COVID-19 testing, timeliness and positivity from ICMR’s laboratory surveillance network in India: Profile of 176 million individuals tested and 188 million tests, March 2020 to January 2021

Background The Indian Council of Medical Research set up a pan-national laboratory network to diagnose and monitor Coronavirus disease 2019 (COVID-19). Based on these data, we describe the epidemiology of the pandemic at national and sub-national levels and the performance of the laboratory network. Methods We included surveillance data for individuals tested and the number of tests from March 2020 to January 2021. We calculated the incidence of COVID-19 by age, gender and state and tests per 100,000 population, the proportion of symptomatic individuals among those tested, the proportion of repeat tests and test positivity. We computed median (Interquartile range—IQR) days needed for selected surveillance activities to describe timeliness. Results The analysis included 176 million individuals and 188 million tests. The overall incidence of COVID-19 was 0.8%, and 12,584 persons per 100,000 population were tested. 6.1% of individuals tested returned a positive result. Ten of the 37 Indian States and Union Territories accounted for about 75.6% of the total cases. Daily testing scaled up from 40,000 initially to nearly one million in March 2021. The median duration between symptom onset and sample collection was two (IQR = 0,3) days, median duration between both sample collection and testing and between testing and data entry were less than or equal to one day. Missing or invalid entries ranged from 0.01% for age to 0.7% for test outcome. Conclusion The laboratory network set-up by ICMR was scaled up massively over a short period, which enabled testing a large section of the population. Although all states and territories were affected, most cases were concentrated in a few large states. Timeliness between the various surveillance activities was acceptable, indicating good responsiveness of the surveillance system.

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Plug-in scripts for EFTEM automation

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100165197 ◽

1996 ◽

Vol 54 ◽

pp. 546-547

Author(s):

N. D. Evans ◽

M. K. Kundmann

Keyword(s):

Electron Microscopy ◽

National Laboratory ◽

Oak Ridge ◽

Multiple User ◽

Transmission Electron ◽

Short Period ◽

User Facility ◽

Instrument Control ◽

And Control ◽

Research Equipment

Post-column energy-filtered transmission electron microscopy (EFTEM) is inherently challenging as it requires the researcher to setup, align, and control both the microscope and the energy-filter. The software behind an EFTEM system is therefore critical to efficient, day-to-day application of this technique. This is particularly the case in a multiple-user environment such as at the Shared Research Equipment (SHaRE) User Facility at Oak Ridge National Laboratory. Here, visiting researchers, who may oe unfamiliar with the details of EFTEM, need to accomplish as much as possible in a relatively short period of time.We describe here our work in extending the base software of a commercially available EFTEM system in order to automate and streamline particular EFTEM tasks. The EFTEM system used is a Philips CM30 fitted with a Gatan Imaging Filter (GIF). The base software supplied with this system consists primarily of two Macintosh programs and a collection of add-ons (plug-ins) which provide instrument control, imaging, and data analysis facilities needed to perform EFTEM.

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Community-based molecular and serological surveillance of subclinical malaria in Myanmar

BMC Medicine ◽

10.1186/s12916-021-01993-8 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Katherine O’Flaherty ◽

Win Han Oo ◽

Sophie G. Zaloumis ◽

Julia C. Cutts ◽

Kyaw Zayar Aung ◽

...

Keyword(s):

Malaria Transmission ◽

Quantitative Polymerase Chain Reaction ◽

Dried Blood Spots ◽

Molecular Testing ◽

Sample Collection ◽

Malaria Surveillance ◽

Surveillance Network ◽

Targeted Interventions ◽

Residual Malaria Transmission ◽

Serological Surveillance

Abstract Background In the Greater Mekong Subregion (GMS), current malaria surveillance strategies rely on a network of village health volunteers (VHVs) reporting the results of rapid diagnostic tests (RDTs), known to miss many asymptomatic infections. Integration of more sensitive diagnostic molecular and serological measures into the VHV network may improve surveillance of residual malaria transmission in hard-to-reach areas in the region and inform targeted interventions and elimination responses. However, data on residual malaria transmission that would be captured by these measures in the VHV-led testing and treatment surveillance network in the GMS is unknown. Methods A total of 114 VHVs were trained to collect dried blood spots from villagers undergoing routine RDTs as part of VHV-led active and passive case detection from April 2015 to June 2016. Samples were subjected to molecular testing (quantitative polymerase chain reaction [qPCR]) to determine Plasmodium falciparum and P. vivax infection and serological testing (against P. falciparum and P. vivax antigens) to determine exposure to P. falciparum and P. vivax. Results Over 15 months, 114 VHVs performed 32,194 RDTs and collected samples for molecular (n = 13,157) and serological (n = 14,128) testing. The prevalence of molecular-detectable P. falciparum and P. vivax infection was 3.2% compared to the 0.16% prevalence of Plasmodium spp. by RDT, highlighting the large burden of infections undetected by standard surveillance. Peaks in anti-P. falciparum, but not P. vivax, merozoite IgG seroprevalence coincided with seasonal P. falciparum transmission peaks, even in those with no molecularly detectable parasites. At the individual level, antibody seropositivity was associated with reduced odds of contemporaneous P. falciparum (OR for PfCSP 0.51 [95%CI 0.35, 0.76], p = 0.001, PfAMA1 0.70 [95%CI 0.52, 0.93], p = 0.01, and PfMSP2 0.81 [95%CI 0.61, 1.08], p = 0.15), but not P. vivax infection (OR PvAMA1 1.02 [95%CI 0.73, 1.43], p = 0.89) indicating a potential role of immunity in protection against molecular-detectable P. falciparum parasitaemia. Conclusions We demonstrated that integration and implementation of sample collection for molecular and serological surveillance into networks of VHV servicing hard-to-reach populations in the GMS is feasible, can capture significant levels of ongoing undetected seasonal malaria transmission and has the potential to supplement current routine RDT testing. Improving malaria surveillance by advancing the integration of molecular and serological techniques, through centralised testing approaches or novel point-of-contact tests, will advance progress, and tracking, towards malaria elimination goals in the GMS.

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Describing the within laboratory and between laboratory agreement of a serum ELISA in a national laboratory network

Preventive Veterinary Medicine ◽

10.1016/j.prevetmed.2011.11.005 ◽

2012 ◽

Vol 104 (3-4) ◽

pp. 240-248 ◽

Cited By ~ 4

Author(s):

David Jordan ◽

Peter Kirkland ◽

Stephen Morris ◽

Ronald Coilparampil

Keyword(s):

National Laboratory ◽

Laboratory Network ◽

Serum Elisa

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On the interpretation of annual oscillations in 32Si and 36Cl decay rate measurements

Scientific Reports ◽

10.1038/s41598-021-95600-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

S. Pommé ◽

K. Pelczar ◽

K. Kossert ◽

I. Kajan

Keyword(s):

Decay Rate ◽

Solar Neutrino ◽

National Laboratory ◽

Neutrino Flux ◽

Measurement Data ◽

Brookhaven National Laboratory ◽

Decay Rates ◽

Dew Point ◽

Annual Variations ◽

Set Up

AbstractThe 32Si decay rate measurement data of Alburger et al. obtained in 1982–1986 at Brookhaven National Laboratory have been presented repeatedly as evidence for solar neutrino-induced beta decay. The count rates show an annual sinusoidal oscillation of about 0.1% amplitude and maximum at February–March. Several authors have claimed that the annual oscillations could not be explained by environmental influences on the set-up, and they questioned the invariability of the decay constant. They hypothesised a correlation with changes in the solar neutrino flux due to annual variations in the Earth-Sun distance, in spite of an obvious mismatch in amplitude and phase. In this work, environmental conditions at the time of the experiment are presented. The 32Si decay rate measurements appear to be inversely correlated with the dew point in a nearby weather station. Susceptibility of the detection set-up to local temperature and humidity conditions is a likely cause of the observed instabilities in the measured decay rates. Similar conclusions apply to 36Cl decay rates measured at Ohio State University in 2005–2012.

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How prediction statistics can help us cope when we are shaken, scared and irrational

10.5194/egusphere-egu21-15219 ◽

2021 ◽

Author(s):

Yavor Kamer ◽

Shyam Nandan ◽

Stefan Hiemer ◽

Guy Ouillon ◽

Didier Sornette

Keyword(s):

Earthquake Prediction ◽

Information Technologies ◽

Predictive Performance ◽

Earthquake Forecasting ◽

Skill Assessment ◽

Surveillance Network ◽

The Public ◽

Predictive Skill ◽

Earthquake Predictability ◽

Set Up

Nature is scary. You can be sitting at your home and next thing you know you are trapped under the ruble of your own house or sucked into a sinkhole. For millions of years we have been the figurines of this precarious scene and we have found our own ways of dealing with the anxiety. It is natural that we create and consume prophecies, conspiracies and false predictions. Information technologies amplify not only our rational but also irrational deeds. Social media algorithms, tuned to maximize attention, make sure that misinformation spreads much faster than its counterpart.What can we do to minimize the adverse effects of misinformation, especially in the case of earthquakes? One option could be to designate one authoritative institute, set up a big surveillance network and cancel or ban every source of misinformation before it spreads. This might have worked a few centuries ago but not in this day and age. Instead we propose a more inclusive option: embrace all voices and channel them into an actual, prospective earthquake prediction platform (Kamer et al. 2020). The platform is powered by a global state-of-the-art statistical earthquake forecasting model that provides near real-time earthquake occurrence probabilities anywhere on the globe (Nandan et al. 2020). Using this model as a benchmark in statistical metrics specifically tailored to the prediction problem, we are able to distill all these voices and quantify the essence of predictive skill. This approach has several advantages. Rather than trying to silence or denounce, we listen and evaluate each claim and report the predictive skill of the source. We engage the public and allow them to take part in a scientific experiment that will increase their risk awareness. We effectively demonstrate that anybody with an internet connected device can make an earthquake prediction, but that it is not so trivial to achieve skillful predictive performance.Here we shall present initial results from our global earthquake prediction experiment that we have been conducting on www.richterx.com for the past two years, yielding more than 10,000 predictions. These results will hopefully demystify the act of predicting an earthquake in the eyes of the public, and next time someone forwards a prediction message it would arouse more scrutiny than panic or distaste. Nandan, S., Kamer, Y., Ouillon, G., Hiemer, S., Sornette, D. (2020). Global models for short-term earthquake forecasting and predictive skill assessment. European Physical Journal ST. doi: 10.1140/epjst/e2020-000259-3 Kamer, Y., Nandan, S., Ouillon, G., Hiemer, S., Sornette, D. (2020). Democratizing earthquake predictability research: introducing the RichterX platform. European Physical Journal ST. doi: 10.1140/epjst/e2020-000260-2&#160;

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Arthur Conan Doyle and Medical London: Reading the Topography of Round the Red Lamp

Victoriographies ◽

10.3366/vic.2021.0435 ◽

2021 ◽

Vol 11 (3) ◽

pp. 295-313

Author(s):

Roger Luckhurst

Keyword(s):

General Practitioner ◽

Full Time ◽

Medical Institutions ◽

Short Period ◽

Arthur Conan Doyle ◽

Set Up

This essay explores the short period of time that Arthur Conan Doyle spent between March and June 1891 when he moved his family into rooms in Bloomsbury and took a consulting room near Harley Street in an attempt to set up as an eye specialist. This last attempt to move up the professional hierarchy from general practitioner to specialist tends to be seen as a final impulsive move before Conan Doyle decided to become a full-time writer in June 1891. The essay aims to elaborate a little on the medical contexts for Conan Doyle’s brief spell in London, and particularly to track the medical topography in which he placed himself, situated between the radical, reformist Bloomsbury medical institutions and the fame and riches of the society doctors of Harley Street. These ambivalences are tracked in the medical fiction he published in Round the Red Lamp, his peculiar collection of medical tales and doctoring in 1894.

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Clinical and multi-omics cross-phenotyping of patients with autoimmune and autoinflammatory diseases: the observational TRANSIMMUNOM protocol

BMJ Open ◽

10.1136/bmjopen-2017-021037 ◽

2018 ◽

Vol 8 (8) ◽

pp. e021037 ◽

Cited By ~ 2

Author(s):

Roberta Lorenzon ◽

Encarnita Mariotti-Ferrandiz ◽

Caroline Aheng ◽

Claire Ribet ◽

Ferial Toumi ◽

...

Keyword(s):

Systems Biology ◽

Good Clinical Practice ◽

Autoinflammatory Diseases ◽

Case Report Form ◽

Sample Collection ◽

Clinical Protocol ◽

Link Type ◽

Systems Immunology ◽

Hospital Ethics ◽

Set Up

IntroductionAutoimmune and autoinflammatory diseases (AIDs) represent a socioeconomic burden as the second cause of chronic illness in Western countries. In this context, the TRANSIMMUNOM clinical protocol is designed to revisit the nosology of AIDs by combining basic, clinical and information sciences. Based on classical and systems biology analyses, it aims to uncover important phenotypes that cut across diagnostic groups so as to discover biomarkers and identify novel therapeutic targets.Methods and analysisTRANSIMMUNOM is an observational clinical protocol that aims to cross-phenotype a set of 19 AIDs, six related control diseases and healthy volunteers . We assembled a multidisciplinary cohort management team tasked with (1) selecting informative biological (routine and omics type) and clinical parameters to be captured, (2) standardising the sample collection and shipment circuit, (3) selecting omics technologies and benchmarking omics data providers, (4) designing and implementing a multidisease electronic case report form and an omics database and (5) implementing supervised and unsupervised data analyses.Ethics and disseminationThe study was approved by the institutional review board of Pitié-Salpêtrière Hospital (ethics committee Ile-De-France 48–15) and done in accordance with the Declaration of Helsinki and good clinical practice. Written informed consent is obtained from all participants before enrolment in the study. TRANSIMMUNOM’s project website provides information about the protocol (https://www.transimmunom.fr/en/) including experimental set-up and tool developments. Results will be disseminated during annual scientific committees appraising the project progresses and at national and international scientific conferences.DiscussionSystems biology approaches are increasingly implemented in human pathophysiology research. The TRANSIMMUNOM study applies such approach to the pathophysiology of AIDs. We believe that this translational systems immunology approach has the potential to provide breakthrough discoveries for better understanding and treatment of AIDs.Trial registration numberNCT02466217; Pre-results.

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HL7 Terminology Management for Disease Surveillance

Online Journal of Public Health Informatics ◽

10.5210/ojphi.v10i1.8364 ◽

2018 ◽

Vol 10 (1) ◽

Author(s):

Emily Roberts ◽

Theron Jeppson ◽

Rachelle Boulton ◽

Josh Ridderhoff

Keyword(s):

Disease Surveillance ◽

Communicable Disease ◽

Laboratory Data ◽

Data Entry ◽

High Volume ◽

Electronic Data ◽

Disease Surveillance System ◽

Department Of Health ◽

Message Structure ◽

Set Up

Objective: The objective of this abstract is to illustrate how the Utah Department of Health processes a high volume of electronic data. We do this by translating what reporters send within an HL7 message into "epidemiologist" language for consumption into our disease surveillance system.Introduction: In 2013, the Utah Department of Health (UDOH) began working with hospital and reference laboratories to implement electronic laboratory reporting (ELR) of reportable communicable disease data. Laboratories utilize HL7 message structure and standard terminologies such as LOINC and SNOMED to send data to UDOH. These messages must be evaluated for validity, translated, and entered into Utah’s communicable disease surveillance system (UT-NEDSS), where they can be accessed by local and state investigators and epidemiologists. Despite the development and use of standardized terminologies, reporters may use different, outdated versions of these terminologies, may not use the appropriate codes, or may send local, home-grown terminologies. These variations cause problems when trying to interpret test results and automate data processing. UDOH has developed a two-step translation process that allows us to first standardize and clean incoming messages, and then translate them for consumption by UT-NEDSS. These processes allow us to efficiently manage several different terminologies and helps to standardize incoming data, maintain data quality, and streamline the data entry process.Methods: UDOH uses the Electronic Message Staging Area (EMSA) to receive ELR messages, manage terminologies such as LOINC and SNOMED, translate messages, and automatically enter laboratory data into UT-NEDSS. LOINCs and other terms, such as facility name, sent by reporting facilities in an HL7 message are considered child terms. All child terms are mapped to a master LOINC or term and each master LOINC or term is mapped to a specific value within UT-NEDSS. In EMSA, the rules engine used for automated processing of electronic data is set to run at the master level and these rules will determine how the message is processed. No rules are set up or run on child terms.Results: As of 09/20/2017, EMSA contains 2,613 unique child LOINCs that are mapped to 906 master LOINCs. Those 906 master LOINCs are mapped to 179 UT-NEDSS test types and 2003 child facility names are mapped to 1043 master facility namesConclusions: Mapping child terminologies from an HL7 message to a master vocabulary helps us to standardize incoming data, allows us to accept non-standard terminologies and correct reporting errors. Translating this data into a format that is understandable to epidemiologists and investigators enables UT-NEDSS to work effectively in identifying outbreaks and improving health outcomes. This framework is working for ELR and will continue to grow and accept more data and the different terminologies that come with that.

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A national measles epidemic in Switzerland in 1997 : consequences for the elimination of measles by the year 2007

Eurosurveillance ◽

10.2807/esm.05.02.00025-en ◽

2000 ◽

Vol 5 (2) ◽

pp. 17-20 ◽

Cited By ~ 10

Author(s):

W J Paget ◽

H Zimmermann ◽

H Vorkauf ◽

Keyword(s):

National Laboratory ◽

Sentinel Surveillance ◽

Surveillance Network ◽

Notification System ◽

Clinical Cases

Clinical cases of measles have been reported to the Swiss Sentinel Surveillance Network (Sentinella) since June 1986 and measles infections have been monitored by the national laboratory notification system since January 1988. These two surveillance syste

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Slow Wave Sleep During a Brief Nap is Related to Reduced Cognitive Deficits During Sleep Deprivation

SLEEP ◽

10.1093/sleep/zsab152 ◽

2021 ◽

Author(s):

Michelle E Stepan ◽

Erik M Altmann ◽

Kimberly M Fenn

Keyword(s):

Sleep Deprivation ◽

Cognitive Processing ◽

Slow Wave ◽

Slow Wave Sleep ◽

Vigilance Task ◽

Attention Task ◽

Performance Deficits ◽

Impaired Performance ◽

Short Period ◽

Set Up

Abstract Sleeping for a short period (i.e., napping) may help mitigate impairments in cognitive processing caused by sleep deprivation, but there is limited research on effects of brief naps in particular. Here, we tested the effect of a brief nap opportunity (30- or 60-min) during a period of sleep deprivation on two cognitive processes with broad scope, placekeeping and vigilant attention. In the evening, participants (N = 280) completed a placekeeping task (UNRAVEL) and a vigilant attention task (Psychomotor Vigilance Task [PVT]) and were randomly assigned to either stay awake overnight or sleep at home. Sleep-deprived participants were randomly assigned to receive either no nap opportunity, a 30-min opportunity, or a 60-min opportunity. Participants who napped were set up with polysomnography. The next morning, sleep participants returned, and all participants completed UNRAVEL and the PVT. Sleep deprivation impaired performance on both tasks, but nap opportunity did not reduce the impairment, suggesting that naps longer than those tested may be necessary to cause group differences. However, in participants who napped, more time spent in slow-wave sleep (SWS) was associated with reduced performance deficits on both tasks, effects we interpret in terms of the role of SWS in alleviating sleep pressure and facilitating memory consolidation.

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