bluuebunny/crossref_metadata_2025_split huggingface dataset:
Foraging behavior and extended phenotype independently affect foraging success in spiders
Authors: DiRienzo N , Schraft H A , Montiglio P O , Bradley C T , Dornhaus A 
Published: August 2020

AbstractMultiple phenotypic traits often interact with each other to determine an individual’s fitness. Behavioral and extended phenotypic traits, such as architectural constructions, can contribute to fitness in an integrated way. The goal of this study was to understand how the interaction between behavioral and extended phenotypic traits can affect foraging success. We tested this question using black widow spiders, where spiders that are aggressive in a foraging context tend to build more gumfooted silk lines that aid in prey capture, while non-aggressive spiders build webs with fewer gumfooted lines. We repeatedly assessed behavior and web structure to quantify relationships between these traits, and then allowed spiders to forage for live prey on their own web or the web of a conspecific that differed in structure. Thus, we assessed how varying combinations of behavior and web structure affect foraging success, and if correlational selection might act on them. We confirmed that aggressiveness and number of gumfooted lines are positively correlated and found that capture success increased with both aggressiveness and the number of gumfooted lines. Yet, we did not find any evidence for correlational selection: aggressiveness and number of gumfooted lines appeared to affect foraging success independently of each other. These findings highlight that a correlation between traits that contribute towards the same ecological function does not necessarily imply correlational selection. Taking advantage of the experimental convenience afforded by extended phenotypic traits can provide insight into the functional consequences of phenotypic variation within and between individuals.
LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers
Authors: Deng Yulan , Luo Hao , Yang Zhenyu , Liu Lunxu 
Published: August 2020

AbstractAccumulating studies demonstrated that the roles of lncRNAs for tumorigenesis were isoform-dependent and their aberrant splicing patterns in cancers contributed to function specificity. However, there is no existing database focusing on cancer-related alternative splicing of lncRNAs. Here, we developed a comprehensive database called LncAS2Cancer, which collected 5335 bulk RNA sequencing and 1826 single-cell RNA sequencing samples, covering over 30 cancer types. By applying six state-of-the-art splicing algorithms, 50 859 alternative splicing events for 8 splicing types were identified and deposited in the database. In addition, the database contained the following information: (i) splicing patterns of lncRNAs under seven different conditions, such as gene interference, which facilitated to infer potential regulators; (ii) annotation information derived from eight sources and manual curation, to understand the functional impact of affected sequences; (iii) survival analysis to explore potential biomarkers; as well as (iv) a suite of tools to browse, search, visualize and download interesting information. LncAS2Cancer could not only confirm the known cancer-associated lncRNA isoforms but also indicate novel ones. Using the data deposited in LncAS2Cancer, we compared gene model and transcript overlap between lncRNAs and protein-coding genes and discusses how these factors, along with sequencing depth, affected the interpretation of splicing signals. Based on recurrent signals and potential confounders, we proposed a reliable score to prioritize splicing events for further elucidation. Together, with the broad collection of lncRNA splicing patterns and annotation, LncAS2Cancer will provide important new insights into the diverse functional roles of lncRNA isoforms in human cancers. LncAS2Cancer is freely available at https://lncrna2as.cd120.com/.
A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data
Authors: Nguyen Hung , Tran Duc , Tran Bang , Pehlivan Bahadir , Nguyen Tin 
Published: August 2020

AbstractGene regulatory network is a complicated set of interactions between genetic materials, which dictates how cells develop in living organisms and react to their surrounding environment. Robust comprehension of these interactions would help explain how cells function as well as predict their reactions to external factors. This knowledge can benefit both developmental biology and clinical research such as drug development or epidemiology research. Recently, the rapid advance of single-cell sequencing technologies, which pushed the limit of transcriptomic profiling to the individual cell level, opens up an entirely new area for regulatory network research. To exploit this new abundant source of data and take advantage of data in single-cell resolution, a number of computational methods have been proposed to uncover the interactions hidden by the averaging process in standard bulk sequencing. In this article, we review 15 such network inference methods developed for single-cell data. We discuss their underlying assumptions, inference techniques, usability, and pros and cons. In an extensive analysis using simulation, we also assess the methods’ performance, sensitivity to dropout and time complexity. The main objective of this survey is to assist not only life scientists in selecting suitable methods for their data and analysis purposes but also computational scientists in developing new methods by highlighting outstanding challenges in the field that remain to be addressed in the future development.
ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm
Authors: Shao Jiangyi , Liu Bin 
Published: August 2020

AbstractAs one of the most important tasks in protein structure prediction, protein fold recognition has attracted more and more attention. In this regard, some computational predictors have been proposed with the development of machine learning and artificial intelligence techniques. However, these existing computational methods are still suffering from some disadvantages. In this regard, we propose a new network-based predictor called ProtFold-DFG for protein fold recognition. We propose the Directed Fusion Graph (DFG) to fuse the ranking lists generated by different methods, which employs the transitive closure to incorporate more relationships among proteins and uses the KL divergence to calculate the relationship between two proteins so as to improve its generalization ability. Finally, the PageRank algorithm is performed on the DFG to accurately recognize the protein folds by considering the global interactions among proteins in the DFG. Tested on a widely used and rigorous benchmark data set, LINDAHL dataset, experimental results show that the ProtFold-DFG outperforms the other 35 competing methods, indicating that ProtFold-DFG will be a useful method for protein fold recognition. The source code and data of ProtFold-DFG can be downloaded from http://bliulab.net/ProtFold-DFG/download
Recognition of Parental Love: Birth Parents’ Experiences with Cooperation When Having a Child Placed in Family Foster Care in Denmark
Authors: Bengtsson Tea Torbenfeldt , Karmsteen Kirstine 
Published: August 2020

AbstractDespite the fact that most children growing up in family foster care remain in contact with their birth parents, the experiences of birth parents have been largely neglected. This article draws on twenty-two in-depth interviews with birth parents to examine their experiences of cooperating with social workers and foster carers. Five patterns of cooperation are empirically identified in the parents’ narratives: (i) constructive cooperation; (ii) ambivalent cooperation; (iii) improved cooperation; (iv) diminishing cooperation and (v) lack of cooperation. While there are key differences in the characteristics of each pattern, there is one central similarity: all the parents seek recognition of their parenthood, especially their love for their child. Thus, actively recognising the role of parental love in parents’ motivation for cooperation can enable social workers to secure better cooperation with birth parents.
‘This is Still All about Love’: Practitioners’ Perspectives of Working with Family Carers Affected by the Harmful Behaviour of the Older Person for Whom They Care
Authors: Isham Louise , Bradbury-Jones Caroline , Hewison Alistair 
Published: August 2020

Abstract
This article explores a hidden and under-acknowledged dimension of caring in family life: when older people with care needs act in a harmful, abusive or violent way towards the family member(s) who cares for them. Thirty-eight health and social care professionals, working in the UK, took part in five focus groups to explore their experience of working with families in this situation. The group discussions were stimulated by vignettes developed from interviews with carers affected by harmful behaviour, and the data generated using this method were analysed using a thematic approach. There were two principal findings: (i) ‘carer harm’ is a serious and under-acknowledged problem, which practitioners have extensive experiential knowledge of and (ii) practitioners face considerable practical and ethical challenges working with affected families. Drawing on Miranda Fricker’s concept of epistemic injustice, we discuss how contemporary social, legal and policy systems can make it difficult for practitioners to identify and meet the needs of affected families. Finally, we explore the role of social workers—and the support they need as a professional group—to work alongside a ‘hidden’ group of families seeking to manage the intersection of care, harm and intimacy in later life.
PET imaging of meningioma with 18F-FLT: a predictor of tumour progression
Authors: Bashir Asma , Vestergaard Mark B , Marner Lisbeth , Larsen Vibeke A , Ziebell Morten , Fugleholm Kåre , Law Ian 
Published: August 2020

Abstract
We have previously reported that PET with 3′-deoxy-3′-18F-fluorothymidine (18F-FLT) provides a non-invasive assessment of cell proliferation in vivo in meningiomas. The purpose of this prospective study was to evaluate the potential of 18F-FLT PET in predicting subsequent tumour progression in asymptomatic meningiomas. Forty-three adult patients harbouring 46 MRI-presumed (n = 40) and residual meningiomas from previous surgery (n = 6) underwent a 60-min dynamic 18F-FLT PET scan prior to radiological surveillance. Maximum and mean tumour-to-blood ratios (TBRmax, TBRmean) of tracer radioactivity were calculated. Tumour progression was defined according to the latest published trial end-point criteria for bidimensional (2D) and corresponding yet exploratory volumetric measurements from the Response Assessment of Neuro-Oncology (RANO) workgroup. Independent-sample t-test, Pearson correlation coefficient, Cox regression, and receiver operating characteristic (ROC) curve analyses were used whenever appropriate. The median follow-up time after 18F-FLT PET imaging was 18 months (range 5–33.5 months). A high concordance rate (91%) was found with regard to disease progression using 2D-RANO (n = 11) versus volumetric criteria (n = 10). Using 2D-RANO criteria, 18F-FLT uptake was significantly increased in patients with progressive disease, compared to patients with stable disease (TBRmax, 5.5 ± 1.3 versus 3.6 ± 1.1, P &lt; 0.0001; TBRmean, 3.5 ± 0.8 versus 2.4 ± 0.7, P &lt; 0.0001). ROC analysis yielded optimal thresholds of 4.4 for TBRmax [sensitivity 82%, specificity 77%, accuracy 78%, and area under curve (AUC) 0.871; P &lt; 0.0001] and 2.8 for TBRmean (sensitivity 82%, specificity 77%, accuracy 78%, AUC 0.848; P = 0.001) for early differentiation of patients with progressive disease from patients with stable disease. Upon excluding patients with residual meningioma or patients with stable disease with less than 12 months follow-up, the thresholds remained unchanged with similar diagnostic accuracies. Moreover, positive correlations were found between absolute and relative tumour growth rates and 18F-FLT uptake (r &lt; 0.513, P &lt; 0.015) that remained similar when excluding patients with residual meningioma or patients with stable disease and shorter follow-up period. Diagnostic accuracies were slightly inferior at 76% when assessing disease progression using volumetric criteria, while the thresholds remained unchanged. Multivariate analysis revealed that TBRmax was the only independent predictor of tumour progression (P &lt; 0.046), while age, gender, baseline tumour size, tumour location, peritumoural oedema, and residual meningioma had no influence. The study reveals that 18F-FLT PET is a promising surrogate imaging biomarker for predicting subsequent tumour progression in treatment-naïve and asymptomatic residual meningiomas.
Splicing machinery dysregulation drives glioblastoma development/aggressiveness: oncogenic role of SRSF3
Authors: Fuentes-Fayos Antonio C , Vázquez-Borrego Mari C , Jiménez-Vacas Juan M , Bejarano Leire , Pedraza-Arévalo Sergio , L.-López Fernando , Blanco-Acevedo Cristóbal , Sánchez-Sánchez Rafael , Reyes Oscar , Ventura Sebastián , Solivera Juan , Breunig Joshua J , Blasco María A , Gahete Manuel D , Castaño Justo P , Luque Raúl M 
Published: August 2020

Abstract
Glioblastomas remain the deadliest brain tumour, with a dismal ∼12–16-month survival from diagnosis. Therefore, identification of new diagnostic, prognostic and therapeutic tools to tackle glioblastomas is urgently needed. Emerging evidence indicates that the cellular machinery controlling the splicing process (spliceosome) is altered in tumours, leading to oncogenic splicing events associated with tumour progression and aggressiveness. Here, we identify for the first time a profound dysregulation in the expression of relevant spliceosome components and splicing factors (at mRNA and protein levels) in well characterized cohorts of human high-grade astrocytomas, mostly glioblastomas, compared to healthy brain control samples, being SRSF3, RBM22, PTBP1 and RBM3 able to perfectly discriminate between tumours and control samples, and between proneural-like or mesenchymal-like tumours versus control samples from different mouse models with gliomas. Results were confirmed in four additional and independent human cohorts. Silencing of SRSF3, RBM22, PTBP1 and RBM3 decreased aggressiveness parameters in vitro (e.g. proliferation, migration, tumorsphere-formation, etc.) and induced apoptosis, especially SRSF3. Remarkably, SRSF3 was correlated with patient survival and relevant tumour markers, and its silencing in vivo drastically decreased tumour development and progression, likely through a molecular/cellular mechanism involving PDGFRB and associated oncogenic signalling pathways (PI3K-AKT/ERK), which may also involve the distinct alteration of alternative splicing events of specific transcription factors controlling PDGFRB (i.e. TP73). Altogether, our results demonstrate a drastic splicing machinery-associated molecular dysregulation in glioblastomas, which could potentially be considered as a source of novel diagnostic and prognostic biomarkers as well as therapeutic targets for glioblastomas. Remarkably, SRSF3 is directly associated with glioblastoma development, progression, aggressiveness and patient survival and represents a novel potential therapeutic target to tackle this devastating pathology.
Lipid Pathology of the Corpus Callosum in Schizophrenia and the Potential Role of Abnormal Gene Regulatory Networks with Reduced Microglial Marker Expression
Authors: Shimamoto-Mitsuyama Chie , Nakaya Akihiro , Esaki Kayoko , Balan Shabeesh , Iwayama Yoshimi , Ohnishi Tetsuo , Maekawa Motoko , Toyota Tomoko , Dean Brian , Yoshikawa Takeo 
Published: August 2020

AbstractStructural changes in the corpus callosum have been reported in schizophrenia; however, the underlying molecular mechanism remains unclear. As the corpus callosum is high in lipid content, we analyzed the lipid contents of the corpora callosa from 15 patients with schizophrenia and 15 age- and sex-matched controls using liquid chromatography coupled to tandem mass spectrometry and identified lipid combinations associated with schizophrenia. Real-time quantitative polymerase chain reaction analyses using extended samples (schizophrenia, n = 95; control, n = 91) showed low expression levels of lipid metabolism-related genes and their potential upstream transcription factors in schizophrenia. Subsequent pathway analysis identified a gene regulatory network where nuclear factor of activated T cells 2 (NFATC2) is placed most upstream. We also observed low gene expression levels of microglial markers, inflammatory cytokines, and colony-stimulating factor 1 receptor (CSF1R), which is known to regulate the density of microglia, in the corpus callosum in schizophrenia. The interactions between CSF1R and several genes in the presently identified gene network originating from NFATC2 have been reported. Collectively, this study provides evidence regarding lipid abnormalities in the corpora callosa of patients with schizophrenia and proposes the potential role of impaired “NFATC2-relevant gene network-microglial axis” as its underlying mechanism.
An Effective Acid–Base-Induced Liquid–Liquid Microextraction Based on Deep Eutectic Solvents for Determination of Testosterone and Methyltestosterone in Milk
Authors: Li Xiao , Yuan Tao , Zhao Ting , Wu Xiaomei , Yang Yaling 
Published: August 2020

AbstractAn environmentally friendly method for the determination of testosterone and methyltestosterone by acid–base-induced deep eutectic solvents liquid–liquid microextraction (DES-ABLLME) combining with high-performance liquid chromatography was established. The deep eutectic solvent (DES) consisting of menthol:lauric acid:decanoic acid (3:1:1) can act as both hydrogen bond donor and hydrogen bond acceptor. In this approach, ammonia solution (NH3•H2O) is used as an emulsifier to react with DESs in the extraction process to generate salt and form milky white solution, achieving high extraction efficiency. Hydrochloric acid was used as a phase separator to change the emulsification state and promote the separation of extraction agent from water phase. A series of parameters were optimized including the volume of DES and the emulsifying agent, glucose concentration as well as hydrochloric acid volume. The method was linear in the range 0.5–100 μg mL−1 with a correlation coefficient (R) of 0.9999, and the limits of detection were 0.067 and 0.2 μg mL−1 for testosterone and methyltestosterone, respectively. This method was applied to analyze testosterone and methyltestosterone in milk samples, and the recoveries were between 89.2 and 108.2%.
Adverse Events Among Young Adults Following a Third Dose of Measles-Mumps-Rubella Vaccine
Authors: Marin Mona , Fiebelkorn Amy Parker , Bi Daoling , Coleman Laura A , Routh Janell , Curns Aaron T , McLean Huong Q 
Published: August 2020

Abstract

Background
A third measles-mumps-rubella vaccine (MMR) dose (MMR3) is recommended in the United States for persons at increased risk for mumps during outbreaks. MMR3 is also likely given to persons who might have received 2 doses of MMR but lack documentation. Since MMR3 safety data are limited, we describe adverse events in persons receiving MMR3 in a nonoutbreak setting.

Methods
Young adults with 2 documented MMR doses were administered MMR3. From 2 weeks before until 4 weeks after MMR3 receipt, participants reported daily on 11 solicited, common symptoms potentially associated with MMR. Weekly rate differences in post- vs prevaccination (baseline) were evaluated by Poisson regression. Baseline rates were subtracted from postvaccination rates of significantly different symptoms to estimate the number and percentage of participants with excess risk for symptoms post-MMR3. Descriptive analyses were performed for 3 postvaccination injection-site symptoms.

Results
The 662 participants were aged 18–28 years (median = 20 years); 56% were women. Headache, joint problems, diarrhea, and lymphadenopathy rates were significantly higher postvaccination vs baseline. We estimate that 119 participants (18%) reported more symptoms after MMR3 than prevaccination. By symptom, 13%, 10%, 8%, and 6% experienced increased symptoms of headache, joint problems, diarrhea, and lymphadenopathy, respectively, after MMR3. The median onset was Days 3–6 postvaccination; the median duration was 1–2 days. One healthcare visit for a potential vaccination-related symptom (urticaria) was reported. Injection-site symptoms were reported by 163 participants (25%); the median duration was 1–2 days.

Conclusions
Reported systemic and local events were mild and transient. MMR3 is safe and tolerable among young adults.
A Pediatric Infectious Disease Perspective on COVID-19
Authors: Wald Ellen R , Schmit Kathryn M , Gusland Daniele Y 
Published: August 2020

Abstract
This review highlights the clinical and epidemiologic characteristics of coronavirus disease 2019 (COVID-19) in children and neonates and contrasts these features with other common respiratory viruses. Although the majority of infections in children are mild, there are many important, as yet, unanswered questions (specifically, the attack rate in children and the role of children as vectors of infection) that will have a major impact on disease in adults. There are no distinctive clinical characteristics that will allow the infectious disease consultant to make the diagnosis without laboratory testing. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appears to be less common, with lower morbidity and mortality than respiratory syncytial virus or influenza, and causes less-severe disease in children with cancer than these more common viruses. The range of severity of infection during pregnancy is comparable to infection in nonpregnant cohorts. Intrauterine infection has been documented but is uncommon. A theme of less-severe disease in individuals with modulated immune systems is emerging.