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Assessment of real-time PCR for Helicobacter pylori DNA detection in stool with co-infection of intestinal parasites: a comparative study of DNA extraction methods
<p>Background</p> <p>Many studies reported high prevalence of <em>H. pylori</em> infection among patients co-infected with intestinal parasites. Molecular approach for the DNA detection of those microbes in stool have been proposed. However there are a few reports that evaluated the effect of bead-beating in relation to the <em>H. pylori</em> outcome. Therefore, we developed and evaluated two TaqMan-based real-time PCR (rt-PCR) qualitative assays for the detection of <em>ureC</em> (<em>glmM</em>) and <em>cagA</em> of <em>Helicobacter pylori</em> on DNA extracted by three procedures.</p> <p>Results</p> <p>The two PCRs were analysed on 100 stool samples from patients who were screened for intestinal parasites. Three DNA extraction procedures were used: 1) automation with bead beating, 2) automation without bead beating and 3) hand column. The specificity of the new assays was confirmed by sequencing the PCR products and by the lack of cross-reactivity with other bacteria or pathogens DNA. Rt-PCR assays showed a detection limit of 10^4 bacteria/200 mg stool. The <em>ureC</em>_PCR with bead beating process was compared to conventional stool antigen test (SAT), with 94.12 and 93.75% of respectively sensitivity and specificity. However, the discordant samples were confirmed by DNA sequencing suggesting a potential higher sensitivity and specificity of PCR.</p> <p>Conclusions</p> <p>Our findings showed that the automation with bead-beating –suggested procedure for intestinal parasitic infections- can reach highly sensitive results in <em>H. pylori</em> detection on stool compared also with SAT. Thus, this work can provide new insights into the practice of a clinical microbiology laboratory in order to optimize detection of gastro-intestinal infections. Further studies are needed to better define the clinical value of this technique.</p>
Development of Dental Implantable Temperature Sensor for Real-time Diagnosis of Infectious Disease
<pre>The two files attached are supplemental data showing how the mechanical stability test of the developed sensor was performed.</pre> <p>Video S1: 180° bending test to verify mechanical stability.</p> <p>Video S2: Stirring test with the microfabricated sensor attached on magnetic bar.</p>
Mobile EEG identifies the re-allocation of attention during real-world activity
<p>All the datasets from the three studies reported in the scientific article "Mobile EEG identifies the re-allocation of attention during real-world activity" <a href="https://www.nature.com/articles/s41598-019-51996-y">10.1038/s41598-019-51996-y </a></p>
On the use of real-time mortality data in modelling and analysis during an epidemic outbreak – extended data
<p>This project contains extended data related to the journal article "On the use of real-time mortality data in modelling and analysis during an epidemic outbreak" by Per Liljenberg</p> <p>This project contains the following extended data:</p> <ul> <li>Liljenberg2020_OGR_Appendix.pdf (Appendix to the main article)</li> <li>swedish_covid_deaths_OGR.R. (R-script to generate graphs and nowcasts in the paper.)</li> <li>MDAR author checklist.pdf (Completed MDAR reporting checklist)</li> </ul>
On the Diversity and Frequency of Code Related to Mathematical Formulas in Real-World Java Projects
<p>Supplementary Material to: On the Diversity and Frequency of Code Related to Mathematical Formulas in Real-World Java Projects. The article available at: https://www.sciencedirect.com/science/article/abs/pii/S0164121220302533</p>
Applying a Multi-platform Architectural Conformance Solution in a Real-World Microservice-based System
<p>Microservice architectures are composed of a set of independent microservices that execute well-defined functionalities, allowing each one to be developed in different programming languages and data management technologies. The problem, however, is that such heterogeneity implies in a harder verification process of communication among microservices and the architectural designs of each microservice. Thereupon, this paper proposes and evaluates a multiplatform architectural conformance solution for the microservice architecture. For this purpose, (i) we specify an architectural constraint language, called DCL+---adapted from the DCL (Dependency Constraint Language) language; (ii) we propose a multiplatform process that restricts the communication between the microservices and verifies the architectural projects of each one of them; (iii) we develop DCL+check, a tool that implements the proposed solution; (iv) we apply our process in a large real-world application composed of eleven microservices, developed in two different languages (JavaScript and Java). As result, we found 16 communication and 171 structural design violations. The communication violations occurred in general due to the lack of knowledge of the developers about the restrictions of communication among the modules of the orchestrator system and other microservices, as well as the evolution of two microservices. </p>
Table 1 : Norms for clinical use of CXM, a real-time marker of height velocity
<p>Table 1 data set</p>
Real-Time Early Detection and Monitoring of Flooding Using Low-Cost Highly Sensitive Ultrasound Sensing of Water Level
<p>Flooding poses safety hazards to motorists, emergency and maintenance crews and may cause costly damage to transportation infrastructure and its operation. Flash flooding, in particular, causes the most flood-related deaths According to NOAA, in 2017 alone, flash flooding also caused $60.7 billion worth of economic damage. Low-water crossings are among the first places where deaths and significant damages to vehicles occur during flooding. With flash flooding, when a critical corridor is blocked by a high level of water, it affects the safety of the general public. To keep the critical corridors open as long as possible, and to minimize losses from flooding, accurate early detection of the rising water level is essential. The flood level detection system has to have flood stage maps in the geographic information system for the street-, roadway-, and critical-freight corridors. This area encompasses public roads in urbanized areas that provide access and connection to the primary roads for ports, public transportation or other transportation facilities. The main goal of this project is to develop cost-effective and high efficient solar-powered water level detection units and implement real-time water level monitoring for water both pavement and river stream. The project was performed with three objectives: to develop the low cost reliable real-time data of the ultrasound water level detection system, increasing its data reliability and resolution; 2) to improve an energy-saving processing system; and to deploy the ultrasound water level detection system and real-time monitoring system for water both pavement and river stream for safety measures. The obtained results and findings imply the developed monitoring system can present reliable water level data with efficient power and data transmission system.</p>
Real-Time Work Zone Traffic Management via Unmanned Air Vehicles
<p>Highway work zones are prone to traffic accidents when congestion and queues develop. Vehicle queues expand at a rate of 1 mile every 2 minutes. Back-of-queue, rear-end crashes are the most common work zone crash, endangering the safety of motorists, passengers, and construction workers. The dynamic nature of queuing in the proximity of highway work zones necessitates traffic management solutions that can monitor and intervene in real time. Fortunately, recent progress in sensor technology, embedded systems, and wireless communication coupled to lower costs are now enabling the development of real-time, automated, “intelligent” traffic management systems that address this problem. The goal of this project was to perform preliminary research and proof of concept development work for the use of UAS in real- time traffic monitoring of highway construction zones in order to create real-time alerts for motorists, construction workers, and first responders. The main tasks of the proposed system was to collect traffic data via the UAV camera, analyze that a UAV based highway construction zone monitoring systems would be capable of detecting congestion and back-of-queue information, and alerting motorists of stopped traffic conditions, delay times, and alternate route options. Experiments were conducted using UAS to monitor traffic and collect traffic videos for processing. Prototype software was created to analyze this data. The software was successful in detecting vehicle speed from zero mph to highway speeds. Review of available mobile traffic apps were conducted for future integration with advanced iterations of the UAV and software system that has been created by this research. This project has proven that UAS monitoring of highway construction zones and real-time alerts to motorists, construction crews, and first responders is possible in the near term and future research is needed to further development and implement the innovative UAS traffic monitoring system developed by this research.</p>
Allochthonous and autochthonous halothermotolerant bioanodes from hypersaline sediment and textile wastewater: A promising microbial electrochemical process for energy recovery coupled with real textile wastewater treatment
<p>16 S sequencing data Askri et al </p>
Data from: Real-world study of efficacy, risk management and reasons for discontinuation of natalizumab for treatment of multiple sclerosis in Russia
Background. NTZ is approved in Russia for the treatment of highly active relapsing remitting multiple sclerosis and is reimbursed via federal budget program. However, no data about NTZ treatment in Russia and the effect of federal reimbursement have been performed so far. Objective. To characterize the population of patients receiving natalizumab and assess the efficacy and risk-management plan (RMP) implementation of NTZ therapy in routine clinical practice in Russia. Methods. We analyzed data for 334 patients, who received at least one infusion of NTZ. Relapse rate, MRI activity, NEDA-3 status after 2 years were assessed. Anti-JC virus antibodies status and RMP implementation were evaluated. Drop-out rate and reasons for therapy discontinuation were analyzed. Results. Patients switched to natalizumab in Russia are mainly female (63%), with median EDSS score of 3.5 and high disease activity: 93% had at least 1 relapse and 58% had both T1Gd+ and new T2 lesion an year before therapy initiation. Introduction of federal reimbursement allowed to start therapy with natalizumab for patients with less relapses. The only predictor of 6-month progression was EDSS score at the baseline of therapy (HR=2.1375, 95%CI 1.0026 – 4.5570, p=0.0492). 82% patients reached NEDA-3 at 24 month of therapy. 25% of patients discontinued NTZ for reasons: tolerability (14.5%), JCV antibody status (61%), and patient's decision (17%). RMP was implemented in only 36% patients. Conclusion. Natalizumab appeared to have high efficacy in Russian clinical practice. Federal reimbursement allowed less active patients to start natalizumab. More efforts should be done to improve RMP implementation.
Data from: Harnessing olfactory bulb oscillations to perform fully brain-based sleep-scoring and real-time monitoring of anesthesia depth
Real-time tracking of vigilance states related to both sleep or anaesthesia has been a goal for over a century. However, sleep scoring cannot currently be performed with brain signals alone, despite the deep neuromodulatory transformations that accompany sleep state changes. Therefore, at heart, the operational distinction between sleep and wake is that of immobility and movement, despite numerous situations in which this one-to-one mapping fails. Here we demonstrate, using local field potential (LFP) recordings in freely moving mice, that gamma (50–70 Hz) power in the olfactory bulb (OB) allows for clear classification of sleep and wake, thus providing a brain-based criterion to distinguish these two vigilance states without relying on motor activity. Coupled with hippocampal theta activity, it allows the elaboration of a sleep scoring algorithm that relies on brain activity alone. This method reaches over 90% homology with classical methods based on muscular activity (electromyography [EMG]) and video tracking. Moreover, contrary to EMG, OB gamma power allows correct discrimination between sleep and immobility in ambiguous situations such as fear-related freezing. We use the instantaneous power of hippocampal theta oscillation and OB gamma oscillation to construct a 2D phase space that is highly robust throughout time, across individual mice and mouse strains, and under classical drug treatment. Dynamic analysis of trajectories within this space yields a novel characterisation of sleep/wake transitions: whereas waking up is a fast and direct transition that can be modelled by a ballistic trajectory, falling asleep is best described as a stochastic and gradual state change. Finally, we demonstrate that OB oscillations also allow us to track other vigilance states. Non-REM (NREM) and rapid eye movement (REM) sleep can be distinguished with high accuracy based on beta (10–15 Hz) power. More importantly, we show that depth of anaesthesia can be tracked in real time using OB gamma power. Indeed, the gamma power predicts and anticipates the motor response to stimulation both in the steady state under constant anaesthetic and dynamically during the recovery period. Altogether, this methodology opens the avenue for multi-timescale characterisation of brain states and provides an unprecedented window onto levels of vigilance.
Solar Thermal Collector (STC) Real Measurements in Switzerland
<h3>Measurements of a solar thermal collector (STC)</h3> <p>These measurements have taken place in Sion, Valais, Switzerland in longitude: 7.364832° and latitude: 46.227372°.</p>
Full sequencing dataset of payload segments for "A Base Multilayer DNA Storage Architecture Enables Real-Time Decoding to Overcome Latency" (Part 2, FASTA file)
<p><span lang="EN-US">This is the full sequencing dataset of payload segments for the manuscript "A Base Multilayer DNA Storage Architecture Enables Real-Time Decoding to Overcome Latency", which is submitted for review.</span></p> <p><span lang="EN-US">We successfully encoded the first color film "Becky Sharp" (54.79 MB) into ~10.08 million DNA strands, achieving a sustained readout throughput of 459 kbit/s.</span></p> <p><span lang="EN-US">This full sequencing dataset contains all base-called data (in BIN and FASTA) of the payload segments. It can be used for recovery of the 28-layer color film data with the <br>DNA-LC software. </span></p> <p><span lang="EN-US">Due to size limitations, the dataset is divided into two parts. Part 1 contains all the files in BIN format, and Part 2 contains the corresponding files in FASTA format. This link is for Part 2.</span></p>
Full sequencing dataset of payload segments for "A Base Multilayer DNA Storage Architecture Enables Real-Time Decoding to Overcome Latency" (Part 1, BIN file)
<p><span lang="EN-US">This is the full sequencing dataset of payload segments for the manuscript "A Base Multilayer DNA Storage Architecture Enables Real-Time Decoding to Overcome Latency", which is submitted for review.</span></p> <p><span lang="EN-US">We successfully encoded the first color film "Becky Sharp" (54.79 MB) into ~10.08 million DNA strands, achieving a sustained readout throughput of 459 kbit/s.</span></p> <p><span lang="EN-US">This full sequencing dataset contains all base-called data (in BIN and FASTA) of the payload segments. It can be used for recovery of the 28-layer color film data with the<br>DNA-LC software. </span></p> <p><span lang="EN-US">Due to size limitations, the dataset is divided into two parts. Part 1 contains all the files in BIN format, and Part 2 contains the corresponding files in FASTA format. This link is for Part 1.</span></p>
Verification dataset of "A Base Multilayer DNA Storage Architecture Enables Real-Time Decoding to Overcome Latency"
<p>This is a dataset for the proposed base-layered DNA data storage. </p> <p>The first color film “Becky Sharp” (54.79 MB) was encoded into ~10.08 million DNA strands<span lang="EN-US">, achieving a sustained readout throughput of 459 kbit/s</span>.</p> <p>For the film, it was used to verify the performance of the proposed DNA data storage method, only for academic research, not related to the content.</p> <p>The dataset consists of three categories: the original data, the oligo sequence data, and the sequencing data (in BIN and FASTA formats).</p>
Figure 1 from: Seitaridou Y, Chamova T, Kamusheva M (2024) Adherence to disease-modifying therapies among patients with multiple sclerosis in Bulgaria – A real world study. Pharmacia 71: 1-7. https://doi.org/10.3897/pharmacia.71.e117681
Figure 1 Adherence level. Legend: 0 – low adherence; 1 – moderate adherence; 2 – high adherence.
Figure 2 from: Neumann M, Ehnert F (2024) Knowledge re-integration in real-world laboratories to transform cities and communities: report on workshop designs. Research Ideas and Outcomes 10: e124018. https://doi.org/10.3897/rio.10.e124018
Figure 2 Template of the online whiteboard for the handbook workshops (translated into English).
Figure 3 from: Neumann M, Ehnert F (2024) Knowledge re-integration in real-world laboratories to transform cities and communities: report on workshop designs. Research Ideas and Outcomes 10: e124018. https://doi.org/10.3897/rio.10.e124018
Figure 3 Flashlight at the end of the DF transfer workshop; photo: Torsten Görg.
Figure 4 from: Neumann M, Ehnert F (2024) Knowledge re-integration in real-world laboratories to transform cities and communities: report on workshop designs. Research Ideas and Outcomes 10: e124018. https://doi.org/10.3897/rio.10.e124018
Figure 4 On-site excursion during the SLS transfer workshop; photo: Nicole Herzog.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.