Low‐cost tools mitigate climate change during reproduction in an endangered marine ectotherm

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordData Availability Statement: Data available via the Dryad Digital Repository https://doi.org/10.5061/dryad.3r2280gfq. (Clarke et al., 2021)The impacts of anthropogenic climate change will be most dramatic for species that live in narrow thermal niches, such as reptiles. Given the imminent threat to biodiversity, and that actions to reduce carbon emissions are not yet sufficient, it is important that a sound evidence base of potential mitigation options is available for conservation managers. Successful incubation and production of male sea turtle hatchlings is threatened by increased global temperatures (sex is determined by the temperature at which eggs incubate). Here we test two conservation tools to reduce incubation temperatures: clutch splitting and clutch shading, on a nesting loggerhead turtle (Caretta caretta) population in the Eastern Atlantic Ocean. During the thermosensitive period of incubation, split and shaded clutches were both 1.00 ˚C cooler than control nests. Clutch splitting (mean: 45 eggs) reduced nest temperatures by reducing metabolic heating during incubation compared to controls (mean: 92 eggs). Modelled primary sex ratios differed between nest treatments, with 1.50 % (± 6 % S.E.) females produced in shaded nests, 45.00 % (± 7 % S.E.) females in split nests and 69.00 % (± 6% S.E.) females in controls. Neither treatment affected hatchling size, success, mass or vigour. When clutch splitting was repeated two years later, hatch success was higher in split clutches compared to controls. Synthesis and Applications: Clutch splitting and clutch shading successfully altered the thermal profile of incubating turtle nests. When there is sufficient knowledge to better understand the effects of intervention on fundamental population demographics, they will be useful for reducing incubation temperatures in sea turtle nests, potentially increasing nest survival and male hatchling production. The effect of clutch splitting in reducing nest temperature was lower relative to clutch shading, but requires significantly less funding, materials and specialist skill, key factors for management of turtle rookeries that are often in remote, resource‐limited areas.Worldwide Fund for NatureWAVE Foundation of Newport Aquariu

Speeding up Simplification of Polygonal Curves using Nested Approximations

We develop a multiresolution approach to the problem of polygonal curve approximation. We show theoretically and experimentally that, if the simplification algorithm A used between any two successive levels of resolution satisfies some conditions, the multiresolution algorithm MR will have a complexity lower than the complexity of A. In particular, we show that if A has a O(N2/K) complexity (the complexity of a reduced search dynamic solution approach), where N and K are respectively the initial and the final number of segments, the complexity of MR is in O(N).We experimentally compare the outcomes of MR with those of the optimal "full search" dynamic programming solution and of classical merge and split approaches. The experimental evaluations confirm the theoretical derivations and show that the proposed approach evaluated on 2D coastal maps either shows a lower complexity or provides polygonal approximations closer to the initial curves.Comment: 12 pages + figure

Assessment of the toll-like receptor 4 Asp299Gly, Thr399Ile and interleukin-8 -251 polymorphisms in the risk for the development of distal gastric cancer

<p>Abstract</p> <p>Background</p> <p>The intensity of the inflammation induced by <it>Helicobacter pylori </it>colonization is associated with the development of distal gastric cancer (GC). The host response to <it>H</it>. <it>pylori </it>has been related to genetic polymorphisms that influence both innate and adaptive immune responses.</p> <p>Our aim was to investigate whether the presence of the <it>TLR4 Asp299Gly</it>, <it>TLR4 Thr399Ile </it>and <it>IL-8-251 </it>A/T polymorphisms had any influence in the development of distal GC in a Mexican population.</p> <p>Methods</p> <p>We studied 337 patients that were divided in two groups: 78 patients with histologically confirmed distal GC and 259 non-cancer controls. The presence of <it>H. pylori </it>in the control population was defined by positive results of at least two of four diagnostic tests: serology, histology, rapid urease test and culture. Human DNA was purified and genotyped for <it>TLR4 Asp299Gly </it>polymorphism by pyrosequencing, for <it>TLR4 Thr399Ile </it>by PCR-RFLP and for <it>IL8-251 </it>by the amplification refractory mutation system (ARMS)-PCR.</p> <p>Results</p> <p>The non-cancer control group was found to be in Hardy-Weinberg equilibrium at the polymorphic loci studied (chi-square _H-W= 0.58 for <it>IL8-251</it>, 0.42 for <it>TLR4 Asp299Gly </it>and 0.17 for <it>TLR4 Thr399Ile</it>). The frequencies of mutated alleles (homozygous plus heterozygous) were compared between cases and controls. We found no significant difference for <it>TLR4- Asp299Gly </it>[the 7.7% of distal GC patients and 7.7 % non-cancer controls (p = 0.82)] and for <it>TLR4 Thr399Ile </it>[the 1.3% of GC patients and the 5% of the control population (p = 0.2)]. In contrast, for <it>IL-8-251 </it>A/T, 80.77% of the GC patients and 66.4% in the control group age and gender matched had at least one copy of mutated allele (OR = 2.12, 95% CI = 1.1–4.2) (p = 0.023).</p> <p>Conclusion</p> <p>This study showed that the <it>IL8-251*A </it>allele could be related to the development of distal gastric cancer in this Mexican population.</p

ER and HER2 expression are positively correlated in HER2 non-overexpressing breast cancer

PMCID: PMC3446380This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

R-parity Conservation via the Stueckelberg Mechanism: LHC and Dark Matter Signals

We investigate the connection between the conservation of R-parity in supersymmetry and the Stueckelberg mechanism for the mass generation of the B-L vector gauge boson. It is shown that with universal boundary conditions for soft terms of sfermions in each family at the high scale and with the Stueckelberg mechanism for generating mass for the B-L gauge boson present in the theory, electric charge conservation guarantees the conservation of R-parity in the minimal B-L extended supersymmetric standard model. We also discuss non-minimal extensions. This includes extensions where the gauge symmetries arise with an additional U(1)_{B-L} x U(1)_X, where U(1)_X is a hidden sector gauge group. In this case the presence of the additional U(1)_X allows for a Z' gauge boson mass with B-L interactions to lie in the sub-TeV region overcoming the multi-TeV LEP constraints. The possible tests of the models at colliders and in dark matter experiments are analyzed including signals of a low mass Z' resonance and the production of spin zero bosons and their decays into two photons. In this model two types of dark matter candidates emerge which are Majorana and Dirac particles. Predictions are made for a possible simultaneous observation of new physics events in dark matter experiments and at the LHC.Comment: 38 pages, 7 fig

Low‐cost tools mitigate climate change during reproduction in an endangered marine ectotherm

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordData Availability Statement: Data available via the Dryad Digital Repository https://doi.org/10.5061/dryad.3r2280gfq. (Clarke et al., 2021)The impacts of anthropogenic climate change will be most dramatic for species that live in narrow thermal niches, such as reptiles. Given the imminent threat to biodiversity, and that actions to reduce carbon emissions are not yet sufficient, it is important that a sound evidence base of potential mitigation options is available for conservation managers. Successful incubation and production of male sea turtle hatchlings is threatened by increased global temperatures (sex is determined by the temperature at which eggs incubate). Here we test two conservation tools to reduce incubation temperatures: clutch splitting and clutch shading, on a nesting loggerhead turtle (Caretta caretta) population in the Eastern Atlantic Ocean. During the thermosensitive period of incubation, split and shaded clutches were both 1.00 ˚C cooler than control nests. Clutch splitting (mean: 45 eggs) reduced nest temperatures by reducing metabolic heating during incubation compared to controls (mean: 92 eggs). Modelled primary sex ratios differed between nest treatments, with 1.50 % (± 6 % S.E.) females produced in shaded nests, 45.00 % (± 7 % S.E.) females in split nests and 69.00 % (± 6% S.E.) females in controls. Neither treatment affected hatchling size, success, mass or vigour. When clutch splitting was repeated two years later, hatch success was higher in split clutches compared to controls. Synthesis and Applications: Clutch splitting and clutch shading successfully altered the thermal profile of incubating turtle nests. When there is sufficient knowledge to better understand the effects of intervention on fundamental population demographics, they will be useful for reducing incubation temperatures in sea turtle nests, potentially increasing nest survival and male hatchling production. The effect of clutch splitting in reducing nest temperature was lower relative to clutch shading, but requires significantly less funding, materials and specialist skill, key factors for management of turtle rookeries that are often in remote, resource‐limited areas.Worldwide Fund for NatureWAVE Foundation of Newport Aquariu

Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori

Helicobacter pylori colonizes the gastric mucosa of half of the human population, causing gastritis, ulcers, and cancer. H. pylori is naturally competent for transformation by exogenous DNA, and recombination during mixed infections of one stomach with multiple H. pylori strains generates extensive allelic diversity. We developed an in vitro transformation protocol to study genomic imports after natural transformation of H. pylori. The mean length of imported fragments was dependent on the combination of donor and recipient strain and varied between 1294 bp and 3853 bp. In about 10% of recombinant clones, the imported fragments of donor DNA were interrupted by short interspersed sequences of the recipient (ISR) with a mean length of 82 bp. 18 candidate genes were inactivated in order to identify genes involved in the control of import length and generation of ISR. Inactivation of the antimutator glycosylase MutY increased the length of imports, but did not have a significant effect on ISR frequency. Overexpression of mutY strongly increased the frequency of ISR, indicating that MutY, while not indispensable for ISR formation, is part of at least one ISR-generating pathway. The formation of ISR in H. pylori increases allelic diversity, and contributes to the uniquely low linkage disequilibrium characteristic of this pathogen

Adjunctive liraglutide treatment in patients with persistent or recurrent type 2 diabetes after metabolic surgery (GRAVITAS): a randomised, double-blind, placebo-controlled trial

Background Many patients with type 2 diabetes do not achieve sustained diabetes remission after metabolic (bariatric) surgery for the treatment of obesity. Liraglutide, a glucagon-like peptide-1 analogue, improves glycaemic control and reduces bodyweight in patients with type 2 diabetes. Our aim was to assess the safety and efficacy of liraglutide 1·8 mg in patients with persistent or recurrent type 2 diabetes after metabolic surgery. Methods In the GRAVITAS randomised double-blind, placebo-controlled trial, we enrolled adults who had undergone Roux-en-Y gastric bypass or vertical sleeve gastrectomy and had persistent or recurrent type 2 diabetes with HbA1c levels higher than 48 mmol/mol (6·5%) at least 1 year after surgery from five hospitals in London, UK. Participants were randomly assigned (2:1) via a computer-generated sequence to either subcutaneous liraglutide 1·8 mg once daily or placebo, both given together with a reduced-calorie diet, aiming for a 500 kcal per day deficit from baseline energy intake, and increased physical activity. The primary outcome was the change in HbA1c from baseline to the end of the study period at 26 weeks, assessed in patients who completed the trial. Safety was assessed in the safety analysis population, consisting of all participants who received either liraglutide or placebo. This trial is registered with EudraCT, number 2014-003923-23, and the ISRCTN registry, number ISRCTN13643081. Findings Between Jan 29, 2016, and May 2, 2018, we assigned 80 patients to receive either liraglutide (n=53) or placebo (n=27). 71 (89%) participants completed the study and were included in the principal complete-cases analysis. In a multivariable linear regression analysis, with baseline HbA1c levels and surgery type as covariates, liraglutide treatment was associated with a difference of −13·3 mmol/mol (−1·22%, 95% CI −19·7 to −7·0; p=0·0001) in HbA1c change from baseline to 26 weeks, compared with placebo. Type of surgery had no significant effect on the outcome. 24 (45%) of 53 patients assigned to liraglutide and 11 (41%) of 27 assigned to placebo reported adverse effects: these were mainly gastrointestinal and in line with previous experience with liraglutide. There was one death during the study in a patient assigned to the placebo group, which was considered unrelated to study treatment. Interpretation These findings support the use of adjunctive liraglutide treatment in patients with persistent or recurrent type 2 diabetes after metabolic surgery

Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of data