Pattern and process in Amazon tree turnover, 1976-2001

Previous work has shown that tree turnover, tree biomass and large liana densities have increased in mature tropical forest plots in the late twentieth century. These results point to a concerted shift in forest ecological processes that may already be having significant impacts on terrestrial carbon stocks, fluxes and biodiversity. However, the findings have proved controversial, partly because a rather limited number of permanent plots have been monitored for rather short periods. The aim of this paper is to characterize regional-scale patterns of 'tree turnover' (the rate with which trees die and recruit into a population) by using improved datasets now available for Amazonia that span the past 25 years. Specifically, we assess whether concerted changes in turnover are occurring, and if so whether they are general throughout the Amazon or restricted to one region or environmental zone. In addition, we ask whether they are driven by changes in recruitment, mortality or both. We find that: (i) trees 10 cm or more in diameter recruit and die twice as fast on the richer soils of southern and western Amazonia than on the poorer soils of eastern and central Amazonia; (ii) turnover rates have increased throughout Amazonia over the past two decades; (iii) mortality and recruitment rates have both increased significantly in every region and environmental zone, with the exception of mortality in eastern Amazonia; (iv) recruitment rates have consistently exceeded mortality rates; (v) absolute increases in recruitment and mortality rates are greatest in western Amazonian sites; and (vi) mortality appears to be lagging recruitment at regional scales. These spatial patterns and temporal trends are not caused by obvious artefacts in the data or the analyses. The trends cannot be directly driven by a mortality driver (such as increased drought or fragmentation-related death) because the biomass in these forests has simultaneously increased. Our findings therefore indicate that long-acting and widespread environmental changes are stimulating the growth and productivity of Amazon forests

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3-prime untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3-prime polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental dataComment: 44 pages, 9 figure

Inheritance of an Epigenetic Mark: The CpG DNA Methyltransferase 1 Is Required for De Novo Establishment of a Complex Pattern of Non-CpG Methylation

Site-specific methylation of cytosines is a key epigenetic mark of vertebrate DNA. While a majority of the methylated residues are in the symmetrical (meC)pG:Gp(meC) configuration, a smaller, but significant fraction is found in the CpA, CpT and CpC asymmetric (non-CpG) dinucleotides. CpG methylation is reproducibly maintained by the activity of the DNA methyltransferase 1 (Dnmt1) on the newly replicated hemimethylated substrates (meC)pG:GpC. On the other hand, establishment and hereditary maintenance of non-CpG methylation patterns have not been analyzed in detail. We previously reported the occurrence of site- and allele-specific methylation at both CpG and non-CpG sites. Here we characterize a hereditary complex of non-CpG methylation, with the transgenerational maintenance of three distinct profiles in a constant ratio, associated with extensive CpG methylation. These observations raised the question of the signal leading to the maintenance of the pattern of asymmetric methylation. The complete non-CpG pattern was reinstated at each generation in spite of the fact that the majority of the sperm genomes contained either none or only one methylated non-CpG site. This observation led us to the hypothesis that the stable CpG patterns might act as blueprints for the maintenance of non-CpG DNA methylation. As predicted, non-CpG DNA methylation profiles were abrogated in a mutant lacking Dnmt1, the enzymes responsible for CpG methylation, but not in mutants defective for either Dnmt3a or Dnmt2

The Tilburg double blind randomised controlled trial comparing inguinal hernia repair according to Lichtenstein and the transinguinal preperitoneal technique

<p>Abstract</p> <p>Background</p> <p>Anterior open treatment of the inguinal hernia with a tension free mesh has reduced the incidence of recurrence and direct postoperative pain. The Lichtenstein procedure rules nowadays as reference technique for hernia treatment. Not recurrences but chronic pain is the main postoperative complication in inguinal hernia repair after Lichtenstein's technique. Preliminary experiences with a soft mesh placed in the preperitoneal space showed good results and less chronic pain.</p> <p>Methods</p> <p>The TULIP is a double-blind randomised controlled trial in which 300 patients will be randomly allocated to anterior inguinal hernia repair according to Lichtenstein or the transinguinal preperitoneal technique with soft mesh. All unilateral primary inguinal hernia patients eligible for operation who meet inclusion criteria will be invited to participate in this trial. The primary endpoint will be direct postoperative- and chronic pain. Secondary endpoints are operation time, postoperative complications, hospital stay, costs, return to daily activities (e.g. work) and recurrence. Both groups will be evaluated.</p> <p>Success rate of hernia repair and complications will be measured as safeguard for quality.</p> <p>To demonstrate that inguinal hernia repair according to the transinguinal preperitoneal (TIPP) technique reduces postoperative pain to <10%, with α = 0,05 and power 80%, a total sample size of 300 patients was calculated.</p> <p>Discussion</p> <p>The TULIP trial is aimed to show a reduction in postoperative chronic pain after anterior hernia repair according to the transinguinal preperitoneal (TIPP) technique, compared to Lichtenstein.</p> <p>In our hypothesis the TIPP technique reduces chronic pain compared to Lichtenstein.</p> <p>Trial registration</p> <p>ISRCTN 93798494</p

J Clin Med

BACKGROUND: During this pandemic situation, some studies have led to hasty conclusions about Corona Virus Disease-19 (COVID-19) treatment, due to a lack of methodology. This pedagogic study aimed to highlight potential biases in research on COVID-19 treatment. METHODS: We evaluate the effect of coffee's active part, 1,3,7-trimethylxanthine (TMX) on patients with COVID-19. A cohort of 93 patients, with a diagnosis of COVID-19 is analyzed. RESULTS: TMX group and control group included, respectively, 26 and 67 patients. In the TMX group, patients had a median length of stay in hospital of 5.5 days shorter than in the control group (9.5 vs. 15 days, p < 0.05). Patients in the control group were more severe than patients in the TMX group with a significantly higher National Early Warning Score 2 (NEWS-2 score) (8 vs. 6, p = 0.002). CONCLUSIONS: Multiple biases prevents us from concluding to an effect of coffee on COVID-19. Despite an important social pressure during this crisis, methodology and conscientiousness are the best way to avoid hasty conclusions that can be deleterious for patients. Identifier: NCT04395742

Variables with time-varying effects and the Cox model: Some statistical concepts illustrated with a prognostic factor study in breast cancer

International audienceBACKGROUND: The Cox model relies on the proportional hazards (PH) assumption, implying that the factors investigated have a constant impact on the hazard - or risk - over time. We emphasize the importance of this assumption and the misleading conclusions that can be inferred if it is violated; this is particularly essential in the presence of long follow-ups. METHODS: We illustrate our discussion by analyzing prognostic factors of metastases in 979 women treated for breast cancer with surgery. Age, tumour size and grade, lymph node involvement, peritumoral vascular invasion (PVI), status of hormone receptors (HRec), Her2, and Mib1 were considered. RESULTS: Median follow-up was 14 years; 264 women developed metastases. The conventional Cox model suggested that all factors but HRec, Her2, and Mib1 status were strong prognostic factors of metastases. Additional tests indicated that the PH assumption was not satisfied for some variables of the model. Tumour grade had a significant time-varying effect, but although its effect diminished over time, it remained strong. Interestingly, while the conventional Cox model did not show any significant effect of the HRec status, tests provided strong evidence that this variable had a non-constant effect over time. Negative HRec status increased the risk of metastases early but became protective thereafter. This reversal of effect may explain non-significant hazard ratios provided by previous conventional Cox analyses in studies with long follow-ups. CONCLUSIONS: Investigating time-varying effects should be an integral part of Cox survival analyses. Detecting and accounting for time-varying effects provide insights on some specific time patterns, and on valuable biological information that could be missed otherwise

Should we welcome robot teachers?

Abstract Current uses of robots in classrooms are reviewed and used to characterise four scenarios: (s1) Robot as Classroom Teacher; (s2) Robot as Companion and Peer; (s3) Robot as Care-eliciting Companion; and (s4) Telepresence Robot Teacher. The main ethical concerns associated with robot teachers are identified as: privacy; attachment, deception, and loss of human contact; and control and accountability. These are discussed in terms of the four identified scenarios. It is argued that classroom robots are likely to impact children’s’ privacy, especially when they masquerade as their friends and companions, when sensors are used to measure children’s responses, and when records are kept. Social robots designed to appear as if they understand and care for humans necessarily involve some deception (itself a complex notion), and could increase the risk of reduced human contact. Children could form attachments to robot companions (s2 and s3), or robot teachers (s1) and this could have a deleterious effect on their social development. There are also concerns about the ability, and use of robots to control or make decisions about children’s behaviour in the classroom. It is concluded that there are good reasons not to welcome fully fledged robot teachers (s1), and that robot companions (s2 and 3) should be given a cautious welcome at best. The limited circumstances in which robots could be used in the classroom to improve the human condition by offering otherwise unavailable educational experiences are discussed

Выращивание из поликристаллического кремния солнечного качества квазимонокристаллических (mono-like) слитков методом направленной кристаллизации

In the frame of permanent objective to increase solar cell efficiency and to decrease production cost the monolike ingot process was designed which combine multicrystalline (mc) productivity and monocrystalline structure performances. As a raw material the mc-Solar Grade silicon (SoG-Si) was used because it is less expensive than the Si purified by gas chemical route (Siemens process or equivalent), Usage of the mc-SoG-Si for growing silicon ingots by monolike process should contribute to the ingot and wafer manufacturing cost decrease. SoG silicon using would be developed all the more fast since it enables to produce high efficiency solar cells. It is why the monolike process have been tested and optimized for Kazakhstan mc-SoG silicon. The objective of this work was study of the higher level content impurities influences on the crystal defect generation (mainly dislocations) of the monocrystalline structure. Visual monocrystalline structure, minority carrier lifetime mapping, and photoluminescence techniques were used to study the monolike ingots obtained from Kazakhstan’s mc-SoG silicon.В целях повышения эффективности солнечных элементов и снижение затрат на производство разработан процесс получения слитков кремния, по так называемой mono-like-технологии. Mono-like-процесс предназначен для получения монокристаллических слитков при использовании технологии производства мультикристаллического кремния (МК-Si). При этом в качестве сырья используют поликристаллический кремний (ПК-Si) «солнечного» качества (solar grade — SoG), технология получения которого является менее затратной, чем очистка кремния газохимическим процессом (Сименс-процесс или его эквивалент). Использование ПК-Si SoG для выращивания слитков по mono-like технологии должно способствовать снижению затрат на получение слитков и пластин. Новые технологии производства солнечных элементов, использующие ПК-Si SoG, разрабатываются быстрыми темпами, так как это позволяет производить при меньших затратах солнечные элементы с достаточно высоким КПД. Именно поэтому mono-like-процесс апробирован и оптимизирован для казахстанского ПК-Si SoG. Изучено влияние более высокой концентрации примесей в ПК-Si SoG на образование кристаллических дефектов (главным образом дислокаций) в монокристаллических структурах. Для исследования свойств mono-like слитка, полученного в промышленных масштабах из казахстанского ПК-Si SoG, использованы визуализация монокристаллической структуры, картирование времени жизни неосновных носителей заряда и фотолюминесценция