cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The nonlinear 2D supercritical inviscid shallow water equations in a rectangle
Creators: name: Huang, Aimin
name: Petcu, Madalina
name: Temam, Roger
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: In this article we consider the inviscid two-dimensional shallow water equations in a rectangle. The flow occurs near a stationary solution in the so called supercritical regime and we establish short term existence of smooth solutions for the corresponding initial and boundary value problem.
description: 30 pages
Supplemental data figure from Oxygen limitation is not the cause of death during lethal heat exposure in an insect
Creators: name: Lehmann, Philipp
name: Javal, Marion
name: Terblanche, John S.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: Developmental Biology

description: Oxygen- and capacity-limited thermal tolerance (OCLTT) is a controversial hypothesis claiming to explain variation in, and mechanistically determine, animal thermal limits. The lack of support from Insecta is typically argued to be a consequence of their high-performance respiratory systems. However, no studies have reported internal body oxygen levels during thermal ramping so it is unclear if changes in ambient gas are partially or fully offset by a compensatory respiratory system. Here we provide such an assessment by simultaneously recording haemolymph oxygen (pO2) levels—as an approximation of tissue oxygenation—while experimentally manipulating ambient oxygen and subjecting organisms to thermal extremes in a series of thermolimit respirometry experiments using pupae of the butterfly Pieris napi. The main results are that while P. napi undergo large changes in haemolymph pO2 that are positively correlated with experimental oxygen levels, haemolymph pO2 is similar pre- and post-death during thermal assays. OCLTT predicts that reduction in body oxygen level should lead to a reduction in CTmax. Despite finding the former, there was no change in CTmax across a wide range of body oxygen levels. Thus, we argue that oxygen availability is not a functional determinant of the upper thermal limits in pupae of P. napi.
From traditional orchards to advanced fruitculture: establishing the bases of commercial horticulture in Afghanistan
Creators: name: Masini, G.
name: Giordani, E.
Publisher: name: Advances in Horticultural Science
Year: 2017

description: The Afghan economy is based essentially on the primary sector and, namely, on fruit production. A cross road of trade along the "Silk route", local traditional fruitculture based on the bagh (home garden) is widely variegated in terms of species and varieties. Afghan fresh and dried fruits (namely raisins) and nuts, sweet and rich in flavors, are demanded by domestic and foreign consumers. The lack of traceability and quality of the propagation material has been considered one of the basic bottle necks hindering development of an advanced horticulture. During the period 2006-2015 the Perennial Horticulture Development Project (PHDP), funded by the EC-EuropeAid Program, has been supporting the Ministry of Agriculture, Irrigation and Livestock of Afghanistan through a process of collection and selection of local fruit varieties in order to improve the private nursery system, as well as perennial horticulture. About 850 accessions of different fruit tree species have been collected and entered into the National Collections at six PHD Centres, where they undergo a standardised characterisation and identification procedure in order to be formally registered in a national list, hence contributing to their safeguard and protection. The best accessions were used as source for a traced propagation system after phytosanitary indexing and also in numerous adaptive experimentations. The PHDP contributed in capacity building at technical and institutional level, fostering the establishment of nursery sector associations, providing expertise and developing the Afghanistan National Nursery Growers Organization (ANNGO) and the apex Afghanistan National Horticulture Development Organization (ANHDO), mainly concerned with value chains.
description: Advances in Horticultural Science, Vol 30 No 4 (2016)
Imaging on a Sphere with Interferometers: the Spherical Wave Harmonic Transform
Creators: name: Carozzi, T. D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: I present an exact and explicit solution to the scalar (Stokes flux intensity) radio interferometer imaging equation on a spherical surface which is valid also for non-coplanar interferometer configurations. This imaging equation is comparable to $w$-term imaging algorithms, but by using a spherical rather than a Cartesian formulation this term has no special significance. The solution presented also allows direct identification of the scalar (spin 0 weighted) spherical harmonics on the sky. The method should be of interest for future multi-spacecraft interferometers, wide-field imaging with non-coplanar arrays, and CMB spherical harmonic measurements using interferometers.
description: (Fixed references missing in previous arxiv version). This is a pre-copyedited, author-produced PDF of an article accepted for publication in MNRAS following peer review
Ets homologous factor regulates pathways controlling response to injury in airway epithelial cells
Creators: name: Harris, Ann
name: Leir, Shih Hsing
name: Dang, Hong
name: Fossum, Sara L.
name: Knowles, Michael R.
name: O'Neal, Wanda K.
name: Mutolo, Michael J.
name: Yang, Rui
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Ets homologous factor (EHF) is an Ets family transcription factor expressed in many epithelial cell types including those lining the respiratory system. Disruption of the airway epithelium is central to many lung diseases, and a network of transcription factors coordinates its normal function. EHF can act as a transcriptional activator or a repressor, though its targets in lung epithelial cells are largely uncharacterized. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq), showed that the majority of EHF binding sites in lung epithelial cells are intergenic or intronic and coincide with putative enhancers, marked by specific histone modifications. EHF occupies many genomic sites that are close to genes involved in intercellular and cell–matrix adhesion. RNA-seq after EHF depletion or overexpression showed significant alterations in the expression of genes involved in response to wounding. EHF knockdown also targeted genes in pathways of epithelial development and differentiation and locomotory behavior. These changes in gene expression coincided with alterations in cellular phenotype including slowed wound closure and increased transepithelial resistance. Our data suggest that EHF regulates gene pathways critical for epithelial response to injury, including those involved in maintenance of barrier function, inflammation and efficient wound repair.
The phytosanitary status of the National Collection of fruits and nuts of Afghanistan and the private Mother Stock Nurseries: a virus survey
Creators: name: Rehman, S.
name: Ahmad, J.
name: Lanzoni, C.
name: Rubies Antonel, C.
name: Ratti, C.
Publisher: name: Advances in Horticultural Science
Year: 2017

description: The horticultural industry is a vital component of the agriculture sector of Afghanistan, the primary engine of the country’s recovering economy which engages approximately 80% of the working population. This sector was thriving in the 1970s, but is today incapable of competing in the international market. To recover and develop the horticulture of the country, the European Community (EC) supports the PHDP (Perennial Horticulture Development Project), to provide true to type/ecotype and healthy planting materials, and the Plant Biotechnology Laboratory, to ensure the health status of local germplasm. This laboratory started screening the health status of the Afghan Germplasm National Collections in order to ensure the multiplication of not only the best-selected varieties or ecotype, but also to avoid production and distribution of virus-infected trees. Inspection for symptoms and sample collection for viral diseases was carried out in all the National Collection fields, including cherry, pear, peach, plum, apricot, almond, apple, grape and citrus plants, located in different areas of the country. Stone fruit plants infected by Apple chlorotic leaf spot virus or Prunus necrotic ringspot virus have been identified in the National Collection experimental farms located in different provinces of Afghanistan. Moreover, many grape plants included in the National Collection located in Herat and Kandahar resulted infected by Grapevine fanleaf virus, but only few imported plants by Grapevine leafroll associated virus 1, Grapevine leafroll associated virus 3 or Grapevine virus A. Finally, in Jalalabad (Nangarhar province) citrus plants showing vein flecking, yellowing and plant decline symptoms were found to be infected by Citrus tristeza virus. Some of the identified viral isolates have been characterized molecularly, amplifying a fragment corresponding to the coat protein gene from a selection of positive samples. The presence of those viruses in different accessions of the national collection is of concern for Afghan horticulture. Implementation of the certification schemes is therefore necessary to quarantine the production and for the employment of virus-free propagating material.
description: Advances in Horticultural Science, Vol 30 No 4 (2016)
fourSig: a method for determining chromosomal interactions in 4C-Seq data
Creators: name: Mieczkowski, Piotr
name: Starmer, Joshua
name: Williams Jr., Rex L.
name: Magnuson, Terry
name: Calabrese, J. Mauro
name: Yee, Della
name: Mugford, Joshua W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-Seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined. 4C-Seq experiments generate large, complicated data sets and it is imperative that signal is properly distinguished from noise. Currently, there are a limited number of methods for analyzing 4C-Seq data. Here, we present a new method, fourSig, which in addition to being precise and simple to use also includes a new feature that prioritizes detected interactions. Our results demonstrate the efficacy of fourSig with previously published and novel 4C-Seq data sets and show that our significance prioritization correlates with the ability to reproducibly detect interactions among replicates.
Amsterdam Declaration on Funding Research Software Sustainability
Creators: name: Barker, Michelle
name: Hong, Neil P. Chue
name: Van Eijnatten, Joris
name: Katz, Daniel S.
Publisher: name: Zenodo
Year: 2023
Subjects: research software
open science
funding
declaration
software sustainability

description: This Declaration on Funding Research Software Sustainability builds on actions undertaken by the Research Software Alliance (ReSA), research funding organisations, and the community surrounding it to develop awareness about the role funders can play in sustaining software in the longer term. It was initiated during an international workshop attended by representatives of funding organisations in Amsterdam on 8-9 November 2022, organised by ReSA and the Netherlands eScience Center. The Declaration is a first step towards formalising, on a global level, the basic principles and recommendations related to funding the sustainability of research software, including the people needed to achieve this goal. The aim of this Declaration is to raise awareness of the role of funding practice in the sustainability of research software, and to improve that practice. The Declaration includes a limited number of recommendations and an accompanying ADORE.software Toolkit. For the purposes of this declaration, research software is defined as “all forms of software that were created during the research process or for a research purpose”. A fuller description is included in the accompanying ADORE.software Toolkit
Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells
Creators: name: Kemp, Michael G.
name: Hu, Jinchuan
name: Sancar, Aziz
name: Choi, Jun Hyuk
name: Kim, So Young
name: Gaddameedhi, Shobhan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisotopic method to directly detect DNA excision repair events in human cells. The approach involves extraction of oligonucleotides from UV-irradiated cells, DNA end-labeling with biotin and streptavidin-mediated chemiluminescent detection of the excised UV photoproduct-containing oligonucleotides that are released from the genome during excision repair. Our novel approach is robust, with essentially no signal in the absence of UV or a functional excision repair system. Furthermore, our non-radioisotopic methodology allows for the sensitive detection of excision products within minutes following UV irradiation and does not require additional enrichment steps such as immunoprecipitation. Finally, this technique allows for quantitative measurements of excision repair in human cells. We suggest that the new techniques presented here will be a useful and powerful approach for studying the mechanism of human nucleotide excision repair in vivo.
Amsterdam Declaration on Funding Research Software Sustainability
Creators: name: Research Software Alliance
Publisher: name: Zenodo
Year: 2024
Subjects: research software
open science
funding
declaration
software sustainability

description: This Declaration on Funding Research Software Sustainability builds on actions undertaken by the Research Software Alliance (ReSA), research funding organisations, and the community surrounding it to develop awareness about the role funders can play in sustaining software in the longer term. It was initiated during an international workshop attended by representatives of funding organisations in Amsterdam on 8-9 November 2022, organised by ReSA and the Netherlands eScience Center. The Declaration is a first step towards formalising, on a global level, the basic principles and recommendations related to funding the sustainability of research software, including the people needed to achieve this goal.

The aim of this Declaration is to raise awareness of the role of funding practice in the sustainability of research software, and to improve that practice. The Declaration includes a limited number of recommendations and an accompanying ADORE.software Toolkit. For the purposes of this declaration, research software is defined as “all forms of software that were created during the research process or for a research purpose”. A fuller description is included in the accompanying ADORE.software Toolkit
Additional file 1 of The new normal for children’s physical activity and screen viewing: a multi-perspective qualitative analysis of behaviours a year after the COVID-19 lockdowns in the UK
Creators: name: Walker, Robert
name: House, Danielle
name: Salway, Ruth
name: Emm-Collison, Lydia
name: Hollander, Lara E.
name: Sansum, Kate
name: Breheny, Katie
name: Churchward, Sarah
name: Williams, Joanna G.
name: de Vocht, Frank
name: Hollingworth, William
name: Foster, Charlie
name: Jago, Russell
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Science Policy
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 1. Interview and focus group topic guides.
Amsterdam Declaration on Funding Research Software Sustainability
Creators: name: Van Eijnatten, Joris
name: Barker, Michelle
name: Azzarà, Valentina
name: Bakker, Tom
name: Katz, Daniel S.
name: Martinez-Ortiz, Carlos
name: Cruz, Maria J.
name: Pang, Veronica
Publisher: name: Zenodo
Year: 2022
Subjects: research software
open science
funding
declaration
software sustainability

description: The Research Software Alliance (ReSA) and the Netherlands eScience Center hosted a two-day international workshop in Amsterdam (the Netherlands) on 8-9 November 2023 to set the future agenda for national and international funders to support sustainable research software. As the importance of software in research has become increasingly apparent, so has the urgent need to sustain it. Funders can play a crucial role in this respect by ensuring structural support. Over the past few years, a variety of methods for sustaining research software have been explored, including improving and extending funding policies and instruments. During the workshop, funding organizations joined forces to explore how they can effectively contribute to making research software sustainable. In preparation of the workshop, a draft of a future international declaration, titled "Amsterdam Declaration on Funding Research Software Sustainability" was created by the Research Software Alliance, the Netherlands eScience Center and with input from stakeholders in the field.
Amsterdam Declaration on Funding Research Software Sustainability
Creators: name: Research Software Alliance
Publisher: name: Zenodo
Year: 2023
Subjects: research software
open science
funding
declaration
software sustainability

description: This Declaration on Funding Research Software Sustainability builds on actions undertaken by the Research Software Alliance (ReSA), research funding organisations, and the community surrounding it to develop awareness about the role funders can play in sustaining software in the longer term. It was initiated during an international workshop attended by representatives of funding organisations in Amsterdam on 8-9 November 2022, organised by ReSA and the Netherlands eScience Center. The Declaration is a first step towards formalising, on a global level, the basic principles and recommendations related to funding the sustainability of research software, including the people needed to achieve this goal. The aim of this Declaration is to raise awareness of the role of funding practice in the sustainability of research software, and to improve that practice. The Declaration includes a limited number of recommendations and an accompanying ADORE.software Toolkit. For the purposes of this declaration, research software is defined as “all forms of software that were created during the research process or for a research purpose”. A fuller description is included in the accompanying ADORE.software Toolkit
Quantifying electronic correlation strength in a complex oxide: a combined DMFT and ARPES study of LaNiO$_3$
Creators: name: Nowadnick, E. A.
name: Ruf, J. P.
name: Park, H.
name: King, P. D. C.
name: Schlom, D. G.
name: Shen, K. M.
name: Millis, A. J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The electronic correlation strength is a basic quantity that characterizes the physical properties of materials such as transition metal oxides. Determining correlation strengths requires both precise definitions and a careful comparison between experiment and theory. In this paper we define the correlation strength via the magnitude of the electron self-energy near the Fermi level. For the case of LaNiO$_3$, we obtain both the experimental and theoretical mass enhancements $m^\star/m$ by considering high resolution angle-resolved photoemission spectroscopy (ARPES) measurements and density functional + dynamical mean field theory (DFT + DMFT) calculations. We use valence-band photoemission data to constrain the free parameters in the theory, and demonstrate a quantitative agreement between the experiment and theory when both the realistic crystal structure and strong electronic correlations are taken into account. These results provide a benchmark for the accuracy of the DFT+DMFT theoretical approach, and can serve as a test case when considering other complex materials. By establishing the level of accuracy of the theory, this work also will enable better quantitative predictions when engineering new emergent properties in nickelate heterostructures.
description: 10 pages, 5 figures
Integrated RNA and DNA sequencing improves mutation detection in low purity tumors
Creators: name: Hoadley, Katherine A.
name: Walter, Vonn
name: Parker, Joel S.
name: Troester, Melissa A.
name: Hammerman, Peter S.
name: Perou, Charles M.
name: Wilkerson, Matthew D.
name: Hayes, D. Neil
name: Sun, Wei
name: Mose, Lisle E.
name: Cabanski, Christopher R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Identifying somatic mutations is critical for cancer genome characterization and for prioritizing patient treatment. DNA whole exome sequencing (DNA-WES) is currently the most popular technology; however, this yields low sensitivity in low purity tumors. RNA sequencing (RNA-seq) covers the expressed exome with depth proportional to expression. We hypothesized that integrating DNA-WES and RNA-seq would enable superior mutation detection versus DNA-WES alone. We developed a first-of-its-kind method, called UNCeqR, that detects somatic mutations by integrating patient-matched RNA-seq and DNA-WES. In simulation, the integrated DNA and RNA model outperformed the DNA-WES only model. Validation by patient-matched whole genome sequencing demonstrated superior performance of the integrated model over DNA-WES only models, including a published method and published mutation profiles. Genome-wide mutational analysis of breast and lung cancer cohorts (n = 871) revealed remarkable tumor genomics properties. Low purity tumors experienced the largest gains in mutation detection by integrating RNA-seq and DNA-WES. RNA provided greater mutation signal than DNA in expressed mutations. Compared to earlier studies on this cohort, UNCeqR increased mutation rates of driver and therapeutically targeted genes (e.g. PIK3CA, ERBB2 and FGFR2). In summary, integrating RNA-seq with DNA-WES increases mutation detection performance, especially for low purity tumors.
Relationships between charge density response functions, exchange holes and localized orbitals
Creators: name: Mussard, Bastien
name: Ángyán, János G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The charge density response function and the exchange hole are closely related to each other via the fundamental fluctuation-dissipation theorem of physics. A simple approximate model of the static response function is visually compared on several examples in order to demonstrate this relationship. This study is completed by illustrating the well-known isomorphism between the exchange hole and the square of the dominant localized orbital lying in the space region of the reference point of the exchange hole function. The implications of these relationships for the interpretation of common chemical concepts, such as delocalization, are discussed.
description: 10 two-columns pages, including 3 figures
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
Creators: name: Zhou, Michelle
name: Tan, Ge
name: Ienasescu, Hans
name: Lim, Jonathan
name: Zhang, Allen W.
name: Shyr, Casper
name: Lenhard, Boris
name: Sandelin, Albin
name: Mathelier, Anthony
name: Parcy, François
name: Worsley-Hunt, Rebecca
name: Chou, Alice
name: Wasserman, Wyeth W.
name: Buchman, Sorana
name: Arenillas, David J.
name: Chen, Chih Yu
name: Zhao, Xiaobei
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR—the JASPAR CORE subcollection, which contains curated, non-redundant profiles—with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods.
Effect of pre- and post-harvest salicylic acid treatments on quality and antioxidant Properties of 'Red Delicious' apples during cold storage
Creators: name: Hadian-Delijou, M.
name: Esna-Ashari, M.
name: Sarikhani, H.
Publisher: name: Advances in Horticultural Science
Year: 2017

description: Salicylic acid is a natural phenolic compound known as a plant hormone having positive effect on storage life and quality of fruits. This study aimed to investigate the effects of pre- and post-harvest application of salicylic acid on antioxidant properties and quality of ‘Red Delicious’ apples during 193 days cold (0±0.5°C) storage. Both pre- and post-harvest salicylic acid treatments did not affect soluble solid content, titratable acidity and fruit firmness, with the exception of 1 mM at pre-harvest application for titratable acidity. Fruit juice pH was reduced in all fruits at the end of storage, while it was not quite uniform during storage. Although there was no significant difference between the concentrations of salicylic acid in terms of fruit weight loss, but the highest amount of weight loss was observed in post-harvest treatments. Salicylic acid application increased total phenolics and antioxidant activity at the earlier stages of storage showing the highest capacity with 2 mM followed by 1 and 4 mM salicylic acid concentrations, while 1 mM concentration belonged to the highest antioxidant capacity at the end of storage. Anthocyanin content showed a gradual increase during storage until day 60, then decreased right afterwards. The highest amounts of anthocyanin were obtained from the concentrations of 1 and 2 mM salicylic acid in pre-harvest treatments, while 4 mM treatment was not encouraging. Overall, salicylic acid treatments could increase apple storage life and quality for a short period of time only.
description: Advances in Horticultural Science, Vol 31 No 1 (2017)
R-code from Heart rate during hyperphagia differs between two bear species.
Creators: name: Fuchs, Boris
name: Yamazaki, Koji
name: Evans, Alina L.
name: Tsubota, Toshio
name: Koike, Shinsuke
name: Naganuma, Tomoko
name: Arnemo, Jon M.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: R-markdown file with modelselection and description
MPEC 2024-R220 : 2024 RW9
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2024
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2024 RW9

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
Model order reduction applied to heat conduction in photovoltaic modules
Creators: name: Ojo, S. O.
name: Grivet-Talocia, S.
name: Paggi, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Modelling of physical systems may be a challenging task when it requires solving large sets of numerical equations. This is the case of photovoltaic (PV) systems which contain many PV modules, each module containing several silicon cells. The determination of the temperature field in the modules leads to large scale systems, which may be computationally expensive to solve. In this context, Model Order Reduction (MOR) techniques can be used to approximate the full system dynamics with a compact model, that is much faster to solve. Among the several available MOR approaches, in this work we consider the Discrete Empirical Interpolation Method (DEIM), which we apply with a suitably modified formulation that is specifically designed for handling the nonlinear terms that are present in the equations governing the thermal behaviour of PV modules. The results show that the proposed DEIM technique is able to reduce significantly the system size, by retaining a full control on the accuracy of the solution.
description: 20 pages, 9 figures
Finite-temperature effects on a triatomic Efimov resonance in ultracold cesium
Creators: name: Huang, Bo
name: Sidorenkov, Leonid A.
name: Grimm, Rudolf
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We report a thorough investigation of finite-temperature effects on three-body recombination near a triatomic Efimov resonance in an ultracold gas of cesium atoms. Our measurements cover a wide range from a near-ideal realization of the zero-temperature limit to a strongly temperature-dominated regime. The experimental results are analyzed within a recently introduced theoretical model based on a universal zero-range theory. The temperature-induced shift of the resonance reveals a contribution that points to an energy-dependence of the three-body parameter. We interpret this contribution in terms of the finite range of the van der Waals interaction in real atomic systems and we quantify it in an empirical way based on length scale arguments. A universal character of the corresponding resonance shift is suggested by observations related to other Efimov resonances and the comparison with a theoretical finite-temperature approach that explicitly takes the van der Waals interaction into account. Our findings are of importance for the precise determination of Efimov resonance positions from experiments at finite temperatures.
description: 8 pages, 5 figures
Additional file 1 of Association of major dietary patterns with advanced glycation end products and high-sensitivity C-reactive protein in people with type 1 diabetes mellitus
Creators: name: Ebrahimi, Zohreh
name: Shojaeian, Zahra
name: Amiri, Fatemehsadat
name: Esmaillzadeh, Ahmad
name: Sadeghi, Omid
name: Esteghamati, Alireza
name: Jahed, Seyed Adel
name: Sedaghat, Sara
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Supplementary Material 1: Food grouping used in the dietary patterns
Requirements for 5′dRP/AP lyase activity in Ku
Creators: name: Carvajal-Garcia, Juan
name: Ramsden, Dale A.
name: Kuhlman, Brian
name: Hallett, Ryan A.
name: Roberts, Steven A.
name: Strom, Christina
name: Waters, Crystal A.
name: Strande, Natasha T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The non-homologous end joining (NHEJ) pathway is used in diverse species to repair chromosome breaks, and is defined in part by a requirement for Ku. We previously demonstrated mammalian Ku has intrinsic 5′ deoxyribosephosphate (5′dRP) and apurinic/apyrimidinic (AP) lyase activity, and showed this activity is important for excising abasic site damage from ends. Here we employ systematic mutagenesis to clarify the protein requirements for this activity. We identify lysine 31 in the 70 kD subunit (Ku70 K31) as the primary candidate nucleophile required for catalysis, but additional mutation of Ku70 K160 and six other lysines within Ku80 were required to eliminate all activity. Ku from Saccharomyces cerevisiae also possesses 5′dRP/AP lyase activity, and robust activity was also reliant on lysines in Ku70 analogous to K31 and K160. By comparison, these lysines are not conserved in Xenopus laevis Ku, and Ku from this species has negligible activity. A role for residues flanking Ku70 K31 in expanding the range of abasic site contexts that can be used as substrate was also identified. Our results suggest an active site well located to provide the substrate specificity required for its biological role.
Stability conditions and related filtrations for $(G,h)$-constellations
Creators: name: Terpereau, Ronan
name: Zamora, Alfonso
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Geometry (math.AG)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: 14D20, 14L24

description: Given an infinite reductive algebraic group $G$, we consider $G$-equivariant coherent sheaves with prescribed multiplicities, called $(G,h)$-constellations, for which two stability notions arise. The first one is analogous to the $θ$-stability defined for quiver representations by King and for $G$-constellations by Craw and Ishii, but depending on infinitely many parameters. The second one comes from Geometric Invariant Theory in the construction of a moduli space for $(G,h)$-constellations, and depends on some finite subset $D$ of the isomorphy classes of irreducible representations of $G$. We show that these two stability notions do not coincide, answering negatively a question raised in [BT15]. Also, we construct Harder-Narasimhan filtrations for $(G,h)$-constellations with respect to both stability notions (namely, the $μ_θ$-HN and $μ_D$-HN filtrations). Even though these filtrations do not coincide in general, we prove that they are strongly related: the $μ_θ$-HN filtration is a subfiltration of the $μ_D$-HN filtration, and the polygons of the $μ_D$-HN filtrations converge to the polygon of the $μ_θ$-HN filtration when $D$ grows.
description: 29 pages, 4 figures. Final version, to appear in International Journal of Mathematics
title: Messungen zum Overshootphänomen in monauralen und diotischen Konfigurationen
Creators: name: Klitzing, Regine von
name: Fassel, Ralf
name: Kohlrausch, Armin
Publisher: name: Deutsche Gesellschaft für Akustik e.V.
Year: 2023

description: Es wurden Messungen zur zeitlichen Struktur der Simultanverdeckung von Breitbandrauschen vorgestellt. Dabei zeigte sich, daß die Mithörschwellen zu Beginn des Maskierers nicht immer erhöht sein müssen (positiver Overshoot), sondern durchaus auch niedriger liegen können als zu späteren Zeitpunkten im Maskierer (negativer Overshoot oder Undershoot). Des weiteren wurde festgestellt, daß dieses Phänomen sich in monauralen und diotischen Konfigurationen pegelabhängig verhält. Das Maximum des Overshoots tritt bei mittleren Rauschpegeln auf. Es konnte gezeigt werden, daß es sich bei dieser Pegelabhängigkeit des Overshoots um eine Abweichung vom Weberschen Gesetz handelt, die sich mit der zeitlichen Lage des Testtones im Maskierer ändert. Ebenfalls zeit- und pegelabhängig ist die Differenz zwischen den monauralen und den diotischen Schwellen. Bei hohen Maskiererpegeln können die diotischen Schwellen deutlich höher liegen als die monauralen. Dieses ungewöhnliche Phänomen und der Overshoot überstreichen den gleichen Zeitbereich.
SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples
Creators: name: Liu, Yufeng
name: Maher, Christopher A.
name: Wilkerson, Matthew D.
name: Johnson, Amy R.
name: Perou, Charles M.
name: Marron, J. S.
name: Kimes, Patrick K.
name: Hayes, D. Neil
name: Cabanski, Christopher R.
name: Makowski, Liza
name: Zhao, Ni
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: High-throughput sequencing technologies, including RNA-seq, have made it possible to move beyond gene expression analysis to study transcriptional events including alternative splicing and gene fusions. Furthermore, recent studies in cancer have suggested the importance of identifying transcriptionally altered loci as biomarkers for improved prognosis and therapy. While many statistical methods have been proposed for identifying novel transcriptional events with RNA-seq, nearly all rely on contrasting known classes of samples, such as tumor and normal. Few tools exist for the unsupervised discovery of such events without class labels. In this paper, we present SigFuge for identifying genomic loci exhibiting differential transcription patterns across many RNA-seq samples. SigFuge combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. We apply SigFuge to RNA-seq cohorts of 177 lung and 279 head and neck squamous cell carcinoma samples from the Cancer Genome Atlas, and identify several cases of differential isoform usage including CDKN2A, a tumor suppressor gene known to be inactivated in a majority of lung squamous cell tumors. By not restricting attention to known sample stratifications, SigFuge offers a novel approach to unsupervised screening of genetic loci across RNA-seq cohorts. SigFuge is available as an R package through Bioconductor.
The Most Luminous Supernova ASASSN-15lh: Signature of a Newborn Rapidly-Rotating Strange Quark Star
Creators: name: Dai, Z. G.
name: Wang, S. Q.
name: Wang, J. S.
name: Wang, L. J.
name: Yu, Y. W.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: In this paper we show that the most luminous supernova discovered very recently, ASASSN-15lh, could have been powered by a newborn ultra-strongly-magnetized pulsar, which initially rotates near the Kepler limit. We find that if this pulsar is a neutron star, its rotational energy could be quickly lost as a result of gravitational-radiation-driven r-mode instability; if it is a strange quark star, however, this instability is highly suppressed due to a large bulk viscosity associated with the nonleptonic weak interaction among quarks and thus most of its rotational energy could be extracted to drive ASASSN-15lh. Therefore, we conclude that such an ultra-energetic supernova provides a possible signature for the birth of a strange quark star.
description: 6 pages, title changed, one figure added, conclusions unchanged, accepted for publication in ApJ
A Thesis Submitted to Addis Ababa University College of Commerce in partial Fulfillment of the Requirements for the Award of the Degree of Masters of Logistics and Supply Chain Management
Creators: name: ATSEDE AYELE
Publisher: name: Zenodo
Year: 2024

description: In the operation of the company, the development of logistics takes the largest part on its day-to-day operation in fuel retail business in Ethiopian oil retail industry. Third party logistics companies play a vital role to the operation and distribution of fuel in the country and contributes to the economic growth of the country; we can say logistics is on its infant stage in Ethiopia. Likewise, in LOEL, logistics in fuel retail business is the largest operation of the organization’s overall performance and in Ethiopia as well; it constitutes more than 50% of the total operation since the company operates mainly on distribution of oil and fuel business, which is the time and place value of logistics. Recently the performance of outsourcing logistics business in Ethiopia has increasing. Almost all oil companies use outsourced logistics service in their operation. However, the challenges of its collaboration, safety and business awareness is mentioned on many instances with the transporter and company management, monthly joint meetings and joint consultations. This research is attempted to describethe outsourced logistics performance of the company in the case of Libya Oil Ethiopia Limited. The scope of the study is assessment on the performance of logistics of Libya Oil Ethiopia Limited in relation to third party logistics service providers. The unit of analysis is assessment of logistics in the case of Libya Oil Ethiopia Limited in relation to its outsourced logistics performance. Semi-structured interview was undertaken to obtain primary data and archival data and some printed and non printed data are used as secondary data.
Phenotypic characterisation of almond accessions collected in Afghanistan
Creators: name: Giordani, E.
name: Berti, M.
name: Yaqubi, M.R.
Publisher: name: Advances in Horticultural Science
Year: 2017

description: Almond [Prunus dulcis (Mill.) D.A. Webb] accessions of Afghanistan have been surveyed, propagated, and grown in ex situ collections. Trees, leaves, flowers, and fruits were characterised following standardized procedures taking into account 48 phenotypic traits. The National Collection of Varieties of Almonds of Afghanistan showed a significant variability in terms of morphological traits, with a predominance of early flowering time accessions. Among the 56 accessions, Sattarbai, a unique group of cultivar typology characterized by crescent dry fruit, soft and thin "paper shell" and high kernel/dry fruit weight ratio (>0.65) was clearly represented by Cluster Analysis. Other accessions resulted closer to the international cultivars Lauranne, Carmel, Ferraduel and Ferragnes, considered as reference.
description: Advances in Horticultural Science, Vol 30 No 4 (2016)
Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for mCpG/TpG mismatches
Creators: name: Cramer, Jason M.
name: Scarsdale, J. Neel
name: Buchwald, William A.
name: Walavalkar, Ninad M.
name: Williams, David C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Unlike other members of the methyl-cytosine binding domain (MBD) family, MBD4 serves as a potent DNA glycosylase in DNA mismatch repair specifically targeting mCpG/TpG mismatches arising from spontaneous deamination of methyl-cytosine. The protein contains an N-terminal MBD (MBD4MBD) and a C-terminal glycosylase domain (MBD4GD) separated by a long linker. This arrangement suggests that the MBD4MBD either directly augments enzymatic catalysis by the MBD4GD or targets the protein to regions enriched for mCpG/TpG mismatches. Here we present structural and dynamic studies of MBD4MBD bound to dsDNA. We show that MBD4MBD binds with a modest preference formCpG as compared to mismatch, unmethylated and hydroxymethylated DNA. We find that while MBD4MBD exhibits slow exchange between molecules of DNA (intermolecular exchange), the domain exhibits fast exchange between two sites in the same molecule of dsDNA (intramolecular exchange). Introducing a single-strand defect between binding sites does not greatly reduce the intramolecular exchange rate, consistent with a local hopping mechanism for moving along the DNA. These results support a model in which the MBD4MBD4 targets the intact protein to mCpG islands and promotes scanning by rapidly exchanging between successive mCpG sites which facilitates repair of nearby mCpG/TpG mismatches by the glycosylase domain.
Selected pomegranate germplasm from Afghanistan: morphological variability and relationship among collected accessions
Creators: name: Giordani, E.
name: Berti, M.
name: Yaqubi, M.R.
name: Stanikzai, S.
name: Amad, A.
name: Zadran, B.
name: Saeedi, A.
name: Ghous, M.
Publisher: name: Advances in Horticultural Science
Year: 2017

description: During the period 2008-09 and in the frame of PHDP 58 Afghan and 18 foreign pomegranate accessions have been collected and grown under homogeneous environmental and cultivation practice conditions in ex situ collections. Standardized procedures were adopted to describe mature trees, leaves, flowers and fruits for a total of 30 phenotypic traits. Within the National Collection of Pomegranate of Afghanistan, coefficients of variability ranged from 8.8 to 31.7% for fruit diameter and weight of non edible part, respectively. Principal component analysis revealed the absence of correlated variables among different organs. The whole set of accessions resulted discriminated on the basis of the studied morphological parameters and all the accessions were grouped into 3 sub-sets by hierarchical cluster analysis. Local accessions resulted distributed in the 3 clusters, nevertheless the largest one held all the foreign varieties while the second one included all the accessions collected under the putative name of ‘Bedana’. The adopted morphological studies allowed to identify one true-to-type ‘Bedana’ accession, considered the best Afghan variety for fresh consume due to its very soft seed, and to solve the cases of homonymy. Analogously, various accessions originally collected from different regions of Afghanistan under the name of ‘Kandahari’ were identified and renamed.
description: Advances in Horticultural Science, Vol 30 No 4 (2016)
R-code from Heart rate during hyperphagia differs between two bear species
Creators: name: Fuchs, Boris
name: Yamazaki, Koji
name: Evans, Alina L.
name: Tsubota, Toshio
name: Koike, Shinsuke
name: Naganuma, Tomoko
name: Arnemo, Jon M.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: R-markdown file with modelselection and description
Effect of pre-harvest putrescine treatment on quality and postharvest life of pear cv. Spadona
Creators: name: Hosseini, M.S.
name: Fakhar, Z.
name: Babalar, M.
name: Askari, M.A.
Publisher: name: Advances in Horticultural Science
Year: 2017

description: The study was conducted to determine the effect of pre-harvest foliar spraying with putrescine (at 0.5, 1 and 2 mM) on quality and postharvest life of Pyrus communis cv. Spadona during cold storage. Fruit quality assessment such as weight loss, firmness, total soluble solids (TSS), titratable acidity (TA), flavor index, skin color (L*, hue angle), vitamin C total phenol (TP), and total antioxidant activity (TAA) were made at harvest and after 3, 6, 9, 12, 15, 18 and 21 weeks of storage at 0±1°C, 80-85% relative humidity. Weight loss, fruit softening, TSS and pH increased during storage but the rate of changes was significantly lower in fruit treated with putrescine at 1 and 2 mM. Putrescine application maintained higher levels of TA, vitamin C, TP, TAA, L*, hue angle and reduced decay incidence compared to control. Furthermore, higher doses of putrescine were effective in terms of prolonging the storage and marketability of fruits more than 127-142 days. In conclusion, pre-harvest application of putrescine could be an effective means for extending the postharvest life of pear cv. Spadona.
description: Advances in Horticultural Science, Vol 31 No 1 (2017)