bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial variation in trophic ecology of small mammals in wetlands: support for hydrological drivers
Authors: van der Merwe Jorista , Hellgren Eric C. 
Published: November 2016

AbstractFood webs composed of similar consumers can vary based on nutrient input, habitat structure, and other factors. For wetland‐associated species, fluctuating water levels can potentially affect habitat quality, which in turn can affect trophic diversity. Our objective was to determine spatiotemporal variation in the trophic structure of small mammals at two wetland complexes (floodplain and mineland) in southern Illinois. We live‐trapped small mammals during 2011–2013 at nine wetland patches on the Mississippi River floodplain and 14 patches at a reclaimed mineland. We collected hair samples from six species of small mammals (n = 428) at these wetland complexes. We analyzed C and N stable isotopes for three mammal taxa (Oryzomys palustris, Peromyscus spp., Microtus ochrogaster) to compare diet between species, sites, and times. Food sources (vegetation and invertebrates) were collected to form the isotopic baseline. We found no seasonal difference in diet composition, but isotopic values varied between sites and species. At the floodplain site, both δ15N and δ13C isotopic values for Oryzomys were more variable and completely enclosed that of Peromyscus. At the mining site, Peromyscus were at a lower trophic level (δ15N) and had a separate and less variable δ13C values from Oryzomys. Microtus was at a lower trophic position than the other two species at both sites. These results point to reduced niche overlap between Oryzomys and Peromyscus at the mining site, perhaps due to lower habitat quality and limited suitable resources. At the floodplain site, we conclude that more dynamic hydrology gave rise to higher biodiversity and more resources allowing small mammals to use similar food items.
Sixty‐year post‐windthrow study of stand dynamics in two natural forests differing in pre‐disturbance composition
Authors: Kosugi Ryota , Shibuya Masato , Ishibashi Satoshi 
Published: November 2016

AbstractWe examined the dynamics of stand structure and composition over 60 years in two natural secondary forest plots in central Hokkaido, Japan, that had been severely disturbed by a stand‐replacing windthrow in 1954. We determined temporal trends in tree density, species richness, species diversity, successional composition, and stand developmental stage. One of the plots contained a coniferous stand prior to the disturbance; the second plot contained a mixed stand. Tree density and species richness increased after the windthrow, and peaked in both stands in 1991, 37 years after the windthrow. Based on the dynamics of tree density and species richness, the stand development phase of both plots remained within the stand initiation stage until 1991, and then progressed to the stem exclusion stage by 2014, 60 years after the windthrow. Based on patterns of increasing tree density by species in both plots, vegetative regeneration was presumed to have contributed abundantly to the recovery of the stand after the windthrow. Species diversity increased after the windthrow as species richness increased in both stands; diversities peaked 23 or 32 years after the windthrow and declined slightly thereafter. Although the successional composition of the pre‐disturbance coniferous stand regressed to an early stage under the influence of the windthrow, the relative importance of late‐successional species approached the pre‐disturbance value as the plot recovered. In contrast, the successional composition of the mixed conifer/hardwood plot was unaffected by the windthrow, but gradually changed to an early stage over several decades following the windthrow. The difference in successional composition between plots was likely a result of differences in pre‐disturbance stand conditions between stands. Our 60‐year permanent plot study determined stand and population dynamics, the duration of the stand initiation stage, and the interrelationships between diversity and species richness. Long‐term permanent plot studies contribute crucial data for the interpretation of forest dynamics following disturbance.
Static and dynamic controls on fire activity at moderate spatial and temporal scales in the Alaskan boreal forest
Authors: Barrett Kirsten , Loboda Tatiana , McGuire A. D. , Genet Hélène , Hoy Elizabeth , Kasischke Eric 
Published: November 2016

AbstractWildfire, a dominant disturbance in boreal forests, is highly variable in occurrence and behavior at multiple spatiotemporal scales. New data sets provide more detailed spatial and temporal observations of active fires and the post‐burn environment in Alaska. In this study, we employ some of these new data to analyze variations in fire activity by developing three explanatory models to examine the occurrence of (1) seasonal periods of elevated fire activity using the number of MODIS active fire detections data set (MCD14DL) within an 11‐day moving window, (2) unburned patches within a burned area using the Monitoring Trends in Burn Severity fire severity product, and (3) short‐to‐moderate interval (<60 yr) fires using areas of burned area overlap in the Alaska Large Fire Database. Explanatory variables for these three models included dynamic variables that can change over the course of the fire season, such as weather and burn date, as well as static variables that remain constant over a fire season, such as topography, drainage, vegetation cover, and fire history. We found that seasonal periods of high fire activity are associated with both seasonal timing and aggregated weather conditions, as well as the landscape composition of areas that are burning. Important static inputs to the model of seasonal fire activity indicate that when fire weather conditions are suitable, areas that typically resist fire (e.g., deciduous stands) may become more vulnerable to burning and therefore less effective as fire breaks. The occurrence of short‐to‐moderate interval fires appears to be primarily driven by weather conditions, as these were the only relevant explanatory variables in the model. The unique importance of weather in explaining short‐to‐moderate interval fires implies that fire return intervals (FRIs) will be sensitive to projected climate changes in the region. Unburned patches occur most often in younger stands, which may be related to a greater deciduous fraction of vegetation as well as lower fuel loads compared with mature stands. The fraction of unburned patches may therefore increase in response to decreasing FRIs and increased deciduousness in the region, or these may decrease if fire weather conditions become more severe.
A macroecological perspective on strategic bat conservation in the U.S. National Park Service
Authors: Rodhouse Thomas J. , Philippi Thomas E. , Monahan William B. , Castle Kevin T. 
Published: November 2016

AbstractNorth American bat populations face unprecedented threats from disease and rapid environmental change, requiring a commensurate strategic conservation response. Protected‐area networks have tremendous potential to support coordinated resource protection, disease surveillance, and population monitoring that could become a cornerstone of 21st‐century bat conservation. To motivate this idea, we develop a macroecological perspective about bat diversity and associated conservation challenges and opportunities on U.S. National Park Service (NPS) lands. We compared occurrence records from parks against published range maps. Only 55 (19%) of parks reported as present ≥90% of the bat species expected based on range maps, highlighting the information‐gap challenge. Discrepancies suggest substantial under‐reporting and under‐sampling of bats on NPS lands; inadequate range maps and habitat specificity are implicated for some species. Despite these discrepancies, 50 species, including several range‐restricted and endangered taxa, were reported in at least one park unit, including those in the Caribbean and tropical Pacific. Species richness increased with park area at a rate (z) of ~0.1, a pattern confounded by covariation with latitude, elevation, and habitat. When accounting for these factors, richness decreased predictably at higher latitudes and increased at mid‐elevations and with greater numbers of keystone underground habitat structures (caves and mines), reflecting a strong species–energy relationship. The inclusion of covariates that represented percentage of natural vs. human‐modified (converted) landscapes and elevation range—a proxy for environmental heterogeneity—was uninformative. White‐nose syndrome (WNS) presents a tremendous challenge to the NPS: All 12 species currently known to be affected by the disease or to host the causal fungus are represented in the NPS system. One hundred and twenty‐seven NPS parks are in counties currently or likely to become WNS‐positive by 2026. All parks are expected to experience increasing temperatures in coming decades; forecasted climate change velocity is particularly high (>1 SD) for 50 parks. Seventeen parks are in the vicinity of high (>1 SD) wind turbine density. Based on these biogeographic patterns, we suggest ways to prioritize NPS parks for additional inventories, monitoring, and resource protection. Our results demonstrate how macroecology and bioinformatics together can guide strategic conservation capacity‐building among protected areas.
Vacant lots as a habitat resource: nesting success and body condition of songbirds
Authors: Rega‐Brodsky Christine C. , Nilon Charles H. 
Published: November 2016

AbstractVacant lots are a common feature throughout many cities and may provide necessary habitat resources for urban bird populations. We evaluated the quality of vacant lots throughout Baltimore, Maryland, by determining how differences in vacant lot properties related to songbirds' nesting success and body condition. We observed 130 nests from American robins (Turdus migratorius), gray catbirds (Dumetella carolinensis), and northern cardinals (Cardinalis cardinalis) across the city and assessed body condition of 19 adult robins. Nesting success for all three species was greatest within areas of vacant lots with high shrub densities. The robins' body condition index did not vary extensively and was not related to any vacant lot site‐ or landscape‐level variables. Even so, we found vacant lots to be actively used by 60 bird species for a variety of resources, with those containing more shrubs to be the most beneficial for bird species' nesting attempts. Vacant lots should no longer be discarded and underestimated; instead, they should be valued for the opportunities they provide for generalist bird species through small‐effort habitat management practices.
Niche partitioning among sexual and unisexual Ambystoma salamanders
Authors: Greenwald Katherine R. , Denton Robert D. , Gibbs H. Lisle 
Published: November 2016

AbstractOrganisms that have ecologically similar sexual and asexual forms present an evolutionary puzzle, as theory predicts that eventually one form should eliminate the other. However, both forms may persist if there is niche partitioning between them. Geographical parthenogenesis is a hypothesis that predicts that in terms of niche use the asexual form in such pairs should be more ecologically successful in marginal habitats. This model has rarely been considered for gynogenetic taxa, as they are sperm dependent and thus constrained to the geographical range of sexual “sperm donor” species. Unisexual Ambystoma salamanders present a unique opportunity to look for evidence of niche partitioning and geographical parthenogenesis in a gynogenetic lineage, as there are multiple possible sperm donor species and so the geographical distributions of unisexuals are less constrained. We used broad sampling, comparative ecological niche models, and a model selection approach to determine (1) whether niche partitioning occurs among sexual and unisexual salamanders and (2) whether unisexual lineages indeed occupy marginal habitat relative to their most similar sexual species. Nearly all unisexual and sexual types showed significant niche differentiation. Predictions consistent with geographical parthenogenesis were upheld for one sexual–unisexual pair (A. jeffersonianum and LJJ unisexuals), but not for a second pair (A. texanum and LTT unisexuals). Our study provides evidence that different biotypes within the unisexual lineage have distinct ecological interactions with sexual taxa, supporting a role for these differences as a mechanism promoting coexistence between some sexual and unisexual forms. However, geographical parthenogenesis is only a partial explanation for sexual–unisexual coexistence, suggesting that other ecological and genetic mechanisms also play important roles in mediating coexistence among these salamanders.
A novel concentration and viability detection method for Brettanomyces using the Cellometer image cytometry
Authors: Martyniak Brian , Bolton Jason , Kuksin Dmitry , Shahin Suzanne M , Chan Leo Li-Ying 
Published: November 2016

Abstract
Brettanomyces spp. can present unique cell morphologies comprised of excessive pseudohyphae and budding, leading to difficulties in enumerating cells. The current cell counting methods include manual counting of methylene blue-stained yeasts or measuring optical densities using a spectrophotometer. However, manual counting can be time-consuming and has high operator-dependent variations due to subjectivity. Optical density measurement can also introduce uncertainties where instead of individual cells counted, an average of a cell population is measured. In contrast, by utilizing the fluorescence capability of an image cytometer to detect acridine orange and propidium iodide viability dyes, individual cell nuclei can be counted directly in the pseudohyphae chains, which can improve the accuracy and efficiency of cell counting, as well as eliminating the subjectivity from manual counting. In this work, two experiments were performed to demonstrate the capability of Cellometer image cytometer to monitor Brettanomyces concentrations, viabilities, and budding/pseudohyphae percentages. First, a yeast propagation experiment was conducted to optimize software counting parameters for monitoring the growth of Brettanomyces clausenii, Brettanomyces bruxellensis, and Brettanomyces lambicus, which showed increasing cell concentrations, and varying pseudohyphae percentages. The pseudohyphae formed during propagation were counted either as multiple nuclei or a single multi-nuclei organism, where the results of counting the yeast as a single multi-nuclei organism were directly compared to manual counting. Second, a yeast fermentation experiment was conducted to demonstrate that the proposed image cytometric analysis method can monitor the growth pattern of B. lambicus and B. clausenii during beer fermentation. The results from both experiments displayed different growth patterns, viability, and budding/pseudohyphae percentages for each Brettanomyces species. The proposed Cellometer image cytometry method can improve efficiency and eliminate operator-dependent variations of cell counting compared with the traditional methods, which can potentially improve the quality of beverage products employing Brettanomyces yeasts.
Intact initiation of autophagy and mitochondrial fission by acute exercise in skeletal muscle of patients with Type 2 diabetes
Authors: Kruse Rikke , Pedersen Andreas J.T. , Kristensen Jonas M. , Petersson Stine J. , Wojtaszewski Jørgen F.P. , Højlund Kurt 
Published: November 2016

Type 2 diabetes (T2D) is characterized by insulin resistance, mitochondrial dysregulation and, in some studies, exercise resistance in skeletal muscle. Regulation of autophagy and mitochondrial dynamics during exercise and recovery is important for skeletal muscle homoeostasis, and these responses may be altered in T2D. We examined the effect of acute exercise on markers of autophagy and mitochondrial fusion and fission in skeletal muscle biopsies from patients with T2D (n=13) and weight-matched controls (n=14) before, immediately after and 3 h after an acute bout of exercise. Although mRNA levels of most markers of autophagy [PIK3C, MAP1LC3B, sequestosome 1 (SQSTM1), BCL-2/adenovirus E1B 19-kDa-interacting protein 3 (BNIP3), BNIP3-like (BNIP3L)] and mitochondrial dynamics [optic atrophy 1 (OPA1), fission protein 1 (FIS1)] remained unchanged, some either increased during and after exercise (GABARAPL1), decreased in the recovery period [BECN1, autophagy-related (ATG) 7, DNM1L] or both [mitofusin (MFN) 2, mitochondrial E3 ubiquitin ligase 1 (MUL1)]. Protein levels of ATG7, p62/SQSTM1, forkhead box O3A (FOXO3A) and MFN2 (only controls) as well as dynamin-related protein 1 (DRP1) Ser616 phosphorylation increased in response to exercise and/or recovery, whereas microtubule-associated protein 1 light chain 3B (LC3B)-II content was reduced immediately after exercise. Exercise increased the activating Ser555 phosphorylation and reduced the inhibitory Ser757 phosphorylation of Unc-51-like kinase-1 (ULK1). The LC3B-II content and phosphorylation of ULK1 and DRP1 returned towards pre-exercise levels in the recovery period. Insulin sensitivity was reduced in T2D, but with no differences in the autophagic response to exercise. Our results demonstrate that initiation of autophagy and mitochondrial fission is activated by exercise in human skeletal muscle, and that these responses are intact in T2D. The exercise-induced decrease in LC3B-II could be due to increased autophagic turnover.
Flexible rectangular waveguide based on cylindrical contactless flange
Authors: Sun Dongquan , Chen Zhenhua , Yao Changfei , Xu Jinping 
Published: November 2016

Contactless waveguide flange is a novel structure to prevent leakage of electromagnetic wave when it propagates across the waveguide flange. The main advantage of contactless waveguide flange is electrical contact of the connected waveguides is not required as long as the gap between the adjacent flanges does not exceed the maximum permitted distance. Therefore, relative motivation or rotation of the contactless connected waveguides is possible. The contactless waveguide flanges have been reported are all planar. A cylindrical contactless flange is first proposed. Then, a novel flexible rectangular waveguide is proposed based on it. A Ka‐band prototype is successfully designed and manufactured. The prototype consists of two bendable contactless flange joints. The maximum bending angle of each joint is limited to ±8° to maintain the return loss performance. The number of joints can be easily increased if larger bending angles are needed. The insertion loss and return loss at different bending angles are measured. The measured insertion loss is better than 0.7 dB from 26 to 37 GHz, and is better than 1.8 dB from 37 to 40 GHz. The measured return loss is 15 dB except frequencies around 37.5 and 40 GHz.
Design of 3D filtering antenna for the application of terahertz
Authors: Li Yang , Yang Lin‐an , Wang Shao‐bo , Du Lin , Hao Yue 
Published: November 2016

A new terahertz (THz) filtering antenna realised by 3D substrate integrated circular waveguide (3D‐SICW) is presented. The filtering antenna is designed on a low‐temperature co‐fired ceramic substrate. Different from traditional planar structure, the direction of power in 3D‐SICW is along Z‐axis and this will significantly enhance the performance of the devices at THz frequency. The filtering antenna is constructed by two 3D‐SICW cavities and a standard substrate integrated waveguide (SIW) cavity, where one SICW cavity and the standard SIW cavity form the bandpass filter by using electric coupling and the other SICW cavity is used as antenna. The results indicate that the passband of filtering antenna range from 170.4 to 177.8 GHz and the gain of antenna is about 5.7 dB. Finally, the filtering antenna is fabricated and measured to verify the simulation prediction. The measured and simulated results are in good agreement at such high frequency.
Association of PD-1/PD-L axis expression with cytolytic activity, mutational load, and prognosis in melanoma and other solid tumors
Authors: Danilova Ludmila , Wang Hao , Sunshine Joel , Kaunitz Genevieve J. , Cottrell Tricia R. , Xu Haiying , Esandrio Jessica , Anders Robert A. , Cope Leslie , Pardoll Drew M. , Drake Charles G. , Taube Janis M. 
Published: November 2016

SignificanceThe Cancer Genome Atlas datasets were used in the current study to explore the relationship of programmed death ligand-1 (PD-L1) expression, a cytotoxic T-cell gene signature, and mutational load to each other, to immunoactive factors, such as programmed cell death protein-1 (PD-1),PD-L2, and other checkpoint molecules, and to survival across multiple solid tumor types. We found thatPD-L2expression is more closely related to an ongoing host immune response in certain tumor types thanPD-L1. Notably, mutational load was not immediately related to inflammation in any tumor type studied, and was inferior to an inflamed tumor microenvironment for predicting survival in patients with metastatic melanoma. Our findings also indicate the need for biomarker assays that are tumor-type–specific and include both expression studies and genomic profiling.
Density of immunogenic antigens does not explain the presence or absence of the T-cell–inflamed tumor microenvironment in melanoma
Authors: Spranger Stefani , Luke Jason J. , Bao Riyue , Zha Yuanyuan , Hernandez Kyle M. , Li Yan , Gajewski Alexander P. , Andrade Jorge , Gajewski Thomas F. 
Published: November 2016

Significance
The T-cell–inflamed tumor microenvironment correlates with efficacy of immunotherapy. It is critical to understand whether non–T-cell–inflamed tumors lack antigens for T-cell recognition. In melanoma, no difference between inflamed and noninflamed tumors for multiple antigen classes was observed. Synthesized peptides corresponding to predicted HLA-A2 binding epitopes showed no differences between inflamed and noninflamed tumors. Extrapolation of a T-cell signature across The Cancer Genome Atlas showed no correlation between gene expression and mutational burden in any cancer type. These results indicate that lack of spontaneous immune infiltration in solid tumors is unlikely to be due to lack of antigens. Rather, transcriptional profiling suggests lack of Batf3-lineage dendritic cells. Our data suggest that strategies to restore T-cell entry into noninflamed tumors should be developed.
Two proofreading steps amplify the accuracy of genetic code translation
Authors: Ieong Ka-Weng , Uzun Ülkü , Selmer Maria , Ehrenberg Måns 
Published: November 2016

Significance
We have discovered that two proofreading steps amplify the accuracy of genetic code reading, not one step, as hitherto believed. We have characterized the molecular basis of each one of these steps, paving the way for structural analysis in conjunction with structure-based standard free energy computations. Our work highlights the essential role of elongation factor Tu for accurate genetic code translation in both initial codon selection and proofreading. Our results have implications for the evolution of efficient and accurate genetic code reading through multistep proofreading, which attenuates the otherwise harmful effects of the obligatory tradeoff between efficiency and accuracy in substrate selection by enzymes.
Catheter-Based Renal Denervation for Resistant Hypertension: Will It Ever Be Ready for “Prime Time”?
Authors: Laffin Luke J , Bakris George L 
Published: November 2016

Abstract
The year 2014 was a turning point for the field of renal denervation (RDN) and its potential use to treat resistant hypertension. Tremendous enthusiasm shifted to sober reflection on the efficacy of a technology once touted as the cure to resistant hypertension. The following review highlights 2 major questions: First, does catheter-based RDN lower blood pressure and, second, will RDN using catheter-directed therapy for the treatment of resistant hypertension ever become more than an investigational technology.