening, diacylglycerol kinase(iota) is excluded as a candidate for the RP10 form of adRP and cannot be a frequent cause of other forms of adRP. Mutations in diacylglycerol kinase(iota) may yet be the cause of recessive forms of retinal degeneration in humans, either in homozygous or compound heterozygous forms. The data provided here will permit testing of this hypothesis.
Prepupal and Pupal Parasitism of Helicoverpa zea and Spodoptera frugiperda (Lepidoptera: Noctuidae) by Steinernema sp. in Cornfields in the Lower Rio Grande Valley (1992)

An indigenous Steinernema sp. (Rhabditida: Steinernematidae) nematode parasitized prepupae and pupae of corn earworm, Helicoverpa zea (Boddie), and fall armyworm, Spodoptera frugiperda (J. E. Smith), collected from fruiting cornfields in the Lower Rio Grande Valley of Texas and northern Tamaulipas, Mexico. Over a 5-yr period, 34% of all fields sampled contained parasitized corn earworm and 24.2% contained parasitized fall annyworm. Of 3,036 corn earwonn prepupae and pupae collected during this study, 11.6% were parasitized; of 1,802 fall armyworm collected, 9.3% were parasitized. Parasitism by Steinernema sp. accounted for 49.4 and 46.1% of the mortality of corn earworm and fall armyworm prepupae and pupae, respectively.
Application of belief propagation to trust and reputation management (2011)

This paper introduces the first application of Belief Propagation (BP) in reputation systems. We view the reputation management as an inference problem, and hence, describe the reputation management problem as computing marginal likelihood distributions from complicated global functions of many variables. However, we observe that computing the marginal probability functions of the reputation variables is computationally prohibitive for large scale reputation systems. Therefore, we propose to utilize the BP algorithm to efficiently (i.e., in linear complexity) compute these marginal probability distributions; leading to a fully iterative probabilistic and BP-based approach (referred to as BP-ITRM). BP-ITRM describes the reputation system on a factor graph, using which we can obtain a qualitative representation of how the service providers (sellers) and consumers (buyers) are related. Further, by using such a graph representation, we compute the marginal probability distribution functions of the variables representing the global reputation values via an iterative message passing algorithm. We show that BP-ITRM significantly outperforms the well-known and commonly used reputation management schemes such as the Averaging Scheme, Bayesian Approach and Cluster Filtering in the presence of attackers. Further, its complexity is linear in the number of service providers and consumers, far exceeding the efficiency of other schemes.
A multi-user Kurtosis algorithm for blind source separation (2002)

In earlier work we presented a set of necessary and sufficient conditions for the blind separation of a number of independent identically distributed (i.i.d.) source signals that share the same distribution and are mutually independent. We present an algorithm for implementing the multi-user Kurtosis (MUK) constrained optimization criterion suggested by these conditions. The algorithm is derived directly from the MUK cost function via a stochastic-gradient update at each iteration, followed by a Gram-Schmidt orthogonalization to project onto the criterion's constraint. A convergence analysis of the derived algorithm reveals that it is globally convergent (in the absence of noise) to a desired setting that recovers all the input sources, up to an arbitrary phase rotation each.
Various functionalities Based on Semiconductor Optical Amplifer for All-Optical Information Processing (2002)

By using a semiconductor optical amplifier and a cross-phase modulation wavelength converter, fundamental all-optical logic gates including NOT, AND, NOR, XOR, and XNOR have been newly proposed and implemented. Realization of these all-optical logic gates will bring up not only all-optical networks but also all-optical computing and signal processing.
Soy-Protein-Based Nanofabrics for Highly Efficient and Multifunctional Air Filtration (2016)

Proteins are well-known by their numerous active functional groups along the polypeptide chain. The variety of functional groups of proteins provides a great potential for proteins to interact with airborne pollutants with varying surface properties. However, to our knowledge, a successful demonstration of this potential has not been reported before. In this work, soy protein, a type of abundant plant protein, has been employed for the first time to fabricate multifunctional air-filtration materials. To take advantage of the functional groups of soy protein for air filtration, the soy protein was first well denatured to unfold the polypeptide chains and then fabricated into nanofibers with the help of poly(vinyl alcohol). It was found that the resultant nanofabrics showed high filtration efficiency not only for airborne particulates with a broad range of size but also for various toxic gaseous chemicals (e.g., formaldehyde and carbon monoxide), a capability that has not been realized by conventional air-filtering materials. This study indicates that protein-based nanofabrics are promising nanomaterials for multifunctional air-filtration applications.
Evolution of a Practical Total Synthesis of Ciguatoxin CTX3C (2004)

More than 20 000 people suffer annually from ciguatera seafood poisoning in subtropical and tropical regions. The extremely low content of the causative neurotoxins, designated as ciguatoxins, in fish has hampered their isolation, detailed biological study, and preparation of anti-ciguatoxin antibodies for detecting these toxins. Ciguatoxins consist of 12 trans-fused polycyclic ethers, ranging from six- to nine-membered, and include a spirally attached five-membered cyclic ether at one end. The large (3 nm in length) and complicated molecular structure of ciguatoxins has impeded chemists from completing their total synthesis. In 2001, we achieved the first total synthesis of ciguatoxin CTX3C by assembly of four structural fragments. Since then, protocols to combine the fragments have significantly improved in terms of overall stereoselectivity, efficiency, and practicality. In this Account, we describe recently evolved methodologies for the total synthesis of CTX3C.
Coulomb-type vibration absorber for suspended cables and suspended cable combined therewith (1984)

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Quadratic form: A robust metric for quantitative comparison of flow cytometric histograms (2008)

Comparison of fluorescence distributions is a fundamental part of the analysis of flow cytometric data. This approach is applied to detect differences between control and test sample and thus analyze a biological response. Comparison of standard test samples over time provides an estimate of instrument stability for quality control. However, application of statistical methods of distribution comparison in flow cytometry is difficult owing to instrument noise and the complex shape of intensity distributions. We applied quadratic form (QF) as a mathematical metric for comparison of flow cytometry histograms. QF operates on histograms as vectors and calculates the total distance in an interbin manner using a matrix of distances between single histogram bins. Euclidean interbin distance and histograms normalized to unity were used. Critical values corresponding to 95% significance level were calculated using Monte-Carlo simulation and single-maximum Gaussian distributions populated with several numbers of events. The QF statistic was then validated for non-Gaussian single-maximum distributions and multiple-maxima distributions. We determined that the critical values for Gaussian distributions depended on standard deviations and number of events in the compared histograms. A simple empirical function was constructed to characterize this dependence. Furthermore, it was verified that critical values (corresponding to 95% significance) for non-Gaussian histograms were similar to values for the Gaussian histograms characterized by the same standard deviation. We applied the QF statistic to estimate the differences between histograms of DNA content (ploidy) in cells of old and young leaf tissue of Brassica campestris. Furthermore, we quantified differences in fluorescence intensity in immunostaining of human lymphocytes. Quadratic form (QF) provides a true (mathematical) metric for estimation of distance between flow cytometry histograms of arbitrary shape. QF can be applied as a statistical test for estimation of significance of the distance measure. The respective critical values depend only on the number of events and standard deviations of compared histograms and are not affected by distribution shape. Therefore, applications of QF do not require assumptions concerning distribution shape and can be easily implemented in practice. This notion was confirmed using empirical distributions of DNA content in plant tissue and distributions of immunofluorescence in human cells.
Design and Fabrication of Magnetically Functionalized Core/Shell Microspheres for Smart Drug Delivery (2008)

Abstract The fabrication of magnetically functionalized core/shell microspheres by using the microfluidic flow‐focusing (MFF) approach is reported. The shell of each microsphere is embedded with magnetic nanoparticles, thereby enabling the microspheres to deform under an applied magnetic field. By encapsulating a drug, for example, aspirin, inside the microspheres, the drug release of the microspheres is enhanced under the compression–extension oscillations that are induced by an AC magnetic field. This active pumping mode of drug release can be controlled by varying the frequency and magnitude of the applied magnetic field as well as the time profile of the magnetic field. UV absorption measurements of cumulative aspirin release are carried out to determine the influence of these factors. The drug release behavior is found to be significantly different depending on whether the applied field varies sinusoidally or in a step‐function manner with time.
ASSL Specification of Emergent Self-Adapting Behavior for NASA Swarm-Based Exploration Missions (2008)

We describe a biologically-inspired approach to modeling self-adapting behavior of NASA swarm-based exploration missions, whereby individual entities in the system can sacrifice themselves for the greater good of the entire system. We investigate aspects of possible emergent self-adapting behavior of swarm-based systems, inspired by the self-sacrifice behavior observed in some hive cultures. Moreover, we propose an ASSL specification model for the self-sacrifice behavior of the swarm individuals. ASSL (Autonomic System Specification Language) is a specification language dedicated to autonomic systems, and with which we have been experimenting with some positive results.
Neurodegeneration is an early event in diabetic retinopathy: therapeutic implications (2012)

Diabetic retinopathy (DR) remains the leading cause of blindness among working-age individuals in developed countries. Current treatments for DR are indicated in advanced stages of the disease and are associated with significant adverse effects. Therefore, new pharmacological treatments for the early stages of DR are needed. DR has been classically considered to be a microcirculatory disease of the retina. However, there is growing evidence to suggest that retinal neurodegeneration is an early event in the pathogenesis of DR, which participates in the microcirculatory abnormalities that occur in DR. Therefore, the study of the underlying mechanisms that lead to neurodegeneration will be essential for identifying new therapeutic targets. From the clinical point of view, the identification of those patients in whom retinal neurodegeneration appears will be crucial for implementing early treatment based on neuroprotective drugs. When the early stages of DR are the therapeutic target, it would be inconceivable to recommend an aggressive treatment such as intravitreous injections. By contrast, topical administration of neuroprotective drugs by using eye drops is a possible option. However, clinical trials to determine the safety and effectiveness of this non-invasive route, as well as a standardisation of the methods for monitoring neurodegeneration, are needed.
On network-aware clustering of Web clients (2000)

Being able to identify the groups of clients that are responsible for a significant portion of a Web site's requests can be helpful to both the Web site and the clients. In a Web application, it is beneficial to move content closer to groups of clients that are responsible for large subsets of requests to an origin server. We introduce clusters ---a grouping of clients that are close together topologically and likely to be under common administrative control. We identify clusters using a ``network-aware" method, based on information available from BGP routing table snapshots.
Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy (2020)

In recent years, the genetic architecture of dilated cardiomyopathy (DCM) has been more thoroughly elucidated. However, there is still insufficient knowledge on the modifiers and regulatory principles that lead to the failure of myocardial function. The current study investigates the association of epigenome-wide DNA methylation and alternative splicing, both of which are important regulatory principles in DCM. We analyzed screening and replication cohorts of cases and controls and identified distinct transcriptomic patterns in the myocardium that differ significantly, and we identified a strong association of intronic DNA methylation and flanking exons usage (<i>p</i> < 2 × 10<sup>-16</sup>). By combining differential exon usage (DEU) and differential methylation regions (DMR), we found a significant change of regulation in important sarcomeric and other DCM-associated pathways. Interestingly, inverse regulation of Titin antisense non-coding RNA transcript splicing and DNA methylation of a locus reciprocal to <i>TTN</i> substantiate these findings and indicate an additional role for non-protein-coding transcripts. In summary, this study highlights for the first time the close interrelationship between genetic imprinting by DNA methylation and the transport of this epigenetic information towards the dynamic mRNA splicing landscape. This expands our knowledge of the genome-environment interaction in DCM besides simple gene expression regulation.
Antigen Delivery to Macrophages Using Liposomal Nanoparticles Targeting Sialoadhesin/CD169 (2012)

Sialoadhesin (Sn, Siglec-1, CD169) is a member of the sialic acid binding Ig-like lectin (siglec) family expressed on macrophages. Its macrophage specific expression makes it an attractive target for delivering antigens to tissue macrophages via Sn-mediated endocytosis. Here we describe a novel approach for delivering antigens to macrophages using liposomal nanoparticles displaying high affinity glycan ligands of Sn. The Sn-targeted liposomes selectively bind to and are internalized by Sn-expressing cells, and accumulate intracellularly over time. Our results show that ligand decorated liposomes are specific for Sn, since they are taken up by bone marrow derived macrophages that are derived from wild type but not Sn(-/-) mice. Importantly, the Sn-targeted liposomes dramatically enhance the delivery of antigens to macrophages for presentation to and proliferation of antigen-specific T cells. Together, these data provide insights into the potential of cell-specific targeting and delivery of antigens to intracellular organelles of macrophages using Sn-ligand decorated liposomal nanoparticles.
A dose delivery verification method for conventional and intensity‐modulated radiation therapy using measured field fluence distributions (2003)

Treatment verification has been a weak link in external beam radiation therapy. As new and more complicated treatment techniques, such as intensity-modulated radiation therapy (IMRT), are implemented into clinical practice, verifying the accuracy of treatment delivery becomes increasingly important. Existing methods for treatment verification are highly labor intensive. We have developed a method for verifying the delivery of external beam radiotherapy and implemented the methodology into a system consisting of both hardware and software components. The system uses grayscale images acquired on the treatment machine from the planned treatment beams. From these images, the photon fluence distribution of each beam is derived. These measured photon fluence maps are then used as input to a separate dose calculation engine to compute the delivered absolute dose and the dose distribution in the same patient, assuming that the patient is set up as required by the treatment plan. The dose distribution generated from the measured fluence maps can then be compared to that of the treatment plan. Software tools, such as overlaying isodose curves generated with this method on those imported from the plan, dose difference maps, dose difference volume histograms, and three-dimensional perspective views of the dose differences, have also been developed. The system thus provides a means to verify the dose, the dose prescription, and the monitor units applied. The potential exists with a suitable electronic portal imaging system to reduce the quality assurance efforts, especially for IMRT.
Hemoglobin A1c and Self-Monitored Average Glucose (2015)

The eA1c procedure developed in type 2 diabetes to track in real-time changes in average glycemia and present the results in HbA1c-equivalent units has shown similar performance in type 1 diabetes. The eA1c calibration factors are highly predictive of the HGI, thereby explaining partially the biological variation causing discrepancies between HbA1c and its linear estimates from SMBG data.
Demonstration of nonlinearity bias in the measurement of the apparent diffusion coefficient in multicenter trials (2015)

The analysis confirms gradient nonlinearity as a major source of spatial DW bias and variability in off-center ADC measurements across MRI platforms, with minor contributions from shim, imaging gradients and eddy currents. The developed protocol enables empiric description of systematic bias in multicenter quantitative DWI studies.