Portable Format Research Articles

Monte Carlo simulation of spatial frequency domain imaging for breast tumors during compression.

Near-infrared optical imaging methods have shown promise for monitoring response to neoadjuvant chemotherapy (NAC) for breast cancer, with endogenous contrast coming from oxy- and deoxyhemoglobin. Spatial frequency domain imaging (SFDI) could be used to detect this contrast in a low-cost and portable format, but it has limited imaging depth. It is possible that local tissue compression could be used to reduce the effective tumor depth. To evaluate the potential of SFDI for therapy response prediction, we aim to predict how changes to tumor size, stiffness, and hemoglobin concentration would be reflected in contrast measured by SFDI under tissue compression. Finite element analysis of compression on an inclusion-containing soft material is combined with Monte Carlo simulation to predict the measured optical contrast. When the effect of compression on blood volume is not considered, contrast gain from compression increases with the size and stiffness of the inclusion and decreases with the inclusion depth. With a model of reduction of blood volume from compression, compression reduces imaging contrast, an effect that is greater for larger inclusions and stiffer inclusions at shallower depths. This computational modeling study represents a first step toward tracking tumor changes induced by NAC using SFDI and local compression.

Digitized Kinetic Analysis Enhances Genotyping Capacity of CRISPR-Based Biosensing.

CRISPR/Cas systems have been widely employed for nucleic acid biosensing and have been further advanced for mutation detection by virtue of the sequence specificity of crRNA. However, existing CRISPR-based genotyping methods are limited by the mismatch tolerance of Cas effectors, necessitating a comprehensive screening of crRNAs to effectively distinguish between wild-type and point-mutated sequences. To circumvent the limitation of conventional CRISPR-based genotyping, here, we introduce Single-Molecule kinetic Analysis via a Real-Time digital CRISPR/Cas12a-assisted assay (SMART-dCRISPR). SMART-dCRISPR leverages the differential kinetics of the signal increase in CRISPR/Cas systems, which is modulated by the complementarity between crRNA and the target sequence. It employs single-molecule digital measurements to discern mutations based on kinetic profiles that could otherwise be obscured by variations in the target concentrations. We applied SMART-dCRISPR to genotype notable mutations in SARS-CoV-2, point mutation (K417N) and deletion (69/70DEL), successfully distinguishing wild-type, Omicron BA.1, and Omicron BA.2 SARS-CoV-2 strains from clinical nasopharyngeal/nasal swab samples. Additionally, we introduced a portable digital real-time sensing device to streamline SMART-dCRISPR and enhance its practicality for point-of-care settings. The combination of a rapid and sensitive isothermal CRISPR-based assay with single-molecule kinetic analysis in a portable format significantly enhances the versatility of CRISPR-based nucleic acid biosensing and genotyping.

Abstract 7420: Optimizing proteomic data access and analysis in the cloud: Leveraging Terra's integration with the Proteomic Data Commons

Abstract The Proteomic Data Commons (PDC) hosts cancer proteomics data with the goal of making this data available to the public to support development of cancer diagnostics, treatment, and progression tracking. As a part of the Cancer Research Data Commons (CRDC), the Terra platform provides a cloud workbench for the PDC data. FireCloud is a Broad Institute project funded by NCI to empower cancer researchers to access data, run analysis tools and collaborate securely in the cloud. It is powered by Terra, a secure, scalable cloud-native platform developed by the Broad Institute, Microsoft, and Verily, an Alphabet company. It provides batch workflow execution, interactive analysis including data visualization, and ~2,900 publicly available tools with the ability to import more tools from Dockstore. The integration of PDC and Terra enables researchers to leverage the data navigation and file-level search capabilities on the PDC web browser (pdc.cancer.gov) and export selected data manifests to a Terra workspace. This integrated hand-off specifically allows metadata and cloud links to PDC data in Portable Format for Bioinformatics (PFB) to be transferred to Terra and used in analysis with cloud resources. A featured workspace for Terra-PDC integration includes tools for (i) downloading data files and relevant additional metadata; (ii) organizing the data and metadata for running the FragPipe workflow, a comprehensive collection of tools for reading and processing raw Mass Spec (MS) data; and (iii) implementing a pre-configured FragPipe workflow to process isobarically labeled MS data from Tandem Mass Tag (TMT) or Isobaric tags for relative and absolute quantitation (iTRAQ) experiments using information automatically imported from PDC via the PFB import. The pipelines can also be customized as needed to process any type of raw MS data the PDC supports. In addition, Terra connects to the NCI Genomic Data Commons (GDC) and hosts The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) datasets allowing users to pull in other data types for co-analysis. As a whole, using the CRDC cloud resources, in conjunction with Terra, allows analysis of data on a massive scale, enabling multi-omic integration spanning the genomic and proteomic commons data, with easy sharing of data and tools. Citation Format: Emily LaPlante, Bingxing Huo, DR Mani, Ratna R. Thangudu. Optimizing proteomic data access and analysis in the cloud: Leveraging Terra's integration with the Proteomic Data Commons [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7420.

Research Status in the Use of Surface-Enhanced Raman Scattering (SERS) to Detect Pesticide Residues in Foods and Plant-Derived Chinese Herbal Medicines.

Surface-enhanced Raman scattering (SERS) technology has unique advantages in the rapid detection of pesticides in plant-derived foods, leading to reduced detection limits and increased accuracy. Plant-derived Chinese herbal medicines have similar sources to plant-derived foods; however, due to the rough surfaces and complex compositions of herbal medicines, the detection of pesticide residues in this context continues to rely heavily on traditional methods, which are time consuming and laborious and are unable to meet market demands for portability. The application of flexible nanomaterials and SERS technology in this realm would allow rapid and accurate detection in a portable format. Therefore, in this review, we summarize the underlying principles and characteristics of SERS technology, with particular focus on applications of SERS for the analysis of pesticide residues in agricultural products. This paper summarizes recent research progress in the field from three main directions: sample pretreatment, SERS substrates, and data processing. The prospects and limitations of SERS technology are also discussed, in order to provide theoretical support for rapid detection of pesticide residues in Chinese herbal medicines.

Digital microfluidics with distance-based detection - a new approach for nucleic acid diagnostics.

There is great enthusiasm for using loop-mediated isothermal amplification (LAMP) in point-of-care nucleic acid amplification tests (POC NAATs), as an alternative to PCR. While isothermal amplification techniques like LAMP eliminate the need for rapid temperature cycling in a portable format, these systems are still plagued by requirements for dedicated optical detection apparatus for analysis and manual off-chip sample processing. Here, we developed a new microfluidic system for LAMP-based POC NAATs to address these limitations. The new system combines digital microfluidics (DMF) with distance-based detection (DBD) for direct signal readout. This is the first report of the use of (i) LAMP or (ii) DMF with DBD - thus, we describe a number of characterization steps taken to determine optimal combinations of reagents, materials, and processes for reliable operation. For example, DBD was found to be quite sensitive to background signals from low molecular weight LAMP products; thus, a Capto™ adhere bead-based clean-up procedure was developed to isolate the desirable high-molecular-weight products for analysis. The new method was validated by application to detection of SARS-CoV-2 in saliva. The method was able to distinguish between saliva containing no virus, saliva containing a low viral load (104 genome copies per mL), and saliva containing a high viral load (108 copies per mL), all in an automated system that does not require detection apparatus for analysis. We propose that the combination of DMF with distance-based detection may be a powerful one for implementing a variety of POC NAATs or for other applications in the future.

Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review.

Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.

RPA-CRISPR/Cas12a-Based Detection of Haemophilus parasuis.

Haemophilus parasuis (H. parasuis, HPS) is a prominent pathogenic bacterium in pig production. Its infection leads to widespread fibrinous inflammation in various pig tissues and organs, often in conjunction with various respiratory virus infections, and leads to substantial economic losses in the pig industry. Therefore, the rapid diagnosis of this pathogen is of utmost importance. In this study, we used recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR) technology to establish a convenient detection and analysis system for H. parasuis that is fast to detect, easy to implement, and accurate to analyze, known as RPA-CRISPR/Cas12a analysis. The process from sample to results can be completed within 1 h with high sensitivity (0.163 pg/μL of DNA template, p < 0.05), which is 104 -fold higher than the common PCR method. The specificity test results show that the RPA-CRISPR/Cas12a analysis of H. parasuis did not react with other common pig pathogens, including Streptococcus suis type II and IX, Actinobacillus pleuropneumoniae, Escherichia coli, Salmonella, Streptococcus suis, and Staphylococcus aureus (p < 0.0001). The RPA-CRISPR/Cas12a assay was applied to 15 serotypes of H. parasuis clinical samples through crude extraction of nucleic acid by boiling method, and all of the samples were successfully identified. It greatly reduces the time and cost of nucleic acid extraction. Moreover, the method allows results to be visualized with blue light. The accurate and convenient detection method could be incorporated into a portable format as point-of-care (POC) diagnostics detection for H. parasuis at the field level.

Sample-to-answer sensing technologies for nucleic acid preparation and detection in the field.

Efficient sample preparation and accurate disease diagnosis under field conditions are of great importance for the early intervention of diseases in humans, animals, and plants. However, in-field preparation of high-quality nucleic acids from various specimens for downstream analyses, such as amplification and sequencing, is challenging. Thus, developing and adapting sample lysis and nucleic acid extraction protocols suitable for portable formats have drawn significant attention. Similarly, various nucleic acid amplification techniques and detection methods have also been explored. Combining these functions in an integrated platform has resulted in emergent sample-to-answer sensing systems that allow effective disease detection and analyses outside a laboratory. Such devices have a vast potential to improve healthcare in resource-limited settings, low-cost and distributed surveillance of diseases in food and agriculture industries, environmental monitoring, and defense against biological warfare and terrorism. This paper reviews recent advances in portable sample preparation technologies and facile detection methods that have been / or could be adopted into novel sample-to-answer devices. In addition, recent developments and challenges of commercial kits and devices targeting on-site diagnosis of various plant diseases are discussed.

Rapid genotyping of 32 insertion/deletion panel for human identification using fluorogenic probes-based multiplex real-time PCR

BackgroundInsertion and deletion (InDel) polymorphisms have considerable potential in the field of forensic genetics because of their low mutation rate and small amplicons. At present, InDel polymorphisms detection based on the technique of capillary electrophoresis is the main technique used in forensic DNA laboratory. However, this method is complicated and time-consuming, and is not suitable for rapid on-site paternity and personal identification. Next-generation sequencing analysis of InDels polymorphisms requires expensive instruments, large upfront reagent and supply costs, computational requirements and complex bioinformatics, increased the time to obtain results. Thus, there is an urgent need to establish a method to provide reliable, rapid, sensitive and economical genotyping for InDels. MethodA rapid InDels (32 InDels) panel was established using fluorogenic probes-based multiplex real-time PCR with microfluidic test cartridge and portable real-time PCR instrument. Then, we performed several validation studies including concordance, accuracy, sensitivity, stability, species specificity. ResultsIt showed that the complete genotypes could be obtained from ≥100 pg of input DNA and from a series of challenging samples with high accuracy and specificity within 90 min. ConclusionThis method provides a rapid and cost-effective solution for InDels genotyping and personal identification in portable format.

In memoriam Klaus Kubitzki (1933–2022)

In memoriam Klaus Kubitzki (1933–2022)

RNAprofiling 2.0: Enhanced Cluster Analysis of Structural Ensembles

Understanding the base pairing of an RNA sequence provides insight into its molecular structure. By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes them into profiles which partition the Boltzmann sample, and highlights key similarities/differences among the most informative, i.e. selected, profiles in a graphical format. Version 2.0 enhances every step of this approach. First, the featured substructures are expanded from helices to stems. Second, profile selection includes low-frequency pairings similar to featured ones. In conjunction, these updates extend the utility of the method to sequences up to length 600, as evaluated over a sizable dataset. Third, relationships are visualized in a decision tree which highlights the most important structural differences. Finally, this cluster analysis is made accessible to experimental researchers in a portable format as an interactive webpage, permitting a much greater understanding of trade-offs among different possible base pairing combinations.

Healthcare Professionals' Perceptions, Barriers, and Facilitators towards Adopting Computerised Clinical Decision Support Systems in Antimicrobial Stewardship in Jordanian Hospitals.

Understanding healthcare professionals' perceptions towards a computerised decision support system (CDSS) may provide a platform for the determinants of the successful adoption and implementation of CDSS. This cross-sectional study examined healthcare professionals' perceptions, barriers, and facilitators to adopting a CDSS for antibiotic prescribing in Jordanian hospitals. This study was conducted among healthcare professionals in Jordan's two tertiary and teaching hospitals over four weeks (June-July 2021). Data were collected in a paper-based format from senior and junior prescribers and non-prescribers (n = 254) who agreed to complete a questionnaire. The majority (n = 184, 72.4%) were aware that electronic prescribing and electronic health record systems could be used specifically to facilitate antibiotic use and prescribing. The essential facilitator made CDSS available in a portable format (n = 224, 88.2%). While insufficient training to use CDSS was the most significant barrier (n = 175, 68.9%). The female providers showed significantly lower awareness (p = 0.006), and the nurses showed significantly higher awareness (p = 0.041) about using electronic prescribing and electronic health record systems. This study examined healthcare professionals' perceptions of adopting CDSS in antimicrobial stewardship (AMS) and shed light on the perceived barriers and facilitators to adopting CDSS in AMS, reducing antibiotic resistance, and improving patient safety. Furthermore, results would provide a framework for other hospital settings concerned with implementing CDSS in AMS and inform policy decision-makers to react by implementing the CDSS system in Jordan and globally. Future studies should concentrate on establishing policies and guidelines and a framework to examine the adoption of the CDSS for AMS.

Towards self-describing and FAIR bulk formats for biomedical data.

We introduce a self-describing serialized format for bulk biomedical data called the Portable Format for Biomedical (PFB) data. The Portable Format for Biomedical data is based upon Avro and encapsulates a data model, a data dictionary, the data itself, and pointers to third party controlled vocabularies. In general, each data element in the data dictionary is associated with a third party controlled vocabulary to make it easier for applications to harmonize two or more PFB files. We also introduce an open source software development kit (SDK) called PyPFB for creating, exploring and modifying PFB files. We describe experimental studies showing the performance improvements when importing and exporting bulk biomedical data in the PFB format versus using JSON and SQL formats.

Cross-cultural forager myth transmission rules: Implications for the emergence of cumulative culture

For most of human evolution, accumulated cultural knowledge has been stored in memory and transmitted orally. This presents a daunting information management problem: how to store and transmit this knowledge in a portable format that resists corruption. One solution–widespread among foragers–is to encode knowledge in narrative. However, this strategy depends on accurate performance of the story. Significantly, some forager cultures have rules regulating myth performance, although the extent of this phenomenon is unknown. We hypothesize that these rules subserve high-fidelity transmission across generations. Accordingly, we predicted that, across forager cultures, myth-telling rules will mandate: (P1) transmission by the most proficient storytellers (P2) under low-distraction conditions with (P3) multiple individuals and (P4) multiple generations present, and the application of measures that (P5) prevent, identify, and/or correct errors, (P6) maintain audience attention, (P7) discourage rule violations and/or (P8) incentivize rule compliance. To test these predictions, we searched the forager ethnographic record for descriptions of myth performance, and coded them for prescriptions/proscriptions regarding narrator age, performance context, audience composition, narrative delivery, and audience comportment, as well as sanctions associated with rule transgression or compliance. Results indicate that rules regulating myth performance are widespread across forager cultures, and are characterized by features that reduce the likelihood of copy errors. These findings help elucidate the role that anthropogenic ratchets played in the emergence of cumulative culture.

Building the nation on 16mm: Film formats and the institutionalization of cinematic portability in 1930s China

This article examines the role played by the 16 mm format in shaping ideas of portable projection in 1930s China. Drawing on research into the Chinese educational film movement, I argue for a format-oriented approach to cinema history that tracks heretofore neglected aspects of how the state—as well as non-state actors—exercised power on and through cinema. As a portable format, 16 mm extracted cinema from urbanized film culture while offering its users access to a broader ‘national’ audience. Educators built a mobile 16 mm network connecting schools and mass education sites and formulated a discourse that sought to codify the place of ‘small scale cinema’ in the Chinese nation and in global media hierarchies. Small scale cinema was deeply contradictory. While promising to make cinema broadly accessible to the Chinese masses, 16 mm also restricted that access. While seemingly liberating cinema from the sway of global film culture and China’s treaty-port cosmopolitanism, 16 mm subjected mass education to other patterns of asymmetrical development. By examining how educational cinema was formed at the intersection of global film technologies and local institutional discourses, I formulate an approach to cine-governmentality that shows how the state’s control of cinema worked from the bottom up, as actors on multiple scales negotiated chaotic circulations of films, equipment, and ideas.

Spectrometers in Wonderland: Shrinking, Shrinking, Shrinking

This article gives a brief overview of the major portable techniques: those based on optical spectroscopy techniques, including near-infrared (NIR), mid-infrared (mid-IR), and Raman spectroscopy; mass spectrometry (MS) systems, including high-pressure MS (HPMS), gas chromatography–MS (GC–MS), ion mobility spectrometry (IMS); elemental techniques, such as X-ray fluorescence (XRF) and laser-induced breakdown spectroscopy (LIBS); and emerging miniaturized techniques like nuclear magnetic resonance (NMR). The above are all “conventional” spectroscopic techniques and reduced to a rugged portable format, containing self-contained data systems. They provide specific and actionable information to their operators working with them outside the laboratory—in the field—and these instruments have well-defined value propositions. A recent development is the availability of low cost (&lt;$100) multispectral sensors operating in the visible and NIR regions. This low cost enables the sensors to be embedded into consumer products, such as smart “white goods” appliances, personal care, fitness products, and even “wearables” products. In the future, miniature and portable spectrometers will be ubiquitous—outside the laboratory, and in your home and pocket.

MarpolBase Expression: A Web-Based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha.

The liverwort Marchantia polymorpha is equipped with a wide range of molecular and genetic tools and resources that have led to its wide use to explore the evo-devo aspects of land plants. Although its diverse transcriptome data are rapidly accumulating, there is no extensive yet user-friendly tool to exploit such a compilation of data and to summarize results with the latest annotations. Here, we have developed a web-based suite of tools, MarpolBase Expression (MBEX, https://marchantia.info/mbex/), where users can visualize gene expression profiles, identify differentially expressed genes, perform co-expression and functional enrichment analyses and summarize their comprehensive output in various portable formats. Using oil body biogenesis as an example, we demonstrated that the results generated by MBEX were consistent with the published experimental evidence and also revealed a novel transcriptional network in this process. MBEX should facilitate the exploration and discovery of the genetic and functional networks behind various biological processes in M. polymorpha and promote our understanding of the evolution of land plants.

Label-free detection of HPV mRNA with an artificial chaperone-enhanced MNAzyme (ACEzyme)-based electrochemical sensor

Nucleic acid biosensors for point-of-care (POC) diagnostic applications are highly desirable. The ability to detect DNA and RNA in a simple, rapid, affordable and portable format leads to a range of important applications for early screening in the field of disease monitoring and management. Herein, we report the development of an isothermal, label-free electrochemical biosensor that was designed on the basis of target-driven MNAzyme cleavage activity. Hybridization with HPV mRNA, a model nucleic acid target, activated MNAzyme and initiated the cleavage of immobilized hairpin substrates, leading to changes in the electrochemical signal. Under optimal conditions, a detection limit of 2.6 pM was obtained with an incubation time of 60 min. Furthermore, an artificial chaperone-enhanced MNAzyme (ACEzyme) system was integrated to an electrochemical biosensor for the first time. The analytical performance of the biosensor was enhanced, and the detection time was significantly reduced by the addition of PLL-g-Dex, which exhibits nucleic acid chaperone-like activity. A detection limit of 0.88 pM was obtained with a threefold decrease in incubation time without prior amplification. The proposed biosensing platform shows the advantages of simple fabrication and operation, good selectivity in the presence of single-base mismatch, and excellent versatility in a complex mixture of total RNA. We believe that this isothermal, label-free, and protein-free nucleic acid analysis platform could provide foundations for the further development of a universal nucleic acid biosensing platform for clinical application.

Blood-Coated Sensor for High-Throughput Ptychographic Cytometry on a Blu-ray Disc.

The Blu-ray drive is an engineering masterpiece that integrates disc rotation, pickup head translation, and three lasers in a compact and portable format. Here, we integrate a blood-coated image sensor with a modified Blu-ray drive for high-throughput cytometric analysis of various biospecimens. In this device, samples are mounted on the rotating Blu-ray disc and illuminated by the built-in lasers from the pickup head. The resulting coherent diffraction patterns are then recorded by the blood-coated image sensor. The rich spatial features of the blood-cell monolayer help down-modulate the object information for sensor detection, thus forming a high-resolution computational biolens with a theoretically unlimited field of view. With the acquired data, we develop a lensless coherent diffraction imaging modality termed rotational ptychography for image reconstruction. We show that our device can resolve the 435 nm line width on the resolution target and has a field of view only limited by the size of the Blu-ray disc. To demonstrate its applications, we perform high-throughput urinalysis by locating disease-related calcium oxalate crystals over the entire microscope slide. We also quantify different types of cells on a blood smear with an acquisition speed of ∼10,000 cells per second. For in vitro experiments, we monitor live bacterial cultures over the entire Petri dish with single-cell resolution. Using biological cells as a computational lens could enable new intriguing imaging devices for point-of-care diagnostics. Modifying a Blu-ray drive with the blood-coated sensor further allows the spread of high-throughput optical microscopy from well-equipped laboratories to citizen scientists worldwide.

StarPEG–heparin biosensors for rapid and portable diagnostics in complex biofluids

We demonstrate impedance chips modified with starPEG–heparin hydrogels as hemocompatible portable biosensors in portable format.