ALVIN dives on the continental margin off the southeastern United States, July 2-13, 1967

Originally issued as Reference No. 67-80, series later renamed WHOI-In late June and July, 1967, the Deep Submergence Research Vehicle (DSRV) ALVIN, aboard its mother snip, LULU, proceeded from the spring base of operations, Nassau, to its home port of Woods Hole. During this trip, from July 2 to July 14, a series of five dives were made by ALVIN on the Blake Plateau off Georgia and South Carolina, and on the continental slope north of Cape Hatteras.U.S. Geological Survey Contracts 14-08-0001-10875 Nonr-3484(00)

Modelling the Health and Economic Impacts of Population-Wide Testing, Contact Tracing and Isolation (PTTI) Strategies for COVID-19 in the UK

Background: The COVID-19 epidemic in the UK has resulted in over 280,000 reported cases and over 40,000 deaths as of 5th June 2020. In the context of a slower increase in reported cases and deaths associated with COVID-19 over the last few weeks compared to earlier in the epidemic, the UK is starting to relax the physical restrictions (‘lockdown’) that have been imposed since 23 March 2020. This has been accompanied by the announcement of a strategy to test people for infection, trace contacts of those tested positive, and isolate positive diagnoses. While such policies are expected to be impactful, there is no conclusive evidence of which approach to this is likely to achieve the most appropriate balance between benefits and costs. This study combines mathematical and economic modelling to estimate the impact, costs, feasibility, and health and economic effects of different strategies. / Methods: We provide detailed description, impact, costing, and feasibility assessment of population-scale testing, tracing, and isolation strategies (PTTI). We estimate the impact of different PTTI strategies with a deterministic mathematical model for SARS-CoV-2 transmission that accurately captures tracing and isolation of contacts of individuals exposed, infectious, and diagnosed with the virus. We combine this with an economic model to project the mortality, intensive care, hospital, and non-hospital case outcomes, costs to the UK National Health Service, reduction in GDP, and intervention costs of each strategy. Model parameters are derived from publicly available data, and the model is calibrated to reported deaths associated with COVID-19. We modelled 31 scenarios in total (Panel 2). The first 18 comprised nine with ‘triggers’ (labelled with the -Trig suffix) for subsequent lockdown periods (>40,000 new infections per day) and lockdown releases (<10,000 new infections per day), and nine corresponding scenarios without triggers, namely: no large-scale PTTI (scenario 1); scale-up of PTTI to testing the whole population every week, with May–July 2020 lockdown release (scenario 2b), or delayed lockdown release until scale-up complete on 31 August 2020 (scenario 2a); these two scenarios with mandatory use of face coverings (scenarios 3a and 3b); and scenarios 2a, 2b, 3a, 3b replacing untargeted PTTI with testing of symptomatic people only (scenarios 4a, 4b, 4c, 4d). The final 13 scenarios looked at: whole population weekly testing to suppress the epidemic with lower tracing success (scenarios 3b-Trig00, 3b-Trig10, 3b-Trig20, 3b-Trig30) and switched to targeted testing after two months when it may suppress the epidemic (scenarios 3b-Trig00-2mo and 3b-Trig30-2mo), and targeted testing with lower tracing success (scenarios 4d-Trig10, 4dTrig20, 4d-Trig30, 4d-Trig40, 4d-Trig50, 4d-Trig60, 4d-Trig70). / Findings: Given that physical distancing measures have already been relaxed in the UK, scenario 4d-Trig (targeted testing of symptomatic people only, with a mandatory face coverings policy and subsequent lockdown triggered to enable PTTI to suppress the epidemic), is a strategy that will result in the fewest deaths (~52,000) and has the lowest intervention costs (~£8bn). The additional lockdown results in total reduction in GDP of ~£503bn, less than half the cost to the economy of subsequent lockdowns triggered in a scenario without PTTI (scenario 1-Trig, ~£1180bn reduction in GDP, ~105,000 deaths). In summer months, with lower cold and flu prevalence, approximately 75,000 symptomatic people per day need to be tested for this strategy to work, assuming 64% of their contacts are effectively traced (~80% traced with 80% success) within the infectious period (most within the first two days and nearly all by seven days) and all are isolated – including those without any symptoms – for 14 days. Untargeted testing of everyone every week, if it were feasible, may work without tracing, but at a higher cost (scenario 3b-Trig00). This cost could be reduced by switching to targeted testing after the epidemic is suppressed (scenario 3b-Trig30-2mo), though we note the epidemic could be suppressed with targeted testing itself providing tracing and isolation has at least a 32% success rate (scenario 4dTrig40). / Interpretation: PTTI strategies to suppress the COVID-19 epidemic within the context of a relaxation of lockdown will necessitate subsequent lockdowns to keep the epidemic suppressed during PTTI scale-up. Targeted testing of symptomatic people only can suppress the epidemic if accompanied by mandated use of face coverings. The feasibility of PTTI depends on sufficient capacity, capabilities, infrastructure and integrated systems to deliver it. The political and public acceptability of alternative scenarios for subsequent lockdowns needs to take account of crucial implications for employment, personal and national debt, education, population mental health and non-COVID-19 disease. Our model is able to incorporate additional scenarios as the situation evolves

Temporal Analysis of Meiotic DNA Double-Strand Break Formation and Repair in Drosophila Females

Using an antibody against the phosphorylated form of His2Av (γ-His2Av), we have described the time course for the series of events leading from the formation of a double-strand break (DSB) to a crossover in Drosophila female meiotic prophase. MEI-P22 is required for DSB formation and localizes to chromosomes prior to γ-His2Av foci. Drosophila females, however, are among the group of organisms where synaptonemal complex (SC) formation is not dependent on DSBs. In the absence of two SC proteins, C(3)G and C(2)M, the number of DSBs in oocytes is significantly reduced. This is consistent with the appearance of SC protein staining prior to γ-His2Av foci. However, SC formation is incomplete or absent in the neighboring nurse cells, and γ-His2Av foci appear with the same kinetics as in oocytes and do not depend on SC proteins. Thus, competence for DSB formation in nurse cells occurs with a specific timing that is independent of the SC, whereas in the oocytes, some SC proteins may have a regulatory role to counteract the effects of a negative regulator of DSB formation. The SC is not sufficient for DSB formation, however, since DSBs were absent from the heterochromatin even though SC formation occurs in these regions. All γ-His2Av foci disappear before the end of prophase, presumably as repair is completed and crossovers are formed. However, oocytes in early prophase exhibit a slower response to X-ray–induced DSBs compared to those in the late pachytene stage. Assuming all DSBs appear as γ-His2Av foci, there is at least a 3:1 ratio of noncrossover to crossover products. From a comparison of the frequency of γ-His2Av foci and crossovers, it appears that Drosophila females have only a weak mechanism to ensure a crossover in the presence of a low number of DSBs

Meiosis in Mice without a Synaptonemal Complex

The synaptonemal complex (SC) promotes fusion of the homologous chromosomes (synapsis) and crossover recombination events during meiosis. The SC displays an extensive structural conservation between species; however, a few organisms lack SC and execute meiotic process in a SC-independent manner. To clarify the SC function in mammals, we have generated a mutant mouse strain (Sycp1−/−Sycp3−/−, here called SC-null) in which all known SC proteins have been displaced from meiotic chromosomes. While transmission electron microscopy failed to identify any remnants of the SC in SC-null spermatocytes, neither formation of the cohesion axes nor attachment of the chromosomes to the nuclear membrane was perturbed. Furthermore, the meiotic chromosomes in SC-null meiocytes achieved pre-synaptic pairing, underwent early homologous recombination events and sustained a residual crossover formation. In contrast, in SC-null meiocytes synapsis and MLH1-MLH3-dependent crossovers maturation were abolished, whereas the structural integrity of chromosomes was drastically impaired. The variable consequences that SC inactivation has on the meiotic process in different organisms, together with the absence of SC in some unrelated species, imply that the SC could have originated independently in different taxonomic groups

Long term records of erosional change from marine ferromanganese crusts

Ferromanganese crusts from the Atlantic, Indian and Pacific Oceans record the Nd and Pb isotope compositions of the water masses from which they form as hydrogenous precipitates. The10Be/9Be-calibrated time series for crusts are compared to estimates based on Co-contents, from which the equatorial Pacific crusts studied are inferred to have recorded ca. 60 Ma of Pacific deep water history. Time series of ɛNd show that the oceans have maintained a strong provinciality in Nd isotopic composition, determined by terrigenous inputs, over periods of up to 60 Ma. Superimposed on the distinct basin-specific signatures are variations in Nd and Pb isotope time series which have been particularly marked over the last 5 Ma. It is shown that changes in erosional inputs, particularly associated with Himalayan uplift and the northern hemisphere glaciation have influenced Indian and Atlantic Ocean deep water isotopic compositions respectively. There is no evidence so far for an imprint of the final closure of the Panama Isthmus on the Pb and Nd isotopic composition in either Atlantic or Pacific deep water masses

corona Is Required for Higher-Order Assembly of Transverse Filaments into Full-Length Synaptonemal Complex in Drosophila Oocytes

The synaptonemal complex (SC) is an intricate structure that forms between homologous chromosomes early during the meiotic prophase, where it mediates homolog pairing interactions and promotes the formation of genetic exchanges. In Drosophila melanogaster, C(3)G protein forms the transverse filaments (TFs) of the SC. The N termini of C(3)G homodimers localize to the Central Element (CE) of the SC, while the C-termini of C(3)G connect the TFs to the chromosomes via associations with the axial elements/lateral elements (AEs/LEs) of the SC. Here, we show that the Drosophila protein Corona (CONA) co-localizes with C(3)G in a mutually dependent fashion and is required for the polymerization of C(3)G into mature thread-like structures, in the context both of paired homologous chromosomes and of C(3)G polycomplexes that lack AEs/LEs. Although AEs assemble in cona oocytes, they exhibit defects that are characteristic of c(3)G mutant oocytes, including failure of AE alignment and synapsis. These results demonstrate that CONA, which does not contain a coiled coil domain, is required for the stable ‘zippering’ of TFs to form the central region of the Drosophila SC. We speculate that CONA's role in SC formation may be similar to that of the mammalian CE proteins SYCE2 and TEX12. However, the observation that AE alignment and pairing occurs in Tex12 and Syce2 mutant meiocytes but not in cona oocytes suggests that the SC plays a more critical role in the stable association of homologs in Drosophila than it does in mammalian cells

Justify your alpha

Benjamin et al. proposed changing the conventional “statistical significance” threshold (i.e.,the alpha level) from p ≤ .05 to p ≤ .005 for all novel claims with relatively low prior odds. They provided two arguments for why lowering the significance threshold would “immediately improve the reproducibility of scientific research.” First, a p-value near .05provides weak evidence for the alternative hypothesis. Second, under certain assumptions, an alpha of .05 leads to high false positive report probabilities (FPRP2 ; the probability that a significant finding is a false positive

Correction for Johansson et al., An open challenge to advance probabilistic forecasting for dengue epidemics.

Correction for “An open challenge to advance probabilistic forecasting for dengue epidemics,” by Michael A. Johansson, Karyn M. Apfeldorf, Scott Dobson, Jason Devita, Anna L. Buczak, Benjamin Baugher, Linda J. Moniz, Thomas Bagley, Steven M. Babin, Erhan Guven, Teresa K. Yamana, Jeffrey Shaman, Terry Moschou, Nick Lothian, Aaron Lane, Grant Osborne, Gao Jiang, Logan C. Brooks, David C. Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni Rosenfeld, Justin Lessler, Nicholas G. Reich, Derek A. T. Cummings, Stephen A. Lauer, Sean M. Moore, Hannah E. Clapham, Rachel Lowe, Trevor C. Bailey, Markel García-Díez, Marilia Sá Carvalho, Xavier Rodó, Tridip Sardar, Richard Paul, Evan L. Ray, Krzysztof Sakrejda, Alexandria C. Brown, Xi Meng, Osonde Osoba, Raffaele Vardavas, David Manheim, Melinda Moore, Dhananjai M. Rao, Travis C. Porco, Sarah Ackley, Fengchen Liu, Lee Worden, Matteo Convertino, Yang Liu, Abraham Reddy, Eloy Ortiz, Jorge Rivero, Humberto Brito, Alicia Juarrero, Leah R. Johnson, Robert B. Gramacy, Jeremy M. Cohen, Erin A. Mordecai, Courtney C. Murdock, Jason R. Rohr, Sadie J. Ryan, Anna M. Stewart-Ibarra, Daniel P. Weikel, Antarpreet Jutla, Rakibul Khan, Marissa Poultney, Rita R. Colwell, Brenda Rivera-García, Christopher M. Barker, Jesse E. Bell, Matthew Biggerstaff, David Swerdlow, Luis Mier-y-Teran-Romero, Brett M. Forshey, Juli Trtanj, Jason Asher, Matt Clay, Harold S. Margolis, Andrew M. Hebbeler, Dylan George, and Jean-Paul Chretien, which was first published November 11, 2019; 10.1073/pnas.1909865116. The authors note that the affiliation for Xavier Rodó should instead appear as Catalan Institution for Research and Advanced Studies (ICREA) and Climate and Health Program, Barcelona Institute for Global Health (ISGlobal). The corrected author and affiliation lines appear below. The online version has been corrected

Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila

Background The synaptonemal complex (SC) is a highly conserved meiotic structure that functions to pair homologs and facilitate meiotic recombination in most eukaryotes. Five Drosophila SC proteins have been identified and localized within the complex: C(3)G, C(2)M, CONA, ORD, and the newly identified Corolla. The SC is required for meiotic recombination in Drosophila and absence of these proteins leads to reduced crossing over and chromosomal nondisjunction. Despite the conserved nature of the SC and the key role that these five proteins have in meiosis in D. melanogaster, they display little apparent sequence conservation outside the genus. To identify factors that explain this lack of apparent conservation, we performed a molecular evolutionary analysis of these genes across the Drosophila genus. Results For the five SC components, gene sequence similarity declines rapidly with increasing phylogenetic distance and only ORD and C(2)M are identifiable outside of the Drosophila genus. SC gene sequences have a higher dN/dS (ω) rate ratio than the genome wide average and this can in part be explained by the action of positive selection in almost every SC component. Across the genus, there is significant variation in ω for each protein. It further appears that ω estimates for the five SC components are in accordance with their physical position within the SC. Components interacting with chromatin evolve slowest and components comprising the central elements evolve the most rapidly. Finally, using population genetic approaches, we demonstrate that positive selection on SC components is ongoing. Conclusions SC components within Drosophila show little apparent sequence homology to those identified in other model organisms due to their rapid evolution. We propose that the Drosophila SC is evolving rapidly due to two combined effects. First, we propose that a high rate of evolution can be partly explained by low purifying selection on protein components whose function is to simply hold chromosomes together. We also propose that positive selection in the SC is driven by its sex-specificity combined with its role in facilitating both recombination and centromere clustering in the face of recurrent bouts of drive in female meiosis

Examining the generalizability of research findings from archival data

This initiative examined systematically the extent to which a large set of archival research findings generalizes across contexts. We repeated the key analyses for 29 original strategic management effects in the same context (direct reproduction) as well as in 52 novel time periods and geographies; 45% of the reproductions returned results matching the original reports together with 55% of tests in different spans of years and 40% of tests in novel geographies. Some original findings were associated with multiple new tests. Reproducibility was the best predictor of generalizability-for the findings that proved directly reproducible, 84% emerged in other available time periods and 57% emerged in other geographies. Overall, only limited empirical evidence emerged for context sensitivity. In a forecasting survey, independent scientists were able to anticipate which effects would find support in tests in new samples