gebhart/patrepeval huggingface dataset:
Hotelling trace criterion and its correlation with human-observer performance (1987)

The Hotelling trace criterion (HTC) is used to find a set of linear features that optimally separate two classes of objects. The objects used in our study were simulated livers with and without tumors, with noise, blur, and object variability. Using the receiver-operating-characteristic parameter da as our measure, we have found that the ability of the HTC to separate these objects into their correct classes, by detecting the presence or absence of a tumor, has a correlation of 0.988 with the ability of humans to separate the same two classes of objects. This suggests, therefore, that the HTC can be used as a figure of merit for optimizing system parameters, since it calculates a single, scalar figure of merit that has a high correlation with human-observer performance.
Neutrophil cytoplasts induce T H 17 differentiation and skew inflammation toward neutrophilia in severe asthma (2018)

Severe asthma is a debilitating and treatment refractory disease. As many as half of these patients have complex neutrophil-predominant lung inflammation that is distinct from milder asthma with type 2 eosinophilic inflammation. New insights into severe asthma pathogenesis are needed. Concomitant exposure of mice to an aeroallergen and endotoxin during sensitization resulted in complex neutrophilic immune responses to allergen alone during later airway challenge. Unlike allergen alone, sensitization with allergen and endotoxin led to NETosis. In addition to neutrophil extracellular traps (NETs), enucleated neutrophil cytoplasts were evident in the lungs. Surprisingly, allergen-driven airway neutrophilia was decreased in peptidyl arginine deiminase 4-deficient mice with defective NETosis but not by deoxyribonuclease treatment, implicating the cytoplasts for the non-type 2 immune responses to allergen. Neutrophil cytoplasts were also present in mediastinal lymph nodes, and the cytoplasts activated lung dendritic cells in vitro to trigger antigen-specific interleukin-17 (IL-17) production from naïve CD4<sup>+</sup> T cells. Bronchoalveolar lavage fluid from patients with severe asthma and high neutrophil counts had detectable NETs and cytoplasts that were positively correlated with IL-17 levels. Together, these translational findings have identified neutrophil cytoplast formation in asthmatic lung inflammation and linked the cytoplasts to T helper 17-mediated neutrophilic inflammation in severe asthma.
Low-Loss and Low-DMD 6-Mode 19-Core Fiber With Cladding Diameter of Less Than 250 μm (2016)

We investigate a few-mode multicore fiber structure suitable for realizing a high spatial density while maintaining a feasible cladding diameter. First, we discuss the impact of cladding diameter on mechanical reliability, and set a target cladding diameter of less than 250 μm to maintain a comparable reliability to conventional fiber. We then optimize the 6-mode core profile to obtain a low differential mode delay (DMD) characteristic and reveal that a hexagonally arranged 19-core structure can realize more than 100 spatial channels with a cladding diameter of less than 250 μm. Finally, we fabricate 6-mode 19-core fiber with a 246 μm cladding diameter and realize a relative core multiplicity factor of more than 60 with a low loss and a DMD of less than 0.24 dB/km and 0.33 ns/km, respectively.
miRNA independent hepacivirus variants suggest a strong evolutionary pressure to maintain miR-122 dependence (2017)

Hepatitis C virus (HCV) requires the liver specific micro-RNA (miRNA), miR-122, to replicate. This was considered unique among RNA viruses until recent discoveries of HCV-related hepaciviruses prompting the question of a more general miR-122 dependence. Among hepaciviruses, the closest known HCV relative is the equine non-primate hepacivirus (NPHV). Here, we used Argonaute cross-linking immunoprecipitation (AGO-CLIP) to confirm AGO binding to the single predicted miR-122 site in the NPHV 5'UTR in vivo. To study miR-122 requirements in the absence of NPHV-permissive cell culture systems, we generated infectious NPHV/HCV chimeric viruses with the 5' end of NPHV replacing orthologous HCV sequences. These chimeras were viable even in cells lacking miR-122, although miR-122 presence enhanced virus production. No other miRNAs bound this region. By random mutagenesis, we isolated HCV variants partially dependent on miR-122 as well as robustly replicating NPHV/HCV variants completely independent of any miRNAs. These miRNA independent variants even replicate and produce infectious particles in non-hepatic cells after exogenous delivery of apolipoprotein E (ApoE). Our findings suggest that miR-122 independent HCV and NPHV variants have arisen and been sampled during evolution, yet miR-122 dependence has prevailed. We propose that hepaciviruses may use this mechanism to guarantee liver tropism and exploit the tolerogenic liver environment to avoid clearance and promote chronicity.
Scaling laws for a High Efficiency Multistage Plasma Thruster (2017)

Upcoming formation flying space missions have unprecedented requirements in both low thrust and low noise-to-thrust ratio for attitude control. With the recent discovery of gravitational waves, LISA (Laser Interferometer Space Antenna) is an outstanding example for such a mission. Its requirements are thrust no more than 100 µN and root of the noise spectral density ≤ 0.1 µN/√Hz. One attempt to reach this regime is to develop a downscaled version of the High Efficiency Multistage Plasma Thruster (HEMPT). One part of this activity is to support the development by computer modeling. In order to simulate the thruster plasma, the Particle-in-Cell (PiC) method is used. We will present analytical considerations and models using the PiC method for a downscaled and an unscaled HEMPT which has been performed in order to investigate the scaling laws of this kind of plasma thruster.
Ebenfurans IV−VIII from Onobrychis ebenoides: Evidence that C-Prenylation is the Key Determinant of the Cytotoxicity of 3-Formyl-2-arylbenzofurans (2008)

Phytochemical investigation of a methanol extract of Onobrychis ebenoides yielded five new 3-formyl-2-arylbenzofurans, namely, ebenfurans IV-VIII (1-5), together with the known compounds ebenfurans I, II (6), and III (7). Only 1 and 7 exhibited growth inhibitory activity against MCF-7 and Ishikawa cells, suggesting that the prenyl moiety at position C-5 is the key determinant of the cytotoxic activity of this group of compounds.
Conformationally rigid histone deacetylase inhibitors correct DF508-CFTR protein function (2011)

Histone deacetylase (HDAC) inhibitors have shown partial efficacy toward correcting cystic fibrosis transmembrane conductance regulator (CFTR) protein function in ΔF508- CFTR models. While current treatment options for CF generally concentrate on disease symptoms such as management of inflammation and bacterial infection, therapy using HDAC inhibitors has the potential to treat and correct the underlying etiology associated with the disorder. Subsequently, we have synthesized conformationally well-defined cyclic tetrapeptide derivatives based on the natural product HDAC inhibitor Apicidin, in order to formulate a pharmacophore model to describe and enhance the bioactivity of these molecules. Through this study we have developed HDAC inhibitors which improve CFTR trafficking from the endoplasmic reticulum (ER) while ultimately increasing ion conductance across the plasma membrane of a lung epithelial cell line expressing ΔF508-CFTR.
Virtual Lash Adjuster for an Electromechanical Valve Actuator Through Iterative Learning Control (2003)

The reduction of impacts which occur in electromechanical valve actuators due to the presence of valve lash have been largely neglected in the literature. Instead, the majority of work in this area has focused on impacts occurring elsewhere. As such, a controller is presented here to account for the impacts which occur during the release phase of the valve opening due to the presence of valve lash. A combination of feed forward and iterative learning control are used to achieve trajectory tracking during the release bounding the impact velocity by 0.4 m/s.
Comparison of clustering approaches for summarizing large populations of images (2010)

This paper compares the efficacy and efficiency of different clustering approaches for selecting a set of exemplar images, to present in the context of a semantic concept. We evaluate these approaches using 900 diverse queries, each associated with 1000 web images, and comparing the exemplars chosen by clustering to the top 20 images for that search term. Our results suggest that Affinity Propagation is effective in selecting exemplars that match the top search images but at high computational cost. We improve on these early results using a simple distribution-based selection filter on incomplete clustering results. This improvement allows us to use more computationally efficient approaches to clustering, such as Hierarchical Agglomerative Clustering (HAC) and Partitioning Around Medoids (PAM), while still reaching the same (or better) quality of results as were given by Affinity Propagation in the original study. The computational savings is significant since these alternatives are 7-27 times faster than Affinity Propagation.
COVID-19 infection in adult patients with hematological malignancies: a European Hematology Association Survey (EPICOVIDEHA) (2021)

This survey confirms that COVID-19 patients with HM are at high risk of lethal complications. However, improved COVID-19 prevention has reduced mortality despite an increase in the number of reported cases.
Optical coherence tomography refraction and optical path length correction for image-guided corneal surgery (2022)

Optical coherence tomography (OCT) may be useful for guidance of ocular microsurgeries such as deep anterior lamellar keratoplasty (DALK), a form of corneal transplantation that requires delicate insertion of a needle into the stroma to approximately 90% of the corneal thickness. However, visualization of the true shape of the cornea and the surgical tool during surgery is impaired in raw OCT volumes due to both light refraction at the corneal boundaries, as well as geometrical optical path length distortion due to the group velocity of broadband OCT light in tissue. Therefore, uncorrected B-scans or volumes may not provide an accurate visualization suitable for reliable surgical guidance. In this article, we introduce a method to correct for both refraction and optical path length distortion in 3D in order to reconstruct corrected OCT B-scans in both natural corneas and corneas deformed by needle insertion. We delineate the separate roles of phase and group index in OCT image distortion correction, and introduce a method to estimate the phase index from the group index which is readily measured in samples. Using the measured group index and estimated phase index of human corneas at 1060 nm, we demonstrate quantitatively accurate geometric reconstructions of the true cornea and inserted needle shape during simulated DALK surgeries.
Intercellular Signaling during Caenorhabditis elegans Vulval Induction (1992)

The essential invariance of Caenorhabditis elegans development has allowed detailed analysis of the mechanisms of cell fate determination. A variety of studies suggest a major role for cell interactions in specifying cell fates during nematode development. The original observations of natural variability of certain cell fates and the cell fate changes after particular cell ablation experiments indicated that the fates of some cells during later embryonic and postembryonic development depend on cell interactions (Sulston and Horvitz 1977; Kimble and Hirsh 1979; Sulston et al. 1983). Blastomere interchange experiments have demonstrated that cell interactions are crucial to specification of fates during early embryogenesis (Priess and Thomson 1987; Schnabel 1991; Wood 1991). Molecular genetic analyses have revealed additional cell interactions and suggest that others will be uncovered. For example, mosaic analysis of the her-1 gene indicates that sex determination involves cell communication (Hunter and Wood 1992). In addition, the pleiotropic effects of...
Supplementary Table S2 from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma (2023)

&lt;p&gt;XLSX file 327K, Supplementary Table S2. Mutations seen exclusively in resistant tumors. For patients with whole exome sequencing data on both pre-treatment and resistant tumors (n = 32), this table summarizes the complete set of non-synonymous mutations and short insertion/deletions called only in the resistant but not pre-treatment tumors. Alterations in this table met the additional criteria of at least 30X coverage in the tumor and an allelic fraction of at least 0.05. Each column is a patient, each row is a gene, and each non-blank entry denotes the protein change that results from the mutation.&lt;/p&gt;
Effects of Patupilone on the Pharmacokinetics and Pharmacodynamics of Warfarin in Patients with Advanced Malignancies: A Phase I Clinical Trial (2011)

Patupilone is a novel microtubule-targeting cytotoxic agent, which exerts its antitumor effect through microtubule stabilization. Pharmacokinetics, pharmacodynamics, and safety of warfarin when administered concomitantly with patupilone were investigated, and antitumor activity was assessed. This was a phase I, two-center, drug-drug interaction study. In the core phase of the study, treatment consisted of warfarin 20 mg orally (days 1 and 29) and patupilone 10 mg/m(2) i.v. (days 8 and 29). Patients benefiting from patupilone treatment continued treatment every 3 weeks (extension phase) until progression of disease, death, or unacceptable toxicity. Seventeen patients were treated (core phase, 17; extension, 9). The geometric mean ratios (comedication/monotherapy) for C(max) and area under the curve(0-168) of warfarin were near unity and their 90% confidence intervals were within the equivalence limits of 0.80 and 1.25. The half-life, plasma clearance, and International Normalized Ratio (INR) of warfarin were not affected by patupilone coadministration. The most common adverse events were diarrhea, nausea, vomiting, abdominal pain, anorexia, dehydration, asthenia, and peripheral neuropathy. Five (29.4%) patients experienced grade 3 study drug-related adverse events (diarrhea, 17.6%; increased INR, 11.8%; dehydration, 5.9%; and neutropenia, 5.9%). One patient with triple-negative breast cancer (estrogen receptor, progesterone receptor, and HER2/neu negative) had a partial response (35% decrease in tumor measurements by Response Evaluation Criteria in Solid Tumors), and 11 had stable disease for 6 weeks or more (≥12 weeks, 6 patients). The pharmacokinetics and pharmacodynamics of warfarin were not affected by patupilone coadministration, suggesting that patupilone has no clinically relevant effect on CYP2C9 metabolism. Patupilone showed antitumor activity in triple-negative breast cancer.
A Class of Optimal Rectangular Filtering Matrices for Single-Channel Signal Enhancement in the Time Domain (2013)

In this paper, we introduce a new class of optimal rectangular filtering matrices for single-channel speech enhancement. The new class of filters exploits the fact that the dimension of the signal subspace is lower than that of the full space. By doing this, extra degrees of freedom in the filters, that are otherwise reserved for preserving the signal subspace, can be used for achieving an improved output signal-to-noise ratio (SNR). Moreover, the filters allow for explicit control of the tradeoff between noise reduction and speech distortion via the chosen rank of the signal subspace. An interesting aspect is that the framework in which the filters are derived unifies the ideas of optimal filtering and subspace methods. A number of different optimal filter designs are derived in this framework, and the properties and performance of these are studied using both synthetic, periodic signals and real signals. The results show a number of interesting things. Firstly, they show how speech distortion can be traded for noise reduction and vice versa in a seamless manner. Moreover, the introduced filter designs are capable of achieving both the upper and lower bounds for the output SNR via the choice of a single parameter.
Identification of RFLP markers linked to a major gene, sw1, conferring resistance to Stewart's wilt in maize. (1999)

The objective of this study was to determine the genetic basis of resistance to Stewart's bacterial wilt (Erwinia stewartii Smith) and to map associated gene(s) in maize (Zea mays L.). It is known that two major dominant genes were involved in the resistance to Stewart's wilt and a single major gene conditions intermediate resistance. Recombinant inbred lines (RILs) were derived in Hawaii from resistant inbred Ki14 an susceptible inbred Hi31, and analyzed by restriction fragment length polymorphism (RFLP). Seventy-one RILs were evaluated for resistance to Stewart's wilt at Henderson, KY. The RILs segregated 1:1 and F 1 hybrids showed intermediate resistance, indicating a single major resistance gene in this population. RFLP markers on the short arm of chromosome 1 showed the largest effect and suggested a major gene in this region. This gene, designated sw1, was mapped on the short arm of chromosome 1 between the RFLP markers umc167 and umc67. This region includes two resistance gene analogs (RGAs) and a major gene for resistance to maize streak virus, msv1. also revealed in RILs produced in Hawaii. In an inoculated trial at Urbana, IL, where disease developed poorly, marker data suggested that none of the more susceptible phenotypes had Sw1 alleles from the resistant parent Ki14.
A neuro-inspired artificial peripheral nervous system for scalable electronic skins (2019)

The human sense of touch is essential for dexterous tool usage, spatial awareness, and social communication. Equipping intelligent human-like androids and prosthetics with electronic skins-a large array of sensors spatially distributed and capable of rapid somatosensory perception-will enable them to work collaboratively and naturally with humans to manipulate objects in unstructured living environments. Previously reported tactile-sensitive electronic skins largely transmit the tactile information from sensors serially, resulting in readout latency bottlenecks and complex wiring as the number of sensors increases. Here, we introduce the Asynchronously Coded Electronic Skin (ACES)-a neuromimetic architecture that enables simultaneous transmission of thermotactile information while maintaining exceptionally low readout latencies, even with array sizes beyond 10,000 sensors. We demonstrate prototype arrays of up to 240 artificial mechanoreceptors that transmitted events asynchronously at a constant latency of 1 ms while maintaining an ultra-high temporal precision of <60 ns, thus resolving fine spatiotemporal features necessary for rapid tactile perception. Our platform requires only a single electrical conductor for signal propagation, realizing sensor arrays that are dynamically reconfigurable and robust to damage. We anticipate that the ACES platform can be integrated with a wide range of skin-like sensors for artificial intelligence (AI)-enhanced autonomous robots, neuroprosthetics, and neuromorphic computing hardware for dexterous object manipulation and somatosensory perception.
Large scale production and semi-purification of kedarcidin in a 1000-L fermentor (1994)

Actinomycete strain ATCC 53650 was grown in a 1000-L fermentor containing 680 L of medium and the production of kedarcidin was monitored by HPLC. The titers of kedarcidin in the fermentor cultures were 0.49-0.53 mg ml-1. A quick and efficient purification method involving the use of anion exchange resin DE23 (batch adsorption-desorption) and an ultrafiltration system yielded high recovery (65% yield) of kedarcidin from the fermentor culture. Over 200 grams of lyophilized kedarcidin of 70% purity was recovered from each of two 1000-L fermentor cultures using this process.
Genome-Wide Somatic Copy Number Alterations in Low-Grade PanINs and IPMNs from Individuals with a Family History of Pancreatic Cancer (2012)

Low- and intermediate-grade PanINs and IPMNs from patients with a family history of pancreatic cancer harbor few if any somatic chromosomal alterations. The absence of a locus of recurrent chromosomal loss in most low-grade pancreatic cancer precursor lesions supports the hypothesis that there is no one tumor suppressor gene locus consistently involved in initiating familial pancreatic neoplasia.
Multi-MW K-Band 7th Harmonic Multiplier for High-Gradient Accelerator R&D (2009)

A preliminary design and current status are presented for a two-cavity 7th harmonic multiplier, intended as a high-power RF source for use in experiments aimed at developing high-gradient structures for a future collider. The harmonic multiplier is to produce power in K-band using as its RF driver an XK-5 S-band klystron (2.856 GHz). The multiplier is to be built with a TE{sub 111} rotating mode input cavity and interchangeable output cavities, a principal example being a TE{sub 711} rotating mode cavity running at 20 GHz. The design that is described uses a 250 kV, 20 A injected laminar electron beam. With 8.5 MW of S-band drive power, 4.4 MW of 20-GHz output power is predicted. The design uses a gun, magnetic coils, and beam collector from an existing waveguide 7th harmonic multiplier. The gun has been re-conditioned and the desired operating parameters have been achieved.
Targeted Nanomedicine for Suppression of CD44 and Simultaneous Cell Death Induction in Ovarian Cancer: An Optimal Delivery of siRNA and Anticancer Drug (2013)

We show a high therapeutic potential for combinatorial treatment of ovarian carcinoma with a novel DDS that effectively transports siRNA targeting to CD44 mRNA simultaneously with cytotoxic agents. Clin Cancer Res; 19(22); 6193-204. ©2013 AACR.
Modulation of a Mr 175,000 c-neu receptor isoform in G8/DHFR cells by serum starvation. (1990)

The neu proto-oncogene product has been found to exist in two interconvertible forms in G8/DHFR mouse fibroblasts. The 185-kilodalton form (p185) present in growing cells is replaced by a 175-kilodalton form (p175) under conditions of serum starvation. This low molecular weight form accounts almost exclusively for the phosphotyrosine content of the receptor and is associated with increased tyrosine kinase activity. Addition of serum, platelet-derived growth factor or tumor promoter induces conversion of p175 to p185 within minutes, and this increase in molecular weight is associated with phosphorylation of serine and threonine; removal of serum growth factors is followed by replacement of p185 with p175 over several hours. Unlike G8/DHFR cells, the human breast cancer cell line SK-Br-3 expresses a high molecular weight neu/HER2 receptor with unchanged phosphotyrosine content in both serum-starved and serum-stimulated cultures. These findings indicate that activation of the neu proto-oncogene product in G8/DHFR cells may be regulated in part by protein kinase C-mediated receptor transmodulation rather than by ligand availability alone.