bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluid Dynamics Simulation and Temperature Gradient Validation along a Greenhouse Temperature Gradient
Authors: Kim Sung Kyeom , Lee Hee Ju , Wi Seung Hwan , Lee Seong-Won , Seo ILHWAN 
Published: September 2020

Abstract
Background: Climate change is increasing the vulnerability of horticultural crop cultivation and production. It is urgent to study such extreme weather phenomena (heatwave, drought, etc.), and in particular, to evaluate crop productivity according to temperature change. For this purpose, the crop physiological response to temperature change in simulated weather conditions was studied. However, there is a limitation in artificial light wavelength, which requires experiments to be carried out in protected facilities or open fields. In this study, we simulated temperature differences with computational fluid dynamics (CFD) in tunnel-type greenhouses. They can create temperature gradients and improve the accuracy of CFD with vertically and horizontally measured temperature profiles. The growth and physiological response of Kimchi cabbage were examined and validated using a temperature gradient within a semi-closed plastic tunnel.Results: Correlation coefficients of measured heights were: 1.120, 0.597, and 0.459. Root mean square error was below 0.1025, which means the CFD simulation values were highly accurate. The error analysis showed that it was possible to accurately predict temperature gradients change within a semi-closed tunnel-type greenhouse using CFD techniques. CFD results showed an average error of 0.597°C compared to field monitoring results. The maximum temperature difference of GTG was 5.7°C, suggesting a well-controlled set point (6°C difference between outside conditions and inside conditions of GTG). In a cloudy day, the gradient temperature of GTG was well maintained by the set differential temperature (dT), which suggests that the set dT was not precisely and accurately performed in GTG of a sunny day. There was a significant difference in the growth, net photosynthetic rate, transpiration rate, and Ci concentration along with temperature differences in GTG.Conclusions: CFD can simulate temperature gradient distribution in a tunnel-type greenhouse and predict the temperature difference for equipment with different specifications. These facilities can be used in climate change-related studies, such as assessment of crop production area optimization, crop physiological response to temperature, vulnerability assessment of crop production under increasing temperatures, or extreme weather.
Targeted Enrichment of Novel Chloroplast-Based Probes Reveals a Large-Scale Phylogeny of 412 Bamboos
Authors: Wang Jiongliang , Mu Weixue , Yang Ting , Song Yue , Hou YinGuang , Wang Yu , Gao Zhimin , Liu Xin , Liu Huan , Zhao Hansheng 
Published: September 2020

Abstract
Background: The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. Moreover, most of the chloroplast DNA sequencing methods cannot meet the requirements of large-scale CpGenome sequencing, which greatly limits and impedes the in-depth research of plant genetics and evolution.Results: To develop a set of bamboo probes, we used 99 high-quality CpGenomes with 6 bamboo CpGenomes as representative species for the probe design, and assembled 15M unique sequences as the final pan-chloroplast genome. A total of 180,519 probes for chloroplast DNA fragments were designed and synthesized by a novel hybridization-based targeted enrichment approach. Another 468 CpGenomes were selected as test data to verify the quality of the newly synthesized probes and the efficiency of the probes for chloroplast capture. We then successfully applied the probes to synthesize, enrich, and assemble 358 non-redundant CpGenomes of woody bamboo in China. Evaluation analysis showed the probes may be applicable to chloroplasts in Magnoliales, Pinales, Poales et al. Moreover, we reconstructed a phylogenetic tree of 412 bamboos (358 in-house and 54 published), supporting a non-monophyletic lineage of the genus Phyllostachys. Additionally, we shared our data by uploading a dataset of bamboo CpGenome into CNGB (https://db.cngb.org/search/project/CNP0000502/) to enrich resources and promote the development of bamboo phylogenetics.Conclusions: The development of the CpGenome enrichment pipeline and its performance on bamboos recommended an inexpensive, high-throughput, time-saving and efficient CpGenome sequencing strategy, which can be applied to facilitate the phylogenetics analysis of most green plants.
Prognostic factors in the pulmonary metastasectomy and efficacy of the repeat pulmonary metastasectomy from colorectal cancer
Authors: Fukada Masahiro , Matsuhashi Nobuhisa , Takahashi Takao , Tanaka Yoshihiro , Okumura Naoki , Yamamoto Hirotaka , Shirahashi Koyo , Iwata Hisashi , Doi Kiyoshi , Yoshida Kazuhiro 
Published: September 2020

Abstract
Background The rate of pulmonary metastasectomy from colorectal cancer (CRC) has increased with recent advances in chemotherapy, diagnostic techniques, and surgical procedures. The purpose of this study was to investigate the prognostic factors for response to pulmonary metastasectomy and the efficacy of repeat pulmonary metastasectomy.Methods This study was a retrospective, single-institution study of 126 CRC patients who underwent pulmonary metastasectomy between 2000 and 2019 at the Gifu University Hospital. Results The 3- and 5- year survival rates were 84.9% and 60.8%, respectively. Among the 126 patients, 47 (37.3%) had pulmonary recurrence after initial pulmonary metastasectomy, and 26 (20.6%) underwent a second pulmonary metastasectomy. Univariate analysis of survival identified seven significant factors: 1) gender (p = 0.04), 2) past history of extra-thoracic metastasis (p = 0.04), 3) maximum tumor size (p = 0.002), 4) mediastinal lymph node metastasis (p = 0.02), 5) preoperative carcinoembryonic antigen (CEA) level (p = 0.01), 6) preoperative carbohydrate antigen 19-9 (CA19-9) level (p = 0.03), and 7) repeat pulmonary metastasectomy for pulmonary recurrence (p < 0.001). On multivariate analysis, only mediastinal lymph node metastasis (p = 0.02, risk ratio: 8.206, 95% confidence interval (CI): 1.566-34.962) and repeat pulmonary metastasectomy for pulmonary recurrence (p < 0.001, risk ratio: 0.054, 95% CI: 0.010-0.202) were significant. Furthermore, there was no significant difference in clinical and surgical characteristics between the initial and the second pulmonary metastasectomy except for intraoperative blood loss. Conclusions Repeat pulmonary metastasectomy is likely to be safe and effective for recurrent cases that meet the surgical criteria. However, mediastinal lymph node metastasis was a significant independent prognostic factor for worse overall survival.
Prognosis Value of Low microRNA-34a Expression in Human Gastrointestinal Cancer: A Meta-Analysis
Authors: Chen Yan-Ling , Liu Xiao-Lin , Li Ling 
Published: September 2020

Abstract
Background: Mounting evidence shows that microRNA-34a (miR-34a) is involved in cancer prognosis. Therefore, we summarize the predictive role of miR-34a for survival in patients with gastrointestinal cancers (GICs). Methods: All the eligible studies were searched by PubMed, Web of Science and EMBASE and survival results were extracted. Then, the hazard ratio (HR) with corresponding 95% confidence intervals (CIs) was calculated to evaluate the prognostic role of miR-34a in GICs. The association between miR-34a expression and clinicopathological characteristics was estimated by odds ratio (OR) and 95%CIs. Results: A total of 20 studies were included in this meta-analysis. For overall survival (OS), the lower miR-34a expression significantly predicted poorer outcome in GICs, with the pooled HR of 1.86 (95% CI: 1.52-2.28, P<0.01). For disease-free survival (DFS), progressive-free survival (PFS), and recurrence-free survival (RFS), the lower miR-34a expression revealed worse DFS/PFS/RFS with the pooled HR of 1.86 (95% CI: 1.31–2.63, P < 0.01). Significant relation of differentiation/TMN stage/lymphatic metastasis and the expression level of miR-34a was identified. Conclusion: This meta-analysis reveals that lower miR-34a expression is significantly connected with worse OS and DFS/PFS/RFS of GICs patients. In addition, miR-34a expression level is relatively lower in patients with lymph node metastasis than patients without, and decreased miR-34a expression level is linked to poor tumor differentiation and late TMN stage. MiR-34a may become a new factor for prognosis prediction and progression of GICs.
Identification of FPR3 as a unique biomarker for targeted therapy in the immune microenvironment of breast cancer
Authors: Qi Jian , Liu Yu , Hu Jiliang , Lu Li , Dou Zhen , Dai Haiming , Wang Hongzhi , Yang Wulin 
Published: September 2020

Abstract
Background

Immunotherapy is in the ascendant, but its use in the treatment of breast cancer remains limited. Thus, identification and evaluation of prognostic biomarkers of tissue microenvironment will reveal new immune-based therapeutic strategies for breast cancer.
Methods

Using in silico bioinformatic approach, we investigated the tumor microenvironmental and genetic factors related to breast cancer. We calculated the Immune score, Stromal score, Estimate score, Tumor purity, Tumor mutation burden (TMB), Mutant-allele tumor heterogeneity (MATH) of breast cancer patients from the Cancer Genome Atlas (TCGA) using the ESTIMATE algorithm and Maftools. Weighted correlation network analysis (WGCNA) was used to identify gene patterns association with the Immune score. Then we use the MCODE plugin of Cytoscape to analyze the protein-protein interaction (PPI) network for mining the functional gene modules. Survival and Cox analysis was further performed to identify the key prognostic targets in immune microenvironment. Gene set enrichment analysis (GSEA) was utilized to explore the carcinogenic pathways associated with the target genes.
Results

Significant correlations between Immune/Stromal scores with breast cancer subtypes and tumor stages were established. Importantly, we found that the Immune score, but not the Stromal score, was significantly related to the patient's prognosis. WGCNA identified a pattern of gene function associated with Immune score, and that almost all of these genes (388 genes) are significantly upregulated in the higher Immune score group. PPI network analysis revealed the enrichment of immune checkpoint genes in the functional module but predicting a good prognosis by survival analysis. Among all the upregulated genes, FPR3, a G protein-coupled receptor essential for neutrophil activation, is the sole factor that predicts poor prognosis. GSEA analysis showed FRP3 upregulation synergizes with the activation of many pathways involved in carcinogenesis.
Conclusions

This study identified FPR3 as a key immune-related biomarker predicting a poor prognosis for breast cancer, revealing it as a promising targetable gene for immunotherapy.
Identification and determination of toxin genes of Vibrio strains causing hemorrhagic disease on red drum (Sciaenops ocellatus) using PCR method
Authors: Linh Nguyen Quang , Pham Yen Thi Hai , Nguyen Tram Duy Quynh 
Published: September 2020

Abstract
Data were isolated from 30 strains of Vibrio and sampled on different organs (brain, hemorrhagic site and digestive tract) of Sciaenops ocellatus infection. The results showed that nucleotide sequences 16S rRNA region are highly, similar to those of V. alginolyticus, V. azureus, V. fluvialis and V. orientalis is published on Genebank, ranging from 98.05 to 100 %. The digestive tract has the most common Vibrio strains (V. alginolyticus, V. azureus and V. fluvialis). Thereout, 25 of 30 strains of Vibrio contained 1 to 3 toxin genes, excepted V. parahaemolyticus. Six parameters were used to measure the DNA polymorphism of 33 homologous DNA sequences in this Vibrio bacteria population. The results indicated number of separate polymorphic sites (S), total number of mutant sites (Eta), number of haplotype (h), haplotype diversity (Hd), average number of nucleotide differences (k), nucleotide diversity (Pi) were 98 (S) 103 (Eta), 9 (h), 0.887 ± 0.032 (Hd), 25.789 (k) and 17.980x10-3 ± 0.003 (Pi), respectively (P < 0,05). The G+C content above 1434 sites positions of nucleotide sequences accounts for 0.542. The phylogenetic tree showed that these strains are divided into six groups. As observed, the appearance of isolated Vibrio on 3 organs of fish (S. ocellatus) hemorrhagic are V. azureus (27,67 %), V. alginolyticus (50 %), V. orientalis (6,67 %) and V. fluvialis (16,67 %). Through this result, we found that the diversity of Vibrio species that appeared on the red drum was used in the 16S rRNA region and the presence of toxin genes in these Vibrio species.
Antibiotic Susceptibility of Staphylococcus Aureus Isolated from Skin Lesions in Children. A Retrospective Analysis from a Tertiary Care Italian Pediatric Hospital
Authors: Lezzi Marilea , Bandettini Roberto , Ugolotti Elisabetta , Saffioti Carolina , Mesini Alessio , Pastorino Carlotta , Manunza Francesca , Ferretti Marta , Brisca Giacomo , Castagnola Elio 
Published: September 2020

Abstract
Background: knowledge on antibiotic susceptibility of S.aureus strains isolated from skin lesions in pediatric Italian patients is limited.Methods: retrospective analysis of antibiotic susceptibility of S.aureus strains isolated from skin infections observed from January 2013 to June 2019 at the IRCCS Istituto Giannina Gaslini, Genoa – ItalyResults: a total of 1833 strains were analyzed. Methicillin resistance was more frequent in cultures from outpatients than from inpatients (18% vs. 14%, p=0.04) as well as resistance to cotrimoxazole (8% vs. 4.1%, p<0.001) Resistance to ampicillin was 99% in both groups, while to clindamycin it was 11% and 14%, respectively. Among topical antibiotics fusidic acid showed the better resistance profile (3%).Conclusions: the proportion of antibiotic resistance in S.aureus skin infections in Italian children is not negligible. This could represent a problem, especially for orally administered drugs.
Hydroxyurea Regressed Atherosclerosis Plaques in ApoE-/- mice: A Discovery Based on Clinic
Authors: Tong Qian , Yang Xinyu , Ma Shu-Rong , Zhang Xian-Feng , Jiang Jian-Dong , Wang Yan 
Published: September 2020

Abstract
Background: A 58-year-old lady was introduced to the clinic because of acute coronary syndrome combined with essential thrombocythemia. After treating her with aspirin, statins and hydroxyurea (HU), the plaques in her coronary arteries showed improvement dramatically. Here, we aim to investigate that whether HU reduces atherosclerosis plaques in ApoE-/- mice.Methods: Wild-type (C57BL/6, n=8) and Apolipoprotein E knockout (ApoE-/-, n=40) mice were used in atherosclerosis model and medication groups. The mice were separated into 7 groups, including the normal control group, the atherosclerosis model group, the dual antiplatelet therapy group (aspirin, and clopidogrel bisulfate), the low-dose and high-dose HU therapy groups [aspirin, clopidogrel bisulfate, and HU (10 or 20 mg/kg/day)], the positive medicine group (aspirin, clopidogrel bisulfate, and atorvastatin calcium), and the combined medicine treatment group [aspirin, clopidogrel bisulfate, atorvastatin calcium, and HU (10 mg/kg/day)]. Fasting serum and aortic vessels were obtained after experiment. The aortic oil red O, hematoxylin-eosin (H&E), and full-length oil red O staining were performed to evaluate the HU’s efficacy of anti- atherosclerosis, and the blood lipid / glucose levels and liver /kidney functions were evaluated after HU treatment.Results: The oil red O and H&E staining results came out that HU therapy with antiplatelet showed an obvious effect in decreasing atherosclerosis plaques and the effect of HU therapy (10 or 20 mg/kg) was stronger than dual antiplatelet therapy plus statin, without liver and kidney toxicity observed. Furthermore, the combined drugs with HU (10 mg/kg/day), statin and antiplatelet nearly eliminated the plaques.Conclusions: A discovery based on clinic reveals that HU regressed atherosclerosis plaques in ApoE-/- mice, which provides us a new insight into anti-atherosclerosis drugs strategy.
Correlation Between the Extension of the Maxillary Sinus Floor and Malocclusion in Adolescent Patients Using a Cone-beam Computed Tomography
Authors: Xu Min , Zhang Xiaoxiao , He Jiacai , Guo Xinxing , Sang Yuanyuan , Zhang Zheng , Wang Yuanyin , Xu Wenhua , Xu Jianguang 
Published: September 2020

Abstract
Background: The correlation between extension of the maxillary sinus floor and vertical facial skeletal patterns is important for designing orthodontic treatment plans. We correlated the extension of the maxillary sinus (MS) floor with different facial skeletal malocclusion in adolescent patients aged 10-19 years old using a cone-beam computed tomography. Methods: The relationship between the root tips of upper posterior teeth and the sinus floor was typed and scored (0-4) using cone-beam computed tomography (CBCT) images. Scores of each tooth and each patient were formulated. The cephalometric radiographs were analyzed with Dolphin software to diagnose patients' facial skeletal types into three groups according to Frankfort mandibular plane angle (FMA) as high-angle, average-angle and low-angle groups and ANB angle as Class I, Class II and Class III groups separately. The influences caused by age, sex, and facial skeletal malocclusion on the tooth and patient score were analyzed. Results: In high-angle group, the first molar (FM) score was significantly higher than that in the average-angle and low-angle groups (P = 0.018). Age has a positive effect on the patient score and some of the tooth scores, such as the second premolar (SPM) score, FM score, and the second molar (SM) score, and in the skeletal facial malocclusion. With increasing age, SM score increased along with FMA angles. No significant difference was found in the distribution of patient and tooth scores by ANB angles. Conclusion: The relationship between the maxillary posterior roots and the sinus floor is correlated with facial skeletal malocclusion in 10- to 19-year-old adolescents. More first molar root tips were inside the sinus in the high-angle group compared with the average-angle and low-angle skeletal patterns. With advancing age, more second molar root tips were more close to contact the sinus floor in the high-angle group. Consideration of the root-sinus position of the posterior maxillary area in different skeletal malocclusion before establishing an orthodontic treatment plan is recommended.
Accuracy of Conventional and Digital Methods for Obtaining Dental Impressions and 3D Printed Models
Authors: Resende CAIO CÉSAR DIAS , Barbosa Tiago Augusto Quirino , Moura Guilherme Faria , Tavares Lucas Nascimento , Rizzante Fabio Antonio Piola , George Furat , Mendonça Gustavo , Neves Flavio Domingues 
Published: September 2020

Abstract
Background: Different sizes of arch could influence in digital methods to obtaining dental impressions and 3D models. The purpose of this study was to evaluate and compare the accuracy of two intra-oral scanners and conventional impression methods for the fabrication of working casts. Methods: Conventional impressions of a reference cast were obtained. Digital impressions were obtained with two intra-oral scanners: Cerec Omnicam (CO) and 3Shape Trios (ST). The obtained digital stereolithographic casts were printed on Zenith D 3D printer. The reference cast and fabricated casts were scanned with a bench top scanner and saved in STL format. All STL records were analyzed in specific software: complete arch (CA), partial arch (PA) and prepared teeth area (PT). One-way and two-way analyses of variance were performed to compare the accuracy, followed by the Tukey test. Results: No significant intergroup differences in trueness and precision were observed for the two intra-oral scanners. 3D printed casts had the lowest trueness when complete arch was analyzed and differed statistically from the stone cast. For complete arch precision, stone cast presented better results, however statistically different only from the CO. Conclusions: The two intraoral scanner systems had similar accuracy. Stone casts had higher trueness than 3D printed casts for CA. For CA precision, 3D printed cast presented similar results to the stone cast.
Prevalence and Associated Risk Factors Analysis of Hepatitis B &amp; C Infections in the Low Socioeconomic Communities; A Cross-Sectional Study from Pakistan
Authors: Noreen Aisha , Adnan Fazal , Alam Naik , Syed Zainab , Aftab Aroosa , Shamim Farah , Najeebullah Syed , Kakar Salik Javed , Ahmed Tahir 
Published: September 2020

Abstract
Background: Pakistan is bearing the second highest global burden of hepatitis C and B virus, infecting 3-4 % of its overall 22 million population. These infections remain unchecked in most of the cases and such incidences become a continuous source of infection to the healthy population. Maximum efforts for screening, prevalence and surveillance of these viral infections is needed to stem the devastating impact on the underprivileged communities living in the outskirt of major cities. Methods: This study was designed to determine the prevalence of hepatitis B & C and the corresponding risk factors among the low socioeconomic communities of Islamabad. Participants (aged 10-70 years) were recruited from six localities inhabited with people living in underprivileged conditions. Relationship between hepatitis B/C incidence, demographics and risk factors was measured using Pearson's Chi-square test, univariate and multivariate regression analysis. A total of 1004 individuals were enrolled in this study.Results: Out of 1004 individuals, almost 4% were found positive for hepatitis C and 1% for hepatitis B after screening with PCR. Pearson’s Chi-square test showed a strong relationship of hepatitis B/C infection with marital status (p= 0.000), hepatitis B vaccination status (p= 0.000), blood or blood product recipient (p= 0.000), having a tattoo, family income (p= 0.026) and participant age (p= 0.000). Multivariable analysis showed hepatitis B vaccination odds ratio (OR) =5.309 (95% confidence interval [CI] 2.812-10.025), population exposed to therapeutic injections four-times/past 6 months OR=4.328 (95% CI 1.319-13.617) dental visit four-time/past six months OR=11.9 (95% CI 3.350-40.098) people having exposure to HCV patients ≥6 times/past six months OR=3.095 (95% CI 1.577-6.074) and age of the participants OR=1.049 (95% CI 1.026-1.072) were independently associated with hepatitis C infection. Conclusions: These findings show that the risk of hepatitis B/C is multifactorial. However, on multivariate analysis, no association was found between hepatitis C incidence and blood donation, blood recipient, nose/ear piercing, barber visit, tattooing, drug abuse, marital status, family income and education status.