Preparation Steps Research Articles

Cutaneous Prototheca wickerhamii infection identified with the matrix-assisted laser desorption/ionization time-of flight mass spectrometry after protein extraction protocol for filamentous fungi isolates from a facial discharge of a 66-year-old female patient in Korea: a case report

Prototheca wickerhamii is an achlorophyllic algae that rarely acts as an opportunistic pathogen in humans. We report the case of a 66-year-old female patient with a history of diabetes mellitus who presented with a pus-like discharge from face, facial redness, and swelling. The patient was admitted to the emergency room with worsening facial pain. Gram staining from pus-like discharge revealed yeast like features; however, an isolated colony on a blood agar plate was not identified using VITEK 2 (Biomerieux) or matrix-assisted laser desorption/ionization time-of flight mass spectrometry (MALDI-TOF) using VITEK®MS (Biomerieux). Lactophenol cotton blue staining of the colony revealed characteristic sporangia and endospore features. After performing the protein extraction procedure for filamentous fungi (mold) isolates using ethanol and formic acid, MALDI-TOF MS identified the colony as Prototheca wickerhamii, with 99.9% confidence. This case indicates that Prototheca spp. require specialized sample preparation steps, such as the ethanol/formic acid extraction procedure, for identification using MALDI-TOF MS.

Evaluation of the extraction methods prior to ICP-MS determination of metal levels in kinetic (magic) sand samples used for children’s play

ABSTRACT Kinetic (magic) sand is widely used in preschool activities in order to improve the children’s creative abilities. Despite its popularity, this study will be the first in literature to assess the heavy metal content of kinetic sand samples. Focusing on the determination of metal content (Hg, Cd, Sb, Sn, Al, Ni, Co, Cu, Pb) of 10 different brands of kinetic sand samples sold in Turkish markets, the significance of sample preparation step was further discussed with the application of wet digestion and microwave digestion methods, prior to analysis by ICP-MS. Based on the acute toxicity classes defined by European Union (EU) As, Cd, Hg belongs to Class 1; Ni, CrVI, Pb belongs to Class 2, whereas Zn and Cu belongs to Class 3. Among the potential toxic elements studied, the Al content of samples attracts attention with its high level exceeding the limits of directives.

Pelatihan Meningkatkan Branding Melalui Implementasi Digital Marketing pada UMKM Aquascape (Aqua Menoreh Gallery)

This community service aims to develop digital technology mastery for MSMEs in entrepreneurship. To provide branding strength and increase market share, it is necessary to implement the use of social media for MSMEs so that their businesses can grow. The community service methods used include preparation, implementation, and evaluation. The preparation steps consist of licensing, observation of obstacles, and preparation of materials. The implementation stage includes explanations and training for MSMEs. The last stage is the evaluation stage by assessing the understanding of MSMEs' knowledge about digital marketing and increasing sales. The material to be provided is related to the concept of marketing content, the use of digital marketing e-commerce applications through social media. The results of community service utilizing digital marketing can provide a positive contribution in optimizing marketing for Aquascape Menoreh Gallery MSMEs. Better understanding and skills for MSMEs in using social media are expected to have a sustainable impact on the growth and development of MSMEs

A Comprehensive Approach to Bias Mitigation for Sentiment Analysis of Social Media Data

Sentiment analysis is a vital component of natural language processing (NLP), enabling the classification of text into positive, negative, or neutral sentiments. It is widely used in customer feedback analysis and social media monitoring but faces a significant challenge: bias. Biases, often introduced through imbalanced training datasets, can distort model predictions and result in unfair outcomes. To address this, we propose a bias-aware sentiment analysis framework leveraging Bias-BERT (Bidirectional Encoder Representations from Transformers), a customized classifier designed to balance accuracy and fairness. Our approach begins with adapting the Jigsaw Unintended Bias in Toxicity Classification dataset by converting toxicity scores into sentiment labels, making it suitable for sentiment analysis. This process includes data preparation steps like cleaning, tokenization, and feature extraction, all aimed at reducing bias. At the heart of our method is a novel loss function incorporating a bias-aware term based on the Kullback–Leibler (KL) divergence. This term guides the model toward fair predictions by penalizing biased outputs while maintaining robust classification performance. Ethical considerations are integral to our framework, ensuring the responsible deployment of AI models. This methodology highlights a pathway to equitable sentiment analysis by actively mitigating dataset biases and promoting fairness in NLP applications.

Guide to microfluidic systems and the preparation of emulsions

AbstractMicrofluidic technology, as an effective method for precise manipulation of microfluid volumes, has demonstrated significant potential in the preparation of emulsions. This guideline introduces key components of a microfluidic operating system, including the design of microfluidic chips (such as T‐junction, flow‐focusing, and co‐flowing structures), fluid driving systems, control systems, and observation and detection systems, explaining how they collaborate to accurately control the droplet generation process. In terms of specific steps for emulsion preparation, the guideline details the workflow utilizing microfluidic technology to fabricate both single‐layer O/W and W/O emulsions, as well as complex multi‐layer emulsions, emphasizing critical considerations during experimentation. Through in‐depth understanding and judicious application of microfluidic technology, there is a promise to advance emulsion preparation techniques across various domains, including drug delivery, food technology, biotechnology, and materials science.

Framework for Dataset Development in Building Energy Balance Simulations

The article presents a structured approach to forming initial datasets necessary for calculating the energy balance of buildings, tailored to the district's level of digitalization. The methodology outlined addresses the often-neglected step of data preparation, which critically influences the outcomes of energy balance simulations. Two distinct process flows for dataset formation are introduced, reflecting high and medium levels of district digitalization. The paper’s novelty lies in formalizing the dataset creation process, enabling more accurate energy simulations, particularly in the early planning stages of positive energy districts.

High-Temperature-Mediated Assembly of Polyoxometalate-Induced Ordered Carbonaceous Superstructures.

Constructing hierarchical superstructures through one-step bottom-up synthesis poses significant challenges due to strong interactions between additives and micelles, which hinders the formation of heterogeneous configurations. Here, we propose a high-temperature-mediated method to weaken these interactions and manipulate the thermal instability of micellar templates. This approach successfully synthesizes hierarchical superstructures that combine a carbonaceous nanosheet substrate with polyoxometalate (POM)-induced, highly ordered discontinuous nanodots in a single preparation step. The surface nanodots have a diameter of approximately 19 nm and are spaced about 32 nm apart. Besides, the nanodots with various arrangements can be generated by simply adjusting the amount of POM. Importantly, the superstructure features more exposed POM catalytic sites than conventional carbonaceous hybrids lacking surface architectures, resulting in excellent electrochemical performance in lithium-sulfur (Li-S) batteries. This high-temperature-mediated approach offers new insights for designing hierarchical superstructures and functional materials with enhanced activities.

Evaluation of Length and Fiber Count Determinations for Natural and Synthetic Microfibers Using the OpTest Fiber Quality Analyzer

Microfibers are small fiber particles that range from 1 µm to 5 mm in length, generated through the home laundering and daily wear of textile garments. Microfibers stemming from synthetic textiles are a global pollution problem marked by their slow biodegradation and steady environmental accumulation. Thus, the quantification and study of factors controlling their generation is of interest. The aim of the current study included exploring the use of a Fiber Quality Analyzer-360 (FQA) for examining fiber counts and lengths of microfibers derived from cotton, flax, ramie, hemp, acrylic, polyester, viscose, and polyamide, and to explore if additional preparation steps, such as sonication, would improve microfiber detection by the system. While probe sonication led to higher fiber counts for most microfiber types, average microfiber lengths were statistically similar for most samples, with only the hemp and ramie samples showing statistically shorter microfibers following sonication. FQA detection estimates for cotton, viscose, and ramie microfibers were high, at 99, 101, and 116% for viscose, flax, and cotton, respectively. In contrast, synthetic microfibers of acrylic, polyamide and polyester showed 77, 43, and 14% detection rates, respectively. The high detection rate for the cotton sample is partly due to the higher fineness value obtained from the gravimetric determination. A similar calculation using AFIS fineness showed 86% detection. These observations confirm the significance of properly suspending the samples to accurately quantify microfibers while using the FQA system. Furthermore, the reduced detection of the examined synthetic microfibers suggests the limitations of the FQA as a technique for the direct comparison of natural and synthetic microfiber counts.

High‐Temperature‐Mediated Assembly of Polyoxometalate‐Induced Ordered Carbonaceous Superstructures

Constructing hierarchical superstructures through one‐step bottom‐up synthesis poses significant challenges due to strong interactions between additives and micelles, which hinders the formation of heterogeneous configurations. Here, we propose a high‐temperature‐mediated method to weaken these interactions and manipulate the thermal instability of micellar templates. This approach successfully synthesizes hierarchical superstructures that combine a carbonaceous nanosheet substrate with polyoxometalate (POM)‐induced, highly ordered discontinuous nanodots in a single preparation step. The surface nanodots have a diameter of approximately 19 nm and are spaced about 32 nm apart. Besides, the nanodots with various arrangements can be generated by simply adjusting the amount of POM. Importantly, the superstructure features more exposed POM catalytic sites than conventional carbonaceous hybrids lacking surface architectures, resulting in excellent electrochemical performance in lithium‐sulfur (Li‐S) batteries. This high‐temperature‐mediated approach offers new insights for designing hierarchical superstructures and functional materials with enhanced activities.

Performance evaluation of an online monitor based on X-ray fluorescence for detecting elemental concentrations in ambient particulate matter

Abstract. Knowledge of the chemical composition of particulate matter (PM) is essential for understanding its source distribution, identifying potential health impacts of toxic elements, and developing efficient air pollution abatement strategies. Traditional methods for analysing PM composition, such as collection on filter substrates and subsequent offline analysis with, for example, inductively coupled plasma mass spectrometry (ICP-MS), are time-consuming and prone to measurement errors due to multiple preparation steps. Emerging near-real-time techniques based on non-destructive energy dispersive X-ray fluorescence (EDXRF) offer advantages for continuous monitoring and source apportionment. This study characterizes the Horiba PX-375 EDXRF monitor by applying a straightforward performance evaluation including (a) limit of detection (LoD), (b) identification and quantification of uncertainty sources, and (c) investigation and comparison of measurement results from three contrasting sites in Luxembourg (urban, semi-urban, rural). We used multi-element reference materials (ME-RMs) from UC Davis for calibration and performed measurements during spring and summer 2023. The LoDs for toxic elements like Ni, Cu, Zn, and Pb were below 3 ng m−3 at 1 h time resolution. Higher LoDs were observed for lighter elements (e.g. Al, Si, S, K, Ca). Expanded uncertainties ranged between 5 % and 25 % for elemental concentrations above 20 ng m−3 and were maximal for concentrations below 10 ng m−3, reaching 60 %–85 %. Elemental analysis revealed S and mineral elements (Fe, Si, Ca, Al) as dominant contributors to PM10. Although the PM mass contribution of toxic trace elements (e.g. Zn, Cu, As) was generally very low, they were found to be enriched at the urban site Belvaux and the semi-urban site Remich compared to the more rural site Vianden. Our results explained on average 51 %–74 % of the gravimetric PM10 mass at the three sites. The study highlights the suitability and importance of the continuous PX-375 particle monitor for future air quality monitoring and source apportionment studies, particularly under changing emission scenarios and air pollution abatement strategies.

Vortex-assisted dispersive solid-phase microextraction of manganese in food samples by using newly synthesized biodegradable poly (3-hydroxy butyrate) diethanol amine

A newly synthesized biodegradable polyhydroxy butyrate diethanol amin (PHB-DEA) was used as adsorbent for vortex assisted dispersive solid phase microextraction (VA-dSPµE) of manganese in food samples. The different parameters were optimized such as pH, amount of adsorbent, time, desorption solvents and time and also number of reuses. After the sample preparation step, the determination of manganese from food samples was carried out using flame atomic absorption spectrometry. The present developed method showed good LOD value 0.15ngmL-1 and LOQ 0.5ngmL-1. The 0.5-300ngmL-1 linearity range was found and enhancement factor was 182. The inter-day RSD% was 2.2-4.1 and intra-day RSD% was 2.8-5.2. The recovery of manganese was found in the 95-98% range. The factorial design was employed such as response surface plots, pareto chart, residual plots and ANOVA was applied to estimate the significant level of the model using central composite design (CCD). The developed VA-dSPµE procedure was successfully implemented to determine manganese in food samples.

Evaluation of Thermodynamic Contributions to Extraction of Medical Devices by Organic Solvents as a Sample Preparation Step in Chemical Characterization of Medical Devices

Evaluation of Thermodynamic Contributions to Extraction of Medical Devices by Organic Solvents as a Sample Preparation Step in Chemical Characterization of Medical Devices

Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology

10X Visium, a popular Spatial transcriptomics (ST) method, faces limited adoption due to its high cost and restricted sample usage per slide. To address these issues, we propose Microarray Integrated Spatial Transcriptomics (MIST), combining conventional tissue microarray (TMA) with Visium, using laser-cutting and 3D printing to enhance slide throughput. Our design facilitates independent replication and customization in individual labs to suit specific experimental needs. We provide a step-by-step guide from designing TMAs to the library preparation step. We demonstrate MIST’s cost-effectiveness and technical benefits over Visium and GeoMx Nanostring. We also introduce ‘AnnotateMap’, a novel computational tool for efficient analysis of multiple ROIs processed through MIST.

A curvature and temperature simultaneous measurement sensor based on micro-taper Formed MZI and an Embedded FBG

Abstract A compact fiber Bragg grating (FBG) and Mach–Zehnder interferometer (MZI) compound for simultaneous measurement of bending and temperature is described. The FBG and MZI are fabricated in fiber forming a compact device, which is different from the previously developed axial cascade of different structures. Experimental results show that the FBG and MZI have different sensitivities for bending and temperature, allowing this device to measure bending and temperature simultaneously. The device has the advantages of small size, simple preparation steps, low cost, short preparation cycle, etc. Due to its excellent performance, it has the potential to become an excellent universal bending and temperature sensor.

A Tool for Reaction Monitoring in Real Time, the Development of a "Walk-Up Automated Reaction Profiling" System.

Optimization of chemical reactions requires a thorough analysis of reaction products and intermediates over a given time course. Chemical reactions are often analyzed by liquid chromatography-mass spectrometry (LC-MS), but generating LC-MS samples and data analysis is time-consuming and produces a significant amount of waste. We sought to remove the sample preparation and data analysis steps by implementing an iChemExplorer/Agilent LC-MS instrument as our reactor and analysis tool, coupled with an automated report generator of reaction progress over time. Herein, we show that our easy-to-use walk-up automated reaction profiling (WARP) system can sample chemical reactions multiple times to produce a data-rich report of reaction progress over time.

Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-Treated Pancreatic Beta Cells

Studying regulation of protein function at a systems level necessitates an understanding of the interplay among diverse post-translational modifications (PTMs). A variety of proteomics sample processing workflows are currently used to study specific PTMs but rarely characterize multiple types of PTMs from the same sample inputs. Method incompatibilities and laborious sample preparation steps complicate large-scale physiological investigations and can lead to variations in results. The single-pot, solid-phase-enhanced sample preparation (SP3) method for sample cleanup is compatible with different lysis buffers and amenable to automation, making it attractive for high-throughput multi-PTM profiling. Herein, we describe an integrative SP3 workflow for multiplexed quantification of protein abundance, cysteine thiol oxidation, phosphorylation, and acetylation. The broad applicability of this approach is demonstrated using cell and tissue samples, and its utility for studying interacting regulatory networks is highlighted in a time-course experiment of cytokine-treated β-cells. We observed a swift response in global regulation of protein abundances consistent with rapid activation of JAK-STAT and NF-κB signaling pathways. Regulators of these pathways as well as proteins involved in their target processes displayed multi-PTM dynamics indicative of a complex cellular response stages: acute, adaptation, and chronic (prolonged stress). PARP14, a negative regulator of JAK-STAT, had multiple co-localized PTMs that may be involved in intraprotein regulatory crosstalk. Our workflow provides a high-throughput platform that can profile multi-PTMomes from the same sample set, which is valuable in unraveling the functional roles of PTMs and their co-regulation.

Tailored Nanoarchitectures: MoS₂/Graphene and MoS2/Graphene Oxide Thin Films via Liquid-Liquid Interfacial Route.

The nanostructured assembly of different two-dimensional (2D) materials in specific organization is crucial for developing materials with synergistic properties. In this study, we present a general methodology to prepare thin, transparent and self-assembled films of 2D/2D composites based on molybdenum sulfide (MoS2)/graphene oxide (GO) or MoS2/reduced graphene oxide (rGO), through the liquid/liquid interfacial route. Different nanoarchitectures are obtained by changing simple experimental parameters during the thin film preparation steps. The films were characterized by UV-Vis and Raman spectroscopy, scanning electron microscopy and cyclic voltammetry, evidencing that the experimental route used plays a role in the organization and properties of the assembled nanoarchitectures. Likewise, nanostructures of MoS2/GO and MoS2/rGO prepared through the same route have different organizations due to the different interactions between the materials. This showcases the potential of the technique to prepare tailored nanoarchitectures with specific properties for various applications, paving the way for innovative nanotechnology and materials science applications.

Getting started with the graded response model: An introduction and tutorial in R.

This tutorial introduces the graded response model (GRM), a tool for testing measurement precision within the item response theory (IRT) paradigm, which is useful for informing researchers about the item and person properties of their measurement. The tutorial aims to guide applied researchers through a unidimensional GRM analysis in the R environment, using the psych, mirt and ggmirt packages. GRM is specifically designed to examine the psychometric properties of psychological scales with polytomous (Likert-style) items. The tutorial illustrates the procedure using data from the Open Psychometrics Database on the right-wing authoritarianism (RWA) scale, outlining the theoretical underpinnings of GRM and steps for data preparation, testing model assumptions, model fitting, plotting item parameters and interpretation of results.

A novel injection device to administer repository corticotropin injection for inflammatory disease treatment: findings from a market research study.

Aim: The goal of this market research study was to determine the usability of a single-dose prefilled injector (SelfJect™) for administration of Acthar® Gel (manufactured by Mallinckrodt Pharmaceuticals, UK) in patients with inflammatory diseases by obtaining feedback from patient and practitioner user groups in the US. Materials & methods: Patients and healthcare professionals (HCPs) representing relevant therapeutic areas were enrolled in the study between February and March 2021. SelfJect was mailed to patients and HCPs prior to 90-minvirtual video-recorded focus group sessions and 60-min1:1 virtual interviews, respectively. Patients completed an online assignment prior to the group session, which included instructions on how to use SelfJect and questions about their initial reaction while handling the device. HCPs were instructed to not open the package until the interview. Feedback from patients and HCPs were captured by open-ended questions and ranking scales. Results: Twelve patients and 42 HCPs participated in the study. Most patients (9/12 [75%]) and HCPs (38/42 [90%]) had experience with injectable medications, and 7/12 (58%) and 30/42 [71%] had experience with Acthar injections, respectively. Most patients and HCPs reported that key benefits of SelfJect were accurate dose delivery and ease of use, including the ergonomic handle and elimination of drawing Acthar from a vial into a syringe. Patients expressed some concerns about storage and disposal, but the need to store SelfJect would not deter them from using it. Most patients (9/12 [75%]) felt prepared to inject Acthar after reviewing the instructions. HCPs anticipated that 75% to 100% of patients would benefit switching from the vial to SelfJect. Conclusion: All participants expressed positive perceptions for SelfJect including easy use, few preparation steps and potential reduced anxiety due to needle phobia. These attributes may help treatment adherence for patients and caregivers.

Profiling of 24-nt phasiRNAs in Rice Anther by Massively Parallel Sequencing and Stem-Loop Reverse Transcription PCR.

Small RNAs are highly abundant and play important roles in plant reproduction. Profiling of small RNAs in reproductive tissues is a critical step in understanding their biology. Here, we describe a protocol for small RNA profiling in rice anthers, with a focus on an abundantly expressed but little-understood reproductive small RNA class named 24-nucleotide phased secondary small interfering RNAs (24-nt phasiRNAs). The protocol details small RNA library preparation steps for high-throughput sequencing, with a subsequent bioinformatic analysis framework. A low-throughput stem-loop reverse transcription PCR protocol for quick semi-quantification of small RNAs is also included as a complementary approach. The collective protocol, although focused on 24-nt phasiRNAs, should be amenable to other small RNA classes in various plant reproductive tissues.