bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling ncRNA regulatory axes in atherosclerosis progression
Authors: Navarro Estanislao , Mallén Adrian , Cruzado Josep M. , Torras Joan , Hueso Miguel 
Published: February 2020

AbstractCompletion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non‐coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non‐coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non‐coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3′UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non‐coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti‐ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks.
Assessment and validation of miniaturized technology for the remote tracking of critically endangered Galápagos pink land iguana (Conolophus marthae)
Authors: Loreti Pierpaolo , Bracciale Lorenzo , Colosimo Giuliano , Vera Carlos , Gerber Glenn P. , De Luca Massimiliano , Gentile Gabriele 
Published: February 2020

Abstract
Background
Gathering ecological data for species of conservation concern inhabiting remote regions can be daunting and, sometimes, logistically infeasible. We built a custom-made GPS tracking device that allows to remotely and accurately collect animal position, environmental, and ecological data, including animal temperature and UVB radiation. We designed the device to track the critically endangered Galápagos pink land iguana, Conolophus marthae. Here we illustrate some technical solutions adopted to respond to challenges associated with such task and present some preliminary results from controlled trial experiments and field implementation.

Results
Our tests show that estimates of temperature and UVB radiation are affected by the design of our device, in particular by its casing. The introduced bias, though, is systematic and can be corrected using linear and quadratic regressions on collected values. Our data show that GPS accuracy loss, although introduced by vegetation and orientation of the devices when attached to the animals, is acceptable, leading to an average error gap of less than 15 m in more than 50% of the cases.

Conclusions
We address some technical challenges related to the design, construction, and operation of a custom-made GPS tracking device to collect data on animals in the wild. Systematic bias introduced by the technological implementation of the device exists. Understanding the nature of the bias is crucial to provide correction models. Although designed to track land iguanas, our device could be used in other circumstances and is particularly useful to track organisms inhabiting locations that are difficult to reach or for which classic telemetry approaches are unattainable.
“It also taught me a lot about myself”: A qualitative exploration of how men understand eating disorder recovery
Authors: Lewke-Bandara Ranidu S. , Thapliyal Priyanka , Conti Janet , Hay Phillipa 
Published: February 2020

Abstract
Background
Eating Disorders (ED) are relatively common in the general population. However, perceived as “female disorders”, EDs in men are often overlooked. Although recovery is often seen as the ideal end goal of ED, there is no single universal definition of recovery. Recovery can be defined in terms of: physical changes, behavioural changes, psychological (cognitive and emotional) and improved quality of life. There is very little research exploring how people with ED define/ understand what recovery is and there is even less research involving men with ED. Therefore, the aim of this study was to explore recovery from men’s perspectives.

Methods
In this qualitative study, eight men from Australia, New Zealand and the United States participated in a semi-structured interview. Data collected on the men’s experiences of recovery were analysed in detail to create a thematic map of their understanding of recovery.

Results
The thematic analysis generated two overarching themes. The first theme focused on psychological recovery in terms of diminished preoccupations with food and disordered eating behaviours, allowing them to eat more freely. They also experienced growth of self-confidence, insight and interpersonal relationships. The second theme viewed recovery as a recursive process without a definite endpoint. The men positioned themselves at different points of the recovery journey and emphasised the importance of support systems and improved resilience to deflect triggers that would otherwise cause relapse.

Conclusions
Recovery was recognised as an improvement in the men’s psychosocial wellbeing from a previous level of functioning. It was a journey which was with no definite endpoint but one that provided benefits such as inner peace, confidence, greater empathy and stronger connections with others around them.
An integrative analysis of genome-wide association study and regulatory SNP annotation datasets identified candidate genes for bipolar disorder
Authors: Qi Xin , Wen Yan , Li Ping , Liang Chujun , Cheng Bolun , Ma Mei , Cheng Shiqiang , Zhang Lu , Liu Li , Kafle Om Prakash , Zhang Feng 
Published: February 2020

AbstractBackgroundBipolar disorder (BD) is a complex mood disorder. The genetic mechanism of BD remains largely unknown.MethodsWe conducted an integrative analysis of genome-wide association study (GWAS) and regulatory SNP (rSNP) annotation datasets, including transcription factor binding regions (TFBRs), chromatin interactive regions (CIRs), mature microRNA regions (miRNAs), long non-coding RNA regions (lncRNAs), topologically associated domains (TADs) and circular RNAs (circRNAs). Firstly, GWAS dataset 1 of BD (including 20,352 cases and 31,358 controls) and GWAS dataset 2 of BD (including 7481 BD patients and 9250 controls) were integrated with rSNP annotation database to obtain BD associated SNP regulatory elements and SNP regulatory element-target gene (E–G) pairs, respectively. Secondly, a comparative analysis of the two datasets results was conducted to identify the common rSNPs and also their target genes. Then, gene sets enrichment analysis (FUMA GWAS) and HumanNet-XC analysis were conducted to explore the functional relevance of identified target genes with BD.ResultsAfter the integrative analysis, we identified 52 TFBRs target genes, 44 TADs target genes, 55 CIRs target genes and 21 lncRNAs target genes for BD, such asITIH4(Pdataset1 = 6.68 × 10−8,Pdataset2 = 6.64 × 10−7),ITIH3(Pdataset1 = 1.09 × 10−8,Pdataset2 = 2.00 × 10−7),SYNE1(Pdataset1 = 1.80 × 10−6,Pdataset2 = 4.33 × 10−9) andOPRM1(Pdataset1 = 1.80 × 10−6,Pdataset2 = 4.33 × 10−9).ConclusionWe conducted a large-scale integrative analysis of GWAS and 6 common rSNP information datasets to explore the potential roles of rSNPs in the genetic mechanism of BD. We identified multiple candidate genes for BD, supporting the importance of rSNP in the development of BD.
Genetic and histologic spatiotemporal evolution of recurrent, multifocal, multicentric and metastatic glioblastoma
Authors: Georgescu Maria-Magdalena , Olar Adriana 
Published: February 2020

AbstractGlioblastoma is the most frequent and aggressive primary brain tumor, characterized by extensive brain invasion and rarely, systemic metastases. The pathogenesis of metastatic glioblastoma is largely unknown. We present the first integrated clinical/histologic/genetic analysis of 5 distinct brain and lung foci from a unique case of recurrent, multifocal, multicentric and metastatic glioblastoma. The initial right frontotemporal gliosarcoma received standard surgical/chemoradiation therapy and recurred 1.5 years later, co-occurring with three additional masses localized to the ipsilateral temporal lobe, cerebellum and lung. Synchronous metastatic lung carcinoma was suspected in this long-term smoker patient with family history of cancer. However, glioblastoma was confirmed in all tumors, although with different morphologic patterns, including ependymomatous and epithelioid. Genomic profiling revealed a germline FANCD2 variant of unknown significance, and a 4-gene somatic mutation signature shared by all tumors, consisting of TERT promoter and PTEN, RB1 and TP53 tumor suppressor mutations. Additional GRIN2A and ATM heterozygous mutations were selected in the cerebellar and lung foci, but were variably present in the supratentorial foci, indicating reduced post-therapeutic genetic evolution in brain foci despite morphologic variability. Significant genetic drift characterized the lung metastasis, likely explaining the known resistance of circulating glioblastoma cells to systemic seeding. MET overexpression was detected in the initial gliosarcoma and lung metastasis, possibly contributing to invasiveness. This comprehensive analysis sheds light on the temporospatial evolution of glioblastoma and underscores the importance of genetic testing for diagnosis and personalized therapy.
RETRACTED ARTICLE: Criminal tendency detection from facial images and the gender bias effect
Authors: Hashemi Mahdi , Hall Margeret 
Published: February 2020

AbstractExplosive performance and memory space growth in computing machines, along with recent specialization of deep learning models have radically boosted the role of images in semantic pattern recognition. In the same way that a textual post on social media reveals individual characteristics of its author, facial images may manifest some personality traits. This work is the first milestone in our attempt to infer personality traits from facial images. With this ultimate goal in mind, here we explore a new level of image understanding, inferring criminal tendency from facial images via deep learning. In particular, two deep learning models, including a standard feedforward neural network (SNN) and a convolutional neural network (CNN) are applied to discriminate criminal and non-criminal facial images. Confusion matrix and training and test accuracies are reported for both models, using tenfold cross-validation on a set of 10,000 facial images. The CNN was more consistent than the SNN in learning to reach its best test accuracy, which was 8% higher than the SNN’s test accuracy. Next, to explore the classifier’s hypothetical bias due to gender, we controlled for gender by applying only male facial images. No meaningful discrepancies in classification accuracies or learning consistencies were observed, suggesting little to no gender bias in the classifier. Finally, dissecting and visualizing convolutional layers in CNN showed that the shape of the face, eyebrows, top of the eye, pupils, nostrils, and lips are taken advantage of by CNN in order to classify the two sets of images.
Smart devices employment in teaching and learning: reality and challenges in Jordan universities
Authors: Al-Hamad Nouwar Q. , AlHamad Asma Q. , Al-Omari Faruq A. 
Published: February 2020

AbstractThe aim of this study was to investigate the reality of smart devices’ employment in teaching and learning in Jordanian universities from the perspective of instructors. A random sample of (364) instructors were targeted. A structured interview was used to collect data and qualitative analysis was performed to reveal results. Obtained results showed that (68.1%) of respondents were against technology use specially inside the class, whereas (31.9%) were in-favor. Although a high percentage were against technology use, yet most of them use the technology by some means. Distraction, misuse, and lack of skills were the most commonly reported drawbacks. On the other hand, enriched interaction and excitement were the main aspects encouraging instructors to employ the technology in the teaching process.
Problematizing teaching and learning mathematics as “given” in STEM education
Authors: Li Yeping , Schoenfeld Alan H. 
Published: February 2020

AbstractMathematics is fundamental for many professions, especially science, technology, and engineering. Yet, mathematics is often perceived as difficult and many students leave disciplines in science, technology, engineering, and mathematics (STEM) as a result, closing doors to scientific, engineering, and technological careers. In this editorial, we argue that how mathematics is traditionally viewed as “given” or “fixed” for students’ expected acquisition alienates many students and needs to be problematized. We propose an alternative approach to changes in mathematics education and show how the alternative also applies to STEM education.
Unravelling the effects of tropical land use conversion on the soil microbiome
Authors: Berkelmann Dirk , Schneider Dominik , Meryandini Anja , Daniel Rolf 
Published: February 2020

Abstract
Background
The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the effects of rainforest conversion to different converted land use systems, including agroforestry (“jungle rubber”) and monoculture plantations comprising rubber and oil palm, on soilborne microbial communities by metagenomic shotgun sequencing in Sumatra, Indonesia.

Results
The diversity of bacteria and archaea decreased whereas diversity of fungi increased in the converted land use systems. The soil microbiome was dominated by bacteria followed by fungi. We detected negative effects of land use conversion on the abundance of Proteobacteria (especially on Rhizobiales and Burkholderiales) and positive effects on the abundance of Acidobacteria and Actinobacteria. These abundance changes were mainly driven by pH, C:N ratio, and Fe, C and N content. With increasing land use intensity, the functional diversity decreased for bacteria, archaea and fungi. Gene abundances of specific metabolisms such as nitrogen metabolism and carbon fixation were affected by land use management practices. The abundance of genes related to denitrification and nitrogen fixation increased in plantations while abundance of genes involved in nitrification and methane oxidation showed no significant difference. Linking taxonomic and functional assignment per read indicated that nitrogen metabolism-related genes were mostly assigned to members of the Rhizobiales and Burkholderiales. Abundances of carbon fixation genes increased also with increasing land use intensity. Motility- and interaction-related genes, especially genes involved in flagellar assembly and chemotaxis genes, decreased towards managed land use systems. This indicated a shift in mobility and interspecific interactions in bacterial communities within these soils.

Conclusions
Rainforest conversion to managed land use systems drastically affects structure and functional potential of soil microbial communities. The decrease in motility- and interaction-related functions from rainforest to converted land use systems indicated not only a shift in nutrient cycling but also in community dynamics. Fertilizer application and correspondingly higher availability of nutrients in intensively managed plantations lead to an environment in which interspecific interactions are not favoured compared to rainforest soils. We could directly link effects of land management, microbial community structure and functional potential for several metabolic processes. As our study is the first study of this size and detail on soil microbial communities in tropical systems, we provide a basis for further analyses.
The efficacy of rhBMP-2 loaded hydrogel composite on bone formation around dental implants in mandible bone defects of minipigs
Authors: Lyu Hao-Zhen , Lee Jae Hyup 
Published: February 2020

Abstract

Background
In dental or orthopedic surgery, bone substitutes are inserted with implants to promote osteogenesis and enhance osseointegration. The purpose of this research was to evaluate the efficacy of rhBMP-2 (recombinant human bone morphogenetic protein-2) loaded hydrogel composite for bone formation around dental implant in minipig mandible bone defect models.

Methods
We made bone defects with a diameter of 4 mm in minipig mandibles and inserted implants of the same size, to mimic the cases of inserting the screws in the bone defect or poor-quality bone. The rhBMP-2 (300 μg) loaded hydrogel composite (0.5 cc) inserted in the bone defect with the implant in the rhBMP-2 group. After 4 weeks, the mandibles were harvested to evaluate the new bone mass around implants using plain radiographs, micro-CT, and histology.

Results
The micro-CT analysis result showed that the quantity of new bone generation around the implant in the rhBMP-2 group was greater than that in the other groups. Comparing the ratios of bone to implant area in three groups by histology, the amount of newly formed bone in the rhBMP-2 group was the most.

Conclusion
The rhBMP-2 loaded hydrogel composite promotes osteogenesis around dental implant in minipig mandible bone defect, and enhance osseointegration between the dental implant and host bone.
Comparison of the effectiveness of manual massage, long-wave diathermy, and sham long-wave diathermy for the management of delayed-onset muscle soreness: a randomized controlled trial
Authors: Visconti Lorenzo , Forni Corrado , Coser Rudi , Trucco Marco , Magnano Elisa , Capra Gianpiero 
Published: February 2020

Abstract
Background
Delayed-onset muscle soreness (DOMS) is a specific symptom that typically arises after unaccustomed eccentric muscular effort. It increases typically 24–72 h post-exercise and can affect physical performance. The pathophysiology of DOMS remains unclear, although it seems to be related to the remodeling phase of myofibrils. Different types of treatments have been proposed to minimize DOMS after exercise; however, no clear gold standard treatment exists. Among the most popular and easy-to-apply treatments, manual massage is often performed by clinicians and has been documented to be effective in reducing symptoms. For several years, long-wave diathermy (LWD) has been performed to manage musculoskeletal complaints, such as DOMS; however, no studies have reported its efficacy thus far.
This study aimed to compare the clinical effectiveness of LWD, sham LWD, and manual massage in participants with lower limb DOMS.

Methods
Participants with lower limb DOMS were included in the study. They were randomly assigned to undergo real LWD, sham LWD, or manual massage. The Numeric Pain Rating Scale (NPRS) score was the primary outcome, and the Patient Global Impression of Change (PGIC) Scale score was the secondary outcome. Outcomes were collected before and immediately after the treatment. Analysis of variance was performed to compare the post-treatment NPRS value variability among the groups and to compare the pre- and post-treatment NPRS differences among the groups.

Results
No clinically relevant differences were observed regarding the NPRS value variability among real LWD, sham LWD and manual massage groups. Differences were observed in the PGIC Scale scores.

Conclusions
Future studies are needed to have a better understanding about the treatment of DOMS in clinical practice.

Trial registration
The trial was registered on 29th February 2016 in ClinicalTrials.gov (NCT02693678).
The role of geographic bias in knowledge diffusion: a systematic review and narrative synthesis
Authors: Skopec Mark , Issa Hamdi , Reed Julie , Harris Matthew 
Published: February 2020

Abstract
Background
Descriptive studies examining publication rates and citation counts demonstrate a geographic skew toward high-income countries (HIC), and research from low- or middle-income countries (LMICs) is generally underrepresented. This has been suggested to be due in part to reviewers’ and editors’ preference toward HIC sources; however, in the absence of controlled studies, it is impossible to assert whether there is bias or whether variations in the quality or relevance of the articles being reviewed explains the geographic divide. This study synthesizes the evidence from randomized and controlled studies that explore geographic bias in the peer review process.

Methods
A systematic review was conducted to identify research studies that explicitly explore the role of geographic bias in the assessment of the quality of research articles. Only randomized and controlled studies were included in the review. Five databases were searched to locate relevant articles. A narrative synthesis of included articles was performed to identify common findings.

Results
The systematic literature search yielded 3501 titles from which 12 full texts were reviewed, and a further eight were identified through searching reference lists of the full texts. Of these articles, only three were randomized and controlled studies that examined variants of geographic bias. One study found that abstracts attributed to HIC sources elicited a higher review score regarding relevance of the research and likelihood to recommend the research to a colleague, than did abstracts attributed to LIC sources. Another study found that the predicted odds of acceptance for a submission to a computer science conference were statistically significantly higher for submissions from a “Top University.” Two of the studies showed the presence of geographic bias between articles from “high” or “low” prestige institutions.

Conclusions
Two of the three included studies identified that geographic bias in some form was impacting on peer review; however, further robust, experimental evidence is needed to adequately inform practice surrounding this topic. Reviewers and researchers should nonetheless be aware of whether author and institutional characteristics are interfering in their judgement of research.