gebhart/patrepeval huggingface dataset:
Update on Grand Challenge Competition to Predict in Vivo Knee Loads (2012)

Validation is critical if clinicians are to use musculoskeletal models to optimize treatment of individual patients with a variety of musculoskeletal disorders. This paper provides an update on the annual Grand Challenge Competition to Predict in Vivo Knee Loads, a unique opportunity for direct validation of knee contact forces and indirect validation of knee muscle forces predicted by musculoskeletal models. Three competitions (2010, 2011, and 2012) have been held at the annual American Society of Mechanical Engineers Summer Bioengineering Conference, and two more competitions are planned for the 2013 and 2014 conferences. Each year of the competition, a comprehensive data set collected from a single subject implanted with a force-measuring knee replacement is released. Competitors predict medial and lateral knee contact forces for two gait trials without knowledge of the experimental knee contact force measurements. Predictions are evaluated by calculating root-mean-square (RMS) errors and R(2) values relative to the experimentally measured medial and lateral contact forces. For the first three years of the competition, competitors used a variety of methods to predict knee contact and muscle forces, including static and dynamic optimization, EMG-driven models, and parametric numerical models. Overall, errors in predicted contact forces were comparable across years, with average RMS errors for the four competition winners ranging from 229 N to 312 N for medial contact force and from 238 N to 326 N for lateral contact force. Competitors generally predicted variations in medial contact force (highest R(2 )= 0.91) better than variations in lateral contact force (highest R(2 )= 0.70). Thus, significant room for improvement exists in the remaining two competitions. The entire musculoskeletal modeling community is encouraged to use the competition data and models for their own model validation efforts.
CANNIBALISM AND INTERSPECIFIC PREDATION:ROLE OF OVIPOSITION BEHAVIOR (1999)

Cannibalism and interspecific predation among insect predators are common, yet these behaviors are frequently omitted from predator–prey theory and empirical studies. Interactions among predators can disrupt, facilitate, or augment biological pest control. We estimated the relative strengths of cannibalism and interspecific predation in a maize–aphid–coccinellid predator system. We know from previous work that Adalia bipunctata females tend to oviposit at the top of the plant near large aphid aggregations and that Coleomegilla maculata females tend to oviposit at the bottom of the plant far from large aphid aggregations. We used this information to design experiments to estimate the relative strength of cannibalism and interspecific predation. At high aphid densities, eggs at the top of the plant, near aphids, were preyed upon more than eggs at the bottom of the plant, far from aphids. This result implies that A. bipunctata suffers greater egg mortality than C. maculata. In part, this was due to the foraging pattern of A. bipunctata and also the large populations of aphidophagous predators that develop as a result of the large aggregations of aphids at the top of the maize plant. In predator-enclosure experiments, A. bipunctata searched primarily near large aggregations of aphids and therefore fed more on eggs at the top of plants near large aggregations of aphids. C. maculata searched throughout, yet tended to feed on more eggs at the bottom of the plant. This demonstrated that for both species the effect of cannibalism was equal to or stronger than that of interspecific predation. These findings suggest that species-specific oviposition behaviors largely determined the relative strength of cannibalism and interspecific predation. Cannibalism and interspecific predation can be analyzed as interference competition. Using competition theory, we were able to make predictions about coccinellid species’ joint impact on aphids and species dominance.
Antiviral responses induced by the TLR3 pathway (2011)

Antiviral responses are successively induced in virus-infected animals, and include primary innate immune responses such as type I interferon (IFN) and cytokine production, secondary natural killer (NK) cell responses, and final cytotoxic T lymphocyte (CTL) responses and antibody production. The endosomal Toll-like receptors (TLRs) and cytoplasmic RIG-I-like receptors (RLRs), which recognize viral nucleic acids, are responsible for virus-induced type I IFN production. RLRs are expressed in most tissues and cells and are primarily implicated in innate immune responses against various viruses through type I IFN production, whereas nucleic acid-sensing TLRs, TLRs 3, 7, 8 and 9, are expressed on the endosomal membrane of dendritic cells (DCs) and play distinct roles in antiviral immunity. TLR3 recognizes viral double-stranded RNA taken up into the endosome and serves to protect the host against viral infection by the induction of a range of responses including type I IFN production and DC-mediated activation of NK cells and CTLs, although the deteriorative role of TLR3 has also been reported in some virus infections. Here, we review the current knowledge on the role of TLR3 during viral infection, and the current understanding of the TLR3-signalling cascade that operates via the adaptor protein TICAM-1 (also called TRIF).
Molecular structures and electron-transfer kinetics for some pentacoordinate Cu(I)/Cu(II) redox-active pairs (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular structures and electron-transfer kinetics for some pentacoordinate Cu(I)/Cu(II) redox-active pairsJohn A. Goodwin, David M. Stanbury, Lon J. Wilson, C. W. Eigenbrot, and W. Robert ScheidtCite this: J. Am. Chem. Soc. 1987, 109, 10, 2979–2991Publication Date (Print):May 1, 1987Publication History Published online1 May 2002Published inissue 1 May 1987https://pubs.acs.org/doi/10.1021/ja00244a021https://doi.org/10.1021/ja00244a021research-articleACS PublicationsRequest reuse permissionsArticle Views320Altmetric-Citations50LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Palladium-Catalyzed Reactions on 1,2-Diazines (2006)

In this report, we review the C- and N-functionalization of the pyridazine nucleus via palladium-catalyzed reactions (Suzuki, Stille, Sonogashira, carbonylation, Heck, Buchwald-Hartwig) in which carbon atoms of the pyridazine nucleus are involved. The efficient use of these reactions in synthetic strategies to build up polycyclic 1,2-diazines is also included. Keywords: pyridazine nucleus, Negishi Reaction, Organometallic reagents, Chloropyridazines, brominated bicyclic fused system
A wirelessly controlled implantable LED system for deep brain optogenetic stimulation (2015)

In recent years optogenetics has rapidly become an essential technique in neuroscience. Its temporal and spatial specificity, combined with efficacy in manipulating neuronal activity, are especially useful in studying the behavior of awake behaving animals. Conventional optogenetics, however, requires the use of lasers and optic fibers, which can place considerable restrictions on behavior. Here we combined a wirelessly controlled interface and small implantable light-emitting diode (LED) that allows flexible and precise placement of light source to illuminate any brain area. We tested this wireless LED system in vivo, in transgenic mice expressing channelrhodopsin-2 in striatonigral neurons expressing D1-like dopamine receptors. In all mice tested, we were able to elicit movements reliably. The frequency of twitches induced by high power stimulation is proportional to the frequency of stimulation. At lower power, contraversive turning was observed. Moreover, the implanted LED remains effective over 50 days after surgery, demonstrating the long-term stability of the light source. Our results show that the wireless LED system can be used to manipulate neural activity chronically in behaving mice without impeding natural movements.
g2scaler_brute Data-to-data fitting (2012)

g2scaler_brute is a collection of MATLAB scripts designed to fit one data set to another data set. It is specifically designed to operate on the second order correlation functions data from our Quantum Feedback in Cavity QED experiment. It achieves this by fixing the scale of one data vector (in this case, the left half of the g2), and transforming the vector until they are optimally matched in a least-squares sense to extract phase, frequency and amplitude differences between the sets.
Beyond the Crystal Structure: Insight into the Function and Vaccine Potential of TbpA Expressed by Neisseria gonorrhoeae (2015)

Neisseria gonorrhoeae, the causative agent of the sexually transmitted infection gonorrhea, is not preventable by vaccination and is rapidly developing resistance to antibiotics. However, the transferrin (Tf) receptor system, composed of TbpA and TbpB, is an ideal target for novel therapeutics and vaccine development. Using a three-dimensional structure of gonococcal TbpA, we investigated two hypotheses, i.e., that loop-derived antibodies can interrupt ligand-receptor interactions in the native bacterium and that the loop 3 helix is a critical functional domain. Preliminary loop-derived antibodies, as well as optimized second-generation antibodies, demonstrated similar modest ligand-blocking effects on the gonococcal surface but different effects in Escherichia coli. Mutagenesis of loop 3 helix residues was employed, generating 11 mutants. We separately analyzed the mutants' abilities to (i) bind Tf and (ii) internalize Tf-bound iron in the absence of the coreceptor TbpB. Single residue mutations resulted in up to 60% reductions in ligand binding and up to 85% reductions in iron utilization. All strains were capable of growing on Tf as the sole iron source. Interestingly, in the presence of TbpB, only a 30% reduction in Tf-iron utilization was observed, indicating that the coreceptor can compensate for TbpA impairment. Complete deletion of the loop 3 helix of TbpA eliminated the abilities to bind Tf, internalize iron, and grow with Tf as the sole iron source. Our studies demonstrate that while the loop 3 helix is a key functional domain, its function does not exclusively rely on any single residue.
Modulation of Voltage-Gated Calcium Channels by Orphanin FQ in Freshly Dissociated Hippocampal Neurons (1996)

Orphanin FQ (OFQ) has recently been reported to be an endogenous ligand for the opioid-like LC132 receptor. The effect of OFQ on high voltage-gated calcium channels (VGCCs) was examined in freshly dissociated rat pyramidal neurons using the whole-cell configuration of the patch-clamp technique. High-threshold Ba2+ currents were reversibly inhibited by OFQ. The depression of the currents was associated with a slowed rate of activation and a change in the activation I-V relationship at step potentials higher than +30 mV. In concentration-response experiments, a mean (+/-SEM) pEC50 value of 7.0 +/- 0.07 and a Hill coefficient of 1.5 +/- 0.08 (n = 5) were obtained. The near-maximum inhibition of the Ba2+ currents by OFQ (1 microM) amounted to 31 +/- 2.2% of control (n = 15). Opioid receptors could not account for the effects of OFQ on VGCCs, because naloxone, a broad spectrum mu-, delta-, and kappa-receptor antagonist, did not reduce the effectiveness of OFQ. When GTP-gamma-S was included in the pipette, the depression of the currents by OFQ was irreversible, whereas currents from neurons preincubated with pertussis toxin were not inhibited by OFQ, consistent with the involvement of a PTX-sensitive G-protein. When selective blockers of VGCCs were used, it was demonstrated that all subtypes of VGCCs were affected by OFQ. In conclusion, the effect of OFQ on VGCCs expressed in hippocampal CA3 and CA1 neurons may play an important role in the regulation of hippocampal cell excitability and neurotransmitter release.
Fast Sparse Gaussian Process Classication With Multiple Classes (2004)

The favourable scaling behaviour of sparse approximations to Bayesian inference for Gaussian Process models makes them attractive for large-scale applications. We show how to generalize the Informative Vector Machine (IVM) [3] to a multi-way classication setting. While being a kernel-based approach, our method yields valid uncertainty estimates and allows for hyperparameter adaption via optimization. Our scheme operates jointly on the data for all classes. Crucially, we still achieve a linear scaling in both the number of classes and the number of training points.
Pharmacologic Differentiation of Inflammation and Fibrosis in the Rat Bleomycin Model (2006)

The response of the BLM model to antifibrotic or antiinflammatory interventions is critically dependent on timing after the initial injury.
Synthesis and Characterization of Al(OH)3/Polystyrene Nanocomposite Latex Particles by Emulsion Polymerization (2007)

Abstract The inorganic/organic core‐shell type nanocomposite particles of Al(OH) 3 /PSt were synthesized through the emulsion polymerization of styrene (St, shell monomer) with ammonium persulfate (APS, initiator), polyoxyethylene (50) nonyl phenyl ether (NP‐1050, nonionic surfactant), and ammonium (POE) alkyl arylether sulfate (EU‐S133D, anionic surfactant) in the presence of the modified Al(OH) 3 particles. The improved compatibility of Al(OH) 3 surface with St achieved by the modification with 3‐(trimethoxysilyl) propyl methacrylate ( γ ‐MPS) enabled to form a polymer shell around the mineral particles. The structure of nanocomposites prepared from different feed ratio of Al(OH) 3 /St was investigated by scanning (SEM) and transmission (TEM) electron microscopies.
An FBG Strain Sensor-Based NPW Method for Natural Gas Pipeline Leakage Detection (2021)

Natural gas pipeline leaks can lead to serious and dangerous accidents that can cause great losses of life and property. Therefore, detecting natural gas pipeline leaks has always been an important subject. The negative pressure wave (NPW) method is currently the most widely used leakage detection method. Generally, this method uses pressure sensors to detect NPW signals to assess the leak and determine the location of the leakage point. However, the installation of a pressure sensor requires penetrating the pipeline structure, so the sensor intervals are often distant, leading to large signal attenuations and the ineffective detection of small leaks. An NPW method based on fiber Bragg grating (FBG) strain sensors is proposed in this paper which detects NPWs by monitoring the annular strain of the pipeline. Moreover, due to the advantages of nondestructive installation FBG strain sensors can be arranged closer along the distance of the pipeline, the attenuation of the NPW is small and the detection of leaks is improved. This method is tested through experiments and compared with a pressure sensor-based method; the experimental results verify that the proposed method is more effective in detecting natural gas pipeline leaks.
Scheduling Policies for Automatic Warehousing Systems: Simulation Results (1978)

Abstract This paper examines and extends previous analytical work on the scheduling of stacker cranes in automatic warehousing systems. In particular, the following are examined by means of a computer simulation: (1) The performance of the closest-open-location rule compared to random storage assignment; (2) The dynamic behavior of the system under stochastic conditions, using various crane and rack utilization levels; (3) The actual versus predicted reduction in crane travel time due to improved scheduling rules; (4) The effect of imperfect information concerning the length of stay of an incoming pallet on system performance. The results of our experiments provide evidence in support of the proposed analytical models. Most important, the experiments demonstrate the value of previously-proposed scheduling rules in a dynamic, stochastic environment operating with imperfect information.
Predicting erlotinib resistance in EGFR wild type NSCLC patients. (2013)

e22065 Background: Cancer patients with wild type EGFR respond to treatment with erlotinib at a lower rate than patients with EGFR mutations. It would be relevant to predict which EGFR wild type patients benefit from erlotinib. We have developed a response predictor based on NCI60 cancer cell lines measurements of erlotinib effect and gene expression measurements. Clinical relevance was improved by filtering the model through expression profiles from more than 3,000 clinical samples.The erlotinib response predictor consists of 94 sensitivity genes and 10 resistance genes and is completely defined before independent validation on patients treated with erlotinib. Methods: Gene expression data from pre-treatment core biopsies from 25 patients with refractory NSCLC (clinicaltrials.gov: NCT00409968) later treated with erlotinib (The BATTLE trial; Kim, ES et al. Cancer Discov. 2011; 1:44-53) were downloaded from Gene Expression Omnibus with accession number GSE33072. PFS after erlotinib treatment was recorded. The erlotinib response predictor was applied retrospectively to the gene expression measurements.Patients with a predicted sensitivity above the 0.15 quantile were categorized as sensitive, patients with a predicted sensitivity below were categorized as resistant.The median was also tested as a cutoff, and correction for multiple testing was taken into consideration. Results: In a Kaplan-Meier analysis of PFS comparing predicted sensitive and predicted resistant patients, the predicted sensitive patients survived longer (PFS 2.3 months (1.9-2.7)) than predicted resistant patients (PFS 1.2 months (0.5-1.8)). A log-rank test for PFS found the difference significant (p=0.005). Hazard ratio 4.6 (1.4-15.2). Conclusions: The small clinical data set validated the cell line derived erlotinib response predictor. It identified a subset of 16% of patients with no apparent benefit from erlotinib. We have performed similar validations for 24 other response predictors in 24 clinical trials. In 20 out of the 24 clinical trials, the agreement between prediction and clinical outcome was statistically significant. Thus, our cell line based method represents a general method for predicting clinical response to cytotoxic or cytostatic agents.
The Most General Planar Transformations that Map Hyperbolas to Hyperbolas (2009)

Abstract. The space of vertical and horizontal right hyperbolas and the lines tangent to these hyperbolas is considered in the double plane. It is proved that an injective map from the middle region of a considered hyperbola that takes hyperbolas and lines in this space to other hyperbolas and lines in this space must be a direct or indirect linear fractional transformation. 1.
Respiratory effort monitoring system for sleep apnea screening for both supine and lateral recumbent positions (2017)

Sleep disorders are a major health problem affecting more than 50 million people in the US alone. Sleep Apnea (SA) is by far the most common of these disorders, causing excessive sleepiness and diminished cognitive functions. Monitoring the respiratory effort is essential for SA detection. Conventional methods are limited to measuring only respiratory effort, and methods based on Inertial Measuring Units have been constrained to supine or standing/sitting positions. In this work, we propose a solution to such limitations, allowing the IMU to detect the respiratory effort on both supine and lateral recumbent positions, based on a sensor fusion algorithm. In addition, the body position is also obtained from the IMU data. Using the Pearson Cross-correlation Coefficient as a success metric, our results show correlation values ranging from 0.8550 to 0.9413 for various tests.
The effect on the electrocatalytic activity of the chemical interaction of selenium with palladium centers: oxygen reduction and methanol oxidation reactions in alkaline medium (2021)

The chemical reactivity of two different selenium precursors (SeO<sub>2</sub>and Se) with nanoparticulated palladium was studied in a simple aqueous phase synthesis to generate palladium selenides (Pd<sub><i>x</i></sub>Se<sub><i>y</i></sub>). As confirmed by XRD, XPS, TEM and energy dispersive spectroscopy analyses, the products generated showed different degrees of selenization according to the nature of the chemical precursor. Such degree of selenization was more important with elemental selenium, in contrast to SeO<sub>2</sub>. Surface electrochemistry and CO stripping in alkaline medium, clearly revealed the different interactions and stability of Pd<sub><i>x</i></sub>Se<sub><i>y</i></sub>achieved with the Pd/C precursor depending on the selenium source. The electrocatalysis of the oxygen reduction reaction was also influenced by the Se source, first in the different degree of reactivity, and second in the selectivity of the reduction product between H<sub>2</sub>O and H<sub>2</sub>O<sub>2</sub>, as well as the tolerance to the methanol oxidation reaction.
Prospect for Developing a Consolidated Bioprocessing (CBP) Strain Using Xylan as the Substrate: the Case Study of Yarrowia lipolytica (2016)

To achieve the goal of developing a direct microbial sugar conversion platform for the production of lipids and drop-in fuels from cellulosic biomass substrate, Yarrowia lipolytica was used to investigate its potential for being developed as CBP strain by expressing cellulase and xylanase enzymes. Y. lipolytica is known to accumulate lipids intracellularly and is capable of metabolizing glucose and xylose to produce lipids; however, due to the lack of the biomass degrading enzymes, it cannot directly utilize lignocellulosic substrates as carbon sources. While research is continuing on the development of a Y. lipolytica strain able to degrade cellulose, in this study, we present successful expression of several xylanases in Y. lipolytica. To the best of our knowledge, this is the first study introducing heterologous hemicellulose genes into the genome of Y. lipolytica. SDS-PAGE and western blotting analysis showed that the endo-xylanase gene XynII and exo-xylosidase gene XlnD were successfully expressed and secreted, and the expressed xylanases were likely either not or sparsely glycosylated, which is advantageous for expression of heterologous proteins from any species. Enzymatic activity tests further demonstrated active expression of XynII and XlnD in Y. lipolytica. Furthermore, synergistic action on converting xylan to xylose was observed when XlnD worked in concert with XynII. XlnD was able to work on the xylo-oligomers generated by XynII, enhancing the xylan conversion to monomeric xylose. The successful expression of these xylanases in Yarrowia further advances us towards our goal to develop a direct microbial conversion process using this organism. and xylose to produce lipids; however, due to the lack of the biomass degrading enzymes, it cannot directly utilize lignocellulosic substrates as carbon sources. While research is continuing on the development of a Y. lipolytica strain able to degrade cellulose, in this study, we present successful expression of several xylanases in Y. lipolytica.