Sample Processing Research Articles

CSP-Former: A Transformer-Based Network for Point Cloud Analysis with Compressed Sensing and Spatial Self-Attention

Point cloud analyzing and processing have attracted extensive attention due to their broad application in numerous sectors. Although many previous deep learning-based frameworks have had significant improvement, they often struggle with processing efficiency and neglect the spatial relationships between points. In this paper, we introduce CSP-Former, a novel framework for point cloud classification and segmentation. Inspired by the impressive strides of self-attention obtained in NLP and CV tasks, we designed a transformer-based network as a backbone for feature extraction; additionally, a fast sampling layer based on compressed sensing theory is proposed to enhance the sampling efficiency, which speeds up the sampling process through only once matrix multiplication. Subsequently, a hierarchical spatial self-attention module is also proposed to better capture the spatial relationships between points, improving segmentation performance. Extensive experiments on the ModelNet40 and ShapeNet part datasets demonstrate that our proposed framework achieves superior performance in point cloud classification and segmentation tasks.

A single microfluidic device for multi-omics analysis sample preparation.

Combining different "omics" approaches, such as genomics and proteomics, is necessary to generate a detailed and complete insight into microbiome comprehension. Proper sample collection and processing and accurate analytical methods are crucial in generating reliable data. We previously developed the ChipFilter device for proteomic analysis of microbial samples. We have shown that this device coupled to LC-MS/MS can successfully be used to identify microbial proteins. In the present work, we have developed our workflow to analyze concomitantly proteins and nucleic acids from the same sample. We performed lysis and proteolysis in the device using cultures of E. coli, B. subtilis, and S. cerevisiae. After peptide recovery for LC-MS/MS analysis, DNA from the same samples was recovered and successfully amplified by PCR for the 3 species. This workflow was further extended to a complex microbial mixture of known compositions. Protein analysis was carried out, enabling the identification of more than 5000 proteins. The recovered DNA was sequenced, performing comparable to DNA extracted with a commercial kit without proteolysis. Our results show that the ChipFilter device is suited to prepare samples for parallel proteomic and genomic analyses, which is particularly relevant in the case of low-abundant samples and drastically reduces sampling bias.

Remote Mapping of Bedrock for Future Cosmogenic Nuclide Exposure Dating Studies in Unvisited Areas of Antarctica

Cosmogenic nuclide exposure dating is an important technique for reconstructing glacial histories. Many of the most commonly applied cosmogenic nuclides are extracted from the mineral quartz, meaning sampling of felsic (silica-rich) rock is often preferred to sampling of mafic (silica-poor) rock for exposure dating studies. Fieldwork in remote regions such as Antarctica is subject to time constraints and considerable logistical challenges, making efficient sample recovery critical to successful research efforts. Remote sensing offers an effective way to map the geology of large areas prior to fieldwork and expedite the sampling process. In this study, we assess the viability of multispectral remote sensing to distinguish felsic from mafic rock outcrops at visible-near infrared (VNIR) and shortwave infrared (SWIR) wavelengths using both the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) and very high-resolution Worldview-3 (WV-3) imagery. We applied a combination of spectral mapping and ground truth from spectral measurements of 17 rock samples from Mount Murphy in the Amundsen Sea sector of West Antarctica. Using this approach, we identified four dominant rock types which we used as a basis for felsic–mafic differentiation: felsic granites and gneisses, and mafic basalts and fragmental hydrovolcanic rocks. Supervised classification results indicate WV-3 performs well at differentiating felsic and mafic rock types and that ASTER, while coarser, could also achieve satisfactory results and be used in concert with more targeted WV-3 image acquisitions. Finally, we present a revised felsic–mafic geological map for Mt Murphy. Overall, our results highlight the potential of spectral mapping for preliminary reconnaissance when planning future cosmogenic nuclide sampling campaigns in remote, unvisited areas of the polar regions.

The Monte Carlo Model and Its Application

This research mainly investigated the Monte Carlo model through literature review and case analysis. This research provides an example of the area of a circle to quickly understand what a Monte Carlo model is. Through Monte Carlo, this paper introduced some other algorithms based on it, such as Markov chain, Monte Carlo Markov chain algorithm and Metropolis algorithm. In addition, the Ising model was introduced and it was found that the model can calculate the energy change corresponding to different probabilities of spin acceptance or rejection flip using the Boltzmann distribution at the same temperature. The main objective of this research is that most Ising models occur in high-dimensional states, changing the spin will affect the adjacent spins, and the difficulty of calculating the energy changes increases dramatically with increasing dimensions. Research has found that Monte Carlo methods enable Ising model problems in high-dimensional or complex interactions to be effectively solved through Monte Carlo simulations. Through extensive random sampling and statistical processing, Monte Carlo simulations can estimate the transition behavior of each spin

Design and fabrication of novel microfluidic-based droplets for drug screening on a chronic myeloid leukemia cell line.

The challenges associated with traditional drug screening, such as high costs and long screening times, have led to an increase in the use of single-cell isolation technologies. Small sample volumes are required for high-throughput, cell-based assays to reduce assay costs and enable rapid sample processing. Using microfluidic chips, single-cell analysis can be conducted more effectively, requiring fewer reagents and maintaining biocompatibility. Due to the chip's ability to manipulate small volumes of fluid, high-throughput screening assays can be developed that are both miniaturized and automated. In the present study, we employ microfluidic chips for drug screening in chronic myeloid leukemia. This study aimed to establish a robust methodology integrating diverse assays, providing a holistic understanding of drug response. Herein, we have used a chronic myeloid leukemia derived cell line (K562) for drug screening with an innovative microfluidic-based drug screening approach to investigate the efficacy of imatinib in K562 cells. Cell viability was assessed using MTT assay. Apoptosis was measured using Annexin/PI staining by flow cytometry. Significant increased apoptosis was seen in K562 cells treated with imatinib in the microfluidic device compared to cells treated with imatinib in 24- and 96-well plates. Moreover, in the microfluidic chip, drug screening time was reduced from 48 hours to 24 hours. Compared to traditional approaches, microfluidic-based drug screening efficiently evaluates the efficacy of imatinib in K562 cells. This approach is promising for drug discovery and treatment optimization, as it increases sensitivity and streamlines the screening process.

PENGARUH MOTIVASI DAN DISIPLIN KERJA TERHADAP KINERJA KARYAWAN DENGAN KEPUASAN KERJA SEBAGAI VARIABEL MEDIASI PADA PT X JAKARTA PUSAT

This study aims to analyze the impact of work discipline and motivation on employee performance, with job satisfaction acting as an intermediary variable. A quantitative research method was utilized in this investigation. The target population consisted of employees at PT X, located in Central Jakarta. The sampling process utilized a purposive sampling method, involving a total of 80 respondents. Data collection was conducted using a questionnaire formatted on a Likert scale. For data analysis, PLS technique was applied with the assistance of SMARTPLS 4.0 software. The PLS-SEM analysis consists of two main components: the Inner Model and the Outer Model. The result showed that motivation positively affects employee performance, but the impact is not significant. In contrast, work discipline has a positive and significant influence on employee performance. Moreover, both motivation and work discipline contribute positively and significantly to job satisfaction. Additionally, job satisfaction acts as a mediator in the relationship between motivation and work discipline with employee performance.

Leveraging mobility data to analyze persistent SARS-CoV-2 mutations and inform targeted genomic surveillance.

Given the rapid cross-country spread of SARS-CoV-2 and the resulting difficulty in tracking lineage spread, we investigated the potential of combining mobile service data and fine-granular metadata (such as postal codes and genomic data) to advance integrated genomic surveillance of the pandemic in the federal state of Thuringia, Germany. We sequenced over 6500 SARS-CoV-2 Alpha genomes (B.1.1.7) across 7 months within Thuringia while collecting patients' isolation dates and postal codes. Our dataset is complemented by over 66,000 publicly available German Alpha genomes and mobile service data for Thuringia. We identified the existence and spread of nine persistent mutation variants within the Alpha lineage, seven of which formed separate phylogenetic clusters with different spreading patterns in Thuringia. The remaining two are subclusters. Mobile service data can indicate these clusters' spread and highlight a potential sampling bias, especially of low-prevalence variants. Thereby, mobile service data can be used either retrospectively to assess surveillance coverage and efficiency from already collected data or to actively guide part of a surveillance sampling process to districts where these variants are expected to emerge. The latter concept was successfully implemented as a proof-of-concept for a mobility-guided sampling strategy in response to the surveillance of Omicron sublineage BQ.1.1. The combination of mobile service data and SARS-CoV-2 surveillance by genome sequencing is a valuable tool for more targeted and responsive surveillance.

Leveraging mobility data to analyze persistent SARS-CoV-2 mutations and inform targeted genomic surveillance

Given the rapid cross-country spread of SARS-CoV-2 and the resulting difficulty in tracking lineage spread, we investigated the potential of combining mobile service data and fine-granular metadata (such as postal codes and genomic data) to advance integrated genomic surveillance of the pandemic in the federal state of Thuringia, Germany. We sequenced over 6500 SARS-CoV-2 Alpha genomes (B.1.1.7) across 7 months within Thuringia while collecting patients’ isolation dates and postal codes. Our dataset is complemented by over 66,000 publicly available German Alpha genomes and mobile service data for Thuringia. We identified the existence and spread of nine persistent mutation variants within the Alpha lineage, seven of which formed separate phylogenetic clusters with different spreading patterns in Thuringia. The remaining two are subclusters. Mobile service data can indicate these clusters’ spread and highlight a potential sampling bias, especially of low-prevalence variants. Thereby, mobile service data can be used either retrospectively to assess surveillance coverage and efficiency from already collected data or to actively guide part of a surveillance sampling process to districts where these variants are expected to emerge. The latter concept was successfully implemented as a proof-of-concept for a mobility-guided sampling strategy in response to the surveillance of Omicron sublineage BQ.1.1. The combination of mobile service data and SARS-CoV-2 surveillance by genome sequencing is a valuable tool for more targeted and responsive surveillance.

Rapid identification of bacterial select agents using loop-mediated isothermal amplification

BackgroundPoint of need diagnostics provide efficient testing capability for remote or austere locations, decreasing the time to answer by minimizing travel or sample transport requirements. Loop-mediated isothermal amplification (LAMP) is an appealing technology for point-of-need diagnostics due to its rapid analysis time and minimal instrumentation requirements.MethodsHere, we designed and optimized nine LAMP assays that are sensitive and specific to targeted bacterial select agents including Bacillus anthracis, Francisella tularensis, Yersinia pestis, and Brucella spp. Evaluation of each assay determined preliminary limit of detection (LOD) with LOD confirmed across 60 replicates (≥ 95% positivity rate). Testing across a robust set of strains of the target agent, common DNA agents, and near-neighbors documented sensitivity and specificity for independent assays.ResultsSpecifically, all assays were 100% specific and sensitive except for Y. pestis Caf1 (90% inclusive across Y. pestis strains).ConclusionHere, we optimized assay turn-around-time, decreasing a standard 60 min traditional polymerase chain reaction (PCR) to 30 min using LAMP with positive results in as little as 5–10 min. Incorporating point of need sample processing and evaluating the potential inhibitory impact of sample matrices such as whole blood and soil would be needed to enable this test system for use on field-forward clinical and environmental sample testing.

Influence of social media on children's dietary habits

Introduction: Dietary habits refer to the consistent choices made by individuals or groups concerning their food consumption. It has a crucial influence in human health and reflects individual eating choices, which are often associated with culture, education, social background, and health status. Dietary habits may be influenced and altered by life stages and lifestyle factors, including physical activity and social interac-tion. Nutritional consumption significantly influences human health and well-being, particularly during childhood and adolescence, and directly impacts children's health due to their physical, mental, and cognitive development. Approaches: Data has been gathered from 100 children to evaluate the impact of social media on their dietary practices. The questionnaire was administered to professionals to establish its validity and subsequently its reliability. The total number of items in the questionnaire was 19. To evaluate children's behavior on social media about eating practices. The data was gathered by a simple random sampling process and analyzed using both descriptive and inferen-tial statistical techniques. Outcomes The results indicated that among 100 children, the mean age of participation was 15.66 years. The cur-rent study demonstrated a moderate impact of social media on children's food habits. The study demonstrated a substantial statistical link between children's age and hours spent on social media, as well as the impact of social media on children's food habits (p < 0.05). The re-sults indicated no statistically significant differences (p > 0.05) between social media usage and other demographic variables. Concludes The findings indicated that social media exerted a moderate influence on children's food habits. The study concluded that a substantial statistical link exists between children's age, hours of social media usage, and the impact of social media on children's food habits. The results indicat-ed no significant statistical differences between social media usage and other demographic variables.

A Reusable Capillary Flow-Driven Microfluidic System for Abscisic Acid Detection Using a Competitive Immunoassay

Point-of-care (PoC) devices offer a promising solution for fast, portable, and easy-to-use diagnostics. These characteristics are particularly relevant in agrifood fields like viticulture where the early detection of plant stresses is crucial to crop yield. Microfluidics, with its low reagent volume requirements, is well-suited for such applications. Self-driven microfluidic devices, which rely on capillary forces for fluid motion, offer an attractive alternative by eliminating the need for external pumps and complex fluid control systems. However, traditional microfluidic prototyping materials like polydimethylsiloxane (PDMS) present challenges due to their hydrophobic nature. This paper presents the development of a reusable, portable, capillary-driven microfluidic platform based on a PDMS-PEG (polyethylene glycol) copolymer designed for the rapid low-cost detection of abscisic acid (ABA), a key biomarker for the onset of ripening of non-climacteric fruits and drought stress in vines. By employing passive fluid transport mechanisms, such as capillary-driven sequential flow, this platform enables precise biological and chemical screenings while maintaining portability and ease of use. A simplified field-ready sample processing method is used to prepare the grapes for analysis.

Proteomics: An In-Depth Review on Recent Technical Advances and Their Applications in Biomedicine.

Proteins hold pivotal importance since many diseases manifest changes in protein activity. Proteomics techniques provide a comprehensive exploration of protein structure, abundance, and function in biological samples, enabling the holistic characterization of overall changes in organisms. Nowadays, the breadth of emerging methodologies in proteomics is unprecedentedly vast, with constant optimization of technologies in sample processing, data collection, data analysis, and its scope of application is steadily transitioning from the bench to the clinic. Here, we offer an insightful review of the technical developments in proteomics and its applications in biomedicine over the past 5 years. We focus on its profound contributions in profiling disease spectra, discovering new biomarkers, identifying promising drug targets, deciphering alterations in protein conformation, and unearthing protein-protein interactions. Moreover, we summarize the cutting-edge technologies and potential breakthroughs in the proteomics pipeline and provide the principal challenges in proteomics. Based on these, we aspire to broaden the applicability of proteomics and inspire researchers to enhance our understanding of complex biological systems by utilizing such techniques.

Large errors in soil carbon measurements attributed to inconsistent sample processing

Large errors in soil carbon measurements attributed to inconsistent sample processing

Breaking the Bone Marrow Barrier: Peripheral Blood as a Gateway to Measurable Residual Disease Detection in Acute Myelogenous Leukemia.

Acute myeloid leukemia (AML) is a genetically heterogeneous disease with high rates of relapse after initial treatment. Identifying measurable residual disease (MRD) following initial therapy is essential to assess response, predict patient outcomes, and identify those in need of additional intervention. Currently, MRD analysis relies on invasive, serial bone marrow (BM) biopsies, which complicate sample availability and processing time and negatively impact patient experience. Additionally, finding a positive result can generate more questions than answers, causing anxiety for both the patient and the provider. Peripheral blood (PB) evaluation has shown promise in detecting MRD and is now recommended by the European Leukemia Net for AML for certain genetic abnormalities. PB-based sampling allows for more frequent testing intervals and better temporal resolution of malignant expansion while sparing patients additional invasive procedures. In this review, we will discuss the current state of PB testing for MRD evaluation with a focus on next-generation sequencing methodologies that are capable of MRD detection across AML subtypes.

Mars Sample Return: From collection to curation of samples from a habitable world

NASA’s Mars 2020 mission has initiated collection of samples from Mars’ Jezero Crater, which has a wide range of ancient rocks and rock types from lavas to lacustrine sedimentary rocks. The Mars Sample Return (MSR) Campaign, a joint effort between NASA and ESA, aims to bring the Perseverance collection back to Earth for intense scientific investigation. As the first return of samples from a habitable world, there are important challenges to overcome for the successful implementation of the MSR Campaign from the point of sample collection on Mars to the long-term curation of the samples on Earth. In particular, the successful execution of planetary protection protocols adds well-warranted complexity to every step of the process from the two MSR Program flight elements to the ground element at the sample receiving facility (SRF). In this contribution, we describe the architecture of the MSR Campaign, with a focus on infrastructure needs for the curation (i.e., the clean storage, processing, and allocation) of pristine Martian samples. Curation is a science-enabling and planetary protection-enabling activity, and the curation practices described in this contribution for the SRF and any long-term curation facility will enable the sample safety assessment, initial scientific investigations of the samples, and establish the MSR collection as a scientific resource that will enable generations of science and discovery through studies of the returned Mars samples. The planetary protection and curation processes established for MSR will provide critical insights into potential future sample return missions from other habitable worlds like Enceladus and Europa.

Assessing Data Adequacy in Qualitative Research Studies.

When undertaking qualitative research studies, researchers often use the concept of data saturation to justify sufficient sampling to cease data collection and analysis. We argue that this reveals a positivist perspective that is incompatible with qualitative research,1 which is instead based on constructivist, interpretivist, or other perspectives. Instead, we recommended the concepts of information power,2conceptual depth,3 and theoretical sufficiency,1,4,5 with data adequacy considered during research design and evaluated iteratively throughout the sampling, data collection, and analysis processes. The table below provides guidelines for when more, or less, data are needed to justify cessation of data collection and analysis. Both researchers and readers can use the criteria for assessing data adequacy.

Droplet-Based Single-Cell 3' mRNA Sequencing of Marburg Virus-Infected Samples.

Single-cell technologies are continually evolving with emerging methods that are gradually uncovering the central DNA-RNA-protein dogma. Single-cell RNA sequencing is one arm of a multi-omic approach that achieves an astounding level of granularity to reveal the complexity of virus-host interactions at the transcriptomic level. Cell tropism, virus replication, pathogenesis, and gene expression changes mediated by the virus and the host's immune response to infection are just some areas of study that are gaining better clarity due to the high-resolution analysis afforded by the technology.We describe a single-cell sequencing protocol for Marburg virus infection in vivo using nonhuman primate blood and the 10× Chromium Next GEM single-cell genomics methodology. Working with pathogens of high consequence is logistically complicated, requiring containment in biosafety level (BSL)-4 laboratories and harsh inactivation procedures before samples can safely be removed to lower biosafety conditions. We provide procedural insight into sample isolation and processing conducted in BSL-4 and describe the requirements for safe sample removal without jeopardizing quality for down-stream sequencing and analysis in BSL-2 conditions. Characterization of complicated biological processes mediated by high-containment pathogens, typically restricted to analogous model systems, e.g., minigenome, can be achieved using live virus.

Collection and Processing of Samples for Next-Generation Sequencing to Study the Gut Microbiome.

16S rRNA gene sequencing is commonly used for identification and quantitation of microorganisms in complex biological mixtures, such as the human gut microbiome. The 16S rRNA gene is an excellent target gene for sequencing DNA in a heterogenous sample, as it is a highly conserved part of the transcriptional machinery. Universal PCR primers are used to amplify the conserved regions of 16S. Thus, it is possible to amplify the gene in a wide range of different microorganisms from a single sample. As the 16S rRNA gene consists of both conserved and variable regions, sequencing of the variable regions can be used to differentiate between different bacterial species.

Molecular detection of Cooperia oncophora and Ostertagia ostertagi in cattle: Comparison of sample processing and detection on ddPCR and qPCR platforms.

Faecal samples were obtained from 77 first season grazers from 20 Norwegian dairy herds in autumn 2020 for analysis of Cooperia oncophora and Ostertagia ostertagi infection. Strongylid eggs per gram of faeces (EPG) were determined for each sample and the samples underwent larval culture. DNA was extracted from the faeces at different stages of the culture preparation: from faecal slurry (FS), direct extraction before culture (DBC), and direct extraction after culture (DAC). Extracted DNA was subject to molecular assay for both C. oncophora and O. ostertagi using both a published ddPCR assay and a modified qPCR duplex assay targeting the ITS-2 gene. For C. oncophora, DBC samples contained significantly less ITS-2 copies than DAC and FS samples (p≤0.0001 for both) for qPCR, but not between DAC and FS samples (p=0.339). Droplet digital PCR with DBC samples yielded significantly fewer ITS-2 copies than DAC and FS samples (p≤0.0001). For O. ostertagi, the ITS-2 copies in DBC samples differed significantly from levels in DAC and FS samples on the qPCR platform (p=0.002 and 0.044, respectively) as was the case with ddPCR (p≤0.0001 and 0.0137). Overall, across the various processing techniques, C. oncophora results obtained on both ddPCR and qPCR platforms correlated with EPG better than was found for equivalent results for O. ostertagi and results are strongly indicative of poor correlation when EPG counts are low. Results from this study suggest that DAC faecal processing was of limited practical use.

A Sociological Study about Effects of Global Media on Youth Culture in Dera Ghazi Khan

The study employs quantitative techniques to support the theory, using a structured approach to forecast causal relationships, measure variations and describe population characteristics. Conducted in Dera Ghazi Khan, the research targets 300 university students selected through a two-stage sampling process. In conclusion, the findings highlight the significant impact of global media on various aspects of culture, including food preferences, music, language, and dressing styles. The majority of respondents acknowledge that global media influences their culture with Chinese cuisine being most prominently promoted, and the widespread appeal of Pop & Rock music. Furthermore, global media's promotion of foreign cultural practices is seen as encouraging the adoption of such practices, especially among the youth. Additionally, there is a clear association between the promotion of global media dressing styles and the perception of cultural changes. The preference for fast food over home-cooked meals and the increasing use of English in academics, influenced by global media's promotion of certain accents, further emphasize the growing influence of global media on lifestyle choices. Recommendations for future research could explore strategies to balance global media influences with the preservation of cultural heritage, especially in educational and community settings.