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المنفى المزدوج : الكتابة في إفريقيا والهند الغربية بين ثقافتين
إيا كان أصل الكتاب الذين يحلل أعمالهم هذا الكتاب، فإنهم جميعا يشتركون في حالة واحدة أدعوها المنفى المزدوج. وعلى الرغم من نشأتهم في بيئة ثقافية مختلفة اختلافا جذريا عن بيئة إنكلترا، فإنهم اختاروا الكتابة باللغة الإنكليزية، وهم لهذا السبب، منفيون ثقافيا عن مصادر تلك اللغة وموروثاتها ومنفيون لغويا عن الأجواء والشعوب التي يكتبون عنها ولما كانت تجارب كتاب أفريقيا وجزر الهند الغربية الذين يستعملون اللغة الإنكليزية مختلفة، فإن هذا الكتاب يعالج منفى مزدوجا بمعنى بسيط جدا.
BOOK
Using single‐cell genomics to understand developmental processes and cell fate decisions
High‐throughput
‐omics
techniques have revolutionised biology, allowing for thorough and unbiased characterisation of the molecular states of biological systems. However, cellular decision‐making is inherently a unicellular process to which “bulk” ‐omics techniques are poorly suited, as they capture ensemble averages of cell states. Recently developed single‐cell methods bridge this gap, allowing high‐throughput molecular surveys of individual cells. In this review, we cover core concepts of analysis of single‐cell gene expression data and highlight areas of developmental biology where single‐cell techniques have made important contributions. These include understanding of cell‐to‐cell heterogeneity, the tracing of differentiation pathways, quantification of gene expression from specific alleles, and the future directions of cell lineage tracing and spatial gene expression analysis.
Graphical Abstract
Single‐cell genomic techniques have advanced our understanding of several developmental processes. This Review summarises advances related to generating and analyzing single‐cell transcriptome data and discusses areas of developmental biology that benefited from such technologies.
Journal Article
Lost kingdoms : Hindu-Buddhist sculpture of early Southeast Asia /
\"Numerous Hindu and Buddhist kingdoms flourished in Southeast Asia from the 5th to the 9th century, yet until recently few concrete details were known about them. Lost Kingdoms reveals newly discovered architectural and sculptural relics from this region, which provide key insights into the formerly mysterious kingdoms. The first publication to use sculpture as a lens to explore this period of Southeast Asian history, Lost Kingdoms offers a significant contribution and a fresh approach to the study of cultures in Cambodia, Thailand, Burma, and other countries\"--Distributor's website.
Book
Seasonal variation in environmental DNA detection in sediment and water samples
The use of aquatic environmental DNA (eDNA) to detect the presence of species depends on the seasonal activity of the species in the sampled habitat. eDNA may persist in sediments for longer than it does in water, and analysing sediment could potentially extend the seasonal window for species assessment. Using the great crested newt as a model, we compare how detection probability changes across the seasons in eDNA samples collected from both pond water and pond sediments. Detection of both aquatic and sedimentary eDNA varied through the year, peaking in the summer (July), with its lowest point in the winter (January): in all seasons, detection probability of eDNA from water exceeded that from sediment. Detection probability of eDNA also varied between study areas, and according to great crested newt habitat suitability and sediment type. As aquatic and sedimentary eDNA show the same seasonal fluctuations, the patterns observed in both sample types likely reflect current or recent presence of the target species. However, given the low detection probabilities found in the autumn and winter we would not recommend using either aquatic or sedimentary eDNA for year-round sampling without further refinement and testing of the methods.
Journal Article
Is the detection of aquatic environmental DNA influenced by substrate type?
The use of environmental DNA (eDNA) to assess the presence-absence of rare, cryptic or invasive species is hindered by a poor understanding of the factors that can remove DNA from the system. In aquatic systems, eDNA can be transported out either horizontally in water flows or vertically by incorporation into the sediment. Equally, eDNA may be broken down by various biotic and abiotic processes if the target organism leaves the system. We use occupancy modelling and a replicated mesocosm experiment to examine how detection probability of eDNA changes once the target species is no longer present. We hypothesise that detection probability falls faster with a sediment which has a large number of DNA binding sites such as topsoil or clay, over lower DNA binding capacity substrates such as sand. Water removed from ponds containing the target species (the great crested newt) initially showed high detection probabilities, but these fell to between 40% and 60% over the first 10 days and to between 10% and 22% by day 15: eDNA remained detectable at very low levels until day 22. Very little difference in detection was observed between the control group (no substrate) and the sand substrate. A small reduction in detection probability was observed between the control and clay substrates, but this was not significant. However, a highly significant reduction in detection probability was observed with a topsoil substrate. This result is likely to have stemmed from increased levels of PCR inhibition, suggesting that incorporation of DNA into the sentiment is of only limited importance. Surveys of aquatic species using eDNA clearly need to take account of substrate type as well as other environmental factors when collecting samples, analysing data and interpreting the results.
Journal Article
Optimising sampling and analysis protocols in environmental DNA studies
Ecological surveys risk incurring false negative and false positive detections of the target species. With indirect survey methods, such as environmental DNA, such error can occur at two stages: sample collection and laboratory analysis. Here we analyse a large qPCR based eDNA data set using two occupancy models, one of which accounts for false positive error by Griffin et al
.
(J R Stat Soc Ser C Appl Stat 69: 377–392, 2020), and a second that assumes no false positive error by Stratton et al
.
(Methods Ecol Evol 11: 1113–1120, 2020). Additionally, we apply the Griffin et al
.
(2020) model to simulated data to determine optimal levels of replication at both sampling stages. The Stratton et al
.
(2020) model, which assumes no false positive results, consistently overestimated both overall and individual site occupancy compared to both the Griffin et al
.
(2020) model and to previous estimates of pond occupancy for the target species. The inclusion of replication at both stages of eDNA analysis (sample collection and in the laboratory) reduces both bias and credible interval width in estimates of both occupancy and detectability. Even the collection of > 1 sample from a site can improve parameter estimates more than having a high number of replicates only within the laboratory analysis.
Journal Article
The Role of Trehalose 6-Phosphate in Crop Yield and Resilience
T6P can be targeted through genetic and chemical methods for crop yield improvements in different environments through the effect of T6P on carbon allocation and biosynthetic pathways.
Journal Article
Detection and removal of barcode swapping in single-cell RNA-seq data
Barcode swapping results in the mislabelling of sequencing reads between multiplexed samples on patterned flow-cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays; however, the severity and consequences of barcode swapping remain poorly understood. We have used two statistical approaches to robustly quantify the fraction of swapped reads in two plate-based single-cell RNA-sequencing datasets. We found that approximately 2.5% of reads were mislabelled between samples on the HiSeq 4000, which is lower than previous reports. We observed no correlation between the swapped fraction of reads and the concentration of free barcode across plates. Furthermore, we have demonstrated that barcode swapping may generate complex but artefactual cell libraries in droplet-based single-cell RNA-sequencing studies. To eliminate these artefacts, we have developed an algorithm to exclude individual molecules that have swapped between samples in 10x Genomics experiments, allowing the continued use of cutting-edge sequencing machines for these assays.
DNA barcode swapping results in mislabelling of sequencing reads between multiplexed samples. Here, the authors investigate the severity and consequences of barcode swapping for single-cell RNA-seq data, and develop a computational method to exclude swapped reads.
Journal Article
A Grassroots Remote Sensing Toolkit Using Live Coding, Smartphones, Kites and Lightweight Drones
This manuscript describes the development of an android-based smartphone application for capturing aerial photographs and spatial metadata automatically, for use in grassroots mapping applications. The aim of the project was to exploit the plethora of on-board sensors within modern smartphones (accelerometer, GPS, compass, camera) to generate ready-to-use spatial data from lightweight aerial platforms such as drones or kites. A visual coding 'scheme blocks' framework was used to build the application ('app'), so that users could customise their own data capture tools in the field. The paper reports on the coding framework, then shows the results of test flights from kites and lightweight drones and finally shows how open-source geospatial toolkits were used to generate geographical information system (GIS)-ready GeoTIFF images from the metadata stored by the app. Two Android smartphones were used in testing-a high specification OnePlus One handset and a lower cost Acer Liquid Z3 handset, to test the operational limits of the app on phones with different sensor sets. We demonstrate that best results were obtained when the phone was attached to a stable single line kite or to a gliding drone. Results show that engine or motor vibrations from powered aircraft required dampening to ensure capture of high quality images. We demonstrate how the products generated from the open-source processing workflow are easily used in GIS. The app can be downloaded freely from the Google store by searching for 'UAV toolkit' (UAV toolkit 2016), and used wherever an Android smartphone and aerial platform are available to deliver rapid spatial data (e.g. in supporting decision-making in humanitarian disaster-relief zones, in teaching or for grassroots remote sensing and democratic mapping).
Journal Article
Effect of Anastomotic Leak on Long-Term Survival After Esophagectomy: Multivariate Meta-analysis and Restricted Mean Survival Times Examination
Background
Anastomotic leak (AL) is a serious complication after esophagectomy. It is associated with prolonged hospital stay, increased costs, and increased risk for 90-day mortality. Controversy exists concerning the impact of AL on survival. This study was designed to investigate the effect of AL on long-term survival after esophagectomy for esophageal cancer.
Methods
PubMed, MEDLINE, Scopus, and Web of Science were searched through October 30, 2022. The included studies evaluated the effect of AL on long-term survival. Primary outcome was long-term overall survival. Restricted mean survival time difference (RMSTD), hazard ratio (HR), and 95% confidence intervals (CI) were used as pooled effect size measures.
Results
Thirteen studies (7118 patients) were included. Overall, 727 (10.2%) patients experienced AL. The RMSTD analysis shows that at 12, 24, 36, 48, and 60 months, patients not experiencing AL live an average of 0.7 (95% CI 0.2–1.2;
p
< 0.001), 1.9 (95% CI 1.1–2.6;
p
< 0.001), 2.6 (95% CI 1.6–3.7;
p
< 0.001), 3.4 (95% CI 1.9–4.9;
p
< 0.001), and 4.2 (95% CI 2.1–6.4;
p
< 0.001) months longer compared with those with AL, respectively. The time-dependent HRs analysis for AL versus no AL shows a higher mortality hazard in patients with AL at 3 (HR 1.94, 95% CI 1.54–2.34), 6 (HR 1.56, 95% CI 1.39–1.75), 12 (HR 1.47, 95% CI 1.24–1.54), and 24 months (HR 1.19, 95% CI 1.02–1.31).
Conclusions
This study seems to suggest a modest clinical impact of AL on long-term OS after esophagectomy. Patients who experience AL seem to have a higher mortality hazard during the first 2 years of follow-up.
Journal Article