Marker selection strategies for circulating tumor DNA guided by phylogenetic inference

Motivation

Blood-based profiling of tumor DNA ("liquid biopsy") has offered great prospects for non-invasive early cancer diagnosis, treatment monitoring, and clinical guidance, but require further advances in computational methods to become a robust quantitative assay of tumor clonal evolution. We propose new methods to better characterize tumor clonal dynamics from circulating tumor DNA (ctDNA), through application to two specific questions: 1) How to apply longitudinal ctDNA data to refine phylogeny models of clonal evolution, and 2) how to quantify changes in clonal frequencies that may be indicative of treatment response or tumor progression. We pose these questions through a probabilistic framework for optimally identifying maximum likelihood markers and applying them to characterizing clonal evolution.

Results

We first estimate a distribution over plausible clonal lineage models, using bootstrap samples over pre-treatment tissue-based sequence data. We then refine these lineage models and the clonal frequencies they imply over successive longitudinal samples. We use the resulting framework for modeling and refining tree distributions to pose a set of optimization problems to select ctDNA markers to maximize measures of utility capturing ability to solve the two questions of reducing uncertain in phylogeny models or quantifying clonal frequencies given the models. We tested our methods on synthetic data and showed them to be effective at refining distributions of tree models and clonal frequencies so as to minimize measures of tree distance relative to the ground truth. Application of the tree refinement methods to real tumor data further demonstrated their effectiveness in refining a clonal lineage model and assessing its clonal frequencies. The work shows the power of computational methods to improve marker selection, clonal lineage reconstruction, and clonal dynamics profiling for more precise and quantitative assays of tumor progression.

Availability

https://github.com/CMUSchwartzLab/Mase-phi.git.

Contact

russells@andrew.cmu.edu.

In ovo injection of AZD6244 suppresses feather follicle development by the inhibition of ERK and Wnt/β-catenin pathways in goose embryos (Anser cygnoides)

1. Feathers are an important product from poultry, and the state of feather growth and development plays an important role in their economic value.2. In total, 120 eggs were selected for immunoblotting and immunolocalisation experiments of ERK and β-catenin proteins in different developmental stages of goose embryos. The ERK protein was highly expressed in the early stage of goose embryo development, while β-catenin protein was highly expressed in the middle stage of embryo development.3. The 120 eggs were divided into four treatment groups, including an uninjected group (BLANK), a group injected with 100 µl of cosolvent (CK), a group injected with 100 µl of AZD6244 containing cosolvent in a dose of 5 mg/kg AZD6244 containing cosolvent (AZD5) and a group injected with 100 µl of AZD6244 containing cosolvent in a dose of 15 mg/kg AZD6244 containing cosolvent (AZD15). The eggs were injected on the ninth day of embryonic development (E9). Samples were collected at E21.5 to observe feather width, feather follicle diameter, ERK and Wnt/β-catenin pathway protein expression.4. The AZD5 and AZD15 doses were within the embryonic safety range compared to the BLANK and CK groups and had no significant effect on the survival rate and weight at the inflection point, but significantly reduced the feather width and feather follicle diameter (p < 0.05). The AZD6244 treatment inhibited ERK protein phosphorylation levels and blocked the Wnt/β-catenin pathway, which in turn significantly down-regulated the expression levels of FZD4, β-catenin, TCF4 and LEF1 (p < 0.05), with an inhibitory effect in the AZD15 group being more significant. The immunohistochemical results of β-catenin and p-ERK were consistent with Western blot results.5. The small molecule inhibitor AZD6244 regulated the growth and development of feather follicles in goose embryos by the ERK and Wnt/β-catenin pathways.

Sc-TUSV-ext: Single-cell clonal lineage inference from single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV)

Clonal lineage inference ("tumor phylogenetics") has become a crucial tool for making sense of somatic evolution processes that underlie cancer development and are increasingly recognized as part of normal tissue growth and aging. The inference of clonal lineage trees from single cell sequence data offers particular promise for revealing processes of somatic evolution in unprecedented detail. However, most such tools are based on fairly restrictive models of the types of mutation events observed in somatic evolution and of the processes by which they develop. The present work seeks to enhance the power and versatility of tools for single-cell lineage reconstruction by making more comprehensive use of the range of molecular variant types by which tumors evolve. We introduce Sc-TUSV-ext, an integer linear programming (ILP) based tumor phylogeny reconstruction method that, for the first time, integrates single nucleotide variants (SNV), copy number alterations (CNA) and structural variations (SV) into clonal lineage reconstruction from single-cell DNA sequencing data. We show on synthetic data that accounting for these variant types collectively leads to improved accuracy in clonal lineage reconstruction relative to prior methods that consider only subsets of the variant types. We further demonstrate the effectiveness on real data in resolving clonal evolution in the presence of multiple variant types, providing a path towards more comprehensive insight into how various forms of somatic mutability collectively shape tissue development.

Convolutional neural networks for classifying healthy individuals practicing or not practicing meditation according to the EEG data

The development of objective methods for assessing stress levels is an important task of applied neuroscience. Analysis of EEG recorded as part of a behavioral self-control program can serve as the basis for the development of test methods that allow classifying people by stress level. It is well known that participation in meditation practices leads to the development of skills of voluntary self-control over the individual's mental state due to an increased concentration of attention to themselves. As a consequence of meditation practices, participants can reduce overall anxiety and stress levels. The aim of our study was to develop, train and test a convolutional neural network capable of classifying individuals into groups of practitioners and non-practitioners of meditation by analysis of eventrelated brain potentials recorded during stop-signal paradigm. Four non-deep convolutional network architectures were developed, trained and tested on samples of 100 people (51 meditators and 49 non-meditators). Subsequently, all structures were additionally tested on an independent sample of 25 people. It was found that a structure using a one-dimensional convolutional layer combining the layer and a two-layer fully connected network showed the best performance in simulation tests. However, this model was often subject to overfitting due to the limitation of the display size of the data set. The phenomenon of overfitting was mitigated by changing the structure and scale of the model, initialization network parameters, regularization, random deactivation (dropout) and hyperparameters of cross-validation screening. The resulting model showed 82 % accuracy in classifying people into subgroups. The use of such models can be expected to be effective in assessing stress levels and inclination to anxiety and depression disorders in other groups of subjects.

The influence of residual plural scattering after deconvolution in electron magnetic chiral dichroism

This work investigated the existence and influence of residual plural scattering in electron magnetic chiral dichroism (EMCD) spectra. A series of low-loss, conventional core-loss, and q-resolved core-loss spectra at Fe-L2,3 edges were detected from areas of different thicknesses in a plane-view sample of Fe/MgO (001) thin film. It reveals by comparison that there remains noticeable plural scattering in q-resolved spectra acquired at two particular chiral positions after deconvolution, and the residual scattering is more significant in thicker areas than thinner ones. Accordingly, the orbital-to-spin moment ratio extracted from EMCD spectra, which is the difference between the two q-resolved spectra after deconvolution, would be in principle increased with increasing sample thickness. The randomly fluctuated moment ratios displayed in our experiments are greatly attributed to a slight and irregular variation of local diffraction conditions due to the bending effect and imperfect epitaxy in detected areas. We suggest EMCD spectra should be acquired from sufficiently thin samples to minimize the plural scattering effect in originally detected spectra before any deconvolution. In addition, great care should be taken for slight misorientation and imperfect epitaxy when performing EMCD investigation on epitaxial thin films using a nano beam.

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

INTRODUCTION

The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures.

METHODS

In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025.

FINDINGS

Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2-6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5-5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4-10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32-4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23-11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation.

INTERPRETATION

After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification.

FUNDING

UK Research and Innovation and National Institute for Health Research.

Impact of shift work on dementia: a systematic review and dose-response meta-analysis

OBJECTIVES

Although shift work has been reported as having a link to dementia, evidence remains inconsistent, and a comprehensive dose-response meta-analysis of the association is still lacking. We therefore conducted this meta-analysis to explore the association between shift work and the risk of dementia.

STUDY DESIGN

Systematic review and dose-response meta-analysis.

METHODS

PubMed, Embase, and Web of Science databases were systematically searched. Fixed or random-effects models were used to estimate the summary relative risks (RRs) and 95% confidence intervals (95% CIs). Generalized least squares regression was used to estimate dose-response associations, and restricted cubic splines were used to examine possible linear or non-linear associations.

RESULTS

Five articles (10 studies) with 72,999 participants and 23,067 cases were eventually included in the meta-analysis. The summary RRs and 95% CIs of dementia risk with shift work and night shift work versus daytime work were 1.13 (95% CI: 1.05-1.21, I2 = 46.70%) and 1.13 (95% CI: 1.03-1.24, I2 = 9.20%), respectively. The risk of dementia increased by 1% (RR = 1.01, 95% CI: 1.01-1.02, I2 = 41.3%) with each 1-year increase in the duration of shift work. We found a non-linear dose-response association between the duration of shift work and the risk of dementia (Pnon-linearity = 0.006). Though the shape of the curve was steeper with the duration of shift work <7 years, the increase was more gradual after 7 years.

CONCLUSION

Our findings suggest that shift work may be a risk factor for future dementia and that controlling the length of shift work is a feasible measure that may contribute to prevent dementia.

Expression of FOXO3 in the skin follicles of goose embryos during embryonic development

1. The Forkhead box O3 (FOXO3) transcription factor is a crucial regulator in controlling cell metabolism, proliferation, apoptosis, migration and response to oxidative stress. However, FOXO3 has not previously been studied much in the embryonic skin follicles of geese.2. This study used Zhedong white geese (Anser cygnoides), Jilin white geese (Anser cygnoides) and Hungarian white geese (Anser anser). The feather follicle structure in the dorsal skin during embryonic stages was examined with haematoxylin and eosin (HE) and Pollak staining. The FOXO3 protein content in the embryonic dorsal skin from feather follicles was detected using western blotting and quantitative real-time PCR.3. The mRNA expression level of FOXO3 in the dorsal skin of Jilin white geese was highly expressed on embryonic day 23 (E23; P < 0.01), while mRNA expression of FOXO3 was highly expressed in the feather follicle of Hungarian white geese at E28 (P < 0.01). The expression of FOXO3 protein mainly concentrated in the early embryonic phase among these goose breeds (P < 0.05). This suggested that FOXO3 plays a crucial role in the development and growth of embryonic dorsal skin of feather follicles. The location of the FOXO3 protein was determined using the IHC technique, which further verified the effect of FOXO3 in the dorsal skin for feather follicles during embryogenesis.4. The study demonstrated the differential expression and localisation of the FOXO3 gene among different goose species. It was speculated that the gene could potentially improve goose feather follicle development and feather-related traits and provide a basis for further understanding of FOXO3 function in the dorsal tissue of goose embryos.

[Analysis of fast-growing culturable bacteria and pathogenic bacteria in the surface water of the northeast coast of Hainan Island in China]

Objective: To obtain the diversity and abundance of fast-growing bacteria in the surface water of the northeast coast of Hainan Island in China, different cultivation methods were employed. This study also aims to provide a reference for isolating bacterial samples from seawater sources and preventing marine-derived pathogens. Methods: Based on the principles of taxonomic design, surface seawater samples were collected from six locations along the northeast coast of Hainan Island in China in March, June, October, and December 2021. Then, bacterial enrichment was performed based on traditional cultivation methods for Salmonella, Vibrio, Burkholderia pseudomallei, Actinomycetes, and general marine bacteria. After that, bacterial species identification was conducted by 16S rDNA amplicon sequencing and metagenomic sequencing. Results: A total of 1 151 fast-growing cultivable bacteria belonging to 66 genera and 213 species were identified using five different culture protocols. In different cultivation protocols, Bacillus and Klebsiella demonstrated extensive discriminatory advantages and ranked among the top genera in terms of abundance. Protocol 1 had Escherichia, Klebsiella, and Citrobacter as dominant genera. Pathogenic bacteria detected by protocol 1 included Klebsiella pneumoniae and Escherichia coli, with 37 and 29 strains respectively, while Salmonella enterica was uniquely detected with seven isolates. Proteus, Enterococcus, and Providencia were the dominant genera in protocol 2, and Proteus mirabilis was the most abundant pathogenic bacteria detected with 66 isolates. Vibrio cholerae was uniquely detected with six isolates at a higher abundance. Klebsiella, Escherichia, and Acinetobacter were the dominant genera in protocol 3, and Klebsiella pneumoniae was the most abundant pathogenic bacteria detected with 53 isolates, while Acinetobacter nosocomialis was uniquely detected with seven isolates. Vibrio and Pseudoalteromonas were the dominant genera in protocol 4, and they showed advantages in isolating and cultivating Marine-derived Vibrio. Exiguobacterium, Staphylococcus, and Bacillus were the dominant genera in protocol 5. Bacillus cereus and Lactococcus lactis were the most abundant pathogenic bacteria detected with 20 and 15 isolates, respectively, while Lactococcus lactis was uniquely detected at higher abundance. Metagenomic sequencing showed that Klebsiella pneumoniae was significantly dominant with a gene abundance of 51.11%, followed by Alcanivorax sp. at 12.57%. Conclusion: The surface water of the northeast coast of Hainan Island in China exhibits a rich diversity of bacteria, with Klebsiella pneumoniae being highly abundant in the studied area. Different cultivation methods demonstrate distinct selective advantages in culturing bacterial genera and pathogens. Therefore, it is necessary to optimize cultivation conditions for specific marine bacteria.

[Bioinformatics analysis and prokaryotic expression of Strongyloides stercoralis serine protease inhibitor 1]

OBJECTIVE

To predict the structure and antigenic epitope of the Strongyloides stercoralis serine protease inhibitor 1 (Ss-SRPN-1) protein using bioinformatics tools, and to construct prokaryotic expression plasmids for expression of recombinant Ss-SRPN-1 protein, so as to provide the basis for unraveling the function of the Ss-SRPN-1 protein.

METHODS

The amino acid sequence of the Ss-SRPN-1 protein was downloaded from the NCBI database, and the physicochemical properties, structure and antigenic epitopes of the Ss-SRPN-1 protein were predicted using bioinformatics tools, including ExPASy, SWISS-MODEL and Protean. Primers were designed according to the nucleotide sequences of Ss-SRPN-1, and the Ss-SRPN-1 gene was amplified, cloned and sequenced with genomic DNA extracted from the infective third-stage larvae of S. stercoralis as a template. The Ss-SRPN-1 protein sequence was cloned into the pET28a (+) expression vector and transformed into Escherichia coli BL21 (DE) cells for induction of the recombinant Ss-SRPN-1 protein expression. The recombinant Ss-SRPN-1 protein was then purified and identified using Western blotting and mass spectrometry.

RESULTS

Bioinformatics analysis showed that the Ss-SRPN-1 protein, which was composed of 372 amino acids and had a molecular formula of C₁₉₄₈H₃₀₄₆N₄₈₈O₅₇₅S₁₆, was a stable hydrophilic protein, and the subcellular localization of the protein was predicted to be extracellular. The Ss-SRPN-1 protein was predicted to contain 11 dominant B-cell antigenic epitopes and 20 T-cell antigenic epitopes. The Ss-SRPN-1 gene with a length of 1 119 bp was successfully amplified, and the recombinant plasmid pET28a (+)/Ss-SRPN-1 was constructed and transformed into E. coli BL21(DE) cells. The expressed recombinant Ss-SRPN-1 protein had a molecular weight of approximately 43 kDa, and was characterized as a Ss-SRPN-1 protein.

CONCLUSIONS

The recombinant Ss-SRPN-1 protein has been expressed successfully, and this recombinant protein may be a potential vaccine candidate against strongyloidiasis.

[Progress of researches on Strongyloides stercoralis co-infection with other pathogens]

Strongyloides stercoralis is an opportunistic pathogenic parasite that can cause severe strongyloidiasis and even death among immunocompromised individuals. Previous clinical studies have reported cases co-infected with S. stercoralis and other pathogens, such as parasites, viruses, bacteria and fungi. This review summarizes strongyloidiasis patients co-infected with pathogens, and analyzes the impact of co-infection on strongyloidiasis, so as to provide insights into the reduction of the morbidity and mortality of disorders associated with S. stercoralis infections.

[Expression of CD47 and its ligands in pregnant mice infected with Toxoplasma gondii during pregnancy]

OBJECTIVE

To investigate the dynamic expression of cluster of differentiation 47 (CD47) and its ligands signaling regulatory protein α (SIRPα) and thrombospondin-1 (TSP-1) in mice infected with Toxoplasma gondii in the second and third trimesters.

METHODS

C57BL/6J mice (6 to 8 weeks old) were used for modeling T. gondii infection in the first trimester, and the pregnant mice were randomly divided into the normal control and infection groups, of 10 mice in each group. Pregnant mice in the infection group were intraperitoneally injected with 150 T. gondii tachyzoites on gestational day (Gd) 6.5, while pregnant mice in the normal control group were intraperitoneally injected with the same volume of physiological saline at the same time. The uterine and placental specimens were collected from all pregnant mice on Gd12.5 and Gd18.5, and the pregnant outcomes were recorded. The pathological damages of mouse uterine and placental specimens were observed using hematoxylin-eosin (HE) staining on Gd12.5 and Gd18.5. The relative expression of CD47, SIRPα, TSP-1, surface antigen 1 (SAG1), interferon-γ (IFN-γ), interleukin-2 (IL-2), IL-4 and IL-13 mRNA was quantified in mouse uterine and placental specimens using real-time fluorescence quantitative PCR (qPCR) assay, and the CD47, SIRPα, TSP-1 expression was determined in mouse uterine and placental specimens using immunohistochemical staining.

RESULTS

As compared with those in the normal control group, the pregnant mice in the infection group showed back arching, bristling, trembling and listlessness during pregnancy, and several mice presented virginal bleeding and abortion. Pathological examinations showed inflammatory cell infiltration, congestion and necrosis in uterine and placental specimens of pregnant mice in the infection group, a higher abortion rate of pregnant mice was seen in the infection group than in the normal control group on Gd12.5 (χ² = 20.405, P < 0.001) and Gd18.5 (χ² = 28.644, P < 0.001). qPCR assay showed significant differences in the expression of CD47, SIRPα, TSP-1, SAG1, INF-γ, IL-2, IL-4 and IL-13 genes in mouse placental specimens between the normal control and infection groups on Gd12.5 and Gd18.5 [F' (F) = 37.511, 29.337, 97.343, 53.755, 67.188, 21.145, 8.658 and 13.930, all P values < 0.001]. Higher CD47, SIRPα and TSP-1 gene expression was quantified in mouse placental specimens in the infection group than in the normal control group on Gd12.5 (all P values < 0.01), and lower CD47, SIRPα and TSP-1 gene expression was quantified in the infection group than in the normal control group on Gd18.5 (all P values < 0.001), while higher SAG1 gene expression was detected in placental specimens of pregnant mice in the infection group than in the normal control group on Gd12.5 and Gd18.5 (both P values < 0.01). In addition, higher INF-γ and IL-2 expression and lower IL-4 and IL-13 expression was detected in mouse placental specimens in the infection group than in the normal control group on Gd12.5 and Gd18.5 (all P values < 0.001), and there were significant differences in the CD47, SIRPα, TSP-1, SAG1, INF-γ, IL-2, IL-4 and IL-13 gene expression in uterine specimens of pregnant mice between the normal control and infection groups on Gd12.5 and Gd18.5 [H(F' and F) = 14.951, 25.977, 18.711, 48.595, 39.318, 14.248 and 15.468, all P values < 0.01], and higher CD47 and TSP-1 expression was detected in mouse uterine specimens in the infection group than in the control group on Gd12.5 and Gd18.5 (all P values < 0.01); however, no significant difference was found in the SIRPα expression (P > 0.05). Higher SAG1 expression was detected in uterine specimens of pregnant mice in the infection group than in the normal control group on Gd12.5 and Gd18.5 (both P values < 0.01), and higher INF-γ and IL-2 gene expression and lower IL-4 and IL-13 gene expression was found in the placental specimens of pregnant mice in the infection group than in the normal control group on Gd12.5 and Gd18.5 (all P values < 0.001). Spearman correlation analysis showed that the CD47 gene expression correlated positively with IFN-γ (r_s = 0.735, P < 0.05) and IL-2 (r_s = 0.655, P < 0.05) and negatively with IL-4 (r_s = -0.689, P < 0.05) and IL-13 expression (r_s = -0.795, P < 0.05) in the placental specimens of pregnant mice in the infection group on Gd12.5, and the CD47 gene expression correlated negatively with IFN-γ (r_s = -0.745, P < 0.05) and IL-2 expression (r_s = -0.816, P < 0.05) and positively with IL-4 (r_s = 0.704, P < 0.05) and IL-13 (r_s = 0.802, P < 0.05) in the placental specimens of pregnant mice in the infection group on Gd18.5. Immunohistochemical staining showed mild CD47, SIRPα and TSP-1 expression in uterine and placental specimens of pregnant mice in the normal control group on Gd12.5 and Gd18.5, strong CD47, SIRPα and TSP-1 expression in the placental specimens of pregnant mice in the infection group on Gd12.5 and strong CD47 and TSP-1 expression in the uterine specimens of pregnant mice in the infection group on Gd12.5.

CONCLUSIONS

T. gondii infection in the first trimester may cause abnormal expression of CD47 and its ligands SIRPα and TSP-1 in the maternal-fetal interface of pregnant mice in the second and third trimesters, which may be associated with the immune escape of T. gondii at the maternal-fetal interface.

Effect of antioxidant procyanidin b2 (pcb2) on ovine oocyte developmental potential in response to in vitro maturation (ivm) and vitrification stress

BACKGROUND

It was demonstrated that external stress, such as in vitro maturation (IVM) and vitrification process can induce significantly reduced development capacity in oocytes. Previous studies indicated that antioxidants play a pivotal part in the acquisition of adaptation in changed conditions. At present, the role of the natural potent antioxidant PCB2 in response to IVM and vitrification during ovine oocyte manipulation has not been explored.

OBJECTIVE

To investigate whether PCB2 treatment could improve the developmental potential of ovine oocytes under IVM and vitrification stimuli.

MATERIALS AND METHODS

The experiment was divided into two parts. Firstly, the effect of PCB2 on the development of oocytes during IVM was evaluated. Un-supplemented and 5 ug per mL PCB2-supplemented in the IVM solution were considered as control and experimental groups (C + 5 ug per mL PCB2). The polar body extrusion (PBE) rate, mitochondrial membrane potential (MMP), ATP, reactive oxygen species (ROS) levels and early apoptosis of oocytes were measured after IVM. Secondly, we further determine whether PCB2 could improve oocyte quality under vitrification stress. The survival rate, PBE rate and early apoptosis of oocytes were compared between fresh group, vitrified group and 5 ug per mL PCB2-supplemented in the IVM solution after vitrification (V + 5 ug per mL PCB2).

RESULTS

Compared to the control group, adding PCB2 significantly increased PBE rate (79.4% vs. 62.8%, P < 0.01) and MMP level (1.9 +/- 0.08 vs. 1.3 +/- 0.04, P < 0.01), and decreased ROS level (47.1 +/- 6.3 vs. 145.3 +/- 8.9, P < 0.01). However, there was no significant difference in ATP content and early apoptosis. Compared to the fresh group, vitrification significantly reduced oocytes viability (43.0% vs. 90.8%, P < 0.01) as well as PBE rate (24.2% vs. 60.6%, P < 0.05). However, 5 ug per mL PCB2-supplemention during maturation had no effect on survival, PBE or early apoptosis in vitrified oocytes.

CONCLUSION

PCB2 could effectively antagonise the oxidative stress during IVM and promote oocyte development. DOI: 10.54680/fr23210110412.

Improving and evaluating deep learning models of cellular organization

MOTIVATION

Cells contain dozens of major organelles and thousands of other structures, many of which vary extensively in their number, size, shape and spatial distribution. This complexity and variation dramatically complicates the use of both traditional and deep learning methods to build accurate models of cell organization. Most cellular organelles are distinct objects with defined boundaries that do not overlap, while the pixel resolution of most imaging methods is n sufficient to resolve these boundaries. Thus while cell organization is conceptually object-based, most current methods are pixel-based. Using extensive image collections in which particular organelles were fluorescently labeled, deep learning methods can be used to build conditional autoencoder models for particular organelles. A major advance occurred with the use of a U-net approach to make multiple models all conditional upon a common reference, unlabeled image, allowing the relationships between different organelles to be at least partially inferred.

RESULTS

We have developed improved Generative Adversarial Networks-based approaches for learning these models and have also developed novel criteria for evaluating how well synthetic cell images reflect the properties of real images. The first set of criteria measure how well models preserve the expected property that organelles do not overlap. We also developed a modified loss function that allows retraining of the models to minimize that overlap. The second set of criteria uses object-based modeling to compare object shape and spatial distribution between synthetic and real images. Our work provides the first demonstration that, at least for some organelles, deep learning models can capture object-level properties of cell images.

AVAILABILITY AND IMPLEMENTATION

http://murphylab.cbd.cmu.edu/Software/2022_insilico.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Research and application of a new multilevel fuzzy comprehensive evaluation method for cold stress in dairy cows

Effective and comprehensive evaluation of cold stress is critical for healthy dairy cow breeding in the winter. Previous studies on dairy cow cold stress have considered thermal environmental factors but not physiological factors or air quality. Therefore, this study aimed to propose a multilevel fuzzy comprehensive evaluation (FCE) method for cold stress in dairy cows based on the analytic hierarchy process (AHP) and a genetic algorithm (GA). First, the AHP was used to construct an evaluation index system for cold stress in dairy cows from 3 dimensions: thermal environment (temperature, relative humidity, wind speed, and illumination), physiological factors (respiratory rate, body surface temperature), and air quality [NH₃, CO₂, inhalable particulate matter (PM₁₀)]. Second, the consistency test of the judgment matrix was transformed into a nonlinear constrained optimization problem and solved using the GA. Next, based on fuzzy set theory, the comment set and membership function were established to classify the degree of cold stress into 5 levels: none, mild, moderate, high, and extreme. Then, the degree of cold stress in cows was obtained using multilevel fuzzy comprehensive judgment. To investigate the effect of illumination indicators on cold stress in dairy cows, 24 prelactation cows from the south and north sides were selected for a 117-d comprehensive cold stress evaluation. The results showed that the mean mild cold stress durations were 605.3 h (25.22 d) and 725.5 h (30.23 d) and the moderate cold stress durations were 67.2 h (2.8 d) and 96 h (4.0 d) on the south and north sides, respectively. Simultaneously, generalized linear mixed model showed that there were significant correlations between the daily cold stress duration and milk yield, feeding time, lying time, and active steps in the cows on both sides. This method can reasonably indicate cow cold stress conditions and better guide cold protection practices in actual production.

Pregnancy of cryopreserved ovine embryos at different developmental stages

BACKGROUND

Developmental stage and cryopreservation method have significant impact on the pregnancy rate after transfer of embryos produced in vivo.

OBJECTIVE

To determine the pregnancy outcomes from ovine embryos cryopreserved at different developmental stages.

MATERIALS AND METHODS

Embryos at different developmental stages were obtained from donor ewes through simultaneous estrus treatment and laparoscopic artificial insemination. Embryos, either cryopreserved via vitrification or slow freezing method, were implanted into recipient ewes. The pregnancy rate was determined 35 days after transfer.

RESULTS

The pregnancy rate of developing embryos increases after transfer from the morula stage, early blastocyst to expanded blastocyst stages (64.9%, 73.9% and 81.3%, respectively). However, cryopreservation significantly decreases the pregnancy rate of embryos at all three developmental stages, and there is no significant difference among developmental stages (43.9%, 43.7%, 52.9%, respectively). There is also no significant difference in the pregnancy rate between slowly-frozen embryos and vitrified embryos.

CONCLUSION

The pregnancy outcomes of embryo transfer is better at the expanded blastocyst stage than at earlier stages. However, no difference is observed in the pregnancy rate of embryos at different developmental stage after cryopreservation, either by slow freezing and vitrification. Cryopreservation methods for ovine embryos, both slow freezing and vitrification, need further improvement. doi.org/10.54680/fr22510110512.

Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study

BACKGROUND

No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge.

METHODS

The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing.

FINDINGS

2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters.

INTERPRETATION

The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials.

FUNDING

UK Research and Innovation and National Institute for Health Research.

Abstract 5031: Improved deconvolution of combined bulk and single-cell RNA-sequencing data

Identifying how cell types and their abundances evolve during tumor progression is critical to understanding the mechanisms and identifying predictors of metastasis. Single-cell RNA sequencing (scRNA-seq) has been especially promising in resolving heterogeneity of expression programs at the single cell level but is not always available, for example for large cohort studies or longitudinal analysis of archived samples. In such cases, cell subpopulations must be inferred by deconvolution, a process that can infer single-cell genomic data from bulk data but has limited ability to resolve fine clonal structure. We extend our previous bulk genomic deconvolution tool, Robust and Accurate Deconvolution (RAD), to establish a new method, scRAD, that can use reference scRNA-seq to interpret sample collections for which only bulk RNA-seq is available for some samples, e.g., clonally resolving archived primary (PRM) tissues using scRNA-seq from metastases (METs). We preprocess scRNA-seq data to accurately represent gene expression profiles, yielding a signature matrix S then extend our RAD method via a regularization term to deconvolve bulk data while maximizing consistency with S. We validate our method on semi-synthetic data derived from human PRM breast cancer cases and bone and ovary METs, showing that scRAD improves inference of single-cell gene expression profiles and their frequencies relative to the prior RAD with random initialization or initialization using the single-cell matrix S (Table 1). We then apply scRAD to a collection of paired PRM and MET tumors to quantify progression changes in common cell types. One-sided Kaplan-Meier analysis shows that tumors inferred to increase the mast cell fraction from PRM to MET exhibit lower overall survival (p&lt;0.05), consistent with the role of mast cells in metastatic growth and propagation. Tumors that show increased macrophage cell fraction from PRM to MET show improved overall survival (p&lt;0.04), consistent with the role of immune infiltration in survival.

mean square error (MSE) of gene expression and mixture fraction inference on semi-simulated data Method RAD with random initialization RAD with random initialization RAD with random initialization RAD initialized with S RAD initialized with S RAD initialized with S scRAD scRAD scRAD Sample number 2 4 8 2 4 8 2 4 8 Gene Expression MSE 0.41 0.28 0.37 0.31 0.27 0.37 0.22 0.15 0.13 Mixture fraction MSE 0.58 0.82 0.59 0.39 0.83 0.58 0.19 0.20 0.22

Citation Format: Haoyun Lei, Xiaoyan A. Guo, Yifeng Tao, Kai Ding, Xuecong Fu, Steffi Oesterreich, Adrian V. Lee, Russell Schwartz. Improved deconvolution of combined bulk and single-cell RNA-sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5031.

POS1234 DMARD DISRUPTION, INCREASED DISEASE ACTIVITY, AND PROLONGED SYMPTOM DURATION AFTER ACUTE COVID-19 AMONG PATIENTS WITH RHEUMATIC DISEASE: A PROSPECTIVE STUDY

Background

Systemic autoimmune rheumatic disease (SARD) patients may be at risk for disease flare and prolonged symptom duration after COVID-19, perhaps related to DMARD disruption and immune activation.

Objectives

To describe DMARD disruption and identify differences in SARD activity among patients with and without prolonged COVID-19 symptom duration.

Methods

We identified all SARD patients with confirmed COVID-19 at the Mass General Brigham healthcare system in Boston, USA; prospective recruitment is ongoing. Surveys were used to collect demographics, clinical characteristics, DMARD disruption, COVID-19 course, and SARD disease activity before and after COVID-19. The survey included validated instruments measuring disease activity, pain, fatigue, functional status, and respiratory quality of life. Prolonged symptom duration was defined as COVID-19 symptoms lasting ≥28 days. We compared differences in patient-reported measures between those with and without prolonged symptoms.

Results

We analyzed survey responses from 174 COVID-19 survivors with SARDs (mean age 52±16 years, 81% female, 80% White). The most common SARDs were RA (40%) and SLE (14%). Fifty-one percent of the 127 respondents on any DMARD reported a disruption to their regimen at COVID-19 onset (Figure 1). Among individual DMARDs, 56-77% were reported to have any change, except for hydroxychloroquine (23%) and rituximab (46%). SARD flare after COVID-19 was reported by 41% of respondents (Table 1). Patient global assessment of SARD activity was worse after COVID-19 (mean 7.6±2.3 before vs. 6.6±2.9 after COVID-19, p<0.001). Prolonged symptom duration was reported by 45% of participants. Those with prolonged symptoms had a higher initial COVID-19 symptom count (median 7 vs. 4, p<0.001) and were more likely to be hospitalized for COVID-19 (28% vs. 17%, p=0.001). Respondents experiencing prolonged symptom duration had higher disease activity on RAPID3 (p=0.007) as well as more pain (p<0.001) and fatigue (p=0.03) compared to those without prolonged symptoms.

Table 1.

Acute COVID-19 course, SARD flare/activity, and patient-reported outcomes among COVID-19 survivors with SARDs.

All COVID-19 survivors with SARDs (n=174)Prolonged symptom duration ≥28 days (n=78)No prolonged symptom duration/(n=96)p-value (prolonged vs. not)Acute COVID-19 courseCOVID-19 symptom duration, days, median [IQR]14 [9, 29]46 [30, 65]11 [7, 14]<0.0001Initial symptom count, median [IQR]6 [3, 8]7 [6, 9]4 [2, 7]<0.001Hospitalized, n (%)38 (22)22 (28)16 (17)0.001SARD flare/activitySelf-reported SARD flare after COVID-19, n (%)71 (41)38 (49)33 (34)0.15Disease activity by RAPID3, median [IQR]9 [4, 14]11.2 [6, 16]7 [3, 13]0.0067RAPID3 categorical score, n (%)0.13Remission (0)11 (7)4 (5)7 (7)Near remission (0.3-1.0)23 (14)5 (7)18 (19)Low severity (1.3-2.0)26 (15)10 (14)16 (17)Moderate severity (2.3-4.0)55 (33)27 (36)28 (29)High severity (4.3-10.0)54 (32)28 (38)26 (27)Patient-reported outcomesPain by SF-MPQ, median [IQR]2 [1, 2]2 [1, 2]1 [0, 2]0.0008Fatigue by FSI, median [IQR]53 [27, 84]66 [31, 91.5]43 [26, 76]0.031mHAQ, median [IQR]0.125 [0, 0.38]0.25 [0, 0.75]0.125 [0, 0.38]0.11Respiratory quality of life by SGRQ, global [IQR]15 [4, 29]16 [4, 36]10 [4, 26]0.49

RAPID3, Routine Assessment of Patient Index Data 3; SF-MPQ, Short-form McGill Pain Questionnaire; FSI, Fatigue Symptom Inventory; mHAQ, modified Health Assessment Questionnaire; SGRQ, Saint George’s Respiratory Questionnaire.

Figure 1.

Frequency of baseline DMARD use and proportion with any disruption at COVID-19 onset.

Conclusion

DMARD disruption, SARD flare, and prolonged symptoms were common in this prospective study of COVID-19 survivors with SARDs. Those with prolonged COVID-19 symptom duration, defined as ≥28 days, had higher SARD activity, more pain, and more fatigue compared to those without prolonged symptoms. These findings suggest that post-acute sequelae of COVID-19 may have a large impact on underlying SARD activity and quality of life.

Disclosure of Interests

Michael Di Iorio: None declared, Claire Cook: None declared, Kathleen Vanni: None declared, Naomi Patel Consultant of: Receives consulting fees from FVC Health unrelated to this work., Kristin D’Silva: None declared, Xiaoqing Fu: None declared, Jiaqi Wang: None declared, Lauren Prisco: None declared, Emily Kowalski: None declared, Alessandra Zaccardelli: None declared, Lily Martin: None declared, Grace Qian: None declared, Tiffany Hsu: None declared, Zachary Wallace Consultant of: Receives consulting fees from Viela Bio, Zenas BioPharma, and MedPace unrelated to this work., Grant/research support from: Receives research support from Bristol-Myers Squibb and Principia/Sanofi., Jeffrey Sparks Consultant of: Receives consultant fees from AbbVie, Amgen, Boehringer Ingelheim, Bristol Myers Squibb, Gilead, Inova Diagnostics, Janssen, Optum, and Pfizer unrelated to this work., Grant/research support from: Receives research support from Bristol Myers Squibb.

OP0251 IMPACT OF INTERSTITIAL LUNG DISEASE ON SEVERE COVID-19 OUTCOMES FOR PATIENTS WITH RHEUMATOID ARTHRITIS: A MULTICENTER STUDY

Background

RA has been associated with poor COVID-19 outcomes, but few studies have investigated outcomes in RA features such as interstitial lung disease.

Objectives

To assess COVID-19 outcomes in patients with RA overall, and those with and without ILD, compared to general population comparators.

Methods

A multicenter, retrospective cohort study was conducted at Mayo Clinic (19 hospitals and affiliated outpatient centers in 4 states) and Mass General Brigham (14 hospitals and affiliated outpatient centers in New England). Consecutive patients with RA meeting ACR/EULAR criteria and a positive COVID-19 test from March 1, 2020 through June 6, 2021 were matched 1:5 on age, sex, race, and COVID-19 test date with general population comparators without RA. RA features assessed included: RA-ILD per Bongartz criteria [1], duration, rheumatoid factor (RF), cyclic citrullinated peptide antibody (CCP), bone erosions, and treatments. The primary outcome was a composite of hospitalization or death following COVID-19 diagnosis. We used multivariable Cox regression to investigate the association of RA, and features such as ILD, with COVID-19 outcomes compared to matched comparators.

Results

We analyzed 582 patients with RA and 2892 comparators without RA, all with COVID-19. Mean age was 62 years, 51% were female, and 79% were White. Mean RA duration was 11 years, 67% were seropositive (52% RF+ and 54% CCP+), 27% had bone erosions, 28% were on steroids, and 79% were on DMARDs. 50/582 (9%) patients with RA had ILD.

The COVID-19 hospitalization or death rate for RA patients was higher than comparators (3.0 per 1,000 days [95% CI 2.5-3.6] vs. 1.9 per 1,000 days [95% CI 1.7-2.1], respectively). Overall, RA patients had a 53% higher risk of hospitalization or death than comparators after adjustment (95% CI 1.20-1.94).

Among those with RA-ILD, the hospitalization or death rate was significantly higher than comparators (10.9 [95% CI 6.7-15.2] vs. 2.5 per 1,000 days [1.8-3.2], respectively). RA-ILD was associated with nearly 3-fold higher risk for hospitalization or death than comparators (multivariable HR 2.84 [95% CI 1.64-4.91], Table 1). There was a significant interaction between RA/comparator status and presence/absence of ILD for risk of severe COVID-19 (p<0.001, Figure 1). The elevated risk for severe COVID-19 was similar for RA subgroups defined by serostatus or bone erosions.

Table 1.

Frequencies, proportions, and hazard ratios for COVID-19 outcomes, comparing all RA patients, and subgroups with or without RA-ILD, to matched comparators.

COVID-19 OutcomesAll RA Patients (n=582)RA-ILD (n=50)RA Patients without ILD (n=532)Comparators (n=2,892)Hospitalization, n (%)121 (21)24 (48)97 (18)402 (14)Unadjusted HR (95% CI)1.58 (1.27, 1.96)2.65 (1.71, 4.09)1.43 (1.12, 1.82)Ref.Adjusted* HR (95% CI)1.45 (1.14, 1.83)2.35 (1.38, 4.00)1.31 (1.00, 1.70)Ref.Death, n (%)26 (4)9 (18)17 (3)63 (2)Unadjusted HR (95% CI)1.72 (0.98, 3.01)5.88 (2.07, 16.71)1.13 (0.56, 2.29)Ref.Adjusted* HR (95% CI)1.24 (0.66, 2.32)13.94 (4.30, 45.18)0.75 (0.35, 1.63)Ref.Hospitalization or death, n (%)126 (22)25 (50)101 (19)419 (14)Unadjusted HR (95% CI)1.66 (1.33, 2.07)3.01 (1.93, 4.70)1.47 (1.14, 1.89)Ref.Adjusted* HR (95% CI)1.53 (1.20, 1.94)2.84 (1.64, 4.91)1.34 (1.02, 1.77)Ref.

*Adjusted for age, sex, race, and smoking

Figure 1.

Multivariable hazard ratios for the composite outcome of hospitalization or death from COVID-19, comparing all RA and subgroups by serostatus, bone erosions, and ILD to matched comparators without RA.

Conclusion

We confirmed that RA was associated with severe COVID-19 outcomes compared to the general population. We found evidence that ILD may be an effect modifier for the relationship between RA and severe COVID-19 outcomes, but RA subgroups defined by serostatus and bone erosions had similarly elevated risk. These findings suggest that ILD or its treatment may be a major contributor to severe COVID-19 outcomes in RA.

References

[1]Bongartz, T, et al, Arthritis Rheum. 2010 Jun;62(6):1583-91.

Disclosure of Interests

None declared

[Risk factors of newly developed nonalcoholic fatty liver disease after pancreaticoduodenectomy]

Objective: To identify the risk factors of newly developed nonalcoholic fatty liver disease(NAFLD) after pancreaticoduodenectomy(PD). Methods: The clinical data of 130 patients who had undergone PD at Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Medical School of Nanjing University from June 2018 to December 2020 were collected retrospectively. There were 74 males and 56 females, with age(M(IQR)) of 62(16) years (range: 22 to 84 years). Twenty-nine patients who developed NAFLD were divided into NAFLD group and 101 patients who did not suffer NAFLD were divided into no NAFLD group. Observation indications included:(1)preoperative demographics,intraoperative and postoperative characteristics; (2)the risk factors of newly developed NAFLD after PD. Count data were analyzed using χ² test or Fisher's exact test. Measurement data were analyzed by student t test or Mann-Whitney U test. Multivariate analysis was performed using Logistic regression model with a stepwise forward approach. Results: All 130 patients successfully underwent PD and 29 cases(22.3%) developed NAFLD in 6 months after PD. The results of univariate analysis showed that gender,diabetic mellitus,the level of triglyceride preoperatively,and pancreatic ductal adenocarcinoma were the related factors of the development of NAFLD after PD(t=-2.655, χ²=4.563,U=-2.192,χ²=7.044;all P<0.05).Multivariate analysis revealed that gender,body mass index,pancreatic ductal adenocarcinoma were independent risk factors for the development of NAFLD after PD(OR=2.849,1.214,4.165,all P<0.05). Conclusion: Gender, body mass index,pancreatic ductal adenocarcinoma were independent risk factors for the development of NAFLD after PD.

OUP accepted manuscript

Motivation

Identifying cell types and their abundances and how these evolve during tumor progression is critical to understanding the mechanisms of metastasis and identifying predictors of metastatic potential that can guide the development of new diagnostics or therapeutics. Single-cell RNA sequencing (scRNA-seq) has been especially promising in resolving heterogeneity of expression programs at the single-cell level, but is not always feasible, e.g. for large cohort studies or longitudinal analysis of archived samples. In such cases, clonal subpopulations may still be inferred via genomic deconvolution, but deconvolution methods have limited ability to resolve fine clonal structure and may require reference cell type profiles that are missing or imprecise. Prior methods can eliminate the need for reference profiles but show unstable performance when few bulk samples are available.

Results

In this work, we develop a new method using reference scRNA-seq to interpret sample collections for which only bulk RNA-seq is available for some samples, e.g. clonally resolving archived primary tissues using scRNA-seq from metastases. By integrating such information in a Quadratic Programming framework, our method can recover more accurate cell types and corresponding cell type abundances in bulk samples. Application to a breast tumor bone metastases dataset confirms the power of scRNA-seq data to improve cell type inference and quantification in same-patient bulk samples.

Availability and implementation

Source code is available on Github at https://github.com/CMUSchwartzLab/RADs.

Genesis of epicardial adipocytes and its association with progenitor markers, muscarinic receptor type 3 and b-blockers intake in patients with cardiovascular disease

Introduction

Epicardial fat thickness or volume was found to be associated with cardiovascular disease (CVD). Our aim was to study the epicardial adipocyte-progenitors' markers and its association with cholinergic or adrenergic activity in patients with cardiovascular disease.

Materials and methods

We have included epicardial adipose tissue (EAT) biopsies from 29 patients underwent open-heart surgery. From 10 patients (69±5 years old, 31±8 kg/ m2, 40% CAD, 40% HF, 60% AF, 0% T2DM) stromal cells from epicardial and subcutaneous fat were isolated after collagenase activity and cultured for 14 days and then submitted to adipogenesis for next 14 days. Samples from 19 patients (60±9 years old, 29±4 kg/m2, 42% CAD, 37% HF, 32% AF, 32% T2DM, 53% β-blockers) were used for “ex vivo assays”. Explants were split into equal pieces (100 mg), treated with or without acetylcholine (ACh) for 30 min. Afterwards RNA was isolated and cDNA was amplified by real time PCR. We selected adipocytes progenitors (CD36, PREF1, COL1A1), adipocytes markers (ADIPO, FABP4), muscarinic (muscarinic receptor type 2 (CHRM2) and 3 (CHRM2)) and β-adrenergic receptors (ABRD1, ABRD2 and ABRD3). Gene expression was represented regarding ACTB as 2HK/GEN.

Results

The stromal vascular cells (SVC) from subcutaneous fat (SAT) had higher expression levels of CD36, PREF1 and COL1A1 than SVC from epicardial fat (EAT). It explains the higher adipocytes markers after adipogenesis induction in SAT than EAT cells. However, an upregulation of fibroblasts markers was detected on EAT. The levels of CD36 and PREF1 in SVC were associated with higher adipogenesis. Although CHRM2 was higher in EAT than SAT SVC, the adipogenesis induction upregulated only CHRM3 (1.48±0.065 vs 1.42±0.036 a.u.) in EAT cells. Thus, this receptor was associated with adipocytes markers in epicardial fat (r=0.777 for CD36 and r=0.746 for FABP4) and incremented in epicardial fat biopsies from patients who were taken β-blockers (1.61±0.011 n=10 vs 1.54±0.097 a.u. n=9; p=0.05) and modulated by ACh treatment (p=0.05).

Conclusions

Our results showed that CD36 and PREF1 in epicardial SVC are adipocytes progenitors. The higher presence of adipocytes markers is associated with higher levels of muscarinic receptor (CHRM3), which are upregulated in epicardial fat from patients who were taken β-blockers and modulated by cholinergic activity. Because a metabolic and lipolytic dysfunction was associated with CHRM3, the sympathetic modulation might play a role in the epicardial adipocytes genesis. Further studies are needed to understand if this mechanism might improve or not future cardiovascular events.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): ISCIII (PFIS2020)

Qualitative and quantitative proteomic approach of epicardial cell secretome from atrial fibrillation patients after cholinergic stimulation

Background

The association between epicardial adipose tissue (EAT) and atrial fibrillation (AF) was already described by several authors. In fact, botulinum toxin injection in this tissue reduces new-onset AF after open-heart surgery. Our previous results showed an elevation of adiposity in epicardial stromal vascular cells (SVC), assessed by the higher levels of fatty acid-binding protein 4 (FABP4) in AF patients; and a higher lipid accumulation in these cells after chronic acetylcholine treatment. We wanted to identify the proteins released from EAT SVC in presence/absence of mature adipocytes, that could be exerting a paracrine effect over the myocardium. The identification of these proteins might shed light on possible triggers in epicardial SVC and the mechanisms underlying botulinum toxin benefits on AF.

Material and methods

Proteomic studies were performed in 32 samples from 8 patients undergoing open-heart surgery (4 with and 4 without AF). Epicardial SVC were isolated by collagenase digestion and cultured in M199 medium. Then, cells were induced or not to adipocyte differentiation. After this intervention, cells were treated or not with acetylcholine (10uM) for 30 min. Conditioned medium was stored until be used. Differential released proteins were identified by nano-high performance liquid chromatography (HPLC) and Triple-Time of flying (TOF) analysis, and quantified by SWATH-Ms proteomics anaylisis.

Results

The quantitative proteomic approach has identified 111 common proteins in EAT SVC from patients with and without AF. A 79,3% of the genes which encoded the proteins identified were citoplasmic. A 78,4% were classified as components of the cellular exosomes, followed by genes related with centrosome (37,1%), nucleosome (15,5%), lysosomes (40,5%) and nucleolus (37,1%). Acute cholinergic treatment with ACh at 10 uM decreased α-defensin 3 (DEFA3, ID: 59666; p-value = 0,0297) secretion from EAT SVC of AF patients in comparison with EAT SVC from non-AF patients. In the same line, Peptidyl-prolyl cis-trans isomerase A (PPIA, ID: P62937) showed a lower secretion from SVC of AF patients (p=0,0326). After adipogenesis-induction, adipocyte presence modified the protein secretion under ACh treatment: Differences between AF and non-AF patients lied on 2 different proteins: profilin 1 (PFN1, ID: P07737, p-value = 0,0286) and β-enolase (ENO3, ID: P13929, p-value = 0,0414), showing a higher and lower secretion in AF patients regarding non-AF patients, respectively.

Conclusions

EAT SVC showed a differential protein secretion according adipocyte and AF presence. Although further studies are needed, the proteins differentially secreted in EAT SVC are related to inflammation (DEFA3), structure (PFN1) and glucose metabolism (ENO3), pointing the pathways that could be modified in AF patients.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Plan Estatal de I+D+I 2016-2020 and ISCIII-Subdirecciόn General de Evaluaciόn y Fomento de la Investigaciόn el Fondo Europeo de Desarrollo Regional (FEDER) Figure 1. Common proteins secreted from EAT SVCFigure 2. Differentially secreted proteins in AF

Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers

Aneuploidy and whole genome duplication (WGD) events are common features of cancers associated with poor outcomes, but the ways they influence trajectories of clonal evolution are poorly understood. Phylogenetic methods for reconstructing clonal evolution from genomic data have proven a powerful tool for understanding how clonal evolution occurs in the process of cancer progression, but extant methods so far have limited the ability to resolve tumor evolution via ploidy changes. This limitation exists in part because single-cell DNA-sequencing (scSeq), which has been crucial to developing detailed profiles of clonal evolution, has difficulty in resolving ploidy changes and WGD. Multiplex interphase fluorescence in situ hybridization (miFISH) provides a more unambiguous signal of single-cell ploidy changes but it is limited to profiling small numbers of single markers. Here, we develop a joint clustering method to combine these two data sources with the goal of better resolving ploidy changes in tumor evolution. We develop a probabilistic framework to maximize the probability of latent variables given the pre-clustered datasets, which we optimize via Markov chain Monte Carlo sampling combined with linear regression. We validate the method by using simulated data derived from a glioblastoma (GBM) case profiled by both scSeq and miFISH. We further apply the method to two GBM cases with scSeq and miFISH data by reconstructing a phylogenetic tree from the joint clustering results, demonstrating their synergistic value in understanding how focal copy number changes and WGD events can collectively contribute to tumor progression.

Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data

MOTIVATION

Computational reconstruction of clonal evolution in cancers has become a crucial tool for understanding how tumors initiate and progress and how this process varies across patients. The field still struggles, however, with special challenges of applying phylogenetic methods to cancers, such as the prevalence and importance of copy number alteration (CNA) and structural variation (SV) events in tumor evolution, which are difficult to profile accurately by prevailing sequencing methods in such a way that subsequent reconstruction by phylogenetic inference algorithms is accurate.

RESULTS

In the present work, we develop computational methods to combine sequencing with multiplex interphase fluorescence in situ hybridization (miFISH) to exploit the complementary advantages of each technology in inferring accurate models of clonal CNA evolution accounting for both focal changes and aneuploidy at whole-genome scales. By integrating such information in an integer linear programming (ILP) framework, we demonstrate on simulated data that incorporation of FISH data substantially improves accurate inference of focal CNA and ploidy changes in clonal evolution from deconvolving bulk sequence data. Analysis of real glioblastoma data for which FISH, bulk sequence, and single cell sequence are all available confirms the power of FISH to enhance accurate reconstruction of clonal copy number evolution in conjunction with bulk and optionally single-cell sequence data.

AVAILABILITY

Source code is available on Github at https://github.com/CMUSchwartzLab/FISH_deconvolution.

Long non-coding RNA DANCR promoted non-small cell lung cancer cells metastasis via modulating of miR-1225-3p/ErbB2 signal

OBJECTIVE

Currently, we aimed to illustrate the role of lncRNA differentiation antagonizing non-protein coding RNA (DANCR) and erb-b2 receptor tyrosine kinase 2 (ErbB2) in non-small cell lung cancer (NSCLC).

PATIENTS AND METHODS

Expression of DANCR, microRNA-1225-3p (miR-1225-3p) and ErbB2 mRNA was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) assays. The clinical value of DANCR was checked by a ROC curve analysis, a Kaplan-Meier analysis and a Pearson Chi-Square test. Transwell chamber assays were performed to determine the migration and invasion ability changes of SPCA1 and A549 cells. The protein expression of ErbB2 was tested by Western blot assays. The targeted binding effect between miR-1225-3p and DANCR or ErbB2 was confirmed by a Dual-Luciferase reporter assay and an RNA pull-down assay, respectively.

RESULTS

In the current study, it was found that DANCR was upregulated and correlated with poor prognosis in patients with NSCLC. DANCR promoted NSCLC cells migration and invasion via upregulation of ErbB2. DANCR regulated ErbB2 at posttranscriptional level. Mechanically, it was illustrated that miR-1225-3p negatively regulated ErbbB2 and it-mediated migration and invasion via directly targeting in NSCLC cells. Meanwhile, it was showed that DANCR interacted with miR-1225-3p in a reciprocal suppression manner. Even further, through a RIP assay and a luciferase assay, we showed that DANCR interacted with miR-1225-3p through a microRNA response element (MRE-1225-3p) via directly binding. Finally, it was demonstrated that DANCR served as a miR-1225-3p sponge to promote ErbB2 expression and to facilitate ErbB2-mediated migration and invasion in NSCLC cells.

CONCLUSIONS

In the current study, it was illustrated that DNACR promoted ErbB2-mediated migration and invasion via working as a ceRNA of miR-1225-3p in NSCLC cells.

Glycosylated hemoglobin levels and the risk for contrast-induced nephropathy in diabetic patients undergoing coronary arteriography/percutaneous coronary intervention

Backgrounds

Diabetes mellitus is an independent risk factor for Contrast-induced nephropathy (CIN) in patients undergoing Coronary arteriography (CAG)/percutaneous coronary intervention (PCI). Glycosylated hemoglobin (HbA1c) is the gold standard to measure blood glucose control, which has important clinical significance for evaluating blood glucose control in diabetic patients in the past 3 months. This study aimed to assess whether preoperative HbA1c levels in diabetic patients who received CAG/PCI impacted the occurrence of postoperative CIN.

Methods

We reviewed the incidence of preoperative HbA1c and postoperative CIN in 670 patients with CAG/PCI from January 1, 2020 to October 30, 2020 and divided the preoperative HbA1c levels into 5 groups. Blood samples were collected at admission, 48 h and 72 h after operation to measure the Scr value of patients. Categorical variables were compared using a chi-square test, and continuous variables were compared using an analysis of variance. Fisher’s exact test was used to compare the percentages when the expected frequency was less than 5. Univariable and multivariable logistic regression analysis was used to exclude the influence of confounding factors, and P for trend was used to analyze the trend between HbA1c levels and the increased risk of CIN.

Results

Patients with elevated HbA1c had higher BMI, FBG, and LDL-C, and they were more often on therapy with hypoglycemic agents, Insulin and PCI. They also had higher basal, 48 h and 72 h Scr. The incidence of CIN in the 5 groups of patients were: 9.8, 11.9, 15.2, 25.3, 48.1%. (p < 0.0001) The multivariate analysis confirmed that in the main high-risk subgroup, patients with elevated HbA1C levels (≥8.8%) had a higher risk of CIN disease. Trend test showed the change of OR (1.000,1.248,1.553,2.625,5.829).

Conclusions

Studies have shown that in diabetic patients undergoing CAG/PCI, elevated HbA1c is independently associated with the risk of CIN, and when HbA1c > 9.5%, the incidence of CIN trends increase. Therefore, we should attach great importance to patients with elevated HbA1c at admission and take more active measures to prevent CIN.

AB0066 MECHANISMS OF TOTAL SAPONINS OF PANAX JAPONICUS MITIGATES COLLAGEN-INDUCED ARTHRITIS

Background:

Total saponins of Panax japonicus (TSPJ) are extracted from Panax japonicus (T.Nees) C.A.Mey and have achieved a good therapeutic effect in the treatment of rheumatoid arthritis (RA). Unfortunately, the mechanism of TSPJ acting on RA is not clear.

Objectives:

To investigate the potential mechanisms and key targets of TSPJ on RA.

Methods:

The raw data were downloaded from the Gene Expression Omnibus (GEO) database, and the RStudio3.6.1 software was used to identify differentially expressed genes (DEGs). The potential targets of active compounds from TSPJ were predicted by the Pharmmapper and SwissTargetPrediction databases. Based on the overlapping genes, we used Cytoscape 3.7.2 software to construct a protein-protein interactions (PPI) network and to determine the mechanisms of the treatment by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Collagen-induced arthritis (CIA) model was established and treated with different doses of TSPJ. Arthritis index (AI) and histology score were used to evaluate the symptoms of CIA. The levels of vascular endothelial growth factor (VEGF), hypoxia-inducible factor 1 (HIF-1), IL-1β, and IL-17A tested by enzyme linked immunosorbent assay and real time-quantitative Polymerase Chain Reaction.

Results:

A total of 2670 DEGs and 371 TSPJ targets were obtained, including 52 overlapping genes. 41 genes had protein interactions that are used to build the PPI network. The results of the KEGG enrichment analysis included VEGF and HIF-1 signaling pathway. Seven negative correlation genes and 16 positive correlation genes were obtained by correlational analysis of DEGs in VEGF and HIF-1 signaling pathway. SRC proto-oncogene, nonreceptor tyrosine kinase (SRC), and the signal transducer and the activator of transcription 3 (STAT 3) had a higher value of degree in PPI and showed a significant correlation in the pathways; they were regarded as key targets. Compared with the CIA model group, TSPJ significantly decreased the AI and histology scores. Moreover, the expression of VEGF-A, HIF-1α, IL-1β, and IL-17A in serum or spleens significantly reduced in a dose-dependent.

Conclusion:

Present study show that SRC and STAT 3 may be the key targets of TSPJ acting on the VEGF and HIF-1 signaling pathways, thus inhibiting angiogenesis and improving RA.

Disclosure of Interests:

None declared

POS1174 HYPERINFLAMMATION AND CLINICAL OUTCOMES FOR PATIENTS WITH SYSTEMIC RHEUMATIC DISEASES HOSPITALIZED FOR COVID-19: A COMPARATIVE COHORT STUDY

Background:

COVID-19 can induce a hyperinflammatory state resulting in cytokine storm, which can lead to poor outcomes. Patients with systemic rheumatic diseases may be at increased risk for respiratory failure with COVID-19. Therefore, we investigated the relationship between rheumatic disease, hyperinflammation, and clinical outcomes among hospitalized COVID-19 patients.

Objectives:

To compare laboratory values, hyperinflammation, and clinical outcomes of hospitalized COVID-19 rheumatic patients and matched comparators.

Methods:

We performed a comparative cohort study of patients with polymerase chain reaction (PCR)-confirmed COVID-19 requiring hospitalization between 3/1/20-7/7/20 at a large health care system. We compared each systemic rheumatic disease case to up to 5 matched (by age, sex, and date of +SARS-CoV-2 PCR) comparators without systemic rheumatic disease. We extracted laboratory values from their hospitalization to compare peaks/troughs of individual laboratory results by case status and derived the COVID-19-associated hyperinflammation score (cHIS), a composite of 6 laboratory domains (0-6, ≥2 indicating hyperinflammation), as previously developed1. We used multivariable logistic regression to estimate ORs for COVID-19 outcomes by hyperinflammation and case status.

Results:

We identified 57 hospitalized rheumatic disease cases (mean age 67 years, 67% female) and 232 matched comparators hospitalized with PCR-confirmed COVID-19. Among cases, 26 (46%) had rheumatoid arthritis and 14 (25%) had systemic lupus erythematosus. Most cases (34, 60%) had active rheumatic disease. At baseline, 15 (27%) of cases were treated with biologic DMARDs, and 32 (56%) were using glucocorticoids. We analyzed 39,900 total laboratory results (median 85 per patient). Cases had higher peak neutrophil-to-lymphocyte ratio (9.6 vs 7.8, p=0.02), LDH (421 vs 345 U/L, p=0.04), creatinine (1.2 vs 1.0 mg/dL, p=0.01), and BUN (31 vs 23 mg/dL, p=0.03) than comparators but similar peak CRP (149 vs 116 mg/L, p=0.11, Figure 1). Cases had higher peak median cHIS (3 vs 2, p=0.01). Peak cHIS ≥2 had higher odds of intensive care unit (ICU) admission (OR 3.45, 95%CI 1.98-5.99), mechanical ventilation (OR 66.0, 95%CI 9.0-487.8), and mortality (OR 16.4, 95%CI 4.8-56.4) compared to cHIS <2 (Table 1). Cases had increased risk of ICU admission (OR 2.0, 95%CI 1.1-3.7) and mechanical ventilation (OR 2.7, 95%CI 1.4-5.2) than comparators.

Table 1.

Associations of peak cHIS and systemic rheumatic disease with COVID-19 hospitalization outcomes

Intensive care unit admissionMechanical ventilationDeath%Adjusted OR (95%CI)%Adjusted OR (95%CI)%Adjusted OR (95%CI)Hospitalization outcomes by hyperinflammation on cHIS1cHIS <2 (n=112)21%1.0 (Ref)1%1.0 (Ref)3%1.0 (Ref)cHIS ≥2 (n=177)48%3.5 (2.0-6.0)37%66.2 (9.0-487.8)27%16.4 (4.8-56.4)Hospitalization outcomes by rheumatic disease statusComparators (n=232)30%1.0 (Ref)19%1.0 (Ref)16%1.0 (Ref)Rheumatic cases (n=57)51%1.87 (1.03-3.40)39%2.46 (1.30-4.67)21%1.32 (0.61-2.88)

Matching factors: age, sex, and date of +PCR.

1Adjusted for age, sex, and case status.

2Adjusted for race, smoking, comorbidities, and body mass index.

cHIS, COVID-19-associated hyperinflammation score; CI, confidence interval; OR, odds ratio; PCR, polymerase chain reaction; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Conclusion:

Patients with systemic rheumatic disease hospitalized for COVID-19 had higher risk for hyperinflammation, kidney injury, and mechanical ventilation than non-rheumatic comparators. We validated the cHIS in our cohort, which was strongly associated with poor COVID-19 outcomes. These findings highlight that hospitalized patients with rheumatic diseases may be vulnerable to poor COVID-19 outcomes.

References:

[1]Webb BJ et al. Clinical criteria for COVID-19-associated hyperinflammatory syndrome. Lancet Rheumatol. 2020 Dec;2(12):e754-e763.

Disclosure of Interests:

Tiffany Hsu: None declared, Kristin D’Silva: None declared, Naomi Serling-Boyd: None declared, Jiaqi Wang: None declared, Alisa Mueller: None declared, Xiaoqing Fu: None declared, Lauren Prisco: None declared, Lily Martin: None declared, Kathleen Vanni: None declared, Alessandra Zaccardelli: None declared, Claire Cook: None declared, Hyon Choi Consultant of: Dr. Choi reports consultancy fees from Takeda, Selecta, GlaxoSmithKline, and Horizon, Grant/research support from: Dr. Choi reports research support from AstraZeneca., Yuqing Zhang: None declared, Ellen Gravallese: None declared, Zachary Wallace Consultant of: Dr. Wallace reports consulting fees from Viela Bio and MedPace., Grant/research support from: Dr. Wallace reports research support from Bristol-Myers Squibb and Principia., Jeffrey Sparks Consultant of: Dr. Sparks reports consultancy fees from Bristol-Myers Squibb, Gilead, Inova, Janssen, Optum, and Pfizer., Grant/research support from: Dr. Sparks reports research support from Amgen and Bristol-Myers Squibb.

Spatiotemporal characteristics and factor analysis of SARS-CoV-2 infections among healthcare workers in Wuhan, China

BACKGROUND

Studying the spatiotemporal distribution of SARS-CoV-2 infections among healthcare workers (HCWs) can aid in protecting them from exposure.

AIM

To describe the spatiotemporal distributions of SARS-CoV-2 infections among HCWs in Wuhan, China.

METHODS

In this study, an open-source dataset of HCW diagnoses was provided. A geographical detector technique was then used to investigate the impacts of hospital level, type, distance from the infection source, and other external indicators of HCW infections.

FINDINGS

The number of daily HCW infections over time in Wuhan followed a log-normal distribution, with its mean observed on January 23rd, 2020, and a standard deviation of 10.8 days. The implementation of high-impact measures, such as the lockdown of the city, may have increased the probability of HCW infections in the short term, especially for those in the outer ring of Wuhan. The infection of HCWs in Wuhan exhibited clear spatial heterogeneity. The number of HCW infections was higher in the central city and lower in the outer city.

CONCLUSION

HCW infections displayed significant spatial autocorrelation and dependence. Factor analysis revealed that hospital level and type had an even greater impact on HCW infections; third-class and general hospitals closer to infection sources were correlated with especially high risks of infection.

Chinese Version of the Baylor Profound Mental Status Examination: A Brief Staging Measure for Patients with Severe Alzheimer's Disease

BACKGROUND

A specialized instrument for assessing the cognition of patients with severe Alzheimer's disease (AD) is needed in China.

OBJECTIVES

To validate the Chinese version of the Baylor Profound Mental Status Examination (BPMSE-Ch).

DESIGN

The BPMSE is a simplified scale which has proved to be a reliable and valid tool for evaluating patients with moderate to severe AD, it is worthwhile to extend the use of it to Chinese patients with AD.

SETTING

Patients were assessed from the Memory Clinic Outpatient.

PARTICIPANTS

All participants were diagnosed as having probable AD by assessment.

MEASUREMENTS

The BPMSE was translated into Chinese and back translated. The BPMSE-Ch was administered to 102 AD patients with a Mini-Mental State Examination (MMSE) score below 17. We assessed the internal consistency, reliability, and construct validity between the BPMSE-Ch and MMSE, Severe Impairment Battery (SIB), Global Deterioration Scale (GDS-1), Geriatric Depression Scale(GDS-2), Instrumental Activities of Daily Living (IADL), Physical Self-Maintenance Scale (PSMS), Neuropsychiatric Inventory (NPI) and Clinical Dementia Rating (CDR).

RESULTS

The BPMSE-Ch showed good internal consistency (α = 0.87); inter-rater and test-retest reliability were both excellent, ranging from 0.91 to 0.99. The construct validity of the measure was also supported by significant correlations with MMSE, SIB. Moreover, as expected, the BMPSE-Ch had a lower floor effect than the MMSE, but a ceiling effect existed for patients with MMSE scores above 11.

CONCLUSIONS

The BPMSE-Ch is a reliable and valid tool for evaluating cognitive function in Chinese patients with severe AD.

Hidden Quantum Hall Stripes in Al_{x}Ga_{1-x}As/Al_{0.24}Ga_{0.76}As Quantum Wells

We report on transport signatures of hidden quantum Hall stripe (hQHS) phases in high (N>2) half-filled Landau levels of Al_{x}Ga_{1-x}As/Al_{0.24}Ga_{0.76}As quantum wells with varying Al mole fraction x<10^{-3}. Residing between the conventional stripe phases (lower N) and the isotropic liquid phases (higher N), where resistivity decreases as 1/N, these hQHS phases exhibit isotropic and N-independent resistivity. Using the experimental phase diagram, we establish that the stripe phases are more robust than theoretically predicted, calling for improved theoretical treatment. We also show that, unlike conventional stripe phases, the hQHS phases do not occur in ultrahigh mobility GaAs quantum wells but are likely to be found in other systems.