gebhart/patrepeval huggingface dataset:
Bubble Liposomes and Ultrasound Exposure Improve Localized Morpholino Oligomer Delivery into the Skeletal Muscles of Dystrophic <i>mdx</i> Mice (2014)

Duchenne muscular dystrophy (DMD) is a genetic disorder that is caused by mutations in the DMD gene that lead to an absence of functional protein. The mdx dystrophic mouse contains a nonsense mutation in exon 23 of the dystrophin gene; a phosphorodiamidate morpholino oligomer (PMO) designed to skip this mutated exon in the mRNA induces dystrophin expression. However, an efficient PMO delivery method is needed to improve treatment strategies for DMD. We previously developed polyethylene glycol (PEG)-modified liposomes (Bubble liposomes) that entrap ultrasound contrast gas and demonstrated that the combination of Bubble liposomes with ultrasound exposure is an effective gene delivery tool in vitro and in vivo. In this study, to evaluate the ability of Bubble liposomes as a PMO delivery tool, we tested the potency of the Bubble liposomes combined with ultrasound exposure to boost the delivery of PMO and increase the skipping of the mutated exon in the mdx mouse. The results indicated that the combination of Bubble liposomes and ultrasound exposure increased the uptake of the PMO targeting a nonsense mutation in exon 23 of the dystrophin gene and consequently increased the PMO-mediated exon-skipping efficiency compared with PMO injection alone, leading to significantly enhanced dystrophin expression. This increased efficiency indicated the potential of the combination of Bubble liposomes with ultrasound exposure to enhance PMO delivery for treating DMD. Thus, this ultrasound-mediated Bubble liposome technique may provide an effective, noninvasive, nonviral method for PMO therapy for DMD muscle as well as for other muscular dystrophies.
Time-frequency analysis of functional optical mammographic images (2003)

We have introduced working technology that provides for time-series imaging of the hemoglobin signal in large tissue structures. In this study we have explored our ability to detect aberrant time-frequency responses of breast vasculature for subjects with Stage II breast cancer at rest and in response to simple provocations. The hypothesis being explored is that time-series imaging will be sensitive to the known structural and functional malformations of the tumor vasculature. Mammographic studies were conducted using an adjustable hemisheric measuring head containing 21 source and 21 detector locations (441 source-detector pairs). Simultaneous dual-wavelength studies were performed at 760 and 830 nm at a framing rate of ~2.7 Hz. Optical measures were performed on women lying prone with the breast hanging in a pendant position. Two class of measures were performed: (1) 20- minute baseline measure wherein the subject was at rest; (2) provocation studies wherein the subject was asked to perform some simple breathing maneuvers. Collected data were analyzed to identify the time-frequency structure and central tendencies of the detector responses and those of the image time series. Imaging data were generated using the Normalized Difference Method (Pei <i>et al., Appl. Opt</i>. <b>40</b>, 5755-5769, 2001). Results obtained clearly document three classes of anomalies when compared to the normal contralateral breast. 1) Breast tumors exhibit altered oxygen supply/demand imbalance in response to an oxidative challenge (breath hold). 2) The vasomotor response of the tumor vasculature is mainly depressed and exhibits an altered modulation. 3) The affected area of the breast wherein the altered vasomotor signature is seen extends well beyond the limits of the tumor itself.
Probiotics as Potential Therapeutics for Colorectal Cancer (2020)

Much health benefits by lactic acid bacteria (LAB) have been observed via in-vivo trials. LAB’s health benefits are described such as improving of intestinal microbial balance between probiotics and harmful bacteria, protecting of pathogen infection and modulating of host’s immunity in gut. Colorectal cancer (CRC) located in intestine and its development leads to invade or spread to other parts of the body result in death. Recent many publications about LAB have demonstrated the immense potential as alternative bio-therapeutics. Actually, LAB have been reported to be the safe bio-therapeutic with positive effects against various cancer types including CRC. In this review, we discuss the evidences of beneficial effects of LAB application and its molecular mechanisms.
Using spectral reflectance to distinguish between tracheal and oesophageal tissue: applications for airway management (2019)

Proper placement of the tracheal tube requires confirmation, and the predominant method in addition to clinical signs is the presence of end-tidal carbon dioxide. Such is the importance of confirmation that novel methods may also have a place. We previously demonstrated using ex-vivo swine tissue a unique spectral reflectance characteristic of tracheal tissue that differs from oesophageal tissue. We hypothesised that this characteristic would be present in living swine tissue and human cadavers. Reflectance spectra in the range 500-650 nm were captured using a customised fibreoptic probe, compact spectrometer and white light source from both the trachea and the oesophagus in anesthetised living swine and in human cadavers. A tracheal detection algorithm using ratio comparisons of reflectance was developed. The existence of the unique tracheal characteristic in both in-vivo swine and cadaver models was confirmed (p < 0.0001 for all comparisons between tracheal and oesophageal tissue at all target wavelengths in both species). Furthermore, our proposed tracheal detection algorithm exhibited a 100% positive predictive value in both models. This has potential utility for incorporation into airway management devices.
DC2: A framework for scalable, scope-bounded software verification (2011)

Software model checking and static analysis have matured over the last decade, enabling their use in automated software verification. However, lack of scalability makes these tools hard to apply. Furthermore, approximations in the models of program and environment lead to a profusion of false alarms. This paper proposes DC2, a verification framework using scope-bounding to bridge these gaps. DC2 splits the analysis problem into manageable parts, relying on a combination of three automated techniques: (a) techniques to infer useful specifications for functions in the form of pre- and post-conditions; (b) stub inference techniques that infer abstractions to replace function calls beyond the verification scope; and (c) automatic refinement of pre- and post-conditions from false alarms identified by a user. DC2 enables iterative reasoning over the calling environment, to help in finding non-trivial bugs and fewer false alarms. We present an experimental evaluation that demonstrates the effectiveness of DC2 on several open-source and industrial software projects.
Sparse methods for Quantitative Susceptibility Mapping (2015)

Quantitative Susceptibility Mapping (QSM) aims to estimate the tissue susceptibility distribution that gives rise to subtle changes in the main magnetic field, which are captured by the image phase in a gradient echo (GRE) experiment. The underlying susceptibility distribution is related to the acquired tissue phase through an ill-posed linear system. To facilitate its inversion, spatial regularization that imposes sparsity or smoothness assumptions can be employed. This paper focuses on efficient algorithms for regularized QSM reconstruction. Fast solvers that enforce sparsity under Total Variation (TV) and Total Generalized Variation (TGV) constraints are developed using Alternating Direction Method of Multipliers (ADMM). Through variable splitting that permits closed-form iterations, the computation efficiency of these solvers are dramatically improved. An alternative approach to improve the conditioning of the ill-posed inversion is to acquire multiple GRE volumes at different head orientations relative to the main magnetic field. The phase information from such multi-orientation acquisition can be combined to yield exquisite susceptibility maps and obviate the need for regularized reconstruction, albeit at the cost of increased data acquisition time.
Supplemental Figure 7 from Tumor Radiosensitization by Monomethyl Auristatin E: Mechanism of Action and Targeted Delivery (2023)

<p>Schematic model of therapeutic strategy utilizing tumor targeted MMAE delivery with ACPP.</p>
High Performance On-demand Video Transcoding Using Cloud Services (2016)

Video streams, either in form of on-demand streaming or live streaming, usually have to be converted (i.e., transcoded) based on the characteristics (e.g., spatial resolution) of clients' devices. Transcoding is a computationally expensive operation, therefore, streaming service providers currently store numerous transcoded versions of the same video to serve different types of client devices. However, recent studies show that accessing video streams have a long tail distribution. That is, there are few popular videos that are frequently accessed while the majority of them are accessed infrequently. The idea we propose in this research is to transcode the infrequently accessed videos in a on-demand (i.e., lazy) manner. Due to the cost of maintaining infrastructure, streaming service providers (e.g., Netflix) are commonly using cloud services. However, the challenge in utilizing cloud services for video transcoding is how to deploy cloud resources in a cost-efficient manner without any major impact on the quality of video streams. To address the challenge, in this research, we present an architecture for on-demand transcoding of video streams. The architecture provides a platform for streaming service providers to utilize cloud resources in a cost-efficient manner and with respect to the Quality of Service (QoS) requirements of video streams. In particular, the architecture includes a QoS-aware scheduling component to efficiently map video streams to cloud resources, and a cost-efficient dynamic (i.e., elastic) resource provisioning policy that adapts the resource acquisition with respect to the video streaming QoS requirements.
ChemInform Abstract: AN IMPROVED ROUTE TO 4‐DEMETHOXYDAUNOMYCINONE. A‐RING FUNCTIONALIZATION AND RESOLUTION STUDIES OF TETRACYCLIC PRECURSORS (1983)

Abstract Das aus dem Keton (Ia) neben dessen Acetat (Ib) zugängliche Derivat (II) (l :1‐Isomerengemisch) wird zum Epoxid (III) oxidiert, aus dem mit verdünnter NaOH das (racemische) Hydroxyketon (IVa) entsteht.
Composites of carbon nanotubes and non-polymeric materials for diagnosing lung cancer via breath samples (2008)

We show here that an array of random network of carbon nanotubes coated with non-polymeric organic materials and conjugated with pattern recognition algorithms has a high potential for diagnosis of lung cancer via breath samples. The results indicate that the sensors array allow excellent discrimination between the volatile organic compounds (VOCs) found in the breath of patients with lung cancer, relative to healthy controls, especially if the sensors array is preceded with either water extractor and/or pre-concentrator of VOCs.
Hypertrophic and Hyperplastic Changes of Mucus-Secreting Epithelial Cells in Rat Airways: Assessment Using a Novel, Rapid, and Simple Technique (1994)

Determination of hyperplastic and hypertrophic changes of mucus-secreting cells in animal airways has been performed in the past by using histologic, immunologic, and/or molecular biologic approaches. Histologic techniques are tedious and time-consuming. The other approaches require specific antibodies and cDNA probes that have proved difficult to develop. Described here is a method for the rapid estimation of hyperplastic and hypertrophic changes of secretory epithelial cells in rat airways. The assay specifically measures acidic and neutral mucoproteins in a linear fashion from 0.5 microgram to at least 10 micrograms. Male Sprague-Dawley rats were exposed to metabisulfite mist (10% wt/vol) for 5 days/wk for 3 wk. The lungs were removed and homogenized in a phosphate-buffered solution containing reducing agents and protease inhibitors. The particulate matter was removed by centrifugation, and the soluble extract was applied to a column packed with Sepharose CL-6B. The material eluting in the void volume was applied to a PVDF membrane and stained for either acidic or neutral mucosubstances using Alcian blue or periodic acid-Schiff (PAS) staining, and the absorbance was read using a 96-well plate reader. Lungs from sodium metabisulfite-exposed animals showed a 7-fold and 3.5-fold increase in PAS-positive and Alcian blue-positive material, respectively. The increase in both PAS and Alcian blue staining was hyaluronidase and chondroitinase insensitive. The observed changes are consistent with morphometric measurements of mucus-containing cells in histologic sections of the tissues. This assay may be useful in determining which neurohumoral mediators might be involved in mucus cell hypertrophy and hyperplasia in animal models of chronic obstructive pulmonary disease.
New Tool for Metabolic Pathway Engineering in <i>Escherichia coli</i> : One-Step Method To Modulate Expression of Chromosomal Genes (2005)

A simple and highly efficient method was developed to produce a library of Escherichia coli clones that express a particular chromosomal gene at a wide range of expression levels. The basic strategy was to replace all or part of the upstream region of a coding sequence containing the elements involved in its expression (promoter, operator, gene coding for a regulator, ribosome binding site, and start codon) with a PCR-generated library of expression cassettes.
Generalized mixed mode reflective liquid crystal displays for three‐panel color projection applications (1999)

Abstract The general parameter space was introduced for generalized mixed mode reflective liquid crystal displays (RLCDs). A contrast ratio parameter space was also derived to provide a better picture of both the voltage‐off and voltage‐on states. A guideline for the optimization of RLCD modes in terms of high light efficiency and high contrast at low operating voltage is given. Such features are important for reflective displays, particularly for crystalline silicon based RLCDs. As a result, we find a number of new RLCD modes with high contrast and high brightness, which are quite suitable for the three‐panel color projection system.
The Influence of Ion Bombardment on Etching Reactions (1985)

Etching involves the interaction of gaseous species (e.g., XeF 2 ) with a solid surface ( e.g., silicon) to produce volatile products ( eg., SiF 4 (gas)). (For recent review papers on this subject see refs. 1-7.) Moreover this type of reaction is frequently enhanced by bombardment with ions, 8,9 electrons, 8 and photons. 10-12
Preliminary results of non-contact THz imaging of cornea (2015)

This paper presents a novel THz optical design that allows the acquisition of THz reflectivity maps of <i>in vivo</i> cornea without the need for a field flattening window and preliminary imaging results of in vivo rabbit cornea. The system's intended use is to sense small changes in corneal tissue water content (CTWC) that can be precursors for a host of diseases and pathologies. Unique beam optics allows the scanning of a curved surface at normal incidence while keeping the source detector and target stationary. Basic system design principles are discussed and image sets of spherical calibration targets and corneal phantom models are presented. The presented design will enable, for the first time, non-contact THz imaging of animal and human cornea.
Effect of Altered Auditory Feedback on People Who Stutter During Scripted Telephone Conversations (1997)

The effect of altered auditory feedback (AAF) conditions on stuttering during scripted telephone conversations was investigated. Nine adult participants made 15 scripted telephone calls to business in New York City. Alterations in the participants' auditory feedback signal were generated by a commercially available digital signal processor (Casa Futura Technologies Desktop Fluency System Model BTD-400) that shifted participants' speech one-half octave down in frequency, produced a 50-ms delay, or produced non-altered auditory feedback. The AAF effects produced by the digital signal processor were not perceived by the recipients of the telephone calls. The proportion of stuttering events per scripted telephone conversations were significantly reduced in the AAF conditions relative to the non-altered auditory feedback condition (p = .0004). Stuttering frequency was reduced by 55% and 60% for the FAF and DAF, respectively. These findings demonstrate the applicability of this technology to situations of daily living involving telephone use.
Immunity to Device Variations in a Spiking Neural Network With Memristive Nanodevices (2013)

Memristive nanodevices can feature a compact multilevel nonvolatile memory function, but are prone to device variability. We propose a novel neural network-based computing paradigm, which exploits their specific physics, and which has virtual immunity to their variability. Memristive devices are used as synapses in a spiking neural network performing unsupervised learning. They learn using a simplified and customized “spike timing dependent plasticity” rule. In the network, neurons' threshold is adjusted following a homeostasis-type rule. We perform system level simulations with an experimentally verified model of the memristive devices' behavior. They show, on the textbook case of character recognition, that performance can compare with traditional supervised networks of similar complexity. They also show that the system can retain functionality with extreme variations of various memristive devices' parameters (a relative standard dispersion of more than 50% is tolerated on all device parameters), thanks to the robustness of the scheme, its unsupervised nature, and the capability of homeostasis. Additionally the network can adjust to stimuli presented with different coding schemes, is particularly robust to read disturb effects and does not require unrealistic control on the devices' conductance. These results open the way for a novel design approach for ultraadaptive electronic systems.
✲-Aware Charging of Lithium-Ion Battery Cells (2016)

Lithium-ion cells are widely used in various platforms, such as electric vehicles (EVs) and mobile devices. Complete and fast charging of cells has always been the goal for sustainable system operation. However, fast charging is not always the best solution, especially in view of a new finding that cells need to rest/relax after being charged with high current to avoid accelerated capacity fading. Fast charging for its typical Charge-and-Go scenario does not allow this needed relaxation. In this paper, we propose ∗-Aware, a novel charging algorithm which maximizes the charged capacity within the user-specified available charging time (i.e., user-awareness) while ensuring enough relaxation (i.e., cell-awareness). We motivate and evaluate ∗-Aware via extensive measurements over 10 months. ∗-Aware is shown to improve the charged capacity by 6.9-50.5% over other charging algorithms that also ensure relaxation, and by almost 3x in some extreme cases. Furthermore, ∗-Aware slows down the capacity fad- ing by 49.55% when compared to fast charging.
Uplink Power Control, Interference Coordination and Resource Allocation for 3GPP E-UTRA (2006)

Evolved UTRA and UTRAN is being standardized in 3GPP standard group as a long term evolution of the 3GPP radio-access technology. The goal is to achieve 2-4 times the spectral efficiency and user throughput and much smaller latency compared to HSDPA/HSUPA. Single carrier FDMA (e.g. DFT-SOFDM) is the multiple access technique of choice for uplink transmission. Interference control is one of the key elements to achieve the target spectral efficiency and user cell- edge performance requirement, especially for uplink. In this paper, interference mitigation is implemented through slow fractional power control and interference coordination through UE alignment and FDM resource allocation. Simulation results show that these techniques significantly improve uplink sector and cell edge user throughput performance.
Model checking a self-stabilizing synchronization protocol for arbitrary digraphs (2012)

This report presents the mechanical verification of a self-stabilizing distributed clock synchronization protocol for arbitrary digraphs in the absence of faults. This protocol does not rely on assumptions about the initial state of the system, other than the presence of at least one node, and no central clock or a centrally generated signal, pulse, or message is used. The system under study is an arbitrary, non-partitioned digraph ranging from fully connected to 1-connected networks of nodes while allowing for differences in the network elements. Nodes are anonymous, i.e., they do not have unique identities. There is no theoretical limit on the maximum number of participating nodes. The only constraint on the behavior of the node is that the interactions with other nodes are restricted to defined links and interfaces. This protocol deterministically converges within a time bound that is a linear function of the self-stabilization period. A bounded model of the protocol is verified using the Symbolic Model Verifier (SMV) for a subset of digraphs. Modeling challenges of the protocol and the system are addressed. The model checking effort is focused on verifying correctness of the bounded model of the protocol as well as confirmation of claims of determinism and linear convergence with respect to the self-stabilization period.
Boron Carbide Reinforced Alumina Composites (1991)

The mechanical properties of alumina have been successfully improved by adding isolated boron carbide particles of two different shapes. A K Ic of 7.26 ± 0.20 MPa · m 1/2 for alumina—boron carbide whiskerlike composites and of 5.27 ± 0.12 MPa · m 1/2 alumina—boron carbide shardlike particle composites has been achieved. The fracture toughness of these composites is dependent on the volume fraction of the boron carbide particles as well as their size and shape. The flexural strength is also appreciably enhanced to a constant value with from 5 to 20 vol% boron carbide additions. The whiskerlike particles increase the flexural strength by 25% and the shardlike particles produce a 47% improvement.
Immunotherapy of disseminated intraperitoneal pancreatic cancer with non-replicating <i>Toxoplasma gondii</i> (P2104) (2013)

Abstract Pancreatic cancer is one of the most devastating and deadly cancers with an overall 5-year survival rate of 5%. Given existing therapies offer limited benefit, there is a strong need for innovative treatments that boost the host immune response to cancer. Toxoplasma gondii is an obligate intracellular parasite that potently stimulates the immune system and elicits CD8 T cell dependent immune responses. Utilizing an intraperitoneal dissemination model of pancreatic cancer, we hypothesize a non-replicating strain of T. gondii (CPS) can alter the tumor microenvironment and elicit strong antitumor responses. Intraperitoneal PAN02 tumors were established and treated with CPS seven days later. CPS treatment significantly increased survival and some treated mice survived long term (&gt;1 year). Treatment efficacy was completely dependent on production of IL-12 and IFN-γ. Within the peritoneal exudate, there is a significant decrease in B cells and classical macrophages and a significant increase in neutrophils, CD4, and CD8 T cells compared to untreated tumors. Therapeutic benefit was dependent on the presence of CD8 T cells whereas CD4 T cells did not significantly contribute to the survival advantage in treated mice. CPS treatment increased the frequency of pancreatic tumor-specific IFN-γ producing CD8 T cells. Further investigation is needed to characterize innate immune mechanisms supporting tumor therapy as well as the potential induction of immune memory.