gebhart/patrepeval huggingface dataset:
Simulation studies of low-emittance muon re-acceleration fo r muon microscopy application (2013)

While conventional muon beam can be used to investigate rather small samples, there is a strong requirement for still lower energy ultra-slow muons that can be stopped near sample surfaces, in thin films and near multi-layer interfaces. A number of muon cooling techniques have been suggested to produce ultra-slow muons, such as twophoton laser resonant ionization of muonium atoms and energy moderation of muons in a thin foil-degrader. In this work, in close collaboration with the Muon Science Establishment (MUSE) at Material and Life science experimental Facility (MLF) of the Japan Proton Accelerator Research Complex (J-PARC), we provide a brief overview of the primary muon production target, where two of the four associated secondary beam transport lines which are dedicated to experiments employing the ultra-slow muons. In particular, we present the simulation results of the ultraslow muon production with tunable energies in the range of energies between 5.65 and 30 keV based on the simple energy moderation of transported muon beam in thin foil-degrader. In addition, we discuss accelerator optics design and beam acceleration simulation results provide a microbeam for muon microscopy.
Performane Modeling of Flash Memory Storage Systems Using Simulink (2011)

The complexity of flash memory based storage systems is high due to diverse host interfaces and other design choices such as mapping granularity, flash memory controller execution models and so on. Thus, it is possible that the actual performance after implementation is not consistent with the target performance. This paper demonstrates that the performance prediction of flash memory based storage systems is possible through performance modeling that takes into account various design parameters. In the performance modeling, the FTL, which is the core element of flash memory based storage systems, is modeled as a set of (copy-on-write) logs and their interactions. Also, the flash memory controller is modeled based on the classification proposed in the design of the Ozone flash controller. In this study, the performance model has been implemented using Simulink and experimental results are presented and analyzed.
Investigating the Neural Basis of the Auditory Continuity Illusion (2005)

In this study, we investigated one type of auditory perceptual grouping phenomena--the auditory continuity illusion (also called temporal induction). We employed a previously developed, neurobiologically realistic, large-scale neural network model of the auditory processing pathway in the cortex, ranging from the primary auditory cortex to the prefrontal cortex, and simulated temporal induction without changing any model parameters. The model processes tonal contour stimuli, composed of combinations of upward and downward FM sweeps and tones, in a delayed match-to-sample task. The local electrical activities of the neuronal units of the model simulated accurately the experimentally observed electrophysiological data, where available, and the model's simulated BOLD-fMRI data were quantitatively matched with experimental fMRI data. In the present simulations, intact stimuli were matched with fragmented versions (i.e., with inserted silent gaps). The ability of the model to match fragmented stimuli declined as the duration of the gaps increased. However, when simulated broadband noise was inserted into these gaps, the matching response was restored, indicating that a continuous stimulus was perceived. The electrical activities of the neuronal units of the model agreed with electrophysiological data, and the behavioral activity of the model matched human behavioral data. In the model, the predominant mechanism implementing temporal induction is the divergence of the feedforward connections along the auditory processing pathway in the temporal cortex. These simulation results not only attest to the robustness of the model, but further predict the primary role of the anatomical connectivity of the auditory processing areas in mediating the continuity illusion.
A computational method for resequencing long DNA targets by universal oligonucleotide arrays (2002)

Universal arrays contain all possible oligonucleotides of a certain length, typically 6-10 bases. They can determine in a single experiment all substrings of that length that occur along a target sequence. That information, also called the spectrum of the sequence, is not sufficient to uniquely reconstruct a sequence longer than a few hundred bases. We have devised a polynomial algorithm that reconstructs the sequence, given the spectrum and an additional reference sequence, homologous to the target sequence. Such a reference is available, for example, in the identification of single-nucleotide polymorphisms. The algorithm can handle errors in the spectrum as well as substitutions, insertions, and deletions in the target sequence. We present extensive simulation results, which show that the algorithm correctly reconstructs target sequences of >2,000 nucleotides from error-prone 8-mer spectra when realistic levels of single-nucleotide polymorphisms are present.
Pharmacological characterization of the chronic phase of the monoiodoacetate‐induced rat model of osteoarthritis pain in the knee joint (2021)

For patients with osteoarthritis (OA) of the knee, pain is the most debilitating symptom. Although it has been proposed that the chronic phase of the monoiodoacetate (MIA)-induced rodent model of knee joint pain may be superior to other chronic or acute OA models for assessing the analgesic efficacy of novel molecules, relatively few pharmacological studies have been conducted in the chronic phase of this model. Hence, this study was designed to use pharmacological methods to characterize the chronic phase of the MIA-induced rat model of knee joint OA pain. Rats received a single intraarticular injection of MIA at 2.5 mg or vehicle (saline) into the left (ipsilateral) knee joint. Pain behaviour was assessed by measuring paw withdrawal thresholds (PWTs) in the hindpaws pre-MIA injection and twice-weekly until study completion on day 42. Mechanical allodynia was fully developed in the ipsilateral hindpaws (PWTs ≤6 g) from day 7 and it persisted until day 42. MIA-injected rats with PWTs ≤6 g in the ipsilateral hindpaws received single doses of one of four clinically available drugs that represent four distinct pharmacological classes, viz gabapentin, amitriptyline, meloxicam and morphine, according to a 'washout' protocol with at least 48 hours between successive doses. Gabapentin evoked dose-dependent anti-allodynia as did morphine whereas amitriptyline and meloxicam were inactive. Our findings are aligned with clinical data showing that gabapentin and morphine alleviated OA pain in the knee. The lack of efficacy of amitriptyline is consistent with the loss of descending diffuse noxious inhibitory controls reported by others in this model.
Obesity and Hypertriglyceridemia Produce Cognitive Impairment (2008)

Obesity is associated with cognitive impairments. Long-term mechanisms for this association include consequences of hyperglycemia, dyslipidemia, or other factors comprising metabolic syndrome X. We found that hypertriglyceridemia, the main dyslipidemia of metabolic syndrome X, is in part responsible for the leptin resistance seen in obesity. Here we determined whether triglycerides have an immediate and direct effect on cognition. Obese mice showed impaired acquisition in three different cognitive paradigms: the active avoidance T-maze, the Morris water maze, and a food reward lever press. These impairments were not attributable to differences in foot shock sensitivity, swim speed, swimming distance, or voluntary milk consumption. Impaired cognition in obese mice was improved by selectively lowering triglycerides with gemfibrozil. Injection into the brain of the triglyceride triolein, but not of the free fatty acid palmitate, impaired acquisition in normal body weight mice. Triolein or milk (97% of fats are triglycerides), but not skim milk (no triglycerides), impaired maintenance of the N-methyl-d-aspartate component of the hippocampal long-term synaptic potential. Measures of oxidative stress in whole brain were reduced by gemfibrozil. We conclude that triglycerides mediate cognitive impairment as seen in obesity, possibly by impairing maintenance of the N-methyl-d-aspartate component of hippocampal long-term potentiation, and that lowering triglycerides can reverse the cognitive impairment and improve oxidative stress in the brain.
Tailings beach slope prediction: a new rheological method (2006)

A new semi-empirical model for tailings beach slope prediction is presented. The model is based on existing non-Newtonian rheology theory combined with some well-established turbulent channel flow equations. It is shown that solid particles do not deposit from the self-formed channels of the tailings slurry as it flows down the beach, and that the slope of the beach is dictated by the channel slope, which is set by the flow parameters and the rheological parameters of the slurry. Two experimental programmes have taken place at tailings storage facilities in Australia, with the experimental results providing validation for the model.
The Effects of Ractopamine on Behavior and Physiology of Finishing Pigs (2002)

The feed additive ractopamine, a beta-adrenergic agonist, acts as a repartitioning agent, promoting lean tissue deposition in market-weight pigs (Watkins et al., 1990; Crome et al., 1996). It has been the focus of widespread research over the last 20 years and has been shown to give substantial improvements in average daily gain, feed conversion efficiency, dressing percent and carcass lean content (Watkins et al., 1990; Gu et al., 1991a,b; Uttaro et al., 1993; Crome et al., 1996). Its usage may also confer environmental benefits such as reduced manure volume, decreased ammonia and volatile fatty acids emissions from slurry (Sutton et al., 2001). It was formally approved for use in swine in the US in 1999, and subsequently, a number of other countries.
Physiological and genetic aspects of a diploid potato population in the Netherlands and Northern Finland (2006)

Tuberization of potatoes exposed to different photoperiod regimes has been earlier investigated in several studies. However, there is still a limited understanding of the entire tuberization process and the factors influencing this process. One of the constraints of the previous studies has been the use of only one or a few genotypes. Furthermore, the experimental designs have not utilised the natural growing conditions with continuous changes in daylength during the growing season. The general aim of the project was to study the developmental dynamics of the broad-based potato (Solanum tuberosum L.) (CxE) population development at different climatical regimes under the very long-day, long-day and short conditions in Finland, the Netherlands and Ecuador/Venezuela, respectively. In this paper we are presenting some of the results achieved in the studies in Finland during the growing season 2004. In addition to population level trait characteristics we also describe here some of the identified QTLs (quantitative trait loci) for stolon related and tuber formation traits. In some cases we also compare the expression of some of the traits both in Finland and Netherlands.The main difference between the CxE population grown in Finland and the Netherlands was that the onset of flowering took place one week later in Finland. The relationship between tuber initiation and onset of flowering differed depending on the day length. In Finland approximately 70 % of the genotypes had swollen stolon tips before the onset of flowering, while in the Netherlands only 30 % of the genotypes had reached this condition. We also found numerous different trait linked QTLs, for example, a QTL associated with tuber formation was identified on chromosome E5, and QTLs associated with stolon characteristics on chromosomes E1, E4, E10 and E12. As a conclusion, the present preliminary results provide a good basis for determining the influence of different environmental conditions on potato development. In addition, the QTLs obtained in this study give a better understanding of the genetics of complex characters, and can be used in improving the potato crop in breeding programs.
Translational advances and novel therapies for pancreatic ductal adenocarcinoma: hope or hype? (2009)

Biological complexity, inaccessible anatomical location, nonspecific symptoms, lack of a screening biomarker, advanced disease at presentation and drug resistance epitomise pancreatic ductal adenocarcinoma (PDA) as a poor-prognosis, lethal disease. Twenty-five years of research (basic, translational and clinical) have barely made strides to improve survival, mainly because of a fundamental lack of knowledge of the biological processes initiating and propagating PDA. However, isolation of pancreas cancer stem cells or progenitors, whole-genome sequencing for driver mutations, advances in functional imaging, mechanistic dissection of the desmoplastic reaction and novel targeted therapies are likely to shed light on how best to treat PDA. Here we summarise current knowledge and areas where the field is advancing, and give our opinion on the research direction the field should be focusing on to better deliver promising therapies for our patients.
Synthetic generation of social network data with endorsements (2014)

In many simulation studies involving networks there is the need to rely on a sample network to perform the simulation experiments. In many cases, real network data is not available due to privacy concerns. In that case we can recourse to synthetic data sets with similar properties to the real data. In this paper we discuss the problem of generating synthetic data sets for a certain kind of online social network, for simulation purposes. Some popular online social networks, such as LinkedIn and ResearchGate, allow user endorsements for specific skills. For each particular skill, the endorsements give rise to a directed subgraph of the corresponding network, where the nodes correspond to network members or users, and the arcs represent endorsement relations. Modelling these endorsement digraphs can be done by formulating an optimization problem, which is amenable to different heuristics. Our construction method consists of two stages: The first one simulates the growth of the network, and the second one solves the aforementioned optimization problem to construct the endorsements.
Functional analysis of keratinocytes in skin color using a human skin substitute model composed of cells derived from different skin pigmentation types (2007)

Skin color is one of the most distinct features in the human race. To assess the mechanisms of skin color variation, human skin substitutes (HSS) were constructed by grafting mixtures of cultured keratinocytes and melanocytes from a combination of donor skin types, together with light skin derived fibroblasts, into chambers inserted onto the back skin of severe combined immunodeficient (SCID) mice. The resulting complexion coloration of the HSS was relatively darker and lighter when dark and light skin derived keratinocytes, respectively, were combined with melanocytes derived from either light or dark skin. The melanin content in the epidermis and the maturation stage of melanosomes in basal keratinocytes were significantly increased in the HSS composed of dark compared to light skin derived keratinocytes. In addition, the ratio of individual/clustered melanosomes in recipient keratinocytes was increased in the former as opposed to the latter HSS. The genetic expression of endothelin-1, proopiomelanocortin, microphthalmia-associated transcription factor, tyrosinase, GP100, and MART1 were increased in HSS composed of dark vs. light skin derived keratinocytes. These data suggest that our HSS is a promising melanogenic model that demonstrates the role of the keratinocyte in regulating in part both melanogenesis and distribution of transferred melanosomes.
Primary Renal Plasmacytoma (2007)

Extramedullary plasmacytoma is a rare malignancy, composed of plasma cell dyscrasias localized to an extramedullary site in the soft tissue. The great majority of extramedullary plasmacytoma occurs in the head and neck region, mainly in the upper respiratory tract and oral cavity. Extramedullary plasmacytoma arising in the kidney, termed a primary renal plasmacytoma, is a very rare malignancy. Primary renal plasmacytoma is not distinguished from a renal cell or transitional cell carcinoma using conventional imaging studies. The diagnosis of a primary renal plasmacytoma is only made on histopathological examination. Herein, a case of primary renal plasmacytoma, in a 39-year-old male patient, is reported. (Korean J Urol 2007;48:878-880) 󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏
Impact of 68Ga-PSMA PET/CT on salvage radiotherapy planning in patients with prostate cancer and persisting PSA values or biochemical relapse after prostatectomy (2016)

<sup>68</sup>Ga-PSMA PET/CT impacts treatment planning in more than 40 % of patients scheduled to undergo SRT. Future prospective studies are needed to confirm this significant therapeutic impact on patients prior to SRT.
Functional Evidence That the 3‘-5‘ Exonuclease Domain of Escherichia coli DNA Polymerase I Employs a Divalent Metal Ion in Leaving Group Stabilization (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTFunctional Evidence That the 3'-5' Exonuclease Domain of Escherichia coli DNA Polymerase I Employs a Divalent Metal Ion in Leaving Group StabilizationJessica F. Curley, Catherine M. Joyce, and Joseph A. PiccirilliView Author Information Departments of Biochemistry and Molecular Biology and Chemistry, Howard Hughes Medical Institute University of Chicago, Chicago, Illinois 60637 Department of Molecular Biophysics and Biochemistry Yale University, New Haven, Connecticut 06520 Cite this: J. Am. Chem. Soc. 1997, 119, 51, 12691–12692Publication Date (Web):December 24, 1997Publication History Received18 June 1997Published online24 December 1997Published inissue 1 December 1997https://pubs.acs.org/doi/10.1021/ja972014jhttps://doi.org/10.1021/ja972014jrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views158Altmetric-Citations31LEARN 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 SUBJECTS:Chemical specificity,Ions,Metals,Peptides and proteins,Transition metals Get e-Alerts
Rapid training of image classifiers through adaptive, multi-frame sampling method (2008)

Computer vision methods, such as automatic target recognition (ATR) techniques, have the potential to improve the accuracy of military systems for weapon deployment and targeting, resulting in greater utility and reduced collateral damage. A major challenge, however, is training the ATR algorithm to the specific environment and mission. Because of the wide range of operating conditions encountered in practice, advanced training based on a pre-selected training set may not provide the robust performance needed. Training on a mission-specific image set is a promising approach, but requires rapid selection of a small, but highly representative training set to support time-critical operations. To remedy these problems and make short-notice seeker missions a reality, we developed learning and mining using bagged augmented decision trees (LAMBAST). LAMBAST examines large databases and extracts sparse, representative subsets of target and clutter samples of interest. For data mining, LAMBAST uses a variant of decision trees, called random decision trees (RDTs). This approach guards against overfitting and can incorporate novel, mission-specific data after initial training via perpetual learning. We augment these trees with a distribution modeling component that eliminates redundant information, ignores misrepresentative class distributions in the database, and stops training when decision boundaries are sufficiently sampled. These augmented random decision trees enable fast investigation of multiple images to train a reliable, mission-specific ATR. This paper presents the augmented random decision tree framework, develops the sampling procedure for efficient construction of the sample, and illustrates the procedure using relevant examples.
A new method to support UMTS/WLAN vertical handover using SCTP (2004)

This article proposes a new method to facilitate seamless vertical handover between wide area cellular data networks such as UMTS and WLANs using the stream control transmission protocol (SCTP). The multihoming capability and dynamic address configuration extension of SCTP are applied in UMTS/WLAN overlay architecture to decrease handover delay and improve throughput performance. Unlike techniques based on mobile IP or session initiation protocol, the SCTP-based vertical handover scheme does not require the addition of components such as home/foreign agents or a SIP server to existing networks. Therefore, the proposed scheme provides a network-independent solution preferred by service providers. Performance evaluations are presented to demonstrate the effectiveness of the proposed scheme.
Intravitreal Bevacizumab for the Treatment of Neovascular Glaucoma Associated With Central Retinal Artery Occlusion (2009)

We report three cases of neovascular glaucoma secondary to central retinal artery occlusion (CRAO) which were effectively managed with intravitreal bevacizumab (IVB) followed by panretinal photocoagulation (PRP). Neovascular glaucoma without peripheral anterior synechiae developed between one and five weeks following CRAO onset. All patients received 0.75 mg (0.03 ml) IVB. In all patients, complete regression of the iris and anterior chamber angle neovascularization was confirmed within one week. PRP was applied two weeks after the injection. The follow-up period was four to seven months (average, five months). Intraocular pressure was controlled in all patients using topical antiglaucoma medications alone. However, one patient experienced a recurrence of neovascularization three months after the initial combination treatment. This patient received another IVB injection and additional PRP, and the recurrent neovascularization resolved. There were no local or systemic adverse events in any patients. Therefore, intravitreal bevacizumab may be an effective adjunct in the treatment of neovascular glaucoma associated with CRAO.