gebhart/patrepeval huggingface dataset:
Orphanin FQ Suppresses NMDA Receptor-Dependent Long-Term Depression and Depotentiation in Hippocampal Dentate Gyrus (1999)

We reported previously that orphanin FQ (OFQ) inhibited NMDA receptor-mediated synaptic currents and consequently suppressed induction of long-term potentiation (LTP) in the hippocampal dentate gyrus. This study examines the effect of OFQ on several other forms of long-term synaptic plasticity in the lateral perforant path of mouse hippocampal dentate gyrus. (1) Long-term depression (LTD): a low frequency stimulation (1 Hz, 15 min) applied to the lateral perforant path induced a long-lasting reduction in the dentate field potentials in slices from 22- to 30-day-old mice. This LTD was sensitive to the NMDA receptor blocker D-AP5, and could be significantly attenuated by bath application of OFQ (1 microM, 25 min). (2) Primed LTD: induction of LTD in slices from 50- to 65-day-old mice required a priming procedure consisting of multiple high frequency stimulus trains delivered in the presence of D-AP5 before the low-frequency stimulation. OFQ applied during the low-frequency stimulation, but not during the priming trains, blocked induction of primed LTD. (3) Depotentiation: high-frequency train-induced dentate LTP could be reversed by a subsequent low-frequency stimulation. This depotentiation was also attenuated by either OFQ or D-AP5 applied during low-frequency stimulation. These results, together with our previous findings, suggest that OFQ inhibits bidirectional changes in synaptic strength in the dentate; and its multiple actions on NMDA receptor-dependent, long-term synaptic plasticity might work in tandem to regulate hippocampus-dependent learning and memory.
Time domain simulation of Shapiro steps in Josephson junctions (1985)

Using the time domain formulation of the theory of the tunnel junction, we investigated Shapiro steps by digital simulation, under the condition of a constant current source given by <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I_{dc} + I_{rf} \sin \omegat</tex> . The integral kernels for the Josephson and the quasiparticle current were computed assuming a nonzero pair breaking parameter <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\delta=0.1</tex> , and T = 0K. We obtained I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rf</inf> dependence of the zeroth and first Shapiro steps, I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> and I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</inf> , and the frequency dependence of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I_{1}^{\MAX}</tex> , the maximum of the first Shapiro step as a function of I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rf</inf> , for a few values of the junction capacitance. we found the following results. (1) <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I_{1}^{\MAX}/I_{c}</tex> (I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</inf> :the critical current), showed the Riedel peak at <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\omega/\omega_{g} \simeq 1</tex> , where ω <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</inf> is the gap frequency 4 Δ/h. (2) For <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\omega/\omega_{g} &gt;1\cdot I_{1}^{\MAX}/I_{c}</tex> agrees well with that for the constant voltage bias. (3) As the frequency becomes smaller below <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\omega_{g} \cdot I_{1}^{\MAX}/I_{c}</tex> is severely depressed compared to that for the constant voltage bias.
ChemInform Abstract: ENHYDRAZINE 7. MITT. CARBAZOLDERIVATE AUS ENHYDRAZINEN (1973)

Abstract Die Enhydrazine (I) bzw. (V) reagieren mit Cyclohexan (II) unter Fischer‐Ringschluß zu den Carbazol‐Derivaten (III) bzw. (VI); bei den Enhydrazinen (VII) werden beide möglichen Reaktionswege beobachtet: Es entstehen nebeneinander die Verbindungen (VIII) und (IX).
Technical note: Intensity‐based quality assurance criteria for deformable image registration in image‐guided radiotherapy (2023)

Intensity-based quality assurance criteria can provide the required confidence in decisions about using mono-modal registrations in clinical workflows. They thereby enable automated quality assurance for deformable image registration in adaptive radiotherapy treatments.
Efficient Analytical Prediction of the Cavity Resonant Behavior of PEC–PMC Metallic Enclosures and Packages (2020)

A metal enclosure whose lid is covered by an array of metal pins is studied in this article. The pins are able to realize a fictitious perfect magnetic conductor surface at the pin end, thus inhibiting cavity resonances in a well-defined frequency band. The article proposes an analytical model for predicting the behavior of the cavity, and thus for estimating the bandgap limits. The method is based on the planar cavity formulation and it embeds analytically the pin to bottom plate capacitance. The obtained cavity response agrees well with the simulated models of various cavity and pins dimensions. Moreover, the method is validated experimentally based on manufactured cavities. An in-depth parametric analysis is carried out for precisely evaluating the limit of validity of the proposed cavity model based approach in the prediction of the bandgap upper and lower limits.
Integrative approaches for large-scale transcriptome-wide association studies (2015)

Abstract Many genetic variants influence complex traits by modulating gene expression, thus altering the abundance levels of one or multiple proteins. In this work we introduce a powerful strategy that integrates gene expression measurements with large-scale genome-wide association data to identify genes whose cis-regulated expression is associated to complex traits. We use a relatively small reference panel of individuals for which both genetic variation and gene expression have been measured to impute gene expression into large cohorts of individuals and identify expression-trait associations. We extend our methods to allow for indirect imputation of the expression-trait association from summary association statistics of large-scale GWAS 1-3 . We applied our approaches to expression data from blood and adipose tissue measured in ∼3,000 individuals overall. We then imputed gene expression into GWAS data from over 900,000 phenotype measurements 4-6 to identify 69 novel genes significantly associated to obesity-related traits (BMI, lipids, and height). Many of the novel genes were associated with relevant phenotypes in the Hybrid Mouse Diversity Panel. Overall our results showcase the power of integrating genotype, gene expression and phenotype to gain insights into the genetic basis of complex traits.
Design, Synthesis and Biological Evaluation of Novel SARS-CoV-2 3CLpro Covalent Inhibitors (2020)

Severe diseases such as the ongoing COVID-19 pandemic, as well as the previous SARS and MERS outbreaks, are the result of coronavirus infections and have demonstrated the urgent need for antiviral drugs to combat these deadly viruses. Due to its essential role in viral replication and function, 3CLpro has been identified as a promising target for the development of antiviral drugs. Previously reported SARS-CoV 3CLpro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CLpro. We report herein our efforts in design and synthesis which led to submicromolar covalent inhibitors when the enzymatic activity of the viral protease was used as a screening platform.
A Grignard-Type Addition of Allyl Unit to Aldehydes by Using Bismuth and Bismuth Salt (1990)

Abstract In the presence of metallic bismuth, bismuth(III) chloride–metallic zinc, or bismuth(III) chloride–metallic iron, allylic halides have been found to react with aldehydes under mild conditions to give the corresponding homoallylic alcohols in high yields with high chemo-, regio-, and stereoselectivity. Allylic halides have been also found to react with aldehydes at room temperature in tetrahydrofuran–water by using bismuth(III) chloride–metallic aluminium to afford the expected homoallylic alcohols in high yields.
Unsteady Aerodynamics of Low-Pressure Steam Turbines Operating Under Low Volume Flow (2013)

Non-synchronous excitation under low volume operation is a major risk to the mechanical integrity of last stage moving blades (LSMBs) in low-pressure (LP) steam turbines. These vibrations are often induced by a rotating aerodynamic instability similar to rotating stall in compressors. Currently extensive validation of new blade designs is required to clarify whether they are subjected to the risk of not admissible blade vibration. Such tests are usually performed at the end of a blade development project. If resonance occurs a costly redesign is required, which may also lead to a reduction of performance. It is therefore of great interest to be able to predict correctly the unsteady flow phenomena and their effects. Detailed unsteady pressure measurements have been performed in a single stage model steam turbine operated with air under ventilation conditions. 3D CFD has been applied to simulate the unsteady flow in the air model turbine. It has been shown that the simulation reproduces well the characteristics of the phenomena observed in the tests. This methodology has been transferred to more realistic steam turbine multi stage environment. The numerical results have been validated with measurement data from a multi stage model LP steam turbine operated with steam. Measurement and numerical simulation show agreement with respect to the global flow field, the number of stall cells and the intensity of the rotating excitation mechanism. Furthermore, the air model turbine and model steam turbine numerical and measurement results are compared. It is demonstrated that the air model turbine is a suitable vehicle to investigate the unsteady effects found in a steam turbine.
Five HLA-DP Molecules Frequently Expressed in the Worldwide Human Population Share a Common HLA Supertypic Binding Specificity (2010)

Compared with DR and DQ, knowledge of the binding repertoires and specificities of HLA-DP alleles is somewhat limited. However, a growing body of literature has indicated the importance of DP-restricted responses in the context of cancer, allergy, and infectious disease. In the current study, we developed high-throughput binding assays for the five most common HLA-DPB1 alleles in the general worldwide population. Using these assays on a comprehensive panel of single-substitution analogs and large peptide libraries, we derived novel detailed binding motifs for DPB1*0101 and DPB1*0501. We also derived more detailed quantitative motifs for DPB1*0201, DPB1*0401, and DPB1*0402, which were previously characterized on the basis of sets of eluted ligands and/or limited sets of substituted peptides. Unexpectedly, all five DP molecules, originally selected only on the basis of their frequency in human populations, were found to share largely overlapping peptide motifs. Testing panels of known DP epitopes and a panel of peptides spanning a set of Phleum pratense Ags revealed that these molecules also share largely overlapping peptide-binding repertoires. This demonstrates that a previously hypothesized DP supertype extends far beyond what was originally envisioned and includes at least three additional very common DP specificities. Taken together, these DP supertype molecules are found in >90% of the human population. Thus, these findings have important implications for epitope-identification studies and monitoring of human class II-restricted immune responses.
Susceptibility of Bacteroides from swine abscesses to 13 antibiotics (1984)

The minimal inhibitory concentrations (MIC) of 129 strains of genus Bacteroides, isolated from abscesses in pigs, for 13 different antimicrobial agents were determined by an agar-dilution method under anaerobic conditions. Clindamycin, the most active antibiotic tested, had a median MIC of 0.8 micrograms/ml. Penicillin G, talampicillin, minocycline, chloramphenicol, and cefoxitin also inhibited all isolates at lower concentrations. Some isolates of B pyogenes were susceptible to gentamicin (MIC, 0.4 micrograms/ml), erythromycin (MIC, 0.8 micrograms/ml), cephalexin (MIC, 0.8 micrograms/ml), and cefoxitin (MIC, 3.2 micrograms/ml). Erythromycin, at a concentration of 3.2 micrograms/ml, was active against 70% of B suis tested, but it was less active against the other Bacteroides species. Some strains tested were resistant to streptomycin and neomycin.
The Power Law and Dynamic Rheology in Cheese Analysis (2012)

The protein networks of food such as cheese are investigated nondestructively by small amplitude oscillatory shear analysis, which provides information on elastic modulus (G′) and viscous modulus (G″). Relationships between frequency and viscoelastic data may be obtained from frequency sweeps by applying the power law, in which G′ and G″ are related to a power of frequency. The power law was applied to the investigation of Queso Fresco cheeses stored at 4 or 10°C for up to 12 wk. The equations revealed changes during aging that were evidently due to leakage of whey from the cheese matrix. Viscous dissipation of energy was not as pronounced as elastic energy storage in the samples. The results demonstrate that a great deal of data may be simplified into two equations that provide insight into the rheological behavior of a food.
Three-dimensional lensless imaging using laser frequency diversity (1992)

A laser radar system for three-dimensional (3-D) lensless imaging is analyzed in theory and experiment. 3-D imaging is accomplished by making use of the relationship between the angular and wavelength dependence of the scattered light and an object's 3-D Fourier transform. The concept is demonstrated by obtaining a 3-D image of an extended object by using a charge-coupled device detector array and an argon-ion laser with a tunable intracavity étalon.
Bacterial inhibition of phagocytosis. Microreview (2000)

The concerted study of molecular mechanisms of phagocytosis and the inhibition of phagocytosis by specific products of extracellular bacterial pathogens has borne considerable fruit. The importance of tyrosine phosphorylation and of the Rho family of GTPases has become clear to cell biologists, but pathogenic bacteria recognized the importance of these signalling pathways in phagocytic cells long ago. The discoveries described in this review are only the beginning. The simultaneous pursuit of the mechanisms and molecules involved in the initiation and regulation of phagocytosis and that pathogenic bacteria use to inhibit phagocytosis will surely identify more interesting pathways on each side of the contest. Are there any obvious possibilities? There are several bacterial factors that have the potential to inhibit known mechanisms of phagocytosis. Clostridium species, for example, make a number of exotoxins of interest. Clostridium botulinum and Clostridium tetani neurotoxins inactivate the regulated secretory machinery by proteolytic cleavage of SNARE proteins, and targets of tetanus toxin and botulinum b toxin inhibit the exocytotic delivery of membrane vesicles needed for phagocytosis of large particles (Hackam et al., 1998). Moreover, the C3 exotoxin of C. botulinum catalyses ADP ribosylation and inactivation of rho family GTPases (Wiegers et al., 1991), and toxins A and B of C. difficile UDP-glucosylate and inactivate rho GTPases and thereby disrupt the actin cytoskeleton (Just et al., 1995a,b). However, as Clostridia lack the machinery for type III secretion, these proteins are not rapidly targeted to the phagocyte cytoplasm. More searching may reveal a pathogen that has combined the type III secretory machinery with clostridia toxin-like substrates. A potentially unique strategy for remaining outside phagocytes is exhibited by Helicobacter pylori, which contain a type IV secretion system. Unopsonized virulent strains of H. pylori bind readily to macrophages but are only internalized after a delay of several minutes. Such a delay appears to be sufficient for the bacteria to remain extracellular (Allen et al., 2000). Elucidation of the mechanism used by H. pylori to delay phagocytosis may reveal one or more novel virulence factors as well as one or more novel targets in the phagocyte that will add to the understanding of a fundamental process in host defence. Another field ripe for further mechanistic investigation is complement receptor-mediated phagocytosis. Dedicated study of the molecular events and molecular mediators of phagocytosis downstream of CR3 is likely to reveal interesting differences from FcgammaR phagocytosis and is just as likely to reveal that microbes have discovered unique mechanisms for circumventing them. Study of extracellular pathogens and the mechanisms that they use to remain outside phagocytic cells has revealed a great deal about the initial encounter between pathogen and phagocyte. We can look forward to additional discoveries about the host-pathogen interactions and the mechanisms and factors that each side uses to battle against the other.
Scale Invariant Feature Transform for n-Dimensional Images (n-SIFT) (2007)

This document describes the implementation of several features previously developed[2], extending the 2D scale invariant feature transform (SIFT)[4, 5] for images of arbitrary dimensionality, such as 3D medical image volumes and time series, using ITK1. Specifically, we provide a scale invariant implementation of a weighted histogram of gradient feature, a rotationally invariant version of the histogram feature, and a SIFT-like feature, adapted to handle images of arbitrary dimensionality. This paper is accompanied with the source code, example input data, parameters and output data, allowing reproduction of the example results in this paper and the results previously reported[2]. Note that usage of SIFT in the United States is governed by US Patent 6,711,293.
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins (2008)

We give further evidence that Jmjd6 most likely has a function as a nonheme-Fe(II)-2-oxoglutarate-dependent dioxygenase as previously suggested. Further, we provide novel insights into the evolution of Jmjd6 and other related members of the superfamily of JmjC domain containing proteins. Finally, we discuss possibilities of the involvement of Jmjd6 and 1110005A03Rik in an antagonistic biochemical pathway.
Tightly coupled cooperation among independent agents (2008)

Coordination is defined as ”the harmonious functioning of parts for effective results” (Mish 1996). When applied to multiple robot systems, coordination is classified by one of two categories: collaboration or cooperation. Each component contributes to the harmonious functioning aspect of Coordination. Collaboration occurs when multiple robots engage in separate independent tasks to fulfill a higher goal. Collaboration is limited to situations where there is no requirement for synchronization on the tasks. An example of this is in distributed mapping: each robot’s progress on generating its portion of the map is unaffected by the progress of other robots. Cooperation, on the other hand, occurs when multiple robots engage in similar or identical tasks that are mutually dependent (coupled) in pursuit of a higher goal. These tasks require at least some degree of synchronization, and cooperative tasks fall on a spectrum that spans from loosely coupled to tightly coupled tasks. More tightly coupled tasks require a greater degree of synchronization. Cooperative box pushing is an example of a somewhat tightly coupled task, since the synchronization requirements are mostly limited to constraining the deviation from the intendended course. Cooperative lifting is a tightly coupled cooperative task because the robots must keep the item fairly level. This way, the robots avoid an uneven distribution of the weight and minimize the risk of damage to themselves and the item. With highly independent autonomous systems, collaboration and loosely coupled cooperation are readily achieved. This is because each individual task completion is seen as a fulfillment of a subgoal pertaining to the overall goal. Though the apparent progress of a loosely coupled cooperative tasking may vary temporally, delaying the deactivation of the task until it remains complete for a minimum time period can ensure successful completion. However, it is much more difficult to construct a system that can perform
Genome sequencing analysis of blood cells identifies germline haplotypes strongly associated with drug resistance in osteosarcoma patients (2019)

We show that combining next generation sequencing data from multiple datasets and defined clinical data can better identify relevant pathway associations and clinically actionable variants, as well as provide insights into drug response mechanisms.
Obesity and vascular complication in percutaneous transfemoral transcatheter aortic valve insertion (2023)

Obesity is not associated with a vascular complication during percutaneous transfemoral transcatheter aortic valve insertion. The operation should not be denied in obese patients.
Thulium fiber laser lithotripsy (2009)

Complications during laser lithotripsy include optical fiber bending failure resulting in endoscope damage and low irrigation rates leading to poor visibility. Both problems are related to fiber diameter and limited by the Holmium:YAG laser (&#955; = 2120 nm) multimode beam profile. This study exploits the Thulium fiber laser (&#955; = 1908 nm) beam profile for higher power transmission through smaller fibers. Thulium fiber laser radiation with 1-ms pulse duration, pulse rates of 10-30 Hz, and 70-&#956;m-diameter spot was coupled into silica fibers with 100, 150, and 200 &#956;m core diameters. Fiber transmission, bending, and endoscope irrigation tests were performed. Damage thresholds for 100, 150, 200 &#956;m fibers averaged 40 W, 60 W, and &gt; 80 W. Irrigation rates measured 35, 26, and 15 ml/min for no fiber, 100, and 200 &#956;m fibers. Thulium fiber laser energy of 70-mJ delivered at 20 Hz through a 100 &#956;m fiber resulted in vaporization and fragmentation rates of 10 and 60 mg/min for uric acid stones. The Thulium fiber laser beam profile provides higher laser power through smaller fibers than the Ho:YAG laser, potentially reducing fiber failure and endoscope damage and allowing greater irrigation rates for improved visibility.