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opencc-zeroDec 2018View details →

Data from: Nathusius' bats optimize long-distance migration by flying at maximum range speed.

Metabolic rate of 12 Pipistrellus nathusii in relation to varying airspeed. We measured the metabolic rate of flying bats in a wind tunnel using the 13C labeled Na-bicarbonate method. The relationship between metabolic rate and airspeed was U-shaped in the majority of individuals. We could not find a U-shaped curve in a few individuals that engaged in flight manoeuvers, including landing. We used the shape of the U-shaped power curve to estimate minimum flight speed and maximum range speed for the study species. Further we present data on migration speed (n=37) and foraging flight speed (n=40) in wild Pipistrellus nathusii at a major miratory corridor in Latvia.

opencc-zeroDec 2013View details →

Data from: Balancing sample accumulation and DNA degradation rates to optimize noninvasive genetic sampling of sympatric carnivores

Noninvasive genetic sampling, or noninvasive DNA sampling (NDS), can be an effective monitoring approach for elusive, wide-ranging species at low densities. However, few studies have attempted to maximize sampling efficiency. We present a model for combining sample accumulation and DNA degradation to identify the most efficient (i.e. minimal cost per successful sample) NDS temporal design for capture–recapture analyses. We use scat accumulation and faecal DNA degradation rates for two sympatric carnivores, kit fox (Vulpes macrotis) and coyote (Canis latrans) across two seasons (summer and winter) in Utah, USA, to demonstrate implementation of this approach. We estimated scat accumulation rates by clearing and surveying transects for scats. We evaluated mitochondrial (mtDNA) and nuclear (nDNA) DNA amplification success for faecal DNA samples under natural field conditions for 20 fresh scats/species/season from <1–112 days. Mean accumulation rates were nearly three times greater for coyotes (0.076 scats/km/day) than foxes (0.029 scats/km/day) across seasons. Across species and seasons, mtDNA amplification success was ≥95% through day 21. Fox nDNA amplification success was ≥70% through day 21 across seasons. Coyote nDNA success was ≥70% through day 21 in winter, but declined to <50% by day 7 in summer. We identified a common temporal sampling frame of approximately 14 days that allowed species to be monitored simultaneously, further reducing time, survey effort and costs. Our results suggest that when conducting repeated surveys for capture–recapture analyses, overall cost-efficiency for NDS may be improved with a temporal design that balances field and laboratory costs along with deposition and degradation rates.

zenodo32/100

Rational design and optimization of synthetic gene switches for controlling cell-fate decisions in pluripotent stem cells

Data underlying the figures in the publication “Rational Design and Optimization of Synthetic Gene Switches for Controlling Cell-fate Decisions in Pluripotent Stem Cells”, published in Metabolic Engineering, 2021, 65, 99-110. <a href="https://doi.org/10.1016/j.ymben.2021.03.009">https://doi.org/10.1016/j.ymben.2021.03.009</a> Table of contents: 1. Dataset 1; Excel file with the curated data underlying the figures. Figure 1. Comparative analysis of synthetic gene switches in HEK-293T and hiPSCs. (A) Erythromycin-responsive synthetic gene switch consisting of a constitutively expressed erythromycin-responsive transactivator (pVH620; PmPGK1-E-VP16-pA) and an inducible Nluc expression vector controlled by an operator containing two erythromycin transcription response (ETR) sites (pVH619; OETR2-PCMVmin-2-Nluc-pA), assessed in terms of production of secreted Nluc 24 h after transfection. EM indicates addition of erythromycin (2.0 µg/mL) to the culture medium. (B) Phloretin-responsive synthetic gene switch consisting of a constitutively expressed phloretin-responsive transactivator (pVH655; PmPGK1-TtgR-VP16-pA) and an inducible Nluc expression vector controlled by an operator containing two TtgR binding sites (pVH654; OTtgO2-PCMVmin-2-Nluc-pA), assessed in terms of production of secreted Nluc 24 h after transfection. Phlo indicates addition of phloretin (50 µM) to the culture medium. (C) Vanillic acid-responsive synthetic gene switch consisting of a constitutively expressed vanillic acid-responsive transactivator (pVH238-1; PmPGK1-VanR-VP16-pA) and an inducible Nluc expression vector controlled by an operator containing two VanR binding sites (pVH294-1.3; OVanO2-PCMVmin-2-Nluc-pA), assessed in terms of production of secreted Nluc 24 h after transfection. VA indicates addition of vanillic acid (500 µM) to the culture medium. Figure 2. Rational design and assembly of a vanillic acid-controlled synthetic gene switch in hiPSCs. (B) Combinatorial analysis of constitutive promoters in hiPSCs for the expression of the VanR-VP16 trans-activator (pVH238-1; PmPGK1-VanR-VP16-pA, pVH238-2; PhEF1a-VanR-VP16-pA) and inducible expression cassette minimal promoters (pVH294-1.1; OVanO2-Pmin-Nluc-pA, pVH294-1.3; OVanO2-PCMVmin-2-Nluc-pA, pVH294-1.2; OVanO2-PCMVmin-1-Nluc-pA), assessed in terms of the production of secreted Nluc 24 h after transfection. (C) Tuning the induction level of the inducible expression cassette in hiPSCs by increasing the number of VanR binding sites within the operator (pVH294-1.1; OVanO2-Pmin-Nluc-pA, pVH294-2.1; OVanO4-Pmin-Nluc-pA, pVH294-3.1; OVanO6-Pmin-Nluc-pA), assessed in terms of the production of secreted Nluc 24 h after co-transfection with PmPGK1-driven VanR-VP16 (pVH238-1; PmPGK1-VanR-VP16-pA). (D) Assessment of the structural assembly of the VanR-VP16 transactivator in hiPSCs, comparing direct fusion of VanR and VP16 (pVH238-1; PmPGK1-VanR-VP16-pA), fusion with a short flexible (pVH261; PmPGK1-VanR-FL1-VP16-pA, FL1; GGGGS) or rigid (pVH263; PmPGK1-VanR-RL1-VP16-pA, RL1; EAAAK) linker, and fusion with a longer flexible (pVH262; PmPGK1-VanR-FL2-VP16-pA, FL2; GGGGSGGGGS) or rigid (pVH264; PmPGK1-VanR-RL2-VP16-pA, RL2; EAAAKEAAAK) linker, assessed in terms of the production of secreted Nluc 24 h after co-transfection with a Pmin-driven reporter construct controlled by four VanR binding sites (pVH294-2.1; OVanO4-Pmin-Nluc-pA). (E) Tuning the induction level of the VA-controlled synthetic gene switch in hiPSCs by promoting active nuclear translocation of VanR-VP16 (pVH238-1; PmPGK1-VanR-VP16-pA) with importin-alpha (pVH250; PmPGK1-NLSSV40-VanR-VP16-pA) or importin-beta (pVH252; PmPGK1-NLSG46-VanR-VP16-pA)-recognized NLS peptide, assessed in terms of the production of secreted Nluc 24 h after co-transfection with a Pmin-driven reporter construct controlled by four VanR binding sites (pVH294-2.1; OVanO4-Pmin-Nluc-pA). (F) Combinatorial analysis for the final assembly of the VA-controlled synthetic gene switch in hiPSCs using a Pmin-driven reporter construct controlled by either four (pVH294-2.1; OVanO4-Pmin-Nluc-pA) or six (pVH294-3.1; OVanO4-Pmin-Nluc-pA) VanR binding sites and different combinations of selected components from previous characterization steps to assemble the transactivator (pVH238-1; PmPGK1-VanR-VP16-pA, pVH263; PmPGK1-VanR-RL1-VP16-pA, pVH262; PmPGK1-VanR-FL2-VP16-pA, pVH250; PmPGK1-NLSSV40-VanR-VP16-pA, pVH252; PmPGK1-NLSG46-VanR-VP16-pA, pVH629; PmPGK1-NLSSV40-VanR-RL1-VP16-pA, pVH628; PmPGK1-NLSSV40-VanR-FL2-VP16-pA, pVH300; PmPGK1-NLSG46-VanR-RL1-VP16-pA, pVH624; PmPGK1-NLSG46-VanR-FL2-VP16-pA), assessed in terms of the production of secreted Nluc 24 h after transfection. (G) Dose-response curves in hiPSCs of the PmPGK1-driven NLSG46-VanR-VP16 (pVH252; PmPGK1-NLSG46-VanR-VP16-pA) and the basic VanR-VP16 (pVH238-1; PmPGK1- VanR-VP16-pA) fusion constructs using the Pmin-driven reporter construct controlled by four VanR binding sites (pVH294-1.2; OVanO4-Pmin-Nluc-pA), assessed in terms of the production of secreted Nluc 24 h after transfection. (B-F) VA indicates addition of vanillic acid (500 µM) to the culture medium. Figure 3. Regulation of the VanA system during the generation of the three germ layers. hiPSCs transiently transfected with the complete VA-controlled expression vector (pVH438; 5’ITR-OVanO4-Pmin-Nluc-pA-PmPGK1-NLSG46-VanR-VP16-2A-NeoR-pA-3’ITR) were specified for 3 days into (A) DE or (B) ME, and for 5 days into (C) EC. The VanA system was maintained in its repressed state by the addition of VA (500 µM) and induced by the removal of VA from the differentiation medium on the last day of differentiation. Induction of the VanA system was assessed in terms of the intracellular production of non-secreted Nluc. Figure 4. Synthetic gene-switch-guided posterior foregut lineage specification. (C) The mRNA expression levels of HHEX and TGIF2 in iHHEX/iTGIF2 hiPSCs cultured for 24 h in the presence of different combinations of VA and DOX were determined by means of qRT-PCR. VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. Values were normalized to those in the VA (+)/DOX(-) condition. (G-H) iHHEX/iTGIF2 hiPSC-derived DE cells were differentiated towards PG with FGF7 (25 ng/mL) for 3 days, and subsequently towards PFG with FGF7 (25 ng/mL), noggin (50 ng/mL), and retinoic acid (RA; 2 µM) for 1 day. During differentiation HHEX and TGIF2 was maintained uninduced/repressed (VA on D0-7, No DOX), or HHEX was induced on day 2-3 by the addition of DOX and TGIF2 was induced on day 3-7 by removal of VA from the differentiation medium (VA on D3-7, DOX on D2-3). VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. (G) Quantification of PDX1-expressing PFG cells. Flow cytometry results quantification of PDX1-expressing PFG cells differentiated using growth-factor-directed (VA on D0-7, No DOX) and TGIF2/HHEX-guided (VA on D0-3, DOX on D2-3) differentiation protocols. (H) Relative mRNA expression levels for PP (PDX1), PFG (SOX9, HNF6), HP (ALB), MHG (CDX2), and AFG (OTX2) genes on day 7 in iHHEX/iTGIF2 hiPSC-derived PFG cells generated with the indicated HHEX and TGIF2 induction conditions were determined by means of qRT-PCR. Values were normalized to those in day 0 iHHEX/iTGIF2 hiPSCs. Figure S1. Effect of constitutive promoter expression strength (pVH238-1; PmPGK1-VanR-VP16-pA, pVH238-2; PhEF1a-VanR-VP16-pA) on the basal expression levels of inducible vectors containing different minimal promoters (pVH294-1.1; OVanO2-Pmin-Nluc-pA, pVH294-1.3; OVanO2-PCMVmin-2-Nluc-pA, pVH294-1.2; OVanO2-PCMVmin-1-Nluc-pA) relative to mock transfection (pColaDuet-1) in hiPSCs, assessed in terms of the production of secreted Nluc 24 h after transfection. VA indicates addition of vanillic acid (500 µM) to the culture medium. Figure S2. Assessment of optimal fusion configurations for NLS peptides. (A) NLSSV40 or (B) NLSG46 was fused to the N-terminus of VanR-VP16 (pVH250; PmPGK1-NLSSV40VanR-VP16-pA, pVH252; PmPGK1-NLSG46-VanR-VP16-pA), in between VanR and VP16 as a linker (pVH260; PmPGK1-VanR-NLSSV40-VP16-pA, pVH622; PmPGK1-VanR-NLSG46-VP16-pA), or to the C-terminus (pVH251; PmPGK1-VanR-VP16-NLSSV40-pA, pVH623; PmPGK1-VanR-VP16-NLSG46-pA) to identify the best conformation in hiPSCs, assessed in terms of the production of secreted Nluc 24 h after co-transfection with a Pmin-driven reporter construct controlled by four VanR binding sites (pVH294-2.1; OVanO4-Pmin-Nluc-pA). (A-B) VA indicates addition of vanillic acid (500 µM) to the culture medium. Figure S3. Complete expression vector design for stable integration encoding OVanO4-Pmin-driven Nluc expression cassette and PmPGK1-driven NLSG46-VanR-VP16 (pVH438; 5’ITR-OVanO4-Pmin-Nluc-pA-PmPGK1-NLSG46-VanR-VP16-2A-NeoR-pA-3’ITR). (B) Transient performance characterization in hiPSCs assessed in terms of the production of intracellular Nluc 24 h after transfection. VA indicates addition of vanillic acid (500 µM) to the culture medium. Figure S4. Generation of the three germ layers from hiPSCs transfected with complete VA-controlled expression vector (pVH438; 5’ITR-OVanO4-Pmin-Nluc-pA-PmPGK1-NLSG46-VanR-VP16-2A-NeoR-pA-3’ITR). (A) Relative mRNA expression levels of definitive endoderm (DE) genes (EOMES, SOX17, FOXA2, CXCR4) in cells transfected with the complete VA system expression vector after 3 days of DE specification with VA. (B) Relative mRNA expression levels of mesoderm (ME) genes (T, PDGFRa, TBX6, HAND1) in cells transfected with the complete VA system expression vector after 3 days of ME specification with VA. (C) Relative mRNA expression levels of ectoderm (EC) genes (PAX6, NES, OTX2, SOX10) in cells transfected with the complete VA system expression vector after 5 days of EC specification with VA. (A-C) Values were normalized to those of day 0 hiPSCs. VA indicates the addition of vanillic acid (500 µM) to the differentiation medium. Figure S5. Performance comparison and multiplexing of the VanA and rtTA systems in hIPSCs. (A) Comparison of selected inducible expression cassette containing four VanR response elements (pVH294-2.1; OVanO4-Pmin-Nluc-pA) in combination with PmPGK1-driven NLSG46-VanR-VP16 (pVH252; PmPGK1-NLSG46-VanR-VP16-pA) fusion construct relative to the DOX-controlled rtTA system (pVH627; OTetO7-Pmin-Nluc-pA / pVH235; PmPGK1-rtTA-pA) in hiPSCs assessed in terms of the production of secreted Nluc 24 h after transfection. (B) Assessment of multiplexing potential of the VA system (pVH425; OVanO4-Pmin-Nluc-pA / pVH252; PmPGK1-NLSG46-VanR-VP16-pA) and the DOX-controlled rtTA system (pVH424; OTetO7-Pmin-Fluc-pA / pVH235; PmPGK1-rtTA-pA) in hiPSCs assessed in terms of the production of intracellular Nluc and Fluc 48 h after transfection. (A-B) VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (1 µg/mL) to the culture medium. Figure S6. (C) iHHEX/iTGIF2 hiPSCs were differentiated towards anterior primitive streak (APS) and DE using the standard combination of exogenous Wnt (GSK3 inhibition CHIR99021 [CHIR]; 3 µM) and TGF-β (Activin A [AA]; 100 ng/mL) induction. During differentiation, TGIF2 was maintained repressed by the addition of VA (VA on D0-3) and HHEX was maintained uninduced (No DOX). VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. Relative mRNA expression levels for pluripotency markers (POU5F1, NANOG, SOX2), and definitive endoderm (DE) markers (EOMES, SOX17, FOXA2, CXCR4) on day 3 in iHHEX/iTGIF2 hiPSC-derived DE cells were determined by means of qRT-PCR. Values were normalized to those of day 0 iHHEX/iTGIF2 hiPSCs. (E) iHHEX/iTGIF2 hiPSC-derived DE cells were differentiation towards PG for 1 day with FGF7 (25 ng/mL). During PG specification, TGIF2 was induced alone (VA on D0-3, No DOX), HHEX was induced alone (VA on D0-4, No DOX), or TGIF2 and HHEX were both maintained uninduced (VA on D0-4, No DOX) on day 3-4 by removal or addition of VA and DOX as specified. VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. The expression levels for HHEX and TGIF2 on day 4 during PG differentiation of iHHEX/iTGIF2 hiPSC-derived DE cells were determined by means of qRT-PCR. Values were normalized to GAPDH and TBP expression levels in day 4 iHHEX/iTGIF2 hiPSCs. Figure S7. (B) iHHEX/iTGIF2 hiPSC-derived DE cells were differentiated towards PG with FGF7 (25 ng/mL) for 3 days, and subsequently towards PFG with FGF7 (25 ng/mL), noggin (50 ng/mL), and retinoic acid (RA; 2 µM) for 1 day. During differentiation TGIF2 was maintained repressed under all conditions by the addition of VA to the differentiation media on day 0-7 (VA on D0-7). HHEX was either maintained uninduced (No DOX) or induced on day 2-3, 2-4, or 2-5 by the addition of DOX to the differentiation media (DOX on D2-3, D2-4, or D2-5). VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. Relative mRNA expression levels for PP (PDX1), HP (ALB), and PFG (SOX9, HNF6) genes on day 7 in iTGIF2/iHHEX hiPSC-derived PFG cells generated with the indicated differentiation protocol and HHEX induction conditions were determined by means of qRT-PCR. Values were normalized to those of day 0 iHHEX/iTGIF2 hiPSCs. (D) iHHEX/iTGIF2 hiPSC-derived DE cells were differentiated towards PG with FGF7 (25 ng/mL) for 3 days, and subsequently towards PFG with FGF7 (25 ng/mL), noggin (50 ng/mL), and retinoic acid (RA; 2 µM) for 1 day. During differentiation HHEX was maintained uninduced under all conditions (No DOX). TGIF2 was either maintained uninduced by the addition of VA (VA on D0-7) or induced on day 5-7, 4-7, or 3-7 by removal of VA from the differentiation medium (VA on D0-5, D0-4, or D0-3). VA indicates addition of vanillic acid (500 µM) and DOX indicates addition of doxycycline (0.75 µg/mL) to the culture medium. Relative mRNA expression levels for PP (PDX1), HP (ALB), and PFG (SOX9, HNF6) genes on day 7 in iHHEX/iTGIF2 hiPSC-derived PFG cells generated with the indicated differentiation protocol and TGIF2 induction conditions were determined by means of qRT-PCR. Values were normalized to those of day 0 iHHEX/iTGIF2 hiPSCs.

opencc-by-4.0Jun 2021View details →

Data from: Multi-objective optimization for plant germplasm collection conservation of genetic resources based on molecular variability

Germplasm collections play a significant role among strategies for conservation of diversity. It is common to select a core collection to represent the genetic diversity of a germplasm collection, in order to minimize the cost of conservation, while ensuring the maximization of genetic variation. We aimed to solve two main problems: (1) to select a set of individuals, from an in situ data set, that is genetically complementary to an existing germplasm collection, and (2) to define a core collection for a germplasm collection. We proposed a new multi-objective optimization (MOO) approach based on principles of systematic conservation planning (SCP) incorporating heterozygosity information; therefore, optimization takes genotypic diversity and variability patterns into account as well. As a case study, we used Dipteryx alata microsatellite loci information from two sources, an ex situ germplasm collection located at the Agronomy School of the Federal University of Goiás (UFG-AS), and an in situ data set composed of 642 sampled individual trees. We were able to identify within a population of several individuals, the exact accessions/samples that should be chosen in order to preserve the species diversity. We found that material from nine in situ individual trees are enough to complement the UFG-AS germplasm collection as it is, and that it is possible to define a core collection of 20 individual trees representing all studied genetic diversity. Moreover, we defined a method (a protocol) to deal with large amounts of accessions in the context of MOO. The proposed approach can be used to help constructing collections with maximal allelic richness and can also be extended to the in situ conservation. As far as we know, this is the first time that principles of SCP and the MOO approach are applied to the problem of complementing a germplasm collection and of finding a core collection for a germplasm collection.

opencc-zeroDec 2013View details →

Data from: Landscape resistance and habitat combine to provide an optimal model of genetic structure and connectivity at the range margin of a small mammal

We evaluated the effect of habitat and landscape characteristics on the population genetic structure of the white-footed mouse. We develop a new approach that uses numerical optimization to define a model that combines site differences and landscape resistance to explain the genetic differentiation between mouse populations inhabiting forest patches in southern Québec. We used ecological distance computed from resistance surfaces with Circuitscape to infer the effect of the landscape matrix on gene flow. We calculated site differences using a site index of habitat characteristics. A model that combined site differences and resistance distances explained a high proportion of the variance in genetic differentiation and outperformed models that used geographical distance alone. Urban and agriculture related land uses were, respectively, the most and the least resistant landscape features influencing gene flow. Our method detected the effect of rivers and highways as highly resistant linear barriers. The density of grass and shrubs on the ground best explained the variation in the site index of habitat characteristics. Our model indicates that movement of white-footed mouse in this region is constrained along routes of low resistance. Our approach can generate models that may improve predictions of future northward range expansion of this small mammal.

opencc-zeroMar 2020View details →

Data from: Oncogene inference optimization using constraint-based modelling incorporated with protein expression in normal and tumour tissues

Cancer cells are known to exhibit unusual metabolic activity and yet, few metabolic cancer driver genes are known. Genetic alterations and epigenetic modi cations of cancer cells result in the abnormal regulation of cellular metabolic pathways that are different when compared to normal cells. Such a metabolic reprogramming can be simulated using constraint-based modelling approaches towards predicting oncogenes. We introduced the tri-level optimization problem to use the metabolic reprogramming towards inferring oncogenes. The algorithm incorporated Recon 2.2 network with the Human Protein Atlas to reconstruct genome-scale metabolic network models of the tissue-speci fic cells at normal and cancer states, respectively. Such reconstructed models were applied to build the templates of the metabolic reprogramming between normal and cancer cell metabolism. The inference optimization problem was formulated to use the templates as a measure towards predicting oncogenes. The nested hybrid differential evolution algorithm was applied to solve the problem to overcome solving difficulty for transferring the inner optimization problem into the single one. Head and neck squamous cells were applied as a case study to evaluate the algorithm. We detected 13 of the top ranked one-hit dysregulations and 17 of the top ranked two-hit oncogenes with high similarity ratios to the templates. According literature survey, most inferred oncogenes are consistent with the observation in various tissues. Furthermore, the inferred oncogenes were highly connected with the TP53/AKT/IGF/MTOR signalling pathway through PTEN, which is one of the most frequently detected tumour suppressor genes in human cancer.

Data from: Optimizing prevention of HIV mother to child transmission: duration of antiretroviral therapy and viral suppression at delivery among pregnant Malawian women

Background: Effective antiretroviral therapy during pregnancy minimizes the risk of vertical HIV transmission. Some women present late in their pregnancy for first antenatal visit; whether these women achieve viral suppression by delivery and how suppression varies with time on ART is unclear. Methods: We conducted a prospective cohort study of HIV-infected pregnant women initiating antiretroviral therapy for the first time from June 2015 to November 2016. Multivariable Poisson models with robust variance estimators were used to estimate risk ratios (RR) and 95% confidence intervals (CI) of the association between duration of ART and both viral load (VL) ≥1000 copies/ml and VL ≥40 copies/ml at delivery. Results: Of the 252 women who had viral load testing at delivery, 40 (16%) and 78 (31%) had VL ≥1000 copies/ml and VL ≥40 copies/ml, respectively. The proportion of women with poor adherence to ART was higher among women who were on ART for ≤12 weeks (9/50 = 18.0%) than among those who were on ART for 13-35 weeks (18/194 = 9.3%). Compared to women who were on ART for ≤12 weeks, women who were on ART for 13-20 weeks (RR = 0.52; 95% CI: 0.36-0.74) or 21-35 weeks (RR = 0.26; 95% CI: 0.14-0.48) had a lower risk of VL ≥40 copies/ml at delivery. Similar comparisons for VL ≥1000 copies/ml at delivery showed decrease in risk although not significant for those on ART 13-20 weeks. Conclusion: Longer duration of ART during pregnancy was associated with suppressed viral load at delivery. Early ANC attendance in pregnancy to facilitate prompt ART initiation for HIV-positive women is essential in the effort to eliminate HIV vertical transmission.

opencc-zeroDec 2015View details →

Data from: Directed flight and optimal airspeeds: homeward-bound gulls react flexibly to wind yet fly slower than predicted

Birds in flight are proposed to adjust their body orientation (heading) and airspeed to wind conditions adaptively according to time and energy constraints. Airspeeds in goal-directed flight are predicted to approach or exceed maximum-range airspeeds, which minimize transport costs (energy expenditure per unit distance) and should increase in headwinds and crosswinds. Diagnosis of airspeed adjustment is however obscured by uncertainty regarding birds' goal-directions, transport costs, interrelations with orientation strategy and the attainability of predicted behaviour. To address these issues, we tested whether gulls minimized transport costs through adjustment of airspeed and heading to wind conditions during extended inbound flight over water (180–360 km) to their breeding colony, and introduce a methodology to assess transport (energy) efficiency given wind conditions. Airspeeds, heading, flight mode and energy expenditure were estimated using GPS tracking, accelerometer and wind data. Predicted flight was determined by simulating each trip according to maximum-range airspeeds and various orientation strategies. Gulls employed primarily flapping flight (93%), and negotiated crosswinds flexibly to exploit both high altitude tailwinds and coastal soaring opportunities. We demonstrate that predicted airspeeds in heavy crosswinds depend strongly on orientation strategy and presumed preferred direction. Measured airspeeds increased with headwind and crosswind similarly to maximum-range airspeeds based on full compensation for wind drift, yet remained ∼ 30% lower than predicted by all strategies, resulting in slower and 30–35% costlier flight. Interestingly, more energy could be saved through adjustment of airspeed (median 40%) than via orientation strategy (median 4%). Therefore, despite remarkably flexible reaction to wind at sea, these gulls evidently minimized neither time nor energy expenditure. However, airspeeds were possibly over-predicted by current aerodynamic models. This study emphasizes the importance of accounting for orientation strategy when assessing airspeed adjustments to wind and indicates that either the cost or adaptive 'currency' of extended flight among gulls may require revision.

Data from: An optimized protocol for large-scale in situ sampling and analysis of volatile organic compounds

Chemical ecology is an ever‐expanding field with a growing interest in population‐ and community‐level studies. Many such studies are hindered due to lack of an efficient and accelerated protocol for large‐scale sampling and analysis of chemical compounds. Here, we present an optimized protocol for such large‐scale study of volatiles. A large‐scale in situ study to understand role of semiochemicals in variation in mating success of lekking blackbuck was conducted. Suitable methods for sampling and statistical analysis were identified by testing and comparing the efficiencies of available techniques to reduce analysis time while retaining sensitivity and comprehensiveness. Solid‐phase extraction using polydimethylsiloxane, analysis using a semiautomated detection of retention time and base peak, and statistical analysis using random forest algorithm were identified as the most efficient methods for large‐scale in situ sampling and analysis of volatiles. The protocol for large‐scale volatile analysis can facilitate evolutionary and metaecological studies of volatiles in situ from all types of biological samples. The protocol has potential for wider application with the analysis and interpretation methods being suitable for all kinds of semiochemicals, including nonvolatile chemicals.

Data from: Context-dependence of maternal effects: testing assumptions of optimal egg size, differential- and sex-allocation models

If offspring develop in adverse conditions, the maternal component of their phenotypic variation might increase due to the stronger dependence of offspring traits on parental investment. This should result in increased parental investment to individual offspring, as assumed by the model of optimal egg size. The opposite pattern, i.e., stronger dependence of offspring fitness on parental investment and consequently larger parental investment under good conditions is assumed by both the theory of differential allocation if attractive males provide material benefits, and reproductive compensation if they invest less into paternal care. Another influential idea is the Trivers-Willard model, which assumes sex-specific dependence of offspring fitness on parental investment. Here we tested these ideas by examining the effects of egg size on offspring fitness across many postnatal contexts in the Collared Flycatcher Ficedula albicollis. We employed a cross-fostering design that generated variation in egg size within nests and used brood means of fledgling mass as a functional measure of the quality of rearing conditions. Effects of egg size on three offspring traits, including lifetime reproductive success of recruits, were more pronounced in low-quality broods. These results support the assumption of the model of optimal egg size. Based on female preference for males providing material benefits, this pattern could support differential allocation, if attractive males invest less in paternal care, or reproductive compensation, if they invest more. By comparison, we did not find any evidence for sex specificity of fitness returns that might explain sex monomorphism of egg size in this species. The challenge for future studies will be the integration of components of parental investment and offspring fitness into their global measures and testing how the former affects the latter across gradients of postnatal conditions.

Data from: Conservation under uncertainty: optimal network protection strategies for worst-case disturbance events

1. Conservation goals are ideally set after a thorough understanding of potential threats; however, predicting future spatial patterns of threats, such as disturbance, remains challenging. Here, we develop a novel extension of network fortification-interdiction models (NFIM) that deals with uncertainty in future spatial patterns of disturbance by optimally selecting sites that will best mitigate a worst-case scenario for a given magnitude of disturbance. 2. This approach uses information on between-patch movement probabilities and patch-specific survival, which can be estimated from mark-recapture data, to optimize life expectancy. Optimization occurs in three interrelated stages: protection, followed by disturbance, and then assessment. 3. We applied the modeling approach to two mark-recapture data sets: Roseate terns Sterna dougallii in the northeastern United States and the Everglade snail kite Rostrhamus sociabilis plumbeus in Florida. We contrasted the results to a more conventional approach of protecting sites that maximize connectivity (by minimizing the distances among protected sites) and a bi-objective model that maximizes connectivity and the number of individuals under protection. 4. Protecting sites that best mitigate future worst-case disturbance scenarios consistently resulted in higher predicted life expectancies than protecting patches that minimize dispersal distance. Predicted life expectancy was similar between NFIM and the biobjective model for the small roseate tern network, yet, the NFIM predicted higher life expectancy than any of the scenarios in the bi-objective model in the snail kite network. 5. Synthesis and applications. This application of interdiction models prescribed a combination of patches for protection that results in the least possible decrease in life expectancy. Our analyses of the snail kite and roseate tern networks suggest that managing to protect these prescribed patches by the network fortification interdiction model (i.e. protecting against the worst-case disturbance scenario) is more beneficial than managing patches that minimize dispersal distance or maximize the number of individuals under protection if the conservation goal is to ensure the long term persistence of a species.

Data from: Optimizing regulatory requirements to aid in the implementation of compensatory mitigation

Governments, companies, and conservation organizations seek to minimize the impacts of development through application of the mitigation hierarchy: avoid, minimize, restore, and offset (McKenney & Kiesecker 2010). Around the world, policies and performance standards for compensatory mitigation are being strengthened not just to reduce impacts to biodiversity, but to achieve goals for biodiversity that range from "no net loss" to "net gains" (IFC 2012). Although use of offsets is still in its infancy, offsets are gaining traction globally as a goal of public policy (Madsen et al. 2011; Villarroya, Barros & Kiesecker 2014), corporate practices (Rainey et al. 2014), and lending standards (IFC 2012; Equator Principles 2013). As such, these new policies and standards will be important drivers for companies to improve mitigation practices.

opencc-zeroDec 2012View details →

Data from: Using semidefinite programming to optimize unequal deployment of genotypes to a clonal seed orchard

Tree breeders must often consider the conservation of genetic diversity, while at the same time, maximizing response to selection. In the case of seed orchards, the buyer of seed wants maximum performance, while satisfying a restriction, sometimes legislated, on the diversity deployed to the forest. Optimal selection will not completely avoid kinship but rather maximize gain while imposing a constraint on average relatedness. Here, we present the application of semidefinite programming (SDP) as a flexible approach to optimize the deployment of genotypes to a clonal seed orchard. We formulate the selection problem as an SDP, where average breeding value is to be maximized, while imposing constraints on relatedness, as well as maximum and minimum contributions from each candidate. An open-source solver, SDPA, was embedded into a tool designed to make the optimization of seed orchards by SDP simple and flexible. Case studies optimizing seed orchards for Scots pine and loblolly pine illustrate how this flexibility can be used to impose additional constraints on the scion material available from some candidate genotypes and optimize selection even when related candidates have varying degrees of coancestry among them. Additional situations where SDP can be employed are discussed.

Data from: Study on the optimization of the deposition rate of planetary GaN-MOCVD films based on CFD simulation and the corresponding surface model

Metal-organic chemical vapour deposition (MOCVD) is a key technique for fabricating GaN thin film structures for light-emitting and semiconductor laser diodes. Film uniformity is an important index to measure equipment performance and chip processes. This paper introduces a method to improve the quality of thin films by optimizing the rotation speed of different substrates of a model consisting of a planetary with seven 6-inch wafers for the planetary GaN-MOCVD. A numerical solution to the transient state at low pressure is obtained using computational fluid dynamics. To evaluate the role of the different zone speeds on the growth uniformity, single factor analysis is introduced. The results show that the growth rate and uniformity are strongly related to the rotational speed. Next, a response surface model was constructed by using the variables and the corresponding simulation results. The optimized combination of the matching of different speeds is also proposed as a useful reference for applications in industry, obtained by a response surface model and genetic algorithm with a balance between the growth rate and the growth uniformity. This method can save time, and the optimization can obtain the most uniform and highest thin film quality.

Data from: Optimal foraging or surplus killing: selective consumption and discarding of salmon by brown bears

Selective consumption of prey by predators, observed in many animals, is often attributed to optimal foraging. Consistent with this idea, brown bears (Ursus arctos) often exhibit partial consumption, feeding exclusively on lipid-rich tissues of Pacific salmon (Oncorhynchus spp.), and discarding remains. However, bears also kill and abandon salmon without consuming any tissue. These discarded fish may be consistent with optimal foraging choices if they are of poor quality and if bears have easy access to better prey, or may reveal non-adaptive surplus killing behavior if fish are killed and discarded at random or solely based on prey abundance. Using 21 consecutive years of data from sockeye salmon (O. nerka) carcass surveys in Alaska, we found that foraging to maximize energy intake best explained prey discarding behavior. Specifically, discarding was more common under high prey abundance, late in the salmon run, and with low quality prey. Patterns of tissue consumption were consistent with these findings; bears were less likely to consume belly, body, and brain tissue when prey condition decreased. Other factors not quantified here (e.g., bear demography, alternative food resources) almost certainly influence prey discard and partial consumption, though the salmon-related factors explored here strongly influenced bear foraging decisions that were consistent with optimal foraging theory. We did not find clear evidence of surplus killing behavior in brown bears foraging on salmon, but prey selectivity manifested itself through both discarding and partial consumption, which contributes to our ability to predict transport of salmon nutrients by bears across ecosystem boundaries.

Data from: Higher rates of pre‐breeding condition gain positively impacts clutch size: a mechanistic test of the condition‐dependent individual optimization model

1. A combination of timing of and body condition (i.e., mass) at arrival on the breeding grounds interact to influence the optimal combination of the timing of reproduction and clutch size in migratory species. This relationship has been formalized by Rowe et al. in a condition-dependent individual optimization model (American Naturalist, 1994, 143, 689-722), which has been empirically tested and validated in avian species with a capital-based breeding strategy. 2. This model makes a key, but currently untested prediction; that variation in the rate of body condition gain will shift the optimal combination of laying date and clutch size. This prediction is essential because it implies that individuals can compensate for the challenges associated with late timing of arrival or poor body condition at arrival on the breeding grounds through adjustment of their life history investment decisions, in an attempt to maximize fitness. 3. Using an 11-year data set in arctic-nesting common eiders (Somateria mollissima), quantification of fattening rates using plasma triglycerides (an energetic metabolite), and a path analysis approach, we test this prediction of this optimization model; controlling for arrival date and body condition, females that fatten more quickly will adjust the optimal combination of lay date and clutch size, in favour of a larger clutch size. 4. As predicted, females fattening at higher rates initiated clutches earlier and produced larger clutch sizes, indicating that fattening rate is an important factor in addition to arrival date and body condition in predicting individual variation in reproductive investment. However, there was no direct effect of fattening rate on clutch size (i.e., birds laying on the same date had similar clutch sizes, independent of their fattening rate). Instead, fattening rate indirectly affected clutch size via earlier lay dates, thus not supporting the original predictions of the optimization model. 5. Our results demonstrate that variation in the rate of condition gain allows individuals to shift flexibly along the seasonal decline in clutch size to presumably optimize the combination of laying date and clutch size.

opencc-zeroAug 2019View details →

Data from: Optimal multisensory integration

Animals are often confronted with potentially informative stimuli from a variety of sensory modalities. While there is a large proximate literature demonstrating multisensory integration, no general framework explains why animals integrate. We developed and tested a quantitative model that explains why multisensory integration is not always adaptive and explain why unimodal decision-making might be favored over multisensory integration. We present our model in terms of a prey that must determine the presence or absence of a predator. A greater chance of encountering a predator, a greater benefit of correctly responding to a predator, a lower benefit of correctly foraging, or a greater uncertainty of the second stimulus favors integration. Uncertainty of the first stimulus may either increase or decreases the favorability of integration. In three field studies, we demonstrate how our model can be empirically tested. We evaluated the model with field studies of yellow-bellied marmots (Marmota flaviventer) by presenting marmots with an olfactory-acoustic predator stimulus at a feed station. We found some support for the model's prediction that integration is favored when the second stimulus is less noisy. We hope additional predictions of the model will guide future empirical work that seeks to understand the extent to which multimodal integration might be situation dependent. We suggest that the model is generalizable beyond antipredator contexts and can be applied within or between individuals, populations or species.

opencc-zeroDec 2012View details →

Data from: Environmental quality predicts optimal egg size in the wild

Parents can maximize their reproductive success by balancing the trade-off between investment per offspring and fecundity. According to theory, environmental quality influences the relationship between investment per offspring and offspring fitness, such that well-provisioned offspring fare better when environmental quality is lower. A major prediction of classic theory, then, is that optimal investment per offspring will increase as environmental quality decreases. To test this prediction, we release over 30,000 juvenile Atlantic salmon (Salmo salar) into eight wild stream environments, and we monitor subsequent growth and survival of juveniles. We estimate the shape of the relationship between investment per offspring (egg size) and offspring fitness in each stream. We find that optimal egg size is greater when the quality of the stream environment is lower (as estimated by a composite index of habitat quality). Across streams, the mean size of stream gravel and the mean amount of incident sunlight are the most important individual predictors of optimal egg size. Within streams, juveniles recaptured in stream subsections that featured larger gravels and greater levels of sunlight also grew relatively quickly, an association that complements our cross-stream analyses. This study provides the first empirical verification that environmental quality alters the relationship between investment per offspring and offspring fitness, such that optimal investment per offspring increases as environmental quality decreases.