bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive analysis of miRNA sequencing profiles identifies novel deregulated and prognostic biomarkers in hepatocellular carcinoma
Authors: Zhang Hui , Ni Senmiao , Li Changxian , Zhou Haoming , Bai Jianling , Pan Xiongxiong , Wu Zhengshan 
Published: April 2020

Abstract
Background: Liver cancer is the fourth most common cause of cancer-related death and rank sixth in terms of incident cases. We aim to identify a set of miRNAs and a miRNA-based signature related to tumorigenesis and prognosis in patients with hepatocellular carcinoma (HCC). Methods: We analyzed the miRNA sequencing profiles of 373 HCC patients downloaded from The Cancer Genome Atlas LIHC program. The isoform quantification profiles were transformed into 5p and 3p mature miRNA names. Differentially expressed (DE) miRNAs between tumor and adjacent normal tissues were identified by Wald test based on the negative binomial distribution. Prognostic miRNAs associated with overall survival were confirmed by multivariate Cox proportional hazards models. The miRNA-based signatures were obtained from the linear predictors of cox regression, and the prognostic performance was compared by Harrel’s C-index and revealed by the restricted mean survival (RMS) curve. Results: The selected twelve DE miRNAs showed a good performance to classify tumor tissues from normal tissues. Meanwhile, a miRNA-based prognostic signature of eight mature miRNAs was constructed, which significantly stratified patients into high- vs low-risk groups in terms of overall survival (hazard ratio, 4.11; 95% CI, 2.71-6.24; P<0.001). When integrated with clinical information, the composite miRNA-clinical signature showed improved prognostic accuracy relative to the eight-miRNA signature alone. As we set the follow-up time at 5 years, the estimated RMST difference between low- and high-risk group stratified by miRNA index was 1.39 (95% CI: 0.95-1.83) months, which is lesser than the difference between miRNA-clinical risk groups (1.63, 95%CI: 1.20-2.06). Functional enrichment analysis indicated that the target mRNAs of selected miRNAs were mainly enriched in cancer-related pathways and vital cell biological processes. Conclusions: The proposed DE miRNAs and miRNA-clinical signature are promising biomarkers for discrimination and predicting overall survival respectively in HCC patients. These biomarkers may have significant relevance for development of new drug research and targeting therapies for HCC patients.
INPP5F translocates into cytoplasm and interacts with ASPH to promote tumor growth in hepatocellular carcinoma
Authors: Zhou Qianlei , Lin Jianhong , Liu Qinghua , Yan Yongcong , Yu Wei , Chen Ruibin , He Chuanchao , Wang Jie , Zhang Jianlong , Mao Kai , Zhou Zhenyu , Xiao Zhiyu 
Published: April 2020

Abstract
Background Increasing evidence has suggested inositol polyphosphate 5-phosphatase family contributes to tumorigenesis and tumor progression. However, the role of INPP5F in hepatocellular carcinoma (HCC) and its underlying mechanisms is unclear. Methods The expression of INPP5F in HCC was analyzed in public databases and our clinical specimens. The biological functions of INPP5F were investigated in vitro and vivo. The molecular mechanism of INPP5F in regulating tumor growth were studied by transcriptome-sequencing analysis, mass spectrometry analysis, immunoprecipitation assay and immunofluorescence assay. Results High expression of INPP5F was found in HCC tissues and was associated with poor prognosis in HCC patients. Overexpression of INPP5F promoted HCC cell proliferation, and vice versa. Knockdown of INPP5F suppressed tumor growth in vivo. Results from transcriptome-sequencing analysis showed INPP5F not only regulated a series of cell cycle related genes expression (c-MYC and cyclin E1), but also promoted many aerobic glycolysis related genes expression. Further study confirmed that INPP5F could enhance lactate production and glucose consumption in HCC cells. Mechanistically, INPP5F interacted with ASPH through which INPP5F activated Notch signaling and subsequently promoted the expression of c-MYC and cyclin E1. Interestingly, INPP5F was commonly nuclear-located in cells of adjacent tissues, while cytoplasmic-located was more common in HCC cells. LMB (nuclear export inhibitor) treatment restricted INPP5F in nucleus and was associated with inhibition of Notch signaling and cell proliferation. Furthermore, sequence of nuclear localization signals (NLSs) and nuclear export signals (NESs) in INPP5F aminoacidic sequence were identified. Alteration of the NLSs or NESs influenced the localization of INPP5F and the expression of its downstream molecules. Conclusion These findings indicate that INPP5F functions as an oncogene in HCC via a translocation mechanism and activating ASPH-mediated Notch signaling pathway. INPP5F may serve as a potential therapeutic target for HCC patients.
Predictive ability of motion sickness susceptibility questionnaire for seasickness individual difference in Chinese military personnel
Authors: Pan Leilei , Qi Ruirui , Xiao Shuifeng , Mao Yuqi , Su Yang , Xu Rong , Gui Li , Wang Junqin , Cai Yiling 
Published: April 2020

Abstract
Background Motion sickness susceptibility questionnaire (MSSQ) has been widely used for assessing individual differences in motion sickness. The present study tried to investigate its efficacy for predicting seasickness susceptible (SUS) and insusceptible (INSUS) subjects among Chinese military personnel. Methods Two cohorts of young male army volunteers were exposed to real ship motion (n=125) and laboratory vertical oscillation motion (n=77). Predictive ability of the MSSQ and its vomiting (MSV) and nausea (MSN) subscales (including child and adult subitems) was examined via analyzing area under the curve (AUC) of receiver operating characteristic (ROC) with seasickness susceptibility defined by Graybiel score or nausea latency. Results Higher Graybiel scores and lower percentage of INSUS subjects was observed in the ship motion trial than the vertical oscillation trial. MSSQ and its subscales positively correlated with the Graybiel score in both trials. The MSN child showed no predictive ability for the INSUS subjects, leading to lower AUC of the MSN than the MSSQ and the MSV for INSUS prediction in ship motion (0.587 vs. 0.647 and 0.644, P < 0.01) and vertical oscillation trial (0.696 vs. 0.761 and 0.788, P < 0.01 and 0.05) when seasickness susceptibility was defined by Graybiel score. Lower AUC in the MSN than the MSSQ (0.691 vs. 0.758, P < 0.05 and 0.01) was observed due to invalidity of MSN child when susceptibility was defined by nausea latency in the vertical oscillation trial. The prediction ability of SUS did not differ among the MSSQ and its subscales in both trials. Relative to the ship motion trial, the vertical oscillation trial showed higher predictive efficacy of the MSSQ for the Graybiel score-defined SUS subjects (0.840 vs. 0.686, P < 0.05) as a result of higher AUC in both the MSV (0.840 vs. 0.690, P < 0.05) and the MSN (0.806 vs. 0.651, P < 0.01). Conclusions The MSSQ was effective for predicting seasickness susceptibility in young male Chinese military members, but the efficacy varies with motion intensity and complexity and the vomiting scale should be recommended for application.
Perinatal Environment Shapes Microbiota Colonization And Infant Growth: Impact On Host Response And Intestinal Function
Authors: Selma-Royo Marta , Calatayud Marta , García-Mantrana Izaskun , Parra-Llorca Anna , Escuriet Ramón , Martínez-Costa Cecilia , Collado Maria Carmen 
Published: April 2020

Abstract
Background Early microbial colonization triggers processes that result in intestinal maturation and immune priming. Perinatal factors, especially those associated with birth, including both mode and place of delivery are critical to shaping the infant gut microbiota with potential health consequences. Methods Gut microbiota profile of 180 healthy infants (n=23 born at home and n=157 born in hospital, 41.7% via caesarean section [CS]) was analyzed by 16S rRNA gene sequencing at birth, seven days and one month of life. Breastfeeding habits, infant clinical data, including length, weight and antibiotic exposure, were collected up to 18 months of life. Long-term personalized in vitro models of the intestinal epithelium and innate immune system were used to assess the link between gut microbiota composition, intestinal function and immune response. Results Microbiota profiles were shaped by the place and mode of delivery, and they had a distinct biological impact on the immune response and intestinal function in epithelial/immune cell models. Bacteroidetes and Bifidobacterium genus were decreased in C-section infants, who showed higher z-scores BMI and W/L during the first 18 months of life. Intestinal simulated epithelium had a stronger epithelial barrier function and intestinal maturation, alongside a higher immunological response (TLR4 route activation and pro-inflammatory cytokine release), when exposed to home-birth fecal supernatants, compared with CS. Distinct host response could be associated with different microbiota profiles. Conclusions Mode and place of birth influence the neonatal gut microbiota, likely shaping its interplay with the host through the maturation of the intestinal epithelium, regulation of the intestinal epithelial barrier and control of the innate immune system during early life, which can affect the phenotypic responses linked to metabolic processes in infants.
MiR-214-3p Promotes Proliferation and Inhibits Estradiol Synthesis In Porcine Granulosa Cells
Authors: Shi Shengjie , Zhou Xiaoge , Li Jingjing , Zhang Lutong , Hu Yamei , Li Yankun , Yang Gongshe , Chu Guiyan 
Published: April 2020

Abstract
Background: Granulosa cells proliferation and estradiol synthesis significantly affect follicular development. The miR-214-3p expression in the ovarian tissues of high-yielding sows is higher than that in low-yielding sows, indicating that miR-214-3p may be involved in sow fertility. However, the functions and mechanisms of miR-214-3p on granulosa cells are unclear. In this study, miR-214-3p was transfected into porcine ovarian granulosa cells to investigate its functions in terms of proliferation and estradiol synthesis via flow cytometry, CCK-8 assay, EdU staining, ElisA, Real-Time PCR, and Western blot analyses. We also identified the targets of miR-214-3p via Luciferase Reporter Assay. Results: Our findings revealed that miR-214-3p promotes proliferation and inhibits estradiol synthesis in porcine granulosa cells. We also found that miR-214-3p up-regulates the expression of cell cycle genes including Cell cycle protein B (Cyclin B), Cell cycle protein D (Cyclin D), Cell cycle protein E (Cyclin E), and Cyclin-dependent kinase 4 (CDK4) at the transcription and translation levels, while down-regulating the mRNA and protein levels of cytochrome P450 family 11 subfamily A member 1 (CYP11A1), cytochrome P450 family 19 subfamily A member 1 (CYP19A1), and steroidogenic acute regulatory protein (StAR) (i.e., the key enzymes in estradiol synthesis). On-line prediction, bioinformatics analysis, a luciferase reporter assay, RT-qPCR, and Western blot results showed that the target genes of miR-214-3p in proliferation and estradiol synthesis are Mfn2 and NR5A1, respectively. Conclusions: Our findings suggest that miR-214-3p plays an important role in the functional regulation of porcine granulosa cells and therefore may be a target gene for regulating follicular development.
Immunohistochemical Evaluation of Angiogenesis in Warts
Authors: Bossart Simon , Hartmeier Lisa , Jafari S. Morteza Seyed , Beltraminelli Helmut , Hunger Robert E. 
Published: April 2020

Abstract
Background

Angiogenesis is a key event in tumour growth. An infection with human papillomavirus (HPV) typically leads to benign tumours, such as warts (papillomas) on the skin and mucous membranes. The role of angiogenesis in skin warts is yet to be established. The present work evaluates the hypothesis that the development of skin warts is associated with alterations in the dermal vascularisation (dermal microvessel density/mm 2 , MVD).

Methods

Seventeen cases of cutaneous warts and eight cases of normal skin were studied. Dermal vessels were immunostained for CD31, CD34 and CD105. The ten areas with the highest number of microvessels were counted.

Results

The number of CD31 + , CD34 + and CD105 + vessels was significantly higher in cutaneous warts compared to that in normal skin (mean±SD: 45.71±22.63 vs 21.27±5.83, P=0.0062; 59.75±24.93 vs 17.13±5.67, P<0.001; and 29.74±7.09 vs 6.58±1.89, P<0.001 respectively).

Conclusion

Higher MVD values in skin warts suggest a possible causal correlation between angiogenesis and development of papillomas in HPV infected skin. Our results shows the morphological histopathological explanation (high number of vessels) for the punk-shaped vessels seen in the dermatoscopical examination.
The current status of Pathology education: A survey among Chinese medical students
Authors: Xu Chun , Li Yiping , Author) Pingsheng Chen(Former Corresponding , Pan Min , Author) Xiaodong Bu(New Corresponding 
Published: April 2020

Abstract
BackgroundPathology education transfers knowledge of Pathology and guides students to become pathologists. Recently, Ministry of Education of the People’s Republic of China strongly advocated establishing the system of ‘Golden Online and Offline Courses’, which indicates online courses will play important roles in college education. Furthermore, the number of pathologists has fallen far behind the clinical needs. To solve this health issue and implement the policy from Ministry of Education, improving current Pathology education is necessary, and first is to know students’ opinions on the present courses and their professional choices.MethodsQuestionnaires covering the quality of traditional courses, the attitude towards the online courses, and the suggestions for optimizing courses were designed and applied via web link. Whether students want to become pathologists and the underlying reasons are also incorporated into this survey. Medical students from certain colleges in Nanjing were participants. The collected data were assessed by corresponding percentages.ResultsOf the 215 valid responses, half of undergraduate students show their interests in Pathology courses, and among them, 50% express that they may become pathologists. However, the percentage is only 18.03% in the group without interest. For optimizing curriculums, the top two suggestions are introducing more clinical cases (undergraduate students, 74.42%; graduate students, 79.09%) and making the classes lively and interesting (undergraduate students, 67.44%; graduate students, 62.79%). Around 80% of students consider online courses as good supplementary materials to traditional courses, and half prefer online-offline mixed learning model. Salary, interest, and employment status are main factors influencing students’ professional choices.ConclusionsStudents are generally satisfied with the traditional Pathology courses, and the online courses are good supplementary materials in their opinions. Clinical cases are suggested to be introduced in classes. It is more likely for the students who have interests in Pathology to become pathologists. The main obstacles students will not become pathologists are boring work and unsatisfactory salary.
Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: Evidence from the frequency of endosymbiotic DNA transfer
Authors: Li Xi-Xi , Fang Cheng , Zhao Jun-Peng , Zhou Xiao-Yu , Ni Zhihua , Niu Deng-Ke 
Published: April 2020

Abstract
Background: Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that are resistant to extreme desiccation and radiation undergo a very high level of HGT, whereas a similar report of another desiccation-resistant invertebrate, the tardigrade, remains controversial. Overall, the DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open a gateway to the nuclear genome for exogenous DNA integration and thus to facilitate the HGT process, thereby enhancing the rate of endosymbiotic DNA transfer (EDT).
Results: We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in five eukaryotes that are highly resistant to desiccation: the bdelloid rotifers Adineta vaga and Adineta ricciae , the tardigrade Ramazzottius varieornatus , and the resurrection plants Dorcoceras hygrometricum and Selaginella tamariscina . Excessive NUMTs or NUPTs were not detected. Furthermore, we compared 24 groups of desiccation-tolerant organisms with their relatively less desiccation-tolerant relatives but did not find a significant difference in NUMT/NUPT contents.
Conclusions: Desiccation may induce DSBs, but it is unlikely to dramatically increase the frequency of exogenous sequence integration in most eukaryotes. The capture of exogenous DNA sequences is possible only when DSBs are repaired through a subtype of non-homologous end joining, named alternative end joining (alt-EJ). Due to the deleterious effects of the resulting insertion mutations, alt-EJ is less frequently initiated than other mechanisms.
High production of triterpenoids in Yarrowia lipolytica through manipulation of lipid components
Authors: Zhang Jin Lai , Bai Qiu Yan , Peng Yang Zi , Fan Jie , Jin Cong Cong , Cao Ying Xiu , Yuan Ying Jin 
Published: April 2020

Abstract
BackgroundLupeol exhibits novel physiological and pharmacological activities, such as anti-cancer and immunity enhancement. However, cytotoxicity is still a challenge for triterpenoids overproduction in microbial cell factories. As lipophilic and relatively small-molecular compounds, triterpenes are generally secreted to the extracellular space. The effect of increasing triterpenes efflux on the synthesis capacity remains unknown.ResultsIn this study, we developed a strategy to enhance the triterpenes efflux through manipulation of lipid components in Y. lipolytica by overexpressing the enzyme of Δ9-fatty acid desaturase (OLE1) and disturbing the phosphatidic acid phosphatase (PAH1) and diacylglycerol kinase (DGK1). As a result, we obtained a high-yield lupeol strain with the highest lupeol production of 411.72 mg/L in shake flasks reported to date, reaching a 33.2-fold improvement over the initial strain. The lipid manipulation led to a two-fold increase of unsaturated fatty acids (UFAs) content, up to 61%~73%, and an exceptionally elongated cell morphology, which might be caused by enhanced membrane phospholipids biosynthesis flux. Both of the phenotypes accelerated the export of toxic products to the extracellular space and ultimately stimulated the capacity of triterpenoids synthesis, which were proved by 5.11-fold higher ratio of extra-/intra-cellular lupeol concentrations, 2.7-fold higher biomass accumulation and 2.60-fold higher lupeol productivity per unit OD in modified strains. This strategy was also highly efficient for biosynthesis of other triterpenes and sesquiterpenes, including α-, β-arymin, longifolene, longipinene and longicyclene.ConclusionsTo conclude, we successfully created a high-yield lupeol strain via lipid manipulation. And we demonstrated that the enhancement of lupeol efflux and synthesis capacity was induced by the increased unsaturated fatty acids content and elongated cell morphology. Our study provides a novel strategy to promote the biosynthesis of valuable but toxic products in microbial cell factories.
Quasi-free limit in the deuteron-deuteron three-body break-up process
Authors: ramazani sharifabadi reza , Amir-Ahmadi Hamid Reza , Bayat M. T. , Ciepał Izabela , Eslami-Kalantari Mohammad , Kalantar Nayestanaki Nasser , Kistryn Stanisław , Kozela Adam , Mahjour-Shafiei Masoud , Mardanpour Hossein , Messchendorp Johan , Mohammadi-Dadkan Maisam , Ramazani-Moghaddam-Aran Ahmad , Stephan Elżbieta , Tavakoli-Zaniani H. 
Published: April 2020

Detailed measurements of vector and tensor analyzing powers of the
^{2}{\rm H}(\vec d,dp){n}
break-up process are presented. The data were obtained using a polarized
deuteron-beam with an energy of 65 MeV/nucleon impinging on a
liquid-deuterium target. The experiment was conducted at the AGOR
facility at KVI using the BINA 4\piπ-detection
system. The focus of this contribution is to analyze data of the
dddd
scattering process in the regime at which the neutron acts as a
spectator, which we refer to as the quasi-free (QF) limit. To achieve
this, events for which the final-state deuteron and proton are coplanar
have been analyzed and the data have been sorted for various
reconstructed momenta of the missing neutron. In the limit of vanishing
neutron momentum and at small deuteron-proton momentum transfer, the
data match very well with measured and predicted spin observables of the
elastic deuteron-proton scattering process. The agreement deteriorates
rapidly with increasing neutron momentum and deuteron-proton momentum
transfer. The results of coplanar configurations in four-body phase
space are compared with the results of recent available theoretical
calculations based on the Single-Scattering Approximation.
Spatial downscaling of radar-derived rainfall field by two-dimensional wavelet transform
Authors: Nourani Vahid , Farshbaf Armin , Adarsh S. 
Published: April 2020

Abstract
Downscaling of rainfall fields, either as images or products of global circulation models, have been the motive of many hydrologists and hydro-meteorologists. The main concern in downscaling is to transform high-resolution properties of the rainfall field to lower resolution without introducing erroneous information. In this paper, rainfall fields obtained from Next Generation Weather Surveillance Radar (NEXRAD) Level III were examined in the wavelet domain which revealed sparsity for wavelet coefficients. The proposed methodology in this work employs a concept named Standardized Rainfall Fluctuation (SRF) to overcome the sparsity of rainfall fields in wavelet domain which also exhibited scaling behaviors in a range of scales. SRFs utilizes such scaling behaviors where upscaled versions of the rainfall fields are downscaled to their actual size, using a two-dimensional discrete wavelet transform, to examine the reproduction of the rainfall fields. Furthermore, model modifications were employed to enhance the accuracy. These modifications include removing the negative values while conserving the mean and applying a non-overlapping kernel to restore high-gradient clusters of rainfall fields. The calculated correlation coefficient, statistical moments, determination coefficient and spatial pattern display a good agreement between the outputs of the downscaling method and the observed rainfall fields.