cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Fish stocking for recreational angling is culpable for the poor condition of many English lakes designated for conservation purposes
Creators: name: Skeate, Eleanor R.
name: Perrow, Martin R.
name: Tomlinson, Mark L.
name: Madgwick, Genevieve
name: Harwood, Andrew J. P.
name: Ottewell, David
name: Berridge, Richard
name: Winfield, Ian J.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Marine Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Contemporary surveys and analysis of previous data identified negative effects of fish stocking for recreational angling in 87% of 23 English lakes (0.2–26 ha and 1–11.9 m mean depth) protected for nature conservation as Sites of Special Scientific Interest (SSSI). All sites except one were in unfavourable condition, with 92% failing to meet targets for characteristic macrophyte species. No lake was judged to have a natural fish community, and 96% had been subjected to fish stocking. The naturalised alien common carp (Cyprinus carpio) was the most widely introduced (87%). The presence of further alien species indicated illegal activity. A combination of estimates from surveys and angler records suggested carp comprised 53% of overall fish biomass density, with values up to 1164 kg ha−1 in individual lakes. Successful recruitment of carp, attributed to a warming climate, was recorded in 44% of the lakes in which it occurred. Consideration of fish impacts on lake ecology from the literature concluded that management of fish stocks, through biomanipulation, was required. The efficacy of biomanipulation was demonstrated by removal of fish from a large exclosure (29% of area) in one study lake and a resultant favourable response of water transparency and macrophyte growth. In the wider SSSI lakes series, we concluded that the retention of carp in any lake was an unacceptable risk to restoration of favourable condition, as were damaging angling practices. A ban on fish stocking in SSSI lakes is recommended, unless fish are introduced to restore natural communities.
Inhaled corticosteroids and FEV 1 decline in chronic obstructive pulmonary disease: a systematic review
Creators: name: Whittaker, Hannah R.
name: Jarvis, Debbie
name: Sheikh, Mohamed R.
name: Kiddle, Steven J.
name: Quint, Jennifer K.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Review
Lung function
COPD
Inhaled corticosteroids

description: Abstract: Rate of FEV1 decline in COPD is heterogeneous and the extent to which inhaled corticosteroids (ICS) influence the rate of decline is unclear. The majority of previous reviews have investigated specific ICS and non-ICS inhalers and have consisted of randomised control trials (RCTs), which have specific inclusion and exclusion criteria and short follow up times. We aimed to investigate the association between change in FEV1 and ICS-containing medications in COPD patients over longer follow up times. MEDLINE and EMBASE were searched and literature comparing change in FEV1 in COPD patients taking ICS-containing medications with patients taking non-ICS-containing medications were identified. Titles, abstract, and full texts were screened and information extracted using the PICO checklist. Risk of bias was assessed using the Cochrane Risk of Bias tool and a descriptive synthesis of the literature was carried out due to high heterogeneity of included studies. Seventeen studies met our inclusion criteria. We found that the difference in change in FEV1 in people using ICS and non-ICS containing medications depended on the study follow-up time. Shorter follow-up studies (1 year or less) were more likely to report an increase in FEV1 from baseline in both patients on ICS and in patients on non-ICS-containing medications, with the majority of these studies showing a greater increase in FEV1 in patients on ICS-containing medications. Longer follow-up studies (greater than 1 year) were more likely to report a decline in FEV1 from baseline in patients on ICS and in patients on non-ICS containing medications but rates of FEV1 decline were similar. Further studies are needed to better understand changes in FEV1 when ICS-containing medications are prescribed and to determine whether ICS-containing medications influence rate of decline in FEV1 in the long term. Results from inclusive trials and observational patient cohorts may provide information more generalisable to a population of COPD patients.
Band flattening in buckled monolayer graphene
Creators: name: Milovanović, S. P.
name: Anđelković, M.
name: Covaci, L.
name: Peeters, F. M.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The strain fields of periodically buckled graphene induce a periodic pseudo-magnetic field (PMF) that modifies the electronic band structure. From the geometry, amplitude, and period of the periodic pseudo-magnetic field, we determine the necessary conditions to access the regime of correlated phases by examining the band flattening. As compared to twisted bilayer graphene the proposed system has the advantages that: 1) only a single layer of graphene is needed, 2) one is not limited to hexagonal superlattices, and 3) narrower flat bandwidth and larger separation between flat bands can be induced. We, therefore, propose that periodically strained graphene single layers can become a platform for the exploration of exotic many-body phases.
description: To appear in Physical Review B
Neuroinflammation and protein pathology in Parkinson’s disease dementia
Creators: name: Kouli, Antonina
name: Camacho, Marta
name: Allinson, Kieren
name: Williams-Gray, Caroline H.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Research
Parkinson’s disease dementia
Neuropathology
Neuroinflammation
Microglia
Infiltrating lymphocytes
Pro-inflammatory cytokines
Toll-like receptors

description: Abstract: Parkinson’s disease dementia is neuropathologically characterized by aggregates of α-synuclein (Lewy bodies) in limbic and neocortical areas of the brain with additional involvement of Alzheimer’s disease-type pathology. Whilst immune activation is well-described in Parkinson’s disease (PD), how it links to protein aggregation and its role in PD dementia has not been explored. We hypothesized that neuroinflammatory processes are a critical contributor to the pathology of PDD. To address this hypothesis, we examined 7 brain regions at postmortem from 17 PD patients with no dementia (PDND), 11 patients with PD dementia (PDD), and 14 age and sex-matched neurologically healthy controls. Digital quantification after immunohistochemical staining showed a significant increase in the severity of α-synuclein pathology in the hippocampus, entorhinal and occipitotemporal cortex of PDD compared to PDND cases. In contrast, there was no difference in either tau or amyloid-β pathology between the groups in any of the examined regions. Importantly, we found an increase in activated microglia in the amygdala of demented PD brains compared to controls which correlated significantly with the extent of α-synuclein pathology in this region. Significant infiltration of CD4+ T lymphocytes into the brain parenchyma was commonly observed in PDND and PDD cases compared to controls, in both the substantia nigra and the amygdala. Amongst PDND/PDD cases, CD4+ T cell counts in the amygdala correlated with activated microglia, α-synuclein and tau pathology. Upregulation of the pro-inflammatory cytokine interleukin 1β was also evident in the substantia nigra as well as the frontal cortex in PDND/PDD versus controls with a concomitant upregulation in Toll-like receptor 4 (TLR4) in these regions, as well as the amygdala. The evidence presented in this study show an increased immune response in limbic and cortical brain regions, including increased microglial activation, infiltration of T lymphocytes, upregulation of pro-inflammatory cytokines and TLR gene expression, which has not been previously reported in the postmortem PDD brain.
of Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression
Creators: name: Jovanovic, Ivan
name: Zivkovic, Maja
name: Kostic, Mirjana
name: Krstic, Zoran
name: Djuric, Tamara
name: Kolic, Ivana
name: Alavantic, Dragan
name: Stankovic, Aleksandra
Publisher: name: figshare
Year: 2019
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Marine Biology
subject: 60506 Virology

description: of Transcriptome-wide based identification of miRs in congenital anomalies of the kidney and urinary tract (CAKUT) in children: the significant upregulation of tissue miR-144 expression
Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development
Creators: name: Adam, Ronja S.
name: Van Neerven, Sanne M.
name: Pleguezuelos-Manzano, Cayetano
name: Simmini, Salvatore
name: Léveillé, Nicolas
name: De Groot, Nina E.
name: Holding, Andrew N.
name: Markowetz, Florian
name: Vermeulen, Louis
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Primary Research
Intestinal cancer
Wnt signalling
Cell of origin

description: Abstract: Background: Cancer results from the accumulation of mutations leading to the acquisition of cancer promoting characteristics such as increased proliferation and resistance to cell death. In colorectal cancer, an early mutation leading to such features usually occurs in the APC or CTNNB1 genes, thereby activating Wnt signalling. However, substantial phenotypic differences between cancers originating within the same organ, such as molecular subtypes, are not fully reflected by differences in mutations. Indeed, the phenotype seems to result from a complex interplay between the cell-intrinsic features and the acquired mutations, which is difficult to disentangle when established tumours are studied. Methods: We use a 3D in vitro organoid model to study the early phase of colorectal cancer development. From three different murine intestinal locations we grow organoids. These are transformed to resemble adenomas after Wnt activation through lentiviral transduction with a stable form of β-Catenin. The gene expression before and after Wnt activation is compared within each intestinal origin and across the three locations using RNA sequencing. To validate and generalize our findings, we use gene expression data from patients. Results: In reaction to Wnt activation we observe downregulation of location specific genes and differentiation markers. A similar effect is seen in patient data, where genes with significant differential expression between the normal left and right colon are downregulated in the cancer samples. Furthermore, the signature of Wnt target genes differs between the three intestinal locations in the organoids. The location specific Wnt signatures are dominated by genes which have been lowly expressed in the tissue of origin, and are the targets of transcription factors that are activated following enhanced Wnt signalling. Conclusion: We observed that the region-specific cell identity has a substantial effect on the reaction to Wnt activation in a simple intestinal adenoma model. These findings provide a way forward in resolving the distinct biology between left- and right-sided human colon cancers with potential clinical relevance.
In-medium spectral functions of charmonia studied by $\bar p + A$ reactions
Creators: name: Golubeva, Ye. S.
name: Bratkovskaya, E. L.
name: Cassing, W.
name: Kondratyuk, L. A.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We study the perspectives of resonant charmonium production in $\bar{p} + A$ reactions within the Multiple Scattering Monte Carlo (MSMC) approach. We calculate the production of the resonances $Ψ(2S)$ and $Ψ(3770)$ on various nuclei, their propagation and decay to dileptons and $D+ \bar{D}$ in the medium and vacuum, respectively, employing parametrizations for the $D,\bar{D}$ self energies taken from QCD sum rule studies. The elastic and inelastic interactions of the charmonia and open charm mesons in the medium are taken into account, too. It is found that the $D, \bar{D}$ invariant mass spectra from light and heavy nuclei are not sufficiently sensitive to the in-medium properties of the $Ψ(2S)$ and $Ψ(3770)$. However, a 'suppression' of low mass dileptons from the $Ψ(3770)$ might be seen experimentally as well as a small broadening of the $Ψ(2S)$ dilepton spectra.
description: 9 pages, LaTeX, including 9 postscript figures, submitted to Eur. Phys. J. A
Roadside snowmelt: a management target to reduce lake and river contamination
Creators: name: Fournier, Isabelle B.
name: Galvez-Cloutier, Rosa
name: Vincent, Warwick F.
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Space Science
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Major ion concentrations have greatly increased in many north temperate lakes and rivers over the last 3 decades as the result of deicing materials applied to their surrounding roads in winter. Salt-based deicing will likely continue or increase in the future, and preventative management strategies require an improved understanding of the flow pathways and timing of road salt and associated contaminant fluxes to downstream receiving waters. In the present study, we focused on the catchment of Saint-Charles River and its reservoir that provides drinking water for Quebec City, Canada. Major ion concentrations were measured in river waters and snowbanks along roads in subcatchments that differed in degree of urbanization, and during the same winter–spring period a mooring system was installed in the reservoir to continuously record conductivity. Large significant differences were found in the concentration and temporal behavior of ions between urbanized and forested watersheds. Snow sampled at 1 m from the roads had elevated concentrations of salts and other contaminants, and the highest solute concentrations in the reservoir and river waters occurred during snowmelt events. The results indicate that management of roadside snowmelt runoff during thawing events may largely prevent salt-associated contamination, and that winter snowmelt will require increasing attention as the climate continues to warm.
title: REINI 2013-10009 NPDES Permit for the Joint Base Lewis-McChord
titleType: AlternativeTitle
title: Endangered Species Act Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response for the Reissuance of the National Pollutant Discharge Elimination System Permit for the Joint Base Lewis-McChord Municipal Separate Storm Sewer System, Permit# WAS026638
Creators: name: United States. National Marine Fisheries Service. West Coast Region
Publisher: name: United States. National Marine Fisheries Service. West Coast Region
Year: 2024

description: WCRO-2023-00605
Identity and Search in Social Networks
Creators: name: Watts, D. J.
name: Dodds, P. S.
name: Newman, M. E. J.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: Social networks have the surprising property of being "searchable": Ordinary people are capable of directing messages through their network of acquaintances to reach a specific but distant target person in only a few steps. We present a model that offers an explanation of social network searchability in terms of recognizable personal identities: sets of characteristics measured along a number of social dimensions. Our model defines a class of searchable networks and a method for searching them that may be applicable to many network search problems, including the location of data files in peer-to-peer networks, pages on the World Wide Web, and information in distributed databases.
description: 4 page, 3 figures, revtex
Novel genome-wide associations for anhedonia, genetic correlation with psychiatric disorders, and polygenic association with brain structure
Creators: name: Ward, Joey
name: Lyall, Laura M.
name: Bethlehem, Richard A. I.
name: Ferguson, Amy
name: Strawbridge, Rona J.
name: Lyall, Donald M.
name: Cullen, Breda
name: Graham, Nicholas
name: Johnston, Keira J. A.
name: Bailey, Mark E. S.
name: Murray, Graham K.
name: Smith, Daniel J.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Article
/631/208/212/748
/692/699/476/1414
/692/699/476/1333
/692/699/476/1799
/45/43
/59/57
article

description: Funder: DJS acknowledges the support of a Lister Prize Fellowship (173096) and the MRC Mental Health Data Pathfinder Award (MC_PC_17217).
description: Funder: JW is supported by the JMAS Sim Fellowship for depression research from the Royal College of Physicians of Edinburgh (173558).
description: Funder: RAIB is supported by a British Academy Post-Doctoral Fellowship.
description: Funder: RJS is supported by a UKRI Innovation- HDR-UK Fellowship (MR/S003061/1).
description: Abstract: Anhedonia is a core symptom of several psychiatric disorders but its biological underpinnings are poorly understood. We performed a genome-wide association study of state anhedonia in 375,275 UK Biobank participants and assessed for genetic correlation between anhedonia and neuropsychiatric conditions (major depressive disorder, schizophrenia, bipolar disorder, obsessive compulsive disorder and Parkinson’s Disease). We then used a polygenic risk score approach to test for association between genetic loading for anhedonia and both brain structure and brain function. This included: magnetic resonance imaging (MRI) assessments of total grey matter volume, white matter volume, cerebrospinal fluid volume, and 15 cortical/subcortical regions of interest; diffusion tensor imaging (DTI) measures of white matter tract integrity; and functional MRI activity during an emotion processing task. We identified 11 novel loci associated at genome-wide significance with anhedonia, with a SNP heritability estimate (h2SNP) of 5.6%. Strong positive genetic correlations were found between anhedonia and major depressive disorder, schizophrenia and bipolar disorder; but not with obsessive compulsive disorder or Parkinson’s Disease. Polygenic risk for anhedonia was associated with poorer brain white matter integrity, smaller total grey matter volume, and smaller volumes of brain regions linked to reward and pleasure processing, including orbito-frontal cortex. In summary, the identification of novel anhedonia-associated loci substantially expands our current understanding of the biological basis of state anhedonia and genetic correlations with several psychiatric disorders confirm the utility of this phenotype as a transdiagnostic marker of vulnerability to mental illness. We also provide the first evidence that genetic risk for state anhedonia influences brain structure, including in regions associated with reward and pleasure processing.
Advancing lake and reservoir water quality management with near-term, iterative ecological forecasting
Creators: name: Carey, Cayelan C.
name: Woelmer, Whitney M.
name: Lofton, Mary E.
name: Figueiredo, Renato J.
name: Bookout, Bethany J.
name: Corrigan, Rachel S.
name: Daneshmand, Vahid
name: Hounshell, Alexandria G.
name: Howard, Dexter W.
name: Lewis, Abigail S. L.
name: McClure, Ryan P.
name: Wander, Heather L.
name: Ward, Nicole K.
name: Thomas, R. Quinn
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Near-term, iterative ecological forecasts with quantified uncertainty have great potential for improving lake and reservoir management. For example, if managers received a forecast indicating a high likelihood of impending impairment, they could make decisions today to prevent or mitigate poor water quality in the future. Increasing the number of automated, real-time freshwater forecasts used for management requires integrating interdisciplinary expertise to develop a framework that seamlessly links data, models, and cyberinfrastructure, as well as collaborations with managers to ensure that forecasts are embedded into decision-making workflows. The goal of this study is to advance the implementation of near-term, iterative ecological forecasts for freshwater management. We first provide an overview of FLARE (Forecasting Lake And Reservoir Ecosystems), a forecasting framework we developed and applied to a drinking water reservoir to assist water quality management, as a potential open-source option for interested users. We used FLARE to develop scenario forecasts simulating different water quality interventions to inform manager decision-making. Second, we share lessons learned from our experience developing and running FLARE over 2 years to inform other forecasting projects. We specifically focus on how to develop, implement, and maintain a forecasting system used for active management. Our goal is to break down the barriers to forecasting for freshwater researchers, with the aim of improving lake and reservoir management globally.
Proof of some supercongruences via the Wilf-Zeilberger method
Creators: name: Mao, Guo-Shuai
Publisher: name: arXiv
Year: 2019
Subjects: subject: Number Theory (math.NT)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: In this paper, we prove some supercongruences via the Wilf-Zeilberger method. For instance, for any odd prime $p$ and positive integer $r$ and $δ\in\{1,2\}$, we have \begin{align*} \sum_{n=0}^{(p^r-1)/δ} \frac{\left(\frac12\right)^5_n}{n!^5}(10n^2+6n+1)(-4)^n &\equiv\begin{cases}p^{2r}\ \pmod{p^{r+4}} &\tt{if}\ r\leq4, \\0\ \pmod{p^{r+4}} &\tt{if}\ r \geq5. \end{cases} \end{align*}
description: 20 pages. This is a preliminary manuscript. Any comments are welcome
Advanced memory effects in the aging of a polymer glass
Creators: name: Bellon, L.
name: Ciliberto, S.
name: Laroche, C.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: A new kind of memory effect on low frequency dielectric measurements on plexiglass (PMMA) is described. These measurements show that cooling and heating the sample at constant rate give an hysteretic dependence on temperature of the dielectric constant $ε$. A temporary stop of cooling produces a downward relaxation of $ε$. Two main features are observed i) when cooling is resumed $ε$ goes back to the values obtained without the cooling stop (i.e. the low temperature state is independent of the cooling history) ii) upon reheating $ε$ keeps the memory of all the cooling stops({\it Advanced memory}). The dependence of this effect on frequency and on the cooling rate is analyzed. The memory deletion is studied too. Finally the results are compared with those of similar experiments done in spin glasses and with the famous experiments of Kovacs.
description: to be published in the European Physical Journal
Norm kernels and the closeness relation for Pauli-allowed basis functions
Creators: name: Filippov, G. F.
name: Lashko, Yu. A.
name: Korennov, S. V.
name: Kato, K.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The norm kernel of the generator-coordinate method is shown to be a symmetric kernel of an integral equation with eigenfunctions defined in the Fock--Bargmann space and forming a complete set of orthonormalized states (classified with the use of SU(3) symmetry indices) satisfying the Pauli exclusion principle. This interpretation allows to develop a method which, even in the presence of the SU(3) degeneracy, provides for a consistent way to introduce additional quantum numbers for the classification of the basis states. In order to set the asymptotic boundary conditions for the expansion coefficients of a wave function in the SU(3) basis, a complementary basis of functions with partial angular momenta as good quantum numbers is needed. Norm kernels of the binary systems 6He+p, 6He+n, 6He+4He, and 8He+4He are considered in detail.
description: 25 pages; submitted to Few-Body Systems
Circulating levels of GDF15 in patients with myalgic encephalomyelitis/chronic fatigue syndrome
Creators: name: Melvin, A.
name: Lacerda, E.
name: Dockrell, H. M.
name: O’Rahilly, S.
name: Nacul, L.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Research
Illnesses of Unknown Etiology
GDF15
Myalgic encephalomyelitis
Chronic fatigue syndrome

description: Abstract: Background: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating condition characterised by fatigue and post-exertional malaise. Its pathogenesis is poorly understood. GDF15 is a circulating protein secreted by cells in response to a variety of stressors. The receptor for GDF15 is expressed in the brain, where its activation results in a range of responses. Among the conditions in which circulating GDF15 levels are highly elevated are mitochondrial disorders, where early skeletal muscle fatigue is a key symptom. We hypothesised that GDF15 may represent a marker of cellular stress in ME/CFS. Methods: GDF15 was measured in serum from patients with ME/CFS (n = 150; 100 with mild/moderate and 50 with severe symptoms), “healthy volunteers” (n = 150) and a cohort of patients with multiple sclerosis (n = 50). Results: Circulating GDF15 remained stable in a subset of ME/CFS patients when sampled on two occasions ~ 7 months (IQR 6.7–8.8) apart, 720 pg/ml (95% CI 625–816) vs 670 pg/ml (95% CI 598–796), P = 0.5. GDF15 levels were 491 pg/ml in controls (95% CI 429–553), 546 pg/ml (95% CI 478–614) in MS patients, 560 pg/ml (95% CI 502–617) in mild/moderate ME/CFS patients and 602 pg/ml (95% CI 531–674) in severely affected ME/CFS patients. Accounting for potential confounders, severely affected ME/CFS patients had GDF15 concentrations that were significantly increased compared to healthy controls (P = 0.01). GDF15 levels were positively correlated (P = 0.026) with fatigue scores in ME/CFS. Conclusions: Severe ME/CFS is associated with increased levels of GDF15, a circulating biomarker of cellular stress that appears which stable over several months.
Form and width of spectral line of Josephson Flux-Flow oscillator
Creators: name: Pankratov, Andrey L.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: The behavior of a Josephson flux-flow oscillator in the presence of both bias current and magnetic field fluctuations has been studied. To derive the equation for slow phase dynamics in the limit of small noise intensity the Poincare method has been used. Both the form of spectral line and the linewidth of the flux-flow oscillator have been derived exactly on the basis of technique presented in the book of Malakhov, known limiting cases are considered, limits of their applicability are discussed and appearance of excess noise is explained. Good coincidence of theoretical description with experimental results has been demonstrated.
description: 10 pages, 5 figures
Biomimetic and electroactive 3D scaffolds for human neural crest-derived stem cell expansion and osteogenic differentiation
Creators: name: Iandolo, Donata
name: Sheard, Jonathan
name: Levy, Galit Karavitas
name: Pitsalidis, Charalampos
name: Tan, Ellasia
name: Dennis, Anthony
name: Kim, Ji-Seon
name: Markaki, Athina E.
name: Widera, Darius
name: Owens, Róisín M.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Research Letter

description: Abstract: Osteoporosis is a skeletal disease characterized by bone loss and bone microarchitectural deterioration. The combination of smart materials and stem cells represents a new therapeutic approach. In the present study, highly porous scaffolds are prepared by combining the conducting polymer PEDOT:PSS with collagen type I, the most abundant protein in bone. The inclusion of collagen proves to be an effective way to modulate their mechanical properties and it induces an increase in scaffolds’ electrochemical impedance. The biomimetic scaffolds support neural crest-derived stem cell osteogenic differentiation, with no need for scaffold pre-conditioning contrarily to other reports.
Phonon anomaly at the charge ordering transition in 1T-TaS2
Creators: name: Gasparov, L. V.
name: Brown, K. G.
name: Wint, A. C.
name: Tanner, D. B.
name: Berger, H.
name: Gaal, R.
name: Forro, L.
name: Margaritondo, G.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: The infrared reflectance of the transition metal chalcogenide 1T-TaS2 has been measured at temperatures from 30K to 360K over 30-45,000cm^-1 (4meV-5.5eV). The optical conductivity was obtained by Kramers-Kronig analysis. At 360K only modest traces of the phonon lines are noticeable. The phonon modes are followed by a pseudogap-like increase of the optical conductivity, with direct optical transitions observed at frequencies above 1eV. As the temperature decreases, the low frequency conductivity also decreases, phonon modes become more pronounced and pseudogap develops into a gap at 800cm^-1 (100meV). We observe an anomalous frequency dependence of the 208cm^-1 infrared-active phonon mode. This mode demonstrates softening as the temperature decreases below the 180K metal-to-insulator transition. The same mode demonstrates strong hysteresis of the frequency and linewidth changes, similar in its temperature behavior to the hysteresis in the dc-resistivity. We discuss a possible relation of the observed softening of the mode to the structural changes associated with the metal-to-insulator transition.
description: 7 pages, 4 figures, 1 table; corrected typos
Thesaurus and Conceptual Framework of Self-Sustaining R&I Ecosystems
Creators: name: Pereira, Carlos Alvarez
Publisher: name: Zenodo
Year: 2020
Subjects: Conceptual framework, systemic thinking, R&I ecosystems, cybernetics, complexity, wellbeing(s) in the biosphere

description: Deliverable of the SeeRRI project ("Building Self-Sustaining Research and Innovation Ecosystems in Europe through Responsible Research and Innovation"). The publication addresses the development of conceptual and integrated frameworks to facilitate the adoption of Responsible Research and Innovation (RRI) concepts and practices in the context of Smart Specialization Strategies (RIS3) at regional level across the European Union. The SeeRRI frameworks are built on leading-edge systems thinking and the publication contains a Thesaurus covering a wide range of concepts from different domains related to systems thinking.
title: Dolberry Seawall
titleType: AlternativeTitle
title: Endangered Species Act - Section 7 Consultation Biological Opinion Shoreline Stabilization, Cape Coral, Lee County, Florida
Creators: name: United States. National Marine Fisheries Service. Southeast Region
Publisher: name: United States. National Marine Fisheries Service. Southeast Region
Year: 2019

description: SERO-2019-02187
Male-Specific Protein Disulphide Isomerase Function is Essential for Plasmodium Transmission and a Vulnerable Target for Intervention
Creators: name: Angrisano, Fiona
name: Sala, Katarzyna A.
name: Tapanelli, Sofia
name: Christophides, George K.
name: Blagborough, Andrew M.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Article
/631/80/304
/631/80/470
/631/326/417/1716
/631/326/417/2552
/64
/82
/14/1
/14/35
/38/109
/64/60
/82/1
/82/80
article

description: Abstract: Inhibiting transmission of Plasmodium is an essential strategy in malaria eradication, and the biological process of gamete fusion during fertilization is a proven target for this approach. Lack of knowledge of the mechanisms underlying fertilization have been a hindrance in the development of transmission-blocking interventions. Here we describe a protein disulphide isomerase essential for malarial transmission (PDI-Trans/PBANKA_0820300) to the mosquito. We show that PDI-Trans activity is male-specific, surface-expressed, essential for fertilization/transmission, and exhibits disulphide isomerase activity which is up-regulated post-gamete activation. We demonstrate that PDI-Trans is a viable anti-malarial drug and vaccine target blocking malarial transmission with the use of PDI inhibitor bacitracin (98.21%/92.48% reduction in intensity/prevalence), and anti-PDI-Trans antibodies (66.22%/33.16% reduction in intensity/prevalence). To our knowledge, these results provide the first evidence that PDI function is essential for malarial transmission, and emphasize the potential of anti-PDI agents to act as anti-malarials, facilitating the future development of novel transmission-blocking interventions.
Elliptic solitons and Heun's equation
Creators: name: Smirnov, A. O.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: Spectral Theory (math.SP)
subject: FOS: Mathematics

description: We find a new class of algebraic geometric solutions of Heun's equation with the accessory parameter belonging to a hyperelliptic curve. Dependence of these solutions from the accessory parameter as well as their relation to Heun's polynomials is studied. Methods of calculating the algebraic genus of the curve, and its branching points, are suggested. Monodromy group is considered. Numerous examples are given.
description: 19 pages, LaTeX2e (AMSLaTeX);Proposition 1 was corrected, two footnotes were added
Type I-F CRISPR-Cas resistance against virulent phages results in abortive infection and provides population-level immunity
Creators: name: Watson, Bridget N. J.
name: Vercoe, Reuben B.
name: Salmond, George P. C.
name: Westra, Edze R.
name: Staals, Raymond H. J
name: Fineran, Peter C.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Article
/631/326/1321
/631/326/4041
/631/326/432
article

description: Funder: Veni grant, Netherlands Organization for Scientific Research (NWO) [016.Veni.171.047 to RHJS] Health Sciences Career Development Award from the University of Otago, NZ
description: Abstract: Type I CRISPR-Cas systems are abundant and widespread adaptive immune systems in bacteria and can greatly enhance bacterial survival in the face of phage infection. Upon phage infection, some CRISPR-Cas immune responses result in bacterial dormancy or slowed growth, which suggests the outcomes for infected cells may vary between systems. Here we demonstrate that type I CRISPR immunity of Pectobacterium atrosepticum leads to suppression of two unrelated virulent phages, ɸTE and ɸM1. Immunity results in an abortive infection response, where infected cells do not survive, but viral propagation is severely decreased, resulting in population protection due to the reduced phage epidemic. Our findings challenge the view of CRISPR-Cas as a system that protects the individual cell and supports growing evidence of abortive infection by some types of CRISPR-Cas systems.
Star Formation and the Initial Mass Function
Creators: name: Nordlund, Aake
name: Padoan, Paolo
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Supersonic turbulence fragments the interstellar medium into dense sheets, filaments, cores and large low density voids. The turbulence is driven on large scales, probably predominantly by supernovae. The scaling properties of supersonic turbulence are well described by a new analytical theory. The distribution of proto-stellar core masses depends primarily on the power spectrum of the turbulent flow, and on the jump conditions for near isothermal shocks in a magnetized gas. For the predicted velocity power spectrum index beta=1.74, consistent with results of numerical experiments of supersonic turbulence as well as with Larson's velocity-size relation, one obtains by scaling arguments a power law mass distribution of dense cores with a slope equal to 3/(4-beta) = 1.33, consistent with the slope of the Salpeter stellar initial mass function (IMF). Results from numerical simulations confirm this scaling. Both the analytical model for the stellar IMF and its numerical estimate show that turbulent fragmentation can also explain the origin of brown dwarfs.
description: 28 pages, 13 figures, invited tutorial for the workshop "Simulations of Magnetohydrodynamic Turbulence in Astrophysics: Recent Achievements and Perspectives", Paris, July 2-6, 2001, Eds. Edith Falgarone & Thierry Passot
title: Zurek Seawall Project
titleType: AlternativeTitle
title: Endangered Species Act - Section 7 Consultation Biological Opinion Shoreline Stabilization, Cape Coral, Lee County, Florida
Creators: name: United States. National Marine Fisheries Service. Southeast Region
Publisher: name: United States. National Marine Fisheries Service. Southeast Region
Year: 2020

description: SERO-2019-02171
Multilingual audio information management system based on semantic knowledge in complex environments
Creators: name: Lopez-De-Ipina, Karmele
name: Barroso, Nora
name: Calvo, Pilar M.
name: Hernandez, Carmen
name: Ezeiza, Aitzol
name: Susperregi, Unai
name: Fernández, Elsa
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Developing Nature-Inspired Intelligence by Neural Systems
Evolutionary computing
Artificial neural networks
Internet information management
Management of complex systems

description: Abstract: This paper proposes a multilingual audio information management system based on semantic knowledge in complex environments. The complex environment is defined by the limited resources (financial, material, human, and audio resources); the poor quality of the audio signal taken from an internet radio channel; the multilingual context (Spanish, French, and Basque that is in under-resourced situation in some areas); and the regular appearance of cross-lingual elements between the three languages. In addition to this, the system is also constrained by the requirements of the local multilingual industrial sector. We present the first evolutionary system based on a scalable architecture that is able to fulfill these specifications with automatic adaptation based on automatic semantic speech recognition, folksonomies, automatic configuration selection, machine learning, neural computing methodologies, and collaborative networks. As a result, it can be said that the initial goals have been accomplished and the usability of the final application has been tested successfully, even with non-experienced users.
Time evolution of many-body localized systems in two spatial dimensions
Creators: name: Kshetrimayum, Augustine
name: Goihl, Marcel
name: Eisert, Jens
Publisher: name: arXiv
Year: 2019
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Many-body localization is a striking mechanism that prevents interacting quantum systems from thermalizing. The absence of thermalization behaviour manifests itself, for example, in a remanence of local particle number configurations, a quantity that is robust over a parameter range. Local particle numbers are directly accessible in programmable quantum simulators, in systems of cold atoms even in two spatial dimensions. Yet, the classical simulation aimed at building trust in quantum simulations is highly challenging. In this work, we present a comprehensive tensor network simulation of a many-body localized systems in two spatial dimensions using a variant of an iPEPS algorithm. The required translational invariance can be restored by implementing the disorder into an auxiliary spin system, providing an exact disorder average under dynamics. We can quantitatively assess signatures of many-body localization for the infinite system: Our methods are powerful enough to provide crude dynamical estimates for the transition between localized and ergodic phases. Interestingly, in this setting of finitely many disorder values, which we also compare with simulations involving non-interacting fermions and for which we discuss the emergent physics, localization emerges in the interacting regime, for which we provide an intuitive argument, while Anderson localization is absent.
description: 14 pages, 8 figures, replaced by final version
Quantum Spin dynamics of the Bilayer Ferromagnet La(1.2)Sr(1.8)Mn2O7
Creators: name: Shannon, Nic
name: Chatterji, Tapan
name: Ouchni, Fatiha
name: Thalmeier, Peter
Publisher: name: arXiv
Year: 2002
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We construct a theory of spin wave excitations in the bilayer manganite La(1.2)Sr(1.8)Mn2O7 based on the simplest possible double-exchange model, but including leading quantum corrections to the spin wave dispersion and damping. Comparison is made with recent inelastic neutron scattering experiments. We find that quantum effects account for some part of the measured damping of spin waves, but cannot by themselves explain the observed softening of spin waves at the zone boundary. Furthermore a doping dependence of the total spin wave dispersion and the optical spin wave gap is predicted.
description: 19 pages revtex, 7 eps figures
Additional file 3: of Kids Out; evaluation of a brief multimodal cluster randomized intervention integrated in health education lessons to increase physical activity and reduce sedentary behavior among eighth graders
Creators: name: M. Aittasalo
name: A-M Jussila
name: K. Tokola
name: H. Sievänen
name: H. Vähä-Ypyä
name: T. Vasankari
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Cancer

description: Day-specific page from the activity diary (DOCX 265 kb)
Serving many masters at once: a framework for assessing ecosystem services delivered by quarry lakes
Creators: name: Seelen, Laura M. S.
name: Teurlincx, Sven
name: Armstrong, Margaret R.
name: Lürling, Miquel
name: van Donk, Ellen
name: de Senerpont Domis, Lisette N.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Globally the number of relatively deep, isolated lakes is increasing because of sand, gravel, or clay excavation activities. The major excavation areas are located within the delta of rivers, and thus the deep freshwater ecosystems formed upon excavation, called quarry lakes, are unique to the landscape. They are embedded in a landscape comprised of shallow, naturally formed lakes. Given that quarry lakes are by definition novel ecosystems, water managers face difficulties in optimally managing them to deliver ecosystem services using existing frameworks designed for natural ecosystems. All lakes in delta areas are subject to similar pressures such as urbanization and eutrophication, leading to shifts in biodiversity and ecosystem functioning, and ultimately changing the ecosystem services the systems can provide. We propose a framework to enable water managers to assess the provision of ecosystem services by quarry lakes based on their ecological quality. For each ecosystem service we determined threshold values of ecological quality based on available scientific literature, an extensive field survey of 51 quarry lakes in the Netherlands, or expert knowledge. To illustrate the usefulness of our approach, we applied our framework to a lake before and after a rehabilitation focused on improving the nutrient status of the waterbody. Assessing ecosystem services under varying levels of ecological health is important to initiate action from legislators, managers, and communities.
Fermi-Löwdin orbital self-interaction correction using the strongly constrained and appropriately normed meta-GGA functional
Creators: name: Yamamoto, Yoh
name: Diaz, Carlos M.
name: Basurto, Luis
name: Jackson, Koblar A.
name: Baruah, Tunna
name: Zope, Rajendra R.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Despite the success of density functional approximations (DFAs) in describing the electronic properties of many-electron systems, the most widely used approximations suffer from self-interaction errors (SIE) that limit their predictive power. Here we describe the effects of removing SIE from the strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (GGA) using the Fermi-Lowdin Orbital Self-Interaction Correction (FLOSIC) method. FLOSIC is a size-extensive implementation of the Perdew-Zunger self-interaction correction (PZ-SIC) formalism. We find that FLOSIC-SCAN calculations require careful treatment of numerical details and describe an integration grid that yields reliable accuracy with this approach. We investigate the performance of FLOSIC-SCAN for predicting a wide array of properties and find that it provides better results than FLOSIC-LDA and FLOSIC-PBE in nearly all cases. It also gives better predictions than SCAN for orbital energies and dissociation energies where self-interaction effects are known to be important, but total energies and atomization energies are made worse. For these properties, we also investigate the use of the self-consistent FLOSIC-SCAN density in the SCAN functional and find that this DFA@FLOSIC-DFA approach yields improved results compared to pure, self-consistent SCAN calculations. Thus FLOSIC-SCAN provides improved results over the parent SCAN functional in cases where SIEs are dominant, and even when they are not, if the SCAN@FLOSIC-SCAN method is used.
description: to appear in Journal of Chemical Physics