gebhart/patrepeval huggingface dataset:
Enumeration, characterization, and collection of intact circulating tumor cells by cross contamination‐free flow cytometry (2011)

Circulating tumor cells (CTC) are an important biomarker for several solid cancers. Most of the commercially available systems for enumeration of CTC are based on immunomagnetic enrichment of epithelial cell adhesion molecule (EpCAM/CD326)-expressing CTC before microscopic cell imaging or reverse-transcription PCR (RT-PCR). The aim of this study was to establish a practical method for enumeration of CTC using a novel flow cytometer that has a disposable microfluidic chip, which is designed to realize absolute cross contamination-free measurements and to collect the analyzed cell sample. Although the process of enumeration and labeling of CTC was optimized for this device, the simplified protocol described here could be applied to other flow cytometers. Cultured cancer cells spiked into normal blood were enriched using MACS® EpCAM-MicroBeads following cell labeling with an allophycocyanin (APC)-conjugated EpCAM mAb, instead of by intracellular staining of cytokeratins (CK). The EpCAM double-positive selection/labeling method allows enumeration of intact CTC, maintenance of cellular integrity, and the concomitant performance of a CTC viability test. The combination of the fine-tuned CTC enrichment process and the cytometric multicolor analysis resulted in a linear relationship between the output cell count and the input cell number from zero to hundreds of cells. In particular, a satisfactory signal/noise ratio was obtained by gate-exclusion of leukocyte signals using an anti-CD45 mAb. The entire process had little influence on the viability of the spiked lung cancer cell PC-9. Measured PC-9 and breast cancer MCF-7 cells bearing EpCAM-MicroBeads, APC-conjugated EpCAM mAb, and the DNA staining dye SYTO9 grew normally, demonstrating the potential usefulness of the collected samples for further studies. This intact CTC enumeration and analysis procedure (iCeap) would be of great benefit to clinicians by providing them with rapid stratification of antitumor therapy, and to basic researchers by permitting further molecular and cellular characterization of CTC.
Oligomerization and Pore Formation of a Sphingomyelin-specific Toxin, Lysenin (2003)

Lysenin is a novel protein derived from coelomic fluid of the earthworm Eisenia foetida, which specifically recognizes sphingomyelin and induces cytolysis. The mechanism underlying lysenin-induced cell lysis has not been clarified. In this report we studied the interaction of lysenin with red blood cells as well as artificial liposomes. Our results showed that lysenin bound membranes and assembled to SDS-resistant oligomers in a sphingomyelin-dependent manner, leading to the formation of pores with a hydrodynamic diameter of approximately 3 nm. Antibody scanning analysis suggested that the C-terminal region of lysenin was exposed, whereas the N-terminal was hidden in the isolated oligomer complex. Differential scanning calorimetry revealed that lysenin interacted with both hydrophilic head group and hydrophobic hydrocarbon tails of sphingomyelin. Oligomerization but not binding was affected by the amide-linked fatty acid composition of sphingomyelin, suggesting the role of membrane fluidity in the oligomerization step.
Online multicast routing with bandwidth guarantees (2000)

This paper presents a new algorithm for on-line routing of bandwidth-guaranteed multicasts where routing requests arrive one-by-one without there being any a priori knowledge of future requests. A multicast routing request consists of a source s, a set of receivers R, and a bandwidth requirement b. This multicast routing problem arises in many contexts. Two applications of interest are routing of point-to-multipoint label-switched paths in Multi-Protocol Label Switched (MPLS) networks, and the provision of bandwidth guaranteed Virtual Private Network (VPN) services under the “hose” service model [17]. Offline multicast routing algorithms cannot be used since they require a priori knowledge of all multicast requests that are to be routed. Instead, on-line algorithms that handle requests arriving one-by-one and that satisfy as many potential future demands as possible are needed. The newly developed algorithm is an on-line algorithm and is based on the idea that a newly routed multicast must follow a route that does not “interfere too much” with network paths that may be critical to satisfy future demands. We develop a multicast tree selection heuristic that is based on the idea of deferred loading of certain “critical” links. These critical links are identified by the algorithm as links that, if heavily loaded, would make it impossible to satisfy future demands between certain ingress-egress pairs. The presented algorithm uses link-state information and some auxilliary capacity information for multicast tree selection and is amenable to distributed implementation. Unlike previous algorithms, the proposed algorithm exploits any available knowledge of the network ingress-egress points of potential future demands even though the demands themselves are unknown and performs very well.
A fast layout algorithm for visual video summaries (2003)

We created an improved layout algorithm for automatically generating visual video summaries reminiscent of comic book pages. The summaries are comprised of images from the video that are sized according to their importance. The algorithm performs a global optimization with respect to a layout cost function that encompasses features such as the number of resized images and the amount of whitespace in the presentation. The algorithm creates summaries that: always fit exactly into the requested area, are varied by containing few rows with images of the same size, and have little whitespace at the end of the last row. The layout algorithm is fast enough to allow the interactive resizing of the summaries and the subsequent generation of a new layout.
Access network discovery and selection in the evolved 3GPP multi‐access system architecture (2010)

Abstract The system architecture evolution (SAE) of mobile networks specified in 3GPP release 8 comprises an evolved packet core (EPC) network to which different types of access networks can be connected. Inter‐system mobility management enables users to change the access network while maintaining ongoing data sessions. One important functionality in a 3GPP system is how a mobile terminal discovers and selects available access networks. In this paper we describe the access network discovery and selection functionality used in 3GPP release 8; we explain the differences of the methods applied for 3GPP access networks (GERAN, UTRAN, E‐UTRAN), for fixed or wireless non‐3GPP access networks (e.g. WLAN, WiMAX), as well as the optimisation used for CDMA2000 access networks. Copyright © 2010 John Wiley & Sons, Ltd.
Nanoporous carbon — metal composites for hydrogen storage (2011)

Abstract Metal-carbon composites have shown considerable hydrogen storage potential at room temperature. In the present work the behaviour of two different Pd amalgam doped carbon substrates, namely a carbogenic foam and a mildly oxidised ordered mesoporous carbon, are compared on the basis of their hydrogen sorption properties at 77 and 298 K and low pressures, aiming to investigate the effect of surface on the storage capacity. In both cases, the introduction of alloy nanoparticles leads to an improvement of the hydrogen uptake with respect to pure carbons. This effect is significant for the carbogenic foam however small for the ordered carbon.
Characterisation of two highly oncogenic strains of Marek's disease virus<sup>1</sup><sup>2</sup> (1982)

The RB-1B and ALA-8 strains of Marek's disease (MD) virus, which were isolated from chickens with MD and which had been vaccinated with the herpesvirus of turkeys (HVT), were evaluated for their oncogenic potential in genetically susceptible (P-line) and resistant (N-line, PDRC) chickens. RB-1B and ALA-8 were both highly oncogenic, causing a high incidence of MD in both susceptible and resistant birds. Vaccination of P-line birds with SB-1 or HVT did not protect satisfactorily against RB-1B. However, a bivalent vaccine consisting of SB-1 and HVT enhanced protection significantly. HVT alone, and the bivalent vaccine, protected PDRC and N-line chickens well against RB-1B, but SB-1 was less protective in PDRC birds. HVT protected equally well against challenge with ALA-8 and the standard JM-10 strain. Differences in the pathogenesis of viral infection could not be detected among ALA-8, RB-1B and JM-10 between 4-7 days post-infection (d.p.i.). However, after d.p.i. 12 RB-1B caused significantly higher levels of viral internal antigen and virus isolation rates than did JM-10 in the same genetic strain. Prior vaccination prevented the expression of ALA-8 at 5 and 20 d.p.i., but not that of RB-1B. Pathogenetic events such as expression of VIA or level of virus infection appeared to be directly related to the level of protection observed in challenged birds.
A no-reference quality measure for DIBR-based 3D videos (2011)

In this paper we present a no-reference objective quality measure for stereoscopic 3D videos generated by depth image-based rendering (DIBR). At first we will derive an ideal depth estimate for each pixel value. The ideal depth estimate will then be used to calculate three distortion measures: temporal outliers (TO), temporal inconsistencies (TI), and spatial outliers (SO). The combination of the three measures constitute the proposed no-reference measure. Its performance is verified using subjective DMO S scores and compared to the full reference version of the proposed algorithm. The subjective results show that the proposed measure highly correlates with subjective scores and is close in performance to the full reference version of the measure.
Clinical-Scale Batch-Mode Production of Hyperpolarized Propane Gas for MRI (2019)

NMR spectroscopy and imaging (MRI) are two of the most important methods to study structure, function, and dynamics from atom to organism scale. NMR approaches often suffer from an insufficient sensitivity, which, however, can be transiently boosted using hyperpolarization techniques. One of these techniques is parahydrogen-induced polarization, which has been used to produce catalyst-free hyperpolarized propane gas with proton polarization that is 3 orders of magnitude greater than equilibrium thermal polarization at a 1.5 T field of a clinical MRI scanner. Here we show that more than 0.3 L of hyperpolarized propane gas can be produced in 2 s. This production rate is more than an order of magnitude greater than that demonstrated previously, and the reported production rate is comparable to that employed for in-human MRI using HP noble gas (e.g., <sup>129</sup>Xe) produced via a spin exchange optical pumping (SEOP) hyperpolarization technique. We show that high polarization values can be retained despite the significant increase in the production rate of hyperpolarized propane. The enhanced signals of produced hyperpolarized propane gas were revealed by stopped-flow MRI visualization at 4.7 T. Achieving this high production rate enables the future use of this compound (already approved for unlimited use in foods by the corresponding regulating agencies, e.g., FDA in the USA, and more broadly as an E944 food additive) as a new inhalable contrast agent for diagnostic detection via MRI.
A unified framework for spectral domain prediction and end-to-end distortion estimation in scalable video coding (2011)

A novel scalable coding approach is proposed for video transmission over lossy networks, which builds on two estimation-theoretic (ET) paradigms previously developed by our group: (1) an ET approach to enhancement layer prediction in scalable video coding (ET-SVC) that optimally combines all available information from both the current base layer and prior enhancement layer frames, and (2) the spectral coefficient-wise optimal recursive estimate (SCORE) of end-to-end distortion. SCORE provides the encoder with an estimate of distortion per decoder-reconstructed transform coefficient, accounting for the effects of quantization, concealment, packet loss and error propagation via the prediction loop. The current work significantly extends the scope of SCORE to encompass the setting of ET-SVC, whose prediction involves non-linear operations. This advance enables optimization of ET-SVC systems for transmission over lossy networks, thereby combining optimal prediction with optimal mode decisions at the enhancement layer. Experiments first demonstrate the estimation accuracy of SCORE in the settings of the ET-SVC coder. They then show considerable gains when SCORE is incorporated into ET-SVC to optimize encoding decisions under a wide range of packet loss and bit rates.
Application of Gold-Tin Solder Paste for Fine Parts and Devices (2005)

Au-Sn solder paste can be applied by various providing methods, such as printing, dispense, pin transfer, etc.. These methods also make it possible to reduce the production cost. However, in the case of using solder paste, the occurrence of void is one of the most undesirable problems. In this study, we have tried to identify the mechanism of void generation and to reduce voids. We found that the most important factor was to prevent both the gases generated during the reflow process and the generation of Au and/or Sn rich phase in molten Au-Sn solder. For details, it was indicated that for the former it is practical to optimize the pre-heat temperature and holding time in reflow process, to make O2 contents of the powder lower, to control the amount of activator in flux, etc.. For the latter it is important to optimize the composition of the Au-Sn alloy for the reduction of Au and/or Sn rich phases in molten solder.
Design, Implementation and Evaluation of a Pump-Controlled Circuit for Single Rod Actuators (2017)

Pump-controlled hydraulic circuits are more efficient than valve-controlled circuits, as they eliminate the energy losses due to flow throttling in valves and require less cooling effort. Presently existing pump-controlled solutions for single rod cylinders encounter an undesirable performance during certain operating conditions. This paper investigates the performance issues in common pump-controlled circuits for the single rod actuators. Detailed analysis is conducted that identifies these regions in a load-velocity plane and the factors affecting them. The findings are validated by experimental results. A new design is then proposed that employs a limited throttling valve alongside two pilot operated check valves for differential flow compensation to improve the performance. The valve is of the flow control type and is chosen to have a throttling effect over critical regions; it has the least throttling over other operating regions, thus maintaining efficiency. Experimental work demonstrates improved performance in a full operating range of the actuator as compared to a circuit that uses only the pilot-operated check valves. This circuit is energy efficient and capable of recuperating energy.
Parallel Unstructured-Solver Methods for Simulation of Complex Giant Reservoirs (2008)

Summary The major issues for parallel solvers in a modern reservoir simulator are robustness, scalability, efficiency, and flexibility. There is significant interest in running fast field-scale simulations for complex giant Middle Eastern reservoirs, which will require tens of millions to hundreds of millions of grid cells to give reasonable resolution. At the same time, significant geologic complexity will require the treatment of dual-permeability regions, faulting and fractures, and high variations of reservoir and fluid properties. Of course, the methods should also work well for extracted-sector simulation with local grid refinements in both the structured and unstructured discretization. The preconditioning methods considered in this work include both the single-stage and multistage frameworks. In the single-stage framework, a novel method is considered in addition to the well-known variants of incomplete lower-upper (ILU) factorizations [ILU0, ILU(k), and ILUT]. The new method is a highly parallel method, which, in this paper, will be referred to as the unstructured line-solve power-series (LSPS) method. The method will be discussed and contrasted in light of key issues for parallel linear solvers. The unstructured LSPS has certain interesting properties in the parallel construct, which make it a highly effective component. The multistage method researched in this work is of the constraint pressure residual (CPR) framework. The method uses approximate pressure solve as the first-stage preconditioning to the full-system preconditioning. A number of original adaptations based on this concept were researched. Here, the use of the parallel algebraic multigrid (PAMG) method and other single-level methods mentioned previously in combinations within the multistage CPR framework were explored. Certain methods constructed in this way are found to be highly efficient, scalable, and robust. The methods developed are discussed, and several test problems are included, in this paper. The largest simulation model tested to date using these solver methods is a 172-million-cell full-field model of a supergiant carbonate complex with more than 3,000 wells and 60 years of history simulation.
Rate-constrained multi-hypothesis motion-compensated prediction for video coding (2002)

Multi-hypothesis prediction extends motion compensation with one prediction signal to the linear superposition of several motion-compensated prediction signals with the result of increased coding efficiency. The multiple hypotheses in this paper are blocks in past decoded frames. These blocks are referenced by individual motion vectors and picture reference parameters incorporating long-term memory motion-compensated prediction. In this work, we at most employ two hypotheses similar to B-frames. However, they are obtained from the past. Due to the increased rate for the motion vectors, rate-constrained coder control is utilized. For this scheme, we demonstrate the coding efficiency of multi-hypothesis prediction in combination with variable block size and long-term memory and present bit-rate savings up to 32% when compared to standard variable block size prediction without long-term memory motion compensation.
Abstract B007: Targeting the ubiquitin signaling system for cancer immunotherapy (2016)

Abstract Studies have been performed to demonstrate that effectors of enzymes of the ubiquitin proteasome pathway associated with T cell activation are able to impair tumor survival by abrogating the immune evasion mechanism. Immune evasion is a collective term for the various strategies employed by tumors to suppress the host immune system's ability to recognize and destroy cancer cells. Significant advances in the understanding of the mechanisms of cancer immune evasion have led to the successful development of biologic immunotherapies that showed clinical efficacy against hematological as well as solid tumors. These include monoclonal antibodies, allogeneic hematopoietic stem cell transplantation, vaccination, cytokines, T cell checkpoint blockade and adoptive transfer of engineered T cells. Owing to the multifaceted nature of cancer immune evasion, however, several different approaches will likely be necessary for effective therapeutic management. We have adopted a dual targeting approach focused on the ubiquitin proteasome pathway to develop novel small molecule cancer immunotherapies. Using the UbiProTM discovery platform, we have identified inhibitors of a deubiquitylase (DUB) that is highly expressed in regulatory T cells (Tregs) and plays a critical role in promoting Treg functions. These inhibitors are shown to suppress Treg functions and promote T-effector cell function ex vivo and in vivo. In addition, we have identified inhibitors of an E3 ubiquitin ligase that negatively regulates T-effector cell function. These inhibitors are shown to activate T-cells and NK cell functions in vitro. A combination of such inhibitors should provide powerful anti-cancer immunotherapy. Citation Format: Suresh Kumar, Liqing Wang, Jian Wu, Feng Wang, Saket Agarwal, Matthew Kodrasov, Wayne Hancock, Michael Mattern. Targeting the ubiquitin signaling system for cancer immunotherapy. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr B007.
Prostate-specific membrane antigen antibody drug conjugate (PSMA ADC): A phase I trial in taxane-refractory prostate cancer. (2011)

158 Background: The unique expression of PSMA type II transmembrane glycoprotein on prostate cancer cells provides a potentially attractive target for antibody therapy. PSMA ADC, a fully humanized antibody to PSMA linked to the potent antitubulin agent monomethyl auristatin E (MMAE), binds PSMA and is internalized within the prostate cancer cell where cleavage and release of free MMAE occur, causing cell cycle arrest and apoptosis. We report results from an ongoing phase I dose escalation study of PSMA ADC in patients (pts) with taxane refractory metastatic prostate cancer (metCRPC). Methods: Eligibility requirements included pts ≥18 years with metCRPC after failure of a taxane- containing regimen and ECOG status of 0 or 1. PSMA ADC is administered by IV infusion Q3W for up to 4 cycles. Adverse events, PK, PSA, circulating tumor cells, clinical disease progression and immunogenic response to PSMA ADC continue to be assessed. Serum concentrations of PSMA ADC and total antibody are measured by an enzyme-linked immunosorbent assay (ELISA) method, and free MMAE is measured by liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS) method. Dosing cohorts ranged from 0.4 mg/kg to 1.8 mg/kg. Results: The demographics of 15 subjects enrolled in the four dosing cohorts (0.4, 0.7, 1.1 and 1.8 mg/kg) were similar. Treatment has to date been generally well tolerated and the most common laboratory abnormalities were reversible changes in liver and hematological parameters. Exposure to PSMA ADC and serum half life (t 1/2 ) increased in a dose-proportional manner. Similar PK metrics were observed after the first and third doses. Exposure to free MMAE was also dose proportional and approximately <0.1% of PSMA ADC. Conclusions: In this first-in-human evaluation, PSMA ADC appears to exhibit dose-proportional PK and limited release of free MMAE. Ongoing enrollment allows for assessment of potential clinical utility of this unique potential treatment of metCRPC. [Table: see text]
Modulation, coding and signal processing for wireless communications - Single-antenna co-channel interference cancellation for TDMA cellular radio systems (2005)

Co-channel interference cancellation is particularly challenging in the downlink of cellular radio systems because usually only one receive antenna is available at the mobile terminal. This tutorial provides an overview of promising a single-antenna co-channel interference cancellation techniques. Focus is on the downlink of time-division multiple access systems. The results may, however, be extended to related applications, including interference suppression in multiple-input multiple-output systems.