cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
IMPaCT-Data Biomedical Cloud: An initial iteration for a federated virtual computing environment in the context of precision medicine in Spain
Creators: name: Chavero-Díez, María
name: Fernández, Jose María
name: Codó, Laia
name: López, Lidia
name: Capella-Gutierrez, Salvador
name: Gelpí, Josep Lluis
name: IMPaCT-Data WP2
Publisher: name: F1000 Research Limited
Year: 2022

description: The Spanish Precision Medicine Infrastructure associated with Science and Technology (IMPaCT), aims to lay the foundations for impulsing precision medicine within the Spanish National Health System. IMPaCT revolves around three main pillars: predictive medicine, data science and genomic medicine.

 As part of the Data Science program, the IMPaCT-Data Biomedical Cloud is being established for providing a scalable and flexible analysis environment, enabling the integration, management and analysis of structured clinical, richly described genomic and annotated medical imaging data available within IMPaCT.

 The infrastructure is designed as a federated cloud system resultant from the interconnection of an increasing number of research organizations functioning under coordinated policies. The infrastructure components include a Life-Sciences-ID-compliant federated authentication system, a data infrastructure to manage public datasets and prospectively sensitive data (leveraging EGA technologies), and a distributed set of computational resources offering platforms like Galaxy, among others. IMPaCT-Data Biomedical Cloud will benefit from services like bio.tools, BioContainers, WorkflowHub and OpenEBench for proper software management and evaluation.

 IMPaCT-Data Biomedical Cloud main objective is to provide a platform as a service that enables the management of resources, and exchange of controlled datasets in their lawful limits, delivering services for data applications and analysis for research and clinical personnel with any kind of experience with information technologies.
Ensemble renormalization group for the random field hierarchical model
Creators: name: Decelle, Aurélien
name: Parisi, Giorgio
name: Rocchi, Jacopo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The Renormalization Group (RG) methods are still far from being completely understood in quenched disordered systems. In order to gain insight into the nature of the phase transition of these systems, it is common to investigate simple models. In this work we study a real-space RG transformation on the Dyson hierarchical lattice with a random field, which led to a reconstruction of the RG flow and to an evaluation of the critical exponents of the model at T = 0. We show that this method gives very accurate estimations of the critical exponents, by comparing our results with the ones obtained by some of us using an independent method.
Post-Brexit, post-Covid-19, which EU citizens are at risk of deportation?
Creators: name: , Morgan
name: , Radziwinowiczówna
Publisher: name: Zenodo
Year: 2020

description: Justice Gap post explaining that with the end of Brexit transition period and with Covid-19 homeless people and other Europeans who fail to live up to the ideal of the ‘good migrant’ are likely to be targeted with enforced removals from the UK.
High-field spectroscopy of singlet-triplet transitions in the spin-dimer systems Sr3Cr2O8 and Ba3Cr2O8
Creators: name: Wang, Zhe
name: Kamenskyi, D.
name: Cépas, O.
name: Schmidt, M.
name: Quintero-Castro, D. L.
name: Islam, A. T. M. N.
name: Lake, B.
name: Aczel, A. A.
name: Dabkowska, H. A.
name: Dabkowski, A. B.
name: Luke, G. M.
name: Wan, Yuan
name: Loidl, A.
name: Ozerov, M.
name: Wosnitza, J.
name: Zvyagin, S. A.
name: Deisenhofer, J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Magnetic excitations in the isostructural spin-dimer systems Sr3Cr2O8 and Ba3Cr2O8 are probed by means of high-field electron spin resonance at sub-terahertz frequencies. Three types of magnetic modes were observed. One mode is gapless and corresponds to transitions within excited states, while two other sets of modes are gapped and correspond to transitions from the ground to the first excited states. The selection rules of the gapped modes are analyzed in terms of a dynamical Dzyaloshinskii-Moriya interaction, suggesting the presence of phonon-assisted effects in the low-temperature spin dynamics of Sr3Cr2O8 and Ba3Cr2O8
description: 6 pages, 4 figures, all comments are welcome and appreciated
Anderson Localization at the Subwavelength Scale and Loss Compensation for Surface-Plasmon Polaritons in Disordered Arrays of Metallic Nanowires
Creators: name: Shi, Xianling
name: Chen, Xianfeng
name: Malomed, Boris A.
name: Panoiu, Nicolae C.
name: Ye, Fangwei
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: Using a random array of coupled metallic nanowires as a generic example of disordered plasmonic systems, we demonstrate that the structural disorder induces localization of light in these nanostructures at a deep-subwavelength scale. The ab initio analysis is based on solving the complete set of 3D Maxwell equations. We find that random variations of the radius of coupled plasmonic nanowires are sufficient to induce the Anderson localization (AL) of surface-plasmon polaritons (SPPs), the size of these trapped modes being significantly smaller than the wavelength. Remarkably, the optical-gain coefficient, needed to compensate losses in the plasmonic components of the system, is much smaller than the loss coefficient of the metal, which is obviously beneficial for the realization of the AL in plasmonic nanostructures. The dynamics of excitation and propagation of the Anderson-localized SPPs are addressed too.
description: 5 pages, 4 figures, to appear in Phys. Rev. B
Chemically-exfoliated single-layer MoS$_2$ : stability, lattice dynamics and catalytic adsorption from first principles
Creators: name: Calandra, Matteo
Publisher: name: arXiv
Year: 2013
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Chemically and mechanically exfoliated MoS$_2$ single-layer samples have substantially different properties. While mechanically exfoliated single-layers are mono-phase (1H polytype with Mo in trigonal prismatic coordination), the chemically exfoliated samples show coexistence of three different phases, 1H, 1T (Mo in octahedral coordination) and 1T$^{'}$ (a distorted $2\times 1$ 1T-superstructure). By using first-principles calculations, we investigate the energetics and the dynamical stability of the three phases. We show that the 1H phase is the most stable one, while the metallic 1T phase, strongly unstable, undergoes a phase transition towards a metastable and insulating 1T$^{'}$ structure composed of separated zig-zag chains. We calculate electronic structure, phonon dispersion, Raman frequencies and intensities for the 1T$^{'}$ structure. We provide a microscopical description of the J$_1$, J$_2$ and J$_3$ Raman features first detected more then $20$ years ago, but unexplained up to now. Finally, we show that H adsorbates, that are naturally present at the end of the chemical exfoliation process, stabilize the 1T$^{\prime}$ over the 1H one.
description: 7 Pages, 8 Pictures, To appear on Phys. Rev. B
Exploring new varieties and applications of trophic cascades using pond species interaction experiments and theory
Creators: name: Rakowski, Chase J.
Publisher: name: The University of Texas at Austin
Year: 2023
Subjects: Biodiversity
Food webs
Algae
Plankton
Intraguild predation
Stability
Wastewater algal cultivation
Biocontrol

description: Global change is altering the diversity, composition, and interactions of predator species even more rapidly than those of lower trophic levels. While many of the most important ecosystem functions and services such as primary production are provided by bottom trophic levels, we know from the classic trophic cascade concept that these ecosystem properties can be strongly impacted by predators via chains of species interactions. However, the relationships between changing attributes of predator communities and these key ecosystem properties at the base of the food web remain unclear. I identify three ways that the trophic cascade concept can be expanded to help fill this knowledge gap. First, ecologists can assess cascading consequences of changes in predator diversity or interactions rather than the less realistic addition or removal of entire top trophic levels. Second, trophic cascade research can move away from an equilibrium approach to incorporate the food web dynamics that determine ecosystem stability. Third, there is understudied potential for the application of trophic cascade theory to improving environmental technologies involving the cultivation of microalgae. In Chapter One I experimentally test the effects of insect predator diversity on the central tendency and variability of pond plankton biomass. I find that the insect species better suppress their collective zooplankton prey when together, leading to less variable phytoplankton biomass. In Chapter Two I analyze a food web model to explore the influence of the degree of intraguild predation on the variability of biomass of lower trophic levels. I show that stronger intraguild predation is associated with biomass fluctuations throughout the food web. Finally, in Chapter Three I experimentally show that fish can provide effective biological control in wastewater algal raceway ponds, increasing algal biomass though not necessarily improving nutrient removal from the wastewater. Overall, the present dissertation describes two novel varieties of trophic cascades and expands upon a new application. These links between the top and bottom ends of food webs predict consequential effects of changes in predator communities, and they also suggest strategies for ecosystem management in pursuit of reliable ecosystem services.
MUQADDAS QADAMJOLAR SAMARQAND SHAHRINING TARIXIY TOPONOMIYASINING MUHIM TARKIBIY QISMI
Creators: name: Tursunov, Javlonbek
Publisher: name: Zenodo
Year: 2023

description: Samarqand toponimiyasi deganda, viloyatning hozirgi hududi bilan bog'liq nomlarni tushunamiz (tarixan viloyatning hududiy-ma'muriy chegaralari turlicha bo'lgan). O'rta Zarafshon vodiysi qadimiy Sug'dning markaziy qismini tashkil qilib, jahon svilizatsiyasida o'ziga xos o'rin tutadi. Ammo turli tarixiy davrlarda Samarqand va unga tegishli regionlar hududi o'zgarib turgan. Siyosiy- iqtisodiy munosabatlar bilan bog'liq bu holat viloyat toponimiyasini o'rganish, material tanlash, ularni qiyosiy tadqiq qilishda muhimdir. Mazkur maqolada muqaddas qadamjolarning Samarqand shahri tarixiy toponimiyasidagi ahamiyati ko`rib chiqiladi.
A Quantitative Analysis of Digital Scholarly Editions
Creators: name: Kurzmeier, Michael
name: O'Sullivan, James
name: Murphy, Órla
name: Pidd, Michael
name: Wessels, Bridgette
Publisher: name: Zenodo
Year: 2023
Subjects: Digital Scholarly Edition
Interview
History
Aufzeichnung
Sprache
Metadaten
Forschungsprozess
DHd2023

description: Eine Posterpräsentation auf der 9. Tagung des Verbands "Digital Humanities im deutschsprachigen Raum" - DHd 2023 Open Humanities Open Culture
Observing Through Wavy Water Surface： Reconstruction the distortion-free image from a distorted video sequcence.
Creators: name: jian, bijian
Publisher: name: figshare
Year: 2022
Subjects: subject: 80104 Computer Vision
subject: FOS: Computer and information sciences
subject: 80106 Image Processing
subject: 80607 Information Engineering and Theory
subject: 80201 Analysis of Algorithms and Complexity

description: We propose an efficient image restoration scheme for the distorted by wavy water surface. The scheme can be used for underwater target detection, coastal target monitoring, and marine biological research.
BiSON data preparation: A correction for differential extinction and the weighted averaging of contemporaneous data
Creators: name: Davies, G. R.
name: Chaplin, W. J.
name: Elsworth, Y.
name: Hale, S. J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The Birmingham Solar Oscillations Network (BiSON) has provided high-quality high-cadence observations from as far back in time as 1978. These data must be calibrated from the raw observations into radial velocity and the quality of the calibration has a large impact on the signal-to-noise ratio of the final time series. The aim of this work is to maximise the potential science that can be performed with the BiSON data set by optimising the calibration procedure. To achieve better levels of signal-to-noise ratio we perform two key steps in the calibration process: we attempt a correction for terrestrial atmospheric differential extinction; and the resulting improvement in the calibration allows us to perform weighted averaging of contemporaneous data from different BiSON stations. The improvements listed produce significant improvement in the signal-to-noise ratio of the BiSON frequency-power spectrum across all frequency ranges. The reduction of noise in the power spectrum will allow future work to provide greater constraint on changes in the oscillation spectrum with solar activity. In addition, the analysis of the low-frequency region suggests we have achieved a noise level that may allow us to improve estimates of the upper limit of g-mode amplitudes.
description: Accepted for publication in MNRAS; 10 pages, 7 figures
Wijsman hyperspaces of non-separable metric spaces
Creators: name: Hernández-Gutiérrez, Rodrigo
name: Szeptycki, Paul
Publisher: name: arXiv
Year: 2013
Subjects: subject: General Topology (math.GN)
subject: FOS: Mathematics
subject: 54B20, 54D15

description: Given a metric space $\langle X,ρ\rangle$, consider its hyperspace of closed sets $CL(X)$ with the Wijsman topology $τ_{W(ρ)}$. It is known that $\langle{CL(X),τ_{W(ρ)}}\rangle$ is metrizable if and only if $X$ is separable and it is an open question by Di Maio and Meccariello whether this is equivalent to $\langle{CL(X),τ_{W(ρ)}}\rangle$ being normal. In this paper we prove that if the weight of $X$ is a regular uncountable cardinal and $X$ is locally separable, then $\langle{CL(X),τ_{W(ρ)}}\rangle$ is not normal. We also solve some questions by Cao, Junnilla and Moors regarding isolated points in Wijsman hyperspaces.
Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion
Creators: name: Jeon, J. -H.
name: Chechkin, A. V.
name: Metzler, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: Anomalous diffusion is frequently described by scaled Brownian motion (SBM), a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is $\langle x^2(t)\rangle\simeq\mathscr{K}(t)t$ with $\mathscr{K}(t)\simeq t^{α-1}$ for $0
description: 7 pages, 5 figures
Missing Burns in the High Northern Latitudes: The Case for Regionally Focused Burned Area Products
Creators: name: Chen, Dong
name: Shevade, Varada
name: Baer, Allison
name: Loboda, Tatiana V.
Publisher: name: MDPI
Year: 2021
Subjects: wildfire
disturbance
Arctic
boreal forests
tundra
MODIS
burned area products
Alaska
Canada

description: Global estimates of burned areas, enabled by the wide-open access to the standard data products from the Moderate Resolution Imaging Spectroradiometer (MODIS), are heavily relied on by scientists and managers studying issues related to wildfire occurrence and its worldwide consequences. While these datasets, particularly the MODIS MCD64A1 product, have fundamentally improved our understanding of wildfire regimes at the global scale, their performance may be less reliable in certain regions due to a series of region- or ecosystem-specific challenges. Previous studies have indicated that global burned area products tend to underestimate the extent of the burned area within some parts of the boreal domain. Despite this, global products are still being regularly used by research activities and management efforts in the northern regions, likely due to a lack of understanding of the spatial scale of their Arctic-specific limitations, as well as an absence of more reliable alternative products. In this study, we evaluated the performance of two widely used global burned area products, MCD64A1 and FireCCI51, in the circumpolar boreal forests and tundra between 2001 and 2015. Our two-step evaluation shows that MCD64A1 has high commission and omission errors in mapping burned areas in the boreal forests and tundra regions in North America. The omission error overshadows the commission error, leading to MCD64A1 considerably underestimating burned areas in these high northern latitude domains. Based on our estimation, MCD64A1 missed nearly half the total burned areas in the Alaskan and Canadian boreal forests and the tundra during the 15-year period, amounting to an area (74,768 km2) that is equivalent to the land area of the United States state of South Carolina. While the FireCCI51 product performs much better than MCD64A1 in terms of commission error, we found that it also missed about 40% of burned areas in North America north of 60° N between 2001 and 2015. Our intercomparison of MCD64A1 and FireCCI51 with a regionally adapted MODIS-based Arctic Boreal Burned Area (ABBA) shows that the latter outperforms both MCD64A1 and FireCCI51 by a large margin, particularly in terms of omission error, and thus delivers a considerably more accurate and consistent estimate of fire activity in the high northern latitudes. Considering the fact that boreal forests and tundra represent the largest carbon pool on Earth and that wildfire is the dominant disturbance agent in these ecosystems, our study presents a strong case for regional burned area products like ABBA to be included in future Earth system models as the critical input for understanding wildfires’ impacts on global carbon cycling and energy budget.
Data for "Machine learning-based sampling of virtual experiments within the full stress state to identify parameters of anisotropic yield models"
Creators: name: Wessel, Alexander
name: Morand, Lukas
name: Butz, Alexander
name: Helm, Dirk
name: Volk, Wolfram
Publisher: name: Fraunhofer-Gesellschaft
Year: 2022
Subjects: subject: yield condition
subject: anisotropic material,
subject: crystal plasticity
subject: machine learning
subject: adaptive sampling
subject: 620 Ingenieurwissenschaften und zugeordnete Tätigkeiten
subject: 531 Klassische Mechanik, Festkörpermechanik
subject: 672 Eisen, Stahl, andere Eisenlegierungen

description: Data for "Machine learning-based sampling of virtual experiments within the full stress state to identify parameters of anisotropic yield models" by A. Wessel, L. Morand, A. Butz, D. Helm and W. Volk.
The effect of Coulomb interactions on thermoelectric properties of quantum dots
Creators: name: Zimbovskaya, Natalya A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Thermoelectric effects in a quantum dot coupled to the source and drain charge reservoirs are explored using a nonequilibrium Green's functions formalism beyond the Hartree-Fock approximation. Thermal transport is analyzed within a linear response regime. A transition from Coulomb blockade regime to Kondo regime in thermoelectric transport through a single-level quantum dot is traced using unified approximations for the relevant Green's functions.
description: 6 pages, 3 figures
Condition-Specific Competitive Effects of the Invasive Mosquito Aedes albopictus on the Resident Culex pipiens among Different Urban Container Habitats May Explain Their Coexistence in the Field
Creators: name: Leisnham, Paul T.
name: LaDeau, Shannon L.
name: Saunders, Megan E. M.
name: Villena, Oswaldo C.
Publisher: name: MDPI
Year: 2021
Subjects: biological invasion
interspecific competition
mosquitoes
trash
urban greenscape
West Nile virus

description: Condition-specific competition, when environmental conditions alter the outcome of competition, can foster the persistence of resident species after the invasion of a competitively superior invader. We test whether condition-specific competition can facilitate the areawide persistence of the resident and principal West Nile virus vector mosquito Culex pipiens with the competitively superior invasive Aedes albopictus in water from different urban container habitats. (2) Methods: We tested the effects of manipulated numbers of A. albopictus on C. pipiens’ survival and development in water collected from common functional and discarded containers in Baltimore, MD, USA. The experiment was conducted with typical numbers of larvae found in field surveys of C. pipiens and A. albopictus and container water quality. (3) Results: We found increased densities of A. albopictus negatively affected the survivorship and development of C. pipiens in water from discarded containers but had little effect in water from functional containers. This finding was driven by water from trash cans, which allowed consistently higher C. pipiens’ survival and development and had greater mean ammonia and nitrate concentrations that can promote microbial food than other container types. (4) Conclusions: These results suggest that the contents of different urban containers alter the effects of invasive A. albopictus competition on resident C. pipiens, that trash cans, in particular, facilitate the persistence of C. pipiens, and that there could be implications for West Nile virus risk as a result.
Density Functional Theory for Chiral Nematic Liquid Crystals
Creators: name: Belli, S.
name: Dussi, S.
name: Dijkstra, M.
name: van Roij, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Even though chiral nematic phases were the first liquid crystals experimentally observed more than a century ago, the origin of the thermodynamic stability of cholesteric states is still unclear. In this Letter we address the problem by means of a novel density functional theory for the equilibrium pitch of chiral particles. When applied to right-handed hard helices, our theory predicts an entropy-driven cholesteric phase, which can be either right- or left-handed, depending not only on the particle shape but also on the thermodynamic state. We explain the origin of the chiral ordering as an interplay between local nematic alignment and excluded-volume differences between left- and right-handed particle pairs.
ON THE PRODUCTION OF SEVERE CONVECTIVE STORM ENVIRONMENTS IN NORTH AND SOUTH AMERICA
Creators: name: Li, Funing
Publisher: name: Purdue University Graduate School
Year: 2023
Subjects: classificationCode: 370199
subject: Atmospheric sciences not elsewhere classified

description: This is a dissertation by Funing Li submitted to the Faculty of Purdue University in partial fulfillment of the requirements for the degree of Doctor of Philosophy.
Mobility-Dependent Selection of Competing Strategy Associations
Creators: name: Dobrinevski, Alexander
name: Alava, Mikko
name: Reichenbach, Tobias
name: Frey, Erwin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences

description: Standard models of population dynamics focus on the the interaction, survival, and extinction of the competing species individually. Real ecological systems, however, are characterized by an abundance of species (or strategies, in the terminology of evolutionary-game theory) that form intricate, complex interaction networks. The description of the ensuing dynamics may be aided by studying associations of certain strategies rather than individual ones. Here we show how such a higher-level description can bear fruitful insight. Motivated from different strains of colicinogenic Escherichia coli bacteria, we investigate a four-strategy system which contains a three-strategy cycle and a neutral alliance of two strategies. We find that the stochastic, spatial model exhibits a mobility-dependent selection of either the three-strategy cycle or of the neutral pair. We analyze this intriguing phenomenon numerically and analytically.
description: 9 pages, six figures; accepted in Physical Review E
Beacon Network goes v2
Creators: name: Repchevsky, Dmitry
name: Baudis, Michael
name: Aguiló-Castillo, Sergi
name: Kataja, Teemu
name: Muilu, Ville
name: Singh, Babita
name: Bruchner, Dominik
name: Törmroos, Juha
name: Rambla, Jordi
name: Fromont, Lauren A.
name: J. Dylan Spalding
name: Gelpí, Josep Lluís
name: Capella-Gutierrez, Salvador
Publisher: name: F1000 Research Limited
Year: 2022

description: With its first concepts going back to 2014, in 2018 the Global Alliance for Genomics and Health (GA4GH) approved Beacon v1 protocol as its standard for genomics data discovery. Warmly welcomed by the genomics community, many institutions implemented the protocol to provide a standardized way to query over their genomic data. The main advantage of these efforts emerged through the federated data discovery enabled by networks of beacons.
 Recently approved by the GA4GH, the completely redesigned Beacon v2 is a big step towards the adoption of Beacon API in clinical genomics and healthcare. The protocol changes require a corresponding redesign of the Beacon Network architecture and infrastructure in order to support new protocol features and datatypes.
 The Barcelona Supercomputing Center (BSC) present together with IT Center for Science Ltd. (CSC), Centre for Genomic Regulation (CRG) and Swiss Institute of Bioinformatics (SIB) the prototype implementation of the ELIXIR Beacon Network v2 service that enables querying individual beacons in the network, the aggregation of Beacon responses, supports ELIXIR AAI with open, registered and controlled access tiers and the handover to ELIXIR Core data resources.
 The service is jointly operated by BSC in Spain and CSC in Finland. We expect that other ELIXIR communities such as Federated Human Data, Rare Diseases, human Copy Number Variation, Proteomics, Plants, Cancer Data, and Health Data will benefit from this service either directly or through the experience from the ELIXIR Beacon Network v2 design and implementation.
Impact of preprocessing in data integration of single-cell RNA-seq data
Creators: name: Youngjun Park
name: Anne-Christin Hauschild
Publisher: name: F1000 Research Limited
Year: 2022

description: Due to technical limitations, single-cell sequencing data has heterogeneity from various noise sources. Over the last years, numerous single-cell data analysis tools have been introduced as de-noising methods. Here, we found that most single-cell studies employed various preprocessing steps without reasoning. This fact is particularly alarming since these read count transformations can significantly alter data distribution and affect downstream cell clustering results. This study aims to investigate the effects of the various data transformation on public datasets and evaluate them with the most commonly used dimensionality reduction and clustering analysis.
Design of Locally E-management System for Technical Education Foundation- Erbil
Creators: name: Ismaeel, Ayad Ghany
name: Mikhail, Dina Y.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computers and Society (cs.CY)
subject: FOS: Computer and information sciences

description: Until now, there is no e-management and automation necessary for the operations or procedures of the departments in the Technical Education Foundation Erbil, and the foundation like any other organization in Kurdistan region is not connected to the network, because there is not infrastructure for that purpose. To solve this problem, comes the proposal DLMS4TEF, which requirements are divided into hardware and software, as hardware will need Fast-Ethernet (LAN) technology to connect the departments of the Foundation via Client-Server network later, when an infrastructure is established for e-governments or e-management, it may be extended to the campus network. The software is represented by installing windows server to implement the proposal design of DLMS4TEF, PHP script is used as web programming that supports the server, where as the HTML and JavaScript are used to support the client side. The dynamic DLMS4TEF will be based on relational database, which is created by using MySQL, to support processing hundreds of queries per second, and the Kurdish Unicode to support Kurdish fonts of GUI's, Moreover, for security DLMS4TEF allows each department in the Foundation to enter its own section and prevent accessing other sections by using HTAccessible program which allows the user to access by using his IP address and his computer only. The important conclusions and advantages of applying DLMS4TEF are making backup to DLMS4TEF's databases using the option (zipped) which allows them to reach the size of (3%) of the original database size, sufficient security techniques, through achieving levels of security, hidden access to the administrator section, and finally DLMS4TEF, when compared with the traditional methods and project of Oman, shows the same efficiency of some, if not better, features of Oman. Keywords- E-management, Client-Server network, Fast-Ethernet, PHP, MySQL
description: 11 pages, 11 figures, 1 tables
Environmental Injustice and Industrial Chicken Farming in Maryland
Creators: name: Hall, Jonathan
name: Galarraga, Joseph
name: Berman, Isabelle
name: Edwards, Camryn
name: Khanjar, Niya
name: Kavi, Lucy
name: Murray, Rianna
name: Burwell-Naney, Kristen
name: Jiang, Chengsheng
name: Wilson, Sacoby
Publisher: name: MDPI
Year: 2021
Subjects: environmental justice
confined animal feeding operations
people of color
disparities
poverty

description: Maryland’s growing chicken industry, including concentrated animal feeding operations (CAFOs) and meat processing plants, raises a number of concerns regarding public health and environmental justice. Using hot spot analysis, we analyzed the totality of Maryland’s CAFOs and meat processing plants and those restricted to the Eastern Shore to assess whether communities of color and/or low socioeconomic status communities disproportionately hosted these types of facilities at the census tract level. We used zero-inflated regression modeling to determine the strength of the associations between environmental justice variables and the location of CAFOs and meatpacking facilities at the State level and on the Eastern Shore. Hot spot analyses demonstrated that CAFO hot spots on the Eastern Shore were located in counties with some of the lowest wealth in the State, including the lowest ranking county—Somerset. Zero-inflated regression models demonstrated that increases in median household income across the state were associated with a 0.04-unit reduction in CAFOs. For every unit increase in the percentage of people of color (POC), there was a 0.02-unit increase in meat processing facilities across the state. The distribution of CAFOs and meat processing plants across Maryland may contribute to poor health outcomes in areas affected by such production, and contribute to health disparities and health inequity.
Is Soil Bonitet an Adequate Indicator for Agricultural Land Appraisal in Ukraine?
Creators: name: Shumilo, Leonid
name: Lavreniuk, Mykola
name: Skakun, Sergii
name: Kussul, Nataliia
Publisher: name: MDPI
Year: 2021
Subjects: bonitet
agricultural land appraisal
soil quality
yield assessment

description: Agriculture land appraisal analysis is an important component of the land market. This task is especially essential for Ukraine, which plans to lift the moratorium on land transactions and legalize farmland sales in 2021. Most post-Soviet countries adopted the notion of a soil bonitet—a quantitative score representing natural soil fertility. This score is also proposed in Ukraine to perform agricultural land appraisals. However, this is a static parameter and does not account for the dynamics of actual crop production on the agricultural lands. Moreover, the bonitet score is not crop-specific. Therefore, in this study, we use maps of bonitet based on the soil map and natural-agricultural districts of Ukraine and crop yields at the village scale to explore the relationships between bonitet values and actual crop production in Ukraine. We found that land appraisal is not correlated with the actual soil bonitet.
Spectral Recalibration of NOAA HIRS Longwave CO2 Channels toward a 40+ Year Time Series for Climate Studies
Creators: name: Zhang, Bin
name: Cao, Changyong
name: Liu, Tung-Chang
name: Shao, Xi
Publisher: name: MDPI
Year: 2021
Subjects: HIRS longwave CO2 channel
HIRS SRF calibration
HIRS SNO
global mean
SRF shift

description: The High-Resolution Infrared Radiation Sounder (HIRS) on NOAA and MetOp A/B satellites has been observing the Earth continuously for over four decades, providing essential data for operational numerical weather prediction, retrieval of atmospheric vertical profile, and total column information on atmospheric temperature, moisture, water vapor, ozone, cloud climatology, and other geophysical parameters globally. Although the HIRS data meets the needs of the short-term weather forecast, there are inconsistencies when the long-term decadal time series is used for time series analysis. The discrepancies are caused by several factors, including spectral response differences between the HIRS models on the satellites and spectral response uncertainties and other calibration issues. Previous studies have demonstrated that significant improvements can be achieved by recalibrating some of the HIRS longwave CO2 channels (Channels 4, 5, 6, and 7), which has helped make the time series more consistent. The current study aims to extend the previous study to the remaining longwave infrared sounding channels, including Channels 1, 2, 3, and 8, using a similar approach. Similar to previous findings, the spectral shift of the HIRS bands has helped improve the consistency in the time series from NOAA-06 to MetOp-A and B for these channels. We also found that HIRS channels on MetOp-B also have bias relative to Infrared Atmospheric Sounding Interferometer (IASI) on the same satellite, especially Channel 4, and a spectral shift significantly reduced the bias. To bridge the observation gap in time series in the mid-1980s between NOAA-07 and NOAA-09, the global mean method has been used since no transfer radiometers between them was available for this period, and the spectral response function corrections, therefore, can be applied to the earliest satellites (NOAA-06) for these channels. The recalibration parameters have been provided to other scientists at the University of Wisconsin for improving the time series in their long-term studies using historical HIRS data and are now made available to the science community.
GenOptics: An intuitive platform of visual analytics for integrative analysis of large-scale multi-omics data
Creators: name: Kyritsis, Konstantinos A.
name: Pechlivanis, Nikolaos
name: Vasileiou, Vasileios
name: Magklara, Angeliki
name: Kougioumtzi, Anastasia
name: Dafopoulos, Panagiotis
name: Ntzioni, Eleni
name: Tsarouchi, Efstathia
name: Sakellariou, Dimitris
name: Kotoulas, Marios
name: Arampatzis, Stratos
name: Chatzikamaris, Panagiotis
name: Siomou, Elisavet
name: Argyraki, Maria
name: Botskaris, Dimitrios
name: Iannis Talianidis
name: Psomopoulos, Fotis
Publisher: name: F1000 Research Limited
Year: 2022

description: During the past two decades, computational analysis has become paramount for biological research. Advancements in high-throughput methods and computational tools resulted in the generation of large amounts of data from different omics fields (multi-omics), such as genomics, epigenomics, transcriptomics, and metabolomics. This plethora of large scale and diverse omics data is being driven by the understanding that a single-omic type does not provide adequate information and integrative analysis of multi-omics data is optimal to gain sufficiently meaningful insights into the actual biological mechanisms. Although various open-source tools have been developed for this purpose, multi-omics data integration and analysis are still beset by a number of problems, including software compatibility, complex parameter selection and creation of functional pipelines with multiple steps of analyses. In this work we present GenOptics, a novel visual analytics platform that aims to facilitate the integration and subsequent analysis of diverse multi-omics datasets as well as meta-data (e.g., clinical data), through a fully interactive environment. The platform comprises of two separate parts. The first incorporates asynchronous analyses of Next-Generation Sequencing raw data, including RNA-, Whole exome-, and ChIP-Seq, using workflows implemented with the Common Workflow Language (doi:10.6084/m9.figshare.3115156.v2) and Docker containers to automate software installation and confer cross-platform portability. The second part constitutes the analytical platform itself, designed to facilitate the execution of robust bioinformatics analyses by life scientists with minimal or no knowledge of programming. GenOptics constitutes an open source (https://genoptics.github.io/), computational biology platform for novel pattern and biomarker detection.
Performance of Ultra-Fast Silicon Detectors
Creators: name: Cartiglia, N.
name: Baselga, M.
name: Dellacasa, G.
name: Ely, S.
name: Fadeyev, V.
name: Galloway, Z.
name: Marchetto, F.
name: Maroiu, S.
name: Mazza, G.
name: Ngo, J.
name: Obertino, M.
name: Parker, C.
name: Rivetti, A.
name: Shumacher, D.
name: Sadrozinski, H. F-W.
name: Seiden, A.
name: Zatserklyaniy, A.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The development of Low-Gain Avalanche Detectors has opened up the possibility of manufacturing silicon detectors with signal larger than that of traditional sensors. In this paper we explore the timing performance of Low-Gain Avalanche Detectors, and in particular we demonstrate the possibility of obtaining ultra-fast silicon detector with time resolution of less than 20 picosecond.
description: 10 pages, 10 figures
Targeting the Gut Mucosal Immune System Using Nanomaterials
Creators: name: McCright, Jacob
name: Ramirez, Ann
name: Amosu, Mayowa
name: Sinha, Arnav
name: Bogseth, Amanda
name: Maisel, Katharina
Publisher: name: MDPI
Year: 2021
Subjects: gastrointestinal tract
lymph node
gut-associated lymphoid tissues
immunotherapy
vaccine
lectins
microfold (M) cells

description: The gastrointestinal (GI) tract is one the biggest mucosal surface in the body and one of the primary targets for the delivery of therapeutics, including immunotherapies. GI diseases, including, e.g., inflammatory bowel disease and intestinal infections such as cholera, pose a significant public health burden and are on the rise. Many of these diseases involve inflammatory processes that can be targeted by immune modulatory therapeutics. However, nonspecific targeting of inflammation systemically can lead to significant side effects. This can be avoided by locally targeting therapeutics to the GI tract and its mucosal immune system. In this review, we discuss nanomaterial-based strategies targeting the GI mucosal immune system, including gut-associated lymphoid tissues, tissue resident immune cells, as well as GI lymph nodes, to modulate GI inflammation and disease outcomes, as well as take advantage of some of the primary mechanisms of GI immunity such as oral tolerance.
Liquid crystal hyperbolic metamaterial for wide-angle negative-positive refraction and reflection
Creators: name: Pawlik, G.
name: Tarnowski, K.
name: Walasik, W.
name: Mitus, A. C.
name: Khoo, I. C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We show that nanosphere dispersed liquid crystal (NDLC) metamaterial can be characterized in near IR spectral region as an indefinite medium whose real parts of effective ordinary and extraordinary permittivities are opposite in signs. Based on this fact we design a novel electrooptic effect: external electric field driven switch between normal refraction, negative refraction and reflection of TM incident electromagnetic wave from the boundary vacuum/NDLC. A detailed analysis of its functionality is given based on effective medium theory combined with a study of negative refraction in anisotropic metamaterials, and Finite Elements simulations.
Modulation of Plasma and Milk Sphingolipids in Dairy Cows Fed High-Starch Diets
Creators: name: Rico, Jorge Eduardo
name: Sandri, Eveline C.
name: Sarmiento, Anrea Celemin
name: Lévesque, Janie
name: Kenéz, Ákos
name: Rico, Daniel C.
Publisher: name: MDPI
Year: 2021
Subjects: high-starch diet
milk
ceramide
sphingomyelin

description: Bovine milk is a significant source of sphingolipids, dietary compounds that can exert anti-inflammatory actions, and which can modulate the host’s microbiome. Because sphingolipid synthesis can be modified by diet, we hypothesized that dietary conditions which reduced FFA availability may result in reduced sphingolipid synthesis. Twelve ruminally cannulated cows (120 ± 52 DIM; 35.5 ± 8.9 kg of milk/d; mean ± SD) were randomly assigned to treatment in a crossover design with 21-d periods. Treatments were (1) High starch (HS), (2) Control. The HS diet contained 29% starch, 24% NDF, and 2.8% fatty acids (FA), whereas the Control diet contained 20% starch, 31% NDF, and 2.3% FA. Plasma and milk samples were obtained on d 21 of each period and sphingolipids were quantified using targeted metabolomics. Univariate and multivariate analyses of generalized log-transformed and Pareto-scaled data included ANOVA (fixed effects of treatment) and discriminant analysis. The lipidomics analysis detected 71 sphingolipids across plasma and milk fat, including sphinganines (n = 3), dihydro-ceramides (n = 8), ceramides (Cer; n = 15), sphingomyelins (SM; n = 17), and glycosylated ceramides (n = 28). Followed by Cer, SM were the most abundant sphingolipids detected in milk and plasma, with a preponderance of 16:0-, 23:0-, and 24:0-carbon sidechains. Although no effects of HS diets were observed on plasma sphingolipids, we detected consistent reductions in the concentrations of several milk Cer (e.g., 22:0- and 24:0-Cer) and SM (17:0- and 23:0-SM) in response to HS. Discriminant analysis revealed distinct metabolite separation of HS and Control groups, with several Cer and SM being distinctively predictive of dietary treatment. We conclude that HS diets can reduce the secretion of milk Cer and SM, even in the absence of changes in circulating sphingolipids.
The failure of DFT-based computations for a stepped-substrate-supported correlated Co wire
Creators: name: Zaki, Nader
name: Park, Hyowon
name: Osgood, Richard M.
name: Millis, Andrew J.
name: Marianetti, Chris A.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: Density functional theory (DFT) has been immensely successful in its ability to predict physical properties, and, in particular, structures of condensed matter systems. Here, however, we show that DFT qualitatively fails to predict the dimerized structural phase for a monatomic Co wire that is self-assembled on a vicinal, i.e. stepped, Cu(111) substrate. To elucidate the nature of this failure, we compute the energetics of a Co chain on a Cu surface, step, notch, and embedded in bulk. The results demonstrate that increasing Co coordination extinguishes the dimerization, indicating that the failure of DFT for Co on the Cu step arises from excessive hybridization, which both weakens the ferromagnetic correlations that drive the dimerization and increases the bonding that opposes dimerization. Additionally, we show that including local interactions via DFT+U or DFT+DMFT does not restore the dimerization for the step-substrate supported wire, though the Co wire does dimerize in DFT+DMFT for the isolated vacuum case. This system can serve as a benchmark for future electronic structure methods.
description: 18 pages, 7 figures
Grain-Scale Anisotropic Analysis of Steady-State Creep in Oligocrystalline SAC Solder Joints
Creators: name: Jiang, Qian
name: Deshpande, Abhishek Nitin
name: Dasgupta, Abhijit
Publisher: name: MDPI
Year: 2021
Subjects: lead-free solder
anistropic steady-state creep
Hill-Norton model
coarse-grained finite element analysis
grain boundary creep
cohesive element

description: Heterogeneous integration is leading to unprecedented miniaturization of solder joints, often with thousands of joints within a single package. The thermomechanical behavior of such SAC solder joints is critically important to assembly performance and reliability, but can be difficult to predict due to the significant joint-to-joint variability caused by the stochastic variability of the arrangement of a few highly-anisotropic grains in each joint. This study relies on grain-scale testing to characterize the mechanical behavior of such oligocrystalline solder joints, while a grain-scale modeling approach has been developed to assess the effect of microstructure that lacks statistical homogeneity. The contribution of the grain boundaries is modeled with isotropic cohesive elements and identified by an inverse iterative method that extracts material properties by comparing simulation with experimental measurements. The properties are extracted from the results of one test and validated by verifying reasonable agreement with test results from a different specimen. Equivalent creep strain heterogeneity within the same specimen and between different specimens are compared to assess typical variability due to the variability of microstructure.