gebhart/patrepeval huggingface dataset:
Assessment of genetic diversity in Australian canola (Brassica napus L.) cultivars using SSR markers (2009)

Australian canola (Brassica napus L.) has been relatively isolated from the global gene pool and limited knowledge is available for genetic variability based on DNA profiling. In the present study, genetic diversity of recent Australian canola cultivars was determined by simple sequence repeat (SSR) marker analysis. In total, 405 individuals from 48 varieties were genotyped with 18 primer pairs, resulting in 112 polymorphic features. The number of polymorphic features amplified by each SSR primer pair varied from 3 to 16. Analysis of molecular variance (AMOVA) detected 53.7% and 46.3% within- and between-cultivar variation, respectively. Intra-cultivar genetic variability differed according to cultivar. The number of polymorphic features per cultivar varied from 35 (Ag-Spectrum) to 72 (Ag-Insignia), while mean sum of squares (MSS) varied from 6.29 (Tornado TT) to 24.76 (Ag-Emblem). Genetic differentiation of cultivars generally reflected pedigree structure and origin by breeding organisation. Clustering and principal coordinate analysis (PCoA) indicated that the individuals were separated into 4 major groups. The genetic diversity information from this study will be useful for future Australian canola breeding programs.
Computational Study of the Allosteric Effects of p5 on CDK5–p25 Hyperactivity as Alternative Inhibitory Mechanisms in Neurodegeneration (2022)

The cyclin-dependent kinase (CDK5) forms a stable complex with its activator p25, leading to the hyperphosphorylation of tau proteins and to the formation of plaques and tangles that are considered to be one of the typical causes of Alzheimer's disease (AD). Hence, the pathological CDK5-p25 complex is a promising therapeutic target for AD. Small peptides, obtained from the truncation of CDK5 physiological activator p35, have shown promise in inhibiting the pathological complex effectively while also crossing the blood-brain barrier. One such small 24-residue peptide, p5, has shown selective inhibition toward the pathological complex in vivo. Our previous research focused on the characterization of a computationally predicted CDK5-p5 binding mode and of its pharmacophore, which was consistent with competitive inhibition. In continuation of our previous work, herein, we investigate four additional binding modes to explore other possible mechanisms of interaction between CDK5 and p5. The quantitative description of the pharmacophore is consistent with both competitive and allosteric p5-induced inhibition mechanisms of CDK5-p25 pathology. The gained insights can direct further in vivo/in vitro tests and help design small peptides, linear or cyclic, or peptidomimetic compounds as adjuvants of orthosteric inhibitors or as part of a cocktail of drugs with enhanced effectiveness and lower side effects.
Wideband probe-type waveguide-to-microstrip transition for V-band applications (2016)

A novel broadband probe-type waveguide-to-microstrip transition adapted for operation in V band is presented. The transition is realized on a standard high frequency printed circuit board (PCB) fixed between a standard WR-15 waveguide and a simple backshort. The microstrip-fed probe is placed at the same side of the PCB with the backshort and acts as an impedance matching element. The proposed transition additionally includes two through holes implemented on the PCB in the center of the transition area. Thus, significant part of the lossy PCB dielectric is removed from that area providing wideband and low-loss performance of the transition. Measurements show that the designed transition has the bandwidth of 50-70 GHz for the -10 dB level of the reflection coefficient with the loss level of only 0.75 dB within the transition bandwidth.
Virus Morphogenesis and Viral Entry as Alternative Targets for Novel Hepatitis C Antivirals (2006)

Hepatitis C virus (HCV) infection is a major public health concern. New antiviral drugs are required urgently to complement and improve the efficacy of current chemotherapies. Molecules specifically targeting viral enzymes are the most attractive in terms of drug development and are, therefore, the most studied. However, an antiviral strategy based uniquely on the utilization of this type of target is expected to encounter problems caused by the emergence of viral escape mutants as has already been widely described for HIV and hepatitis B virus. HCV morphogenesis and viral entry represent interesting, and yet unexploited, novel molecular targets. Inhibitors of morphogenesis have recently been identified and studied in different virus–cell systems. Some of these are currently being evaluated in clinical trials against HCV. This review focuses on HCV morphogenesis, viral entry and inhibition and presents clinical development perspectives of this new generation of antivirals.
Hadronic mass spectrum analysis of D+→K−π+μ+ν decay and measurement of the K∗(892)0 mass and width (2005)

We present a Kπ mass spectrum analysis of the four-body semileptonic charm decay D+→K-π+μ+ν in the range of 0.65 GeV/c2&lt;1.5 GeV/c2. We observe a non-resonant contribution of 5.30±0.74-0.96+0.99% with respect to the total D+→K-π+μ+ν decay. For the K*(892)0 resonance, we obtain a mass of 895.41±0.32-0.43+0.35 MeV/c2, a width of 47.79±0.86-1.06+1.32 MeV/c2, and a Blatt-Weisskopf damping factor parameter of 3.96±0.54-0.90+1.31 GeV-1. We also report 90% CL upper limits of 4% and 0.64% for the branching ratios Γ(D+→K̄*(1680)0μ+ν)Γ(D+→K-π+μ+ν) and Γ(D+→K̄0*(1430)0μ+ν) Γ(D+→K-π+μ+ν), respectively.
HTN planning with preferences (2009)

In this paper we address the problem of generating preferred plans by combining the procedural control knowledge specified by Hierarchical Task Networks (HTNs) with rich user preferences. To this end, we extend the popular Planning Domain Definition Language, PDDL3, to support specification of simple and temporally extended preferences over HTN constructs. To compute preferred HTN plans, we propose a branch-and-bound algorithm, together with a set of heuristics that, leveraging HTN structure, measure progress towards satisfaction of preferences. Our preference-based planner, HTNPLAN-P, is implemented as an extension of the SHOP2 planner. We compared our planner with SGPlan5 and HPLAN-P – the top performers in the 2006 International Planning Competition preference tracks. HTNPLAN-P generated plans that in all but a few cases equalled or exceeded the quality of plans returned by HPLAN-P and SGPlan5. While our implementation builds on SHOP2, the language and techniques proposed here are relevant to a broad range of HTN planners. 1
Improving Automated Hemorrhage Detection in Sparse-view Computed Tomography via Deep Convolutional Neural Network based Artifact Reduction (2023)

This is a preprint. The latest version has been published here: https://pubs.rsna.org/doi/10.1148/ryai.230275 Purpose: Sparse-view computed tomography (CT) is an effective way to reduce dose by lowering the total number of views acquired, albeit at the expense of image quality, which, in turn, can impact the ability to detect diseases. We explore deep learning-based artifact reduction in sparse-view cranial CT scans and its impact on automated hemorrhage detection. Methods: We trained a U-Net for artefact reduction on simulated sparse-view cranial CT scans from 3000 patients obtained from a public dataset and reconstructed with varying levels of sub-sampling. Additionally, we trained a convolutional neural network on fully sampled CT data from 17,545 patients for automated hemorrhage detection. We evaluated the classification performance using the area under the receiver operator characteristic curves (AUC-ROCs) with corresponding 95% confidence intervals (CIs) and the DeLong test, along with confusion matrices. The performance of the U-Net was compared to an analytical approach based on total variation (TV). Results: The U-Net performed superior compared to unprocessed and TV-processed images with respect to image quality and automated hemorrhage diagnosis. With U-Net post-processing, the number of views can be reduced from 4096 (AUC-ROC: 0.974; 95% CI: 0.972-0.976) views to 512 views (0.973; 0.971-0.975) with minimal decrease in hemorrhage detection (P&lt;.001) and to 256 views (0.967; 0.964-0.969) with a slight performance decrease (P&lt;.001). Conclusion: The results suggest that U-Net based artifact reduction substantially enhances automated hemorrhage detection in sparse-view cranial CTs. Our findings highlight that appropriate post-processing is crucial for optimal image quality and diagnostic accuracy while minimizing radiation dose.
<title>Microscopic pick-and-place teleoperation</title> (1993)

A three degree-of-freedom direct drive mini robot has been developed for biomedical applications. The design approach of the mini robot relies heavily upon electromechanical components from the Winchester disk drive industry. In the current design, the first joint is driven by actuators from a 5.25' drive, and the following joints are driven by actuators typical of 3.5' drives. The system has 5 - 10 micrometers of position repeatability and resolution in all three axes. A mini gripper attachment has been fabricated for the robot to explore manipulation of objects ranging from 50 micrometers to 500 micrometers . Mounted on the robot, the gripper has successfully performed pick and place operations under teleoperated control. The mini robot serves to precisely position the gripper, and a needle-like finger of the gripper deflects so the fingers can grip a target object. The gripper finger capable of motion is fabricated with a piezoelectric bimorph crystal which deflects with an applied DC voltage. The experimental results are promising, and the mini gripper may be modified for future biomedical and micro assembly applications.
Experimental Digital VCR with New DCT-Based Bit-Rate Reduction and Channel Coding (1992)

To achieve a more compact and longer-playing videocassette recorder (VCR), the number and the size of its recording bits must become smaller. The authors have achieved a data rate of 28 Mbits/sec for a component-coded video that normally requires approximately 200 Mbits/sec, maintaining high picture quality with less noticeable degradation by using a new discrete cosine transform (DCT)-based bit-rate reduction method. The authors have developed a data format based on the triple Reed-Solomon product code and a new 8/14 modulation scheme to make the recording density higher. An experiment showing the feasibility of the authors' new system concept is discussed in this article.
Impact of Cysteine Residues on MHC Binding Predictions and Recognition by Tumor-Reactive T Cells (2020)

The availability of MHC-binding prediction tools has been useful in guiding studies aimed at identifying candidate target Ags to generate reactive T cells and to characterize viral and tumor-reactive T cells. Nevertheless, prediction algorithms appear to function poorly for epitopes containing cysteine (Cys) residues, which can oxidize and form disulfide bonds with other Cys residues under oxidizing conditions, thus potentially interfering with their ability to bind to MHC molecules. Analysis of the results of HLA-A*02:01 class I binding assays carried out in the presence and absence of the reducing agent 2-ME indicated that the predicted affinity for 25% of Cys-containing epitopes was underestimated by a factor of 3 or more. Additional analyses were undertaken to evaluate the responses of human CD8<sup>+</sup> tumor-reactive T cells against 10 Cys-containing HLA class I-restricted minimal determinants containing substitutions of α-aminobutyric acid (AABA), a cysteine analogue containing a methyl group in place of the sulfhydryl group present in Cys, for the native Cys residues. Substitutions of AABA for Cys at putative MHC anchor positions often significantly enhanced T cell recognition, whereas substitutions at non-MHC anchor positions were neutral, except for one epitope where this modification abolished T cell recognition. These findings demonstrate the need to evaluate MHC binding and T cell recognition of Cys-containing peptides under conditions that prevent Cys oxidation, and to adjust current prediction binding algorithms for HLA-A*02:01 and potentially additional class I alleles to more accurately rank peptides containing Cys anchor residues.
Capability analysis for an inductively coupled power transfer system (2002)

This paper reviews a computer-aided analytical technique for predicting the power transfer capability of an AC inverter energizing a separable inductive coupling. The capability curve is obtained using a switching model of the output rectifier and a readily available software package such as MATLAB(R). The capability curve is useful, among other applications, for evaluating candidate separable transformer designs. Conceptually, it can be used to analyze any transformer-isolated, DC-DC power conversion stage.
Sergestidæ of the Siboga expedition (1919)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Adenosine and Preexcitation Variants: Reappraisal of Electrocardiographic Changes (2016)

Intravenous adenosine is a short-acting blocker of the atrioventricular node that has been used to unmask subtle or latent preexcitation, and also to enable catheter ablation in selected patients with absent or intermittent preexcitation. Depending on the accessory pathway characteristics, intravenous adenosine may produce specific electrocardiographic changes highly suggestive of the preexcitation variant. Herein, we view different ECG responses to this pharmacological test in various preexcitation patterns that were confirmed by electrophysiological studies. Careful analysis of electrocardiographic changes during adenosine test, with emphasis on P-delta interval, preexcitation degree, and atrioventricular block, can be helpful to diagnose the preexcitation variant/pattern.
SUMO1 Modification of Tau in Progressive Supranuclear Palsy (2022)

Small ubiquitin-like modifiers (SUMO) have been implicated in several neurodegenerative diseases. SUMO1 conjugation has been shown to promote aggregation and regulate phosphorylation of the tau protein linked to Alzheimer's disease and related tauopathies. The current study has demonstrated that SUMO1 co-localizes with intraneuronal tau inclusions in progressive supranuclear palsy (PSP). Immunoprecipitation of isolated and solubilized tau fibrils from PSP tissues revealed SUMO1 conjugation to a cleaved and N-terminally truncated tau. The effects of SUMOylation were examined using tau-SUMO fusion proteins which showed a higher propensity for tau oligomerization of PSP-truncated tau and accumulation on microtubules as compared to the full-length protein. This was found to be specific for SUMO1 as the corresponding SUMO2 fusion protein did not display a significantly altered cytoplasmic distribution or aggregation of tau. Blocking proteasome-mediated degradation promoted the aggregation of the tau fusion proteins with the greatest effect observed for truncated tau-SUMO1. The SUMO1 modification of the truncated tau in PSP may represent a detrimental event that promotes aggregation and impedes the ability of cells to remove the resulting protein deposits. This combination of tau truncation and SUMO1 modification may be a contributing factor in PSP pathogenesis.
Prognostic Enhancements to Diagnostic Systems for Improved Condition-Based Maintenance (2002)

Abstract : In recent years, numerous machinery health monitoring technologies have been developed by the U.S. Navy to aid in the detection and classification of developing machinery faults for various Naval platforms. Existing Naval condition assessment systems such as ICAS (Integrated Condition Assessment System) employ several fault detection and diagnostic technologies ranging from simple thresholding to rule-based algorithms. However, these technologies have not specifically focused on the ability to predict the future condition (prognostics) of a machine based on the current diagnostic state of the machinery and its available operating and failure history data. An advanced prognostic capability is desired because the ability to forecast this future condition enables a higher level of condition-based maintenance for optionally managing total Life Cycle Costs (LCC). A second issue is that a framework does not exist for 'plug 'n play' integration of new diagnostic and prognostic technologies into existing Naval platforms. This paper will outline such Prognostic Enhancements to Diagnostic Systems (PEDS) using a generic framework for developing interoperable prognostic 'modules'. Specific prognostic module examples developed for gas turbine engines and gearbox systems are also provided.
Recombinant Human Osteogenic Protein-1 (Bone Morphogenetic Protein-7) as an Osteoinductive Agent in Spinal Fusion (2002)

Animal studies support the ability of osteogenic protein-1 to enhance or replace autograft for spinal arthrodesis in both the posterolateral and interbody environment. Human trials ultimately will provide data to clarify the optimal role of osteogenic protein-1 in human spinal surgery.
JNJ-40255293, a Novel Adenosine A2A/A1Antagonist with Efficacy in Preclinical Models of Parkinson’s Disease (2014)

Adenosine A2A antagonists are believed to have therapeutic potential in the treatment of Parkinson's disease (PD). We have characterized the dual adenosine A2A/A1 receptor antagonist JNJ-40255293 (2-amino-8-[2-(4-morpholinyl)ethoxy]-4-phenyl-5H-indeno[1,2-d]pyrimidin-5-one). JNJ-40255293 was a high-affinity (7.5 nM) antagonist at the human A2A receptor with 7-fold in vitro selectivity versus the human A1 receptor. A similar A2A:A1 selectivity was seen in vivo (ED50's of 0.21 and 2.1 mg/kg p.o. for occupancy of rat brain A2A and A1 receptors, respectively). The plasma EC50 for occupancy of rat brain A2A receptors was 13 ng/mL. In sleep-wake encephalographic (EEG) studies, JNJ-40255293 dose-dependently enhanced a consolidated waking associated with a subsequent delayed compensatory sleep (minimum effective dose: 0.63 mg/kg p.o.). As measured by microdialysis, JNJ-40255293 did not affect dopamine and noradrenaline release in the prefrontal cortex and the striatum. However, it was able to reverse effects (catalepsy, hypolocomotion, and conditioned avoidance impairment in rats; hypolocomotion in mice) produced by the dopamine D2 antagonist haloperidol. The compound also potentiated the agitation induced by the dopamine agonist apomorphine. JNJ-40255293 also reversed hypolocomotion produced by the dopamine-depleting agent reserpine and potentiated the effects of l-dihydroxyphenylalanine (L-DOPA) in rats with unilateral 6-hydroxydopamine-induced lesions of the nigro-striatal pathway, an animal model of Parkinson's disease. Extrapolating from the rat receptor occupancy dose-response curve, the occupancy required to produce these various effects in rats was generally in the range of 60-90%. The findings support the continued research and development of A2A antagonists as potential treatments for PD.
Molecular mechanisms involved in activity of h7C10, a humanized monoclonal antibody, to IGF‐1 receptor (2008)

IGF-1 receptor (IGF-1R) plays a key role in the development of numerous tumors. Blockade of IGF-1R axis using monoclonal antibodies constitutes an interesting approach to inhibit tumor growth. We have previously shown that h7C10, a humanized anti-IGF-1R Mab, exhibited potent antitumor activity in vivo. However, mechanisms of action of h7C10 are still unknown. Here, we showed that h7C10 inhibited IGF-1-induced IGF-1R phosphorylation in a dose-dependent manner. Also, h7C10 abolished IGF-1-induced activation of PI3K/AKT and MAPK pathways. Cell cycle progression and colony formation were affected in the presence of h7C10 probably because of the inhibition of IGF-1-induced cyclin D1 and E expression. In addition, we demonstrated that h7C10 induced a rapid IGF-1R internalization leading to an accumulation into cytoplasm resulting in receptor degradation. Using lysosome and proteasome inhibitors, we observed that the IGF-1R alpha- and beta-chains could follow different degradation routes. Thus, we demonstrated that antitumoral properties of h7C10 are the result of IGF-1-induced cell signaling inhibition and down-regulation of IGF-1R level suggesting that h7C10 could be a candidate for therapeutic applications.
Does agency change the perceived timing of events? (2004)

If one believes that his action has caused an event, does that change the way he perceives the timing of his action and/or the event? Haggard et al (2002) reported that when subjects voluntarily pressed a key, which was followed by a beep 250 msec later, the keypress was judged to take place later in time, and the beep earlier in time — i.e., the two events seemed closer together (Eagleman & Holcombe, 2002). Further, in a report by Cunningham et al (2001), subjects anecdotally reported that their actions and delayed effects began to seem simultaneous. To further examine temporal attraction between intentional action and effect, we had subjects play a game in which they adapted to a 100ms delay between their keypress and a resultant flash. Occasionally, a computer opponent would cause this same flash in a time window after the subject's keypress, but before the subject's flash was expected to arrive. After adapting to the action-effect delay, Ss often erroneously answered that flashes appearing in this time window actually occurred before they pressed the button. When they played the same game with no inserted delay, this timing illusion disappeared. One hypothesis is that the keypress was judged by Ss to be later in time. Given this, we attempted to replicate the Haggard et al study, and found that subjects reported a beep to indeed happen earlier in the voluntary condition and later in the involuntary condition (average difference 155+−47 msec). However, it is unclear whether all subjects perceived the *keypress* to be pulled later in time. Further, we were surprised to find that several other versions of causality games that we constructed did not show any significant temporal attractin as a result of agency. This indicates that the putative ‘temporal attraction’ between actions and their effects is not straightforward, but might be overridden by stimuli that give more information. We propose a temporal Bayesian model to partially explain our results.
Evaluation of chloride/bicarbonate. Exchange in the human colon in vivo. (1983)

During perfusion of a plasma-like solution, colonic absorption rate of chloride was much higher than the secretion rate of bicarbonate (34 vs. 3.5 meq/h, respectively). This might suggest that anion exchange (Cl/HCO3) accounts for only a small fraction of total chloride absorption. However, if the colon absorbs as well as secretes bicarbonate, this reasoning would underestimate the magnitude of the anion exchange. To see if the colon absorbs bicarbonate, we perfused a chloride-free solution (which would eliminate bicarbonate secretion via (Cl/HCO3 exchange) and found that the colon absorbed bicarbonate at a rate of 5.1 meq/h. Calculation of electrochemical gradients and measurement of luminal fluid PCO2 indicated that this bicarbonate absorption was mediated passively in response to electrical gradients, rather than via reversed Cl/HCO3 exchange or acid secretion. The combined results of the plasma-like and chloride-free perfusion experiments suggest Cl/HCO3 exchange at a rate of 8.6 meq/h (the sum of bicarbonate movements, 3.5 and 5.1 meq/h, observed in the two experiments). To obtain a second estimate under different experimental conditions, a choline chloride-choline bicarbonate (sodium-free) solution was perfused; with this solution, chloride and bicarbonate absorption dependent on active sodium transport should be eliminated or markedly reduced, and the magnitude of Cl/HCO3 exchange should be revealed. This experiment suggested a Cl/HCO3 exchange rate of 9.3 meq/h, similar to the first estimate. As chloride was absorbed at a rate of 34 meq/h during perfusion of the plasma-like solution, the Cl/HCO3 exchange provides for approximately one-fourth of total chloride absorption.