Landscape context outweighs local habitat quality in its effects on herbivore dispersal and distribution

Past studies with spatially structured herbivore populations have emphasized the primacy of intrinsic factors (e.g., patch quality), patch geometry (e.g., patch size and isolation), and more recently landscape context (e.g., matrix composition) in affecting local population abundance and dispersal rate. However, few studies have examined the relative importance of each factor, or how they might interact to affect herbivore abundance or dispersal. Here, we performed a factorial field experiment to examine the independent and interactive effects of patch quality (plant biomass, leaf protein, leaf phenolics) and matrix composition [mudflat or non-host grass (Bromus inermis)] on planthopper (Prokelisia crocea) emigration from host-plant patches (prairie cordgrass, Spartina pectinata). In addition, a field survey was conducted to examine the relative importance of patch quality, geography, and matrix composition on planthopper occupancy and density. In the experiment, we found that rates of emigration from low and intermediate quality patches were, on average, 21% percent higher for patches embedded in brome than mudflat. In contrast, the emigration rate was unaffected by matrix composition in nutrient-rich patches. Within matrix types, plant quality had little effect on emigration. In the survey, planthopper density and the patch occupancy rate of planthoppers increased nonadditively with increasing patch size and the percentage of the surrounding matrix composed of mudflat. This study suggests that landscape-level factors, such as the matrix, may be more important than factors intrinsic to the patches. © 2006 Springer-Verlag

Genome-wide association reveals three SNPs associated with sporadic amyotrophic lateral sclerosis through a two-locus analysis

<p>Abstract</p> <p>Background</p> <p>Amyotrophic lateral sclerosis (ALS) is a fatal, degenerative neuromuscular disease characterized by a progressive loss of voluntary motor activity. About 95% of ALS patients are in "sporadic form"-meaning their disease is not associated with a family history of the disease. To date, the genetic factors of the sporadic form of ALS are poorly understood.</p> <p>Methods</p> <p>We proposed a two-stage approach based on seventeen biological plausible models to search for two-locus combinations that have significant joint effects to the disease in a genome-wide association study (GWAS). We used a two-stage strategy to reduce the computational burden associated with performing an exhaustive two-locus search across the genome. In the first stage, all SNPs were screened using a single-marker test. In the second stage, all pairs made from the 1000 SNPs with the lowest p-values from the first stage were evaluated under each of the 17 two-locus models.</p> <p>Results</p> <p>we performed the two-stage approach on a GWAS data set of sporadic ALS from the SNP Database at the NINDS Human Genetics Resource Center DNA and Cell Line Repository <url>http://ccr.coriell.org/ninds/</url>. Our two-locus analysis showed that two two-locus combinations--rs4363506 (SNP1) and rs3733242 (SNP2), and rs4363506 and rs16984239 (SNP3) -- were significantly associated with sporadic ALS. After adjusting for multiple tests and multiple models, the combination of SNP1 and SNP2 had a p-value of 0.032 under the Dom∩Dom epistatic model; SNP1 and SNP3 had a p-value of 0.042 under the Dom × Dom multiplicative model.</p> <p>Conclusion</p> <p>The proposed two-stage analytical method can be used to search for joint effects of genes in GWAS. The two-stage strategy decreased the computational time and the multiple testing burdens associated with GWAS. We have also observed that the loci identified by our two-stage strategy can not be detected by single-locus tests.</p

A population-based study of tumor gene expression and risk of breast cancer death among lymph node-negative patients

INTRODUCTION: The Oncotype DX assay was recently reported to predict risk for distant recurrence among a clinical trial population of tamoxifen-treated patients with lymph node-negative, estrogen receptor (ER)-positive breast cancer. To confirm and extend these findings, we evaluated the performance of this 21-gene assay among node-negative patients from a community hospital setting. METHODS: A case-control study was conducted among 4,964 Kaiser Permanente patients diagnosed with node-negative invasive breast cancer from 1985 to 1994 and not treated with adjuvant chemotherapy. Cases (n = 220) were patients who died from breast cancer. Controls (n = 570) were breast cancer patients who were individually matched to cases with respect to age, race, adjuvant tamoxifen, medical facility and diagnosis year, and were alive at the date of death of their matched case. Using an RT-PCR assay, archived tumor tissues were analyzed for expression levels of 16 cancer-related and five reference genes, and a summary risk score (the Recurrence Score) was calculated for each patient. Conditional logistic regression methods were used to estimate the association between risk of breast cancer death and Recurrence Score. RESULTS: After adjusting for tumor size and grade, the Recurrence Score was associated with risk of breast cancer death in ER-positive, tamoxifen-treated and -untreated patients (P = 0.003 and P = 0.03, respectively). At 10 years, the risks for breast cancer death in ER-positive, tamoxifen-treated patients were 2.8% (95% confidence interval [CI] 1.7–3.9%), 10.7% (95% CI 6.3–14.9%), and 15.5% (95% CI 7.6–22.8%) for those in the low, intermediate and high risk Recurrence Score groups, respectively. They were 6.2% (95% CI 4.5–7.9%), 17.8% (95% CI 11.8–23.3%), and 19.9% (95% CI 14.2–25.2%) for ER-positive patients not treated with tamoxifen. In both the tamoxifen-treated and -untreated groups, approximately 50% of patients had low risk Recurrence Score values. CONCLUSION: In this large, population-based study of lymph node-negative patients not treated with chemotherapy, the Recurrence Score was strongly associated with risk of breast cancer death among ER-positive, tamoxifen-treated and -untreated patients

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Confined deep water system development on the accretionary wedge (Miocene, Kahramanmaras Foreland Basin, S turkey)

WOS: 000309620500001According to theoretical studies, the foreland basin consists of: accretionary wedge (including wedge top or piggyback basin), foredeep, forebulge and backbulge depozones. All of them are parallel to the orogenic belts of the overlying and underlying plates. The closure of the southern branch of the Neotethys during the Late Cretaceous led to an oblique collision of the Arabian Plate and the Anatolide-Taurides Platform, leading to the development of the Miocene Kahramanmaras Foreland Basin (KFB). Thus, the promontory shape of the Arabian Plate prevented the development of an accretionary wedge parallel to the orogenic belt. The accretionary wedge of the KFB includes blocks of various sizes and age (mainly Mesozoic limestone) scattered within an Early Tertiary matrix (mass wasting deposits and shallow to deep marine sediments). At the beginning of the Miocene, transtensional tectonism led to the development of half-graben basins on top of the accretionary wedge. These basins (namely: the Tekir and Cukurhisar) also cut the foredeep of the KFB obliquely (in contrast with the theoretical study). This paper focuses on the evolution and fillings of those basins. Initially, claystone and basin margin reef deposits filled the half-graben basins as a consequence of the Lower Miocene sea invasion. Then, long and narrow conglomeratic channels starting from the northern edge of the basins (fan-delta) progressed southwards, passing into sandy lobes, then into claystones. An activation of the boundary faults of the wedge top basin stopped the progression of the Lower Middle Miocene sediments and led to their deformation. Then, the sedimentation of the KFB shifted towards the basin centre during the Middle Miocene. (C) 2012 Elsevier B.V. All rights reserved.Research Fund of cukurova UniversityCukurova University [MMF 2003 D1]; TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK)The authors express their gratitude to Prof. Dr. Atike Nazik, Prof. Dr. Niyazi Avsar (cukurova University) and Assist. Prof. Dr. Guldemin Darbas (Kahramanmaras Sutcu Imam University) for their help with the palaeontological data. The authors are also grateful for financial support provided by the Research Fund of cukurova University (Grant MMF 2003 D1) and TUBITAK. We also thank to two anonymous reviewers and editor (Prof. Dr. A. D. Miall) for their comments, which enhanced this paper

Provenance of the northern part of the Kahramanmaras Peripheral Foreland Basin (Miocene, S Turkey)

WOS: 000286846400004The Miocene Miocene Kahramanmaras Peripheral Foreland Basin (KPFB) resemble to classic foreland basin model, with small differences. In the classic model, both the accretionary wedge and foredeep extend lengthways parallel to the plate margin. In addition, accretionary wedge includes wedge top basin or piggy back basin that extends parallel to foredeep. However, the accretionary wedge of the KPFB contains small half-graben type basins that obliquely intersect the plate margin between the Arabian Plate and the Anatolide-Taurides Platform (due to the irregular shape of the plate boundary). Tectonic lineaments controlled the shape and orientation of these basins and larger main depocentre of the KFPB, which were predominantly filled with deep-sea sediments. This paper focuses on the provenance of features of the KFPB, predominantly was fed from the northern basin margin, while also aiming to resolve the complex basin evolution that occurred during the Miocene. Clasts of Palaeozoic and Mesozoic limestone and ophiolites are common components of the confined deep-water clastic systems, which evolved as elongated trenches in the north-western sector of the KPFB during the Early-Middle Miocene. During the Middle Miocene, continuous thrusting of the northern basin margin to south caused depocentre migration to south-east, through the basin interior. At that time, the north-east and central depocentres of the KPFB were filled primarily by clasts of ophiolite and metamorphic units. The tectonic control on basin fill architecture can be observed anywhere in the KFPB. The principal tectonic features controlled the geometry and orientation of the canyon, the channel geometry of the deep-water slope on the northern basin margin, the frequency and distribution of slump-slide-debris flows and the overall pattern of sedimentation cycles in the stratigraphy of the slope and the central basin floor. Some basin sectors have continuously reactivated and as a result, different sediment entry points with substantial local accumulation of sediment and deformation have evolved on the slope and basin floor. Three scales of provenance were used to investigate the source rock: (a) field-based observation and analysis of conglomerate clasts, (b) modal analysis of sandstone facies and (c) geochemical analysis, all of which were in agreement. (C) 2010 Elsevier Ltd. All rights reserved.Cukurova UniversityCukurova University [MMF2003BAP1, MMF2003D1]; Aberdeen University, Scotland; UNOCAL, BPThe authors gratefully acknowledge the financial support of the Cukurova University Research Funds MMF2003BAP1 and MMF2003D1 and also the "Turkey 2 Consortium Project of deep-sea sediment" from Aberdeen University, Scotland, sponsored by UNOCAL, BP and ConocoPhillips. Dr. Gill would also like to thank TUBITAK for his PhD scholarship. The authors warmly thank Andrew Racey from BG Energy for chemical analysis of samples and Dr. N. Emre Altun from Mug la University for his editorial contribution. Finally the authors thank Dr. Sarah Boulton, an anonymous reviewer and Prof. Dr. Boris Natalin (associate editor) for their constructive criticism of the paper