Protocol for phage matching, treatment, and monitoring for compassionate bacteriophage use in non-resolving infections

Phage therapy has re-emerged as a promising treatment for non-resolving infections. Given the lack of approved phage treatments, there is a need to establish a compassionate use pipeline. Here, we present a protocol for phage matching, treatment, and monitoring for compassionate bacteriophage use in non-resolving infections. We describe steps for consultation and request implementation, evaluating and comparing different aspects of phage activity, and phage production. We then detail procedures for multidisciplinary meetings, ethics approvals, phage therapy, and follow-up. For complete details on the use and execution of this protocol, please refer to Onallah et al.1,2.

Protocol to identify biomarkers in patients with post-COVID condition using multi-omics and machine learning analysis of human plasma

Here, we present a workflow for analyzing multi-omics data of plasma samples in patients with post-COVID condition (PCC). Applicable to various diseases, we outline steps for data preprocessing and integrating diverse assay datasets. Then, we detail statistical analysis to unveil plasma profile changes and identify biomarker-clinical variable associations. The last two steps discuss machine learning techniques for unsupervised clustering of patients based on their inherent molecular similarities and feature selection to identify predictive biomarkers. For complete details on the use and execution of this protocol, please refer to Wang et al.1.

Protocol for postmortem bedside endoscopic procedure to sample human respiratory and olfactory cleft mucosa, olfactory bulbs, and frontal lobe

We present a protocol for the rapid postmortem bedside procurement of selected tissue samples using an endoscopic endonasal surgical technique that we adapted from skull base surgery. We describe steps for the postmortem collection of blood, cerebrospinal fluid, a nasopharyngeal swab, and tissue samples; the clean-up procedure; and the initial processing and storage of the samples. This protocol was validated with tissue samples procured postmortem from COVID-19 patients and can be applied in another emerging infectious disease. For complete details on the use and execution of this protocol, please refer to Khan et al. (2021)1 and Khan et al. (2022).2.

Protocol for assessing total antioxidant capacity in minimal volumes of varying clinical human samples

Total antioxidant capacity (TAC), representative of the capacity to combat oxidative stress, is closely linked to numerous diseases. Here, we present a protocol for measuring TAC using minimal samples that are stable across varying pH levels and at room temperature. We describe steps for preparing and loading samples and working solutions and conducting and analyzing the colorimetric reaction. Sample sources include aqueous humor, vitreous, tears, and plasma, which allow the protocol to be used in various clinical diagnostic settings. For complete details on the use and execution of this protocol, please refer to publications by Tsao et al. (2022).1,2.

Protocol for investigating data quality and reporting outcomes of pediatric gliomas in population-based cancer registry research

Cancer registry data on pediatric gliomas come with inherent limitations as inclusion criteria and registration practices of these tumors differ between registries due to specific guidelines that are lacking. These limitations can lead to biased estimates in incidence and survival outcomes. Here, we present a protocol to investigate data quality and comparability for retrospective population-based pediatric glioma studies. We describe steps for obtaining institutional permissions, dealing with data quality issues, regrouping tumors, and reporting tumors in a clinically relevant manner. For complete details on the use and execution of this protocol, please refer to Hoogendijk et al.1.

Protocol to study immunodynamics in the tumor microenvironment using a tyramide signal amplification-based immunofluorescent multiplex panel

Immunodynamics in the tumor microenvironment can be precisely examined by using multiple antigen identification approaches. Here, we present a protocol for capturing expression levels of multiple target proteins in the same specimen at single-cell resolution using a tyramide signal amplification-based immunofluorescent multiplexing system. We describe steps for tumor tissue microarray preparation, multiplex immunohistochemistry staining, image acquisition, and quantification. This protocol can quantify immune cells in tissues from patients or experimental disease models at a protein level. For complete details on the use and execution of this protocol, please refer to Chung et al. (2023),1 Tang et al. (2022),2 and Tang et al. (2022).3.

Protocol to measure apoptosis-associated speck-like protein containing a CARD specks in human cerebrospinal fluid via imaging flow cytometry

Apoptosis-associated speck-like protein containing a c-terminal caspase activation and recruitment domain (ASC) specks are elevated in the cerebrospinal fluid (CSF) of Alzheimer's disease and related dementias (AD/ADRDs) patients. Here, we present a flow cytometry protocol to quantify ASC specks. We describe steps for fluorescently labeling ASC specks using antibody technology, visualizing with imaging flow cytometry, and gating based on physical characteristics. CSF ASC specks levels positively correlate with phosphorylated tau (Thr181) and negatively correlate with amyloid β ratio (42/40), thus serving as a neuroinflammatory biomarker for diagnosing AD/ADRDs. For complete details on the use and execution of this protocol, please refer to Jiang et al.1.

Protocol for programing a degree-to-careers dashboard in R using Posit and Shiny

Here, we present a protocol for programing a degree-to-careers dashboard in R using Posit and Shiny. We describe steps for installing software, obtaining datasets, and munging and joining data. We then detail procedures for programing and publishing the dashboard in Shiny web application that includes a filtered data table. The resulting dashboard links academic programs with careers and income data and may be useful to inform decision-making by higher education leaders and policymakers. For complete details on the use and execution of this protocol, please refer to Perkins and Carrier (2023).1.

Generation of post-surgical minimal residual disease models to investigate metastasis in soft tissue sarcoma patient-derived orthotopic xenografts

Despite optimal multimodal treatment including surgical resection, 50%-80% of high-grade soft tissue sarcoma (STS) patients metastasize. Here, we present a protocol for the generation and use of post-surgical minimal residual disease models to investigate metastatic relapse in STS patient-derived xenografts. We describe steps for orthotopic engraftment of high-grade STS patient-derived tumor tissue. We then detail procedures for primary tumor resection with broad, negative resection margins and follow-up until metastases using MRI. For complete details on the use and execution of this protocol, please refer to Fischer et al. (2023).1.

Protocol for immunophenotyping out-of-hospital cardiac arrest patients

Immunophenotyping of out-of-hospital cardiac arrest (OHCA) patients is of increasing interest but has challenges. Here, we describe steps for the design of the clinical cohort, planning patient enrollment and sample collection, and ethical review of the study protocol. We detail procedures for blood sample collection and cryopreservation of peripheral blood mononuclear cells (PBMCs). We detail steps to modulate immune checkpoints in OHCA PBMC ex vivo. This protocol also has relevance for immunophenotyping other types of critical illness. For complete details on the use and execution of this protocol, please refer to Tamura et al. (2023).1.

Protocol for training MERGE: A federated multi-input neural network for COVID-19 prognosis

Federated learning is a cooperative learning approach that has emerged as an effective way to address privacy concerns. Here, we present a protocol for training MERGE: a federated multi-input neural network (NN) for COVID-19 prognosis. We describe steps for collecting and preprocessing datasets. We then detail the process of training a multi-input NN. This protocol can be adapted for use with datasets containing both image- and table-based input sources. For complete details on the use and execution of this protocol, please refer to Casella et al.1.

Protocol for identifying metabolite biomarkers in patient uterine fluid for early ovarian cancer detection

High mortality of ovarian cancer (OC) is primarily attributed to the lack of effective early detection methods. Uterine fluid, pooling molecules from neighboring ovaries, presents an organ-specific advantage over conventional blood samples. Here, we present a protocol for identifying metabolite biomarkers in uterine fluid for early OC detection. We describe steps for uterine fluid collection from patients, metabolite extraction, metabolomics experiments, and candidate metabolite biomarker screening. This standardized workflow holds the potential to achieve early OC diagnosis in clinical practice. For complete details on the use and execution of this protocol, please refer to Wang et al.1.

Comparison In Vitro Fertilization Outcomes between DouStim and Minimal Stimulation Protocols in Poor Ovarian Responders: A Randomized Clinical Trial

BACKGROUND

Various protocols have been approved to improve the response rate leading to successful fertilization in poor ovarian responders (PORs). The application of double ovarian stimulation (DuoStim) in the follicular and luteal phases of the same ovarian cycle has been shown as an intriguing option to achieve more oocyte retrievals in the shortest time. The aim of the current study is to compare the outcomes of different protocols, minimal stimulation (MS) and Duostim.

MATERIALS AND METHODS

This randomized clinical trial was performed on 42 in vitro fertilization (IVF) candidates with POR diagnosis. Patients were classified into two equal groups and treated with the DuoStim protocol and MS protocol. The IVF outcomes, including retrieved follicles, oocytes, metaphase II (MII) oocytes and embryos, were compared between these groups.

RESULTS

The patients' characteristics including age, anti-mullerian hormone (AMH), follicle stimulating hormone (FSH), luteinizing hormone (LH), and antral follicle count (AFC) were collected and compared. It showed there was no significant difference between the two groups baseline characteristics (P>0.05). We observed that the DuoStim protocol resulted in a significantly higher score in comparison with the MS protocols , including the number of follicles (6.23 ± 2.93 vs. 1.77 ± 1.66, P<0.001), retrieved oocytes (3.86 ± 2.57 vs. 1.68 ± 1.58, P=0.002), MII oocytes (3.36 ± 2.42 vs. 1.27 ± 1.27, P=0.001) and obtained embryos (2.04 ± 1.64 vs. 0.77 ± 0.86, P=0.003).

CONCLUSION

The DuoStim protocol is a favourable and time saving plan that is associated with more oocytes in a single stimulation cycle. The DuoStim protocol significantly can result in more frequent MII oocytes and embryos. We figured that the higher number of oocytes and embryos might have led to a higher rate of pregnancy (registration number: IRCT20200804048303N1).

An optimized protocol for isolation of hepatic leukocytes retrieved from murine and NASH liver biopsies

Immune dysregulation and inflammation by hepatic-resident leukocytes is considered a key step in disease progression of non-alcoholic fatty liver disease and non-alcoholic steatohepatitis toward cirrhosis and hepatocellular carcinoma. Here, we provide a protocol for isolation and characterization of liver-resident immune cells from fine-needle biopsies obtained from a rodent model and humans. We describe steps for isolating leukocytes, cell sorting, and RNA extraction and sequencing. We then detail procedures for low-input mRNA sequencing analyses.

Protocol for evaluating mechanistic pathways associated with HIV acquisition via nested Least Absolute Shrinkage and Selective Operator analysis

Statistical analysis to evaluate mechanistic pathways can be limited by non-causal associations as well as co-linearity of high-dimensional data. Here, we present a protocol evaluating statistical associations between multiple exposure variables (sociodemographic and behavioral), immune biomarkers, and HIV acquisition. We describe steps for study setup, combining Least Absolute Shrinkage and Selective Operator with the standard regression approach, and building nested models. This approach can determine to what extent associations between risks for exposure contributes to HIV acquisition with or without associated changes in immune activation. For complete details on the use and execution of this protocol, please refer to Bender Ignacio et al.1.

Ultrasound-guided lymph node fine-needle aspiration for evaluating post-vaccination germinal center responses in humans

The lymph node (LN) is a critical biological site for immune maturation after vaccination as it includes several cell populations critical for priming the antibody response. Here, we present a protocol for sampling the LN and isolating cell populations to evaluate immunogens targeting germline cells. We describe steps for media and tube preparation and sample collection using an ultrasound-guided LN fine-needle aspiration procedure. This protocol is safe, quick, low-cost, and less invasive than excisional biopsy. For complete details on the use and execution of this protocol, please refer to Leggat et al. (2022).1.

Protocol for isolating single cells from human pancreatic cancer tissues and analyzing major immune cell populations using flow cytometry

Here, we present a protocol for collecting, dissociating, isolating, staining, and analyzing immune cells from pancreatic cancer tissues for flow cytometry. The isolated cells can also be used for single-cell RNA sequencing and other related procedures. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2023).1.

Protocol to analyze fundus images for multidimensional quality grading and real-time guidance using deep learning techniques

Data quality issues have been acknowledged as one of the greatest obstacles in medical artificial intelligence research. Here, we present DeepFundus, which employs deep learning techniques to perform multidimensional classification of fundus image quality and provide real-time guidance for on-site image acquisition. We describe steps for data preparation, model training, model inference, model evaluation, and the visualization of results using heatmaps. This protocol can be implemented in Python using either the suggested dataset or a customized dataset. For complete details on the use and execution of this protocol, please refer to Liu et al.1.

Protocol for detecting Helicobacter suis infection in gastric biopsies and serum by PCR and ELISA

Infection with Helicobacter suis, which causes many cases of gastric disease, is not reliably diagnosed. Here, we present a protocol for detecting H. suis infection. We describe steps for collecting gastric biopsies and sera from patients, preparing DNA for PCR, and targeting the H. suis-specific gene. We then define procedures for inoculating biopsies onto primary agar plates and transferring colonies to secondary agar plates. Finally, we detail whole-genome sequencing of bacteria and assess H. suis infection in sera with ELISA. For complete details on the use and execution of these protocols, please refer to Matsui et al.1.

Proteomics protocol for obtaining extracellular vesicle from human plasma using asymmetrical flow field-flow fractionation technology

Plasma extracellular vesicles (EVs) represent a potential resource for biomarkers of multiple diseases. Here, we present a protocol for obtaining EVs from human plasma using asymmetrical flow field-flow fractionation technology. We describe steps for using tandem mass tags to perform comparative proteomic studies of a large clinical cohort. We then detail targeted quantitative analysis of differential proteins based on a parallel reaction monitoring technique. For complete details on the use and execution of this protocol, please refer to Wu et al. (2020)1 and Li et al. (2023).2.

Protocol to conduct functional magnetic resonance spectroscopy in different age groups of human participants

We present a protocol to conduct functional magnetic resonance spectroscopy (fMRS) in human participants before, during, and after training on a visual task. We describe steps for participant setup, volume-of-interest placement, fMRS measurement, and post-scan tests. We discuss the design, analysis, and interpretation of fMRS experiments. This protocol can be adapted to investigate the dynamics of chief excitatory and inhibitory neurotransmitters (glutamate and γ-aminobutyric acid, GABA, respectively) while participants perform or learn perceptual, motor, or cognitive tasks. For complete details on the use and execution of this protocol, please refer to Frank et al. (2022).1.

Protocol for the automatic extraction of epidemiological information via a pre-trained language model

The lack of systems to automatically extract epidemiological fields from open-access COVID-19 cases restricts the timeliness of formulating prevention measures. Here we present a protocol for using CCIE, a COVID-19 Cases Information Extraction system based on the pre-trained language model.1 We describe steps for preparing supervised training data and executing python scripts for named entity recognition and text category classification. We then detail the use of machine evaluation and manual validation to illustrate the effectiveness of CCIE. For complete details on the use and execution of this protocol, please refer to Wang et al.2.

Protocol for deep proteomic profiling of formalin-fixed paraffin-embedded specimens using a spectral library-free approach

Formalin-fixed paraffin-embedded (FFPE) samples are valuable archived bio-specimens of individuals and are commonly used in biomedical research. Here, we present a protocol for deep proteomic profiling of FFPE specimens using a spectral library-free approach. We describe steps for FFPE tissue collection, tissue lysis, homogenization, protein lysate cleanup, on-beads digestion, and de-salting. We then detail data acquisition and statistical analysis. This protocol is highly sensitive, reproducible, and applicable for high-throughput proteomic profiling and can be used on various types of specimens.

Antimicrobial susceptibility testing to evaluate minimum inhibitory concentration values of clinically relevant antibiotics

Antimicrobial susceptibility testing is used to determine the minimum inhibitory concentration (MIC), the standard measurement of antibiotic activity. Here, we present a protocol for evaluating MIC values of clinically relevant antibiotics against bacterial isolates cultured in standard bacteriologic medium and in mammalian cell culture medium. We describe steps for pathogen identification, culturing bacteria, preparing MIC plates, MIC assay incubation, and determining MIC. This protocol can potentially optimize the use of existing antibiotics while enhancing efforts to discover new ones. For complete details on the use and execution of this protocol, please refer to Heithoff et al.1.

Protocol to acquire time series data on adverse reactions following vaccination using a smartphone or web-based platform

Data collection on adverse reactions in recipients after vaccination is vital to evaluate potential health issues, but health observation diaries are onerous for participants. Here, we present a protocol to collect time series information using a smartphone or web-based platform, thus eliminating the need for paperwork and data submission. We describe steps for setting up the platform using the Model-View-Controller web framework, uploading lists of recipients, sending notifications, and managing respondent data. For complete details on the use and execution of this protocol, please refer to Ikeda et al. (2022).¹.

Protocol to identify novel immunotherapy biomarkers based on transcriptomic data in human cancers

Immune checkpoint inhibitors have transformed the management of advanced cancers, but biomarkers for the prediction of therapeutic responses have not been fully uncovered. Here, we provide a step-by-step approach for the identification of novel biomarkers from public transcriptomic datasets. We comprehensively summarize the available transcriptomic datasets containing immunotherapy information and describe the necessary procedures to evaluate the effectiveness of a novel immunotherapy biomarker, which may accelerate the identification of novel immunotherapy biomarkers. For complete details on the use and execution of this protocol, please refer to Mei et al.¹.

Protocol for quantitative characterization of human retinotopic maps using quasiconformal mapping

High-field functional magnetic resonance imaging generates in vivo retinotopic maps, but quantifying them remains challenging. Here, we present a pipeline based on conformal geometry and Teichmüller theory for the quantitative characterization of human retinotopic maps. We describe steps for cortical surface parameterization and surface-spline-based smoothing. We then detail Beltrami coefficient-based mapping, which provides a quantitative and re-constructible description of the retinotopic maps. This framework has been successfully used to analyze the Human Connectome Project's V1 retinotopic maps. For complete details on the use and execution of this protocol, please refer to Ta et al. (2022).¹.

An optimized protocol to isolate quiescent washed platelets from human whole blood and generate platelet releasate under clinical conditions

The contents of the platelet releasate (PR) play significant roles in hemostasis, inflammation, and pathologic sequelae. Careful platelet isolation to ensure quiescence and subsequent activation is key to the successful generation of PR. Here, we describe steps to isolate and aggregate quiescent washed platelets from whole blood of a clinical patient cohort. We then detail the generation of PR from isolated human washed platelets under clinical conditions. This protocol allows the investigation of platelet cargoes released through various activation pathways.

Protocol for measuring intrahepatic triglyceride content in adults with non-alcohol fatty liver disease

Here, we present a protocol for conducting magnetic resonance imaging proton density fat fraction (MRI-PDFF) to measure intrahepatic triglyceride (IHTG) content in adults with non-alcohol fatty liver disease (NAFLD). We describe steps for screening patients for NAFLD, MRI-PDFF scanning, and using MRI-PDFF data to quantify IHTG. This protocol can be repeated sequentially and used in weight loss trials. However, it is limited to patients with NAFLD as it does not assess non-alcoholic steatohepatitis or hepatic fibrosis. For complete details on the use and execution of this protocol, please refer to Ezpeleta et al. (2023).¹.

In vivo imaging of the human retina using a two-photon excited fluorescence ophthalmoscope

Noninvasive imaging of endogenous retinal fluorophores, including vitamin A derivatives, is vital to developing new treatments for retinal diseases. Here, we present a protocol for obtaining in vivo two-photon excited fluorescence images of the fundus in the human eye. We describe steps for laser characterization, system alignment, positioning human subjects, and data registration. We detail data processing and demonstrate analysis with example datasets. This technique allays safety concerns by allowing for the acquisition of informative images at low laser exposure. For complete details on the use and execution of this protocol, please refer to Bogusławski et al. (2022).¹.

Chimerism and phenotypic analysis of intraepithelial and lamina propria T cells isolated from human ileal biopsies after intestinal transplantation

Understanding immune cell dynamics after intestinal transplantation has provided new insights into human lymphocyte biology. However, isolating and characterizing such cells can be challenging. Here, we provide a protocol to isolate intraepithelial and lamina propria lymphocytes from human ileal biopsies. We describe techniques for flow cytometric analysis and determination of multilineage chimerism and T lymphocyte phenotypes. This protocol can be modified to isolate and analyze lymphocytes from other tissues. For complete details on the use and execution of this protocol, please refer to Fu et al. (2019)¹ and Fu et al. (2021).².

Protocol to detect antigen-specific nasal-resident T cells in humans

Specialized T cells are located in the nasal cavity and act as the first line of defense against respiratory viral infection. Here, we present a protocol for the detection and characterization of antigen-specific nasal-resident T cells. We detail steps for localized nasal swabbing to collect the nasal samples. We then describe IFN-γ ELISpot and an activation-induced marker assay to detect and characterize antigen-specific nasal-resident T cells. For complete details on the use and execution of this protocol, please refer to Lim et al. (2022).1.

Precision mapping and transcranial magnetic stimulation of individual-specific functional brain networks in humans

Spatial targeting in transcranial magnetic stimulation protocols does not typically account for the idiosyncratic functional organization of individual human brains. Here, we provide a protocol for implementing targeted functional network stimulation (TANS), which accounts for each individual's unique functional neuroanatomy and cortical folding patterns. Using an example dataset, we describe how to create a head model and estimate the best coil placement and stimulation intensity to minimize off-target effects. For complete details on the use and execution of this protocol, please refer to Lynch et al. (2022).1.

Measuring VLDL1 secretion in humans with an intravenous fat emulsion test

Tracer techniques to assess very-low-density lipoprotein (VLDL) secretion in humans are expensive, are time consuming, and require mathematical models to estimate VLDL kinetics. Here, we describe an alternative, time- and cost-efficient protocol to directly determine VLDL1 secretion with an intravenous (i.v.) lipid emulsion test that does not require tracers and compartmental modeling. We describe steps for intralipid infusion, blood sampling, and removal of intralipid from plasma samples, followed by density gradient ultracentrifugation to isolate VLDL1 fraction and measure the secretion rate. For complete details on the use and execution of this protocol, please refer to Bjorkegren et al. (1996),1 Al-Shayji et al. (2007),2 and Metz et al. (2022).3.

Protocol for assessing the effects of exogenous hormone administration on human postprandial glucose metabolism, appetite sensations, and food intake

Here, we present a protocol for a randomized, double-blind, placebo-controlled, crossover trial to evaluate the effects of a continuous intravenous infusion of a native liver-derived hormone, liver-expressed antimicrobial peptide 2 (LEAP2), on postprandial glucose metabolism, appetite and satiety sensations, and ad libitum food intake in humans. We describe the preparation of the exogenous hormone administration and participants. We then detail the liquid mixed meal, ad libitum meal test, and blood sampling procedures for assessing postprandial glucose metabolism and food intake. For complete details on the use and execution of this protocol, please refer to Hagemann et al. (2022).1.

Protocol to examine the neural basis of symbolic and non-symbolic quantity processing in human brain with fMRI

Number perception is among the basic cognitive abilities necessary to understand our environment. Here, we present a protocol to examine the neural underpinnings of numerosity comparison regarding symbolic and non-symbolic stimuli using functional magnetic resonance imaging (fMRI). This protocol gives instructions for screening participants, followed by steps to perform an event-related fMRI experiment and data analysis with SPM12. This protocol will be informative for investigating numerical cognition in various groups including children with dyscalculia or people at different developmental stages. For complete details on the use and execution of this protocol, please refer to Üstün et al. (2021) and Vatansever et al. (2020).

Isolation of five different primary cell types from a single sample of human skin

We have developed a technique to isolate primary keratinocytes, melanocytes, fibroblasts, preadipocytes, and microvascular endothelial cells from an individual sample of human skin. The protocol describes step-by-step instructions for processing, cells isolation, and culture of neonatal foreskin, with adaptation for more demanding adult tissues. The availability of multiple isogenic cell types derived from individual skin samples offers the ability to investigate various areas of biology, in the context of cell-type specificity without potential confounding influence of inter-individual or genetic differences.

For complete details on the use and execution of this protocol, please refer to Holliman et al. (2017), Horvath et al. (2019), Horvath et al. (2018), Kabacik et al. (2018), Lowe et al. (2020), Lu et al. (2019), and Lu et al. (2018).

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Protocol to isolate five different primary cell types from human skin sample

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Modification for more demanding adult tissue

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Extensive characterization of each cell type

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Expansion and cryopreservation for biobanking

Speech-to-Speech Synchronization protocol to classify human participants as high or low auditory-motor synchronizers

The ability to synchronize a motor action to a rhythmic auditory stimulus is often considered an innate human skill. However, some individuals lack the ability to synchronize speech to a perceived syllabic rate. Here, we describe a simple and fast protocol to classify a single native English speaker as being or not being a speech synchronizer. This protocol consists of four parts: the pretest instructions and volume adjustment, the training procedure, the execution of the main task, and data analysis. For complete details on the use and execution of this protocol, please refer to Assaneo et al. (2019a).

Protocol to generate xenogeneic-free/serum-free human dental pulp stem cells

Human dental pulp stem cell (hDPSCs)-based therapy is a feasible option for regenerative medicine, such as dental pulp regeneration. Here, we show the steps needed to colony-forming unit-fibroblasts (CFU-F)-based isolation, expansion, and cryopreservation of hDPSCs for manufacturing clinical-grade products under a xenogeneic-free/serum-free condition. We also demonstrate the characterization of hDPSCs by CFU-F, flow cytometric, and in vitro multipotent assays. For complete details on the use and execution of this protocol, please refer to Iwanaka et al. (2020).

Simplified mass cytometry protocol for in-plate staining, barcoding, and cryopreservation of human PBMC samples in clinical trials

With the increasing use of mass cytometry in clinical research, a simplified and standardized protocol for immunophenotyping human peripheral blood mononuclear cells (PBMCs) in clinical trials is needed. We present a simplified in-plate staining protocol for up to 80 samples, for laboratories of all mass cytometry expertise levels, aimed to generate reproducible datasets for large clinical cohorts. In this protocol, we provide details on the requirements to obtain meaningful results, spanning from sample quality, barcoding, and batch-freezing of stained samples.

Global metabolome profiling of COVID-19 respiratory specimen using high-resolution mass spectrometry (HRMS)

Here we describe a protocol for identifying metabolites in respiratory specimens of patients that are SARS-CoV-2 positive, SARS-CoV-2 negative, or H1N1 positive. This protocol provides step-by-step instructions on sample collection from patients, followed by metabolite extraction. We use ultra-high-pressure liquid chromatography (UHPLC) coupled with high-resolution mass spectrometry (HRMS) for data acquisition and describe the steps for data analysis. The protocol was standardized with specific customization for SARS-CoV-2-containing respiratory specimens. For complete details on the use and execution of this protocol, please refer to Maras et al. (2021).

Identifying patients and assessing variant pathogenicity for an autosomal dominant disease-driving gene

Identifying a disease gene and determining its causality in patients can be challenging. Here, we present an approach to predicting the pathogenicity of deletions and missense variants for an autosomal dominant gene. We provide online resources for identifying patients and determining constraint metrics to isolate the causal gene among several candidates encompassed in a shared region of deletion. We also provide instructions for optimizing functional annotation programs that may be otherwise inaccessible to a nonexpert or novice in computational approaches. For complete details on the use and execution of this protocol, please refer to Gennarino et al. (2018).

A transcranial magnetic stimulation protocol for decreasing the craving of methamphetamine-dependent patients

Transcranial magnetic stimulation (TMS) is a non-invasive brain stimulation technique. Many substance use disorders lack effective treatments, and TMS is expected to reduce cravings and risk of relapse by regulating brain function. Here, we introduce three alternative TMS settings and specific operations to interfere with methamphetamine use disorders. Theoretically, this protocol can also be applied to diseases with similar brain damage characteristics. For complete details on the use and execution of this protocol, please refer to Chen et al. (2020).

Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein

Nucleocapsid proteins are essential for SARS-CoV-2 life cycle. Here, we describe protocols to gather domain-specific insights about essential properties of nucleocapsids. These assays include dynamic light scattering to characterize oligomerization, fluorescence polarization to quantify RNA binding, hydrogen-deuterium exchange mass spectrometry to map RNA binding regions, negative-stain electron microscopy to visualize oligomeric species, interferon reporter assay to evaluate interferon signaling modulation, and a serology assay to reveal insights for improved sensitivity and specificity. These assays are broadly applicable to RNA-encapsidated nucleocapsids. For complete details on the use and execution of this protocol, please refer to Wu et al. (2021).

Flow-cytometry-based protocols for human blood/marrow immunophenotyping with minimal sample perturbation

This protocol provides instructions to improve flow cytometry analysis of marrow/peripheral blood cells by avoiding erythrolytic solutions, density gradients, and washing steps. We describe two basic approaches for identifying cell surface antigens with minimal sample perturbation, which have been successfully used to identify healthy and pathologically rare cells. The greatest advantage of these approaches is that they minimize the unwanted effect caused by sample preparation, allowing for improved study of live cells at the point of analysis.

For complete details on the use and execution of this protocol, please refer to Petriz et al. (2018).

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Optimized protocol to identify cell surface antigens with minimal sample perturbation

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Efficient identification of target cells avoiding artifacts from erythrolytic solutions

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Suitable for the simultaneous phenotypic and functional analysis of blood/marrow cells

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Detailed gating strategies to discriminate nucleated from non- nucleated cells

Spatially resolved sampling of the human oral cavity for metabolic profiling

Here, we present a spatially resolved sampling protocol for the oral human cavity aimed at untargeted metabolomics. We describe the spatial collection of salivary biospecimens, their preparation, and subsequent mass-spectrometry-based untargeted metabolomics analysis. Our protocol avoids complex procedures generally required for gland-specific saliva collection. For the human oral cavity, we provide an easy, flexible, and reproducible solution to comprehensively map the highly heterogeneous environment and elucidate the functionality of salivary components. For complete details on the use and execution of this protocol, please refer to Ciurli et al. (2021).

UnCovid: A versatile, low-cost, and open-source protocol for SARS-CoV-2 RNA detection

Here, we describe a detailed step-by-step protocol to detect SARS-CoV-2 RNA using RT-PCR-mediated amplification and CRISPR/Cas-based visualization. The optimized assay uses basic molecular biology equipment such as conventional thermocyclers and transilluminators for qualitative detection. Alternatively, a fluorescence plate reader can be used for quantitative measurements. The protocol detects two regions of the SARS-CoV-2 genome in addition to the human RNaseP sample control. Aiming to reach remote regions, this work was developed to use the portable molecular workstation from BentoLab. For complete details on the use and execution of this protocol, please refer to Alcántara et al., 2021.

Coregistration of magnetic resonance spectroscopy and polysomnography for sleep analysis in human subjects

We developed a protocol for simultaneous magnetic resonance spectroscopy (MRS) and polysomnography (PSG) recordings while subjects are in sleep. The approach is useful to estimate plasticity-stability balances by measuring neurochemical changes in the brain during sleep. We detail the steps needed to minimize artifacts in PSG recordings and the setup and coregistration of MRS data to sleep stages. We also describe useful information for various types of electroencephalogram (EEG) experiments in magnetic resonance imaging (MRI) environments.

For complete details on the use and execution of this protocol, please refer to Tamaki et al. (2020b).

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Avoid instructions that may cause subjects to feel pressured to sleep well

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Introduce an adaptation sleep session before a main sleep session

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Segment PSG data and align them with MRS data for MRI artifact removal

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Assign sleep stage to each MRS segment to obtain E/I balance for the stage

Protocol for one-step selective lysis of red blood cells and platelets with long-term preservation of white blood cells (human) at ambient temperature

Current protocols for storage of white blood cells (WBCs) rely on constant refrigeration. The protocol described below explains the preparation of a fixative combination saline (FCS) formulation, which allows fixation of human WBCs and lysis of red blood cells and platelets (at ambient temperature, 4–35^oC) in whole blood samples in one step. FCS can be used for storing and transporting blood at ambient temperatures for up to 4 months, without altering the nuclear morphology and genomic integrity of WBCs.

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FCS for single-step preparation of human WBCs

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FCS fixes and preserves WBCs; FCS selectively lyses RBCs and platelets

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Fixed WBCs can be stored and transported at ambient temperature up to 4 months

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FCS can overcome the constraint of refrigeration of blood samples

Protocol to assess performance of crisis standards of care guidelines for clinical triage

During the COVID-19 pandemic, US states developed Crisis Standards of Care (CSC) algorithms to triage allocation of scarce resources to maximize population-wide benefit. While CSC algorithms were developed by ethical debate, this protocol guides their quantitative assessment. For CSC algorithms, this protocol addresses (1) adapting algorithms for empirical study, (2) quantifying predictive accuracy, and (3) simulating clinical decision-making. This protocol provides a framework for healthcare systems and governments to test the performance of CSC algorithms to ensure they meet their stated ethical goals.

For complete details on the use and execution of this protocol, please refer to Jezmir et al. (2021).

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Scoring with Crisis Standards of Care (CSC) triage algorithms

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Assessing the predictive accuracy of triage algorithms

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Simulating clinical decision-making by triage algorithms

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Troubleshooting disease severity, comorbidity scoring, and ties