A method for under-sampled ecological network data analysis: plant-pollination as case study

In this paper, we develop a method, termed the Interaction Distribution (ID) method, for analysis of quantitative ecological network data. In many cases, quantitative network data sets are under-sampled, i.e. many interactions are poorly sampled or remain unobserved. Hence, the output of statistical analyses may fail to differentiate between patterns that are statistical artefacts and those which are real characteristics of ecological networks. The ID method can support assessment and inference of under-sampled ecological network data. In the current paper, we illustrate and discuss the ID method based on the properties of plant-animal pollination data sets of flower visitation frequencies. However, the ID method may be applied to other types of ecological networks. The method can supplement existing network analyses based on two definitions of the underlying probabilities for each combination of pollinator and plant species: (1), pi,j: the probability for a visit made by the i’th pollinator species to take place on the j’th plant species; (2), qi,j: the probability for a visit received by the j’th plant species to be made by the i’th pollinator. The method applies the Dirichlet distribution to estimate these two probabilities, based on a given empirical data set. The estimated mean values for pi,j and qi,j reflect the relative differences between recorded numbers of visits for different pollinator and plant species, and the estimated uncertainty of pi,j and qi,j decreases with higher numbers of recorded visits.

A comparison of thiolated and disulfide‐crosslinked polyethylenimine for nonviral gene delivery

Branched polyethylenimine (25 kDa) is thiolated and compared with redox-sensitive crosslinked derivatives. Both polymers thiol contents are assessed; the thiolated polymers have 390–2300 mmol SH groups/mol, whereas the crosslinked polymers have lower thiol contents. Cytotoxicity assays show that both modified polymers give lower hemolysis than unmodified PEI. Increased thiol content increases gene transfer efficiency but also elevates cytotoxicity. Crosslinking improves plasmid DNA condensation and enhances transfection efficiency, but extensive crosslinking overstabilizes the polyplexes and decreases transfection, emphasizing the need to balance polyplex stabilization and unpacking. Thus, at low levels of crosslinking, 25 kDa PEI can be an efficient redox-sensitive carrier system.

The Gly482Ser genotype at the PPARGC1A gene and elevated blood pressure: a meta-analysis involving 13,949 individuals.

The protein encoded by the PPARGC1A gene is expressed at high levels in metabolically active tissues and is involved in the control of oxidative stress via reactive oxygen species detoxification. Several recent reports suggest that the PPARGC1A Gly482Ser (rs8192678) missense polymorphism may relate inversely with blood pressure. We used conventional meta-analysis methods to assess the association between Gly482Ser and systolic (SBP) or diastolic blood pressures (DBP) or hypertension in 13,949 individuals from 17 studies, of which 6,042 were previously unpublished observations. The studies comprised cohorts of white European, Asian, and American Indian adults, and adolescents from South America. Stratified analyses were conducted to control for population stratification. Pooled genotype frequencies were 0.47 (Gly482Gly), 0.42 (Gly482Ser), and 0.11 (Ser482Ser). We found no evidence of association between Gly482Ser and SBP [Gly482Gly: mean = 131.0 mmHg, 95% confidence interval (CI) = 130.5-131.5 mmHg; Gly482Ser mean = 133.1 mmHg, 95% CI = 132.6-133.6 mmHg; Ser482Ser: mean = 133.5 mmHg, 95% CI = 132.5-134.5 mmHg; P = 0.409] or DBP (Gly482Gly: mean = 80.3 mmHg, 95% CI = 80.0-80.6 mmHg; Gly482Ser mean = 81.5 mmHg, 95% CI = 81.2-81.8 mmHg; Ser482Ser: mean = 82.1 mmHg, 95% CI = 81.5-82.7 mmHg; P = 0.651). Contrary to previous reports, we did not observe significant effect modification by sex (SBP, P = 0.966; DBP, P = 0.715). We were also unable to confirm the previously reported association between the Ser482 allele and hypertension [odds ratio: 0.97, 95% CI = 0.87-1.08, P = 0.585]. These results were materially unchanged when analyses were focused on whites only. However, statistical evidence of gene-age interaction was apparent for DBP [Gly482Gly: 73.5 (72.8, 74.2), Gly482Ser: 77.0 (76.2, 77.8), Ser482Ser: 79.1 (77.4, 80.9), P = 4.20 x 10(-12)] and SBP [Gly482Gly: 121.4 (120.4, 122.5), Gly482Ser: 125.9 (124.6, 127.1), Ser482Ser: 129.2 (126.5, 131.9), P = 7.20 x 10(-12)] in individuals <50 yr (n = 2,511); these genetic effects were absent in those older than 50 yr (n = 5,088) (SBP, P = 0.41; DBP, P = 0.51). Our findings suggest that the PPARGC1A Ser482 allele may be associated with higher blood pressure, but this is only apparent in younger adults.

An investigation of the role of business analysts in IS development

Business analysis has developed since the early 1990s as an IS discipline that is concerned with understanding business problems, defining requirements and evaluating relevant solutions. However, this discipline has had limited recognition within the academic community and little research has been conducted into the practices and standards employed by business analysts. This paper reports on a study into business analysis that considered the activities conducted and the outcomes experienced on IS projects. Senior business analysts were interviewed in order to gain insights into the business analyst role and the techniques and approaches applied when conducting this work. The Context, Content, Process, Outcomes framework was adopted as a basis for developing the interview questions. The data collected was analysed using the template analysis technique and the template was based upon this framework. Additional themes concerning aspects of business analysis that may contribute to IS success emerged during data analysis. These included the key business analysis activities and the skills business analysts require to perform these activities. The organisational attitude was also identified as a key factor in enabling the use and contribution of business analysis.

Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes

5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions,and mainly located in transposable element (TE) genes, especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification.

Earth's ion upflow associated with polar cap patches: global and in-situ observations

We report simultaneous global monitoring of a patch of ionization and in situ observation of ion upflow at the center of the polar cap region during a geomagnetic storm. Our observations indicate strong fluxes of upwelling O+ ions originating from frictional heating produced by rapid antisunward flow of the plasma patch. The statistical results from the crossings of the central polar cap region by Defense Meteorological Satellite Program F16–F18 from 2010 to 2013 confirm that the field-aligned flow can turn upward when rapid antisunward flows appear, with consequent significant frictional heating of the ions, which overcomes the gravity effect. We suggest that such rapidly moving patches can provide an important source of upwelling ions in a region where downward flows are usually expected. These observations give new insight into the processes of ionosphere-magnetosphere coupling.

Aligning IS programs with industry: linking business analysis curricula design with the professional body

Aligning information systems (IS) solutions with business goals and needs are crucial for IS activities. IS professionals who are able to work closely with both the business and technical staff are key enablers of business and IT alignment. IS programs in higher education (HE) institutions have a long tradition of enabling graduates to develop the appropriate skills needed for their future careers. Yet, organizations are still having difficulty finding graduates who possess both the knowledge and skills that are best suited to their specific requirements. Prior studies suggest that IS curricula are often ill-matched with industry/business needs. This study reports on the business analysis curricula (re) design which was undertaken to align it with a key professional body for the IS industry. This study presents the approaches taken in the (re) design of the module, and provides a discussion of the wider implications for IS curricula design. The results show a positive outcome for the HE and professional body partnership.

TNF-alpha Promotes an Odontoblastic Phenotype in Dental Pulp Cells

Dental pulp cells can differentiate toward an odontoblastic phenotype to produce reparative dentin beneath caries lesions. However, the mechanisms involved in pulp cell differentiation under pro-inflammatory stimuli have not been well-explored. Thus, we hypothesized that the pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-alpha) could be a mediator involved in dental pulp cell differentiation toward an odontoblastic phenotype. We observed that TNF-alpha-challenged pulp cells exhibited increased mineralization and early and increased expression of dentin phosphoprotein (DPP), dentin sialoprotein (DSP), dentin matrix protein-1, and osteocalcin during a phase of reduced matrix metalloproteinase (MMP) expression. We investigated whether these events were related and found that p38, a mitogen-activated protein kinase, differentially regulated MMP-1 and DSP/DPP expression and mediated mineralization upon TNF-alpha treatment. These findings indicate that TNF-alpha stimulates differentiation of dental pulp cells toward an odontoblastic phenotype via p38, while negatively regulating MMP-1 expression.

Percolation in a network with long-range connections: Implications for cytoskeletal structure and function

Cell shape, signaling, and integrity depend on cytoskeletal organization. In this study we describe the cytoskeleton as a simple network of filamentary proteins (links) anchored by complex protein structures (nodes). The structure of this network is regulated by a distance-dependent probability of link formation as P = p/d(s), where p regulates the network density and s controls how fast the probability for link formation decays with node distance (d). It was previously shown that the regulation of the link lengths is crucial for the mechanical behavior of the cells. Here we examined the ability of the two-dimensional network to percolate (i.e. to have end-to-end connectivity), and found that the percolation threshold depends strongly on s. The system undergoes a transition around s = 2. The percolation threshold of networks with s < 2 decreases with increasing system size L, while the percolation threshold for networks with s > 2 converges to a finite value. We speculate that s < 2 may represent a condition in which cells can accommodate deformation while still preserving their mechanical integrity. Additionally, we measured the length distribution of F-actin filaments from publicly available images of a variety of cell types. In agreement with model predictions, cells originating from more deformable tissues show longer F-actin cytoskeletal filaments. (C) 2008 Elsevier B.V. All rights reserved.

Dilepton mass spectra in p plus p collisions at root s=200 GeV

PHENIX has measured the electron-positron pair mass spectrum from 0 to 8 GeV/c(2) in p + p collisions at root s = 200 GeV. The contributions from light meson decays to e(+)e(-) pairs have been determined based on measurements of hadron production cross sections by PHENIX. Within the systematic uncertainty of similar to 20% they account for all e(+)e(-) pairs in the mass region below similar to 1 GeV/c(2). The e(+)e(-) pair yield remaining after subtracting these contributions is dominated by semileptonic decays of charmed hadrons correlated through flavor conservation. Using the spectral shape predicted by PYTHIA, we estimate the charm production cross section to be 544 +/- 39(stat) +/- 142(syst) +/- 200(model) pb. which is consistent with QCD calculations and measurements of single leptons by PHENIX. (C) 2008 Elsevier BV. All rights reserved.

Praktiska effekter av begreppsförvirring för en databas konceptuella design : En fallstudie om databas- och begreppsmodellering

Company X develops a laboratory information system (LIS) called System Y. The informationsystem has a two-tier database architecture consisting of a production database and a historicaldatabase. A database constitutes the backbone of a IS, which makes the design of the databasevery important. A poorly designed database can cause major problems within an organization.The two databases in System Y are poorly modeled, particularly the historical database. Thecause of the poor modeling was unclear concepts. The unclear concepts have remained in thedatabase and in the company organization and caused a general confusion of concepts. The splitdatabase architecture itself has evolved into a bottleneck and is the cause of many problemsduring the development of System Y.Company X investigates the possibility of integrating the historical database with the productiondatabase. The goal of our thesis is to conduct a consequence analysis of such integration andwhat the effects would be on System Y, and to create a new design for the integrated database.We will also examine and describe the practical effects of confusion of concepts for a databaseconceptual design.To achieve the goal of the thesis, five different method steps have been performed: a preliminarystudy of the organization, a change analysis, a consequence analysis and an investigation of theconceptual design of the database. These method steps have helped identify changes necessaryfor the organization, a new design proposal for an integrated database, the impact of theproposed design and a number of effects of confusion for the database.

Småhusens framtida utformning : -Hur påverkar Boverkets nya byggregler?

Från och med 1:a jan 2010 gäller nya byggregler avseende energianvändning och effektbehov för nya byggnader. De nya kraven innebär en skärpning för alla byggnader som använder el för uppvärmning. För att begränsa effektbehovet för elvärmda hus införs krav på maximal installerad eleffekt och kraven på köpt energimängd blir lägre i hus med elvärme än i hus som har annat uppvärmningssätt. Denna rapport undersöker hur byggandet kan komma att påverkas av de nya byggreglerna och vilka system som kan komma att bli dominerande i småhusen framöver. En villa med olika isolerstandard simulerades på fyra olika orter från Malmö i söder till Kiruna i norr och energianvändningen för de olika uppvärmningssystemen beräknades sedan scha-blonmässigt med hjälp av tillverkarnas data. Två olika isolerstandarder och ett passivhus simu-lerades med respektive utan från och tilluft med värmeåtervinning. Resultaten visar att traditionella frånluftvärmepumpar inte klarar kraven, både vad gäller ener-gi och effekt, förutom möjligen i sydligaste Sverige i ett välisolerat hus. En kondenserande frånluftvärmepump som kyler frånluften kraftigare och utvinner kondensationsvärme klarar kraven om den uppfyller vad tillverkaren lovar. En frånluft/jordvärmepump klarar också kra-ven, men ligger nära gränsen i Mellansverige. De uppvärmningsalternativ som klarar de nya energikraven med god marginal i alla klimatzoner är kondenserande frånluftvärmepump, bergvärmepump, fjärrvärme (FTX krävs i norra Sverige), pelletkamin med FTX samt passiv-huset. De el-baserade uppvärmningsalternativ som ger lägst elanvändning är bergvärmepump samt passivhus alternativet. Dessa ligger på alla orter långt under kravgränserna från BBR.Uppvärmning med enbart pellets eller fjärrvärme (utan FTX eller solvärme) klarar inte energi-kraven med tillräcklig marginal förutom i Malmö. Det krävs ytterligare åtgärder som kan vara tilläggsisolering, värmeåtervinning med FTX, frånluftvärmepump eller solvärme. Pelletvärme-systemen får lite svårare att klara energikraven, pga pelletkaminens verkningsgrad. Det blir alltså i praktiken krav på FTX med ved, pellets och oftast med fjärrvärme.En ekonomisk utvärdering har genomförts baserad på första årets energi-, kapital- och under-hållskostnader. Kapitalkostnader delas upp på komponentens förväntade livslängd med annui-tetsmetoden. Framtida underhållskostnader diskonteras ett nuvärde och delas upp med annui-tetsmetoden. Dagens energipriser och en kalkylränta på 4,5 % används som utgångspunkt, men varieras för olika scenarier. Fjärrvärme tycks ge bland de lägsta kostnaderna av de studerade alternativen. I alla fall i de kommuner som ligger under medelpriset för svensk fjärrvärme. Vedeldning har inte studerats här, men ger säkerligen lägst totalkostnader om man accepterar den tid som krävs för att han-tera ved och elda. Det studerade passivhuset hör också till de alternativ som har bland de lägs-ta kostnaderna då investering och energianvändning vägs samman. Men räntenivån har en stor inverkan på systemens totalkostnad. Låg ränta har en utjämnande effekt på totalkostnaden. Vid högre ränta ökar kostnaden mest för system med lång livslängd (avskrivningstid), vilket gör passivhusen dyrare. Pelleteldning i nybyggda hus kommer nog att utgöra en mindre del av installationerna, då det krävs FTX och investeringskostnaden blir ganska hög, men om lösningar med frånluftvärme-pump och luftburen pelletkamin mot förmodan skulle komma att uppfylla kraven för ett icke elvärmt hus kan det bli ett uppsving av sådana lösningar.