bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene co-expression and histone modification signatures are associated with melanoma progression, epithelial-to-mesenchymal transition, and metastasis
Authors: Azevedo Hátylas , Pessoa Guilherme Cavalcante , de Luna Vitorino Francisca Nathália , Nsengimana Jérémie , Newton-Bishop Julia , Reis Eduardo Moraes , da Cunha Júlia Pinheiro Chagas , Jasiulionis Miriam Galvonas 
Published: August 2020

Abstract
Background
We have previously developed a murine cellular system that models the transformation from melanocytes to metastatic melanoma cells. This model was established by cycles of anchorage impediment of melanocytes and consists of four cell lines: differentiated melanocytes (melan-a), pre-malignant melanocytes (4C), malignant (4C11−), and metastasis-prone (4C11+) melanoma cells. Here, we searched for transcriptional and epigenetic signatures associated with melanoma progression and metastasis by performing a gene co-expression analysis of transcriptome data and a mass-spectrometry-based profiling of histone modifications in this model.

Results
Eighteen modules of co-expressed genes were identified, and some of them were associated with melanoma progression, epithelial-to-mesenchymal transition (EMT), and metastasis. The genes in these modules participate in biological processes like focal adhesion, cell migration, extracellular matrix organization, endocytosis, cell cycle, DNA repair, protein ubiquitination, and autophagy. Modules and hub signatures related to EMT and metastasis (turquoise, green yellow, and yellow) were significantly enriched in genes associated to patient survival in two independent melanoma cohorts (TCGA and Leeds), suggesting they could be sources of novel prognostic biomarkers. Clusters of histone modifications were also linked to melanoma progression, EMT, and metastasis. Reduced levels of H4K5ac and H4K8ac marks were seen in the pre-malignant and tumorigenic cell lines, whereas the methylation patterns of H3K4, H3K56, and H4K20 were related to EMT. Moreover, the metastatic 4C11+ cell line showed higher H3K9me2 and H3K36me3 methylation, lower H3K18me1, H3K23me1, H3K79me2, and H3K36me2 marks and, in agreement, downregulation of the H3K36me2 methyltransferase Nsd1.

Conclusions
We uncovered transcriptional and histone modification signatures that may be molecular events driving melanoma progression and metastasis, which can aid in the identification of novel prognostic genes and drug targets for treating the disease.
CFDSD: a Communication Framework for Distributed Software Development
Authors: L’Erario Alexandre , Gonçalves José Antônio , Fabri José Augusto , Pagotto Tiago , Cunha Palácios Rodrigo Henrique 
Published: August 2020

AbstractDue to geographical and/or temporal dispersion, communication between teams in distributed software projects is a critical factor for success. Notably, distributed teams suffer adverse physical and temporal dispersion effects during an information exchange. To mitigate problems arising from interactions, it is important to understand the communication structure of teams during distributed projects. The objective of this work is to present the Communication Framework for Distributed Software Development. This framework groups a set of distributed projects communication concepts and enables a unified view of all stakeholders’ intercommunications that use many interaction technologies. The goal of this framework is to portray the dynamics of the interaction between distributed teams in a multi-tier structure, and each tier approaches a single function in the intercommunication process. We analyzed all interactions from distributed teams after developing an experimental IT Project, using the content analysis method to validate the Communication Framework for Distributed Software Development. The main contribution of this work is the framework specification, and the investigation, which has the potential to help mapping communication patterns in DSD. Moreover, this framework comprises interfaces for communication assessment and includes intercommunications from automated engineering tools as bots.
Visual short-term memory relates to tau and amyloid burdens in preclinical autosomal dominant Alzheimer’s disease
Authors: Norton Daniel J. , Parra Mario A. , Sperling Reisa A. , Baena Ana , Guzman-Velez Edmarie , Jin David S. , Andrea Nicholas , Khang Juna , Schultz Aaron , Rentz Dorene M. , Pardilla-Delgado Enmanuelle , Fuller Joshua , Johnson Keith , Reiman Eric M. , Lopera Francisco , Quiroz Yakeel T. 
Published: August 2020

Abstract
Background
Over the past decade, visual short-term memory (VSTM) binding tests have been shown to be one of the most sensitive behavioral indicators of Alzheimer’s disease (AD), especially when they require the binding of multiple features (e.g., color and shape). Recently, it has become possible to directly measure amyloid and tau levels in vivo via positron emission tomography (PET). To this point, these behavioral and neurochemical markers have not been compared in humans with AD or at risk for it.

Methods
In a cross-sectional study, we compared VSTM performance to tau and amyloid concentrations, measured by PET, in individuals certain to develop AD by virtue of their inheritance of the presenilin-1 E280A mutation. These included 21 clinically unimpaired subjects and 7 subjects with early mild cognitive impairment (MCI), as well as 30 family members who were not carriers of the mutation.

Results
We found that VSTM performance correlated strongly with tau in entorhinal cortex and inferior temporal lobe, and also with amyloid when examining asymptomatic carriers only. The condition requiring binding was not preferentially linked to tau—in fact, the non-binding “shape only” condition showed a stronger relationship.

Conclusions
The results confirm VSTM’s status as an early marker of AD pathology and raise interesting questions as to the course of binding-specific versus non-binding aspects of VSTM in early AD.
Sex differences in circulating proteins in heart failure with preserved ejection fraction
Authors: Stienen Susan , Ferreira João Pedro , Kobayashi Masatake , Preud’homme Gregoire , Dobre Daniela , Machu Jean-Loup , Duarte Kevin , Bresso Emmanuel , Devignes Marie-Dominique , Andrés Natalia López , Girerd Nicolas , Aakhus Svend , Ambrosio Giuseppe , Rocca Hans-Peter Brunner-La , Fontes-Carvalho Ricardo , Fraser Alan G. , van Heerebeek Loek , de Keulenaer Gilles , Marino Paolo , McDonald Kenneth , Mebazaa Alexandre , Papp Zoltàn , Raddino Riccardo , Tschöpe Carsten , Paulus Walter J. , Zannad Faiez , Rossignol Patrick 
Published: August 2020

Abstract
Background
Many patients with heart failure with preserved ejection fraction (HFpEF) are women. Exploring mechanisms underlying the sex differences may improve our understanding of the pathophysiology of HFpEF. Studies focusing on sex differences in circulating proteins in HFpEF patients are scarce.

Methods
A total of 415 proteins were analyzed in 392 HFpEF patients included in The Metabolic Road to Diastolic Heart Failure: Diastolic Heart Failure study (MEDIA-DHF). Sex differences in these proteins were assessed using adjusted logistic regression analyses. The associations between candidate proteins and cardiovascular (CV) death or CV hospitalization (with sex interaction) were assessed using Cox regression models.

Results
We found 9 proteins to be differentially expressed between female and male patients. Women expressed more LPL and PLIN1, which are markers of lipid metabolism; more LHB, IGFBP3, and IL1RL2 as markers of transcriptional regulation; and more Ep-CAM as marker of hemostasis. Women expressed less MMP-3, which is a marker associated with extracellular matrix organization; less NRP1, which is associated with developmental processes; and less ACE2, which is related to metabolism. Sex was not associated with the study outcomes (adj. HR 1.48, 95% CI 0.83–2.63), p = 0.18.

Conclusion
In chronic HFpEF, assessing sex differences in a wide range of circulating proteins led to the identification of 9 proteins that were differentially expressed between female and male patients. These findings may help further investigations into potential pathophysiological processes contributing to HFpEF.
Bond Behavior Between Steel Fiber Reinforced Polymer (SRP) and Concrete
Authors: Zou Xingxing , Sneed Lesley H. 
Published: August 2020

AbstractSteel fiber reinforced polymer (SRP) composite materials, which consist of continuous unidirectional steel wires (cords) embedded in a polymeric matrix, have recently emerged as an effective solution for strengthening of reinforced concrete (RC) structures. SRP is bonded to the surface of RC structures by the same matrix to provide external reinforcement. Interfacial debonding between the SRP and concrete is a primary concern in this type of application. This study aimed to investigate the bond characteristics between SRP and concrete determined by single-lap direct shear tests with different composite bonded lengths and fiber sheet densities (cord spacings). Specimens with medium density fibers failed mainly due to composite debonding, whereas those with low density fibers failed due to fiber rupture. Results of specimens that exhibited debonding were used to determine the bond-slip relationship of the SRP-concrete interface and to predict the full-range load response, which was in good agreement with the experimental results. A database of SRP-concrete direct shear tests reported in the literature was also established. Four analytical equations derived for fiber reinforced polymer (FRP)-concrete debonding were evaluated based on the database results and were found to predict the maximum load within approximately 15% error on average, however, they all underestimated the effective bond length.
Impact of a global leader on pharmaceutical practice and policy around the world
Authors: Alves da Costa F. , Henman M. , Hughes C. , Leufkens H. , Babar Z. , McElnay J. , Schulz M. 
Published: August 2020

AbstractThis commentary describes the contributions of a Dutch pharmacist who contributed in a unique manner to the development of community pharmacy practice in Europe, to the evolution of practice-based research and to its publication. With an interest in pharmaceutical care and in clinical pharmacy, Dr. van Mil changed practice and policy in Europe over the last decades in a very visible way, here documented through a summary of some of his main written contributions. We write this to honour his memory and contribute to the preservation of his legacy.
Uniformity, diversity, harmony, and emotional energy in a Chinese STEM classroom
Authors: Davis James P. , Du Juan , Tang Jia-Hui , Qiao Lu , Liu Yan-Qiu , Chiang Feng-Kuang 
Published: August 2020

AbstractBackgroundUnderstanding cultural diversity in STEM education is important for inclusivity and teaching STEM literacy for all. We explore diversity at a micro-cultural classroom level involving students’ emotional experiences and interactional practices as they engage with learning, which has received limited attention in naturalistic studies of STEM education, especially in East Asian cultures. In this study, we explore emotional experiences of students during a guided inquiry lesson in a Chinese primary school using an interpretive methodology informed by concepts of emotional energy, uniformity, and harmony. Emotional energy is an individual and collective experience of togetherness and solidarity emerging from successful social interaction. Uniformity and harmony are emotion-related concepts experienced in Confucian heritage cultures. The aims of this study are to explore Chinese students’ emotional experiences during a STEM inquiry lesson and to refine the conceptualization of emotional energy from Confucian cultural perspectives.ResultsIn a STEM inquiry, context knowledge about micro-cultural diversity and the interplay between Chinese emotional experiences and engagement with ideas are explored. Notions of uniformity and harmony are described through cultural practices as they relate to emotional energy. The study contributes to understanding the diversity of emotional energy as a student experience and social form of engagement, during a STEM inquiry activity in a Confucian heritage context.ConclusionsThis study contributes to understandings of student experiences of uniformity, harmony, and variations to intensity of emotional energy during learning via STEM inquiry. Modifications to the conceptualization of emotional energy in STEM education are indicated. Our findings inform an understanding of student emotive experiences of STEM education in East Asian and multi-cultural education systems internationally.
Evaluating the impact of sampling schemes on leaf area index measurements from digital hemispherical photography in Larix principis-rupprechtii forest plots
Authors: Zou Jie , Hou Wei , Chen Ling , Wang Qianfeng , Zhong Peihong , Zuo Yong , Luo Shezhou , Leng Peng 
Published: August 2020

Abstract
Background
Digital hemispherical photography (DHP) is widely used to estimate the leaf area index (LAI) of forest plots due to its advantages of high efficiency and low cost. A crucial step in the LAI estimation of forest plots via DHP is choosing a sampling scheme. However, various sampling schemes involving DHP have been used for the LAI estimation of forest plots. To date, the impact of sampling schemes on LAI estimation from DHP has not been comprehensively investigated.

Methods
In this study, 13 commonly used sampling schemes which belong to five sampling types (i.e. dispersed, square, cross, transect and circle) were adopted in the LAI estimation of five Larix principis-rupprechtii plots (25 m × 25 m). An additional sampling scheme (with a sample size of 89) was generated on the basis of all the sample points of the 13 sampling schemes. Three typical inversion models and four canopy element clumping index (Ωe) algorithms were involved in the LAI estimation. The impacts of the sampling schemes on four variables, including gap fraction, Ωe, effective plant area index (PAIe) and LAI estimation from DHP were analysed. The LAI estimates obtained with different sampling schemes were then compared with those obtained from litter collection measurements.

Results
Large differences were observed for all four variable estimates (i.e. gap fraction, Ωe, PAIe and LAI) under different sampling schemes. The differences in impact of sampling schemes on LAI estimation were not obvious for the three inversion models, if the four Ωe algorithms, except for the traditional gap-size analysis algorithm were adopted in the estimation. The accuracy of LAI estimation was not always improved with an increase in sample size. Moreover, results indicated that with the appropriate inversion model, Ωe algorithm and sampling scheme, the maximum estimation error of DHP-estimated LAI at elementary sampling unit can be less than 20%, which is required by the global climate observing system, except in forest plots with extremely large LAI values (~ > 6.0). However, obtaining an LAI from DHP with an estimation error lower than 5% is impossible regardless of which combination of inversion model, Ωe algorithm and sampling scheme is used.

Conclusion
The LAI estimation of L. principis-rupprechtii forests from DHP was largely affected by the sampling schemes adopted in the estimation. Thus, the sampling scheme should be seriously considered in the LAI estimation. One square and two transect sampling schemes (with sample sizes ranging from 3 to 9) were recommended to be used to estimate the LAI of L. principis-rupprechtii forests with the smallest mean relative error (MRE). By contrast, three cross and one dispersed sampling schemes were identified to provide LAI estimates with relatively large MREs.
Effects of climate, biotic factors, and phylogeny on allometric relationships: testing the metabolic scaling theory in plantations and natural forests across China
Authors: Sun Han , Wang Xiangping , Fan Dayong 
Published: August 2020

Abstract
Background
Metabolic scaling theory (MST) is still in debate because observed allometric exponents often deviate from MST predictions, and can change significantly depending on environment, phylogeny, and disturbance. We assembled published scaling exponents from literatures for three allometric relationships linked to biomass allocation: leaf biomass-diameter (L-D), stem biomass-diameter (S-D), and root biomass-diameter (R-D). We used data from natural forests and plantations across China to test the following hypotheses: 1) the allometric relationships of trees support the predictions of MST on a broad scale; 2) the observed deviations from MST predictions are caused by climate, biotic factors, and/or phylogeny; 3) abiotic and biotic factors influence allometric relationships in plantations and natural forests differently, and different allometric relationships (i.e. L-D, S-D, and R-D) are affected differently. We related these scaling exponents to geographic climate gradient, successional stage, stand density, leaf form and phenology, and phylogeny. We used mixed-effect models to examine the major factors affecting tree allometries.

Results
In natural forests, S-D and R-D scaling exponents were consistent with MST predictions in primary forests, but were significantly lower in secondary forests. Both S-D and R-D scaling exponents in plantations had a medium value that fell between those of the secondary and primary forests, despite plantations being similar in species characteristics and age to secondary forests. The S-D and R-D exponents were significantly affected by factors that are not yet considered in MST, including winter coldness which explained 2.76% – 3.24% of variations, successional stage (7.91% – 8.20% of variations), density (a surrogate for competition, 5.86% – 8.54% of variations), and especially phylogeny (45.86% – 56.64% of variations explained). However, the L-D scaling exponents conformed to MST predictions in primary, secondary, and plantation forests, and was not strongly explained by most factors.

Conclusion
MST is only applicable to primary (steady-state) forests, and climate, biotic factors and phylogeny are causes of the observed deviations of allometric relationships from MST predictions. Forest management practices in plantations have a strong influence on tree allometries. L-D allometry is more strongly controlled by biophysical constraints than S-D and R-D allometries, however, the mechanisms behind this difference still need further examinations.
Should we investigate mitochondrial disorders in progressive adult-onset undetermined ataxias?
Authors: Pedroso José Luiz , de Rezende Pinto Wladimir Bocca Vieira , Barsottini Orlando Graziani Povoas , Oliveira Acary Souza Bulle 
Published: August 2020

Abstract
Background
Despite the broad development of next-generation sequencing approaches recently, such as whole-exome sequencing, diagnostic workup of adult-onset progressive cerebellar ataxias without remarkable family history and with negative genetic panel testing for SCAs remains a complex and expensive clinical challenge.

Case presentation
In this article, we report a Brazilian man with adult-onset slowly progressive pure cerebellar ataxia, which developed neuropathy and hearing loss after fifteen years of ataxia onset, in which a primary mitochondrial DNA defect (MERRF syndrome - myoclonus epilepsy with ragged-red fibers) was confirmed through muscle biopsy evaluation and whole-exome sequencing.

Conclusions
Mitochondrial disorders are a clinically and genetically complex and heterogenous group of metabolic diseases, resulting from pathogenic variants in the mitochondrial DNA or nuclear DNA. In our case, a correlation with histopathological changes identified on muscle biopsy helped to clarify the definitive diagnosis. Moreover, in neurodegenerative and neurogenetic disorders, some symptoms may be evinced later during disease course. We suggest that late-onset and adult pure undetermined ataxias should be considered and investigated for mitochondrial disorders, particularly MERRF syndrome and other primary mitochondrial DNA defects, together with other more commonly known nuclear genes.
Surface roughness of titanium disks influences the adhesion, proliferation and differentiation of osteogenic properties derived from human
Authors: Martinez Maria Alejandra Frias , Balderrama Ísis de Fátima , Karam Paula Stephania Brandão Hage , de Oliveira Rodrigo Cardoso , de Oliveira Flávia Amadeu , Grandini Carlos Roberto , Vicente Fábio Bossoi , Stavropoulos Andreas , Zangrando Mariana Schutzer Ragghianti , Sant’Ana Adriana Campos Passanezi 
Published: August 2020

Abstract
Purpose
The aim of this study was to investigate the response of osteogenic cell lineage and gingival fibroblastic cells to different surface treatments of grade IV commercially pure Titanium (cpTi) disks.

Material and methods
Grade IV cpTi disks with different surfaces were produced: machined (M), sandblasting (B), sandblasting and acid subtraction (NP), and hydrophilic treatment (ACQ). Surface microtopography characteristics and chemical composition were investigated by scanning electron microscopy (SEM) and energy dispersive x-ray spectrometry (EDS). Adhesion and proliferation of SC-EHAD (human surgically-created early healing alveolar defects) and HGF-1 (human gingival fibroblasts) on Ti disks were investigated at 24 and 48 h, and osteogenic differentiation and mineralization were evaluated by assessing alkaline phosphatase (ALP) activity and alizarin red staining, respectively.

Results
No significant differences were found among the various surface treatments for all surface roughness parameters, except for skewness of the assessed profile (Rsk) favoring M (p = 0.035 ANOVA). M disks showed a slightly higher (p > 0.05; Kruskal-Wallis/Dunn) adhesion of HGF-1 (89.43 ± 9.13%) than SC-EHAD cells (57.11 ± 17.72%). ACQ showed a significantly higher percentage of SC-EHAD (100%) than HGF-1 (69.67 ± 13.97%) cells adhered at 24 h. SC-EHAD cells expressed increased ALP activity in osteogenic medium at M (213%) and NP (235.04%) surfaces, but higher mineralization activity on ACQ (54.94 ± 4.80%) at 14 days.

Conclusion
These findings suggest that surface treatment influences the chemical composition and the adhesion and differentiation of osteogenic cells in vitro.

Clinical relevance
Hydrophilic surface treatment of grade IV cpTi disks influences osteogenic cell adhesion and differentiation, which might enhance osseointegration.
An extremely rare case of neuromuscular and vascular hamartoma of the appendix
Authors: Sasaki Takahiro , Furuhata Tomohisa , Nishimura Masashige , Ono Tatsunori , Noda Akiyoshi , Koizumi Hirotaka , Miyajima Nobuyoshi , Otsubo Takehito 
Published: August 2020

Abstract
Background
Neuromuscular and vascular hamartoma is a rare lesion of the small intestine, with only 26 cases reported since its initial description in 1982. No occurrence of hamartoma in the appendix has been reported until now.

Case presentation
A 60-year-old man had been suffering from longstanding right lower quadrant pain. Abdominal computed tomography showed a slight swelling of the appendix as the possible cause of his pain. Laparoscopic appendectomy with partial resection of the cecum was performed for diagnostic and therapeutic purposes. An 18 × 10-mm lesion located on the tip of the appendix was found in the resected specimen. Pathological examination showed that the lesion was covered with normal mucosa and consisted of adipose tissue, smooth muscle fibers, small vessels, and neural fibers. These findings were consistent with neuromuscular and vascular hamartoma of the appendix.

Conclusion
This is the first report of neuromuscular and vascular hamartoma arising from the appendix.