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- ItemBaseline predictors of treatment gains in peak propulsive force in individuals poststroke(Biomed Central Ltd, 1/15/16) Hsiao,HaoYuan; Higginson,Jill S.; Binder-Macleod,Stuart A.; HaoYuan Hsiao, Jill S. Higginson, Stuart A. Binder-Macleod; Higginson, Jill Startzell; Binder-Macleod, StuartBackground: Current rehabilitation for individuals poststroke focuses on increasing walking speed because it is an indicator of community walking ability and quality of life. Propulsive force generated from the paretic limb is critical to walking speed and may reflect actual neural recovery that restores the affected neural systems. A wide variation across individuals in the improvements in paretic propulsive force was observed following an intervention that targeted paretic propulsive force. This study aimed to determine if specific baseline characteristics can be used to predict patients who would respond to the intervention. Methods: Participants (N = 19) with chronic poststroke hemiparesis walked at their self-selected and maximal walking speeds on a treadmill before and after a 12-week gait training program. Propulsive forces from the paretic limb were analyzed. Pearson correlation coefficient was used to determine the relationships between (1) treatment gains in walking speed and propulsive force following intervention, and (2) treatment gains in propulsive force and baseline propulsive forces. Results: Treatment gains in self-selected walking speed were correlated to treatment gains in paretic propulsive force following intervention. In addition, changes in paretic propulsive force between self-selected and maximal walking speeds at baseline were strongly correlated to treatment gains in paretic propulsive force. Conclusions: The capacity to modulate paretic propulsive force, rather than the absolute propulsive force during self-selected or maximal walking speed, predicted treatment gains in propulsive force following the intervention. Findings from this research could help to inform clinicians and researchers to target the appropriate patient population for rehabilitation interventions.
- ItemA parallel fictitious domain method for the interface-resolved simulation of particle-laden flows and its application to the turbulent channel flow(Hong Kong Polytechnic University, Department of Civil and Structural Engineering, 1/20/16) Yu,Zhaosheng; Lin,Zhaowu; Shao,Xueming; Wang,Lian-Ping; Zhaosheng Yu, Zhaowu Lin, Xueming Shao , Lian-Ping Wang; Wang, Lian-PingA parallel direct-forcing (DF) fictitious domain (FD) method for the simulation of particulate flows is reported in this paper. The parallel computing strategies for the solution of flow fields and particularly the distributed Lagrange multiplier are presented, and the high efficiency of the parallel code is demonstrated. The new code is then applied to study the effects of particle density (or particle inertia) on the turbulent channel flow. The results show that the large-scale vortices are weakened more severely, and the flow friction drag increases first and then reduces, as particle inertia is increased.
- ItemRoad-Aided Ground Slowly Moving Target 2D Motion Estimation for Single-Channel Synthetic Aperture Radar(MDPI Ag, 1/31/16) Wang,Zhirui; Xu,Jia; Huang,Zuzhen; Zhang,Xudong; Xia,Xiang-Gen; Long,Teng; Bao,Qian; Zhirui Wang, Jia Xu, Zuzhen Huang , Xudong Zhang, Xiang-Gen Xia, Teng Long and Qian Bao; Xia, Xiang-GenTo detect and estimate ground slowly moving targets in airborne single-channel synthetic aperture radar (SAR), a road-aided ground moving target indication (GMTI) algorithm is proposed in this paper. First, the road area is extracted from a focused SAR image based on radar vision. Second, after stationary clutter suppression in the range-Doppler domain, a moving target is detected and located in the image domain via the watershed method. The target's position on the road as well as its radial velocity can be determined according to the target's offset distance and traffic rules. Furthermore, the target's azimuth velocity is estimated based on the road slope obtained via polynomial fitting. Compared with the traditional algorithms, the proposed method can effectively cope with slowly moving targets partly submerged in a stationary clutter spectrum. In addition, the proposed method can be easily extended to a multi-channel system to further improve the performance of clutter suppression and motion estimation. Finally, the results of numerical experiments are provided to demonstrate the effectiveness of the proposed algorithm.
- ItemHeat Stress and Lipopolysaccharide Stimulation of Chicken Macrophage-Like Cell Line Activates Expression of Distinct Sets of Genes(Public Library Science, 10/13/16) Slawinska,Anna; Hsieh,John C.; Schmidt,Carl J.; Lamont,Susan J.; Anna Slawinska, John C. Hsieh, Carl J. Schmidt, Susan J. Lamont; Schmidt, Carl JAcute heat stress requires immediate adjustment of the stressed individual to sudden changes of ambient temperatures. Chickens are particularly sensitive to heat stress due to Developmentelopment of insufficient physiological mechanisms to mitigate its effects. One of the symptoms of heat stress is endotoxemia that results from release of the lipopolysaccharide (LPS) from the guts. Heat-related cytotoxicity is mitigated by the innate immune system, which is comprised mostly of phagocytic cells such as monocytes and macrophages. The objective of this study was to analyze the molecular responses of the chicken macrophage-like HD11 cell line to combined heat stress and lipopolysaccharide treatment in vitro. The cells were heat-stressed and then allowed a temperature-recovery period, during which the gene expression was investigated. LPS was added to the cells to mimic the heat-stress-related endotoxemia. Semi high-throughput gene expression analysis was used to study a gene panel comprised of heat shock proteins, stress-related genes, signaling molecules and immune response genes. HD11 cell line responded to heat stress with increased mRNA abundance of the HSP25, HSPA2 and HSPH1 chaperones as well as DNAJA4 and DNAJB6 co-chaperones. The anti-apoptotic gene BAG3 was also highly up-regulated, providing evidence that the cells expressed pro-survival processes. The immune response of the HD11 cell line to LPS in the heat stress environment (up-regulation of CCL4, CCL5, IL1B, IL8 and iNOS) was higher than in thermoneutral conditions. However, the peak in the transcriptional regulation of the immune genes was after two hours of temperature-recovery. Therefore, we propose the potential influence of the extracellular heat shock proteins not only in mitigating effects of abiotic stress but also in triggering the higher level of the immune responses. Finally, use of correlation networks for the data analysis aided in discovering subtle differences in the gene expression (i.e. the role of the CASP3 and CASP9 genes).
- ItemKilling Two Birds with One Stone: Natural Rice Rhizospheric Microbes Reduce Arsenic Uptake and Blast Infections in Rice(Frontiers Media S.A., 10/13/16) Lakshmanan,Venkatachalam; Cottone,Jonathon; Bais,Harsh P.; Venkatachalam Lakshmanan, Jonathon Cottone and Harsh P.Bais; Harsh P.BaisOur recent work has shown that a rice thizospheric natural isolate, a Paritoea sp (hereafter EA106) attenuates Arsenic (As) uptake in rice. In parallel, yet another natural rice rhizospheric isolate, a Pseuclomonas chlororaphis (hereafter EA105), was shown to inhibit rice blast pathogen Magnaporthe oryzae. Considering the above, we envisaged to evaluate the importance of mixed stress regime in rice plants subjected to both As toxicity and blast infections. Plants subjected to As regime showed increased susceptibility to blast infections compared to As-untreated plants. Rice blast pathogen M. oryzae showed significant resistance against As toxicity compared to other non host fungal pathogens. Interestingly, plants treated with EA106 showed reduced susceptibility against blast infections in plants pre-treated with As. This data also corresponded with lower As uptake in plants primed with EA106. In addition, we also evaluated the expression of defense related genes in host plants subjected to As treatment. The data showed that plants primed with EA106 upregulated defense-related genes with or without As treatment. The data shows the first evidence of how rice plants cope with mixed stress regimes. Our work highlights the importance of natural association of plant microbiome which determines the efficacy of benign microbes to promote the Developmentelopment of beneficial traits in plants.
- ItemSingle nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences(Biomed Central Ltd, 10/19/16) Fleming,D. S.; Koltes,J. E.; Fritz-Waters,E. R.; Rothschild,M. F.; Schmidt,C. J.; Ashwell,C. M.; Persia,M. E.; Reecy,J. M.; Lamont,S. J.; D. S. Fleming, J. E. Koltes, E. R. Fritz-Waters, M. F. Rothschild, C. J. Schmidt, C. M. Ashwell, M. E. Persia, J. M. Reecy and S. J. Lamont; Schmidt, Carl JBackground: Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within-and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation. Results: Downstream fixation test (FST) analysis and subsequent gene ontology (GO) enrichment analysis elucidated major differences between the two lines. The genes with high FST values for both breeds were used to identify enriched gene ontology terms. Over-enriched GO annotations were uncovered for functions indicative of breed-related traits of pathogen resistance and reproductive ability for Fayoumi and Leghorn, respectively. Conclusions: Variant analysis elucidated GO functions indicative of breed-predominant phenotypes related to genomic variation in the lines, showing a possible link between the genetic variants and breed traits.
- ItemSingle-Cell Transcriptional Analysis Reveals Novel Neuronal Phenotypes and Interaction Networks Involved in the Central Circadian Clock(Frontiers Media Sa, 10/25/16) Park,James; Zhu,Haisun; O'Sullivan,Sean; Ogunnaike,Babatunde A.; Weaver,David P.; Schwaber,James S.; Vadigepalli,Rajanikanth; James Park, Haisun Zhu, Sean O'Sullivan, Babatunde A. Ogunnaike, David R.Weaver , James S. Schwaber and RajanikanthVadigepalli; Ogunnaike, Babatunde A; Schwaber, James S; Vadigepalli, RajanikanthSingle-cell heterogeneity confounds efforts to understand how a population of cells organizes into cellular networks that underlie tissue-level function. This complexity is prominent in the mammalian suprachiasmatic nucleus (SCN). Here, individual neurons exhibit a remarkable amount of asynchronous behavior and transcriptional heterogeneity. However, SCN neurons are able to generate precisely coordinated synaptic and molecular outputs that synchronize the body to a common circadian cycle by organizing into cellular networks. To understand this emergent cellular network property, it is important to reconcile single-neuron heterogeneity with network organization. In light of recent studies suggesting that transcriptionally heterogeneous cells organize into distinct cellular phenotypes, we characterized the transcriptional, spatial, and functional organization of 352 SCN neurons from mice experiencing phase-shifts in their circadian cycle. Using the community structure detection method and multivariate analytical techniques, we identified previously undescribed neuronal phenotypes that are likely to participate in regulatory networks with known SCN cell types. Based on the newly discovered neuronal phenotypes, we Developmenteloped a data-driven neuronal network structure in which multiple cell types interact through known synaptic and paracrine signaling mechanisms. These results provide a basis from which to interpret the functional variability of SCN neurons and describe methodologies toward understanding how a population of heterogeneous single cells organizes into cellular networks that underlie tissue-level function.
- ItemTsunamis caused by submarine slope failures along western Great Bahama Bank(Nature Publishing Group, 10/7/16) Schnyder,Jara S. D.; Eberli,Gregor P.; Kirby,James T.; Shi,Fengyan; Tehranirad,Babak; Mulder,Thierry; Ducassou,Emmanuelle; Hebbeln,Dierk; Wintersteller,Paul; Jara S.D. Schnyder1, Gregor P. Eberli1, James T. Kirby2, Fengyan Shi2, Babak Tehranirad2, Thierry Mulder3, Emmanuelle Ducassou3, Dierk Hebbeln4 & Paul Wintersteller4; Kirby Jr, James T; Shi, FengyanSubmarine slope failures are a likely cause for tsunami generation along the East Coast of the United States. Among potential source areas for such tsunamis are submarine landslides and margin collapses of Bahamian platforms. Numerical models of past events, which have been identified using high-resolution multibeam bathymetric data, reveal possible tsunami impact on Bimini, the Florida Keys, and northern Cuba. Tsunamis caused by slope failures with terminal landslide velocity of 20 ms(-1) will either dissipate while traveling through the Straits of Florida, or generate a maximum wave of 1.5 m at the Florida coast. Modeling a worst-case scenario with a calculated terminal landslide velocity generates a wave of 4.5 m height. The modeled margin collapse in southwestern Great Bahama Bank potentially has a high impact on northern Cuba, with wave heights between 3.3 to 9.5 m depending on the collapse velocity. The short distance and travel time from the source areas to densely populated coastal areas would make the Florida Keys and Miami vulnerable to such low-probability but high-impact events.
- ItemNo Apparent Influence of Reward upon Visual Statistical Learning(Frontiers Media SA, 11/2/16) Rogers,Leeland L.; Friedman,Kyle G.; Vickery,Timothy J.; Leeland L. Rogers, Kyle G. Friedman and Timothy J. Vickery; Vickery, Timothy JohnHumans are capable of detecting and exploiting a variety of environmental regularities, including stimulus stimulus contingencies (e.g., visual statistical learning) and stimulus reward contingencies. However, the relationship between these two types of learning is poorly understood. In two experiments, we sought evidence that the occurrence of rewarding events enhances or impairs visual statistical learning. Across all of our attempts to find such evidence, we employed a training stage during which we grouped shapes into triplets and presented triplets one shape at a time in an undifferentiated stream. Participants subsequently performed a surprise recognition task in which they were tested on their knowledge of the underlying structure of the triplets. Unbeknownst to participants, triplets were also assigned no-, low-, or high reward status. In Experiments 1A and 1B, participants viewed shape streams while low and high rewards were "randomly" given, presented as low- and high-pitched tones played through headphones. Rewards were always given on the third shape of a triplet (Experiment 1A) or the first shape of a triplet (Experiment 1B), and high- and low-reward sounds were always consistently paired with the same triplets. Experiment 2 was similar to Experiment 1, except that participants were required to learn value associations of a subset of shapes before viewing the shape stream. Across all experiments, we observed significant visual statistical learning effects, but the strength of learning did not differ amongst no-, low-, or high-reward conditions for any of the experiments. Thus, our experiments failed to find any influence of rewards on statistical learning, implying that visual statistical learning may be unaffected by the occurrence of reward. The system that detects basic stimulus stimulus regularities may operate independently of the system that detects reward contingencies.
- ItemBioluminescence as an ecological factor during high Arctic polar night(Nature Publishing Group, 11/2/16) Cronin,Heather A.; Cohen,Jonathan H.; Berge,Jorgen; Johnsen,Geir; Moline,Mark A.; Heather A. Cronin, Jonathan H. Cohen, J�rgen Berge, Geir Johnsen, Mark A. Moline; Cohen, Jonathan Hirsch; Moline, Mark AlanBioluminescence commonly influences pelagic trophic interactions at mesopelagic depths. Here we characterize a vertical gradient in structure of a generally low species diversity bioluminescent community at shallower epipelagic depths during the polar night period in a high Arctic fjord with in situ bathyphotometric sampling. Bioluminescence potential of the community increased with depth to a peak at 80 m. Community composition changed over this range, with an ecotone at 20-40 m where a dinoflagellate-dominated community transitioned to dominance by the copepod Metridia longa. Coincident at this depth was bioluminescence exceeding atmospheric light in the ambient pelagic photon budget, which we term the bioluminescence compensation depth. Collectively, we show a winter bioluminescent community in the high Arctic with vertical structure linked to attenuation of atmospheric light, which has the potential to influence pelagic ecology during the light-limited polar night.
- ItemLiver transcriptome response to hyperthermic stress in three distinct chicken lines(Biomed Central LTD, 11/22/16) Lan,Xi; Hsieh,John C. F.; Schmidt,Carl J.; Zhu,Qing; Lamont,Susan J.; Xi Lan, John C. F. Hsieh, Carl J. Schmidt, Qing Zhu, Susan J. Lamont; Schmidt, Carl J.Background: High ambient temperatures cause stress in poultry, especially for broiler lines, which are genetically selected for rapid muscle growth. RNA-seq technology provides powerful insights into environmental response from a highly metabolic tissue, the liver. We investigated the effects of acute (3 h, 35 degrees C) and chronic (7d of 35 degrees C for 7 h/d) heat stress on the liver transcriptome of 3-week-old chicks of a heat-susceptible broiler line, a heat-resistant Fayoumi line, and their advanced intercross line (AIL). Results: Transcriptome sequencing of 48 male chickens using Illumina HiSeq 2500 technology yielded an average of 33.9 million, 100 base-pair, single-end reads per sample. There were 8 times more differentially expressed genes (DEGs) (FDR < 0.05) in broilers (n = 627) than Fayoumis (n = 78) when comparing the acute-heat samples to the control (25 degrees C) samples. Contrasting genetic lines under similar heat treatments, the highest number of DEGs appeared between Fayoumi and broiler lines. Principal component analysis of gene expression and analysis of the number of DEGs suggested that the AIL had a transcriptomic response more similar to the Fayoumi than the broiler line during acute heat stress. The number of DEGs also suggested that acute heat stress had greater impact on the broiler liver transcriptome than chronic heat stress. The angiopoietin-like 4 (ANGPTL4) gene was identified as differentially expressed among all 6 contrasts. Ingenuity Pathway Analysis (IPA) created a novel network that combines the heat shock protein family with immune response genes. Conclusions: This study extends our understanding of the liver transcriptome response to different heat exposure treatments in distinct genetic chicken lines and provides information necessary for breeding birds to be more resilient to the negative impacts of heat. The data strongly suggest ANGPTL4 as a candidate gene for improvement of heat tolerance in chickens.
- ItemThe Spatial Properties of Radical Environmental Organizations in the UK: Do or Die!(The Public Library of Science, 11/29/16) Almquist,Zack W.; Bagozzi,Benjamin E.; Zack W. Almquist,Benjamin E. Bagozzi; Bagozzi, Benjamin EdwardRadical environmental groups and their members have a wide and varied agenda which often encompasses both local and global issues. In their efforts to call attention to environmental problems, communicate with like-minded groups, and mobilize support for their activities, radical environmental organizations also produce an enormous amount of text, which can be used to estimate the complex communications and task-based networks that underlie these organizations. Moreover, the tactics employed to garnish attention for these groups' agenda can range from peaceful activities such as information dissemination to violent activities such as fire-bombing buildings. To obtain these varied objectives, radical environmental organizations must harness their networks, which have an important spatial component that structures their ability to communicate, coordinate and act on any given agenda item. Here, we analyze a network built from communications and information provided by the semi-annual "Do or Die" (DoD) magazine published in the UK over a 10 year period in the late 1990s and early 2000s. We first employ structural topic model methods to discover violent and nonviolent actors within the larger environmental community. Using this designation, we then compare the spatial structure of these groups, finding that violent groups are especially likely to engage in coordination and/or communication if they are sufficiently close, but exhibit a quickly decreasing probability of interaction over even a few kilometers. Further, violent and nonviolent groups each have a higher probability of coordination with their own group than across groups over even short distances. In these respects, we see that violent groups are especially local in their organization and that their geographic reach is likely very limited. This suggests that nonviolent environmental groups seek each other out over both large and short distances for communication and coordination, but violent groups tend to be highly localized.
- ItemSomatostatin signaling via SSTR1 contributes to the quiescence of colon cancer stem cells(Biomed Central LTD, 12/7/16) Modarai,Shirin R.; Opdenaker,Lynn M.; Viswanathan,Vignesh; Fields,Jeremy Z.; Boman,Bruce M.; Shirin R. Modarai, Lynn M. Opdenaker, Vignesh Viswanathan, Jeremy Z. Fields, Bruce M. Boman; Modarai, Shirin R.; Opdenaker, Lynn Marie.; Viswanathan, Vignesh; Boman, Bruce MillringBackground: Neuroendocrine cells (NECs) reside adjacent to colonic stem cells (SCs) in the crypt stem cell (SC) niche, but how NECs are involved in regulation of SCs is unclear. We investigated NECs expressing somatostatin (SST) and somatostatin receptor type 1 (SSTR1) because SST inhibits intestinal proliferation. Hypothesis: SSTR1 cells maintain SCs in a quiescent state, and aberrant SST signaling contributes to SC overpopulation in colorectal cancer (CRC). Methods: The proportion of SCs to NECs cells was quantified, by flow cytometry, in CRC cell lines and primary normal/tumor tissues based on cellular ALDH and SSTR1 levels, respectively. Doubling time and sphere-formation was used to evaluate cell proliferation and stemness. CRC cell lines were treated with exogenous SST and SST inhibitor cyclosomatostatin (cycloSST) and analyzed for changes in SCs and growth rate. Paracrine signaling between NECs and SCs was ascertained using transwell cultures of ALDH+ and SSTR1+ cells. Results: In CRC cell lines, the proportion of ALDH+ cells inversely correlates with proportion of SSTR1+ cells and with rate of proliferation and sphere-formation. While primary normal tissue shows SST and SSTR1 expression, CRC shows only SSTR1 expression. Moreover, ALDH+ cells did not show SST or SSTR1 expression. Exogenous SST suppressed proliferation but not ALDH+ population size or viability. Inhibition of SSTR1 signaling, via cycloSST treatment, decreased cell proliferation, ALDH+ cell population size and sphere-formation. When co-cultured with SSTR1+ cells, sphere-formation and cell proliferation of ALDH+ cells was inhibited. Conclusion: That each CRC cell line has a unique ALDH+/SSTR1+ ratio which correlates with its growth dynamics, suggests feedback mechanisms exist between SCs and NECs that contribute to regulation of SCs. The growth suppression by both SST and cycloSST treatments suggests that SST signaling modulates this feedback mechanism. The ability of SSTR1+ cells to decrease sphere formation and proliferation of ALDH+ cells in transwell cultures indicates that the ALDH subpopulation is regulated by SSTR1 via a paracrine mechanism. Since ALDH+ cells lack SST and SSTR1 expression, we conjecture that SST signaling controls the rate of NEC maturation as SCs mature along the NEC lineage, which contributes to quiescence of SCs and inhibition of proliferation.
- ItemYear-round pack ice in the Weddell Sea, Antarctica: Response and sensitivity to atmospheric and oceanic forcing(International Glaciology Society, 1997) Geiger, Cathleen A.; Ackley, Stephen F.; Hibler, W. D., III; Geiger, Cathleen A., Ackley, S. F., Hibler, M. D.; Geiger, Cathleen A.Using a dynamic-thermodynamic numerical sea-ice model, external oceanic and atmospheric forcings on sea ice in the Weddell Sea are examined to identify physical processes associated with the seasonal cycle of pack ice, and to identify further the parameters that coupled models need to consider in predicting the response of the pack ice to climate and ocean-circulation changes. In agreement with earlier studies, the primary influence on the winter ice-edge maximum extent is air temperature. Ocean heat flux has more impact on the minimum ice-edge extent and in reducing pack-ice thickness, especially in the eastern Weddell Sea. Low relative humidity enhances ice growth in thin ice and open-water regions, producing a more realistic ice edge along the coastal areas of the western Weddell Sea where dry continental air has an impact. The modeled extent of the Weddell summer pack is equally sensitive to ocean heat flux and atmospheric relative humidity variations with the more dynamic responses being from the atmosphere. Since the atmospheric regime in the eastern Weddell is dominated by marine intrusions from lower latitudes, with high humidity already, it is unlikely that either the moisture transport could be further raised or that it could be significantly lowered because of its distance from the continent (the lower humidity source). Ocean heat-transport variability is shown to lead to overall ice thinning in the model response and is a known feature of the actual system, as evidenced by the occurrence of the Weddell Polynya in the mid 1970s.
- ItemLarge-scale sea ice drift and deformation: Comparison between models and observations in the western weddell sea during 1992(American Geophysical Union, 1998) Geiger, Cathleen A.; Hibler, W. D., III; Ackley, Stephen F.; Geiger, Cathleen A., Hibler, W. D., Ackley, S. F.; Geiger, Cathleen A.Statistical comparisons between numerical sea ice models and an observed large-scale strain array in the western Weddell Sea during 1992 are used to evaluate the performance of three of the more generally utilized sea ice rheology formulations. Results show that sea ice velocity is reproduced with relatively high accuracy (90% coherence, >80% normalized cross correlation) in models having high-quality atmospheric forcing fields (e.g., the European Centre for Medium-Range Weather Forecasts). On the other hand, temporal and spatial variability of the velocity field, as exemplified by progressive vector plots and ice deformation, respectively, are reproduced less accurately (coherence and normalized cross correlation <50%). In terms of model sensitivity, this means that deformation and temporal variability are more discriminating in terms of elucidating specifics about the constitutive relation and mechanical properties of sea ice on a large scale. For example, inclusion of both compressive and shear stresses is important in attaining a proper probability distribution of deformation relative to observations. Additional analysis shows that adjustments to specific model parameters improve the model results for either drift or select deformation components, but no best solution could be found, given the models examined here. Results suggest that inclusion of more physically based processes, such as subdaily tidal and inertial oscillations; reconsideration of the boundary layer formulation, and consideration of anisotropy, may be necessary to include in next-generation sea ice models, especially those that are intended for coupling with high-resolution (eddy resolving) ocean models.
- ItemMitochondrial DNA analysis of population structure in the Atlantic croaker, Micropogonias undulatus (Perciformes: Sciaenidae)(United States. National Marine Fisheries Service., 1999) Lankford, Thomas E. Jr.; Targett, Timothy E.; Gaffney, Patrick M.; Thomas E. Lankford Jr., Timothy E. Targett, Patrick M. Gaffney; Lankford, Thomas E. Jr.; Targett, Timothy E.; Gaffney, Patrick M.Genetic population struc- ture in Atlantic croaker ( Micropogonias undulatus Linnaeus) was examined by using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis of mi- tochondrial DNA (mtDNA). Juvenile croaker from three U.S. Atlantic locali- ties (Delaware, North Carolina, and Florida) and one Gulf of Mexico local- ity (Louisiana) were screened to docu- ment the magnitude and spatial distri- bution of mtDNA variation in M. undulatus ; to evaluate the integrity of Cape Hatteras, North Carolina, as a genetic stock boundary; and to estimate levels of gene flow among Atlantic lo- calities to provide an improved basis for future decisions regarding coastwide management of this fishery resource. RFLP analysis of the ATPase 6 and D-loop mtDNA regions revealed a total of 15 composite haplotypes in 93 indi- viduals. Monte Carlo simulations re- vealed no geographic heterogeneity in mtDNA haplotype frequencies among Atlantic localities and no evidence that juveniles collected north and south of Cape Hatteras originated from sepa- rate gene pools (net sequence diver- gence=–0.002%). There was significant heterogeneity between Atlantic and Gulf of Mexico samples, suggesting re- stricted gene flow between these two re- gions. Analysis of molecular variance also indicated regional (Atlantic versus Gulf) population structure, but pro- vided no evidence that Cape Hatteras represents a genetic stock boundary. AMOVA indicated relatively high gene flow ( N e m U = 12–23 effective female mi- grants per generation) among Atlantic localities. These findings are consistent with 1) a single genetic stock of M . undulatus on the Atlantic coast and 2) separate, weakly differentiated stocks in the Atlantic and Gulf of Mexico.
- ItemEvaluating sex as a biological variable in preclinical research: the Developmental in the details(Biomed Central Ltd, 2/11/16) Tannenbaum,Cara; Schwarz,Jaclyn M.; Clayton,Janine A.; de Vries,Geert J.; Sullivan,Casey; Cara Tannenbaum, Jaclyn M. Schwarz, Janine A. Clayton, Geert J. de Vries, and Casey Sullivan; Schwarz, Jaclyn MarieTranslating policy into action is a complex task, with much debate surrounding the process whereby US and Canadian health funding agencies intend to integrate sex and gender science as an integral component of methodological rigor and reporting in health research. Effective January 25, 2016, the US National Institutes of Health implemented a policy that expects scientists to account for the possible role of sex as a biological variable (SABV) in vertebrate animal and human studies. Applicants for NIH-funded research and career Developmentelopment awards will be asked to explain how they plan to factor consideration of SABV into their research design, analysis, and reporting; strong justification will be required for proposing single-sex studies. The Canadian Institutes of Health Research is revising their peer review accreditation process to ensure that peer reviewers are skilled in applying a critical lens to protocols that should be incorporating sex and gender science. The current paper outlines the components that peer reviewers in North America will be asked to assess when considering whether SABV is appropriately integrated into research designs, analyses, and reporting. Consensus argues against narrowly defining rules of engagement in applying SABV, with criteria provided for reviewers as guidance only. Scores will not be given for each criterion; applications will be judged on the overall merit of scientific innovation, rigor, reproducibility, and potential impact.
- ItemThe Guaymas Basin Hiking Guide to Hydrothermal Mounds, Chimneys, and Microbial Mats: Complex Seafloor Expressions of Subsurface Hydrothermal Circulation(Frontiers Media Sa, 2/18/16) Teske,Andreas; de Beer,Dirk; McKay,Luke J.; Tivey,Margaret K.; Biddle,Jennifer F.; Hoer,Daniel; Lloyd,Karen G.; Lever,Mark A.; Roy,Hans; Albert,Daniel B.; Mendlovitz,Howard P.; MacGregor,Barbara J.; Andreas Teske, Dirk de Beer, Luke J. McKay, Margaret K. Tivey, Jennifer F. Biddle, Daniel Hoer, Karen G. Lloyd, Mark A. Lever, Hans Roy, Daniel B. Albert, Howard P. Mendlovitz and Barbara J. MacGregor; Biddle, Jennifer FrancesThe hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.
- ItemThe UniProtKB guide to the human proteome(Oxford University Press, 2/19/16) Breuza,Lionel; Poux,Sylvain; Estreicher,Anne; Famiglietti,Maria Livia; Magrane,Michele; Tognolli,Michael; Bridge,Alan; Baratin,Delphine; Redaschi,Nicole; UniProt Consortium; Lionel Breuza, Sylvain Poux, Anne Estreicher, Maria Livia Famiglietti, Michele Magrane, Michael Tognolli, Alan Bridge, Delphine Baratin, Nicole Redaschi and The UniProt Consortium; Wu, Cathy Huey-HwaAdvances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. Using the example of the human proteome, we will describe the content of a complete proteome in the UniProt Knowledgebase (UniProtKB). We will show how manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation to build a comprehensive, high-quality and traceable resource. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB.
- ItemSpectral Reflectance of Palauan Reef-Building Coral with Different Symbionts in Response to Elevated Temperature(MDPI Ag, 2/23/16) Russell,Brandon J.; Dierssen,Heidi M.; LaJeunesse,Todd C.; Hoadley,Kenneth D.; Warner,Mark E.; Kemp,Dustin W.; Bateman,Timothy G.; Brandon J. Russell, Heidi M. Dierssen, Todd C. LaJeunesse, Kenneth D. Hoadley, Mark E. Warner, Dustin W. Kemp and Timothy G. Bateman; Hoadley, Kenneth D;Warner, Mark ESpectral reflectance patterns of corals are driven largely by the pigments of photosynthetic symbionts within the host cnidarian. The warm inshore bays and cooler offshore reefs of Palau share a variety of coral species with differing endosymbiotic dinoflagellates (genus: Symbiodinium), with the thermally tolerant Symbiodinium trenchii (S. trenchii) (= type D1a or D1-4) predominating under the elevated temperature regimes inshore, and primarily Clade C types in the cooler reefs offshore. Spectral reflectance of two species of stony coral, Cyphastrea serailia (C. serailia) and Pachyseris rugosa (P. rugosa), from both inshore and offshore locations shared multiple features both between sites and to similar global data from other studies. No clear reflectance features were evident which might serve as markers of thermally tolerant S. trenchii symbionts compared to the same species of coral with different symbionts. Reflectance from C. serailia colonies from inshore had a fluorescence peak at approximately 500 nm which was absent from offshore animals. Integrated reflectance across visible wavelengths had an inverse correlation to symbiont cell density and could be used as a relative indicator of the symbiont abundance for each type of coral. As hypothesized, coral colonies from offshore with Clade C symbionts showed a greater response to experimental heating, manifested as decreased symbiont density and increased reflectance or "bleaching" than their inshore counterparts with S. trenchii. Although no unique spectral features were found to distinguish species of symbiont, spectral differences related to the abundance of symbionts could prove useful in field and remote sensing studies.