cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Bradykinin B1 and B2 receptors both have protective roles in renal ischemia/reperfusion injury
Creators: name: Kim, H.-S.
name: Smithies, O.
name: Kakoki, M.
name: McGarrah, R. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: To explore the role of the kallikrein–kinin system in relation to ischemia/reperfusion injury in the kidney, we generated mice lacking both the bradykinin B1 and B2 receptor genes (B1RB2R-null, Bdkrb1−/−/Bdkrb2−/−) by deleting the genomic region encoding the two receptors. In 4-month-old mice, blood pressures were not significantly different among B1RB2R-null, B2R-null (Bdkrb2−/−), and WT mice. After 30 min of bilateral renal artery occlusion and 24 h of reperfusion, mortality rates, renal histological and functional changes, 8-hydroxy-2′-deoxyguanosine levels in total DNA, mtDNA deletions, and the number of TUNEL-positive cells in the kidneys increased progressively in the following order (from lowest to highest): WT, B2R-null, and B1RB2R-null mice. Increases in mRNA levels of TGF-β1, connective tissue growth factor, and endothelin-1 after ischemia/reperfusion injury were also exaggerated in the same order (from lowest to highest): WT, B2R-null, and B1RB2R-null. Thus, both the B1 and B2 bradykinin receptors play an important role in reducing DNA damage, apoptosis, morphological and functional kidney changes, and mortality during renal ischemia/reperfusion injury.
Shade tolerant legumes
Creators: name: Franca, Antonello
name: Re, Giovanni A.
name: Sanna, Federico
Publisher: name: Zenodo
Year: 2017
Subjects: Silvopasture
Legume-rich mixtures

description: In silvopastoral systems, light interception affects productivity of flora beneath the canopy in various ways. In general, herbage production decreases with reduced light intensity. Thus, the use of shade tolerant cultivars of selected species can play an important role in successful silvopastoral management.

Due to their nitrogen fixing ability, the incorporation of shade tolerant legume species may have a special role in increasing the quality and productivity of silvopastures and in enhancing soil fertility.
Rediscovering valonia oak acorns
Creators: name: Papadopoulos, Andreas
Publisher: name: Zenodo
Year: 2017
Subjects: Agroforestry
Silvopastoral
Agrosilvopastoral
Valonia oak
Acorn cups

description: Two valonia oak systems are present in Greece: ancient open forests (silvopastoral systems) and agricultural fields with valonia oak trees (agro-silvopastoral systems). Both have significant socio-economic, ecological and cultural value. They provide ecosystem services and support traditional uses including, grazing, acorn cup and nut collection, harvesting wood (for shipbuilding, firewood and charcoal) and collection of aromatic and medicinal plants.Valonia oak forests are one of the habitats of the NATURA 2000 network and include monumental trees in many places in Greece. The harvesting of acorn cups for leather tanning rendered it a very important traditional economic activity up to 1970s, significantly contributing to the localeconomy. The average annual production of acorn cups in the past reached 14,000 tonnes. Most were exported as raw material or processed to produce powder, liquid or extract. In recent years, there has been a growing interest in reassessing the productive value of these systems within the context of acorn harvesting, organic agriculture and animal husbandry, as well as for environmental protection reasons. There is also increasing interest in the history of this traditional practice.
Modelling livestock carrying capacity in montados
Creators: name: Palma, Joao
name: Oliveira, Tânia Sofia
name: Moreno, Gerardo
name: Crous-Duran, Josep
name: Paulo, Joana Amaral
Publisher: name: Zenodo
Year: 2017
Subjects: Carrying capacity
Montado
Pasture
Yield-SAFE
Microclimate

description: First impressions are often that the presence of trees in pasture systems will lead to a reduction in pasture production due to the light and water competition. However, other effects on the system dynamics and water availability may be beneficial to nutrient cycling, yield, and pasture productivity. Trees affect wind speed and temperature, creating a milder climate by providing shade under the canopies. This microclimate can improve pasture production and availability (more production in winter and delayed drying in early summer), and reduce livestock energy requirements.
Factores asociados a la homofobia en estudiantes de enfermería de las universidades de la ciudad de Cartagena.
Creators: name: López Roca, Yessica Alejandra
name: Martínez Arango, Angie Carolina
name: Negrete González, Yiseth María
name: Paternina Mejía, Saira Luz
Publisher: name: Universidad de Cartagena
Year: 2016
Subjects: Estudiantes de enfermería - Investigaciones
Homofobia - Investigaciones

description: Tesis (Enfermero). -- Universidad de Cartagena. Facultad de Enfermería, 2016
description: El término “Homofobia” fue utilizado por primera vez por Weinberg para referirse a “la condena irracional hacia los individuos homosexuales cuya consecuencia es la violencia, deprivación y separación. Diversos factores se asocian a esta conducta tales como, la religión, el género, estrato social, edad, nivel educativo, entre otros. Se concluye que el alto nivel de homofobia es frecuente en estudiantes de enfermería de mayor nivel de estudios. Esta actitud negativa hacia personas de la comunidad LGTBI, podría tener efectos desfavorables en la atención en salud brindada por el personal de enfermería.
Ca2+ sparks operated by membrane depolarization require isoform 3 ryanodine receptor channels in skeletal muscle
Creators: name: Pouvreau, S.
name: Meissner, G.
name: Brum, G.
name: Yi, J.
name: Royer, L.
name: Zhou, J.
name: Rios, E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Stimuli are translated to intracellular calcium signals via opening of inositol trisphosphate receptor and ryanodine receptor (RyR) channels of the sarcoplasmic reticulum or endoplasmic reticulum. In cardiac and skeletal muscle of amphibians the stimulus is depolarization of the transverse tubular membrane, transduced by voltage sensors at tubular–sarcoplasmic reticulum junctions, and the unit signal is the Ca2+ spark, caused by concerted opening of multiple RyR channels. Mammalian muscles instead lose postnatally the ability to produce sparks, and they also lose RyR3, an isoform abundant in spark-producing skeletal muscles. What does it take for cells to respond to membrane depolarization with Ca2+ sparks? To answer this question we made skeletal muscles of adult mice expressing exogenous RyR3, demonstrated as immunoreactivity at triad junctions. These muscles showed abundant sparks upon depolarization. Sparks produced thusly were found to amplify the response to depolarization in a manner characteristic of Ca2+-induced Ca2+ release processes. The amplification was particularly effective in responses to brief depolarizations, as in action potentials. We also induced expression of exogenous RyR1 or yellow fluorescent protein-tagged RyR1 in muscles of adult mice. In these, tag fluorescence was present at triad junctions. RyR1-transfected muscle lacked voltage-operated sparks. Therefore, the voltage-operated sparks phenotype is specific to the RyR3 isoform. Because RyR3 does not contact voltage sensors, their opening was probably activated by Ca2+, secondarily to Ca2+ release through junctional RyR1. Physiologically voltage-controlled Ca2+ sparks thus require a voltage sensor, a master junctional RyR1 channel that provides trigger Ca2+, and a slave parajunctional RyR3 cohort.
White Paper on Food and Drink Waste Management
Creators: name: Model2Bio project team
name: Fernández Arévalo, Tamara
Publisher: name: Zenodo
Year: 2023
Subjects: Agri-food by-products
Valorisation
Decision Support System (DSS) tool
Waste management and optimisation
Bio-based industries (BBIs)

description: This white paper shows the potential of some of the most prominent and relevant agri-food byproducts in Europe and it identifies some of the innovative treatments for their valorisation, as well as promising value chains. After an analysis of the potential of the most relevant sectors of the agri-food industry (vegetable, dairy, alcoholic beverage and meat sector), the focus has been on five key residual streams such as potato steam peels, cheese whey, brewer's spent grain, grape seeds & peels, and olive leaves. Each of these byproducts presents unique challenges, yet they also offer numerous opportunities for innovative and sustainable valorisation. The case studies presented have allowed us to exemplify the potential of biorefinery approaches that could be implemented using by-products as substrate valorisation processes. Thanks to these approaches, it is possible to obtain a wide range of high-value products, from biodegradable films and bioplastics to antioxidants and biofuels. This strategic approach not only addresses the environmental concerns associated with waste disposal, but also aligns with the growing demand for sustainable solutions and the promotion of circular economies.
In parallel to technological innovation, it is necessary to develop tools for managing information, analysing solutions in an agile manner and also for making decisions. One such tool worth is the pioneering Model2Bio decision support (DSS) tool (https:// www.model2bio.eu/). It is based on mathematical models to predict agri-food residual streams and to identify the best routes for valorising them. Based on current innovation, the obvious strategy to follow is to maximise the conversion and extraction processes to obtain value-added compounds. But is it the best valuation option in all cases? Considering only technical criteria, the answer would be yes. But what is the point of obtaining valuable products if the cost of their production and logistics exceeds their market value? Under this holistic perspective the problem becomes complex and it is necessary to use tools that allow all variables to be analysed as a whole. The Model2Bio-DSS tool considers technical, economic, environmental and social aspects together to make the best valuation option in each specific case, helping in decision-making with multiple factors.
Managing shrub encroachment in cork oak montado
Creators: name: Paulo, Joana Amaral
name: Faias, Sónia
name: Palma, Joao
Publisher: name: Zenodo
Year: 2017
Subjects: Montado
Cork oak
Understorey management

description: The impact of the shrub layers that naturally occupy the montado ecosystem can often be positive. Benefits include: natural tree regeneration; protection from excessive light exposure and animal predation; soil protection; increased carbon sequestration; increased fodder diversity; increased biodiversity.However, there can also be negative impacts. These include: tree-shrub-pasture competition for natural resources (water, nutrients and light); increased fire risk.The balance between positive and negative impacts varies between farms and even within a single farm. It depends on factors such as: species composition and age; tree age and vitality; climate conditions; soil water holding capacity; grazing animals.
title: Book review : Pallett, C., Blackeby, K., Bengo, C., Yule, W., Weissman, R., Scott, S. &Fursland, E. (2015). Managing difficult behaviour: How to improve relationships. London: CoramBAAF. 128pp. ISBN: 9781910039366
Creators: name: Barr, Erica
Publisher: name: Strathprints - University of Strathclyde
Year: 2017

description: Managing difficult behaviour, or as it is sometimes referred 'challenging behaviour' is the subject of many books, articles and training courses within various fields including education, residential child care, foster care, mental health, learning disabilities and elderly care. Working with trauma-experienced and relationally resistant youth can be very challenging. Their early childhood experiences of abuse, neglect and often trauma means that they have very complex needs and difficulty regulating their emotions, which are often expressed through their behaviour (Cairns, 2016). Managing challenging behaviour, or pain-based behaviour (Anglin, 2003) (which I feel is a more helpful and informed term), can be very difficult and is often the cause of multiple placement breakdowns both within residential child care and foster care. Supporting carers to develop the necessary skills to confidently and competently respond to young people in an emotionally attuned way is vital to improving stability of placements and long-term outcomes (Fahlberg, 2012).
Global Inversion of Functions: an Introduction
Creators: name: De Marco, Giuseppe
name: Gorni, Gianluca
name: Zampieri, Gaetano
Publisher: name: arXiv
Year: 2014
Subjects: subject: Functional Analysis (math.FA)
subject: FOS: Mathematics

description: This is an exposition of some basic ideas in the realm of Global Inverse Function theorems. We address ourselves mainly to readers who are interested in the applications to Differential Equations. But we do not deal with those applications and we give a `self-contained' elementary exposition.
Stability Characteristics of a Single Injector Combustor through Acoustic Solutions with Large Eddy Simulated Heat Sources
Creators: name:  MUSA ONUR OZTURKMEN
name:   YUSUF OZYORUK
Publisher: name: Proceedings of the Aerospace Europe Conference - EUCASS - CEAS - 2023
Year: 2023
Subjects: HELMHOLTZ SOLVER
THERMO-ACOUSTIC INSTABILITIES
FLAME TRANSFER FUNCTION

description: The stability characteristics of the experimental combustion chamber known as CVRC (Continuously Variable Resonance Chamber) in literature are investigated through frequency domain solutions of the nonhomogeneous wave equation with heat sources that are computed by large eddy simulation. The heat sources are represented by flame transfer functions and the discretized nonhomogeneous wave equation is cast into a non-linear quadratic eigenvalue problem which is first linearized, and then solved iteratively. By varying the oxidizer post length, the combustion chamber exhibits different stability characteristics due to acoustic and combustion interactions. An oxidizer post length of 13.97 cm is chosen for the study. The computed results exhibit consistent characteristics with those from literature.
Factores asociados a la susceptibilidad al consumo de cigarrillo en escolares de 10 y 11 años de la ciudad de Cartagena
Creators: name: Amador Herrera, Rocío
name: Ayola Marrugo, Elymer
name: Ballesteros Estrada, Laura
name: Orozco Gómez, Yarlys
Publisher: name: Universidad de Cartagena
Year: 2013
Subjects: Enfermería de salud pública
Salud pública - Investigaciones

description: Tesis (Enfermero)-- Universidad de Cartagena. Facultad de enfermería, 2013
description: La susceptibilidad al consumo de cigarrillo en estudiantes de 6° y 7° grado, están asociados a ser del genero masculino, la disfuncionalidad familiar y haber fumado alguna vez en la vida. Los niños son los mas vulnerables de adquirir conductas de riesgo y en estas edades la modificación de hábitos es mas fácil, en la edad escolar en la que se produce habitualmente la experimentación y adquisición del habito. Esto es preocupante para la salud pública.
CCR4/NOT complex associates with the proteasome and regulates histone methylation
Creators: name: Roguev, A.
name: Weissman, J. S.
name: Strahl, B. D.
name: Kemmeren, P.
name: Krogan, N. J.
name: Mersman, D. P.
name: Shibata, Y.
name: Laribee, R. N.
name: Collins, S. R.
name: Briggs, S. D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: The proteasome regulates histone lysine methylation and gene transcription, but how it does so is poorly understood. To better understand this process, we used the epistatic miniarray profile (E-MAP) approach to identify factors that genetically interact with proteasomal subunits. In addition to members of the Set1 complex that mediate histone H3 lysine 4 methylation (H3K4me), we found that deleting members of the CCR4/NOT mRNA processing complex exhibit synthetic phenotypes when combined with proteasome mutants. Further biochemical analyses revealed physical associations between CCR4/NOT and the proteasome in vivo. Consistent with the genetic and biochemical interactions linking CCR4/NOT with proteasome and Set1-mediated methylation, we find that loss of Not4 decreases global and gene-specific H3K4 trimethylation (H3K4me3) and decreases 19S proteasome recruitment to the PMA1 gene. Similar to proteasome regulation of histone methylation, loss of CCR4/NOT members does not affect ubiquitinated H2B. Mapping of Not4 identified the RING finger domain as essential for H3K4me3, suggesting a role for ubiquitin in this process. Consistent with this idea, loss of the Not4-interacting protein Ubc4, a known ubiquitin-conjugating enzyme, decreases H3K4me3. These studies implicate CCR4/NOT in the regulation of H3K4me3 through a ubiquitin-dependent pathway that likely involves the proteasome.
Surveying 1 Civil SVN11P1
Creators: name: Kieck, Ray
Publisher: name: Walter Sisulu University
Year: 2022
Subjects: Civil engineering not elsewhere classified

description: Subject : Surveying I Subject code : SVN11P1 Qualification : National Diploma Engineering: Civil Examiners : Mr. R Kieck Moderator : Mr J van Heerden Date : June 2019
From short to too-short arcs: admissible states region theory and boundary use for surveillance observations
Creators: name:  LAURA PIROVANO
name:   MATTEO LOSACCO
name:   ROBERTO ARMELLIN
name:   CARLOS YANEZ
name:   EMMANUEL DELANDE
name:   STEPHANIE LIZY-DESTREZ
Publisher: name: Proceedings of the Aerospace Europe Conference - EUCASS - CEAS - 2023
Year: 2023
Subjects: INITIAL ORBIT DETERMINATION
ADMISSIBLE REGIONS
SHORT ARCS
SPACE DEBRIS

description: This work develops a rigorous metric for the identification of the boundary between the short and the tooshort arcs regimes in the initial orbit determination process. The proposed approach makes use of differential algebra and domain-splitting techniques to investigate the presence of singularities in the formulation of the initial orbit determination process. When these are detected, a six-dimensional reformulation of the classical admissible region concept is employed. Examples for ground and space-based sensor types are then presented.
Basic phenomenology for relativistic heavy-ion collisions
Creators: name: Florkowski, Wojciech
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: Basic concepts used to interpret the soft-hadronic data collected in relativistic heavy-ion collisions are reviewed at the elementary level.
description: introductory lectures presented at the Cracow School of Theoretical Physics, LIV Course, 2014
Hidden magnetic fields in stellar interiors probed by asteroseismology
Creators: name: Fort, Antoine
name: Ouazzani, Rhita-Maria
name: Goupil, Marie-Jo
Publisher: name: Zenodo
Year: 2024

description: Understanding the distribution and evolution of angular momentum is crucial for comprehending star formation processes, stellar evolution and activity, and their influence on planet formation and environment. Recent space photometry missions, such as CoRoT and Kepler, have revolutionized our understanding of stellar structure and evolution by highlighting discrepancies in current angular momentum transport models. However, incorporating magnetic fields into these models could offer a solution to this transport problem. Even though detecting and measuring magnetic fields within stellar interiors utilizing perturbative methods through asteroseismology is a recent breakthrough, there remains a need for a non-perturbative model, of which the first steps of the development will be presented in this poster. This model would comprehensively consider both stellar rotation and magnetic fields in a two-dimensional framework, testing the existing perturbative methods, surpassing their limitations and tackling the area of strong and complex internal magnetic fields.
Control of Emi2 activity and stability through Mos-mediated recruitment of PP2A
Creators: name: Freel, C. D.
name: Wang, M. Z.
name: Kornbluth, S.
name: Tung, J. J.
name: Jackson, P. K.
name: Hansen, D. V.
name: Wu, J. Q.
name: Tang, W.
name: Guo, Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Before fertilization, vertebrate eggs are arrested in meiosis II by cytostatic factor (CSF), which holds the anaphase-promoting complex (APC) in an inactive state. It was recently reported that Mos, an integral component of CSF, acts in part by promoting the Rsk-mediated phosphorylation of the APC inhibitor Emi2/Erp1. We report here that Rsk phosphorylation of Emi2 promotes its interaction with the protein phosphatase PP2A. Emi2 residues adjacent to the Rsk phosphorylation site were important for PP2A binding. An Emi2 mutant that retained Rsk phosphorylation but lacked PP2A binding could not be modulated by Mos. PP2A bound to Emi2 acted on two distinct clusters of sites phosphorylated by Cdc2, one responsible for modulating its stability during CSF arrest and one that controls binding to the APC. These findings provide a molecular mechanism for Mos action in promoting CSF arrest and also define an unusual mechanism, whereby protein phosphorylation recruits a phosphatase for dephosphorylation of distinct sites phosphorylated by another kinase.
Cryopyrin/NALP3 binds ATP/dATP, is an ATPase, and requires ATP binding to mediate inflammatory signaling
Creators: name: Willingham, S. B.
name: Wang, Y.
name: Duncan, J. A.
name: Zimmermann, A. G.
name: Ting, J. P.-Y.
name: Ye, Z.
name: Bergstralh, D. T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: The CATERPILLER (CLR/NLR) gene family encodes a family of putative nucleotide-binding proteins important for host defense. Although nucleotide binding is thought to be central to this family, this aspect is largely unstudied. The CATERPILLER protein cryopyrin/NALP3 regulates IL-1β processing by assembling the multimeric inflammasome complex. Mutations within the exon encoding the nucleotide-binding domain are associated with hereditary periodic fevers characterized by constitutive IL-1β production. We demonstrate that purified cryopyrin binds ATP, dATP, and ATP-agarose, but not CTP, GTP, or UTP, and exhibits ATPase activity. Mutation of the nucleotide-binding domain reduces ATP binding, caspase-1 activation, IL-1β production, cell death, macromolecular complex formation, self-association, and association with the inflammasome component ASC. Disruption of nucleotide binding abolishes the constitutive activation of disease-associated mutants, identifying nucleotide binding by cryopyrin as a potential target for antiinflammatory pharmacologic intervention.
title: Cycloadditionen des Azulens unter hohem Druck
Creators: name: Klärner, Frank-Gerrit
name: Dogan, Barbara
name: Roth, Wolfgang R.
name: Hafner, Klaus
Publisher: name: Wiley
Year: 2023

description: Die Umsetzung von Acetylendicarbonshre-dimethylester 2a mit Azulen 1 (siedendes Tetralin, 207.6 °C) führt zum Heptalendicarbonsäure dimethylester 7a[¹].
Geotechnical Engineering II GEN22B1 EGEN22B1
Creators: name: Mbugua, Rose
name: Gangerdine, Angelo
Publisher: name: Walter Sisulu University
Year: 2022
Subjects: Civil geotechnical engineering
Civil engineering not elsewhere classified
Water resources engineering
Transport engineering
Timber engineering
Structural engineering
Construction materials

description: Subject : Geotechnical Engineering II Subject code : GEN22B1; EGEN22B1 Qualification : National Diploma Engineering: Civil Examiners : DR. Rose Mbugua & Mr. Angelo Gangerdine Moderator : Mr Jan van der Merwe Date : June 2019
Delayed upwelling alters nearshore coastal ocean ecosystems in the northern California current
Creators: name: Kirincich, A. R.
name: Barth, J. A.
name: McManus, M. A.
name: Bane, J. M.
name: Menge, B. A.
name: Chan, F.
name: Pierce, S. D.
name: Nielsen, K. J.
name: Lubchenco, J.
name: Washburn, L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Wind-driven coastal ocean upwelling supplies nutrients to the euphotic zone near the coast. Nutrients fuel the growth of phytoplankton, the base of a very productive coastal marine ecosystem [Pauly D, Christensen V (1995) Nature 374:255–257]. Because nutrient supply and phytoplankton biomass in shelf waters are highly sensitive to variation in upwelling-driven circulation, shifts in the timing and strength of upwelling may alter basic nutrient and carbon fluxes through marine food webs. We show how a 1-month delay in the 2005 spring transition to upwelling-favorable wind stress in the northern California Current Large Marine Ecosystem resulted in numerous anomalies: warm water, low nutrient levels, low primary productivity, and an unprecedented low recruitment of rocky intertidal organisms. The delay was associated with 20- to 40-day wind oscillations accompanying a southward shift of the jet stream. Early in the upwelling season (May–July) off Oregon, the cumulative upwelling-favorable wind stress was the lowest in 20 years, nearshore surface waters averaged 2°C warmer than normal, surf-zone chlorophyll-a and nutrients were 50% and 30% less than normal, respectively, and densities of recruits of mussels and barnacles were reduced by 83% and 66%, respectively. Delayed early-season upwelling and stronger late-season upwelling are consistent with predictions of the influence of global warming on coastal upwelling regions.
Cold stress induces differential gene expression of retained homeologs in Camelina sativa cv Suneson
Creators: name: Fang, Chao
name: Hamilton, John
name: Vaillancourt, Brieanne
name: Wang, Yi-Wen
name: Wood, Joshua
name: Deans, Natalie C.
name: Strayhorn, Taylor
name: Carlton, Lemor
name: Mailloux, Kathrine
name: Douches, David S.
name: Nadakuduti, S. Swathi
name: Jiang, Jiming
name: Buell, C. Robin
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 310899
subject: Plant biology not elsewhere classified
classificationCode: 310802
subject: Plant biochemistry

description: Abstract:
Camelina sativa (L.) Crantz, a member of the Brassicaceae, has potential as a biofuel feedstock which is attributable to the production of fatty acids in its seeds, its fast growth cycle, and low input requirements. While a genome assembly is available for camelina, it was generated from short sequence reads and is thus highly fragmented in nature. Using long read sequences, we generated a chromosome-scale, highly contiguous genome assembly (644,491,969 bp) for the spring biotype cultivar ‘Suneson’ with an N50 contig length of 12,031,512 bp and a scaffold N50 length of 32,184,682 bp. Annotation of protein-coding genes revealed 91,877 genes that encode 133,355 gene models. We identified a total of 4,467 genes that were significantly up-regulated under cold stress which were enriched in gene ontology terms associated with ‘response to cold’ and ‘response to abiotic stress’. Coexpression analyses revealed multiple coexpression modules that were enriched in genes differentially expressed following cold stress that had putative functions involved in stress adaptation, specifically within the plastid. With access to a highly contiguous genome assembly, comparative analyses with Arabidopsis thaliana revealed 23,625 A. thaliana genes syntenic with 45,453 Suneson genes. Of these, 24,960 Suneson genes were syntenic to 8,320 A. thaliana genes reflecting a 3 camelina homeolog to 1 Arabidopsis gene relationship and retention of all three homeologs. Some of the retained triplicated homeologs showed conserved gene expression patterns under control and cold-stressed conditions whereas other triplicated homeologs displayed diverged expression patterns revealing sub- and neo-functionalization of the homeologs at the transcription level. Access to the chromosome-scale assembly of Suneson will enable both basic and applied research efforts in the improvement of camelina as a sustainable biofuel feedstock.
Differential Apaf-1 levels allow cytochrome c to induce apoptosis in brain tumors but not in normal neural tissues
Creators: name: Smith, M. I.
name: Zhang, Q.
name: Kornbluth, S.
name: Vaughn, A. E.
name: Van Dyke, T.
name: Deshmukh, M.
name: Wechsler-Reya, R. J.
name: Parrish, A. B.
name: Wright, K. M.
name: Huang, Y. Y.
name: Johnson, C. E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Brain tumors are typically resistant to conventional chemotherapeutics, most of which initiate apoptosis upstream of mitochondrial cytochrome c release. In this study, we demonstrate that directly activating apoptosis downstream of the mitochondria, with cytosolic cytochrome c, kills brain tumor cells but not normal brain tissue. Specifically, cytosolic cytochrome c is sufficient to induce apoptosis in glioblastoma and medulloblastoma cell lines. In contrast, primary neurons from the cerebellum and cortex are remarkably resistant to cytosolic cytochrome c. Importantly, tumor tissue from mouse models of both high-grade astrocytoma and medulloblastoma display hypersensitivity to cytochrome c when compared with surrounding brain tissue. This differential sensitivity to cytochrome c is attributed to high Apaf-1 levels in the tumor tissue compared with low Apaf-1 levels in the adjacent brain tissue. These differences in Apaf-1 abundance correlate with differences in the levels of E2F1, a previously identified activator of Apaf-1 transcription. ChIP assays reveal that E2F1 binds the Apaf-1 promoter specifically in tumor tissue, suggesting that E2F1 contributes to the expression of Apaf-1 in brain tumors. Together, these results demonstrate an unexpected sensitivity of brain tumors to postmitochondrial induction of apoptosis. Moreover, they raise the possibility that this phenomenon could be exploited therapeutically to selectively kill brain cancer cells while sparing the surrounding brain parenchyma.
Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase
Creators: name: Guogas, L. M.
name: Lujan, S. A.
name: Ragonese, H.
name: Matson, S. W.
name: Redinbo, M. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Conjugative transfer of plasmid DNA via close cell–cell junctions is the main route by which antibiotic resistance genes spread between bacterial strains. Relaxases are essential for conjugative transfer and act by cleaving DNA strands and forming covalent phosphotyrosine linkages. Based on data indicating that multityrosine relaxase enzymes can accommodate two phosphotyrosine intermediates within their divalent metal-containing active sites, we hypothesized that bisphosphonates would inhibit relaxase activity and conjugative DNA transfer. We identified bisphosphonates that are nanomolar inhibitors of the F plasmid conjugative relaxase in vitro. Furthermore, we used cell-based assays to demonstrate that these compounds are highly effective at preventing DNA transfer and at selectively killing cells harboring conjugative plasmids. Two potent inhibitors, clodronate and etidronate, are already clinically approved to treat bone loss. Thus, the inhibition of conjugative relaxases is a potentially novel antimicrobial approach, one that selectively targets bacteria capable of transferring antibiotic resistance and generating multidrug resistant strains.
Enhanced EGFP-chromophore-assisted laser inactivation using deficient cells rescued with functional EGFP-fusion proteins
Creators: name: Vitriol, E. A.
name: Shen, F.
name: Bear, J. E.
name: Uetrecht, A. C.
name: Jacobson, K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Chromophore-assisted laser inactivation (CALI) is a light-mediated technique that offers precise spatiotemporal control of protein inactivation, enabling better understanding of the protein's role in cell function. EGFP has been used effectively as a CALI chromophore, and its cotranslational attachment to the target protein avoids having to use exogenously added labeling reagents. A potential drawback to EGFP-CALI is that the CALI phenotype can be obscured by the endogenous, unlabeled protein that is not susceptible to light inactivation. Performing EGFP-CALI experiments in deficient cells rescued with functional EGFP-fusion proteins permits more complete loss of function to be achieved. Here, we present a modified lentiviral system for rapid and efficient generation of knockdown cell lines complemented with physiological levels of EGFP-fusion proteins. We demonstrate that CALI of EGFP-CapZβ increases uncapped actin filaments, resulting in enhanced filament growth and the formation of numerous protrusive structures. We show that these effects are completely dependent upon knocking down the endogenous protein. We also demonstrate that CALI of EGFP-Mena in Mena/VASP-deficient cells stabilizes lamellipodial protrusions.
On zero-rate error exponents of finite-state channels with input-dependent states
Creators: name: Merhav, Neri
Publisher: name: arXiv
Year: 2014
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: We derive a single-letter formula for the zero-rate reliability (error exponent) of a finite-state channel whose state variable depends deterministically (and recursively) on past channel inputs, where the code complies with a given channel input constraint. Special attention is then devoted to the important special case of the Gaussian channel with inter-symbol interference (ISI), where more explicit results are obtained.
description: 22 pages; submitted to IEEE Transactions on Information Theory
Consumer Factors Affecting the Gap between Food Price Index and Consumer Sentiment Price
Creators: name: Heo, Taeho
name: Heo, Taeho
Publisher: name: Unknown
Year: 2020
Subjects: subject: Agricultural and Food Policy
subject: Demand and Price Analysis
subject: Food price index
subject: consumer sentiment price
subject: Price Index and Cognition Difference Index (PICDI)

description: In this study, we calculated the Price Index and Cognition Difference Index(PICDI) by analyzing the difference between the real food price index and consumer sentiment price. Our analysis of the PICDI calculated in this study shows that most consumers perceive the consumer sentiment price index higher than the real food price index. We also analyzed the factors influencing this difference. The result shows that both the real food price index and consumer sentiment price are influenced by gender, occupation, purchasing frequency, purchasing location, income, and expenditure.
Existence of transient functional double-stranded DNA intermediates during recombinant AAV transduction
Creators: name: Samulski, R. J.
name: Wang, J.
name: Xiao, W.
name: Hauck, B.
name: Chen, L.
name: Xie, J.
name: Lu, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Previous studies have documented that 0.1≈1% of input recombinant adeno-associated virus (rAAV) vectors could be stabilized and lead to transgene expression. To characterize the steps involving massive AAV DNA loss, we designed an“AAV footprinting” strategy that can track newly formed AAV dsDNA genomes. This strategy is based on an ROSA26R mouse model or cell line that carries a lacZ gene flanked by two loxP sites. When it is transduced by a rAAV vector carrying the Cre recombinase, the lacZ gene can be activated and remain active even when rAAV genomes are later lost. By using this sensitive AAV footprinting technique, we confirmed the existence of transient AAV dsDNA that went undetected by conventional DNA methods. Although these dsDNA intermediates could be efficiently formed in almost every cell and were competent for mRNA transcription and protein synthesis in vivo, they got lost continuously. Only a small fraction was eventually stabilized for sustained gene expression. Although both rAAV2 and rAAV8 can potentially have similar levels of dsDNA formation, AAV8 dsDNA was formed much faster than that of AAV2, which explains why rAAV8 is more efficient than rAAV2 in transducing the liver. Collectively, our studies suggested that rather than receptor binding, viral entry, and ssDNA to dsDNA conversion, the instability of newly formed AAV dsDNA was the primary contributing factor for the low rAAV transduction efficacy. The uncoating step significantly influenced the stability of AAV transient dsDNA. The identification of transient AAV dsDNA provided a new pathway for improving rAAV transduction.
Quality characteristics of chicken meat belonging to the different market categories available in Italy
Creators: name: Soglia, Francesca
name: Gagliano, Mara Antonia
name: Mancinelli, Alice Cartoni
name: Petracci, Massimiliano
Publisher: name: Zenodo
Year: 2023

description: The present study aims at evaluating the quality traits and technological properties of chicken breast meat belonging to the different market categories available in Italy.
Photoionization of atoms and molecules studied by Crank-Nicolson method
Creators: name: Bian, Xue-Bin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Crank-Nicolson (C-N) Method combined with $ B $-spline basis set can be used in both time-dependent and time-independent calculations of the photoionization cross sections of atoms and molecules. For time-independent systems, it is found that C-N method in imaginary-time propagation (ITP) can converge directly to not only the ground state, but also excited and continuum states by controlling the time step size. The C-N method can also be directly applied in time-dependent calculations. Both time-dependent and time-independent calculations agree very well with previous results. This method can also be extended to two-electron systems directly.
GTPase acceleration as the rate-limiting step in Arabidopsis G protein-coupled sugar signaling
Creators: name: Chen, J.-G.
name: Willard, F. S.
name: Jones, A. M.
name: Kimple, A. J.
name: Grigston, J. C.
name: Johnston, C. A.
name: Taylor, J. P.
name: Gao, Y.
name: Siderovski, D. P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Heterotrimeric G protein signaling is important for cell-proliferative and glucose-sensing signal transduction pathways in the model plant organism Arabidopsis thaliana. AtRGS1 is a seven-transmembrane, RGS domain-containing protein that is a putative membrane receptor for d-glucose. Here we show, by using FRET, that d-glucose alters the interaction between the AtGPA1 and AtRGS1 in vivo. AtGPA1 is a unique heterotrimeric G protein α subunit that is constitutively GTP-bound given its high spontaneous nucleotide exchange coupled with slow GTP hydrolysis. Analysis of a point mutation in AtRGS1 that abrogates GTPase-accelerating activity demonstrates that the regulation of AtGPA1 GTP hydrolysis mediates sugar signal transduction during Arabidopsis development, in contrast to animals where nucleotide exchange is the limiting step in the heterotrimeric G protein nucleotide cycle.
High-resolution design of a protein loop
Creators: name: Kuhlman, B.
name: Hu, X.
name: Wang, H.
name: Ke, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Despite having irregular structure, protein loops often adopt specific conformations that are critical to protein function. Most studies in de novo protein design have focused on creating proteins with regular elements of secondary structure connected by very short loops or turns. To design longer protein loops that adopt specific conformations, we have developed a protocol within the Rosetta molecular modeling program that iterates between optimizing the sequence and conformation of a loop in search of low-energy sequence–structure pairs. We have tested the procedure by designing 10-residue loops for the connection between the second and third strand in the β-sandwich protein tenascin. Three low-energy designs from 7,200 flexible backbone trajectories were selected for experimental characterization. All three designs, called LoopA, LoopB, and LoopC, adopt stable folded structures. High-resolution crystal structures of LoopA and LoopB have been solved. LoopB adopts a structure very similar to the design model (0.46 Å rmsd), and all but one of the side chains are modeled in the correct rotamers. LoopA crystallized at low pH in a structure that differs dramatically from our design model. It forms a strand-swapped dimer mediated by hydrogen bonds to protonated glutamic acids. Gel filtration indicates that the protein is not a dimer at neutral pH. These results suggest that the high-resolution design of protein loops is possible; however, they also highlight how small changes in protein energetics can dramatically perturb the low free energy structure of a protein.
An Analysis of Forestry Companies’ Willingness to Pay for Forest-certified Timber
Creators: name: Jeon, Chulhyun
name: Jeon, Chulhyun
Publisher: name: Unknown
Year: 2020
Subjects: subject: International Relations/Trade
subject: Resource /Energy Economics and Policy
subject: timber legality
subject: non-tariff barrier
subject: forest certification

description: The purpose of this research is to carry out an analysis of the business’s perception against non-tariff barriers to the timber trade, the impact on the Act of Legal Timber Trade Promotion, and estimate the willingness to pay off the forest certified-timber for legality certification acquisition. We conducted an interview survey targeting representatives or managers between June 12~September 30, 2018. The samples for the survey were allocated to 140 units in the metropolitan area, 30 units in the Gyungsang area, 30 units in the Chungcheong/Jeonra area, considering the proportion based on the registered companies as timber production. To summarize the main results, 66.2% of the surveyed companies in the importation of timber answered that they faced problems concerning the recognition and responses of non-tariff barriers. Regarding the areas for the national response, 60.7% of respondents pointed to ‘precise technical regulatory information’ and 60.2% to ‘provision of solutions for technical regulations.’ As for the instrument to be recognized as legality in case of a restriction on illegal timber trade among the number of measures to obtain legalization was harvesting permits (58.2%) and the acquisition of forest-related certification(FSC, PEFC) (57.2%). Regarding the estimation of payments for the recognition of timber legality, 24.4% of respondents representing additional costs to purchase forest-certified wood as a means of obtaining legality of timber pay additional costs approximately average WTP ￦28,059/㎥, Truncated WTP ￦13,188/㎥, Median WTP ￦28,428/㎥ using DBCV. This result could be useful as policy-making against NTB in timber-related business. As well, it is necessary to make an advertisement of the instrument for reducing adverse effects before implementing the new institution.
SHERPA Position Paper - Climate Change and Environmental Sustainability
Creators: name: Miller, David
name: Bourneix, Julie
name: Cooksley, Susan
name: Irvine, Kate
name: Kuulia, Vilma
name: Martino, Giulia
name: Nijnik, Maria
name: Schwarz, Gerald
name: Wang, Chen
Publisher: name: Zenodo
Year: 2022
Subjects: Climate change
Environmental sustainability
Climate neutrality

description: Tackling climate change and striving for environmental sustainability cross almost all aspects of the lives of citizens, and over multiple generations as individuals take on different responsibilities through their life course. The transitions required to achieve net zero Greenhouse Gas (GHG) emissions by 2050 requires all citizens to be agents of change, including rural citizens. SHERPA Position Paper on Climate Change and Environmental Sustainability aims to contributesto the process of making Europe - and rural areas within the European continent- climate neutral. Through a concerted discussion of different Multi-Stakeholder Platforms (MAPs), SHERPA gathered evidence of the types of transformational changes which are necessary to transition in an effective and just manner to climate neutrality by 2050.
description: {"references": ["Miller, D., Bourneix, J., Cooksley, S., Irvine, K., Kuulia, V., Martino, G., Nijnik, M., Schwarz, G. and Wang, C. (2022). SHERPA Position Paper on Climate Change and Environmental Sustainability, Sustainable Hub to Engage into Rural Policies with Actors (SHERPA), pp39."]}
Effect of the iron valence in the two types of layers in LiFeO$_2$Fe$_2$Se$_2$
Creators: name: Heil, Christoph
name: Boeri, Lilia
name: Sormann, Heinrich
name: von der Linden, Wolfgang
name: Aichhorn, Markus
Publisher: name: arXiv
Year: 2014
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We perform electronic structure calculations for the recently synthesized iron-based superconductor LiFeO$_2$Fe$_2$Se$_2$. In contrast to other iron-based superconductors, this material comprises two different iron atoms in 3$d^5$ and 3$d^6$ configurations. In band theory, both contribute to the low-energy electronic structure. Spin-polarized density functional theory calculations predict an antiferromagnetic metallic ground state with different moments on the two Fe sites. However, several other almost degenerate magnetic configurations exist. Due to their different valences, the two iron atoms behave very differently when local quantum correlations are included through the dynamical mean-field theory. The contributions from the half-filled 3$d^5$ atoms in the LiFeO$_2$ layer are suppressed and the 3$d^6$ states from the FeSe layer restore the standard iron-based superconductor fermiology.
description: 9 pages, 11 figures
In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut
Creators: name: Rawls, J. F.
name: Mahowald, M. A.
name: Trent, C. M.
name: Gordon, J. I.
name: Goodman, A. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Complex microbial communities reside within the intestines of humans and other vertebrates. Remarkably little is known about how these microbial consortia are established in various locations within the gut, how members of these consortia behave within their dynamic ecosystems, or what microbial factors mediate mutually beneficial host–microbial interactions. Using a gnotobiotic zebrafish–Pseudomonas aeruginosa model, we show that the transparency of this vertebrate species, coupled with methods for raising these animals under germ-free conditions can be used to monitor microbial movement and localization within the intestine in vivo and in real time. Germ-free zebrafish colonized with isogenic P. aeruginosa strains containing deletions of genes related to motility and pathogenesis revealed that loss of flagellar function results in attenuation of evolutionarily conserved host innate immune responses but not conserved nutrient responses. These results demonstrate the utility of gnotobiotic zebrafish in defining the behavior and localization of bacteria within the living vertebrate gut, identifying bacterial genes that affect these processes, and assessing the impact of these genes on host–microbial interactions.