gebhart/patrepeval huggingface dataset:
Abstract 3754: A prospective imaging biomarker trial for early identification of GBM patients resistant to first line therapy (2010)

Abstract We assessed whether quantification of therapeutic-associated tumor cellularity and hemodynamic alterations may help in the early assessment of treatment resistance in patients with high grade glioma. Patients with high grade glioma (n=45) received concurrent chemoradiation. Apparent diffusion coefficient (ADC) and relative cerebral blood volume (rCBV) maps were acquired prior to chemoradiation and at week 3 during treatment on a prospective IRB-approved study. Clinical and conventional MR parameters, including average baseline ADC and rCBV and radiological response, were evaluated as prognostic indicators of one-year survival. Parametric response map (PRM), an innovative, voxel-by-voxel method of image analysis, was also performed. Of 45 patients, median survival was found to be 14.9 months with 44% of patients living shorter than one year (median survival of 6.6 months). Baseline ADC was the only single model not found to be predictive of survival at one year, whereas in a multivariate analysis PRMADC+ and PRMrCBV- had a stronger correlation to survival than baseline rCBV. Overall, a composite model of PRMADC+ and PRMrCBV- was found to have the strongest correlation with one-year survival. This study demonstrates the potential of a composite parametric model sensitive to both tumor cellularity and hemodynamic alterations following first line therapy for providing an early assessment of patient resistant to chemoradiation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3754.
Cyclic diGMP Regulates Production of Sortase Substrates of Clostridium difficile and Their Surface Exposure through ZmpI Protease-mediated Cleavage (2015)

In Gram-positive pathogens, surface proteins may be covalently anchored to the bacterial peptidoglycan by sortase, a cysteine transpeptidase enzyme. In contrast to other Gram-positive bacteria, only one single sortase enzyme, SrtB, is conserved between strains of Clostridium difficile. Sortase-mediated peptidase activity has been reported in vitro, and seven potential substrates have been identified. Here, we demonstrate the functionality of sortase in C. difficile. We identify two sortase-anchored proteins, the putative adhesins CD2831 and CD3246, and determine the cell wall anchor structure of CD2831. The C-terminal PPKTG sorting motif of CD2831 is cleaved between the threonine and glycine residues, and the carboxyl group of threonine is amide-linked to the side chain amino group of diaminopimelic acid within the peptidoglycan peptide stem. We show that CD2831 protein levels are elevated in the presence of high intracellular cyclic diGMP (c-diGMP) concentrations, in agreement with the control of CD2831 expression by a c-diGMP-dependent type II riboswitch. Low c-diGMP levels induce the release of CD2831 and presumably CD3246 from the surface of cells. This regulation is mediated by proteolytic cleavage of CD2831 and CD3246 by the zinc metalloprotease ZmpI, whose expression is controlled by a type I c-diGMP riboswitch. These data reveal a novel regulatory mechanism for expression of two sortase substrates by the secondary messenger c-diGMP, on which surface anchoring is dependent.
A novel array processing method for precise depth detection of ultrasound point scatter (2016)

A signal based algorithm resulting in increased depth resolution is presented for medical ultrasound. It relies on multiple foci beamforming that is enabled by current ultrasound imaging systems. The concept stems from optical microscopy and is translated here into ultrasound using the Field II simulation software. A 7 MHz linear transducer is used to scan a single point scatterer phantom that can move in the axial direction. Individual beamformer outputs from 3 different foci are post-processed using the highly-dependent on focusing errors, metric of sharpness to estimate the position of the point scatter. A 37.8 μm uncertainty in depth estimation is achieved, which attains an almost 3-fold improvement compared to conventional ultrasound imaging axial resolution. Future work on the development of this algorithm requires experimental validation in tissue-like materials that provide strong aberrations.
G202 A Study of Noise Reduction Effect on Blade Shape of Cross Flow Fan(2) (2006)

Recently, it's necessary for saving energy of air-conditioner to reduce fan noise. In this study, the new type of cross flow fan is developed, which has pretty high performance of noise reduction. That new fan is called "saw-edged blade fan" whose blade has a lot of cutouts. In this paper, PIV (Particle Image Velocimetry) measurement is carried out to analyze the flow structure of blade passage of the fans, and it's found out that the decrease of wake by saw-edged blade effects the noise reduction of the fan.
The Conversational Web (2012)

There is currently significant interest in the speech, language, and human computer interaction (HCI) scientific communities in creating a conversational interface to the web. Through the combination of natural language (spoken and written) with gesture, touch, and gaze, this natural user interface (NUI) could help you complete online tasks, find what you want, and answer any question as naturally as having a conversation – anytime, anywhere. This talk explores the emergence of this Conversational Web and the fundamental trends in the industry that are providing significant opportunities, and in some cases challenges, for spoken language technologists. The first trend that the talk will cover is the availability of massive data from the Web. A Web of Intents has emerged from the feedback loop of click streams in Web search engines and browsers, capturing many hundreds of millions of queries, page views, and clicks from billions of users every day. This Web of Intents has begun to radically increase the predictive power of statistical learning algorithms underlying modern conversational systems. Second, the talk will discuss the emergence of the Web of Structured Knowledge. With the broadly adopted structuring of web sites through well-formed APIs, the Programmable Web has already enabled the emergence of mobile virtual personal assistants. And with the commitment to adopt standard semantic ontologies, the large search engine companies (Microsoft, Google) are finally making the structured “Semantic Web” a reality. Third, the “Applification” of the Web, which is decentralizing the web into highly structured but fragmented, specialized functional islands. This talk will explore all three trends, and propose some particular approaches to leveraging the first two and turning the third into an asset for the Conversational Web.
Investigation of Medium Chain Fatty Acid Feed Supplementation for Reducing Salmonella Typhimurium Colonization in Turkey Poults (2017)

Studies indicate that persistent Salmonella colonization occurs in poultry that are infected early in life, leading to both food safety and public health concerns. Development of improved preharvest Salmonella management strategies is needed to reduce poultry product contamination. The objective of this study was to evaluate the efficacy of a product containing medium chain fatty acids (MCFA) for reducing early Salmonella colonization in turkey poults. Day-of-hatch turkeys were provided a standard starter diet supplemented with MCFA at 0 (negative and positive controls), 1.5, 3, 4.5, or 6 lbs/ton of feed. Positive control and MCFA treated birds were also crop-gavaged with 10<sup>8</sup> colony forming units (CFU) of bioluminescent Salmonella Typhimurium. Gastrointestinal tissue samples were collected at 3 days postinoculation for bioluminescence imaging (Meckel's diverticulum to the cloaca) and selective enumeration (cecal contents). Quantification of bioluminescence indicated that the 4.5 and 6 lbs/ton MCFA groups had significantly less colonization than the positive control group (p = 0.0412 and p < 0.0001, respectively). Similarly, significantly lower numbers (1-log<sub>10</sub> CFU/g reduction) of Salmonella were observed in the ceca of the 6 lbs/ton MCFA group compared to the positive control group (p = 0.0153). These findings indicate that incorporation of MCFA in turkey diets can significantly reduce early Salmonella colonization. In addition, this study highlights the utility of bioluminescence imaging as a screening methodology for assessing the efficacy of treatments that may reduce Salmonella in poultry.
High‐Speed Router Chip Set (2006)

This chapter contains sections titled: Network Processors (NPs) Co-Processors for Packet Classification Traffic Management Chips Switching Fabric Chips
Supplementary Table 1 from PARP-1 Inhibition as a Targeted Strategy to Treat Ewing's Sarcoma (2023)

&lt;p&gt;PDF file - 31K&lt;/p&gt;
Organized assemblies of colloids formed at the poles of micrometer-sized droplets of liquid crystal (2014)

We report on the formation of organized assemblies of 1 μm-in-diameter colloids (polystyrene (PS)) at the poles of water-dispersed droplets (diameters 7-20 μm) of nematic liquid crystal (LC). For 4-cyano-4'-pentylbiphenyl droplets decorated with two to five PS colloids, we found 32 distinct arrangements of the colloids to form at the boojums of bipolar droplet configurations. Significantly, all but one of these configurations (a ring comprised of five PS colloids) could be mapped onto a local (non-close packed) hexagonal lattice. To provide insight into the origin of the hexagonal lattice, we investigated planar aqueous-LC interfaces, and found that organized assemblies of PS colloids did not form at these interfaces. Experiments involving the addition of salts revealed that a repulsive interaction of electrostatic origin prevented formation of assemblies at planar interfaces, and that regions of high splay near the poles of the LC droplets generated cohesive interactions between colloids that could overcome the repulsion. Support for this interpretation was obtained from a model that included (i) a long-range attraction between adsorbed colloids and the boojum due to the increasing rate of strain (splay) of LC near the boojum (splay attraction), (ii) an attractive inter-colloid interaction that reflects the quadrupolar symmetry of the strain in the LC around the colloids, and (iii) electrostatic repulsion between colloids. The model predicts that electrostatic repulsion between colloids can lead to a ∼1000kBT energy barrier at planar interfaces of LC films, and that the repulsive interaction can be overcome by splay attraction of the colloids to the boojums of the LC droplets. Overall, the results reported in this paper advance our understanding of the directed assembly of colloids at interfaces of LC droplets.
On-chip circuit for measuring multi-GHz clock signal waveforms (2013)

An on-chip circuit to measure full analog waveforms of internal signals is described. It can measure signals up to a repetition rate of at least 7 GHz, a bandwidth of at least 12 GHz, with accuracy required to detect subtle differences in signals, and it can measure overshoot above the rail voltage. It has been demonstrated on an experimental clock grid with optional resonant operation.
Admission Control in Cellular Radio Systems Based on Relative Load Estimates (2001)

When operating a cellular radio system nearly at full capacity, admitting yet another user may jeopardize the stability of the system as well as the performance of the individual users. Therefore, ...
Analysis of very large radio telescope antennas using multilevel physical optics algorithm (2015)

Analysis of very large multi-reflector antennas like that of RATAN-600 radio telescope presents a formidable computational challenge. At mm-wave frequencies of interest, the RATAN-600 main reflector measures roughly 20,000 by 1000 square wavelengths. Such reflector antennas are often analyzed as quasi-optical systems in two main steps. In the first stage, the field is propagated from the feed to an equivalent aperture using geometrical optics (GO), while in the second, the radiation pattern is computed by aperture integration, which for planar apertures can be accelerated using the Fast Fourier Transform (FFT) (R.E. Collin, Antennas and Radio Wave Propagation, McGraw-Hill, 1985). This line of modeling completely neglects the wave phenomena involved in the inter-reflector propagation and introduces phase errors due to introduction of the artificial planar equivalent aperture required for the radiation pattern evaluation using the FFT.
Un-masking the latent immunogenicity of neoepitopes by checkpoint blockade (TUM2P.1031) (2015)

Abstract Comparison of transcriptome sequences of the BALB/c mouse fibrosarcoma Meth A with the normal BALB/c genome led to identification of 1528 heterozygous tumor-specific point mutations, which, using the NetMHC algorithm, generated 203 Kd-restricted potential neoepitopes1. BALB/c mice were immunized with each of 11 candidate-neoepitopes which had a high binding affinity to Kd (IC50 &amp;lt;500 nM), and were challenged with live Meth A cells. Not a single candidate-neoepitope elicited tumor rejection. Mice were then immunized with the same candidate-neoepitopes in combination with 9D9, an antagonistic antibody to CTLA-4 (mouse anti-mouse IgG2b). In preliminary results, a small number of candidate-neoepitopes that did not elicit tumor rejection on their own appear to be active in tumor rejection, when combined with checkpoint blockade of CTLA-4. These results as well as a mechanistic dissection of this un-covering of latent immunogenicity by checkpoint blockade shall be presented. 1Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II, Srivastava PK. Genomic and Bioinformatic Profiling of Mutational Neoepitopes Reveals New Rules to Predict Anticancer Immunogenicity." J Exp Med. 211 (2014): 2231-248. PMID: 25245761
Effective duty cycle of galvanometer-based scanners: impact on OCT imaging (2015)

We study experimentally the scanning functions of galvanometer-based scanners (GSs) in order to optimize them for biomedical imaging in general, and for Optical Coherence Tomography (OCT) in particular. The main scanning parameters of the scanning process are taken into account: theoretical duty cycle (of the input signal of the GS), scan frequency (<i>f</i><sub>s</sub>), and scan amplitude (θ<sub>m</sub>). Triangular to sawtooth scanning regimes are thus considered. We demonstrate that when increasing the scan frequency and amplitude, the scanning function (i.e., the angular position of the galvomirror) is not able to follow anymore the input signal. Furthermore, as the theoretical duty cycle is increased, the result is unexpected: the effective duty cycle actually decreases – for high <i>f</i><sub>s</sub> and θ<sub>m</sub>. A saturation of the device therefore occurs. The practical limits of this phenomenon are discussed. GS users are thus provided with a multi-parameter analysis that allows them for optimizing their scanning regimes and to avoid pushing the devices to their limit – when that actually results in decreasing the quality of the images obtained, by example in OCT. Gabor Domain Optical Coherence Microscopy (GD-OCM) images are made to show effects of this phenomenon.
Unraveling the Dual Functionality of High‐Donor‐Number Anion in Lean‐Electrolyte Lithium‐Sulfur Batteries (2020)

Abstract Minimizing electrolyte use is essential to achieve high practical energy density of lithium–sulfur (Li–S) batteries. However, the sulfur cathode is more readily passivated under a lean electrolyte condition, resulting in low sulfur utilization. In addition, continuous electrolyte decomposition on the Li metal anode aggravates the problem, provoking rapid capacity decay. In this work, the dual functionalities of NO 3 − as a high‐donor‐number (DN) salt anion is presented, which improves the sulfur utilization and cycling stability of lean‐electrolyte Li–S batteries. The NO 3 − anion elevates the solubility of the sulfur species based on its high electron donating ability, achieving a high sulfur utilization of above 1200 mA h g −1 . Furthermore, the anion suppresses electrolyte decomposition on the Li metal by regulating the lithium ion (Li + ) solvation sheath, enhancing the cycle performance of the lean electrolyte cell. By understanding the anionic effects, this work demonstrates the potential of the high‐DN electrolyte, which is beneficial for both the cathode and anode of Li–S batteries.
Towards systematic design of distance functions for data mining applications (2003)

Distance function computation is a key subtask in many data mining algorithms and applications. The most effective form of the distance function can only be expressed in the context of a particular data domain. It is also often a challenging and non-trivial task to find the most effective form of the distance function. For example, in the text domain, distance function design has been considered such an important and complex issue that it has been the focus of intensive research over three decades. The final design of distance functions in this domain has been reached only by detailed empirical testing and consensus over the quality of results provided by the different variations. With the increasing ability to collect data in an automated way, the number of new kinds of data continues to increase rapidly. This makes it increasingly difficult to undertake such efforts for each and every new data type. The most important aspect of distance function design is that since a human is the end-user for any application, the design must satisfy the user requirements with regard to effectiveness. This creates the need for a systematic framework to design distance functions which are sensitive to the particular characteristics of the data domain. In this paper, we discuss such a framework. The goal is to create distance functions in an automated waywhile minimizing the work required from the user. We will show that this framework creates distance functions which are significantly more effective than popularly used functions such as the Euclidean metric.
Structure–Activity Relationship Studies of the Natural Product Gq/11 Protein Inhibitor YM‐254890 (2019)

G proteins act as molecular switches in G protein-coupled receptor signaling pathways and are key mediators for numerous important physiological processes. The natural product, cyclic depsipeptide YM-254890, together with the structurally similar FR900359, is the only known selective inhibitor of the G<sub>q/11</sub> subfamily of G proteins. We recently reported the first total synthesis of YM-254890 and FR900359, followed by synthesizing analogues to perform structure-activity relationship studies. However, incomplete information about their structure-activity relationship prevents the further development of potent and structurally simplified analogues. Herein we report the first systematic structure-activity relationship study toward the N-methyldehydroalanine moiety in YM-254890, by designing and synthesizing seven new analogues. Pharmacological characterization of the seven compounds for G<sub>q/11</sub> -, G<sub>i/o</sub> - and G<sub>s</sub> -mediated signaling showed that the simplified analogue YM-19 is the most potent G<sub>q/11</sub> inhibitor among the new analogues. This study provides information for the future design of potent and simplified YM-254890 analogues.
ONC201/TIC10 Is Empowered by 2-Deoxyglucose and Causes Metabolic Reprogramming in Medulloblastoma Cells in Vitro Independent of C-Myc Expression (2021)

The purpose of this study was to examine whether the imipridone ONC201/TIC10 affects the metabolic and proliferative activity of medulloblastoma cells <i>in vitro</i>. Preclinical drug testing including extracellular flux analyses (agilent seahorse), MTT assays and Western blot analyses were performed in high and low c-myc-expressing medulloblastoma cells. Our data show that treatment with the imipridone ONC201/TIC10 leads to a significant inihibitory effect on the cellular viability of different medulloblastoma cells independent of c-myc expression. This effect is enhanced by glucose starvation. While ONC201/TIC10 decreases the oxidative consumption rates in D458 (c-myc high) and DAOY (c-myc low) cells extracellular acidification rates experienced an increase in D458 and a decrease in DAOY cells. Combined treatment with ONC201/TIC10 and the glycolysis inhibitor 2-Deoxyglucose led to a synergistic inhibitory effect on the cellular viability of medulloblastoma cells including spheroid models. In conclusion, our data suggest that ONC201/TIC10 has a profound anti-proliferative activity against medulloblastoma cells independent of c-myc expression. Metabolic targeting of medulloblastoma cells by ONC201/TIC10 can be significantly enhanced by an additional treatment with the glycolysis inhibitor 2-Deoxyglucose. Further investigations are warranted.
Ectodomain Structures of the CGRP and AM Receptors (2013)

Receptor activity-modifying proteins (RAMPs) 1-3, which are classified as type I transmembrane proteins, serve as the partner proteins of several family B GPCRs for physiologically active peptides, including the calcitonin receptor- like receptor (CLR). The properties of the GPCRs are defined by the RAMP and peptide ligand combination. The CLR•RAMP1 heterodimer functions mainly as the calcitonin gene-related peptide (CGRP) receptor, while the CLR•RAMP2 and CLR•RAMP3 heterodimers primarily function as the adrenomedullin 1 and adrenomedullin 2 (AM₁ and AM₂) receptors, respectively. The crystal structures of the RAMP1 and RAMP2 ectodomains exhibited three-helix bundles, and those of their complexes with the N-terminal extracellular domain of CLR revealed how the two ectodomains associate to form the CGRP and AM₁ receptors, respectively. On this structural framework, the various intermolecular interactions of CLR with RAMP1 and RAMP2 result in the distinct shapes of the putative ligand-binding sites, where several residues are uniquely presented. Therefore, the differences in the shapes and the presented residues of the binding sites determine the specificities of the receptors to either CGRP or AM. These structural features of the ectodomains are consistent with mutagenesis results, and are useful to further examine the binding modes of the peptide ligands to the full-length CGRP and AM₁ receptors.
Reverse shoulder arthroplasty for type 1 sequelae of a fracture of the proximal humerus (2018)

RSA is an effective form of treatment for patients with type 1 sequelae of a fracture of the proximal humerus associated with rotator cuff deficiency or stiffness of the shoulder, with high rates of satisfaction. Rotator cuff tears and stiffness of the shoulder had an adverse effect on the clinical outcome. Cite this article: Bone Joint J 2018;100-B:318-23.