Camera traps and genetic identification of faecal samples for detection and monitoring of an Endangered ungulate.

Almost all Indochinese ungulates are classified as globally threatened but efforts to assess and monitor population status have been hampered by their rarity, cryptic nature and uncertainty in accurate identification from sightings. An improved approach is urgently needed to gather information about threatened ungulate species in order to effectively conserve them as, a lack of reliable monitoring methods means that basic information such as population sizes, distribution and habitat associations is currently unknown. Here, we used a combination of camera trapping and genetic detection of the Endangered Eld’s deer, Rucervus eldii, to investigate the utility of these methods to infer intensity of site use within a protected Cambodian dry forest. We asked: 1) Are Eld's deer present in our study area?; 2) How is site use influenced by local habitat?; and 3) Do camera traps or genetic detection perform better in terms of detection and monitoring? Camera traps were deployed and faecal samples collected from Chhaeb Wildlife Sanctuary in Northern Cambodia during the 2017 dry season. Faecal samples were identified as Eld’s deer using newly developed species-specific mitochondrial DNA primers. Camera traps recorded 20 Eld’s deer observations across 3905 trap-nights and 44 out of 71 collected faecal samples, identified by fieldworkers as likely to belong to Eld’s deer, were positively identified to be so. Camera trap surveys and genetic detection demonstrated that Eld’s deer were present in Chhaeb Wildlife Sanctuary, although the number of detections relative to sampling effort was low in both methods (detected at 29% and 1% of sample sites, respectively). Occupancy models showed that water level and tree diameter both had positive relationships, whilst human and domestic or feral pig activity had a negative relationship, with the relative intensity of Eld’s deer site use. Overall, our data suggest that both of our methods can prove effective for monitoring Eld’s deer but that repeated sampling is necessary to account for their low detectability in this area. We suggest that faecal samples are collected during future camera trap monitoring visits to maximise efficiency, increase detectability, and provide the most information to support conservation

The importance of long-term genetic monitoring of reintroduced populations: inbreeding in the natterjack toad (Epidalea calamita)

Genetic monitoring is an important, but frequently lacking, component of management actions to support long-term persistence in reintroduced populations. Populations that remain small, due to demographic processes and genetic diversity, are more likely to experience a second extinction event. The natterjack toad (Epidelea calamita) is legally protected in Britain and was the subject of a reintroduction programme in the 1990s. However, subsequent genetic assessment has been mostly lacking. The aim of this study was to assess the genetic diversity of two reintroduced populations of natterjack toads in order to inform conservation management. Adults were sampled and nine microsatellites amplified to assess neutral genetic variation within each site and for comparison with the source population. Inbreeding was observed at the reintroduction sites, as evidenced by high FIS values (0.43 and 0.72), low observed compared to expected heterozygosities, and significant deviation from Hardy-Weinberg equilibrium. Observed heterozygosity is currently lower in the reintroduction sites than it was in the source population at the time of the reintroductions (Red Rocks: 0.15±0.20; Talacre: 0.12±0.20; Ainsdale (source): 0.29). Evidence for a bottleneck was not found, although this is likely a result of sampling overlapping generations. No within-site population structuring was observed. Such low genetic diversity has not previously been recorded in any natterjack population. Genetic rescue, combined with pool creation, is the most viable option for safeguarding the species at these sites into the future. Our work highlights the importance of ongoing genetic monitoring, in collaboration with conservation organisations, to support conservation management

Camera Traps Confirm the Presence of the White-naped Mangabey Cercocebus lunulatus in Cape Three Points Forest Reserve, Western Ghana

The white-naped mangabey Cercocebus lunulatus is severely threatened by logging, mining, and hunting. In the last decade, wild populations have been confirmed in just three forested areas in Ghana and a handful of sites in neighboring Côte d’Ivoire and Burkina Faso. Sightings of this species were recently reported in a fourth area in Ghana, the Cape Three Points Forest Reserve, a forest patch in western Ghana, 60 km from the nearest recorded wild population, which is in the Ankasa Conservation Area. We deployed 14 camera traps across 21 different locations throughout the reserve, with the intention of confirming the presence of this species. Images of the white-naped mangabey were captured at four locations, consolidating recent evidence for a fourth sub-population of this species in Ghana and providing only the second-ever photograph of a wild member of this species in the country. We observed evidence of numerous illegal anthropogenic activities in the reserve, which threaten these mangabeys, and we make recommendations for the protection of the reserve, essential for the conservation of this highly endangered species

A novel blood proteomic signature for prostate cancer

International audienceSimple Summary Despite intensive research, effective tools for detection and monitoring of prostate cancer remain to be found. Prostate-specific antigen (PSA), commonly used in prostate cancer assessments, can lead to overdiagnosis and overtreatment of indolent disease. This highlights the need for supporting non-invasive diagnostic, prognostic, and disease stratification biomarkers that could complement PSA in clinical decision-taking via increased sensitivity and specificity. In order to address this need, we uncover novel prostate cancer protein signatures by leveraging a cutting-edge analytical technique to measure proteins in patient samples. This strategy was used as a discovery tool to identify changes in protein levels in the serum of newly diagnosed patients as compared with healthy controls; the feature set was then further validated by reference to a second cohort of patients, achieving a high discriminatory ability. The proteomic maps generated also identified relevant changes in biological functions, notably the complement cascade. Prostate cancer is the most common malignant tumour in men. Improved testing for diagnosis, risk prediction, and response to treatment would improve care. Here, we identified a proteomic signature of prostate cancer in peripheral blood using data-independent acquisition mass spectrometry combined with machine learning. A highly predictive signature was derived, which was associated with relevant pathways, including the coagulation, complement, and clotting cascades, as well as plasma lipoprotein particle remodeling. We further validated the identified biomarkers against a second cohort, identifying a panel of five key markers (GP5, SERPINA5, ECM1, IGHG1, and THBS1) which retained most of the diagnostic power of the overall dataset, achieving an AUC of 0.91. Taken together, this study provides a proteomic signature complementary to PSA for the diagnosis of patients with localised prostate cancer, with the further potential for assessing risk of future development of prostate cancer. Data are available via ProteomeXchange with identifier PXD025484

Starting New Accreditation Council for Graduate Medical Education (ACGME) Residency Programs in a Teaching Hospital

Starting a new ACGME approved residency program can positively impact patient care, medical education, hospital operations, and the community as whole. This requires a significant amount of commitment, time, and preparation. The initial application and accreditation process should start early and requires a thorough understanding on the ACGME requirements. Building a new residency program involves collaboration among various stakeholders, starting with the teaching hospital, ACGME, and the Center of Medicare and Medicaid services (CMS). It is prudent to also consider the operational and logistical issues such as budget, faculty and administrative staff hire, faculty time for administrative duties, and educational space for faculty and residents. It is vital to recognize how the institution’s strengths and weaknesses match up to these requirements. A robust educational and clinical curriculum in line with ACGME’s core competencies and useful educational collaboration among various programs is critical for effective program. Recruiting and developing the appropriate faculty members is another important aspect for a successful program. The final challenge is recruiting residents that will fit well into the new residency program. Lastly, we discuss the challenges and tips to mitigate the risks of disappointment in the process of starting and creating a flagship residency program

Survey of Period Variations of Superhumps in SU UMa-Type Dwarf Novae

We systematically surveyed period variations of superhumps in SU UMa-type dwarf novae based on newly obtained data and past publications. In many systems, the evolution of superhump period are found to be composed of three distinct stages: early evolutionary stage with a longer superhump period, middle stage with systematically varying periods, final stage with a shorter, stable superhump period. During the middle stage, many systems with superhump periods less than 0.08 d show positive period derivatives. Contrary to the earlier claim, we found no clear evidence for variation of period derivatives between superoutburst of the same object. We present an interpretation that the lengthening of the superhump period is a result of outward propagation of the eccentricity wave and is limited by the radius near the tidal truncation. We interpret that late stage superhumps are rejuvenized excitation of 3:1 resonance when the superhumps in the outer disk is effectively quenched. Many of WZ Sge-type dwarf novae showed long-enduring superhumps during the post-superoutburst stage having periods longer than those during the main superoutburst. The period derivatives in WZ Sge-type dwarf novae are found to be strongly correlated with the fractional superhump excess, or consequently, mass ratio. WZ Sge-type dwarf novae with a long-lasting rebrightening or with multiple rebrightenings tend to have smaller period derivatives and are excellent candidate for the systems around or after the period minimum of evolution of cataclysmic variables (abridged).Comment: 239 pages, 225 figures, PASJ accepte

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

Qualitative data sharing and re-use for socio-environmental systems research: A synthesis of opportunities, challenges, resources and approaches

Researchers in many disciplines, both social and natural sciences, have a long history of collecting and analyzing qualitative data to answer questions that have many dimensions, to interpret other research findings, and to characterize processes that are not easily quantified. Qualitative data is increasingly being used in socio-environmental systems research and related interdisciplinary efforts to address complex sustainability challenges. There are many scientific, descriptive and material benefits to be gained from sharing and re-using qualitative data, some of which reflect the broader push toward open science, and some of which are unique to qualitative research traditions. However, although open data availability is increasingly becoming an expectation in many fields and methodological approaches that work on socio-environmental topics, there remain many challenges associated the sharing and re-use of qualitative data in particular. This white paper discusses opportunities, challenges, resources and approaches for qualitative data sharing and re-use for socio-environmental research. The content and findings of the paper are a synthesis and extension of discussions that began during a workshop funded by the National Socio-Environmental Synthesis Center (SESYNC) and held at the Center Feb. 28-March 2, 2017. The structure of the paper reflects the starting point for the workshop, which focused on opportunities, challenges and resources for qualitative data sharing, and presents as well the workshop outputs focused on developing a novel approach to qualitative data sharing considerations and creating recommendations for how a variety of actors can further support and facilitate qualitative data sharing and re-use. The white paper is organized into five sections to address the following objectives: (1) Define qualitative data and discuss the benefits of sharing it along with its role in socio-environmental synthesis; (2) Review the practical, epistemological, and ethical challenges regarding sharing such data; (3) Identify the landscape of resources available for sharing qualitative data including repositories and communities of practice (4) Develop a novel framework for identifying levels of processing and access to qualitative data; and (5) Suggest roles and responsibilities for key actors in the research ecosystem that can improve the longevity and use of qualitative data in the future.This work was supported by the National Socio-Environmental Synthesis Center (SESYNC) under funding received from the National Science Foundation DBI-1052875

A call to action for climate change research on Caribbean dry forests

The final publication is available at Springer via https://doi.org/10.1007/s10113-018-1334-6Tropical dry forest (TDF) is globally one of the most threatened forest types. In the insular Caribbean, limited land area and high population pressure have resulted in the loss of over 60% of TDF, yet local people’s reliance on these systems for ecosystem services is high. Given the sensitivity of TDF to shifts in precipitation regimes and the vulnerability of the Caribbean to climate change, this study examined what is currently known about the impacts of climate change on TDF in the region. A systematic review (n = 89) revealed that only two studies addressed the ecological response of TDF to climate change. Compared to the rapidly increasing knowledge of the effects of climate change on other Caribbean systems and on TDF in the wider neotropics, this paucity is alarming given the value of these forests. We stress the need for long-term monitoring of climate change responses of these critical ecosystems, including phenological and hotspot analyses as priorities

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease