Geographic distribution of tree species occurring in the region of Manaus, Brazil: implications for regional diversity and conservation

The alpha-diversity of trees found in the region of Manaus, Brazil is among the highest recorded for one-hectare plots in Amazonia or any tropical forest. Based on a survey of the distributions of 2541 Neotropical tree species, we analyzed the geographic distribution of 364 species of terra firme forest trees that occur in the region and that are not edaphic specialists. Fifteen distinct distribution patterns were recognized for trees occurring in Manaus. The great majority of species (84.9%) have continuous, somewhat restricted distributions, 35 (9.6%) show broad distributions and 20 species (5.5%) show disjunction between Amazonia and Eastern Brazil. A remarkable 150 (41.2%) of these species showed the region of Manaus as one of their distribution limits. Using the same pool of 2541 species distributions, the percentage of species with a distribution limit in Manaus was compared with that for other localities known to be centers of botanical collection. The null hypothesis that the difference in proportion of species with distribution limits among these localities and Manaus is insignificant was rejected. We conclude that the results are not an artifact of collecting density, that Manaus is indeed a crossroads of distinct phytogeographic regions, and that this explains part of the high species diversity of trees in the region of Manaus. A number of scenarios proposed for the Pleistocene in Amazonia postulate some degree of fragmentation of Amazonian forests or at least populations. As much as these theories may conflict with each other in some respects, they are compatible with the concept of Manaus as a region of re-convergence of isolated or disrupted floras and faunas. The significance of the vicinity of Manaus in the history of the Amazon flora and its current status as a repository for surprisingly high tree diversity highlights the need to make this region a conservation priority.     

Evolution of the Hepatitis C Virus Second Envelope Protein Hypervariable Region in Chronically Infected Patients Receiving Alpha Interferon Therapy

Sustained hepatitis C virus (HCV) RNA clearance is achieved in 8 to 12% of patients with chronic HCV infection treated with alpha interferon (IFN-alpha) at the approved dose of 3 MU three times a week for 6 months and in about 25% of those receiving this treatment for 12 months. We used single-strand conformation polymorphism analysis combined with cloning and sequencing strategies to characterize the genetic evolution of HCV second envelope gene hypervariable region 1 (HVR1) quasispecies during and after IFN therapy in patients who failed to clear HCV RNA. Sustained HCV RNA clearance was achieved in 6% of patients. Profound changes in HVR1 quasispecies major variants were estimated to occur in 70% of the patients during and after therapy. These changes were evolutionary and were characterized by shifts in the virus population, related to selection and subsequent diversification of minor pretreatment variants. The quasispecies changes appeared to be induced by changes in the host environment likely resulting from the IFN-induced enhancement and post-IFN attenuation of neutralizing and possibly cytotoxic responses against HVR1. The remaining patients had no apparent changes in HVR1 quasispecies major variants, suggesting selection of major pretreatment variants, but some changes were observed in other genomic regions. We conclude that IFN-alpha administration and withdrawal profoundly alters the nature of circulating HCV quasispecies, owing to profound changes in virus-host interactions, in patients in whom sustained HCV RNA clearance fails to occur. These changes are associated with profound alterations of the natural outcome of HCV-related liver disease, raising the hypothesis of a causal relationship.     

Identifying mismatches between conservation area networks and vulnerable populations using spatial randomization

Grassland birds are among the most globally threatened bird groups due to substantial degradation of native grassland habitats. However, the current network of grassland conservation areas may not be adequate for halting population declines and biodiversity loss. Here, we evaluate a network of grassland conservation areas within Wisconsin, U.S.A., that includes both large Focal Landscapes and smaller targeted conservation areas (e.g., Grassland Bird Conservation Areas, GBCAs) established within them. To date, this conservation network has lacked baseline information to assess whether the current placement of these conservation areas aligns with population hot spots of grassland‐dependent taxa. To do so, we fitted data from thousands of avian point‐count surveys collected by citizen scientists as part of Wisconsin''s Breeding Bird Atlas II with multinomial N‐mixture models to estimate habitat–abundance relationships, develop spatially explicit predictions of abundance, and establish ecological baselines within priority conservation areas for a suite of obligate grassland songbirds. Next, we developed spatial randomization tests to evaluate the placement of this conservation network relative to randomly placed conservation networks. Overall, less than 20% of species statewide populations were found within the current grassland conservation network. Spatial tests demonstrated a high representation of this bird assemblage within the entire conservation network, but with a bias toward birds associated with moderately tallgrasses relative to those associated with shortgrasses or tallgrasses. We also found that GBCAs had higher representation at Focal Landscape rather than statewide scales. Here, we demonstrated how combining citizen science data with hierarchical modeling is a powerful tool for estimating ecological baselines and conducting large‐scale evaluations of an existing conservation network for multiple grassland birds. Our flexible spatial randomization approach offers the potential to be applied to other protected area networks and serves as a complementary tool for conservation planning efforts globally.     

Complications after breast reconstruction with alloplastic material in breast cancer patients submitted or not to post mastectomy radiotherapy

Background and purposeBreast reconstruction following mastectomy is a relevant element of breast cancer treatment. The purpose of this study was to evaluate the influence of radiotherapy (RT) on local complications in patients with breast cancer that had undergone breast reconstruction with alloplastic material.Materials and methodsRetrospective study of breast cancer patients submitted to mastectomy and breast reconstruction from 2009 to 2013. Clinical and treatment variables were correlated with early and late complications.Results251 patients were included; mean age was 49.7 (25 to 78) years. Reconstruction was immediate in 94% of the patients, with 88% performed with a temporary tissue expander. Postoperative radiotherapy (RT) was delivered to 167 patients (66.5%). Early complications were present in 26.3% of the patients. Irradiated patients presented 5.4% incidence of late complications versus 2.4% for non-irradiated patients (p = 0.327). Diabetes (OR = 3.41 95% CI: 1.23–9.45, p = 0.018) and high body mass index (BMI) (OR = 2.65; 95% CI: 1.60–4.37, p < 0.0001) were the main risk factors. The overall incidence of late complications was 4.4%, with predominance of severe capsular contracture (8/11). Arterial hypertension (OR = 4.78; 95% CI: 1.97–11.63, p = 0.001), BMI (OR = 0.170; 95% CI: 0.048–0.607, p = 0.006) and implant placement (OR = 3.55; 95% CI: 1.26–9.99, p = 0.016) were related to late complications.ConclusionsThe overall rate of complications was low in this population. Radiotherapy delivery translated into a higher but not statistically significant risk of late complications when compared with the non-irradiated patients. Already well-known clinical risk factors for complications after breast reconstruction were identified.     

Ten simple rules on writing clean and reliable open-source scientific software

Functional, usable, and maintainable open-source software is increasingly essential to scientific research, but there is a large variation in formal training for software development and maintainability. Here, we propose 10 “rules” centered on 2 best practice components: clean code and testing. These 2 areas are relatively straightforward and provide substantial utility relative to the learning investment. Adopting clean code practices helps to standardize and organize software code in order to enhance readability and reduce cognitive load for both the initial developer and subsequent contributors; this allows developers to concentrate on core functionality and reduce errors. Clean coding styles make software code more amenable to testing, including unit tests that work best with modular and consistent software code. Unit tests interrogate specific and isolated coding behavior to reduce coding errors and ensure intended functionality, especially as code increases in complexity; unit tests also implicitly provide example usages of code. Other forms of testing are geared to discover erroneous behavior arising from unexpected inputs or emerging from the interaction of complex codebases. Although conforming to coding styles and designing tests can add time to the software development project in the short term, these foundational tools can help to improve the correctness, quality, usability, and maintainability of open-source scientific software code. They also advance the principal point of scientific research: producing accurate results in a reproducible way. In addition to suggesting several tips for getting started with clean code and testing practices, we recommend numerous tools for the popular open-source scientific software languages Python, R, and Julia.     

Photo-identification and satellite telemetry connect southern right whales from South Georgia Island (Islas Georgias del Sur) with multiple feeding and calving grounds in the southwest Atlantic

The sub-Antarctic waters of South Georgia Island (Islas Georgias del Sur, SG/IG) are a regularly visited feeding ground for southern right whales (Eubalaena australis, SRW) in the southwest Atlantic. Satellite telemetry and photo-identification records were compared to better understand the role of SG/IG in the SRW migratory network. We present the first insights from SRW satellite-tracked from the SG/IG feeding ground, habitat use patterns in the Scotia Arc, and movements to Antarctic habitats. Photo-identification comparisons to calving and feeding areas across the South Atlantic and a review of sightings of cetaceans reported from Bird Island (west of SG/IG) since 1979 illuminate long-term habitat use patterns in SG/IG. We present the first recorded migratory movement between SG/IG and multiple countries: Argentina, Uruguay, and Brazil. Photo-identification (1) linked SG/IG to a female SRW with a long-term sighting history in Brazil, and (2) provided the first match between SG/IG and the western Antarctic Peninsula, suggesting the latter could extend the feeding area for southwest Atlantic SRW. Satellite tracking and opportunistic sightings suggest that shelf and coastal waters west of SG/IG represent an important multi-season SRW feeding habitat and add to our overall understanding of habitats and ranges occupied by recovering southwest Atlantic SRW.     

popharvest: An R package to assess the sustainability of harvesting regimes of bird populations

Bird harvest for recreational purposes or as a source for food is an important activity worldwide. Assessing or mitigating the impact of these additional sources of mortality on bird populations is therefore crucial issue. The sustainability of harvest levels is however rarely documented, because knowledge of their population dynamics remains rudimentary for many bird species. Some helpful approaches using limited demographic data can be used to provide initial assessment of the sustainable use of harvested bird populations, and help adjusting harvest levels accordingly. The Demographic Invariant Method (DIM) is used to detect overharvesting. In complement, the Potential Take Level (PTL) approach may allow setting a level of take with regard to management objectives and/or to assess whether current harvest levels meet these objectives. Here, we present the R package popharvest that implements these two approaches in a simple and straightforward way. The package provides users with a set of flexible functions whose arguments can be adapted to existing knowledge about population dynamics. Also, popharvest enables users to test scenarios or propagate uncertainty in demographic parameters to the assessment of sustainability through easily programming Monte Carlo simulations. The simplicity of the package makes it a useful toolbox for wildlife managers or policymakers. This paper provides them with backgrounds about the DIM and PTL approaches and illustrates the use of popharvest''s functionalities in this context.     

Chronic wounds in Sierra Leone: Searching for Buruli ulcer,a NTD caused by Mycobacterium ulcerans,at Masanga Hospital

BackgroundChronic wounds pose a significant healthcare burden in low- and middle-income countries. Buruli ulcer (BU), caused by Mycobacterium ulcerans infection, causes wounds with high morbidity and financial burden. Although highly endemic in West and Central Africa, the presence of BU in Sierra Leone is not well described. This study aimed to confirm or exclude BU in suspected cases of chronic wounds presenting to Masanga Hospital, Sierra Leone.MethodologyDemographics, baseline clinical data, and quality of life scores were collected from patients with wounds suspected to be BU. Wound tissue samples were acquired and transported to the Swiss Tropical and Public Health Institute, Switzerland, for analysis to detect Mycobacterium ulcerans using qPCR, microscopic smear examination, and histopathology, as per World Health Organization (WHO) recommendations.FindingsTwenty-one participants with wounds suspected to be BU were enrolled over 4-weeks (Feb-March 2019). Participants were predominantly young working males (62% male, 38% female, mean 35yrs, 90% employed in an occupation or as a student) with large, single, ulcerating wounds (mean diameter 9.4cm, 86% single wound) exclusively of the lower limbs (60% foot, 40% lower leg) present for a mean 15 months. The majority reported frequent exposure to water outdoors (76%). Self-reports of over-the-counter antibiotic use prior to presentation was high (81%), as was history of trauma (38%) and surgical interventions prior to enrolment (48%). Regarding laboratory investigation, all samples were negative for BU by microscopy, histopathology, and qPCR. Histopathology analysis revealed heavy bacterial load in many of the samples. The study had excellent participant recruitment, however follow-up proved difficult.ConclusionsBU was not confirmed as a cause of chronic ulceration in our cohort of suspected cases, as judged by laboratory analysis according to WHO standards. This does not exclude the presence of BU in the region, and the definitive cause of these treatment-resistance chronic wounds is uncertain.