gebhart/patrepeval huggingface dataset:
Investigation of a dual modal method for bone pathologies using quantitative ultrasound and photoacoustics (2015)

Osteoporosis is a widespread disease that has a catastrophic impact on patient's lives and overwhelming related healthcare costs. In recent works, we have developed a multi-spectral, frequency domain photoacoustic method for the evaluation of bone pathologies. This method has great advantages over pure ultrasonic or optical methods as it provides both molecular information from the bone absorption spectrum and bone mechanical status from the characteristics of the ultrasound propagation. These characteristics include both the Speed of Sound (SOS) and Broadband Ultrasonic Attenuation (BUA). To test the method's quantitative predictions, we have constructed a combined ultrasound and photoacoustic setup. Here, we experimentally present a dual modality system, and compares between the methods on bone samples in-vitro. The differences between the two modalities are shown to provide valuable insight into the bone structure and functional status.
A mild method for the conversion of 1,3-glycols into unsaturated alcohols (1988)

Some transformations of 1,3-glycols utilizing dimethylformamide dimethyl acetal have been examined with the diterpenoids aphidicolin and foliol and some steroids as substrates. Axial alcohols with a suitably disposed trans hydrogen atom undergo an elimination reaction to give the formate of an unsaturated alcohol via the quaternary salt of the cyclic formamido acetal.
Coexpression of two functionally independent p58 inhibitory receptors in human natural killer cell clones results in the inability to kill all normal allogeneic target cells. (1995)

In the present study, we define a group of natural killer (NK) clones (group 0) that fails to lyse all of the normal allogeneic target cells analyzed. Their specificity for HLA class I molecules was suggested by their ability to lyse class I-negative target cells and by the fact that they could lyse resistant target cells in the presence of selected anti-class I monoclonal antibodies. The use of appropriate target cells represented by either HLA-homozygous cell lines or cell transfectants revealed that these clones recognized all the HLA-C alleles. By the use of monoclonal antibodies directed to either GL183 or EB6 molecules, we showed that the EB6 molecules were responsible for the recognition of Cw4 and related alleles, while the GL183 molecules recognized Cw3 (and related C alleles). These data suggest that the GL183 and the EB6 molecules can function, in individual NK clones, as independent receptors for two different groups of HLA-C alleles, (which include all known alleles for locus C), thus resulting in their inability to lyse all normal HLA-C+ target cells. Indirect immunofluorescence and fluorescence-activated cell sorting analysis revealed that the presently defined GL183+EB6+ group 0 NK clones brightly express EB6 molecules (EB6bright) while the GL183+EB6+ group 2 clones (unable to recognize Cw4) express an EB6dull phenotype. These data also imply that the density of EB6 receptors may be critical for the generation of an optimal negative signal upon interaction with appropriate HLA-C alleles.
Acadesine Reduces Indium-Labeled Platelet Deposition After Photothrombosis of the Common Carotid Artery in Rats (1995)

These results support a prophylactic role for acadesine in reducing the accumulation of platelet emboli during vascular thrombosis and subsequent brain infarction. Acadesine treatment in patients at risk for embolic stroke could potentially lead to cerebral protection.
The performance of a distributed combat simulation with the time warp operating system (1989)

Abstract This paper analyzes the performance of a discrete‐event combat simulation executed on a parallel processor under control of the Time Warp Operating System. Time Warp is in a class of distributed simulation methods called Optimistic methods which have proven to be useful over a wide range of simulations. The combat simulation used for this performance study, called STB88, is a division‐corps model incorporating a number of different types of computations. The speed‐up for three versions of this model on the Caltech/JPL Mark III Hypercube and the BBN Butterfly parallel processors was measured relative to an efficient sequential execution of the same model on the same hardware. The results indicate that STB88 version 1 achieves a speed‐up of 28.6 on 60 Mark III processors, while STB88 version 2 achieves a speed‐up of 36.8 on 100 Butterfly processors. Version 3 of STB88 achieved a speed‐up of 38.5 on 128 Mark III processors. The versions differed only in their interface to Time Warp. On the Butterfly, the sequential execution completed in 2 hours, while the 100 processor execution completed in 3.2 minutes.
Comparison of the H-2Kk- and H-2Kkm1-Restricted Peptide Motifs (1993)

Self-peptide pools eluted from purified H-2Kk or H-2Kkm1 molecules were sequenced. The majority of self-peptides associated with H-2Kk molecules were found to be octamers with two anchor positions. Position 2 is invariantly occupied with Glu, and the C-terminal residue at position 8 is almost always Ile. Comparison of this motif with synthetic peptides known to contain viral or parasite T-cell epitopes could be well aligned with this motif, except that the C-terminal Ile residue frequently appears to be at position 9 of the aligned sequences, instead of 8. Self-peptides eluted from mutant H-2Kkm1 molecules also appear to be mostly octamers with the same Ile residues at position 8 as with Kk. Position 2 is still dominantly occupied by Glu; in contrast to the Kk motif, however, Gln, Gly, and Pro are also allowed. Other differences between the two motifs indicate that a certain number of peptides presented by one of the molecules are not presented by the other.
Competitive HIF Prolyl Hydroxylase Inhibitors Show Protection against Oxidative Stress by a Mechanism Partially Dependent on Glycolysis (2012)

The hypoxia inducible factor 1 (HIF-1) is a central transcription factor involved in the cellular and molecular adaptation to hypoxia and low glucose supply. The level of HIF-1 is to a large degree regulated by the HIF prolyl hydroxylase enzymes (HPHs) belonging to the Fe(II) and 2-oxoglutarate-dependent dioxygenase superfamily. In the present study, we compared competitive and noncompetitive HPH-inhibitor compounds in two different cell types (SH-SY5Y and PC12). Although the competitive HPH-inhibitor compounds were found to be pharmacologically more potent than the non-competitive compounds at inhibiting HPH2 and HPH1, this was not translated into the cellular effects of the compounds, where the non-competitive inhibitors were actually more potent than the competitive in stabilizing and translocatingHIF1 α to the nucleus (quantified with Cellomics ArrayScan technology). This could be explained by the high cellular concentrations of the cofactor 2-oxoglutarate (2-OG) as the competitive inhibitors act by binding to the 2-OG site of the HPH enzymes. Both competitive and non-competitive HPH inhibitors protected the cells against 6-OHDA induced oxidative stress. In addition, the protective effect of a specific HPH inhibitor was partially preserved when the cells were serum starved and exposed to 2-deoxyglucose, an inhibitor of glycolysis, indicating that other processes than restoring energy supply could be important for the HIF-mediated cytoprotection.
<i>Drosophila</i> AD3 mutation of synaptotagmin impairs calcium‐dependent self‐oligomerization activity (2000)

Genetic analysis of a Drosophila synaptotagmin (Syt) I mutant (AD3) has revealed that Tyr-334 within the C2B domain is essential for efficient Ca(2+)-dependent neurotransmitter release. However, little is known as to why a missense mutation (Tyr-334-Asn) disrupts the function of the C2B domain at the molecular level. Here, we present evidence that a Tyr-312 to Asn substitution in mouse Syt II, which corresponds to the Drosophila AD3 mutation, completely impairs Ca(2+)-dependent self-oligomerization activity mediated by the C2B domain but allows partial interaction with wild-type proteins in a Ca(2+)-dependent manner. This observation is consistent with the fact that the AD3 allele is homozygous lethal but complements another mutant phenotype. We also showed that the Ca(2+)-dependent C2B self-oligomerization is inhibited by inositol 1,3,4, 5-tetrakisphosphate, a potent inhibitor of neurotransmitter release. All of these findings strongly support the idea that self-oligomerization of Syt I or II is essential for neurotransmitter release in vivo.
MEDICATION ERRORS (2012)

In Brief Never use insulin pens on multiple patients...teach patients that APAP means acetaminophen...an I.V. syringe isn't a toy... eribulin confused with epirubicin
Scattering by a Blade on a Metallic Plane (2005)

The scattering from a metal plane with a ridge is considered for the cases of plane wave and line source illumination and both polarizations. Exact analytical results are expressed using series that contain products of radial and angular Mathieu functions. The exact analytical results are computed and compared with high-frequency approximations and with measurements.
Optically detected magnetic resonance of the phosphorescent bases of Escherichia coli valine-specific transfer ribonucleic acid (1981)

Phosphorescence spectroscopy and optical detection of triplet state magnetic resonance (ODMR) spectroscopy have been used to characterize bases that contribute to the phosphorescence emission of Escherichia coli valine-specific transfer ribonucleic acid. When it is excited with 335-nm light, a short-lived phosphorescence with an origin near 435 nm is observed and is assigned to 4-thiouridine (s4U) at position 8 of the tRNA sequence. With excitation at 290-300 nm, a structured, long-lived phosphorescence is observed with an origin near 380 nm, in addition to the s4U phosphorescence. Comparison was made of the phosphorescence and ODMR spectra between Mg2+-containing and Mg2+-free tRNA samples. The s4U phosphorescence of the Mg2+-containing sample is more structured, and the peak is blue shifted relative to the Mg2+-free sample. Both samples give a single low-frequency (ca. 2.9 GHz) ODMR signal, but the high-frequency signal region (ca. 19-20 GHz) is structured. The Mg2+-containing sample has a partially resolved group of lines centered at 19.3 GHz, whereas the Mg2+-free sample has two broad bands centered at 19.2 and 20.0 gHz. The differences are attributed to effects of Mg2+ on the tRNA conformation. The ODMR signals observed by monitoring the long-lived phosphorescence are assigned to a pyrimidine nucleoside, possibly 5-(carboxy-methoxy)uridine in the anticodon.
Battery capacity of deferrable energy demand (2016)

We investigate the ability of a homogeneous collection of deferrable energy loads to behave as a battery; that is, to absorb and release energy in a controllable fashion up to fixed and predetermined limits on volume, charge rate and discharge rate. We derive bounds on the battery capacity that can be realized and show that there are fundamental tradeoffs between battery parameters. By characterizing the state trajectories under scheduling policies that emulate two illustrative batteries, we show that the trade-offs occur because the states that allow the loads to absorb and release energy at high aggregate rates are conflicting.
Experimental basis of determining maximum coronary, myocardial, and collateral blood flow by pressure measurements for assessing functional stenosis severity before and after percutaneous transluminal coronary angioplasty. (1993)

These results provide the experimental basis for determining relative maximum flow or fractional flow reserve of both the epicardial coronary artery and the myocardium, including collateral flow, from pressure measurements during maximum arteriolar vasodilation. With a suitable guide wire for reliably measuring distal coronary pressure clinically, this method may have potential applications during percutaneous transluminal coronary angioplasty for assessing changes in the functional severity of coronary artery stenoses and for estimating collateral flow achievable during occlusion of the coronary artery.
Reverse Engineering Legacy Finite Element Code (2012)

The development of code for finite elements-based field computation has been going on at a pace since the 1970s, yielding code that was not put through the software lifecycle – where code is developed through a sequential process of requirements elicitation from the user/client to design, analysis, implementation and testing and release and maintenance. As a result, today we have legacy code running into millions of lines, implemented without planning and not using proper state-of-the-art software design tools. It is necessary to redo this code to exploit new object oriented facilities and make corrections or run on the web with Java. Object oriented code’s principal advantage is reusability. Recent advances in software make such reverse engineering/re-engineering of this code into object oriented form possible. The purpose of this paper is to show how existing finite element code can be reverse/re-engineered to improve it. Taking sections of working finite element code, especially matrix computation for equation solution as examples, we put it through reverse engineering to arrive at the effective UML design by which development was done and then translate it to Java. This then is the starting point for analyzing the design and improving it without having to throw away any of the old code. Using auto-translators and then visually rewriting parts by the design so revealed, has no match in terms of speed and efficiency of re-engineering legacy code.
Ascl1‐induced neuronal differentiation of P19 cells requires expression of a specific inhibitor protein of cyclic AMP‐dependent protein kinase (2011)

cAMP-dependent protein kinase (PKA) plays a critical role in nervous system development by modulating sonic hedgehog and bone morphogenetic protein signaling. In the current studies, P19 embryonic carcinoma cells were neuronally differentiated by expression of the proneural basic helix-loop-helix transcription factor Ascl1. After expression of Ascl1, but prior to expression of neuronal markers such as microtubule associated protein 2 and neuronal β-tubulin, P19 cells demonstrated a large, transient increase in both mRNA and protein for the endogenous protein kinase inhibitor (PKI)β. PKIβ-targeted shRNA constructs both reduced the levels of PKIβ expression and blocked the neuronal differentiation of P19 cells. This inhibition of differentiation was rescued by transfection of a shRNA-resistant expression vector for the PKIβ protein, and this rescue required the PKA-specific inhibitory sequence of the PKIβ protein. PKIβ played a very specific role in the Ascl1-mediated differentiation process as other PKI isoforms were unable to rescue the deficit conferred by shRNA-mediated knockdown of PKIβ. Our results define a novel requirement for PKIβ and its inhibition of PKA during neuronal differentiation of P19 cells.
Advances in ladar components and subsystems at Raytheon (2012)

Raytheon is developing NIR sensor chip assemblies (SCAs) for scanning and staring 3D LADAR systems. High sensitivity is obtained by integrating high performance detectors with gain, i.e., APDs with very low noise Readout Integrated Circuits (ROICs). Unique aspects of these designs include: independent acquisition (non-gated) of pulse returns, multiple pulse returns with both time and intensity reported to enable full 3D reconstruction of the image. Recent breakthrough in device design has resulted in HgCdTe APDs operating at 300K with essentially no excess noise to gains in excess of 100, low NEP <1nW and GHz bandwidths and have demonstrated linear mode photon counting. SCAs utilizing these high performance APDs have been integrated and demonstrated excellent spatial and range resolution enabling detailed 3D imagery both at short range and long ranges. In the following we will review progress in real-time 3D LADAR imaging receiver products in three areas: (1) scanning 256 × 4 configuration for the Multi-Mode Sensor Seeker (MMSS) program and (2) staring 256 × 256 configuration for the Autonomous Landing and Hazard Avoidance Technology (ALHAT) lunar landing mission and (3) Photon-Counting SCAs which have demonstrated a dramatic reduction in dark count rate due to improved design, operation and processing.
Microtechnology For Realization Of Dielectrophoresis Enhanced Microwells For Biomedical Applications (2007)

Microtechnologies are widely used in many applications as e.g. for the automotive or telecommunication industry. But it could be also a versatile tool for biological and biomedical applications. Microwells have been established long in this application field but remained without any additional functionality up to now. Merging new fabrication techniques and handling concepts with microelectronics enables the realization of intelligent microwells suitable for future applications e.g. improved cancer treatment. For the implementation of a dielectrophoresis enhanced microwell device a technology based on standard PCB technology has been developed. But as materials from PCB technology are not biocompatible new materials have to be selected, tested and processes adapted to these new packaging materials. With promising preselected materials for an enhanced microwell device biocompatibility tests have been carried out. As base conducting metal layer Aluminum has been selected. Different dielectric materials were evaluated with focus on their processability. Goal of this preselection study was to find materials, which allow a fine structuring and realization of thin layers for the required application geometries. Thin aluminum foils are structured by laser micro machining and laminated successively to obtain minimum registration tolerances of the respective layers. The microwells are also laser machined into the laminate, allowing capturing and handling individual cells within a dielectrophoretic cage realized by the structured aluminum as well as providing access holes for the layer-to-layer interconnection. Furthermore, surface treatments with e.g.
Analysis of NLRP3 in the Development of Allergic Airway Disease in Mice (2012)

The contribution of NLRP3, a member of the nucleotide-binding domain leucine-rich repeat-containing (NLR) family, to the development of allergic airway disease is currently controversial. In this study, we used multiple allergic asthma models to examine the physiologic role of NLRP3. We found no significant differences in airway eosinophilia, histopathologic condition, mucus production, and airway hyperresponsiveness between wild-type and Nlrp3(-/-) mice in either acute (alum-dependent) or chronic (alum-independent) OVA models. In addition to the OVA model, we did not detect a role for NLRP3 in the development of allergic airway disease induced by either acute or chronic house dust mite Ag exposure. Although we did not observe significant phenotypic differences in any of the models tested, we did note a significant reduction of IL-13 and IL-33 in Nlrp3(-/-) mice compared with wild-type controls in the chronic OVA model without added alum. In all of the allergic airway disease models, the NLRP3 inflammasome-associated cytokines IL-1β and IL-18 in the lung were below the level of detection. In sum, this report surveyed four different allergic asthma models and found a modest and selected role for NLRP3 in the alum-free OVA model. However, this difference did not greatly alter the clinical outcome of the disease. This finding suggests that the role of NLRP3 in allergic asthma must be re-evaluated.
Biogeochemical Control on Metal Distribution and Accumulation in Louisiana Sediments (1988)

Abstract Metal accumulation rates were determined from sedimentation rates and the distribution of 137 Cs and total metal content in cores collected from freshwater, brackish, and saltwater bay bottoms in Barataria Basin, LA. Vertical accretion rates ranged from 0.65 cm/yr in the northern freshwater part of the basin up to 1.1 cm/yr in the lower saline estuary. Metal sedimentation and accumulation rate estimates along this salinity gradient indicated that metals were concentrated by a factor of two to four in the saline end‐member. Manganese, however, exhibited an estimated depletion of 1.95 g/(m 2 yr) in the lower part of the basin, due to its postdepositional mobility. A principal component and regression analysis of total metal distribution showed that the metal content could be predicted by the C content of the substrate ( R = 0.89**; significant at the 0.01 probability level). This suggested the sedimentation of metal‐rich organic matter, most likely originating from adjacent marshes. Clay and silt content were insignificant as predictor variables. In the subsurface layer (0–4 cm), 18% of the variability in Fe and 27% in the variability in Mn content were attributed to redox processes, and were adequately predicted by the redox potential of the sediment ( R = 0.60*; significant at the 0.05 probability level). Partial metal partitioning in soluble, exchangeable, and reducible fractions indicated that Fe, Al, Cu, Zn, Pb, and Cd held in the water soluble and exchangeable phase represented a minor part of the total metal content. However, water soluble plus exchangeable Mn accounted for 19,10, and 1% of the total Mn in freshwater, brackish, and saltwater environments, respectively. Iron and manganese oxides were found to scavenge metals to 50% of the total heavy metal content.
A Comparison of Enthalpies of Formation in Solution and Enthalpies for HPLC Retention for Hydrogen‐Bonded Host—Guest Complexes (1995)

From the temperature-dependent HPLC retention of a guest or host on a chemically bonded stationary phase containing the complementary component (as shown schematically on the right), the complexation enthalpies of a series of hydrogen-bonded host-guest complexes can be rapidly and conveniently determined. The ΔH̊ values determined in this way agree within experimental error with the complexation enthalpies measured in free solution by traditional methods.
Linear Discriminant and Support Vector Classifiers (2000)

This chapter contains sections titled: Introduction, What is a Linear Discriminant?, Formulation of the Linear Discriminant Training Problem, Training Algorithms, Which Linear Discriminant?, Conclusion, Acknowledgments
Purification of Serine-specific Transfer Ribonucleic Acid from Bakers' Yeast (1967)

By a combination of partition chromatography and countercurrent distribution, serine-specific transfer RNA has been obtained in essentially pure form.The methods described
Multiple Regulatory Mechanisms Act on the 5′ Untranslated Region of the S-Layer Gene from <i>Thermus thermophilus</i> HB8 (2001)

The role of the 5' untranslated region (5'UTR) of the S-layer gene from Thermus thermophilus was analyzed through the isolation of Delta 5'UTR mutants. In these mutants the half-life of splA mRNA was strongly reduced and slpA transcription was no longer subjected to growth phase-dependent repression. Overproduction and detachment of the external envelopes of the mutants were observed in stationary phase.
Quantitative positron emission tomography reveals regional differences in aerobic glycolysis within the human brain (2018)

Glucose and oxygen metabolism are tightly coupled in the human brain, with the preponderance of the brain's glucose supply used to generate ATP via oxidative phosphorylation. A fraction of glucose is consumed outside of oxidative phosphorylation despite the presence of sufficient oxygen to do so. We refer to this process as aerobic glycolysis. A recent positron emission tomography study reported that aerobic glycolysis is uniform within gray matter. Here, we analyze the same data and demonstrate robust regional differences in aerobic glycolysis within gray matter, a finding consistent with previously published data.