gebhart/patrepeval huggingface dataset:
Immunogenetic Risk and Protective Factors for the Idiopathic Inflammatory Myopathies (2006)

The idiopathic inflammatory myopathies (IIM) are systemic connective tissue diseases defined by chronic muscle inflammation and weakness associated with autoimmunity. We have performed low to high resolution molecular typing to assess the genetic variability of major histocompatibility complex loci (HLA-A, -B, -Cw, -DRB1, and -DQA1) in a large population of European American patients with IIM (n = 571) representing the major myositis autoantibody groups. We established that alleles of the 8.1 ancestral haplotype (8.1 AH) are important risk factors for the development of IIM in patients producing anti-synthetase/anti-Jo-1, -La, -PM/Scl, and -Ro autoantibodies. Moreover, a random forests classification analysis suggested that 8.1 AH-associated alleles B*0801 and DRB1*0301 are the principal HLA risk markers. In addition, we have identified several novel HLA susceptibility factors associated distinctively with particular myositis-specific (MSA) and myositis-associated autoantibody (MAA) groups of the IIM. IIM patients with anti-PL-7 (anti-threonyl-tRNA synthetase) autoantibodies have a unique HLA Class I risk allele, Cw*0304 (pcorr = 0.046), and lack the 8.1 AH markers associated with other anti-synthetase autoantibodies (for example, anti-Jo-1 and anti-PL-12). In addition, HLA-B*5001 and DQA1*0104 are novel potential risk factors among anti-signal recognition particle autoantibody-positive IIM patients (pcorr = 0.024 and p = 0.010, respectively). Among those patients with MAA, HLA DRB1*11 and DQA1*06 alleles were identified as risk factors for myositis patients with anti-Ku (pcorr = 0.041) and anti-La (pcorr = 0.023) autoantibodies, respectively. Amino acid sequence analysis of the HLA DRB1 third hypervariable region identified a consensus motif, 70D (hydrophilic)/71R (basic)/74A (hydrophobic), conferring protection among patients producing anti-synthetase/anti-Jo-1 and -PM/Scl autoantibodies. Together, these data demonstrate that HLA signatures, comprising both risk and protective alleles or motifs, distinguish IIM patients with different myositis autoantibodies and may have diagnostic and pathogenic implications. Variations in associated polymorphisms for these immune response genes may reflect divergent pathogenic mechanisms and/or responses to unique environmental triggers in different groups of subjects resulting in the heterogeneous syndromes of the IIM.
In vivo evidence of htid suppressive activity on ErbB-2 in breast cancers over expressing the receptor (2010)

Our findings provide in vivo evidence that htid is a tissue independent and evolutionarily conserved suppressor of ErbB-2.
Electrical performance and physics of isolation region structures for VLSI (1984)

A two-dimensional effect in isolation structures is described. It is shown with computer simulations, mathematical analysis, and experimental measurements that the use of trench-like isolation structures significantly improves device electrical isolation, provided junction depths are less than the trench depth. A potential barrier exists at the corners of the isolation region that dominates the parasitic device's I - V characteristics. A mathematical relation for the subthreshold slope as a function of the interface radius is derived which predicts the slope is flatter and the threshold voltage is increased compared to conventional LOCOS structures. This significantly improves the isolation. The position of the potential barrier is shown to allow scaling of the isolation region width without degrading the isolation. Experimental results have verified the predictions of extensive computer simulations.
Divalent Cations Stimulate Preferential Recognition of a Viral DNA End by HIV-1 Integrase (1999)

In the presence of a divalent metal cofactor (Mg2+ or Mn2+), retroviral-encoded integrase (IN) catalyzes two distinct reactions: site-specific cleavage of two nucleotides from both 3' ends of viral DNA, and sequence-independent joining of the recessed viral ends to staggered phosphates in a target DNA. Here we investigate human immunodeficiency virus type 1 (HIV-1) IN-DNA interactions using surface plasmon resonance. The results show that IN forms tight complexes both with duplex oligonucleotides that represent the viral DNA ends and with duplex oligonucleotides with an unrelated sequence that represent a target DNA substrate. The IN-DNA complexes are stable in 4.0 M NaCl, or 50% (v/v) methanol, but they are not resistant to low concentrations of SDS, indicating that their stability is highly dependent on structural features of the protein. Divalent metal cofactors exert two distinct effects on the IN-DNA interaction. Mn2+ inhibits IN binding to a model target DNA with the apparent Kd increasing approximately 3-fold in the presence of this cation. On the other hand, Mn2+ (or Mg2+) stimulates the binding of IN to a model viral DNA end, decreasing the apparent Kd of this IN-viral DNA complex approximately 6-fold. Such metal-mediated stimulation of the binding of IN to the viral DNA is totally abolished by substitution of the subterminal conserved CA/GT bp with a GT/CA bp, and is greatly diminished when the viral DNA end is recessed or "pre-processed." IN binds to a viral duplex oligonucleotide whose end was extended with nonviral sequences with kinetics similar to the nonviral model target DNA. This suggests that IN can distinguish the integrated DNA product from the viral donor DNA in the presence of divalent metal ion. Thus, our results show that preferential recognition of viral DNA by HIV-1 IN is achieved only in the presence of metal cofactor, and requires a free, wild-type viral DNA end.
Diffusion of In and Ga in selenized Cu-In and Cu-Ga precursors (1996)

The interdiffusion of Ga and In in a CuGaSe/sub 2//CuInSe/sub 2/ thin film diffusion couple and the diffusion of In into CuGaSe/sub 2/ thin films were studied by Auger depth profiling. CuGaSe/sub 2/ and CuInSe/sub 2/ were obtained via selenization by H/sub 2/Se of sequentially deposited Cu-Ga and Cu-In layers, respectively. The CuGaSe/sub 2//CuInSe/sub 2/ diffusion couple was annealed at 650/spl deg/C for 30 minutes in an argon atmosphere. The thin film source of In was diffused into CuGaSe/sub 2/ in the temperature range of 400/spl deg/C to 600/spl deg/C for 30 minutes in an argon atmosphere. Bulk interdiffusion coefficients of In and Ga in the CuGaSe/sub 2//GuInSe/sub 2/ couple annealed at 650/spl deg/C, and the diffusion coefficients of In in CuGaSe/sub 2/ films diffusion annealed at various temperatures were determined. The interdiffusion coefficients of In and Ga at 650/spl deg/C in the diffusion couple are similar (D/sub In/=1.5/spl times/10/sup -11/ cm/sup 2//sec and D/sub Ga/=4.0/spl times/10/sup -11/ cm/sup 2//sec). The diffusion coefficients of In in CuGaSe/sub 2/ thin films varied from 2.0/spl times/10/sup -13/ cm/sup 2//sec to 4.5/spl times/10/sup -12/ cm/sup 2//sec in the temperature range of 400/spl deg/C to 600/spl deg/C.
Cellulose Nanofiber/Nanocrystal Reinforced Capsules: A Fast and Facile Approach Toward Assembly of Liquid-Core Capsules with High Mechanical Stability (2014)

Liquid-core capsules of high mechanical stability open up for many solid state-like applications where functionality depending on liquid mobility is vital. Herein, a novel concept for fast and facile improvement of the mechanical properties of walls of liquid-core capsules is reported. By imitating nature's own way of enhancing the mechanical properties in liquid-core capsules, the parenchyma plant cells found in fruits and vegetables, a blend of short cellulose nanofibers (<1 μm, NFC) and nanocrystals (CNC) was exploited in the creation of the capsule walls. The NFC/CNC blend was prepared from a new version of the classical wood pulp hydrolysis. The capsule shell consisted of a covalently (by aromatic diisocyanate) cross-linked NFC/CNC structure at the outer capsule wall and an inner layer dominated by aromatic polyurea. The mechanical properties revealed an effective capsule elastic modulus of 4.8 GPa at 17 wt % NFC/CNC loading, about six times higher compared to a neat aromatic polyurea capsule (0.79 GPa) and 3 orders of magnitude higher than previously reported capsules from regenerated cellulose (0.0074 GPa). The outstanding mechanical properties are ascribed to the dense nanofiber structure, present in the outer part of the capsule wall, that is formed by oriented NFC/CNC of high average aspect ratio (L/d ∼ 70) and held together by both covalent (urethane bonds) and physical bonds (hydrogen bonds).
Mitral Valve Prolapse With Mid-Late Systolic Mitral Regurgitation (2012)

MR of mitral valve prolapse that is purely mid-late systolic causes more benign consequences and outcomes than holosystolic MR. Assessment may be misleading because jet area and ERO by flow convergence appear similar to those of holosystolic MR. However, shorter MR yields lower regurgitant volume, consequences, and benign outcomes. Instantaneous ERO by flow convergence should be interpreted in context, and in mid-late systolic MR, regurgitant volume provides information more reflective of MR severity. Therefore, for clinical management and surgical referral, clinicians should carefully take into account the timing and consequences of MR.
Combining Generative and Discriminative Representation Learning for Lung CT Analysis With Convolutional Restricted Boltzmann Machines (2016)

The choice of features greatly influences the performance of a tissue classification system. Despite this, many systems are built with standard, predefined filter banks that are not optimized for that particular application. Representation learning methods such as restricted Boltzmann machines may outperform these standard filter banks because they learn a feature description directly from the training data. Like many other representation learning methods, restricted Boltzmann machines are unsupervised and are trained with a generative learning objective; this allows them to learn representations from unlabeled data, but does not necessarily produce features that are optimal for classification. In this paper we propose the convolutional classification restricted Boltzmann machine, which combines a generative and a discriminative learning objective. This allows it to learn filters that are good both for describing the training data and for classification. We present experiments with feature learning for lung texture classification and airway detection in CT images. In both applications, a combination of learning objectives outperformed purely discriminative or generative learning, increasing, for instance, the lung tissue classification accuracy by 1 to 8 percentage points. This shows that discriminative learning can help an otherwise unsupervised feature learner to learn filters that are optimized for classification.
Top-Down Proteomics (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Field‐evolved resistance to Cry1Ab maize by Spodoptera frugiperda in Brazil (2015)

The decrease in susceptibility to Cry1Ab was expected, but the specific contributions to this resistance by MON 810 maize cannot be distinguished from cross-resistance to Cry1Ab caused by exposure to Cry1F maize. Technologies combining multiple novel insecticidal traits with no cross-resistance to the current Cry1 proteins and high activity against the same target pests should be pursued in Brazil and similar environments. © 2015 Society of Chemical Industry.
[Scatter and attenuation correction for quantitative myocardial SPECT imaging]. (1996)

We performed scatter and attenuation compensation in 201Tl myocardial SPECT using the triple-energy-window (TEW) scatter correction method and 99mTc transmission scan (TCT). A dual-headed SPECT gammacamera system equipped with parallel-hole collimators was employed for imaging and a sheet source for TCT was attached to the surface of one of the two detectors. Two imaging protocols, a sequential mode and a simultaneous mode, were examined. In the sequential mode, TCT was performed prior to the administration of the tracer and then ECT was carried out. On the other hand, the injection was followed by a simultaneous transmission-emission scan, in the simultaneous mode. Results of phantom studies showed that reconstructed SPECT values of the whole myocardium were almost equal to the true value with errors of less than 5 per cent, and that more homogeneous images were obtained by performing scatter and attenuation correction. We conclude that this correction method was clinically practical and cost-effective because it uses parallel-hole collimators and does not require fan-beam collimators which may produce truncation artifacts.
Sensitivity Minimization by Stable Controllers for a Class of Unstable Time-Delay Systems (2006)

In this paper sensitivity minimization problem is considered for a class of unstable time delay systems. Our goal is to find a stable controller stabilizing the feedback system and giving rise to smallest H <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">infin</sup> norm for the sensitivity function. This problem has been solved by Ganesh and Pearson (1986) for finite dimensional plants using Nevanlinna-Pick interpolation. We extend their technique to include possibly unstable time delay systems. Moreover, we illustrate suboptimal solutions, and their robust implementation
Investigations of breast cancer screening using a novel in vitro diagnostics technology. (2015)

13 Background: A newly developed in-vitro diagnostic technology named Cancer Differentiation Analysis Technology (CDA) was investigated for breast cancer screening. The CDA technology is a blood-sample based, multi-level, multi-parameter diagnostic method which detects signals from both proteins and cells, in which multiple aspects and parameters of information were collected to improve diagnostic accuracy. Methods: Blood samples from breast cancer group (n = 222), and control subjects (n = 204) were collected in EDTA tubes. CDA values were measured using a CDA medical device. The results were shown in Table 1 and Figure 1 below. Results: The average CDA values of breast cancer and control groups were 50.43 and 34.03 (rel. units) respectively. The results indicated that breast cancer could be significantly distinguished from the control (p &lt; 0.001). Area under ROC curve was 0.914. When Youden Index reached the maximum, sensitivity and specificity was 82.0% and 89.2% respectively. Conclusions: Initial results showed that CDA technology could be a potential candidate for breast cancer screening. [Table: see text]
Radiolabeling and PET-MRI microdosing of the experimental cancer therapeutic, MN-anti-miR10b, demonstrates delivery to metastatic lesions in a murine model of metastatic breast cancer (2021)

Abstract Background In our earlier work, we identified microRNA-10b (miR10b) as a master regulator of the viability of metastatic tumor cells. This knowledge allowed us to design a miR10b-targeted therapeutic consisting of anti-miR10b and ultrasmall iron oxide magnetic nanoparticles (MN), termed MN-anti-miR10b. In mouse models of breast cancer, we demonstrated that MN-anti-miR10b caused durable regressions of established metastases with no evidence of systemic toxicity. As a first step towards translating MN-anti-miR10b for the treatment of metastatic breast cancer, we needed to determine if MN-anti-miR10b, which is so effective in mice, will also accumulate in human metastases. Results In this study, we devised a method to efficiently radiolabel MN-anti-miR10b with Cu-64 ( 64 Cu) and evaluated the pharmacokinetics and biodistribution of the radiolabeled product at two different doses: a therapeutic dose, referred to as macrodose, corresponding to 64 Cu-MN-anti-miR10b co-injected with non-labeled MN-anti-miR10b, and a tracer level dose of 64 Cu-MN-anti-miR10b, referred to as microdose. In addition, we evaluated the uptake of 64 Cu-MN-anti-miR10b by metastatic lesions using both in vivo and ex vivo positron emission tomography-magnetic resonance imaging (PET-MRI). A comparable distribution of the therapeutic was observed after administration of a microdose or macrodose. Uptake of the therapeutic by metastatic lymph nodes, lungs, and bone was also demonstrated by PET-MRI with a significantly higher PET signal than in the same organs devoid of metastatic lesions. Conclusion Our results demonstrate that PET-MRI following a microdose injection of the agent will accurately reflect the innate biodistribution of the therapeutic. The tools developed in the present study lay the groundwork for the clinical testing of MN-anti-miR10b and other similar therapeutics in patients with cancer.
Optimal training signals for MIMO OFDM channel estimation (2006)

This paper presents general classes of optimal training signals for the estimation of frequency-selective channels in MIMO OFDM systems. Basic properties of the discrete Fourier transform are used to derive the optimal training signals which minimize the channel estimation mean square error. Both single and multiple OFDM training symbols are considered. Several optimal pilot tone allocations across the transmit antennas are presented and classified as frequency-division multiplexing, time-division multiplexing, code-division multiplexing in the frequency-domain, code-division multiplexing in the time-domain, and combinations thereof. All existing optimal training signals in the literature are special cases of the presented optimal training signals and our designs can be applied to pilot-only schemes as well as pilot-data-multiplexed schemes.
A Probabilistic Approach for Maintaining Trust Based on Evidence (2011)

Leading agent-based trust models address two important needs. First, they show how an agent may estimate the trustworthiness of another agent based on prior interactions. Second, they show how agents may share their knowledge in order to cooperatively assess the trustworthiness of others. However, in real-life settings, information relevant to trust is usually obtained piecemeal, not all at once. Unfortunately, the problem of maintaining trust has drawn little attention. Existing approaches handle trust updates in a heuristic, not a principled, manner. This paper builds on a formal model that considers probability and certainty as two dimensions of trust. It proposes a mechanism using which an agent can update the amount of trust it places in other agents on an ongoing basis. This paper shows via simulation that the proposed approach (a) provides accurate estimates of the trustworthiness of agents that change behavior frequently; and (b) captures the dynamic behavior of the agents. This paper includes an evaluation based on a real dataset drawn from Amazon Marketplace, a leading e-commerce site.
Fragmentation and constitutive response of tailored mesostructured aluminum compacts (2016)

The fragmentation and constitutive response of aluminum-based compacts were examined under dynamic conditions using mesostructured powder compacts in which the interfaces between the powders (sizes of 40, 100, and 400 μm) were tailored during the swaging fabrication process. Fragmentation was induced in ring samples of this material through explosive loading and was examined through high speed photography, laser interferometry, and soft capture of fragments. Fragment velocities of around 100 m/s were recorded. The fragment mass distributions obtained correlated in general with the interfacial strength of the compacts as well as with the powder size. Experimental results are compared with fragmentation theories to characterize the behavior of reactive powders based on the material's mesostructure by introducing the fracture toughness of the compacts. The mean fragment size is calculated using a modified form of Mott's theory and successfully compared with experimental results.
3D visualization of aurora considering the physical characteristics (2016)

In this paper, we proposed a novel method to measure and visualize 3D shape of aurora accurately. The proposed method considers not only information of aurora images taken by stereo camera system but also constraints based on the mechanism and physical knowledge of aurora generation. The corresponding points between a pair of stereo images were detected for measurement by triangulation. At the corresponding point detection, detection accuracy was improved drastically by using the information of geomagnetism and altitude of aurora's lower end. Then the shape was visualized by fitting NURBS surface to the detected corresponding point. Figure 1 shows the visualization result. Applying this method, the 3D shape of aurora which didn't contradict the physical knowledge could be visualized.
Replication of pressure-volume loop with controllable ESPVR and EDPVR curves on a personalized mock circulatory loop based on elastance function (2017)

In the development of a left ventricular assist device (LVAD), it is important to evaluate the LVAD's hemodynamic effect on the compromised left ventricle (LV) before surgical implantation. The mock circulatory loop (MCL) is widely accepted as an in vitro test platform to evaluate LVADs across a wide range of operational conditions as a way to examine how the device and the cardiovascular system interact. Unfortunately, most MCLs represent an oversimplified model of cardiac function, with disease states simulated through generalized changes in heart rate and stroke volume. Because heart failure (HF) severity varies substantially among patients, an MCL is needed that can mimic the pressure-volume loop of an individual patient. In this work, two numerical elastance models, derived from a specific pressure volume loop template, were used to control the LV simulator of the MCL to simulate different degrees of HF. The numerical elastance model was then scaled to change the slopes of the end-systolic (ESPVR) and end-diastolic (EDPVR) pressure volume relationship curves to simulate systolic and diastolic dysfunction. The resulting experimental pressure volume loops are consistent with theoretical loops, demonstrating the feasibility of creating an MCL that can be customized for the patient.