Farms, pipes, streams and reforestation : reasoning about structured parallel processes using types and hylomorphisms

The increasing importance of parallelism has motivated the creation of better abstractions for writing parallel software, including structured parallelism using nested algorithmic skeletons. Such approaches provide high-level abstractions that avoid common problems, such as race conditions, and often allow strong cost models to be defined. However, choosing a combination of algorithmic skeletons that yields good parallel speedups for a program on some specific parallel architecture remains a difficult task. In order to achieve this, it is necessary to simultaneously reason both about the costs of different parallel structures and about the semantic equivalences between them. This paper presents a new type-based mechanism that enables strong static reasoning about these properties. We exploit well-known properties of a very general recursion pattern, hylomorphisms, and give a denotational semantics for structured parallel processes in terms of these hylomorphisms. Using our approach, it is possible to determine formally whether it is possible to introduce a desired parallel structure into a program without altering its functional behaviour, and also to choose a version of that parallel structure that minimises some given cost model.Postprin

Methods of identifying and recruiting older people at risk of social isolation and loneliness: A mixed methods review

BackgroundLoneliness and social isolation are major determinants of mental wellbeing, especially among older adults. The effectiveness of interventions to address loneliness and social isolation among older adults has been questioned due to the lack of transparency in identifying and recruiting populations at risk. This paper aims to systematically review methods used to identify and recruit older people at risk of loneliness and social isolation into research studies that seek to address loneliness and social isolation.MethodsIn total, 751 studies were identified from a structured search of eleven electronic databases combined with hand searching of reference bibliography from identified studies for grey literature. Studies conducted between January 1995 and December 2017 were eligible provided they recruited community living individuals aged 50 and above at risk of social isolation or loneliness into an intervention study.ResultA total of 22 studies were deemed eligible for inclusion. Findings from these studies showed that the most common strategy for inviting people to participate in intervention studies were public-facing methods including mass media and local newspaper advertisements. The majority of participants identified this way were self-referred, and in many cases self-identified as lonely. In most cases, there was no standardised tool for defining loneliness or social isolation. However, studies that recruited via referral by recognised agencies reported higher rates of eligibility and enrolment. Referrals from primary care were only used in a few studies. Studies that included agency referral either alone or in combination with multiple forms of recruitment showed more promising recruitment rates than those that relied on only public facing methods. Further research is needed to establish the cost-effectiveness of multiple forms of referral.ConclusionFindings from this study demonstrate the need for transparency in writing up the methods used to approach, assess and enrol older adults at risk of becoming socially isolated. None of the intervention studies included in this review justified their recruitment strategies. The ability of researchers to share best practice relies greatly on the transparency of research

The subpopulation pattern of eel sperm is affected by post-activation time, hormonal treatment and thermal regime

[EN] There has been a marked reduction in natural stocks of eels (genus Anguilla) over the past 60 years, and the culture of eels is still based on the capture of very large quantities of juveniles. It is necessary to close the life cycle in captivity in order to ease the pressure on wild populations. The aims of the present study were to evaluate sperm subpopulations (through cluster analysis of computer-aided sperm analysis data) in the European eel (Anguilla anguilla) and to assess the effects of motility acquisition time after activation (i.e. at 30, 60 and 90 s), the thermal regimen (i.e. 10 degrees C (T10) or 15 degrees C (T15) and up to 20 degrees C, or constant at 20 degrees C (T20)) and hormonal treatments (i.e. human chorionic gonadotropin (hCG), recombinant (r) hCG or pregnant mare serum gonadotropin (PMSG)) on these subpopulations. In all cases, we obtained three subpopulations of spermatozoa: low velocity and linear (S1); high velocity with low linearity (S2); and high velocity and linear (S3; considered high quality). Total motility and S1 were affected by acquisition time; thus, 30 s is recommended as the standard time for motility acquisition. When eels were kept at 20 degrees C (T20), motility data fitted quadratic models, with the highest motility and proportion of S3 between Weeks 8 and 12 after the first injection. Lower temperatures (T10, T15) delayed spermiation and the obtaining of high-quality spermatozoa (S3), but did not seem to alter the spermiation process (similar subpopulation pattern). Conversely, the hormonal treatments altered both the dynamics of the subpopulation pattern and the onset of spermiation (with PMSG delaying it). Total motility and the yield of S3 with the widely used hCG treatment varied throughout the spermiation period. However, using rhCG allowed us to obtain high-quality and constant motility for most of the study (Weeks 7-20), and the S3 yield was also higher overall (61.8 +/- 1.3%; mean +/- s.e.m.) and more stable over time than the other hormonal treatments (averaging 53.0 +/- 1.4%). Using T20 and rhCG would be more economical and practical, allowing us to obtain a higher number of S3 spermatozoa over an extended time.This study was funded by the European Community's 7th Framework Program under the Theme 2 'Food, Agriculture and Fisheries, and Bio-technology', grant agreement no. 245257 (PRO-EEL) and Generalitat Valenciana (ACOMP/2012/086). VG and MCV have predoctoral grants from the Spanish Ministry of Economy and Competitiveness (AGL2010-16009) and Universitat Politecnica de Valencia (UPV) PAID Program (2011-S2-02-6521), respectively. DSP was supported by a contract cofinanced by Ministry of Science and Innovation (MICINN) and UPV (PTA2011-4948-I). FM-P was supported by the Ramon y Cajal program (MICINN, RYC-2008-02560).Gallego Albiach, V.; Vilchez Olivencia, MC.; Peñaranda, D.; Pérez Igualada, LM.; Herraez, MP.; Asturiano Nemesio, JF.; Martinez-Pastor, F. (2015). The subpopulation pattern of eel sperm is affected by post-activation time, hormonal treatment and thermal regime. Reproduction, Fertility and Development. 27(3):529-543. https://doi.org/10.1071/RD13198S52954327

The dating of shallow faults in the Earth's crust

Direct dating of ductile shear zones and calculation of uplift/exhumation rates can be done using various radiometric dating techniques. But radiometric dating of shallow crustal faulting, which occurs in the crust's brittle regime, has remained difficult(1-4) because the low temperatures typical of shallow crusted faults prevent the complete syntectonic mineral recrystallization that occurs in deeper faults. Both old (detrital) and newly grown (authigenic) fine-grained phyllosilicates are thus preserved in shallow fault zones and therefore their radiometric ages reflect a mixture of both mineral populations. Also, the loss of Ar-39 during neutron irradiation in dating of clay minerals can produce erroneously old ages. Here we present a method of characterizing the clay populations in fault gouge, using X-ray modelling, combined with sample encapsulation, and show how it can be used to date near-surface fault activity reliably. We examine fault gouge from the Lewis thrust of the southern Canadian Rockies, which we determine to be similar to 52 Myr old. This result requires the western North America stress regime to have changed from contraction to extension in only a few million years during the Eocene. We also estimate the uplift/exhumation age and sedimentary source of these rocks to be similar to 172 Myr.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62567/1/412172a0.pd

Satellite remote sensing data can be used to model marine microbial metabolite turnover

Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes’ predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10−6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ~3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology

Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study

Peer reviewedPublisher PD

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Measurement of the Forward-Backward Asymmetry in the B -> K(*) mu+ mu- Decay and First Observation of the Bs -> phi mu+ mu- Decay

We reconstruct the rare decays $B^+ \to K^+\mu^+\mu^-$, $B^0 \to K^{*}(892)^0\mu^+\mu^-$, and $B^0_s \to \phi(1020)\mu^+\mu^-$ in a data sample corresponding to $4.4 {\rm fb^{-1}}$ collected in $p\bar{p}$ collisions at $\sqrt{s}=1.96 {\rm TeV}$ by the CDF II detector at the Fermilab Tevatron Collider. Using $121 \pm 16$ $B^+ \to K^+\mu^+\mu^-$ and $101 \pm 12$ $B^0 \to K^{*0}\mu^+\mu^-$ decays we report the branching ratios. In addition, we report the measurement of the differential branching ratio and the muon forward-backward asymmetry in the $B^+$ and $B^0$ decay modes, and the $K^{*0}$ longitudinal polarization in the $B^0$ decay mode with respect to the squared dimuon mass. These are consistent with the theoretical prediction from the standard model, and most recent determinations from other experiments and of comparable accuracy. We also report the first observation of the $B^0_s \to \phi\mu^+\mu^- decay and measure its branching ratio${\mathcal{B}}(B^0_s \to \phi\mu^+\mu^-) = [1.44 \pm 0.33 \pm 0.46] \times 10^{-6}$using$27 \pm 6$signal events. This is currently the most rare$B^0_s$ decay observed.Comment: 7 pages, 2 figures, 3 tables. Submitted to Phys. Rev. Let

Search for a New Heavy Gauge Boson Wprime with Electron + missing ET Event Signature in ppbar collisions at sqrt(s)=1.96 TeV

We present a search for a new heavy charged vector boson $W^\prime$ decaying to an electron-neutrino pair in $p\bar{p}$ collisions at a center-of-mass energy of 1.96\unit{TeV}. The data were collected with the CDF II detector and correspond to an integrated luminosity of 5.3\unit{fb}^{-1}. No significant excess above the standard model expectation is observed and we set upper limits on $\sigma\cdot{\cal B}(W^\prime\to e\nu)$. Assuming standard model couplings to fermions and the neutrino from the $W^\prime$ boson decay to be light, we exclude a $W^\prime$ boson with mass less than 1.12\unit{TeV/}c^2 at the 95\unit{%} confidence level.Comment: 7 pages, 2 figures Submitted to PR

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO