Induction of cyclophilin A by influenza A virus infection facilitates group A Streptococcus coinfection

During influenza A epidemics, bacterial coinfection is a major cause of increased morbidity and mortality. However, the roles of host factors in regulating influenza A virus (IAV)-triggered bacterial coinfection remain elusive. Cyclophilin A (CypA) is an important regulator of infection and immunity. Here, we show that IAV-induced CypA expression facilitates group A Streptococcus (GAS) coinfection both in vitro and in vivo. Upon IAV infection, CypA interacts with focal adhesion kinase (FAK) and inhibited E3 ligase cCbl-mediated, K48-linked ubiquitination of FAK, which positively regulates integrin α5 expression and actin rearrangement via the FAK/Akt signaling pathway to facilitate GAS colonization and invasion. Notably, CypA deficiency or inhibition by cyclosporine A significantly inhibits IAV-triggered GAS coinfection in mice. Collectively, these findings reveal that CypA is critical for GAS infection, and induction of CypA expression is another way for IAV to promote bacterial coinfection, suggesting that CypA is a promising therapeutic target for the secondary bacterial infection.

Dual-wavelength visible photodetector based on vertical (In,Ga)N nanowires grown by molecular beam epitaxy

Due to the wide applications of blue and red photodetectors, dual-wavelength (blue/red) photodetectors are promising for future markets. In this work, a dual-wavelength photodetector based on vertical (In,Ga)N nanowires and graphene has been fabricated successfully. By using the transparent graphene, both blue and red responses can be clearly detected. The rise time of response can reach 3.5 ms. Furthermore, the underlying mechanism of double responses has also been analyzed. The main reason contributing to the dual-wavelength response could be the different diameters of nanowires, leading to different In components within (In,Ga)N sections.

Adverse childhood experiences and co-occurring psychological distress and substance abuse among juvenile offenders: the role of protective factors

OBJECTIVE

The purpose of this study was to estimate associations between cumulative exposure to adverse childhood experiences (ACEs), protective factors, and co-occurrence among male and female juvenile offenders.

STUDY DESIGN

Cross-sectional study.

METHODS

Validated measures of ACEs, internal resilience, external youth assets, psychological distress, and substance abuse were collected from 429 youths involved in the juvenile justice system in Nevada. A three-level outcome variable was created using the psychological distress and substance use measures: no problems, one problem, or co-occurring problems. Hierarchical multinomial logistic regression models were used to determine the independent, direct, and moderating impact of the protective factors on ACEs and the outcome.

RESULTS

Internal resilience, family communication, school connectedness, peer role models, and non-parental adult role models were associated with lower odds of co-occurrence compared to having no problems (adjusted odds ratios [AORs] ranged from 0.11 to 0.33). When ACEs were added to the model, internal resilience and all assets except for one (non-parental adult role models) continued to offer protection against co-occurrence. Internal resilience was the only protective factor that significantly moderated the association between ACEs and co-occurrence (AOR, 0.24; 95% CI, 0.06, 0.99).

CONCLUSION

Most protective factors decreased co-occurring mental health and substance abuse problems in the presence of ACE exposure and internal resilience moderated the relationship between ACEs and co-occurrence. Juvenile justice systems should use positive youth development approaches to help prevent co-occurrence among youths.

Snipe: highly sensitive pathogen detection from metagenomic sequencing data

Metagenomics data provide rich information for the detection of foodborne pathogens from food and environmental samples that are mixed with complex background bacteria strains. While pathogen detection from metagenomic sequencing data has become an activity of increasing interest, shotgun sequencing of uncultured food samples typically produces data that contain reads from many different organisms, making accurate strain typing a challenging task. Particularly, as many pathogens may contain a common set of genes that are highly similar to those from normal bacteria in food samples, traditional strain-level abundance profiling approaches do not perform well at detecting pathogens of very low abundance levels. To overcome this limitation, we propose an abundance correction method based on species-specific genomic regions to achieve high sensitivity and high specificity in target pathogen detection at low abundance.

LncRNA APPAT regulated miR-328a/Pkp1 signal pathway to participate in breast cancer

OBJECTIVE

Recent studies indicated long non-coding RNA (lncRNA) is involved in the development of breast cancer, which is the pathological basis of breast cancer. Here, we reported the molecular mechanisms by which lncRNA APPAT regulated in the progression of breast cancer.

MATERIALS AND METHODS

QPCR was used to inspect the expression of lncRNA APPAT and miR-328a in breast cancer cell lines. Luciferase reporter assay confirmed the direct target effect of APPAT and miR-328a. Western blot was used to check Pkp1 protein expression in breast cancer cell lines.

RESULTS

The expressions of lncRNA APPAT, Pkp1 protein levels and miR-328a were commonly expressed in breast cancer cells. The inhibition of lncRNA APPAT expression repressed cell proliferation, migration and invasion in breast cancer and reverse results were found after lncRNA APPAT overexpressing. Mechanistically, the binding targets of lncRNA APPAT vs. miR-328a and Pkp1 vs. miR-328a were checked in breast cancer. Meanwhile, miR-328a silencing enhanced the proliferation, migration and invasion of breast cancer cells. Moreover, the effect caused by Pkp1 silencing on cell proliferation, migration and invasion was reversed by miR-328a inhibitor in MCF-7 and BT594 cells. Additionally, Pkp1 knockout reversed the effect of cell proliferation, migration and invasion triggered by APPAT elevated. Taken together, these results showed miR-328a as a downstream target of lncRNA APPAT linking lncRNA APPAT to Pkp1.

CONCLUSIONS

LncRNA APPAT regulated the proliferation, migration, invasion of breast cancer by regulating miR-328a/Pkp1 signaling pathway, providing a novel possible strategy for the treatment of breast cancer.

Circular RNA-ABCB10 suppresses hepatocellular carcinoma progression through upregulating NRP1/ABL2 via sponging miR-340-5p/miR-452-5p

OBJECTIVE

Hepatocellular carcinoma (HCC) is one of the most common liver malignancies worldwide with a high rate of recurrence and mortality. Circular RNA-ABCB10 (circ-ABCB10), 724 nucleotides in length, plays a pro-oncogenic role in tumor progression. However, the role of circ-ABCB10 in HCC is still unknown. Therefore, the objective of this study was to determine the role of circ-ABCB10 in HCC progression in vitro and in vivo and to elucidate the underlying mechanism.

PATIENTS AND METHODS

Tumor tissues from patients with HCC and multiple HCC cell lines were used for in vitro experiments and a mouse xenograft model was used for in vivo experiments. Quantitative Real Time-PCR, Western blots, lentivirus transfection, cell proliferation assays, cloning formation, migration, and invasion assays, flow cytometry, Luciferase reporter assays, and biotin-coupled probe pull-down assays were performed to investigate the mechanism underlying the effect of circ-ABCB10 on HCC.

RESULTS

The results revealed that the expression of circ-ABCB10 was downregulated in both HCC tissues and cell lines and was positively correlated with histological grade and tumor size. The overexpression of circ-ABCB10 exerted inhibitory effects on HCC cell proliferation, invasion, and migration. Mechanistic and functional evidence together showed that circ-ABCB10 elevated expressions of neuropilin-1 (NRP1) and ABL related gene (ABL2) by sponging miR-340-5p and miR-452-5p, which inhibited the progression of HCC. Furthermore, the in vivo study suggests that circ-ABCB10 inhibited tumor growth in nude mice.

CONCLUSIONS

In brief, the results demonstrate that circ-ABCB10 exerts anti-tumor roles via miR-340-5p/miR-452-5p-NRP1/ABL2 signaling axis, providing a promising biomarker and therapeutic target for HCC.

Genomic scan revealed KIT gene underlying white/gray plumage color in Chinese domestic geese

Goose is an important type of domesticated poultry. The wild geese that are regarded as the ancestors of modern domestic geese present gray plumage. Domesticated, geese have both white and gray feathers. To elucidate the genetic mechanisms underlying the formation of white and gray plumage in geese, we resequenced the whole genome of 18 geese from six populations including white and gray goose breeds. The average sequencing depth per individual was 9.81× and the average genome coverage was 96.8%. A total of 346 genes were detected in the top 1% of F_ST scores of gray- and white-feathered geese, and a significant F_ST site was located in the intron region within the KIT gene, the 18 bp deletion in KIT having the strongest potential association with white feathers. It has been reported that a number of genes are associated with plumage colors in birds. However, no studies have identified the relationship between KIT and plumage color in birds at present, although the white coat can be attributed to mutations in KIT in some mammals. Our study showed that that KIT is a plausible candidate gene for white/gray plumage color in Chinese domestic geese.

Design of Geiger Muller detector system for searching lost γ-ray source

If a radiation source is lost, it will do harm to human being, especially for the searching person. In order to find the lost radiation source easily, a detector system, including 3 detectors, was designed to search the lost c-ray radiation source autonomously in any environment. First, based on GEANT4 simulation, the radiation dose rates in 3 Geiger Muller (GM) counters were simulated at the different source-detector distances, distances between detectors and angles. Various analyses were performed by experimentally and verified the simulated detector designed system. A Mono-energetic 137Cs c-ray source with energy 662 keV and activity of 1.11 GBq was used for the observation. The simulated results were compared with the experimental dose rate values and obtained good agreements for various cases. Only based on the dose rates in three detectors, the radiation source was searched in a different location at a specific source activity and angle. The corresponding angles of deviation and detection limit were calculated for sensitivity and ability of detector designed system. The proposed detector designed system can be used to navigate radiation sources in the low level and high radiation environments.

Ratio of the interferon-γ signature to the immunosuppression signature predicts anti-PD-1 therapy response in melanoma

Immune checkpoint inhibitor (ICI) treatments produce clinical benefit in many patients. However, better pretreatment predictive biomarkers for ICI are still needed to help match individual patients to the treatment most likely to be of benefit. Existing gene expression profiling (GEP)-based biomarkers for ICI are primarily focused on measuring a T cell-inflamed tumor microenvironment that contributes positively to the response to ICI. Here, we identified an immunosuppression signature (IMS) through analyzing RNA sequencing data from a combined discovery cohort (n = 120) consisting of three publicly available melanoma datasets. Using the ratio of an established IFN-γ signature and IMS led to consistently better prediction of the ICI therapy outcome compared to a collection of nine published GEP signatures from the literature on a newly generated internal validation cohort (n = 55) and three published datasets of metastatic melanoma treated with anti-PD-1 (n = 54) and anti-CTLA-4 (n = 42), as well as in patients with gastric cancer treated with anti-PD-1 (n = 45), demonstrating the potential utility of IMS as a predictive biomarker that complements existing GEP signatures for immunotherapy.

Diamond: A Multi-Modal DIA Mass Spectrometry Data Processing Pipeline

MOTIVATION

We developed Diamond, a Nextflow-based, containerized, multi-modal data-independent acquisition (DIA) mass spectrometry (MS) data processing pipeline for peptide identification and quantification. Diamond integrated two mainstream workflows for DIA data analysis, namely, spectrum-centric scoring (SCS) and peptide-centric scoring (PCS), for use cases both with and without assay libraries. This multi-modal pipeline serves as a versatile, easy-to-use, and easily extendable toolbox for large-scale DIA data processing.

AVAILABILITY

The Docker image is available at https://hub.docker.com/r/zeroli/diamond and the source codes are freely accessible at https://github.com/xmuyulab/Diamond.

Effect of Polyphenols on Cognitive Function: Evidence from Population-Based Studies and Clinical Trials

Due to progressive population aging, a new dementia case occurs at every 3 seconds, placing a heavy burden of disease. Identifying potential risk or preventive factors is emphasized owing to a lack of effective treatment for dementia. There has been emerging evidence on the link of certain dietary components, particularly polyphenols, to brain wellness and cognitive outcomes. Findings from animal and in vitro studies appear more consistent and conclusive. However, such an association has not been investigated in depth in human beings. In this review, we examined studies on the effect of dietary polyphenols (including flavonoids, curcumin, and resveratrol) on cognitive function. Intervention in early stages of dementia/Alzheimer's disease might be a target to slow down age-related cognitive decline before disease onset. We summarized 28 epidemiological studies (8 cross-sectional and 20 cohort studies) and 55 trials in this review. Preliminary evidence from epidemiological data provides the necessity for intervention trials, even though the measures of polyphenol intake tend to be less precise. Clinical trials are in favor of the role of some polyphenols in benefiting specific domains of cognition. This review also describes the divergence of results and current limitations of research in this field.

Using deep learning to predict anti-PD-1 response in melanoma and lung cancer patients from histopathology images

BACKGROUND

Recent studies showed that immune-checkpoint blockade (ICB) has significantly improved clinical outcomes of melanoma and lung cancer patients. However, only a small subset of patients can benefit from ICB. Deep learning has been successfully implemented in complementary clinical diagnosis. The aim of this study is to demonstrate the potential of deep learning to facilitate the prediction of anti-PD-1 response from H&E images directly.

METHODS

In this study, 190 H&E slides of melanoma were segmented into 256 × 256 tiles which were used as the training set for the convolutional neural network (CNN). Additional 54 melanoma and 55 lung cancer H&E slides were collected as independent testing sets.

FINDINGS

An AUC of 0.778(95% CI: 63.8%-90.5%) was achieved for 54 melanoma testing samples with 15(65.2%) responders and 23(74.2%) non-responders correctly classified. We also obtained an AUC of 0.645(95% CI: 49.4%-78.4%) for 55 lung cancer samples.

INTERPRETATION

To our knowledge, this is the first study of using deep learning to determine patients' anti-PD-1 response from H&E slides directly. Our CNN model achieved the state-of-the-art performance and has the potential to screen ICB beneficial patients in routine clinical practice.

Performance evaluation of lossy quality compression algorithms for RNA-seq data

Background

Recent advancements in high-throughput sequencing technologies have generated an unprecedented amount of genomic data that must be stored, processed, and transmitted over the network for sharing. Lossy genomic data compression, especially of the base quality values of sequencing data, is emerging as an efficient way to handle this challenge due to its superior compression performance compared to lossless compression methods. Many lossy compression algorithms have been developed for and evaluated using DNA sequencing data. However, whether these algorithms can be used on RNA sequencing (RNA-seq) data remains unclear.

Results

In this study, we evaluated the impacts of lossy quality value compression on common RNA-seq data analysis pipelines including expression quantification, transcriptome assembly, and short variants detection using RNA-seq data from different species and sequencing platforms. Our study shows that lossy quality value compression could effectively improve RNA-seq data compression. In some cases, lossy algorithms achieved up to 1.2-3 times further reduction on the overall RNA-seq data size compared to existing lossless algorithms. However, lossy quality value compression could affect the results of some RNA-seq data processing pipelines, and hence its impacts to RNA-seq studies cannot be ignored in some cases. Pipelines using HISAT2 for alignment were most significantly affected by lossy quality value compression, while the effects of lossy compression on pipelines that do not depend on quality values, e.g., STAR-based expression quantification and transcriptome assembly pipelines, were not observed. Moreover, regardless of using either STAR or HISAT2 as the aligner, variant detection results were affected by lossy quality value compression, albeit to a lesser extent when STAR-based pipeline was used. Our results also show that the impacts of lossy quality value compression depend on the compression algorithms being used and the compression levels if the algorithm supports setting of multiple compression levels.

Conclusions

Lossy quality value compression can be incorporated into existing RNA-seq analysis pipelines to alleviate the data storage and transmission burdens. However, care should be taken on the selection of compression tools and levels based on the requirements of the downstream analysis pipelines to avoid introducing undesirable adverse effects on the analysis results.

A machine learning framework to determine geolocations from metagenomic profiling

BACKGROUND

Studies on metagenomic data of environmental microbial samples found that microbial communities seem to be geolocation-specific, and the microbiome abundance profile can be a differentiating feature to identify samples' geolocations. In this paper, we present a machine learning framework to determine the geolocations from metagenomics profiling of microbial samples.

RESULTS

Our method was applied to the multi-source microbiome data from MetaSUB (The Metagenomics and Metadesign of Subways and Urban Biomes) International Consortium for the CAMDA 2019 Metagenomic Forensics Challenge (the Challenge). The goal of the Challenge is to predict the geographical origins of mystery samples by constructing microbiome fingerprints.First, we extracted features from metagenomic abundance profiles. We then randomly split the training data into training and validation sets and trained the prediction models on the training set. Prediction performance was evaluated on the validation set. By using logistic regression with L2 normalization, the prediction accuracy of the model reaches 86%, averaged over 100 random splits of training and validation datasets.The testing data consists of samples from cities that do not occur in the training data. To predict the "mystery" cities that are not sampled before for the testing data, we first defined biological coordinates for sampled cities based on the similarity of microbial samples from them. Then we performed affine transform on the map such that the distance between cities measures their biological difference rather than geographical distance. After that, we derived the probabilities of a given testing sample from unsampled cities based on its predicted probabilities on sampled cities using Kriging interpolation. Results show that this method can successfully assign high probabilities to the true cities-of-origin of testing samples.

CONCLUSION

Our framework shows good performance in predicting the geographic origin of metagenomic samples for cities where training data are available. Furthermore, we demonstrate the potential of the proposed method to predict metagenomic samples' geolocations for samples from locations that are not in the training dataset.

Analysis of adoption trends of in-parlor technologies over a 10-year period for labor saving and data capture on pasture-based dairy farms

The use of precision technology is increasingly seen as an option to improve productivity, animal welfare, resource use efficiency, and workplace features on dairy farms. There is limited research related to longitudinal adoption patterns of precision dairy technologies and reasons for any patterns. The aim of this analysis was to investigate trends in technology adoption regarding both the amount (number of farms with a technology) and intensity (number of technologies per farm) of adoption. Surveys of parlor technology adoption were conducted on New Zealand dairy farms in 2008, 2013, and 2018, with 532, 500, and 500 respondents, respectively. Technologies were grouped into labor-saving (LS, such as automatic cluster removers) or data-capture (DC, such as in-line milk meters) categories. Trends were examined for farms that had only LS, only DC, or LS+DC technologies. Technology adoption increased over time; the likelihood of technology adoption in 2018 (and 2013 in parentheses) increased by 21 (22), 7 (68), and 378% (165) for LS, DC, and LS+DC technology groups, respectively, compared to 2008. Farms with LS+DC technologies also had a greater proportion of LS technologies compared to non-LS+DC farms, although this relationship declined over the 10-yr period. The use of a rotary versus herringbone parlor was estimated to be associated with 356 and 470% increase in the likelihood of adopting LS technologies and LS+DC, respectively, from 2008 to 2018. Regional differences in adoption were also found, with the likelihood of adopting DC and LS+DC technologies found to be 46 and 59% greater, respectively, in the South Island of New Zealand, compared to the base region of Waikato. The results highlight the importance of understanding spatial and temporal farm characteristics when considering future effect and adoption of precision dairy technologies. For example, the analysis indicates the occurrence of 2 trajectories to technology investment on farms, where larger farms are able to take advantage of technology opportunities, but smaller farms may be constrained by factors such as lack of economies of scale, limited capital to invest, and inability to retrofit technology into aging parlor infrastructure.

Implications of new-onset atrial fibrillation for in-hospital and long-term prognosis in patients with acute myocardial infarction: the CBD Bank study

Background

Atrial fibrillation (AF) often coexists with coronary artery disease. Data on the incidence and prognostic impact of new-onset AF following acute myocardial infarction (AMI) with current optimal therapy are insufficient, especially in Asian populations.

Purpose

To investigate the incidence of new-onset AF following AMI and to assess its impact on in-hospital and long-term prognosis.

Methods

We included consecutive AMI patients between December 2012 and July 2019, and excluded those with prior known AF on presentation. New-onset AF was defined as newly detected AF during the index hospitalization following AMI. The primary outcomes comprised of all-cause death and cardiovascular death occurred during hospitalization; and all-cause death and cardiovascular death during long-term follow-up among those AMI survivors. Follow-up visits were routinely scheduled after discharge, at 1 month, 3 months, 6 months, 12 months and every 12 months thereafter.

Results

Of 3686 patients enrolled, new-onset AF was documented in 138 (3.7%) patients during a mean duration of hospitalization of 8.8±5.8 days. Independent risk factors of new-onset AF were age ≥75 years, left atrial diameter ≥40mm, high levels of cardiac troponin-I or high sensitive C reactive protein. During hospitalization, all-cause death occurred in 22 (15.9%) new-onset AF patients and 67 (1.9%) non-AF patients (p<0.001); cardiovascular death occurred in 19 (13.8%) new-onset AF patients and 58 (1.6%) non-AF patients (p<0.001). On multivariable logistic analysis, new-onset AF was an independent predictor of in-hospital all-cause death (OR 5.85, 95% CI: 3.24–10.55) and cardiovascular death (OR 5.44, 95% CI: 2.90–10.20). Apart from the in-hospital deaths, another 265 (7.7%) were lost to follow-up; thus, 3332 patients were included in the long-term follow-up analysis: 106 new-onset AF and 3226 non-AF patients. After a mean follow-up period of 1096.7±682.0 days, all-cause death occurred in 19 new-onset AF patients and 249 non-AF patients; corresponding rates were 8.08 (95% CI: 5.15–12.67) vs. 2.55 (95% CI: 2.25, 2.88) per 100 person-years, respectively (p<0.001). Cardiovascular death occurred in 11 new-onset AF patients and 150 non-AF patients; corresponding rates were 4.68 (95% CI: 2.59–8.45) vs. 1.53 (95% CI: 1.31–1.80) per 100 person-years, respectively (p=0.002). After multivariable Cox adjustment, there was no significant association between new-onset AF and long-term all-cause death (HR 1.45, 95% CI: 0.90–2.35) or cardiovascular death (HR 1.21, 95% CI: 0.65–2.26).

Conclusion

New-onset AF following AMI was an independent predictor of increased risk of in-hospital mortality, but had no independent association with long-term death.

Funding Acknowledgement

Type of funding source: None

ScaleQC: a scalable lossy to lossless solution for NGS data compression

Motivation

Per-base quality values in Next Generation Sequencing data take a significant portion of storage even after compression. Lossy compression technologies could further reduce the space used by quality values. However, in many applications, lossless compression is still desired. Hence, sequencing data in multiple file formats have to be prepared for different applications.

Results

We developed a scalable lossy to lossless compression solution for quality values named ScaleQC (Scalable Quality value Compression). ScaleQC is able to provide the so-called bit-stream level scalability that the losslessly compressed bit-stream by ScaleQC can be further truncated to lower data rates without incurring an expensive transcoding operation. Despite its scalability, ScaleQC still achieves comparable compression performance at both lossless and lossy data rates compared to the existing lossless or lossy compressors.

Availability and implementation

ScaleQC has been integrated with SAMtools as a special quality value encoding mode for CRAM. Its source codes can be obtained from our integrated SAMtools (https://github.com/xmuyulab/samtools) with dependency on integrated HTSlib (https://github.com/xmuyulab/htslib).

Supplementary information

Supplementary data are available at Bioinformatics online.

SIRT5 deficiency enhances the proliferative and therapeutic capacities of adipose-derived mesenchymal stem cell via metabolic switching

Background

Mesenchymal stem/stromal cells (MSCs) render potential therapies for multiple ischemic diseases. However, in vitro expansion of MSCs before application leads to a metabolic switch from glycolysis to oxidative phosphorylation, drastically impairing their proliferative and therapeutic capacities.

Purpose

Here we aim to identify the role of SIRT5, a master metabolic regulator, in culture expansion of adipose-derived MSCs (ADMSCs).

Methods

SIRT5 deficiencyADMSCs was obtained from Sirt5−/− mice and their metabolic pattern and proliferation capacity were tested during in vitro expansion. Hind limb ischemic model was established to evaluated the therapeutic function of Sirt5−/−ADMSCs.

Results

SIRT5 protein level was upregulated in ADMCSs undergoing culture expansion. Sirt5−/−ADMSCs during in vitro expansion exhibited higher proliferation rate, delayed senescence and enhanced antioxidant capacity. SIRT5 deficiency induced hypersuccinylation of metabolic-related proteins, leading to attenuated mitochondrial respiration with elevated glycolysis and pentose phosphate pathway. Furthermore, lowering succinylation level by glycine treatment reversed the altered metabolism and enhanced proliferation of Sirt5−/−ADMSCs. In mice hind limb ischemic model, SIRT5−/−ADMSCs treatment achieved better blood flow recovery and angiogenesis compared to WT ADMSCs treatment.

Conclusion

We reveal that SIRT5 is a key regulator of ADMSCs undergoing in vitro culture. Ablation of SIRT5 leads to reversed metabolic pattern, enhanced proliferative capacity and improved therapeutic outcomes. Our data provide a potential target for enhancing MSC functional properties during bio-manufacturing in future MSC therapy. Such work may not only benefit MSC cell therapy, but could extent to a wide variety of other stem cells that share similar metabolic pattern.

Graphic Abstract

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Major Research Plan of the National Natural Science Foundation of China. National Science Fund for Distinguished Young Scholars.

Fabry-Pérot Oscillations in Correlated Carbon Nanotubes

We report the observation of an intriguing behavior in the transport properties of nanodevices operating in a regime between the Fabry-Pérot and the Kondo limits. Using ultrahigh quality nanotube devices, we study how the conductance oscillates when sweeping the gate voltage. Surprisingly, we observe a fourfold enhancement of the oscillation period upon decreasing temperature, signaling a crossover from single-electron tunneling to Fabry-Pérot interference. These results suggest that the Fabry-Pérot interference occurs in a regime where electrons are correlated. The link between the measured correlated Fabry-Pérot oscillations and the SU(4) Kondo effect is discussed.

A joint analysis strategy reveals genetic changes associated with artificial selection between egg-type and meat-type ducks

Egg-type ducks and meat-type ducks are predominantly commercial or indigenous and have been subjected to artificial directional selection. These two duck types differ substantially in body shape, production performance and reproductivity. However, the genetic changes associated with phenotypic differences remain unclear. Here, we compared the two duck types at the genomic and transcriptomic levels. We identified a large number of SNPs and genes in genomic divergent regions in terms of F_ST and θπ values. The corresponding genes were mainly enriched in embryonic development function and metabolic pathway. RNA-seq analysis also revealed differential gene expression in the liver and gonads. The differentially expressed genes were functionally associated with signal transmission and substance metabolism respectively. Furthermore, we found that seven genes were related to differentiation between the two types by both g genome and transcriptome analysis and were plausible candidate genes. These genes were annotated to GO categories of cell development and disease immunity. These findings will enable a better understanding of the artificial selection history of meat and egg ducks and provide a valuable resource for future research on the breeding of these two lineages.

Profiling the effects of physicochemical indexes on the microbial diversity and its aroma substances in pit mud

Microbial diversity of pit mud (PM) plays a significant role in Baijiu's flavour. Here we explored the microbial community structures and aroma substances of Wenwang Winery with high-throughput sequencing coupling with headspace solid-phase microextraction-gas chromatography-mass spectrometry. We discovered that the odorant was mainly derived from 14 aroma compounds because of their OAVs ≥ 1 (OAV, the ratio of substance concentration to aroma threshold; s, on behalf of the plural), such as ethyl hexanoate (2438), ethyl octanoate (975), caproic acid (52) and etc. Moreover we also revealed that Lactobacillaceae (97·08%) was the mainly bacterial microbial community in 2-year-old PM, companied by the primarily fungi including Aspergillaceae (55·45%), Unclassified Ascomycota (11·13%) and Dipodascaceae (5·72%). Compared with the 2-year-old PM, bacterial floras in 20-year-old PM and 30-year-old PM were more abundant (i.e. Dysgonomonadaceae, Clostridium and Synerggstaceas), while no fungi were detected. Besides, the physicochemical analysis showed that the content of Lactobacillaceae was inversely associated with moisture, pH and ammonia nitrogen. By further Spearman's correlation coefficient analysis, we verified that the content of Lactobacillaceae was positively correlated with ethyl hexanoate, while negatively correlated with ethyl octanoate and caproic acid. Meanwhile, ethyl octanoate and caproic acid were positively correlated with most flora including Ruminococcaceae, Dysgonomonadaceae and Clostridiacea, which were related to physicochemical indexes. This work demonstrates promise for adjusting the physicochemical indexes of PM to affect the micro-organisms and aroma, which may provide a reference for the production of high-quality Baijiu.

Identification of risk factors for falls in postmenopausal women: a systematic review and meta-analysis

The purpose of this study was to identify risk factors for falls in postmenopausal women and provide evidence for the primary prevention of falls in postmenopausal women. The protocol for this meta-analysis is registered with PROSPERO (CRD42020170927). We searched PubMed, the Cochrane Library and EMBASE for observational studies on the risk factors for falls in postmenopausal women. Review Manager 5.3 was used to calculate the relative risk (RR) or weighted mean difference (WMD) of potential risk factors related to falls. STATA 14.0 was used for the quantitative evaluation of publication bias. Eleven studies with 42,429 patients from 7 countries were included. The main risk factors for falls in postmenopausal women were patient sociodemographic risk factors (age: WMD = 0.37, 95% CI 0.07 to 0.68; body weight: WMD = 0.88, 95% CI 0.56 to 1.12; BMI: WMD = 0.34, 95% CI 0.21 to 0.46; exercise: RR = 0.97, 95% CI 0.94 to 0.99; and FES-I: WMD = 6.60, 95% CI 0.72 to 12.47) and medical risk factors (dietary calcium intake: WMD = - 16.91, 95% CI - 25.80 to - 8.01; previous fracture history: RR = 1.21, 95% CI 1.13 to 1.29; previous falls: RR = 2.02, 95% CI 1.91 to 2.14; number of diseases, ˃ 2: RR = 1.17, 95% CI 1.11 to 1.23; and number of reported chronic health disorders: WMD = 0.30, 95% CI 0.10 to 0.49). Knowledge of the many risk factors associated with falls in postmenopausal women can aid in fall prevention. However, we cannot rule out some additional potential risk factors (age at the onset of menopause, years since last menstruation, hormone therapy and BMD) that need further clinical research.

Naringenin induces neuroprotection against homocysteine-induced PC12 cells via the upregulation of superoxide dismutase 1 expression by decreasing miR-224-3p expression

Naringenin is a flavonoid compound with antioxidant effects. It is used to treat oxidative stress-related diseases, but its mechanism is unclear. In this experiment, we explored whether naringenin can increase the expression of superoxide dismutase 1(SOD1), reduce the oxidative stress of PC12 cells induced by homocysteine (Hcy), and decrease the apoptosis of PC12 cells induced by Hcy by inhibiting the expression of mir-224-3p. Different concentrations of Hcy (1, 3, 5, 8, and 10 mmol/L) was used to analyze effect of homocysteine on PC12 cells. A total of 5 mmol/L Hcy was used to induce the excitatory and neurotoxicity model of PC12 cells in vitro. The cells were divided into normal control, Hcy induction, Hcy + Naringenin (25 μM), Hcy + Naringenin (50 μM), Hcy + Naringenin (75 μM), Hcy + Naringenin (100 μM), and Hcy + Naringenin (150 μM) groups. The relative survival rate and activities of the PC12 cells were determined by the MTT method, and the apoptosis rate of the PC12 cells was determined by using flow cytometry. The Western blot method was used to determine the expressions of SOD1, Bax, Caspase-3, Caspase-8, and Bcl-2 in the PC12 cells induced by Hcy. The expressions of SOD1 mRNA and miR-224-3p in the Hcy-induced PC12 cells were determined by RT-PCR. Results found that Hcy increased the expression of miR-224-3p in a dose-dependent manner but decreased that of SOD1 mRNA and protein. Hcy also increased oxidative stress in the PC12 cells and the proapoptotic proteins Bax, Caspase-3, and Caspase-9. Furthermore, it decreased the expression of anti-apoptotic protein Bcl-2 and the activity and survival rate of the HT22 cells, but it increased the apoptosis of the PC12 cells. The treatment of Hcy-induced PC12 cells with different concentrations of naringenin for 24 h decreased the expression of miR-224-3p in a dose-dependent manner and increased the expressions of SOD1 mRNA and protein. The treatment also decreased the oxidative stress in the PC12 cells and the expressions of pro-apoptotic proteins Bax, Caspase-3, and Caspase-9; increased the expression of anti-apoptotic protein Bcl- 2; decreased the apoptosis of the PC12 cells; and increased the PC12 cells.The results suggest that Naringenin can decrease the apoptosis and oxidative stress of PC12 cells induced by Hcy and increase the activities and survival rates of PC12 cells. The mechanism may be related to naringenin decreasing the expression of miR-224-3p in PC12 cells induced by Hcy and increasing the expressions of SOD1 mRNA and protein.

Comparison of high-throughput single-cell RNA sequencing data processing pipelines

With the development of single-cell RNA sequencing (scRNA-seq) technology, it has become possible to perform large-scale transcript profiling for tens of thousands of cells in a single experiment. Many analysis pipelines have been developed for data generated from different high-throughput scRNA-seq platforms, bringing a new challenge to users to choose a proper workflow that is efficient, robust and reliable for a specific sequencing platform. Moreover, as the amount of public scRNA-seq data has increased rapidly, integrated analysis of scRNA-seq data from different sources has become increasingly popular. However, it remains unclear whether such integrated analysis would be biassed if the data were processed by different upstream pipelines. In this study, we encapsulated seven existing high-throughput scRNA-seq data processing pipelines with Nextflow, a general integrative workflow management framework, and evaluated their performance in terms of running time, computational resource consumption and data analysis consistency using eight public datasets generated from five different high-throughput scRNA-seq platforms. Our work provides a useful guideline for the selection of scRNA-seq data processing pipelines based on their performance on different real datasets. In addition, these guidelines can serve as a performance evaluation framework for future developments in high-throughput scRNA-seq data processing.

Differential proteomics analysis of serum exosomein burn patients

The exosome is an emerging concepts biomarkers due to their abnormal expression in various diseases. Research on exosome has already shifted from the laboratory to clinical application. This study uses bioinformatics technology to identify functional changes in proteins of serum exosomes from burn patients. A total of 231 quantifiable differentially-expressed proteins were screened out, 31 of them had statistically significant changes in expression levels. In the test group, expression of2 proteins had downregulated, whereas that of 29 proteins upregulated. Gene Ontology analysis demonstrates that differentially-expressed proteins were primarily identified in extracellular vesicles and platelet α granules, which can alter enzyme inhibitor activities, heparin-binding, coagulation, and lipid transport. Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrates that ITGA2B and ITGB3 proteins, which were significantly upregulated in the burn group, were primarily involved in the PI3K/AKT signaling pathway. Western blotting confirmed that the expressions of ITGA2B and ITGB3 in burn patient tissue samples were higher than those in the control group; conversely, the expression of CD9 was lower than that in the control group. In burn patients, the upregulated proteins ITGA2B and ITGB3 of serum exosomes likely participate in injury detection and repair via PI3K/AKT signaling pathways.

[Application of intestinal stent in prevention of anastomotic leakage after rectal cancer operation]

Objective: To observe preventive effect of intestinal stent against anastomotic leakage after rectal cancer operation. Methods: A retrospective cohort study was carried out. Clinical data of 107 patients with low rectal cancer undergoing laparoscopic radical resection from January 2015 to August 2019 were retrospectively analyzed. Intestinal stent was placed intraoperatively in 48 cases and was not placed in 59 cases. Postoperative Wexner score for anal function and incidence of anastomotic leakage were compared between patients with and without intstinal stent. Results: There was no significant differences in age, distance between tumor and the anal verge, operative time and postoperative Wexner score for anal function between the two groups (all P>0.05). After a month of follow-up, the incidence of anastomotic leakage was 16.9% (10/59) in the non-stent group, while no anastomotic leakage was found in the stent group (P=0.002). Conclusion: Placement of intestinal stent can effectively prevent anastomotic leakage after low rectal cancer surgery.

Subnanosecond phase transition dynamics in laser-shocked iron

Iron is one of the most studied chemical elements due to its sociotechnological and planetary importance; hence, understanding its structural transition dynamics is of vital interest. By combining a short pulse optical laser and an ultrashort free electron laser pulse, we have observed the subnanosecond structural dynamics of iron from high-quality x-ray diffraction data measured at 50-ps intervals up to 2500 ps. We unequivocally identify a three-wave structure during the initial compression and a two-wave structure during the decaying shock, involving all of the known structural types of iron (α-, γ-, and ε-phase). In the final stage, negative lattice pressures are generated by the propagation of rarefaction waves, leading to the formation of expanded phases and the recovery of γ-phase. Our observations demonstrate the unique capability of measuring the atomistic evolution during the entire lattice compression and release processes at unprecedented time and strain rate.

OP0297 EFFICACY AND SAFETY OF ROMOSOZUMAB AMONG POSTMENOPAUSAL WOMEN WITH OSTEOPOROSIS AND MILD-TO-MODERATE CHRONIC KIDNEY DISEASE

Background:

Osteoporosis and renal insufficiency are coexisting disease states in a substantial proportion of postmenopausal women. Since bisphosphonates are generally contraindicated in patients with estimated glomerular filtration rate (eGFR) <35 mL/min, it is important to evaluate other osteoporosis treatments in this setting.

Objectives:

To determine if baseline renal function affects the efficacy and safety of romosozumab.

Methods:

We performed post hoc analyses of two clinical trials of romosozumab in postmenopausal women with osteoporosis. In ARCH (NCT01631214), 4,093 patients were randomised 1:1 to romosozumab 210 mg monthly or alendronate 70 mg weekly for 12 months (mean age: 74.3 years; 96.1% with prevalent vertebral fractures [VFx]). In FRAME (NCT01575834), 7,180 patients were randomised 1:1 to romosozumab 210 mg or placebo monthly for 12 months (mean age: 70.9 years; 18.3% with prevalent VFx). For these analyses, patients were categorised by baseline eGFR (mL/min/1.73m2): normal renal function (eGFR ≥90), mild renal insufficiency (eGFR 60–89), or moderate renal insufficiency (eGFR 30–59). Least squares mean (LSM) percent change from baseline in bone mineral density (BMD) at the lumbar spine, total hip, and femoral neck; incidence of new VFx and adverse events (AEs); and changes in renal function were assessed for each eGFR category at Month 12 of the double-blind treatment period.

Results:

At baseline, most patients had mild/moderate renal insufficiency: 84% in ARCH, 88% in FRAME. In both studies, change from baseline in BMD was significantly higher in the romosozumab group across baseline eGFR categories (Figure). There was an interaction between BMD increase and renal function, and although BMD increase was not as large in women with impaired renal function, differences between romosozumab and control groups remained significant (Figure). In ARCH, among patients with eGFR ≥90, 60–89, and 30–59, the incidence of new VFx (romosozumab vs alendronate) at Month 12 was 3.3% vs 7.3%, 3.2% vs 3.9%, and 3.4% vs 6.2% in ARCH. In FRAME, the incidence of new VFx (romosozumab vs placebo) at Month 12 was 0.5% vs 3.0%, 0.4% vs 1.5%, and 0.6% vs 2.1%.

In both studies, the incidences of AEs and serious AEs were similar in both treatment groups within and across eGFR categories. AEs of mild-to-moderate hypocalcaemia (investigator reported) occurred in two patients in ARCH (one romosozumab [eGFR 60–89] and one alendronate [eGFR ≥90]), and one patient in FRAME (romosozumab [eGFR 60–89]). Five patients in ARCH (all in the alendronate group) and 19 patients in FRAME (14 romosozumab, 5 placebo) had decreases in serum Ca levels (albumin adjusted); in the romosozumab group all were mild (<LLN–8.0 mg/dL) or moderate (<8.0–7.0 mg/dL). A similar percentage of patients in each group had changes in renal function over 12 months of treatment.

Conclusion:

The efficacy and safety of romosozumab vs alendronate or placebo was similar among postmenopausal women with osteoporosis and different levels of renal function.

Acknowledgments:

This study was funded by Amgen, Astellas and UCB Pharma. Editorial services were provided by Costello Medical.

Disclosure of Interests:

Paul Miller Grant/research support from: Amgen, Radius Health, Ultragenyx, Consultant of: Amgen, Radius Health, Jonathan Adachi Consultant of: Amgen, Speakers bureau: Amgen, Ben-Hur Albergaria Consultant of: Amgen Inc., Eli Lilly, Speakers bureau: Amgen Inc., Eli Lilly, Angela M Cheung Consultant of: Amgen, Eli Lilly, Arkadi Chines Shareholder of: Amgen Inc., Employee of: Amgen Inc., Evelien Gielen Consultant of: Amgen Inc., Takeda, Sandoz and UCB Pharma, Speakers bureau: Amgen Inc., Takeda, Sandoz and UCB Pharma, Bente Langdahl Grant/research support from: Amgen, NovoNordisk, Consultant of: Amgen Inc., Eli Lilly, UCB Pharma, Akimitsu Miyauchi Consultant of: Amgen Inc., Astellas BioPharma K.K., Teijin Pharma, Mary Oates Shareholder of: Amgen Inc., Employee of: Amgen Inc., Ian Reid Consultant of: Amgen Inc., Eli Lilly, Speakers bureau: Amgen Inc., Eli Lilly, Norma Ruiz Santiago Shareholder of: Amgen Inc., Employee of: Amgen Inc., Mark Vanderkelen Employee of: UCB Pharma, Wenjing Yang Shareholder of: Amgen Inc., Employee of: Amgen Inc., Zhigang Yu Shareholder of: Amgen Inc., Employee of: Amgen Inc.

Research on the quality changes of grass carp during brine salting

The research on the quality changes of grass carp during brine salting with 6%, 8%, and 10% salt additions was evaluated by chemical and physical indicators, as well as a sensory assessment and microbiological analysis. The NaCl content was proportional to salt addition and salting time. The increase of salt addition could lead to the increase of hardness and chewiness in which change trends were contrary to the pH within 24 hr. All K values were less than 10% during brine salting. The effect of 8% salt additions on free amino acids was relatively smaller. Higher levels of salt additions could inhibit bacterial growth. Combined with sensory assessment, equivalent umami concentration (EUC), and taste activity value (TAV) to analysis comprehensively, it was suggested that grass carp meat should be eaten at 4-8 hr of brine salting with 8% salt additions or processed for the next step, in which the grass carp meat had a better taste and quality.

[Efficacy and prognosis of phentolamine in the treatment of patients with myocardial injury due to sepsis]

Objective: To explore the effect of phenolamine on the outcome and prognosis of patients with myocardial injury due to sepsis. Methods: From January 2015 to December 2017, 62 septic patients with myocardial injury were randomly divided into study group (n=32) and control group (n=30). Two groups were given conventional treatment, while the study group was treated with phentolamine. The NT-pro brain natriuretic pepitide (NT-proBNP), cardiac troponin I (cTnI), lactate dehydrogenase (LDH), creatine kinase isoenzymes (CK-MB) and tumor necrosis factor (TNF)-α, high-sensitivity C-reactive protein (hs-CRP), interleukin (IL)-1β, IL-6 were detected at 0,12, 24, 48, 72 h and 7 d after hospitalization. And left ventricular ejection fraction (LVEF), e', E and A in each time period were observed. The 28 d survival rate and length of ICU stay were observed in both groups. The data were compared with single sample t test between the two groups. Results: After 12, 24, 48, 72 h and 7 d, NT-proBNP, cTnI, LDH, CK-MB, TNF-α, hs-CRP, IL-1β, IL-6 in the study group were all significantly lower than those in the control group (all P<0.05). The cardiac function indexes of LVEF, E/A and E/e' in the study group were all significantly improved when compared with those in the control group (all P<0.05). The length of ICU stay and 28-day mortality in the study group were significantly lower than those in the control group ((9.8±3.6) d vs (13.0±4.1) d, t=3.152, P=0.004; 21.9% vs 36.7%, χ(2)=5.078, P=0.021). Conclusion: Combined application of phentolamine can significantly improve the outcome of sepsis patients with myocardial injury and improve the survival rate.

ILC3 cells promote the proliferation and invasion of pancreatic cancer cells through IL-22/AKT signaling

PURPOSE

Type 3 innate lymphocytes (ILC3s) are reported to be involved in lung cancer, possibly by producing interleukin-22 (IL-22). However, whether ILC3s and their secreted IL-22 molecules contribute to the pathogenesis of pancreatic cancer (PC) remains unclear. To this end, in this study, we investigated the effects and possible mechanisms of ILC3s on PC pathogenesis.

METHOD

The IL-22 and IL-2i2R levels and the ILC3s' frequency in cancer tissues from PC patients and in peripheral blood from PC patients and healthy controls were analyzed by flow cytometry, immunochemistry, or immunofluorescence. The effects of IL-22-induced AKT signaling on the proliferation, invasion, and migration of PC cells were examined by co-culturing PC cell lines with ILC3s isolated from PC tissues, with or without the addition of neutralizing IL-22 antibody, IL-22R antibody or AKT inhibitor.

RESULTS

Our results showed that IL-22 and ILC3s were significantly upregulated in the PBMCs and cancer tissues of PC patients, and the IL-22R level was increased in PC cells. The increased frequency of ILC3s was positively correlated with the clinical features of PC patients. Co-culture experiments indicated that ILC3s promoted the proliferation, invasion, and migration of PC cell lines by secreting IL-22 to activate AKT signaling because IL-22/IL-22R or AKT blockage markedly counteracted such effects on PC cells.

CONCLUSION

Our data demonstrated that ILC3s may promote PC pathogenesis through IL-22/IL-22R-AKT signaling, suggesting a potential intervention target for PC treatment in the future.