Tracing Tool Research Articles

Convergent olfactory circuits for courtship in Drosophila revealed by ds-Tango.

Animals exhibit sex-specific behaviors that are governed by sexually dimorphic circuits. One such behavior in male Drosophila melanogaster, courtship, is regulated by various sensory modalities, including olfaction. Here, we reveal how sexually dimorphic olfactory pathways in male flies converge at the third-order, onto lateral horn output neurons, to regulate courtship. To achieve this, we developed ds-Tango, a modified version of the monosynaptic tracing and manipulation tool trans-Tango. In ds-Tango, two distinct configurations of trans-Tango are positioned in series, thus providing selective genetic access not only to the monosynaptic partners of starter neurons but also to their disynaptic connections. Using ds-Tango, we identified a node of convergence for three sexually dimorphic olfactory pathways. Silencing this node results in deficits in sex recognition of potential partners. Our results identify lateral horn output neurons required for proper courtship behavior in male flies and establish ds-Tango as a tool for disynaptic circuit tracing.

Application of tracing tools for analysis of microcontroller failures arising under the 14 MeV neutrons exposure

The trace support tools capabilities for a microcontroller (МС) with a Cortex-M3 core are analyzed to investigation of failures arising under the 14 MeV neutrons exposure. It has been shown that in most cases, MC hang is caused by the microcontroller going into a handling an inactive exception infinite loop. The cross-section values for the single event functional interrupt and the single event latch-up are estimated.

CRISPR-AMRtracker: A novel toolkit to monitor the antimicrobial resistance gene transfer in fecal microbiota

The spread of antibiotic resistance genes (ARGs), particularly those carried on plasmids, poses a major risk to global health. However, the extent and frequency of ARGs transfer in microbial communities among human, animal, and environmental sectors is not well understood due to a lack of effective tracking tools. We have developed a novel fluorescent tracing tool, CRISPR-AMRtracker, to study ARG transfer. It combines CRISPR/Cas9 fluorescence tagging, fluorescence-activated cell sorting, 16S rRNA gene sequencing, and microbial community analysis. CRISPR-AMRtracker integrates a fluorescent tag immediately downstream of ARGs, enabling the tracking of ARG transfer without compromising the host cell's antibiotic susceptibility, fitness, conjugation, and transposition. Notably, our experiments demonstrate that sfGFP-tagged plasmid-borne mcr-1 can transfer across diverse bacterial species within fecal samples. This innovative approach holds the potential to illuminate the dynamics of ARG dissemination and provide valuable insights to shape effective strategies in mitigating the escalating threat of antibiotic resistance.

A Free-Space Diffraction BSDF

Free-space diffractions are an optical phenomenon where light appears to "bend" around the geometric edges and corners of scene objects. In this paper we present an efficient method to simulate such effects. We derive an edge-based formulation of Fraunhofer diffraction, which is well suited to the common (triangular) geometric meshes used in computer graphics. Our method dynamically constructs a free-space diffraction BSDF by considering the geometry around the intersection point of a ray of light with an object, and we present an importance sampling strategy for these BSDFs. Our method is unique in requiring only ray tracing to produce free-space diffractions, works with general meshes, requires no geometry preprocessing, and is designed to work with path tracers with a linear rendering equation. We show that we are able to reproduce accurate diffraction lobes, and, in contrast to any existing method, are able to handle complex, real-world geometry. This work serves to connect free-space diffractions to the efficient path tracing tools from computer graphics.

Deciphering visceral adipose tissue regulatory T cells: Key contributors to metabolic health.

Regulatory T cells (Tregs) within the visceral adipose tissue (VAT) play a crucial role in controlling tissue inflammation and maintaining metabolic health. VAT Tregs display a unique transcriptional profile and T cell receptor (TCR) repertoire, and closely interact with adipocytes, stromal cells, and other immune components within the local VAT microenvironment. However, in the context of obesity, there is a notable decline in VAT Tregs, resulting in heightened VAT inflammation and insulin resistance. A comprehensive understanding of the biology of VAT Tregs is essential for the development of Treg-based therapies for mitigating obesity-associated metabolic diseases. Recent advancements in lineage tracing tools, genetic mouse models, and various single cell "omics" techniques have significantly progressed our understandings of the origin, differentiation, and regulation of this unique VAT Treg population at steady state and during obesity. The identification of VAT-Treg precursor cells in the secondary lymphoid organs has also provided important insights into the timing, location, and mechanisms through which VAT Tregs acquire their distinctive phenotype that enables them to function within a lipid-rich microenvironment. In this review, we highlight key recent breakthroughs in the VAT-Treg field while discussing pivotal questions that remain unanswered.

Determination of the larval precursor configuration of the Drosophila adult hindgut by G-TRACE analysis

The Drosophila hindgut is a classical model to study organogenesis. The adult hindgut originates from the precursor cells in the larval hindgut. However, the territory of these cells has still not been well determined. A ring of wingless (wg)-expressing cells lies at the anterior zone of both the larval and adult hindgut. The larval Wg ring was thought as a portion of precursor of the adult hindgut. By applying a cell lineage tracing tool (G-TRACE), we demonstrate that larval wg-expressing cells have no cell lineage contribution to the adult hindgut. Additionally, adult Wg ring cells do not divide and move posteriorly to replenish the hindgut tissue. Instead, we determine that the precursors of the adult pylorus and ileum are situated in the cubitus interruptus (ci)-expressing cells in the anterior zone, and deduce that the precursor stem cells of the adult rectum locate in the trunk region of the larval pylorus including hedgehog (hh)-expressing cells. Together, this research advances our understanding of cell lineage origins and the development of the Drosophila hindgut.

Spatial organization of astrocyte clones: The role of developmental progenitor timing.

Astrocytes represent a diverse and morphologically complex group of glial cells critical for shaping and maintaining nervous system homeostasis, as well as responding to injuries. Understanding the origins of astroglial heterogeneity, originated from a limited number of progenitors, has been the focus of many studies. Most of these investigations have centered on protoplasmic and pial astrocytes, while the clonal relationship of fibrous astrocytes or juxtavascular astrocytes has remained relatively unexplored. In this study, we sought to elucidate the morphological diversity and clonal distribution of astrocytes across adult cortical layers, with particular emphasis on their ontogenetic origins. Using the StarTrack lineage tracing tool, we explored the characteristics of adult astroglial clones derived from single and specific progenitors at various embryonic stages. Our results revealed a heterogeneous spatial distribution of astroglial clones, characterized by variations in location, clonal size, and rostro-caudal dispersion. While a considerable proportion of clones were confined within specific cortical layers, others displayed sibling cells crossing layer boundaries. Notably, we observed a correlation between clone location and developmental stage at earlier embryonic stages, although this relationship diminished in later stages. Fibrous astrocyte clones were exclusively confined to the corpus callosum. In contrast, protoplasmic or juxtavascular clones were located in either the upper or lower cortical layers, with certain clones displayed sibling cells distributed across both regions. Our findings underscore the developmental origins and spatial distribution of astroglial clones within cortical layers, providing new insights into the interplay between their morphology, clonal sizes, and progenitor heterogeneity.

Does integration with national registers improve the data completeness of local COVID-19 contact tracing tools? A register-based study in Norway, May 2020 - September 2021

BackgroundDuring the COVID-19 response in Norway, many municipalities used the Fiks contact tracing tool (FiksCT) to register positive individuals and follow-up contacts. This tool is based on DHIS2, an open source, web-based platform. In this study we examined if data completeness in FiksCT improved after integration with national registers between May 2020 and September 2021.MethodsData from municipalities using FiksCT was extracted from the Norwegian Emergency Preparedness Register for COVID-19 (Beredt C19). We linked FiksCT data to the Norwegian Surveillance System for Communicable Diseases (MSIS), the National Population Register (FREG), and the Norwegian Vaccine Registry (SYSVAK) using unique identification numbers (ID). Completeness for each variable linked with a national register was calculated before and after integration with these registers.ResultsOf the 125 municipalities using FiksCT, 87 (69.6%) agreed to share and upload their data to Beredt C19. Data completeness for positive individuals improved after integration with national registers. After integration with FREG, the proportion of missing values decreased from 12.5 to 1.6% for ID, from 4.5 to 0.9% for sex, and from 1.2 to 0.4% for date of birth. Missing values for vaccine type decreased from 63.0 to 15.2% and 39.3–36.7% for first and second dose, respectively. In addition, direct reporting from FiksCT to MSIS increased the proportion of complete records in MSIS (on the selected variables) from 68.6% before to 77.0% after integration.ConclusionThe completeness of local contact tracing data can be improved by enabling integration with established national registers. In addition, providing the option to submit local data to the national registers could ease workload and reduce the need to collect duplicate data.

A Qualitative Interview Study of Distributed Tracing Visualisation: A Characterisation of Challenges and Opportunities.

Distributed tracing tools have emerged in recent years to enable operators of modern internet applications to troubleshoot cross-component problems in deployed applications. Due to the rich, detailed diagnostic data captured by distributed tracing tools, effectively presenting this data is important. However, use of visualisation to enable sensemaking of this complex data in distributed tracing tools has received relatively little attention. Consequently, operators struggle to make effective use of existing tools. In this article we present the first characterisation of distributed tracing visualisation through a qualitative interview study with six practitioners from two large internet companies. Across two rounds of 1-on-1 interviews we use grounded theory coding to establish users, extract concrete use cases and identify shortcomings of existing distributed tracing tools. We derive guidelines for development of future distributed tracing tools and expose several open research problems that have wide reaching implications for visualisation research and other domains.

Annelids as models of germ cell and gonad regeneration.

Germ cells (reproductive cells and their progenitors) give rise to the next generation in sexually reproducing organisms. The loss or removal of germ cells often leads to sterility in established research organisms such as the fruit fly, nematodes, frog, and mouse. The failure to regenerate germ cells in these organisms reinforced the dogma of germline-soma barrier in which germ cells are set-aside during embryogenesis and cannot be replaced by somatic cells. However, in stark contrast, many animals including segmented worms (annelids), hydrozoans, planaria, sea stars, sea urchins, and tunicates can regenerate germ cells. Here I review germ cell and gonad regeneration in annelids, a rich history of research that dates back to the early 20th century in this highly regenerative group. Examples include annelids from across the annelid phylogeny, across developmental stages, and reproductive strategies. Adult annelids regenerate germ cells as a part of regeneration, grafting, and asexual reproduction. Annelids can also recover germ cells after ablation of germ cell progenitors in the embryos. I present a framework to investigate cellular sources of germ cell regeneration in annelids, and discuss the literature that supports different possibilities within this framework, where germ-soma separation may or may not be preserved. With contemporary genetic-lineage tracing and bioinformatics tools, and several genetically enabled annelid models, we are at the brink of answering the big questions that puzzled many for over more than a century.

Geometrical and optical analysis of small-sized parabolic trough collector using ray tracing tool SolTrace

Geometrical and optical analysis of small-sized parabolic trough collector using ray tracing tool SolTrace

Emission of Energetic Neutral Atoms From the Magnetosphere‐Atmosphere Interactions at Callisto and Europa

AbstractWe analyze the emission of energetic neutral atom (ENA) flux from charge exchange between Jovian magnetospheric ions and the atmospheres of Callisto and Europa. For this purpose, we combine the draped electromagnetic fields from a hybrid plasma model with a particle tracing tool for the energetic ions. We determine the ENA flux through a concentric sphere located just outside of each moon's atmosphere, thereby capturing the complete physics imprinted in these emission patterns. In order to constrain the modifications to the ENA emissions that arise from the periodic change of the ambient plasma conditions, we calculate the emission morphology at multiple positions during a Jovian synodic rotation. To isolate the influence of field line draping, we compare to the emission patterns in uniform fields. Our major results are: (a) At Europa and Callisto, the majority of detectable ENA emissions are concentrated into a band normal to the Jovian magnetospheric field. (b) The fraction of observable ENA flux that contributes to this band depends on the number of complete gyrations that the parent ions can complete within the moon's atmosphere. (c) Field line draping partially deflects impinging parent ions around both moons, thereby attenuating the ENA flux and driving significant morphological changes to the emission patterns. (d) The band of elevated ENA flux is locally maximized on the opposite (antipodal) side of the moon where the flux is locally minimized. At Europa, detectable ENA emissions are maximized slightly west of the ramside apex. At Callisto, they maximize near the Jupiter‐facing apex.

Building a Simple Model to Assess the Impact of Case Investigation and Contact Tracing for Sexually Transmitted Diseases: Lessons From COVID-19

During the COVID-19 pandemic, the U.S. Centers for Disease Control and Prevention developed a simple spreadsheet-based tool to help state and local public health officials assess the performance and impact of COVID-19 case investigation and contact tracing in their jurisdiction. The applicability and feasibility of building such a tool for sexually transmitted diseases were assessed. The key epidemiologic differences between sexually transmitted diseases and respiratory diseases (e.g., mixing patterns, incubation period, duration of infection, and the availability of treatment) were identified, and their implications for modeling case investigation and contact tracing impact with a simple spreadsheet tool were remarked on. Existing features of the COVID-19 tool that are applicable for evaluating the impact of case investigation and contact tracing for sexually transmitted diseases were also identified. Our findings offer recommendations for the future development of a spreadsheet-based modeling tool for evaluating the impact of sexually transmitted disease case investigation and contact tracing efforts. Generally, we advocate for simplifying sexually transmitted disease-specific complexities and performing sensitivity analyses to assess uncertainty. The authors also acknowledge that more complex modeling approaches might be required but note that it is possible that a sexually transmitted disease case investigation and contact tracing tool could incorporate features from more complex models while maintaining a user-friendly interface. A sexually transmitted disease case investigation and contact tracing tool could benefit from the incorporation of key features of the COVID-19 model, namely its user-friendly interface. The inherent differences between sexually transmitted diseases and respiratory viruses should not be seen as a limitation to the development of such tool.

Detection of malicious PE files using synthesized DNA artifacts

The availability of sophisticated IT tools has provided computer system attackers with the capacity to develop dangerous metamorphic or polymorphic malware. Such malware presents behaviors similar to biological viruses enabling them to evade detection from conventional anti-malware methods. To circumvent this challenge, we carried out this research experiment to build and train machine learning models, and our proposed models achieved 99% & 99.6% accuracy in detecting and classifying PE-oriented malware. This excellent performance of our proposed models is undoubtedly a function of several factors but majorly on the synthesized DNA datasets (from our previous research works), which we used to train our proposed models. The synthesized DNA datasets are composed of salient features (dynamic and static) extracted from behaviors of nonmalicious programs (.exe, .dll, etc.) before and after infection by malware using reverse engineering and tracing tools. Then using a encoding algorithm and bioinformatics tools, we synthesized these features into a DNA-like representation (data sets) akin to the biological Deoxyribonucleic acid(DNA).

Harnessing a real-time location system for contact tracing in a busy emergency department

With the persistent threat of emerging infectious diseases (EID), digital contact tracing (CT) tools can augment conventional CT for the prevention of healthcare-associated infectious disease transmissions. However, their performance has yet to be comprehensively evaluated in the fast-paced emergency department (ED). We compared the CT performance of the radiofrequency identification (RFID) based real time location system (RTLS) with conventional Electronic Medical Records (EMR review), against continuous direct observations of close contacts ("gold-standard") in a busy ED during pandemic period. The cross-sectional study was conducted at the ED in a large tertiary-care hospital in Singapore, from December-2020 to April-2021. We computed the CT performance (sensitivity, specificity, PPV, NPV, kappa) of RTLS, EMR and combination of the 2 approaches (Hybrid-CT), with respect to the direct observations. Finally, we calculated the Mean Absolute Error (MAE) between the duration of each contact episode found via RTLS and direct observations. Both RTLS and the hybrid-CT approach had the highest sensitivity of 0.955 (vs EMR 0.455) and highest NPV of 0.997 (vs EMR 0.968). RTLS also had the highest PPV of 0.777 (vs EMR 0.714; vs hybrid-CT 0.712). RTLS had the strongest agreement with the direct observation (kappa= 0.848). MAE between contact durations of 80 direct observations and their respective RTLS contact time was 1.81 minutes. RTLS was validated to be a high-performing CT tool, with significantly higher sensitivity than conventional CT via EMR review. RTLS can be used with confidence in time-strapped EDs for time-sensitive CT for the prevention of healthcare-associated transmission of EIDs.

Digital exposure notification tools: A global landscape analysis.

As the COVID-19 pandemic continues, digital exposure notification systems are increasingly used to support traditional contact tracing and other preventive strategies. Likewise, a plethora of COVID-19 mobile applications have emerged. Objective: To characterize the global landscape of pandemic related mobile applications, including digital exposure notification and contact tracing tools. The following queries were entered into the Google search engine: "(*country name* COVID app) OR (COVID app *country name*) OR (COVID app *country name*+) OR (*country name*+ COVID app)". The App Store, Google Play, and official government websites were then accessed to collect descriptive data for each application. Descriptive data were qualified and quantified using standard methods. COVID-19 Exposure Notification Systems (ENS) and non-Exposure Notification products were categorized and summarized to provide a global landscape review. Our search resulted in a global count of 224 COVID-19 mobile applications, in 127 countries. Of these 224 apps, 128 supported exposure notification, with 75 employing the Google Apple Exposure Notification (GAEN) application programming interface (API). Of the 75 apps using the GAEN API, 15 apps were developed using Exposure Notification Express, a GAEN turnkey solution. COVID-19 applications that did not include exposure notifications (n = 96) focused on COVID-19 Self-Assessment (35·4%), COVID-19 Statistics and Information (32·3%), and COVID-19 Health Advice (29·2%). The digital response to COVID-19 generated diverse and novel solutions to support non-pharmacologic public health interventions. More research is needed to evaluate the extent to which these services and strategies were useful in reducing viral transmission.

An open-source digital contact tracing system tailored to haulage.

Digital contact tracing presents numerous advantages compared to manual contact tracing methods, especially in terms of enhanced speed and automation. Nevertheless, a lack of comprehensive evaluation regarding functionality, efficiency, benefits, and acceptance within communities remains. Here we primarily focus on the functionality of THEA-GS, an open-source digital contact tracing tool developed through consultation with stakeholders. Additionally, we provide insights from its implementation on a limited sample of haulage drivers in Uganda, serving as a representative case for a low- and middle-income country. THEA-GS comprises two primary components: (a) a smartphone application, and (b) a suite of server-programs responsible for data processing and analysis, including databases and a web-based interface featuring dashboards. In essence, the mobile application records the timestamped location of haulage drivers within the road network and identifies possible transmission hotspots by analyzing factors such as the duration of stops and the communities associated with them. The tool can be integrated with national infrastructure to compare drivers' diagnostic results and contact structure, thereby generating individual and community risk assessments relative to the road network. During the Omicron-variant wave of the COVID-19 pandemic, a total of 3,270 haulage drivers were enrolled between October 2021 and October 2022. Around 75% of these drivers utilized THEA-GS for approximately two months. Based on an analysis of 3,800 test results, which included 48 positive cases, 125 contacts, and 40 million time-stamped GPS points, THEA-GS shows a significant speed improvement, being approximately 90 times faster than MCT. For instance, the average time from sample collection to notifying a case and their contacts was approximately 70 and 80 min, respectively. The adoption of this tool encountered challenges, mainly due to drivers' awareness of its purpose and benefits for public health. THEA-GS is a place-based digital contact tracing tool specifically designed to assist National Public Health Institutions in managing infectious disease outbreaks involving the haulage industry as a high-risk group. While its utility, acceptance, and accuracy have not been fully evaluated, our preliminary tests conducted in Uganda indicate the tool's functionality is robust, but social acceptance and adoption are heavily reliant on establishing trust among users.

COVID-19 Contact Tracing Experience at a Tertiary Healthcare Center in Saudi Arabia.

Introduction As of May 2023, the end of the pandemic, the cumulative number of COVID-19 cases reached more than 841,000 cases. Healthcare workers (HCWs) especially have been at the frontline during this pandemic and are at a higher chance of contracting COVID-19. Approximately half of all high-risk exposures were to healthcare personnel with COVID-19. While several tools for contact tracing were developed for the general public, contact tracing for infectious diseases in the healthcare setting is limited, and global testing of HCWs, or in-hospital digital tracing, is not performed in most facilities. The King Faisal Specialist Hospital and Research Center (KFSH&RC) collaborated with the Infection Control and Health Information Technology Affairs (HITA)to create an automated COVID-19 contact tracing tool specifically for HCWs who worked at the institute. This study aims to describe the contact tracing experience at KFSH&RC. Methods A retrospective study was conducted to describe the use of an automated tool that was developed to assist in the contact tracing process and that was to be used by KFSH&RC employees who had been in contact with a COVID-19-positiveindividual. This tool is utilized for the early identification of possible COVID-19 cases and risk stratification of the exposed individuals. The tool can be accessed through the KFSH&RC website; it also collects information about the COVID-19 exposure rate among the different departments such as administration, capital projects/facilities, and healthcare at a tertiary care hospital in Riyadh, Saudi Arabia Results The tool has been utilized 7,353 times by contact cases. Approximately 7% of those tested later developed a COVID-19 infection. When assessing the positivity rates per department, The Environmental Services Department had the highest positivity rate of 28.21%, followed by Health Information Technology and Analytics (HITA), and then the Central Transportation Department. Conclusion This study acts as the first of its kind to describe the successful use of the healthcare contact tracing system in one of Saudi Arabia's largest hospitals (KFSH&RC) and describe the infection trends in different departments of the hospital. Through the tracing system, the departments with the highest COVID-19 infection occurrences at the hospital were identified in a timely manner, and safety protocols were implemented.

Open tracing tools: Overview and critical comparison

Background:Coping with the rapid growing complexity in contemporary software architecture, tracing has become an increasingly critical practice and been adopted widely by software engineers. By adopting tracing tools, practitioners are able to monitor, debug, and optimize distributed software architectures easily. However, with excessive number of valid candidates, researchers and practitioners have a hard time finding and selecting the suitable tracing tools by systematically considering their features and advantages. Objective:To such a purpose, this paper aims to provide an overview of popular Open tracing tools via comparison. Methods:Herein, we first identified 30 tools in an objective, systematic, and reproducible manner adopting the Systematic Multivocal Literature Review protocol. Then, we characterized each tool looking at the 1) measured features, 2) popularity both in peer-reviewed literature and online media, and 3) benefits and issues. We used topic modeling and sentiment analysis to extract and summarize the benefits and issues. Specially, we adopted ChatGPT to support the topic interpretation. Results:As a result, this paper presents a systematic comparison amongst the selected tracing tools in terms of their features, popularity, benefits and issues. Conclusion:The result mainly shows that each tracing tool provides a unique combination of features with also different pros and cons. The contribution of this paper is to provide the practitioners better understanding of the tracing tools facilitating their adoption.

Making applications faster by asynchronous execution: Slowing down processes or relaxing MPI collectives

Comprehending the performance bottlenecks at the core of the intricate hardware–software interactions exhibited by highly parallel programs on HPC clusters is crucial. This paper sheds light on the issue of automatically asynchronous MPI communication in memory-bound parallel programs on multicore clusters and how it can be facilitated. For instance, slowing down MPI processes by deliberate injection of delays can improve performance if certain conditions are met. This leads to the counter-intuitive conclusion that noise, independent of its source, is not always detrimental but can be leveraged for performance improvements. We employ phase-space graphs as a new tool to visualize parallel program dynamics. They are useful in spotting certain patterns in parallel execution that will easily go unnoticed with traditional tracing tools. We investigate five different microbenchmarks and applications on different supercomputer platforms: an MPI-augmented STREAM Triad, two implementations of Lattice-Boltzmann fluid solvers (D3Q19 and SPEChpc D2Q37), the LULESH and HPCG proxy applications.