bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of urban particulate matter-induced disruption of human respiratory mucosa integrity using whole transcriptome analysis and organ-on-a chip
Authors: Byun Junhyoung , Song Boa , Lee Kyungwoo , Kim Byoungjae , Hwang Hae Won , Ok Myung-Ryul , Jeon Hojeong , Lee Kijeong , Baek Seung-Kuk , Kim Sang-Heon , Oh Seung Ja , Kim Tae Hoon 
Published: November 2019

Abstract
Background
Exposure to air particulate matter (PM) is associated with various diseases in the human respiratory system. To date, most in vitro studies showing cellular responses to PM have been performed in cell culture using a single cell type. There are few studies considering how multicellular networks communicate in a tissue microenvironment when responding to the presence of PM. Here, an in vitro three-dimensional (3D) respiratory mucosa-on-a-chip, composed of human nasal epithelial cells, fibroblasts, and endothelial cells, is used to recapitulate and better understand the effects of urban particulate matter (UPM) on human respiratory mucosa.

Results
We hypothesized that the first cells to contact with UPM, the nasal epithelial cells, would respond similar to the tissue microenvironment, and the 3D respiratory mucosa model would be a suitable platform to capture these events. First, whole transcriptome analysis revealed that UPM induced gene expression alterations in inflammatory and adhesion-related genes in human nasal epithelial cells. Next, we developed an in vitro 3D respiratory mucosa model composed of human nasal epithelial cells, fibroblasts, and endothelial cells and demonstrated that the model is structurally and functionally compatible with the respiratory mucosa. Finally, we used our model to expose human nasal epithelial cells to UPM, which led to a disruption in the integrity of the respiratory mucosa by decreasing the expression of zonula occludens-1 in both the epithelium and endothelium, while also reducing vascular endothelial cadherin expression in the endothelium.

Conclusions
We demonstrate the potential of the 3D respiratory mucosa model as a valuable tool for the simultaneous evaluation of multicellular responses caused by external stimuli in the human respiratory mucosa. We believe that the evaluation strategy proposed in the study will move us toward a better understanding of the detailed molecular mechanisms associated with pathological changes in the human respiratory system.
SEQdata-BEACON: a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500
Authors: Zhou Yanqiu , Liu Chen , Zhou Rongfang , Lu Anzhi , Huang Biao , Liu Liling , Chen Ling , Luo Bei , Huang Jin , Tian Zhijian 
Published: November 2019

Abstract
Background
The sequencing platform BGISEQ-500 is based on DNBSEQ technology and provides high throughput with low costs. This sequencer has been widely used in various areas of scientific and clinical research. A better understanding of the sequencing process and performance of this system is essential for stabilizing the sequencing process, accurately interpreting sequencing results and efficiently solving sequencing problems. To address these concerns, a comprehensive database, SEQdata-BEACON, was constructed to accumulate the run performance data in BGISEQ-500.

Results
A total of 60 BGISEQ-500 instruments in the BGI-Wuhan lab were used to collect sequencing performance data. Lanes in paired-end 100 (PE100) sequencing using 10 bp barcode were chosen, and each lane was assigned a unique entry number as its identification number (ID). From November 2018 to April 2019, 2236 entries were recorded in the database containing 65 metrics about sample, yield, quality, machine state and supplies information. Using a correlation matrix, 52 numerical metrics were clustered into three groups signifying yield-quality, machine state and sequencing calibration. The distributions of the metrics also delivered information about patterns and rendered clues for further explanation or analysis of the sequencing process. Using the data of a total of 200 cycles, a linear regression model well simulated the final outputs. Moreover, the predicted final yield could be provided in the 15th cycle of the early stage of sequencing, and the corresponding R2 of the 200th and 15th cycle models were 0.97 and 0.81, respectively. The model was run with the test sets obtained from May 2019 to predict the yield, which resulted in an R2 of 0.96. These results indicate that our simulation model was reliable and effective.

Conclusions
Data sources, statistical findings and application tools provide a constantly updated reference for BGISEQ-500 users to comprehensively understand DNBSEQ technology, solve sequencing problems and optimize run performance. These resources are available on our website http://seqBEACON.genomics.cn:443/home.html.
The prevalence and impact of self‐reported foot and ankle pain in the over 55 age group: a secondary data analysis from a large community sample
Authors: Keenan Anne‐Maree , Drake Chris , Conaghan Philip G. , Tennant Alan 
Published: November 2019

AbstractBackgroundWhile the prevalence and impact of musculoskeletal problems are high, most attention has been directed towards the back, knee and hip disorders. Foot pain is known to be common in older adults and accounts for a significant burden on health services. The aim of this study was to assess the impact of foot and ankle joint pain, considering age, presence of co‐morbidities and other site joint pain, in a large community sample.MethodsIn the North Yorkshire Health study, 16,222 people over 55 years participated in a detailed survey of the prevalence and impact of lower limb joint problems. Self‐assessment of overall body pain and functional activities of daily living were assessed. Participants indicated the presence of joint pain, stiffness or swelling during the last 3 months which had lasted for more than 6 weeks on a manikin: data were captured on the foot and the ankle.ResultsThe prevalence of self‐reported foot and ankle joint pain was substantial: 184.33 per 1000, second only to knee problems. While foot pain was common, it was mostly associated with joint pain at other sites; only 1 in 11 of those with foot and ankle pain reported it only in the foot. Logistic regression modeling revealed while established factors such as co‐morbidities, knee and hip problems contributed to functional impairment, foot and ankle problems contributed to an additional increased risk of having difficulty standing and walking by two fold (OR = 2.314, 95%CI 2.061–2.598), going up and down stairs by 71% (OR = 1.711, 95%CI 1.478–1.980) and getting up from a seated position by 44% (OR = 1.438, 95%CI 1.197–1.729).ConclusionThese results suggest that not only are foot problems in the over 55 age group extremely prevalent, they have a considerable impact on functional abilities.
MicroRNA-326-5p enhances therapeutic potential of endothelial progenitor cells for myocardial infarction
Authors: Li Xiaoting , Xue Xiang , Sun Yuejun , Chen Lei , Zhao Ting , Yang Wentao , Chen Yongbing , Zhang Zhiwei 
Published: November 2019

Abstract
Background
Our study sought to investigate the therapeutic effects and mechanisms of miR-326-5p-overexpressing endothelial progenitor cells (EPCs) on acute myocardial infarction (AMI).

Methods
Mouse EPCs were isolated, purified, and identified by flow cytometry and uptake of DiI-ac-LDL. The target gene of miR-326-5p was predicted using target prediction algorithms and verified by dual-luciferase reporter assay, RT-qPCR, and Western blot. After EPCs were transfected with the agomir or antagomir of miR-326-5p, tube formation assay and Matrigel plug angiogenesis assay were conducted in four groups (NC, miR-326-5p agomir, miR-326-5p antagomir, and miR-326-5p agomir+Wnt1 agonist). In addition, a mouse model of MI was established and treated with the injection of miR-326-5p-EPCs, miR-326-5p-EPCs+ Wnt1 agonist, EPCs-NC, or PBS/control into the peri-infarcted myocardium. Subsequently, cardiac function was monitored by echocardiography at 7 and 28 days postoperatively. Finally, the infarcted hearts were collected at 28 days, and the size of myocardial infarction was measured by Masson’s trichrome staining and the neovascularization in the peri-infarcted area was examined through immunofluorescence staining.

Results
Luciferase reporter assay indicated that Wnt1 was a direct target of miR-326-5p. Using RT-qPCR and Western blot analysis, we further demonstrated that the expression level of Wnt1 was negatively correlated with miR-326-5p expression in EPCs. Both in vitro study of tube formation assay and in vivo investigation of subcutaneous Matrigel plug assay revealed that the miR-326-5p agomir could significantly enhance the angiogenic capacity of EPCs, and this effect was partially inhibited by Wnt1 agonist. Meanwhile, miR-326-5p antagomir could obviously reduce the the angiogenic capacity of EPCs in vivo compared with that in the NC group. Moreover, the transplantation of miR-326-5p-overexpressing EPCs in the ischemic hearts of mice significantly enhanced the angiogenesis in the peri-infarcted zone and improved the cardiac function. However, the enhanced capacity of angiogenesis of miR-326-5p-overexpressing EPCs was remarkably neutralized by Wnt1 agonist, accompanied by the decreased improvement in cardiac function.

Conclusion
miR-326-5p significantly enhanced the angiogenic capacity of EPCs. Transplantation of miR-326-5p-overexpressing EPCs improved cardiac function for AMI therapy, which can be a novel strategy for enhancing therapeutic angiogenesis in ischemic heart diseases.
Supplementation of vitamin C promotes early germ cell specification from human embryonic stem cells
Authors: Li Zili , Fang Fang , Zhao Qian , Li Honggang , Xiong Chengliang 
Published: November 2019

Abstract
Background
As the precursors of sperm and eggs, human primordial germ cells (hPGCs) emerge as early as weeks 2 to 3 of post-implantation development. Recently, robust hPGC induction models have been established in vitro with different protocols, but global 5mC/5hmC epigenetic reprogramming is not initiated in vitro. Previous studies found that vitamin C can enhance Tet (ten-eleven translocation) enzyme expression and improve 5hmC level in cells. But the effect of vitamin C supplementation on hPGC in vitro induction is still unknown.

Methods
We generated a gene-edited human embryonic stem cell (hESC) line carrying a BLIMP1-mkate2 reporter by CRISPR/Cas9 technology and used flow cytometry to optimize the PGC differentiation protocol; meanwhile, the expression of PGC genes (BLIMP1, TFAP2C, SOX17, OCT4) was evaluated by qRT-PCR. When different concentrations of vitamin C were added to the induction medium, the percentage of hPGCLCs (hPGC-like cells) was analyzed by flow cytometry; dot blot and ELISA were used to detect the levels of 5hmC and 5mC. The expression of TET enzymes was also evaluated by qRT-PCR.

Results
We optimized the PGC differentiation protocol with the BLIMP1-mkate reporter hESCs, and the efficiency of PGC induction in vitro can be improved to 30~40%. When 50 μg/mL vitamin C was added, the derived hPGCLCs not only upregulated the expression of key genes involved in human early germ cell development such as NANOS3, TFAP2C, BLIMP1, and SOX17, but also increased the levels of 5hmC and TET enzymes.

Conclusions
Taken together, supplementation of vitamin C can promote the in vitro induction of hPGCLCs from hESCs, which might be related to vitamin C-mediated epigenetic regulations during the differentiation process.
Intra-pancreatic tissue-derived mesenchymal stromal cells: a promising therapeutic potential with anti-inflammatory and pro-angiogenic profiles
Authors: Khiatah Bashar , Qi Meirigeng , Du Weiting , T-Chen Kuan , van Megen Kayleigh M. , Perez Rachel G. , Isenberg Jeffrey S. , Kandeel Fouad , Roep Bart O. , Ku Hsun Teresa , Al-Abdullah Ismail H. 
Published: November 2019

AbstractBackgroundHuman pancreata contain many types of cells, such as endocrine islets, acinar, ductal, fat, and mesenchymal stromal cells (MSCs). MSCs are important and shown to have a promising therapeutic potential to treat various disease conditions.MethodsWe investigated intra-pancreatic tissue-derived (IPTD) MSCs isolated from tissue fractions that are routinely discarded during pancreatic islet isolation of human cadaveric donors. Furthermore, whether pro-angiogenic and anti-inflammatory properties of these cells could be enhanced was investigated.ResultsIPTD-MSCs were expanded in GMP-compatible CMRL-1066 medium supplemented with 5% human platelet lysate (hPL). IPTD-MSCs were found to be highly pure, with > 95% positive for CD90, CD105, and CD73, and negative for CD45, CD34, CD14, and HLA-DR. Immunofluorescence staining of pancreas tissue demonstrated the presence of CD105+cells in the vicinity of islets. IPTD-MSCs were capable of differentiation into adipocytes, chondrocytes, and osteoblasts in vitro, underscoring their multipotent features. When these cells were cultured in the presence of a low dose of TNF-α, gene expression of tumor necrosis factor alpha-stimulated gene-6 (TSG-6) was significantly increased, compared to control. In contrast, treating cells with dimethyloxallyl glycine (DMOG) (a prolyl 4-hydroxylase inhibitor) enhanced mRNA levels of nuclear factor erythroid 2-related factor 2 (NRF2) and vascular endothelial growth factor (VEGF). Interestingly, a combination of TNF-α and DMOG stimulated the optimal expression of all three genes in IPTD-MSCs. Conditioned medium of IPTD-MSCs treated with a combination of DMOG and TNF-α contained higher levels of pro-angiogenic (VEGF, IL-6, and IL-8) compared to controls, promoting angiogenesis of human endothelial cells in vitro. In contrast, levels of MCP-1, a pro-inflammatory cytokine, were reduced in the conditioned medium of IPTD-MSCs treated with a combination of DMOG and TNF-α.ConclusionsThe results demonstrate that IPTD-MSCs reside within the pancreas and can be separated as part of a standard islet-isolation protocol. These IPTD-MSCs can be expanded and potentiated ex vivo to enhance their anti-inflammatory and pro-angiogenic profiles. The fact that IPTD-MSCs are generated in a GMP-compatible procedure implicates a direct clinical application.
Digital spotlighting filtering optimization for SAR imaging
Authors: Balster Eric J. , Mundy David B. , Kordik Andrew M. , Hill Kerry L. 
Published: November 2019

AbstractIn this paper, a synthetic aperture radar (SAR) image formation simulator is used to objectively evaluate the parameter selection within the digital spotlighting process. Specifically, recommendations for the filter type and filter order of the low-pass filters used in the range and azimuth decimation processes within the digital spotlighting algorithm are determined to maximize image quality and minimize computational cost. Results show that a finite impulse response low-pass filter with a Taylor $(\overline {n}=5)$(n¯=5) window applied provides the highest image quality over a wide range of filter orders and decimation factors. Additionally, a linear relationship between filter length and decimation factor is found.
Lipiodol retention pattern after TACE for HCC is a predictor for local progression in lesions with complete response
Authors: Dioguardi Burgio Marco , Sartoris Riccardo , Libotean Claudia , Zappa Magaly , Sibert Annie , Vilgrain Valérie , Ronot Maxime 
Published: November 2019

AbstractBackgroundTo evaluate the predictive value of the lipiodol retention pattern for local progression of HCC with a complete response (CR) on CT according to mRECIST criteria after a first session of conventional chemoembolization (cTACE).MethodsFrom January 2014 to May 2016 all consecutive patients undergoing a first cTACE session for HCC were identified. Inclusion criteria were the presence of ≤3 HCCs and available pre- and post-cTACE CT. Tumor response was classified according to mRECIST criteria. The analysis focused on tumors with a CR. The lipiodol retention pattern in these tumors was classified as complete (C-Lip, covering the entire tumor volume), or incomplete (I-Lip). Local progression was defined as the reappearance of areas of enhancement on arterial-phase images with washout on portal/delayed phase images within 2 cm from treated tumors on follow-up CT.ResultsThe final population included 50 patients with 82 HCCs. A total of 46 (56%) HCCs were classified with a CR, including 16 (35%) with I-Lip, and 30 (65%) with C-Lip. After a median follow-up of 14 months (3.2–35.9 months), 15/16 (94%) and 10/30 (30%) of I-Lip and C-Lip HCCs showed local progression on CT, respectively (p < 0.001), with no significant difference in the time to progression (mean 11.1 ± 2 vs. 13.4 ± 3 months for I-Lip and C-Lip, respectivelyp = 0.51).ConclusionsHCCs with incomplete lipiodol retention after a first cTACE session have a high risk of local progression even when there is a CR according to mRECIST, and should be considered to be incompletely treated.
Effective erector spinae plane block for postoperative analgesia in a pyothorax patient who underwent emergency re-open thoracotomy—a case report
Authors: Kawagoe Izumi , Satoh Daizoh , Fukui Mariko , Suzuki Kenji , Inada Eiichi 
Published: November 2019

Abstract
Background
The appropriate choice of postoperative analgesia for pyothorax surgery is unclear since local infection could contaminate the catheter used for regional blocks and bacteremia can lead to disordered coagulation. We performed erector spinae plane block (ESPB) in a pyothorax patient undergoing emergency re-open thoracotomy.

Case presentation
An 81-year-old male with internal jugular vein stenosis on aspirin therapy was scheduled for pyothorax drainage and residual middle lobectomy 14 days after he underwent open right lower lung lobectomy for lung cancer.
ESPB was performed with injection of 20 ml of 0.375% levobupivacaine at the Th5 transverse process of the right side under ultrasound guidance.
Although he needed intravenous pentazocine for pain on postoperative day 0, no more analgesics were required postoperatively. NRS score ranged from 0 to 1 thereafter.

Conclusions
ESPB provided effective postoperative analgesia following emergency re-open thoracotomy for our pyothorax patient. ESPB might be the appropriate choice for postoperative analgesia following pyothorax surgery.
Lower genital tract infections in young female juvenile idiopathic arthritis patients
Authors: Ferreira Gabriela R. V. , Tomioka Renato B. , Queiroz Ligia B. , Kozu Katia , Aikawa Nadia E. , Sallum Adriana M. E. , Serafini Paulo , Tacla Maricy , Baracat Edmund C. , Pereira Rosa M. R. , Bonfá Eloisa , Silva Clovis A. 
Published: November 2019

Abstract
Background
To evaluate human papillomavirus (HPV), Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections in juvenile idiopathic arthritis (JIA) patients.

Methods
After exclusion, 33 female adolescent and young JIA patients (ILAR criteria) and 28 healthy controls were selected for this study. Demographic data, gynecological, sexual function, cervical cytology and histological abnormalities were evaluated. JIA clinical/laboratorial parameters and treatment were also assessed. HPV-DNA, CT-DNA and NG-DNA testing in cervical specimens were performed by Hybrid Capture 2 assays.

Results
The mean current age was similar in JIA patients and controls (23.3 ± 6.24 vs. 26.1 ± 6.03 years, p = 0.09). The frequencies of sexual intercourse (76% vs. 89%, p = 0.201) and abnormal cervical cytology (24% vs. 11%, p = 0.201) were similar in JIA compared to controls. The higher frequency of HPV infection in JIA patients than controls (30% vs. 11%, p = 0.155) did not reach statistical significance. CT (0% vs. 7%, p = 0.207) and NG infections (0% vs. 4%, p = 0.459) were also alike in both groups. Further evaluation of JIA patients with abnormal and normal cervical cytology showed that the former group had a higher frequency of HPV infection (87% vs. 12%, p = 0.0002) with a low frequency of HPV vaccination (0% vs. 8%, p = 1.0). No differences were evidenced between these two JIA groups regarding demographic data, sexual function and clinical/laboratorial parameters. The frequencies of methotrexate (p = 0.206) and biological agent use (p = 0.238) were similar in both JIA groups.

Conclusions
To our knowledge, this was the first study to assess lower genital infections in JIA patients allowing the identification of HPV as main cause of cervical dysplasia. Methotrexate and biological agents do not seem to increase risk of lower genital tract infections in JIA patients.
Large-scale inversions majorly drive upland cotton population differentiation
Authors: TIAN Shilin , MA Zhiying 
Published: November 2019

AbstractRecently, Li and his team hosted a project on roles of inversion in upland cotton population differentiation. Strikingly, genomic comparison identified, and subsequent RIL population and germplasm panel haplotype analyses confirmed, that large-scale inversions on chromosome At08 are widely distributed and have over time mediated the reduction of meiotic recombination that has ultimately driven genetically isolated haplotypes of G. hirsutum. This work is likely to become the new benchmark for cotton functional genomics research, and the scientific insights from the comparative analyses contributed substantially to our basic understanding of how genomic inversions influence meiotic recombination and thus lower genetic diversity in plant populations.
Determination of physiological parameters for endogenous glucose production in individuals using diurnal data
Authors: van Stee Mariël F. , Krishnan Shaji , Groen Albert K. , de Graaf Albert A. 
Published: November 2019

AbstractBackgroundTriple tracer meal experiments used to investigate organ glucose-insulin dynamics, such as endogenous glucose production (EGP) of the liver are labor intensive and expensive. A procedure was developed to obtain individual liver related parameters to describe EGP dynamics without the need for tracers.ResultsThe development used an existing formula describing the EGP dynamics comprising 4 parameters defined from glucose, insulin and C-peptide dynamics arising from triple meal studies. The method employs a set of partial differential equations in order to estimate the parameters for EGP dynamics. Tracer-derived and simulated data sets were used to develop and test the procedure. The predicted EGP dynamics showed an overall meanR2of 0.91.ConclusionsIn summary, a method was developed for predicting the hepatic EGP dynamics for healthy, pre-diabetic, and type 2 diabetic individuals without applying tracer experiments.
Meeting the mental health needs of low- and middle-income countries: the start of a long journey
Authors: Kisely Steve , Siskind Dan 
Published: November 2019

Summary
Mental health is increasingly recognised as an important component of global health. In recognition of this fact, the European Union funded the Emerald programme (Emerging Mental Health Systems in Low- and Middle-Income Countries). The aims were to improve mental health in the following six low- and middle-income countries (LMICs): Ethiopia, India, Nepal, Nigeria, South Africa and Uganda. The Emerald programme offers valuable insights into addressing the mental health needs of LMICs. It provides a framework and practical tools. However, it will be important to evaluate longer-term effects including improvements in mental health outcomes, as well as the applicability to LMICs beyond existing participant countries. Importantly, this must be coupled with efforts to improve health worker retention in LMICs.