University of Amsterdam

About: University of Amsterdam is a education organization based out in Amsterdam, Noord-Holland, Netherlands. It is known for research contribution in the topics: Population & Context (language use). The organization has 59309 authors who have published 140894 publications receiving 5984137 citations. The organization is also known as: UvA & Universiteit van Amsterdam.

Human fetal lymphoid tissue–inducer cells are interleukin 17–producing precursors to RORC + CD127 + natural killer–like cells

Abstract: Mouse lymphoid tissue–inducer (LTi) cells require the transcription factor RORγt. Cupedo's group identifies RORγt+ human LTi cell equivalents as committed natural killer cell precursors, and teams led by Vivier and Diefenbach describe RORγt-expressing interleukin 22–producing natural killer cells in mouse gut. The human body contains over 500 individual lymph nodes, yet the biology of their formation is poorly understood. Here we identify human lymphoid tissue–inducer cells (LTi cells) as lineage-negative RORC+ CD127+ cells with the functional ability to interact with mesenchymal cells through lymphotoxin and tumor necrosis factor. Human LTi cells were committed natural killer (NK) cell precursors that produced interleukin 17 (IL-17) and IL-22. In vitro, LTi cells gave rise to RORC+ CD127+ NK cells that retained the ability to produce IL-17 and IL-22. Postnatally, similar populations of LTi cell–like cells and RORC+ CD127+ NK cells were present in tonsils, and both secreted IL-17 and IL-22 but no interferon-γ. Our data indicate that lymph node organogenesis is controlled by an NK cell precursor population with adaptive immune features and demonstrate a previously unappreciated link between the innate and adaptive immune systems.

The fate of intertidal microphytobenthos carbon: An in situ 13C-labeling study

Abstract: At two intertidal sites (one sandy and one silty, in the Scheldt estuary, The Netherlands), the fate of microphytobenthos was studied through an in situ C-13 pulse- chase experiment. Label was added at the beginning of low tide, and uptake of C-13 by algae was linear during the whole period of tidal exposure (about 27 mg m(-2) h(-1) in the top millimeter at both sites). The C-13 fixed by microphytobenthos was rapidly displaced toward deeper sediment layers (down to 6 cm), in particular at the dynamic, sandy site. The residence times of microphytobenthos with respect to external losses (resuspension and respiration) were about 2.4 and 5.6 d at the sandy and silly stations, respectively. The transfer of carbon from microphytobenthos to benthic consumers was estimated from the appearance of C-13 in bacterial biomarkers, handpicked nematodes, and macrofauna. The incorporation of C-13 into bacterial biomass was quantified by carbon isotope analysis of polar lipid derived fatty acids specific for bacteria. The bacterial polar lipid-derived fatty acids (i14:0, i15:0, a15:0, i16:0, and 18:1 omega 7c) showed rapid, significant transfer from benthic algae to bacteria with maximum labeling after 1 d. Nematodes became enriched after 1 h, and C-13 assimilation increased until day 3. Microphytobenthos carbon entered all heterotrophic components in proportion to heterotrophic biomass distribution (bacteria > macrofauna > meiofauna). Our results indicate a central role for microphytobenthos in moderating carbon flow in coastal sediments. [KEYWORDS: Water marine habitats; microbenthic communities; westerschelde estuary; microbial biomass; epipelic diatoms; ecological role; organic-matter; grazing rates; chlorophyll-a; secret garden]

Antibody tests for identification of current and past infection with SARS‐CoV‐2

Abstract: Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and resulting COVID-19 pandemic present important diagnostic challenges. Several diagnostic strategies are available to identify current infection, rule out infection, identify people in need of care escalation, or to test for past infection and immune response. Serology tests to detect the presence of antibodies to SARS-CoV-2 aim to identify previous SARS-CoV-2 infection, and may help to confirm the presence of current infection. Objectives To assess the diagnostic accuracy of antibody tests to determine if a person presenting in the community or in primary or secondary care has SARS-CoV-2 infection, or has previously had SARS-CoV-2 infection, and the accuracy of antibody tests for use in seroprevalence surveys. Search methods We undertook electronic searches in the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern, which is updated daily with published articles from PubMed and Embase and with preprints from medRxiv and bioRxiv. In addition, we checked repositories of COVID-19 publications. We did not apply any language restrictions. We conducted searches for this review iteration up to 27 April 2020. Selection criteria We included test accuracy studies of any design that evaluated antibody tests (including enzyme-linked immunosorbent assays, chemiluminescence immunoassays, and lateral flow assays) in people suspected of current or previous SARS-CoV-2 infection, or where tests were used to screen for infection. We also included studies of people either known to have, or not to have SARS-CoV-2 infection. We included all reference standards to define the presence or absence of SARS-CoV-2 (including reverse transcription polymerase chain reaction tests (RT-PCR) and clinical diagnostic criteria). Data collection and analysis We assessed possible bias and applicability of the studies using the QUADAS-2 tool. We extracted 2x2 contingency table data and present sensitivity and specificity for each antibody (or combination of antibodies) using paired forest plots. We pooled data using random-effects logistic regression where appropriate, stratifying by time since post-symptom onset. We tabulated available data by test manufacturer. We have presented uncertainty in estimates of sensitivity and specificity using 95% confidence intervals (CIs). Main results We included 57 publications reporting on a total of 54 study cohorts with 15,976 samples, of which 8526 were from cases of SARS-CoV-2 infection. Studies were conducted in Asia (n = 38), Europe (n = 15), and the USA and China (n = 1). We identified data from 25 commercial tests and numerous in-house assays, a small fraction of the 279 antibody assays listed by the Foundation for Innovative Diagnostics. More than half (n = 28) of the studies included were only available as preprints. We had concerns about risk of bias and applicability. Common issues were use of multi-group designs (n = 29), inclusion of only COVID-19 cases (n = 19), lack of blinding of the index test (n = 49) and reference standard (n = 29), differential verification (n = 22), and the lack of clarity about participant numbers, characteristics and study exclusions (n = 47). Most studies (n = 44) only included people hospitalised due to suspected or confirmed COVID-19 infection. There were no studies exclusively in asymptomatic participants. Two-thirds of the studies (n = 33) defined COVID-19 cases based on RT-PCR results alone, ignoring the potential for false-negative RT-PCR results. We observed evidence of selective publication of study findings through omission of the identity of tests (n = 5). We observed substantial heterogeneity in sensitivities of IgA, IgM and IgG antibodies, or combinations thereof, for results aggregated across different time periods post-symptom onset (range 0% to 100% for all target antibodies). We thus based the main results of the review on the 38 studies that stratified results by time since symptom onset. The numbers of individuals contributing data within each study each week are small and are usually not based on tracking the same groups of patients over time. Pooled results for IgG, IgM, IgA, total antibodies and IgG/IgM all showed low sensitivity during the first week since onset of symptoms (all less than 30.1%), rising in the second week and reaching their highest values in the third week. The combination of IgG/IgM had a sensitivity of 30.1% (95% CI 21.4 to 40.7) for 1 to 7 days, 72.2% (95% CI 63.5 to 79.5) for 8 to 14 days, 91.4% (95% CI 87.0 to 94.4) for 15 to 21 days. Estimates of accuracy beyond three weeks are based on smaller sample sizes and fewer studies. For 21 to 35 days, pooled sensitivities for IgG/IgM were 96.0% (95% CI 90.6 to 98.3). There are insufficient studies to estimate sensitivity of tests beyond 35 days post-symptom onset. Summary specificities (provided in 35 studies) exceeded 98% for all target antibodies with confidence intervals no more than 2 percentage points wide. False-positive results were more common where COVID-19 had been suspected and ruled out, but numbers were small and the difference was within the range expected by chance. Assuming a prevalence of 50%, a value considered possible in healthcare workers who have suffered respiratory symptoms, we would anticipate that 43 (28 to 65) would be missed and 7 (3 to 14) would be falsely positive in 1000 people undergoing IgG/IgM testing at days 15 to 21 post-symptom onset. At a prevalence of 20%, a likely value in surveys in high-risk settings, 17 (11 to 26) would be missed per 1000 people tested and 10 (5 to 22) would be falsely positive. At a lower prevalence of 5%, a likely value in national surveys, 4 (3 to 7) would be missed per 1000 tested, and 12 (6 to 27) would be falsely positive. Analyses showed small differences in sensitivity between assay type, but methodological concerns and sparse data prevent comparisons between test brands. Authors' conclusions The sensitivity of antibody tests is too low in the first week since symptom onset to have a primary role for the diagnosis of COVID-19, but they may still have a role complementing other testing in individuals presenting later, when RT-PCR tests are negative, or are not done. Antibody tests are likely to have a useful role for detecting previous SARS-CoV-2 infection if used 15 or more days after the onset of symptoms. However, the duration of antibody rises is currently unknown, and we found very little data beyond 35 days post-symptom onset. We are therefore uncertain about the utility of these tests for seroprevalence surveys for public health management purposes. Concerns about high risk of bias and applicability make it likely that the accuracy of tests when used in clinical care will be lower than reported in the included studies. Sensitivity has mainly been evaluated in hospitalised patients, so it is unclear whether the tests are able to detect lower antibody levels likely seen with milder and asymptomatic COVID-19 disease. The design, execution and reporting of studies of the accuracy of COVID-19 tests requires considerable improvement. Studies must report data on sensitivity disaggregated by time since onset of symptoms. COVID-19-positive cases who are RT-PCR-negative should be included as well as those confirmed RT-PCR, in accordance with the World Health Organization (WHO) and China National Health Commission of the People's Republic of China (CDC) case definitions. We were only able to obtain data from a small proportion of available tests, and action is needed to ensure that all results of test evaluations are available in the public domain to prevent selective reporting. This is a fast-moving field and we plan ongoing updates of this living systematic review.

Spatially Inhomogeneous Metal-Insulator Transition in Doped Manganites

Abstract: Scanning tunneling spectroscopy was used to investigate single crystals and thin films of La1– x Ca x MnO3(with x of about 0.3), which exhibit colossal magnetoresistance. The different spectroscopic signatures of the insulating (paramagnetic) and metallic (ferromagnetic) phases enable their spatial extent to be imaged down to a lateral scale of the order of 10 nanometers. Above the bulk transition temperature T c, the images show mostly insulating behavior. Below T c, a phase separation is observed where inhomogeneous structures of metallic and more insulating areas coexist and are strongly field dependent in their size and structure. Insulating areas are found to persist far below T c. These results suggest that the transition and the associated magnetoresistance behavior should be viewed as a percolation of metallic ferromagnetic domains.

Plant strategies of manipulating predator- prey interactions through allelochemicals: prospects for application in pest control

Abstract: To understand the role of allelochemicals in predator-prey interactions it is not sufficient to study the behavioral responses of predator and prey. One should elucidate the origin of the allelochemicals and be aware that it may be located at another trophic level. These aspects are reviewed for predator-prey interactions in general and illustrated in detail for interactions between predatory mites and herbivorous mites. In the latter system there is behavioral and chemical evidence for the involvement of the host plant in production of volatile allelochemicals upon damage by the herbivores with the consequence of attracting predators. These volatiles not only influence predator behavior, but also prey behavior and even the attractiveness of nearby plants to predators. Herbivorous mites disperse away from places with high concentrations of the volatiles, and undamaged plants attract more predators when previously exposed to volatiles from infested conspecific plants rather than from uninfested plants. The latter phenomenon may well be an example of plant-to-plant communication. The involvement of the host plant is probably not unique to the predator-herbivore-plant system under study. It may well be widespread since it makes sense from an evolutionary point of view. If so, prospects for application in pest control are wide open. These are discussed, and it is concluded that crop protection in the future should include tactics whereby man becomes an ally to plants in their strategies to manipulate predator-prey interactions through allelochemicals.