gebhart/patrepeval huggingface dataset:
Detecting and assessing macrophages <i>in vivo</i> to evaluate atherosclerosis noninvasively using molecular MRI (2007)

We investigated the ability of targeted immunomicelles to detect and assess macrophages in atherosclerotic plaque using MRI in vivo. There is a large clinical need for a noninvasive tool to assess atherosclerosis from a molecular and cellular standpoint. Macrophages play a central role in atherosclerosis and are associated with plaques vulnerable to rupture. Therefore, macrophage scavenger receptor (MSR) was chosen as a target for molecular MRI. MSR-targeted immunomicelles, micelles, and gadolinium-diethyltriaminepentaacetic acid (DTPA) were tested in ApoE-/- and WT mice by using in vivo MRI. Confocal laser-scanning microscopy colocalization, macrophage immunostaining and MRI correlation, competitive inhibition, and various other analyses were performed. In vivo MRI revealed that at 24 h postinjection, immunomicelles provided a 79% increase in signal intensity of atherosclerotic aortas in ApoE-/- mice compared with only 34% using untargeted micelles and no enhancement using gadolinium-DTPA. Confocal laser-scanning microscopy revealed colocalization between fluorescent immunomicelles and macrophages in plaques. There was a strong correlation between macrophage content in atherosclerotic plaques and the matched in vivo MRI results as measured by the percent normalized enhancement ratio. Monoclonal antibodies to MSR were able to significantly hinder immunomicelles from providing contrast enhancement of atherosclerotic vessels in vivo. Immunomicelles provided excellent validated in vivo enhancement of atherosclerotic plaques. The enhancement seen is related to the macrophage content of the atherosclerotic vessel areas imaged. Immunomicelles may aid in the detection of high macrophage content associated with plaques vulnerable to rupture.
Unsupervised deconvolution of molecular heterogeneity uncovers novel signatures and glia-neuron ratio (2018)

While the two major types of cells in the brain are known to be glia and neuron, the true ratio of glia to neurons in the brain remains a mystery. One of recent studies reveals that the ratio of glia to neurons in the brain varies from one region to another, sometimes dramatically. Here we report a study that applies UNsupervised DecOnvolution version 2 (UNDO2.0) software tool to the gene expression and DNA methylation data acquired from heterogeneous brain tissues. UNDO2.0 can automatically detect cell-specific markers located on the scatter radii of mixed gene expressions, estimate cellular proportions in each sample, and deconvolve mixed expressions into cell-specific expression profiles. The in-silico analysis uncovers many novel marker genes and provides a molecularly-defined 2.2:1 ratio of glia to neurons in the brain.
Characterization of fluctuations of impedance and scattering matrices in wave chaotic scattering (2006)

In wave chaotic scattering, statistical fluctuations of the scattering matrix S and the impedance matrix Z depend both on universal properties and on nonuniversal details of how the scatterer is coupled to external channels. This paper considers the impedance and scattering variance ratios, Xi(z) and Xi(s), where Xi(z) = Var[Z(ij)]/{Var[Z(ii)]Var[Z(jj)]}1/2, Xi(s) = Var[S(ij)]/{Var[S(ii)]Var[S(jj)]}1/2, and Var[.] denotes variance. Xi(z) is shown to be a universal function of distributed losses within the scatterer. That is, Xi(z) is independent of nonuniversal coupling details. This contrasts with s for which universality applies only in the large loss limit. Explicit results are given for Xi(z) for time reversal symmetric and broken time reversal symmetric systems. Experimental tests of the theory are presented using data taken from scattering measurements on a chaotic microwave cavity.
Long-term outcomes of patients undergoing tricuspid valve surgery† (2019)

TV surgery is associated with poor outcomes due to multiple patient comorbidities. TV repair results in better survival compared to replacement in patients with similar comorbidities with no increased risk of getting a reoperation.
Novel peptides extracted from Muraenesox cinereus bone promote calcium transport, osteoblast differentiation, and calcium absorption (2022)

Extracting peptides from fish bones as calcium supplements is of great significance for patients with osteoporosis. Novel peptides were obtained from Muraenesox cinereus bone (MCBP) by enzymatic hydrolysis and membrane separation. Molecular dynamics simulation and electron microscope analysis shown MCBP could chelate with calcium ions. A Caco-2 cell monolayer model was used to investigate the effect of peptide–calcium chelates on promoting calcium transport. MC3T3-E1 osteoblasts were treated with different concentrations of MCBP (0, 0.25, 0.5, or 1 mg/mL) to analyze the effects of MCBP on calcium absorption and cell differentiation factors. The bone formation of zebrafish evaluate the therapeutic effect of MCBP on the zebrafish OP model. The results showed that there were at least 13 kinds of calcium chelation modes in the mixed peptide, and peptide–calcium chelate could significantly improve calcium transport in the Caco-2 cell monolayer. After 14 days of culture with different concentrations of MCBP, the calcium deposition in MC3T3-E1 cells increased significantly. The type I collagen (COL-I), osteocalcin (OCN) and run-related transcription factor 2 (RUNX2), and activities of alkaline phosphatase (ALP) were dose-dependent with MCBP. MCBP can increase bone mineral density in an OP model of zebrafish. After being treated with MCBP, the expression levels of ALP, OCN, osteoprotegerin (OPG) and transforming growth factor-β (TGF-β) in the model group increased, while the expression levels of tartrate-resistant acid phosphatase (TRAP) decreased. The results indicated that MCBP may act as a nutritional food and provide an effective means for dietary supplementation in OP patients.
Replication of Centromere II of <i>Schizosaccharomyces pombe</i> (1995)

The centromeric DNAs of Schizosaccharomyces pombe chromosomes resemble those of higher eukaryotes in being large and composed predominantly of repeated sequences. To begin a detailed analysis of the mode of replication of a complex centromere, we examined whether any sequences within S. pombe centromere II (cen2) have the ability to mediate autonomous replication. We found a high density of segments with such activity, including at least eight different regions comprising most of the repeated and unique centromeric DNA elements. A physical mapping analysis using two-dimensional gels showed that autonomous replication initiated within the S. pombe sequences in each plasmid. A two-dimensional gel analysis of replication on the chromosomes revealed that the K and L repeat elements, which occur in multiple copies at all three centromeres and comprise approximately 70% of total centromeric DNA mass in S. pombe, are both sites of replication initiation. In contrast, the unique cen2 central core, which contains multiple segments that can support autonomous replication, appears to be repressed for initiation on the chromosome. We discuss the implications of these findings for our understanding of DNA replication and centromere function.
Overview: The Design, Adoption, and Analysis of a Visual Document Mining Tool for Investigative Journalists (2014)

For an investigative journalist, a large collection of documents obtained from a Freedom of Information Act request or a leak is both a blessing and a curse: such material may contain multiple newsworthy stories, but it can be difficult and time consuming to find relevant documents. Standard text search is useful, but even if the search target is known it may not be possible to formulate an effective query. In addition, summarization is an important non-search task. We present Overview, an application for the systematic analysis of large document collections based on document clustering, visualization, and tagging. This work contributes to the small set of design studies which evaluate a visualization system "in the wild", and we report on six case studies where Overview was voluntarily used by self-initiated journalists to produce published stories. We find that the frequently-used language of "exploring" a document collection is both too vague and too narrow to capture how journalists actually used our application. Our iterative process, including multiple rounds of deployment and observations of real world usage, led to a much more specific characterization of tasks. We analyze and justify the visual encoding and interaction techniques used in Overview's design with respect to our final task abstractions, and propose generalizable lessons for visualization design methodology.
ALMmap: Technology Mapping for FPGAs With Adaptive Logic Modules (2012)

Modern field programmable gate arrays like Altera's Stratix Series have adopted the adaptive logic module (ALM) structure due to its potential performance and area advantages. An ALM can implement a single logic function or can be fractured into two smaller lookup tables (LUTs). In this paper, we propose an ALM mapping algorithm, ALMmap, for area minimization with bounded depth. We revamp the traditional iterative cut-based mapping flow and introduce a procedure for bounded depth mapping generation with dynamic area recovery that effectively combines cut selection, mapping, and area recovery together. In addition, we introduce a new procedure for computing cut set for ALM minimization under a depth constraint. The notion of area flow which has been used successfully for cut selection to reduce LUT count is revised for cut selection to reduce ALM count. ALMmap obtains depth optimal solutions that are 25.6% and 11.6% smaller, on average, than those produced by a classical mapper and WireMap, respectively.
31P Nuclear Magnetic Resonance Spectroscopy: Neurodevelopment and Schizophrenia (1993)

A number of studies have demonstrated alterations in the structure and function of the frontolimbic system in some schizophrenic patients. Recent in vivo phosphorus-31 nuclear magnetic resonance studies of the dorsal prefrontal cortex in neuroleptic-naive, first-episode schizophrenic patients and matched controls have shown evidence of alterations in membrane phospholipid and energy metabolism. The membrane alterations observed in the schizophrenic patients are compatible with either premature aging or altered timing and exaggeration of regressive events occurring during normal brain development. These molecular changes may precede onset of clinical symptoms and brain structural changes in schizophrenia and suggest fresh approaches to the pathogenesis and treatment of this illness.
A Novel Minimum-Phase Dual-Inductor Hybrid Boost Converter with PWM Voltage-Mode Controller (2021)

This paper presents a new dual-inductor hybrid boost converter (DI-HBOC) with two inductors located at the output. This structure allows continuous current delivered to the load, thus, reducing the output filtering capacitor size and the output voltage ripple. By relocating the inductor at the output, which is the lower current path, the conduction loss on the inductor can be significantly reduced. The right half plane zero (RHPZ) in the control-to-output transfer function can also be eliminated; therefore, a simple pulse-width modulation (PWM) voltage-mode controller can be used for the proposed DI-HBOC while still achieving high closed-loop bandwidth and fast transient response. The distinct features of the proposed converter are analytically demonstrated. A 12-to 24 V DI-HBOC and a conventional BOC (CBOC) using low-ÆoN GaN switches with PWM voltage-mode controller are also implemented in PSIM for verification and comparison. The simulated peak power efficiency is 97.4 % that is 1.17 % higher than the CBOC. At 3 A load current, the power efficiency is improved by 9.7 % and the output ripple is only 17.5 mV, 6x lower than in CBOC.
A comparison of pressure calculation methods that subtract near field singularities from analytical expressions developed for triangular apertures (2006)

Previous simulation studies have shown that the fast nearfield method (FNM) is faster and more accurate than the impulse response and rectangular radiator methods for nearfield pressure calculations. The FNM achieves this advantage by subtracting a singularity from a one-dimensional integral expression, which improves the numerical convergence relative to these other techniques. A related approach subtracts a singularity from the two-dimensional (2D) Rayleigh integral, thereby separating the Rayleigh integral into two parts. In this approach, one integral is evaluated analytically and the remaining terms are evaluated numerically. Numerical calculations are performed with a seven point Gauss quadrature rule. This approach is evaluated for a triangular source and compared to results obtained from FNM calculations. For larger triangular sources, the 2D Rayleigh integral is subdivided into smaller triangular patches, and then the results are superposed. Results show that for an equilateral triangle with sides equal to one wavelength, this approach achieves a 10% peak error without subdividing the source, and a 1% peak error is obtained when the source is subdivided into four smaller triangles. Computation times with this approach are 0.140s and 0.2190s for 10% and 1% peak errors, respectively, whereas the FNM results for the same peak errors are 0.031s and 0.047s for a reduction in the computation time by a factor of 4.52 and 4.66, respectively. This shows that FNM calculations converge more rapidly than the method that subtracts the singularity from the 2D Rayleigh integral.
Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques (2019)

The proposed models have been adopted to implement a web-based tool (GBSTyper), which is now freely accessible at http://csb.cse.yzu.edu.tw/GBSTyper/, for providing efficient and effective detection of GBS serotypes based on a MALDI-TOF MS spectrum. Overall, this work has demonstrated that the combination of MALDI-TOF MS and machine intelligence could provide a practical means of clinical pathogen testing.
Phosphite cannot be used as a phosphorus source but is non-toxic for microalgae (2014)

Phosphorous (P) plays a critical role for all living organisms as a structural component of RNA, DNA and phospholipids. Microalgae are autotrophs organisms that have been reported to only assimilate the fully oxidized phosphate (Pi) as P source. However, there are microorganisms capable of utilizing P reduced compounds (i.e. phosphite (Phi) and hypophosphite) as a sole P source, such as bacteria and cyanobacteria. In this study, we evaluated whether microalgae, such as Chlamydomonas reinhardtii, Botryococcus braunii and Ettlia oleoabundans, are capable of using Phi as a sole P source. Our studies revealed that these three microalgae are unable to use Phi as a sole P source. We also found that when Phi is present at concentrations equal or higher than that of Pi, Phi has an inhibitory effect on C. reinhardtii growth. However, since C. reinhardtii was able to survive for a long period of cultivation in the presence of high concentrations of Phi and to recover cell division capacity after transfer to media containing Pi, we noticed that Phi is not toxic for this microalga. We propose that the inhibitory effect of Phi on C. reinhardtii growth might be caused, at least in part, by a competition between the transport of Pi and Phi.
Efficacy of a Temperature-Sensitive Mycoplasma synoviae Live Vaccine (1998)

A temperature-sensitive clone of Mycoplasma synoviae (MS), MS-H, derived from the chemical mutagenesis of the Australian field isolate 86079/7NS, was investigated for efficacy as a live vaccine. Titers of MS-H vaccine ranged between 1.16 x 10(8) and 8.4 x 10(8) color changing units/ml when incubated at 33 C and were consistently > or = 10(2) lower when incubated at 39.5 C. Laboratory-produced MS-H vaccine protected 8 out of 10 specific-pathogen-free Webster white leghorn chickens against a combined experimental challenge of aerosols of the virulent wild MS strain 88064/FP and T-strain infectious bronchitis vaccine administered intratracheally. Laboratory and commercially produced vaccines were compared for efficacy against thoracic air sac challenge, with both achieving similar levels of air sac protection. Air sac lesion incidences of five air sacs with lesions out of 32 and four out of 32 were seen in groups vaccinated with laboratory and commercial vaccines, respectively, compared with 13 out of 20 in nonvaccinated specific-pathogen-free hybrid white leghorn chickens. An attempt to determine the dose response of the commercial vaccine was conducted with 0.5, 2, and 4 times the standard dose. Air sac lesion incidences of 16 air sacs with lesions out of 32 in the 0.5 times, 11 out of 32 in the 2 times, and 1 out of 32 in the 4 times dose groups were observed.
Critical Fujita Exponent for the Porous Medium Equation in ${\mathbb R}^{{N}}$ with hole (2020)

We study the large time behavior of solutions to the Neumann Problem of the porous medium equation. It is shown that the critical Fujita exponent is determined not only by the spatial dimension and the nonlinear exponent, but also by the coefficient $k$ of the first-order term.
Ab Initio Study on Oxygen Doping of (5,4), (6,4), (6,5), and (8,6) Carbon Nanotubes (2015)

Oxygen doping of single-wall carbon nanotubes (SWCNTs) exposed to ozone and light has attracted attention because of their greater luminescence quantum yield than that of pristine CNTs. The luminescence at E11*, which is red-shifted from E11 for pristine CNTs, originating from the oxidation appears to be also observed for small-diameter CNTs in chirality separation experiments without a particular oxidation treatment. To understand this phenomenon, we performed ab initio calculations for the adsorption of oxygen molecules (O2) onto realistic models of chiral CNTs. We found that the energy barrier from the physisorption of O2 to the chemisorption is lower than that of the reverse reaction for (6,4) nanotubes, whereas the relation is opposite for (8,6) nanotubes, consistent with the distinct luminescence peak at E11* observed for (6,4) nanotubes and with the lack of a pronounced luminescence peak for larger-diameter (8,6) nanotubes in the chirality separation experiments. As also proposed for ozone oxidation, one of the final products was found to be the isolated ether structure, whose ground state band gap is slightly narrower than that of pristine CNTs.
Refinement and expansion of signaling pathways: The osmotic response network in yeast (2007)

The analysis of large-scale genome-wide experiments carries the promise of dramatically broadening our understanding on biological networks. The challenge of systematic integration of experimental results with established biological knowledge on a pathway is still unanswered. Here we present a methodology that attempts to answer this challenge when investigating signaling pathways. We formalize existing qualitative knowledge as a probabilistic model that depicts known interactions between molecules (genes, proteins, etc.) as a network and known regulatory relations as logics. We present algorithms that analyze experimental results (e.g., transcription profiles) vis-à-vis the model and propose improvements to the model based on the fit to the experimental data. These algorithms refine the relations between model components, as well as expand the model to include new components that are regulated by components of the original network. Using our methodology, we have modeled together the knowledge on four established signaling pathways related to osmotic shock response in Saccharomyces cerevisiae. Using over 100 published transcription profiles, our refinement methodology revealed three cross talks in the network. The expansion procedure identified with high confidence large groups of genes that are coregulated by transcription factors from the original network via a common logic. The results reveal a novel delicate repressive effect of the HOG pathway on many transcriptional target genes and suggest an unexpected alternative functional mode of the MAP kinase Hog1. These results demonstrate that, by integrated analysis of data and of well-defined knowledge, one can generate concrete biological hypotheses about signaling cascades and their downstream regulatory programs.
Investigation of Initial Growth Process of GaN Film on Sapphire Using Computational Chemistry (2000)

We have performed molecular dynamics (MD) simulations and periodic density functional calculations to investigate the interatomic interactions of the GaN/sapphire (0001) interface and the energetically stable site of GaN molecule on the sapphire (0001) surface. The MD simulations indicate that the mobility of the Ga atoms is larger than that of the N atoms on the sapphire (0001) surface, as the Al–N interaction is stronger than the O–Ga interaction. The density functional calculations also suggest that the formation of the Al–N bond is most energetically stable on the sapphire (0001) surface. Since the sapphire (0001) substrate is terminated with Al atoms in the reductive atmosphere, we assumed that the formation of Al–N bonds is dominant at the GaN/sapphire (0001) interface.
Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division (2015)

To maintain cellular structure and integrity during division, Gram-negative bacteria must carefully coordinate constriction of a tripartite cell envelope of inner membrane, peptidoglycan (PG), and outer membrane (OM). It has remained enigmatic how this is accomplished. Here, we show that envelope machines facilitating septal PG synthesis (PBP1B-LpoB complex) and OM constriction (Tol system) are physically and functionally coordinated via YbgF, renamed CpoB (Coordinator of PG synthesis and OM constriction, associated with PBP1B). CpoB localizes to the septum concurrent with PBP1B-LpoB and Tol at the onset of constriction, interacts with both complexes, and regulates PBP1B activity in response to Tol energy state. This coordination links PG synthesis with OM invagination and imparts a unique mode of bifunctional PG synthase regulation by selectively modulating PBP1B cross-linking activity. Coordination of the PBP1B and Tol machines by CpoB contributes to effective PBP1B function in vivo and maintenance of cell envelope integrity during division.
Significance of HBsAg and HDVRNA levels in patients with delta hepatitis recruited in the Hep-Net/International HDV intervention trial (2006)

Aims: Hepatitis delta virus (HDV) infection is associated with severe liver disease with limited treatment options. We investigated the significance of HDV-RNA, HBsAg and HBV-DNA levels and analysed histological, biochemical and demographic parameters in patients recruited in an International-multicenter intervention trial.