gebhart/patrepeval huggingface dataset:
A peak detector that picks more than peaks (2003)

The sensor measurement data supplied to an automatic tracking system is often provided by a peak detector or peak picker. Here it is assumed that digital processing is used for all steps from signal processing onwards. The peak detector follows the signal processing step and converts the received signals into radar measurements. It does this by interpolating the position about local peaks which are above a detection threshold. The peak detector output gives target and clutter measurements which are described by different probability density functions (PDFs). The probabilistic data association filter (PDAF) uses a priori models for the target and clutter distributions. The PDAF has since been extended to include a nonuniform clutter distribution. This paper outlines this extension and also describes another peak detector derived parameter, namely the curvature of a peak. It shows the difference between the peak curvature PDFs for targets and clutter from experimental over-the-horizon radar (OTHR) data. The extension of the PDAF to effectively use peak curvature is then outlined. The examples of performance show the impact of including these extra parameters from a peak detector. These results are based on data recorded from Australia's OTHR, Jindalee.
Reflecting Microscopes with Spherical Mirrors (1951)

Previous designs of reflecting microscope objectives using spherical mirrors have approximated to a design derived from theory due to Schwarzschild, consisting of two concentric mirrors giving a central obstruction of the numerical aperture of 45 percent. Except for the designs of Matsukov, where the central obstruction takes even higher values, the numerical aperture has been limited to 0.5. Theory has been taken as indicating that there was little room for improvement without a high degree of asphericity in one of the mirrors. By an experimental approach, using a microscope interferometer, it is shown in the present work that the Schwarzschild conditions may be forgotten completely and very useful designs of objectives still produced for purposes where a large field area is not required. Such reflecting systems may be made little bigger than refracting objectives and have numerical aperture 0.60 and 35 percent central obstruction, and are free from spherical aberration. No refracting components or compensating lenses are employed. Mechanical parts for these objectives and a microscope stand are described.
De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2006)

The recent proliferation of novel mass spectrometers such as Fourier transform, QTOF, and OrbiTrap marks a transition into the era of precision mass spectrometry, providing a 2 orders of magnitude boost to the mass resolution, as compared to low-precision ion-trap detectors. We investigate peptide de novo sequencing by precision mass spectrometry and explore some of the differences when compared to analysis of low-precision data. We demonstrate how the dramatically improved performance of de novo sequencing with precision mass spectrometry paves the way for novel approaches to peptide identification that are based on direct sequence lookups, rather than comparisons of spectra to a database. With the direct sequence lookup, it is not only possible to search a database very efficiently, but also to use the database in novel ways, such as searching for products of alternative splicing or products of fusion proteins in cancer. Our de novo sequencing software is available for download at http://peptide.ucsd.edu/.
Monocular image depth estimation using dilated convolution and spatial pyramid polling structure (2019)

In this work, we address the problem of depth estimation from a single image. This is a challenging task because a single still image on its own does not give much depth cue, while recent advances in CNNs have made learning and predicting depth from a single image possible. We propose a new residual convolutional neural network (CNN) with dilated convolution and spatial pyramid pooling (SPP) structure to model the ambiguous mapping from a monocular 2D image to its depth map. The advantages of our method come from the use of dilated convolution and multi spatial scale information. Compared with existing deep CNN based methods, our method achieves much better results in indoor and outdoor scenarios.
Home Bus System (HBS) Interface LSI and ITS Standard Protocol Example (1986)

We first proposed in 1983 a plan for standardization of in-house information distribution networks called Home Bus System (HBS) to realize effective Home Automation (HA) in the world. In the HBS, digital data, audio and visual information of base-band and broad-band are transmitted on a single coax cable by frequency-division multiplex. In order to realize economical HA, a standard protocol for HBS was established and standardized interface LSIs were developed. These LSIs were incorporated into various equipment made by different manufacturers and usefulness of the HBS was verified by system experiments undertaken in two model houses. In this paper, the standard protocol and interface LSIs for the HBS base-band agreed on by many Japanese companies and a concrete control system for realization of HA are presented in detail.
Novel association between serum pentraxin‐2 levels and advanced fibrosis in well‐characterised patients with non‐alcoholic fatty liver disease (2015)

PTX-2 levels are significantly lower in patients with NAFLD compared to non-NAFLD controls, and decline further in patients with advanced fibrosis. PTX-2 may therefore be both a biomarker of disease and a potential target for anti-fibrotic therapy with the recombinant pentraxin-2.
Abstract P3-06-14: Identification of Prognosis-Relevant Subgroups in Patients with Chemoresistant Triple Negative Breast Cancer (2012)

Abstract Purpose: Triple-negative breast cancer (TNBC) is a highly heterogeneous disease. TNBC patients with pathologic complete response (pCR) have excellent survival, but those with residual disease after neoadjuvant chemotherapy have significantly worse outcome. However, some patients having extensive residual cancer burden after neoadjuvant chemotherapy do not relapse, and we hypothesize that there may be subgroups with diverse prognosis among these chemoresistant TNBC patients. Methods: Forty-nine cases with residual cancer from 111 TNBC patients treated with neoadjuvant chemotherapy (in M.D. Anderson Cancer Center, 2000–2006) constituted the discovery cohort. Twenty-five chemoresistant samples from 47 neoadjuvant chemotherapy-treated TNBC (in Baylor College of Medicine and Methodist Hospital, 2002–2006) were chosen for validation. Extended validation was performed in 269 operable TNBC predicted to be chemoresistant (using a JAMA-published genomic predictor) from public databases. Results: By comparing the gene expression data from cases in relapse with those from un-relapsed cases, we established a 7-gene prognostic signature (including AR, ESR2, GATA3, GBX2, KRT16, MMP28, and WNT11) using dChip and gene enrichment analyses. In the discovery cohort, the signature showed positive predictive value (PPV; i.e., cumulative relapse rate of patients predicted to relapse in 3 years) of 95.4% and negative predictive values (NPV; i.e., relapse-free survival of patients predicted not to relapse in 3 years) of 100%. In the validation cohort, the classifier predicted correctly with PPV of 75.0% and NPV of 76.9% at 3 years. Compared with patients predicted not to relapse, those predicted to relapse had a hazard ratio of 3.37 (95% CI, 1.15–9.85) for disease recurrence or death in 3 years. In an extended validation cohort of 269 patients, our signature discriminated chemoresistant TNBC in overall cohort (PPV, 52.4%; NPV, 77.7%; log rank P &lt; 0.0001), or each subset (e.g., log rank p = 0.001 for Rotterdam set; p = 0.013 for Frankfurt set), with adjusted overall hazard ratio of 2.07 (95% CI, 1.26–3.39). This signature was the only marker that could effectively predict the relapse in patients with chemoresistant TNBC. Of note, the subgroup predicted not to relapse was characterized by high expression of luminal-like genes (AR, GATA3), while the subgroup predicted to have high possibility of relapse was characterized by high expression of cancer stem cell and epithelial-to-mesenchymal transition associated genes (WNT11, MMP28). The former corresponded to the luminal AR subtype and the latter to the mesenchymal stem-like subtype, according to Pietenpol's TNBC subtype classification. Conclusion: We developed a clinically useful prognostic signature for chemoresistant TNBC. For these chemoresistant TNBC patients, new therapeutic strategies targeting AR-activation or cancer stem cells need to be developed. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-06-14.
Measuring Quantitative Virulence in the Wheat Pathogen<i>Zymoseptoria tritici</i>Using High-Throughput Automated Image Analysis (2014)

Zymoseptoria tritici, causal agent of Septoria tritici blotch on wheat, produces pycnidia in chlorotic and necrotic lesions on infected leaves. A high-throughput phenotyping method was developed based on automated digital image analysis that accurately measures the percentage of leaf area covered by lesions (PLACL) as well as pycnidia size and number. A seedling inoculation assay was conducted using 361 Z. tritici isolates originating from a controlled cross and two different winter wheat cultivars. Pycnidia size and density were found to be quantitative traits that showed a continuous distribution in the progeny. There was a weak correlation between pycnidia density and size (r = -0.27) and between pycnidia density and PLACL (r = 0.37). There were significant differences in PLACL and pycnidia density on resistant and susceptible cultivars. In all, >20% of the offspring exhibited significantly different pycnidia density on the two cultivars, consistent with host specialization. Automated image analysis provided greater accuracy and precision compared with traditional visual estimates of virulence. These results show that digital image analysis provides a powerful tool for measuring differences in quantitative virulence among strains of Z. tritici.
Multi-product allocation under imperfect raw material supply conditions: the case of fish products (1996)

Abstract An otherwise conventional model of multi-product supply is applied to circumstances in which the raw material is provided under highly imperfect market conditions. Satisfactory results are obtained from a specification in which the supply allocation is a function of both the price and the quantity of the raw material.
Calvarial development: cells and mechanics (2005)

Purpose of review: Calvarial skeletal structures are derivatives of mesenchymal cells. In development, mesenchymal cells derived from the neural crest and mesoderm differentiate to form most craniofacial structures, including calvarial bone and cranial sutures, teeth, periodontal ligament, cartilage, muscles and subcutaneous fibrous and adipose tissues. The present review synthesizes recent key findings of mechanical modulation of calvarial growth. Recent findings: All mechanically regulated genes and matrix molecules in cranial sutures are some of the same genes and molecules involved in natural development. Intrinsic mechanical stress, likely in the magnitude of nanoNewtons or picoNewtons, is involved in calvarial development and skeletal patterning. The cranial vault consists of a soft cranial suture interface between mineralized bones and presents a compelling model for studying mechanical modulation of skeletal patterning. Summary: Recent findings have enhanced our understanding of mechanical modulation of calvarial growth. What was previously considered to be exclusively hereditarily programmed development of the cranial base growth plate is now demonstrated to be readily modulated by mechanical stress. By contrast, cranial sutures have been assumed to be incapable of self-initiated growth and to grow only when the two sutural edges are separated by tensile forces resulting from the rapidly growing brain. Recent data suggest not only that sutural strain from daily brain growth is too small to induce sutural osteogenesis, but also that substantial brain growth is over before the completion of sutural growth. In-vivo studies demonstrate strain-induced sutural osteogenesis in response to both tensile and compressive strain experienced at the suture. Thus, genetic inheritance and mechanical stress play inseparable roles in calvarial development.
Oil debris monitoring in aerospace engines and helicopter transmissions (2012)

Oil debris monitoring is one of the important elements of an engine condition monitoring system. It is the activity that detects impending failures of bearings, gears, splines and other oil wetted components. There are three traditional methods or devices that are in common use in aircraft gas turbine engines: spectrometric oil analysis (SOA), magnetic chip collectors (also called magnetic plugs or magnetic chip detectors) and electric chip detectors. The traditional methods are described in sufficient detail to provide an understanding of what is driving the need for advanced debris monitoring technologies. New areas of development are introduced in the proceeding to the extent that proprietary and patentable features are not disclosed.
Update on current and potential nanoparticle cancer therapies (2013)

A number of intriguing nanoparticle therapies are being tested in preclinical and clinical trials. Nanoparticles with increasing molecular sophistication, specific targeting properties, and unique mechanisms of action will find their way to the clinic. Certainly, nanoparticle-based therapies will be increasingly represented in drug development pipelines, and will continue to provide efficacious and well tolerated drug options for patients with cancer.
Lentiviral Vectors for the Treatment and Prevention of Cystic Fibrosis Lung Disease (2019)

Despite the continued development of cystic fibrosis transmembrane conductance regulator (CFTR) modulator drugs for the treatment of cystic fibrosis (CF), the need for mutation agnostic treatments remains. In a sub-group of CF individuals with mutations that may not respond to modulators, such as those with nonsense mutations, CFTR gene transfer to airway epithelia offers the potential for an effective treatment. Lentiviral vectors are well-suited for this purpose because they transduce nondividing cells, and provide long-term transgene expression. Studies in primary cultures of human CF airway epithelia and CF animal models demonstrate the long-term correction of CF phenotypes and low immunogenicity using lentiviral vectors. Further development of CF gene therapy requires the investigation of optimal CFTR expression in the airways. Lentiviral vectors with improved safety features have minimized insertional mutagenesis safety concerns raised in early clinical trials for severe combined immunodeficiency using γ-retroviral vectors. Recent clinical trials using improved lentiviral vectors support the feasibility and safety of lentiviral gene therapy for monogenetic diseases. While work remains to be done before CF gene therapy reaches the bedside, recent advances in lentiviral vector development reviewed here are encouraging and suggest it could be tested in clinical studies in the near future.
An Experimental Study of Flow and Heat Transfer in Wavy Passages (1997)

Wavy passages are one of the many devices being considered by manufacturers in the\nHV ACIR industry to increase the air-side heat transfer coefficient for a variety of heat\nexchanger applications. The purpose of this research is to obtain a better understanding of\nthe flow instabilities and heat transfer in wavy passages so that design guidelines may be\ndeveloped. Flow visualization experiments on twelve different geometries revealed the flow\npatterns and behavior in laminar wavy-channel flow. At low Reynolds numbers, there is\nevidence of macroscopic mixing between the core flow and the near-wall fluid. The onset\nlocation of this macroscopic mixing moves closer to the entrance of the channel with\nincreasing Reynolds number. The instabilities in the cp=180?? geometry appear to be\nfundamentally different from the instabilities in the cp=O?? and the cp=90?? geometries. A\nparametric study revealed that for a given Reynolds number, instabilities in the cp=00 and the\ncp=90?? geometries occur at a farther upstream location than in the cp=180?? geometries.\nRelative wavelength did not affect channel performance in the experimental range. An\nincrease in the relative amplitude of the channel delayed the intial onset of instability in the\nwavy passage, but had little effect as the location of the onset of instabiltiy moved closer to\nthe entrance of the channel. Heat transfer experiments confirmed that the instabilities\nobserved in the flow visualization experiments enhance heat transfer. The results of this\nresearch may help in determining wavy channel geometries with high heat transfer rates for a\nparticular application.
Multifunctional nanocomposites constructed from Fe3O4–Au nanoparticle cores and a porous silica shell in the solution phase (2011)

This work is directed towards the synthesis of multifunctional nanoparticles composed of Fe(3)O(4)-Au nanocomposite cores and a porous silica shell (Fe(3)O(4)-Au/pSiO(2)), aimed at ensuring the stability, magnetic, and optical properties of magnetic-gold nanocomposite simultaneously. The prepared Fe(3)O(4)-Au/pSiO(2) core/shell nanoparticles are characterized by means of TEM, N(2) adsorption-desorption isotherms, FTIR, XRD, UV-vis, and VSM. Meanwhile, as an example of the applications, catalytic activity of the porous silica shell-encapsulated Fe(3)O(4)-Au nanoparticles is investigated by choosing a model reaction, reduction of o-nitroaniline to benzenediamine by NaBH(4). Due to the existence of porous silica shells, the reaction with Fe(3)O(4)-Au/pSiO(2) core/shell nanoparticles as a catalyst follows second-order kinetics with the rate constant (k) of about 0.0165 l mol(-1) s(-1), remarkably different from the first-order kinetics with the k of about 0.002 s(-1) for the reduction reaction with the core Fe(3)O(4)-Au nanoparticles as a catalyst.
Horizontal Transfer of the High-Pathogenicity Island of<i>Yersinia pseudotuberculosis</i> (2005)

The horizontal transfer of genetic elements plays a major role in bacterial evolution. The high-pathogenicity island (HPI), which codes for an iron uptake system, is present and highly conserved in various Enterobacteriaceae, suggesting its recent acquisition by lateral gene transfer. The aim of this work was to determine whether the HPI has kept its ability to be transmitted horizontally. We demonstrate here that the HPI is indeed transferable from a donor to a recipient Yersinia pseudotuberculosis strain. This transfer was observable only when the donor and recipient bacteria were cocultured at low temperatures in a liquid medium. When optimized conditions were used (bacteria actively growing in an iron-deprived medium at 4 degrees C), the frequency of HPI transfer reached approximately 10(-8). The island was transferable to various serotype I strains of Y. pseudotuberculosis and to Yersinia pestis, but not to Y. pseudotuberculosis strains of serotypes II and IV or to Yersinia enterocolitica. Upon transfer, the HPI was inserted almost systematically into the asn3 tRNA locus. Acquisition of the HPI resulted in the loss of the resident island, suggesting an incompatibility between two copies of the HPI within the same strain. Transfer of the island did not require a functional HPI-borne insertion-excision machinery and was RecA dependent in the recipient but not the donor strain, suggesting that integration of the island into the recipient chromosome occurs via a mechanism of homologous recombination. This lateral transfer also involved the HPI-adjacent sequences, leading to the mobilization of a chromosomal region at least 46 kb in size.
Sustained Activation of the Raf-MEK-ERK Pathway Elicits Cytokine Unresponsiveness in T Cells (1999)

Activation of T cells via the TCR and other costimulatory receptors triggers a number of signaling cascades. Among them, the Ras-activated Raf-mitogen-activated protein/extracellular signal-related kinase (ERK) kinase (MEK)-ERK signaling cascade has been demonstrated to be crucial for both T cell development and activation. It has previously been demonstrated that high doses of Ag or anti-CD3 mAb are able to induce in T cells a nonresponsive state to subsequent treatment with cytokines such as IL-2. The precise biochemical mechanisms underlying this effect are not fully characterized. In this study, we demonstrate that cytokine nonresponsiveness is accompanied by the induction of the cyclin-dependent kinase inhibitor p21Cip1 that is mediated, at least in part, by the activation of the Raf-MEK-ERK pathway. Furthermore, we demonstrate that selective activation of the Raf-MEK-ERK signaling pathway in T cells is sufficient to induce cytokine nonresponsiveness in both a T cell clone and naive primary T cells. In this case, nonresponsiveness is accompanied by the induction of p21Cip1 and the prevention of p27Kip1 down-regulation, leading to inhibition of cyclin E/cyclin-dependent kinase 2 activity. These data suggest that anti-CD3 mAb-induced cytokine nonresponsiveness may be a consequence of hyperactivation of the Raf-MEK-ERK pathway, leading to alterations in the expression of key cell cycle regulators. These observations may provide a novel insight into the mechanisms of induction of peripheral tolerance.
Investigation with chitosan-oxalate oxidase-catalase conjugate for degrading oxalate from hyperoxaluric rat chyme. (1997)

Enteric hyperoxaluria manifests due to hyperabsorption of dietary oxalate, secondary to a variety of chronic gastrointestinal disorders. The potential use of chitosan immobilized oxalate oxidase-catalase conjugate to deplete the oxalate content of food materials, while they are in the digestive tract has been evaluated by treating rat stomach chyme with such an enzyme preparation. Oxalate oxidase, obtained from beet stem, was adsorbed on chitosan along with catalase and then cross linked with glutaraldehyde to stabilize the derivative. This chemical modification of oxalate oxidase brought about a shift in its optimal pH from 4.2 to 3.8 with a marginal increase in its K(m). Compared to native enzyme, the modified oxalate oxidase exhibited increased storage stability, higher thermal stability and enhanced resistance to proteolytic digestion and heavy metal inactivation. These improved properties of the immobilized oxalate oxidase possibly render it suitable for oral administration under hyperoxaluric conditions.
Inferring MicroRNA Activities by Combining Gene Expression with MicroRNA Target Prediction (2008)

A huge amount of gene expression data sets are available in the literature, but miRNA regulation underlying these data sets is largely unknown. The method is easy to be implemented and can be used to investigate the miRNA effective regulation underlying the expression change profiles obtained from microarray experiments.
Mesoporous carbon nanofibers with a high surface area electrospun from thermoplastic polyvinylpyrrolidone (2012)

Carbon nanofibers (CNFs) have been synthesized from thermoplastic polyvinylpyrrolidone (PVP) using electrospinning in combination with a novel three-step heat treatment process, which successfully stabilizes the fibrous morphology before carbonization that was proven to be difficult for thermoplastic polymers other than polyacrylonitrile (PAN). These CNFs are both mesoporous and microporous with high surface areas without subsequent activation, and thus overcome the limitations of PAN based CNFs, and are processed in an environmentally friendly and more cost effective manner. The effects of heat treatment parameters and precursor concentration on the morphologies and porous properties of CNFs have been investigated, and their application as anodes for lithium ion batteries has also been demonstrated.