bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated analysis of differential lncRNA and mRNA expression in cholelithiasis based on high-throughput sequencing and bioinformatics
Authors: Xu Conghui , Sun Yanbo , Li Yijun , Xu Qingwen , Li Weiming , Xu Pengyuan 
Published: June 2022

Abstract
Background: The etiology of GSD (gallstone disease)has not been fully elucidated. Thus, the current study was designed to analyze the expression profiles of lncRNAs and mRNAs to unveil the potential mechanisms and investigate the role of lncRNA in GSD.Methods:Four gallstone and four control samples were collected and used for RNA sequencing. Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified between gallstone and control samples by limma R package. The biological function of DElncRNAs and DEmRNAs were analyzed by clusterProfiler R package and IPA software. The Pearson correlation between DElncRNAs and DEmRNAs were calculated to construct the co-expression network of DElncRNAs and DEmRNAs. Moreover, to explore the role of lncRNA in gallstone, the cis- and trans-regulatory network of selected lncRNAs were constructed and visualized by Cytoscape software. In addition, we also constructed a ceRNA regulatory network in gallstone disease. To validate the RNA-sequencing data, we performed RT-qPCR to determine the expressions of top 4 DEmRNAs and DElncRNAs in gallstone and control samples.Results:A total of 934 DEmRNAs and 304 DElncRNAs were identified between gallstone and control samples, respectively. Functional enrichment analysis revealed that both DElncRNAs and DEmRNAs were involved in metabolism-related biological functions. The results of correlation analysis showed that the expressions of 597 DEmRNAs had extremely strong relationship with the expressions of 194 DElncRNAs. A cis-lncRNA-mRNA and trans-lncRNA-TF-mRNA regulatory network were constructed. In addition, a ceRNA composed of 24 DElncRNAs, 201 DEmRNAs and 120 predicted miRNAs was constructed by Cytoscape software. Moreover, by RT-qPCR, we found that the expressions of AC004692.4, HECW1-IT1, SFRP4 and COMP were significantly higher, whereas the expressions of LINC01564, SLC26A3, RP1-27K12.2 and GSTA2 were remarkedly lower in gallstone samples compared with those in control ones, which were consistent with the sequencing results.Conclusion: Our study investigated the role of DElncRNAs and DEmRNAs in gallstone, which may help us understand the etiology of gallstone on the genetic level.
Carbon sequestration in vegetation and its change in the Three-North Shelter Forest region of China in 2000-2021
Authors: Wang Li-xia , Gao Ji-xi , Zhang Wen-guo , Shen Wen-ming , Cai Ming-yong , Xiao Tong , Zhang Xin-sheng , Tai Wen-fei 
Published: June 2022

Abstract
Carbon sequestration in vegetation can offset a large proportion of carbon emissions, and plays an important role in mitigation climate change. Based on satellite data and ground observation data, we examined carbon sequestration rate and its long-term change in the Three-North Shelter Forest Program (TNSFP) region, where a series of large-scale ecological projects have been implemented. The results indicated that carbon sequestration rate in vegetation was 458.3 ± 45 g C m− 2yr− 1 in the TNSFP region during the period 2000–2021. Obvious increase trend of carbon sequestration rate was observed covering approximately 90% of the TNSFP region, with an average increase rate of 5.06 ± 4.3 g C m− 2yr− 1. There was a larger increase rate of 7.78 ± 2.07 g C m− 2yr− 1 in forest than that of 3.27 ± 0.55 g C m− 2yr− 1in grassland. Total carbon sequestration into vegetation was 26.1054 P g C (1 P g = 1015 g) in the TNSFP region, with annual carbon sequestration of 1186.6 ± 122.6 T g C (1 T g = 1012 g) during the period 2000–2021. Our results revealed that both human activities and climate change have positive effect on carbon sequestration rate. Human activities contribute to carbon sequestration increment of 1.7905 Pg C approximately under assumptions that the existing forest transformed from original natural grass land due to afforestation and reforestation. Climate change has promoted carbon sequestration rate due to increase in annual precipitation, but the increase in annual air temperature is harmful in enhancing carbon sequestration rate.
The effect of adjuvant radiotherapy on one- and two-stage prosthetic breast reconstruction and on autologous reconstruction: a multicenter Italian study among 18 Senonetwork Breast Centres
Authors: Lisa Andrea , Salgarello Marzia , Huscher Alessandra , Corsi Fabio , Piovani Daniele , Rubbino Federica , Andreoletti Stefania , Papa Giovanni , Klinger Francesco , Vinci Valeriano , Klinger Marco Attilio Ettore 
Published: June 2022

Abstract
Purpose: In modern breast cancer treatment we observed breast reconstruction growing role together with an extension in clinical indications for postmastectomy radiotherapy(PMRT). Optimal integration between reconstruction procedures and PMRT is still under debate. For this reason we performed a multicenter national study which aims to analyze the impact of PMRT on breast reconstruction.Methods: we conducted a retrospective case-control multicenter study on women undergoing breast reconstruction. Data were collected from 18 Italian Breast Centres, and stored in a cumulative database which included: autologous reconstruction, direct-to-implant (DTI), and tissue expander/immediate (TE/I). For all patients, we described complications and surgical endpoints to complications such as reconstruction failure, explant, change in type of reconstruction and reintervention. Results: From 2001 to April 2020, 3116 patients were evaluated. The risk for any complication was significantly increased in patients receiving PMRT (aOR, 1.73; 95% CI, 1.33‒2.24; p<0.001). PMRT was associated with a significant increase in the risk of capsular contracture in the DTI and TE/I groups (aOR, 2.24; 95% CI, 1.57‒3.20; p<0.001). Comparing type of procedures, the risk of failure (aOR, 1.82; 95% CI, 1.06‒3.12, p=0.030), explant (aOR, 5.49; 95% CI, 3.85‒7.83, p<0.001) and severe complications (aOR, 2.54; 95% CI, 1.88‒3.43, p<0.001) was significantly higher in the group undergoing DTI reconstruction as compared to TE/I reconstruction.Conclusion: Our study confirms that autologous reconstruction is the one least impacted by PMRT while DTI appears to be the most impacted by PMRT if compared with TE/I which shows a lower rate of explant and reconstruction failure. Trial registration number NCT04783818 and date of registration 1 March 2021 retrospectively registered
Spatiotemporal polymorphism analysis and influencing factors of diatom community in tropical freshwater （Wanquan River）
Authors: Wang Bo , CAI Jie , XU Yu-Zhao , QU Yi-hong , SONG Tao , CHEN Jian-hua , DENG Jian-qiang 
Published: June 2022

Abstract
The high temperature and rainy climate conditions make the diatom community in tropical freshwater ecosystem significantly different from other regions, which has specific laws and differences. Taking the diatom community structure of Wanquan River in Hainan Island as the research object, the regularity and difference factors were analyzed. In this study, 18 water samples were collected from 9 sampling sites in Wanquan River of Hainan Island in dry season (February) and wet season (August). High-throughput sequencing of eukaryotic plankton in water samples was carried out by using 18S rDNA meta-barcoding, and diatom classification information was extracted from each sampling point in different seasons. In this study, a total of 67 species, 38 genera, 7 families, 5 orders, 4 classes of diatoms were obtained. The dominant diatoms in Wanquan River were Mediophyceae and Bacillariophyceae. According to Alpha and Beta analysis, the total number and species of diatom in dry season were more, and the diatom community difference in each sampling site was also greater than those in wet season. There were five diatom species with significant differences between two seasons (P > 0.05),,Thalassiosira, Guinardia, Gomphonema, Mediophyceae and Discostella. In addition, the influence degree and trend of different environmental variables on diatom community composition were also analyzed. Three environmental variables, temperature, wind speed and water temperature, had the greatest impact on the diatom community. Dissolved oxygen, chromium ion and total alkalinity, also had a certain impact on the diatom community distribution. The diatom community structure and influencing factors in tropical fresh water differs greatly from that in other regions.
Insights into the quality of recombinant proteins produced by two different Bombyx mori expression systems
Authors: Kajiura Hiroyuki , Tatematsu Ken-ichiro , Nomura Tsuyoshi , Miyazawa Mitsuhiro , Usami Akihiro , Tamura Toshiki , Sezutsu Hideki , Fujiyama Kazuhito 
Published: June 2022

Abstract
The silkworm, Bombyx mori, is an attractive host for recombinant protein production due to its high expression efficiency, quality, and quantity. Two expression systems have been widely used for recombinant protein production in B. mori: baculovirus/silkworm expression system and transgenic silkworm expression system. Both expression systems enable high protein production, but the qualities of the resulting recombinant proteins have not been well evaluated. In this study, we expressed bovine interferon g (IFN-g) using the two systems and examined the quality of the resulting proteins in terms of N-glycosylation and protein cleavage. Both expression systems successfully produced IFN-g as an N-glycoprotein. Although the production in the baculovirus/silkworm expression system was much more efficient than that in the transgenic silkworm expression system, unexpected variants of IFN-g were also produced in the former system due to the different N-glycosylation and C-terminal truncations. These results indicate that while high protein production could be achieved in the baculovirus/silkworm expression system, unintentional protein modification might occur, and therefore protein expression in the transgenic silkworm expression system is preferable from the point-of-view of N-glycosylation of the recombinant protein and evasion of unexpected attack by a protease in B. mori.
Electronic origin of ultrafast laser-induced ferroelectricity in SrTiO3
Authors: Zhang Cui , Song Chenchen , Yang Qing , Liu Xinbao , Zhao Hui , Meng Sheng 
Published: June 2022

Abstract
Following an ultrafast laser excitation, paraelectric SrTiO3 can be driven non-thermally into a metastable ferroelectricity state. Despite achieving ultrafast control of ferroelectricity, the fundamental mechanism and dynamics of the photoinduced phase transition remain ambiguous. Here, the determinant formation mechanism of ultrafast ferroelectricity in SrTiO3 is traced by non-adiabatic dynamics simulations. That is, the selective excitation of multiple phonons, induced by photoexcited electrons through the strong correlation between electronic excitation and lattice distortion, result in the breaking of the crystal central symmetry and the onset of ferroelectricity on the ultrafast time scale. Laser illumination leads to a uniaxially stretched lattice deformation along the laser polarization direction, generated by nonequilibrium forces from optically excited electrons. The accompanying population transition between 3dz2 and 3d(x2-y2) orbitals excites multiple phonon branches, including the two high-energy longitudinal optical modes, so as to drive titanium ion away from the center of oxygen octahedron and generate a metastable ferroelectric phase. These findings provide new insights into the understanding and manipulation of laser-induced ferroelectric phase transition, and suggests new schemes for the optical control of electronic and structural quantum states in complex materials.
Integrated Metabolomics and Transcriptomics Analyses Reveal Anthocyanin and Carotenoid Biosynthesis Involved in Color Development in Willow Bark
Authors: Zhou Jie , Guo Jiahui , Chen Qingsheng , Wang Baosong , He Xudong , Zhuge Qiang , Wang Pu 
Published: June 2022

Abstract
Background The rich yellow-orange to vividly deep red bark of willow (Salix spp.) branches have great ornamental and economic value. The mechanism of willow branch color has not been clarified yet. ResultsTo study the mechanisms regulating color development, we performed metabolomics and transcriptomics analyses using purple, green, and red willow barks. Seven anthocyanins were isolated; pelargonidin, petunidin 3-O-rutinoside, and cyanin chloride were the most abundant in the red bark and pelargonin chloride in the purple bark. Among the barks, green bark had the highest level of malvidin, but its level was not significantly higher than in the red bark; the purple bark had the highest amount of canthaxanthin, a carotenoid pigment. The integrated biosynthetic pathway of flavonoid, carotenoid, and chlorophyll was constructed for willow barks. Among the three barks, the expression of the structural genes ANS, ANR, and BZ1, involved in anthocyanin synthesis, was highest in the red bark, likely causing anthocyanin accumulation. The highest expression of CrtZ, involved in the carotenoid pathway, was observed in the purple bark, likely causing canthaxanthin accumulation. The high expression of DVR, POR, and CRD1 may be associated with the green pigment synthesis in chlorophyll biosynthetic pathway. Our research findings will facilitate genetic breeding to improve the color and luster of willows. ConclusionsIn conclusion, the purple bark is co-regulated by anthocyanins and carotenoids. The red bark is characterized by anthocyanin accumulation and chlorophyll degradation. The green pigment is regulated by maintaining of chlorophyll synthesis. The key regulation genes BZ1, CrtZ could be candidate genes regulating anthocyanin and canthaxanthin accumulation in red and purple barks. Our research findings facilitate the genetic breeding and cultivation of colorful willows with improved color and luster.
Pulmonary Function Changes After Sublobar Resection In Patients With Peripheral Non-Subpleural Nodules
Authors: Feng Kun-Peng , Shen Zi-Qing , Xu Chun , Ding Cheng , Feng Yu , Zhu Xin-Yu , Pan Bin , Jia Xin-Yu , Zhao Jun , li Chang 
Published: June 2022

Abstract
Background: in the treatment of peripheral early-staged lung cancer and benign lesions, segmentectomy and wedge resection are both reliable treatment methods. It is debatable that how much pulmonary function will be lost after different sublobar resection in the treatment of early-staged deep-located peripheral NSCLC (non-small cell lung cancer). The purpose of this study was to explore postoperative pulmonary function changes of sublobar resection in enrolled patients with non-subpleural peripheral nodules. Methods: we collected clinical data of patients undergoing VATS (video-assisted thoracoscopic surgery) segmentectomy or wedge resection for single nodule. These nodules were confirmed as peripheral non-subpleural nodules by preoperative 3D imaging. Patients were divided into two groups according to the operation procedure. Demographic characteristics, pulmonary function, postoperative outcomes，and others were collected. All data was gathered at the First Affiliated Hospital of Soochow University. Outcomes after wedge resection were compared with those after segmentectomy resection. Results: A total of 88 patients were included in this study, including 46 patients with VATS wedge resection and 42 patients with VATS segmentectomy. No difference was detected when comparing FEV1 (Forced Expiratory Volume in One Second) loss between these two groups (17.6389±2.18267%, wedge resection vs. 19.401±5.42039%, segmentectomy, P=0.176). FVC (Forced Vital Capacity) loss (8.7922±2.36723%, wedge resection vs. 17.1267±2.26517%, segmentectomy, P<0.001) and MVV (Maximum Ventilatory Volume) loss (11.543±3.1547%, wedge resection vs. 20.639±7.8527%, segmentectomy, P<0.001) in segmentectomy group was significantly higher than those in wedge resection group. Discrepancies were investigated when comparing duration of surgery (70.43±22.615mins, wedge resection vs. 111.76±52.455mins, segmentectomy, P=0.0002), postoperative drainage (85.65±45.209mL, wedge resection vs. 287.62±672.115mL, segmentectomy, P=0.0123), and treatment hospitalization expenses [35148±889CNY, wedge resection vs. 52502(38276~57772) CNY, segmentectomy, P<0.0002]. No significant difference was found between air leak time (1.78±0.736days, wedge resection vs. 2.57±1.72days, segmentectomy, P=0.062) and hospitalization time (2.78±0.736days, wedge resection vs. 3.57±1.72days, segmentectomy, P=0.051). Conclusions: For patients with peripheral non-subpleural nodules, wedge resection did not cause more loss of lung function than segmental resection. Patients undergoing wedge resection had partial advantages over patients with segmental resection in terms of hospitalization cost, operation time and postoperative drainage, etc. Wedge resection, as a treatment for peripheral non-subpleural pulmonary nodules, had no worse outcome than segmentectomy.
Understanding the Rain-shelter and Water and Fertilizer Management in Reducing Root rot of Panax notoginseng
Authors: Zhang Yan , Zang Zhennan , Tang Zhenya , Yang Qiliang 
Published: June 2022

Abstract
Purpose Panax notoginseng (Burk) F. H. Chen, a valuable Chinese medicinal herb,is widely used in chinese medicine products. The frequent root-rot, however, caused a large reduction of Panax notoginseng yields, which greatly affected the development of Panax notoginseng planting. Panax notoginseng root-rot is related to its warm and humid growing environment.Methods Thus, five-year-old Panax ginseng was selected to investigate the effects of water and fertilizer conditions in rain-sheltered and non-rain-sheltered environments on the incidence of Panax ginseng root-rot disease in field trials. Two irrigation (W1: 50% of field water holding capacity, W2: 70% field water holding capacity), and four fertilizer amounts (F0:0 kg ha-1, F1:75 kg ha-1, F2:105 kg ha-1, and F3:135 kg ha-1) were chosed in rain-sheltered and non-rain-sheltered, respectively.Results The results showed that water and fertilizer coupling under rain-sheltered or non-rain-sheltered conditions had significant effects on Panax notoginseng root-rot disease as well as agronomic traits. Compared with non-rain shelter cultivation, the rain-shelter treatments led to higher net photosynthetic rate, and root volume of Panax notoginseng, and promoted the soil respiration and soil enzyme activity, as well as decreased the soil moisture. Additionally, The incidence of root-rot in 50% irrigation level non-rain shelter treatment (RWF) were 52.97% -88.46% higher than that in corresponding 50% rain shelter treatment (P<0.05), and 97.80% -137.30% in 70% irrigation level. F2 fertilizer led to the lowest root-rot in rain-shelter treated Panax notoginseng, and F1 in non-rain-shelter treated Panax notoginseng. Structural equation modeling showed soil moisture was the main factor affecting root-rot with contribution of 0.545.Conclusions Comprehensive analysis of detected parameter of plant and soil, the DW2F2 was recommended with higher root valume and lower root-rot than the other treatments.
Anatomical basis for the trigeminal autonomic cephalalgia-like response produced by formalin injection into the facial cheek in rats
Authors: Wang Ming R , Tseng Ching J , Kuo Jon S 
Published: June 2022

Abstract
Trigeminal autonomic cephalalgias (TACs) comprise cluster headaches and are characterized by unilateral neuralgiform headache attacks associated with autonomic responses and somatic responses. An animal model for evaluating the anatomical basis of the TAC-like response is not currently available. Twenty-five rats weighing 550-650 g were anaesthetized with urethane. The TAC-like response was produced either by subcutaneous injection of formalin into the unilateral facial cheek or by electrical stimulation of the unilateral intact trigeminal nerve. The induced TAC-like response, which included ipsilateral common carotid arterial flow (iCCAF) and other autonomic responses, was studied in intact nerves or after cutting either the ipsilateral trigeminal nerve or the ipsilateral facial nerve. The formalin injections produced concentration-dependent iCCAF increases accompanied by ipsilateral autonomic responses of rhinitis-like nasal congestion, nasal mucus, meiosis, lacrimation, red eye, and eyelid oedema. The formalin (5% or 10%, 0.5 cc)-induced responses were nearly abolished by sectioning of either the facial or trigeminal nerve. The electrical stimulation (15 V, 60 Hz, and 0.4 ms) of the intact trigeminal nerve or its ophthalmo-maxillary branch also produced stimulation strength-dependent iCCAF increases as well as autonomic responses; however, the electrical stimulation-induced iCCAF increases and other autonomic responses could still be induced by electrical stimulation of the central but not the peripheral end of the ophthalmo-maxillary branch (n = 8) or the trigeminal nerve (n = 2). Thus, an animal model for inducing the TAC-like response by subcutaneous formalin injection into the rat facial cheek was established. The TAC-like response could be sequentially mediated via the afferent trigeminal nerve, trigeminal nucleus, dorsal facial nucleus, and efferent facial nerve.
KBTBD11, encoding a novel PPARγ target gene, is involved in NFATc1 proteolysis by interacting with HSC70 and HSP60
Authors: Watanabe Kazuhisa , Matsumoto Ayumi , Tsuda Hidetoshi , Iwamoto Sadahiko 
Published: June 2022

Abstract
We previously revealed that Kbtbd11 mRNA levels increase during 3T3-L1 differentiation and Kbtbd11 knockdown suppresses whereas its overexpression promotes adipogenesis. However, how Kbtbd11 mRNA is regulated during adipocyte differentiation and how the KBTBD11 protein functions in adipocytes remain elusive. This study aimed to examine the transcriptional regulatory mechanism of Kbtbd11 during adipocyte differentiation, KBTBD11-interacting protein functions, and elucidate the role of KBTBD11 in adipocytes. First, we identified the PPRE consensus sequences in the Kbtbd11 exon 1- and intron 1-containing region and demonstrated that PPARγ acts on this region to regulate Kbtbd11 expression. Next, we purified the KBTBD11 protein complex from 3T3-L1 adipocytes and identified heat shock proteins HSC70 and HSP60 as novel KBTBD11-interacting proteins. HSC70 and HSP60 inhibition increased KBTBD11 protein levels that promoted NFATc1 ubiquitination. These data suggested that HSC70 and HSP60 are involved in KBTBD11 stabilization and are responsible for NFATc1 regulation on the protein level. In summary, this study describes first the protein regulatory mechanism of NFATc1 through the HSC70/HSP60-KBTBD11 interaction that could provide a potential new target for the differentiation and proliferation of various cells, including adipocytes and tumors.