Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data

We present Farseer-NMR (https://git.io/vAueU), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems’ responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension

Successional Change in Phosphorus Stoichiometry Explains the Inverse Relationship between Herbivory and Lupin Density on Mount St. Helens

The average nitrogen-to-phosphorus ratio (N?P) of insect herbivores is less than that of leaves, suggesting that P may mediate plant-insect interactions more often than appreciated. We investigated whether succession-related heterogeneity in N and P stoichiometry influences herbivore performance on N-fixing lupin (Lupinus lepidus) colonizing primary successional volcanic surfaces, where the abundances of several specialist lepidopteran herbivores are inversely related to lupin density and are known to alter lupin colonization dynamics. We examined larval performance in response to leaf nutritional characteristics using gelechiid and pyralid leaf-tiers, and a noctuid leaf-cutter.Apple JL, Wink M, Wills SE, Bishop JG (2009) Successional Change in Phosphorus Stoichiometry Explains the Inverse Relationship between Herbivory and Lupin Density on Mount St. Helens. PLoS ONE 4(11): e7807. doi:10.1371/journal.pone.000780

An integrated model of care to counter high incidence of HIV and sexually transmitted diseases in men who have sex with men – initial analysis of service utilizers in Zurich

BACKGROUND: As other countries, Switzerland experiences a high or even rising incidence of HIV and sexually transmitted infections (STI) among men who have sex with men (MSM). An outpatient clinic for gay men ("Checkpoint") was opened in 2006 in Zurich (Switzerland) in order to provide sexual health services. The clinic provides counselling, testing, medical treatment and follow-up at one location under an "open-door-policy" and with a high level of personal continuity. We describe first experiences with the new service and report the characteristics of the population that utilized it. METHODS: During the 6-month evaluation period, individuals who requested counselling, testing or treatment were asked to participate in a survey at their first visit prior to the consultation. The instrument includes questions regarding personal data, reasons for presenting, sexual behaviour, and risk situations. Number and results of HIV/STI tests and treatments for STI were also recorded. RESULTS: During the evaluation period, 632 consultations were conducted and 247 patients were seen by the physician. 406 HIV tests were performed (3.4% positive). 402 men completed the entry survey (64% of all consultations). The majority of respondents had 4 and more partners during the last 12 months and engaged in either receptive, insertive or both forms of anal intercourse. More than half of the responders used drugs or alcohol to get to know other men or in conjunction with sexual activity (42% infrequently, 10% frequently and 0.5% used drugs always). The main reasons for requesting testing were a prior risk situation (46.3%), followed by routine screening without a prior risk situation (24.1%) and clarification of HIV/STI status due to a new relationship (29.6%). A fifth of men that consulted the service had no history of prior tests for HIV or other STIs. CONCLUSION: Since its first months of activity, the service achieved high levels of recognition, acceptance and demand in the MSM community. Contrary to common concepts of "testing clinics", the Checkpoint service provides post-exposure prophylaxis, HIV and STI treatment, psychological support and counselling and general medical care. It thus follows a holistic approach to health in the MSM community with the particular aim to serve as a "door opener" between the established system of care and those men that have no access to, or for any reason hesitate to utilize traditional health care

The effectiveness of digital storytelling in the classrooms: a comprehensive study

In recent years the use of new technologies in educational systems has increased worldwide as digital cameras, personal computers, scanners, and easy-to-use software have become available to educators to harness the digital world. The impact of new technologies in educational contexts has been mostly positive as new technologies have given educators the opportunity to enhance their knowledge, skills, and therefore enhance the standard of education. Researchers have found that student engagement, achievement and motivation are enhanced through integration of such technologies. However, education systems still face many challenges: one of these challenges is how to enhance student engagement to provide better educational outcomes. It has become increasingly important to use innovative pedagogical models to engage learners. Digital storytelling is one of the innovative pedagogical approaches that can engage students in deep and meaningful learning. This research project aimed to create a constructivist learning environment with digital storytelling. The research investigated the pedagogical aspects of digital storytelling and the impact of digital storytelling on student learning when teachers and students use digital stories. A multi-site case study was conducted in one Australian school at primary and secondary levels. In selected classrooms, students and teachers had the opportunity to engage in innovative learning experiences based on digital storytelling. In order to enhance the reliability and validity of the research, multiple methods of data collection and analysis were used. Data was collected with qualitative and quantitative methods. An evaluation rubric was used to collect quantitative data, while interviews and observation were used to collect qualitative data. Data collection was guided by a mixed methods research design in order to evaluate if and how digital storytelling enhances teaching and learning outcomes. The findings from this study suggest that digital storytelling is a powerful tool to integrate instructional messages with learning activities to create more engaging and exciting learning environments. It is a meaningful approach for creating a constructivist learning environment based on novel principles of teaching and learning. Thus, this approach has the potential to enhance student engagement and provide better educational outcomes for learners

Seasonal Climate Effects Anemotaxis in Newly Emerged Adult Anopheles gambiae Giles in Mali, West Africa

The direction and magnitude of movement by the malaria vector Anopheles gambiae Giles has been of great interest to medical entomologists for over 70 years. This direction of movement is likely to be affected by many factors, from environmental conditions and stage of life history of the mosquito to the existence of attractants in the vicinity. We report here the direction of movement of newly emerged An. gambiae in nature, around the village of Donéguébougou, Mali. We assessed the direction of movement for individual mosquitoes by placing them in a novel enclosure with exit traps oriented in the direction of the cardinal and intermediate points of the compass. We consistently found predominantly Southward directions of movement during 2009 and 2010, with an additional Eastward component during the dry season and a Westward one during the wet season. Our data indicate that wind has an important effect on the direction of movement, but that this effect varied by season: Average directions of movement were downwind during the dry season and upwind during the wet season. A switch in anemotactic response suggests that the direction of movement of An. gambiae relative to the wind immediately after emergence under varying conditions of humidity should be further investigated under controlled conditions

The willingness of final year medical and dental students to perform bystander cardiopulmonary resuscitation in an Asian community

Background Despite the importance of early effective chest compressions to improve the chance of survival of an out-of-hospital cardiac arrest victim, it is still largely unknown how willing our Malaysian population is to perform bystander cardiopulmonary resuscitation (CPR). Aims We conducted a voluntary, anonymous self-administered questionnaire survey of a group of 164 final year medical students and 60 final year dental students to unravel their attitudes towards performing bystander CPR. Methods Using a 4-point Likert scale of “definitely yes,” “probably yes,” “probably no,” and “definitely no,” the students were asked to rate their willingness to perform bystander CPR under three categories: chest compressions with mouth-to-mouth ventilation (CC + MMV), chest compressions with mask-to-mouth ventilation (CC + PMV), and chest compressions only (CC). Under each category, the students were given ten hypothetical victim scenarios. Categorical data analysis was done using the McNemar test, chi-square test, and Fisher exact test where appropriate. For selected analysis, “definitely yes” and “probably yes” were recoded as a “positive response.” Results Generally, we found that only 51.4% of the medical and 45.5% of the dental students are willing to perform bystander CPR. When analyzed under different hypothetical scenarios, we found that, except for the scenario where the victim is their own family member, all other scenarios showed a dismally low rate of positive responses in the category of CC + MMV, but their willingness was significantly improved under the CC + PMV and CC categories. Conclusion This study shows that there are unique sociocultural factors that contribute to the reluctance of our students to perform CC + MMV. Keywords Cardiopulmonary resuscitation Mouth-to-mouth resuscitation Basic cardiac life support Asian communit

Evidence for modulation of pericryptal sheath myofibroblasts in rat descending colon by Transforming Growth Factor β and Angiotensin II.

BACKGROUND: Absorption of water and Na(+) in descending colonic crypts is dependent on the barrier function of the surrounding myofibroblastic pericryptal sheath. Here the effects of high and low Na(+) diets and exposure to whole body ionising radiation on the growth and activation of the descending colonic pericryptal myofibroblasts are evaluated. In addition the effect of a post-irradiation treatment with the angiotensin converting enzyme inhibitor Captopril was investigated. METHODS: The levels of Angiotensin II type 1 receptor (AT1), ACE, collagen type IV, transforming growth factor-β type 1 receptor (TGF-βR1), OB cadherin and α-smooth muscle actin in both descending colon and caecum were evaluated, using immunocytochemistry and confocal microscopy, in rats fed on high and low Na(+) diets (LS). These parameters were also determined during 3 months post-irradiation with 8Gy from a (60)Co source in the presence and absence of the angiotensin converting enzyme inhibitor, Captopril. RESULTS: Increases in AT1 receptor (135.6% ± 18.3, P < 0.001); ACE (70.1% ± 13.1, P < 0.001); collagen type IV (49.6% ± 15.3, P < 0.001); TGF-β1 receptors (291.0% ± 26.5, P < 0.001); OB-cadherin (26.3% ± 13.8, P < 0.05) and α-smooth muscle actin (82.5% ± 12.4, P < 0.001) were observed in the pericryptal myofibroblasts of the descending colon after LS diet. There are also increases in AT1 receptor and TGF-β1 receptor, smooth muscle actin and collagen type IV after irradiation. Captopril reduced all these effects of irradiation on the pericryptal sheath and also decreased the amount of collagen and smooth muscle actin in control rats (P < 0.001). CONCLUSIONS: These results demonstrate an activation of descending colonic myofibroblasts to trophic stimuli, or irradiation, which can be attenuated by Captopril, indicative of local trophic control by angiotensin II and TGF-β release

Unraveling the forcings controlling the vegetation and climate of the best orbital analogues for the present interglacial in SW Europe

The suitability of MIS 11c and MIS 19c as analogues of our present interglacial and its natural evolution is still debated. Here we examine the regional expression of the Holocene and its orbital analogues over SW Iberia using a model-data comparison approach. Regional tree fraction and climate based on snapshot and transient experiments using the LOVECLIM model are evaluated against the terrestrial-marine profiles from Site U1385 documenting the regional vegetation and climatic changes. The pollen-based reconstructions show a larger forest optimum during the Holocene compared to MIS 11c and MIS 19c, putting into question their analogy in SW Europe. Pollen-based and model results indicate reduced MIS 11c forest cover compared to the Holocene primarily driven by lower winter precipitation, which is critical for Mediterranean forest development. Decreased precipitation was possibly induced by the amplified MIS 11c latitudinal insolation and temperature gradient that shifted the westerlies northwards. In contrast, the reconstructed lower forest optimum at MIS 19c is not reproduced by the simulations probably due to the lack of Eurasian ice sheets and its related feedbacks in the model. Transient experiments with time-varying insolation and CO2 reveal that the SW Iberian forest dynamics over the interglacials are mostly coupled to changes in winter precipitation mainly controlled by precession, CO2 playing a negligible role. Model simulations reproduce the observed persistent vegetation changes at millennial time scales in SW Iberia and the strong forest reductions marking the end of the interglacial "optimum".SFRH/BD/9079/2012, SFRH/BPD/108712/2015, SFRH/BPD/108600/2015info:eu-repo/semantics/publishedVersio

A Poorly Known High-Latitude Parasitoid Wasp Community: Unexpected Diversity and Dramatic Changes through Time

Climate change will have profound and unanticipated effects on species distributions. The pace and nature of this change is largely unstudied, especially for the most diverse elements of terrestrial communities – the arthropods – here we have only limited knowledge concerning the taxonomy and the ecology of these groups. Because Arctic ecosystems have already experienced significant increases in temperature over the past half century, shifts in community structure may already be in progress. Here we utilise collections of a particularly hyperdiverse insect group – parasitoid wasps (Hymenoptera; Braconidae; Microgastrinae) – at Churchill, Manitoba, Canada in the early and mid-twentieth century to compare the composition of the contemporary community to that present 50–70 years ago. Morphological and DNA barcoding results revealed the presence of 79 species of microgastrine wasps in collections from Churchill, but we estimate that 20% of the local fauna awaits detection. Species composition and diversity between the two time periods differ significantly; species that were most common in historic collections were not found in contemporary collections and vice versa. Using barcodes we compared these collections to others from across North America; contemporary Churchill species are most affiliated with more south-western collections, while historic collections were more affiliated with eastern collections. The past five decades has clearly seen a dramatic change of species composition within the area studied coincident with rising temperature

Ontogeny of juvenile freshwater pearl mussels, Margaritifera margaritifera (Bivalvia: Margaritiferidae).

The gills of juvenile freshwater bivalves undergo a complex morphogenesis that may correlate with changes in feeding ecology, but ontogenic studies on juvenile mussels are rare. Scanning electron microscopy was used to examine the ultrastructure and ontogeny of 117 juvenile freshwater pearl mussels (Margaritifera margaritifera) ranging in age from 1–44 months and length from 0.49–8.90 mm. Three stages of gill development are described. In Stage 1 (5–9 inner demibranch filaments), only unreflected inner demibranch filaments were present. In Stage 2 (9–17 inner demibranch filaments), inner demibranch filaments began to reflect when shell length exceeded 1.13 mm, at 13–16 months old. Reflection began in medial filaments and then proceeded anterior and posterior. In Stage 3 (28–94 inner demibranch filaments), outer demibranch filaments began developing at shell length > 3.1 mm and about 34 months of age. The oral groove on the inner demibranch was first observed in 34 month old specimens > 2.66 mm but was never observed on the outer demibranch. Shell length (R2 = 0.99) was a better predictor of developmental stage compared to age (R2 = 0.84). The full suite of gill ciliation was present on filaments in all stages. Interfilamentary distance averaged 31.3 μm and did not change with age (4–44 months) or with size (0.75–8.9 mm). Distance between laterofrontal cirri couplets averaged 1.54 μm and did not change significantly with size or age. Labial palp primordia were present in even the youngest individuals but ciliature became more diverse in more developed individuals. Information presented here is valuable to captive rearing programmes as it provides insight in to when juveniles may be particularly vulnerable to stressors due to specific ontogenic changes. The data are compared with two other recent studies of Margaritifera development.N/