gebhart/patrepeval huggingface dataset:
Achieving a near‐optimum erasure correction performance with low‐complexity LDPC codes (2010)

Abstract Low‐density parity‐check (LDPC) codes are shown to tightly approach the performance of idealized maximum distance separable (MDS) codes over memoryless erasure channels, under maximum likelihood (ML) decoding. This is possible down to low error rates and even for small and moderate block sizes. The decoding complexity of ML decoding is kept low thanks to a class of decoding algorithms, which exploit the sparseness of the parity‐check matrix to reduce the complexity of Gaussian elimination. ML decoding of LDPC codes is reviewed at first. A performance comparison among various classes of LDPC codes is then carried out, including a comparison with fixed‐rate Raptor codes for the same parameters. The results confirm that a judicious LDPC code design allows achieving a near‐optimum performance over the erasure channel, with very low error floors. Furthermore, it is shown that LDPC and Raptor codes, under ML decoding, provide almost identical performance in terms of decoding failure probability vs. overhead. Copyright © 2010 John Wiley & Sons, Ltd.
Radiocolloids in the Treatment of Ovarian Cancer (1979)

Though radiocolloids have been used for over twenty years in the treatment of ovarian cancer, no comprehensive review of the literature exists. This review incorporates the historical development of radiocolloids, discusses the physical properties and physics of the two commonly used colloids, radioactive gold (Au-198) and radioactive phosphorus (P-32), discusses instillation and distribution of intraperitoneally administered P-32, and reviews result of treatment. The conclusions reached from this review are that Au-198 is a very different radiocolloid than P-32; that the dose of clinically used P-32 is determined from an empirically determined dose of Au-198; and that the dose of 100 mCi to 150 mCi of Au-198 yields significantly greater radiation than 10 mCi to 15 mCi of P-32. The complications associated with Au-198 are results of a possibly excessive dose, with a significant gamma component, delivered over a shorter period of time. It is clear that in greater than 99% of distintegrations each beta particle is associated with a gamma component. The review of the literature also shows that no propsective randomized well controlled study has indicated the effectiveness of P-32 over other treatment modalities. The clinical applicability of P-32 awaits prospective randomized trials and the ability to accurately determine dose and dose-distribution in-vivo.
Apoptosis induced clustering of IP3R1 in nuclei of non-differentiated PC12 cells (2011)

Inositol 1,4,5-trisphosphate (IP(3)) receptors are emerging as key sites for regulation by pro- and anti-apoptotic factors. Induction of apoptosis for 3 h increased mRNA and protein levels of type 1 IP(3) receptors in non-differentiated (ND), but not in differentiated (D) PC12 cells. Inhibitors of the IP(3) R's calcium release-2-aminoethoxydiphenyl borate (2-APB) and xestospongin-completely prevented Bax and caspase-3 mRNA increase after treatment with the apoptosis inducer set (AIK), and this reinforces the importance of IP(3) R1 in the apoptosis of ND PC12 cells. Apoptosis induction not only increases the IP(3) R1 protein, but it also causes formation of IP(3) R1 clusters in the nucleus which most likely result from fusion of the nucleoplasmic reticulum and/or IP(3) R1 translocation to the nucleus. This is quite similar to the observations noted after overexpression of IP(3) R1 in PC12 cells. The amount of IP(3) induced calcium release was higher in control than in AIK-treated cells. From our results we propose that after the apoptosis induction the amount of intranuclear calcium decreased dramatically due to the increase of calcium permeability of the nuclear calcium store vesicles. Therefore, increase of the calcium permeability may result from IP(3) receptors translocation to nuclei that can boost the calcium transport through IP(3) receptors.
ESR1 and ESR2 Differentially Regulate Daily and Circadian Activity Rhythms in Female Mice (2014)

Estrogenic signaling shapes and modifies daily and circadian rhythms, the disruption of which has been implicated in psychiatric, neurologic, cardiovascular, and metabolic disease, among others. However, the activational mechanisms contributing to these effects remain poorly characterized. To determine the activational impact of estrogen on daily behavior patterns and differentiate between the contributions of the estrogen receptors ESR1 and ESR2, ovariectomized adult female mice were administered estradiol, the ESR1 agonist propylpyrazole triol, the ESR2 agonist diarylpropionitrile, or cholesterol (control). Animals were singly housed with running wheels in a 12-hour light, 12-hour dark cycle or total darkness. Estradiol increased total activity and amplitude, consolidated activity to the dark phase, delayed the time of peak activity (acrophase of wheel running), advanced the time of activity onset, and shortened the free running period (τ), but did not alter the duration of activity (α). Importantly, activation of ESR1 or ESR2 differentially impacted daily and circadian rhythms. ESR1 stimulation increased total wheel running and amplitude and reduced the proportion of activity in the light vs the dark. Conversely, ESR2 activation modified the distribution of activity across the day, delayed acrophase of wheel running, and advanced the time of activity onset. Interestingly, τ was shortened by estradiol or either estrogen receptor agonist. Finally, estradiol-treated animals administered a light pulse in the early subjective night, but no other time, had an attenuated response compared with controls. This decreased phase response was mirrored by animals treated with diarylpropionitrile, but not propylpyrazole triol. To conclude, estradiol has strong activational effects on the temporal patterning and expression of daily and circadian behavior, and these effects are due to distinct mechanisms elicited by ESR1 and ESR2 activation.
Controlling Graph Dynamics with Reinforcement Learning and Graph Neural Networks (2020)

We consider the problem of controlling a partially-observed dynamic process on a graph by a limited number of interventions. This problem naturally arises in contexts such as scheduling virus tests to curb an epidemic; targeted marketing in order to promote a product; and manually inspecting posts to detect fake news spreading on social networks. We formulate this setup as a sequential decision problem over a temporal graph process. In face of an exponential state space, combinatorial action space and partial observability, we design a novel tractable scheme to control dynamical processes on temporal graphs. We successfully apply our approach to two popular problems that fall into our framework: prioritizing which nodes should be tested in order to curb the spread of an epidemic, and influence maximization on a graph.
Visualization and PIV Measurements of the Transonic Flowaround the Leading Edge of an eroded Fan Airfoil (2012)

The influence of blade deterioration on the time-averaged and instantaneous flow around a fan airfoil is investigated by PIV, schlieren imaging and high speed shock-shadowgraphs in a transonic cascade windtunnel. In addition to a global characterization of the time-averaged flow using PIV, the instantaneous passage shock position was extracted from single shot PIV measurements by matching the tracer velocity across the normal shock with an exponential fit. From this the relaxation time of paraffine-ethanol seeding was verified to have a response time in the sub-microsecond range. The instantaneous shock positions, defined by the onset of the exponential decay, are assigned to a probability density distribution in order to obtain the average position and the width of fluctuations. Finally the distributions from the generic blunted edge geometry and the unaffected reference geometry are compared under near stall and under choked conditions. At similar back-pressure conditions the passage shock of the blunted edge geometry is located further upstream in comparison to the reference geometry. The amplitude of shock fluttering is significantly higher for the blunted edge. In order to extract the frequency range of the shock motion the direct shadow of the shock wave was tracked in high-speed shadowgraphs and spectrally analyzed. A comparison of the power spectra of the shock motion indicates that under choked conditions the blunted edge geometry exhibits a more continuous spectrum with a broader frequency range. The paper discusses details on the experimental implementation such as a specifically designed purged light sheet probe.
Refinery Upgrading of Hydropyrolysis Oil From Biomass (2015)

Cellulosic and woody biomass can be converted to bio-oils containing less than 10% oxygen by a hydropyrolysis process. Hydropyrolysis is the first step in Gas Technology Institute’s (GTI) integrated Hydropyrolysis and Hydroconversion IH2®. These intermediate bio-oils can then be converted to drop-in hydrocarbon fuels using existing refinery hydrotreating equipment to make hydrocarbon blending components, which are fully compatible with existing fuels. Alternatively, cellulosic or woody biomass can directly be converted into drop-in hydrocarbon fuels containing less than 0.4% oxygen using the IH2 process located adjacent to a refinery or ethanol production facility. Many US oil refineries are actually located near biomass resources and are a logical location for a biomass to transportation fuel conversion process. The goal of this project was to work directly with an oil refinery partner, to determine the most attractive route and location for conversion of biorenewables to drop in fuels in their refinery and ethanol production network. Valero Energy Company, through its subsidiaries, has 12 US oil refineries and 11 ethanol production facilities, making them an ideal partner for this analysis. Valero is also part of a 50- 50 joint venture with Darling Ingredients called Diamond Green Diesel. Diamond Green Diesel’s production capacity is approximately 11,000 barrels per day of renewable diesel. The plant is located adjacent to Valero’s St Charles, Louisiana Refinery and converts recycled animal fats, used cooking oil, and waste corn oil into renewable diesel. This is the largest renewable diesel plant in the U.S. and has successfully operated for over 2 years For this project, 25 liters of hydropyrolysis oil from wood and 25 liters of hydropyrolysis oils from corn stover were produced. The hydropyrolysis oil produced had 4-10% oxygen. Metallurgical testing of hydropyrolysis liquids was completed by Oak Ridge National Laboratories (Oak Ridge) and showed the hydropyrolysis oils had low acidity and caused almost no corrosion in comparison to pyrolysis oils, which had high acidity and caused significant levels of corrosion.
Reproducible Research as a Community Effort: Lessons from the Madagascar Project (2014)

Reproducible research is the discipline of attaching software code and data to publications, which enables the reader to reproduce, verify, and extend published computational experiments. Instead of being the responsibility of an individual author, computational reproducibility should become the responsibility of open source scientific-software communities. A dedicated community effort can keep a body of computational research alive by actively maintaining its reproducibility. The Madagascar open source software project offers an example of such a community.
Transmission of Vibronic Signals in Molecular Circuits (2005)

It is proposed and demonstrated using molecular dynamics and digital signal processing techniques that molecular vibrations can be used to transport signals in molecular circuits, revealing that signals transmitted along polypeptide molecules by a frequency-modulated carrier in the terahertz domain consume only 0.2 eV to successfully transfer one information bit; this energy is several orders of magnitude smaller than the several thousands of electronvolts needed using electrons in present electronic devices.
Pre-mRNA Splicing and the Nuclear Matrix (1987)

We examined the relationship between pre-mRNA splicing and the nuclear matrix by using an in vivo system that we have developed. Plasmids containing the inducible herpesvirus tk gene promoter linked to an intron-containing segment of the rabbit beta-globin gene were transfected into HeLa cells, and then the promoter was transactivated by infection with a TK- virus. Northern analysis revealed that the globin pre-mRNA and all its splicing intermediates and products are associated with the nuclear matrix prepared from such transfected cells. When the nuclear matrix was incubated with a HeLa cell in vitro splicing extract in the presence of ATP, the amount of matrix-associated precursor progressively decreased without a temporal lag in the reaction, with a corresponding increase in free intron lariat. Thus, most of the events of the splicing process (endonucleolytic cuts and branching) occur in this in vitro complementation reaction. However, ligation of exons cannot be monitored in this system because of the abundance of preexisting mature mRNA. Since the matrix is not a self-splicing entity, whereas the in vitro splicing system cannot process efficiently deproteinized matrix RNA, we conclude from our in vitro complementation results (which can be reproduced by using micrococcal nuclease-treated splicing extract) that the nuclear matrix preparation retains parts of preassembled ribonucleoprotein complexes that have the potential to function when supplemented with soluble factors (presumably other than most of the small nuclear ribonucleoproteins known to participate in splicing) present in the HeLa cell extract.
Holographic second harmonic generation imaging (2012)

Keywords: [MVD] Reference EPFL-CHAPTER-169987 URL: http://www.crcpress.com/product/isbn/9781439849149 Record created on 2011-11-03, modified on 2017-05-10
In vitro measurement of P50-the pH correction, and use of frozen red blood cells as controls (1979)

The Unicam Spectrophotometer, the IL 282 CO-Oximeter, and the Hemoscan were used to measure the in vitro P50 using 1, 20–45, and 50% hematocrit values of red blood cells suspended in autologous plasma or phosphate buffered saline at pH of 6.7–7.7. The relation between pH and P50 was a linear correlation for washed red blood cells by all three methods whereas the relation between pH and P50 was a log correlation for red blood cells in plasma. Multiple units of red blood cells with low 2,3 diphosphoglycerate (2,3 DPG) and increased affinity for oxygen, with normal 2,3 DPG and normal affinity for oxygen, and above normal 2,3 DPG and decreased affinity for oxygen, were frozen in 10 ml aliquots with 40% w/v glycerol and maintained at −80°C. One tube of each level of 2,3 DPG was thawed, washed, and suspended in buffer daily to yield P50 values of 17.5 ± 0.67, 29.7 ± 0.92, or 41.2 ± 0.72 torr at pH 7.2 in order to have a control of both instrumentation and personnel.
Random access schemes for satellite networks, from VSAT to M2M: a survey (2016)

Summary In this survey paper, we review the random access (RA) techniques with particular emphasis on the issues and the possible solutions applicable to satellite networks. RA dates back to the 1970s when the ALOHA protocol was developed to solve the problem of interconnecting university computers located in different Hawaiian islands. Since then, several evolutions of the ALOHA protocol have been developed. In particular, solutions were devised to mitigate the problem of packet collisions severely degrading the RA protocols performance. The approach followed for many years has been to avoid the occurrence of collisions rather than solving them. More recently, techniques tackling the RA packet collision problem have appeared triggered by the need of improving RA performance in satellite and terrestrial wireless networks. In particular, satellite networks large propagation delay does not allow the adoption of enhanced terrestrial RA techniques based on channel sensing. Adopting conventional demand assignment multiple access protocols is not suitable for supporting a large number of sensors or devices transmitting small‐size low duty cycle packets as required for machine‐to‐machine communications. This provided the stimulus to exploit successive interference cancelation schemes to solve packet collision issues. The use of successive interference cancelation in RA is relatively new and has opened up a promising research area. We provide an extensive review of recent high‐performance RA techniques achieving more than three orders of magnitude throughput increase compared with the original ALOHA at low packet loss rate. In this survey, we cover both slotted and unslotted techniques. Finally, we review the use of RA in satellite systems and related standards including recent proposals for machine‐to‐machine applications. Copyright © 2016 John Wiley & Sons, Ltd.
High Performance Magnetic Bearings for Aero Applications (1997)

Several previous annual reports were written and numerous papers published on the topics for this grant. That work is not repeated here in this final report. Only the work completed in the final year of the grant is presented in this final report. This final year effort concentrated on power loss measurements in magnetic bearing rotors. The effect of rotor power losses in magnetic bearings are very important for many applications. In some cases, these losses must be minimized to maximize the length of time the rotating machine can operate on a fixed energy or power supply. Examples include aircraft gas turbine engines, space devices, or energy storage flywheels. In other applications, the heating caused by the magnetic bearing must be removed. Excessive heating can be a significant problem in machines as diverse as large compressors, electric motors, textile spindles, and artificial heart pumps.
Synthesis of Polymer with Bisstyrylanthracene Chromophore on Polymer Skeleton and Application to Electroluminescent Devices (1996)

Abstract Novel EL polymer, in which 9,10-bis[4-(N,N-diphenylamino)-styryl]anthracene chromophore (polymer-BSA) was synthesized. Two kinds of EL devices were fabricated: One is a single-layer device, ITO/polymer-BSA/MgAg, and the other is a double-layer device, ITO/polymer-BSA/OXD-7/MgAg, in which a vacuum-sublimed 1,3-bis(4-tert-butylphenyl-1,3,4-oxadiazoly)phenylene (OXD-7) layer plays the roles of electron transport and hole blocking. The quantum efficiency of the double-layer device was observed about 60 times higher than that of the single-layer device. In the double-layer device, the maximum current density of 40 mA/cm2 was observed at the applied voltage of 23 V and the maximum luminance was about 60 cd/m2. EL spectra of the single-layer and double-layer devices have peaks at about 595 nm, which coincided with a photoluminescence spectrum of a polymer-BSA film.
"Color Timer" mice: visualization of neuronal differentiation with fluorescent proteins (2010)

The molecular mechanisms governing the differentiation of neural stem cells (NSCs) into neuronal progenitor cells and finally into neurons are gradually being revealed. The lack of convenient means for real-time determination of the stages of differentiation of individual neural cells, however, has been hindering progress in elucidating the mechanisms. In order to be able to easily identify the stages of differentiation of neural cells, we have been attempting to establish a mouse system that would allow progression of neuronal differentiation to be visualized based on transitions between fluorescence colors by using a combination of mouse genetics and the ever-expanding repertoire of fluorescent proteins. In this study we report the initial version of such a mouse system, which we call "Color Timer." We first generated transgenic (Tg; nestin/KOr Tg) mice in which production of the fluorescent protein Kusabira-Orange (KOr) is controlled by the gene regulatory elements within the 2nd intronic enhancer of the nestin gene, which is a good marker for NSCs, so that NSCs would emit orange fluorescence upon excitation. We then confirmed by immunohistochemical and immunocytochemical analyses that the KOr fluorescence closely reflected the presence of the Nestin protein. We also confirmed by a neurosphere formation assay that the intensity of the KOr fluorescence correlated with "stemness" of the cell and it was possible to readily identify NSCs in the two neurogenic regions, namely the dentate gyrus of the hippocampus and the subventricular zone of the lateral ventricle, in the brain of adult nestin/KOr Tg mice by the orange fluorescence they emitted. We then crossed nestin/KOr mice with doublecortin-enhanced Green Fluorescent Protein Tg mice, whose immature neurons emit green fluorescence upon excitation, and it was possible to visualize the progress of NSC-to-neuron differentiation by the transition between fluorescence colors from orange to green. This two-color initial version of the "Color Timer" mouse system will provide a powerful new tool for neurogenesis research.
Genetic Analysis of Vascular Factors in Alzheimer's Disease (2002)

Genetic risk factors for Alzheimer's disease (AD) have been extensively examined. Several risk factors for AD are shared with vascular dementia (VaD). We performed genetic case-control studies on polymorphisms of the apolipoprotein E (ApoE) gene, the methylene tetrahydrofolate reductase (MTHFR) gene, and the angiotensin-converting enzyme (ACE) gene. The most acceptable genetic risk factor for the development of AD is the ApoE epsilon-4 (ApoE epsilon4) allele. ApoE promoter polymorphisms have also been reported to be associated with AD. As expected, the ApoE epsilon4 allele had strong association with AD in our samples. The ApoE epsilon4 allele was also estimated as a risk factor for VaD. An ApoE promoter polymorphism (-291T/G) did not show positive association with AD or any other diseases. Common MTHFR phenotypes are thought to genetically regulate blood homocysteine level, which has been associated with AD. We failed to show independent associations between AD and the common MTHFR polymorphisms (C677T and A1298C). A deletion polymorphism at intron 16 of the ACE gene has also been associated with AD. In our study, we found a significant ethnic difference of the genotype distribution, but failed to replicate the positive association between the I allele and AD.
Supplemental Figure 1 from A Phase I Study of Veliparib (ABT-888) in Combination with Low-Dose Fractionated Whole Abdominal Radiation Therapy in Patients with Advanced Solid Malignancies and Peritoneal Carcinomatosis (2023)

<p>CTC number and ɣ-H2AX-positive CTC changes during treatment with radiotherapy and veliparib.</p>
Design considerations and experimental results of a 100 W, 500 000 rpm electrical generator (2006)

Mesoscale gas turbine generator systems are a promising solution for high energy and power density portable devices. This paper focuses on the design of a 100 W, 500 000 rpm generator suitable for use with a gas turbine. The design procedure selects the suitable machine type and bearing technology, and determines the electromagnetic characteristics. The losses caused by the high frequency operation are minimized by optimizing the winding and the stator core material. The final design is a permanent-magnet machine with a volume of 3 cm3 and experimental measurements from a test bench are presented.
Yeast as a Model System for Studying Glucose Transport (2002)

In the yeast Saccharomyces cerevisiae uptake of hexoses is mediated by a large family of transporter proteins. These transporters differ in their substrate specificities, their kinetic properties and their expression profiles. Two of the transporter proteins act as glucose sensors and control expression of the hexose transporters according to the availability and concentration of carbon sources. Deletion of at least 20 genes was necessary to block uptake of hexoses completely. The resulting hxt-null yeast strain provides a valuable tool for the cloning and characterization of hexose transporters from other organisms.