Provenance effects in Banksia attenuata germination and emergence: implications for restoration seed sourcing under climate change

The rapidity of climate change and its effects have contributed to the complexity of selecting an appropriate seed source for restoration projects. The use of a traditional local provenancing seed sourcing strategy has been critiqued as it may fail to facilitate long-term sustainability of a restoration site. Alternative strategies such as climate-adjusted provenancing may enhance lasting survival of a restored community, by purposefully selecting seed sources that match future climate predictions for the site. This study assessed the population-level variation (that is, a provenance effect) in Banksia attenuata seed germination and emergence in response to a variety of environmental stimuli. Specifically, laboratory trials of seed germination highlight that Banksia attenuata shows significant provenance effects in response to temperature, with seed sourced from hotter climates achieving greater germination under hotter incubation temperatures than seed sourced from cooler climates. All sampled populations displayed a significant interactive effect with water potential (MPa), whereby a decrease in MPa resulted in a varied reduction in germination between populations. Four trial locations were established to investigate any provenance effects in Banksia attenuata emergence. No overall significant provenance effect was observed at unmined or postmining restoration sites 16 weeks after seeds had been sown. These findings indicate that provenance does not play a significant role in Banksia attenuata seedling emergence in field trials, suggesting that local seed sourcing for restoration of Banksia attenuata is no more effective than using non-local seed. The results from the field trial provide little evidence to support a climate-adjusted seed sourcing strategy for restoration in the future. The contrasting results between laboratory (germination) and field (emergence) trials points to the need for future research quantifying determinants of species provenance in a practical restoration context

Feasibility of mapping benthic biotopes in the Hudson River

Successful management of aquatic resources requires comprehensive maps that identify the spatial distribution and extent of potentially vulnerable habitats and their resident biota (e.g., essential fish habitat). We illustrate a technique that describes submerged landscapes not only in terms of geophysical properties, but also in terms of the resident biotic communities. Biological community distribution was highly correlated with the geophysical provinces initially identified by Bell et al. (2000). However, fewer groups of stations (created mainly by combining provinces) explained almost as much of the variation in benthic community structure and was a better description of the major biotopes in this stretch of the Hudson River Estuary. The findings of this pilot study can lead to sampling design criteria for the rest of the Hudson River Estuary

Benthic Mapping for Habitat Classification in the Peconic Estuary: Phase I Groundtruth Studies

Benthic habitat maps of the estuary seafloor will increase our knowledge of range and variability in benthic habitats, will assist managers in their efforts to protect and/or restore commercially and recreationally important finfish and shellfish, will link land usage (e.g. developed vs. undeveloped areas) and water quality data to benthic habitat quality, and will make it possible to utilize faunal data as a long-term indicator of the overall “health” of the estuary. We are developing benthic habitat maps by combining high-resolution remote sensing techniques with detailed study of the physical and faunal characteristics at point locations in different seafloor environments. In Phase I, six critical natural resource areas (CNRA: Robins Island, Shelter Island, Flanders Bay, Orient Bay, Northwest Harbor, and Gardiners Island) were acoustically mapped and sampled. Acoustic mapping used side-scan sonar and multibeam swath bathymetry and backscatter to generate bathymetric and backscatter images that provide high resolution detail about bottom morphology, sediment processes, and geophysical habitat, and that allow classification of the sea bed into regions. Samples for macrofauna and sediment properties were collected within each bottom region to provide ground truth for the acoustic maps. Robins Island and Shelter Island areas were sampled at 30 and 35 locations, respectively, with two replicate samples at each location. The other four CNRA areas were sampled at 7-15 locations each, with no replication. Results suggest that the acoustic provinces identified do indeed represent areas of similar faunal and sedimentary characteristics, and that this approach can provide new insights into benthic community structure. Phase II benthic habitat studies will extend mapping from nearly shore to shore (north-south) across four different reaches of the Peconic Estuary

Interferon-λ in HCV Infection and Therapy

Chronic infection with hepatitis C virus (HCV) is associated with significant liver disease and is therefore an important public health problem. The current standard-of-care therapy for chronic HCV infection consists of a combination of pegylated (PEG) interferon (IFN)-α and ribavirin. Although this therapy effectively generates a sustained viral response in approximately half of treated individuals, it is associated with significant hematological and neurological side effects. A new family of IFN-related proteins (IFN-λ1, 2, and 3; or alternately, IL-29, 28A, 28B, respectively) possesses properties that may make these cytokines superior to PEG-IFN-α for HCV therapy. Genetic studies have also implicated these proteins in both the natural and therapy-induced resolution of HCV infection. This review summarizes the basic aspects of IFN-λ biology, the potential role of these cytokines in HCV infection, and the outlook for their therapeutic application

The influence of dynamics and speech on understanding humanoid facial expressions

Human communication relies mostly on nonverbal signals expressed through body language. Facial expressions, in particular, convey emotional information that allows people involved in social interactions to mutually judge the emotional states and to adjust its behavior appropriately. First studies aimed at investigating the recognition of facial expressions were based on static stimuli. However, facial expressions are rarely static, especially in everyday social interactions. Therefore, it has been hypothesized that the dynamics inherent in a facial expression could be fundamental in understanding its meaning. In addition, it has been demonstrated that nonlinguistic and linguistic information can contribute to reinforce the meaning of a facial expression making it easier to be recognized. Nevertheless, few studies have been performed on realistic humanoid robots. This experimental work aimed at demonstrating the human-like expressive capability of a humanoid robot by examining whether the effect of motion and vocal content influenced the perception of its facial expressions. The first part of the experiment aimed at studying the recognition capability of two kinds of stimuli related to the six basic expressions (i.e. anger, disgust, fear, happiness, sadness, and surprise): static stimuli, that is, photographs, and dynamic stimuli, that is, video recordings. The second and third parts were focused on comparing the same six basic expressions performed by a virtual avatar and by a physical robot under three different conditions: (1) muted facial expressions, (2) facial expressions with nonlinguistic vocalizations, and (3) facial expressions with an emotionally neutral verbal sentence. The results show that static stimuli performed by a human being and by the robot were more ambiguous than the corresponding dynamic stimuli on which motion and vocalization were associated. This hypothesis has been also investigated with a 3-dimensional replica of the physical robot demonstrating that even in case of a virtual avatar, dynamic and vocalization improve the emotional conveying capability

L’impact d’un campus clinique régional en milieu urbain : les perceptions des parties prenantes de la collectivité

Background: Regional medical campuses (RMC) have shown promise in addressing physician shortages. RMCs have been positively evaluated in rural/remote communities, however, it is unclear whether this model will be as beneficial in underserved urban areas. This study evaluated the impact of a RMC on a midsized urban city (Windsor, Ontario). We compare our results with a similar study conducted in a remote community in British Columbia (BC). Methods: A broad array of community stakeholders representing different sectors were consulted using a semi-structured interview format replicated from the BC Northern Medical Program (NMP) study. Thematic analysis based on the resulting rich data was conducted within a grounded theory context. Results: Twenty-three participants (52% male) representing healthcare, education, business, community and government/politico sectors were consulted. Their views regarding the Windsor Regional Medical Campus (WRMC) aligned around several themes: improved healthcare, enhanced community reputation, stimulated economic/community development, expanded training opportunities and an engaged community regarding the WRMC. These results were compared to the main findings of the NMP study with both similarities (e.g. increased community pride) and differences (e.g. resource concerns) discussed. Conclusion: Community stakeholders provided strong support for the WRMC through their perceptions of its positive impact on this urban region. These findings are consistent with similar RMC studies in rural/remote areas. Those interested in developing a RMC might benefit from considering these findings.Contexte : Les campus cliniques régionaux (CCR) se sont révélés prometteurs pour remédier à la pénurie de médecins. Les CCR ont été évalués positivement dans les collectivités rurales/éloignées, mais il n’est pas certain que ce modèle soit aussi bénéfique dans les zones urbaines mal desservies. La présente étude évalue l’impact d’un CCR dans une ville de taille moyenne (Windsor, Ontario). Nous comparons nos résultats avec ceux d’une étude similaire menée dans une collectivité éloignée en Colombie-Britannique (BC). Méthode : Un large éventail de parties prenantes de la collectivité représentant différents secteurs a été consulté par le biais d’entrevues semi-structurées calquées sur celles de l’étude du BC Northern Medical Program (NMP). L’analyse thématique des riches données obtenues a été faite selon l’approche de la Grounded Theory (théorie ancrée). Résultats : Vingt-trois participants (52 % d’hommes) des secteurs de la santé, de l’éducation, des affaires, de la vie communautaire, du gouvernement ou encore du monde politique ont été consultés. Leurs opinions concernant le campus clinique régional de Windsor (WRMC) s’articulaient autour de plusieurs thèmes : l’amélioration des soins de santé, le renforcement de la réputation de la collectivité, la stimulation du développement économique et communautaire, l’élargissement des possibilités de formation et l’engagement de la communauté envers le WRMC. Les résultats ont été comparés aux principales conclusions de l’étude du NMP, en analysant aussi bien les similitudes (par exemple, fierté accrue de la collectivité) que les différences (par exemple, les préoccupations en matière de ressources). Conclusion : Percevant l’impact positif qu’a eu le WRMC dans la région urbaine, les acteurs de la collectivité témoignent d’un ferme appui à son égard. Ces résultats sont conformes aux études similaires portant sur des CCR dans les zones rurales/éloignées. Les résultats de l’étude seraient utiles à tous ceux qui souhaitant mettre sur pied un CCR

From Micro to Macro-Contaminants: The Impact of Low-Energy Titanium Dioxide Photocatalysis Followed by Filtration on The Mitigation of Drinking Water Organics

This study evaluated strategies targeting macro- and micro-organic contaminant mitigation using low-energy titanium dioxide photocatalysis. Energy inputs of 1, 2, and 5 kWh m−3 resulted in incomplete oxidation of macro-organic natural organic matter, signified by greater reductions of UV254 and specific ultraviolet UV absorbance (SUVA) in comparison to dissolved organic carbon (DOC). The rate of UV254 removal was 3 orders of magnitude greater than the rate of DOC degradation. Incomplete oxidation improved operation of downstream filtration processes. Photocatalysis at 2 kWh m−3 increased the bed life of downstream granular activated carbon (GAC) filtration by 340% relative to direct filtration pretreatment. Likewise, photocatalysis operated ahead of microfiltration decreased fouling, resulting in longer filter run times. Using 2 kWh m−3 photocatalysis increased filter run time by 36 times in comparison to direct filtration. Furthermore, levels of DOC and UV254 in the membrane permeate improved (with no change in removal across the membrane) using low-energy photocatalysis pretreatments. While high-energy UV inputs provided high levels of removal of the estrogenic micro-organics estrone (E1), 17β-estradiol (E2), estriol (E3), and 17α-ethynlestradiol (EE2), low-energy photocatalysis did not enhance removal of estrogens beyond levels achieved by photolysis alone. In the cases of E1 and E3, the addition of TiO2 as a photocatalyst reduced degradation rates of estrogens compared to UV photolysis. Overall, process electrical energy per order magnitude reductions (EEOs) greatly improved using photocatalysis, versus photolysis, for the macro-organics DOC, UV254, and SUVA; however, energy required for removal of estrogens was similar between photolysis and photocatalysis

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

BACKGROUND: Long intergenic non-coding RNAs (lncRNAs) represent an emerging and under-studied class of transcripts that play a significant role in human cancers. Due to the tissue- and cancer-specific expression patterns observed for many lncRNAs it is believed that they could serve as ideal diagnostic biomarkers. However, until each tumor type is examined more closely, many of these lncRNAs will remain elusive. RESULTS: Here we characterize the lncRNA landscape in lung cancer using publicly available transcriptome sequencing data from a cohort of 567 adenocarcinoma and squamous cell carcinoma tumors. Through this compendium we identify over 3,000 unannotated intergenic transcripts representing novel lncRNAs. Through comparison of both adenocarcinoma and squamous cell carcinomas with matched controls we discover 111 differentially expressed lncRNAs, which we term lung cancer-associated lncRNAs (LCALs). A pan-cancer analysis of 324 additional tumor and adjacent normal pairs enable us to identify a subset of lncRNAs that display enriched expression specific to lung cancer as well as a subset that appear to be broadly deregulated across human cancers. Integration of exome sequencing data reveals that expression levels of many LCALs have significant associations with the mutational status of key oncogenes in lung cancer. Functional validation, using both knockdown and overexpression, shows that the most differentially expressed lncRNA, LCAL1, plays a role in cellular proliferation. CONCLUSIONS: Our systematic characterization of publicly available transcriptome data provides the foundation for future efforts to understand the role of LCALs, develop novel biomarkers, and improve knowledge of lung tumor biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0429-8) contains supplementary material, which is available to authorized users

Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A

The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by \u3e60◦. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are ‘captured’ by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18- base-pair DNA oligomer indeed remains bound to yNhp6A while unbent. In 100 mM NaCl, yNhp6Abound DNA unbends as the temperature is raised, with no significant dissociation of the complex detected up to ∼45◦C. In 200 mM NaCl, DNA unbending in the intact yNhp6A complex is again detected up to ∼35◦C. Microseconds-resolved laser temperaturejump perturbation of the yNhp6a–DNA complex revealed relaxation kinetics that yielded unimolecular DNA bending/unbending rates on timescales of 500 s−1 ms. These data provide the first direct observation of bending/unbending dynamics of DNA in complex with yNhp6A, suggesting a bind-then-bend mechanism for this protein