gebhart/patrepeval huggingface dataset:
Frequency domain measurements in the P3 approximation (2000)

We have applied the P3 approximation to multi-distance frequency domain measurements in turbid media. Phase noise and amplitude-phase cross talk are critical parameters for these experiments. Good agreement with theory is obtained.
Role of DOCK2 and DOCK180 in fetal thymus colonization (2009)

Fetal thymus colonization is initiated before the vascularization of the thymus primordium. This prevascular colonization of the fetal thymus by T-lymphoid progenitor cells is guided by the coordination of CCR7- and CCR9-mediated chemokine signals. However, the intracellular signals that mediate the prevascular migration of T-lymphoid progenitor cells to the fetal thymus are unknown. Here we show that T-lymphoid progenitor cells in fetal mice express two closely related CDM family molecules, DOCK2 and DOCK180. We found that the prevascular fetal thymus accumulation in vivo was significantly reduced in mice doubly deficient for DOCK2 and DOCK180 but not in mice deficient for either DOCK2 or DOCK180. Immature T-lymphoid cells from mice doubly deficient for DOCK2 and DOCK180 were defective in their in vitro migration towards fetal thymus lobes. The T-lymphoid progenitor cells generated in mice lacking DOCK2 and DOCK180 were capable of T-cell development after their transfer into a fetal thymus environment, and the impaired fetal thymus colonization in mice deficient for DOCK2 and DOCK180 was not as severe as that in mice doubly deficient for CCR7 and CCR9. These results indicate that the combination of DOCK2 and DOCK180 plays a significant but not essential role in prevascular fetal thymus colonization.
Human herpesvirus 6 infection and transient acquired myelodysplasia in children (2005)

Our results indicate that severe HHV-6 infection may induce reversible myelodysplastic changes. These findings contribute to elucidate the pathogenicity of HHV-6 and furthermore suggest that HHV-6 infection must also be considered as a cause of dysplasia in the differential diagnosis of MDS.
MatKG: The Largest Knowledge Graph in Materials Science -- Entities, Relations, and Link Prediction through Graph Representation Learning (2022)

This paper introduces MatKG, a novel graph database of key concepts in material science spanning the traditional material-structure-property-processing paradigm. MatKG is autonomously generated through transformer-based, large language models and generates pseudo ontological schema through statistical co-occurrence mapping. At present, MatKG contains over 2 million unique relationship triples derived from 80,000 entities. This allows the curated analysis, querying, and visualization of materials knowledge at unique resolution and scale. Further, Knowledge Graph Embedding models are used to learn embedding representations of nodes in the graph which are used for downstream tasks such as link prediction and entity disambiguation. MatKG allows the rapid dissemination and assimilation of data when used as a knowledge base, while enabling the discovery of new relations when trained as an embedding model.
Antibody targeting to the murine lymphoma ESb‐MP: Increased accumulation due to reduced internauzation into lymphoma cells as compared to normal lymphoid cells (1988)

Using rat monoclonal antibody (MAb) 12-15A against the spontaneously metastasizing mouse lymphoma variant ESb-MP, we elaborated conditions for targeting. In vitro, high binding of labelled antibody to ESb-MP cells and low binding to lymphoid cells (e.g., spleen cells) was noted. In vivo, we observed pronounced accumulation in spleen, lymph nodes and bone marrow, the uptake kinetics indicating high accessibility of the target antigen in these tissues, and rapid clearance of radioactivity from blood and most normal tissues, indicating degradation of the antibody and excretion of the label. Binding to lymphoma tissue was slow but persistent, resulting in high tumor:tissue ratios only after 2-3 days. Biodistribution could be dramatically changed by pre-treatment of animals with excess cold antibody, which reduced trapping of labelled antibody in normal lymphatic tissue, leading to prolonged persistence in the blood and preferential uptake into tumor tissue. Monovalent 12-15A fragments showed less pronounced binding to lymphatic tissue, while being rapidly cleared from the circulation by virtue of their inherent tendency to bind to kidney tissue. Tumor:tissue ratios up to 56:1 were obtained by a combination of pre-treatment with unlabelled 12-15A IgG or Fab fragment, followed by injection of labelled fragment or IgG, respectively. This is interpreted on the basis of differences in the internalization and retention of antigen-antibody complexes. Pre-treatment obviously leads to a temporary blockade or removal of the target antigen, which is much more efficient with normal lymphoid cells than with tumor cells. Thus, it may become possible to target antibodies into the tumor despite concurrent antigen expression on normal tissue.
Silver Nanowires with Pristine Graphene Oxidation Barriers for Stable and High Performance Transparent Conductive Films (2018)

One-dimensional (1D) silver nanowires (AgNWs) have emerged as a leading candidate for the development of next-generation optoelectronic and wearable electronic devices. However, a key limitation of AgNW electrodes is that they are readily oxidized, resulting in a shift in properties leading to devices becoming erratic over time. To address this problem, we report a facile method to improve both the stability and performance of AgNW films. The AgNWs were combined with pristine graphene (pG) using an optimal (30/70 wt %) with the goals to prove that the pG sheets can provide a barrier shielding to protect against AgNW oxidation and have the additional benefit of improving the connections between wires and stability of the films. The fabrication of these films was demonstrated on wide range of substrates including glass, plastic, textile, and paper. A surface resistance of 18.23 Ω/sq and an optical transparency of 89% were obtained on the glass substrates, 50 Ω/sq and 88% transparency for poly(ethylene terephthalate) (PET), and 0.35 Ω/sq resistance on the textile substrate. Atmospheric pressure plasma jets (APPJ) treatment was further used to enhance the performance of the film (i.e., glass), resulting in a significant reduction of 30.6% in sheet resistance (15.20 Ω/sq) and an improvement of transparency to 91%. The stability of AgNW/pG film under environmental conditions and higher temperatures was significantly improved, showing only a minor increase in the sheet resistance after 30 days and at temperature increases up to 300 °C when compared with control (AgNW film) which shows a sharp increase after 8–10 days and is thermally stable until 150 °C as a result of Ag oxidation.
Ecogenomics of Human and Animal Basidiomycetous Yeast Pathogens (2013)

This chapter provides an overview on the diversity of basidiomycetous yeasts with emphasis on the human and animal pathogens. Comparative genomics studies clearly show that these yeast pathogens are well adapted to the human host and are able to circumvent the host defense systems. A discussion is provided on the diversity of mating type systems that regulate the (a)sexual development of basidiomycetes, including the human, animal, and plant pathogens. Two groups of fungi are discussed in detail as examples. The first includes Cryptococcus neoformans, which is causing a significant number of attributable mortalities among people infected with HIV, and its sibling species Cryptococcus gattii that is a primary pathogen causing outbreaks occurring in distinct locales involving a majority of individuals who have no known immunodeficiency. The second example is the adaptation of lipophilic or lipid-dependent Malassezia yeasts to the human and animal skin.
Interacting queues with server selection and coordinated scheduling—application to cellular data networks (2008)

We consider a system of parallel servers handling users of various classes, whose service rates depend not only on user classes, but also on the set of active servers. We investigate the stability under two types of allocation strategies: (i) server assignment where the users are assigned to servers based on rates, load, and other considerations, and (ii) coordinated scheduling where the activity states of servers are coordinated. We show how the model may be applied to evaluate the downlink capacity of wireless data networks. Specifically, we examine the potential gains in wireless capacity from the two types of resource allocation strategies.
Local Stiffness in Nylon 6/Rubber Blends Determined by DigitalPulsed Force Mode-SPM (2005)

The incorporation of soft rubber into a thermoplastic matrix can lead to tough blends. Generally, such binary blends are immiscible and exhibit poor mechanical properties caused by the unfavorable interactions between the two phases. Thus, there is an enormous interest in polymer blend compatibility to improve the properties of the polymer blends by the addition of an appropriate compatibilizer [1,2].
Computing Cellulase Kinetics with a Two-Domain Linear Interaction Energy Approach (2021)

While heterogeneous enzyme reactions play an essential role in both nature and green industries, computational predictions of their catalytic properties remain scarce. Recent experimental work demonstrated the applicability of the Sabatier principle for heterogeneous biocatalysis. This provides a simple relationship between binding strength and the catalytic rate and potentially opens a new way for inexpensive computational determination of kinetic parameters. However, broader implementation of this approach will require fast and reliable prediction of binding free energies of complex two-phase systems, and computational procedures for this are still elusive. Here, we propose a new framework for the assessment of the binding strengths of multidomain proteins, in general, and interfacial enzymes, in particular, based on an extended linear interaction energy (LIE) method. This two-domain LIE (2D-LIE) approach was successfully applied to predict binding and activation free energies of a diverse set of cellulases and resulted in robust models with high accuracy. Overall, our method provides a fast computational screening tool for cellulases that have not been experimentally characterized, and we posit that it may also be applicable to other heterogeneously acting biocatalysts.
Protein Microarrays: A New Tool for the Study of Autoantibodies in Immunodeficiency (2015)

Autoimmunity is highly coincident with immunodeficiency. In a small but growing number of primary immunodeficiencies, autoantibodies are diagnostic of a given disease and implicated in disease pathogenesis. In order to improve our understanding of the role of autoantibodies in immunodeficiencies and to discover novel autoantibodies, new proteomic tools are needed. Protein microarrays have the ability to screen for reactivity to hundreds to many thousands of unique autoantigens simultaneously on a single chip using minimal serum input. Here, we review different types of protein microarrays and how they can be useful in framing the study of primary and secondary immunodeficiencies.
Directly Estimating Nonclassicality (2011)

We establish a method of directly measuring and estimating nonclassicality--operationally defined in terms of the distinguishability of a given state from one with a positive Wigner function. It allows us to certify nonclassicality, based on possibly much fewer measurement settings than necessary for obtaining complete tomographic knowledge, and is at the same time equipped with a full certificate. We find that even from measuring two conjugate variables alone, one may infer the nonclassicality of quantum mechanical modes. This method also provides a practical tool to eventually certify such features in mechanical degrees of freedom in opto-mechanics. The proof of the result is based on Bochner's theorem characterizing classical and quantum characteristic functions and on semidefinite programming. In this joint theoretical-experimental work we present data from experimental optical Fock state preparation.
&lt;title&gt;Evaluation of 3D vs. 2D compression of medical images with set partitioning in hierarchical trees&lt;/title&gt; (1998)

Wavelet-based image compression is a very effective technique for medical images, giving significantly better results than the JPEG algorithm. Recent advanced wavelet techniques, such as embedded zerotree wavelet coding or set partitioning in hierarchical trees (SPIHT), have further improved compression efficiency by exploiting the natural relationship between corresponding coefficients at different scales and by progressively refining coefficient values. It is also well known that full 3-D wavelet compression of 3-D data sets is significantly more efficient than 2-D compression of individual slices, but the memory requirements are very high. We explore the extension of the SPIHT algorithm to three dimensions, and also of intermediate approaches such as the encoding of a 3-D image in 'slabs' of 16 slices at a time or simple subtraction of neighboring slices, which yield different tradeoffs between speed and memory requirements on the one hand and compression efficiency on the other for a variety of possible approaches on typical 3-D CT and MRI data sets.
Field programmable gate array implementation of wheel–rail contact laws (2010)

This study presents the development of a field programmable gate array (FPGA)-based accelerator that is highly suited to the implementation of complex and computationally demanding control or real-time simulation tasks. The application studied in this article is for the real-time simulation of wheel–rail contact laws, which may be used for hardware-in-the-loop experimental studies of the latest active control technology for wheelset stabilisation and steering. The complex wheel–rail contact laws are implemented using a single FPGA chip that outperforms substantially modern general-purpose CPU or DSP in the aspects of processing time, configuration flexibility and cost. The algorithms are restructured to utilise the FPGA&apos;s parallel processing capability. Reusable IP core are used for the floating point operations. The scheduling of the operations is optimised to ensure effective and efficient use of the FPGA&apos;s resources.
ChemInform Abstract: INTRAMOLECULAR CARBON‐HYDROGEN INSERTION: SYNTHESIS OF (.+‐.)‐PENTALENOLACTONE E METHYL ESTER (1985)

Abstract H Insertion: Synthesis of (±)‐Pentalenolactone E Methyl Ester.
MEASUREMENT OF FUNCTIONAL RESIDUAL CAPACITY USING CO2 WASH-IN (2004)

SOCIETY OF CRITICAL CARE MEDICINE 34TH CRITICAL CARE CONGRESS PHOENIX, ARIZONA, USA JANUARY 15-19, 2005: Poster: Clinical Science: Pulmonary Disease or Dysfuntion/Mechanical Ventilation/Weaning (Adult) I
MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA-seq data. (2015)

Single-cell transcriptomic profiling enables the unprecedented interrogation of gene expression heterogeneity in rare cell populations that would otherwise be obscured in bulk RNA sequencing experiments. The stochastic nature of transcription is revealed in the bimodality of single-cell transcriptomic data, a feature shared across single-cell expression platforms. There is, however, a paucity of computational tools that take advantage of this unique characteristic. We present a new methodology to analyze single-cell transcriptomic data that models this bimodality within a coherent generalized linear modeling framework. We propose a two-part, generalized linear model that allows one to characterize biological changes in the proportions of cells that are expressing each gene, and in the positive mean expression level of that gene. We introduce the cellular detection rate, the fraction of genes turned on in a cell, and show how it can be used to simultaneously adjust for technical variation and so-called “extrinsic noise” at the single-cell level without the use of control genes. Our model permits direct inference on statistics formed by collections of genes, facilitating gene set enrichment analysis. The residuals defined by such models can be manipulated to interrogate cellular heterogeneity and gene-gene correlation across cells and conditions, providing insights into the temporal evolution of networks of co-expressed genes at the single-cell level. Using two single-cell RNA-seq datasets, including newly generated data from Mucosal Associated Invariant T (MAIT) cells, we show how model residuals can be used to identify significant changes across biologically relevant gene sets that are missed by other methods and characterize cellular heterogeneity in response to stimulation.
Production and characterization of recombinant human CLN2 protein for enzyme-replacement therapy in late infantile neuronal ceroid lipofuscinosis (2001)

Late infantile neuronal ceroid lipofuscinosis (LINCL) is a fatal recessive childhood disease caused by mutations in the CLN2 gene, which encodes the lysosomal enzyme tripeptidyl peptidase I. As a step towards understanding the protein and developing therapeutics for the disease, we have produced and characterized recombinant human CLN2 (ceroid lipofuscinosis, neuronal 2) protein from Chinese-hamster ovary cells engineered to secrete high levels of the enzyme. The protein was secreted as an inactive soluble proenzyme of ≈ 65kDa that appears as a monomer by gel filtration. Upon acidification, the protein is processed to mature form and acquires activity. The enzyme is efficiently delivered to the lysosomes of LINCL fibroblasts by mannose 6-phosphate-receptor-mediated endocytosis (EC50≈ 2nM), where it remains active for long periods of time (t1/2≈ 12 days). In addition, the enzyme is taken up by rat cerebellar granule neurons by mannose 6-phosphate-dependent and -independent mechanisms. Treatment of LINCL fibroblasts with recombinant CLN2 protein restores normal enzyme activity and ameliorates accumulation of the major storage protein, mitochondrial ATP synthase subunit c.
Isolation and partial characterisation of a Chinese hamster O6-alkylguanine-DNA alky It ransferase cDNA (1992)

The cDNA encoding Chinese hamster O6-alkylguanine-DNA-alkyltransferase (ATase) has been isolated from a library prepared from RNA isolated from V79 lung fibroblasts which had an upregulated level of this repair activity following stepwise selection with a chloroethylating agent (1, 2). Expression of the cDNA in E. coli produced functionally active ATase at levels of 2.5% of total cellular protein as determined by in vitro assay. The recombinant hamster protein has a molecular weight of 28 kDa as estimated by SDS-PAGE and fluorography and this was identical to that in the upregulated cells. The characteristic PCHRV pentapeptide of the alkyl acceptor site has been identified and there is a 68 amino acid residue region which is 90% conserved across all the mammalian proteins so far analysed: in contrast, the N- and C-terminal domains diverge by as much as 50% between species. Polyclonal antibodies to the human and rat ATases hybridised to the hamster protein on western analysis suggesting at least one common epitope shared across species. However, in antibody inhibition experiments neither of the antisera cross reacted with the hamster ATase in a way which interfered with functional activity whereas the anti-human antibodies inhibited the human ATase and the anti-rat antibodies inhibited the rat and mouse ATases. There may therefore be significant tertiary structural differences between the hamster protein and the other mammalian ATases.
Homogeneous Differential Magnetic Assay (2019)

Assays are widely used for detection of various targets, including pathogens, drugs, and toxins. Homogeneous assays are promising for the realization of point-of-care diagnostics as they do not require separation, immobilization, or washing steps. For low concentrations of target molecules, the speed and sensitivity of homogeneous assays have hitherto been limited by slow binding kinetics, time-consuming amplification steps, and the presence of a high background signal. Here, we present a homogeneous differential magnetic assay that utilizes a differential magnetic readout that eliminates previous limitations of homogeneous assays. The assay uses a gradiometer sensor configuration combined with precise microfluidic sample handling. This enables simultaneous differential measurement of a positive test sample containing a synthesized <i>Vibrio cholerae</i> target and a negative control sample, which reduces the background signal and increases the readout speed. Very low concentrations of targets down to femtomolar levels are thus detectable without any additional amplification of the number of targets. Our homogeneous differential magnetic assay method opens new possibilities for rapid and highly sensitive diagnostics at the point of care.
Assessment of a Novel Non-Axial Counter-Rotating Compressor Concept for Aero-Engines (2018)

This paper presents the first assessment of a new non-axial counter-rotating compressor concept. This concept consists of replacing the stator of a mixed-flow compressor stage or the diffuser of a centrifugal compressor stage with a counter-rotating rotor that will turn the flow back to the axial direction with much lower diffusion factor, while providing the equivalent in work of the upstream mixed-flow rotor or impeller. This concept has two advantages. First, the very high stage pressure rise means that only a single counter-rotating rotor may be required, making mechanical implementation simpler than for multi-stage axial counter-rotating compressors. Second, the replacement of the high flow turning (high loss) stator/diffuser in a non-axial stage with a low flow turning counter-rotating rotor gives the new concept potential for achieving higher efficiency than conventional non-axial compressors. As a first proof of concept, a subsonic counter-rotating mixed-flow compressor and its conventional (i.e. rotor-stator) equivalent have been designed with the intent of being implemented in a test rig. CFD simulations have been carried out for a comparative evaluation of both configurations. Results show that the counter-rotating mixed-flow compressor produces more than double the pressure rise of its conventional version with a slightly higher peak-efficiency while having a smaller axial length. Moreover, the counter-rotating configuration has a better stall margin than its conventional counterpart, for which the boundary layer separation from excessive flow turning in the stator causes early stall.
ICEPT-an integrated cellular network planning tool (2002)

In this paper, we present ICEPT, a new mobile radio network planning tool that is based on an integrated design approach. The new approach starts with the analysis of the spatial distribution of the expected teletraffic within the service area of the cellular system. Employing this principle, the ICEPT tool considers concurrently the four major design areas of cellular networks: radio transmission, mobile subscriber, resource allocation, and system architecture. ICEPT uses these factors as input for the automatic network design algorithm ABPA which locates the base stations in the supplying area.
102W picosecond all fiber one-stage MOPA laser (2011)

We report a high power picosecond pulses all fiber, one-stage MOPA system. A passively mode-locked ytterbium-doped fiber laser was used as seed source. Average output power as high as 102W was obtained in 76 ps pulses at 18.6 MHz repetition rate at 1064 nm with bandwidth of 0. 5 nm.