cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Motivations For Dams Migration
Creators: name: Stein, Ayla
name: Thompson, Santi
Publisher: name: Zenodo
Year: 2015
Subjects: digital asset management systems
digital repositories
digital library systems
digital libraries
system migration

description: Based on results from "Identifying Motivations for DAMS Migration: A Survey," this presentation discusses themes and features desired in future digital asset management systems (DAMS). It outlines specific topical areas that will inform future system and workflow development and governing body/vendor relations. Presenters conclude by reviewing lessons learned from the project as well as discussing future areas of research related to this study.
OPTIMIZING MUCOADHESIVE TABLETS OF LERCANIDIPINE: FORMULATION DEVELOPMENT AND EVALUATION
Creators: name: Vikash Singh*, Mrs. Reena Shende, Dr. Satkar Prasad
Publisher: name: Zenodo
Year: 2023

description: Arterial hypertension, the prevailing cardiovascular ailment associated with escalating obesity rates and sedentary lifestyles, often necessitates changes in therapy due to the challenges posed by traditional antihypertensive medications. This study endeavors to address these issues through the development and evaluation of mucoadhesive buccal tablets of Lercanidipine. Formulation and evaluation procedures were conducted according to standard protocols, resulting in six formulations with varying ingredient concentrations. The results indicated that the bulk density of the formulations ranged from 0.374 to 0.385, while tapped density varied from 0.473 to 0.492. The compressibility index fell within the range of 21.75 to 23.00, and the Hausner ratio ranged from 1.278 to 1.299. Formulation F3 exhibited the highest drug content at 99.45±0.20%. The thickness and hardness for F3 were 3.11±0.04 mm and 5.4±0.4 kg/cm^2, respectively, while weight variation and friability were measured at 246±7 mg and 0.658±0.013%. The maximum swelling in the F3 formulation at 12 hours reached 103.25%, indicating its potential for effective drug release. The % Cumulative Drug Release for F3 at 12 hours was observed to be 99.45%. Regression coefficient values were compared, revealing that the 'r2' values of the First Order kinetics were maximized, reaching 0.978. This suggests that drug release from the formulations follows First Order kinetics. In conclusion, the F3 formulation demonstrated ideal parameters, ensuring rapid action and offering a viable alternative to traditional tablets for the management of arterial hypertension.
Keywords: Hypertension, Buccal drug delivery, Muucoadhesive tablets, Lercanidipine
Nonperturbative tuning of an improved relativistic heavy-quark action with application to bottom spectroscopy
Creators: name: Aoki, Yasumichi
name: Christ, Norman H.
name: Flynn, Jonathan M.
name: Izubuchi, Taku
name: Lehner, Christoph
name: Li, Min
name: Peng, Hao
name: Soni, Amarjit
name: Van de Water, Ruth S.
name: Witzel, Oliver
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We calculate the masses of bottom mesons using an improved relativistic action for the b-quarks and the RBC/UKQCD Iwasaki gauge configurations with 2+1 flavors of dynamical domain-wall light quarks. We analyze configurations with two lattice spacings: a^{-1} = 1.729 GeV (a ~ 0.11 fm) and a^{-1} = 2.281 GeV (a ~ 0.086 fm). We use an anisotropic, clover-improved Wilson action for the b-quark, and tune the three parameters of the action nonperturbatively such that they reproduce the experimental values of the B_s and B_s* heavy-light meson states. The masses and mass-splittings of the low-lying bottomonium states (such as the eta_b and Upsilon) can then be computed with no additional inputs, and comparison between these predictions and experiment provides a test of the validity of our method. We obtain bottomonium masses with total uncertainties of ~0.5-0.6% and fine-structure splittings with uncertainties of ~35-45%; for all cases we find good agreement with experiment. The parameters of the relativistic heavy-quark action tuned for b-quarks presented in this work can be used for precise calculations of weak matrix elements such as B-meson decay constants and mixing parameters with lattice discretization errors that are of the same size as in light pseudoscalar meson quantities. This general method can also be used for charmed meson masses and matrix elements if the parameters of the heavy-quark action are appropriately tuned.
description: 30 pages, 14 figures, 14 tables
Dacryolithogenesis or dacryolithiasis : the story so far
Creators: name: Ali, Mohammad Javed
name: Heichel, Jens
name: Paulsen, Friedrich
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 2024
Subjects: subject: 610

description: The term dacryoliths refers to the concretions found within the lacrimal system. When the term dacryoliths is unspecified, it usually refers to the noninfectious dacryoliths commonly isolated from the lacrimal sac and the nasolacrimal duct. More often, they are diagnosed incidentally during a dacryocystorhinostomy, and the reported incidence among all dacryocystorhinostomy surgeries is 5.7% to as high as 18%. Dacryolithiasis is a complex process occurring within the lacrimal system, and current evidence suggests a multifactorial etiology. The sequence of events can be summarized broadly into 4 stages: stage of susceptibility, stage of initiation/trigger, stage of development, and stage of maintenance. The triggering event is the breach of the lacrimal sac or nasolacrimal duct epithelium, resulting in microtrauma with blood leakage. The blood clots act as a nidus for subsequent sequential laying of mucopeptides, cellular debris present locally, debris washed from the ocular surface, and extraneous agents in tears. This process is aided by altered rheology and composition of the tear film. After the formation of dacryoliths, extracellular neutrophil traps usually form on the surface, which help to maintain the dacryoliths (which do not dissolve). This review highlights and discusses the possible sequence of events during dacryolithiasis.
St. Gallen/Vienna 2023 : optimization of rreatment for patients with primary breast cancer - a brief summary of the consensus discussion
Creators: name: Balic, Marija
name: Thomssen, Christoph
name: Gnant, Michael
name: Harbeck, Nadia
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 2023
Subjects: subject: 610

description: The St. Gallen Consensus Conference on early breast cancer treatment 2023 was again a live event and took place in Vienna, Austria. After 4 years and one virtual event due to the pandemic, more than 2,800 participants from over 100 countries came together in Vienna, and the 2023 St. Gallen/Vienna conference was a great success. Over 3 days, the global faculty reviewed the most important evidence published during the last 2 years and debated over controversial topics, and finally, the consensus votes aimed to define the impact of the new data on everyday routine practice. Focuses of this year's conference were radiotherapy and local management of the axilla, genetics, and their impact on treatment, as well as the role of the immune system and tumor-infiltrating lymphocytes in pathological reports and treatment decision-making. The traditional panel votes were moderated for the first time by Harold Burstein from Boston, and with questions previously voted on and live voting, the panel managed for the most part to clarify the critical questions. This report by editors of BREAST CARE summarizes the results of the 2023 international panel votes with respect to locoregional and systemic treatment as a brief news update but does not intend to replace the official St. Gallen Consensus publication that not just reports but also interprets the panel votes and will follow shortly in a major oncological journal. The next (19th) St. Gallen International Breast Cancer Conference will again take place in Vienna (save the date: March 12-15, 2025).
mGPT: A Probabilistic Planner Based on Heuristic Search
Creators: name: Bonet, B.
name: Geffner, H.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: We describe the version of the GPT planner used in the probabilistic track of the 4th International Planning Competition (IPC-4). This version, called mGPT, solves Markov Decision Processes specified in the PPDDL language by extracting and using different classes of lower bounds along with various heuristic-search algorithms. The lower bounds are extracted from deterministic relaxations where the alternative probabilistic effects of an action are mapped into different, independent, deterministic actions. The heuristic-search algorithms use these lower bounds for focusing the updates and delivering a consistent value function over all states reachable from the initial state and the greedy policy.
Statika: Managing Cloud Resources, Bioinformatics Tools And Data
Creators: name: Alekhin, Alexey
Publisher: name: Zenodo
Year: 2014

description: Next Generation Sequencing (NGS) has brought a revolution to the bioinformatics landscape, definitely reshaping fields such as genomics and transcriptomics, by offering sheer amounts of data about previously inaccessible domains in a cheap and scalable way. Thus biological data analysis demands, more than ever, high performance computing architectures; in particular, Cloud Computing, a comparable breakthrough in the IT world, holds promise for being the foundation on which a solution could be built (as already demonstrated by pioneering efforts such as Galaxy or CloudBioLinux). It provides a perfect framework for high throughput data analysis: deploying architectures with as much computing capacity as needed, scaling in an horizontal way, being also able to scale down adjusting to the computing needs real time, or the pay-as-you-go model make for a strong case.

However, fast, reproducible, and cost-effective data analysis in the cloud at such scale remains elusive. Certainly, one fundamental prerequisite for achieving this is having the ability to manage both the tools and data to be used in a robust, reproducible, and automated way. High throughput analysis, where a lot of resources are to be used and paid for, needs to have a robust configuration system to rely on. In the cloud computing world, due to its on-demand nature, automated resource configuration is a critical factor. This is even more so in the case of bioinformatics analysis where pretty often a pretty intricated and unstable chain of dependencies underlies tools and data; knowing beforehand that all the resources to be used are properly configured is invaluable.

Statika (http://ohnosequences.com/statika) aims to be a basic tool for the declaration and deployment of composable, versioned and reproducible cloud infrastructures for the bioinformatics space.

Data, tools and infrastructure are treated on an equal footing, and a expressive domain specific language allows the user to express complex dependency relationships, check for possible version conflicts and automatically choose a safe resource creation order.

By making use of advanced features of the Scala programming language such as dependent types and type-level computations a great deal of structure can be expressed abstractly, and checked at compile time before any cost is incurred. A strong versioning system where both data and tools are included makes reproducibility not only possible but actually enforced.

Statika has been put to work on scenarios as different as a cloud-based system for scaling inherently parallel computations in the bioinformatics domain: Nispero, or by providing versioned and modular automated deployments of Bio4j, a graph database integrating all data from key resources in the bioinformatics data space, including: UniProt, Gene Ontology, the NCBI Taxonomy or UniRef. We use it internally for the integration and automated deployment of all sort of bioinformatics tools and data.

Statika is open source, available under the AGPLv3 license.
Distances to dense cores that contain Very Low Luminosity Objects
Creators: name: Maheswar, G.
name: Lee, Chang Won
name: Dib, Sami
Publisher: name: arXiv
Year: 2011
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The aim of the paper is to estimate distances to dense molecular cores that harbour Very Low Luminosity Objects (VeLLO) detected by Spitzer Space Telescope and to confirm their VeLLO nature. The cloud distances are estimated using near-IR photometric method. We use a technique that provides spectral classification of stars lying towards the fields containing the clouds into main sequence and giants. In this technique, the observed (J-H) and (H-Ks) colours are dereddened simultaneously using trial values of A_V and a normal interstellar extinction law. The best fit of the dereddened colours to the intrinsic colours giving a minimum value of chi^{2} then yields the corresponding spectral type and A_V for the star. The main sequence stars, thus classified, are then utilized in an A_V versus distance plot to bracket the cloud distances. The typical error in the estimation of distances to the clouds are found to be ~18%.We estimated distances to seven cloud cores, IRAM04191, L1521F, BHR111, L328, L673-7, L1014, and L1148 using the above method. These clouds contain VeLLO candidates. The estimated distances to the cores are found to be 127\pm25 pc (IRAM04191), 136\pm36 pc (L1521F), 355\pm65 pc (BHR111), 217\pm30 pc (L328), 240\pm45 pc (L673-7), 258\pm50 pc (L1014), and 301\pm55 pc (L1148). We re-evaluated the internal luminosities of the VeLLOs discovered in these seven clouds using the distances estimated from this work. Except for L1014-IRS (L_{int}=0.15 L_{\odot}), all other VeLLO candidates are found to be consistent with the definition of a VeLLO (L_{int}<=0.1L_{\odot}). In addition to the cores that harbour VeLLO candidates, we also obtained distances to the clouds L323, L675, L676, CB 188, L1122, L1152, L1155, L1157 and L1158 which are located in the directions of the above seven cores. Towards L1521F and L1148 we found evidence of the presence of multiple dust layers.
description: 23 figures, accepted for publication in A&A
Agnes Sós, Die Ausgrabungen Géza Fehérs in Zalavár und Sandor Bökönyi / Die Wirbeltierfaune der Ausgrabungen in Zalavár
Creators: name: Hinz, Hermann
Publisher: name: Bonner Jahrbücher
Year: 2020

description: Rezension zu: Agnes Sós, Die Ausgrabungen Géza Fehérs in Zalavár (210 Seiten, 98 Tafeln, 18 Karten, 84 Abbildungen) und Sandor Bökönyi, Die Wirbeltierfauna der Ausgrabungen in Zalavár (58 Seiten, 12 Tafeln). Archaeologia Hungarica, Series Nova 41. Budapest 1963.
description: Bonner Jahrbücher, Bd. 164.1964: Bonner Jahrbücher
BFKL equation for the adjoint representation of the gauge group in the next-to-leading approximation at N=4 SUSY
Creators: name: Fadin, V. S.
name: Lipatov, L. N.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We calculate the eigenvalues of the next-to-leading kernel for the BFKL equation in the adjoint representation of the gauge group $SU(N_c)$ in the N=4 supersymmetric Yang-Mills model. These eigenvalues are used to obtain the high energy behavior of the remainder function for the 6-point scattering amplitude with the maximal helicity violation in the kinematical regions containing the Mandelstam cut contribution. The leading and next-to-leading singularities of the corresponding collinear anomalous dimension are calculated in all orders of perturbation theory. We compare our result with the known collinear limit and with the recently suggested ansatz for the remainder function in three loops and obtain the full agreement providing that the numerical parameters in this anzatz are chosen in an appropriate way.
description: 13 pages
APHRODITE criteria : addressing male patients with hypogonadism and/or infertility owing to altered idiopathic testicular function
Creators: name: Esteves, Sandro
name: Humaidan, Peter
name: Ubaldi, Filippo M.
name: Alviggi, Carlo
name: Antonio, Leen
name: Barratt, Christopher
name: Behre, Hermann M.
name: Jørgensen, Niels
name: Pacey, Allan A.
name: Simoni, Manuela
name: Santi, Daniele
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 2024
Subjects: subject: 610

description: Research question: Can a novel classification system of the infertile male – ‘APHRODITE’ (Addressing male Patients with Hypogonadism and/or infeRtility Owing to altereD, Idiopathic TEsticular function) – stratify different subgroups of male infertility to help scientists to design clinical trials on the hormonal treatment of male infertility, and clinicians to counsel and treat the endocrinological imbalances in men and, ultimately, increase the chances of natural and assisted conception? Design: A collaboration between andrologists, reproductive urologists and gynaecologists, with specialization in reproductive medicine and expertise in male infertility, led to the development of the APHRODITE criteria through an iterative consensus process based on clinical patient descriptions and the results of routine laboratory tests, including semen analysis and hormonal testing. Results: Five patient groups were delineated according to the APHRODITE criteria; (1) Hypogonadotrophic hypogonadism (acquired and congenital); (2) Idiopathic male infertility with lowered semen analysis parameters, normal serum FSH and normal serum total testosterone concentrations; (3) A hypogonadal state with lowered semen analysis parameters, normal FSH and reduced total testosterone concentrations; (4) Lowered semen analysis parameters, elevated FSH concentrations and reduced or normal total testosterone concentrations; and (5) Unexplained male infertility in the context of unexplained couple infertility. Conclusion: The APHRODITE criteria offer a novel and standardized patient stratification system for male infertility independent of aetiology and/or altered spermatogenesis, facilitating communication among clinicians, researchers and patients to improve reproductive outcomes following hormonal therapy. APHRODITE is proposed as a basis for future trials of the hormonal treatment of male infertility.
Bio4J: Bigger, Faster, Leaner
Creators: name: Alekhin, Alexey
Publisher: name: Zenodo
Year: 2014

description: Bio4j (http://bio4j.com) is a high-performance cloud-enabled graph-based bioinformatics data platform. It is one of the first and most important graph databases for biological data, specially designed to cope with and manage the huge amount of data brought by NGS technologies: it integrates most data available in UniProt KB (SwissProt + Trembl), Gene Ontology (GO), UniRef (50, 90, 100), RefSeq, NCBI taxonomy, and Expasy Enzyme DBs. Data is organized in a way semantically equivalent to what it represents by taking advantage of the graph structure; in this paradigm it is easy to have many different types of relationships and nodes thus making it perfect for highly interconnected complex data (as it is the case of biological data). From a performance point of view, relational databases with their tabular data structure are not able to respond to some complex queries that are possible to resolve using the graph paradigm; graph databases give you fast local access to all the elements related with each entity, through the edges that connect them with others. In this way, queries which would even be impossible to perform with a standard Relational DB, just take a couple of seconds with Bio4j.

This year has seen important updates and new developments on Bio4j; it now includes 1,216,993,547 relationships and 190,625,351 nodes, close to triplicating the figures from one year ago. We have introduced a new level of abstraction for the domain model, by decoupling the inner database implementation from the relationships among entities themselves. Interfaces has been developed for each node and relationship present in the database, including methods to access both the properties of the entity it represents and utility methods that allow to easily navigate to the entities that will be linked to it.

Implementing that set of interfaces we have developed another layer for the domain model using Blueprints, the de-facto standard for graph data modeling, thus making the domain model independent from the choice of database technology. Building on that, we now offer specifically tuned data binary distributions for TitanDB, yielding a dramatic increase in performance due to vertex-local edge-typed indexes.

The introduction of a module system based in Statika makes now possible to deploy only selected components of the integrated data sets, with Amazon Web Services deployments on hardware specifically configured for them.

Bio4j is open source, available under the AGPLv3 license.
Statika: Managing Bioinformatics Tools And Resources In The Cloud
Creators: name: Alekhin, Alexey
Publisher: name: Zenodo
Year: 2014

description: Next Generation Sequencing has revolutionized the bioinformatics landscape, reshaping fields such as genomics and transcriptomics, by offering huge amounts of data about previously inaccessible domains in a cheap and scalable way. Thus, biological data analysis demands, more than ever, high performance computing architectures. Cloud Computing, a comparable breakthrough in the IT world, holds promise for being the foundation on which a solution could be built (as already demonstrated by pioneering efforts such as Galaxy or CloudBioLinux). It provides a perfect framework for high throughput data analysis: deploying architectures with as much computing capacity as needed, scaling in a horizontal way, being also able to scale down adjusting to the computing needs real time, with the pay-as-you-go model.

However, fast and cost-effective data analysis in the cloud at such scale remains elusive. High throughput analysis, where a lot of resources are to be used and paid for, critically needs to have an ability to manage both the tools and data in a robust, reproducible and automated way. As in bioinformatics analysis often a pretty complex and unstable chain of dependencies underlies tools and data, knowing beforehand that all the resources to be used are properly configured is invaluable.

Statika (http://ohnosequences.com/statika) aims to be a basic tool for the declaration and automated deployment of composable cloud infrastructures for the bioinformatics space. Using Statika data, tools and infrastructure are treated on an equal basis with a expressive domain specific language that allows the user to express complex dependency relationships. Statika will automatically check for possible version conflicts and choose a safe resource creation order.

Statika has been applied in different scenarios: from a cloud-based system for scalable and composable parallel computations in the bioinformatics domain as in Nispero tool, to modular automated deployments of complex databases as Bio4j. Bio4j (bio4j.com)is a graph database integrating all data from key resources in the bioinformatics data space, including UniProt, Gene Ontology, the NCBI Taxonomy or UniRef. We use Statika internally for the integration and automated deployment of all sort of bioinformatics tools and data.

Statika is open source, available under the AGPLv3 license.
Bio4J: The Bioinformatics Data Platform
Creators: name: Alekhin, Alexey
Publisher: name: Zenodo
Year: 2014

description: Bio4j (http://bio4j.com) is a cloud-based high-performance bioinformatics graph database. It is one of the first and most important graph databases for biological data with a special focus on data integration: it integrates most data available in UniProt KB (SwissProt + Trembl), Gene Ontology (GO), UniRef (50, 90, 100), RefSeq, NCBI taxonomy, and Expasy Enzyme DBs. All this data in Bio4j is organized in a semantically equivalent graph structure. It allows having many different types of nodes and relationships, making it perfect for highly interconnected complex biological data. Graph databases allow fast local access to all the elements related with each entity, through the edges that connect them with others. So, from a performance point of view, queries which would even be impossible to perform with a standard relational database take no more than a couple of seconds with Bio4j.

Bio4j is in active development and grows rapidly: it includes now 1,216,993,547 relationships and 190,625,351 nodes, which is close to triplicating the figures from one year ago. A flexible module system based on Statika is provided with Bio4j enabling the user to build and deploy only the modules needed for the analysis.

Bio4j is now based on an abstract domain model which decoupling the inner database implementation from the relationships among entities themselves. This allowed us to have a default implementation using Blueprints, the de-facto standard for graph data modeling, thus making the domain model independent from the choice of database technology. Building on that, we now offer binary distributions for Neo4j and TitanDB backends, yielding a dramatic increase of performance using the backend-specific optimizations, such as vertex-local edge-typed indexes in TitanDB for instance.

Bio4j is open source, available under the AGPLv3 license.
Income distribution patterns from a complete social security database
Creators: name: Derzsy, N.
name: Neda, Z.
name: Santos, M. A.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Statistical Finance (q-fin.ST)
subject: FOS: Physical sciences
subject: FOS: Economics and business

description: We analyze the income distribution of employees for 9 consecutive years (2001-2009) using a complete social security database for an economically important district of Romania. The database contains detailed information on more than half million taxpayers, including their monthly salaries from all employers where they worked. Besides studying the characteristic distribution functions in the high and low/medium income limits, the database allows us a detailed dynamical study by following the time-evolution of the taxpayers income. To our knowledge, this is the first extensive study of this kind (a previous japanese taxpayers survey was limited to two years). In the high income limit we prove once again the validity of Pareto's law, obtaining a perfect scaling on four orders of magnitude in the rank for all the studied years. The obtained Pareto exponents are quite stable with values around $α\approx 2.5$, in spite of the fact that during this period the economy developed rapidly and also a financial-economic crisis hit Romania in 2007-2008. For the low and medium income category we confirmed the exponential-type income distribution. Following the income of employees in time, we have found that the top limit of the income distribution is a highly dynamical region with strong fluctuations in the rank. In this region, the observed dynamics is consistent with a multiplicative random growth hypothesis. Contrarily with previous results obtained for the japanese employees, we find that the logarithmic growth-rate is not independent of the income.
description: 10 pages, 7 Figures
Regulation of ethylene biosynthesis and its possible role in phenotypic plasticity in Stellaria longipes
Creators: name: Kathiresan, Arumugam
Publisher: name: University of Calgary
Year: 1997
Subjects: subject: QK981.3.K38 1997
subject: Plant biochemical genetics
subject: Plants - Evolution
subject: Stellaria

description: Bibliography: p. 203-229.
Supporting material for "Ensemble flow reconstruction in the atmospheric boundary layer from spatially limited measurements through latent diffusion models"
Creators: name: Rybchuk, Alex
name: Hassanaly, Malik
name: Hamilton, Nicholas
name: Doubrawa, Paula
name: Fulton, Mitchell
name: Martínez-Tossas, Luis A.
Publisher: name: Zenodo
Year: 2023

description: In addition to the code for our manuscript, here we upload two large files associated with our manuscript. `data.zip` contains a truncated dataset that the LDM was trained on. `models.zip` contains the training checkpoints that were used for the autoencoder and the diffusion model.
Analytical and experimental studies of the stability limits of nonpremixed flames in a co-flowing stream
Creators: name: Karbassi, Massoumeh
Publisher: name: University of Calgary
Year: 1997
Subjects: subject: TP254.5.K37 1997
subject: Combustion - Analysis
subject: Combustion engineering
subject: Combustion gases

description: Bibliography: p. 190-203.
Deconfinement vs. chiral symmetry and higher representation matter
Creators: name: Kähärä, T.
name: Ruggieri, M.
name: Tuominen, K.
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: The interplay of deconfinement and chiral symmetry restoration are considered in terms of effective theories. We generalize the earlier model studies by considering fermions in higher representations, and study the finite temperature phase diagrams of SU(2) and SU(3) gauge theories with two fermion flavors in fundamental, adjoint or two-index symmetric representations. We discuss our results in relation to recent lattice simulations on these theories and outline possible applications in the context of dynamical electroweak symmetry breaking.
description: 13 pages, 6 figures
Mode conversion of radiatively damped magnetogravity waves in the solar chromosphere
Creators: name: Newington, Marie E.
name: Cally, Paul S.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Modelling of adiabatic gravity wave propagation in the solar atmosphere showed that mode conversion to field guided acoustic waves or Alfvén waves was possible in the presence of highly inclined magnetic fields. This work aims to extend the previous adiabatic study, exploring the consequences of radiative damping on the propagation and mode conversion of gravity waves in the solar atmosphere. We model gravity waves in a VAL-C atmosphere, subject to a uniform, and arbitrarily orientated magnetic field, using the Newton cooling approximation for radiatively damped propagation. The results indicate that the mode conversion pathways identified in the adiabatic study are maintained in the presence of damping. The wave energy fluxes are highly sensitive to the form of the height dependence of the radiative damping time. While simulations starting from 0.2 Mm result in modest flux attenuation compared to the adiabatic results, short damping times expected in the low photosphere effectively suppress gravity waves in simulations starting at the base of the photosphere. It is difficult to reconcile our results and observations of propagating gravity waves with significant energy flux at photospheric heights unless they are generated in situ, and even then, why they are observed to be propagating as low as 70 km where gravity waves should be radiatively overdamped.
description: 9 pages, 10 figures, accepted for publication in MNRAS (June 27 2011)
Pathways And Genes Under Positive Selection In Metabolic Diseases
Creators: name: Vatsiou Alexandra
Publisher: name: Zenodo
Year: 2015

description: Uncovering signatures of positive selection has been a long-standing interest in the field of genomics. The high prevalence of metabolic diseases such as diabetes has been suggested to be associated with positive selective pressures. Advantageous alleles increase in frequency and linked surrounding deleterious mutations rise in frequency as well, therefore the high prevalence of many diseases. High-density SNP maps of the human genome enable us to look for such regions involved in the susceptibility to diseases, particularly diabetes, obesity and metabolic syndrome. Firstly, we conduct a sensitivity analysis to evaluate the performance of several existing methods to detect positive selection. Out of the 7 methods (EHHST, XPEHHST, XP-EHH, iHS, nSL, XPCLR and hapFLK) that were compared under various demographic scenarios, XPCLR and iHS were found to perform best. These two methods were used for a genome scan of the HapMap Phase II database. Based on these results, we carried out an enrichment analysis to uncover signals enriched for positive selection. Two methods to conduct the enrichment analysis were used: the SUMSTAT statistic and Gowinda, an already available tool. String, Intact and Bio4j databases were also used to extract information about possible Protein-Protein Interactions associated with the ‘interesting genes’. Our results indicate that selection has affected in a large percentage the evolution of diseases in the human history. More specifically, 64 pathways were discovered to have undergone selection and a total of 16 positively selected genes were found to have a direct or indirect links with diabetes, obesity or metabolic syndrome.
description: http://epidemiology.conferenceseries.com/abstract/2015/pathways-and-genes-under-positive-selection-in-metabolic-diseases
Macro-FF: Improving AI Planning with Automatically Learned Macro-Operators
Creators: name: Botea, A.
name: Enzenberger, M.
name: Mueller, M.
name: Schaeffer, J.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Despite recent progress in AI planning, many benchmarks remain challenging for current planners. In many domains, the performance of a planner can greatly be improved by discovering and exploiting information about the domain structure that is not explicitly encoded in the initial PDDL formulation. In this paper we present and compare two automated methods that learn relevant information from previous experience in a domain and use it to solve new problem instances. Our methods share a common four-step strategy. First, a domain is analyzed and structural information is extracted, then macro-operators are generated based on the previously discovered structure. A filtering and ranking procedure selects the most useful macro-operators. Finally, the selected macros are used to speed up future searches. We have successfully used such an approach in the fourth international planning competition IPC-4. Our system, Macro-FF, extends Hoffmanns state-of-the-art planner FF 2.3 with support for two kinds of macro-operators, and with engineering enhancements. We demonstrate the effectiveness of our ideas on benchmarks from international planning competitions. Our results indicate a large reduction in search effort in those complex domains where structural information can be inferred.
Enhanced H2O formation through dust grain chemistry in X-ray exposed environments
Creators: name: Meijerink, R.
name: Cazaux, S.
name: Spaans, M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The ULIRG Mrk 231 exhibits very strong water rotational lines between λ= 200-670μm, comparable to the strength of the CO rotational lines. High redshift quasars also show similar CO and H2O line properties, while starburst galaxies, such as M82, lack these very strong H2O lines in the same wavelength range, but do show strong CO lines. We explore the possibility of enhancing the gas phase H2O abundance in X-ray exposed environments, using bare interstellar carbonaceous dust grains as a catalyst. Cloud-cloud collisions cause C and J shocks, and strip the grains of their ice layers. The internal UV field created by X-rays from the accreting black hole does not allow to reform the ice. We determine formation rates of both OH and H2O on dust grains, having temperature T_dust=10-60 K, using both Monte Carlo as well as rate equation method simulations. The acquired formation rates are added to our X-ray chemistry code, that allows us to calculate the thermal and chemical structure of the interstellar medium near an active galactic nucleus. We derive analytic expressions for the formation of OH and H2O on bare dust grains as a catalyst. Oxygen atoms arriving on the dust are released into the gas phase under the form of OH and H2O. The efficiencies of this conversion due to the chemistry occurring on dust are of order 30 percent for oxygen converted into OH and 60 percent for oxygen converted into H_2O between T_dust=15-40 K. At higher temperatures, the efficiencies rapidly decline. When the gas is mostly atomic, molecule formation on dust is dominant over the gas-phase route, which is then quenched by the low H2 abundance. Here, it is possible to enhance the warm (T> 200 K) water abundance by an order of magnitude in X-ray exposed environments. This helps to explain the observed bright water lines in nearby and high-redshift ULIRGs and Quasars.
description: 13 pages, 8 figures, accepted by A&A
Signals Enriched For Positive Selection
Creators: name: Vatsiou Alexandra
name: Bazin Eric
name: Gaggiotti Oscar
Publisher: name: Zenodo
Year: 2014

description: Abstract: Motivation: The identification of genetic variations that contribute to a genetic disease remains a major challenge in the research in human genetics. One of the factors that could have shaped the genetic diversity in a population is natural selection. Many studies investigate the effects of mutations and genes in the phenotype independently and therefore do not consider for large functional and gemonic effects that could originate from multiple small ones. Assessing and analyzing large-scale genomic data based on the gene sets level or in the network of gene-sets could provide further biological insight. Our objective in this work is to detect signals enriched for positive selection in the biological pathway level that could improve our knowledge in the biological interpretation of these effects. Methods & Results: We used the HapMap data phase II for genetic data http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2007-08_rel22/, the human genes from coding regions from the Entrez NCBI database (data downloaded on 5/2014) and the human pathways from the Biosystems database http://www.ncbi.nlm.nih.gov/biosystems (data downloaded on 5/2014). The analysis consists of the following steps: 1. Analyze the haplotype and SNP data using a composite likelihood method to test for positive selection between populations. The method XPCLR was chosen as it was proved to detect the wider range of signals over other methods (Vatsiou et al. in prep). Three comparisons were conducted: a. CEU-YRI, b. CEU-CHB/JTP and c. YRI-CHB/JTP. 2. Match the SNPs to 27081 genes according to their start and end position that were extracted from the Entrez database. We also included 50kb upstream or downstream away from the gene to account for intergenic regions. 3. We considered the highest XPCLR normalized score as the representative of the whole gene. A further normalization though was made to account for genes with large number of SNPs. 4. We tested for enrichment signals for positive selection calculating the sum of all the scores in each of the gene sets (total number of gene sets: 2362) and we estimated the significance taking into account the different gene set sizes. Conclusions: It is about to be shown the exact signals we observe from the human genome pathways and the way that they could possibly be involved in adaptation events. Even though many enrichment analysis have been conducted before (Daud et al. 2013), our study will possibly reveal more biological pathways enriched for positive selection as we are mainly based on pairwise comparisons between populations using XPCLR, and such an analysis has not yet been considered.
description: http://eccb14.loria.fr/poster_proceedings/poster_proc_track_F.pdf
title: Exploratory vocabulary collection session (speaker M28; Labai dialect)
title: Séance exploratoire d'enquête de vocabulaire
Creators: name: Michaud, Alexis
Publisher: name: Pangloss
Year: 2013
Subjects: subject: Linguistique
subject: Na

description: Work with Lamu Gatusa only extended over two sessions, on August 11th and August 12th, 2009. The second session was recorded. This is an exploratory elicitation session: the items were transcribed as they were being said; the speaker and the investigator discussed in Chinese over the meaning of words, cases of homophony, issues of transcription, and so on. The purpose was to devise a first version of a transcription system in the International Phonetic Alphabet, which Mr. Lamu would then use (and develop further) for transcribing Na stories, proverbs and rituals and preparing annotated bilingual editions. A note about Mr. Lamu Gatusa's name: his name in Na is /lɑ˧mbv˧ kɤ˧tʰv˥sɑ˥/. The phonetic approximation of this Na name in Mandarin Chinese is Lamu Gatusa (Chinese characters: 拉木•嘎吐萨). His pen-name is 石高峰: Shi Gaofeng.
Parish rationalisation : A case study of the effects the clustering of three Catholic parishes has had on the Religious Education Curricula of the parish primary schools
Creators: name: Waldron, Peter
Publisher: name: Australian Catholic University
Year: 2001
Subjects: Catholic parishes
religious education
Catholic education
primary schools
Catholic Church

description: The study sets out to examine the impact of the clustering on the relationship between the individual school and the Parish Priest, on the relationship between the individual schools, and on the relationship between the schools and their parish communities. It seeks to propose findings and recommendations to assist similar initiatives in Australia and beyond.
Comparison Of Haplotype Methods To Detect Selection
Creators: name: Vatsiou Alexandra
name: Bazin Eric
name: Gaggiotti Oscar
Publisher: name: Zenodo
Year: 2013

description: Motivation: The main topic of research in human genetics is the identification of genes and mutations that contribute to a genetic disease. One of the factors that can influence the genetic diversity in a population is natural selection. In this work, we will compare the existing long-range haplotype methods to detect selection. Our primary objective is to obtain a clear view about their power and validity under complex demographic scenarios. Methods & Results: Literature review: A systematic review that was conducted revealed five haplotype methods with available software to identify loci that have undergone selection. The five methods are the following: LRH (Sabeti, 2002; Nature 419:832-837), iHS (Voight, 2006; PLos Biol 4:72), xp-EHH (Sabeti, 2007; Nature 449:913-8), EHHST (Zhong, 2010; Hum Genet 18:1148-59) and xp-EHHST (Zhong, 2011; Stat & Its Interface 4:51–63). All of them used simulations to test their performance with the ms (Hudson, 2002; Bioinf 18:337-8) and SelSim programs (Spencer, 2004; Bioinf 20:3673-5). Sensitivity Analysis: Ms program can consider different demographic models, without selection and SelSim provides simulations under natural selection with a simple population structure. To determine the best method, we will generate simulated data using SimuPOP. SimuPOP is a forward-in-time simulation program that can construct models with selection under complex evolutionary scenarios. We will begin with an island model, a stepping stone model incorporating an environmental gradient and more complex scenarios including a hierarchically structured population. Conclusions: We will thoroughly investigate their behavior under complex scenarios. Our study sets the basis to identify the advantages and disadvantages of each method under each modeling assumption. Here, we restrict ourselves to the comparison of the methods but an extension to a model to detect selection to N populations could be developed at a later stage.
description: http://www.eseb2013.com/delegates/avatsiou
Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1
Creators: name: Zhang, Yue
name: Soubias, Olivier
name: Pant, Shashank
name: Heinrich, Frank
name: Vogel, Alexander
name: Li, Jess
name: Li, Yifei
name: Clifton, Luke A.
name: Daum, Sebastian
name: Bacia, Kirsten
name: Huster, Daniel
name: Randazzo, Paul A.
name: Lösche, Mathias
name: Tajkhorshid, Emadeddin
name: Byrd, R. Andrew
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 2023
Subjects: subject: 610

description: ADP-ribosylation factor 1 (Arf1) interacts with multiple cellular partners and membranes to regulate intracellular traffic, organelle structure and actin dynamics. Defining the dynamic conformational landscape of Arf1 in its active form, when bound to the membrane, is of high functional relevance and key to understanding how Arf1 can alter diverse cellular processes. Through concerted application of nuclear magnetic resonance (NMR), neutron reflectometry (NR) and molecular dynamics (MD) simulations, we show that, while Arf1 is anchored to the membrane through its N-terminal myristoylated amphipathic helix, the G domain explores a large conformational space, existing in a dynamic equilibrium between membrane-associated and membrane-distal conformations. These configurational dynamics expose different interfaces for interaction with effectors. Interaction with the Pleckstrin homology domain of ASAP1, an Arf-GTPase activating protein (ArfGAP), restricts motions of the G domain to lock it in what seems to be a conformation exposing functionally relevant regions.
The X-factor in Galaxies: I. Dependence on Environment and Scale
Creators: name: Feldmann, Robert
name: Gnedin, Nickolay Y.
name: Kravtsov, Andrey V.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Characterizing the conversion factor between CO emission and column density of molecular hydrogen, X_CO, is crucial in studying the gaseous content of galaxies, its evolution, and relation to star formation. In most cases the conversion factor is assumed to be close to that of giant molecular clouds (GMCs) in the Milky Way, except possibly for mergers and star-bursting galaxies. However, there are physical grounds to expect that it should also depend on the gas metallicity, surface density, and strength of the interstellar radiation field. The XCO factor may also depend on the scale on which CO emission is averaged due to effects of limited resolution. We study the dependence of X_CO on gas properties and averaging scale using a model that is based on a combination of results of sub-pc scale magneto-hydrodynamic simulations and on the gas distribution from self-consistent cosmological simulations of galaxy formation. Our model predicts a value of X_CO that is consistent with the Galactic value for interstellar medium conditions typical for the Milky Way. For such conditions the predicted X_CO varies by only a factor of two for gas surfaced densities in the range \sim 50 - 500 M_sun / pc^2. However, the model also predicts that more generally on the scale of GMCs, X_CO is a strong function of metallicity, and depends on the column density and the interstellar UV flux. We show explicitly that neglecting these dependencies in observational estimates can strongly bias the inferred distribution of H2 column densities of molecular clouds to have a narrower and offset range compared to the true distribution. We find that when averaged on \sim kpc scales the X-factor depends only weakly on radiation field and column density, but is still a strong function of metallicity. The predicted metallicity dependence can be approximated as X_CO \sim Z^{-γ} with γ ~ 0.5 - 0.8.
description: 23 pages, 14 figures, revised version following referee report, APJ submitted