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Introduction Studying arterial thrombus formation by in vitro flow assays is a widely used approach. Incorporating human atherosclerotic plaque material as a thrombogenic surface in these assays represents a method to model the pathophysiological environment of thrombus formation upon plaque disruption. Up until now, achieving a homogeneous coating of plaque material and subsequent reproducible platelet adhesion has been challenging. Here, we characterized a novel method for coating of plaque material on glass coverslips for use in thrombosis microfluidic assays. Methods A homogenate of human atherosclerotic plaques was coated on glass coverslips by conventional manual droplet coating or by spin coating. Prior to coating, a subset of coverslips was plasma treated. Water contact angle measurements were performed as an indicator for the hydrophilicity of the coverslips. Homogeneity of plaque coatings was determined using profilometric analysis and scanning electron microscopy. Thrombogenicity of the plaque material was assessed in real time by microscopic imaging while perfusing whole blood at a shear rate of 1500 s−1 over the plaque material. Results Plasma treatment of glass coverslips, prior to spin coating with plaque material, increased the hydrophilicity of the coverslip compared to no plasma treatment. The most homogeneous plaque coating and highest platelet adhesion was obtained upon plasma treatment followed by spin coating of the plaque material. Manual plaque coating on non-plasma treated coverslips yielded lowest coating homogeneity and platelet adhesion and activation. Conclusion Spin coating of atherosclerotic plaque material on plasma treated coverslips leads to a more homogenous coating and improved platelet adhesion to the plaque when compared to conventional droplet coating on non-plasma treated coverslips. These properties are beneficial in ensuring the quality and reproducibility of flow experiments.

Methods to quantify biological aging are emerging as new measurement tools for epidemiology and population science and have been proposed as surrogate measures for healthy lifespan extension in geroscience clinical trials. Publicly available software packages to compute biological aging measurements from DNA methylation data have accelerated dissemination of these measures and generated rapid gains in knowledge about how different measures perform in a range of datasets. Biological age measures derived from blood chemistry data were introduced at the same time as the DNA methylation measures and, in multiple studies, demonstrate superior performance to these measures in prediction of healthy lifespan. However, their dissemination has been slow by comparison, resulting in a significant gap in knowledge. We developed a software package to help address this knowledge gap. The BioAge R package, available for download at GitHub (http://github.com/dayoonkwon/BioAge), implements three published methods to quantify biological aging based on analysis of chronological age and mortality risk: Klemera-Doubal biological age, PhenoAge, and homeostatic dysregulation. The package allows users to parametrize measurement algorithms using custom sets of biomarkers, to compare the resulting measurements to published versions of the Klemera-Doubal method and PhenoAge algorithms, and to score the measurements in new datasets. We applied BioAge to safety lab data from the CALERIE™ randomized controlled trial, the first-ever human trial of long-term calorie restriction in healthy, non-obese adults, to test effects of intervention on biological aging. Results contribute evidence that CALERIE intervention slowed biological aging. BioAge is a toolkit to facilitate measurement of biological age for geroscience. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11357-021-00480-5.

While novel statistical methods quantifying the shared heritability of traits and diseases between ancestral distinct populations have been recently proposed, a thorough evaluation of these approaches under differing circumstances remain elusive. Brown et al.2016 proposed the method Popcorn to estimate the shared heritability, i.e. genetic correlation, using only summary statistics. Here, we evaluate Popcorn under several parameters and circumstances: sample size, number of SNPs, sample size of external reference panel, various population pairs, inappropriate external reference panel, and admixed population involved. Our results determined the minimum sample size of the external reference panel, summary statistics, and number of SNPs required to accurately estimate both the genetic correlation and heritability. Moreover, the number of individuals and SNPs required to produce accurate and stable estimates was directly proportional with heritability in Popcorn. Misrepresentation of the reference panel overestimated the genetic correlation by 20% and heritability by 60%. Lastly, applying Popcorn to homogeneous (EUR) and admixed (ASW) populations underestimated the genetic correlation by 15%. Although statistical approaches estimating the shared heritability between ancestral populations will provide novel etiologic insight, caution is required ensuring results are based on the appropriate sample size, number of SNPs, and the generalizability of the reference panel to the discovery populations.

Selection of pharmacological agents based on potency measurements performed at equilibrium fail to incorporate the kinetic aspects of the drug–target interaction. Here we describe a method for screening or characterization of enzyme inhibitors that allows the concomitant determination of the equilibrium inhibition constant in unison with rates of complex formation and dissociation. The assay is distinct from conventional enzymatic assays and is based on the analysis of inhibition curves recorded prior to full equilibration of the system. The methodology is illustrated using bicyclic peptide inhibitors of the serine protease plasma kallikrein.

Key message Biolistic delivery into pollen. Abstract In recent years, genome editing techniques, such as the CRISPR/Cas9 system, have been highlighted as a new approach to plant breeding. Agrobacterium-mediated transformation has been widely utilized to generate transgenic plants by introducing plasmid DNA containing CRISPR/Cas9 into plant cells. However, this method has general limitations, such as the limited host range of Agrobacterium and difficulties in tissue culture, including callus induction and regeneration. To avoid these issues, we developed a method to genetically modify germ cells without the need for Agrobacterium-mediated transfection and tissue culture using tobacco as a model. In this study, plasmid DNA containing sequences of Cas9, guide RNA, and fluorescent reporter was introduced into pollen using a biolistic delivery system. Based on the transient expression of fluorescent reporters, the Arabidopsis UBQ10 promoter was found to be the most suitable promoter for driving the expression of the delivered gene in pollen tubes. We also evaluated the delivery efficiency in male germ cells in the pollen by expression of the introduced fluorescent marker. Mutations were detected in the target gene in the genomic DNA extracted from CRISPR/Cas9-introduced pollen tubes, but were not detected in the negative control. Bombarded pollen germinated pollen tubes and delivered their contents into the ovules in vivo. Although it is necessary to improve biolistic delivery efficiency and establish a method for the screening of genome-modified seeds, our findings provide important insights for the detection and production of genome-modified seeds by pollen biolistic delivery.

Real-world emotions are often more vivid, personally meaningful, and consequential than those evoked in the lab. Therefore, studying emotions in daily life is essential to test theories, discover new phenomena, and understand healthy emotional functioning; in short, to move affective science forward. The past decades have seen a surge of research using daily diary, experience sampling, or ecological momentary assessment methods to study emotional phenomena in daily life. In this paper, we will share some of the insights we have gained from our collective experience applying such daily life methods to study everyday affective processes. We highlight what we see as important considerations and caveats involved in using these methods and formulate recommendations to improve their use in future research. These insights focus on the importance of (i) theory and hypothesis-testing; (ii) measurement; (iii) timescale; and (iv) context, when studying emotions in their natural habitat. ispartof: Affective Science vol:3 issue:2 pages:505-515 ispartof: location:Switzerland status: published

Although the CRISPR/Cas9 system has been successfully used for crop breeding, its application remains limited in forest trees. Here, we describe an efficient gene editing strategy for hybrid poplar, (Populus tremula × alba INRA clone 717-1B4) based on the Golden Gate MoClo cloning. To test the system efficiency for generating single gene mutants, two single guide RNAs (sgRNAs) were designed and incorporated into the MoClo Tool Kit level 2 binary vector with the Cas9 expression cassette to mutate the SHORT ROOT (SHR) gene. Moreover, we also tested its efficiency for introducing mutations in two genes simultaneously by expressing one sgRNA targeting a single site of the YUC4 gene and the other sgRNA targeting the PLT1 gene. For a robust evaluation of the approach, we repeated the strategy to target the LBD12 and LBD4 genes simultaneously, using an independent construct. We generated hairy roots by Agrobacterium rhizogenes-mediated leaf transformation. Sequencing results confirmed the CRISPR/Cas9-mediated mutation in the targeted sites of PtaSHR. Biallelic and homozygous knockout mutations were detected. A deletion spanning both target sites and small insertions/deletions were the most common mutations. Out of the 22 SHR alleles sequenced, 21 were mutated. The phenotype’s characterization showed that transgenic roots with biallelic mutations for the SHR gene lacked a defined endodermal single cell layer, suggesting a conserved gene function similar to its homolog in Arabidopsis Arabidopsis thaliana (L.) Heynh. Sequencing results also revealed the high efficiency of the system for generating double mutants. Biallelic mutations for both genes in the yuc4/plt1 and lbd12/lbd4 roots were detected in three (yuc4/plt1) and two (lbd12/lbd4) out of four transgenic roots evaluated. A small deletion or a single nucleotide insertion at the single target site was the most common mutations. This CRISPR/Cas9 strategy arises as a rapid, simple and standardized gene-editing tool to evaluate the gene role in essential developmental programs such as radial cell differentiation of poplar roots.

Aims We sought to develop a novel experimental system which enabled application of iodinated contrast media to in vivo plant roots intact in soil and was compatible with time-resolved synchrotron X-ray computed tomography imaging. The system was developed to overcome issues of low contrast to noise within X-ray computed tomography images of plant roots and soil environments, the latter of which can complicate image processing and result in the loss of anatomical information. Methods To demonstrate the efficacy of the system we employ the novel use of both synchrotron X-ray computed tomography and synchrotron X-ray fluorescence mapping to capture the translocation of the contrast media through root vasculature into the leaves. Results With the application of contrast media we identify fluid flow in root vasculature and visualise anatomical features, which are otherwise often only observable in ex vivo microscopy, including: the xylem, metaxylem, pith, fibres in aerenchyma and leaf venation. We are also able to observe interactions between aerenchyma cross sectional area and solute transport in the root vasculature with depth. Conclusions Our novel system was capable of successfully delivering sufficient contrast media into root and leaf tissues such that anatomical features could be visualised and internal fluid transport observed. We propose that our system could be used in future to study internal plant transport mechanisms and parameterise models for fluid flow in plants.

Analysis of the angioarchitecture and quantification of the conduit vessels and microvasculature is of paramount importance for understanding the physiological and pathological processes within the central nervous system (CNS). Most of the available in vivo imaging methods lack penetration depth and/or resolution. Some ex vivo methods may provide better resolution, but are mainly destructive, as they are designed for imaging the CNS tissues after their removal from the skull or vertebral column. The removal procedure inevitably alters the in situ relations of the investigated structures and damages the dura mater and leptomeninges. µAngiofil, a polymer-based contrast agent, permits a qualitatively novel postmortem microangio-computed tomography (microangioCT) approach with excellent resolution and, therefore, visualization of the smallest brain capillaries. The datasets obtained empower a rather straightforward quantitative analysis of the vascular tree, including the microvasculature. The µAngiofil has an excellent filling capacity as well as a radio-opacity higher than the one of bone tissue, which allows imaging the cerebral microvasculature even within the intact skull or vertebral column. This permits in situ visualization and thus investigation of the dura mater and leptomeningeal layers as well as their blood supply in their original geometry. Moreover, the methodology introduced here permits correlative approaches, i.e., microangioCT followed by classical histology, immunohistochemistry and even electron microscopy. The experimental approach presented here makes use of common desktop microCT scanners, rendering it a promising everyday tool for the evaluation of the (micro)vasculature of the central nervous system in preclinical and basic research. Electronic supplementary material The online version of this article (10.1007/s00429-020-02158-8) contains supplementary material, which is available to authorized users.

High-quality pollen is a prerequisite for plant reproductive success. Pollen viability and sterility can be routinely assessed using common stains and manual microscope examination, but with low overall statistical power. Current automated methods are primarily directed towards the analysis of pollen sterility, and high throughput solutions for both pollen viability and sterility evaluation are needed that will be consistent with emerging biotechnological strategies for crop improvement. Our goal is to refine established labelling procedures for pollen, based on the combination of fluorescein (FDA) and propidium iodide (PI), and to develop automated solutions for accurately assessing pollen grain images and classifying them for quality. We used open-source software programs (CellProfiler, CellProfiler Analyst, Fiji and R) for analysis of images collected from 10 pollen taxa labelled using FDA/PI. After correcting for image background noise, pollen grain images were examined for quality employing thresholding and segmentation. Supervised and unsupervised classification of per-object features was employed for the identification of viable, dead and sterile pollen. The combination of FDA and PI dyes was able to differentiate between viable, dead and sterile pollen in all the analysed taxa. Automated image analysis and classification significantly increased the statistical power of the pollen viability assay, identifying more than 75,000 pollen grains with high accuracy (R2 = 0.99) when compared to classical manual counting. Overall, we provide a comprehensive set of methodologies as baseline for the automated assessment of pollen viability using fluorescence microscopy, which can be combined with manual and mechanized imaging systems in fundamental and applied research on plant biology. We also supply the complete set of pollen images (the FDA/PI pollen dataset) to the scientific community for future research. Electronic supplementary material The online version of this article (10.1007/s00497-020-00398-6) contains supplementary material, which is available to authorized users.

The ability to generate in vitro cultures of neuronal cells has been instrumental in advancing our understanding of the nervous system. Rodent models have been the principal source of brain cells used in primary cultures for over a century, providing insights that are widely applicable to human diseases. However, therapeutic agents that showed benefit in rodent models, particularly those pertaining to aging and age-associated dementias, have frequently failed in clinical trials. This discrepancy established a potential “translational gap” between human and rodent studies that may at least partially be explained by the phylogenetic distance between rodent and primate species. Several non-human primate (NHP) species, including the common marmoset (Callithrix jacchus), have been used extensively in neuroscience research, but in contrast to rodent models, practical approaches to the generation of primary cell culture systems amenable to molecular studies that can inform in vivo studies are lacking. Marmosets are a powerful model in biomedical research and particularly in studies of aging and age-associated diseases because they exhibit an aging phenotype similar to humans. Here, we report a practical method to culture primary marmoset neurons and astrocytes from brains of medically euthanized postnatal day 0 (P0) marmoset newborns that yield highly pure primary neuron and astrocyte cultures. Primary marmoset neuron and astrocyte cultures can be generated reliably to provide a powerful NHP in vitro model in neuroscience research that may enable mechanistic studies of nervous system aging and of age-related neurodegenerative disorders. Because neuron and astrocyte cultures can be used in combination with in vivo approaches in marmosets, primary marmoset neuron and astrocyte cultures may help bridge the current translational gap between basic and clinical studies in nervous system aging and age-associated neurological diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11357-020-00284-z) contains supplementary material, which is available to authorized users.

Background: Autologous myoblasts have been tested in the treatment of muscle-related diseases. However, the standardization of manufacturing myoblasts is still not established. Here we report a flask and animal-free medium-based method of manufacturing clinical-grade myoblast together with establishing releasing criteria for myoblast products under Good Manufacturing Practice (GMP). Methods: Quadriceps muscle biopsy samples were donated from three patients with myogenic ptosis. After biopsy samples were digested through enzymatic dissociation, the cells were grown in T175 flasks (passage 0) and hyperflasks (passage 1) in the animal-free SkGM(TM)-2 skeletal muscle cell growth medium containing 5% human platelet lysate for 15–17 days. The harvested cells were released based on cell morphology, cell dose, viability, sterility, endotoxin, mycoplasma and immunophenotype. Myotube differentiation was also evaluated. Results: 400 to 500 million myoblast cells were manufactured within 15 to 17 days by the end of passage 1, which met pre-determined releasing criteria. The manufactured myoblast cells could differentiate and fuse into myotubes in vitro, with the possible trend that the donor age may impact the differentiation ability of myoblasts. Conclusions: The present study establishes a flask-based method of manufacturing myoblast in the animal-free medium together with releasing criteria, which is simple, robust, inexpensive and easily reproducible. This study will serve as the validation for a planned phase 1 clinical trial to assess the use of autologous myoblast transplants for the treatment of myogenic ptosis and other myogenic diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10616-020-00420-9) contains supplementary material, which is available to authorized users.

The Dynamic model has been described as one of the most accurate models to quantify chill accumulation based on hourly temperatures in nuts and temperate fruits. This model considers that a dynamic process occurs at a biochemical level that determines the endodormancy breaking through the accumulation of the so-called portions. The kinetic parameters present in the model should reflect how the fruit trees integrate chilling exposure and thus they should be characteristic for each species. However, the original parameter values, reported in the late 1980s, are still being used. Even if the use of such parameter values is useful to compare among chilling requirements (CRs) for different species or cultivars, it is not the optimal choice when one intends to explain the CR variations in different years for a given cultivar. In this work we propose a data-based model calibration that makes use of phenological data for different apricot cultivars within different years to obtain model parameters, which minimize the variations among years and that have, at the same time, physical meaning to characterize the incumbent species. Results reveal that the estimation not only reduces the accumulated portion dispersion within the considered time periods but also allows to improve the CR predictions for subsequent years. We propose a set of model parameter values to predict endodormancy breaking dates in the apricot cultivars studied here., The financial support of this research work was provided by the Ministry of Economy and Competitiveness (MINECO) of the Spanish Government and European Regional Development Fund (ERDF) through project AGL2017-86627-R

In vitro models of angiogenesis are valuable tools for understanding the underlying mechanisms of pathological conditions and for the preclinical evaluation of therapies. Our laboratory developed the rat mesentery culture model as a new tool for investigating mechanistic cell–cell interactions at specific locations across intact blood and lymphatic microvascular networks ex vivo. The objective of this study was to report a method for evaluating the effect of aging on human stem cell differentiation into pericytes during angiogenesis in cultured microvascular networks. DiI labeled exogenous stem cells were seeded onto harvested adult Wistar rat mesenteric tissues and cultured in alpha-MEM + 1% serum for up to 5 days according to four experimental groups: (1) adult human adipose–derived stem cells (hASCs), (2) aged hASCs, (3) adult human bone marrow-derived stem cells (hBMSCs), and (4) aged hBMSCs. Angiogenesis per experimental group was supported by observation of increased vessel density and capillary sprouting. For each tissue per experimental group, a subset of cells was observed in typical pericyte location wrapped along blood vessels. Stem cell differentiation into pericytes was supported by the adoption of elongated pericyte morphology along endothelial cells and positive NG2 labeling. The percentage of cells in pericyte locations was not significantly different across the experimental groups, suggesting that aged mesenchymal stem cells are able to retain their differentiation capacity. Our results showcase an application of the rat mesentery culture model for aging research and the evaluation of stem cell fate within intact microvascular networks.

Social information processing is vital for inferring emotional states in others, yet affective neuroscience has only begun to scratch the surface of how we represent emotional information in the brain. Most previous affective neuroscience work has used isolated stimuli such as static images of affective faces or scenes to probe affective processing. While this work has provided rich insight to the initial stages of emotion processing (encoding cues), activation to isolated stimuli provides limited insight into later phases of emotion processing such as interpretation of cues or interactions between cues and established cognitive schemas. Recent work has highlighted the potential value of using complex video stimuli to probe socio-emotional processing, highlighting the need to develop standardized video coding schemas as this exciting field expands. Toward that end, we present a standardized and open-source coding system for complex videos, two fully coded videos, and a video and code processing Python library. The EmoCodes manual coding system provides an externally validated and replicable system for coding complex cartoon stimuli, with future plans to validate the system for other video types. The emocodes Python library provides automated tools for extracting low-level features from video files as well as tools for summarizing and analyzing the manual codes for suitability of use in neuroimaging analysis. Materials can be freely accessed at https://emocodes.org/. These tools represent an important step toward replicable and standardized study of socio-emotional processing using complex video stimuli. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42761-021-00100-7.

Supplemental Digital Content is available in the text., Background: Most patients with congenital heart disease survive into adulthood; however, residual abnormalities remain and management of the patients is life-long and personalized. Patients with surgical repair of transposition of the great arteries, for example, face the risk to develop neoaortic valve regurgitation. Cardiologists update the prognosis of the patient intuitively with updated information of the cardiovascular status of the patient, for instance from echocardiographic imaging. Methods: Usually a time-dependent version of the Cox model is used to analyze repeated measurements with a time-to-event outcome. New statistical methods have been developed with multiple advantages, of which the most prominent one being the joint model for longitudinal and time-to-event outcome. In this tutorial, the joint modeling framework is introduced and applied to patients with transposition of the great arteries after surgery with a long-term follow-up, where repeated echocardiographic values of the neoaortic root are evaluated against the risk of neoaortic valve regurgitation. Results: The data are analyzed with the time-dependent Cox model as benchmark method, and the results are compared with a joint model, leading to different conclusions. The flexibility of the joint model is shown by adding the growth rate of the neoaortic root to the model and adding repeated values of body surface area to obtain a multimarker model. Lastly, it is demonstrated how the joint model can be used to obtain personalized dynamic predictions of the event. Conclusions: The joint model for longitudinal and time-to-event data is an attractive method to analyze data in follow-up studies with repeated measurements. Benefits of the method include using the estimated natural trajectory of the longitudinal outcome, great flexibility through multiple extensions, and dynamic individualized predictions.

The AGE Presents Introduction to Geroscience video lecture series is a collection of high-quality didactic video lectures and associated teaching materials focused on foundational topics in aging biology. The videos are made freely available on YouTube and are targeted toward an audience familiar with concepts learned in the first year of a college undergraduate biology/biomedical major. Members of the American Aging Association also receive the original lecture slides and lecture notes, with additional course materials to be developed in the future. We expect that these lectures will enhance understanding of geroscience among the general public while also providing tools that educators can use in the classroom for high school, undergraduate, and graduate level curricula.

Introduction: Precision mapping of the functional structure of platelet populations holds great promise for the identification of hyper-reactive subtypes that are likely to be disease drivers, having value in prognostics and as therapeutic targets. However, the ability to measure the intrinsic functional capacity of individual platelets is confounded by potent paracrine cross-talk, resulting in phenotypic remodeling of the entire platelet population, and in doing so obscuring the identity of hyper-reactive platelets.Methods: To address this we have developed a droplet microfluidics strategy for single platelet confinement to exclude paracrine signaling. Consideration of the Poisson distribution was used for high throughput single platelet encapsulation and the preparation of minimal platelet collectives serving as digital models for understanding the role of hyper-reactive platelets coordinating system-level behavior by paracrine signaling. Platelets are retrieved from the droplets for phenotyping using standard flow cytometry. In addition, we have incorporated a staggered herringbone micromixing element for accurate agonist and antibody dispensing in droplets.Results: The methodology was used for characterizing sensitivity distributions from healthy blood donors in response to convulxin (agonist of the GPVI receptor, the major platelet receptor for collagen). P-selectin exposure and α IIb β 3 integrin activation were used as analytical end-points to demonstrate the existence of hyper-reactive platelets that direct 20-fold gains in system level sensitivity. Conclusions: The analytical workflow represents an enabling tool for the accurate classification of platelet subtypes and description of their underlying biology.Supplementary information: The online version of this article (10.1007/s12195-020-00665-6) contains supplementary material, which is available to authorized users.

Teixit adipós; Medul·la òssia; Cèl·lules estromals mesenquimals multipotents Tejido adiposo; Médula ósea; Células estromales mesenquimales multipotentes Adipose tissue; Bone marrow; Multipotent mesenchymal stromal cells Multipotent mesenchymal stromal cells (MSCs) are currently the most extensively studied type of adult stem cells in advanced stages of development in the field of regenerative medicine. The biological properties of MSCs have generated great hope for their therapeutic use in degenerative and autoimmune conditions that, at present, lack effective treatment options. Over the last decades, MSCs have been typically obtained from adult bone marrow, but the extraction process is highly invasive and the quality and numbers of isolated cells is drastically influenced by patient age, medication and associated comorbidities. Therefore, there is currently an open discussion on the convenience of allogeneic over autologous treatments, despite potential disadvantages such as rejection by the host. This shift to the allogeneic setting entails the need for high production of MSCs to ensure availability of sufficient cell numbers for transplantation, and therefore making the search for alternative tissue sources of highly proliferative MSC cultures with low levels of senescence occurrence, which is one of the greatest current challenges in the scale up of therapeutic cell bioprocessing. Herein we (i) present the main isolation protocols of MSCs from bone marrow, adipose tissue and Wharton’s jelly of the umbilical cord; and (ii) compare their qualities from a bioprocess standpoint, addressing both quality and regulatory aspects, in view of their anticipated clinical use. This work has been developed in the context of the Spanish Cell Therapy Network (TerCel, expedient number: RD16/0011/0028) and project PI19/01788, which is funded by Instituto de Salud Carlos III and co-funded by European Union (ERDF/ESF)—A way to build Europe.

Background and Aims Nursing home research may involve eliciting information from managers, yet response rates for Directors of Nursing have not been recently studied. As a part of a more extensive study, we surveyed all nursing homes in three states in 2018 and 2019, updating how to survey these leaders effectively. We focus on response rates as a measure of non‐response error and comparison of nursing home's characteristics to their population values as a measure of representation error. Methods We surveyed Directors of Nursing or their designees in nursing homes serving adult residents with at least 30 beds in California, Massachusetts, and Ohio (N = 2389). We collected contact information for respondents and then emailed survey invitations and links, followed by three email reminders and a paper version. Nursing home associations in two of the states contacted their members on our behalf. We compared the response rates across waves and states. We also compared the characteristics of nursing homes based on whether the response was via email or paper. In a multivariable logit regression, we used characteristics of the survey and the nursing homes to predict whether their DON responded to the survey using adjustments for multiple comparisons. Results The response rate was higher for the first wave than for the second (30% vs 20.5%). The highest response rate was in Massachusetts (31.8%), followed by Ohio (25.8%) and California (19.5%). Nursing home characteristics did not vary by response mode. Additionally, we did not find any statistically significant predictors of whether a nursing home responded. Conclusion A single‐mode survey may provide a reasonably representative sample at the cost of sample size. With that said, however, switching modes can increase sample size without potentially biasing the sample.

Improvements in ischemic heart disease (IHD) management have been unbalanced between sexes, with coronary microvascular dysfunction considered the likely underlying reason. The Endocrine Vascular disease Approach (EVA) is an observational study (Clinicaltrial.gov NCT02737982) aiming to assess sex and gender interactions between coronary circulation, sexual hormones, and platelet function. Consecutive patients with IHD undergoing coronary angiography will be recruited: (1) to assess sex and gender differences in angiographic reperfusion indexes; (2) to evaluate the effects of estrogen/androgen on sex-related differences in myocardial ischemia; (3) to investigate the platelet biology differences between men and women with IHD; (4) to verify sex- and gender-driven interplay between response to percutaneous coronary intervention, platelets, sex hormones, and myocardial damage at baseline and its impact on 12-month outcomes. The integration of sex and gender in this translational project on IHD will contribute to the identification of new targets for further innovative clinical interventions.

Backgrounds and aims This article develops a Specialty Intensity Score, which uses patient diagnosis codes to estimate the number of specialist physicians a patient will need to access. Conceptually, the score can serve as a proxy for a patient's need for care coordination across doctors. Such a measure may be valuable to researchers studying care coordination practices for complex patients. In contrast with previous comorbidity scores, which focus primarily on mortality and utilization, this comorbidity score approximates the complexity of a patient's the interaction with the health care system. Methods We use 2015 inpatient claims data from the Centers for Medicare and Medicaid Services to model the relationship between a patient's diagnoses and physician specialty usage. We estimate usage of specialist doctors by using a least absolute shrinkage and selection operator Poisson model. The Specialty Intensity Score is then constructed using this predicted specialty usage. To validate our score, we test its power to predict the occurrence of patient safety incidents and compare that with the predictive power of the Charlson comorbidity index. Results Our model uses 127 of the 279 International Classification of Disease, 10th Revision, Clinical Modification (ICD‐10‐CM) diagnosis subchapters to predict specialty usage, thus creating the Specialty Intensity Score. This score has significantly greater power in predicting patient safety complications than the widely used Charlson comorbidity index. Conclusion The Specialty Intensity Score developed in this article can be used by health services researchers and administrators to approximate a patient's need for care coordination across multiple specialist doctors. It, therefore, can help with evaluation of care coordination practices by allowing researchers to restrict their analysis of outcomes to the patients most impacted by those practices.

Supplemental Digital Content is available in the text., Background: Iron deficiency (ID) has a prevalence of ≈40% to 50% among patients in heart failure (HF) with reduced ejection fraction and is associated with worse prognosis. Several trials demonstrated that intravenous ferric carboxymaltose leads to early and sustained improvement in patient-reported outcomes and functional capacity in patients with HF with reduced ejection fraction with ID, yet morbidity and mortality data are limited. Methods: The objective of the HEART-FID trial (Ferric Carboxymaltose in Heart Failure With Iron Deficiency) is to assess efficacy and safety of ferric carboxymaltose compared with placebo as treatment for symptomatic HF with reduced ejection fraction with ID. HEART-FID is a multicenter, randomized, double-blind, placebo-controlled trial enrolling ≈3014 patients at ≈300 international centers. Eligible patients are aged ≥18 years in stable chronic HF with New York Heart Association functional class II to IV symptoms, ejection fraction ≤40%, ID (ferritin

Background: Iron deficiency (ID) has a prevalence of ≈40% to 50% among patients in heart failure (HF) with reduced ejection fraction and is associated with worse prognosis. Several trials demonstrated that intravenous ferric carboxymaltose leads to early and sustained improvement in patient-reported outcomes and functional capacity in patients with HF with reduced ejection fraction with ID, yet morbidity and mortality data are limited. Methods: The objective of the HEART-FID trial (Ferric Carboxymaltose in Heart Failure With Iron Deficiency) is to assess efficacy and safety of ferric carboxymaltose compared with placebo as treatment for symptomatic HF with reduced ejection fraction with ID. HEART-FID is a multicenter, randomized, double-blind, placebo-controlled trial enrolling ≈3014 patients at ≈300 international centers. Eligible patients are aged ≥18 years in stable chronic HF with New York Heart Association functional class II to IV symptoms, ejection fraction ≤40%, ID (ferritin Conclusions: The HEART-FID trial will inform clinical practice by clarifying the role of long-term treatment with intravenous ferric carboxymaltose, added to usual care, in ambulatory patients with symptomatic HF with reduced ejection fraction with ID. Registration: URL: https://www.clinicaltrials.gov ; Unique identifier: NCT03037931.

Supplemental Digital Content is available in the text., Background: The expense of clinical trials mandates new strategies to efficiently generate evidence and test novel therapies. In this context, we designed a decentralized, patient-centered randomized clinical trial leveraging mobile technologies, rather than in-person site visits, to test the efficacy of 12 weeks of canagliflozin for the treatment of heart failure, regardless of ejection fraction or diabetes status, on the reduction of heart failure symptoms. Methods: One thousand nine hundred patients will be enrolled with a medical record-confirmed diagnosis of heart failure, stratified by reduced (≤40%) or preserved (>40%) ejection fraction and randomized 1:1 to 100 mg daily of canagliflozin or matching placebo. The primary outcome will be the 12-week change in the total symptom score of the Kansas City Cardiomyopathy Questionnaire. Secondary outcomes will be daily step count and other scales of the Kansas City Cardiomyopathy Questionnaire. Results: The trial is currently enrolling, even in the era of the coronavirus disease 2019 (COVID-19) pandemic. Conclusions: CHIEF-HF (Canagliflozin: Impact on Health Status, Quality of Life and Functional Status in Heart Failure) is deploying a novel model of conducting a decentralized, patient-centered, randomized clinical trial for a new indication for canagliflozin to improve the symptoms of patients with heart failure. It can model a new method for more cost-effectively testing the efficacy of treatments using mobile technologies with patient-reported outcomes as the primary clinical end point of the trial. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT04252287.

Bacteriophages with long DNA genomes are of interest due to their diverse mutations dependent on environmental factors. By lowering the ionic strength of a hydrophobic (PPh4Cl) antagonistic salt (at 1 mM), single long T4 DNA strand fluctuations were clearly observed, while condensed states of T4 DNA globules were formed above 5–10 mM salt. These long DNA strands were treated with fluorescently labeled probes, for which photo bleaching is often unavoidable over a short time of measurement. In addition, long (few tens of $$\upmu m$$ μ m ) length scales are required to have larger fields of view for better sampling, with shorter temporal resolutions. Thus, an optimization between length and time is crucial to obtain useful information. To facilitate the challenge of detecting large biomacromolecules, we here introduce an effective method of live image data analysis for direct visualization and quantification of local thermal fluctuations. The motions of various conformations for the motile long DNA strands were examined for the single- and multi-T4 DNA strands. We find that the unique correlation functions exhibit a relatively high-frequency oscillatory behavior superimposed on the overall slower decay of the correlation function with a splitting of amplitudes deriving from local activities of the long DNA strands. This work shows not only the usefulness of an image–time correlation for analyzing large biomacromolecules, but also provides insight into the effects of a hydrophobic antagonistic salt on active T4 bacteriophage long DNA strands, including thermal translocations in their electrostatic interactions.

Tree stem CO2 efflux is an important component of ecosystem carbon fluxes and has been the focus of many studies. While CO2 efflux can easily be measured, a growing number of studies have shown that it is not identical with actual in situ respiration. Complementing measurements of CO2 flux with simultaneous measurements of O2 flux provides an additional proxy for respiration, and the combination of both fluxes can potentially help getting closer to actual measures of respiratory fluxes. To date, however, the technical challenge to measure relatively small changes in O2 concentration against its high atmospheric background has prevented routine O2 measurements in field applications. Here, we present a new and low-cost field-tested device for autonomous real-time and quasi-continuous long-term measurements of stem respiration by combining CO2 (NDIR-based) and O2 (quenching-based) sensors in a tree stem chamber. Our device operates as a cyclic-closed system and measures changes in both CO2 and O2 concentration within the chamber over time. The device is battery powered with a >1-week power independence, and data acquisition is conveniently achieved by an internal logger. Results from both field and laboratory tests document that our sensors provide reproducible measurements of CO2 and O2 exchange fluxes under varying environmental conditions.

Quantifying the intensity of animals’ reaction to stimuli is notoriously difficult as classic unidimensional measures of responses such as latency or duration of looking can fail to capture the overall strength of behavioural responses. More holistic rating can be useful but have the inherent risks of subjective bias and lack of repeatability. Here, we explored whether crowdsourcing could be used to efficiently and reliably overcome these potential flaws. A total of 396 participants watched online videos of dogs reacting to auditory stimuli and provided 23,248 ratings of the strength of the dogs’ responses from zero (default) to 100 using an online survey form. We found that raters achieved very high inter-rater reliability across multiple datasets (although their responses were affected by their sex, age, and attitude towards animals) and that as few as 10 raters could be used to achieve a reliable result. A linear mixed model applied to PCA components of behaviours discovered that the dogs’ facial expressions and head orientation influenced the strength of behaviour ratings the most. Further linear mixed models showed that that strength of behaviour ratings was moderately correlated to the duration of dogs’ reactions but not to dogs’ reaction latency (from the stimulus onset). This suggests that observers’ ratings captured consistent dimensions of animals’ responses that are not fully represented by more classic unidimensional metrics. Finally, we report that overall participants strongly enjoyed the experience. Thus, we suggest that using crowdsourcing can offer a useful, repeatable tool to assess behavioural intensity in experimental or observational studies where unidimensional coding may miss nuance, or where coding multiple dimensions may be too time-consuming. Supplementary Information The online version contains supplementary material available at 10.1007/s10071-021-01490-8.

Introduction Cellular bone matrices (CBM) are allograft products that provide three components essential to new bone formation: an osteoconductive scaffold, extracellular growth factors for cell proliferation and differentiation, and viable cells with osteogenic potential. This is an emerging technology being applied to augment spinal fusion procedures as an alternative to autografts. Methods We aim to compare the ability of six commercially‐available human CBMs (Trinity ELITE®, ViviGen®, Cellentra®, Osteocel® Pro, Bio4® and Map3®) to form a stable spinal fusion using an athymic rat model of posterolateral fusion. Iliac crest bone from syngeneic rats was used as a control to approximate the human gold standard. The allografts were implanted at L4‐5 according to vendor specifications in male athymic rats, with 15 rats in each group. MicroCT scans were performed at 48 hours and 6 weeks post‐implantation. The rats were euthanized 6 weeks after surgery and the lumbar spines were harvested for X‐ray, manual palpation and histology analysis by blinded reviewers. Results By manual palpation, five of 15 rats of the syngeneic bone group were fused at 6 weeks. While Trinity ELITE had eight of 15 and Cellentra 11 of 15 rats with stable fusion, only 2 of 15 of ViviGen‐implanted spines were fused and zero of 15 of the Osteocel Pro, Bio4 and Map3 produced stable fusion. MicroCT analysis indicated that total bone volume increased from day 0 to week 6 for all groups except syngeneic bone group. Trinity ELITE (65%) and Cellentra (73%) had significantly greater bone volume increases over all other implants, which was consistent with the histological analysis. Conclusion Trinity ELITE and Cellentra were significantly better than other implants at forming new bone and achieving spinal fusion in this rat model at week 6. These results suggest that there may be large differences in the ability of different CBMs to elicit a successful fusion in the posterolateral spine., We aim to compare the ability of six commercially‐available human CBMs (Trinity ELITE, ViviGen, Cellentra, Osteocel Pro, Bio4 and Map3) to form a stable spinal fusion using an athymic rat model of posterolateral fusion. Our results showed that Trinity ELITE and Cellentra were significantly better than other implants at forming new bone and achieving spinal fusion in this rat model at week 6.

Introduction Intervertebral disc (IVD) degeneration is often associated with low back pain and radiating leg pain. The purpose of this study is to develop a reproducible and standardized preclinical model of painful lumbar IVD degeneration by evaluation of structural and behavioral changes in response to IVD injury with increasing needle sizes. This model can be used to develop new therapies for IVD degeneration. Methods Forty‐five female Sprague Dawley rats underwent anterior lumbar disc needle puncture at levels L4‐5 and L5‐6 under fluoroscopic guidance. Animals were randomly assigned to four different experimental groups: needle sizes of 18 Gauge (G), 21G, 23G, and sham control. To monitor the progression of IVD degeneration and pain, the following methods were employed: μMRI, qRT‐PCR, histology, and biobehavioral analysis. Results T1‐ and T2‐weighted μMRI analysis showed a correlation between the degree of IVD degeneration and needle diameter, with the most severe degeneration in the 18G group. mRNA expression of markers for IVD degeneration markers were dysregulated in the 18G and 21G groups, while pro‐nociceptive markers were increased in the 18G group only. Hematoxylin and Eosin (H&E) and Alcian Blue/Picrosirius Red staining confirmed the most pronounced IVD degeneration in the 18G group. Randall‐Selitto and von Frey tests showed increased hindpaw sensitivity in the 18G group. Conclusion Our findings demonstrate that anterior disc injury with an 18G needle creates severe IVD degeneration and mechanical hypersensitivity, while the 21G needle results in moderate degeneration with no increased pain sensitivity. Therefore, needle sizes should be selected depending on the desired phenotype for the pre‐clinical model., Study Design Overview This study establishes and validates a rat model for lumbar IVD degeneration that is reflected in painful behavior. Based on our findings we conclude that annular disc injury with a 18G needle creates severe, painful IVD degeneration, while 21G needle injury results in moderate degeneration.

Although machine learning (ML) has made significant improvements in radiology, few algorithms have been integrated into clinical radiology workflow. Complex radiology IT environments and Picture Archiving and Communication System (PACS) pose unique challenges in creating a practical ML schema. However, clinical integration and testing are critical to ensuring the safety and accuracy of ML algorithms. This study aims to propose, develop, and demonstrate a simple, efficient, and understandable hardware and software system for integrating ML models into the standard radiology workflow and PACS that can serve as a framework for testing ML algorithms. A Digital Imaging and Communications in Medicine/Graphics Processing Unit (DICOM/GPU) server and software pipeline was established at a metropolitan county hospital intranet to demonstrate clinical integration of ML algorithms in radiology. A clinical ML integration schema, agnostic to the hospital IT system and specific ML models/frameworks, was implemented and tested with a breast density classification algorithm and prospectively evaluated for time delays using 100 digital 2D mammograms. An open-source clinical ML integration schema was successfully implemented and demonstrated. This schema allows for simple uploading of custom ML models. With the proposed setup, the ML pipeline took an average of 26.52 s per second to process a batch of 100 studies. The most significant processing time delays were noted in model load and study stability times. The code is made available at “ http://bit.ly/2Z121hX ”. We demonstrated the feasibility to deploy and utilize ML models in radiology without disrupting existing radiology workflow.

Purpose Neutral zone (NZ) parameters in spinal biomechanics studies are sensitive to spinal instability, disc degeneration, and repair. Multiple methods in the literature quantify NZ, yet no consensus exists on applicability and comparability of methods. This study compares five different NZ quantification methods using two different load‐deflection profiles. Methods Rat caudal and lumbar motion segments were tested in axial rotation to generate load‐deflection curves with profiles exhibiting prominent distinction between elastic and NZ regions (ie, triphasic) and profiles that did not (ie, viscoelastic). NZ was quantified using five methods: trilinear, double sigmoid (DS), zero load, stiffness threshold (ST), and extrapolated elastic zone. Absolute agreement and consistency of NZ parameters were assessed using intraclass correlation (ICC), Bland‐Altman analyses, and analysis of variance. Results For triphasic profiles, NZ magnitude exhibited high consistency (methods correlate but differ in absolute values), and only some methods exhibited agreement. For viscoelastic profiles, NZ magnitude showed limited consistency and no absolute agreement. NZ stiffness had high agreement and consistency across most methods and profiles. For triphasic profiles, the linear NZ regions for all methods were not well‐described by a linear fit yet for viscoelastic profiles all methods characterized a linear NZ region. Conclusion This NZ comparison study showed surprisingly limited agreement and consistency among NZ parameters with approximately 5% to 100% difference depending on the method and load‐deflection profile. Nevertheless, the DS and ST methods appeared to be most comparable. We conclude that most NZ quantification methods cannot be applied interchangeably, highlighting a need to clearly state NZ calculation methods. Future studies are required to identify which methods are most sensitive to disc degeneration and repair in order to identify a “best” method., The neutral zone (NZ) is a clinically relevant metric of spinal motion segment laxity, but measuring it is difficult due to the viscoelastic nature of the intervertebral disc. Various NZ quantification methods are currently used in the field, yet the degree of agreeability and interchangeability between methods remains unknown. Our findings indicate that methods rarely agree in measurement and should therefore not be considered interchangeable, highlighting the need to clearly describe the underlying methodology in order to contextualize NZ results.

The morphological structure of neurons provides the basis for their functions and is a major focus of contemporary neuroscience studies. Intracellular staining of single cells in acute slices is a well-established approach, offering high-resolution information on neuronal morphology, complementing their physiology. Despite major technical advances, however, a common histological artifact often precludes precise morphological analysis: shrinkage of the sampled tissue after embedding for microscopy. Here, we describe a new approach using a metal spacer, sandwiched between two coverslips to reduce shrinkage of whole-mount slice preparations during embedding with aqueous mounting medium under a coverslip. This approach additionally allows imaging the slices from both sides to obtain better quality images of deeper structures. We demonstrate that the use of this spacer system can efficiently and stably reduce the shrinkage of slices, whereas conventional embedding methods without spacer or with agar spacer cause severe, progressive shrinkage after embedding. We further show that the shrinkage of slices is not uniform and artifacts in morphology and anatomical parameters produced cannot be compensated using linear correction algorithms. Our study, thus, emphasizes the importance of preventing the deformation of slice preparations and offers an effective means for reducing shrinkage and associated artifacts during embedding. Electronic supplementary material The online version of this article (10.1007/s00429-020-02141-3) contains supplementary material, which is available to authorized users.

Background and aims\ud Understanding the structures and functions of carbon-based molecules in soils is an important goal in the context of soils as an ecosystem function of immense importance. Polysaccharides are implicated in maintaining soil aggregate status but have not been extensively dissected in terms of their structures and soil adhesion properties. This is largely because of the technical difficulties in identifying polysaccharide structures and quantifying any functional properties.\ud \ud Methods\ud Here, we describe the use of a novel nitrocellulose-based adhesion assay to determine the relative capacities for soil adhesion of over twenty plant and microbial polysaccharides that are likely to be present in soil and to contribute to organic matter content and properties. Weights of soil adhered to spots of known amounts of specific polysaccharides were quantified by scanning of the nitrocellulose sheets.\ud \ud Results\ud The most effective polysaccharides identified from this survey included chitosan, β-1,3-glucan, gum tragacanth, xanthan and xyloglucan. We also demonstrate that the soil adhesion assay is suitable to assess the soil-binding properties of plant exudates.\ud \ud Conclusions\ud The soil adhesion assay will be useful for the functional dissection of the organic matter components of soils and also of the factors involved in soil attachment to plant roots and in rhizosheath formation.

Clinical use of multipotent Mesenchymal Stromal Cell (MSC)-based medicinal products requires their production in compliance with Good Manufacturing Practices, thus ensuring that the final drug product meets specifications consistently from batch to batch in terms of cell viability, identity, purity and potency. Potency relates to the efficacy of the medicine in its target clinical indication, so adequate release tests need to be defined and validated as quality controls. Herein we report the design and optimisation of parameters affecting the performance of an in vitro cell-based assay for assessing immunomodulatory potential of clinical grade MSC for human use, based on their capacity to inhibit proliferation of T lymphocytes under strong polyclonal stimuli. The resulting method was demonstrated to be reproducible and relatively simple to execute. Two case studies using clinical grade MSC are presented as examples to illustrate the applicability of the methodology described in this work.

Non-structural carbohydrates (NSCs), the stored products of photosynthesis, building blocks for growth and fuel for respiration, are central to plant metabolism, but their measurement is challenging. Differences in methods and procedures among laboratories can cause results to vary widely, limiting our ability to integrate and generalize patterns in plant carbon balance among studies. A recent assessment found that NSC concentrations measured for a common set of samples can vary by an order of magnitude, but sources for this variability were unclear. We measured a common set of nine plant material types, and two synthetic samples with known NSC concentrations, using a common protocol for sugar extraction and starch digestion, and three different sugar quantification methods (ion chromatography, enzyme, acid) in six laboratories. We also tested how sample handling, extraction solvent and centralizing parts of the procedure in one laboratory affected results. Non-structural carbohydrate concentrations measured for synthetic samples were within about 11.5% of known values for all three methods. However, differences among quantification methods were the largest source of variation in NSC measurements for natural plant samples because the three methods quantify different NSCs. The enzyme method quantified only glucose, fructose and sucrose, with ion chromatography we additionally quantified galactose, while the acid method quantified a large range of mono- and oligosaccharides. For some natural samples, sugars quantified with the acid method were two to five times higher than with other methods, demonstrating that trees allocate carbon to a range of sugar molecules. Sample handling had little effect on measurements, while ethanol sugar extraction improved accuracy over water extraction. Our results demonstrate that reasonable accuracy of NSC measurements can be achieved when different methods are used, as long as protocols are robust and standardized. Thus, we provide detailed protocols for the extraction, digestion and quantification of NSCs in plant samples, which should improve the comparability of NSC measurements among laboratories.

Key message An easy and highly reproducible nondestructive method named the Leaf Collar Method is described to identify and characterize the different stages of pollen development in maize. Abstract In plants, many cellular events such as meiosis, asymmetric cell division, cell cycle regulation, cell fate determination, nucleus movement, vacuole formation, chromatin condensation and epigenetic modifications take place during pollen development. In maize, pollen development occurs in tassels that are confined within the internal stalk of the plant. Hence, identification of the different pollen developmental stages as a tool to investigate above biological processes is impossible without dissecting the entire plant. Therefore, an efficient and reproducible method is necessary to isolate homogeneous cell populations at individual stages throughout pollen development without destroying the plant. Here, we describe a method to identify the various stages of pollen development in maize. Using the Leaf Collar Method in the maize inbreed line B73, we have determined the duration of each stage from pollen mother cells before meiosis to mature tricellular pollen. Anther and tassel size as well as percentage of pollen stages were correlated with vegetative stages, which are easily recognized. The identification of stage-specific genes indicates the reproducibility of the method. In summary, we present an easy and highly reproducible nondestructive method to identify and characterize the different stages of pollen development in maize. This method now opens the way for many subsequent physiological, morphological and molecular analyses to study, for instance, transcriptomics, metabolomics, DNA methylation and chromatin patterns during normal and stressful conditions throughout pollen development in one of the economically most important grass species. Electronic supplementary material The online version of this article (10.1007/s00497-017-0311-4) contains supplementary material, which is available to authorized users.

Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making. Here, we explored the potential of a pocket-size nanopore sequencing device for multimodal and rapid molecular diagnostics of cancer. Low-pass whole genome sequencing was used to simultaneously generate copy number (CN) and methylation profiles from native tumor DNA in the same sequencing run. Single nucleotide variants in IDH1, IDH2, TP53, H3F3A, and the TERT promoter region were identified using deep amplicon sequencing. Nanopore sequencing yielded ~0.1X genome coverage within 6 h and resulting CN and epigenetic profiles correlated well with matched microarray data. Diagnostically relevant alterations, such as 1p/19q codeletion, and focal amplifications could be recapitulated. Using ad hoc random forests, we could perform supervised pan-cancer classification to distinguish gliomas, medulloblastomas, and brain metastases of different primary sites. Single nucleotide variants in IDH1, IDH2, and H3F3A were identified using deep amplicon sequencing within minutes of sequencing. Detection of TP53 and TERT promoter mutations shows that sequencing of entire genes and GC-rich regions is feasible. Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost. It outperforms hybridization-based and current sequencing technologies with respect to time to diagnosis and required laboratory equipment and expertise, aiming to make precision medicine possible for every cancer patient, even in resource-restricted settings. Electronic supplementary material The online version of this article (doi:10.1007/s00401-017-1743-5) contains supplementary material, which is available to authorized users.

The study of CD8 positive cells in peripheral blood has become an essential part of research in the field of cancer immunotherapies, vaccine development, inflammation, autoimmune disease, etc. In this study, an 8-color flow cytometry panel, containing lineage and functional markers, was developed for the identification of CD8+ cytotoxic T cells in previously cryopreserved peripheral blood mononuclear cells from healthy human donors. By studying functional markers in naïve and CD3/CD28 activated T cells we demonstrate that the panel is capable of detecting protein markers corresponding to different T cell activation statuses. Data generated by flow cytometry were corroborated by different antibody based assay technologies to detect soluble cytokines. Our findings suggest that there is an inter donor variability in both baseline and activation responses. We have also successfully developed an antibody panel for flow cytometry that could be used to study cytotoxic function of CD8 T cells in clinical immunology research areas.

Background: Variable selection is an important issue when developing prognostic models. Missing data occur frequently in clinical research. Multiple imputation is increasingly used to address the presence of missing data in clinical research. The effect of different variable selection strategies with multiply imputed data on the external performance of derived prognostic models has not been well examined. Methods and Results: We used backward variable selection with 9 different ways to handle multiply imputed data in a derivation sample to develop logistic regression models for predicting death within 1 year of hospitalization with an acute myocardial infarction. We assessed the prognostic accuracy of each derived model in a temporally distinct validation sample. The derivation and validation samples consisted of 11 524 patients hospitalized between 1999 and 2001 and 7889 patients hospitalized between 2004 and 2005, respectively. We considered 41 candidate predictor variables. Missing data occurred frequently, with only 13% of patients in the derivation sample and 31% of patients in the validation sample having complete data. Regardless of the significance level for variable selection, the prognostic model developed using only the complete cases in the derivation sample had substantially worse performance in the validation sample than did the models for which variables were selected using the multiply imputed versions of the derivation sample. The other 8 approaches to handling multiply imputed data resulted in prognostic models with performance similar to one another. Conclusions: Ignoring missing data and using only subjects with complete data can result in the derivation of prognostic models with poor performance. Multiple imputation should be used to account for missing data when developing prognostic models.

Fusion of somatic cells to pluripotent cells such as mouse embryonic stem (ES) cells induces reprogramming of the somatic nucleus, and can be used to study the effect of trans-acting factors from the pluripotent cell on the somatic nucleus. Moreover, fusion of cells from different species permits the identification of the transcriptome of each cell, so the gene expression changes can be monitored. However, fusion only happens in a small proportion of the cells exposed to fusogenic conditions, hence the need for a protocol that produces high fusion rate with minimal cell damage, coupled with a method capable of identifying and selecting fusion events from the bulk of the cells. Polyethylene glycol (PEG) is a polymer of repeated ethylene oxide units known to induce cell fusion within a certain range of molecular weight. Here, we describe a method to induce formation of bi-species heterokaryons from adherent mammalian cells, which can then be specifically labeled and selected using live cell immunostaining and a combination of imaging and traditional flow cytometry. First, we tested several PEG-based fusion conditions to optimize a protocol to consistently produce both mouse NIH/3T3 fibroblast and primary bovine fetal fibroblast (bFF) homokaryons. Initially, we obtained 7.28% of NIH/3T3 homokaryons when using 50% PEG 1500. Addition of 10% of DMSO to the PEG solution increased the percentage of NIH/3T3 homokaryons to 11.71%. In bFFs, treatment with 50% PEG 1500 plus 10% DMSO produced 11.05% of homokaryons. We then produced interspecies heterokaryons by fusing mouse embryonic stem (mES) cells to bFFs. To identify bi-species fusion products, heterokaryons were labeled using indirect immunostaining in live cells and selected using imaging (Amnis ImageStream Mark II) and traditional (BD FACSAria I) flow cytometry. Heterokaryons selected with this method produced ES cell-like colonies when placed back in culture. The method described here can also be combined with downstream applications such as nucleic acid isolation for RT-PCR and RNA-seq, and used as a tool to study cellular processes in which the effect of trans-acting factors is relevant, such as in nuclear reprogramming.

INTRODUCTION: The orientation of collagen fibers in native tissues plays an important role in cell signaling and mediates the progression of tumor cells in breast cancer by a contact guidance mechanism. Understanding how migration of epithelial cells is directed by the alignment of collagen fibers requires in vitro assays with standardized orientations of collagen fibers. METHODS: To address this issue, we produced micro-stripes with aligned collagen fibers using an easy-to-use and versatile approach based on the aspiration of a collagen solution within a microchannel. Glass coverslips were functionalized with a (3-aminopropyl)triethoxysilane/glutaraldehyde linkage to covalently anchor micro-stripes of aligned collagen fibers, whereas microchannels were functionalized with a poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) nonionic triblock polymer to prevent adhesion of the collagen micro-stripes. RESULTS: Using this strategy, microchannels can be peeled off to expose micro-stripes of aligned collagen fibers without affecting their mechanical integrity. We used time-lapse confocal reflection microscopy to characterize the polymerization kinetics of collagen networks for different concentrations and the orientation of collagen fibers as a function of the microchannel width. Our results indicate a non-linear concentration dependence of the area of fluorescence, suggesting that the architecture of collagen networks is sensitive to small changes in concentration. We show the possibility to influence the collagen fibril coverage by adjusting the concentration of the collagen solution. CONCLUSION: We applied this novel approach to study the migration of epithelial cells, demonstrating that collagen micro-stripes with aligned fibers represent a valuable in-vitro assay for studying cell contact guidance mechanisms. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12195-019-00600-4) contains supplementary material, which is available to authorized users.

C3H10T1/2, a mouse mesenchymal stem cell line, is a well-known in vitro model of chondrogenesis that can be easily employed to recapitulate some of the mechanisms intervening in this process. Moreover, these cells can be used to validate the effect of candidate molecules identified by high throughput screening approaches applied to the development of targeted therapy for human disorders in which chondrogenic differentiation may be involved, as in conditions characterized by heterotopic endochondral bone formation. Chondrogenic differentiation of C3H10T1/2 cells can be monitored by applying quantitative polymerase chain reaction (qPCR), one of the most sensitive methods that allows detection of small dynamic changes in gene expression between samples obtained under different experimental conditions. In this work, we have used qPCR to monitor the expression of specific markers during chondrogenic differentiation of C3H10T1/2 cells in micromass cultures. Then we have applied the geNorm approach to identify the most stable reference genes suitable to get a robust normalization of the obtained expression data. Among 12 candidate reference genes (Ap3d1, Csnk2a2, Cdc40, Fbxw2, Fbxo38, Htatsf1, Mon2, Pak1ip1, Zfp91, 18S, ActB, GAPDH) we identified Mon2 and Ap3d1 as the most stable ones during chondrogenesis. ActB, GAPDH and 18S, the most commonly used in the literature, resulted to have an expression level too high compared to the differentiation markers (Sox9, Collagen type 2a1, Collagen type 10a1 and Collagen type 1a1), therefore are actually less recommended for these experimental conditions. In conclusion, we identified nine reference genes that can be equally used to obtain a robust normalization of the gene expression variation during the C3H10T1/2 chondrogenic differentiation. Electronic supplementary material The online version of this article (10.1007/s11033-019-04713-x) contains supplementary material, which is available to authorized users.

Much of the worldwide dissemination of antibiotic resistance has been driven by resistance gene associations with mobile genetic elements (MGEs), such as plasmids and transposons. Although increasing, our understanding of resistance spread remains relatively limited, as methods for tracking mobile resistance genes through multiple species, strains and plasmids are lacking. We have developed a bioinformatic pipeline for tracking variation within, and mobility of, specific transposable elements (TEs), such as transposons carrying antibiotic resistance genes. TETyper takes short-read whole-genome sequencing data as input and identifies single-nucleotide mutations and deletions within the TE of interest, to enable tracking of specific sequence variants, as well as the surrounding genetic context(s), to enable identification of transposition events. To investigate global dissemination ofKlebsiella pneumoniaecarbapenemase (KPC) and its associated transposon Tn4401, we applied TETyper to a collection of >3000 publicly available Illumina datasets containingblaKPC. This revealed surprising diversity, with >200 distinct flanking genetic contexts for Tn4401, indicating high levels of transposition. Integration of sample metadata revealed insights into associations between geographic locations, host species, Tn4401sequence variants and flanking genetic contexts. To demonstrate the ability of TETyper to cope with high copy number TEs and to track specific short-term evolutionary changes, we also applied it to the insertion sequence IS26within a definedK. pneumoniaeoutbreak. TETyper is implemented in python and is freely available athttps://github.com/aesheppard/TETyper.

We report for the first time the use of coaxial cutting needle biopsy, guided by post-mortem computed tomography (PMCT), to sample internal body tissues for bacterioplankton PCR analysis to investigate drowning. This technical report describes the biopsy technique, the comparison of the needle biopsy and the invasive autopsy sampling results, as well as the PMCT and autopsy findings. By using this new biopsy sampling approach for bacterioplankton PCR, we have developed on previous papers describing the minimally invasive PMCT approach for the diagnosis of drowning. When such a system is used, the operator must take all precautions to avoid contamination of the core biopsy samples due to the sensitivity of PCR-based analytic systems.

The heterogeneous presentation and progression of atrial fibrillation (AF) implicate the existence of different pathophysiological processes. Individualized diagnosis and therapy of the arrhythmogenic substrate underlying AF may be required to improve treatment outcomes. Therefore, this single-center study aims to identify the arrhythmogenic areas underlying AF by intra-operative, high-resolution, multi-site epicardial mapping in 600 patients with different heart diseases. Participants are divided into 12 groups according to the underlying heart diseases and presence of prior AF episodes. Mapping is performed with a 192-electrode array for 5–10 s during sinus rhythm and (induced) AF of the entire atrial surface. Local activation times are converted into activation and wave maps from which various electrophysiological parameters are derived. Postoperative cardiac rhythm registrations and a 5-year follow-up will show the incidence of postoperative and persistent AF. This project provides the first step in the development of a tool for individual AF diagnosis and treatment. Electronic supplementary material The online version of this article (doi:10.1007/s12265-016-9685-1) contains supplementary material, which is available to authorized users.

Accurate temporal and spatial measurements of leaf optical traits (i.e., absorption, reflectance and transmittance) are paramount to photosynthetic studies. These optical traits are also needed to couple radiative transfer and physiological models to facilitate the interpretation of optical data. However, estimating leaf optical traits in leaves with complex morphologies remains a challenge. Leaf optical traits can be measured using integrating spheres, either by placing the leaf sample in one of the measuring ports (External Method) or by placing the sample inside the sphere (Internal Method). However, in leaves with complex morphology (e.g., needles), the External Method presents limitations associated with gaps between the leaves, and the Internal Method presents uncertainties related to the estimation of total leaf area. We introduce a modified version of the Internal Method, which bypasses the effect of gaps and the need to estimate total leaf area, by painting the leaves black and measuring them before and after painting. We assess and compare the new method with the External Method using a broadleaf and two conifer species. Both methods yielded similar leaf absorption estimates for the broadleaf, but absorption estimates were higher with the External Method for the conifer species. Factors explaining the differences between methods, their trade-offs and their advantages and limitations are also discussed. We suggest that the new method can be used to estimate leaf absorption in any type of leaf independently of its morphology, and be used to study further the impact of gap fraction in the External Method.