bluuebunny/crossref_metadata_2025_split huggingface dataset:
PAX8 expression in high-grade serous ovarian cancer positively regulates attachment to ECM via Integrin β3
Authors: Soriano Amata Amy , de Cristofaro Tiziana , Di Palma Tina , Dotolo Serena , Gokulnath Priyanka , Izzo Antonella , Calì Gaetano , Facchiano Angelo , Zannini Mariastella 
Published: November 2019

Abstract
Background
Ovarian cancer is the third most common cause of death among gynecologic malignancies worldwide. Understanding the biology and molecular pathogenesis of ovarian epithelial tumors is key to developing improved prognostic indicators and effective therapies. We aimed to determine the effects of PAX8 expression on the migrative, adhesive and survival capabilities of high-grade serous carcinoma cells.

Methods
PAX8 depleted Fallopian tube secretory cells and ovarian cancer cells were generated using short interfering siRNA. Anoikis resistance, cell migration and adhesion properties of PAX8 silenced cells were analyzed by means of specific assays. Chromatin immunoprecipitation (ChIP) was carried out using a PAX8 polyclonal antibody to demonstrate that PAX8 is able to bind to the 5′-flanking region of the ITGB3 gene positively regulating its expression.

Results
Here, we report that RNAi silencing of PAX8 sensitizes non-adherent cancer cells to anoikis and affects their tumorigenic properties. We show that PAX8 plays a critical role in migration and adhesion of both Fallopian tube secretory epithelial cells and ovarian cancer cells. Inhibition of PAX8 gene expression reduces the ability of ovarian cancer cells to migrate and adhere to the ECM and specifically to fibronectin and/or collagen substrates. Moreover, loss of PAX8 strongly reduces ITGB3 expression and consequently the correct expression of the αvβ3 heterodimer on the plasma membrane.

Conclusions
Our results demonstrate that PAX8 modulates the interaction of tumor cells with the extracellular matrix (ECM). Notably, we also highlight a novel pathway downstream this transcription factor. Overall, PAX8 could be a potential therapeutic target for high-grade serous carcinoma.
Behavioral mapping of children’s physical activities and social behaviors in an indoor preschool facility: methodological challenges in revealing the influence of space in play
Authors: Onojeghuo Ajoke R. , Nykiforuk Candace I. J. , Belon Ana Paula , Hewes Jane 
Published: November 2019

Abstract
Background
GIS (Geographic Information Systems) based behavior maps are useful for visualizing and analyzing how children utilize their play spaces. However, a GIS needs accurate locational information to ensure that observations are correctly represented on the layout maps of play spaces. The most commonly used tools for observing and coding free play among children in indoor play spaces require that locational data be collected alongside other play variables. There is a need for a practical, cost-effective approach for extending most tools for analyzing free play by adding geospatial locational information to children’s behavior data collected in indoor play environments.

Results
We provide a non-intrusive approach to adding locational information to behavior data acquired from video recordings of preschool children in their indoor play spaces. The gridding technique showed to be a cost-effective method of gathering locational information about children from video recordings of their indoor physical activities and social behaviors. Visualizing the proportions of categories and observed intervals was done using bubble pie charts which allowed for the merging of multiple categorical information on one map. The addition of locational information to other play activity and social behavior data presented the opportunity to assess what types of equipment or play areas may encourage different physical activities and social behaviors among preschool children.

Conclusions
Gridding is an effective method for providing locational data when analyzing physical activities and social behaviors of preschool children in indoor spaces. It is also reproducible for most GIS behavior mapping focusing on indoor environments. This bypasses the need to have positioning devices attached to children during observations, which can raise ethical considerations regarding children’s privacy and methodological implications with children playing less naturally. It also supports visualizations on behavior maps making them easier to interpret.
Predicting drug−disease associations via sigmoid kernel-based convolutional neural networks
Authors: Jiang Han-Jing , You Zhu-Hong , Huang Yu-An 
Published: November 2019

AbstractBackgroundIn the process of drug development, computational drug repositioning is effective and resource-saving with regards to its important functions on identifying new drug–disease associations. Recent years have witnessed a great progression in the field of data mining with the advent of deep learning. An increasing number of deep learning-based techniques have been proposed to develop computational tools in bioinformatics.MethodsAlong this promising direction, we here propose a drug repositioning computational method combining the techniques of Sigmoid Kernel and Convolutional Neural Network (SKCNN) which is able to learn new features effectively representing drug–disease associations via its hidden layers. Specifically, we first construct similarity metric of drugs using drug sigmoid similarity and drug structural similarity, and that of disease using disease sigmoid similarity and disease semantic similarity. Based on the combined similarities of drugs and diseases, we then use SKCNN to learn hidden representations for each drug-disease pair whose labels are finally predicted by a classifier based on random forest.ResultsA series of experiments were implemented for performance evaluation and their results show that the proposed SKCNN improves the prediction accuracy compared with other state-of-the-art approaches. Case studies of two selected disease are also conducted through which we prove the superior performance of our method in terms of the actual discovery of potential drug indications.ConclusionThe aim of this study was to establish an effective predictive model for finding new drug–disease associations. These experimental results show that SKCNN can effectively predict the association between drugs and diseases.
Elamipretide (SS-31) improves mitochondrial dysfunction, synaptic and memory impairment induced by lipopolysaccharide in mice
Authors: Zhao Weixing , Xu Zhipeng , Cao Jiangbei , Fu Qiang , Wu Yishuang , Zhang Xiaoying , Long Yue , Zhang Xuan , Yang Yitian , Li Yunfeng , Mi Weidong 
Published: November 2019

Abstract
Background
It is widely accepted that mitochondria have a direct impact on neuronal function and survival. Oxidative stress caused by mitochondrial abnormalities play an important role in the pathophysiology of lipopolysaccharide (LPS)-induced memory impairment. Elamipretide (SS-31) is a novel mitochondrion-targeted antioxidant. However, the impact of elamipretide on the cognitive sequelae of inflammatory and oxidative stress is unknown.

Methods
We utilized MWM and contextual fear conditioning test to assess hippocampus-related learning and memory performance. Molecular biology techniques and ELISA were used to examine mitochondrial function, oxidative stress, and the inflammatory response. TUNEL and Golgi-staining was used to detect neural cell apoptosis and the density of dendritic spines in the mouse hippocampus.

Results
Mice treated with LPS exhibited mitochondrial dysfunction, oxidative stress, an inflammatory response, neural cell apoptosis, and loss of dendritic spines in the hippocampus, leading to impaired hippocampus-related learning and memory performance in the MWM and contextual fear conditioning test. Treatment with elamipretide significantly ameliorated LPS-induced learning and memory impairment during behavioral tests. Notably, elamipretide not only provided protective effects against mitochondrial dysfunction and oxidative stress but also facilitated the regulation of brain-derived neurotrophic factor (BDNF) signaling, including the reversal of important synaptic-signaling proteins and increased synaptic structural complexity.

Conclusion
These findings indicate that LPS-induced memory impairment can be attenuated by the mitochondrion-targeted antioxidant elamipretide. Consequently, elamipretide may have a therapeutic potential in preventing damage from the oxidative stress and neuroinflammation that contribute to perioperative neurocognitive disorders (PND), which makes mitochondria a potential target for treatment strategies for PND.
“A herder’s duty is to think”: landscape partitioning and folk habitats of Mongolian herders in a mountain forest steppe (Khuvsugul-Murun region)
Authors: Gantuya B. , Avar Á. , Babai D. , Molnár Á. , Molnár Zs 
Published: November 2019

AbstractBackgroundTraditional habitat knowledge, like the classification of folk habitats and how people partition their landscape into habitats, is an emerging but still understudied part of traditional ecological knowledge. Our objectives were to reconstruct the folk habitats and the partitioning of the landscape into these folk habitats by Mongolian herders in Northern Mongolia and to compare it with other Northern Hemisphere boreal-temperate classifications.MethodsThe study area is located in Seruun Gilad (Khuvsugul province) and belongs to the mountain forest steppe of the Khangai region (dominated by meadow steppes and larch forests). Most herder families use the area for summer pasturing. Data collection was based on indoor and outdoor, structured and semi-structured interviews and interviews during landscape walks and participatory fieldwork. We interviewed 20 people using 76+ photos of plant species and 25+ photos of habitats and asked them to name and describe the habitats and describe the habitat preferences of the species.ResultsMongolian herders distinguished at least 88 folk habitat categories and knew well the habitat preferences of the 76 plant species. They argued that a herder has to be observant of nature. The habitat classification was moderately lexicalized, with many descriptive expressions. Most habitats (77%) belonged to the meso-scale, while macro-scale habitats (liketaiga,Gobi) and micro-scale habitats (likemarmot burrow,top of the tussock) were few. Habitat names did not reflect directly the usefulness of the habitat. Classification was multidimensional; key dimensions were geomorphological and edaphic. There were some species (e.g.,botyuul,hyag,shireg) and species groups (hot plants,leafy plants) that were often used to describe habitat types.ConclusionsLandscape partitionings in the Northern Hemisphere differed considerably in the importance of various dimensions used, with edaphic, geomorphological, hydrological, and dominant species-based dimensions having higher importance, while land use, successional, and zoological dimensions having lower importance. We argue that conducting research on folk habitats will contribute to a deeper understanding of how nature is perceived by locals and to a more efficient management of the Mongolian pastures.
Preoperative irrigation and vacuum sealing drainage with antibiotic-containing drainage fluid of foot and ankle wounds improves outcome of reconstructive skin flap surgery
Authors: Gao Xu , Yin Hailei , Sun Jixia 
Published: November 2019

Abstract
Objectives
By observing the infection and soft tissue defect on the wound surface of the foot and ankle, this paper attempts to explore the effect of preoperative irrigation and vacuum sealing drainage with antibiotic-containing drainage fluid (abPI-VSD) on the bacterial quantity and the local inflammatory response at the flap, and further to provide a basis for applying this technique before a reconstructive skin flap surgery of foot and ankle wounds.

Methods
Seventy-five patients were randomly divided into two groups, and all surgeries were done by one physician. The flap reconstructions were done to 31 cases with the abPI-VSD being used (group A); the flap reconstructions were done to the rest 44 cases after wound cleaning using antibiotic irrigation solution without the use of the abPI-VSD (group B). Quantitative bacteriology was made to group A before and after the use of abPI-VSD; quantitative bacteriology was made to group B before and after wound cleaning. Then, the reconstructive skin flap surgery was done. After the surgeries, the time of local inflammatory response at the flap in both groups were recorded. The measured bacterial quantity was evaluated in logarithm and by t test.

Results
The bacterial quantity was 3.2 ± 1.9 × 107 cfu/g in group A before the use of abPI-VSD and 2.3 ± 2.0 × 107 in group B (P > 0.05) before debridement. The bacterial quantity was 1.2 ± 2.0 × 104 cfu/g in group A after abPI-VSD and was 2.9 ± 4.0 × 106 in group B after wound cleaning (P < 0.05). The time of postoperative inflammatory response in the flap was 8 ± 2.5 days in group A and 13 ± 3.4 days in group B (P < 0.05).

Conclusions
abPI-VSD can distinctly reduce the bacterial quantity on the surface of the wound, provide a good condition of tissue bed for the flap reconstruction, and effectively control the local inflammatory response at the flap and hence improve the survival quality of the flap.
Long noncoding RNA 00976 promotes pancreatic cancer progression through OTUD7B by sponging miR-137 involving EGFR/MAPK pathway
Authors: Lei Shan , He Zhiwei , Chen Tengxiang , Guo Xingjun , Zeng Zhirui , Shen Yiyi , Jiang Jianxin 
Published: November 2019

Abstract
Background
Accumulation evidence indicates the vital role of long non-coding RNAs (lncRNAs) in tumorigenesis and the progression of malignant tumors, including pancreatic cancer (PC). However, the role and the molecular mechanism of long non-coding RNA 00976 is unclear in pancreatic cancer.

Methods
In situ hybridization (ISH) and qRT-PCR was performed to investigate the association between linc00976 expression and the clinicopathological characteristics and prognosis of patients with PC. Subsequently, linc00976 over-expression vector and shRNAs were transfected into PC cells to up-regulate or down-regulate linc00976 expression. Loss- and gain-of function assays were performed to investigate the role of linc00976 in proliferation and metastasis in vitro and vivo. ITRAQ, bioinformatic analysis and rescue assay were used to illustrate the ceRNA mechanism network of linc00976/miR-137/OTUD7B and its downstream EGFR/MAPK signaling pathway.

Results
linc00976 expression was overexpressed in PC tissues and cell lines and was positively associated with poorer survival in patients with PC. Function studies revealed that linc00976 knockdown significantly suppressed cell proliferation, migration and invasion in vivo and in vitro, whereas its overexpression reversed these effects. Based on Itraq results and online database prediction, Ovarian tumor proteases OTUD7B was found as a downstream gene of linc00976, which deubiquitinated EGFR mediates MAPK signaling activation. Furthermore, Bioinformatics analysis and luciferase assays and rescue experiments revealed that linc00976/miR137/OTUD7B established the ceRNA network modulating PC cell proliferation and tumor growth.

Conclusion
The present study demonstrates that linc00976 enhances the proliferation and invasion ability of PC cells by upregulating OTUD7B expression, which was a target of miR-137. Ultimately, OTUD7B mediates EGFR and MAPK signaling pathway, suggesting that linc00976/miR-137/OTUD7B/EGFR axis may act as a potential biomarker and therapeutic target for PC.
Upregulation of ERp57 promotes clear cell renal cell carcinoma progression by initiating a STAT3/ILF3 feedback loop
Authors: Liu Yan , Wang Jian-Xing , Nie Zi-Yuan , Wen Yue , Jia Xin-Ju , Zhang Li-Na , Duan Hui-Jun , Shi Yong-Hong 
Published: November 2019

Abstract

Background
ERp57 dysfunction has been shown to contribute to tumorigenesis in multiple malignances. However, the role of ERp57 in clear cell renal carcinoma (ccRCC) remains unclear.

Methods
Cell proliferation ability was measured by MTT and colony forming assays. Western blotting and quantitative real-time PCR (qRT-PCR) were performed to measure protein and mRNA expression. Co-immunoprecipitation (CoIP) and proximity ligation assay (PLA) were performed to detect protein-protein interaction. Chromatin immunoprecipitation (ChIP), ribonucleoprotein immunoprecipitation (RIP), and oligo pull-down were used to confirm DNA–protein and RNA–protein interactions. Promoter luciferase analysis was used to detect transcription factor activity.

Results
Here we found ERp57 was overexpressed in ccRCC tissues, and the higher levels of ERp57 were correlated with poor survival in patients with ccRCC. In vivo and in vitro experiments showed that ccRCC cell proliferation was enhanced by ERp57 overexpression and inhibited by ERp57 deletion. Importantly, we found ERp57 positively regulated ILF3 expression in ccRCC cells. Mechanically, ERp57 was shown to bind to STAT3 protein and enhance the STAT3-mediated transcriptional activity of ILF3. Furthermore, ILF3 levels were increased in ccRCC tissues and associated with poor prognosis. Interestingly, we revealed that ILF3 could bind to ERp57 and positively regulate its expression by enhancing its mRNA stability. Furthermore, ccRCC cell proliferation was moderated via the ERp57/STAT3/ILF3 feedback loop.

Conclusions
In summary, our results indicate that the ERp57/STAT3/ILF3 feedback loop plays a key role in the oncogenesis of ccRCC and provides a potential therapeutic target for ccRCC treatment.
Factors affecting breast-feeding practice among a sample of Iranian women: a structural equation modeling approach
Authors: Rafizadeh Reyhaneh , Heidari Zahra , Karimy Mahmood , Zamani-Alavijeh Fereshteh , Araban Marzieh 
Published: November 2019

Abstract
Background
Breastfeeding is one of the most sensitive stages in the development of children, having many benefits for the mother and the child. The present study aimed to determine factors associated with breastfeeding intention and behavior in mothers living in Taft County, Iran.

Methods
In this cross-sectional design, the statistical population consisted of 420 mothers with infants under 1 year of age living in Taft County of Yazd province, Iran. The research data were collected from health records of infants under one in health centers of the county as well as a researcher-made questionnaire including demographic information, knowledge and attitude towards breastfeeding, social support and perceived self-efficacy, and breastfeeding intention and behavior. Structural Equation Modeling (SEM) based on AMOS 18 were employed to analyze the relationship between research variables.

Results
The mean age of mothers was 28.04 ± 6.49 year and the children were 10 ± 6 months. Half of the mothers (50.3%) had cesarean sections and more than half (55.8%) of the children were males. Mothers’ attitude (β = 0.442; 95% CI: 0.284, 0.599), self-efficacy (β = 0.186; 95% CI: 0.047, 0.324) and perceived social support (β = 0.178; 95% CI: 0.035, 0.322) were respectively the strongest predictors of breastfeeding intention. Besides, the breastfeeding intention affected breastfeeding behavior with a high coefficient (0.857; 95% CI: 0.735, 0.979).

Conclusions
The study provided informative pathways on the association of maternal attitude, social support and self-efficacy with breast feeding behavior. These findings could be useful for designing health education and promotion programs about breast feeding among women.
A simple strategy to effectively produce d-lactate in crude glycerol-utilizing Escherichia coli
Authors: Wang Yao-De , Liao Jin-Yi , Chiang Chung-Jen , Chao Yun-Peng 
Published: November 2019

AbstractBackgroundFed-batch fermentation has been conventionally implemented for the production of lactic acid with a high titer and high productivity. However, its operation needs a complicated control which increases the production cost.ResultsThis issue was addressed by simplifying the production scheme.Escherichia coliwas manipulated for its glycerol dissimilation andd-lactate synthesis pathways and then subjected to adaptive evolution under high crude glycerol. Batch fermentation in the two-stage mode was performed by controlling the dissolved oxygen (DO), and the evolved strain deprived ofpoxBenabled production of 100 g/Ld-lactate with productivity of 1.85 g/L/h. To increase productivity, the producer strain was further evolved to improve its growth rate on crude glycerol. The fermentation was performed to undergo the aerobic growth with low substrate, followed by the anaerobic production with high substrate. Moreover, the intracellular redox of the strain was balanced by fulfillment of the anaerobic respiratory chain with nitrate reduction. Without controlling the DO, the microbial fermentation resulted in the homofermentative production ofd-lactate (ca. 0.97 g/g) with a titer of 115 g/L and productivity of 3.29 g/L/h.ConclusionsThe proposed fermentation strategy achieves the highest yield based on crude glycerol and a comparable titer and productivity as compared to the approach by fed-batch fermentation. It holds a promise to sustain the continued development of the crude glycerol-based biorefinery.
Genetic diversity, natural selection and haplotype grouping of Plasmodium vivax Duffy-binding protein genes from eastern and western Myanmar borders
Authors: Hu Yubing , Wang Lin , Mbenda Huguette Gaelle Ngassa , Soe Myat Thu , Yu Chunyun , Feng Hui , Kyaw Myat Phone , Cui Liwang , Zhu Xiaotong , Cao Yaming 
Published: November 2019

AbstractBackgroundMerozoite proteins of the malaria parasites involved in the invasion of red blood cells are selected by host immunity and their diversity is greatly influenced by changes in malaria epidemiology. In the Greater Mekong Subregion (GMS), malaria transmission is concentrated along the international borders and there have been major changes in malaria epidemiology withPlasmodium vivaxbecoming the dominant species in many regions. Here, we aimed to evaluate the genetic diversity ofP. vivax Duffy-binding proteingene domain II (pvdbp-II) in isolates from the eastern and western borders of Myanmar, and compared it with that from globalP. vivaxpopulations.Methodspvdbp-II sequences were obtained from 85 and 82 clinicalP. vivaxisolates from the eastern and western Myanmar borders, respectively. In addition, 504pvdbp-II sequences from nineP. vivaxpopulations of the world were retrieved from GenBank and used for comparative analysis of genetic diversity, recombination and population structure of the parasite population.ResultsThe nucleotide diversity of thepvdbp-II sequences from the Myanmar border parasite isolates was not uniform, with the highest diversity located between nucleotides 1078 and 1332. Western Myanmar isolates had a unique R391C mutation. Evidence of positive natural selection was detected inpvdbp-II gene inP. vivaxisolates from the eastern Myanmar area.P. vivaxparasite populations in the GMS, including those from the eastern, western, and central Myanmar as well as Thailand showed low-level genetic differentiation (FST, 0.000–0.099). Population genetic structure analysis of thepvdbp-II sequences showed a division of the GMS populations into four genetic clusters. A total of 60 PvDBP-II haplotypes were identified in 210 sequences from the GMS populations. Among the epitopes in PvDBP-II, high genetic diversity was found in epitopes 45 (379-SIFGT(D/G)(E/K)(K/N)AQQ(R/H)(R/C)KQ-393, π = 0.029) and Ia (416-G(N/K)F(I/M)WICK(L/I)-424], Ib [482-KSYD(Q/E)WITR-490, π = 0.028) inP. vivaxpopulations from the eastern and western borders of Myanmar.ConclusionsThepvdbp-II gene is genetically diverse in the eastern and western Myanmar borderP. vivaxpopulations. Positive natural selection and recombination occurred inpvdbp-II gene. Low-level genetic differentiation was identified, suggesting extensive gene flow of theP. vivaxpopulations in the GMS. These results can help understand the evolution of theP. vivaxpopulations in the course of regional malaria elimination and guide the design of PvDBP-II-based vaccine.