gebhart/patrepeval huggingface dataset:
Two-photon near- and far-field fluorescence microscopy with continuous-wave excitation (1998)

We report on scanning far- and near-field two-photon microscopy of cell nuclei stained with DAPI and bisbenzimidazole Hoechst 33342 (BBI-342) with the 647-nm laser line of a cw ArKr mixed-gas laser. Two-photon-excited fluorescence images are obtained for 50-200 mW of average power at the sample. A nearly quadratic dependence of fluorescence intensity on laser power confirmed the two-photon effect. The nonlinearity was further supported by evidence of three-dimensional sectioning in a scanning far-field microscope. We find that the cw two-photon irradiation sufficient for imaging within typically 5 s does not significantly impair cell cycling of BBI-342-labeled live cells. Finally, high-resolution imaging in scanning near-field microscopy with good contrast is demonstrated.
Detection of classical and newly described staphylococcal superantigen genes in coagulase-negative staphylococci isolated from bovine intramammary infections (2010)

The coagulase-negative staphylococci (CNS) are the most prevalent mastitis pathogen group yet their virulence characteristics have not been well described. We investigated the presence of 19 classical and newly described staphylococcal superantigen (SAg) genes in CNS isolates from bovine intramammary infections (IMI). A total of 263 CNS representing 11 different Staphylococcus spp. were examined, and 31.2% (n=82) of CNS isolates had one or more SAg genes; there were 21 different SAg gene combinations. The most prevalent combination of SAg genes (seb, seln and selq; n=45) was found in S. chromogenes, S. xylosus, S. haemolyticus, S. sciuri subsp. carnaticus, S. simulans and S. succinus. The genes for SAgs appear to be widely distributed amongst CNS isolated from bovine IMI.
P‐type doping in GaN through Be implantation (2005)

P-type doping through Be implantation in GaN is achieved by a two-step annealing process. Combined photoluminescence-Raman measurements showed Be-related band, indicating a low acceptor ionization energy of 140 meV, and resonance Raman features. X-ray diffraction revealed the lattice expansion due to Be-implantation. Scanning electron microscopy exhibited the surface defects morphology with hexagonal plane like inverse open pyramids. The effect of new annealing process on Be activation is discussed. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
A Generalized Model for Linear-Periodically-Time-Variant Circulators (2019)

Magnetic-free non-reciprocity based on linear-periodically-time-variant (LPTV) circuits has received significant research and commercial attention since it could revolutionize wireless communications. LPTV circuits are formed by two main components: linear-time-invariant (LTI) networks and periodically-modulated switches. The modulated switches are the core elements to break the reciprocity of LTI networks. To understand and design LPTV circulators, a universal and intuitive analytical model is required. However, such model does not exist as it is extremely challenging to accurately model and fully understand the LPTV behaviour of energy storage networks. To address this limitation, this work introduces a novel analysis method, which is broadly applicable to any LPTV networks, and validates it experimentally. The novelty of this methodology comes from two main contributions: (1) modelling of the switch as a resistor in parallel with a current-controlled current source; (2) the decomposition of the LPTV network into the linear superposition of two LTI networks. We apply this technique to model the exact behaviour of an LPTV circulator in the frequency domain.
Elevated levels of hydroxylated phosphocholine lipids in the blood serum of breast cancer patients (2009)

The difference in serum phospholipid content between stage-IV breast cancer patients and disease-free individuals was studied by employing a combination of chemometric statistical analysis tools and mass spectrometry. Chloroform-extracted serum samples were profiled for their lipid class composition and structure using precursor ion, neutral loss, and product ion tandem mass spectrometric (MS/MS) scanning experiments. Changes in the relative abundance of phospholipids in serum as a consequence of cancer progression, measured through electrospray ionization (ESI) mass spectrometry of flow-injected serum samples collected from 25 disease-free individuals and 50 patients diagnosed with stage-IV breast cancer, were statistically evaluated using principal component analysis (PCA), analysis of variance (ANOVA) and receiver operating characteristic (ROC) analysis. Lipids whose abundance changed significantly as a consequence of cancer progression were structurally characterized using product ion spectra, and independently quantified using precursor ion scan experiments against an internal standard of known concentration. Phosphocholine lipids that displayed a statistically significant change as a consequence of cancer progression were found to contain an oxidized fatty acid moiety as determined by MS3 experiments.
Comprehensive transcriptomic analyses of tissue, serum, and serum exosomes from hepatocellular carcinoma patients (2019)

Our combined data point to altered miRNA and mRNA expression contributing to both generally impaired lipid metabolism and increased cell proliferation and a miRNA-driven increase in collagen synthesis in HCC. Our results further indicate a correlation in miRNA expression between exosomes, serum, and tissue samples suggesting export from tumors via exosomes. This correlation could provide a basis for a more tumor-specific miRNA profile in serum.
Applications for Progressive Barcodes (2014)

Color barcodes offer increased density over two-dimensional barcodes, which can be taken advantage of to embed longer data strings in the same printed/displayed area. However, the color channels also offer the possibility of containing multiple, distinct sets of data in the same &#x201C;hybrid&#x201D; mark.The four-dimensional progressive barcode is a printed mark that does not change in size as it is used to represent different stages (or &#x201C;states&#x201D;) in a workflow. The addition of progressive information to a barcode allows it to change through time&#x2014;supporting many different information lifecycles.1,2 This means that the use of the same barcode location for multiple barcodes through time is possible. Progressive barcodes can be also used to support two (or more) applications or services in the same object. One of these can be standards compliant and another can be proprietary or customized. Thus, a &#x201C;hybrid&#x201D; of two functions, represented by two planes of information, is combined in a single mark.These two planes of information include different densities of information. The first plane is binary, with high contrast between the two binary encoding (usually black and white) tiles in the barcode. The second is n-ary, and utilizes inks that are invisible to the binary barcode reading software. This is accomplished with highly saturated colors, but it can also be used with IR, UV or other &#x201C;invisible&#x201D; inks.In this article, the authors will demonstrate several types of applications and services that are enabled by the progressive barcode. They are most effectively deployed when there are multiple types of information payloads needed for a single object&#x2014;e.g., point-of-sale and customer interrogation of the product. This also makes them useful in a variety of document/physical item workflows.
Detection and Quantitation of Amyloid-β Aggregates in Body Fluids may be Suitable for Early Diagnosis of Alzheimer’s Disease (2014)

The post mortem identification of amyloid plaques, consisting of the amyloid-β (Aβ) peptide, and neurofibrillary tangles in the brains of patients still leads to the most reliable diagnosis for Alzheimer’s disease (AD). Substantial efforts have been made to identify reliable biomarkers for AD that can be used for early diagnosis of AD. Body fluids of AD patients have been investigated for their content of total or soluble Aβ(1-40) or Aβ(1-42), either using classical ELISA procedures, or non-classical assays with more innovative read-out signals, or a combination of both. The concentration of total soluble Aβ(1-42) in cerebrospinal fluid (CSF) is reduced by 40 to 50 % in AD patients compared to age-matched healthy controls, as confirmed in more than 30 studies, with both sensitivity and specificity exceeding 80 to 90 %. Thus, it was suggested that detection of low levels of Aβ(1-42) in CSF might help preclinical diagnosis. The achievable sensitivity using such CSF biomarkers, however, is 85 % or less. Therefore, these assays cannot deliver any increase in the diagnostic outcome as compared to existing algorithms based on neuropsychological and imaging modalities. Regarding the amyloid cascade hypothesis, Aβ oligomers and aggregates are directly involved in the pathologic process. The presence of Aβ aggregates in CSF could thus be the most direct and most reliable biomarker for AD and increasing efforts are undertaken to develop methods that are suitable to quantify and characterize Aβ aggregate species present in body fluids, especially in CSF. Here, we present an overview of the current status of the development of methods for Aβ aggregate specific detection and quantitation, which is an update of a previous review.
Electrophysiology and ocular blood flow in a family with dominant optic nerve atrophy and a mutation in the OPA1 gene (2003)

Patients with a mutation in the OPA1 gene have a very variable phenotype. MVEP and blood flow measurements are two new objective methods for an easier detection of this specific genetic optic nerve atrophy.
Cardiac Energetic Impairment in Heart Disease and the Potential Role of Metabolic Modulators (2014)

Cardiac energetic impairment is a frequent finding in patients with both inherited and acquired diseases of heart muscle. In this review the mechanisms of energy generation in the healthy heart and their disturbances in heart muscle diseases are described. Therapeutic agents targeted at correcting cardiac energetic impairment are discussed.
Immunomodulating Effect of Methisoprinol on the Pronephros Macrophage and Lymphocyte Activity after Suppression Induced by Infectious Haematopoietic Necrosis Virus (IHNV) in Rainbow Trout (Oncorhynchus mykiss) (2008)

The purpose of this in vitro study was to determine the influence of methisoprinol on the activity of pronephros macrophages and lymphocytes after suppression induced by infectious haematopoietic necrosis virus (IHNV). For this study IHNV-free rainbow trout were used. Pronephros from 20 fish were removed and single leukocyte suspensions were separated. The IHNV significantly ( P &lt; 0.05) decreased the respiratory burst activity and potential killing activity of pronephros macrophages and proliferative response of lymphocytes stimulated by mitogens ConA and LPS. The results of our in vitro study showed that methisoprinol at a concentration of 50 mg/ml modulated (restored) the metabolic and potential killing activity of macrophages and proliferative response of lymphocytes suppressed by IHNV.
Energetics of Defects on Graphene through Fluorination (2014)

Functionalized graphene sheets (FGSs) comprise a unique member of the carbon family, demonstrating excellent electrical conductivity and mechanical strength. However, the detailed chemical composition of this material is still unclear. Herein, we take advantage of the fluorination process to semiquantitatively probe the defects and functional groups on graphene surface. Functionalized graphene sheets are used as substrate for low-temperature (<150 °C) direct fluorination. The fluorine content has been modified to investigate the formation mechanism of different functional groups such as C-F, CF2, O-CF2 and (C=O)F during fluorination. The detailed structure and chemical bonds are simulated by density functional theory (DFT) and quantified experimentally by nuclear magnetic resonance (NMR). The electrochemical properties of fluorinated graphene are also discussed extending the use of graphene from fundamental research to practical applications.
Magnetic properties and microstructures of the Nd-Fe-B magnet powder produced by hydrogen treatment (1991)

The hydrogen treatment of the Nd-Fe-B alloy ingots was found to produce magnet powders with good magnetic properties. Typical magnetic properties of these powders are as follows; 4πIs = 9.5 kG, Br = 7.7 kG, iHc = 9.4 kOe, and (BH)max = 12.2 MGOe. Microstructural studies of these powders showed that they are made of fine crystalline grains of ∼0.3 μm diameter and that these crystalline grains in the individual magnet powder are not necessarily enclosed with boundary phase(s), which is quite different from previously known Nd-Fe-B magnets, i.e., the sintered magnet (the nucleation type magnet) or the amorphous ribbon magnet (the pinning type magnet). It is also noted that the size of these crystalline grains is comparable to that of the single magnetic domain of the tetragonal Nd2Fe14B intermetallic compound and the coercive force of these powders appears to be related to their fine crystalline grain size.
Association Between Perceived Barriers to Diabetes Self-management and Diabetic Retinopathy in Asian Patients With Type 2 Diabetes (2017)

These results suggest that greater perceived barriers to DSM are independently associated with severity of DR. Although longitudinal data are needed, these findings suggest that evidence-based interventions to reduce patient-, practitioner-, and system-related barriers to diabetes care may help reduce the risk of DR.
Calcium regulates estrogen increase in permeability of cultured CaSki epithelium by eNOS-dependent mechanism (2000)

Estrogen increases baseline transepithelial permeability across CaSki cultures and augments the increase in permeability in response to hypertonic gradients. In estrogen-treated cells, lowering cytosolic calcium abrogated the hypertonicity-induced augmented increase in permeability and decreased baseline permeability to a greater degree than in estrogen-deprived cells. Steady-state levels of cytosolic calcium in estrogen-deprived cells were higher than in estrogen-treated cells. Increases in extracellular calcium increased cytosolic calcium more in estrogen-deprived cells than in estrogen-treated cells. However, in estrogen-treated cells, increasing cytosolic calcium was associated with greater increases in permeability in response to hypertonic gradients than in estrogen-deprived cells. Lowering cytosolic calcium blocked the estrogen-induced increase in nitric oxide (NO) release and in the in vitro conversion of L-[(3)H]arginine to L-[(3)H]citrulline. Treatment with estrogen upregulated mRNA of the NO synthase isoform endothelial nitric oxide synthase (eNOS). These results indicate that cytosolic calcium mediates the responses to estrogen and suggest that the estrogen increase in permeability and the augmented increase in permeability in response to hypertonicity involve an increase in NO synthesis by upregulation of the calcium-dependent eNOS.
Molecular Interdiffusion between Stacked Layers by Solution and Thermal Annealing Processes in Organic Light Emitting Devices (2015)

In organic light emitting devices (OLEDs), interfacial structures between multilayers have large impacts on the characteristics of OLEDs. Herein, we succeeded in revealing the interdiffusion in solution processed and thermal annealed OLEDs by neutron reflectometry. We investigated interfaces between a polymer under layer and small molecules upper layer. The small molecules diffused into the swollen polymer layer during the interfacial formation by the solution process, but the polymer did not diffuse into the small molecules layer. At temperatures close to the glass transition temperatures of the materials, asymmetric molecular diffusion was observed. We elucidated the effects of the interdiffusion on the characteristics of OLEDs. Partially mixing the interface improved the current efficiencies due to suppressed triplet-polaron quenching at the interface. Controlling and understanding the interfacial structures of the miultilayers will be more important to improve the OLED characteristics.
Effect of thermal processing on silver thin films of varying thickness deposited on zinc oxide and indium tin oxide (2009)

Silver films of varying thicknesses (25, 45, and 60 nm) were deposited on indium tin oxide (ITO) on silicon and zinc oxide (ZnO) on silicon. The films were annealed in vacuum for 1 h at different temperatures (300–650 °C). Four-point-probe measurements were used to determine the resistivity of the films. All films showed an abrupt change in resistivity beyond an onset temperature that varied with thickness. Rutherford backscattering spectrometry measurements revealed agglomeration of the Ag films upon annealing as being responsible for the resistivity change. X-ray pole figure analysis determined that the annealed films took on a preferential ⟨111⟩ texturing; however, the degree of texturing was significantly higher in Ag/ZnO/Si than in Ag/ITO/Si samples. This observation was accounted for by interface energy minimization. Atomic force microscopy (AFM) measurements revealed an increasing surface roughness of the annealed films with temperature. The resistivity behavior was explained by the counterbalancing effects of increasing crystallinity and surface roughness. Average surface roughness obtained from the AFM measurements were also used to model the agglomeration of Ag based on Ostwald ripening theory.
Split to Learn: Gradient Split for Multi-Task Human Image Analysis (2023)

This paper presents an approach to train a unified deep network that simultaneously solves multiple human-related tasks. A multi-task framework is favorable for sharing information across tasks under restricted computational resources. However, tasks not only share information but may also compete for resources and conflict with each other, making the optimization of shared parameters difficult and leading to suboptimal performance. We propose a simple but effective training scheme called GradSplit that alleviates this issue by utilizing asymmetric inter-task relations. Specifically, at each convolution module, it splits features into T groups for T tasks and trains each group only using the gradient back-propagated from the task losses with which it does not have conflicts. During training, we apply GradSplit to a series of convolution modules. As a result, each module is trained to generate a set of task-specific features using the shared features from the previous module. This enables a network to use complementary information across tasks while circumventing gradient conflicts. Experimental results show that GradSplit achieves a better accuracy-efficiency trade-off than existing methods. It minimizes accuracy drop caused by task conflicts while significantly saving compute resources in terms of both FLOPs and memory at inference. We further show that GradSplit achieves higher cross-dataset accuracy compared to single-task and other multi-task networks.
The InterMesh Network Architecture (2007)

The rapid spread of mobile devices, the emergence of key wireless technologies, and the nomadic user and computing lifestyles on current networks are continuously evolving in synergy. MANETs, WSNs, and WMNs are examples of self-organizing unstructured networks that have their local communication paradigms and are optimized to perform under their particular physical constraints. Wireless Mesh Networks (WMNs) are particularly interesting because of their ability to operate in a pure ad-hoc mode or to include some infrastructural components, making them suitable for a multitude of applications. Inter-networking among the heterogeneous access networks is currently offered by the Internet Protocol (IP). However, the evolution of and the innovation within these networks is greatly hindered by the rigidity of the current Internet implementation and its lag in efficiently supporting flexible unstructured communication paradigms. To broaden the user's innovation space and to efficiently embrace the characteristics of emerging networks, clean-slate architectural approaches are being pursued. In this paper, we propose InterMesh, a novel iner-networking platform for wireless mesh networks. InterMesh enables heterogeneous access networks to converge at novel Persistent Identification and Networking Layer (PINL), providing a seamless service to individual network entities. This paper identifies the key concepts behind the InterMesh network platform, presents an interesting prototype implementation that can coexist with today's Internet while still be able to evolve separately, and discusses some preliminary performance results of the prototype.
Practical methods for generating alternating magnetic fields for biomedical research (2017)

Alternating magnetic fields (AMFs) cause magnetic nanoparticles (MNPs) to dissipate heat while leaving surrounding tissue unharmed, a mechanism that serves as the basis for a variety of emerging biomedical technologies. Unfortunately, the challenges and costs of developing experimental setups commonly used to produce AMFs with suitable field amplitudes and frequencies present a barrier to researchers. This paper first presents a simple, cost-effective, and robust alternative for small AMF working volumes that uses soft ferromagnetic cores to focus the flux into a gap. As the experimental length scale increases to accommodate animal models (working volumes of 100s of cm3 or greater), poor thermal conductivity and volumetrically scaled core losses render that strategy ineffective. Comparatively feasible strategies for these larger volumes instead use low loss resonant tank circuits to generate circulating currents of 1 kA or greater in order to produce the comparable field amplitudes. These principles can be extended to the problem of identifying practical routes for scaling AMF setups to humans, an infrequently acknowledged challenge that influences the extent to which many applications of MNPs may ever become clinically relevant.
CD8+ T cell clonotypes from prior SARS-CoV-2 infection predominate during the cellular immune response to mRNA vaccination (2022)

Almost three years into the SARS-CoV-2 pandemic, hybrid immunity is highly prevalent worldwide and more protective than vaccination or prior infection alone. Given emerging resistance of variant strains to neutralizing antibodies (nAb), it is likely that T cells contribute to this protection. To understand how sequential SARS-CoV-2 infection and mRNA-vectored SARS-CoV-2 spike (S) vaccines affect T cell clonotype-level expansion kinetics, we identified and cross-referenced TCR sequences from thousands of S-reactive single cells against deeply sequenced peripheral blood TCR repertoires longitudinally collected from persons during COVID-19 convalescence through booster vaccination. Successive vaccinations recalled memory T cells and elicited antigen-specific T cell clonotypes not detected after infection. Vaccine-related recruitment of novel clonotypes and the expansion of S-specific clones were most strongly observed for CD8<sup>+</sup> T cells. Severe COVID-19 illness was associated with a more diverse CD4<sup>+</sup> T cell response to SARS-CoV-2 both prior to and after mRNA vaccination, suggesting imprinting of CD4<sup>+</sup> T cells by severe infection. TCR sequence similarity search algorithms revealed myriad public TCR clusters correlating with human leukocyte antigen (HLA) alleles. Selected TCRs from distinct clusters functionally recognized S in the predicted HLA context, with fine viral peptide requirements differing between TCRs. Most subjects tested had S-specific T cells in the nasal mucosa after a 3rd mRNA vaccine dose. The blood and nasal T cell responses to vaccination revealed by clonal tracking were more heterogeneous than nAb boosts. Analysis of bulk and single cell TCR sequences reveals T cell kinetics and diversity at the clonotype level, without requiring prior knowledge of T cell epitopes or HLA restriction, providing a roadmap for rapid assessment of T cell responses to emerging pathogens.