Detecting wildlife in unmanned aerial systems imagery using convolutional neural networks trained with an automated feedback loop

Using automated processes to detect wildlife in uncontrolled outdoor imagery in the field of wildlife ecology is a challenging task. This is especially true in imagery provided by an Unmanned Aerial System (UAS), where the relative size of wildlife is small and visually similar to its background. This work presents an automated feedback loop which can be used to train convolutional neural networks with extremely unbalanced class sizes, which alleviates some of these challenges. This work utilizes UAS imagery collected by the Wildlife@Home project, which has employed citizen scientists and trained experts to go through collected UAS imagery and classify it. Classified data is used as inputs to convolutional neural networks (CNNs) which seek to automatically mark which areas of the imagery contain wildlife. The output of the CNN is then passed to a blob counter which returns a population estimate for the image. The feedback loop was developed to help train the CNNs to better differentiate between the wildlife and the visually similar background and deal with the disparate amount of wildlife training images versus background training images. Utilizing the feedback loop dramatically reduced population count error rates from previously published work, from +150% to −3.93% on citizen scientist data and +88% to +5.24% on expert data

Evidence of recent dengue exposure among malaria parasite-positive children in three urban centers in Ghana.

Blood samples of 218 children ages 2-14 years old with confirmed malaria in hospitals across Ghana were tested for dengue virus exposure. We detected dengue-specific immunoglobulin M (IgM) antibodies in 3.2% of the children, indicating possible coinfection, and IgG antibodies in 21.6% of them, which suggests previous exposure. Correlates of exposure are discussed

Computational Identification of Uncharacterized Cruzain Binding Sites

Chagas disease, caused by the unicellular parasite Trypanosoma cruzi, claims 50,000 lives annually and is the leading cause of infectious myocarditis in the world. As current antichagastic therapies like nifurtimox and benznidazole are highly toxic, ineffective at parasite eradication, and subject to increasing resistance, novel therapeutics are urgently needed. Cruzain, the major cysteine protease of Trypanosoma cruzi, is one attractive drug target. In the current work, molecular dynamics simulations and a sequence alignment of a non-redundant, unbiased set of peptidase C1 family members are used to identify uncharacterized cruzain binding sites. The two sites identified may serve as targets for future pharmacological intervention

Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: the PLANET study

Intra-tumor heterogeneity (ITH) is a key challenge in cancer treatment, but previous studies have focused mainly on the genomic alterations without exploring phenotypic (transcriptomic and immune) heterogeneity. Using one of the largest prospective surgical cohorts for Hepatocellular Carcinoma (HCC) with multi-region sampling, we sequenced whole genomes and paired transcriptomes from 67 HCC patients (331 samples). We found that while genomic ITH was rather constant across TNM stages, phenotypic ITH had a very different trajectory and quickly diversified in stage II patients. Most strikingly, 30% patients were found to contain more than one transcriptomic subtype within a single tumor. Such phenotypic ITH was found to be much more informative in predicting patient survival than genomic ITH and explains the poor efficacy of single-target systemic therapies in HCC. Taken together, we not only revealed an unprecedentedly dynamic landscape of phenotypic heterogeneity in HCC, but also highlighted the importance of studying phenotypic evolution across cancer types

Differences between urban and rural hedges in England revealed by a citizen science project

Background: Hedges are oth ecologically and culturally important and are a distinctive feature of the British landscape. However the overall length of hedges across Great Britain is decreasing. Current challenges in studying hedges relate to the dominance of research on rural, as opposed to urban, hedges, and their variability and geographical breadth. To help address these challenges and to educate the public on the importance of hedge habitats for wildlife, in 2010 the Open Air Laboratories (OPAL) programme coordinated a hedge-focused citizen science survey. Results: Results from 2891 surveys were analysed. Woody plant species differed significantly between urban and rural areas. Beech, Holly, Ivy, Laurel, Privet and Yew were more commonly recorded in urban hedges whereas Blackthorn, Bramble, Dog Rose, Elder and Hawthorn were recorded more often in rural hedges. Urban and rural differences were shown for some groups of invertebrates. Ants, earwigs and shieldbugs were recorded more frequently in urban hedges whereas blowflies, caterpillars, harvestmen, other beetles, spiders and weevils were recorded more frequently in rural hedges. Spiders were the most frequently recorded invertebrate across all surveys. The presence of hard surfaces adjacent to the hedge was influential on hedge structure, number and diversity of plant species, amount of food available for wildlife and invertebrate number and diversity. In urban hedges with one adjacent hard surface, the food available for wildlife was significantly reduced and in rural hedges, one adjacent hard surface affected the diversity of invertebrates. Conclusions: This research highlights that urban hedges may be important habitats for wildlife and that hard surfaces may have an impact on both the number and diversity of plant species and the number and diversity of invertebrates. This study demonstrates that citizen science programmes that focus on hedge surveillance can work and have the added benefit of educating the public on the importance of hedgerow habitats

Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy

Background The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89.6 per cent) compared with that in countries with a middle (753 of 1242, 60.6 per cent; odds ratio (OR) 0.17, 95 per cent c.i. 0.14 to 0.21, P <0001) or low (363 of 860, 422 per cent; OR 008, 007 to 010, P <0.001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference -94 (95 per cent c.i. -11.9 to -6.9) per cent; P <0001), but the relationship was reversed in low-HDI countries (+121 (+7.0 to +173) per cent; P <0001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0.60, 0.50 to 073; P <0.001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.Peer reviewe

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Global variation in anastomosis and end colostomy formation following left-sided colorectal resection

Background End colostomy rates following colorectal resection vary across institutions in high-income settings, being influenced by patient, disease, surgeon and system factors. This study aimed to assess global variation in end colostomy rates after left-sided colorectal resection. Methods This study comprised an analysis of GlobalSurg-1 and -2 international, prospective, observational cohort studies (2014, 2016), including consecutive adult patients undergoing elective or emergency left-sided colorectal resection within discrete 2-week windows. Countries were grouped into high-, middle- and low-income tertiles according to the United Nations Human Development Index (HDI). Factors associated with colostomy formation versus primary anastomosis were explored using a multilevel, multivariable logistic regression model. Results In total, 1635 patients from 242 hospitals in 57 countries undergoing left-sided colorectal resection were included: 113 (6·9 per cent) from low-HDI, 254 (15·5 per cent) from middle-HDI and 1268 (77·6 per cent) from high-HDI countries. There was a higher proportion of patients with perforated disease (57·5, 40·9 and 35·4 per cent; P < 0·001) and subsequent use of end colostomy (52·2, 24·8 and 18·9 per cent; P < 0·001) in low- compared with middle- and high-HDI settings. The association with colostomy use in low-HDI settings persisted (odds ratio (OR) 3·20, 95 per cent c.i. 1·35 to 7·57; P = 0·008) after risk adjustment for malignant disease (OR 2·34, 1·65 to 3·32; P < 0·001), emergency surgery (OR 4·08, 2·73 to 6·10; P < 0·001), time to operation at least 48 h (OR 1·99, 1·28 to 3·09; P = 0·002) and disease perforation (OR 4·00, 2·81 to 5·69; P < 0·001). Conclusion Global differences existed in the proportion of patients receiving end stomas after left-sided colorectal resection based on income, which went beyond case mix alone