gebhart/patrepeval huggingface dataset:
Absolute vs. relative error characterization of electromagnetic tracking accuracy (2010)

Electromagnetic (EM) tracking systems are often used for real time navigation of medical tools in an Image Guided Therapy (IGT) system. They are specifically advantageous when the medical device requires tracking within the body of a patient where line of sight constraints prevent the use of conventional optical tracking. EM tracking systems are however very sensitive to electromagnetic field distortions. These distortions, arising from changes in the electromagnetic environment due to the presence of conductive ferromagnetic surgical tools or other medical equipment, limit the accuracy of EM tracking, in some cases potentially rendering tracking data unusable. We present a mapping method for the operating region over which EM tracking sensors are used, allowing for characterization of measurement errors, in turn providing physicians with visual feedback about measurement confidence or reliability of localization estimates. In this instance, we employ a calibration phantom to assess distortion within the operating field of the EM tracker and to display in real time the distribution of measurement errors, as well as the location and extent of the field associated with minimal spatial distortion. The accuracy is assessed relative to successive measurements. Error is computed for a reference point and consecutive measurement errors are displayed relative to the reference in order to characterize the accuracy in near-real-time. In an initial set-up phase, the phantom geometry is calibrated by registering the data from a multitude of EM sensors in a non-ferromagnetic ("clean") EM environment. The registration results in the locations of sensors with respect to each other and defines the geometry of the sensors in the phantom. In a measurement phase, the position and orientation data from all sensors are compared with the known geometry of the sensor spacing, and localization errors (displacement and orientation) are computed. Based on error thresholds provided by the operator, the spatial distribution of localization errors are clustered and dynamically displayed as separate confidence zones within the operating region of the EM tracker space.
DM2 intronic expansions: evidence for CCUG accumulation without flanking sequence or effects on ZNF9 mRNA processing or protein expression (2006)

Myotonic dystrophy type 2 (DM2) is caused by a CCTG expansion mutation in intron 1 of the zinc finger protein 9 (ZNF9) gene. The mean expansion size in patients is larger than for DM1 or any previously reported disorder (mean=5000 CCTGs; range=75-11 000), and similar to DM1, repeats containing ribonuclear inclusions accumulate in affected DM2 tissue. Although an RNA gain-of-function mechanism involving DM1 CUG or DM2 CCUG expansion transcripts is now well established, still debated are the potential role that flanking sequences within the DMPK 3'-UTR may have on disease pathogenesis and whether or not decreased expression of DMPK, ZNF9 or neighboring genes at these loci contribute to disease. To address these questions in DM2, we have examined the nucleic acid content of the ribonuclear inclusions and the effects of these large expansions on ZNF9 expression. Using cell lines either haploid or homozygous for the expansion, as well as skeletal muscle biopsy tissue, we demonstrate that pre-mRNAs containing large CCUG expansions are normally spliced and exported from the nucleus, that the expansions do not decrease ZNF9 expression at the mRNA or protein level, and that the ribonuclear inclusions are enriched for the CCUG expansion, but not intronic flanking sequences. These data suggest that the downstream molecular effects of the DM2 mutation are triggered by the accumulation of CCUG repeat tract alone.
Improved Reconstruction Quality of Bioluminescent Images by Combining SP<sub><b>3</b></sub>Equations and Bregman Iteration Method (2013)

Bioluminescence tomography (BLT) has a great potential to provide a powerful tool for tumor detection, monitoring tumor therapy progress, and drug development; developing new reconstruction algorithms will advance the technique to practical applications. In the paper, we propose a BLT reconstruction algorithm by combining SP(3) equations and Bregman iteration method to improve the quality of reconstructed sources. The numerical results for homogeneous and heterogeneous phantoms are very encouraging and give significant improvement over the algorithms without the use of SP(3) equations and Bregman iteration method.
Screening the Sequence Selectivity of DNA-Binding Molecules Using a Gold Nanoparticle-Based Colorimetric Approach (2007)

We have developed a novel competition assay that uses a gold nanoparticle (Au NP)-based, high-throughput colorimetric approach to screen the sequence selectivity of DNA-binding molecules. This assay hinges on the observation that the melting behavior of DNA-functionalized Au NP aggregates is sensitive to the concentration of the DNA-binding molecule in solution. When short, oligomeric hairpin DNA sequences were added to a reaction solution consisting of DNA-functionalized Au NP aggregates and DNA-binding molecules, these molecules may either bind to the Au NP aggregate interconnects or the hairpin stems based on their relative affinity for each. This relative affinity can be measured as a change in the melting temperature (Tm) of the DNA-modified Au NP aggregates in solution. As a proof of concept, we evaluated the selectivity of 4',6-diamidino-2-phenylindone (an AT-specific binder), ethidium bromide (a nonspecific binder), and chromomycin A (a GC-specific binder) for six sequences of hairpin DNA having different numbers of AT pairs in a five-base pair variable stem region. Our assay accurately and easily confirmed the known trends in selectivity for the DNA binders in question without the use of complicated instrumentation. This novel assay will be useful in assessing large libraries of potential drug candidates that work by binding DNA to form a drug/DNA complex.
Impaired glomerulogenesis and endothelial cell migration in Pkd1-deficient renal organ cultures (2014)

The PKD1 gene is essential for a number of biological functions, and its loss-of-function causes autosomal dominant polycystic kidney disease (ADPKD). The gene is developmentally regulated and believed to play an essential role in renal development. Previous studies have shown that manipulating murine renal organ cultures with dominant-negative forms of the Pkd1 gene impaired ureteric bud (UB) branching. In the current study, we analyzed different stages of renal development in two distinct mouse models carrying either a null mutation or inactivation of the last two exons of Pkd1. Surprisingly, metanephric explants from Pkd1-deleted kidneys harvested at day E11.5 did not show defects of UB branching and elongation, estimated by cytokeratin staining on fixed tissues or by Hoxb7-GFP time-lapse imaging. However, renal explants from Pkd1-mutants isolated at day E14.5 showed impaired nephrogenesis. Notably, we observed cell migratory defects in the developing endothelial compartment. Previous studies had implicated the Pkd1 gene in controlling cell migration and collagen deposition through PI3 kinases. In line with these studies, our results show that wild-type explants treated with PI3-kinase inhibitors recapitulate the endothelial defects observed in Pkd1 mutants, whereas treatment with VEGF only partially rescued the defects. Our data are consistent with a role for the Pkd1 gene in the endothelium that may be required for proper nephrogenesis.
Post-occlusive reactive hyperemia in patients with peripheral vascular disease. (2004)

We measured tissue oxygen saturation (StO2) changes during a post-occlusive reactive hyperemia (PORH) test on lower extremities of peripheral vascular disease (PVD) patients and healthy controls. The StO2 changes were measured by the near-infrared tissue oximeter prototyped by ViOptix Inc. We found that PVD indicators may include the post-occlusive StO2 reperfusion rate, the time duration of the reperfusion phase in a PORH test, and the StO2 dispersion rate in reactive hyperemia. We suggest critical values of these indicators for PVD assessments.
The Unique Characteristics of Covalently Polymerized Bovine Serum Albumin Solutions When Used as Antibody Detection Media (1978)

Bovine Serum Albumin solutions (BSA) have been chemically polymerized to give solutions (PBSA) with superior serological properties. The new PBSA reagents are shown to contain covalently bonded dimers, trimers, tetramers, and larger polymers, the presence of which is directly related to hemagglutination by IgG antibody. Data are presented which show that reagents containing increased amounts of higher molecular weight polymers enhance hemagglutination, as demonstrated by serum albumin titrations of various antisera. Additionally, isolated polymers are shown to enhance hemagglutination as a function of their molecular weight with the high molecular weight tetramers being more effective than the trimeric form, which in turn is more effective than the dimeric and monomeric forms. The protein concentration does not play any significant role in these events. The data establish that the polymeric content of bovine serum albumin reagents is a major factor in the potentiating properties of such solutions. Additionally, it is shown that these reagents act not only on the second stage of hemagglutination as a function of the bovine albumin present, but also on the first stage of hemagglutination as a function of the ionic strength of these reagents. The polymeric content and ionic strength of albumin solutions are the major criteria in determining the effectiveness of these potentiating reagents.
Colocalization and differential expression of PBAN‐ and FMRFamide‐like immunoreactivity in the subesophageal ganglion of <i>Helicoverpa zea</i> (Lepidoptera: Noctuidae) during development (1992)

Abstract Pheromone biosynthesis activating neuropeptide (PBAN) stimulates sex pheromone production in several species of moths. We have used an antiserum to PBAN to map the distribution of PBAN‐like immunoreactivity (PLI) in the subesophageal ganglion (SEG) of the larval and pupal stages of the corn earworm, Helicoverpa zea , and compared this distribution with that of the adult. The distribution of PLI within the SEG of larvae and pupae was quite similar to that found in adults, suggesting a function for PBAN other than the stimulation of pheromone biosynthesis. In all developmental stages studied, three groups of nerve cells in the SEG, and their projections, contained PLI. In adults and larvae, most of the cells containing PLI also had FMRFamide‐like immunoreactivity (FLI). In pupae, however, a number of cells which appeared to have PLI and FLI in both larvae and adults, did not contain andy detectable FLI, while the PLI appeared unchanged. The FLI returns to these cells during adult development. These immunocytochemical observations were corroborated by quantifying PLI and FLI by competitive ELISA; the level of extractable FLI in pupae was about 25% of that found in larvae, while PLI levels were unchanged. © 1992 Wiley‐Liss, Inc.
Answering order-based queries over XML data (2005)

Order-based queries over XML data include XPath navigation axes such as following-sibling and following. In this paper, we present holistic algorithms that evaluate such order-based queries. An experimental comparison with previous approaches shows the performance benefits of our algorithms.
The Role of GnRH Receptor Autoantibodies in Polycystic Ovary Syndrome (2020)

GnRHR-ECL2-AAb are significantly elevated in patients with PCOS compared with NCs. Their presence raises important etiological, diagnostic, and therapeutic implications.
Manipulating the Tumor Microenvironment <i>Ex Vivo</i> for Enhanced Expansion of Tumor-Infiltrating Lymphocytes for Adoptive Cell Therapy (2014)

Our results highlight a previously unrecognized concept in TIL ACT that the tumor microenvironment can be dynamically regulated in the initial tumor fragment cultures to regulate the types of T cells expanded and their functional characteristics.
Low molecular weight gels: potential in remediation of crude oil spillage and recovery (2016)

A molecular gelator which has strong gelation ability for different crude oils (light to heavy crudes), and a wide range of refinery products is reported for the first time for its potential application in oil spillage/recovery.
Oral administration of a Ketone Ester regulates blood cholesterol in rats and humans (2015)

Control of cholesterol in Type 2 Diabetics and Pre‐diabetics has been problematic as statins increase blood glucose. We propose that a unique β‐hydroxybutyrate (βHB) Ester can provide non‐lipogenic calories and decrease cholesterol synthesis without increasing glucose. The ketone bodies, βHB and Acetoacetate, can be metabolized by most tissues, but not liver, limiting cholesterol precursors. In humans, a single meal containing this ketone ester (KE) dose dependently decreased plasma mevalonate, a marker for cholesterol synthesis, without directly inhibiting HMG‐CoA Reductase. After two days of KE, rats had 31% lower plasma cholesterol and 26% lower mevalonate than controls. In a 30 day study, KE fed rats had lower plasma total cholesterol (‐40%) and mevalonate (‐27%) than controls. Levels of mevalonate precursors, Acetoacetyl‐CoA and HMG‐CoA were lower by 33% and 54% respectively, but Acetyl‐CoA was unaffected. Low liver cholesterol increases absorption of cholesterol through the Low Density Lipoprotein receptor (LDL‐R), KE feeding increased LDL‐R levels in whole cell (+24%) and membrane preparations (+67%). KE fed animals had increased protein levels of SREBP‐2, a key transcriptional activator of LDL‐R, both full length and transcriptionally active forms increased, by 91% and 140%. A 5 day study of KE effect on cholesterol in human Type 2 Diabetics showed not only lower total cholesterol (‐10%) but also lower fasting glucose (‐17%) and Triglycerides (‐18%). We report preliminary findings that KE decreases cholesterol and its synthetic precursors while decreasing fasting blood glucose and triglycerides.
The Inductrack: a simpler approach to magnetic levitation (2000)

Arising out of research at the Lawrence Livermore National Laboratory on passive magnetic bearings, a new magnetic levitation system, the Inductrack, has been developed and tested at model scale. The system employs special arrays of permanent magnets (Halbach arrays) on the moving car. The magnetic field from the arrays induces repelling currents in a close-packed array of shorted circuits in the track. Above a low transition speed (a few kilometers per hour), levitation forces approach a constant value, while drag forces decrease inversely with speed, with L/D reaching 200:1 or more at operating speeds. The high magnetic efficiency of the Halbach arrays, plus the use of close-packed track circuits, results in levitating forces approaching 40 metric tonnes per square meter (using NdFeB permanent magnet arrays, whose weight in typical cases is a few percent of the levitated weight). The system is passively stable: only motion is required for levitation. Failure of the drive system only results in the train slowing down and settling onto auxiliary wheels at a low speed. A detailed theoretical analysis of the Inductrack was made, on the basis of which a small-scale model was constructed and operated. The Laboratory is building a new small-scale model system (under NASA sponsorship) to demonstrate the acceleration rates and speeds (10-g and Mach 0.4 in the model) needed to magnetically launch rockets.
Dynamic Data Stability in Low-power SRAM Design (2007)

SRAM cell stability measurement is traditionally based on static criteria of data stability requiring 3 coincident points in butterfly curves. We introduce <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dynamic criteria</i> of stability for the cell knowing that the cell operates in a dynamic environment. It reveals that the true noise margin of the cell can be made considerably higher than the SNM once the cell access time is sufficiently shorter than the cell time-constant. This behavior enables enhancing SRAM yield as well as reducing cell operating voltage without compromising reliability. A 40Kb SRAM designed using SVGND scheme exploits the dynamic behavior of the cell in order to increase the stability and reduce the static and dynamic power consumption. The SRAM unit realized in 0.13μm CMOS consumes 702μW at 100MHz during write operation and offers a 27pA/Cell leakage current.
Phase 1 Safety and Immunogenicity Study of a Respiratory Syncytial Virus Vaccine With an Adenovirus 26 Vector Encoding Prefusion F (Ad26.RSV.preF) in Adults Aged ≥60 Years (2020)

Ad26.RSV.preF (LD and HD) had an acceptable safety profile and elicited sustained humoral and cellular immune responses after a single immunization in older adults.
Fatty Acid Desaturases And Elongases And Uses Thereof (Patent US 9493520 B2 ) (2016)

The invention provides isolated nucleic acid molecules which encode novel fatty acid desaturases and elongases from the organism Emiliana huxleyi. The invention also provides recombinant expression vectors containing desaturase or elongase nucleic acid molecules, host cells into which the expression vectors have been introduced, and methods for large-scale production of long chain polyunsaturated fatty acids (LCPUFAs), e.g. arachidonic acid (ARA), eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA).
Para‐Hydrogen‐Enhanced Hyperpolarized Gas‐Phase Magnetic Resonance Imaging (2007)

Gas-phase MRI phantom: Magnetic resonance imaging (MRI) in the gas phase was demonstrated using para-hydrogen-induced polarization. H2 enriched in the para (antiparallel) spin state and propylene gas were flowed over solid-supported Wilkinson's catalyst, and the product, propane gas, was collected in an NMR tube. Enhanced signal intensities were observed in the images of phantoms placed inside the NMR tube (see picture).
Lyotropic liquid crystalline phases from helical β-peptides as alignment media (2010)

Lyotropic liquid crystalline (LLC) phases from helical β-peptides are proposed as novel water-based alignment media. In contrast to α-peptides, β-peptides form LLCs at very short chain lengths and at concentrations as low as 1 percent. Spectra obtained in these LLC phases are artefact-free and lead to RDCs of the desired size. First indications towards enantiodiscrimination are provided.
Towards an Elasticity Framework for Legacy Highly Available Applications in the Cloud (2015)

Elasticity is a key characteristic of cloud computing where the provisioning of resources can be directly proportional to the runtime demand. Legacy highly available applications typically rely on the underlying platform to manage their availability by monitoring heartbeats, executing recoveries, and attempting repairs to bring the system back to normal. Migrating such applications to the cloud can be particularly challenging, especially if the elasticity policies target the application only, without considering the underlying platform contributing to its high availability (HA). In this paper, we present a comprehensive framework for the elasticity of highly available applications that considers the elastic deployment of the platform and the HA placement of the application's components. We apply our approach to an IP multimedia subsystem (IMS) application and demonstrate how, within a matter of seconds, the IMS application can be scaled up while maintaining its HA status.
A unified maximum likelihood approach to acoustic mismatch compensation: application to noisy Lombard speech recognition (2002)

In the context of continuous density hidden Markov model (CDHMM) we present a unified maximum likelihood (ML) approach to acoustic mismatch compensation. This is achieved by introducing additive Gaussian biases at the state level in both the mel cepstral and linear spectral domains. Flexible modelling of different mismatch effects can be obtained through appropriate bias tying. A maximum likelihood approach for joint estimation of both mel cepstral and linear spectral biases from the observed mismatched speech given only one set of clean speech models is presented, where the obtained bias estimates are used for the compensation of clean speech models during decoding. The proposed approach is applied to the recognition of noisy Lombard speech, and significant improvement in the word recognition rate is achieved.
Compact High Power THz Source (2003)

In this paper a new type of THz radiation source, based on recirculating an electron beam through a high gradient superconducting radio frequency cavity, and using this beam to drive a standard electromagnetic undulator, is discussed. Because the beam is recirculated, short bunches may be produced that radiate coherently in the undulator, yielding high average THz power for relatively low average beam power. Deceleration from the coherent emission, and the detuning it causes is discussed.
Overexpression of the Glucose Transporter Gene with a Herpes Simplex Viral Vector Protects Striatal Neurons against Stroke (1996)

Herpes simplex virus vectors bearing a glucose transporter (GT) gene and a marker gene were found to protect neurons against a 1-h focal ischemic insult. Rats receiving the GT vector v alpha22beta gal alpha4GT exhibited a 67.4 +/- 35.3% survival of virally targeted neurons in the ischemic hemisphere compared with the contralateral control (n = 7), whereas rats receiving a control vector exhibited only 32.8 +/- 17.9% survival (n = 9). This significant improvement in survival (105%, p=0.022) suggests that energy failure is an important contributor to the neuropathology of ischemic damage in the striatum, and that it can be alleviated by gene transfer. This is the first demonstration of protection against ischemic cerebral injury by the direct transfer of GT genes to neurons.
High Throughput Methodology for Synthesis, Screening, and Optimization of Solid State Lithium Ion Electrolytes (2011)

A study of the lithium ion conductor Li(3x)La(2/3-x)TiO(3) solid solution and the surrounding composition space was carried out using a high throughput physical vapor deposition system. An optimum total ionic conductivity value of 5.45 × 10(-4) S cm(-1) was obtained for the composition Li(0.17)La(0.29)Ti(0.54) (Li(3x)La(2/3-x)TiO(3)x = 0.11). This optimum value was calculated using an artificial neural network model based on the empirical data. Due to the large scale of the data set produced and the complexity of synthesis, informatics tools were required to analyze the data. Partition analysis was carried out to determine the synthetic parameters of importance and their threshold values. Multivariate curve resolution and principal component analysis were applied to the diffraction data set. This analysis enabled the construction of phase distribution diagrams, illustrating both the phases obtained and the compositional zones in which they occur. The synthetic technique presented has significant advantages over other thin film and bulk methodologies, in terms of both the compositional range covered and the nature of the materials produced.