gebhart/patrepeval huggingface dataset:
Data from A 3-Plex Methylation Assay Combined with the <i>FGFR3</i> Mutation Assay Sensitively Detects Recurrent Bladder Cancer in Voided Urine (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; DNA methylation is associated with bladder cancer and these modifications could serve as useful biomarkers. &lt;i&gt;FGFR3&lt;/i&gt; mutations are present in 60% to 70% of non–muscle invasive bladder cancer (NMIBC). Low-grade bladder cancer recurs in more than 50% of patients. The aim of this study is to determine the sensitivity and specificity of a urine assay for the diagnosis of recurrences in patients with a previous primary NMIBC G1/G2 by using cystoscopy as the reference standard.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We selected eight CpG islands (CGI) methylated in bladder cancer from our earlier genome-wide study. Sensitivity of the CGIs for recurrences detection was investigated on a test set of 101 preTUR urines. Specificity was determined on 70 urines from healthy males aged more than 50 years. A 3-plex assay for the best combination was developed and validated on an independent set of 95 preTUR, recurrence free, and nonmalignant urines (&lt;i&gt;n&lt;/i&gt; = 130).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The 3-plex assay identified recurrent bladder cancer in voided urine with a sensitivity of 74% in the validation set. In combination with the &lt;i&gt;FGFR3&lt;/i&gt; mutation assay, a sensitivity of 79% was reached (specificity of 77%). Sensitivity of &lt;i&gt;FGFR3&lt;/i&gt; and cytology was 52% and 57%, respectively.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; The combination of methylation and &lt;i&gt;FGFR3&lt;/i&gt; assays efficiently detects recurrent bladder cancer without the need for stratification of patients regarding methylation/mutation status of the primary tumor. We conclude that the sensitivity of this combination is in the same range as cystoscopy and paves the way for a subsequent study that investigates a modified surveillance protocol consisting of the urine test followed by cystoscopy only when the urine test is positive. &lt;i&gt;Clin Cancer Res; 19(17); 4760–9. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Role of Computed Tomography for Diagnosis and Risk Stratification of Patients With Suspected or Known Coronary Artery Disease (2014)

Cardiac computed tomographic angiography (CCTA) has emerged as a powerful imaging modality for the detection and prognostication of individuals with suspected coronary artery disease. Because calcification of coronary plaque occurs in proportion to the total atheroma volume, the initial diagnostic potential of CCTA focused on the identification and quantification of coronary calcium in low- to intermediate-risk individuals, a finding that tracks precisely with the risk of incident adverse clinical events. Beyond noncontrast detection of coronary calcium, CCTA using iodinated contrast yields incremental information about the degree and distribution of coronary plaques and stenosis, as well as vessel wall morphology and atherosclerotic plaque features. This additive information offers the promise of CCTA to provide a more comprehensive view of total atherosclerotic burden because it relates to myocardial ischemia and future adverse clinical events. Furthermore, emerging data suggest the prognostic and diagnostic importance of stenosis severity detection and atherosclerotic plaque features described by CCTA including positive remodeling, low-attenuation plaque, and spotty calcification, which have been associated with the vulnerability of plaque. We report a summary of the evidence supporting the role of CCTA in the detection of subclinical and clinical coronary artery disease in both asymptomatic and symptomatic patients and discuss the potential of CCTA to augment the identification of at-risk individuals. CCTA and coronary artery calcium scoring offer the ability to improve risk stratification, discrimination, and reclassification of the risk in patients with suspected coronary artery disease and to noninvasively determine the measures of stenosis severity and atherosclerotic plaque features.
Probabilistic Graphical Model for Auto-Annotation, Content-Based Retrieval, and Classification of TV Clips Containing Audio, Video, and Text (2007)

We present a probabilistic graphical model that learns the joint statistical structures of text, audio, and video for the purpose of classification and retrieval of multimedia documents. The proposed model, which we call multi-modal LDA (MM-LDA), builds on the basic latent Dirichlet allocation (LDA) model by postulating common hidden factors, termed topics, that are shared among the 3 data modalities. These hidden topics correspond to patterns of word co-occurrences in multimedia documents and describe how text words co-occur with certain visual and acoustic features. We demonstrate the power of MM-LDA in representing TV clips containing closed-captions, video, and audio, and show promising results in 3 challenging applications: TV clip classification, retrieval, and auto-annotation.
Animal silks: their structures, properties and artificial production (2009)

This feature article reviews recent progress in the understanding of the hierarchically organized structures, the perfectly balanced mechanical properties and the structure-property relationship of the natural animal silk fibres, as well as the experimental attempts to fabricate man-made silk fibres by means of wet spinning, dry spinning, electrospinning and transgenosis.
Statistical Development of a Duty Cycle for Plug-in Vehicles in a North American Urban Setting Using Fleet Information (2010)

Development of a daily duty cycle based on real-world driving behavior and parking times is a critical requirement in the optimal design of power-train components of a plug-in vehicle. Standard driving cycles cannot completely emulate the real-world power demand of a vehicle and its downtimes in particular. To address these shortcomings, a large database of one year of measured data collected from a fleet of 76 cars in the city of Winnipeg, MB, Canada, is obtained and is then used to develop a new duty cycle. This paper describes a methodology for statistical analysis of the fleet data, including while a vehicle is parked. Due to the intrinsic differences in vehicle usage profiles during weekdays and weekends, two 24-h duty cycles with suitable windows of opportunity for charging are developed for weekday and weekend driving patterns. The uniqueness of the proposed statistical methodology and the resulting duty cycles contribute to addressing the present shortcomings of standard driving cycles.
Theoretical Study of the Si/C Mixed Benzenes and Their Major Valence Isomers (2020)

Changes in the structures and relative stabilities of benzene and the major valence isomers fulvene, Dewar benzene, benzvalene, and prismane on the substitution of the skeletal carbons with silicon atoms in a stepwise manner have been systematically investigated by ab initio molecular orbital methods. The number and arrangement of the formal C═C, C═Si and Si═Si double bonds were found to be considerably important factors controlling the structure and relative stability of a series of the compounds for fulvene, Dewar benzene, and benzvalene analogues. Also, the applicability of “π-electron-holding ability” proposed for the planarity of heavy ethenes or polyenes in our previous study to the benzene analogues was confirmed. On the other hand, the angle strain is the key for the properties of prismane analogues, as expected. The noteworthy point is that benzene-type compounds tend to have a planar structure in comparison to fulvene analogues with a partially conjugated structure, and the stability relative to the other isomers is not extremely lowered even though the skeletal silicon atoms increase. Among them, the Si/C alternately mixed benzene (1,3,5-trisilabenzene) is an attractive “intermediate compound” between benzene and hexasilabenzene, as it has a planar and electronic structure similar to those of benzene. Therefore, in order to provide some useful information for its synthesis and isolation, the thermodynamic and kinetic stabilities were investigated. As a result, the Si/C alternately mixed benzene was found to be highly reactive for addition reactions, especially for a dimerization. However, as a cure for that, some promising cross-linking substituents considerably effective at preventing isomerization and dimerization were finally proposed.
Two decades of axillary management in breast cancer (2015)

This population-based study demonstrated the radical transformation in management of the axilla since the introduction of SLNB and following the recent publication of trials on management of the axilla with a low metastatic burden.
Potential and force between a magnet and a bulk Y1Ba2Cu3O7-δsuperconductor studied by a mechanical pendulum (1990)

The interaction between a magnet and a high Tc superconductor (HTSC) is investigated by a novel method. A permanent magnet mounted at one end of a stiff rod hanging by a knife's edge forms a mechanical pendulum. When a HTSC is placed below the magnet the frequency v and damping factor Gamma will be changed due to the interaction between the magnet and the HTSC. The experiments show that, as the separation between the magnet and the HTSC decreases, the flux lines start to penetrate the sample via intergranules and grain boundaries, which results in a horizontal restoring force even for the field range B<<Bc1. The present experimental results are consistent with the theoretical model of weak links for bulk HTSC. The power-law-like potential Veff, and force, Feff, are introduced to describe the interaction. The behaviour of Veff and Feff obtained from the present measurements is in disagreement with the dipole-image model even for the field range B<<Bc1.
Electronically Reconfigurable Microwave Lens Antennas (2005)

Abstract : The purpose of this report is to present the results of further investigations into the operation and design of two-dimensional Luneburg Lenses at 24 GHz, with the possibility for electronic control of their behavior. Various lens design techniques are illustrated; these include a holey dielectric lens (drilled dielectric), and a holey plate lens (etched holes on the upper metal plate). Ray tracing theory is presented which shows the general properties of the gradient index lens. These results indicate that it may be possible to synthesize a tuneable lens whose focal length and/or radiation pattern can be adjusted by electronic modification of the lens dielectric properties. In addition, a uniform outer layer lens and a two-shell lens are also demonstrated. Some preliminary investigations are presented with regard to the general properties of Liquid Crystal materials for tuneable lens use. Also, we present preliminary design work on a MMIC reflection amplifier for ultimate deployment in active planar lens reflector for RCS enhancement.
Three-dimensional semi-automatic segmentation of intracranial aneurysms in CTA (2010)

This paper proposes a method for the semi-automatic segmentation of cerebral aneurysms from CTA datasets. The method consists of two phases: a region growing-based approach followed by a level set method, firstly to extract the cerebral artery and then to segment the aneurysm. The first phase automatically locates a seed point for initialization of the region growing in a seed slice, detection of which is based on a measure of maximum entropy, combined with prior anatomical knowledge. Two masks are defined to confine the region growing. A halting criterion is defined as the intensity difference between each voxel and its neighbour.
Red/green Dual Fluorescence Detection of Both the Nucleus and Nucleolus in Living Cells (2009)

Abstract The nucleolus represents a highly dynamic nuclear domain arising from an equilibrium between the level of ribosomal RNA synthesis and the efficiency of ribosomal RNA processing [1, 2]. Although the nucleolus is primarily associated with ribosome biogenesis, several lines of evidence now demonstrate that it has additional functions, such as regulation of mitosis, cell-cycle progression and proliferation, many forms of stress response, and biogenesis of multiple ribonucleoprotein particles. Ribosome biogenesis is regulated throughout interphase and ceases during mitosis (Figure 1). Thus, there is a direct relationship between cell growth and nucleolar activities. Nucleoli are well known to be dramatically modified in cancer cells. Additionally, a large number of key proteins from both DNA- and RNA-containing viruses are localized in the nucleolus, including the human immunodeficiency virus (HIV)-1 Rev and Tat proteins. Targeting of viral proteins to the nucleolus not only facilitates virus replication, but may also be required for pathogenic processes. The nucleolus can also be considered a sensor of stress due to the redistribution of the ribosomal proteins in the nucleoplasm through its disruption.
Dietary Pattern Score, Diet Quality, and Major Neurodegenerative Diseases: A Meta-analysis of Observational Cohort Studies (OR33-07-19) (2019)

Diet is an important lifestyle factor that may prevent or slow the onset and progression of neurodegeneration. Recent studies suggest that adherence to a healthy dietary pattern is associated with reduced risk of cognitive decline. Few studies have examined the relationships between dietary patterns and risk of clinical neurodegenerative disease outcomes. In this meta-analysis, we examined the associations between overall dietary patterns, assessed a priori and a posteriori, and risk of major neurodegenerative disease including dementia, Alzheimer’s disease, and Parkinson’s disease. We systematically searched in the PubMed, Web of Science, and Cumulative Index for Nursing and Allied Health databases starting from 1981 to October 10, 2018. Observational cohort studies published in English with prospective and case-control designs were included. Diet assessment approaches (a priori or a posteriori) were utilized to assist in determining whether the exposure was dietary pattern score or diet quality. Generic inverse variance method was used to calculate the pooled risk ratios and 95% confidence intervals (CIs) among the highest versus the lowest diet quality/dietary pattern score groups in random effect models. Seventeen studies with 173,283 participants were identified. Various diet quality indexes or dietary pattern scores, such as the Healthy Eating Index, the Mediterranean diet score, and dietary pattern scores generated by principal component analysis or reduced rank regression, were used among studies. Our meta-analysis of cohorts showed significant associations between adherence to high diet quality or healthy dietary pattern and lower risk of dementia (pooled risk ratio = 0.70; 95% CI: 0.56-0.86) and Parkinson’s disease (pooled risk ratio = 0.72; 95% CI: 0.54-0.97) relative to those with low diet quality or unhealthy dietary pattern. Adherence to high diet quality or healthy dietary pattern may provide protective effects on risk of neurodegenerative diseases. Additional observational studies and randomized controlled trials are needed to address our study limitations and provide further evidence about the role of a poor diet on the development and progression of neurodegenerative diseases as well as the benefits of a healthy diet on the prevention of major neurodegenerative diseases. United States Department of Agriculture, Agricultural Research Service agreement.
Multiply driven and loaded coaxial circular loop arrays (1980)

Characteristics of single- or double-loaded coaxial loop arrays with arbitrary circumferences are studied when the sources or loads are located diagonally on the loops. For finite gaps at the deriving points and finite lengths of the loads, integral equations for the loop currents are obtained. These integral equations are then reduced to a matrix one by expanding the currents and the kernel in Fourier series of the azimuthal coordinate. For the special case of loaded Yagi arrays numerical results for the gain and the input impedance are presented. These results reveal that a capacitive loading of the array generally broadens the gain bandwidth of the array over which the gain remains essentially constant. A resistive loading of the exciter, on the other hand, yields a broadband characteristic for the driving-point admittance.
CENNA: Cost-Effective Neural Network Accelerator (2020)

Convolutional neural networks (CNNs) are widely adopted in various applications. State-of-the-art CNN models deliver excellent classification performance, but they require a large amount of computation and data exchange because they typically employ many processing layers. Among these processing layers, convolution layers, which carry out many multiplications and additions, account for a major portion of computation and memory access. Therefore, reducing the amount of computation and memory access is the key for high-performance CNNs. In this study, we propose a cost-effective neural network accelerator, named CENNA, whose hardware cost is reduced by employing a cost-centric matrix multiplication that employs both Strassen’s multiplication and a naïve multiplication. Furthermore, the convolution method using the proposed matrix multiplication can minimize data movement by reusing both the feature map and the convolution kernel without any additional control logic. In terms of throughput, power consumption, and silicon area, the efficiency of CENNA is up to 88 times higher than that of conventional designs for the CNN inference.
Anti-nephrin antibodies in idiopathic nephrotic syndrome in Japanese children (2023)

Abstract Background Many patients with childhood idiopathic nephrotic syndrome are steroid-sensitive. Several genome-wide association studies have suggested a polygenic contribution, particularly in the HLA DR/DQ region and a locus including nephrin, but the etiology remains unclear. Anti-nephrin antibodies have recently been reported in both adults and children with biopsy proven minimal change disease (MCD), but the presence of anti-nephrin antibodies in Japanese childhood idiopathic nephrotic syndrome (INS) has not been investigated. Methods Anti-nephrin antibodies were measured by ELISA in paired plasma samples obtained from 14 Japanese pediatric patients with INS (male/female: 8/6), at onset (active disease) and following steroid monotherapy. Results The median age at the onset was 75.5 months (interquartile range (IQR): 45-113). Steroid sensitivity resulted in complete remission in 13 patients and almost complete remission in one patient after 4 weeks of glucocorticoid monotherapy. Circulating anti-nephrin antibodies were detected in seven of 14 patients during active disease. In all cases, anti-nephrin antibodies were significantly reduced following treatment concordant with clinical response. There were no differences between the positive and negative groups in pre-treatment parameters. Of the 13 patients who achieved complete remission, nine had at least one relapse during a median follow-up of 851 days (IQR: 808-973). There was also no significant difference in the relapse-free period after the onset between the two groups (P=0.658). Conclusions We identified circulating anti-nephrin antibodies in half of Japanese pediatric patients with INS at initial presentation, which is higher than has been previously reported in a North American cohort.
AL3810, a multi‐tyrosine kinase inhibitor, exhibits potent anti‐angiogenic and anti‐tumour activity via targeting VEGFR, FGFR and PDGFR (2012)

Angiogenesis plays an important role in neoplastic transformation and progression as well as in the metastasis process of most human cancers. Herein, we identified AL3810 as a novel and orally bioavailable small molecular inhibitor with potent inhibitory activity against multiple tyrosine kinases involved in the process of angiogenesis. We found that AL3810 substantially inhibited the autophosphorylation of VEGFR2, PDGFRβ and FGFR1 in endothelial cells. Moreover, AL3810 exhibited potent anti-angiogenesis activity, manifested by significant inhibition of microvessel outgrowth of rat arterial ring and chickallantochorion membrane (CAM) in ex vivo angiogenesis models. Daily dosing of AL3810 has shown broad-spectrum anti-tumour activity in human kidney, pancreas, liver cancer xenograft models. Importantly, immunohistochemistry results demonstrated that the anti-tumour activity of AL3810 was closely correlated with its anti-angiogenesis activity, as demonstrated by a decreased microvessel area and reduced microvessel numbers in tumour tissues. The overall pharmacological profiles of AL3810 are superior to sorafenib. The clinical trials of AL3810 will soon be launched in China.
Spatial Multiplexing Architectures with Jointly Designed Rate-Tailoring and Ordered BLAST Decoding Part-II: A Practical Method for Rate and Power Allocation (2008)

The study of the class of new spatial multiplexing architectures (SMAs) is continued. As introduced in Part I of this paper, the SMAs consist of joint design of rate and power allocation to the spatially-multiplexed substreams at the transmitter and ordered nulling/canceling detection/decoding at the receiver. This was studied in Part I under the diversitymultiplexing tradeoff framework. Here the more detailed and practical problem of allocating rates and powers across the transmit antennas is investigated to minimize the overall system (uncoded or outage) error probability. Since the layer gains are unavailable to the transmitter, the rates and powers must be allocated based on the statistics of the layer gains. However, the channel dependent ordering rules make the precise distributions of the layer gains complicated or intractable. To solve this problem, a simple, yet effective, four-parameter hyperbola model is proposed to closely approximate the error probability of each layer. With this approximation, the computation of rate and power allocation according to the criterion of minimizing the maximal error probability of all the substreams is given. Simulation results validate the superior performance of the proposed SMAs, especially that of the Greedy ordering Rate Tailored SMA (GRT-SMA). Although the rate and power allocation method is obtained under the assumption of iid Rayleigh fading channel, the proposed SMAs also work well in other types of fading channels (such as in correlated and Rician channels).
Radioimmunoassay for the pyridinoline cross-linked carboxy-terminal telopeptide of type I collagen: a new serum marker of bone collagen degradation (1993)

We developed a radioimmunoassay (RIA) for the carboxy-terminal telopeptides of type I collagen (ICTP), cross-linked with the helical domain of another type I collagen molecule, after isolation from human femoral bone. The cross-linked peptide was liberated by digesting insoluble, denatured bone collagen either with bacterial collagenase or with trypsin, and purified by two successive reversed-phase separations on HPLC, with monitoring of pyridinoline-specific fluorescence. The purity of the peptide was verified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and its origin in the type I collagen fibers was determined by amino-terminal amino acid sequencing. Polyclonal antibodies and a separation reagent containing second antibody and polyethylene glycol are used in the RIA. An immunologically identical, somewhat larger antigen is present in human serum; its concentration increases in multiple myeloma and in rheumatoid arthritis. The ICTP antigen seems to be cleared from the circulation by the kidneys, because glomerular filtration rates that are two-thirds of normal or less are associated with increased circulating ICTP concentrations. The CVs of the method are between 3% and 8% for a wide range of concentrations. The analysis of 40 serum samples can be completed in 4 h.