612 research outputs found
Die Auswirkungen der Wasserstände am Bodensee auf das Deschampsietum rhenanae zwischen 1989 und 2003
AbstractThe Deschampsietum rhenanae is an endemic and endangered lakeshore community growing in the upper littoral of Lake Constance, the occurrence of which has been reduced dramatically during the last 100 years. The existence of this community depends on the seasonal water level changes of the unregulated, prealpine Lake Constance. Long-term monitoring indicates that the typical species of the Deschampsietum rhenanae and their competitors may be strongly affected by extreme water levels. An earlier onset of the water level increase in spring could potentially pose a threat to the Deschampsietum rhenanae, especially if the water level rises before seed ripening in the Deschampsietum rhenanae
Machine learning in and out of equilibrium
The algorithms used to train neural networks, like stochastic gradient
descent (SGD), have close parallels to natural processes that navigate a
high-dimensional parameter space -- for example protein folding or evolution.
Our study uses a Fokker-Planck approach, adapted from statistical physics, to
explore these parallels in a single, unified framework. We focus in particular
on the stationary state of the system in the long-time limit, which in
conventional SGD is out of equilibrium, exhibiting persistent currents in the
space of network parameters. As in its physical analogues, the current is
associated with an entropy production rate for any given training trajectory.
The stationary distribution of these rates obeys the integral and detailed
fluctuation theorems -- nonequilibrium generalizations of the second law of
thermodynamics. We validate these relations in two numerical examples, a
nonlinear regression network and MNIST digit classification. While the
fluctuation theorems are universal, there are other aspects of the stationary
state that are highly sensitive to the training details. Surprisingly, the
effective loss landscape and diffusion matrix that determine the shape of the
stationary distribution vary depending on the simple choice of minibatching
done with or without replacement. We can take advantage of this nonequilibrium
sensitivity to engineer an equilibrium stationary state for a particular
application: sampling from a posterior distribution of network weights in
Bayesian machine learning. We propose a new variation of stochastic gradient
Langevin dynamics (SGLD) that harnesses without replacement minibatching. In an
example system where the posterior is exactly known, this SGWORLD algorithm
outperforms SGLD, converging to the posterior orders of magnitude faster as a
function of the learning rate.Comment: 24 pages, 6 figure
Overlap of heritable influences between Cannabis Use Disorder, frequency of use and opportunity to use cannabis: Trivariate twin modelling and implications for genetic design
Background: The genetic component of Cannabis Use Disorder may overlap with influences acting more generally on early stages of cannabis use. This paper aims to determine the extent to which genetic influences on the development of cannabis abuse/dependence are correlated with those acting on the opportunity to use cannabis and frequency of use. Methods: A cross-sectional study of 3303 Australian twins, measuring age of onset of cannabis use opportunity, lifetime frequency of cannabis use, and lifetime DSM-IV cannabis abuse/dependence. A trivariate Cholesky decomposition estimated additive genetic (A), shared environment (C) and unique environment (E) contributions to the opportunity to use cannabis, the frequency of cannabis use, cannabis abuse/dependence, and the extent of overlap between genetic and environmental factors associated with each phenotype. Results: Variance components estimates were A = 0.64 [95% confidence interval (CI) 0.58–0.70] and E = 0.36 (95% CI 0.29–0.42) for age of opportunity to use cannabis, A = 0.74 (95% CI 0.66–0.80) and E = 0.26 (95% CI 0.20–0.34) for cannabis use frequency, and A = 0.78 (95% CI 0.65–0.88) and E = 0.22 (95% CI 0.12–0.35) for cannabis abuse/dependence. Opportunity shares 45% of genetic influences with the frequency of use, and only 17% of additive genetic influences are unique to abuse/dependence from those acting on opportunity and frequency. Conclusions: There are significant genetic contributions to lifetime cannabis abuse/dependence, but a large proportion of this overlaps with influences acting on opportunity and frequency of use. Individuals without drug use opportunity are uninformative, and studies of drug use disorders must incorporate individual exposure to accurately identify aetiology
On Approximation of the Eigenvalues of Perturbed Periodic Schrodinger Operators
This paper addresses the problem of computing the eigenvalues lying in the
gaps of the essential spectrum of a periodic Schrodinger operator perturbed by
a fast decreasing potential. We use a recently developed technique, the so
called quadratic projection method, in order to achieve convergence free from
spectral pollution. We describe the theoretical foundations of the method in
detail, and illustrate its effectiveness by several examples.Comment: 17 pages, 2 tables and 2 figure
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High Throughput siRNA Screening Identifies Phosphatidylinositol 3-kinase Class II Alpha as Important for Production of Human Cytomegalovirus Virions.
High throughput siRNA screening is a useful methodology to identify cellular factors required for virus replication. Here we utilized a high throughput siRNA screen based on detection of a viral antigen by microscopy to interrogate cellular protein kinases and phosphatases for their importance during human cytomegalovirus (HCMV) replication, and identified the Class II Phosphatidylinositol 3-kinase PI3K-C2A as being involved in HCMV replication. Confirming this observation, infected cells treated with either pooled or individual siRNAs targeting PI3K-C2A mRNA produced approximately 10-fold less infectious virus compared to controls. Western blotting and quantitative PCR analysis of infected cells treated with siRNAs indicated that depletion of PI3K-C2A slightly reduced accumulation of late, but not immediate-early or early, viral antigens and had no appreciable effect of viral DNA synthesis. Analysis of siRNA treated cells by electron microscopy and western blotting indicated that PI3K-C2A was not required for production of viral capsids, but did lead to increased numbers of enveloped capsids in the cytoplasm that had undergone secondary envelopment and reduction of viral particles exiting the cell. Therefore, PI3K-C2A is a factor important for HCMV replication and has a role in production of HCMV virions. IMPORTANCE: There is limited information about the cellular factors required for human cytomegalovirus (HCMV) replication. Therefore, to identify proteins involved in HCMV replication we developed a methodology to conduct a high throughput siRNA screen in HCMV infected cells. From our screening data we focused our studies on the top "hit" from our screen, the lipid kinase phosphatidylinositol 3-kinase Class II Alpha (PI3K-C2A), as its role in HCMV replication was unknown. Interestingly, we found that PI3K-C2A is important for the production of HCMV virions and is involved in virion production after secondary envelopment of viral capsids, the encapsidation of HCMV capsids by a lipid bilayer that occurs before virions exit the cell
Results of the 2016 Indianapolis Biodiversity Survey, Marion County, Indiana
Surprising biodiversity can be found in cities, but urban habitats are understudied. We report on a bioblitz conducted primarily within a 24-hr period on September 16 and 17, 2016 in Indianapolis, Indiana, USA. The event focused on stretches of three waterways and their associated riparian habitat: Fall Creek (20.6 ha; 51 acres), Pleasant Run (23.5 ha; 58 acres), and Pogue’s Run (27.1 ha; 67 acres). Over 75 scientists, naturalists, students, and citizen volunteers comprised 14 different taxonomic teams. Five hundred ninety taxa were documented despite the rainy conditions. A brief summary of the methods and findings are presented here. Detailed maps of survey locations and inventory results are available on the Indiana Academy of Science website (https://www.indianaacademyofscience.org/)
TbGT8 is a bifunctional glycosyltransferase that elaborates<em> N</em>-linked glycans on a protein phosphatase AcP115 and a GPI-anchor modifying glycan in <em>Trypanosoma brucei</em>
AbstractThe procyclic form of Trypanosoma brucei expresses procyclin surface glycoproteins with unusual glycosylphosphatidylinositol-anchor side chain structures that contain branched N-acetyllactosamine and lacto-N-biose units. The glycosyltransferase TbGT8 is involved in the synthesis of the branched side chain through its UDP-GlcNAc: βGal β1-3N-acetylglucosaminyltransferase activity. Here, we explored the role of TbGT8 in the mammalian bloodstream form of the parasite with a tetracycline-inducible conditional null T. brucei mutant for TbGT8. Under non-permissive conditions, the mutant showed significantly reduced binding to tomato lectin, which recognizes poly-N-acetyllactosamine-containing glycans. Lectin pull-down assays revealed differences between the wild type and TbGT8 null-mutant T. brucei, notably the absence of a broad protein band with an approximate molecular weight of 110kDa in the mutant lysate. Proteomic analysis revealed that the band contained several glycoproteins, including the acidic ecto-protein phosphatase AcP115, a stage-specific glycoprotein in the bloodstream form of T. brucei. Western blotting with an anti-AcP115 antibody revealed that AcP115 was approximately 10kDa smaller in the mutant. Enzymatic de-N-glycosylation demonstrated that the underlying protein cores were the same, suggesting that the 10-kDa difference was due to differences in N-linked glycans. Immunofluorescence microscopy revealed the colocalization of hemagglutinin epitope-tagged TbGT8 and the Golgi-associated protein GRASP. These data suggest that TbGT8 is involved in the construction of complex poly-N-acetyllactosamine-containing type N-linked and GPI-linked glycans in the Golgi of the bloodstream and procyclic parasite forms, respectively
Treatment and Intervention for Opiate Dependence in the United Kingdom:Lessons from Triumph and Failure
The history of opiate treatment in the United Kingdom (UK) since the early 1980s is a rich source of learning about the benefits and pitfalls of drug treatment policy. We present five possible lessons to be learnt about how factors outside the clinic, including government, charities and researchers can influence treatment and outcomes. First, do not let a crisis go to waste. The philosophical shift from abstinence to harm reduction in the 1980s, in response to an HIV outbreak in injecting users, facilitated expansion in addiction services and made a harm reduction approach more acceptable. Second, studies of drug-related deaths can lead to advances in care. By elucidating the pattern of mortality, and designing interventions to address the causes, researchers have improved patient safety in certain contexts, though significant investment in Scotland has not arrested rising mortality. Third, collection of longitudinal data and its use to inform clinical guidelines, as pursued from the mid-1990s, can form an enduring evidence base and shape policy, sometimes in unintended ways. Fourth, beware of the presentation of harm reduction and recovery as in conflict. At the least, this reduces patient choice, and at worst, it has caused some services to be redesigned in a manner that jeopardises patient safety. Fifth, the relationship between the third and state sectors must be carefully nurtured. In the UK, early collaboration has been replaced by competition, driven by changes in funding, to the detriment of service provision
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