STAMPS: Software Tool for Automated MRI Post-processing on a supercomputer.

PubMed

Bigler, Don C; Aksu, Yaman; Miller, David J; Yang, Qing X

2009-08-01

This paper describes a Software Tool for Automated MRI Post-processing (STAMP) of multiple types of brain MRIs on a workstation and for parallel processing on a supercomputer (STAMPS). This software tool enables the automation of nonlinear registration for a large image set and for multiple MR image types. The tool uses standard brain MRI post-processing tools (such as SPM, FSL, and HAMMER) for multiple MR image types in a pipeline fashion. It also contains novel MRI post-processing features. The STAMP image outputs can be used to perform brain analysis using Statistical Parametric Mapping (SPM) or single-/multi-image modality brain analysis using Support Vector Machines (SVMs). Since STAMPS is PBS-based, the supercomputer may be a multi-node computer cluster or one of the latest multi-core computers.

Laser-assisted cataract surgery: benefits and barriers.

PubMed

Hatch, Kathryn M; Talamo, Jonathan H

2014-01-01

The use of the femtosecond laser (FSL) in cataract surgery may represent the largest advancement in the field since the inception of phacoemulsification. The goal of this review is to outline the benefits of and barriers to this technology. There are several significant potential benefits of the FSL in cataract surgery over conventional manual cataract surgery: precise capsulotomy formation, clear corneal and limbal relaxing incision construction, lens fragmentation, and lens softening. Evidence suggests that refractive benefits include more precise effective lens position as well as reduced effective phacoemulsification time with the use of FSL compared with manual surgery. Patients with conditions such as Fuchs' endothelial dystrophy, pseudoexfoliation, history of trauma, or brunescent cataracts may particularly benefit from this technology. There are significant financial and logistical issues to consider prior to the purchase of a FSL, including the cost of the laser, and charges to patients, and how the laser affects the patient flow in the operating room. The FSL may significantly change the current approach to cataract surgery.

Accurate GM atrophy quantification in MS using lesion-filling with co-registered 2D lesion masks☆

PubMed Central

Popescu, V.; Ran, N.C.G.; Barkhof, F.; Chard, D.T.; Wheeler-Kingshott, C.A.; Vrenken, H.

2014-01-01

Background In multiple sclerosis (MS), brain atrophy quantification is affected by white matter lesions. LEAP and FSL-lesion_filling, replace lesion voxels with white matter intensities; however, they require precise lesion identification on 3DT1-images. Aim To determine whether 2DT2 lesion masks co-registered to 3DT1 images, yield grey and white matter volumes comparable to precise lesion masks. Methods 2DT2 lesion masks were linearly co-registered to 20 3DT1-images of MS patients, with nearest-neighbor (NNI), and tri-linear interpolation. As gold-standard, lesion masks were manually outlined on 3DT1-images. LEAP and FSL-lesion_filling were applied with each lesion mask. Grey (GM) and white matter (WM) volumes were quantified with FSL-FAST, and deep gray matter (DGM) volumes using FSL-FIRST. Volumes were compared between lesion mask types using paired Wilcoxon tests. Results Lesion-filling with gold-standard lesion masks compared to native images reduced GM overestimation by 1.93 mL (p < .001) for LEAP, and 1.21 mL (p = .002) for FSL-lesion_filling. Similar effects were achieved with NNI lesion masks from 2DT2. Global WM underestimation was not significantly influenced. GM and WM volumes from NNI, did not differ significantly from gold-standard. GM segmentation differed between lesion masks in the lesion area, and also elsewhere. Using the gold-standard, FSL-FAST quantified as GM on average 0.4% of the lesion area with LEAP and 24.5% with FSL-lesion_filling. Lesion-filling did not influence DGM volumes from FSL-FIRST. Discussion These results demonstrate that for global GM volumetry, precise lesion masks on 3DT1 images can be replaced by co-registered 2DT2 lesion masks. This makes lesion-filling a feasible method for GM atrophy measurements in MS. PMID:24567908

Root Zone Microbial Communities and Restoration of Plant Communities in Owens Valley, California - Phase 1

DTIC Science & Technology

2007-09-01

Distichlis spicata (saltgrass), Glycyrrhiza lepidota (wild licorice), Jun- cus balticus (Baltic rush), Sida leprosa (alkali mallow), and Sporobolus...E 4138005 N N under vegetation Glycyrrhiza lepidota licorice FSL201 N-3 367579 E 4138377 N N under shrub Atriplex canescens fourwing...Big sagebrush) Dryland nonalkaline scrub FSL201 N2 Qa Glycyrrhiza lepidota (Wild licorice) High-ground-water alkaline meadow FSL201 N3 Qa

Bayesian automated cortical segmentation for neonatal MRI

NASA Astrophysics Data System (ADS)

Chou, Zane; Paquette, Natacha; Ganesh, Bhavana; Wang, Yalin; Ceschin, Rafael; Nelson, Marvin D.; Macyszyn, Luke; Gaonkar, Bilwaj; Panigrahy, Ashok; Lepore, Natasha

2017-11-01

Several attempts have been made in the past few years to develop and implement an automated segmentation of neonatal brain structural MRI. However, accurate automated MRI segmentation remains challenging in this population because of the low signal-to-noise ratio, large partial volume effects and inter-individual anatomical variability of the neonatal brain. In this paper, we propose a learning method for segmenting the whole brain cortical grey matter on neonatal T2-weighted images. We trained our algorithm using a neonatal dataset composed of 3 fullterm and 4 preterm infants scanned at term equivalent age. Our segmentation pipeline combines the FAST algorithm from the FSL library software and a Bayesian segmentation approach to create a threshold matrix that minimizes the error of mislabeling brain tissue types. Our method shows promising results with our pilot training set. In both preterm and full-term neonates, automated Bayesian segmentation generates a smoother and more consistent parcellation compared to FAST, while successfully removing the subcortical structure and cleaning the edges of the cortical grey matter. This method show promising refinement of the FAST segmentation by considerably reducing manual input and editing required from the user, and further improving reliability and processing time of neonatal MR images. Further improvement will include a larger dataset of training images acquired from different manufacturers.

Software Library: A Reusable Software Issue.

DTIC Science & Technology

1984-06-01

On reverse aide it neceeary aid Identify by block number) Software Library; Program Library; Reusability; Generator 20 ABSTRACT (Cmlnue on revere... Software Library. A particular example of the Software Library, the Program Library, is described as a prototype of a reusable library. A hierarchical... programming libraries are described. Finally, non code products in the Software Library are discussed. Accesson Fo NTIS R~jS DrrC TA Availability Codes 0

NLS Flight Simulation Laboratory (FSL) documentation

NASA Technical Reports Server (NTRS)

1995-01-01

The Flight Simulation Laboratory (FSL) Electronic Documentation System design consists of modification and utilization of the MSFC Integrated Engineering System (IES), translation of the existing FSL documentation to an electronic format, and generation of new drawings to represent the Engine Flight Simulation Laboratory design and implementation. The intent of the electronic documentation is to provide ease of access, local print/plot capabilities, as well as the ability to correct and/or modify the stored data by network users who are authorized to access this information.

Elevation of Il6 is associated with disturbed let-7 biogenesis in a genetic model of depression

PubMed Central

Wei, Y B; Liu, J J; Villaescusa, J C; Åberg, E; Brené, S; Wegener, G; Mathé, A A; Lavebratt, C

2016-01-01

Elevation of the proinflammatory cytokine IL-6 has been implicated in depression; however, the mechanisms remain elusive. MicroRNAs (miRNAs) are small non-coding RNAs that inhibit gene expression post-transcriptionally. The lethal-7 (let-7) miRNA family was suggested to be involved in the inflammation process and IL-6 was shown to be one of its targets. In the present study, we report elevation of Il6 in the prefrontal cortex (PFC) of a genetic rat model of depression, the Flinders Sensitive Line (FSL) compared to the control Flinders Resistant Line. This elevation was associated with an overexpression of LIN28B and downregulation of let-7 miRNAs, the former an RNA-binding protein that selectively represses let-7 synthesis. Also DROSHA, a key enzyme in miRNA biogenesis was downregulated in FSL. Running was previously shown to have an antidepressant-like effect in the FSL rat. We found that running reduced Il6 levels and selectively increased let-7i and miR-98 expression in the PFC of FSL, although there were no differences in LIN28B and DROSHA expression. Pri-let-7i was upregulated in the running FSL group, which associated with increased histone H4 acetylation. In conclusion, the disturbance of let-7 family biogenesis may underlie increased proinflammatory markers in the depressed FSL rats while physical activity could reduce their expression, possibly through regulating primary miRNA expression via epigenetic mechanisms. PMID:27529677

Elevation of Il6 is associated with disturbed let-7 biogenesis in a genetic model of depression.

PubMed

Wei, Y B; Liu, J J; Villaescusa, J C; Åberg, E; Brené, S; Wegener, G; Mathé, A A; Lavebratt, C

2016-08-16

Elevation of the proinflammatory cytokine IL-6 has been implicated in depression; however, the mechanisms remain elusive. MicroRNAs (miRNAs) are small non-coding RNAs that inhibit gene expression post-transcriptionally. The lethal-7 (let-7) miRNA family was suggested to be involved in the inflammation process and IL-6 was shown to be one of its targets. In the present study, we report elevation of Il6 in the prefrontal cortex (PFC) of a genetic rat model of depression, the Flinders Sensitive Line (FSL) compared to the control Flinders Resistant Line. This elevation was associated with an overexpression of LIN28B and downregulation of let-7 miRNAs, the former an RNA-binding protein that selectively represses let-7 synthesis. Also DROSHA, a key enzyme in miRNA biogenesis was downregulated in FSL. Running was previously shown to have an antidepressant-like effect in the FSL rat. We found that running reduced Il6 levels and selectively increased let-7i and miR-98 expression in the PFC of FSL, although there were no differences in LIN28B and DROSHA expression. Pri-let-7i was upregulated in the running FSL group, which associated with increased histone H4 acetylation. In conclusion, the disturbance of let-7 family biogenesis may underlie increased proinflammatory markers in the depressed FSL rats while physical activity could reduce their expression, possibly through regulating primary miRNA expression via epigenetic mechanisms.

AGN-2979, an inhibitor of tryptophan hydroxylase activation, does not affect serotonin synthesis in Flinders Sensitive Line rats, a rat model of depression, but produces a significant effect in Flinders Resistant Line rats

PubMed Central

Kanemaru, Kazuya; Nishi, Kyoko; Diksic, Mirko

2009-01-01

The neurotransmitter, serotonin, is involved in several brain functions, including both normal, physiological functions, and pathophysiological functions. Alterations in any of the normal parameters of serotonergic neurotransmission can produce several different psychiatric disorders, including major depression. In many instances, brain neurochemical variables are not able to be studied properly in humans, thus making the use of good animal models extremely valuable. One of these animal models is the Flinders Sensitive Line (FSL) of rats, which has face, predictive and constructive validities in relation to human depression. The objective of this study was to quantify the effect of the tryptophan hydroxylase (TPH) activation inhibitor, AGN-2979, on the FSL rats (rats with depression-like behaviour), and compare it to the effect on the Flinders Resistant Line (FRL) of rats used as the control rats. The effect was evaluated by measuring changes in regional serotonin synthesis in the vehicle treated rats (FSL-VEH and FRL-VEH) relative to those measured in the AGN-2979 treated rats (FSL-AGN and FRL-AGN). Regional serotonin synthesis was measured autoradiographically in more than thirty brain regions. The measurements were performed using α-[14C]methyl-L-tryptophan as the tracer. The results indicate that AGN-2979 did not produce a significant reduction of TPH activity in the AGN-2979 group relative to the vehicle group (a reduction would have been observed if there had been an activation of TPH by the experimental set up) in the FSL rats. On the other hand, there was a highly significant reduction of synthesis in the FRL rats treated by AGN-2979, relative to the vehicle group. Together, the results demonstrate that in the FSL rats, AGN-2979 does not affect serotonin synthesis. This suggests that there was no activation of TPH in the FSL rats during the experimental procedure, but such activation did occur in the FRL rats. Because of this finding, it could be hypothesised that TPH in the FSL rats cannot be easily activated. This may contribute to the development of depressive-like symptoms in the FSL rats (“depressed” rats), as they cannot easily modulate their need for elevated amounts of this neurotransmitter, and possibly other neurotransmitters. Further, because these rats represent a very good model of human depression, one can hypothesize that humans who do not have readily activated TPH may be more prone to develop depression. PMID:19463878

Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA.

PubMed

Weller, Daniel; Andrus, Alexis; Wiedmann, Martin; den Bakker, Henk C

2015-01-01

Sampling of seafood and dairy processing facilities in the north-eastern USA produced 18 isolates of Listeria spp. that could not be identified at the species-level using traditional phenotypic and genotypic identification methods. Results of phenotypic and genotypic analyses suggested that the isolates represent two novel species with an average nucleotide blast identity of less than 92% with previously described species of the genus Listeria. Phylogenetic analyses based on whole genome sequences, 16S rRNA gene and sigB gene sequences confirmed that the isolates represented by type strain FSL M6-0635(T) and FSL A5-0209 cluster phylogenetically with Listeria cornellensis. Phylogenetic analyses also showed that the isolates represented by type strain FSL A5-0281(T) cluster phylogenetically with Listeria riparia. The name Listeria booriae sp. nov. is proposed for the species represented by type strain FSL A5-0281(T) ( =DSM 28860(T) =LMG 28311(T)), and the name Listeria newyorkensis sp. nov. is proposed for the species represented by type strain FSL M6-0635(T) ( =DSM 28861(T) =LMG 28310(T)). Phenotypic and genotypic analyses suggest that neither species is pathogenic. © 2015 IUMS.

Accuracy and precision of flash glucose monitoring sensors inserted into the abdomen and upper thigh compared with the upper arm.

PubMed

Charleer, Sara; Mathieu, Chantal; Nobels, Frank; Gillard, Pieter

2018-06-01

Nowadays, most Belgian patients with type 1 diabetes use flash glucose monitoring (FreeStyle Libre [FSL]; Abbott Diabetes Care, Alameda, California) to check their glucose values, but some patients find the sensor on the upper arm too visible. The aim of the present study was to compare the accuracy and precision of FSL sensors when placed on different sites. A total of 23 adults with type 1 diabetes used three FSL sensors simultaneously for 14 days on the upper arm, abdomen and upper thigh. FSL measurements were compared with capillary blood glucose (BG) measurements obtained with a built-in FSL BG meter. The aggregated mean absolute relative difference was 11.8 ± 12.0%, 18.5 ± 18.4% and 12.3 ± 13.8% for the arm, abdomen (P = .002 vs arm) and thigh (P = .5 vs arm), respectively. Results of Clarke error grid analysis for the arm and thigh were similar (zone A: 84.9% vs 84.5%; P = .6), while less accuracy was seen for the abdomen (zone A: 69.4%; P = .01). Apart from the first day, the accuracy of FSL sensors on the arm and thigh was more stable across the 14-day wear duration than accuracy of sensors on the abdomen, which deteriorated mainly during week 2 (P < .0005). The aggregated precision absolute relative difference was markedly lower for the arm/thigh (10.9 ± 11.9%) compared with the arm/abdomen (20.9 ± 22.8%; P = .002). Our results indicate that the accuracy and precision of FSL sensors placed on the upper thigh are similar to the upper arm, whereas the abdomen performed unacceptably poorly. © 2018 John Wiley & Sons Ltd.

Neuropeptide S alters anxiety, but not depression-like behaviour in Flinders Sensitive Line rats: a genetic animal model of depression.

PubMed

Wegener, Gregers; Finger, Beate C; Elfving, Betina; Keller, Kirsten; Liebenberg, Nico; Fischer, Christina W; Singewald, Nicolas; Slattery, David A; Neumann, Inga D; Mathé, Aleksander A

2012-04-01

Neuropeptide S (NPS) and its receptor (NPSR) have been implicated in the mediation of anxiolytic-like behaviour in rodents. However, little knowledge is available regarding the NPS system in depression-related behaviours, and whether NPS also exerts anxiolytic effects in an animal model of psychopathology. Therefore, the aim of this work was to characterize the effects of NPS on depression- and anxiety-related parameters, using male and female rats in a well-validated animal model of depression: the Flinders Sensitive Line (FSL), their controls, the Flinders Resistant Line (FRL), and Sprague-Dawley (SD) rats. We found that FSL showed greater immobility in the forced swim test (FST) than FRL, confirming their phenotype. However, NPS did not affect depression-related behaviour in any rat line. No significant differences in baseline anxiety levels between the FSL and FRL strains were observed, but FSL and FRL rats displayed less anxiety-like behaviour compared to SD rats. NPS decreased anxiety-like behaviour on the elevated plus-maze in all strains. The expression of the NPSR in the amygdala, periventricular hypothalamic nucleus, and hippocampus was equal in all male strains, although a trend towards reduced expression within the amygdala was observed in FSL rats compared to SD rats. In conclusion, NPS had a marked anxiolytic effect in FSL, FRL and SD rats, but did not modify the depression-related behaviour in any strain, in spite of the significant differences in innate level between the strains. These findings suggest that NPS specifically modifies anxiety behaviour but cannot overcome/reverse a genetically mediated depression phenotype.

The Toll-Like Receptor 2/6 Agonist, FSL-1 Lipopeptide, Therapeutically Mitigates Acute Radiation Syndrome.

PubMed

Kurkjian, Cathryn J; Guo, Hao; Montgomery, Nathan D; Cheng, Ning; Yuan, Hong; Merrill, Joseph R; Sempowski, Gregory D; Brickey, W June; Ting, Jenny P-Y

2017-12-11

Risks of radiation exposure from nuclear incidents and cancer radiotherapy are undeniable realities. These dangers urgently compel the development of agents for ameliorating radiation-induced injuries. Biologic pathways mediated by myeloid differentiation primary response gene 88 (MyD88), the common adaptor for toll-like receptor (TLR) and Interleukin-1 receptor signaling, are critical for radioprotection. Treating with agonists prior to radiation enhances survival by activating TLR signaling, whereas radiomitigating TLR-activating therapeutics given after exposure are less defined. We examine the radiomitigation capability of TLR agonists and identify one that is superior for its efficacy and reduced toxic consequences compared to other tested agonists. We demonstrate that the synthetic TLR2/6 ligand Fibroblast-stimulating lipopeptide (FSL-1) substantially prolongs survival in both male and female mice when administered 24 hours after radiation and shows MyD88-dependent function. FSL-1 treatment results in accelerated hematopoiesis in bone marrow, spleen and periphery, and augments systemic levels of hematopoiesis-stimulating factors. The ability of FSL-1 to stimulate hematopoiesis is critical, as hematopoietic dysfunction results from a range of ionizing radiation doses. The efficacy of a single FSL-1 dose for alleviating radiation injury while protecting against adverse effects reveals a viable radiation countermeasures agent.

[Changes of brain pain center and default mode network an electro acupuncture in Weizhong and Dachangshu acupoints: a task-fMRI study].

PubMed

Zhou, S; Cao, H X; Yu, L C; Jin, Y J; Jia, R H; Wen, Y R; Chen, X F

2016-02-23

To investigate the functional brain pain center and default mode network response to electro acupuncture stimulate in weizhong acupoints(BL40) and dachangshu acupoints(BL25). During January to February 2015, volunteers were enrolled in this study from the staff and student interns of Gansu Province Traditional Chinese Medicine Hospital. A total of 20 healthy, right-handed subjects, male 9, female 11, age (23±3) years, participated in this study. Block design task functional magnetic resonance imaging(fMRI) 3.0 T was performed in all subjects by electro acupuncture stimulating at BL40 and BL25 from the same experienced acupuncturist.The needle connected electric acupuncture apparatus through tow long coaxial-cable. A block design with five 120 s blocks of rest time (OFF block, electric acupuncture turn off ) interspersed between five 60 s blocks of stimulation (ON block, electric acupuncture turn on) fMRI scan. Magnetic resonance data of brain function was collected and FSL(fMRI Software Library) software was used to analyze the data. All subjects' data were analyzed except 2 cases whose head movement were more than 2 mm. Activated brain function regions by electro acupuncture stimulate included temporal lobe lateral sulcus, lobus insularis, thalamus, supramarginal gyrus, prefrontal medial frontal gyrus. Negative activated brain regions included middle frontal gyrus, parahippocampal gyrus, cingulate cortex abdominal segment, parietal cortex.The functional pain central and default mode network were changed when electro acupuncture stimulate in(BL40) and(BL25). There are several brain activation regions and negative activated brain regions when administering electro acupuncture stimulation at BL40 and BL25.

Evaluation of Soft Tissue Sarcoma Tumors Electrical Conductivity Anisotropy Using Diffusion Tensor Imaging for Numerical Modeling on Electroporation.

PubMed

Ghazikhanlou-Sani, K; Firoozabadi, S M P; Agha-Ghazvini, L; Mahmoodzadeh, H

2016-06-01

There is many ways to assessing the electrical conductivity anisotropy of a tumor. Applying the values of tissue electrical conductivity anisotropy is crucial in numerical modeling of the electric and thermal field distribution in electroporation treatments. This study aims to calculate the tissues electrical conductivity anisotropy in patients with sarcoma tumors using diffusion tensor imaging technique. A total of 3 subjects were involved in this study. All of patients had clinically apparent sarcoma tumors at the extremities. The T1, T2 and DTI images were performed using a 3-Tesla multi-coil, multi-channel MRI system. The fractional anisotropy (FA) maps were performed using the FSL (FMRI software library) software regarding the DTI images. The 3D matrix of the FA maps of each area (tumor, normal soft tissue and bone/s) was reconstructed and the anisotropy matrix was calculated regarding to the FA values. The mean FA values in direction of main axis in sarcoma tumors were ranged between 0.475-0.690.  With assumption of isotropy of the electrical conductivity, the FA value of electrical conductivity at each X, Y and Z coordinate axes would be equal to 0.577. The gathered results showed that there is a mean error band of 20% in electrical conductivity, if the electrical conductivity anisotropy not concluded at the calculations. The comparison of FA values showed that there is a significant statistical difference between the mean FA value of tumor and normal soft tissues (P<0.05). DTI is a feasible technique for the assessment of electrical conductivity anisotropy of tissues.  It is crucial to quantify the electrical conductivity anisotropy data of tissues for numerical modeling of electroporation treatments.

Reproducibility of neuroimaging analyses across operating systems

PubMed Central

Glatard, Tristan; Lewis, Lindsay B.; Ferreira da Silva, Rafael; Adalat, Reza; Beck, Natacha; Lepage, Claude; Rioux, Pierre; Rousseau, Marc-Etienne; Sherif, Tarek; Deelman, Ewa; Khalili-Mahani, Najmeh; Evans, Alan C.

2015-01-01

Neuroimaging pipelines are known to generate different results depending on the computing platform where they are compiled and executed. We quantify these differences for brain tissue classification, fMRI analysis, and cortical thickness (CT) extraction, using three of the main neuroimaging packages (FSL, Freesurfer and CIVET) and different versions of GNU/Linux. We also identify some causes of these differences using library and system call interception. We find that these packages use mathematical functions based on single-precision floating-point arithmetic whose implementations in operating systems continue to evolve. While these differences have little or no impact on simple analysis pipelines such as brain extraction and cortical tissue classification, their accumulation creates important differences in longer pipelines such as subcortical tissue classification, fMRI analysis, and cortical thickness extraction. With FSL, most Dice coefficients between subcortical classifications obtained on different operating systems remain above 0.9, but values as low as 0.59 are observed. Independent component analyses (ICA) of fMRI data differ between operating systems in one third of the tested subjects, due to differences in motion correction. With Freesurfer and CIVET, in some brain regions we find an effect of build or operating system on cortical thickness. A first step to correct these reproducibility issues would be to use more precise representations of floating-point numbers in the critical sections of the pipelines. The numerical stability of pipelines should also be reviewed. PMID:25964757

Reproducibility of neuroimaging analyses across operating systems.

PubMed

Glatard, Tristan; Lewis, Lindsay B; Ferreira da Silva, Rafael; Adalat, Reza; Beck, Natacha; Lepage, Claude; Rioux, Pierre; Rousseau, Marc-Etienne; Sherif, Tarek; Deelman, Ewa; Khalili-Mahani, Najmeh; Evans, Alan C

2015-01-01

Neuroimaging pipelines are known to generate different results depending on the computing platform where they are compiled and executed. We quantify these differences for brain tissue classification, fMRI analysis, and cortical thickness (CT) extraction, using three of the main neuroimaging packages (FSL, Freesurfer and CIVET) and different versions of GNU/Linux. We also identify some causes of these differences using library and system call interception. We find that these packages use mathematical functions based on single-precision floating-point arithmetic whose implementations in operating systems continue to evolve. While these differences have little or no impact on simple analysis pipelines such as brain extraction and cortical tissue classification, their accumulation creates important differences in longer pipelines such as subcortical tissue classification, fMRI analysis, and cortical thickness extraction. With FSL, most Dice coefficients between subcortical classifications obtained on different operating systems remain above 0.9, but values as low as 0.59 are observed. Independent component analyses (ICA) of fMRI data differ between operating systems in one third of the tested subjects, due to differences in motion correction. With Freesurfer and CIVET, in some brain regions we find an effect of build or operating system on cortical thickness. A first step to correct these reproducibility issues would be to use more precise representations of floating-point numbers in the critical sections of the pipelines. The numerical stability of pipelines should also be reviewed.

FSL_FASES

NASA Image and Video Library

2013-06-19

ISS036-E-009550 (19 June 2013) --- European Space Agency astronaut Luca Parmitano, Expedition 36 flight engineer, installs the Fundamental and Applied Studies of Emulsion Stability (FASES) experiment container into the Central Experiment Module (CEM) Lower of Fluid Science Laboratory (FSL) in the Columbus laboratory of the International Space Station.

Femtosecond laser modification of an array of vertically aligned carbon nanotubes intercalated with Fe phase nanoparticles

PubMed Central

2013-01-01

Femtosecond lasers (FSL) are playing an increasingly important role in materials research, characterization, and modification. Due to an extremely short pulse width, interactions of FSL irradiation with solid surfaces attract special interest, and a number of unusual phenomena resulted in the formation of new materials are expected. Here, we report on a new nanostructure observed after the interaction of FSL irradiation with arrays of vertically aligned carbon nanotubes (CNTs) intercalated with iron phase catalyst nanoparticles. It was revealed that the FSL laser ablation transforms the topmost layer of CNT array into iron phase nanospheres (40 to 680 nm in diameter) located at the tip of the CNT bundles of conical shape. Besides, the smaller nanospheres (10 to 30 nm in diameter) are found to be beaded at the sides of these bundles. Some of the larger nanospheres are encapsulated into carbon shells, which sometime are found to contain CNTs. The mechanism of creation of such nanostructures is proposed. PMID:24004518

Femtosecond laser modification of an array of vertically aligned carbon nanotubes intercalated with Fe phase nanoparticles.

PubMed

Labunov, Vladimir; Prudnikava, Alena; Bushuk, Serguei; Filatov, Serguei; Shulitski, Boris; Tay, Beng Kang; Shaman, Yury; Basaev, Alexander

2013-09-03

Femtosecond lasers (FSL) are playing an increasingly important role in materials research, characterization, and modification. Due to an extremely short pulse width, interactions of FSL irradiation with solid surfaces attract special interest, and a number of unusual phenomena resulted in the formation of new materials are expected. Here, we report on a new nanostructure observed after the interaction of FSL irradiation with arrays of vertically aligned carbon nanotubes (CNTs) intercalated with iron phase catalyst nanoparticles. It was revealed that the FSL laser ablation transforms the topmost layer of CNT array into iron phase nanospheres (40 to 680 nm in diameter) located at the tip of the CNT bundles of conical shape. Besides, the smaller nanospheres (10 to 30 nm in diameter) are found to be beaded at the sides of these bundles. Some of the larger nanospheres are encapsulated into carbon shells, which sometime are found to contain CNTs. The mechanism of creation of such nanostructures is proposed.

Navigating Native-Speaker Ideologies as FSL Teacher

ERIC Educational Resources Information Center

Wernicke, Meike

2017-01-01

Although a well-established domain of research in English language teaching, native-speaker ideologies have received little attention in French language education. This article reports on a study that examined the salience of "authentic French" in the identity construction of French as a second language (FSL) teachers in English-speaking…

Online Synchronous Communication in the Second-Language Classroom

ERIC Educational Resources Information Center

Murphy, Elizabeth

2009-01-01

The study reported on in this paper used a framework of benefits, challenges and solutions to categorize data from a design experiment using synchronous online communication for learning French as a second language (FSL). Participants were 92 Grade 6, FSL students and four teachers from urban and rural areas of Newfoundland, Canada. Data…

Importance of Muscle Power Variables in Repeated and Single Sprint Performance in Soccer Players

PubMed Central

López-Segovia, Manuel; Dellal, Alexandre; Chamari, Karim; González-Badillo, Juan José

2014-01-01

This study examined the relationship between lower body power and repeated as well as single sprint performance in soccer players. The performance of nineteen male soccer players was examined. The first testing session included the countermovement jump (CMJL) and the progressive full squat (FSL), both with external loads. Power in the CMJL and FSL was measured with each load that was lifted. The second session included a protocol of 40-m repeated sprints with a long recovery period (2 min). The number of sprints executed until there was a 3% decrease in performance for the best 40-m sprint time was recorded as a repeated sprint index (RSI). The RSI was moderately associated with power output relative to body mass in the CMJL and FSL (r = 0.53/0.54, p ≤ 0.05). The most and least powerful players (determined by FSL) showed significant differences in the RSI (9.1 ± 4.2 vs. 6.5 ± 1.6) and 10 m sprint time (p ± 0.01). Repeated and single sprints are associated with relatively lower body power in soccer players. PMID:25031688

First-spike latency in Hodgkin's three classes of neurons.

PubMed

Wang, Hengtong; Chen, Yueling; Chen, Yong

2013-07-07

We study the first-spike latency (FSL) in Hodgkin's three classes of neurons with the Morris-Lecar neuron model. It is found that all the three classes of neurons can encode an external stimulus into FSLs. With DC inputs, the FSLs of all of the neurons decrease with input intensity. With input current decreased to the threshold, class 1 neurons show an arbitrary long FSL whereas class 2 and 3 neurons exhibit the short-limit FSLs. When the input current is sinusoidal, the amplitude, frequency and initial phase can be encoded by all the three classes of neurons. The FSLs of all of the neurons decrease with the input amplitude and frequency. When the input frequency is too high, all of the neurons respond with infinite FSLs. When the initial phase increases, the FSL decreases and then jumps to a maximal value and finally decreases linearly. With changes in the input parameters, the FSLs of the class 1 and 2 neurons exhibit similar properties. However, the FSL of the class 3 neurons became slightly longer and only produces responses for a narrow range of initial phase if input frequencies are low. Moreover, our results also show that the FSL and firing rate responses are mutually independent processes and that neurons can encode an external stimulus into different FSLs and firing rates simultaneously. This finding is consistent with the current theory of dual or multiple complementary coding mechanisms. Copyright © 2013 Elsevier Ltd. All rights reserved.

The antidepressant effect of running is associated with increased hippocampal cell proliferation.

PubMed

Bjørnebekk, Astrid; Mathé, Aleksander A; Brené, Stefan

2005-09-01

A common trait of antidepressant drugs, electroconvulsive treatment and physical exercise is that they relieve depression and up-regulate neurotrophic factors as well as cell proliferation and neurogenesis in the hippocampus. In order to identify possible biological underpinnings of depression and the antidepressant effect of running, we analysed cell proliferation, the level of the neurotrophic factor BDNF in hippocampus and dynorphin in striatum/accumbens in 'depressed' Flinders Sensitive Line rats (FSL) and Flinders Resistant Line (FRL) rats with and without access to running-wheels. The FRL strain exhibited a higher daily running activity than the FSL strain. Wheel-running had an antidepressant effect in the 'depressed' FSL rats, as indicated by the forced swim test. In the hippocampus, cell proliferation was lower in the 'depressed' rats compared to the control FRL rats but there was no difference in BDNF or dynorphin levels in striatum/accumbens. After 5 wk of running, cell proliferation increased in FSL but not in FRL rats. BDNF and dynorphin mRNA levels were increased in FRL but not to the same extent in the in FSL rats; thus, increased BDNF and dynorphin levels were correlated to the running activity but not to the antidepressant effect of running. The only parameter that was associated to basal level of 'depression' and to the antidepressant effect was cell proliferation in the hippocampus. Thus, suppression of cell proliferation in the hippocampus could constitute one of the mechanisms that underlie depression, and physical activity might be an efficient antidepressant.

Femtosecond laser cutting of multiple thin corneal stromal lamellae for endothelial bioengineering.

PubMed

Bernard, Aurélien; He, Zhiguo; Forest, Fabien; Gauthier, Anne-Sophie; Peocʼh, Michel; Dumollard, Jean-Marc; Acquart, Sophie; Montard, Romain; Delbosc, Bernard; Gain, Philippe; Thuret, Gilles

2015-02-01

To assess the feasibility of cutting multiple thin stromal lamellae in human donor corneas using a commercial femtosecond laser (FSL) to provide cell carriers for future endothelial graft bioengineering. Eight edematous organ-cultured corneas not suitable for grafting for endothelial reasons were mounted on a Ziemer anterior chamber and cut with a Z6 FSL with 6 successive parallel cuts, from depth to surface. Target thickness of each lamella ranged from 100 to 150 μm depending on initial corneal thickness. Thickness was measured using anterior segment optical coherence tomography before and after cutting on mounted corneas, and on each stromal lamella after detachment. Scanning electron microscopy observation was performed on 4 lamellae and histological cross sections on 1 cornea before detachment. A median of 5 (minimum 3, maximum 7) lamellae was obtained per cornea. All lamellae still attached were the most posterior ones, suggesting that FSL was less efficient because of light scattering by edematous stroma. Cut precision and postdetachment swelling were correlated with anterior-posterior position within the cornea. Median lamella thickness was 127 μm (56-222 μm) before detachment and 196 μm (80-304 μm) after detachment. Surface state was consistent with previously reported FSL lamellar cuts during Descemet stripping automated endothelial keratoplasty. Up to 7 thin lamellae can be cut in stored corneas with an FSL. This method, once optimized primarily by using deswelled, more transparent corneas, could prove effective for recycling unsuitable donor corneas in corneal bioengineering processes.

Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments

PubMed Central

Miller, Rachel A.; Beno, Sarah M.; Kent, David J.; Carroll, Laura M.; Martin, Nicole H.; Boor, Kathryn J.

2016-01-01

A facultatively anaerobic, spore-forming Bacillus strain, FSL W8-0169T, collected from raw milk stored in a silo at a dairy powder processing plant in the north-eastern USA was initially identified as a Bacillus cereus group species based on a partial sequence of the rpoB gene and 16S rRNA gene sequence. Analysis of core genome single nucleotide polymorphisms clustered this strain separately from known B. cereus group species. Pairwise average nucleotide identity blast values obtained for FSL W8-0169T compared to the type strains of existing B. cereus group species were <95 % and predicted DNA–DNA hybridization values were <70 %, suggesting that this strain represents a novel B. cereus group species. We characterized 10 additional strains with the same or closely related rpoB allelic type, by whole genome sequencing and phenotypic analyses. Phenotypic characterization identified a higher content of iso-C16 : 0 fatty acid and the combined inability to ferment sucrose or to hydrolyse arginine as the key characteristics differentiating FSL W8-0169T from other B. cereus group species. FSL W8-0169T is psychrotolerant, produces haemolysin BL and non-haemolytic enterotoxin, and is cytotoxic in a HeLa cell model. The name Bacillus wiedmannii sp. nov. is proposed for the novel species represented by the type strain FSL W8-0169T (=DSM 102050T=LMG 29269T). PMID:27520992

The long-term effects of methamphetamine exposure during pre-adolescence on depressive-like behaviour in a genetic animal model of depression.

PubMed

Mouton, Moné; Harvey, Brian H; Cockeran, Marike; Brink, Christiaan B

2016-02-01

Methamphetamine (METH) is a psychostimulant and drug of abuse, commonly used early in life, including in childhood and adolescence. Adverse effects include psychosis, anxiety and mood disorders, as well as increased risk of developing a mental disorder later in life. The current study investigated the long-term effects of chronic METH exposure during pre-adolescence in stress-sensitive Flinders Sensitive Line (FSL) rats (genetic model of depression) and control Flinders Resistant Line (FRL) rats. METH or vehicle control was administered twice daily from post-natal day 19 (PostND19) to PostND34, followed by behavioural testing at either PostND35 (early effects) or long-lasting after withdrawal at PostND60 (early adulthood). Animals were evaluated for depressive-like behaviour, locomotor activity, social interaction and object recognition memory. METH reduced depressive-like behaviour in both FSL and FRL rats at PostND35, but enhanced this behaviour at PostND60. METH also reduced locomotor activity on PostND35 in both FSL and FRL rats, but without effect at PostND60. Furthermore, METH significantly lowered social interaction behaviour (staying together) in both FRL and FSL rats at PostND35 and PostND60, whereas self-grooming time was significantly reduced only at PostND35. METH treatment enhanced exploration of the familiar vs. novel object in the novel object recognition test (nORT) in FSL and FRL rats on PostND35 and PostND60, indicative of reduced cognitive performance. Thus, early-life METH exposure induce social and cognitive deficits. Lastly, early-life exposure to METH may result in acute antidepressant-like effects immediately after chronic exposure, whereas long-term effects after withdrawal are depressogenic. Data also supports a role for genetic predisposition as with FSL rats.

Library and Classroom Use of Copyrighted Videotapes and Computer Software.

ERIC Educational Resources Information Center

Reed, Mary Hutchings; Stanek, Debra

1986-01-01

This pullout guide addresses issues regarding library use of copyrighted videotapes and computer software. Guidelines for videotapes cover in-classroom use, in-library use in public library, loan, and duplication. Guidelines for computer software cover purchase conditions, avoiding license restrictions, loaning, archival copies, and in-library and…

Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods

PubMed Central

de Bresser, Jeroen; Hendrikse, Jeroen; Siero, Jeroen C. W.; Petersen, Esben T.; De Vis, Jill B.

2018-01-01

Objective In previous work we have developed a fast sequence that focusses on cerebrospinal fluid (CSF) based on the long T2 of CSF. By processing the data obtained with this CSF MRI sequence, brain parenchymal volume (BPV) and intracranial volume (ICV) can be automatically obtained. The aim of this study was to assess the precision of the BPV and ICV measurements of the CSF MRI sequence and to validate the CSF MRI sequence by comparison with 3D T1-based brain segmentation methods. Materials and methods Ten healthy volunteers (2 females; median age 28 years) were scanned (3T MRI) twice with repositioning in between. The scan protocol consisted of a low resolution (LR) CSF sequence (0:57min), a high resolution (HR) CSF sequence (3:21min) and a 3D T1-weighted sequence (6:47min). Data of the HR 3D-T1-weighted images were downsampled to obtain LR T1-weighted images (reconstructed imaging time: 1:59 min). Data of the CSF MRI sequences was automatically segmented using in-house software. The 3D T1-weighted images were segmented using FSL (5.0), SPM12 and FreeSurfer (5.3.0). Results The mean absolute differences for BPV and ICV between the first and second scan for CSF LR (BPV/ICV: 12±9/7±4cc) and CSF HR (5±5/4±2cc) were comparable to FSL HR (9±11/19±23cc), FSL LR (7±4, 6±5cc), FreeSurfer HR (5±3/14±8cc), FreeSurfer LR (9±8, 12±10cc), and SPM HR (5±3/4±7cc), and SPM LR (5±4, 5±3cc). The correlation between the measured volumes of the CSF sequences and that measured by FSL, FreeSurfer and SPM HR and LR was very good (all Pearson’s correlation coefficients >0.83, R2 .67–.97). The results from the downsampled data and the high-resolution data were similar. Conclusion Both CSF MRI sequences have a precision comparable to, and a very good correlation with established 3D T1-based automated segmentations methods for the segmentation of BPV and ICV. However, the short imaging time of the fast CSF MRI sequence is superior to the 3D T1 sequence on which segmentation with established methods is performed. PMID:29672584

Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods.

PubMed

van der Kleij, Lisa A; de Bresser, Jeroen; Hendrikse, Jeroen; Siero, Jeroen C W; Petersen, Esben T; De Vis, Jill B

2018-01-01

In previous work we have developed a fast sequence that focusses on cerebrospinal fluid (CSF) based on the long T2 of CSF. By processing the data obtained with this CSF MRI sequence, brain parenchymal volume (BPV) and intracranial volume (ICV) can be automatically obtained. The aim of this study was to assess the precision of the BPV and ICV measurements of the CSF MRI sequence and to validate the CSF MRI sequence by comparison with 3D T1-based brain segmentation methods. Ten healthy volunteers (2 females; median age 28 years) were scanned (3T MRI) twice with repositioning in between. The scan protocol consisted of a low resolution (LR) CSF sequence (0:57min), a high resolution (HR) CSF sequence (3:21min) and a 3D T1-weighted sequence (6:47min). Data of the HR 3D-T1-weighted images were downsampled to obtain LR T1-weighted images (reconstructed imaging time: 1:59 min). Data of the CSF MRI sequences was automatically segmented using in-house software. The 3D T1-weighted images were segmented using FSL (5.0), SPM12 and FreeSurfer (5.3.0). The mean absolute differences for BPV and ICV between the first and second scan for CSF LR (BPV/ICV: 12±9/7±4cc) and CSF HR (5±5/4±2cc) were comparable to FSL HR (9±11/19±23cc), FSL LR (7±4, 6±5cc), FreeSurfer HR (5±3/14±8cc), FreeSurfer LR (9±8, 12±10cc), and SPM HR (5±3/4±7cc), and SPM LR (5±4, 5±3cc). The correlation between the measured volumes of the CSF sequences and that measured by FSL, FreeSurfer and SPM HR and LR was very good (all Pearson's correlation coefficients >0.83, R2 .67-.97). The results from the downsampled data and the high-resolution data were similar. Both CSF MRI sequences have a precision comparable to, and a very good correlation with established 3D T1-based automated segmentations methods for the segmentation of BPV and ICV. However, the short imaging time of the fast CSF MRI sequence is superior to the 3D T1 sequence on which segmentation with established methods is performed.

Can an Interactive Digital Game Help French Learners Improve Their Pronunciation?

ERIC Educational Resources Information Center

Cardoso, Walcir; Rueb, Avery; Grimshaw, Jennica

2017-01-01

This study examines the effects of the pedagogical use of an interactive mobile digital game, Prêt à Négocier (PàN), on improving learners' pronunciation of French as a Second Language (FSL), using three holistic measures: comprehensibility, fluency, and overall pronunciation. Two groups of FSL learners engaged in different types of game-playing…

Study Abroad as Professional Development for FSL Teachers

ERIC Educational Resources Information Center

Wernicke, Meike

2010-01-01

In July 2009, a group of over 80 FSL teachers from British Columbia (BC) participated in a two-week sojourn at the "Centre d'Approches vivantes des Langues et des Medias" (CAVILAM) in Vichy, France, as part of an initiative to address the critical shortage of qualified French language teachers in the province. After almost four decades…

Hierarchies of Authenticity in Study Abroad: French from Canada versus French from France?

ERIC Educational Resources Information Center

Wernicke, Meike

2016-01-01

For many decades, Francophone regions in Canada have provided language study exchanges for French as a second language (FSL) learners within their own country. At the same time, FSL students and teachers in Canada continue to orient to a native speaker standard associated with European French. This Eurocentric orientation manifested itself in a…

Library-Specific Microcomputer Software.

ERIC Educational Resources Information Center

Levert, Virginia M.

1985-01-01

Discusses number and type of microcomputer software programs useful to libraries and types of hardware on which they run, as identified by Nolan Information Management Services. Highlights include general application programs, applications designed to support library technical processes, producers of library software, and choosing among options.…

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2012 CFR

2012-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2013 CFR

2013-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2011 CFR

2011-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2010 CFR

2010-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

37 CFR 201.24 - Warning of copyright for software lending by nonprofit libraries.

Code of Federal Regulations, 2014 CFR

2014-07-01

... software lending by nonprofit libraries. 201.24 Section 201.24 Patents, Trademarks, and Copyrights U.S... copyright for software lending by nonprofit libraries. (a) Definition. A Warning of Copyright for Software... States Code, as amended by the Computer Software Rental Amendments Act of 1990, Public Law 101-650. As...

Sex differences in the effect of puberty on hippocampal morphology.

PubMed

Satterthwaite, Theodore D; Vandekar, Simon; Wolf, Daniel H; Ruparel, Kosha; Roalf, David R; Jackson, Chad; Elliott, Mark A; Bilker, Warren B; Calkins, Monica E; Prabhakaran, Karthik; Davatzikos, Christos; Hakonarson, Hakon; Gur, Raquel E; Gur, Ruben C

2014-03-01

Puberty is the defining process of adolescence, and is accompanied by divergent trajectories of behavior and cognition for males and females. Here we examine whether sex differences exist in the effect of puberty on the morphology of the hippocampus and amygdala. T1-weighted structural neuroimaging was performed in a sample of 524 pre- or postpubertal individuals ages 10 to 22 years. Hippocampal and amygdala volume and shape were quantified using the Functional Magnetic Resonance Imaging of the Brain (FMRIB) Software Library (FSL) FIRST procedure and scaled by intracranial volume. The effects on regional volume of age, sex, puberty, and their interactions were examined using linear regression. Postpubertal sex differences were examined using a vertex analysis. Prepubertal males and females had similar hippocampal volumes, whereas postpubertal females had significantly larger bilateral hippocampi, resulting in a significant puberty-by-sex interaction even when controlling for age and age-by-sex. This effect was regionally specific and was not apparent in the amygdala. Vertex analysis revealed that postpubertal differences were most prominent in the lateral aspect of the hippocampus bilaterally, corresponding to the CA1 subfield. These results establish that there are regionally specific sex differences in the effect of puberty on the hippocampus. These findings are relevant for the understanding of psychiatric disorders that have both hippocampal dysfunction and prominent gender disparities during adolescence. Copyright © 2014 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

Neurological Effects of Exposure to Non-Hypoxic Hypobaria

DTIC Science & Technology

2014-04-16

be at risk for subclinical brain injury, raising concern about the long-term impact in aircrew. Altitude chamber personnel are a second...flight surgeon FSL BET brain extraction tool FSL FLIRT FMRIB’s linear image registration tool IQ intelligence quotient IRB Institutional Review...population would potentially have similar risks and findings. Chronic brain injury in other neurological diseases is associated with lower

Running Opposes the Effects of Social Isolation on Synaptic Plasticity and Transmission in a Rat Model of Depression

PubMed Central

Gómez-Galán, Marta; Femenía, Teresa; Åberg, Elin; Graae, Lisette; Van Eeckhaut, Ann; Smolders, Ilse; Brené, Stefan; Lindskog, Maria

2016-01-01

Stress, such as social isolation, is a well-known risk factor for depression, most probably in combination with predisposing genetic factors. Physical exercise on the other hand, is depicted as a wonder-treatment that makes you healthier, happier and live longer. However, the published results on the effects of exercise are ambiguous, especially when it comes to neuropsychiatric disorders. Here we combine a paradigm of social isolation with a genetic rat model of depression, the Flinders Sensitive Line (FSL), already known to have glutamatergic synaptic alterations. Compared to group-housed FSL rats, we found that social isolation further affects synaptic plasticity and increases basal synaptic transmission in hippocampal CA1 pyramidal neurons. These functional synaptic alterations co-exist with changes in hippocampal protein expression levels: social isolation in FSL rats reduce expression of the glial glutamate transporter GLT-1, and increase expression of the GluA2 AMPA-receptor subunit. We further show that physical exercise in form of voluntary running prevents the stress-induced synaptic effects but do not restore the endogenous mechanisms of depression already present in the FSL rat. PMID:27764188

Running Opposes the Effects of Social Isolation on Synaptic Plasticity and Transmission in a Rat Model of Depression.

PubMed

Gómez-Galán, Marta; Femenía, Teresa; Åberg, Elin; Graae, Lisette; Van Eeckhaut, Ann; Smolders, Ilse; Brené, Stefan; Lindskog, Maria

2016-01-01

Stress, such as social isolation, is a well-known risk factor for depression, most probably in combination with predisposing genetic factors. Physical exercise on the other hand, is depicted as a wonder-treatment that makes you healthier, happier and live longer. However, the published results on the effects of exercise are ambiguous, especially when it comes to neuropsychiatric disorders. Here we combine a paradigm of social isolation with a genetic rat model of depression, the Flinders Sensitive Line (FSL), already known to have glutamatergic synaptic alterations. Compared to group-housed FSL rats, we found that social isolation further affects synaptic plasticity and increases basal synaptic transmission in hippocampal CA1 pyramidal neurons. These functional synaptic alterations co-exist with changes in hippocampal protein expression levels: social isolation in FSL rats reduce expression of the glial glutamate transporter GLT-1, and increase expression of the GluA2 AMPA-receptor subunit. We further show that physical exercise in form of voluntary running prevents the stress-induced synaptic effects but do not restore the endogenous mechanisms of depression already present in the FSL rat.

Software Repository

NASA Technical Reports Server (NTRS)

Merwarth, P., D.

1983-01-01

The Common Software Module Repository (CSMR) is computerized library system with high product and service visibility to potential users. Online capabilities of system allow both librarian and user to interact with library. Librarian is responsible for maintaining information in CSMR library. User searches library to locate software modules that meet his or her current needs.

Points of Departure: Developing the Knowledge Base of ESL and FSL Teachers for K-12 Programs in Canada

ERIC Educational Resources Information Center

Faez, Farahnaz

2011-01-01

In this paper I examine similarities and differences between the required knowledge base of teachers of English as a second language (ESL) and French as a second language (FSL) for teaching in Kindergarten through Grade 12 programs in Canada. Drawing on knowledge base frameworks in language teacher education (Freeman and Johnson, 1998; Richards,…

Language Learning Strategies Use and Challenges Faced by Adult Arab Learners of Finnish as a Second Language in Finland

ERIC Educational Resources Information Center

Naif, Ahmed H.; Saad, Noor Saazai Mat

2017-01-01

Adult Arab learners of Finnish as second language (FSL) often encounter communication difficulty when dealing with official documents. They also cannot help their children in their school homework. FSL proficiency is an essential requirement to get an employment and to obtain the Finnish citizenship. The aim of this paper is to explore the use of…

Application Reuse Library for Software, Requirements, and Guidelines

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Thronesbery, Carroll

1994-01-01

Better designs are needed for expert systems and other operations automation software, for more reliable, usable and effective human support. A prototype computer-aided Application Reuse Library shows feasibility of supporting concurrent development and improvement of advanced software by users, analysts, software developers, and human-computer interaction experts. Such a library expedites development of quality software, by providing working, documented examples, which support understanding, modification and reuse of requirements as well as code. It explicitly documents and implicitly embodies design guidelines, standards and conventions. The Application Reuse Library provides application modules with Demo-and-Tester elements. Developers and users can evaluate applicability of a library module and test modifications, by running it interactively. Sub-modules provide application code and displays and controls. The library supports software modification and reuse, by providing alternative versions of application and display functionality. Information about human support and display requirements is provided, so that modifications will conform to guidelines. The library supports entry of new application modules from developers throughout an organization. Example library modules include a timer, some buttons and special fonts, and a real-time data interface program. The library prototype is implemented in the object-oriented G2 environment for developing real-time expert systems.

Computer Software: Copyright and Licensing Considerations for Schools and Libraries. ERIC Digest.

ERIC Educational Resources Information Center

Reed, Mary Hutchings

This digest notes that the terms and conditions of computer software package license agreements control the use of software in schools and libraries, and examines the implications of computer software license agreements for classroom use and for library lending policies. Guidelines are provided for interpreting the Copyright Act, and insuring the…

Running has differential effects on NPY, opiates, and cell proliferation in an animal model of depression and controls.

PubMed

Bjørnebekk, Astrid; Mathé, Aleksander A; Brené, Stefan

2006-02-01

Physical activity has documented beneficial effect in treatment of depression. Recently, we found an antidepressant-like effect of running in an animal model of depression, the Flinders Sensitive Line (FSL) and demonstrated that it was associated with increased hippocampal cell proliferation. In this study, we analyzed levels of mRNAs encoding the neuropeptide Y (NPY) and the opioid peptides dynorphin and enkephalin in hippocampus and correlated these to cell proliferation in the FSL and in the 'nondepressed' Flinders Resistant Line (FRL) strain, with/without access to running wheels. Running increased NPY mRNA in dentate gyrus and the CA4 region in FSL, but not in FRL rats. NPY mRNA increase was correlated to increased cell proliferation in the subgranular zone of dentate gyrus. Baseline dynorphin and enkephalin mRNA levels in the dentate gyrus were lower in the FSL compared to the FRL strain. Running had no effect on dynorphin and enkephalin mRNAs in the FSL strain but it decreased dynorphin mRNA, and there was a trend to increased enkephalin mRNA in the FRL rats. Thus, it would appear that the CNS effects of running are different in 'depressed' and control animals; modification of NPY, a peptide associated with depression and anxiety, in depressed animals, vs effects on opioids, associated with the reward systems, in healthy controls. Our data support the hypothesis that NPY neurotransmission in hippocampus is malfunctioning in depression and that antidepressive treatment, in this case wheel running, will normalize it. In addition, we also show that the increased NPY after running is correlated to increased cell proliferation, which is associated with an antidepressive-like effect.

The effects of antecedent dry days on the nitrogen removal in layered soil infiltration systems for storm run-off control.

PubMed

Cho, Kang-Woo; Yoon, Min-Hyuk; Song, Kyung-Guen; Ahn, Kyu-Hong

2011-01-01

The effects of antecedent dry days (ADD) on nitrogen removal efficiency were investigated in soil infiltration systems, with three distinguishable layers: mulch layer (ML), coarse soil layer (CSL) and fine soil layer (FSL). Two sets of lab-scale columns with loamy CSL (C1) and sandy CSL (C2) were dosed with synthetic run-off, carrying chemical oxygen demand of 100 mg L(-1) and total nitrogen of 13 mg L(-1). The intermittent dosing cycle was stepwise adjusted for 5, 10 and 20 days. The influent ammonium and organic nitrogen were adsorbed to the entire depth in C1, while dominantly to the FSL in C2. In both columns, the effluent ammonium concentration increased while the organic nitrogen concentration decreased, as ADD increased from 5 to 20 days. The effluent of C1 always showed nitrate concentration exceeding influent, caused by nitrification, by increasing amounts as ADD increased. However, the wash-out of nitrate in C1 was not distinct in terms of mass since the effluent flow rate was only 25% of the influent. In contrast, efficient reduction (>95%) of nitrate loading was observed in C2 under ADD of 5 and 10 days, because of insignificant nitrification in the CSL and denitrification in the FSL. However, for the ADD of 20 days, a significant nitrate wash-out appeared in C2 as well, possibly because of the re-aeration by the decreasing water content in the FSL. Consequently, the total nitrogen load escaping with the effluent was always smaller in C2, supporting the effectiveness of sandy CSL over loamy FSL for nitrogen removal under various ADDs.

Microcomputer Software Packages--Choose with Caution.

ERIC Educational Resources Information Center

Naumer, Janet Noll

1983-01-01

Briefly discusses types of software available for library and media center operations and library instruction, suggests three sources of software reviews, and describes almost 50 specific application programs available for bibliographic management, cataloging, circulation, inventory and purchasing, readability, and teaching library skills in…

Advanced Transport Operating System (ATOPS) utility library software description

NASA Technical Reports Server (NTRS)

Clinedinst, Winston C.; Slominski, Christopher J.; Dickson, Richard W.; Wolverton, David A.

1993-01-01

The individual software processes used in the flight computers on-board the Advanced Transport Operating System (ATOPS) aircraft have many common functional elements. A library of commonly used software modules was created for general uses among the processes. The library includes modules for mathematical computations, data formatting, system database interfacing, and condition handling. The modules available in the library and their associated calling requirements are described.

Proposal for a CLIPS software library

NASA Technical Reports Server (NTRS)

Porter, Ken

1991-01-01

This paper is a proposal to create a software library for the C Language Integrated Production System (CLIPS) expert system shell developed by NASA. Many innovative ideas for extending CLIPS were presented at the First CLIPS Users Conference, including useful user and database interfaces. CLIPS developers would benefit from a software library of reusable code. The CLIPS Users Group should establish a software library-- a course of action to make that happen is proposed. Open discussion to revise this library concept is essential, since only a group effort is likely to succeed. A response form intended to solicit opinions and support from the CLIPS community is included.

Selecting Software for Libraries.

ERIC Educational Resources Information Center

Beiser, Karl

1993-01-01

Discusses resources and strategies that libraries can use to evaluate competing database management software for purchase. Needs assessments, types of software available, features of good software, evaluation aids, shareware, and marketing and product trends are covered. (KRN)

PD5: a general purpose library for primer design software.

PubMed

Riley, Michael C; Aubrey, Wayne; Young, Michael; Clare, Amanda

2013-01-01

Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for primer design would considerably improve the development time, the processing speed, and the reliability of bespoke primer design software applications. The PD5 software library is an open-source collection of classes and utilities, providing a complete collection of software building blocks for primer design and analysis. It is written in object-oriented C(++) with an emphasis on classes suitable for efficient and rapid development of bespoke primer design programs. The modular design of the software library simplifies the development of specific applications and also integration with existing third party software where necessary. We demonstrate several applications created using this software library that have already proved to be effective, but we view the project as a dynamic environment for building primer design software and it is open for future development by the bioinformatics community. Therefore, the PD5 software library is published under the terms of the GNU General Public License, which guarantee access to source-code and allow redistribution and modification. The PD5 software library is downloadable from Google Code and the accompanying Wiki includes instructions and examples: http://code.google.com/p/primer-design.

Preparation of cherry-picked combinatorial libraries by string synthesis.

PubMed

Furka, Arpád; Dibó, Gábor; Gombosuren, Naran

2005-03-01

String synthesis [1-3] is an efficient and cheap manual method for preparation of combinatorial libraries by using macroscopic solid support units. Sorting the units between two synthetic steps is an important operation of the procedure. The software developed to guide sorting can be used only when complete combinatorial libraries are prepared. Since very often only selected components of the full libraries are needed, new software was constructed that guides sorting in preparation of non-complete combinatorial libraries. Application of the software is described in details.

libdrdc: software standards library

NASA Astrophysics Data System (ADS)

Erickson, David; Peng, Tie

2008-04-01

This paper presents the libdrdc software standards library including internal nomenclature, definitions, units of measure, coordinate reference frames, and representations for use in autonomous systems research. This library is a configurable, portable C-function wrapped C++ / Object Oriented C library developed to be independent of software middleware, system architecture, processor, or operating system. It is designed to use the automatically-tuned linear algebra suite (ATLAS) and Basic Linear Algebra Suite (BLAS) and port to firmware and software. The library goal is to unify data collection and representation for various microcontrollers and Central Processing Unit (CPU) cores and to provide a common Application Binary Interface (ABI) for research projects at all scales. The library supports multi-platform development and currently works on Windows, Unix, GNU/Linux, and Real-Time Executive for Multiprocessor Systems (RTEMS). This library is made available under LGPL version 2.1 license.

A Padawan Programmer's Guide to Developing Software Libraries.

PubMed

Yurkovich, James T; Yurkovich, Benjamin J; Dräger, Andreas; Palsson, Bernhard O; King, Zachary A

2017-11-22

With the rapid adoption of computational tools in the life sciences, scientists are taking on the challenge of developing their own software libraries and releasing them for public use. This trend is being accelerated by popular technologies and platforms, such as GitHub, Jupyter, R/Shiny, that make it easier to develop scientific software and by open-source licenses that make it easier to release software. But how do you build a software library that people will use? And what characteristics do the best libraries have that make them enduringly popular? Here, we provide a reference guide, based on our own experiences, for developing software libraries along with real-world examples to help provide context for scientists who are learning about these concepts for the first time. While we can only scratch the surface of these topics, we hope that this article will act as a guide for scientists who want to write great software that is built to last. Copyright © 2017 Elsevier Inc. All rights reserved.

The Vendors' Corner: Biblio-Techniques' Library and Information System (BLIS).

ERIC Educational Resources Information Center

Library Software Review, 1984

1984-01-01

Describes online catalog and integrated library computer system designed to enhance Washington Library Network's software. Highlights include system components; implementation options; system features (integrated library functions, database design, system management facilities); support services (installation and training, software maintenance and…

Connecting the Library's Patron Database to Campus Administrative Software: Simplifying the Library's Accounts Receivable Process

ERIC Educational Resources Information Center

Oliver, Astrid; Dahlquist, Janet; Tankersley, Jan; Emrich, Beth

2010-01-01

This article discusses the processes that occurred when the Library, Controller's Office, and Information Technology Department agreed to create an interface between the Library's Innovative Interfaces patron database and campus administrative software, Banner, using file transfer protocol, in an effort to streamline the Library's accounts…

Sharing brain mapping statistical results with the neuroimaging data model

PubMed Central

Maumet, Camille; Auer, Tibor; Bowring, Alexander; Chen, Gang; Das, Samir; Flandin, Guillaume; Ghosh, Satrajit; Glatard, Tristan; Gorgolewski, Krzysztof J.; Helmer, Karl G.; Jenkinson, Mark; Keator, David B.; Nichols, B. Nolan; Poline, Jean-Baptiste; Reynolds, Richard; Sochat, Vanessa; Turner, Jessica; Nichols, Thomas E.

2016-01-01

Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices. This standardized representation allows authors to relay methods and results in a platform-independent regularized format that is not tied to a particular neuroimaging software package. Tools are available to export NIDM-Result graphs and associated files from the widely used SPM and FSL software packages, and the NeuroVault repository can import NIDM-Results archives. The specification is publically available at: http://nidm.nidash.org/specs/nidm-results.html. PMID:27922621

Marked brain asymmetry with intact cognitive functioning in idiopathic Parkinson’s disease: A longitudinal analysis

PubMed Central

Tanner, Jared J.; Levy, Shellie-Anne; Schwab, Nadine A.; Hizel, Loren P.; Nguyen, Peter T.; Okun, Michael S.; Price, Catherine C.

2016-01-01

Objective A 71-year old (MN) with an 11-year history of left onset tremor diagnosed as Parkinson’s disease (PD) completed longitudinal brain magnetic resonance imaging (MRI) and neuropsychological testing. MRI scans showed an asymmetric caudate nucleus (right< left volume). We describe this asymmetry at baseline and the progression over time relative to other subcortical gray, frontal white matter, and cortical gray matter regions of interest. Isolated structural changes are compared to MN’s cognitive profiles. Method MN completed yearly MRIs and neuropsychological assessments. For comparison, left onset PD (n=15) and non-PD (n=43) peers completed the same baseline protocol. All MRI scans were processed with FreeSurfer and the FMRIB Software Library (FSL) to analyze gray matter structures and frontal fractional anisotropy (FA) metrics. Processing speed, working memory, language, verbal memory, abstract reasoning, visuospatial, and motor functions were examined using reliable change methods. Results At baseline MN had striatal volume and frontal lobe thickness asymmetry relative to peers with mild prefrontal white matter FA asymmetry. Over time only MN’s right caudate nucleus showed accelerated atrophy. Cognitively, MN had slowed psychomotor speed and visuospatial-linked deficits with mild visuospatial working memory declines longitudinally. Conclusions This is a unique report using normative neuroimaging and neuropsychology to describe an individual diagnosed with PD who had striking striatal asymmetry followed secondarily by cortical thickness asymmetry and possible frontal white matter asymmetry. His decline and variability in visual working memory could be linked to ongoing atrophy of his right caudate nucleus. PMID:27813459

MB-COMT promoter DNA methylation is associated with working-memory processing in schizophrenia patients and healthy controls

PubMed Central

Walton, Esther; Liu, Jingyu; Hass, Johanna; White, Tonya; Scholz, Markus; Roessner, Veit; Gollub, Randy; Calhoun, Vince D; Ehrlich, Stefan

2014-01-01

Many genetic studies report mixed results both for the associations between COMT polymorphisms and schizophrenia and for the effects of COMT variants on common intermediate phenotypes of the disorder. Reasons for this may include small genetic effect sizes and the modulation of environmental influences. To improve our understanding of the role of COMT in the disease etiology, we investigated the effect of DNA methylation in the MB-COMT promoter on neural activity in the dorsolateral prefrontal cortex during working memory processing as measured by fMRI - an intermediate phenotype for schizophrenia. Imaging and epigenetic data were measured in 102 healthy controls and 82 schizophrenia patients of the Mind Clinical Imaging Consortium (MCIC) study of schizophrenia. Neural activity during the Sternberg Item Recognition Paradigm was acquired with either a 3T Siemens Trio or 1.5T Siemens Sonata and analyzed using the FMRIB Software Library (FSL). DNA methylation measurements were derived from cryo-conserved blood samples. We found a positive association between MB-COMT promoter methylation and neural activity in the left dorsolateral prefrontal cortex in a model using a region-of-interest approach and could confirm this finding in a whole-brain model. This effect was independent of disease status. Analyzing the effect of MB-COMT promoter DNA methylation on a neuroimaging phenotype can provide further evidence for the importance of COMT and epigenetic risk mechanisms in schizophrenia. The latter may represent trans-regulatory or environmental risk factors that can be measured using brain-based intermediate phenotypes. PMID:24837210

Magnetic Resonance Imaging Measurement of Transmission of Arterial Pulsation to the Brain on Propranolol Versus Amlodipine.

PubMed

Webb, Alastair J S; Rothwell, Peter M

2016-06-01

Cerebral arterial pulsatility is associated with leukoaraiosis and depends on central arterial pulsatility and arterial stiffness. The effect of antihypertensive drugs on transmission of central arterial pulsatility to the cerebral circulation is unknown, partly because of limited methods of assessment. In a technique-development pilot study, 10 healthy volunteers were randomized to crossover treatment with amlodipine and propranolol. At baseline and on each drug, we assessed aortic (Sphygmocor) and middle cerebral artery pulsatility (TCDtranscranial ultrasound). We also performed whole-brain, 3-tesla multiband blood-oxygen level dependent magnetic resonance imaging (multiband factor 6, repetition time=0.43s), concurrent with a novel method of continuous noninvasive blood pressure monitoring. Drug effects on relationships between cardiac cycle variation in blood pressure and blood-oxygen level dependent imaging were determined (fMRI Expert Analysis Tool, fMRIB Software Library [FEAT-FSL]). Aortic pulsatility was similar on amlodipine (27.3 mm Hg) and propranolol (27.9 mm Hg, P diff=0.33), while MCA pulsatility increased nonsignificantly more from baseline on propranolol (+6%; P=0.09) than amlodipine (+1.5%; P=0.58). On magnetic resonance imaging, cardiac frequency blood pressure variations were found to be significantly more strongly associated with blood-oxygen level dependent imaging on propranolol than amlodipine. We piloted a novel method of assessment of arterial pulsatility with concurrent high-frequency blood-oxygen level dependent magnetic resonance imaging and noninvasive blood pressure monitoring. This method was able to identify greater transmission of aortic pulsation on propranolol than amlodipine, which warrants further investigation. © 2016 American Heart Association, Inc.

Flight Software Math Library

NASA Technical Reports Server (NTRS)

McComas, David

2013-01-01

The flight software (FSW) math library is a collection of reusable math components that provides typical math utilities required by spacecraft flight software. These utilities are intended to increase flight software quality reusability and maintainability by providing a set of consistent, well-documented, and tested math utilities. This library only has dependencies on ANSI C, so it is easily ported. Prior to this library, each mission typically created its own math utilities using ideas/code from previous missions. Part of the reason for this is that math libraries can be written with different strategies in areas like error handling, parameters orders, naming conventions, etc. Changing the utilities for each mission introduces risks and costs. The obvious risks and costs are that the utilities must be coded and revalidated. The hidden risks and costs arise in miscommunication between engineers. These utilities must be understood by both the flight software engineers and other subsystem engineers (primarily guidance navigation and control). The FSW math library is part of a larger goal to produce a library of reusable Guidance Navigation and Control (GN&C) FSW components. A GN&C FSW library cannot be created unless a standardized math basis is created. This library solves the standardization problem by defining a common feature set and establishing policies for the library s design. This allows the libraries to be maintained with the same strategy used in its initial development, which supports a library of reusable GN&C FSW components. The FSW math library is written for an embedded software environment in C. This places restrictions on the language features that can be used by the library. Another advantage of the FSW math library is that it can be used in the FSW as well as other environments like the GN&C analyst s simulators. This helps communication between the teams because they can use the same utilities with the same feature set and syntax.

Integrated Online Software for Libraries: An Overview of Today's Best-Selling IOLS. Options from the U.S. Perspective.

ERIC Educational Resources Information Center

Cibbarelli, Pamela

1996-01-01

Profiles the top-selling IOLS (integrated online library systems) software for libraries based on sales figures reported in the 1996 "Library Journal" annual survey of the library automation marketplace. Highlights include microcomputer-based systems and minicomputer-based systems, system components, MARC formats, and market sectors.…

Mining Software Usage with the Automatic Library Tracking Database (ALTD)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadri, Bilel; Fahey, Mark R

2013-01-01

Tracking software usage is important for HPC centers, computer vendors, code developers and funding agencies to provide more efficient and targeted software support, and to forecast needs and guide HPC software effort towards the Exascale era. However, accurately tracking software usage on HPC systems has been a challenging task. In this paper, we present a tool called Automatic Library Tracking Database (ALTD) that has been developed and put in production on several Cray systems. The ALTD infrastructure prototype automatically and transparently stores information about libraries linked into an application at compilation time and also the executables launched in a batchmore » job. We will illustrate the usage of libraries, compilers and third party software applications on a system managed by the National Institute for Computational Sciences.« less

Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments.

PubMed

den Bakker, Henk C; Warchocki, Steven; Wright, Emily M; Allred, Adam F; Ahlstrom, Christina; Manuel, Clyde S; Stasiewicz, Matthew J; Burrell, Angela; Roof, Sherry; Strawn, Laura K; Fortes, Esther; Nightingale, Kendra K; Kephart, Daniel; Wiedmann, Martin

2014-06-01

Sampling of agricultural and natural environments in two US states (Colorado and Florida) yielded 18 Listeria-like isolates that could not be assigned to previously described species using traditional methods. Using whole-genome sequencing and traditional phenotypic methods, we identified five novel species, each with a genome-wide average BLAST nucleotide identity (ANIb) of less than 85% to currently described species. Phylogenetic analysis based on 16S rRNA gene sequences and amino acid sequences of 31 conserved loci showed the existence of four well-supported clades within the genus Listeria; (i) a clade representing Listeria monocytogenes, L. marthii, L. innocua, L. welshimeri, L. seeligeri and L. ivanovii, which we refer to as Listeria sensu stricto, (ii) a clade consisting of Listeria fleischmannii and two newly described species, Listeria aquatica sp. nov. (type strain FSL S10-1188(T) = DSM 26686(T) = LMG 28120(T) = BEI NR-42633(T)) and Listeria floridensis sp. nov. (type strain FSL S10-1187(T) = DSM 26687(T) = LMG 28121(T) = BEI NR-42632(T)), (iii) a clade consisting of Listeria rocourtiae, L. weihenstephanensis and three novel species, Listeria cornellensis sp. nov. (type strain TTU A1-0210(T) = FSL F6-0969(T) = DSM 26689(T) = LMG 28123(T) = BEI NR-42630(T)), Listeria grandensis sp. nov. (type strain TTU A1-0212(T) = FSL F6-0971(T) = DSM 26688(T) = LMG 28122(T) = BEI NR-42631(T)) and Listeria riparia sp. nov. (type strain FSL S10-1204(T) = DSM 26685(T) = LMG 28119(T) = BEI NR- 42634(T)) and (iv) a clade containing Listeria grayi. Genomic and phenotypic data suggest that the novel species are non-pathogenic. © 2014 IUMS.

Age differences in the associations between sick leave and aspects of health, psychosocial workload and family life: a cross-sectional study

PubMed Central

Bos, Judith T; van der Velden, Koos; van der Gulden, Joost W J

2012-01-01

Objectives To investigate differences in associations between sick leave and aspects of health, psychosocial workload, family life and work–family interference between four age groups (<36, 36–45, 46–55 and 55+ years). Design A cross-sectional study; a questionnaire was sent to the home addresses of all employees of a university. Setting A Dutch university. Participants 1843 employees returned the questionnaire (net response: 49.1%). The age distribution was as follows: <36: 32%; 36–45: 26%; 46–55: 27% and 55+: 12%. Primary outcomes Frequent sick leave (FSL, ≥3 times in the past 12 months) and prolonged sick leave (PSL, >2 weeks in total in the past 12 months). Differences between the age groups in independent variables and outcomes were investigated. Logistic regression analysis was used to calculate associations between various variables and the sick leave outcomes. Interaction terms were included to detect differences between the age groups. Results Age differences were found for many work- and family-related characteristics but not in the mean scores for health-related aspects. Presence of chronic disease was reported more frequently with increasing age. The 55+ age group had almost two times less chance of FSL, but 1.6 times more chance of PSL than the <36 age group. Age moderates the associations between career opportunities, partner's contribution in domestic tasks and sex, and FSL. Job security and pay, support from supervisor, challenging work and being breadwinner have different associations with PSL. However, life events in private lives and perceived health complaints are important in all age groups. FSL and PSL have some determinants in common, but there are differences between the outcomes as well. Conclusions Age should be treated as a variable of interest instead of a control variable. Employers and occupational physicians need to be aware that each phase in life has specific difficulties that can lead to FSL and PSL. PMID:22855622

A Computerized Cataloging System for an Outdoor Program Library or Resource Center.

ERIC Educational Resources Information Center

Watters, Ron

The Outdoor Resource Library Cataloging System is a computer software program designed primarily for outdoor programs with small to medium-sized resource centers. The software is free to nonprofit organizations and is available from the Idaho State University Outdoor Program. The software is used to construct a database of library materials, which…

Demographic Variables as Factors Influencing Accessibility and Utilisation of Library Software by Undergraduates in Two Private Universities in Nigeria

ERIC Educational Resources Information Center

Tolulope, Akano

2017-01-01

Libraries before the 21st century carried out daily routine library task such as cataloguing and classification, acquisition, reference services etc using manual procedures only but the advent of Information Technology as transformed these routine task that libraries can now automate their activities by deploying the use of library software in…

CycloPs: generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids.

PubMed

Duffy, Fergal J; Verniere, Mélanie; Devocelle, Marc; Bernard, Elise; Shields, Denis C; Chubb, Anthony J

2011-04-25

We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical measurements, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experiments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at http://bioware.ucd.ie .

Nuclear Data Online Services at Peking University

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fan, T.S.; Guo, Z.Y.; Ye, W.G.

2005-05-24

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

Nuclear Data Online Services at Peking University

NASA Astrophysics Data System (ADS)

Fan, T. S.; Guo, Z. Y.; Ye, W. G.; Liu, W. L.; Liu, T. J.; Liu, C. X.; Chen, J. X.; Tang, G. Y.; Shi, Z. M.; Huang, X. L.; Chen, J. E.

2005-05-01

The Institute of Heavy Ion Physics at Peking University has developed a new nuclear data online services software package. Through the web site (http://ndos.nst.pku.edu.cn), it offers online access to main relational nuclear databases: five evaluated neutron libraries (BROND, CENDL, ENDF, JEF, JENDL), the ENSDF library, the EXFOR library, the IAEA photonuclear library and the charged particle data of the FENDL library. This software allows the comparison and graphic representations of the different data sets. The computer programs of this package are based on the Linux implementation of PHP and the MySQL software.

Software Defined GPS API: Development and Implementation of GPS Correlator Architectures Using MATLAB with Focus on SDR Implementations

DTIC Science & Technology

2014-05-18

intention of offering improved software libraries for GNSS signal acquisition. It has been the team mission to implement new and improved techniques...with the intention of offering improved software libraries for GNSS signal acquisition. It has been the team mission to implement new and improved...intention of offering improved software libraries for GNSS signal acquisition. It has been the team mission to implement new and improved techniques to

Library Automation Alternatives in 1996 and User Satisfaction Ratings of Library Users by Operating System.

ERIC Educational Resources Information Center

Cibbarelli, Pamela

1996-01-01

Examines library automation product introductions and conversions to new operating systems. Compares user satisfaction ratings of the following library software packages: DOS/Windows, UNIX, Macintosh, and DEC VAX/VMS. Software is rated according to documentation, service/support, training, product reliability, product capabilities, ease of use,…

Paralogous Outer Membrane Proteins Mediate Uptake of Different Forms of Iron and Synergistically Govern Virulence in Francisella tularensis tularensis*

PubMed Central

Ramakrishnan, Girija; Sen, Bhaswati; Johnson, Richard

2012-01-01

Francisella tularensis subsp. tularensis is a highly infectious bacterium causing acute disease in mammalian hosts. Mechanisms for the acquisition of iron within the iron-limiting host environment are likely to be critical for survival of this intracellular pathogen. FslE (FTT0025) and FupA (FTT0918) are paralogous proteins that are predicted to form β-barrels in the outer membrane of virulent strain Schu S4 and are unique to Francisella species. Previous studies have implicated both FupA, initially identified as a virulence factor and FslE, encoded by the siderophore biosynthetic operon, in iron acquisition. Using single and double mutants, we demonstrated that these paralogs function in concert to promote growth under iron limitation. We used a 55Fe transport assay to demonstrate that FslE is involved in siderophore-mediated ferric iron uptake, whereas FupA facilitates high affinity ferrous iron uptake. Optimal replication within J774A.1 macrophage-like cells required at least one of these uptake systems to be functional. In a mouse model of tularemia, the ΔfupA mutant was attenuated, but the ΔfslE ΔfupA mutant was significantly more attenuated, implying that the two systems of iron acquisition function synergistically to promote virulence. These studies highlight the importance of specific iron acquisition functions, particularly that of ferrous iron, for virulence of F. tularensis in the mammalian host. PMID:22661710

Improving Software Sustainability: Lessons Learned from Profiles in Science.

PubMed

Gallagher, Marie E

2013-01-01

The Profiles in Science® digital library features digitized surrogates of historical items selected from the archival collections of the U.S. National Library of Medicine as well as collaborating institutions. In addition, it contains a database of descriptive, technical and administrative metadata. It also contains various software components that allow creation of the metadata, management of the digital items, and access to the items and metadata through the Profiles in Science Web site [1]. The choices made building the digital library were designed to maximize the sustainability and long-term survival of all of the components of the digital library [2]. For example, selecting standard and open digital file formats rather than proprietary formats increases the sustainability of the digital files [3]. Correspondingly, using non-proprietary software may improve the sustainability of the software--either through in-house expertise or through the open source community. Limiting our digital library software exclusively to open source software or to software developed in-house has not been feasible. For example, we have used proprietary operating systems, scanning software, a search engine, and office productivity software. We did this when either lack of essential capabilities or the cost-benefit trade-off favored using proprietary software. We also did so knowing that in the future we would need to replace or upgrade some of our proprietary software, analogous to migrating from an obsolete digital file format to a new format as the technological landscape changes. Since our digital library's start in 1998, all of its software has been upgraded or replaced, but the digitized items have not yet required migration to other formats. Technological changes that compelled us to replace proprietary software included the cost of product licensing, product support, incompatibility with other software, prohibited use due to evolving security policies, and product abandonment. Sometimes these changes happen on short notice, so we continually monitor our library's software for signs of endangerment. We have attempted to replace proprietary software with suitable in-house or open source software. When the replacement involves a standalone piece of software with a nearly equivalent version, such as replacing a commercial HTTP server with an open source HTTP server, the replacement is straightforward. Recently we replaced software that functioned not only as our search engine but also as the backbone of the architecture of our Web site. In this paper, we describe the lessons learned and the pros and cons of replacing this software with open source software.

Software Quality Assurance and Verification for the MPACT Library Generation Process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yuxuan; Williams, Mark L.; Wiarda, Dorothea

This report fulfills the requirements for the Consortium for the Advanced Simulation of Light-Water Reactors (CASL) milestone L2:RTM.P14.02, “SQA and Verification for MPACT Library Generation,” by documenting the current status of the software quality, verification, and acceptance testing of nuclear data libraries for MPACT. It provides a brief overview of the library generation process, from general-purpose evaluated nuclear data files (ENDF/B) to a problem-dependent cross section library for modeling of light-water reactors (LWRs). The software quality assurance (SQA) programs associated with each of the software used to generate the nuclear data libraries are discussed; specific tests within the SCALE/AMPX andmore » VERA/XSTools repositories are described. The methods and associated tests to verify the quality of the library during the generation process are described in detail. The library generation process has been automated to a degree to (1) ensure that it can be run without user intervention and (2) to ensure that the library can be reproduced. Finally, the acceptance testing process that will be performed by representatives from the Radiation Transport Methods (RTM) Focus Area prior to the production library’s release is described in detail.« less

Update on PISCES

NASA Technical Reports Server (NTRS)

Pearson, Don; Hamm, Dustin; Kubena, Brian; Weaver, Jonathan K.

2010-01-01

An updated version of the Platform Independent Software Components for the Exploration of Space (PISCES) software library is available. A previous version was reported in Library for Developing Spacecraft-Mission-Planning Software (MSC-22983), NASA Tech Briefs, Vol. 25, No. 7 (July 2001), page 52. To recapitulate: This software provides for Web-based, collaborative development of computer programs for planning trajectories and trajectory- related aspects of spacecraft-mission design. The library was built using state-of-the-art object-oriented concepts and software-development methodologies. The components of PISCES include Java-language application programs arranged in a hierarchy of classes that facilitates the reuse of the components. As its full name suggests, the PISCES library affords platform-independence: The Java language makes it possible to use the classes and application programs with a Java virtual machine, which is available in most Web-browser programs. Another advantage is expandability: Object orientation facilitates expansion of the library through creation of a new class. Improvements in the library since the previous version include development of orbital-maneuver- planning and rendezvous-launch-window application programs, enhancement of capabilities for propagation of orbits, and development of a desktop user interface.

NA-42 TI Shared Software Component Library FY2011 Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knudson, Christa K.; Rutz, Frederick C.; Dorow, Kevin E.

The NA-42 TI program initiated an effort in FY2010 to standardize its software development efforts with the long term goal of migrating toward a software management approach that will allow for the sharing and reuse of code developed within the TI program, improve integration, ensure a level of software documentation, and reduce development costs. The Pacific Northwest National Laboratory (PNNL) has been tasked with two activities that support this mission. PNNL has been tasked with the identification, selection, and implementation of a Shared Software Component Library. The intent of the library is to provide a common repository that is accessiblemore » by all authorized NA-42 software development teams. The repository facilitates software reuse through a searchable and easy to use web based interface. As software is submitted to the repository, the component registration process captures meta-data and provides version control for compiled libraries, documentation, and source code. This meta-data is then available for retrieval and review as part of library search results. In FY2010, PNNL and staff from the Remote Sensing Laboratory (RSL) teamed up to develop a software application with the goal of replacing the aging Aerial Measuring System (AMS). The application under development includes an Advanced Visualization and Integration of Data (AVID) framework and associated AMS modules. Throughout development, PNNL and RSL have utilized a common AMS code repository for collaborative code development. The AMS repository is hosted by PNNL, is restricted to the project development team, is accessed via two different geographic locations and continues to be used. The knowledge gained from the collaboration and hosting of this repository in conjunction with PNNL software development and systems engineering capabilities were used in the selection of a package to be used in the implementation of the software component library on behalf of NA-42 TI. The second task managed by PNNL is the development and continued maintenance of the NA-42 TI Software Development Questionnaire. This questionnaire is intended to help software development teams working under NA-42 TI in documenting their development activities. When sufficiently completed, the questionnaire illustrates that the software development activities recorded incorporate significant aspects of the software engineering lifecycle. The questionnaire template is updated as comments are received from NA-42 and/or its development teams and revised versions distributed to those using the questionnaire. PNNL also maintains a list of questionnaire recipients. The blank questionnaire template, the AVID and AMS software being developed, and the completed AVID AMS specific questionnaire are being used as the initial content to be established in the TI Component Library. This report summarizes the approach taken to identify requirements, search for and evaluate technologies, and the approach taken for installation of the software needed to host the component library. Additionally, it defines the process by which users request access for the contribution and retrieval of library content.« less

A Hybrid Hierarchical Approach for Brain Tissue Segmentation by Combining Brain Atlas and Least Square Support Vector Machine

PubMed Central

Kasiri, Keyvan; Kazemi, Kamran; Dehghani, Mohammad Javad; Helfroush, Mohammad Sadegh

2013-01-01

In this paper, we present a new semi-automatic brain tissue segmentation method based on a hybrid hierarchical approach that combines a brain atlas as a priori information and a least-square support vector machine (LS-SVM). The method consists of three steps. In the first two steps, the skull is removed and the cerebrospinal fluid (CSF) is extracted. These two steps are performed using the toolbox FMRIB's automated segmentation tool integrated in the FSL software (FSL-FAST) developed in Oxford Centre for functional MRI of the brain (FMRIB). Then, in the third step, the LS-SVM is used to segment grey matter (GM) and white matter (WM). The training samples for LS-SVM are selected from the registered brain atlas. The voxel intensities and spatial positions are selected as the two feature groups for training and test. SVM as a powerful discriminator is able to handle nonlinear classification problems; however, it cannot provide posterior probability. Thus, we use a sigmoid function to map the SVM output into probabilities. The proposed method is used to segment CSF, GM and WM from the simulated magnetic resonance imaging (MRI) using Brainweb MRI simulator and real data provided by Internet Brain Segmentation Repository. The semi-automatically segmented brain tissues were evaluated by comparing to the corresponding ground truth. The Dice and Jaccard similarity coefficients, sensitivity and specificity were calculated for the quantitative validation of the results. The quantitative results show that the proposed method segments brain tissues accurately with respect to corresponding ground truth. PMID:24696800

Microcomputer Software for Libraries: A Survey.

ERIC Educational Resources Information Center

Nolan, Jeanne M.

1983-01-01

Reports on findings of research done by Nolan Information Management Services concerning availability of microcomputer software for libraries. Highlights include software categories (specific, generic-database management programs, original); number of programs available in 1982 for 12 applications; projections for 1983; and future software…

Garcinia mangostana Linn displays antidepressant-like and pro-cognitive effects in a genetic animal model of depression: a bio-behavioral study in the Flinders Sensitive Line rat.

PubMed

Oberholzer, Inge; Möller, Marisa; Holland, Brendan; Dean, Olivia M; Berk, Michael; Harvey, Brian H

2018-04-01

There is abundant evidence for both disorganized redox balance and cognitive deficits in major depressive disorder (MDD). Garcinia mangostana Linn (GM) has anti-oxidant activity. We studied the antidepressant-like and pro-cognitive effects of raw GM rind in Flinders Sensitive Line (FSL) rats, a genetic model of depression, following acute and chronic treatment compared to a reference antidepressant, imipramine (IMI). The chemical composition of the GM extract was analysed for levels of α- and γ-mangostin. The acute dose-dependent effects of GM (50, 150 and 200 mg/kg po), IMI (20 mg/kg po) and vehicle were determined in the forced swim test (FST) in FSL rats, versus Flinders Resistant Line (FRL) control rats. Locomotor testing was conducted using the open field test (OFT). Using the most effective dose above coupled with behavioral testing in the FST and cognitive assessment in the novel object recognition test (nORT), a fixed dose 14-day treatment study of GM was performed and compared to IMI- (20 mg/kg/day) and vehicle-treated animals. Chronic treated animals were also assessed with respect to frontal cortex and hippocampal monoamine levels and accumulation of malondialdehyde. FSL rats showed significant cognitive deficits and depressive-like behavior, with disordered cortico-hippocampal 5-hydroxyindole acetic acid (5-HIAA) and noradrenaline (NA), as well as elevated hippocampal lipid peroxidation. Acute and chronic IMI treatment evoked pronounced antidepressant-like effects. Raw GM extract contained 117 mg/g and 11 mg/g α- and γ-mangostin, respectively, with acute GM demonstrating antidepressant-like effects at 50 mg/kg/day. Chronic GM (50 mg/kg/d) displayed significant antidepressant- and pro-cognitive effects, while demonstrating parity with IMI. Both behavioral and monoamine assessments suggest a more prominent serotonergic action for GM as opposed to a noradrenergic action for IMI, while both IMI and GM reversed hippocampal lipid peroxidation in FSL animals. Concluding, FSL rats present with cognitive deficits and depressive-like behaviors that are reversed by acute and chronic GM treatment, similar to that of IMI.

Femtosecond laser beam propagation through corneal tissue: Evaluation of therapeutic laser-stimulated second and third- harmonic generation

NASA Astrophysics Data System (ADS)

Calhoun, William R., III

One of the most recent advancements in laser technology is the development of ultrashort pulsed femtosecond lasers (FSLs). FSLs are improving many fields due to their unique extreme precision, low energy and ablation characteristics. In the area of laser medicine, ophthalmic surgeries have seen very promising developments. Some of the most commonly performed surgical operations in the world, including laser-assisted in-situ keratomileusis (LASIK), lens replacement (cataract surgery), and keratoplasty (cornea transplant), now employ FSLs for their unique abilities that lead to improved clinical outcome and patient satisfaction. The application of FSLs in medical therapeutics is a recent development, and although they offer many benefits, FSLs also stimulate nonlinear optical effects (NOEs), many of which were insignificant with previously developed lasers. NOEs can change the laser characteristics during propagation through a medium, which can subsequently introduce unique safety concerns for the surrounding tissues. Traditional approaches for characterizing optical effects, laser performance, safety and efficacy do not properly account for NOEs, and there remains a lack of data that describe NOEs in clinically relevant procedures and tissues. As FSL technology continues to expand towards new applications, FSL induced NOEs need to be better understood in order to ensure safety as FSL medical devices and applications continue to evolve at a rapid pace. In order to improve the understanding of FSL-tissue interactions related to NOEs stimulated during laser beam propagation though corneal tissue, research investigations were conducted to evaluate corneal optical properties and determine how corneal tissue properties including corneal layer, collagen orientation and collagen crosslinking, and laser parameters including pulse energy, repetition rate and numerical aperture affect second and third-harmonic generation (HG) intensity, duration and efficiency. The results of these studies revealed that all laser parameters and tissue properties had a substantial influence on HG. The dynamic relationship between optical breakdown and HG was responsible for many observed changes in HG metrics. The results also demonstrated that the new generation of therapeutic FSLs has the potential to generate hazardous effects if not carefully controlled. Finally, recommendations are made to optimize current and guide future FSL applications.

[Femtosecond laser in cataract surgery. A critical appraisal].

PubMed

Menapace, R M; Dick, H B

2014-01-01

The use of femtosecond lasers (FSL) is increasingly spreading in cataract surgery. Potential advantages over standard manual cataract surgery are the superior precision of corneal incisions and capsular openings as well as the reduction of ultrasound energy for lens nucleus work-up. Exact positioning and dimensioning of the anterior capsular opening should help reduce decentration and tilt of the intraocular lens (IOL) optics and thus achieve better target refraction. Together with the possibility to correct low-grade corneal astigmatism by precise arcuate incision, FSL technology is expected to convert cataract surgery from a purely curative into a refractive procedure. Apart from own experiences this review article critically analyses the pertinent literature published so far as well as congress presentations and personal reports of other FSL surgeons. The advantages and disadvantages are scrutinized with regard to their impact on the surgical and refractive results and compared with those experienced by the authors with manual cataract surgery over several decades. Economic and healthcare political aspects are also addressed. The use of FSL surgery improves the precision and reproducibility of corneal incisions and the capsular opening and reduces the amount of ultrasound energy required for lens nucleus work-up. However, the clinical benefits must be put into perspective due to the subsequent surgical manipulation of the incisions (during lens emulsification, aspiration and IOL injection), the lacking possibility to visualize the crystalline lens equator as the reference for correct capsulotomy centration and the relativity of ultrasound energy consumption on the corneal endothelial trauma. This is of particular relevance against the background of the significantly higher costs. Conversely, tears of the anterior capsule edge which, apart from interfering with correct IOL positioning, may entail serious complications presently occur more frequently with all FSL instruments. From the economic and healthcare political viewpoint, thought should be given to the possible acquisition of the cataract surgical business by the industry or investors, as cataract surgery is a high-volume standardized procedure with enormous future potential. This could fundamentally change our currently decentralized and individualized structures and subsequently the steam of patient and make surgeons largely dependent or superfluous.

Effect of laser polarization and pulse energy on therapeutic, femtosecond laser-induced second harmonic generation in corneal tissue (Conference Presentation)

NASA Astrophysics Data System (ADS)

Calhoun, William R.; Ilev, Ilko K.

2016-03-01

Some of the most commonly performed surgical operations in the world, including laser-assisted in-situ keratomileusis (LASIK), lens replacement (e.g. cataract surgery), and keratoplasty (cornea transplant), now employ therapeutic infrared femtosecond lasers (FSLs) for their extreme precision, low energy delivered into tissue and advanced ablation characteristics. Although the widely exploited applications of FSLs in medical therapeutics offer significant benefits, FSLs must generate very high intensities in order to achieve optical breakdown, the predominant tissue ablative mechanism, which can also stimulate nonlinear optical effects such as harmonic generation, an effect that generates coherent visible and UV light in the case of second- (SHG) and third-harmonic generation (THG), respectively. In order to improve the understanding of HG in corneal tissue, the effect of FSL polarization and pulse energy were investigated. FSL stimulated SHG intensity in corneal tissue was measured as the laser polarization was rotated 360 degrees. Further, the pulse energy at the SHG wavelength were measured for single FSL pulses as the pulse energy at the fundamental wavelength was varied through a range of clinically relevant values. The results of this study revealed SHG intensity oscillated with laser polarization, having a variation greater than 20%. This relationship seems to due to the intrinsic anisotropy of collagen fibril hyperpolarizability, not related to tissue birefringence. SHG pulse energy measurements showed an increase in SHG pulse energy with increasing FSL pulse energy, however conversion efficiency decreased. This may be related to the dynamic relationship between optical breakdown leading to tissue destruction and HG evolution.

A Robust and Scalable Software Library for Parallel Adaptive Refinement on Unstructured Meshes

NASA Technical Reports Server (NTRS)

Lou, John Z.; Norton, Charles D.; Cwik, Thomas A.

1999-01-01

The design and implementation of Pyramid, a software library for performing parallel adaptive mesh refinement (PAMR) on unstructured meshes, is described. This software library can be easily used in a variety of unstructured parallel computational applications, including parallel finite element, parallel finite volume, and parallel visualization applications using triangular or tetrahedral meshes. The library contains a suite of well-designed and efficiently implemented modules that perform operations in a typical PAMR process. Among these are mesh quality control during successive parallel adaptive refinement (typically guided by a local-error estimator), parallel load-balancing, and parallel mesh partitioning using the ParMeTiS partitioner. The Pyramid library is implemented in Fortran 90 with an interface to the Message-Passing Interface (MPI) library, supporting code efficiency, modularity, and portability. An EM waveguide filter application, adaptively refined using the Pyramid library, is illustrated.

A Framework for Linear and Non-Linear Registration of Diffusion-Weighted MRIs Using Angular Interpolation

PubMed Central

Duarte-Carvajalino, Julio M.; Sapiro, Guillermo; Harel, Noam; Lenglet, Christophe

2013-01-01

Registration of diffusion-weighted magnetic resonance images (DW-MRIs) is a key step for population studies, or construction of brain atlases, among other important tasks. Given the high dimensionality of the data, registration is usually performed by relying on scalar representative images, such as the fractional anisotropy (FA) and non-diffusion-weighted (b0) images, thereby ignoring much of the directional information conveyed by DW-MR datasets itself. Alternatively, model-based registration algorithms have been proposed to exploit information on the preferred fiber orientation(s) at each voxel. Models such as the diffusion tensor or orientation distribution function (ODF) have been used for this purpose. Tensor-based registration methods rely on a model that does not completely capture the information contained in DW-MRIs, and largely depends on the accurate estimation of tensors. ODF-based approaches are more recent and computationally challenging, but also better describe complex fiber configurations thereby potentially improving the accuracy of DW-MRI registration. A new algorithm based on angular interpolation of the diffusion-weighted volumes was proposed for affine registration, and does not rely on any specific local diffusion model. In this work, we first extensively compare the performance of registration algorithms based on (i) angular interpolation, (ii) non-diffusion-weighted scalar volume (b0), and (iii) diffusion tensor image (DTI). Moreover, we generalize the concept of angular interpolation (AI) to non-linear image registration, and implement it in the FMRIB Software Library (FSL). We demonstrate that AI registration of DW-MRIs is a powerful alternative to volume and tensor-based approaches. In particular, we show that AI improves the registration accuracy in many cases over existing state-of-the-art algorithms, while providing registered raw DW-MRI data, which can be used for any subsequent analysis. PMID:23596381

PANDA: a pipeline toolbox for analyzing brain diffusion images.

PubMed

Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

2013-01-01

Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named "Pipeline for Analyzing braiN Diffusion imAges" (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

Brain Structures Associated with Internet Addiction Tendency in Adolescent Online Game Players

PubMed Central

Pan, Nannan; Yang, Yongxin; Du, Xin; Qi, Xin; Du, Guijin; Zhang, Yang; Li, Xiaodong; Zhang, Quan

2018-01-01

With the development of the Internet, an increasing number of adolescents play online game excessively, which leads to adverse effects on individuals and society. Previous studies have demonstrated altered gray-matter volume (GMV) in individuals with Internet gaming disorder (IGD), but the relationship between the tendency to IGD and the GMV across whole brain is still unclear in adolescents. In the present study, anatomical imaging with high resolution was performed on 67 male adolescents who played online game; and Young’s Internet addiction test (IAT) was conducted to test the tendency to IGD. FMRIB Software Library (FSL) was used to calculate the voxel-based correlations between the GMV and the IAT score after controlling for the age and years of education. The GMVs of the bilateral postcentral gyri (postCG), the bilateral precentral gyri (preCG), the right precuneus, the left posterior midcingulate cortex (pMCC), the left inferior parietal lobe (IPL), and the right middle frontal gyrus (MFG) were negatively correlated with the IAT score. The correlation still existed between the IAT score and the GMVs of the bilateral postCG, the left preCG, the left pMCC, and the right MFG after controlling for the total time of playing online game. When the participants were divided into two groups according to the IAT score, the GMVs of these IAT-related brain regions were lower in high IAT score subgroup (IAT score >50) than in low IAT score subgroup (IAT score ≤50). Our results suggested that the GMVs of brain regions involved in sensorimotor process and cognitive control were associated with the IGD tendency. These findings may lead to new targets for preventing and treating the IGD. PMID:29559931

PANDA: a pipeline toolbox for analyzing brain diffusion images

PubMed Central

Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

2013-01-01

Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named “Pipeline for Analyzing braiN Diffusion imAges” (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies. PMID:23439846

Brain Structures Associated with Internet Addiction Tendency in Adolescent Online Game Players.

PubMed

Pan, Nannan; Yang, Yongxin; Du, Xin; Qi, Xin; Du, Guijin; Zhang, Yang; Li, Xiaodong; Zhang, Quan

2018-01-01

With the development of the Internet, an increasing number of adolescents play online game excessively, which leads to adverse effects on individuals and society. Previous studies have demonstrated altered gray-matter volume (GMV) in individuals with Internet gaming disorder (IGD), but the relationship between the tendency to IGD and the GMV across whole brain is still unclear in adolescents. In the present study, anatomical imaging with high resolution was performed on 67 male adolescents who played online game; and Young's Internet addiction test (IAT) was conducted to test the tendency to IGD. FMRIB Software Library (FSL) was used to calculate the voxel-based correlations between the GMV and the IAT score after controlling for the age and years of education. The GMVs of the bilateral postcentral gyri (postCG), the bilateral precentral gyri (preCG), the right precuneus, the left posterior midcingulate cortex (pMCC), the left inferior parietal lobe (IPL), and the right middle frontal gyrus (MFG) were negatively correlated with the IAT score. The correlation still existed between the IAT score and the GMVs of the bilateral postCG, the left preCG, the left pMCC, and the right MFG after controlling for the total time of playing online game. When the participants were divided into two groups according to the IAT score, the GMVs of these IAT-related brain regions were lower in high IAT score subgroup (IAT score >50) than in low IAT score subgroup (IAT score ≤50). Our results suggested that the GMVs of brain regions involved in sensorimotor process and cognitive control were associated with the IGD tendency. These findings may lead to new targets for preventing and treating the IGD.

A Framework for Linear and Non-Linear Registration of Diffusion-Weighted MRIs Using Angular Interpolation.

PubMed

Duarte-Carvajalino, Julio M; Sapiro, Guillermo; Harel, Noam; Lenglet, Christophe

2013-01-01

Registration of diffusion-weighted magnetic resonance images (DW-MRIs) is a key step for population studies, or construction of brain atlases, among other important tasks. Given the high dimensionality of the data, registration is usually performed by relying on scalar representative images, such as the fractional anisotropy (FA) and non-diffusion-weighted (b0) images, thereby ignoring much of the directional information conveyed by DW-MR datasets itself. Alternatively, model-based registration algorithms have been proposed to exploit information on the preferred fiber orientation(s) at each voxel. Models such as the diffusion tensor or orientation distribution function (ODF) have been used for this purpose. Tensor-based registration methods rely on a model that does not completely capture the information contained in DW-MRIs, and largely depends on the accurate estimation of tensors. ODF-based approaches are more recent and computationally challenging, but also better describe complex fiber configurations thereby potentially improving the accuracy of DW-MRI registration. A new algorithm based on angular interpolation of the diffusion-weighted volumes was proposed for affine registration, and does not rely on any specific local diffusion model. In this work, we first extensively compare the performance of registration algorithms based on (i) angular interpolation, (ii) non-diffusion-weighted scalar volume (b0), and (iii) diffusion tensor image (DTI). Moreover, we generalize the concept of angular interpolation (AI) to non-linear image registration, and implement it in the FMRIB Software Library (FSL). We demonstrate that AI registration of DW-MRIs is a powerful alternative to volume and tensor-based approaches. In particular, we show that AI improves the registration accuracy in many cases over existing state-of-the-art algorithms, while providing registered raw DW-MRI data, which can be used for any subsequent analysis.

Copyright: Know Your Electronic Rights!

ERIC Educational Resources Information Center

Valauskas, Edward J.

1992-01-01

Defines copyright and examines the interests of computer software publishers. Issues related to the rights of libraries in the circulation of software are discussed, including the fair use principle, software vendors' licensing agreements, and cooperation between libraries and vendors. An inset describes procedures for internal auditing of…

Teaching Reprint File Management: Basic Principles and Software Programs.

ERIC Educational Resources Information Center

Wood, Elizabeth H.

1989-01-01

Describes a workshop for teaching library users how to manage reprint files which was developed at the University of Southern California Norris Medical Library. Software programs designed for this purpose are suggested, and a sidebar lists software features to consider. (eight references) (MES)

Apples in the Apple Library--How One Library Took a Byte.

ERIC Educational Resources Information Center

Ertel, Monica

1983-01-01

Summarizes automation of a specialized library at Apple Computer, Inc., describing software packages chosen for the following functions: word processing/text editing; cataloging and circulation; reference; and in-house databases. Examples of each function and additional sources of information on software and equipment mentioned in the article are…

A Multi-User Microcomputer System for Small Libraries.

ERIC Educational Resources Information Center

Leggate, Peter

1988-01-01

Describes the development of Bookshelf, a multi-user microcomputer system for small libraries that uses an integrated software package. The discussion covers the design parameters of the package, which were based on a survey of seven small libraries, and some characteristics of the software. (three notes with references) (CLB)

One library's experience with review and selection of chat software for reference.

PubMed

Behm, Leslie M

2003-01-01

When Michigan State University (MSU) Libraries decided to make the foray into virtual reference, the first thing that needed to be done was to decide on the software to use. This article discusses the process used including the items considered essential (deal-breakers) for software to make the first cut, what other features needed to be included, and what features would be useful but were not critical. A literature review of some useful current articles on virtual reference is included. The vendor and software ultimately selected was not one of the original vendors; how MSU Libraries was able to evaluate and select Docutek is presented. A matrix for software comparison is included in the appendix.

Public Access to Digital Material; A Call to Researchers: Digital Libraries Need Collaboration across Disciplines; Greenstone: Open-Source Digital Library Software; Retrieval Issues for the Colorado Digitization Project's Heritage Database; Report on the 5th European Conference on Digital Libraries, ECDL 2001; Report on the First Joint Conference on Digital Libraries.

ERIC Educational Resources Information Center

Kahle, Brewster; Prelinger, Rick; Jackson, Mary E.; Boyack, Kevin W.; Wylie, Brian N.; Davidson, George S.; Witten, Ian H.; Bainbridge, David; Boddie, Stefan J.; Garrison, William A.; Cunningham, Sally Jo; Borgman, Christine L.; Hessel, Heather

2001-01-01

These six articles discuss various issues relating to digital libraries. Highlights include public access to digital materials; intellectual property concerns; the need for collaboration across disciplines; Greenstone software for construction and presentation of digital information collections; the Colorado Digitization Project; and conferences…

GeoTess: A generalized Earth model software utility

DOE PAGES

Ballard, Sanford; Hipp, James; Kraus, Brian; ...

2016-03-23

GeoTess is a model parameterization and software support library that manages the construction, population, storage, and interrogation of data stored in 2D and 3D Earth models. Here, the software is available in Java and C++, with a C interface to the C++ library.

Designing a Decision Support System (DSS) for Academic Library Managers Using Preprogrammed Application Software on a Microcomputer.

ERIC Educational Resources Information Center

McDonald, Joseph

1986-01-01

Focusing on management decisions in academic libraries, this article compares management information systems (MIS) with decision support systems (DSS) and discusses the decision-making process, information needs of library managers, sources of data, reasons for choosing microcomputer, preprogrammed application software, prototyping a system, and…

Digital Preservation in Open-Source Digital Library Software

ERIC Educational Resources Information Center

Madalli, Devika P.; Barve, Sunita; Amin, Saiful

2012-01-01

Digital archives and digital library projects are being initiated all over the world for materials of different formats and domains. To organize, store, and retrieve digital content, many libraries as well as archiving centers are using either proprietary or open-source software. While it is accepted that print media can survive for centuries with…

The Elusive Cost of Library Software

ERIC Educational Resources Information Center

Breeding, Marshall

2009-01-01

Software pricing is not a straightforward issue, since each procurement involves a special business arrangement between a library and its chosen vendor. The author thinks that it is reasonable to scale the cost of a product to such factors as the size of the library, the complexity of the installation, the number of simultaneous users, or the…

A basic analysis toolkit for biological sequences

PubMed Central

Giancarlo, Raffaele; Siragusa, Alessandro; Siragusa, Enrico; Utro, Filippo

2007-01-01

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL. PMID:17877802

Femtosecond laser cutting of endothelial grafts: comparison of endothelial and epithelial applanation.

PubMed

Bernard, Aurélien; He, Zhiguo; Gauthier, Anne Sophie; Trone, Marie Caroline; Baubeau, Emmanuel; Forest, Fabien; Dumollard, Jean Marc; Peocʼh, Michel; Thuret, Gilles; Gain, Philippe

2015-02-01

Stromal surface quality of endothelial lamellae cut for endothelial keratoplasty with a femtosecond laser (FSL) with epithelial applanation remains disappointing. Applanation of the endothelial side of the cornea, mounted inverted on an artificial chamber, has therefore been proposed to improve cut quality. We compared lamellar quality after FSL cutting using epithelial versus endothelial applanation. Lamellae were cut with an FSL from organ-cultured corneas. After randomization, 7 were cut with epithelial applanation and 7 with endothelial applanation. Lamellae of 50-, 75-, and 100-μm thickness were targeted. Thickness was measured by optical coherence tomography before and immediately after cutting. Viable endothelial cell density was quantified immediately after cutting using triple labeling with Hoechst/ethidium/calcein-AM coupled with image analysis with ImageJ. The stromal surface was evaluated by 9 masked observers using semiquantitative scoring of scanning electronic microscopy images. Histology of 2 samples was also analyzed before lamellar detachment. Precision (difference in target/actual thickness) and thickness regularity [coefficient of variation (CV) of 10 measurements] were significantly better with endothelial applanation (precision: 18 μm; range, 10-30; CV: 11%; range, 8-12) than with epithelial applanation (precision: 84 μm; range, 54-107; P = 0.002; CV: 24%; range, 13-47; P = 0.001). Endothelial applanation provided thinner lamellae. However, viable endothelial cell density was significantly lower after endothelial applanation (1183 cells/mm2; range, 787-1725 versus 1688 cells/mm2; range, 1288-2025; P = 0.018). FSL cutting of endothelial lamellae using endothelial applanation provides thinner more regular grafts with more predictable thickness than with conventional epithelial applanation but strongly reduces the pool of viable endothelial cells.

Dissociation between learning and memory impairment and other sickness behaviours during simulated Mycoplasma infection in rats.

PubMed

Swanepoel, Tanya; Harvey, Brian H; Harden, Lois M; Laburn, Helen P; Mitchell, Duncan

2011-11-01

To investigate potential consequences for learning and memory, we have simulated the effects of Mycoplasma infection, in rats, by administering fibroblast-stimulating lipopepide-1 (FSL-1), a pyrogenic moiety of Mycoplasma salivarium. We measured the effects on body temperature, cage activity, food intake, and on spatial learning and memory in a Morris Water Maze. Male Sprague-Dawley rats had radio transponders implanted to measure abdominal temperature and cage activity. After recovery, rats were assigned randomly to receive intraperitoneal (I.P.) injections of FSL-1 (500 or 1000 μg kg(-1) in 1 ml kg(-1) phosphate-buffered saline; PBS) or vehicle (PBS, 1 ml kg(-1)). Body mass and food intake were measured daily. Training in the Maze commenced 18 h after injections and continued daily for four days. Spatial memory was assessed on the fifth day. In other rats, we measured concentrations of brain pro-inflammatory cytokines, interleukin (IL)-1β and IL-6, at 3 and 18 h after injections. FSL-1 administration induced a dose-dependent fever (∼1°C) for two days, lethargy (∼78%) for four days, anorexia (∼65%) for three days and body mass stunting (∼6%) for at least four days. Eighteen hours after FSL-1 administration, when concentrations of IL-1β, but not that of IL-6, were elevated in both the hypothalamus and the hippocampus, and when rats were febrile, lethargic and anorexic, learning in the Maze was unaffected. There also was no memory impairment. Our results support emerging evidence that impaired learning and memory is not inevitable during simulated infection. Copyright © 2011 Elsevier Inc. All rights reserved.

Differential interaction with the serotonin system by S-ketamine, vortioxetine, and fluoxetine in a genetic rat model of depression.

PubMed

du Jardin, Kristian Gaarn; Liebenberg, Nico; Müller, Heidi Kaastrup; Elfving, Betina; Sanchez, Connie; Wegener, Gregers

2016-07-01

The mechanisms mediating ketamine's antidepressant effect have only been partly resolved. Recent preclinical reports implicate serotonin (5-hydroxytryptamine; 5-HT) in the antidepressant-like action of ketamine. Vortioxetine is a multimodal-acting antidepressant that is hypothesized to exert its therapeutic activity through 5-HT reuptake inhibition and modulation of several 5-HT receptors. The objective of this study was to evaluate the therapeutic-like profiles of S-ketamine, vortioxetine, and the serotonin reuptake inhibitor fluoxetine in response to manipulation of 5-HT tone. Flinders Sensitive Line (FSL) rats, a genetic model of depression, were depleted of 5-HT by repeated administration of 4-chloro-DL-phenylalanine methyl ester HCl (pCPA). Using pCPA-pretreated and control FSL rats, we investigated the acute and sustained effects of S-ketamine (15 mg/kg), fluoxetine (10 mg/kg), or vortioxetine (10 mg/kg) on recognition memory and depression-like behavior in the object recognition task (ORT) and forced swim test (FST), respectively. The behavioral phenotype of FSL rats was unaffected by 5-HT depletion. Vortioxetine, but not fluoxetine or S-ketamine, acutely ameliorated the memory deficits of FSL rats in the ORT irrespective of 5-HT tone. No sustained effects were observed in the ORT. In the FST, all three drugs demonstrated acute antidepressant-like activity but only S-ketamine had sustained effects. Unlike vortioxetine, the antidepressant-like responses of fluoxetine and S-ketamine were abolished by 5-HT depletion. These observations suggest that the acute and sustained antidepressant-like effects of S-ketamine depend on endogenous stimulation of 5-HT receptors. In contrast, the acute therapeutic-like effects of vortioxetine on memory and depression-like behavior may be mediated by direct activity at 5-HT receptors.

DOCLIB: a software library for document processing

NASA Astrophysics Data System (ADS)

Jaeger, Stefan; Zhu, Guangyu; Doermann, David; Chen, Kevin; Sampat, Summit

2006-01-01

Most researchers would agree that research in the field of document processing can benefit tremendously from a common software library through which institutions are able to develop and share research-related software and applications across academic, business, and government domains. However, despite several attempts in the past, the research community still lacks a widely-accepted standard software library for document processing. This paper describes a new library called DOCLIB, which tries to overcome the drawbacks of earlier approaches. Many of DOCLIB's features are unique either in themselves or in their combination with others, e.g. the factory concept for support of different image types, the juxtaposition of image data and metadata, or the add-on mechanism. We cherish the hope that DOCLIB serves the needs of researchers better than previous approaches and will readily be accepted by a larger group of scientists.

The CECAM Electronic Structure Library: community-driven development of software libraries for electronic structure simulations

NASA Astrophysics Data System (ADS)

Oliveira, Micael

The CECAM Electronic Structure Library (ESL) is a community-driven effort to segregate shared pieces of software as libraries that could be contributed and used by the community. Besides allowing to share the burden of developing and maintaining complex pieces of software, these can also become a target for re-coding by software engineers as hardware evolves, ensuring that electronic structure codes remain at the forefront of HPC trends. In a series of workshops hosted at the CECAM HQ in Lausanne, the tools and infrastructure for the project were prepared, and the first contributions were included and made available online (http://esl.cecam.org). In this talk I will present the different aspects and aims of the ESL and how these can be useful for the electronic structure community.

Component Technology for High-Performance Scientific Simulation Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Epperly, T; Kohn, S; Kumfert, G

2000-11-09

We are developing scientific software component technology to manage the complexity of modem, parallel simulation software and increase the interoperability and re-use of scientific software packages. In this paper, we describe a language interoperability tool named Babel that enables the creation and distribution of language-independent software libraries using interface definition language (IDL) techniques. We have created a scientific IDL that focuses on the unique interface description needs of scientific codes, such as complex numbers, dense multidimensional arrays, complicated data types, and parallelism. Preliminary results indicate that in addition to language interoperability, this approach provides useful tools for thinking about themore » design of modem object-oriented scientific software libraries. Finally, we also describe a web-based component repository called Alexandria that facilitates the distribution, documentation, and re-use of scientific components and libraries.« less

INTERIM -- Starlink Software Environment

NASA Astrophysics Data System (ADS)

Pearce, Dave; Pavelin, Cliff; Lawden, M. D.

Early versions of this paper were based on a number of other papers produced at a very early stage of the Starlink project. They contained a description of a specific implementation of a subroutine library, speculations on the desirable attributes of a software environment, and future development plans. They reflected the experimental nature of the Starlink software environment at that time. Since then, the situation has changed. The implemented subroutine library, INTERIM_DIR:INTERIM.OLB, is now a well established and widely used piece of software. A completely new Starlink software environment (ADAM) has been developed and distributed. Thus the library released in 1980 as `STARLINK' and now called `INTERIM' has reached the end of its development cycle and is now frozen in its current state, apart from bug corrections. This paper has, therefore, been completely rewritten and restructured to reflect the new situation. Its aim is to describe the facilities of the INTERIM subroutine library as clearly and concisely as possible. It avoids speculation, discussion of design decisions, and announcements of future plans.

Software Library for Bruker TopSpin NMR Data Files

DOE Office of Scientific and Technical Information (OSTI.GOV)

A software library for parsing and manipulating frequency-domain data files that have been processed using the Bruker TopSpin NMR software package. In the context of NMR, the term "processed" indicates that the end-user of the Bruker TopSpin NMR software package has (a) Fourier transformed the raw, time-domain data (the Free Induction Decay) into the frequency-domain and (b) has extracted the list of NMR peaks.

Software for Real-Time Analysis of Subsonic Test Shot Accuracy

DTIC Science & Technology

2014-03-01

used the C++ programming language, the Open Source Computer Vision ( OpenCV ®) software library, and Microsoft Windows® Application Programming...video for comparison through OpenCV image analysis tools. Based on the comparison, the software then computed the coordinates of each shot relative to...DWB researchers wanted to use the Open Source Computer Vision ( OpenCV ) software library for capturing and analyzing frames of video. OpenCV contains

Assessing the Effects of Software Platforms on Volumetric Segmentation of Glioblastoma

PubMed Central

Dunn, William D.; Aerts, Hugo J.W.L.; Cooper, Lee A.; Holder, Chad A.; Hwang, Scott N.; Jaffe, Carle C.; Brat, Daniel J.; Jain, Rajan; Flanders, Adam E.; Zinn, Pascal O.; Colen, Rivka R.; Gutman, David A.

2017-01-01

Background Radiological assessments of biologically relevant regions in glioblastoma have been associated with genotypic characteristics, implying a potential role in personalized medicine. Here, we assess the reproducibility and association with survival of two volumetric segmentation platforms and explore how methodology could impact subsequent interpretation and analysis. Methods Post-contrast T1- and T2-weighted FLAIR MR images of 67 TCGA patients were segmented into five distinct compartments (necrosis, contrast-enhancement, FLAIR, post contrast abnormal, and total abnormal tumor volumes) by two quantitative image segmentation platforms - 3D Slicer and a method based on Velocity AI and FSL. We investigated the internal consistency of each platform by correlation statistics, association with survival, and concordance with consensus neuroradiologist ratings using ordinal logistic regression. Results We found high correlations between the two platforms for FLAIR, post contrast abnormal, and total abnormal tumor volumes (spearman’s r(67) = 0.952, 0.959, and 0.969 respectively). Only modest agreement was observed for necrosis and contrast-enhancement volumes (r(67) = 0.693 and 0.773 respectively), likely arising from differences in manual and automated segmentation methods of these regions by 3D Slicer and Velocity AI/FSL, respectively. Survival analysis based on AUC revealed significant predictive power of both platforms for the following volumes: contrast-enhancement, post contrast abnormal, and total abnormal tumor volumes. Finally, ordinal logistic regression demonstrated correspondence to manual ratings for several features. Conclusion Tumor volume measurements from both volumetric platforms produced highly concordant and reproducible estimates across platforms for general features. As automated or semi-automated volumetric measurements replace manual linear or area measurements, it will become increasingly important to keep in mind that measurement differences between segmentation platforms for more detailed features could influence downstream survival or radio genomic analyses. PMID:29600296

Student project of optical system analysis API-library development

NASA Astrophysics Data System (ADS)

Ivanova, Tatiana; Zhukova, Tatiana; Dantcaranov, Ruslan; Romanova, Maria; Zhadin, Alexander; Ivanov, Vyacheslav; Kalinkina, Olga

2017-08-01

In the paper API-library software developed by students of Applied and Computer Optics Department (ITMO University) for optical system design is presented. The library performs paraxial and real ray tracing, calculates 3d order (Seidel) aberration and real ray aberration of axis and non-axis beams (wave, lateral, longitudinal, coma, distortion etc.) and finally, approximate wave aberration by Zernike polynomials. Real aperture can be calculated by considering of real rays tracing failure on each surface. So far we assume optical system is centered, with spherical or 2d order aspherical surfaces. Optical glasses can be set directly by refraction index or by dispersion coefficients. The library can be used for education or research purposes in optical system design area. It provides ready to use software functions for optical system simulation and analysis that developer can simply plug into their software development for different purposes, for example for some specific synthesis tasks or investigation of new optimization modes. In the paper we present an example of using the library for development of cemented doublet synthesis software based on Slusarev's methodology. The library is used in optical system optimization recipes course for deep studying of optimization model and its application for optical system design. Development of such software is an excellent experience for students and help to understanding optical image modeling and quality analysis. This development is organized as student group joint project. We try to organize it as a group in real research and development project, so each student has his own role in the project and then use whole library functionality in his own master or bachelor thesis. Working in such group gives students useful experience and opportunity to work as research and development engineer of scientific software in the future.

Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries

PubMed Central

Urbach, Jonathan M.; Wei, Tao; Liberati, Nicole; Grenfell-Lee, Daniel; Villanueva, Jacinto; Wu, Gang; Ausubel, Frederick M.

2015-01-01

PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software. PMID:19343706

Biocompatibility of the micro-patterned NiTi surface produced by femtosecond laser

NASA Astrophysics Data System (ADS)

Liang, Chunyong; Wang, Hongshui; Yang, Jianjun; Li, Baoe; Yang, Yang; Li, Haipeng

2012-11-01

Biocompatibility of the micro-patterned NiTi surface produced by femtosecond laser (FSL) was studied in this work. The surface characteristics of the laser treated NiTi alloys were investigated by scanning electron microscopy (SEM), atom force microscopy (AFM), X-ray diffractometry (XRD) and X-ray photoelectron spectrum (XPS). The biocompatibility was evaluated by in vitro cell culture test. The results showed that, grooves, ripples, which covered by nanoparticles were formed on the sample surfaces, and the Ni/Ti ratio on the alloy surface increased with increasing laser energy. The crystal structure was not changed by laser treatment. However, the cell culture test proved that the micro-patterns induced by FSL were beneficial to improve the biocompatibility of NiTi alloys: the growth of osteoblasts oriented along the grooves, a large amount of synapses and filopodias were formed due to the ripples, holes and nanoparticles on the alloy surface, and the proliferation rate and alkaline phosphatase (ALP) content of cells were increased after FSL treatment. However, due to the toxicity of Ni ions on cell growth, the NiTi alloy surface should not be treated by laser fluence of more than 3.82 J/cm2 to obtain the ideal biocompatibility.

Automation and Networking of Public Libraries in India Using the E-Granthalaya Software from the National Informatics Centre

ERIC Educational Resources Information Center

Matoria, Ram Kumar; Upadhyay, P. K.; Moni, Madaswamy

2007-01-01

Purpose: To describe the development of the library management system, e-Granthalaya, for public libraries in India. This is an initiative of the Indian government's National Informatics Centre (NIC). The paper outlines the challenges and the potential of a full-scale deployment of this software at a national level. Design/methodology/approach:…

A user's guide to Sandia's latin hypercube sampling software : LHS UNIX library/standalone version.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, Laura Painton; Wyss, Gregory Dane

2004-07-01

This document is a reference guide for the UNIX Library/Standalone version of the Latin Hypercube Sampling Software. This software has been developed to generate Latin hypercube multivariate samples. This version runs on Linux or UNIX platforms. This manual covers the use of the LHS code in a UNIX environment, run either as a standalone program or as a callable library. The underlying code in the UNIX Library/Standalone version of LHS is almost identical to the updated Windows version of LHS released in 1998 (SAND98-0210). However, some modifications were made to customize it for a UNIX environment and as a librarymore » that is called from the DAKOTA environment. This manual covers the use of the LHS code as a library and in the standalone mode under UNIX.« less

A Language for Specifying Compiler Optimizations for Generic Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willcock, Jeremiah J.

2007-01-01

Compiler optimization is important to software performance, and modern processor architectures make optimization even more critical. However, many modern software applications use libraries providing high levels of abstraction. Such libraries often hinder effective optimization — the libraries are difficult to analyze using current compiler technology. For example, high-level libraries often use dynamic memory allocation and indirectly expressed control structures, such as iteratorbased loops. Programs using these libraries often cannot achieve an optimal level of performance. On the other hand, software libraries have also been recognized as potentially aiding in program optimization. One proposed implementation of library-based optimization is to allowmore » the library author, or a library user, to define custom analyses and optimizations. Only limited systems have been created to take advantage of this potential, however. One problem in creating a framework for defining new optimizations and analyses is how users are to specify them: implementing them by hand inside a compiler is difficult and prone to errors. Thus, a domain-specific language for librarybased compiler optimizations would be beneficial. Many optimization specification languages have appeared in the literature, but they tend to be either limited in power or unnecessarily difficult to use. Therefore, I have designed, implemented, and evaluated the Pavilion language for specifying program analyses and optimizations, designed for library authors and users. These analyses and optimizations can be based on the implementation of a particular library, its use in a specific program, or on the properties of a broad range of types, expressed through concepts. The new system is intended to provide a high level of expressiveness, even though the intended users are unlikely to be compiler experts.« less

Building a Library Web Server on a Budget.

ERIC Educational Resources Information Center

Orr, Giles

1998-01-01

Presents a method for libraries with limited budgets to create reliable Web servers with existing hardware and free software available via the Internet. Discusses staff, hardware and software requirements, and security; outlines the assembly process. (PEN)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ballard, Sanford; Hipp, James; Kraus, Brian

GeoTess is a model parameterization and software support library that manages the construction, population, storage, and interrogation of data stored in 2D and 3D Earth models. Here, the software is available in Java and C++, with a C interface to the C++ library.

Lean and Efficient Software: Whole-Program Optimization of Executables

DTIC Science & Technology

2015-09-30

libraries. Many levels of library interfaces—where some libraries are dynamically linked and some are provided in binary form only—significantly limit...software at build time. The opportunity: Our objective in this project is to substantially improve the performance, size, and robustness of binary ...executables by using static and dynamic binary program analysis techniques to perform whole-program optimization directly on compiled programs

National Software Reference Library (NSRL)

National Institute of Standards and Technology Data Gateway

National Software Reference Library (NSRL) (PC database for purchase)   A collaboration of the National Institute of Standards and Technology (NIST), the National Institute of Justice (NIJ), the Federal Bureau of Investigation (FBI), the Defense Computer Forensics Laboratory (DCFL),the U.S. Customs Service, software vendors, and state and local law enforement organizations, the NSRL is a tool to assist in fighting crime involving computers.

Moving Reference to the Web.

ERIC Educational Resources Information Center

McGlamery, Susan; Coffman, Steve

2000-01-01

Explores the possibility of using Web contact center software to offer reference assistance to remote users. Discusses a project by the Metropolitan Cooperative Library System/Santiago Library System consortium to test contact center software and to develop a virtual reference network. (Author/LRW)

Libraries for Software Use on Peregrine | High-Performance Computing | NREL

Science.gov Websites

-specific libraries. Libraries List Name Description BLAS Basic Linear Algebra Subroutines, libraries only managing hierarchically structured data. LAPACK Standard Netlib offering for computational linear algebra

The U. S. Geological Survey, Digital Spectral Library: Version 1 (0.2 to 3.0um)

USGS Publications Warehouse

Clark, Roger N.; Swayze, Gregg A.; Gallagher, Andrea J.; King, Trude V.V.; Calvin, Wendy M.

1993-01-01

We have developed a digital reflectance spectral library, with management and spectral analysis software. The library includes 498 spectra of 444 samples (some samples include a series of grain sizes) measured from approximately 0.2 to 3.0 um . The spectral resolution (Full Width Half Maximum) of the reflectance data is <= 4 nm in the visible (0.2-0.8 um) and <= 10 nm in the NIR (0.8-2.35 um). All spectra were corrected to absolute reflectance using an NIST Halon standard. Library management software lets users search on parameters (e.g. chemical formulae, chemical analyses, purity of samples, mineral groups, etc.) as well as spectral features. Minerals from borate, carbonate, chloride, element, halide, hydroxide, nitrate, oxide, phosphate, sulfate, sulfide, sulfosalt, and the silicate (cyclosilicate, inosilicate, nesosilicate, phyllosilicate, sorosilicate, and tectosilicate) classes are represented. X-Ray and chemical analyses are tabulated for many of the entries, and all samples have been evaluated for spectral purity. The library also contains end and intermediate members for the olivine, garnet, scapolite, montmorillonite, muscovite, jarosite, and alunite solid-solution series. We have included representative spectra of H2O ice, kerogen, ammonium-bearing minerals, rare-earth oxides, desert varnish coatings, kaolinite crystallinity series, kaolinite-smectite series, zeolite series, and an extensive evaporite series. Because of the importance of vegetation to climate-change studies we have include 17 spectra of tree leaves, bushes, and grasses. The library and software are available as a series of U.S.G.S. Open File reports. PC user software is available to convert the binary data to ascii files (a separate U.S.G.S. open file report). Additionally, a binary data files are on line at the U.S.G.S. in Denver for anonymous ftp to users on the Internet. The library search software enables a user to search on documentation parameters as well as spectral features. The analysis system includes general spectral analysis routines, plotting packages, radiative transfer software for computing intimate mixtures, routines to derive optical constants from reflectance spectra, tools to analyze spectral features, and the capability to access imaging spectrometer data cubes for spectral analysis. Users may build customized libraries (at specific wavelengths and spectral resolution) for their own instruments using the library software. We are currently extending spectral coverage to 150 um. The libraries (original and convolved) will be made available in the future on a CD-ROM.

ValWorkBench: an open source Java library for cluster validation, with applications to microarray data analysis.

PubMed

Giancarlo, R; Scaturro, D; Utro, F

2015-02-01

The prediction of the number of clusters in a dataset, in particular microarrays, is a fundamental task in biological data analysis, usually performed via validation measures. Unfortunately, it has received very little attention and in fact there is a growing need for software tools/libraries dedicated to it. Here we present ValWorkBench, a software library consisting of eleven well known validation measures, together with novel heuristic approximations for some of them. The main objective of this paper is to provide the interested researcher with the full software documentation of an open source cluster validation platform having the main features of being easily extendible in a homogeneous way and of offering software components that can be readily re-used. Consequently, the focus of the presentation is on the architecture of the library, since it provides an essential map that can be used to access the full software documentation, which is available at the supplementary material website [1]. The mentioned main features of ValWorkBench are also discussed and exemplified, with emphasis on software abstraction design and re-usability. A comparison with existing cluster validation software libraries, mainly in terms of the mentioned features, is also offered. It suggests that ValWorkBench is a much needed contribution to the microarray software development/algorithm engineering community. For completeness, it is important to mention that previous accurate algorithmic experimental analysis of the relative merits of each of the implemented measures [19,23,25], carried out specifically on microarray data, gives useful insights on the effectiveness of ValWorkBench for cluster validation to researchers in the microarray community interested in its use for the mentioned task. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Towards a high performance geometry library for particle-detector simulations

DOE PAGES

Apostolakis, J.; Bandieramonte, M.; Bitzes, G.; ...

2015-05-22

Thread-parallelization and single-instruction multiple data (SIMD) ”vectorisation” of software components in HEP computing has become a necessity to fully benefit from current and future computing hardware. In this context, the Geant-Vector/GPU simulation project aims to re-engineer current software for the simulation of the passage of particles through detectors in order to increase the overall event throughput. As one of the core modules in this area, the geometry library plays a central role and vectorising its algorithms will be one of the cornerstones towards achieving good CPU performance. Here, we report on the progress made in vectorising the shape primitives, asmore » well as in applying new C++ template based optimizations of existing code available in the Geant4, ROOT or USolids geometry libraries. We will focus on a presentation of our software development approach that aims to provide optimized code for all use cases of the library (e.g., single particle and many-particle APIs) and to support different architectures (CPU and GPU) while keeping the code base small, manageable and maintainable. We report on a generic and templated C++ geometry library as a continuation of the AIDA USolids project. As a result, the experience gained with these developments will be beneficial to other parts of the simulation software, such as for the optimization of the physics library, and possibly to other parts of the experiment software stack, such as reconstruction and analysis.« less

Towards a high performance geometry library for particle-detector simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Apostolakis, J.; Bandieramonte, M.; Bitzes, G.

Thread-parallelization and single-instruction multiple data (SIMD) ”vectorisation” of software components in HEP computing has become a necessity to fully benefit from current and future computing hardware. In this context, the Geant-Vector/GPU simulation project aims to re-engineer current software for the simulation of the passage of particles through detectors in order to increase the overall event throughput. As one of the core modules in this area, the geometry library plays a central role and vectorising its algorithms will be one of the cornerstones towards achieving good CPU performance. Here, we report on the progress made in vectorising the shape primitives, asmore » well as in applying new C++ template based optimizations of existing code available in the Geant4, ROOT or USolids geometry libraries. We will focus on a presentation of our software development approach that aims to provide optimized code for all use cases of the library (e.g., single particle and many-particle APIs) and to support different architectures (CPU and GPU) while keeping the code base small, manageable and maintainable. We report on a generic and templated C++ geometry library as a continuation of the AIDA USolids project. As a result, the experience gained with these developments will be beneficial to other parts of the simulation software, such as for the optimization of the physics library, and possibly to other parts of the experiment software stack, such as reconstruction and analysis.« less

Electronic Library: A TERI Experiment.

ERIC Educational Resources Information Center

Kar, Debal C.; Deb, Subrata; Kumar, Satish

2003-01-01

Discusses the development of Electronic Library at TERI (The Energy and Resources Institute, New Delhi). Highlights include: hardware and software used; the digital library/Virtual Electronic Library; directory of Internet journals; virtual reference resources; electronic collection/Physical Electronic Library; downloaded online full-length…

Comparison of four methods of surface roughness assessment of corneal stromal bed after lamellar cutting

PubMed Central

Jumelle, Clotilde; Hamri, Alina; Egaud, Gregory; Mauclair, Cyril; Reynaud, Stephanie; Dumas, Virginie; Pereira, Sandrine; Garcin, Thibaud; Gain, Philippe; Thuret, Gilles

2017-01-01

Corneal lamellar cutting with a blade or femtosecond laser (FSL) is commonly used during refractive surgery and corneal grafts. Surface roughness of the cutting plane influences postoperative visual acuity but is difficult to assess reliably. For the first time, we compared chromatic confocal microscopy (CCM) with scanning electron microscopy, atomic force microscopy (AFM) and focus-variation microscopy (FVM) to characterize surfaces of variable roughness after FSL cutting. The small area allowed by AFM hinders conclusive roughness analysis, especially with irregular cuts. FVM does not always differentiate between smooth and rough surfaces. Finally, CCM allows analysis of large surfaces and differentiates between surface states. PMID:29188095

Library Computing.

ERIC Educational Resources Information Center

Goodgion, Laurel; And Others

1986-01-01

Eight articles in special supplement to "Library Journal" and "School Library Journal" cover a computer program called "Byte into Books"; microcomputers and the small library; creating databases with students; online searching with a microcomputer; quality automation software; Meckler Publishing Company's…

Library Computing

ERIC Educational Resources Information Center

Library Computing, 1985

1985-01-01

Special supplement to "Library Journal" and "School Library Journal" covers topics of interest to school, public, academic, and special libraries planning for automation: microcomputer use, readings in automation, online searching, databases of microcomputer software, public access to microcomputers, circulation, creating a…

Managing Automation: A Process, Not a Project.

ERIC Educational Resources Information Center

Hoffmann, Ellen

1988-01-01

Discussion of issues in management of library automation includes: (1) hardware, including systems growth and contracts; (2) software changes, vendor relations, local systems, and microcomputer software; (3) item and authority databases; (4) automation and library staff, organizational structure, and managing change; and (5) environmental issues,…

ENCOMPASS: A SAGA based environment for the compositon of programs and specifications, appendix A

NASA Technical Reports Server (NTRS)

Terwilliger, Robert B.; Campbell, Roy H.

1985-01-01

ENCOMPASS is an example integrated software engineering environment being constructed by the SAGA project. ENCOMPASS supports the specification, design, construction and maintenance of efficient, validated, and verified programs in a modular programming language. The life cycle paradigm, schema of software configurations, and hierarchical library structure used by ENCOMPASS is presented. In ENCOMPASS, the software life cycle is viewed as a sequence of developments, each of which reuses components from the previous ones. Each development proceeds through the phases planning, requirements definition, validation, design, implementation, and system integration. The components in a software system are modeled as entities which have relationships between them. An entity may have different versions and different views of the same project are allowed. The simple entities supported by ENCOMPASS may be combined into modules which may be collected into projects. ENCOMPASS supports multiple programmers and projects using a hierarchical library system containing a workspace for each programmer; a project library for each project, and a global library common to all projects.

PTools: an opensource molecular docking library

PubMed Central

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-01-01

Background Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. Results We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. Conclusion The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation. PMID:19409097

PTools: an opensource molecular docking library.

PubMed

Saladin, Adrien; Fiorucci, Sébastien; Poulain, Pierre; Prévost, Chantal; Zacharias, Martin

2009-05-01

Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.

Climbing the Mountain: The Americans with Disabilities Act and Libraries.

ERIC Educational Resources Information Center

Lenn, Katy

1993-01-01

Provides suggestions for academic libraries to comply with the Americans with Disabilities Act. Topics addressed are planning, including patron surveys; physical access to buildings; signage; library security systems; furniture; library services; staff development; telephone access; library acquisitions; and equipment and software. A sidebar lists…

GLCF: Library

Science.gov Websites

Global Land Cover Facility About GLCF Research Publications Data & Products Gallery Library Services Contact Site Map Go Library Documents Proposal Reports Publications FAQ Display Materials Release News Archive Library * Display Materials * Documents * News Archive * Software e-link 4321

GridKit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peles, Slaven

2016-11-06

GridKit is a software development kit for interfacing power systems and power grid application software with high performance computing (HPC) libraries developed at National Labs and academia. It is also intended as interoperability layer between different numerical libraries. GridKit is not a standalone application, but comes with a suite of test examples illustrating possible usage.

Software, Copyright, and Site-License Agreements: Publishers' Perspective of Library Practice.

ERIC Educational Resources Information Center

Happer, Stephanie K.

Thirty-one academic publishers of stand-alone software and book/disk packages were surveyed to determine whether publishers have addressed the copyright issues inherent in circulating these packages within the library environment. Twenty-two questionnaires were returned, providing a 71% return rate. There were 18 usable questionnaires. Publishers…

Copyright Handbook for Videotapes and Microcomputer Software.

ERIC Educational Resources Information Center

Ensign, David; And Others

Developed to help library media personnel, administrators, and educators understand and work with the copyright law as it applies to videotape and microcomputer software, this handbook provides: (1) an overview of copyright, including rights granted to copyright holders and libraries and court interpretation of the copyright law; (2) suggestions…

User’s Manual for the Modular Analysis-Package Libraries ANAPAC and TRANL

DTIC Science & Technology

1977-09-01

number) Computer software Fourier transforms Computer software library Interpolation software Digitized data...disregarded to give the user a simplified plot. (b) The last digit of ISPACE determines the type of line to be drawn, provided KODE is not...negative. If the last digit of ISPACE is 0 a solid line is drawn 1 a dashed line is drawn - - - 2 a dotted line is drawn .... 3 a dash-dot line is

Libraries Online!: Microsoft Partnering with American Library Association (ALA).

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Describes Libraries Online, a pilot project created by Microsoft and the American Library Association to develop ways to provide access to information technologies to underserved populations. Presents the nine public libraries that will receive cash grants, staff training, computer hardware and software, and technical support to help support local…

Wyoming: Open Range for Library Technology.

ERIC Educational Resources Information Center

Maul, Helen Meadors

1996-01-01

Describes the development of library technology and the need for telecommunications in a state with a lack of population density. Topics include the state library's role; shared library resources and library networks; government information; the Wyoming State Home Page on the World Wide Web; Ariel software; network coordinating; and central…

Introduction to Minicomputers in Federal Libraries.

ERIC Educational Resources Information Center

Young, Micki Jo; And Others

This book for library administrators and Federal library staff covers the application of minicomputers in Federal libraries and offers a review of minicomputer technology. A brief overview of automation explains computer technology, hardware, and software. The role of computers in libraries is examined in terms of the history of computers and…

Sex, Kids, and the Public Library.

ERIC Educational Resources Information Center

Mason, Marilyn Gell

1997-01-01

Considers issues relating to children's access to information on the Internet in public libraries. Topics include censorship versus selection; First Amendment rights; the American Library Association's challenge to the Communications Decency Act; filtering software; and the role of the public library. (LRW)

Comparison of Cortical and Subcortical Measurements in Normal Older Adults across Databases and Software Packages

PubMed Central

Rane, Swati; Plassard, Andrew; Landman, Bennett A.; Claassen, Daniel O.; Donahue, Manus J.

2017-01-01

This work explores the feasibility of combining anatomical MRI data across two public repositories namely, the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the Progressive Parkinson’s Markers Initiative (PPMI). We compared cortical thickness and subcortical volumes in cognitively normal older adults between datasets with distinct imaging parameters to assess if they would provide equivalent information. Three distinct datasets were identified. Major differences in data were scanner manufacturer and the use of magnetization inversion to enhance tissue contrast. Equivalent datasets, i.e., those providing similar volumetric measurements in cognitively normal controls, were identified in ADNI and PPMI. These were datasets obtained on the Siemens scanner with TI = 900 ms. Our secondary goal was to assess the agreement between subcortical volumes that are obtained with different software packages. Three subcortical measurement applications (FSL, FreeSurfer, and a recent multi-atlas approach) were compared. Our results show significant agreement in the measurements of caudate, putamen, pallidum, and hippocampus across the packages and poor agreement between measurements of accumbens and amygdala. This is likely due to their smaller size and lack of gray matter-white matter tissue contrast for accurate segmentation. This work provides a segue to combine imaging data from ADNI and PPMI to increase statistical power as well as to interrogate common mechanisms in disparate pathologies such as Alzheimer’s and Parkinson’s diseases. It lays the foundation for comparison of anatomical data acquired with disparate imaging parameters and analyzed with disparate software tools. Furthermore, our work partly explains the variability in the results of studies using different software packages. PMID:29756095

Comparison of Cortical and Subcortical Measurements in Normal Older Adults across Databases and Software Packages.

PubMed

Rane, Swati; Plassard, Andrew; Landman, Bennett A; Claassen, Daniel O; Donahue, Manus J

2017-01-01

This work explores the feasibility of combining anatomical MRI data across two public repositories namely, the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Progressive Parkinson's Markers Initiative (PPMI). We compared cortical thickness and subcortical volumes in cognitively normal older adults between datasets with distinct imaging parameters to assess if they would provide equivalent information. Three distinct datasets were identified. Major differences in data were scanner manufacturer and the use of magnetization inversion to enhance tissue contrast. Equivalent datasets, i.e., those providing similar volumetric measurements in cognitively normal controls, were identified in ADNI and PPMI. These were datasets obtained on the Siemens scanner with TI = 900 ms. Our secondary goal was to assess the agreement between subcortical volumes that are obtained with different software packages. Three subcortical measurement applications (FSL, FreeSurfer, and a recent multi-atlas approach) were compared. Our results show significant agreement in the measurements of caudate, putamen, pallidum, and hippocampus across the packages and poor agreement between measurements of accumbens and amygdala. This is likely due to their smaller size and lack of gray matter-white matter tissue contrast for accurate segmentation. This work provides a segue to combine imaging data from ADNI and PPMI to increase statistical power as well as to interrogate common mechanisms in disparate pathologies such as Alzheimer's and Parkinson's diseases. It lays the foundation for comparison of anatomical data acquired with disparate imaging parameters and analyzed with disparate software tools. Furthermore, our work partly explains the variability in the results of studies using different software packages.

Three-Dimensional Audio Client Library

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.

2005-01-01

The Three-Dimensional Audio Client Library (3DAudio library) is a group of software routines written to facilitate development of both stand-alone (audio only) and immersive virtual-reality application programs that utilize three-dimensional audio displays. The library is intended to enable the development of three-dimensional audio client application programs by use of a code base common to multiple audio server computers. The 3DAudio library calls vendor-specific audio client libraries and currently supports the AuSIM Gold-Server and Lake Huron audio servers. 3DAudio library routines contain common functions for (1) initiation and termination of a client/audio server session, (2) configuration-file input, (3) positioning functions, (4) coordinate transformations, (5) audio transport functions, (6) rendering functions, (7) debugging functions, and (8) event-list-sequencing functions. The 3DAudio software is written in the C++ programming language and currently operates under the Linux, IRIX, and Windows operating systems.

Documentation Library Application (DLA) Version 2.0.0.1, User Guide

DTIC Science & Technology

2013-05-08

document DIScard chotnoes and undo <ht:dc-oot. View AN Library ~IR8librMY ~ooc~~.tiOn Llbt~ry View W AA Library View ~MI Libr -ary...Windows XP and access to the DLA SQL Server database. To install the DLA, navigate to N:\\Dept 161\\3 - PRODUCTS\\ Software Installation...Health Research Center. You should see the DLA menu item listed under the NHRC programs there. Contact the DLA software POC if you encounter any

Development of an Ada package library

NASA Technical Reports Server (NTRS)

Burton, Bruce; Broido, Michael

1986-01-01

A usable prototype Ada package library was developed and is currently being evaluated for use in large software development efforts. The library system is comprised of an Ada-oriented design language used to facilitate the collection of reuse information, a relational data base to store reuse information, a set of reusable Ada components and tools, and a set of guidelines governing the system's use. The prototyping exercise is discussed and the lessons learned from it have led to the definition of a comprehensive tool set to facilitate software reuse.

The Social Ties That Bind. Online Treasures

ERIC Educational Resources Information Center

Balas, Janet L.

2006-01-01

This article discusses how, in the new world of the information age, libraries must seek to bring relevant services to their technically savvy patrons. This includes designing a library that can serve not only the geographic community, but also the virtual online community. Software used to create online communities is known as social software and…

Using Web Metric Software to Drive: Mobile Website Development

ERIC Educational Resources Information Center

Tidal, Junior

2011-01-01

Many libraries have developed mobile versions of their websites. In order to understand their users, web developers have conducted both usability tests and focus groups, yet analytical software and web server logs can also be used to better understand users. Using data collected from these tools, the Ursula C. Schwerin Library has made informed…

Linux Adventures on a Laptop. Computers in Small Libraries

ERIC Educational Resources Information Center

Roberts, Gary

2005-01-01

This article discusses the pros and cons of open source software, such as Linux. It asserts that despite the technical difficulties of installing and maintaining this type of software, ultimately it is helpful in terms of knowledge acquisition and as a beneficial investment librarians can make in themselves, their libraries, and their patrons.…

Securing PCs and Data in Libraries and Schools: A Handbook with Menuing, Anti-Virus, and Other Protective Software.

ERIC Educational Resources Information Center

Benson, Allen C.

This handbook is designed to help readers identify and eliminate security risks, with sound recommendations and library-tested security software. Chapter 1 "Managing Your Facilities and Assessing Your Risks" addresses fundamental management responsibilities including planning for a secure system, organizing computer-related information, assessing…

A Survey on the Use of Microcomputers in Special Libraries.

ERIC Educational Resources Information Center

Krieger, Tillie

1986-01-01

Describes a survey on the use of microcomputers in special libraries. The discussion of the findings includes types of hardware and software in use; applications in public services, technical processes, and administrative tasks; data back-up techniques; training received; evaluation of software; and future plans for microcomputer applications. (1…

After Losing Users in Catalogs, Libraries Find Better Search Software

ERIC Educational Resources Information Center

Parry, Marc

2010-01-01

Traditional online library catalogs do not tend to order search results by ranked relevance, and they can befuddle users with clunky interfaces. However, that's changing because of two technology trends. First, a growing number of universities are shelling out serious money for sophisticated software that makes exploring their collections more…

Real Time with the Librarian: Using Web Conferencing Software to Connect to Distance Students

ERIC Educational Resources Information Center

Riedel, Tom; Betty, Paul

2013-01-01

A pilot program to provide real-time library webcasts to Regis University distance students using Adobe Connect software was initiated in fall of 2011. Previously, most interaction between librarians and online students had been accomplished by asynchronous discussion threads in the Learning Management System. Library webcasts were offered in…

ALSC 2011 Notable Videos, Recordings & Interactive Software

ERIC Educational Resources Information Center

School Library Journal, 2011

2011-01-01

This article presents the Notable Children's Videos, Recordings, and Interactive Software for Kids lists which are compiled annually by committees of the Association for Library Service to children (ALSC), a division of the American Library Association (ALA). These lists were released in January 2011 at the ALA Midwinter meeting in San Diego,…

PVM Wrapper

NASA Technical Reports Server (NTRS)

Katz, Daniel

2004-01-01

PVM Wrapper is a software library that makes it possible for code that utilizes the Parallel Virtual Machine (PVM) software library to run using the message-passing interface (MPI) software library, without needing to rewrite the entire code. PVM and MPI are the two most common software libraries used for applications that involve passing of messages among parallel computers. Since about 1996, MPI has been the de facto standard. Codes written when PVM was popular often feature patterns of {"initsend," "pack," "send"} and {"receive," "unpack"} calls. In many cases, these calls are not contiguous and one set of calls may even exist over multiple subroutines. These characteristics make it difficult to obtain equivalent functionality via a single MPI "send" call. Because PVM Wrapper is written to run with MPI- 1.2, some PVM functions are not permitted and must be replaced - a task that requires some programming expertise. The "pvm_spawn" and "pvm_parent" function calls are not replaced, but a programmer can use "mpirun" and knowledge of the ranks of parent and child tasks with supplied macroinstructions to enable execution of codes that use "pvm_spawn" and "pvm_parent."

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

Kessner, Darren; Chambers, Matt; Burke, Robert; Agus, David; Mallick, Parag

2008-11-01

The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.

How Much Security Does Your Library Need?

ERIC Educational Resources Information Center

Banerjee, Kyle

2003-01-01

Explains how to keep library systems healthy and functioning by taking sensible security measures. Examines why hackers would target library systems and how library systems are compromised. Describes tools that can help, including: firewalls; antivirus software; alarms; network analysis tools; and encryption. Identifies several strategies for…

Technology for Libraries.

ERIC Educational Resources Information Center

Phenix, Katharine; And Others

1990-01-01

Five articles discuss information technology in libraries: (1) "Software for Libraries" (Katharine Phenix); (2) "Online Update: European Online Services" (Martin Kesselman); (3) "Connect Time: Online Pricing Breakthroughs" (Barbara Quint); (4) "Microcomputing: Micro Biology Computer Viruses" (James LaRue);…

Hippocampal volume and auditory attention on a verbal memory task with adult survivors of pediatric brain tumor.

PubMed

Jayakar, Reema; King, Tricia Z; Morris, Robin; Na, Sabrina

2015-03-01

We examined the nature of verbal memory deficits and the possible hippocampal underpinnings in long-term adult survivors of childhood brain tumor. 35 survivors (M = 24.10 ± 4.93 years at testing; 54% female), on average 15 years post-diagnosis, and 59 typically developing adults (M = 22.40 ± 4.35 years, 54% female) participated. Automated FMRIB Software Library (FSL) tools were used to measure hippocampal, putamen, and whole brain volumes. The California Verbal Learning Test-Second Edition (CVLT-II) was used to assess verbal memory. Hippocampal, F(1, 91) = 4.06, ηp² = .04; putamen, F(1, 91) = 11.18, ηp² = .11; and whole brain, F(1, 92) = 18.51, ηp² = .17, volumes were significantly lower for survivors than controls (p < .05). Hippocampus and putamen volumes were significantly correlated (r = .62, p < .001) with each other, but not with total brain volume (r = .09; r = .08), for survivors and controls. Verbal memory indices of auditory attention list span (Trial 1: F(1, 92) = 12.70, η² = .12) and final list learning (Trial 5: F(1, 92) = 6.01, η² = .06) were significantly lower for survivors (p < .05). Total hippocampal volume in survivors was significantly correlated (r = .43, p = .01) with auditory attention, but none of the other CVLT-II indices. Secondary analyses for the effect of treatment factors are presented. Volumetric differences between survivors and controls exist for the whole brain and for subcortical structures on average 15 years post-diagnosis. Treatment factors seem to have a unique effect on subcortical structures. Memory differences between survivors and controls are largely contingent upon auditory attention list span. Only hippocampal volume is associated with the auditory attention list span component of verbal memory. These findings are particularly robust for survivors treated with radiation. PsycINFO Database Record (c) 2015 APA, all rights reserved.

Low-intensity daily walking activity is associated with hippocampal volume in older adults.

PubMed

Varma, Vijay R; Chuang, Yi-Fang; Harris, Gregory C; Tan, Erwin J; Carlson, Michelle C

2015-05-01

Hippocampal atrophy is associated with memory impairment and dementia and serves as a key biomarker in the preclinical stages of Alzheimer's disease. Physical activity, one of the most promising behavioral interventions to prevent or delay cognitive decline, has been shown to be associated with hippocampal volume; specifically increased aerobic activity and fitness may have a positive effect on the size of the hippocampus. The majority of older adults, however, are sedentary and have difficulty initiating and maintaining exercise programs. A modestly more active lifestyle may nonetheless be beneficial. This study explored whether greater objectively measured daily walking activity was associated with larger hippocampal volume. We additionally explored whether greater low-intensity walking activity, which may be related to leisure-time physical, functional, and social activities, was associated with larger hippocampal volume independent of exercise and higher-intensity walking activity. Segmentation of hippocampal volumes was performed using Functional Magnetic Resonance Imaging of the Brain's Software Library (FSL), and daily walking activity was assessed using a step activity monitor on 92, nondemented, older adult participants. After controlling for age, education, body mass index, cardiovascular disease risk factors, and the Mini Mental State Exam, we found that a greater amount, duration, and frequency of total daily walking activity were each associated with larger hippocampal volume among older women, but not among men. These relationships were specific to hippocampal volume, compared with the thalamus, used as a control brain region, and remained significant for low-intensity walking activity, independent of moderate- to vigorous-intensity activity and self-reported exercise. This is the first study, to our knowledge, to explore the relationship between objectively measured daily walking activity and hippocampal volume in an older adult population. Findings suggest the importance of examining whether increasing nonexercise, lifestyle physical activities may produce measurable cognitive benefits and affect hippocampal volume through molecular pathways unique to those related to moderate-intensity exercise. © 2014 Wiley Periodicals, Inc.

Information Technology in Libraries. A Pakistani Perspective.

ERIC Educational Resources Information Center

Mahmood, Khalid

This book presents an overview of the present status of the use of library automation hardware and software in Pakistan. The following 20 articles are included: (1) "The Status of Library Automation in Pakistan"; (2) "Promoting Information Technology in Pakistan: the Netherlands Library Development Project"; (3) "Library…

Earth Science Markup Language: Transitioning From Design to Application

NASA Technical Reports Server (NTRS)

Moe, Karen; Graves, Sara; Ramachandran, Rahul

2002-01-01

The primary objective of the proposed Earth Science Markup Language (ESML) research is to transition from design to application. The resulting schema and prototype software will foster community acceptance for the "define once, use anywhere" concept central to ESML. Supporting goals include: 1. Refinement of the ESML schema and software libraries in cooperation with the user community. 2. Application of the ESML schema and software libraries to a variety of Earth science data sets and analysis tools. 3. Development of supporting prototype software for enhanced ease of use. 4. Cooperation with standards bodies in order to assure ESML is aligned with related metadata standards as appropriate. 5. Widespread publication of the ESML approach, schema, and software.

The simulation library of the Belle II software system

NASA Astrophysics Data System (ADS)

Kim, D. Y.; Ritter, M.; Bilka, T.; Bobrov, A.; Casarosa, G.; Chilikin, K.; Ferber, T.; Godang, R.; Jaegle, I.; Kandra, J.; Kodys, P.; Kuhr, T.; Kvasnicka, P.; Nakayama, H.; Piilonen, L.; Pulvermacher, C.; Santelj, L.; Schwenker, B.; Sibidanov, A.; Soloviev, Y.; Starič, M.; Uglov, T.

2017-10-01

SuperKEKB, the next generation B factory, has been constructed in Japan as an upgrade of KEKB. This brand new e+ e- collider is expected to deliver a very large data set for the Belle II experiment, which will be 50 times larger than the previous Belle sample. Both the triggered physics event rate and the background event rate will be increased by at least 10 times than the previous ones, and will create a challenging data taking environment for the Belle II detector. The software system of the Belle II experiment is designed to execute this ambitious plan. A full detector simulation library, which is a part of the Belle II software system, is created based on Geant4 and has been tested thoroughly. Recently the library has been upgraded with Geant4 version 10.1. The library is behaving as expected and it is utilized actively in producing Monte Carlo data sets for various studies. In this paper, we will explain the structure of the simulation library and the various interfaces to other packages including geometry and beam background simulation.

Evaluating Open Source Software for Use in Library Initiatives: A Case Study Involving Electronic Publishing

ERIC Educational Resources Information Center

Samuels, Ruth Gallegos; Griffy, Henry

2012-01-01

This article discusses best practices for evaluating open source software for use in library projects, based on the authors' experience evaluating electronic publishing solutions. First, it presents a brief review of the literature, emphasizing the need to evaluate open source solutions carefully in order to minimize Total Cost of Ownership. Next,…

Hammond Workforce 2000: A Three-Year Project. October 1989 to September 1992.

ERIC Educational Resources Information Center

Meyers, Arthur S.; Somerville, Deborah J.

A 3-year Library Services and Construction Act grant project from 1989-1992 provided for adult learning centers, equipped with Apple IIGS computers and software at each location of the Hammond Public Library (Indiana). User-friendly, job-based software to strengthen reading, writing, mathematics, spelling, and grammar skills, as well as video and…

Library iTour: Introducing the iPod Generation to the Academic Library

ERIC Educational Resources Information Center

Cairns, Virginia; Dean, Toni C.

2009-01-01

Purpose: For many years, the Lupton Library offered a traditional library introduction class to first year students participating in the Freshman Seminar Program at the University of Tennessee at Chattanooga. In 2007, the library applied for and received a campus grant to purchase thirty iPod Touches, along with accompanying hardware and software.…

Use of the Femtosecond Lasers in Ophthalmology

NASA Astrophysics Data System (ADS)

Roszkowska, Anna M.; Urso, Mario; Signorino, Alberto; Aragona, Pasquale

2018-01-01

Femtosecond laser (FSL) is an infrared laser with a wavelength of 1053 nm. FS laser works producing photodisruption or photoionization of the optically transparent tissue such as cornea. Currently FS lasers have a wide range of applications in ophthalmic surgery. They are used above all in corneal surgery in refractive procedures and keratoplasty, and recently in cataract surgery. The use of the FSL in corneal refractive surgery includes LASIK flap creation, astigmatic keratotomy, Femtosecond Lenticule Extraction (FLEx), Small Incision Lenticule Extraction (SMILE) and channels creation for implantation of the intrastromal corneal rings. As to the corneal grafting, the FS lasers are used in laser-assisted anterior and posterior lamellar keratoplasty and customized trephination in the penetrating keratoplasty. FS Laser Assisted Cataract Surgery (FLACS) includes capsulorrhexis and nuclear fragmentation that enhance safety and efficacy of the procedure.

Analysis of Bacterial Community Structure in Sulfurous-Oil-Containing Soils and Detection of Species Carrying Dibenzothiophene Desulfurization (dsz) Genes

PubMed Central

Duarte, Gabriela Frois; Rosado, Alexandre Soares; Seldin, Lucy; de Araujo, Welington; van Elsas, Jan Dirk

2001-01-01

The selective effects of sulfur-containing hydrocarbons, with respect to changes in bacterial community structure and selection of desulfurizing organisms and genes, were studied in soil. Samples taken from a polluted field soil (A) along a concentration gradient of sulfurous oil and from soil microcosms treated with dibenzothiophene (DBT)-containing petroleum (FSL soil) were analyzed. Analyses included plate counts of total bacteria and of DBT utilizers, molecular community profiling via soil DNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and detection of genes that encode enzymes involved in the desulfurization of hydrocarbons, i.e., dszA, dszB, and dszC.Data obtained from the A soil showed no discriminating effects of oil levels on the culturable bacterial numbers on either medium used. Generally, counts of DBT degraders were 10- to 100-fold lower than the total culturable counts. However, PCR-DGGE showed that the numbers of bands detected in the molecular community profiles decreased with increasing oil content of the soil. Analysis of the sequences of three prominent bands of the profiles generated with the highly polluted soil samples suggested that the underlying organisms were related to Actinomyces sp., Arthrobacter sp., and a bacterium of uncertain affiliation. dszA, dszB, and dszC genes were present in all A soil samples, whereas a range of unpolluted soils gave negative results in this analysis. Results from the study of FSL soil revealed minor effects of the petroleum-DBT treatment on culturable bacterial numbers and clear effects on the DBT-utilizing communities. The molecular community profiles were largely stable over time in the untreated soil, whereas they showed a progressive change over time following treatment with DBT-containing petroleum. Direct PCR assessment revealed the presence of dszB-related signals in the untreated FSL soil and the apparent selection of dszA- and dszC-related sequences by the petroleum-DBT treatment. PCR-DGGE applied to sequential enrichment cultures in DBT-containing sulfur-free basal salts medium prepared from the A and treated FSL soils revealed the selection of up to 10 distinct bands. Sequencing a subset of these bands provided evidence for the presence of organisms related to Pseudomonas putida, a Pseudomonas sp., Stenotrophomonas maltophilia, and Rhodococcus erythropolis. Several of 52 colonies obtained from the A and FSL soils on agar plates with DBT as the sole sulfur source produced bands that matched the migration of bands selected in the enrichment cultures. Evidence for the presence of dszB in 12 strains was obtained, whereas dszA and dszC genes were found in only 7 and 6 strains, respectively. Most of the strains carrying dszA or dszC were classified as R. erythropolis related, and all revealed the capacity to desulfurize DBT. A comparison of 37 dszA sequences, obtained via PCR from the A and FSL soils, from enrichments of these soils, and from isolates, revealed the great similarity of all sequences to the canonical (R. erythropolis strain IGTS8) dszA sequence and a large degree of internal conservation. The 37 sequences recovered were grouped in three clusters. One group, consisting of 30 sequences, was minimally 98% related to the IGTS8 sequence, a second group of 2 sequences was slightly different, and a third group of 5 sequences was 95% similar. The first two groups contained sequences obtained from both soil types and enrichment cultures (including isolates), but the last consisted of sequences obtained directly from the polluted A soil. PMID:11229891

Small but Pristine--Lessons for Small Library Automation.

ERIC Educational Resources Information Center

Clement, Russell; Robertson, Dane

1990-01-01

Compares the more positive library automation experiences of a small public library with those of a large research library. Topics addressed include collection size; computer size and the need for outside control of a data processing center; staff size; selection process for hardware and software; and accountability. (LRW)

The Generalized Support Software (GSS) Domain Engineering Process: An Object-Oriented Implementation and Reuse Success at Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Condon, Steven; Hendrick, Robert; Stark, Michael E.; Steger, Warren

1997-01-01

The Flight Dynamics Division (FDD) of NASA's Goddard Space Flight Center (GSFC) recently embarked on a far-reaching revision of its process for developing and maintaining satellite support software. The new process relies on an object-oriented software development method supported by a domain specific library of generalized components. This Generalized Support Software (GSS) Domain Engineering Process is currently in use at the NASA GSFC Software Engineering Laboratory (SEL). The key facets of the GSS process are (1) an architecture for rapid deployment of FDD applications, (2) a reuse asset library for FDD classes, and (3) a paradigm shift from developing software to configuring software for mission support. This paper describes the GSS architecture and process, results of fielding the first applications, lessons learned, and future directions

Microcomputers in Libraries.

ERIC Educational Resources Information Center

Ertel, Monica M.

1984-01-01

This discussion of current microcomputer technologies available to libraries focuses on software applications in four major classifications: communications (online database searching); word processing; administration; and database management systems. Specific examples of library applications are given and six references are cited. (EJS)

Expanding roles in a library-based bioinformatics service program: a case study

PubMed Central

Li, Meng; Chen, Yi-Bu; Clintworth, William A

2013-01-01

Question: How can a library-based bioinformatics support program be implemented and expanded to continuously support the growing and changing needs of the research community? Setting: A program at a health sciences library serving a large academic medical center with a strong research focus is described. Methods: The bioinformatics service program was established at the Norris Medical Library in 2005. As part of program development, the library assessed users' bioinformatics needs, acquired additional funds, established and expanded service offerings, and explored additional roles in promoting on-campus collaboration. Results: Personnel and software have increased along with the number of registered software users and use of the provided services. Conclusion: With strategic efforts and persistent advocacy within the broader university environment, library-based bioinformatics service programs can become a key part of an institution's comprehensive solution to researchers' ever-increasing bioinformatics needs. PMID:24163602

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

PubMed

Ayres, Daniel L; Darling, Aaron; Zwickl, Derrick J; Beerli, Peter; Holder, Mark T; Lewis, Paul O; Huelsenbeck, John P; Ronquist, Fredrik; Swofford, David L; Cummings, Michael P; Rambaut, Andrew; Suchard, Marc A

2012-01-01

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

PubMed Central

Ayres, Daniel L.; Darling, Aaron; Zwickl, Derrick J.; Beerli, Peter; Holder, Mark T.; Lewis, Paul O.; Huelsenbeck, John P.; Ronquist, Fredrik; Swofford, David L.; Cummings, Michael P.; Rambaut, Andrew; Suchard, Marc A.

2012-01-01

Abstract Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software. PMID:21963610

SU-G-BRB-02: An Open-Source Software Analysis Library for Linear Accelerator Quality Assurance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerns, J; Yaldo, D

Purpose: Routine linac quality assurance (QA) tests have become complex enough to require automation of most test analyses. A new data analysis software library was built that allows physicists to automate routine linear accelerator quality assurance tests. The package is open source, code tested, and benchmarked. Methods: Images and data were generated on a TrueBeam linac for the following routine QA tests: VMAT, starshot, CBCT, machine logs, Winston Lutz, and picket fence. The analysis library was built using the general programming language Python. Each test was analyzed with the library algorithms and compared to manual measurements taken at the timemore » of acquisition. Results: VMAT QA results agreed within 0.1% between the library and manual measurements. Machine logs (dynalogs & trajectory logs) were successfully parsed; mechanical axis positions were verified for accuracy and MLC fluence agreed well with EPID measurements. CBCT QA measurements were within 10 HU and 0.2mm where applicable. Winston Lutz isocenter size measurements were within 0.2mm of TrueBeam’s Machine Performance Check. Starshot analysis was within 0.2mm of the Winston Lutz results for the same conditions. Picket fence images with and without a known error showed that the library was capable of detecting MLC offsets within 0.02mm. Conclusion: A new routine QA software library has been benchmarked and is available for use by the community. The library is open-source and extensible for use in larger systems.« less

The Weakest Link: Library Catalogs.

ERIC Educational Resources Information Center

Young, Terrence E., Jr.

2002-01-01

Describes methods of correcting MARC records in online public access catalogs in school libraries. Highlights include in-house methods; professional resources; conforming to library cataloging standards; vendor services, including Web-based services; software specifically developed for record cleanup; and outsourcing. (LRW)

DSPSR: Digital Signal Processing Software for Pulsar Astronomy

NASA Astrophysics Data System (ADS)

van Straten, W.; Bailes, M.

2010-10-01

DSPSR, written primarily in C++, is an open-source, object-oriented, digital signal processing software library and application suite for use in radio pulsar astronomy. The library implements an extensive range of modular algorithms for use in coherent dedispersion, filterbank formation, pulse folding, and other tasks. The software is installed and compiled using the standard GNU configure and make system, and is able to read astronomical data in 18 different file formats, including FITS, S2, CPSR, CPSR2, PuMa, PuMa2, WAPP, ASP, and Mark5.

Enhancements to the EPANET-RTX (Real-Time Analytics) ...

EPA Pesticide Factsheets

Technical brief and software The U.S. Environmental Protection Agency (EPA) developed EPANET-RTX as a collection of object-oriented software libraries comprising the core data access, data transformation, and data synthesis (real-time analytics) components of a real-time hydraulic and water quality modeling system. While EPANET-RTX uses the hydraulic and water quality solvers of EPANET, the object libraries are a self-contained set of building blocks for software developers. “Real-time EPANET” promises to change the way water utilities, commercial vendors, engineers, and the water community think about modeling.

Quantification of phase retardation in corneal tissues using a femtosecond laser

NASA Astrophysics Data System (ADS)

Calhoun, William R.; Beylin, Alexander; Weiblinger, Richard; Ilev, Ilko

2013-03-01

The use of femtosecond lasers (FSL) in ophthalmic procedures, such as LASIK, lens replacement (cataract surgery), as well as several other treatments, is growing rapidly. The treatment effect is based on photo ablation of ocular tissues by a series of ultra-short laser pulses. However, the laser beam characteristics change dynamically due to interactions with birefringent corneal tissue, which may affect the outcome of the laser treatment. To better understand the effect the cornea has on the laser characteristics, we developed a system for measuring retardation and validated it with precise, standard phase retarders. Then we measured the phase retardation of FSLs through bovine corneas and found that there is a considerable, location dependent, variation in retardation values. This information can potentially help optimize FSL parameters to make their application in ophthalmic procedures safer and more effective.

7α-Hydroxycholesterol Elicits TLR6-Mediated Expression of IL-23 in Monocytic Cells.

PubMed

Seo, Hyun Chul; Kim, Sun-Mi; Eo, Seong-Kug; Rhim, Byung-Yong; Kim, Koanhoi

2015-01-01

We investigated the question of whether 7-oxygenated cholesterol derivatives could affect inflammatory and/or immune responses in atherosclerosis by examining their effects on expression of IL-23 in monocytic cells. 7α-Hydroxycholesterol (7αOHChol) induced transcription of the TLR6 gene and elevated the level of cell surface TLR6 protein in THP-1 monocytic cells. Addition of an agonist of TLR6, FSL-1, to TLR6-expressing cells by treatment with 7αOHChol resulted in enhanced production of IL-23 and transcription of genes encoding the IL-23 subunit α (p19) and the IL-12 subunit β (p40). However, treatment with 7-ketocholesterol (7K) and 7β-hydroxycholesterol (7βOHChol) did not affect TLR6 expression, and addition of FSL-1 to cells treated with either 7K or 7βOHChol did not influence transcription of the genes. Pharmacological inhibition of ERK, Akt, or PI3K resulted in attenuated transcription of TLR6 induced by 7αOHChol as well as secretion of IL-23 enhanced by 7αOHChol plus FSL-1. Inhibition of p38 MAPK or JNK resulted in attenuated secretion of IL-23. These results indicate that a certain type of 7-oxygenated cholesterol like 7αOHChol can elicit TLR6-mediated expression of IL-23 by monocytic cells via PI3K/Akt and MAPKs pathways.

7α-Hydroxycholesterol Elicits TLR6-Mediated Expression of IL-23 in Monocytic Cells

PubMed Central

Seo, Hyun Chul; Kim, Sun-Mi; Eo, Seong-Kug; Rhim, Byung-Yong; Kim, Koanhoi

2015-01-01

We investigated the question of whether 7-oxygenated cholesterol derivatives could affect inflammatory and/or immune responses in atherosclerosis by examining their effects on expression of IL-23 in monocytic cells. 7α-Hydroxycholesterol (7αOHChol) induced transcription of the TLR6 gene and elevated the level of cell surface TLR6 protein in THP-1 monocytic cells. Addition of an agonist of TLR6, FSL-1, to TLR6-expressing cells by treatment with 7αOHChol resulted in enhanced production of IL-23 and transcription of genes encoding the IL-23 subunit α (p19) and the IL-12 subunit β (p40). However, treatment with 7-ketocholesterol (7K) and 7β-hydroxycholesterol (7βOHChol) did not affect TLR6 expression, and addition of FSL-1 to cells treated with either 7K or 7βOHChol did not influence transcription of the genes. Pharmacological inhibition of ERK, Akt, or PI3K resulted in attenuated transcription of TLR6 induced by 7αOHChol as well as secretion of IL-23 enhanced by 7αOHChol plus FSL-1. Inhibition of p38 MAPK or JNK resulted in attenuated secretion of IL-23. These results indicate that a certain type of 7-oxygenated cholesterol like 7αOHChol can elicit TLR6-mediated expression of IL-23 by monocytic cells via PI3K/Akt and MAPKs pathways. PMID:25593648

An object-oriented class library for medical software development.

PubMed

O'Kane, K C; McColligan, E E

1996-12-01

The objective of this research is the development of a Medical Object Library (MOL) consisting of reusable, inheritable, portable, extendable C++ classes that facilitate rapid development of medical software at reduced cost and increased functionality. The result of this research is a library of class objects that range in function from string and hierarchical file handling entities to high level, procedural agents that perform increasingly complex, integrated tasks. A system built upon these classes is compatible with any other system similarly constructed with respect to data definitions, semantics, data organization and storage. As new objects are built, they can be added to the class library for subsequent use. The MOL is a toolkit of software objects intended to support a common file access methodology, a unified medical record structure, consistent message processing, standard graphical display facilities and uniform data collection procedures. This work emphasizes the relationship that potentially exists between the structure of a hierarchical medical record and procedural language components by means of a hierarchical class library and tree structured file access facility. In doing so, it attempts to establish interest in and demonstrate the practicality of the hierarchical medical record model in the modern context of object oriented programming.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Jong, Wibe A.; Walker, Andrew M.; Hanwell, Marcus D.

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XMLmore » files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.« less

The Australian Bibliographic Network--An Introduction.

ERIC Educational Resources Information Center

Hannan, Chris

1982-01-01

Focuses on the centralized, online, shared-cataloging facility of the Australian Bibliographic Network operated by the National Library of Australia. Existing automated library systems in Australia, selection and implementation of Washington Library Network software, comparison of Australian and U.S. automation, and projections for future…

From LAMP to Koha: Case Study of the Pakistan Legislative Assembly Libraries

ERIC Educational Resources Information Center

Shafi-Ullah, Farasat; Qutab, Saima

2012-01-01

Purpose: This paper aims to elaborate the library data migration process from LAMP (Library Automation Management Program) to the open source software Koha's (2.2.8 Windows based) Pakistani flavour PakLAG-Koha in six legislative assembly libraries of Pakistan. Design/methodology/approach: The paper explains different steps of the data migration…

Using the Intel Math Kernel Library on Peregrine | High-Performance

Science.gov Websites

Computing | NREL the Intel Math Kernel Library on Peregrine Using the Intel Math Kernel Library on Peregrine Learn how to use the Intel Math Kernel Library (MKL) with Peregrine system software. MKL architectures. Core math functions in MKL include BLAS, LAPACK, ScaLAPACK, sparse solvers, fast Fourier

Perceptions of Personnel at Selected Texas Community Colleges Regarding the Impact of Technology on Their Libraries

ERIC Educational Resources Information Center

Kenan, Sharon K.

2012-01-01

Technological innovations have transformed all areas of community college libraries. Automated library systems, office software, and Internet access have altered work processes for library personnel and have changed research methodologies for students and faculty. The purpose of this bounded multiple case study was to explore how the adoption of…

Automated software development workstation

NASA Technical Reports Server (NTRS)

Prouty, Dale A.; Klahr, Philip

1988-01-01

A workstation is being developed that provides a computational environment for all NASA engineers across application boundaries, which automates reuse of existing NASA software and designs, and efficiently and effectively allows new programs and/or designs to be developed, catalogued, and reused. The generic workstation is made domain specific by specialization of the user interface, capturing engineering design expertise for the domain, and by constructing/using a library of pertinent information. The incorporation of software reusability principles and expert system technology into this workstation provide the obvious benefits of increased productivity, improved software use and design reliability, and enhanced engineering quality by bringing engineering to higher levels of abstraction based on a well tested and classified library.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

PubMed

Ueno, Yutaka; Ito, Shuntaro; Konagaya, Akihiko

2014-12-01

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

Software to Go--And It Goes!

ERIC Educational Resources Information Center

Abrams, Mary; Kurlychek, Ken

1989-01-01

This article describes the Software Evaluation Clearinghouse for Educators of the Hearing Impaired at Gallaudet University (Washington, DC). Software compatible with Apple and IBM hardware is collected, rated by clearinghouse members, and described in a printed catalog. Tips on starting a software lending library are offered. (PB)

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heroux, Michael A.; Bartlett, Roscoe; Demeshko, Irina

Here, extreme-scale computational science increasingly demands multiscale and multiphysics formulations. Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities. Scientific libraries provide high-quality, reusable software components for constructing applications with improved robustness and portability. However, without coordination, many libraries cannot be easily composed. Namespace collisions, inconsistent arguments, lack of third-party software versioning, and additional difficulties make composition costly. The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos, and Alquimia) and provides a foundationmore » for addressing broader issues in software interoperability, performance portability, and sustainability. The xSDK provides turnkey installation of member software and seamless combination of aggregate capabilities, and it marks first steps toward extreme-scale scientific software ecosystems from which future applications can be composed rapidly with assured quality and scalability.« less

What makes computational open source software libraries successful?

NASA Astrophysics Data System (ADS)

Bangerth, Wolfgang; Heister, Timo

2013-01-01

Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects.

xSDK Foundations: Toward an Extreme-scale Scientific Software Development Kit

DOE PAGES

Heroux, Michael A.; Bartlett, Roscoe; Demeshko, Irina; ...

2017-03-01

Here, extreme-scale computational science increasingly demands multiscale and multiphysics formulations. Combining software developed by independent groups is imperative: no single team has resources for all predictive science and decision support capabilities. Scientific libraries provide high-quality, reusable software components for constructing applications with improved robustness and portability. However, without coordination, many libraries cannot be easily composed. Namespace collisions, inconsistent arguments, lack of third-party software versioning, and additional difficulties make composition costly. The Extreme-scale Scientific Software Development Kit (xSDK) defines community policies to improve code quality and compatibility across independently developed packages (hypre, PETSc, SuperLU, Trilinos, and Alquimia) and provides a foundationmore » for addressing broader issues in software interoperability, performance portability, and sustainability. The xSDK provides turnkey installation of member software and seamless combination of aggregate capabilities, and it marks first steps toward extreme-scale scientific software ecosystems from which future applications can be composed rapidly with assured quality and scalability.« less

An Online Library Catalogue.

ERIC Educational Resources Information Center

Alloro, Giovanna; Ugolini, Donatella

1992-01-01

Describes the implementation of an online catalog in the library of the National Institute for Cancer Research and the Clinical and Experimental Oncology Institute of the University of Genoa. Topics addressed include automation of various library functions, software features, database management, training, and user response. (10 references) (MES)

Hagerstown-Jefferson Township Public Library Internet Web Site.

ERIC Educational Resources Information Center

Albertson, Marie

1997-01-01

Describes the development of the Hagerstown (Indiana) public library's Web site. Highlights include writing successful grant proposals for funding; software from Microsoft; community support; free community access to the Internet from home computers as well as at the library; problems encountered; and future plans. (LRW)

Continuous quality improvement using intelligent infusion pump data analysis.

PubMed

Breland, Burnis D

2010-09-01

The use of continuous quality-improvement (CQI) processes in the implementation of intelligent infusion pumps in a community teaching hospital is described. After the decision was made to implement intelligent i.v. infusion pumps in a 413-bed, community teaching hospital, drug libraries for use in the safety software had to be created. Before drug libraries could be created, it was necessary to determine the epidemiology of medication use in various clinical care areas. Standardization of medication administration was performed through the CQI process, using practical knowledge of clinicians at the bedside and evidence-based drug safety parameters in the scientific literature. Post-implementation, CQI allowed refinement of clinically important safety limits while minimizing inappropriate, meaningless soft limit alerts on a few select agents. Assigning individual clinical care areas (CCAs) to individual patient care units facilitated customization of drug libraries and identification of specific CCA compliance concerns. Between June 2007 and June 2008, there were seven library updates. These involved drug additions and deletions, customization of individual CCAs, and alterations of limits. Overall compliance with safety software use rose over time, from 33% in November 2006 to over 98% in December 2009. Many potentially clinically significant dosing errors were intercepted by the safety software, prompting edits by end users. Only 4-6% of soft limit alerts resulted in edits. Compliance rates for use of infusion pump safety software varied among CCAs over time. Education, auditing, and refinement of drug libraries led to improved compliance in most CCAs.

Rehabilitation and Prosthetic Services

MedlinePlus

... VA Learning University (VALU) SimLearn Libraries (VALNET) VA Software Documentation Library (VDL) About VHA Learn about VHA Forms & ... & Sensory Aids Service (PSAS) Our Mission The mission of the Prosthetic & ...

DMG-α--a computational geometry library for multimolecular systems.

PubMed

Szczelina, Robert; Murzyn, Krzysztof

2014-11-24

The DMG-α library grants researchers in the field of computational biology, chemistry, and biophysics access to an open-sourced, easy to use, and intuitive software for performing fine-grained geometric analysis of molecular systems. The library is capable of computing power diagrams (weighted Voronoi diagrams) in three dimensions with 3D periodic boundary conditions, computing approximate projective 2D Voronoi diagrams on arbitrarily defined surfaces, performing shape properties recognition using α-shape theory and can do exact Solvent Accessible Surface Area (SASA) computation. The software is written mainly as a template-based C++ library for greater performance, but a rich Python interface (pydmga) is provided as a convenient way to manipulate the DMG-α routines. To illustrate possible applications of the DMG-α library, we present results of sample analyses which allowed to determine nontrivial geometric properties of two Escherichia coli-specific lipids as emerging from molecular dynamics simulations of relevant model bilayers.

Stereo Vision Inside Tire

DTIC Science & Technology

2015-08-21

using the Open Computer Vision ( OpenCV ) libraries [6] for computer vision and the Qt library [7] for the user interface. The software has the...depth. The software application calibrates the cameras using the plane based calibration model from the OpenCV calib3D module and allows the...6] OpenCV . 2015. OpenCV Open Source Computer Vision. [Online]. Available at: opencv.org [Accessed]: 09/01/2015. [7] Qt. 2015. Qt Project home

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

PubMed Central

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-01-01

Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects. PMID:18402700

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

PubMed

Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

2008-04-10

Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

Finding the Right Educational Software for Your Child.

ERIC Educational Resources Information Center

Moore, Jack

1990-01-01

Ideas are presented for identifying, evaluating, and selecting instructional software for children with special needs. The article notes several library research tools as sources of information and lists specific questions to consider when evaluating software. (JDD)

International Inventory of Software Packages in the Information Field.

ERIC Educational Resources Information Center

Keren, Carl, Ed.; Sered, Irina, Ed.

Designed to provide guidance in selecting appropriate software for library automation, information storage and retrieval, or management of bibliographic databases, this inventory describes 188 computer software packages. The information was obtained through a questionnaire survey of 600 software suppliers and developers who were asked to describe…

Cataloging and Organizing Microcomputer Software--Where Do We Go from First Base?

ERIC Educational Resources Information Center

Choi, Susan E.

This position paper addresses general topics to be considered when organizing library software collections. Tasks involved in organizing and cataloging educational software collections are discussed, including arrangement/classification; the type of catalog; descriptions of the software; the general materials designator; storage requirements; and…

A real-time MPEG software decoder using a portable message-passing library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwong, Man Kam; Tang, P.T. Peter; Lin, Biquan

1995-12-31

We present a real-time MPEG software decoder that uses message-passing libraries such as MPL, p4 and MPI. The parallel MPEG decoder currently runs on the IBM SP system but can be easil ported to other parallel machines. This paper discusses our parallel MPEG decoding algorithm as well as the parallel programming environment under which it uses. Several technical issues are discussed, including balancing of decoding speed, memory limitation, 1/0 capacities, and optimization of MPEG decoding components. This project shows that a real-time portable software MPEG decoder is feasible in a general-purpose parallel machine.

Logic Model Checking of Time-Periodic Real-Time Systems

NASA Technical Reports Server (NTRS)

Florian, Mihai; Gamble, Ed; Holzmann, Gerard

2012-01-01

In this paper we report on the work we performed to extend the logic model checker SPIN with built-in support for the verification of periodic, real-time embedded software systems, as commonly used in aircraft, automobiles, and spacecraft. We first extended the SPIN verification algorithms to model priority based scheduling policies. Next, we added a library to support the modeling of periodic tasks. This library was used in a recent application of the SPIN model checker to verify the engine control software of an automobile, to study the feasibility of software triggers for unintended acceleration events.

SAGA: A project to automate the management of software production systems

NASA Technical Reports Server (NTRS)

Campbell, Roy H.; Laliberte, D.; Render, H.; Sum, R.; Smith, W.; Terwilliger, R.

1987-01-01

The Software Automation, Generation and Administration (SAGA) project is investigating the design and construction of practical software engineering environments for developing and maintaining aerospace systems and applications software. The research includes the practical organization of the software lifecycle, configuration management, software requirements specifications, executable specifications, design methodologies, programming, verification, validation and testing, version control, maintenance, the reuse of software, software libraries, documentation, and automated management.

Integration of the NRL Digital Library.

ERIC Educational Resources Information Center

King, James

2001-01-01

The Naval Research Laboratory (NRL) Library has identified six primary areas that need improvement: infrastructure, InfoWeb, TORPEDO Ultra, journal data management, classified data, and linking software. It is rebuilding InfoWeb and TORPEDO Ultra as database-driven Web applications, upgrading the STILAS library catalog, and creating other support…

Library Programming with LEGO MINDSTORMS, Scratch, and PicoCricket: Analysis of Best Practices for Public Libraries

ERIC Educational Resources Information Center

Romero, Juan Suarez

2010-01-01

Public libraries are redefining their roles in order to stay relevant to the needs of the communities they serve. Today, libraries are places where reading meets hands-on learning and where quietness coexists with voices and music. The latest advances in technology for children and teens, specifically, robotics sets and media-rich software, are…

Migration of Data from One Library Management System to Another: A Case Study in India

ERIC Educational Resources Information Center

Matoria, Ram Kumar; Upadhyay, P. K.

2005-01-01

Purpose: To share the experiences gained during the migration of library data from one library management system (LibSys[TM]) to another (e-Granthalaya[TM]). Design/methodology/approach: The paper describes the step-by-step approach taken to migrate the existing library data to the new software. The paper also discusses the peculiarities of the…

The New York City Subways: The First Ten Years. A Library Research Exercise Using a Computer.

ERIC Educational Resources Information Center

Machalow, Robert

This document presents a library research exercise developed at York College which uses the Apple IIe microcomputer and word processing software--the Applewriter--to teach library research skills. Unlike some other library research exercises on disk, this program allows the student to decide on alternative approaches to solving the given problem:…

Library Operations Policies and Procedures, Volume 2. Central Archive for Reusable Defense Software (CARDS)

DTIC Science & Technology

1994-02-28

improvements. Pare 10 ka•- V •DkI U Release Manager The Release Manager provides franchisees with media copies of existing libraries, as needed. Security...implementors, and potential library franchisees . Security Team The Security Team assists the Security Officer with security analysis. Team members are...and Franchisees . A Potential User is an individual who requests a Library Account. A User Recruit has been sent a CARDS Library Account Registration

Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages

PubMed Central

Nunez-Iglesias, Juan; Kennedy, Ryan; Plaza, Stephen M.; Chakraborty, Anirban; Katz, William T.

2014-01-01

The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them. PMID:24772079

Hippocampal Morphology in a Rat Model of Depression: The Effects of Physical Activity

PubMed Central

Sierakowiak, Adam; Mattsson, Anna; Gómez-Galán, Marta; Feminía, Teresa; Graae, Lisette; Aski, Sahar Nikkhou; Damberg, Peter; Lindskog, Mia; Brené, Stefan; Åberg, Elin

2015-01-01

Accumulating in vivo and ex vivo evidences show that humans suffering from depression have decreased hippocampal volume and altered spine density. Moreover, physical activity has an antidepressant effect in humans and in animal models, but to what extent physical activity can affect hippocampal volume and spine numbers in a model for depression is not known. In this study we analyzed whether physical activity affects hippocampal volume and spine density by analyzing a rodent genetic model of depression, Flinders Sensitive Line Rats (FSL), with Magnetic Resonance Imaging (MRI) and ex vivo Golgi staining. We found that physical activity in the form of voluntary wheel running during 5 weeks increased hippocampal volume. Moreover, runners also had larger numbers of thin spines in the dentate gyrus. Our findings support that voluntary wheel running, which is antidepressive in FSL rats, is associated with increased hippocampal volume and spine numbers. PMID:25674191

Hippocampal morphology in a rat model of depression: the effects of physical activity.

PubMed

Sierakowiak, Adam; Mattsson, Anna; Gómez-Galán, Marta; Feminía, Teresa; Graae, Lisette; Aski, Sahar Nikkhou; Damberg, Peter; Lindskog, Mia; Brené, Stefan; Åberg, Elin

2014-01-01

Accumulating in vivo and ex vivo evidences show that humans suffering from depression have decreased hippocampal volume and altered spine density. Moreover, physical activity has an antidepressant effect in humans and in animal models, but to what extent physical activity can affect hippocampal volume and spine numbers in a model for depression is not known. In this study we analyzed whether physical activity affects hippocampal volume and spine density by analyzing a rodent genetic model of depression, Flinders Sensitive Line Rats (FSL), with Magnetic Resonance Imaging (MRI) and ex vivo Golgi staining. We found that physical activity in the form of voluntary wheel running during 5 weeks increased hippocampal volume. Moreover, runners also had larger numbers of thin spines in the dentate gyrus. Our findings support that voluntary wheel running, which is antidepressive in FSL rats, is associated with increased hippocampal volume and spine numbers.

Operating and environmental characteristics of Sigma Tau hydrogen masers used in the Very Long Baseline Array (VLBA)

NASA Technical Reports Server (NTRS)

Tucker, T. K.

1989-01-01

Presented here are the results obtained from performance evaluation of a pair of Sigma Tau Standards Corporation Model VLBA-112 active hydrogen maser frequency standards. These masers were manufactured for the National Radio Astronomy Observatory (NRAO) for use on the Very Long Baseline Array (VLBA) project and were furnished to the Jet Propulsion Laboratory (JPL) for the purpose of these tests. Tests on the two masers were performed in the JPL Frequency Standards Laboratory (FSL) and included the characterization of output frequency stability versus environmental factors such as temperature, humidity, magnetic field, and barometric pressure. The performance tests also included the determination of phase noise and Allan variance using both FSL and Sigma Tau masers as references. All tests were conducted under controlled laboratory conditions, with only the desired environmental and operational parameters varied to determine sensitivity to external environment.

Using component technology to facilitate external software reuse in ground-based planning systems

NASA Technical Reports Server (NTRS)

Chase, A.

2003-01-01

APGEN (Activity Plan GENerator - 314), a multi-mission planning tool, must interface with external software to vest serve its users. AP-GEN's original method for incorporating external software, the User-Defined library mechanism, has been very successful in allowing APGEN users access to external software functionality.

The tensor network theory library

NASA Astrophysics Data System (ADS)

Al-Assam, S.; Clark, S. R.; Jaksch, D.

2017-09-01

In this technical paper we introduce the tensor network theory (TNT) library—an open-source software project aimed at providing a platform for rapidly developing robust, easy to use and highly optimised code for TNT calculations. The objectives of this paper are (i) to give an overview of the structure of TNT library, and (ii) to help scientists decide whether to use the TNT library in their research. We show how to employ the TNT routines by giving examples of ground-state and dynamical calculations of one-dimensional bosonic lattice system. We also discuss different options for gaining access to the software available at www.tensornetworktheory.org.

A Security-façade Library for Virtual-observatory Software

NASA Astrophysics Data System (ADS)

Rixon, G.

2009-09-01

The security-façade library implements, for Java, IVOA's security standards. It supports the authentication mechanisms for SOAP and REST web-services, the sign-on mechanisms (with MyProxy, AstroGrid Accounts protocol or local credential-caches), the delegation protocol, and RFC3820-enabled HTTPS for Apache Tomcat. Using the façade, a developer who is not a security specialist can easily add access control to a virtual-observatory service and call secured services from an application. The library has been an internal part of AstroGrid software for some time and it is now offered for use by other developers.

The Microcomputer in the Library: VI. Implementation and Future Development.

ERIC Educational Resources Information Center

Leggate, Peter; Dyer, Hilary

1986-01-01

This sixth article in a series discusses planning for the installation and implementation of automated systems in the library, workstation design and location, scheduling of software implementation, security, data input, staff and reader training, job design, impact of automation on library procedures, evaluation of system performance, and future…

101 Computer Projects for Libraries. 101 Micro Series.

ERIC Educational Resources Information Center

Dewey, Patrick R.

The projects collected in this book represent a wide cross section of the way microcomputers are used in libraries. Each project description includes organization and contact information, hardware and software used, cost and project length estimates, and Web or print references when available. Projects come from academic and public libraries,…

Library Users: How They Adapt to Changing Roles.

ERIC Educational Resources Information Center

Miido, Helis

Traditional library tasks, for example database searching, are increasingly performed by library users, forcing both the librarian and the user to assume at times dichotomous roles of teacher and student. Modern librarians install new software and guide organizations in multimedia applications. Librarians need to be cognizant of the human factor,…

Opening up Library Automation Software

ERIC Educational Resources Information Center

Breeding, Marshall

2009-01-01

Throughout the history of library automation, the author has seen a steady advancement toward more open systems. In the early days of library automation, when proprietary systems dominated, the need for standards was paramount since other means of inter-operability and data exchange weren't possible. Today's focus on Application Programming…

An Integrated Library System from Existing Microcomputer Programs.

ERIC Educational Resources Information Center

Kuntz, Lynda S.

1988-01-01

Demonstrates how three commercial microcomputer software packages--PC-Talk III, Wordstar, and dBase III--were combined to produce an integrated library system at the U.S. Army Concepts Analysis Agency library. The retrospective conversion process is discussed, and the four modules of the system are described: acquisitions/cataloging; online…

Mini-Micro CDS/ISIS in the Thailand Development Research Institute Library.

ERIC Educational Resources Information Center

Wongkoltoot, Poonsin; Indee, Somsak

1992-01-01

Describes the Thailand Development Research Institute Library's development of an integrated bibliographic system using UNESCO's Micro-ISIS software. Linkages between databases were made using an in-house application (TIBIS) written in CDS/ISIS Pascal. The library system is available on a local area network (LAN). (three references) (EA)

Washington Public Libraries Online: Collaborating in Cyberspace.

ERIC Educational Resources Information Center

Wildin, Nancy

1997-01-01

Discussion of public libraries, the Internet, and the World Wide Web focuses on development of a Web site in Washington. Highlights include access to the Internet through online public access catalogs; partnerships between various types of libraries; hardware and software; HTML training; content design; graphics design; marketing; evaluation; and…

CONTENTdm Digital Collection Management Software and End-User Efficacy

ERIC Educational Resources Information Center

Dickson, Maggie

2008-01-01

Digital libraries and collections are a growing facet of today's traditional library. Digital library technologies have become increasingly more sophisticated in the effort to provide more and better access to the collections they contain. The evaluation of the usability of these technologies has not kept pace with technological developments,…

Software To Go: A Catalog of Software Available for Loan.

ERIC Educational Resources Information Center

Kurlychek, Ken, Comp.

This catalog lists the holdings of the Software To Go software lending library and clearinghouse for programs and agencies serving students or clients who are deaf or hard of hearing. An introduction describes the clearinghouse and its collection of software, much of it commercial and copyrighted material, for Apple, Macintosh, and IBM (MS-DOS)…

A conceptual model for megaprogramming

NASA Technical Reports Server (NTRS)

Tracz, Will

1990-01-01

Megaprogramming is component-based software engineering and life-cycle management. Magaprogramming and its relationship to other research initiatives (common prototyping system/common prototyping language, domain specific software architectures, and software understanding) are analyzed. The desirable attributes of megaprogramming software components are identified and a software development model and resulting prototype megaprogramming system (library interconnection language extended by annotated Ada) are described.

Maintenance of Automated Library Systems.

ERIC Educational Resources Information Center

Epstein, Susan Baerg

1983-01-01

Discussion of the maintenance of both the software and hardware in an automated library system highlights maintenance by the vendor, contracts and costs, the maintenance log, downtime, and planning for trouble. (EJS)

An application of machine learning to the organization of institutional software repositories

NASA Technical Reports Server (NTRS)

Bailin, Sidney; Henderson, Scott; Truszkowski, Walt

1993-01-01

Software reuse has become a major goal in the development of space systems, as a recent NASA-wide workshop on the subject made clear. The Data Systems Technology Division of Goddard Space Flight Center has been working on tools and techniques for promoting reuse, in particular in the development of satellite ground support software. One of these tools is the Experiment in Libraries via Incremental Schemata and Cobweb (ElvisC). ElvisC applies machine learning to the problem of organizing a reusable software component library for efficient and reliable retrieval. In this paper we describe the background factors that have motivated this work, present the design of the system, and evaluate the results of its application.

Automated Reuse of Scientific Subroutine Libraries through Deductive Synthesis

NASA Technical Reports Server (NTRS)

Lowry, Michael R.; Pressburger, Thomas; VanBaalen, Jeffrey; Roach, Steven

1997-01-01

Systematic software construction offers the potential of elevating software engineering from an art-form to an engineering discipline. The desired result is more predictable software development leading to better quality and more maintainable software. However, the overhead costs associated with the formalisms, mathematics, and methods of systematic software construction have largely precluded their adoption in real-world software development. In fact, many mainstream software development organizations, such as Microsoft, still maintain a predominantly oral culture for software development projects; which is far removed from a formalism-based culture for software development. An exception is the limited domain of safety-critical software, where the high-assuiance inherent in systematic software construction justifies the additional cost. We believe that systematic software construction will only be adopted by mainstream software development organization when the overhead costs have been greatly reduced. Two approaches to cost mitigation are reuse (amortizing costs over many applications) and automation. For the last four years, NASA Ames has funded the Amphion project, whose objective is to automate software reuse through techniques from systematic software construction. In particular, deductive program synthesis (i.e., program extraction from proofs) is used to derive a composition of software components (e.g., subroutines) that correctly implements a specification. The construction of reuse libraries of software components is the standard software engineering solution for improving software development productivity and quality.

BASKET on-board software library

NASA Astrophysics Data System (ADS)

Luntzer, Armin; Ottensamer, Roland; Kerschbaum, Franz

2014-07-01

The University of Vienna is a provider of on-board data processing software with focus on data compression, such as used on board the highly successful Herschel/PACS instrument, as well as in the small BRITE-Constellation fleet of cube-sats. Current contributions are made to CHEOPS, SAFARI and PLATO. The effort was taken to review the various functions developed for Herschel and provide a consolidated software library to facilitate the work for future missions. This library is a shopping basket of algorithms. Its contents are separated into four classes: auxiliary functions (e.g. circular buffers), preprocessing functions (e.g. for calibration), lossless data compression (arithmetic or Rice coding) and lossy reduction steps (ramp fitting etc.). The "BASKET" has all functionality that is needed to create an on-board data processing chain. All sources are written in C, supplemented by optimized versions in assembly, targeting popular CPU architectures for space applications. BASKET is open source and constantly growing

Software support for SBGN maps: SBGN-ML and LibSBGN.

PubMed

van Iersel, Martijn P; Villéger, Alice C; Czauderna, Tobias; Boyd, Sarah E; Bergmann, Frank T; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I; Mi, Huaiyu; Moodie, Stuart L; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

2012-08-01

LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. sbgn-libsbgn@lists.sourceforge.net.

TimeBench: a data model and software library for visual analytics of time-oriented data.

PubMed

Rind, Alexander; Lammarsch, Tim; Aigner, Wolfgang; Alsallakh, Bilal; Miksch, Silvia

2013-12-01

Time-oriented data play an essential role in many Visual Analytics scenarios such as extracting medical insights from collections of electronic health records or identifying emerging problems and vulnerabilities in network traffic. However, many software libraries for Visual Analytics treat time as a flat numerical data type and insufficiently tackle the complexity of the time domain such as calendar granularities and intervals. Therefore, developers of advanced Visual Analytics designs need to implement temporal foundations in their application code over and over again. We present TimeBench, a software library that provides foundational data structures and algorithms for time-oriented data in Visual Analytics. Its expressiveness and developer accessibility have been evaluated through application examples demonstrating a variety of challenges with time-oriented data and long-term developer studies conducted in the scope of research and student projects.

Noiseless Vlasov-Poisson simulations with linearly transformed particles

DOE PAGES

Pinto, Martin C.; Sonnendrucker, Eric; Friedman, Alex; ...

2014-06-25

We introduce a deterministic discrete-particle simulation approach, the Linearly-Transformed Particle-In-Cell (LTPIC) method, that employs linear deformations of the particles to reduce the noise traditionally associated with particle schemes. Formally, transforming the particles is justified by local first order expansions of the characteristic flow in phase space. In practice the method amounts of using deformation matrices within the particle shape functions; these matrices are updated via local evaluations of the forward numerical flow. Because it is necessary to periodically remap the particles on a regular grid to avoid excessively deforming their shapes, the method can be seen as a development ofmore » Denavit's Forward Semi-Lagrangian (FSL) scheme (Denavit, 1972 [8]). However, it has recently been established (Campos Pinto, 2012 [20]) that the underlying Linearly-Transformed Particle scheme converges for abstract transport problems, with no need to remap the particles; deforming the particles can thus be seen as a way to significantly lower the remapping frequency needed in the FSL schemes, and hence the associated numerical diffusion. To couple the method with electrostatic field solvers, two specific charge deposition schemes are examined, and their performance compared with that of the standard deposition method. Finally, numerical 1d1v simulations involving benchmark test cases and halo formation in an initially mismatched thermal sheet beam demonstrate some advantages of our LTPIC scheme over the classical PIC and FSL methods. Lastly, benchmarked test cases also indicate that, for numerical choices involving similar computational effort, the LTPIC method is capable of accuracy comparable to or exceeding that of state-of-the-art, high-resolution Vlasov schemes.« less

Search for biological correlates of depression and mechanisms of action of antidepressant treatment modalities. Do neuropeptides play a role?

PubMed

Mathé, Aleksander A; Husum, Henriette; El Khoury, Aram; Jiménez-Vasquez, Patricia; Gruber, Susanne H M; Wörtwein, Gitta; Nikisch, Georg; Baumann, Pierre; Agren, Hans; Andersson, Weronica; Södergren, Asa; Angelucci, Francesco

2007-09-10

Dysregulation of the monoaminergic systems is likely a sufficient but not a necessary cause of depression. A wealth of data indicates that neuropeptides, e.g., NPY, CRH, somatostatin, tachykinins and CGRP play a role in affective disorders and alcohol use/abuse. This paper focuses on NPY in etiology and pathophysiology of depression. Decreased peptide and mRNA NPY were found in hippocampus of both the genetic, e.g., the FSL strain, and environmental rat models of depression, e.g., chronic mild stress and early life maternal separation paradigms. Rat models of alcoholism also show altered NPY. Furthermore, NPY is also reduced in CSF of depressed patients. Antidepressive treatments tested so far (lithium, topiramate, SSRIs, ECT and ECS, wheel running) increase NPY selectively in rat hippocampus and in human CSF. Moreover, NPY given icv to rat has antidepressive effects which are antagonized by NPY-Y1 blockers. The data support our hypothesis that the NPY system dysregulation constitutes one of the biological underpinnings of depression and that one common mechanism of action of antidepressive treatment modalities may be effects on NPY and its receptors. In a novel paradigm, early life maternal separation was superimposed on "depressed" FSL and control rats and behavioral and brain neurochemistry changes observed in adulthood. The consequences were more deleterious in genetically vulnerable FSL. Early antidepressive treatment modulated the adult sequelae. Consequently, if these data are confirmed, the ethical and medical question that will be asked is whether it is permissible and advisable to consider prophylactically treating persons at risk.

Mapping the fine specificity of ABO monoclonal reagents with A and B type-specific function-spacer-lipid constructs in kodecytes and inkjet printed on paper.

PubMed

Barr, Katie; Korchagina, Elena; Ryzhov, Ivan; Bovin, Nicolai; Henry, Stephen

2014-10-01

Monoclonal (MoAb) reagents are routinely used and are usually very reliable for the serologic determination of ABO blood types. However, the fine specificity and cross-reactivity of these reagents are often unknown, particularly against synthetic antigens used in some diagnostic assays. If nonserologic assays or very sensitive techniques other than those specifically prescribed by the manufacturer are used, then there is a risk of incorrect interpretation of results. Forty-seven MoAbs and two polyclonal ABO reagents were tested against red blood cell (RBC) kodecytes prepared with A trisaccharide, A Type 1, A Type 2, A Type 3, A Type 4, B trisaccharide, B Type 1, B Type 2, acquired B trisaccharide, and Le(a) trisaccharide function-spacer-lipid (FSL) constructs. Natural RBCs were tested in parallel. In addition these FSL constructs were printed onto paper with a desktop inkjet printer and used in a novel immunoassay that identifies reactivity through the appearance of alphanumeric characters. Mapping of MoAbs with kodecytes and printed FSL constructs revealed a series of broad recognition patterns. All ABO MoAbs tested were reactive with the RBC dominant Type 2 ABO antigens. Unexpectedly some anti-A reagents were reactive against the B Type 1 antigen, while others were poorly reactive with trisaccharide antigens. All ABO MoAbs detect the RBC dominant Type 2 ABO antigens; however, some reagents may show minor reactivity with inappropriate blood group antigens, which needs to be considered when using these reagents in alternative or highly sensitive analytic systems. © 2014 AABB.

Shoestring Digital Library: If Existing Digital Library Software Doesn't Suit Your Needs, Create Your Own

ERIC Educational Resources Information Center

Weber, Jonathan

2006-01-01

Creating a digital library might seem like a task best left to a large research collection with a vast staff and generous budget. However, tools for successfully creating digital libraries are getting easier to use all the time. The explosion of people creating content for the web has led to the availability of many high-quality applications and…

Preliminary Specifications (Hardware and Software) for a Center for Information Services. Final Report on Mechanized Information Services in the University Library, Phase I - Planning. Part 10.

ERIC Educational Resources Information Center

California Univ., Los Angeles. Inst. of Library Research.

The general conclusions of the planning study on Mechanized Information Services in the University Library are that such services represent a desirable, even necessary, extension of the library's traditional functions. Preliminary specifications for such a library-based "Center for Information Services" (CIS) are presented in this report. Covered…

Parallel computation and the Basis system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, G.R.

1992-12-16

A software package has been written that can facilitate efforts to develop powerful, flexible, and easy-to-use programs that can run in single-processor, massively parallel, and distributed computing environments. Particular attention has been given to the difficulties posed by a program consisting of many science packages that represent subsystems of a complicated, coupled system. Methods have been found to maintain independence of the packages by hiding data structures without increasing the communication costs in a parallel computing environment. Concepts developed in this work are demonstrated by a prototype program that uses library routines from two existing software systems, Basis and Parallelmore » Virtual Machine (PVM). Most of the details of these libraries have been encapsulated in routines and macros that could be rewritten for alternative libraries that possess certain minimum capabilities. The prototype software uses a flexible master-and-slaves paradigm for parallel computation and supports domain decomposition with message passing for partitioning work among slaves. Facilities are provided for accessing variables that are distributed among the memories of slaves assigned to subdomains. The software is named PROTOPAR.« less

Parallel computation and the basis system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, G.R.

1993-05-01

A software package has been written that can facilitate efforts to develop powerful, flexible, and easy-to use programs that can run in single-processor, massively parallel, and distributed computing environments. Particular attention has been given to the difficulties posed by a program consisting of many science packages that represent subsystems of a complicated, coupled system. Methods have been found to maintain independence of the packages by hiding data structures without increasing the communications costs in a parallel computing environment. Concepts developed in this work are demonstrated by a prototype program that uses library routines from two existing software systems, Basis andmore » Parallel Virtual Machine (PVM). Most of the details of these libraries have been encapsulated in routines and macros that could be rewritten for alternative libraries that possess certain minimum capabilities. The prototype software uses a flexible master-and-slaves paradigm for parallel computation and supports domain decomposition with message passing for partitioning work among slaves. Facilities are provided for accessing variables that are distributed among the memories of slaves assigned to subdomains. The software is named PROTOPAR.« less

Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example.

PubMed

Gunalan, Kabilar; Chaturvedi, Ashutosh; Howell, Bryan; Duchin, Yuval; Lempka, Scott F; Patriat, Remi; Sapiro, Guillermo; Harel, Noam; McIntyre, Cameron C

2017-01-01

Deep brain stimulation (DBS) is an established clinical therapy and computational models have played an important role in advancing the technology. Patient-specific DBS models are now common tools in both academic and industrial research, as well as clinical software systems. However, the exact methodology for creating patient-specific DBS models can vary substantially and important technical details are often missing from published reports. Provide a detailed description of the assembly workflow and parameterization of a patient-specific DBS pathway-activation model (PAM) and predict the response of the hyperdirect pathway to clinical stimulation. Integration of multiple software tools (e.g. COMSOL, MATLAB, FSL, NEURON, Python) enables the creation and visualization of a DBS PAM. An example DBS PAM was developed using 7T magnetic resonance imaging data from a single unilaterally implanted patient with Parkinson's disease (PD). This detailed description implements our best computational practices and most elaborate parameterization steps, as defined from over a decade of technical evolution. Pathway recruitment curves and strength-duration relationships highlight the non-linear response of axons to changes in the DBS parameter settings. Parameterization of patient-specific DBS models can be highly detailed and constrained, thereby providing confidence in the simulation predictions, but at the expense of time demanding technical implementation steps. DBS PAMs represent new tools for investigating possible correlations between brain pathway activation patterns and clinical symptom modulation.

The Electronic Hermit: Trends in Library Automation.

ERIC Educational Resources Information Center

LaRue, James

1988-01-01

Reviews trends in library software development including: (1) microcomputer applications; (2) CD-ROM; (3) desktop publishing; (4) public access microcomputers; (5) artificial intelligence; (6) mainframes and minicomputers; and (7) automated catalogs. (MES)

Development of the FITS tools package for multiple software environments

NASA Technical Reports Server (NTRS)

Pence, W. D.; Blackburn, J. K.

1992-01-01

The HEASARC is developing a package of general purpose software for analyzing data files in FITS format. This paper describes the design philosophy which makes the software both machine-independent (it runs on VAXs, Suns, and DEC-stations) and software environment-independent. Currently the software can be compiled and linked to produce IRAF tasks, or alternatively, the same source code can be used to generate stand-alone tasks using one of two implementations of a user-parameter interface library. The machine independence of the software is achieved by writing the source code in ANSI standard Fortran or C, using the machine-independent FITSIO subroutine interface for all data file I/O, and using a standard user-parameter subroutine interface for all user I/O. The latter interface is based on the Fortran IRAF Parameter File interface developed at STScI. The IRAF tasks are built by linking to the IRAF implementation of this parameter interface library. Two other implementations of this parameter interface library, which have no IRAF dependencies, are now available which can be used to generate stand-alone executable tasks. These stand-alone tasks can simply be executed from the machine operating system prompt either by supplying all the task parameters on the command line or by entering the task name after which the user will be prompted for any required parameters. A first release of this FTOOLS package is now publicly available. The currently available tasks are described, along with instructions on how to obtain a copy of the software.

The Organization of a Computer Software Collection Using an Information Storage and Retrieval Software Package.

ERIC Educational Resources Information Center

Davies, Denise M.

1985-01-01

Discusses design, development, and use of a database to provide organization and access to a computer software collection at the University of Hawaii School of Library Studies. Field specifications, samples of report forms, and a description of the physical organization of the software collection are included. (MBR)

Observation Scheduling System

NASA Technical Reports Server (NTRS)

Chien, Steve A.; Tran, Daniel Q.; Rabideau, Gregg R.; Schaffer, Steven R.

2011-01-01

Software has been designed to schedule remote sensing with the Earth Observing One spacecraft. The software attempts to satisfy as many observation requests as possible considering each against spacecraft operation constraints such as data volume, thermal, pointing maneuvers, and others. More complex constraints such as temperature are approximated to enable efficient reasoning while keeping the spacecraft within safe limits. Other constraints are checked using an external software library. For example, an attitude control library is used to determine the feasibility of maneuvering between pairs of observations. This innovation can deal with a wide range of spacecraft constraints and solve large scale scheduling problems like hundreds of observations and thousands of combinations of observation sequences.

Cognitive Foundry v. 3.0 (OSS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basilico, Justin; Dixon, Kevin; McClain, Jonathan

2009-11-18

The Cognitive Foundry is a unified collection of tools designed for research and applications that use cognitive modeling, machine learning, or pattern recognition. The software library contains design patterns, interface definitions, and default implementations of reusable software components and algorithms designed to support a wide variety of research and development needs. The library contains three main software packages: the Common package that contains basic utilities and linear algebraic methods, the Cognitive Framework package that contains tools to assist in implementing and analyzing theories of cognition, and the Machine Learning package that provides general algorithms and methods for populating Cognitive Frameworkmore » components from domain-relevant data.« less

Advanced data acquisition and display techniques for laser velocimetry

NASA Technical Reports Server (NTRS)

Kjelgaard, Scott O.; Weston, Robert P.

1991-01-01

The Basic Aerodynamics Research Tunnel (BART) has been equipped with state-of-the-art instrumentation for acquiring the data needed for code validation. This paper describes the three-component LDV and the workstation-based data-acquisition system (DAS) which has been developed for the BART. The DAS allows the use of automation and the quick integration of advanced instrumentation, while minimizing the software development time required between investigations. The paper also includes a description of a graphics software library developed to support the windowing environment of the DAS. The real-time displays generated using the graphics library help the researcher ensure the test is proceeding properly. The graphics library also supports the requirements of posttest data analysis. The use of the DAS and graphics libraries is illustrated by presenting examples of the real-time and postprocessing display graphics for LDV investigations.

The Use of BookshelF in Teaching Students of Information and Library Management.

ERIC Educational Resources Information Center

Rowley, Jenny E.; Fisher, Shelagh

1992-01-01

Describes how BookshelF software, a library management system, has been integrated into the library and information management curriculum at Manchester Polytechnic (England), and discusses the learning objectives that have been achieved. The use of BookshelF modules for ordering, circulation control, cataloging, OPAC (online public access…

Introduction of Electronic Book Ordering with EDIFACT in a Special Library: A Case Study.

ERIC Educational Resources Information Center

Stadler, Peter; Thomas, Martin; Mernke, Ernst

1999-01-01

Describes book ordering procedures at a German pharmaceutical library using the Electronic Data Interchange for Administration, Commerce and Transport (EDIFACT) guidelines developed by the United Nations. Topics include advantages for libraries and for the book trade, changes needed in software, productivity gains, and EDIFACT versus the Internet.…

A Survey of Popular R Packages for Cluster Analysis

ERIC Educational Resources Information Center

Flynt, Abby; Dean, Nema

2016-01-01

Cluster analysis is a set of statistical methods for discovering new group/class structure when exploring data sets. This article reviews the following popular libraries/commands in the R software language for applying different types of cluster analysis: from the stats library, the kmeans, and hclust functions; the mclust library; the poLCA…

Automation Challenges of the 80's: What to Do until Your Integrated Library System Arrives.

ERIC Educational Resources Information Center

Allan, Ferne C.; Shields, Joyce M.

1986-01-01

A medium-sized aerospace library has developed interim solutions to automation needs by using software and equipment that were available in-house in preparation for an expected integrated library system. Automated processes include authors' file of items authored by employees, journal routing (including routing slips), statistics, journal…

Library Information System Time-Sharing (LISTS) Project. Final Report.

ERIC Educational Resources Information Center

Black, Donald V.

The Library Information System Time-Sharing (LISTS) experiment was based on three innovations in data processing technology: (1) the advent of computer time-sharing on third-generation machines, (2) the development of general-purpose file-management software and (3) the introduction of large, library-oriented data bases. The main body of the…

Two Ways to Set Up Wireless Hotspot: Comparing Apples and Oranges

ERIC Educational Resources Information Center

Mutch, Andrew; Ventura, Karen

2006-01-01

Every place has it--coffee shops, bookstores, universities ... and now libraries are offering wireless Internet access too. At the Waterford Township Public Library (Waterford, Michigan), Andrew Mutch created a wide-open wireless network using Public IP open source software. About 20 miles away, at the Novi Public Library (Novi, Michigan), Karen…

A Tour of the Stacks--HyperCard for Libraries.

ERIC Educational Resources Information Center

Ertel, Monica; Oros, Jane

1989-01-01

Description of HyperCard, a software package that runs on Macintosh microcomputers, focuses on its use in the Apple Computer, Inc., Library as a user guide to the library. Examples of screen displays are given, and a list of resources is included to help use and understand HyperCard more completely. (LRW)

The Philip Morris Information Network: A Library Database on an In-House Timesharing System.

ERIC Educational Resources Information Center

DeBardeleben, Marian Z.; And Others

1983-01-01

Outlines a database constructed at Philip Morris Research Center Library which encompasses holdings and circulation and acquisitions records for all items in the library. Host computer (DECSYSTEM-2060), software (BASIC), database design, search methodology, cataloging, and accessibility are noted; sample search, circ-in profile, end user profiles,…

Surviving the First Three Months as a Community College Library Director

ERIC Educational Resources Information Center

Kelly, Robert E., IV

2003-01-01

The experiences of a first-time community college library director during the initial three months on the job are detailed. The process of automation software migration is used as a vehicle for demonstrating activities performed to improve knowledge. Marketing, customer service, and identification of core library supporters are addressed. Concern…

The UNIX Operating System in Libraries: Advantages of LAN's and Bulletin Board Systems in Your Library.

ERIC Educational Resources Information Center

Rose, Phillip E.

1988-01-01

Describes the experiences of the AT&T Technical Library in installing a local area network (LAN) and bulletin board using the UNIX operating system. Reasons why a LAN was needed, how the system works, and hardware and software used are discussed. (1 reference) (MES)

Library and Classroom Use of Copyrighted Videotapes and Computer Software.

ERIC Educational Resources Information Center

Reed, Mary Hutchings; Stanek, Debra

Designed to provide guidance for librarians, this publication expresses the opinion of the legal counsel of the American Library Association (ALA) regarding library and classroom use of copyrighted videotapes and computer programs. A discussion of videotapes considers the impact of the Copyright Revision Act of 1976 on in-classroom use, in-library…

Visual programming for next-generation sequencing data analytics.

PubMed

Milicchio, Franco; Rose, Rebecca; Bian, Jiang; Min, Jae; Prosperi, Mattia

2016-01-01

High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone. Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a 'cultural' gap between the end user and the developer. Generic software template libraries specifically developed for NGS can help in dealing with the former problem, whilst coupling template libraries with visual programming may help with the latter. Here we scrutinize the state-of-the-art low-level software libraries implemented specifically for NGS and graphical tools for NGS analytics. An ideal developing environment for NGS should be modular (with a native library interface), scalable in computational methods (i.e. serial, multithread, distributed), transparent (platform-independent), interoperable (with external software interface), and usable (via an intuitive graphical user interface). These characteristics should facilitate both the run of standardized NGS pipelines and the development of new workflows based on technological advancements or users' needs. We discuss in detail the potential of a computational framework blending generic template programming and visual programming that addresses all of the current limitations. In the long term, a proper, well-developed (although not necessarily unique) software framework will bridge the current gap between data generation and hypothesis testing. This will eventually facilitate the development of novel diagnostic tools embedded in routine healthcare.

Performance testing of 3D point cloud software

NASA Astrophysics Data System (ADS)

Varela-González, M.; González-Jorge, H.; Riveiro, B.; Arias, P.

2013-10-01

LiDAR systems are being used widely in recent years for many applications in the engineering field: civil engineering, cultural heritage, mining, industry and environmental engineering. One of the most important limitations of this technology is the large computational requirements involved in data processing, especially for large mobile LiDAR datasets. Several software solutions for data managing are available in the market, including open source suites, however, users often unknown methodologies to verify their performance properly. In this work a methodology for LiDAR software performance testing is presented and four different suites are studied: QT Modeler, VR Mesh, AutoCAD 3D Civil and the Point Cloud Library running in software developed at the University of Vigo (SITEGI). The software based on the Point Cloud Library shows better results in the loading time of the point clouds and CPU usage. However, it is not as strong as commercial suites in working set and commit size tests.

A design for a reusable Ada library

NASA Technical Reports Server (NTRS)

Litke, John D.

1986-01-01

A goal of the Ada language standardization effort is to promote reuse of software, implying the existence of substantial software libraries and the storage/retrieval mechanisms to support them. A searching/cataloging mechanism is proposed that permits full or partial distribution of the database, adapts to a variety of searching mechanisms, permits a changine taxonomy with minimal disruption, and minimizes the requirement of specialized cataloger/indexer skills. The important observation is that key words serve not only as indexing mechanism, but also as an identification mechanism, especially via concatenation and as support for a searching mechanism. By deliberately separating these multiple uses, the modifiability and ease of growth that current libraries require, is achieved.

Climate tools in mainstream Linux distributions

NASA Astrophysics Data System (ADS)

McKinstry, Alastair

2015-04-01

Debian/meterology is a project to integrate climate tools and analysis software into the mainstream Debian/Ubuntu Linux distributions. This work describes lessons learnt, and recommends practices for scientific software to be adopted and maintained in OS distributions. In addition to standard analysis tools (cdo,, grads, ferret, metview, ncl, etc.), software used by the Earth System Grid Federation was chosen for integraion, to enable ESGF portals to be built on this base; however exposing scientific codes via web APIs enables security weaknesses, normally ignorable, to be exposed. How tools are hardened, and what changes are required to handle security upgrades, are described. Secondly, to enable libraries and components (e.g. Python modules) to be integrated requires planning by writers: it is not sufficient to assume users can upgrade their code when you make incompatible changes. Here, practices are recommended to enable upgrades and co-installability of C, C++, Fortran and Python codes. Finally, software packages such as NetCDF and HDF5 can be built in multiple configurations. Tools may then expect incompatible versions of these libraries (e.g. serial and parallel) to be simultaneously available; how this was solved in Debian using "pkg-config" and shared library interfaces is described, and best practices for software writers to enable this are summarised.

Mathematical and Statistical Software Index. Final Report.

ERIC Educational Resources Information Center

Black, Doris E., Comp.

Brief descriptions are provided of general-purpose mathematical and statistical software, including 27 "stand-alone" programs, three subroutine systems, and two nationally recognized statistical packages, which are available in the Air Force Human Resources Laboratory (AFHRL) software library. This index was created to enable researchers…

Software for quantitative analysis of radiotherapy: overview, requirement analysis and design solutions.

PubMed

Zhang, Lanlan; Hub, Martina; Mang, Sarah; Thieke, Christian; Nix, Oliver; Karger, Christian P; Floca, Ralf O

2013-06-01

Radiotherapy is a fast-developing discipline which plays a major role in cancer care. Quantitative analysis of radiotherapy data can improve the success of the treatment and support the prediction of outcome. In this paper, we first identify functional, conceptional and general requirements on a software system for quantitative analysis of radiotherapy. Further we present an overview of existing radiotherapy analysis software tools and check them against the stated requirements. As none of them could meet all of the demands presented herein, we analyzed possible conceptional problems and present software design solutions and recommendations to meet the stated requirements (e.g. algorithmic decoupling via dose iterator pattern; analysis database design). As a proof of concept we developed a software library "RTToolbox" following the presented design principles. The RTToolbox is available as open source library and has already been tested in a larger-scale software system for different use cases. These examples demonstrate the benefit of the presented design principles. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Habib, Salman; Roser, Robert

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3)more » Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.« less

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Habib, Salman; Roser, Robert; LeCompte, Tom

2015-10-29

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3)more » Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.« less

Clinical data miner: an electronic case report form system with integrated data preprocessing and machine-learning libraries supporting clinical diagnostic model research.

PubMed

Installé, Arnaud Jf; Van den Bosch, Thierry; De Moor, Bart; Timmerman, Dirk

2014-10-20

Using machine-learning techniques, clinical diagnostic model research extracts diagnostic models from patient data. Traditionally, patient data are often collected using electronic Case Report Form (eCRF) systems, while mathematical software is used for analyzing these data using machine-learning techniques. Due to the lack of integration between eCRF systems and mathematical software, extracting diagnostic models is a complex, error-prone process. Moreover, due to the complexity of this process, it is usually only performed once, after a predetermined number of data points have been collected, without insight into the predictive performance of the resulting models. The objective of the study of Clinical Data Miner (CDM) software framework is to offer an eCRF system with integrated data preprocessing and machine-learning libraries, improving efficiency of the clinical diagnostic model research workflow, and to enable optimization of patient inclusion numbers through study performance monitoring. The CDM software framework was developed using a test-driven development (TDD) approach, to ensure high software quality. Architecturally, CDM's design is split over a number of modules, to ensure future extendability. The TDD approach has enabled us to deliver high software quality. CDM's eCRF Web interface is in active use by the studies of the International Endometrial Tumor Analysis consortium, with over 4000 enrolled patients, and more studies planned. Additionally, a derived user interface has been used in six separate interrater agreement studies. CDM's integrated data preprocessing and machine-learning libraries simplify some otherwise manual and error-prone steps in the clinical diagnostic model research workflow. Furthermore, CDM's libraries provide study coordinators with a method to monitor a study's predictive performance as patient inclusions increase. To our knowledge, CDM is the only eCRF system integrating data preprocessing and machine-learning libraries. This integration improves the efficiency of the clinical diagnostic model research workflow. Moreover, by simplifying the generation of learning curves, CDM enables study coordinators to assess more accurately when data collection can be terminated, resulting in better models or lower patient recruitment costs.

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

PubMed Central

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23467006

Automation and hypermedia technology applications

NASA Technical Reports Server (NTRS)

Jupin, Joseph H.; Ng, Edward W.; James, Mark L.

1993-01-01

This paper represents a progress report on HyLite (Hypermedia Library technology): a research and development activity to produce a versatile system as part of NASA's technology thrusts in automation, information sciences, and communications. HyLite can be used as a system or tool to facilitate the creation and maintenance of large distributed electronic libraries. The contents of such a library may be software components, hardware parts or designs, scientific data sets or databases, configuration management information, etc. Proliferation of computer use has made the diversity and quantity of information too large for any single user to sort, process, and utilize effectively. In response to this information deluge, we have created HyLite to enable the user to process relevant information into a more efficient organization for presentation, retrieval, and readability. To accomplish this end, we have incorporated various AI techniques into the HyLite hypermedia engine to facilitate parameters and properties of the system. The proposed techniques include intelligent searching tools for the libraries, intelligent retrievals, and navigational assistance based on user histories. HyLite itself is based on an earlier project, the Encyclopedia of Software Components (ESC) which used hypermedia to facilitate and encourage software reuse.

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

PubMed

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013 Elsevier B.V. All rights reserved.

An open-source java platform for automated reaction mapping.

PubMed

Crabtree, John D; Mehta, Dinesh P; Kouri, Tina M

2010-09-27

This article presents software applications that have been built upon a modular, open-source, reaction mapping library that can be used in both cheminformatics and bioinformatics research. We first describe the theoretical underpinnings and modular architecture of the core software library. We then describe two applications that have been built upon that core. The first is a generic reaction viewer and mapper, and the second classifies reactions according to rules that can be modified by end users with little or no programming skills.

NRL Hyperspectral Imagery Trafficability Tool (HITT): Software andSpectral-Geotechnical Look-up Tables for Estimation and Mapping of Soil Bearing Strength from Hyperspectral Imagery

DTIC Science & Technology

2012-09-28

spectral-geotechnical libraries and models developed during remote sensing and calibration/ validation campaigns conducted by NRL and collaborating...geotechnical libraries and models developed during remote sensing and calibration/ validation campaigns conducted by NRL and collaborating institutions in four...2010; Bachmann, Fry, et al, 2012a). The NRL HITT tool is a model for how we develop and validate software, and the future development of tools by

YAP Version 4.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Eric M.

2004-05-20

The YAP software library computes (1) electromagnetic modes, (2) electrostatic fields, (3) magnetostatic fields and (4) particle trajectories in 2d and 3d models. The code employs finite element methods on unstructured grids of tetrahedral, hexahedral, prism and pyramid elements, with linear through cubic element shapes and basis functions to provide high accuracy. The novel particle tracker is robust, accurate and efficient, even on unstructured grids with discontinuous fields. This software library is a component of the MICHELLE 3d finite element gun code.

Image analysis library software development

NASA Technical Reports Server (NTRS)

Guseman, L. F., Jr.; Bryant, J.

1977-01-01

The Image Analysis Library consists of a collection of general purpose mathematical/statistical routines and special purpose data analysis/pattern recognition routines basic to the development of image analysis techniques for support of current and future Earth Resources Programs. Work was done to provide a collection of computer routines and associated documentation which form a part of the Image Analysis Library.

Two Years on: Koha 3.0 in Use at the CAMLIS Library, Royal London Homoeopathic Hospital

ERIC Educational Resources Information Center

Bissels, Gerhard; Chandler, Andrea

2010-01-01

Purpose: The purpose of this paper is to describe the further development of the Koha 3.0 library management system (LMS) and the involvement of external software consultants at the Complementary and Alternative Medicine Library and Information Service (CAMLIS), Royal London Homoeopathic Hospital. Design/methodology/approach: The paper takes the…

Expert Systems for Libraries at SCIL [Small Computers in Libraries]'88.

ERIC Educational Resources Information Center

Kochtanek, Thomas R.; And Others

1988-01-01

Six brief papers on expert systems for libraries cover (1) a knowledge-based approach to database design; (2) getting started in expert systems; (3) using public domain software to develop a business reference system; (4) a music cataloging inquiry system; (5) linguistic analysis of reference transactions; and (6) a model of a reference librarian.…

Who Moved My Intranet? The Human Side of Introducing Collaborative Technologies to Library Staff

ERIC Educational Resources Information Center

Jeffery, Keven; Dworak, Ellie

2010-01-01

Intranets can be crucial tools in fostering communication within an academic library. This article describes the successful implementation of an intranet wiki at the San Diego State University Library & Information Access. The steps involved with implementing, marketing, and supporting the MediaWiki software are described, and the results of a…

Do We Really Have an Internet Problem? Statistics, Credibility and Issues Concerning Public Internet Access in Academic Libraries.

ERIC Educational Resources Information Center

Cubbage, Charlotte

2002-01-01

Discusses problems with patron Internet access in academic libraries and describes a study conducted at Northwestern University (Illinois) that used Internet tracking software to assess user Internet behavior. Topics include Internet use policies; pornography; and loss of control over library services and information content that is provided. (LRW)

Competencies for Librarians. Proceedings from the 1985 Spring Meeting of the Nebraska Library Association: College and University Section (Omaha, Nebraska, April 26, 1985).

ERIC Educational Resources Information Center

Krzywkowski, Valerie I., Ed.

Based on the conference theme, "Competencies for Librarians," papers presented at the 1985 meeting of the association include: (1) "Planning a Library-Based Public Access Microcomputer Facility" (Suzanne Kehm); (2) "Processing and Circulating Microcomputer Software in the Academic Library: A Sharing Session" (Jan…

Experiences Using an Open Source Software Library to Teach Computer Vision Subjects

ERIC Educational Resources Information Center

Cazorla, Miguel; Viejo, Diego

2015-01-01

Machine vision is an important subject in computer science and engineering degrees. For laboratory experimentation, it is desirable to have a complete and easy-to-use tool. In this work we present a Java library, oriented to teaching computer vision. We have designed and built the library from the scratch with emphasis on readability and…

Special Features of the Advanced Loans Module of the ABCD Integrated Library System

ERIC Educational Resources Information Center

de Smet, Egbert

2011-01-01

Purpose: The "advanced loans" module of the relatively new library software, ABCD, is an addition to the normal loans module and it offers a "generic transaction decision-making engine" functionality. The module requires extra installation effort and parameterisation, so this article aims to explain to the many potentially interested libraries,…

Assessing Homegrown Library Collections: Using Google Analytics to Track Use of Screencasts and Flash-Based Learning Objects

ERIC Educational Resources Information Center

Betty, Paul

2009-01-01

Increasing use of screencast and Flash authoring software within libraries is resulting in "homegrown" library collections of digital learning objects and multimedia presentations. The author explores the use of Google Analytics to track usage statistics for interactive Shockwave Flash (.swf) files, the common file output for screencast and Flash…

Upgrading a ColdFusion-Based Academic Medical Library Staff Intranet

ERIC Educational Resources Information Center

Vander Hart, Robert; Ingrassia, Barbara; Mayotte, Kerry; Palmer, Lisa A.; Powell, Julia

2010-01-01

This article details the process of upgrading and expanding an existing academic medical library intranet to include a wiki, blog, discussion forum, and photo collection manager. The first version of the library's intranet from early 2002 was powered by ColdFusion software and existed primarily to allow staff members to author and store minutes of…

Open Source Software and the Intellectual Commons.

ERIC Educational Resources Information Center

Dorman, David

2002-01-01

Discusses the Open Source Software method of software development and its relationship to control over information content. Topics include digital library resources; reference services; preservation; the legal and economic status of information; technical standards; access to digital data; control of information use; and copyright and patent laws.…

CGNS Mid-Level Software Library and Users Guide

NASA Technical Reports Server (NTRS)

Poirier, Diane; Smith, Charles A. (Technical Monitor)

1998-01-01

The "CFD General Notation System" (CGNS) consists of a collection of conventions, and conforming software, for the storage and retrieval of Computational Fluid Dynamics (CFD) data. It facilitates the exchange of data between sites and applications, and helps stabilize the archiving of aerodynamic data. This effort was initiated in order to streamline the procedures in exchanging data and software between NASA and its customers, but the goal is to develop CGNS into a National Standard for the exchange of aerodynamic data. The CGNS development team is comprised of members from Boeing Commercial Airplane Group, NASA-Ames, NASA-Langley, NASA-Lewis, McDonnell-Douglas Corporation (now Boeing-St. Louis), Air Force-Wright Lab., and ICEM-CFD Engineering. The elements of CGNS address all activities associated with the storage of data on external media and its movement to and from application programs. These elements include: - The Advanced Data Format (ADF) Database manager, consisting of both a file format specification and its I/O software, which handles the actual reading and writing of data from and to external storage media; - The Standard Interface Data Structures (SIDS), which specify the intellectual content of CFD data and the conventions governing naming and terminology; - The SIDS-to-ADF File Mapping conventions, which specify the exact location where the CFD data defined by the SIDS is to be stored within the ADF file(s); and - The CGNS Mid-level Library, which provides CFD-knowledgeable routines suitable for direct installation into application codes. The CGNS Mid-level Library was designed to ease the implementation of CGNS by providing developers with a collection of handy I/O functions. Since knowledge of the ADF core is not required to use this library, it will greatly facilitate the task of interfacing with CGNS. There are currently 48 user callable functions that comprise the Mid-level library and are described in the Users Guide. The library is written in C, but each function has a FORTRAN counterpart.

Video Discs in Libraries.

ERIC Educational Resources Information Center

Barker, Philip

1986-01-01

Discussion of developments in information storage technology likely to have significant impact upon library utilization focuses on hardware (videodisc technology) and software developments (knowledge databases; computer networks; database management systems; interactive video, computer, and multimedia user interfaces). Three generic computer-based…

AUTONOMIC AND BEHAVIORAL RESPONSES OF SELECTIVELY BRED HYPERCHOLINERGIC RATS TO OXOTREMORINE AND DIISOPROPYL FLUOROPHOSPHATE

EPA Science Inventory

The hypercholinergic Flinders Sensitive Line (FSL) rat was significantly more sensitive than the Flinders Resistant Line (FRL) rat to the biotelemetrically recorded hypothermic effects of oxotremorine, a directly acting muscarinic agonist, and diisopropyl fluorophosphate (DFP), a...

Perl Extension to the Bproc Library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grunau, Daryl W.

2004-06-07

The Beowulf Distributed process Space (Bproc) software stack is comprised of UNIX/Linux kernel modifications and a support library by which a cluster of machines, each running their own private kernel, can present itself as a unified process space to the user. A Bproc cluster contains a single front-end machine and many back-end nodes which receive and run processes given to them by the front-end. Any process which is migrated to a back-end node is also visible as a ghost process on the fron-end, and may be controlled there using traditional UNIX semantics (e.g. ps(1), kill(1), etc). This software is amore » Perl extension to the Bproc library which enables the Perl programmer to make direct calls to functions within the Bproc library. See http://www.clustermatic.org, http://bproc.sourceforge.net, and http://www.perl.org« less

An FPGA-Based People Detection System

NASA Astrophysics Data System (ADS)

Nair, Vinod; Laprise, Pierre-Olivier; Clark, James J.

2005-12-01

This paper presents an FPGA-based system for detecting people from video. The system is designed to use JPEG-compressed frames from a network camera. Unlike previous approaches that use techniques such as background subtraction and motion detection, we use a machine-learning-based approach to train an accurate detector. We address the hardware design challenges involved in implementing such a detector, along with JPEG decompression, on an FPGA. We also present an algorithm that efficiently combines JPEG decompression with the detection process. This algorithm carries out the inverse DCT step of JPEG decompression only partially. Therefore, it is computationally more efficient and simpler to implement, and it takes up less space on the chip than the full inverse DCT algorithm. The system is demonstrated on an automated video surveillance application and the performance of both hardware and software implementations is analyzed. The results show that the system can detect people accurately at a rate of about[InlineEquation not available: see fulltext.] frames per second on a Virtex-II 2V1000 using a MicroBlaze processor running at[InlineEquation not available: see fulltext.], communicating with dedicated hardware over FSL links.

Pore size assessment during corneal endothelial cells permeabilization by femtosecond laser activated carbon nanoparticles

NASA Astrophysics Data System (ADS)

Jumelle, C.; Mauclair, C.; Houzet, J.; Bernard, A.; He, Z.; Piselli, S.; Perrache, C.; Egaud, G.; Baubeau, E.; Gain, P.; Thuret, G.

2015-07-01

Corneal therapeutic molecules delivery represents a promising solution to maintain human corneal endothelial cells (HCECs) viability, but the difficulty is transport across cell membrane. A new delivery method published recently consists in ephemerally permeabilizing cell membranes using a photo-acoustic reaction produced by carbon nanoparticles (CNPs) and femtosecond laser (FsL). The aim of this work is to investigate the size of pores formed at cell membrane by this technique. To induce cell permeabilization, HCECs were put in contact with CNPs and irradiated with a 500 μm diameter Ti:Sa FsL focalized spot. Four sizes of marker molecules were delivered into HCECs to investigate pore sizes: calcein (1.2 nm), FITC-Dextran 4kDa (2.8 nm) and FITC-Dextran 70kDa (12 nm) and FITC-Dextran 2MDa (50 nm). Delivery of each molecule was assessed by flow cytometry, a technique able to measure their presence into cells. We showed that the delivery rate was dependent of their size. Calcein was delivered in 56.1±8.2% of HCECs, FITC-Dextran 4kDa in 42.2±3.5%, FITC-Dextran 70 kDa in 21.5±2.7% and finally FITC-Dextran 2MDa in 12.9±2.0%. It means that a large number of pores in the size ranging from 1.2 to 2.8 nm were formed. However, 12 nm and larger pores were almost half more infrequent. Pore sizes formed at cell membrane by the technique of cell permeabilization by FsL activated CNPs was investigated. The results indicated that the pore sizes are large enough for the efficient delivery of small, medium and big therapeutics molecules on HCECs by this technique.

QuBiLS-MIDAS: a parallel free-software for molecular descriptors computation based on multilinear algebraic maps.

PubMed

García-Jacas, César R; Marrero-Ponce, Yovani; Acevedo-Martínez, Liesner; Barigye, Stephen J; Valdés-Martiní, José R; Contreras-Torres, Ernesto

2014-07-05

The present report introduces the QuBiLS-MIDAS software belonging to the ToMoCoMD-CARDD suite for the calculation of three-dimensional molecular descriptors (MDs) based on the two-linear (bilinear), three-linear, and four-linear (multilinear or N-linear) algebraic forms. Thus, it is unique software that computes these tensor-based indices. These descriptors, establish relations for two, three, and four atoms by using several (dis-)similarity metrics or multimetrics, matrix transformations, cutoffs, local calculations and aggregation operators. The theoretical background of these N-linear indices is also presented. The QuBiLS-MIDAS software was developed in the Java programming language and employs the Chemical Development Kit library for the manipulation of the chemical structures and the calculation of the atomic properties. This software is composed by a desktop user-friendly interface and an Abstract Programming Interface library. The former was created to simplify the configuration of the different options of the MDs, whereas the library was designed to allow its easy integration to other software for chemoinformatics applications. This program provides functionalities for data cleaning tasks and for batch processing of the molecular indices. In addition, it offers parallel calculation of the MDs through the use of all available processors in current computers. The studies of complexity of the main algorithms demonstrate that these were efficiently implemented with respect to their trivial implementation. Lastly, the performance tests reveal that this software has a suitable behavior when the amount of processors is increased. Therefore, the QuBiLS-MIDAS software constitutes a useful application for the computation of the molecular indices based on N-linear algebraic maps and it can be used freely to perform chemoinformatics studies. Copyright © 2014 Wiley Periodicals, Inc.

Algorithm-Based Fault Tolerance for Numerical Subroutines

NASA Technical Reports Server (NTRS)

Tumon, Michael; Granat, Robert; Lou, John

2007-01-01

A software library implements a new methodology of detecting faults in numerical subroutines, thus enabling application programs that contain the subroutines to recover transparently from single-event upsets. The software library in question is fault-detecting middleware that is wrapped around the numericalsubroutines. Conventional serial versions (based on LAPACK and FFTW) and a parallel version (based on ScaLAPACK) exist. The source code of the application program that contains the numerical subroutines is not modified, and the middleware is transparent to the user. The methodology used is a type of algorithm- based fault tolerance (ABFT). In ABFT, a checksum is computed before a computation and compared with the checksum of the computational result; an error is declared if the difference between the checksums exceeds some threshold. Novel normalization methods are used in the checksum comparison to ensure correct fault detections independent of algorithm inputs. In tests of this software reported in the peer-reviewed literature, this library was shown to enable detection of 99.9 percent of significant faults while generating no false alarms.

FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

PubMed

Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

2014-06-14

Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis.

PubMed

Trümbach, Dietrich; Pfeiffer, Susanne; Poppe, Manuel; Scherb, Hagen; Doll, Sebastian; Wurst, Wolfgang; Schick, Joel A

2017-11-25

As CRISPR/Cas9 mediated screens with pooled guide libraries in somatic cells become increasingly established, an unmet need for rapid and accurate companion informatics tools has emerged. We have developed a lightweight and efficient software to easily manipulate large raw next generation sequencing datasets derived from such screens into informative relational context with graphical support. The advantages of the software entitled ENCoRE (Easy NGS-to-Gene CRISPR REsults) include a simple graphical workflow, platform independence, local and fast multithreaded processing, data pre-processing and gene mapping with custom library import. We demonstrate the capabilities of ENCoRE to interrogate results from a pooled CRISPR cellular viability screen following Tumor Necrosis Factor-alpha challenge. The results not only identified stereotypical players in extrinsic apoptotic signaling but two as yet uncharacterized members of the extrinsic apoptotic cascade, Smg7 and Ces2a. We further validated and characterized cell lines containing mutations in these genes against a panel of cell death stimuli and involvement in p53 signaling. In summary, this software enables bench scientists with sensitive data or without access to informatic cores to rapidly interpret results from large scale experiments resulting from pooled CRISPR/Cas9 library screens.

Open source libraries and frameworks for biological data visualisation: a guide for developers.

PubMed

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-04-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Open source libraries and frameworks for biological data visualisation: A guide for developers

PubMed Central

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-01-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. PMID:25475079

Software for Teaching Physiology and Biophysics.

ERIC Educational Resources Information Center

Weiss, Thomas F.; And Others

1992-01-01

Describes a software library developed to teach biophysics and physiology undergraduates that includes software on (1) the Hodgkin-Huxley model for excitation of action potentials in electrically excitable cells; (2) a random-walk model of diffusion; (3) single voltage-gated ion channels; (4) steady-state chemically mediated transport; and (5)…

A Public Domain Software Library for Reading and Language Arts.

ERIC Educational Resources Information Center

Balajthy, Ernest

A three-year project carried out by the Microcomputers and Reading Committee of the New Jersey Reading Association involved the collection, improvement, and distribution of free microcomputer software (public domain programs) designed to deal with reading and writing skills. Acknowledging that this free software is not without limitations (poor…

Microcomputers in Libraries: The Quiet Revolution.

ERIC Educational Resources Information Center

Boss, Richard

1985-01-01

This article defines three separate categories of microcomputers--personal, desk-top, multi-user devices--and relates storage capabilities (expandability, floppy disks) to library applications. Highlghts include de facto standards, operating systems, database management systems, applications software, circulation control systems, dumb and…

iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data.

PubMed

Groppe, David M; Bickel, Stephan; Dykstra, Andrew R; Wang, Xiuyuan; Mégevand, Pierre; Mercier, Manuel R; Lado, Fred A; Mehta, Ashesh D; Honey, Christopher J

2017-04-01

Intracranial electrical recordings (iEEG) and brain stimulation (iEBS) are invaluable human neuroscience methodologies. However, the value of such data is often unrealized as many laboratories lack tools for localizing electrodes relative to anatomy. To remedy this, we have developed a MATLAB toolbox for intracranial electrode localization and visualization, iELVis. NEW METHOD: iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging coregistration, and manual identification of electrodes in postimplant neuroimaging. Subsequently, iELVis implements methods for correcting electrode locations for postimplant brain shift with millimeter-scale accuracy and provides interactive visualization on 3D surfaces or in 2D slices with optional functional neuroimaging overlays. iELVis also localizes electrodes relative to FreeSurfer-based atlases and can combine data across subjects via the FreeSurfer average brain. It takes 30-60min of user time and 12-24h of computer time to localize and visualize electrodes from one brain. We demonstrate iELVis's functionality by showing that three methods for mapping primary hand somatosensory cortex (iEEG, iEBS, and functional MRI) provide highly concordant results. COMPARISON WITH EXISTING METHODS: iELVis is the first public software for electrode localization that corrects for brain shift, maps electrodes to an average brain, and supports neuroimaging overlays. Moreover, its interactive visualizations are powerful and its tutorial material is extensive. iELVis promises to speed the progress and enhance the robustness of intracranial electrode research. The software and extensive tutorial materials are freely available as part of the EpiSurg software project: https://github.com/episurg/episurg. Copyright © 2017 Elsevier B.V. All rights reserved.

Zooming In on Copyright with Integrated Library Software Services

ERIC Educational Resources Information Center

Oye, Karen

2007-01-01

Over the last decade, many of Kelvin Smith Library's (KSL) content delivery services have gone digital, and some, such as enhanced course reserves products, are new to the market. The best digital library services have given KSL options and integrated solutions that allow it to do more than it thought possible just a few years ago. As with many…

Largenet2: an object-oriented programming library for simulating large adaptive networks.

PubMed

Zschaler, Gerd; Gross, Thilo

2013-01-15

The largenet2 C++ library provides an infrastructure for the simulation of large dynamic and adaptive networks with discrete node and link states. The library is released as free software. It is available at http://biond.github.com/largenet2. Largenet2 is licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported License. gerd@biond.org

Effective e-Training: Using a Course Management System and e-Learning Tools to Train Library Employees

ERIC Educational Resources Information Center

See, Andrew; Teetor, Travis Stephen

2014-01-01

In the summer of 2012, the University of Arizona Libraries implemented an online training program to effectively train Access Services staff and student employees at a large academic research library. This article discusses the program, which was built using a course management system (D2L) and various e-Learning software applications (Articulate…

Computers in Libraries, 2000: Proceedings (15th, Washington, D.C., March 15-17, 2000).

ERIC Educational Resources Information Center

Nixon, Carol, Comp.; Burmood, Jennifer, Comp.

Topics of the Proceedings of the 15th Annual Computers in Libraries Conference (March 15-17, 2000) include: Linux and open source software in an academic library; a Master Trainer Program; what educators need to know about multimedia and copyright; how super searchers find business information online; managing print costs; new technologies in wide…

Active learning based segmentation of Crohns disease from abdominal MRI.

PubMed

Mahapatra, Dwarikanath; Vos, Franciscus M; Buhmann, Joachim M

2016-05-01

This paper proposes a novel active learning (AL) framework, and combines it with semi supervised learning (SSL) for segmenting Crohns disease (CD) tissues from abdominal magnetic resonance (MR) images. Robust fully supervised learning (FSL) based classifiers require lots of labeled data of different disease severities. Obtaining such data is time consuming and requires considerable expertise. SSL methods use a few labeled samples, and leverage the information from many unlabeled samples to train an accurate classifier. AL queries labels of most informative samples and maximizes gain from the labeling effort. Our primary contribution is in designing a query strategy that combines novel context information with classification uncertainty and feature similarity. Combining SSL and AL gives a robust segmentation method that: (1) optimally uses few labeled samples and many unlabeled samples; and (2) requires lower training time. Experimental results show our method achieves higher segmentation accuracy than FSL methods with fewer samples and reduced training effort. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes

PubMed Central

Li, Erna; Wei, Xiao; Ma, Yanyan; Yin, Zhe; Li, Huan; Lin, Weishi; Wang, Xuesong; Li, Chao; Shen, Zhiqiang; Zhao, Ruixiang; Yang, Huiying; Jiang, Aimin; Yang, Wenhui; Yuan, Jing; Zhao, Xiangna

2016-01-01

Enterobacter aerogenes (Enterobacteriaceae) is an important opportunistic pathogen that causes hospital-acquired pneumonia, bacteremia, and urinary tract infections. Recently, multidrug-resistant E. aerogenes have been a public health problem. To develop an effective antimicrobial agent, bacteriophage phiEap-2 was isolated from sewage and its genome was sequenced because of its ability to lyse the multidrug-resistant clinical E. aerogenes strain 3-SP. Morphological observations suggested that the phage belongs to the Siphoviridae family. Comparative genome analysis revealed that phage phiEap-2 is related to the Salmonella phage FSL SP-031 (KC139518). All of the structural gene products (except capsid protein) encoded by phiEap-2 had orthologous gene products in FSL SP-031 and Serratia phage Eta (KC460990). Here, we report the complete genome sequence of phiEap-2 and major findings from the genomic analysis. Knowledge of this phage might be helpful for developing therapeutic strategies against E. aerogenes. PMID:27320081

Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes.

PubMed

Li, Erna; Wei, Xiao; Ma, Yanyan; Yin, Zhe; Li, Huan; Lin, Weishi; Wang, Xuesong; Li, Chao; Shen, Zhiqiang; Zhao, Ruixiang; Yang, Huiying; Jiang, Aimin; Yang, Wenhui; Yuan, Jing; Zhao, Xiangna

2016-06-20

Enterobacter aerogenes (Enterobacteriaceae) is an important opportunistic pathogen that causes hospital-acquired pneumonia, bacteremia, and urinary tract infections. Recently, multidrug-resistant E. aerogenes have been a public health problem. To develop an effective antimicrobial agent, bacteriophage phiEap-2 was isolated from sewage and its genome was sequenced because of its ability to lyse the multidrug-resistant clinical E. aerogenes strain 3-SP. Morphological observations suggested that the phage belongs to the Siphoviridae family. Comparative genome analysis revealed that phage phiEap-2 is related to the Salmonella phage FSL SP-031 (KC139518). All of the structural gene products (except capsid protein) encoded by phiEap-2 had orthologous gene products in FSL SP-031 and Serratia phage Eta (KC460990). Here, we report the complete genome sequence of phiEap-2 and major findings from the genomic analysis. Knowledge of this phage might be helpful for developing therapeutic strategies against E. aerogenes.

Control of polarization rotation in nonlinear propagation of fully structured light

NASA Astrophysics Data System (ADS)

Gibson, Christopher J.; Bevington, Patrick; Oppo, Gian-Luca; Yao, Alison M.

2018-03-01

Knowing and controlling the spatial polarization distribution of a beam is of importance in applications such as optical tweezing, imaging, material processing, and communications. Here we show how the polarization distribution is affected by both linear and nonlinear (self-focusing) propagation. We derive an analytical expression for the polarization rotation of fully structured light (FSL) beams during linear propagation and show that the observed rotation is due entirely to the difference in Gouy phase between the two eigenmodes comprising the FSL beams, in excellent agreement with numerical simulations. We also explore the effect of cross-phase modulation due to a self-focusing (Kerr) nonlinearity and show that polarization rotation can be controlled by changing the eigenmodes of the superposition, and physical parameters such as the beam size, the amount of Kerr nonlinearity, and the input power. Finally, we show that by biasing cylindrical vector beams to have elliptical polarization, we can vary the polarization state from radial through spiral to azimuthal using nonlinear propagation.

Computer Program User’s Manual for FIREFINDER Digital Topographic Data Verification Library Dubbing System. Volume II. Dubbing.

DTIC Science & Technology

1982-01-29

N - Nw .VA COMPUTER PROGRAM USER’S MANUAL FOR . 0FIREFINDER DIGITAL TOPOGRAPHIC DATA VERIFICATION LIBRARY DUBBING SYSTEM VOLUME II DUBBING 29 JANUARY...Digital Topographic Data Verification Library Dubbing System, Volume II, Dubbing 6. PERFORMING ORG. REPORT NUMER 7. AUTHOR(q) S. CONTRACT OR GRANT...Software Library FIREFINDER Dubbing 20. ABSTRACT (Continue an revWee *Ide II necessary end identify by leek mauber) PThis manual describes the computer

Tools for Modeling & Simulation of Molecular and Nanoelectronics Devices

DTIC Science & Technology

2012-06-14

implemented a prototype DFT simulation software using two different open source Finite Element (FE) libraries: DEALII and FENICS . These two libraries have been...ATK. In the first part of this Phase I project we investigated two different candidate finite element libraries, DEAL II and FENICS . Although both...element libraries, Deal.II and FEniCS /dolfin, for use as back-ends to a finite element DFT in ATK, Quantum Insight and QuantumWise A/S, October 2011.

Distinct effects of ASD and ADHD symptoms on reward anticipation in participants with ADHD, their unaffected siblings and healthy controls: a cross-sectional study.

PubMed

van Dongen, Eelco V; von Rhein, Daniel; O'Dwyer, Laurence; Franke, Barbara; Hartman, Catharina A; Heslenfeld, Dirk J; Hoekstra, Pieter J; Oosterlaan, Jaap; Rommelse, Nanda; Buitelaar, Jan

2015-01-01

Autism spectrum disorder (ASD) traits are continuously distributed throughout the population, and ASD symptoms are also frequently observed in patients with attention-deficit/hyperactivity disorder (ADHD). Both ASD and ADHD have been linked to alterations in reward-related neural processing. However, whether both symptom domains interact and/or have distinct effects on reward processing in healthy and ADHD populations is currently unknown. We examined how variance in ASD and ADHD symptoms in individuals with ADHD and healthy participants was related to the behavioural and neural response to reward during a monetary incentive delay (MID) task. Participants (mean age: 17.7 years, range: 10-28 years) from the NeuroIMAGE study with a confirmed diagnosis of ADHD (n = 136), their unaffected siblings (n = 83), as well as healthy controls (n = 105) performed an MID task in a magnetic resonance imaging (MRI) scanner. ASD and ADHD symptom scores were used as predictors of the neural response to reward anticipation and reward receipt. Behavioural responses were modeled using linear mixed models; neural responses were analysed using FMRIB's Software Library (FSL) proprietary mixed effects analysis (FLAMEO). ASD and ADHD symptoms were associated with alterations in BOLD activity during reward anticipation, but not reward receipt. Specifically, ASD scores were related to increased insular activity during reward anticipation across the sample. No interaction was found between this effect and the presence of ADHD, suggesting that ASD symptoms had no differential effect in ADHD and healthy populations. ADHD symptom scores were associated with reduced dorsolateral prefrontal activity during reward anticipation. No interactions were found between the effects of ASD and ADHD symptoms on reward processing. Variance in ASD and ADHD symptoms separately influence neural processing during reward anticipation in both individuals with (an increased risk of) ADHD and healthy participants. Our findings therefore suggest that both symptom domains affect reward processing through distinct mechanisms, underscoring the importance of multidimensional and multimodal assessment in psychiatry.

SCIL Executive Summaries.

ERIC Educational Resources Information Center

Samuels, Alan R.; And Others

1987-01-01

These five papers by speakers at the Small Computers in Libraries 1987 conference include: "Acquiring and Using Shareware in Building Small Scale Automated Information systems" (Samuels); "A Software Lending Collection" (Talab); "Providing Subject Access to Microcomputer Software" (Mitchell); "Interfacing Vendor…

Computers and Library Management.

ERIC Educational Resources Information Center

Cooke, Deborah M.; And Others

1985-01-01

This five-article section discusses changes in the management of the school library resulting from use of the computer. Topics covered include data management programs (record keeping, word processing, and bibliographies); practical applications of a database; evaluation of "Circulation Plus" software; ergonomics and computers; and…

Prediction of Hydrolysis Products of Organic Chemicals under Environmental pH Conditions

EPA Science Inventory

Cheminformatics-based software tools can predict the molecular structure of transformation products using a library of transformation reaction schemes. This paper presents the development of such a library for abiotic hydrolysis of organic chemicals under environmentally relevant...

The Electronic Library Workstation--Today.

ERIC Educational Resources Information Center

Nolte, James

1990-01-01

Describes the components--hardware, software and applications, CD-ROM and online reference resources, and telecommunications links--of an electronic library workstation in use at Clarkson University (Potsdam, New York). Data manipulation, a hypothetical research scenario, and recommended workstation capabilities are also discussed. (MES)

DiffPy-CMI-Python libraries for Complex Modeling Initiative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

Videotex--The Library of the Future.

ERIC Educational Resources Information Center

Mischo, Lare; Hegarty, Kevin

1982-01-01

Discusses a presentation prepared by Boeing Computer Services in cooperation with the Tacoma Public Library staff, which demonstrates the potential of interactive cable systems based on the Canadian Telidon system. Features of this videotex system, software, and equipment, including microcomputers, are noted. (EJS)

Geospatial Data Stream Processing in Python Using FOSS4G Components

NASA Astrophysics Data System (ADS)

McFerren, G.; van Zyl, T.

2016-06-01

One viewpoint of current and future IT systems holds that there is an increase in the scale and velocity at which data are acquired and analysed from heterogeneous, dynamic sources. In the earth observation and geoinformatics domains, this process is driven by the increase in number and types of devices that report location and the proliferation of assorted sensors, from satellite constellations to oceanic buoy arrays. Much of these data will be encountered as self-contained messages on data streams - continuous, infinite flows of data. Spatial analytics over data streams concerns the search for spatial and spatio-temporal relationships within and amongst data "on the move". In spatial databases, queries can assess a store of data to unpack spatial relationships; this is not the case on streams, where spatial relationships need to be established with the incomplete data available. Methods for spatially-based indexing, filtering, joining and transforming of streaming data need to be established and implemented in software components. This article describes the usage patterns and performance metrics of a number of well known FOSS4G Python software libraries within the data stream processing paradigm. In particular, we consider the RTree library for spatial indexing, the Shapely library for geometric processing and transformation and the PyProj library for projection and geodesic calculations over streams of geospatial data. We introduce a message oriented Python-based geospatial data streaming framework called Swordfish, which provides data stream processing primitives, functions, transports and a common data model for describing messages, based on the Open Geospatial Consortium Observations and Measurements (O&M) and Unidata Common Data Model (CDM) standards. We illustrate how the geospatial software components are integrated with the Swordfish framework. Furthermore, we describe the tight temporal constraints under which geospatial functionality can be invoked when processing high velocity, potentially infinite geospatial data streams. The article discusses the performance of these libraries under simulated streaming loads (size, complexity and volume of messages) and how they can be deployed and utilised with Swordfish under real load scenarios, illustrated by a set of Vessel Automatic Identification System (AIS) use cases. We conclude that the described software libraries are able to perform adequately under geospatial data stream processing scenarios - many real application use cases will be handled sufficiently by the software.

HPC Software Stack Testing Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garvey, Cormac

The HPC Software stack testing framework (hpcswtest) is used in the INL Scientific Computing Department to test the basic sanity and integrity of the HPC Software stack (Compilers, MPI, Numerical libraries and Applications) and to quickly discover hard failures, and as a by-product it will indirectly check the HPC infrastructure (network, PBS and licensing servers).

An Overview of Public Access Computer Software Management Tools for Libraries

ERIC Educational Resources Information Center

Wayne, Richard

2004-01-01

An IT decision maker gives an overview of public access PC software that's useful in controlling session length and scheduling, Internet access, print output, security, and the latest headaches: spyware and adware. In this article, the author describes a representative sample of software tools in several important categories such as setup…

Surgical pathology report in the era of desktop publishing.

PubMed

Pillarisetti, S G

1993-01-01

Since it is believed that "a picture is worth a thousand words," incorporation of computer-generated line art was used as a adjunct to gross description in surgical pathology reporting in selected cases. The lack of an integrated software program was overcome by using commercially available graphic and word processing software. A library of drawings was developed over the last few years. Most time-consuming is the development of templates and the graphic library. With some effort it is possible to integrate graphics of high quality into surgical pathology reports.

AstroBus On-Board Software

NASA Astrophysics Data System (ADS)

Biscarros, D.; Cantenot, C.; Séronie-Vivien, J.; Schmidt, G.

AstroBus on-board software is a customisable software for ERC32 based avionics implementing standard ESA Packet Utilization Standard functions. Its architecture based on generic design templates and relying on a library providing standard PUS TC, TM and event services enhances its reusability on various programs. Finally, AstroBus on-board software development and validation environment is based on last generation tools providing an optimised customisation environment.

Adaptive Integration of Nonsmooth Dynamical Systems

DTIC Science & Technology

2017-10-11

controlled time stepping method to interactively design running robots. [1] John Shepherd, Samuel Zapolsky, and Evan M. Drumwright, “Fast multi-body...software like this to test software running on my robots. Started working in simulation after attempting to use software like this to test software... running on my robots. The libraries that produce these beautiful results have failed at simulating robotic manipulation. Postulate: It is easier to

Airland Battlefield Environment (ALBE) Tactical Decision Aid (TDA) Demonstration Program,

DTIC Science & Technology

1987-11-12

Management System (DBMS) software, GKS graphics libraries, and user interface software. These components of the ATB system software architecture will be... knowlede base ano auqent the decision mak:n• process by providing infocr-mation useful in the formulation and execution of battlefield strategies...Topographic Laboratories as an Engineer. Ms. Capps is managing the software development of the AirLand Battlefield Environment (ALBE) geographic

Assessing the accuracy of software predictions of mammalian and microbial metabolites

EPA Science Inventory

New chemical development and hazard assessments benefit from accurate predictions of mammalian and microbial metabolites. Fourteen biotransformation libraries encoded in eight software packages that predict metabolite structures were assessed for their sensitivity (proportion of ...

Open Access, Open Source and Digital Libraries: A Current Trend in University Libraries around the World

ERIC Educational Resources Information Center

Krishnamurthy, M.

2008-01-01

Purpose: The purpose of this paper is to describe the open access and open source movement in the digital library world. Design/methodology/approach: A review of key developments in the open access and open source movement is provided. Findings: Open source software and open access to research findings are of great use to scholars in developing…

Below the Surface: New Tools--And Savvy Librarians--Are Turning the ILS into a Gold Mine for Making More Informed Decisions

ERIC Educational Resources Information Center

Cummins, Caroline

2006-01-01

In this article, the author discusses the benefits offered by integrated library systems (ILS) for making more informed decisions. Library software vendors, realizing ILS products can reveal business intelligence, have begun to offer tools like Director's Station to help library managers get more out of their data, and librarians are taking…

Characterizing and Modeling the Cost of Rework in a Library of Reusable Software Components

NASA Technical Reports Server (NTRS)

Basili, Victor R.; Condon, Steven E.; ElEmam, Khaled; Hendrick, Robert B.; Melo, Walcelio

1997-01-01

In this paper we characterize and model the cost of rework in a Component Factory (CF) organization. A CF is responsible for developing and packaging reusable software components. Data was collected on corrective maintenance activities for the Generalized Support Software reuse asset library located at the Flight Dynamics Division of NASA's GSFC. We then constructed a predictive model of the cost of rework using the C4.5 system for generating a logical classification model. The predictor variables for the model are measures of internal software product attributes. The model demonstrates good prediction accuracy, and can be used by managers to allocate resources for corrective maintenance activities. Furthermore, we used the model to generate proscriptive coding guidelines to improve programming, practices so that the cost of rework can be reduced in the future. The general approach we have used is applicable to other environments.

The Advent of Portals.

ERIC Educational Resources Information Center

Jackson, Mary E.

2002-01-01

Explains portals as tools that gather a variety of electronic information resources, including local library resources, into a single Web page. Highlights include cross-database searching; integration with university portals and course management software; the ARL (Association of Research Libraries) Scholars Portal Initiative; and selected vendors…

Technology and Microcomputers for an Information Centre/Special Library.

ERIC Educational Resources Information Center

Daehn, Ralph M.

1984-01-01

Discusses use of microcomputer hardware and software, telecommunications methods, and advanced library methods to create a specialized information center's database of literature relating to farm machinery and food processing. Systems and services (electronic messaging, serials control, database creation, cataloging, collections, circulation,…

The Virginia Tech Library System (VTLS).

ERIC Educational Resources Information Center

McGrath, Deborah Hall; Lee, Carl R.

1989-01-01

Discusses topics relating to the Virginia Tech Library System: the company (VTLS, Inc.); the software; data structure; cataloging, status, and authority control; circulation; serials control and acquisitions; the online catalog; management reporting; networking; and the operating environment. Sidebars discuss the Vanilla Network; LINNEA--a network…

75 FR 32692 - Schools and Libraries Universal Service Support Mechanism

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-09

..., wireless Internet access applications, and web hosting. We propose to revise the Commission's rules to.../anti-spam software, scheduling services, wireless Internet access applications, and web hosting should... schools and libraries may receive discounts for eligible telecommunications services, Internet access, and...

Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example

PubMed Central

Gunalan, Kabilar; Chaturvedi, Ashutosh; Howell, Bryan; Duchin, Yuval; Lempka, Scott F.; Patriat, Remi; Sapiro, Guillermo; Harel, Noam; McIntyre, Cameron C.

2017-01-01

Background Deep brain stimulation (DBS) is an established clinical therapy and computational models have played an important role in advancing the technology. Patient-specific DBS models are now common tools in both academic and industrial research, as well as clinical software systems. However, the exact methodology for creating patient-specific DBS models can vary substantially and important technical details are often missing from published reports. Objective Provide a detailed description of the assembly workflow and parameterization of a patient-specific DBS pathway-activation model (PAM) and predict the response of the hyperdirect pathway to clinical stimulation. Methods Integration of multiple software tools (e.g. COMSOL, MATLAB, FSL, NEURON, Python) enables the creation and visualization of a DBS PAM. An example DBS PAM was developed using 7T magnetic resonance imaging data from a single unilaterally implanted patient with Parkinson’s disease (PD). This detailed description implements our best computational practices and most elaborate parameterization steps, as defined from over a decade of technical evolution. Results Pathway recruitment curves and strength-duration relationships highlight the non-linear response of axons to changes in the DBS parameter settings. Conclusion Parameterization of patient-specific DBS models can be highly detailed and constrained, thereby providing confidence in the simulation predictions, but at the expense of time demanding technical implementation steps. DBS PAMs represent new tools for investigating possible correlations between brain pathway activation patterns and clinical symptom modulation. PMID:28441410

Implementing the HDF-EOS5 software library for data products in the UNAVCO InSAR archive

NASA Astrophysics Data System (ADS)

Baker, Scott; Meertens, Charles; Crosby, Christopher

2017-04-01

UNAVCO is a non-profit university-governed consortium that operates the U.S. National Science Foundation (NSF) Geodesy Advancing Geosciences and EarthScope (GAGE) facility and provides operational support to the Western North America InSAR Consortium (WInSAR). The seamless synthetic aperture radar archive (SSARA) is a seamless distributed access system for SAR data and higher-level data products. Under the NASA-funded SSARA project, a user-contributed InSAR archive for interferograms, time series, and other derived data products was developed at UNAVCO. The InSAR archive development has led to the adoption of the HDF-EOS5 data model, file format, and library. The HDF-EOS software library was designed to support NASA Earth Observation System (EOS) science data products and provides data structures for radar geometry (Swath) and geocoded (Grid) data based on the HDF5 data model and file format provided by the HDF Group. HDF-EOS5 inherits the benefits of HDF5 (open-source software support, internal compression, portability, support for structural data, self-describing file metadata enhanced performance, and xml support) and provides a way to standardize InSAR data products. Instrument- and datatype-independent services, such as subsetting, can be applied to files across a wide variety of data products through the same library interface. The library allows integration with GIS software packages such as ArcGIS and GDAL, conversion to other data formats like NetCDF and GeoTIFF, and is extensible with new data structures to support future requirements. UNAVCO maintains a GitHub repository that provides example software for creating data products from popular InSAR processing software packages like GMT5SAR and ISCE as well as examples for reading and converting the data products into other formats. Digital object identifiers (DOI) have been incorporated into the InSAR archive allowing users to assign a permanent location for their processed result and easily reference the final data products. A metadata attribute is added to the HDF-EOS5 file when a DOI is minted for a data product. These data products are searchable through the SSARA federated query providing access to processed data for both expert and non-expert InSAR users. The archive facilitates timely distribution of processed data with particular importance for geohazards and event response.

Why Students Should Use Multimedia.

ERIC Educational Resources Information Center

Bucher, Katherine

1995-01-01

Examines benefits of multimedia presentation software for teachers, librarians, and elementary and secondary school students. Discusses an example of two school library media specialists working with an English class using the library's reference collection (print and CD-ROM) and HyperCard. Suggests presentation assignments for various subjects.…

Microcomputers and Workstations in Libraries: Trends and Opportunities.

ERIC Educational Resources Information Center

Welsch, Erwin K.

1990-01-01

Summarizes opinions of scholars in various disciplines on workstation history, definition, and functions. Networks and configurations for library workstations, including hardware and software recommendations, are described. The impact of workstations on the workplace resulting in task, process, and institutional transformation, is also considered.…

Exploring Planet PDA: The Librarian as Astronaut, Innovator, and Expert.

ERIC Educational Resources Information Center

Galganski, Carol; Peters, Tom; Bell, Lori

2002-01-01

Describes the integration of personal digital assistants into a medical center library's services in Illinois. Discusses training for users; hardware selection; software selection and content; technical support; the role of libraries, including the creation of policies and procedures; and future challenges. (LRW)

The Future of Library Automation in Schools.

ERIC Educational Resources Information Center

Anderson, Elaine

2000-01-01

Addresses the future of library automation programs for schools. Discusses requirements of emerging OPACs and circulation systems; the Schools Interoperability Framework (SIF), an industry initiatives to develop an open specification for ensuring that K-12 instructional and administrative software applications work together more effectively; home…

Providing Services to Virtual Patrons.

ERIC Educational Resources Information Center

Hulshof, Robert

1999-01-01

Discusses the types of services libraries need to support patrons who access the library via the Internet or e-mail. Highlights include issues in technical support; establishing policies and procedures; tools for technical support, including hardware and software; impacts of technical support on staff; and future possibilities. (LRW)

Protecting Public-Access Computers in Libraries.

ERIC Educational Resources Information Center

King, Monica

1999-01-01

Describes one public library's development of a computer-security plan, along with helpful products used. Discussion includes Internet policy, physical protection of hardware, basic protection of the operating system and software on the network, browser dilemmas and maintenance, creating clear intuitive interface, and administering fair use and…

Virtually Usable: A Test of the Information Gardens

ERIC Educational Resources Information Center

Johnson, Megan; Ochoa, Louise; Purpur, Geraldine

2007-01-01

This paper presents the results of a usability study conducted to determine the functionality of a desktop, three-dimensional virtual library designed and supported by the Appalachian State University Distance Learning Library Services team. Formative evaluations were performed with representative students utilizing Morae software. Results…

75 FR 25185 - Broadband Initiatives Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

..., excluding desktop or laptop computers, computer hardware and software (including anti-virus, anti-spyware, and other security software), audio or video equipment, computer network components... 10 desktop or laptop computers and individual workstations to be located within the rural library...

A portable structural analysis library for reaction networks.

PubMed

Bedaso, Yosef; Bergmann, Frank T; Choi, Kiri; Medley, Kyle; Sauro, Herbert M

2018-07-01

The topology of a reaction network can have a significant influence on the network's dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the network configuration and are important considerations before any dynamical analysis is made. Most established simulation software tools usually carry out some kind of structural analysis of a network before any attempt is made at dynamic simulation. In this paper, we describe a portable software library, libStructural, that can carry out a variety of popular structural analyses that includes conservation analysis, flux dependency analysis and enumerating elementary modes. The library employs robust algorithms that allow it to be used on large networks with more than a two thousand nodes. The library accepts either a raw or fully labeled stoichiometry matrix or models written in SBML format. The software is written in standard C/C++ and comes with extensive on-line documentation and a test suite. The software is available for Windows, Mac OS X, and can be compiled easily on any Linux operating system. A language binding for Python is also available through the pip package manager making it simple to install on any standard Python distribution. The bulk of the source code is licensed under the open source BSD license with other parts using as either the MIT license or more simply public domain. All source is available on GitHub (https://github.com/sys-bio/Libstructural). Copyright © 2018 Elsevier B.V. All rights reserved.

Open source clustering software.

PubMed

de Hoon, M J L; Imoto, S; Nolan, J; Miyano, S

2004-06-12

We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

Providing Access to CD-ROM Databases in a Campus Setting. Part II: Networking CD-ROMs via a LAN.

ERIC Educational Resources Information Center

Koren, Judy

1992-01-01

The second part of a report on CD-ROM networking in libraries describes LAN (local area network) technology; networking software and towers; gateway software for connecting to campuswide networks; Macintosh LANs; and network licenses. Several product and software reviews are included, and a sidebar lists vendor addresses. (NRP)

Research flight software engineering and MUST, an integrated system of support tools

NASA Technical Reports Server (NTRS)

Straeter, T. A.; Foudriat, E. C.; Will, R. W.

1977-01-01

Consideration is given to software development to support NASA flight research. The Multipurpose User-Oriented Software Technology (MUST) program, designed to integrate digital systems into flight research, is discussed. Particular attention is given to the program's special interactive user interface, subroutine library, assemblers, compiler, automatic documentation tools, and test and simulation subsystems.

"Computers: Cure-All or Snake Oil?" Proceedings from the Spring Meeting of the Nebraska Library Association, College and University Section (Bellevue, Nebraska, April 20, 1984).

ERIC Educational Resources Information Center

Krzywkowski, Valerie I., Ed.

The 15 papers in this collection discuss various aspects of computer use in libraries and several other aspects of library service not directly related to computers. Following an introduction and a list of officers, the papers are: (1) "Criminal Justice and Related Databases" (Kate E. Adams); (2) "Software and Hard Thought:…

Using geographic information systems to identify prospective marketing areas for a special library.

PubMed

McConnaughy, Rozalynd P; Wilson, Steven P

2006-05-04

The Center for Disability Resources (CDR) Library is the largest collection of its kind in the Southeastern United States, consisting of over 5,200 books, videos/DVDs, brochures, and audiotapes covering a variety of disability-related topics, from autism to transition resources. The purpose of the library is to support the information needs of families, faculty, students, staff, and other professionals in South Carolina working with individuals with disabilities. The CDR Library is funded on a yearly basis; therefore, maintaining high usage is crucial. A variety of promotional efforts have been used to attract new patrons to the library. Anyone in South Carolina can check out materials from the library, and most of the patrons use the library remotely by requesting materials, which are then mailed to them. The goal of this project was to identify areas of low geographic usage as a means of identifying locations for future library marketing efforts. Nearly four years worth of library statistics were compiled in a spreadsheet that provided information per county on the number of checkouts, the number of renewals, and the population. Five maps were created using ArcView GIS software to create visual representations of patron checkout and renewal behavior per county. Out of the 46 counties in South Carolina, eight counties never checked out materials from the library. As expected urban areas and counties near the library's physical location have high usage totals. The visual representation of the data made identification of low usage regions easier than using a standalone database with no visual-spatial component. The low usage counties will be the focus of future Center for Disability Resources Library marketing efforts. Due to the impressive visual-spatial representations created with Geographic Information Systems, which more efficiently communicate information than stand-alone database information can, librarians may benefit from the software's use as a supplemental tool for tracking library usage and planning promotional efforts.

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.

PubMed

Sand, Andreas; Kristiansen, Martin; Pedersen, Christian N S; Mailund, Thomas

2013-11-22

Hidden Markov models are widely used for genome analysis as they combine ease of modelling with efficient analysis algorithms. Calculating the likelihood of a model using the forward algorithm has worst case time complexity linear in the length of the sequence and quadratic in the number of states in the model. For genome analysis, however, the length runs to millions or billions of observations, and when maximising the likelihood hundreds of evaluations are often needed. A time efficient forward algorithm is therefore a key ingredient in an efficient hidden Markov model library. We have built a software library for efficiently computing the likelihood of a hidden Markov model. The library exploits commonly occurring substrings in the input to reuse computations in the forward algorithm. In a pre-processing step our library identifies common substrings and builds a structure over the computations in the forward algorithm which can be reused. This analysis can be saved between uses of the library and is independent of concrete hidden Markov models so one preprocessing can be used to run a number of different models.Using this library, we achieve up to 78 times shorter wall-clock time for realistic whole-genome analyses with a real and reasonably complex hidden Markov model. In one particular case the analysis was performed in less than 8 minutes compared to 9.6 hours for the previously fastest library. We have implemented the preprocessing procedure and forward algorithm as a C++ library, zipHMM, with Python bindings for use in scripts. The library is available at http://birc.au.dk/software/ziphmm/.

The JPL Library information retrieval system

NASA Technical Reports Server (NTRS)

Walsh, J.

1975-01-01

The development, capabilities, and products of the computer-based retrieval system of the Jet Propulsion Laboratory Library are described. The system handles books and documents, produces a book catalog, and provides a machine search capability. Programs and documentation are available to the public through NASA's computer software dissemination program.

Bibliographic Utilities and the Use of Microcomputers in Libraries: Current and Projected Practices.

ERIC Educational Resources Information Center

McAninch, Glen

1986-01-01

Bibliographic utilities are marketing specially designed hardware and software that permit libraries to patch together automated cataloging, acquisitions, serials control, reference, online public catalogs, circulation, interlibrary loan, and administrative functions. The increasing complexity of the technology is making it more difficult to…

Development and Evaluation of a Measure of Library Automation.

ERIC Educational Resources Information Center

Pungitore, Verna L.

1986-01-01

Construct validity and reliability estimates indicate that study designed to measure utilization of automation in public and academic libraries was successful in tentatively identifying and measuring three subdimensions of level of automation: quality of hardware, method of software development, and number of automation specialists. Questionnaire…

Public Access Workstations in the Library: New Trends.

ERIC Educational Resources Information Center

Beecher, Henry

1991-01-01

Discusses the use of microcomputer-based workstations that are provided for public access in libraries. Criteria for workstations are discussed, including standard hardware, open-design software, scalable interface, and connectivity options for networking; systems that provide full-text access are described; and the need for standards is…

Search without Boundaries Using Simple APIs

ERIC Educational Resources Information Center

Tong, Qi (Helen)

2009-01-01

The U.S. Geological Survey (USGS) Library, where the author serves as the digital services librarian, is increasingly challenged to make it easier for users to find information from many heterogeneous information sources. Information is scattered throughout different software applications (i.e., library catalog, federated search engine, link…

Ringling School of Art and Design Builds a CASTLE.

ERIC Educational Resources Information Center

Morse, Yvonne; Davis, Wendy

1984-01-01

Describes the development and installation of the Computer Automated Software for the Total Library Environment System (CASTLE), which uses a microcomputer to automate operations of small academic library in six main areas: circulation, online catalog, inventory and file maintenance, audiovisual equipment, accounting, and information and…

Imaging Technology in Libraries: Photo CD Offers New Possibilities.

ERIC Educational Resources Information Center

Beiser, Karl

1993-01-01

Describes Kodak's Photo CD technology, a format for the storage and retrieval of photographic images in electronic form. Highlights include current and future Photo CD formats; computer imaging technology; ownership issues; hardware for using Photo CD; software; library and information center applications, including image collections and…

The Quebec National Library on the Web.

ERIC Educational Resources Information Center

Kieran, Shirley; Sauve, Diane

1997-01-01

Provides an overview of the Quebec National Library (Bibliotheque Nationale du Quebec, or BNQ) Web site. Highlights include issues related to content, design, and technology; IRIS, the BNQ online public access catalog; development of the multimedia catalog; software; digitization of documents; links to bibliographic records; and future…

Going Prime Time with Live Chat Reference.

ERIC Educational Resources Information Center

Hoag, Tara J.; Cichanowicz, Edana McCaffrey

2001-01-01

Describes the development of the Suffolk Cooperative Library System's live, online chat reference service, a pilot project for public libraries in Suffolk County (New York). Topics include chat software selection; a virtual reference collection; marketing; funding; staffing; evaluation; expanded hours of service; email; and extracting data from…

Design of Inhouse Automated Library Systems.

ERIC Educational Resources Information Center

Cortez, Edwin M.

1984-01-01

Examines six steps inherent to development of in-house automated library system: (1) problem definition, (2) requirement specifications, (3) analysis of alternatives and solutions, (4, 5) design and implementation of hardware and software, and (6) evaluation. Practical method for comparing and weighting options is illustrated and explained. A…

Who Goes There? Measuring Library Web Site Usage.

ERIC Educational Resources Information Center

Bauer, Kathleen

2000-01-01

Discusses how libraries can gather data on the use of their Web sites. Highlights include Web server log files, including the common log file, referrer log file, and agent log file; log file limitations; privacy concerns; and choosing log analysis software, both free and commercial. (LRW)

Tips for Good Electronic Presentations.

ERIC Educational Resources Information Center

Strasser, Dennis

1996-01-01

Describes library uses of presentation graphics software and offers tips for creating electronic presentations. Tips include: audience retention; visual aid options; software package options; presentation planning; presentation showing; and use of text, colors, and graphics. Sidebars note common presentation errors and popular presentation…

OSIRIX: open source multimodality image navigation software

NASA Astrophysics Data System (ADS)

Rosset, Antoine; Pysher, Lance; Spadola, Luca; Ratib, Osman

2005-04-01

The goal of our project is to develop a completely new software platform that will allow users to efficiently and conveniently navigate through large sets of multidimensional data without the need of high-end expensive hardware or software. We also elected to develop our system on new open source software libraries allowing other institutions and developers to contribute to this project. OsiriX is a free and open-source imaging software designed manipulate and visualize large sets of medical images: http://homepage.mac.com/rossetantoine/osirix/

CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries.

PubMed

Heigwer, Florian; Zhan, Tianzuo; Breinig, Marco; Winter, Jan; Brügemann, Dirk; Leible, Svenja; Boutros, Michael

2016-03-24

Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs. CLD predicts a high fraction of functional sgRNAs and is publicly available at https://github.com/boutroslab/cld.

The Keck keyword layer

NASA Technical Reports Server (NTRS)

Conrad, A. R.; Lupton, W. F.

1992-01-01

Each Keck instrument presents a consistent software view to the user interface programmer. The view consists of a small library of functions, which are identical for all instruments, and a large set of keywords, that vary from instrument to instrument. All knowledge of the underlying task structure is hidden from the application programmer by the keyword layer. Image capture software uses the same function library to collect data for the image header. Because the image capture software and the instrument control software are built on top of the same keyword layer, a given observation can be 'replayed' by extracting keyword-value pairs from the image header and passing them back to the control system. The keyword layer features non-blocking as well as blocking I/O. A non-blocking keyword write operation (such as setting a filter position) specifies a callback to be invoked when the operation is complete. A non-blocking keyword read operation specifies a callback to be invoked whenever the keyword changes state. The keyword-callback style meshes well with the widget-callback style commonly used in X window programs. The first keyword library was built for the two Keck optical instruments. More recently, keyword libraries have been developed for the infrared instruments and for telescope control. Although the underlying mechanisms used for inter-process communication by each of these systems vary widely (Lick MUSIC, Sun RPC, and direct socket I/O, respectively), a basic user interface has been written that can be used with any of these systems. Since the keyword libraries are bound to user interface programs dynamically at run time, only a single set of user interface executables is needed. For example, the same program, 'xshow', can be used to display continuously the telescope's position, the time left in an instrument's exposure, or both values simultaneously. Less generic tools that operate on specific keywords, for example an X display that controls optical instrument exposures, have also been written using the keyword layer.

The software and algorithms for hyperspectral data processing

NASA Astrophysics Data System (ADS)

Shyrayeva, Anhelina; Martinov, Anton; Ivanov, Victor; Katkovsky, Leonid

2017-04-01

Hyperspectral remote sensing technique is widely used for collecting and processing -information about the Earth's surface objects. Hyperspectral data are combined to form a three-dimensional (x, y, λ) data cube. Department of Aerospace Research of the Institute of Applied Physical Problems of the Belarusian State University presents a general model of the software for hyperspectral image data analysis and processing. The software runs in Windows XP/7/8/8.1/10 environment on any personal computer. This complex has been has been written in C++ language using QT framework and OpenGL for graphical data visualization. The software has flexible structure that consists of a set of independent plugins. Each plugin was compiled as Qt Plugin and represents Windows Dynamic library (dll). Plugins can be categorized in terms of data reading types, data visualization (3D, 2D, 1D) and data processing The software has various in-built functions for statistical and mathematical analysis, signal processing functions like direct smoothing function for moving average, Savitzky-Golay smoothing technique, RGB correction, histogram transformation, and atmospheric correction. The software provides two author's engineering techniques for the solution of atmospheric correction problem: iteration method of refinement of spectral albedo's parameters using Libradtran and analytical least square method. The main advantages of these methods are high rate of processing (several minutes for 1 GB data) and low relative error in albedo retrieval (less than 15%). Also, the software supports work with spectral libraries, region of interest (ROI) selection, spectral analysis such as cluster-type image classification and automatic hypercube spectrum comparison by similarity criterion with similar ones from spectral libraries, and vice versa. The software deals with different kinds of spectral information in order to identify and distinguish spectrally unique materials. Also, the following advantages should be noted: fast and low memory hypercube manipulation features, user-friendly interface, modularity, and expandability.

Beam Instrument Development System

DOE Office of Scientific and Technical Information (OSTI.GOV)

DOOLITTLE, LAWRENCE; HUANG, GANG; DU, QIANG

Beam Instrumentation Development System (BIDS) is a collection of common support libraries and modules developed during a series of Low-Level Radio Frequency (LLRF) control and timing/synchronization projects. BIDS includes a collection of Hardware Description Language (HDL) libraries and software libraries. The BIDS can be used for the development of any FPGA-based system, such as LLRF controllers. HDL code in this library is generic and supports common Digital Signal Processing (DSP) functions, FPGA-specific drivers (high-speed serial link wrappers, clock generation, etc.), ADC/DAC drivers, Ethernet MAC implementation, etc.

System and method for memory allocation in a multiclass memory system

DOEpatents

Loh, Gabriel; Meswani, Mitesh; Ignatowski, Michael; Nutter, Mark

2016-06-28

A system for memory allocation in a multiclass memory system includes a processor coupleable to a plurality of memories sharing a unified memory address space, and a library store to store a library of software functions. The processor identifies a type of a data structure in response to a memory allocation function call to the library for allocating memory to the data structure. Using the library, the processor allocates portions of the data structure among multiple memories of the multiclass memory system based on the type of the data structure.

Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases.

PubMed

Rossetti, Lia; Giraffa, Giorgio

2005-11-01

About a thousand lactic acid bacteria (LAB) isolated from dairy products, especially cheeses, were identified and typed by species-specific PCR and RAPD-PCR, respectively. RAPD-PCR profiles, which were obtained by using the M13 sequence as a primer, allowed us to implement a large database of different fingerprints, which were analysed by BioNumerics software. Cluster analysis of the combined RAPD-PCR fingerprinting profiles enabled us to implement a library, which is a collection of library units, which in turn is a selection of representative database entries. A library unit, in this case, can be considered to be a definable taxon. The strains belonged to 11 main RAPD-PCR fingerprinting library units identified as Lactobacillus casei/paracasei, Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacillus helveticus, Lactobacillus delbrueckii, Lactobacillus fermentum, Lactobacillus brevis, Enterococcus faecium, Enterococcus faecalis, Streptococcus thermophilus and Lactococcus lactis. The possibility to routinely identify newly typed, bacterial isolates by consulting the library of the software was valued. The proposed method could be suggested to refine previous strain identifications, eliminate redundancy and dispose of a technologically useful LAB strain collection. The same approach could also be applied to identify LAB strains isolated from other food ecosystems.

Template-based combinatorial enumeration of virtual compound libraries for lipids

PubMed Central

2012-01-01

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license. PMID:23006594

Template-based combinatorial enumeration of virtual compound libraries for lipids.

PubMed

Sud, Manish; Fahy, Eoin; Subramaniam, Shankar

2012-09-25

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomopy is a Python toolbox to perform x-ray data processing, image reconstruction and data exchange tasks at synchrotron facilities. The dependencies of the software are currently as follows: -Python related python standard library (http://docs.python.org/2/library/) numpy (http://www.numpy.org/) scipy (http://scipy.org/) matplotlib (http://matplotlip.org/) sphinx (http://sphinx-doc.org) pil (http://www.pythonware.com/products/pil/) pyhdf (http://pysclint.sourceforge.net/pyhdf/) h5py (http://www.h5py.org) pywt (http://www.pybytes.com/pywavelets/) file.py (https://pyspec.svn.sourceforge.net/svnroot/pyspec/trunk/pyspec/ccd/files.py) -C/C++ related: gridec (anonymous?? C-code written back in 1997 that uses standard C library) fftw (http://www.fftw.org/) tomoRecon (multi-threaded C++ verion of gridrec. Author: Mark Rivers from APS. http://cars9.uchicago.edu/software/epics/tomoRecon.html) epics (http://www.aps.anl.gov/epics/)

Virtual Libraries: Interactive Support Software and an Application in Chaotic Models.

ERIC Educational Resources Information Center

Katsirikou, Anthi; Skiadas, Christos; Apostolou, Apostolos; Rompogiannakis, Giannis

This paper begins with a discussion of the characteristics and the singularity of chaotic systems, including dynamic systems theory, chaotic orbit, fractals, chaotic attractors, and characteristics of chaotic systems. The second section addresses the digital libraries (DL) concept and the appropriateness of chaotic models, including definition and…

Administrative Issues in Planning a Library End User Searching Program. ERIC Digest.

ERIC Educational Resources Information Center

Machovec, George S.

This digest presents a reprint of an article which examines management principles that should be considered when implementing library end user searching programs. A brief discussion of specific implementation issues includes needs assessment, hardware, software, training, budgeting, what systems to offer, publicity and marketing, policies and…

Working toward Transparency in Library Automation

ERIC Educational Resources Information Center

Breeding, Marshall

2007-01-01

In this article, the author argues the need for transparency with regard to the automation systems used in libraries. As librarians make decisions regarding automation software and services, they should have convenient access to information about the organizations it will potentially acquire technology from and about the collective experiences of…

The Librarian and the Library User: What the Future Holds.

ERIC Educational Resources Information Center

Electronic Library, 1997

1997-01-01

Discusses the role of information professionals in the future, based on a session at the Online Information 96 conference in London (England). Topics include equipment and software needs; technological advances; a trend toward distance education; how library users are adapting to change; interlibrary loans; online public access catalogs; and…

15 CFR 734.7 - Published information and software.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Ready availability at libraries open to the public or at university libraries (See supplement No. 1 to this part, Question A(6)); (3) Patents and open (published) patent applications available at any patent office; and (4) Release at an open conference, meeting, seminar, trade show, or other open gathering. (i...

15 CFR 734.7 - Published information and software.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Ready availability at libraries open to the public or at university libraries (See Supplement No. 1 to this part, Question A(6)); (3) Patents and open (published) patent applications available at any patent office; and (4) Release at an open conference, meeting, seminar, trade show, or other open gathering. (i...

Directory of Library Automation Software, Systems, and Services. 1998 Edition.

ERIC Educational Resources Information Center

Cibbarelli, Pamela R., Ed.; Cibbarelli, Shawn E., Ed.

This book includes basic information to locate and compare available options for library automation based on various criteria such as hardware requirements, operating systems, components and applications, and price, and provides the necessary contact information to allow further investigation. The major part of the directory lists 211 software…

"Library Quarterly," 1956-2004: An Exploratory Bibliometric Analysis

ERIC Educational Resources Information Center

Young, Arthur P.

2006-01-01

"Library Quarterly's" seventy-fifth anniversary invites an analysis of the journal's bibliometric dimension, including contributor attributes, various author rankings, and citation impact. Eugene Garfield's HistCite software, linked to Thomson Scientific's Web of Science, as made available by Garfield, for the period 1956-2004, was used as the…

Tracking the Integration of Library Skills in the Curriculum.

ERIC Educational Resources Information Center

Gill, Suzanne L.

2003-01-01

Describes the use of IMSeries software, a relational database capable of implementing curriculum design, in an elementary school. Topics include Big6 research skills; tracking the scope and sequence of curriculum; tying library skills to curricular disciplines; information literacy; and examples of a lesson unit and assessment strategy. (LRW)

Distance Education and Virtual Reference: Where Are We Headed?

ERIC Educational Resources Information Center

Coffman, Steve

2001-01-01

Discusses changes in distance education and considers the resulting need for new types of library services. Topics include new Web-based contact center software; how to conduct virtual reference interviews; online reference service; the role of the physical library; staffing changes; and future possibilities, including impacts on costs of library…

Making Information Available to Partially Sighted and Blind Clients.

ERIC Educational Resources Information Center

Long, C. A.

1993-01-01

Provides an empirical review of problems facing library users with visual impairments using computers, and reviews some of the technology that can help alleviate these problems. Highlights include software; GUI (Graphical User Interfaces); advising and training; library automation; and appendices that list further sources of relevant information.…

CD-ROM and Local Area Networks.

ERIC Educational Resources Information Center

Marks, Kenneth E.; And Others

1993-01-01

This special section on local area networks includes three articles: (1) a description of migration at Joyner Library, East Carolina University (North Carolina) to a new network server; (2) a discussion of factors to consider for network planning in school libraries; and (3) a directory of companies supplying cable, hardware, software, and…

Retrospective Catalog Conversion in Mid-Sized Law Libraries: Some Practical Guidelines for Automation.

ERIC Educational Resources Information Center

Riger, Robert E.

1992-01-01

Discusses retrospective catalog conversion from the viewpoint of a law firm library. Topics discussed include reasons for retrospective conversion; preplanning; suggestions for the selection of software; conducting an inventory of the collection; sources of MARC bibliographic records; setting up an online public access catalog; and marketing…

Apocalypse Soon? The Bug.

ERIC Educational Resources Information Center

Clyde, Anne

1999-01-01

Discussion of the Year 2000 (Y2K) problem, the computer-code problem that affects computer programs or computer chips, focuses on the impact on teacher-librarians. Topics include automated library systems, access to online information services, library computers and software, and other electronic equipment such as photocopiers and fax machines.…

Laser Printing for a Variety of Library Applications.

ERIC Educational Resources Information Center

Kelly, Glen J.

1988-01-01

Summarizes the current status of laser printers in terms of cost, hardware and software requirements, measurement and operational considerations, ease of use, and maintenance. The cost effectiveness of laser printing in libraries for applications such as spine labels, purchase orders, and reports, is explored. (9 notes with references) (CLB)

Assessing the Effectiveness of Online Library Instruction with Finance Students

ERIC Educational Resources Information Center

Friehs, Curt G.; Craig, Cindy L.

2008-01-01

Many academic librarians use online information literacy tutorials as an alternative or a supplement to in-class library instruction. Tutorials created with streaming media software such as Camtasia Studio have become increasingly popular. Librarians at a mid-sized Midwestern university have created several such tutorials demonstrating various…

Information Resources on Microcomputers in Libraries: Public Services. A Selected ERIC Bibliography.

ERIC Educational Resources Information Center

ERIC Clearinghouse on Information Resources, Syracuse, NY.

Twelve articles published between 1982 and 1984 and cited in "Current Index to Journals in Education" are listed in this bibliography on public service applications of microcomputers in libraries. Topics include provision of free public access to microcomputers (justification, objectives, equipment specifications, uses and software,…

Modular Filter and Source-Management Upgrade of RADAC

NASA Technical Reports Server (NTRS)

Lanzi, R. James; Smith, Donna C.

2007-01-01

In an upgrade of the Range Data Acquisition Computer (RADAC) software, a modular software object library was developed to implement required functionality for filtering of flight-vehicle-tracking data and management of tracking-data sources. (The RADAC software is used to process flight-vehicle metric data for realtime display in the Wallops Flight Facility Range Control Center and Mobile Control Center.)

An Enhanced Z39.50 Gateway to the WorldWideWeb.

ERIC Educational Resources Information Center

Cunningham, David; Sloan, Stephen

1994-01-01

Describes how a university library uses the WorldWideWeb (WWW) to enable users to access resources mounted on a local Z39.50 server and to order prints from articles stored on a CD-ROM jukebox. The software used in the construction of the system, necessary modifications to the software, and software ordering information are covered. (KRN)

Campus Energy Model for Control and Performance Validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-09-19

The core of the modeling platform is an extensible block library for the MATLAB/Simulink software suite. The platform enables true co-simulation (interaction at each simulation time step) with NREL's state-of-the-art modeling tools and other energy modeling software.

An Automation Survival Guide for Media Centers.

ERIC Educational Resources Information Center

Whaley, Roger E.

1989-01-01

Reviews factors that should affect the decision to automate a school media center and offers suggestions for the automation process. Topics discussed include getting the library collection ready for automation, deciding what automated functions are needed, evaluating software vendors, selecting software, and budgeting. (CLB)

Deductive Verification of Cryptographic Software

NASA Technical Reports Server (NTRS)

Almeida, Jose Barcelar; Barbosa, Manuel; Pinto, Jorge Sousa; Vieira, Barbara

2009-01-01

We report on the application of an off-the-shelf verification platform to the RC4 stream cipher cryptographic software implementation (as available in the openSSL library), and introduce a deductive verification technique based on self-composition for proving the absence of error propagation.

Digital Equipment Corporation's CRDOM Software and Database Publications.

ERIC Educational Resources Information Center

Adams, Michael Q.

1986-01-01

Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

Selecting Data-Base Management Software for Microcomputers in Libraries and Information Units.

ERIC Educational Resources Information Center

Pieska, K. A. O.

1986-01-01

Presents a model for the evaluation of database management systems software from the viewpoint of librarians and information specialists. The properties of data management systems, database management systems, and text retrieval systems are outlined and compared. (10 references) (CLB)

Toward a digital library strategy for a National Information Infrastructure

NASA Technical Reports Server (NTRS)

Coyne, Robert A.; Hulen, Harry

1993-01-01

Bills currently before the House and Senate would give support to the development of a National Information Infrastructure, in which digital libraries and storage systems would be an important part. A simple model is offered to show the relationship of storage systems, software, and standards to the overall information infrastructure. Some elements of a national strategy for digital libraries are proposed, based on the mission of the nonprofit National Storage System Foundation.

A verification library for multibody simulation software

NASA Technical Reports Server (NTRS)

Kim, Sung-Soo; Haug, Edward J.; Frisch, Harold P.

1989-01-01

A multibody dynamics verification library, that maintains and manages test and validation data is proposed, based on RRC Robot arm and CASE backhoe validation and a comparitive study of DADS, DISCOS, and CONTOPS that are existing public domain and commercial multibody dynamic simulation programs. Using simple representative problems, simulation results from each program are cross checked, and the validation results are presented. Functionalities of the verification library are defined, in order to automate validation procedure.

Use of OsiriX in developing a digital radiology teaching library.

PubMed

Shamshuddin, S; Matthews, H R

2014-10-01

Widespread adoption of digital imaging in clinical practice and for the image-based examinations of the Royal College of Radiologists has created a desire to provide a digital radiology teaching library in many hospital departments around the UK. This article describes our experience of using OsiriX software in developing digital radiology teaching libraries. Copyright © 2014 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Integration of New Technology in Army Libraries

DTIC Science & Technology

1982-07-02

libraries in Alaska that belong to WLN. However, three of the NIorth American bibliographic utilities either are marketing minicomputer-based systems...OCLC and UT’LAS3) or a vendor will be marketing a suitable -66- modificatioxi of the software to operate on a minicomputer (WLN/BLIS). There is no...integrated and contain more II special ,features than the Claremont system which OCLC currently is marketing . -75- OCLC’s Claremont Total Library System (TLS

The Weapons Laboratory Technical Library: Automating with ’Stilas’

DTIC Science & Technology

1990-03-01

version of the system to LC in October 1988. -X- A small business specializing in library automation, SIRSI was founded in 1979 by library and...computer specialists, and has a strong reputation based upon the success of their UNIX-based Unicorn Collection Management System. SIRSI offers a complete...system based on the Unicorn and BRS/ Search systems. The contracted STILAS package includes UNISYS hardware, software written in the C language

Standardizing Activation Analysis: New Software for Photon Activation Analysis

NASA Astrophysics Data System (ADS)

Sun, Z. J.; Wells, D.; Segebade, C.; Green, J.

2011-06-01

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

Fuzzy Logic Engine

NASA Technical Reports Server (NTRS)

Howard, Ayanna

2005-01-01

The Fuzzy Logic Engine is a software package that enables users to embed fuzzy-logic modules into their application programs. Fuzzy logic is useful as a means of formulating human expert knowledge and translating it into software to solve problems. Fuzzy logic provides flexibility for modeling relationships between input and output information and is distinguished by its robustness with respect to noise and variations in system parameters. In addition, linguistic fuzzy sets and conditional statements allow systems to make decisions based on imprecise and incomplete information. The user of the Fuzzy Logic Engine need not be an expert in fuzzy logic: it suffices to have a basic understanding of how linguistic rules can be applied to the user's problem. The Fuzzy Logic Engine is divided into two modules: (1) a graphical-interface software tool for creating linguistic fuzzy sets and conditional statements and (2) a fuzzy-logic software library for embedding fuzzy processing capability into current application programs. The graphical- interface tool was developed using the Tcl/Tk programming language. The fuzzy-logic software library was written in the C programming language.

The Astrophysics Source Code Library: Supporting software publication and citation

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter

2018-01-01

The Astrophysics Source Code Library (ASCL, ascl.net), established in 1999, is a free online registry for source codes used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using the unique ascl ID assigned to each code. In addition to registering codes, the ASCL can house archive files for download and assign them DOIs. The ASCL advocations for software citation on par with article citation, participates in multidiscipinary events such as Force11, OpenCon, and the annual Workshop on Sustainable Software for Science, works with journal publishers, and organizes Special Sessions and Birds of a Feather meetings at national and international conferences such as Astronomical Data Analysis Software and Systems (ADASS), European Week of Astronomy and Space Science, and AAS meetings. In this presentation, I will discuss some of the challenges of gathering credit for publishing software and ideas and efforts from other disciplines that may be useful to astronomy.

Mobile Learning to Improve Writing in ESL Teaching

ERIC Educational Resources Information Center

Noriega, Heidy Selene Robles

2016-01-01

This article reports on the results of a study concerning the type of texts and their features produced by a student after using mobile technology as a support to improve the development of the students' writing skills in a second language. The Functional Systemic Linguistic (FSL), Genre Pedagogical Approach (GPA), and mobile learning concepts…

Observing the Interactive Qualities of L2 Instructional Practices in ESL and FSL Classrooms

ERIC Educational Resources Information Center

Zuniga, Michael; Simard, Daphnée

2016-01-01

Discourse features that promote the generation of interactionally modified input and output, such as negotiation for meaning, have been shown to significantly enhance second language acquisition. Research has also identified several characteristics of instructional practices that render them more or less propitious to the generation of these…

Research Perspectives on Core French: A Literature Review

ERIC Educational Resources Information Center

Lapkin, Sharon; Mady, Callie; Arnott, Stephanie

2009-01-01

This article reviews the research literature on core French in three main areas: student diversity, delivery models for the core French program, and instructional approaches. These topics are put into context through a discussion of studies on community attitudes to French as a second language (FSL), dissatisfaction with core French outcomes and…

Brain Neurons as Quantum Computers:

NASA Astrophysics Data System (ADS)

Bershadskii, A.; Dremencov, E.; Bershadskii, J.; Yadid, G.

The question: whether quantum coherent states can sustain decoherence, heating and dissipation over time scales comparable to the dynamical timescales of brain neurons, has been actively discussed in the last years. A positive answer on this question is crucial, in particular, for consideration of brain neurons as quantum computers. This discussion was mainly based on theoretical arguments. In the present paper nonlinear statistical properties of the Ventral Tegmental Area (VTA) of genetically depressive limbic brain are studied in vivo on the Flinders Sensitive Line of rats (FSL). VTA plays a key role in the generation of pleasure and in the development of psychological drug addiction. We found that the FSL VTA (dopaminergic) neuron signals exhibit multifractal properties for interspike frequencies on the scales where healthy VTA dopaminergic neurons exhibit bursting activity. For high moments the observed multifractal (generalized dimensions) spectrum coincides with the generalized dimensions spectrum calculated for a spectral measure of a quantum system (so-called kicked Harper model, actively used as a model of quantum chaos). This observation can be considered as a first experimental (in vivo) indication in the favor of the quantum (at least partially) nature of brain neurons activity.

A Comparison of Science and Technology Funding for DoD’s Space and Nonspace Programs

DTIC Science & Technology

2008-01-15

Artificial intelligence for HAARP Multispectral signature libraries Environmental conditions that Ionospheric prediction HAARP Weather software for...Hardware and software for solar HAARP Electromagnetic interference for Plasma theory in the space Subproject details were not available Subproject

Software Products - Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You astronomy. Available as Fortran, C, or Python source code. Current version: 3.1 Software Products by Our computer or programmable calculator. Standards Of Fundamental Astronomy (SOFA) Libraries The International

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Z. J.; Wells, D.; Green, J.

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switchingmore » the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.« less

Generalized Support Software: Domain Analysis and Implementation

NASA Technical Reports Server (NTRS)

Stark, Mike; Seidewitz, Ed

1995-01-01

For the past five years, the Flight Dynamics Division (FDD) at NASA's Goddard Space Flight Center has been carrying out a detailed domain analysis effort and is now beginning to implement Generalized Support Software (GSS) based on this analysis. GSS is part of the larger Flight Dynamics Distributed System (FDDS), and is designed to run under the FDDS User Interface / Executive (UIX). The FDD is transitioning from a mainframe based environment to systems running on engineering workstations. The GSS will be a library of highly reusable components that may be configured within the standard FDDS architecture to quickly produce low-cost satellite ground support systems. The estimates for the first release is that this library will contain approximately 200,000 lines of code. The main driver for developing generalized software is development cost and schedule improvement. The goal is to ultimately have at least 80 percent of all software required for a spacecraft mission (within the domain supported by the GSS) to be configured from the generalized components.

Development of an e-VLBI Data Transport Software Suite with VDIF

NASA Technical Reports Server (NTRS)

Sekido, Mamoru; Takefuji, Kazuhiro; Kimura, Moritaka; Hobiger, Thomas; Kokado, Kensuke; Nozawa, Kentarou; Kurihara, Shinobu; Shinno, Takuya; Takahashi, Fujinobu

2010-01-01

We have developed a software library (KVTP-lib) for VLBI data transmission over the network with the VDIF (VLBI Data Interchange Format), which is the newly proposed standard VLBI data format designed for electronic data transfer over the network. The software package keeps the application layer (VDIF frame) and the transmission layer separate, so that each layer can be developed efficiently. The real-time VLBI data transmission tool sudp-send is an application tool based on the KVTP-lib library. sudp-send captures the VLBI data stream from the VSI-H interface with the K5/VSI PC-board and writes the data to file in standard Linux file format or transmits it to the network using the simple- UDP (SUDP) protocol. Another tool, sudp-recv , receives the data stream from the network and writes the data to file in a specific VLBI format (K5/VSSP, VDIF, or Mark 5B). This software system has been implemented on the Wettzell Tsukuba baseline; evaluation before operational employment is under way.

Efficacy of Distortion Correction on Diffusion Imaging: Comparison of FSL Eddy and Eddy_Correct Using 30 and 60 Directions Diffusion Encoding

PubMed Central

Yamada, Haruyasu; Abe, Osamu; Shizukuishi, Takashi; Kikuta, Junko; Shinozaki, Takahiro; Dezawa, Ko; Nagano, Akira; Matsuda, Masayuki; Haradome, Hiroki; Imamura, Yoshiki

2014-01-01

Diffusion imaging is a unique noninvasive tool to detect brain white matter trajectory and integrity in vivo. However, this technique suffers from spatial distortion and signal pileup or dropout originating from local susceptibility gradients and eddy currents. Although there are several methods to mitigate these problems, most techniques can be applicable either to susceptibility or eddy-current induced distortion alone with a few exceptions. The present study compared the correction efficiency of FSL tools, “eddy_correct” and the combination of “eddy” and “topup” in terms of diffusion-derived fractional anisotropy (FA). The brain diffusion images were acquired from 10 healthy subjects using 30 and 60 directions encoding schemes based on the electrostatic repulsive forces. For the 30 directions encoding, 2 sets of diffusion images were acquired with the same parameters, except for the phase-encode blips which had opposing polarities along the anteroposterior direction. For the 60 directions encoding, non–diffusion-weighted and diffusion-weighted images were obtained with forward phase-encoding blips and non–diffusion-weighted images with the same parameter, except for the phase-encode blips, which had opposing polarities. FA images without and with distortion correction were compared in a voxel-wise manner with tract-based spatial statistics. We showed that images corrected with eddy and topup possessed higher FA values than images uncorrected and corrected with eddy_correct with trilinear (FSL default setting) or spline interpolation in most white matter skeletons, using both encoding schemes. Furthermore, the 60 directions encoding scheme was superior as measured by increased FA values to the 30 directions encoding scheme, despite comparable acquisition time. This study supports the combination of eddy and topup as a superior correction tool in diffusion imaging rather than the eddy_correct tool, especially with trilinear interpolation, using 60 directions encoding scheme. PMID:25405472

S-Ketamine Mediates Its Acute and Sustained Antidepressant-Like Activity through a 5-HT1B Receptor Dependent Mechanism in a Genetic Rat Model of Depression.

PubMed

du Jardin, Kristian G; Liebenberg, Nico; Cajina, Manuel; Müller, Heidi K; Elfving, Betina; Sanchez, Connie; Wegener, Gregers

2017-01-01

Rationale: The mechanisms responsible for the unique antidepressant properties of ketamine have only been partly resolved. Recent preclinical reports implicate the neurotransmitter serotonin [5-hydroxytryptamine (5-HT)] in the antidepressant-like response of ketamine, and modulation of 5-HT 1B receptors has been hypothesized to attain an important role. Objectives: To evaluate the role of endogenous stimulation of 5-HT 1B heteroreceptors in the antidepressant-like activity of S -ketamine. Method: Flinders sensitive line (FSL) rats, a genetic model of depression, were depleted of endogenous 5-HT by 4-chloro-DL-phenylalanine methyl ester HCl administration (pCPA; 86 mg/kg/day for 3 days). In pCPA-pretreated and control FSL rats, the acute and sustained effects of a single dose of S -ketamine (15 mg/kg) and the selective 5-HT 1B receptor agonist CP94253 (1-6 mg/kg) alone and in combination with S -ketamine were studied in the forced swim test (FST), a commonly used assay that detects antidepressant activity. Results: pCPA pretreatment decreased cortical 5-HT levels to ∼6% but did not affect the baseline behavioral phenotype of FSL rats. S -ketamine demonstrated acute and sustained antidepressant-like activity, both of which were abolished by 5-HT depletion. Combining S -ketamine with a sub-effective dose of CP94253 (1 mg/kg) rescued S -ketamine's acute and sustained antidepressant-like effects, when CP94253 was administered 2 h prior to the FST. Co-administration of S -ketamine and CP94253 did not affect the plasma level of either compound, suggesting that the observed behavioral interaction could not be ascribed to a kinetic drug-drug interaction. Conclusion: 5-HT 1B receptor activation during testing appears to be critical for S -ketamine's antidepressant-like potentials in this model.

Efficacy of distortion correction on diffusion imaging: comparison of FSL eddy and eddy_correct using 30 and 60 directions diffusion encoding.

PubMed

Yamada, Haruyasu; Abe, Osamu; Shizukuishi, Takashi; Kikuta, Junko; Shinozaki, Takahiro; Dezawa, Ko; Nagano, Akira; Matsuda, Masayuki; Haradome, Hiroki; Imamura, Yoshiki

2014-01-01

Diffusion imaging is a unique noninvasive tool to detect brain white matter trajectory and integrity in vivo. However, this technique suffers from spatial distortion and signal pileup or dropout originating from local susceptibility gradients and eddy currents. Although there are several methods to mitigate these problems, most techniques can be applicable either to susceptibility or eddy-current induced distortion alone with a few exceptions. The present study compared the correction efficiency of FSL tools, "eddy_correct" and the combination of "eddy" and "topup" in terms of diffusion-derived fractional anisotropy (FA). The brain diffusion images were acquired from 10 healthy subjects using 30 and 60 directions encoding schemes based on the electrostatic repulsive forces. For the 30 directions encoding, 2 sets of diffusion images were acquired with the same parameters, except for the phase-encode blips which had opposing polarities along the anteroposterior direction. For the 60 directions encoding, non-diffusion-weighted and diffusion-weighted images were obtained with forward phase-encoding blips and non-diffusion-weighted images with the same parameter, except for the phase-encode blips, which had opposing polarities. FA images without and with distortion correction were compared in a voxel-wise manner with tract-based spatial statistics. We showed that images corrected with eddy and topup possessed higher FA values than images uncorrected and corrected with eddy_correct with trilinear (FSL default setting) or spline interpolation in most white matter skeletons, using both encoding schemes. Furthermore, the 60 directions encoding scheme was superior as measured by increased FA values to the 30 directions encoding scheme, despite comparable acquisition time. This study supports the combination of eddy and topup as a superior correction tool in diffusion imaging rather than the eddy_correct tool, especially with trilinear interpolation, using 60 directions encoding scheme.

Relationship between suicidality and impulsivity in bipolar I disorder: a diffusion tensor imaging study

PubMed Central

Mahon, Katie; Burdick, Katherine E; Wu, Jinghui; Ardekani, Babak A; Szeszko, Philip R

2012-01-01

Background Impulsivity is characteristic of individuals with bipolar disorder and may be a contributing factor to the high rate of suicide in patients with this disorder. Although white matter abnormalities have been implicated in the pathophysiology of bipolar disorder, their relationship to impulsivity and suicidality in this disorder has not been well-investigated. Methods Diffusion tensor imaging scans were acquired in 14 bipolar disorder patients with a prior suicide attempt, 15 bipolar disorder patients with no prior suicide attempt, and 15 healthy volunteers. Bipolar disorder patients received clinical assessments including measures of impulsivity, depression, mania, and anxiety. Images were processed using the Tract-Based Spatial Statistics method in the FSL software package. Results Bipolar disorder patients with a prior suicide attempt had lower fractional anisotropy (FA) within the left orbital frontal white matter (p < 0.05, corrected) and higher overall impulsivity compared to patients without a previous suicide attempt. Among patients with a prior suicide attempt, FA in the orbital frontal white matter region correlated inversely with motor impulsivity. Conclusions Abnormal orbital frontal white matter may play a role in impulsive and suicidal behavior among patients with bipolar disorder. PMID:22329475

Automated volumetry for unilateral hippocampal sclerosis detection in patients with temporal lobe epilepsy.

PubMed

Martins, Cristina; Moreira da Silva, Nadia; Silva, Guilherme; Rozanski, Verena E; Silva Cunha, Joao Paulo

2016-08-01

Hippocampal sclerosis (HS) is the most common cause of temporal lobe epilepsy (TLE) and can be identified in magnetic resonance imaging as hippocampal atrophy and subsequent volume loss. Detecting this kind of abnormalities through simple radiological assessment could be difficult, even for experienced radiologists. For that reason, hippocampal volumetry is generally used to support this kind of diagnosis. Manual volumetry is the traditional approach but it is time consuming and requires the physician to be familiar with neuroimaging software tools. In this paper, we propose an automated method, written as a script that uses FSL-FIRST, to perform hippocampal segmentation and compute an index to quantify hippocampi asymmetry (HAI). We compared the automated detection of HS (left or right) based on the HAI with the agreement of two experts in a group of 19 patients and 15 controls, achieving 84.2% sensitivity, 86.7% specificity and a Cohen's kappa coefficient of 0.704. The proposed method is integrated in the "Advanced Brain Imaging Lab" (ABrIL) cloud neurocomputing platform. The automated procedure is 77% (on average) faster to compute vs. the manual volumetry segmentation performed by an experienced physician.

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors

PubMed Central

Castro-García, Juan A.; Lebrato-Vázquez, Clara

2018-01-01

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive. PMID:29596394

Real-Time Processing Library for Open-Source Hardware Biomedical Sensors.

PubMed

Molina-Cantero, Alberto J; Castro-García, Juan A; Lebrato-Vázquez, Clara; Gómez-González, Isabel M; Merino-Monge, Manuel

2018-03-29

Applications involving data acquisition from sensors need samples at a preset frequency rate, the filtering out of noise and/or analysis of certain frequency components. We propose a novel software architecture based on open-software hardware platforms which allows programmers to create data streams from input channels and easily implement filters and frequency analysis objects. The performances of the different classes given in the size of memory allocated and execution time (number of clock cycles) were analyzed in the low-cost platform Arduino Genuino. In addition, 11 people took part in an experiment in which they had to implement several exercises and complete a usability test. Sampling rates under 250 Hz (typical for many biomedical applications) makes it feasible to implement filters, sliding windows and Fourier analysis, operating in real time. Participants rated software usability at 70.2 out of 100 and the ease of use when implementing several signal processing applications was rated at just over 4.4 out of 5. Participants showed their intention of using this software because it was percieved as useful and very easy to use. The performances of the library showed that it may be appropriate for implementing small biomedical real-time applications or for human movement monitoring, even in a simple open-source hardware device like Arduino Genuino. The general perception about this library is that it is easy to use and intuitive.

BioSig: The Free and Open Source Software Library for Biomedical Signal Processing

PubMed Central

Vidaurre, Carmen; Sander, Tilmann H.; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals. PMID:21437227

BioSig: the free and open source software library for biomedical signal processing.

PubMed

Vidaurre, Carmen; Sander, Tilmann H; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hart, David; Klise, Katherine A.

The PyEPANET package is a set of commands for the Python programming language that are built to wrap the EPANET toolkit library commands, without requiring the end user to program using the ctypes package. This package does not contain the EPANET code, nor does it implement the functions within the EPANET software, and it requires the separately downloaded or compiled EPANET2 toolkit dynamic library (epanet.dll, libepanent.so, or epanet.dylib) and/or the EPANET-MSX dynamic library in order to function.

compomics-utilities: an open-source Java library for computational proteomics.

PubMed

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

The Digital Marketplace and Library and Information Education in the GCC Member Nations: A Critical Review.

ERIC Educational Resources Information Center

Rehman, Sajjad ur; Al-Ansari, Husain

2003-01-01

Assessed six library and information education programs in preparing manpower for the digital environment in three countries in the Gulf Cooperation Council (GCC): Saudi Arabia, Kuwait, and Oman. Highlights include curriculum changes; student-teacher ratio; technological, physical and instructional resources; hardware; software; vendors;…

MicroUse: The Database on Microcomputer Applications in Libraries and Information Centers.

ERIC Educational Resources Information Center

Chen, Ching-chih; Wang, Xiaochu

1984-01-01

Describes MicroUse, a microcomputer-based database on microcomputer applications in libraries and information centers which was developed using relational database manager dBASE II. The description includes its system configuration, software utilized, the in-house-developed dBASE programs, multifile structure, basic functions, MicroUse records,…

Collection Analysis: Powerful Ways To Collect, Analyze, and Present Your Data.

ERIC Educational Resources Information Center

Hart, Amy

2003-01-01

Discussion of collection analysis in school libraries focuses on the kinds of data used and how to use library automation software to collect the data. Describes the use of Microsoft Excel and its chart-making capabilities to enhance the presentation of the analysis and suggests ways to use collection analysis output. (LRW)

BIBLIO: A Computer System Designed to Support the Near-Library User Model of Information Retrieval.

ERIC Educational Resources Information Center

Belew, Richard K.; Holland, Maurita Peterson

1988-01-01

Description of the development of the Information Exchange Facility, a prototype microcomputer-based personal bibliographic facility, covers software selection, user selection, overview of the system, and evaluation. The plan for an integrated system, BIBLIO, and the future role of libraries are discussed. (eight references) (MES)

Implementing LibGuides 2: An Academic Case Study

ERIC Educational Resources Information Center

Duncan, Vicky; Lucky, Shannon; McLean, Jaclyn

2015-01-01

Since 1997, the University of Saskatchewan Library has used "subject pages" to highlight key library resources. When Springshare announced it was launching LibGuides v2, a project team was assembled to transition a mixture of locally produced guides and guides created with the original LibGuides v1 software. This article synthesizes best…

VTLS Inc.: The Company, the Products, the Services, the Vision.

ERIC Educational Resources Information Center

Chachra, Vinod; And Others

1993-01-01

Describes the range of products and services offered by VTLS, a company that offers comprehensive, integrated library automation software and customer support. VTLS's growth and development in the United States and abroad is described, and nine sidebar articles detail system features and applications in public, academic, and virtual libraries. (20…

Access to Full-Text Journal Articles: Some Practical Considerations.

ERIC Educational Resources Information Center

Racine, Drew

1992-01-01

Discusses some of the issues and problems involved in using electronic full-text journals in the University of Texas at Austin libraries. Issues addressed include different standards; subjects represented and the time period covered; hardware considerations; software; printing; skills and training needed for library staff and for users; and costs.…

Library Signage: Applications for the Apple Macintosh and MacPaint.

ERIC Educational Resources Information Center

Diskin, Jill A.; FitzGerald, Patricia

1984-01-01

Describes specific applications of the Macintosh computer at Carnegie-Mellon University Libraries, where MacPaint was used as a flexible, easy to use, and powerful tool to produce informational, instructional, and promotional signage. Profiles of system hardware and software, an evaluation of the computer program MacPaint, and MacPaint signage…

The Structure of the Library Market for Scientific Journals: The Case of Chemistry.

ERIC Educational Resources Information Center

Bensman, Stephen J.

1996-01-01

An analysis of price and scientific value of chemistry journals concluded that scientific value does not play a role in the pricing of scientific journals and that consequently little relationship exists between scientific value and the prices charged libraries for journals. Describes a software package, Serials Evaluator, being developed at…

Use of Information and Communication Technology to Enhance the Information Literacy Skills of Distance Students

ERIC Educational Resources Information Center

Pastula, Matthew

2010-01-01

Information and Communication Technology (ICT) has become an integral tool in enhancing library services worldwide. This article looks at ways technology is utilized at Massey University to bridge the gap between distance students and traditional library services. There are a variety of software providers, formats and implementation practices…

Technology in the Public Library: Results from the 1992 PLDS Survey of Technology.

ERIC Educational Resources Information Center

Fidler, Linda M.; Johnson, Debra Wilcox

1994-01-01

Discusses and compares the incorporation of technology by larger public libraries in Canada and the United States. Technology mentioned includes online public access catalogs; remote and local online database searching; microcomputers and software for public use; and fax, voice mail, and Telecommunication Devices for the Deaf and Teletype writer…

The New Philanthropist: Eric Schnell--Ohio State University

ERIC Educational Resources Information Center

Library Journal, 2005

2005-01-01

As head of information technology at the Prior Health Sciences Library, Eric Schnell likes to improve products that don't fully meet his library's purposes. His first major software product, the award-winning Prospero Electronic Delivery Project, is a web-based document delivery system designed to complement Ariel[R] by converting documents to a…

An object-oriented data reduction system in Fortran

NASA Technical Reports Server (NTRS)

Bailey, J.

1992-01-01

A data reduction system for the AAO two-degree field project is being developed using an object-oriented approach. Rather than use an object-oriented language (such as C++) the system is written in Fortran and makes extensive use of existing subroutine libraries provided by the UK Starlink project. Objects are created using the extensible N-dimensional Data Format (NDF) which itself is based on the Hierarchical Data System (HDS). The software consists of a class library, with each class corresponding to a Fortran subroutine with a standard calling sequence. The methods of the classes provide operations on NDF objects at a similar level of functionality to the applications of conventional data reduction systems. However, because they are provided as callable subroutines, they can be used as building blocks for more specialist applications. The class library is not dependent on a particular software environment thought it can be used effectively in ADAM applications. It can also be used from standalone Fortran programs. It is intended to develop a graphical user interface for use with the class library to form the 2dF data reduction system.

Marathon: An Open Source Software Library for the Analysis of Markov-Chain Monte Carlo Algorithms

PubMed Central

Rechner, Steffen; Berger, Annabell

2016-01-01

We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time. PMID:26824442

Chemkin-II: A Fortran chemical kinetics package for the analysis of gas-phase chemical kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kee, R.J.; Rupley, F.M.; Miller, J.A.

1989-09-01

This document is the user's manual for the second-generation Chemkin package. Chemkin is a software package for whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides an especially flexible and powerful tool for incorporating complex chemical kinetics into simulations of fluid dynamics. The package consists of two major software components: an Interpreter and Gas-Phase Subroutine Library. The Interpreter is a program that reads a symbolic description of an elementary, user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Gas-Phase Subroutinemore » Library. This library is a collection of about 100 highly modular Fortran subroutines that may be called to return information on equation of state, thermodynamic properties, and chemical production rates.« less

The Astrophysics Source Code Library by the numbers

NASA Astrophysics Data System (ADS)

Allen, Alice; Teuben, Peter; Berriman, G. Bruce; DuPrie, Kimberly; Mink, Jessica; Nemiroff, Robert; Ryan, PW; Schmidt, Judy; Shamir, Lior; Shortridge, Keith; Wallin, John; Warmels, Rein

2018-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) was founded in 1999 by Robert Nemiroff and John Wallin. ASCL editors seek both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and add entries for the found codes to the library. Software authors can submit their codes to the ASCL as well. This ensures a comprehensive listing covering a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL is indexed by both NASA’s Astrophysics Data System (ADS) and Web of Science, making software used in research more discoverable. This presentation covers the growth in the ASCL’s number of entries, the number of citations to its entries, and in which journals those citations appear. It also discusses what changes have been made to the ASCL recently, and what its plans are for the future.

Front End Software for Online Database Searching. Part 2: The Marketplace.

ERIC Educational Resources Information Center

Levy, Louise R.; Hawkins, Donald T.

1986-01-01

This article analyzes the front end software marketplace and discusses some of the complex forces influencing it. Discussion covers intermediary market; end users (library customers, scientific and technical professionals, corporate business specialists, consumers); marketing strategies; a British front end development firm; competitive pressures;…

PyMICE: APython library for analysis of IntelliCage data.

PubMed

Dzik, Jakub M; Puścian, Alicja; Mijakowska, Zofia; Radwanska, Kasia; Łęski, Szymon

2018-04-01

IntelliCage is an automated system for recording the behavior of a group of mice housed together. It produces rich, detailed behavioral data calling for new methods and software for their analysis. Here we present PyMICE, a free and open-source library for analysis of IntelliCage data in the Python programming language. We describe the design and demonstrate the use of the library through a series of examples. PyMICE provides easy and intuitive access to IntelliCage data, and thus facilitates the possibility of using numerous other Python scientific libraries to form a complete data analysis workflow.

Interface for the documentation and compilation of a library of computer models in physiology.

PubMed Central

Summers, R. L.; Montani, J. P.

1994-01-01

A software interface for the documentation and compilation of a library of computer models in physiology was developed. The interface is an interactive program built within a word processing template in order to provide ease and flexibility of documentation. A model editor within the interface directs the model builder as to standardized requirements for incorporating models into the library and provides the user with an index to the levels of documentation. The interface and accompanying library are intended to facilitate model development, preservation and distribution and will be available for public use. PMID:7950046

AMPHION: Specification-based programming for scientific subroutine libraries

NASA Technical Reports Server (NTRS)

Lowry, Michael; Philpot, Andrew; Pressburger, Thomas; Underwood, Ian; Waldinger, Richard; Stickel, Mark

1994-01-01

AMPHION is a knowledge-based software engineering (KBSE) system that guides a user in developing a diagram representing a formal problem specification. It then automatically implements a solution to this specification as a program consisting of calls to subroutines from a library. The diagram provides an intuitive domain oriented notation for creating a specification that also facilitates reuse and modification. AMPHION'S architecture is domain independent. AMPHION is specialized to an application domain by developing a declarative domain theory. Creating a domain theory is an iterative process that currently requires the joint expertise of domain experts and experts in automated formal methods for software development.

MAVEN Data Analysis and Visualization Toolkits

NASA Astrophysics Data System (ADS)

Harter, B., Jr.; DeWolfe, A. W.; Brain, D.; Chaffin, M.

2017-12-01

The Mars Atmospheric and Volatile Evolution (MAVEN) mission has been collecting data at Mars since September 2014. The MAVEN Science Data Center has developed software toolkits for analyzing and visualizing the science data. Our Data Intercomparison and Visualization Development Effort (DIVIDE) toolkit is written in IDL, and utilizes the widely used "tplot" IDL libraries. Recently, we have converted DIVIDE into Python in an effort to increase the accessibility of the MAVEN data. This conversion also necessitated the development of a Python version of the tplot libraries, which we have dubbed "PyTplot". PyTplot is generalized to work with missions beyond MAVEN, and our software is available on Github.

Optimizing the Performance of Radionuclide Identification Software in the Hunt for Nuclear Security Threats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fotion, Katherine A.

2016-08-18

The Radionuclide Analysis Kit (RNAK), my team’s most recent nuclide identification software, is entering the testing phase. A question arises: will removing rare nuclides from the software’s library improve its overall performance? An affirmative response indicates fundamental errors in the software’s framework, while a negative response confirms the effectiveness of the software’s key machine learning algorithms. After thorough testing, I found that the performance of RNAK cannot be improved with the library choice effect, thus verifying the effectiveness of RNAK’s algorithms—multiple linear regression, Bayesian network using the Viterbi algorithm, and branch and bound search.

Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data.

PubMed

Lu, Emily; Elizondo-Riojas, Miguel-Angel; Chang, Jeffrey T; Volk, David E

2014-06-10

Next-generation sequencing results from bead-based aptamer libraries have demonstrated that traditional DNA/RNA alignment software is insufficient. This is particularly true for X-aptamers containing specialty bases (W, X, Y, Z, ...) that are identified by special encoding. Thus, we sought an automated program that uses the inherent design scheme of bead-based X-aptamers to create a hypothetical reference library and Markov modeling techniques to provide improved alignments. Aptaligner provides this feature as well as length error and noise level cutoff features, is parallelized to run on multiple central processing units (cores), and sorts sequences from a single chip into projects and subprojects.

The Environment for Application Software Integration and Execution (EASIE), version 1.0. Volume 2: Program integration guide

NASA Technical Reports Server (NTRS)

Jones, Kennie H.; Randall, Donald P.; Stallcup, Scott S.; Rowell, Lawrence F.

1988-01-01

The Environment for Application Software Integration and Execution, EASIE, provides a methodology and a set of software utility programs to ease the task of coordinating engineering design and analysis codes. EASIE was designed to meet the needs of conceptual design engineers that face the task of integrating many stand-alone engineering analysis programs. Using EASIE, programs are integrated through a relational data base management system. In volume 2, the use of a SYSTEM LIBRARY PROCESSOR is used to construct a DATA DICTIONARY describing all relations defined in the data base, and a TEMPLATE LIBRARY. A TEMPLATE is a description of all subsets of relations (including conditional selection criteria and sorting specifications) to be accessed as input or output for a given application. Together, these form the SYSTEM LIBRARY which is used to automatically produce the data base schema, FORTRAN subroutines to retrieve/store data from/to the data base, and instructions to a generic REVIEWER program providing review/modification of data for a given template. Automation of these functions eliminates much of the tedious, error prone work required by the usual approach to data base integration.

A web-based library consult service for evidence-based medicine: Technical development.

PubMed

Schwartz, Alan; Millam, Gregory

2006-03-16

Incorporating evidence based medicine (EBM) into clinical practice requires clinicians to learn to efficiently gain access to clinical evidence and effectively appraise its validity. Even using current electronic systems, selecting literature-based data to solve a single patient-related problem can require more time than practicing physicians or residents can spare. Clinical librarians, as informationists, are uniquely suited to assist physicians in this endeavor. To improve support for evidence-based practice, we have developed a web-based EBM library consult service application (LCS). Librarians use the LCS system to provide full text evidence-based literature with critical appraisal in response to a clinical question asked by a remote physician. LCS uses an entirely Free/Open Source Software platform and will be released under a Free Software license. In the first year of the LCS project, the software was successfully developed and a reference implementation put into active use. Two years of evaluation of the clinical, educational, and attitudinal impact on physician-users and librarian staff are underway, and expected to lead to refinement and wide dissemination of the system. A web-based EBM library consult model may provide a useful way for informationists to assist clinicians, and is feasible to implement.

Award ER25750: Coordinated Infrastructure for Fault Tolerance Systems Indiana University Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lumsdaine, Andrew

2013-03-08

The main purpose of the Coordinated Infrastructure for Fault Tolerance in Systems initiative has been to conduct research with a goal of providing end-to-end fault tolerance on a systemwide basis for applications and other system software. While fault tolerance has been an integral part of most high-performance computing (HPC) system software developed over the past decade, it has been treated mostly as a collection of isolated stovepipes. Visibility and response to faults has typically been limited to the particular hardware and software subsystems in which they are initially observed. Little fault information is shared across subsystems, allowing little flexibility ormore » control on a system-wide basis, making it practically impossible to provide cohesive end-to-end fault tolerance in support of scientific applications. As an example, consider faults such as communication link failures that can be seen by a network library but are not directly visible to the job scheduler, or consider faults related to node failures that can be detected by system monitoring software but are not inherently visible to the resource manager. If information about such faults could be shared by the network libraries or monitoring software, then other system software, such as a resource manager or job scheduler, could ensure that failed nodes or failed network links were excluded from further job allocations and that further diagnosis could be performed. As a founding member and one of the lead developers of the Open MPI project, our efforts over the course of this project have been focused on making Open MPI more robust to failures by supporting various fault tolerance techniques, and using fault information exchange and coordination between MPI and the HPC system software stack from the application, numeric libraries, and programming language runtime to other common system components such as jobs schedulers, resource managers, and monitoring tools.« less

Planning a new library in an age of transition: the Washington University School of Medicine Library and Biomedical Communications Center.

PubMed Central

Crawford, S; Halbrook, B

1990-01-01

In an era of great technological and socioeconomic changes, the Washington University School of Medicine conceptualized and built its first Library and Biomedical Communications Center in seventy-eight years. The planning process, evolution of the electronic library, and translation of functions into operating spaces are discussed. Since 1983, when the project was approved, a whole range of information technologies and services have emerged. The authors consider the kind of library that would operate in a setting where people can do their own searches, order data and materials through an electronic network, analyze and manage information, and use software to create their own publications. Images PMID:2393757

The medical matters wiki: building a library Web site 2.0.

PubMed

Robertson, Justin; Burnham, Judy; Li, Jie; Sayed, Ellen

2008-01-01

New and innovative information technologies drive the ever-evolving library profession. From clay tablet to parchment scroll to manufactured paper to computer screen pixel, information storage, retrieval, and delivery methods continue to evolve, and each advance irrevocably affects the way libraries, and librarians, work. The Internet has forever altered information and library science, both in theory and practice, but even within this context the progression continues. Though ambiguously defined, Web 2.0 offers a new outlook and new software, presenting librarians with potentially invaluable new tools and methods. This paper discusses the creation, implementation, and maintenance of a Web 2.0 technology, the wiki, as a resource tool for an academic biomedical library.

Chapter 24: Programmatic Interfaces - IDL VOlib

NASA Astrophysics Data System (ADS)

Miller, C. J.

In this chapter, we describe a library for working with the VO using IDL (the Interactive Data Language). IDL is a software environment for data analysis, visualization, and cross-platform application development. It has wide-usage in astronomy, including NASA (e.g. http://seadas.gsfc.nasa.gov/), the Sloan Digital Sky Survey (http://www.sdss.org), and the Spitzer Infrared Spectrograph Instrument (http://ssc.spitzer.caltech.edu/archanaly/contributed/smart/). David Stern, the founder of Research Systems, Inc. (RSI), began the development of IDL while working with NASA's Mars Mariner 7 and 9 data at the Laboratory for Atmospheric and Space Physics at the University of Colorado. In 1981, IDL was rewritten in assembly language and FORTRAN for VAX/VMS. IDL's usage has expanded over the last decade into the fields of medical imaging and engineering, among many others. IDL's programming style carries over much of this FORTRAN-legacy, and has a familiar feel to many astronomers who learned their trade using FORTRAN. The spread of IDL-usage amongst astronomers can in part be attributed to the wealth of publicly astronomical libraries. The Goddard Space Flight Center (GSFC) maintains a list of astronomy-related IDL libraries, including the well known Astronomy User's Library (hereafter ASTROLIB2). We will use some of these GSFC IDL libraries. We note that while IDL is a licensed-software product, the source code of user-written procedures are typically freely available to the community. To make the most out of this section as a reader, it is important that many of the data discovery, access, and analysis protocols are understood before reading this chapter. In the next section, we provide an overview of some of the NVO terminology with which the reader should be familiar. The IDL library discussed here is specifically for use with the Virtual Observatory and is named VOlib. IDL's VOlib is available at http://nvo.noao.edu and is included with the software distrubution for this book.

STARLSE -- Starlink Extensions to the VAX Language Sensitive Editor

NASA Astrophysics Data System (ADS)

Warren-Smith, R. F.

STARLSE is a ``Starlink Sensitive'' editor based on the VAX Language Sensitive Editor (LSE). It exploits the extensibility of LSE to provide additional features which assist in the writing of portable Fortran 77 software with a standard Starlink style. STARLSE is intended mainly for use by those writing ADAM applications and subroutine libraries for distribution as part of the Starlink Software Collection, although it may also be suitable for other software projects. It is designed to integrate with the SST (Simple Software Tools) package.

75 FR 13689 - Airworthiness Directives; Empresa Brasileira de Aeronautica S.A. (EMBRAER) Model EMB-135ER...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-23

... the Critical Design Configuration Control Limitations (CDCCL) and in the Fuel System Limitations (FSL... necessary to maintain the design features required to preclude the existence or development of an ignition... amend this proposed AD based on those comments. We will post all comments we receive, without change, to...

Gender Differences in Motivation to Learn French

ERIC Educational Resources Information Center

Kissau, Scott

2006-01-01

There is concern among second language educators in Canada that male students are losing interest in studying French as a second language (FSL). In response, in the fall of 2003, a study was conducted to investigate gender differences in second language (L2) motivation among Grade 9 core French students. Building upon the traditional model of L2…

Second Language Text Comprehension: Processing within a Multilayered System

ERIC Educational Resources Information Center

Donin, Janet; Graves, Barbara; Goyette, Els

2004-01-01

The results of a within-subject cross-language study of text comprehension in adult second language (L2) learners are presented. Text comprehension and sentence reading time measures were obtained for matched narrative and procedural texts in English and French from adult learners of French as a second language (FSL) at two levels of French…

Bibliographic Management Software Seminars: Funding and Implementation.

ERIC Educational Resources Information Center

Henry, Marcia

This paper contains the grant proposal and final report for a project conducted by the California State University at Northridge library to demonstrate online database searching and introduce the use of bibliographic management software to faculty and graduate students. Day-long, discipline-oriented seminars were planned to increase the…

Creating an X Window Terminal-Based Information Technology Center.

ERIC Educational Resources Information Center

Klassen, Tim W.

1997-01-01

The creation of an information technology center at the University of Oregon Science Library is described. Goals included providing access to Internet-based resources and multimedia software, platforms for running science-oriented software, and resources so students can create multimedia materials. A mixed-lab platform was created with Unix-based…

Choosing and Using Text-to-Speech Software

ERIC Educational Resources Information Center

Peters, Tom; Bell, Lori

2007-01-01

This article describes a computer-based technology for generating speech called text-to-speech (TTS). This software is ready for widespread use by libraries, other organizations, and individual users. It offers the affordable ability to turn just about any electronic text that is not image-based into an artificially spoken communication. The…

MLS data segmentation using Point Cloud Library procedures. (Polish Title: Segmentacja danych MLS z użyciem procedur Point Cloud Library)

NASA Astrophysics Data System (ADS)

Grochocka, M.

2013-12-01

Mobile laser scanning is dynamically developing measurement technology, which is becoming increasingly widespread in acquiring three-dimensional spatial information. Continuous technical progress based on the use of new tools, technology development, and thus the use of existing resources in a better way, reveals new horizons of extensive use of MLS technology. Mobile laser scanning system is usually used for mapping linear objects, and in particular the inventory of roads, railways, bridges, shorelines, shafts, tunnels, and even geometrically complex urban spaces. The measurement is done from the perspective of use of the object, however, does not interfere with the possibilities of movement and work. This paper presents the initial results of the segmentation data acquired by the MLS. The data used in this work was obtained as part of an inventory measurement infrastructure railway line. Measurement of point clouds was carried out using a profile scanners installed on the railway platform. To process the data, the tools of 'open source' Point Cloud Library was used. These tools allow to use templates of programming libraries. PCL is an open, independent project, operating on a large scale for processing 2D/3D image and point clouds. Software PCL is released under the terms of the BSD license (Berkeley Software Distribution License), which means it is a free for commercial and research use. The article presents a number of issues related to the use of this software and its capabilities. Segmentation data is based on applying the templates library pcl_ segmentation, which contains the segmentation algorithms to separate clusters. These algorithms are best suited to the processing point clouds, consisting of a number of spatially isolated regions. Template library performs the extraction of the cluster based on the fit of the model by the consensus method samples for various parametric models (planes, cylinders, spheres, lines, etc.). Most of the mathematical operation is carried out on the basis of Eigen library, a set of templates for linear algebra.

Specification of Fenix MPI Fault Tolerance library version 1.0.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gamble, Marc; Van Der Wijngaart, Rob; Teranishi, Keita

This document provides a specification of Fenix, a software library compatible with the Message Passing Interface (MPI) to support fault recovery without application shutdown. The library consists of two modules. The first, termed process recovery , restores an application to a consistent state after it has suffered a loss of one or more MPI processes (ranks). The second specifies functions the user can invoke to store application data in Fenix managed redundant storage, and to retrieve it from that storage after process recovery.

The Region 4 collaborative virtual reference project.

PubMed

Parker, Sandi K; Johnson, E Diane

2003-01-01

In May 2002, the Denison Memorial Library at the University of Colorado Health Sciences Center and the J. Otto Lottes Health Sciences Library at the University of Missouri-Columbia, with funding from the National Network of Libraries of Medicine-Midcontinental Region, embarked on a collaborative, real-time reference project using the 24/7 Reference, Inc., software package. This paper describes how the project was conceived, and includes details on the service hours, staffing, training, marketing, lessons learned, and future plans for the service.

Spending Smart: How To Budget and Finance. Making Sense of Your Budget Dollars; Success with Budget Proposals; Encumbering Grants: Managing the Money; Write a Grant? Me?; Using Microsoft[R] Excel To Plan and Budget in Your School Library; Charging Ahead; The No-Money Lottery; Coffee, Anyone?

ERIC Educational Resources Information Center

Bernstein, Allison; Baule, Steve; Farmer, Lesley S. J.; Anderson, Cyndee; Barringer, Crystal; Buchanan, Peggy; Fullner, Sheryl Kindle; Knop, Kathi; Larson, Chris

2002-01-01

Includes eight articles that address issues related to budgeting and finances in secondary school libraries. Topics include limited budgets; budget proposals; administering grants; writing grants; using Microsoft's Excel software for budgeting; using credit cards for library purchases; offering prizes for donating books; and offering coffee and…

JAMI: a Java library for molecular interactions and data interoperability.

PubMed

Sivade Dumousseau, M; Koch, M; Shrivastava, A; Alonso-López, D; De Las Rivas, J; Del-Toro, N; Combe, C W; Meldal, B H M; Heimbach, J; Rappsilber, J; Sullivan, J; Yehudi, Y; Orchard, S

2018-04-11

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

The Visible Human Data Sets (VHD) and Insight Toolkit (ITk): Experiments in Open Source Software

PubMed Central

Ackerman, Michael J.; Yoo, Terry S.

2003-01-01

From its inception in 1989, the Visible Human Project was designed as an experiment in open source software. In 1994 and 1995 the male and female Visible Human data sets were released by the National Library of Medicine (NLM) as open source data sets. In 2002 the NLM released the first version of the Insight Toolkit (ITk) as open source software. PMID:14728278

Managing Digital Archives Using Open Source Software Tools

NASA Astrophysics Data System (ADS)

Barve, S.; Dongare, S.

2007-10-01

This paper describes the use of open source software tools such as MySQL and PHP for creating database-backed websites. Such websites offer many advantages over ones built from static HTML pages. This paper will discuss how OSS tools are used and their benefits, and after the successful implementation of these tools how the library took the initiative in implementing an institutional repository using DSpace open source software.

Activity and task of the saveMLAK and aid for library

NASA Astrophysics Data System (ADS)

Okamoto, Makoto

We report the activities of saveMLAK, an organization dedicated to supporting museums, libraries, archives, and kominkans damaged by the Great East Japan Earthquake, focusing on the activities for libraries. saveMLAK provides a website using MediaWiki collaborative editing software for accumulating information regarding damage and support activities, offering information support, indirect support, and intermediary support. We also report the collaboration with Miyagi Prefectural Library based on the accumulated, shared information as an example of support for libraries in the disaster area. We describe the process of the activities of saveMLAK and problems emerging so far, and provide constructive criticism and proposals to other support activities for libraries. In conclusion, we suggest establishment of permanent organizations/functions to prepare for emergencies and to cope with disasters in the future.

Software for Studying and Enhancing Educational Uses of Geospatial Semantics and Data

ERIC Educational Resources Information Center

Nodenot, Thierry; Sallaberry, Christian; Gaio, Mauro

2010-01-01

Geographically related queries form nearly one-fifth of all queries submitted to the Excite search engine and the most frequently occurring terms are names of places. This paper focuses on digital libraries and extends the basic services of existing library management systems to include new ones that are dedicated to geographic information…