bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlabeling and quantitative assessment of chondrocyte viability in articular cartilage with intrinsic nonlinear optical signatures
Authors: Li Yang , Chen Xun , Watkins Beckham , Saini Neal , Gannon Steven , Nadeau Elizabeth , Reeves Russell , Gao Bruce , Pelligrini Vincent , Yao Hai , Mercuri Jeremy , Ye Tong 
Published: January 2020

Chondrocyte viability is a crucial factor for evaluating cartilage health. Most prevalent cell viability assays rely on dyes and are not applicable for in vivo or longitudinal studies. Here we demonstrated that the two-photon excited autofluorescence and second harmonic generation microscopy provided high-resolution imaging of cartilage tissue and distinguished live/dead chondrocytes by visual assessment. Furthermore, the normalized autofluorescence ratio was proposed as a quantitative indicator to determine chondrocyte viability. Based on the indicator, a curve fitting and simulated receiver operating characteristic method was proposed to identify the live/dead cell populations as well as the indicator threshold without dye labeling. Thus, it established the label-free imaging method for chondrocyte viability assay in cartilage tissue. Impact statement Chondrocytes are the only cellular component found in the cartilage, playing a critical role in maintaining the homeostasis of articular cartilage. The viability of chondrocytes is a crucial factor for evaluating cartilage health. However, the current prevalent cell viability assays rely on dye staining and thereby are not applicable in vivo or in longitudinal assessments. In this study, we demonstrate that the intrinsic signals such as two-photon excited autofluorescence and second harmonic generation can be used to classify live and dead chondrocytes in cartilage tissue. A quantitative measure is also proposed allowing development of automated assessment algorithms. The nonlabeling nature of this method suggests the potential applicability to nondestructive and in vivo assessment of cartilage health.
In vivoevaluation of posterior eye elasticity using shaker-based optical coherence elastography
Authors: Qian Xuejun , Li Runze , Li Yan , Lu Gengxi , He Youmin , Humayun Mark S , Chen Zhongping , Zhou Qifa 
Published: January 2020

Age-related macular degeneration (AMD) is a progressive retinal disease and becomes the leading cause of blindness. It is well established that early detection is the key to preservation of functional vision. However, it is very difficult to diagnose AMD in very early stages, before structural changes are evident. Consequently, investigating the biomechanical properties of the retina maybe essential for understanding its physiological function. In this study, we present a shear wave-based quantitative method for estimating the elasticity of the posterior eye using shaker-based optical coherence elastography. This technique has been developed and validated on both a homogeneous phantom and a healthy rabbit in vivo. The shear wave speed from the ganglion side to the photoreceptor side of the rabbit eye is 4.1 m/s, 4.9 m/s, and 6.7 m/s, respectively. In addition, the most stiff sclera region has an average shear wave speed of 9.1 m/s. The results demonstrate the feasibility of using this technique to quantify biomechanical properties of the posterior eye and its potential translation to the clinical study.Impact statementHerein, we propose a potentially clinical applicable shaker-based optical coherence elastography (OCE) technique to characterize the biomechanical properties of the posterior eye, including different layers of the retina. Compared with either acoustic radiation force OCE or air-puff OCE, the newly developed method can induce sufficient shear wave propagation at the posterior eye with high resolution and large field of view.
Saturated hydrogen improves lipid metabolism disorders and dysbacteriosis induced by a high-fat diet
Authors: Qiu Xiangjie , Ye Qiaona , Sun Mengxing , Wang Lili , Tan Yurong , Wu Guojun 
Published: January 2020

Studies have shown that metabolic diseases, such as obesity, are significantly associated with intestinal flora imbalance. The amplification of opportunistic pathogens induced by the glyoxylic acid cycle contributes to intestinal flora imbalance. Promising, though, is that saturated hydrogen can effectively improve the occurrence and development of metabolic diseases, such as obesity. However, the specific mechanism of how saturated hydrogen operates is still not very clear. In this study, after a high-fat diet, the level of total cholesterol, total glyceride, and low-density lipoprotein in the peripheral blood of mice increased, and that of high-density lipoprotein decreased. Intestinal fatty acid metabolism-related gene Apolipoprotein E (ApoE), fatty acid synthase (FAS), intestinal fatty acid-binding protein (I-FAPB), acetyl-CoA carboxylase 1 (ACC1), peroxisome proliferator-activated receptor γ (PPARγ), and stearoyl-CoA desaturase 1 (SCD1) increased significantly. Bacteroides, Bifidobacteria, and Lactobacillus counts in feces decreased considerably, while Enterobacter cloacae increased. The activity of isocitrate lyase in feces increased markedly. Treatment of mice with saturated hydrogen led to decreased total cholesterol, total glyceride, and low-density lipoprotein and increased high-density lipoprotein in the peripheral blood. FAS and I-FAPB gene expression in the small intestine decreased. Bacteroides, Bifidobacteria, and Lactobacillus in feces increased significantly, whereas Enterobacter cloacae decreased. The activity of isocitrate lyase also diminished remarkably. These results suggest that saturated hydrogen could improve intestinal structural integrity and lipid metabolism disorders by inhibiting the glyoxylic acid cycle of the intestinal flora. Impact statement Past studies have shown that hydrogen can improve metabolic disorders, but its mechanism of action remains unclear. It is well known that metabolic diseases, such as obesity, are significantly associated with changes in the intestinal flora. The glyoxylic acid cycle is an essential metabolic pathway in prokaryotes, lower eukaryotes, and plants and could be the portal for mechanisms related to metabolic disorders. Many opportunistic pathogenic bacteria can recycle fatty acids to synthesize sugars and other pathogenic substances using the glyoxylic acid cycle. So, the glyoxylic acid cycle may be involved in intestinal dysbacteriosis under high-fat diet. This study, therefore, seeks to provide the mechanism of how hydrogen improves metabolic diseases and a new basis for the use of hydrogen in the treatment of metabolic disorders.
Nivolumab treatment of relapsed/refractory Epstein-Barr virus–associated hemophagocytic lymphohistiocytosis in adults
Authors: Liu Pengpeng , Pan Xiangyu , Chen Chong , Niu Ting , Shuai Xiao , Wang Jian , Chen Xuelan , Liu Jiazhuo , Guo Yong , Xie Liping , Wu Yu , Liu Yu , Liu Ting 
Published: January 2020

Abstract
Epstein-Barr virus (EBV)-associated hemophagocytic lymphohistiocytosis (EBV-HLH) is a life-threatening hyperinflammatory syndrome triggered by EBV infection. It often becomes relapsed or refractory (r/r), given that etoposide-based regimens cannot effectively clear the virus. r/r EBV-HLH is invariably lethal in adults without allogeneic hematopoietic stem cell transplantation. Here, we performed a retrospective analysis of 7 r/r EBV-HLH patients who were treated with nivolumab on a compassionate-use basis at West China Hospital. All 7 patients tolerated the treatment and 6 responded to it. Five of them achieved and remained in clinical complete remission with a median follow-up of 16 months (range, 11.4-18.9 months). Importantly, both plasma and cellular EBV-DNAs were completely eradicated in 4 patients. Single-cell RNA-sequencing analysis showed that HLH syndrome was associated with hyperactive monocytes/macrophages and ineffective CD8 T cells with a defective activation program. Nivolumab treatment expanded programmed death protein-1–positive T cells and restored the expression of HLH-associated degranulation and costimulatory genes in CD8 T cells. Our data suggest that nivolumab, as a monotherapy, provides a potential cure for r/r EBV-HLH, most likely by restoring a defective anti-EBV response.
CNCC: an analysis tool to determine genome-wide DNA break end structure at single-nucleotide resolution
Authors: Szlachta Karol , Raimer Heather M. , Comeau Laurey D. , Wang Yuh-Hwa 
Published: January 2020

Abstract
Background
DNA double-stranded breaks (DSBs) are potentially deleterious events in a cell. The end structures (blunt, 3′- and 5′-overhangs) at DSB sites contribute to the fate of their repair and provide critical information concerning the consequences of the damage. Therefore, there has been a recent eruption of DNA break mapping and sequencing methods that aim to map at single-nucleotide resolution where breaks are generated genome-wide. These methods provide high resolution data for the location of DSBs, which can encode the type of end-structure present at these breaks. However, genome-wide analysis of the resulting end structures has not been investigated following these sequencing methods.

Results
To address this analysis gap, we develop the use of a coverage-normalized cross correlation analysis (CNCC) to process the high-precision genome-wide break mapping data, and determine genome-wide break end structure distributions at single-nucleotide resolution. We take advantage of the single-nucleotide position and the knowledge of strandness from every mapped break to analyze the relative shifts between positive and negative strand encoded break nucleotides. By applying CNCC we can identify the most abundant end structures captured by a break mapping technique, and further can make comparisons between different samples and treatments. We validate our analysis with restriction enzyme digestions of genomic DNA and establish the sensitivity of the analysis using end structures that only exist as a minor fraction of total breaks. Finally, we demonstrate the versatility of our analysis by applying CNCC to the breaks resulting after treatment with etoposide and study the variety of resulting end structures.

Conclusion
For the first time, on a genome-wide scale, our analysis revealed the increase in the 5′ to 3′ end resection following etoposide treatment, and the global progression of the resection. Furthermore, our method distinguished the change in the pattern of DSB end structure with increasing doses of the drug. The ability of this method to determine DNA break end structures without a priori knowledge of break sequences or genomic position should have broad applications in understanding genome instability.
Identification of a novel anthocyanin synthesis pathway in the fungus Aspergillus sydowii H-1
Authors: Bu Congfan , Zhang Qian , Zeng Jie , Cao Xiyue , Hao Zhaonan , Qiao Dairong , Cao Yi , Xu Hui 
Published: January 2020

Abstract
Background
Anthocyanins are common substances with many agro-food industrial applications. However, anthocyanins are generally considered to be found only in natural plants. Our previous study isolated and purified the fungus Aspergillus sydowii H-1, which can produce purple pigments during fermentation. To understand the characteristics of this strain, a transcriptomic and metabolomic comparative analysis was performed with A. sydowii H-1 from the second and eighth days of fermentation, which confer different pigment production.

Results
We found five anthocyanins with remarkably different production in A. sydowii H-1 on the eighth day of fermentation compared to the second day of fermentation. LC-MS/MS combined with other characteristics of anthocyanins suggested that the purple pigment contained anthocyanins. A total of 28 transcripts related to the anthocyanin biosynthesis pathway was identified in A. sydowii H-1, and almost all of the identified genes displayed high correlations with the metabolome. Among them, the chalcone synthase gene (CHS) and cinnamate-4-hydroxylase gene (C4H) were only found using the de novo assembly method. Interestingly, the best hits of these two genes belonged to plant species. Finally, we also identified 530 lncRNAs in our datasets, and among them, three lncRNAs targeted the genes related to anthocyanin biosynthesis via cis-regulation, which provided clues for understanding the underlying mechanism of anthocyanin production in fungi.

Conclusion
We first reported that anthocyanin can be produced in fungus, A. sydowii H-1. Totally, 31 candidate transcripts were identified involved in anthocyanin biosynthesis, in which CHS and C4H, known as the key genes in anthocyanin biosynthesis, were only found in strain H1, which indicated that these two genes may contribute to anthocyanins producing in H-1. This discovery expanded our knowledges of the biosynthesis of anthocyanins and provided a direction for the production of anthocyanin.
Over-expression of poplar NAC15 gene enhances wood formation in transgenic tobacco
Authors: Yao Wenjing , Zhang Dawei , Zhou Boru , Wang Jianping , Li Renhua , Jiang Tingbo 
Published: January 2020

Abstract
Background
NAC (NAM/ATAF/CUC) is one of the largest plant-specific transcription factor (TF) families known to play significant roles in wood formation. Acting as master gene regulators, a few NAC genes can activate secondary wall biosynthesis during wood formation in woody plants.

Results
In the present study, firstly, we screened 110 differentially expressed NAC genes in the leaves, stems, and roots of di-haploid Populus simonii×P. nigra by RNA-Seq. Then we identified a nucleus-targeted gene, NAC15 gene, which was one of the highly expressed genes in the stem among 110 NAC family members. Thirdly, we conducted expression pattern analysis of NAC15 gene, and observed NAC15 gene was most highly expressed in the xylem by RT-qPCR. Moreover, we transferred NAC15 gene into tobacco and obtained 12 transgenic lines overexpressing NAC15 gene (TLs). And the relative higher content of hemicellulose, cellulose and lignin was observed in the TLs compared to the control lines containing empty vector (CLs). It also showed darker staining in the culms of the TLs with phloroglucinol staining, compared to the CLs. Furthermore, the relative expression level of a few lignin- and cellulose-related genes was significantly higher in the TLs than that in the CLs.

Conclusions
The overall results indicated that NAC15 gene is highly expressed in the xylem of poplar and may be a potential candidate gene playing an important role in wood formation in transgenic tobacco.
Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7
Authors: Oblessuc Paula Rodrigues , Matiolli Cleverson Carlos , Melotto Maeli 
Published: January 2020

Abstract
Background
Food contamination with Salmonella enterica and enterohemorrhagic Escherichia coli is among the leading causes of foodborne illnesses worldwide and crop plants are associated with > 50% of the disease outbreaks. However, the mechanisms underlying the interaction of these human pathogens with plants remain elusive. In this study, we have explored plant resistance mechanisms against these enterobacteria and the plant pathogen Pseudomonas syringae pv. tomato (Pst) DC3118, as an opportunity to improve food safety.

Results
We found that S. enterica serovar Typhimurium (STm) transcriptionally modulates stress responses in Arabidopsis leaves, including induction of two hallmark processes of plant defense: ROS burst and cell wall modifications. Analyses of plants with a mutation in the potentially STm-induced gene EXO70H4 revealed that its encoded protein is required for stomatal defense against STm and E. coli O157:H7, but not against Pst DC3118. In the apoplast however, EXO70H4 is required for defense against STm and Pst DC3118, but not against E. coli O157:H7. Moreover, EXO70H4 is required for callose deposition, but had no function in ROS burst, triggered by all three bacteria. The salicylic acid (SA) signaling and biosynthesis proteins NPR1 and ICS1, respectively, were involved in stomatal and apoplastic defense, as well as callose deposition, against human and plant pathogens.

Conclusions
The results show that EXO70H4 is involved in stomatal and apoplastic defenses in Arabidopsis and suggest that EXO70H4-mediated defense play a distinct role in guard cells and leaf mesophyll cells in a bacteria-dependent manner. Nonetheless, EXO70H4 contributes to callose deposition in response to both human and plant pathogens. NPR1 and ICS1, two proteins involved in the SA signaling pathway, are important to inhibit leaf internalization and apoplastic persistence of enterobacteria and proliferation of phytopathogens. These findings highlight the existence of unique and shared plant genetic components to fight off diverse bacterial pathogens providing specific targets for the prevention of foodborne diseases.
Metabolomic analyses reveal substances that contribute to the increased freezing tolerance of alfalfa (Medicago sativa L.) after continuous water deficit
Authors: Xu Hongyu , Li Zhenyi , Tong Zongyong , He Feng , Li Xianglin 
Published: January 2020

Abstract
Background
Alfalfa is a high-quality forage cultivated widely in northern China. Recently, the failure of alfalfa plants to survive the winter has caused substantial economic losses. Water management has attracted considerable attention as a method for the potential improvement of winter survival. The aim of this study was to determine whether and how changes in the water regime affect the freezing tolerance of alfalfa.

Results
The alfalfa variety WL353LH was cultivated under water regimes of 80 and 25% of water-holding capacity, and all the plants were subjected to low temperatures at 4/0 °C (light/dark) and then − 2/− 6 °C (light/dark). The semi-lethal temperatures were lower for water-stressed than well-watered alfalfa. The pool sizes of total soluble sugars, total amino acids, and proline changed substantially under water-deficit and low-temperature conditions. Metabolomics analyses revealed 72 subclasses of differential metabolites, among which lipid and lipid-like molecules (e.g., fatty acids, unsaturated fatty acids, and glycerophospholipids) and amino acids, peptides, and analogues (e.g., proline betaine) were upregulated under water-deficit conditions. Some carbohydrates (e.g., D-maltose and raffinose) and flavonoids were also upregulated at low temperatures. Finally, Kyoto Encyclopedia of Genes and Genomes analyses revealed 18 significantly enriched pathways involved in the biosynthesis and metabolism of carbohydrates, unsaturated fatty acids, amino acids, and glycerophospholipids.

Conclusions
Water deficit significantly enhanced the alfalfa’ freezing tolerance, and this was correlated with increased soluble sugar, amino acid, and lipid and lipid-like molecule contents. These substances are involved in osmotic regulation, cryoprotection, and the synthesis, fluidity, and stability of the cellular membrane. Our study provides a reference for improving alfalfa’ winter survival through water management.
Adding dexmedetomidine to morphine-based analgesia reduces early postoperative nausea in patients undergoing gynecological laparoscopic surgery: a randomized controlled trial
Authors: Li Huai Jin , Liu Shan , Geng Zhi Yu , Li Xue Ying 
Published: January 2020

Abstract
Background
Few studies have investigated the effect of dexmedetomidine on postoperative nausea and vomiting (PONV) in patients underwent gynecological laparoscopic surgery. We investigated if adding dexmedetomidine to a morphine-based patient-controlled analgesia (PCA) could decrease the incidence of PONV in this high-risk patient population.

Methods
In this prospective, randomized, double-blind and placebo-controlled study, 122 patients underwent gynecological laparoscopic surgery were assigned into two groups. Patients in the dexmedetomidine group (Group Dex) received a loading dose of dexmedetomidine 0.4 μg/kg before the end of surgery, followed by morphine 0.5 mg/ml plus dexmedetomidine 1 μg/ml for postoperative i.v. PCA. Patients in the control group (Group Ctrl) received normal saline before the end of surgery, followed by morphine 0.5 mg/ml alone for postoperative i.v. PCA. PCA pump was programmed as followed: bolus dose 2 ml, lockout interval 8 min and background infusion at a rate of 1 ml/h. The primary outcome was the incidence of nausea and vomiting within the first postoperative 24 h.

Results
Although there were no significant differences in regard to the total incidence of PONV (41.0% vs 52.5%, P = 0.204), PONV score, time to first onset of PONV, or the need for rescue antiemetics within the first postoperative 24 h between the two groups, the incidence of nausea and total PONV during the first 2 h period was significantly lower in the Group Dex than in the Group Ctrl (9.8% vs 24.6%, P = 0.031 and 0.031, respectively). More patients in Group Dex were over sedated or had bradycardia during the PACU compared with Group Ctrl (P = 0.040 and 0.036, respectively).

Conclusion
Our protocol in which dexmedetomidine was administered postoperatively – after a loading dose – to intravenous PCA morphine in patients undergoing gynecological laparoscopic surgery, had only early antiemetic effects, while no clinically meaningful antiemetic effect could be evidenced within the first 24 h after surgery.

Trial registration
Current control trial registered at Chictr.org.cn: ChiCTR1800017172. Date registered: 07/16/2018.
Preoperative exercise and recovery after cardiac surgery: a meta-analysis
Authors: Zheng Yu-Ting , Zhang Jiang-Xu 
Published: January 2020

Abstract
Background
To evaluate the association between preoperative exercise and recovery after cardiac surgery.

Methods
Literature comparing preoperative exercise and the control group for patients receiving cardiac surgery was retrieved in multiple databases. Review Manager 5.2 was adopted for meta-analysis, sensitivity analysis and bias analysis.

Results
Finally, 6 relevant studies satisfied the inclusion criteria. There was significant difference in length of stay in intensive care unit (ICU) (MD- = 1.35, 95%CI [− 2.64, − 0.06], P = 0.04; P for heterogeneity < 0.0001, I2 = 88%) and physical function after operation (P of heterogeneity = 0.32, I2 = 12%, Z = 9.92, P of over effect< 0.00001). The meta-analysis suggested that there was no significant difference in white blood cell count (WBC) at postoperative day 7 and mental health after operation between the exercise group and the control group. Limited publication bias was observed in this study.

Conclusion
Preoperative exercise including inhaled muscle training, aerobics, resistance training and stretching could promote recovery after cardiac surgery.