bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perceiving Aesthetic Properties
Authors: Voltolini Alberto 
Published: May 2023

AbstractIn this paper, I want to claim that, in conformity with overall intuitions, there are some aesthetic properties that are perceivable. For they are high-level properties that are not only grasped immediately, but also attended to holistically—just like the grouping properties they depend on and that are responsible for the Gestalt effects or switches through which they are grasped. Yet, unlike such grouping properties, they are holistically attended to in a disinterested modality, where objects and their properties are regarded for their own sake.
The diversification of CaribbeanBuxusin time and space: elevated speciation rates in lineages that accumulate nickel and spreading to other islands from Cuba in non-obligate ultramafic species
Authors: González Gutiérrez Pedro A , Fuentes-Bazan Susy , Di Vincenzo Vanessa , Berazaín-Iturralde Rosalina , Borsch Thomas 
Published: May 2023

AbstractBackground and AimsThe genus Buxus has high levels of endemism in the Caribbean flora, with ~50 taxa. In Cuba, 82 % grow on ultramafic substrates and 59 % are nickel (Ni) accumulators or Ni hyperaccumulators. Hence it is an ideal model group to study if this diversification could be related to adaptation to ultramafic substrates and to Ni hyperaccumulation.MethodsWe generated a well-resolved molecular phylogeny, including nearly all of the Neotropical and Caribbean Buxus taxa. To obtain robust divergence times we tested for the effects of different calibration scenarios, and we reconstructed ancestral areas and ancestral character states. Phylogenetic trees were examined for trait-independent shifts in diversification rates and we used multi-state models to test for state-dependent speciation and extinction rates. Storms could have contributed to Cuba acting as a species pump and to Buxus reaching other Caribbean islands and northern South America’.Key ResultsWe found a Caribbean Buxus clade with Mexican ancestors, encompassing three major subclades, which started to radiate during the middle Miocene (13.25 Mya). Other Caribbean islands and northern South America were reached from ~3 Mya onwards.ConclusionsAn evolutionary scenario is evident in which Buxus plants able to grow on ultramafic substrates by exaptation became ultramafic substrate endemics and evolved stepwise from Ni tolerance through Ni accumulation to Ni hyperaccumulation, which has triggered species diversification of Buxus in Cuba. Storms could have contributed to Cuba acting as a species pump and to Buxus reaching other Caribbean islands and northern South America’.
Single-cell RNA-seq data clustering by deep information fusion
Authors: Ren Liangrui , Wang Jun , Li Wei , Guo Maozu , Yu Guoxian 
Published: May 2023

Abstract
Determining cell types by single-cell transcriptomics data is fundamental for downstream analysis. However, cell clustering and data imputation still face the computation challenges, due to the high dropout rate, sparsity and dimensionality of single-cell data. Although some deep learning based solutions have been proposed to handle these challenges, they still can not leverage gene attribute information and cell topology in a sensible way to explore the consistent clustering. In this paper, we present scDeepFC, a deep information fusion-based single-cell data clustering method for cell clustering and data imputation. Specifically, scDeepFC uses a deep auto-encoder (DAE) network and a deep graph convolution network to embed high-dimensional gene attribute information and high-order cell–cell topological information into different low-dimensional representations, and then fuses them to generate a more comprehensive and accurate consensus representation via a deep information fusion network. In addition, scDeepFC integrates the zero-inflated negative binomial (ZINB) into DAE to model the dropout events. By jointly optimizing the ZINB loss and cell graph reconstruction loss, scDeepFC generates a salient embedding representation for clustering cells and imputing missing data. Extensive experiments on real single-cell datasets prove that scDeepFC outperforms other popular single-cell analysis methods. Both the gene attribute and cell topology information can improve the cell clustering.
RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor
Authors: Ramos Marcel , Morgan Martin , Geistlinger Ludwig , Carey Vincent J , Waldron Levi 
Published: May 2023

Abstract

Summary
The RaggedExperiment R / Bioconductor package provides lossless representation of disparate genomic ranges across multiple specimens or cells, in conjunction with efficient and flexible calculations of rectangular-shaped summaries for downstream analysis. Applications include statistical analysis of somatic mutations, copy number, methylation, and open chromatin data. RaggedExperiment is compatible with multimodal data analysis as a component of MultiAssayExperiment data objects, and simplifies data representation and transformation for software developers and analysts.

Motivation and Results
Measurement of copy number, mutation, single nucleotide polymorphism, and other genomic attributes that may be stored as VCF files produce “ragged” genomic ranges data: i.e. across different genomic coordinates in each sample. Ragged data are not rectangular or matrix-like, presenting informatics challenges for downstream statistical analyses. We present the RaggedExperiment R/Bioconductor data structure for lossless representation of ragged genomic data, with associated reshaping tools for flexible and efficient calculation of tabular representations to support a wide range of downstream statistical analyses. We demonstrate its applicability to copy number and somatic mutation data across 33 TCGA cancer datasets.
BRGenomics for analyzing high-resolution genomics data in R
Authors: DeBerardine Michael 
Published: May 2023

Abstract

Summary
I present here the R/Bioconductor package BRGenomics, which provides fast and flexible methods for post-alignment processing and analysis of high-resolution genomics data within an interactive R environment. Utilizing GenomicRanges and other core Bioconductor packages, BRGenomics provides various methods for data importation and processing, read counting and aggregation, spike-in and batch normalization, re-sampling methods for robust ‘metagene’ analyses, and various other functions for cleaning and modifying sequencing and annotation data. Simple yet flexible, the included methods are optimized for handling multiple datasets simultaneously, make extensive use of parallel processing, and support multiple strategies for efficiently storing and quantifying different kinds of data, including whole reads, quantitative single-base data, and run-length encoded coverage information. BRGenomics has been used to analyze ATAC-seq, ChIP-seq/ChIP-exo, PRO-seq/PRO-cap, and RNA-seq data; is built to be unobtrusive and maximally compatible with the Bioconductor ecosystem; is extensively tested; and includes complete documentation, examples, and tutorials.

Availability and implementation
BRGenomics is an R package distributed through Bioconductor (https://bioconductor.org/packages/BRGenomics). Full documentation with examples and tutorials are available online (https://mdeber.github.io).
‘Caring as a Female Concern’: Social Work Students’ Choices within the Boundaries of care
Authors: Cowan Fiona , Robinson Kim 
Published: May 2023

Abstract
Australian social work university cohorts are increasingly made up of female, mature-aged students. The Australian Association of Social Workers (AASW) mandates a requirement of 1,000 h of unpaid field education across two placements, with full-time attendance as the norm. There is a growing body of research that suggests students experience financial, social, emotional and psychological stress during lengthy unpaid field placements. Yet little is currently known about the impacts specific to female students who have caring responsibilities at the time of their placement. In response, this initial Honours research conducted by a student with this lived experience explored the experiences of fifteen female social work students who had caring responsibilities at the time of their field placements. The analysis was situated in a feminist paradigm and generated five themes from the student responses, and this article focuses on one theme, ‘caring as a female concern’. The findings suggest that mature aged female students who juggle caring responsibilities, unpaid placement and other life responsibilities are particularly disadvantaged at the time of field placement, to the detriment of their own and their families’ financial, social, emotional, and psychological wellbeing. It calls for urgent changes to the AASW accreditation standards.
Cerebrospinal fluid transcripts may predict shunt surgery responses in normal pressure hydrocephalus
Authors: Levin Zachary , Leary Owen P , Mora Victor , Kant Shawn , Brown Sarah , Svokos Konstantina , Akbar Umer , Serre Thomas , Klinge Petra , Fleischmann Alexander , Ruocco Maria Grazia 
Published: May 2023

Abstract
Molecular biomarkers for neurodegenerative diseases are critical for advancing diagnosis and therapy. Normal pressure hydrocephalus (NPH) is a neurological disorder characterized by progressive neurodegeneration, gait impairment, urinary incontinence and cognitive decline. In contrast to most other neurodegenerative disorders, NPH symptoms can be improved by the placement of a ventricular shunt that drains excess CSF. A major challenge in NPH management is the identification of patients who benefit from shunt surgery. Here, we perform genome-wide RNA sequencing of extracellular vesicles in CSF of 42 NPH patients, and we identify genes and pathways whose expression levels correlate with gait, urinary or cognitive symptom improvement after shunt surgery. We describe a machine learning algorithm trained on these gene expression profiles to predict shunt surgery response with high accuracy. The transcriptomic signatures we identified may have important implications for improving NPH diagnosis and treatment and for understanding disease aetiology.
Cognitive and neuropsychiatric endophenotypes in amyotrophic lateral sclerosis
Authors: Costello Emmet , Ryan Marie , Donohoe Bronagh , Kavanagh Caoimhe , Pinto-Grau Marta , Doherty Mark , McLaughlin Russell Lewis , McHutchison Caroline , Abrahams Sharon , Heverin Mark , Hardiman Orla , Pender Niall 
Published: May 2023

Abstract
First- and second-degree relatives of people with amyotrophic lateral sclerosis report higher rates of neuropsychiatric disorders, indicating that risk genes may be pleiotropic, causing multiple phenotypes within kindreds. Such phenotypes may constitute a disease endophenotype that associates with disease liability. We have directly investigated cognitive functioning and neuropsychiatric traits among relatives of people with amyotrophic lateral sclerosis to identify potential endophenotypes of the disease. In a family-based, cross-sectional study design, first- and second-degree relatives of people with amyotrophic lateral sclerosis (n = 149) were compared to controls (n = 60) using an in-depth neuropsychological and neuropsychiatric assessment. Subgroup analyses examined the effect of family history and C9orf72 repeat expansion status (n = 16 positive carriers). Relatives of people with amyotrophic lateral sclerosis had lower scores on executive functioning, language and memory tasks compared to controls, with large effect sizes observed on object naming (d = 0.91, P = 0.00001) and phonemic verbal fluency (d = 0.81, P = 0.0003). Relatives also had higher autism quotient attention to detail traits (d = −0.52, P = 0.005), lower conscientiousness (d = 0.57, P = 0.003) and lower openness to experience personality traits (d = 0.54, P = 0.01) than controls. These effects were typically larger in relatives of people with familial, rather than sporadic, amyotrophic lateral sclerosis and were present in both gene carrier and non-carrier relatives of probands with a C9orf72 repeat expansion. Poorer phonemic fluency and object naming, along with autism and personality traits, are more frequent in relatives of people with amyotrophic lateral sclerosis. Among kindreds carrying the C9orf72 repeat expansion, these traits were identified in relatives regardless of their carrier status, suggesting the presence of a disease-associated endophenotype that is not exclusively mediated by the C9orf72 expansion.
Risk and resilience: exploring the potential of LGBTQ third sector and academic partnership
Authors: Nodin Nuno , Pestano Catherine , Peel Elizabeth , Rivers Ian , Tyler Allan 
Published: May 2023

Abstract
The Risk and Resilience Explored [RaRE] Project (2010–2016) was a collaborative process involving a third sector agency, university partners and volunteers to better understand the risk and resilience factors associated with specific mental health issues among lesbian, gay, bisexual, trans, and queer (LGBTQ) people. In this article, we discuss the project’s collaborative ethos, based on a Community-Based Participatory Research (CBPR) approach. We explain how the CBPR approach benefitted from including academic partners from the onset of the project, as well as from the direct and indirect engagement of community volunteers. We then explore some of our experience of third sector and academic partner collaboration in more depth, highlighting topic summaries salient to this partnership: support and continuity, upskilling of staff and volunteers for mutual benefit, accessible communication across sectors, and aligning priorities. We conclude by setting out recommendations based on our experience for those interested in developing similarly collaborative projects.
Determination of Related Substances in Promethazine Hydrochloride and Dextromethorphan Hydrobromide in Oral Solution by RP-HPLC Method
Authors: Patil Amruta Sainath , Amrutkar Sunil V , Nalwade Santaji 
Published: May 2023

Abstract
The goal of this study is to provide a single, widely applicable high-performance liquid chromatographic (HPLC) technique for the determination of related substances in multicomponent oral solution of promethazine hydrochloride and dextromethorphan hydrobromide. For the assessment of impurities of promethazine hydrochloride and dextromethorphan hydrobromide in oral solution, a unique, sensitive, quick, stability-indicating gradient HPLC technique has been created. For chromatographic separation, an Agilent Eclipse XDB-C18, 250 mm × 4.6 mm, 5 μm column was used with a buffered mobile phase consisting of a mixture of potassium dihydrogen phosphate pH 3.0:acetonitrile (80:20) v/v as mobile phase A and potassium dihydrogen phosphate pH 3.0:acetonitrile:methanol (10:10:80) v/v/v as mobile phase B. The separation was performed at a flow rate of 1.2 mL/min and a detection wavelength of 224 nm. The temperature of the column oven was regulated at 40°C. With good sensitivity and resolution, all compounds were effectively separated on a reverse-phase HPLC column. Acid, base, photolytic, thermal, oxidative and humidity stress conditions significantly degraded dextromethorphan hydrobromide and promethazine hydrochloride. The developed technique was validated according to the criteria of the International Conference on Harmonization for all validation parameters such as specificity, accuracy, linearity, precision, the limit of detection, the limit of quantitation and robustness.
Information-based estimation of causality networks from high-dimensional multivariate time series
Authors: Fotiadis Akylas , Kugiumtzis Dimitris 
Published: May 2023

Abstract
One of the most challenging aspects in the study of the complex dynamical systems is the estimation of their underlying, interdependence structure. Being in the era of Big Data, this problem gets even more complicated since more observed variables are available. To estimate direct causality effects in this setting, dimension reduction has to be employed in the Granger causality measure. The measure should also be capable to detect non-linear effects, persistently present in real-world complex systems. The model-free information-based measure of partial mutual information from mixed embedding (PMIME) has been developed to address these issues and it was found to perform well on multivariate time series of moderately high dimension. Here, the problem of forming complex networks from direct, possibly non-linear, high-dimensional time series at the order of hundreds is investigated. The performance of the measure PMIME is tested on two coupled dynamical systems in discrete time (coupled Hénon maps) and continuous time (coupled Mackey–Glass delay differential equations). It is concluded that the correct detection of the underlying causality network depends mainly on the network density rather than on its size (number of nodes). Finally, the effect of network size is investigated in the study of the British stock market in the period around Brexit.
Infectious agents and their physiological correlates in early marine Chinook salmon (Oncorhynchus tshawytscha)
Authors: Wang Yuwei , Bass Arthur L , Hinch Scott G , Li Shaorong , Di Cicco Emiliano , Kaukinen Karia H , Ferguson Hugh , Ming Tobi J , Patterson David A , Miller Kristina M 
Published: May 2023

Abstract The early marine life of Pacific salmon is believed to be a critical period limiting population-level survival. Recent evidence suggests that some infectious agents are associated with survival but linkages with underlying physiological mechanisms are lacking. While challenge studies can demonstrate cause and effect relationships between infection and pathological change or mortality, in some cases pathological change may only manifest in the presence of environmental stressors; thus, it is important to gain context from field observations. Herein, we examined physiological correlates with infectious agent loads in Chinook salmon during their first ocean year. We measured physiology at the molecular (gene expression), metabolic (plasma chemistry) and cellular (histopathology) levels. Of 46 assayed infectious agents, 27 were detected, including viruses, bacteria and parasites. This exploratory study identified: Importantly, our study provides the first evidence that the molecular activation of viral disease response and the lesions observed during the development of the PRV-related disease jaundice/anemia in farmed Chinook salmon are also observed in wild juvenile Chinook salmon.
Defining Biological Remission in Crohn’s Disease: Interest, Challenges and Future Directions
Authors: Pierre Nicolas , Vieujean Sophie , Peyrin-Biroulet Laurent , Meuwis Marie-Alice , Louis Edouard 
Published: May 2023

Abstract
In Crohn’s disease, the treat-to-target strategy has been greatly encouraged and has become a standard of care. In this context, defining the target [remission] constitutes a major stake and is fuelling the literature. Currently, clinical remission [symptom control] is no longer the only objective of treatments since it does not allow to closely control inflammation-induced tissue damage. The introduction of endoscopic remission as a therapeutic target clearly represented progress but this examination remains invasive, costly, not well accepted by patients and does not allow tight control of disease activity. More fundamentally, morphological techniques [e.g. endoscopy, histology, ultrasonography] are limited since they do not evaluate the biological activity of the disease but only its consequences. Besides, emerging evidence suggests that biological signs of disease activity could better guide treatment decisions than clinical parameters. In this context, we stress the necessity to define a novel treatment target: biological remission. Based on our previous work, we propose a conceptual definition of biological remission which goes beyond the classical normalization of inflammatory markers [C-reactive protein and faecal calprotectin]: absence of biological signs associated with the risk of short-term relapse and mid-/long-term relapse. The risk of short-term relapse seems essentially to be characterized by a persistent inflammatory state while the risk of mid-/long-term relapse implies a more heterogeneous biology. We discuss the value of our proposal [guiding treatment maintenance, escalation or de-escalation] but also the fact that its clinical implementation would require overcoming major challenges. Finally, future directions are proposed to better define biological remission.
A case report of percutaneous MitraClip implantation in an adult with a double-outlet right ventricle
Authors: Kumar Preetham , Gordon Brent M , Kheiwa Ahmed , Abudayyeh Islam 
Published: May 2023

Abstract

Background
Atrioventricular valve regurgitation (AVVR) is present in up to 75% of Fontan patients, and it is associated with an increased risk of Fontan circulation failure, morbidity, and mortality. Traditional treatment options include surgical repair vs. surgical replacement. We present, to the best of our knowledge, one of the first cases of successful trans-catheter repair of severe common AVVR using the MitraClip device.

Case summary
A 20-year-old male with a history of double-outlet right ventricle (DORV) with unbalanced common atrioventricular canal to the right ventricle, severely hypoplastic left ventricle, and total anomalous pulmonary venous return status post-Fontan procedure presented with progressively worsening dyspnoea on exertion. Transoesophageal echocardiogram demonstrated severe common AVVR. After discussion of the case during the adult congenital heart disease multidisciplinary conference, patient underwent successful placement of two MitraClip devices, reducing the regurgitation from torrential to moderate.

Discussion
MitraClip therapy can be used to alleviate symptoms in patients deemed as high risk for surgery. However, careful attention must be paid to haemodynamics before and after clip placement, which may predict short-term clinical outcomes.
Irisin reduces orthodontic tooth movement in rats by promoting the osteogenic potential in the periodontal ligament
Authors: Yang Yang , Pullisaar Helen , Stunes Astrid Kamilla , Nogueira Liebert Parreiras , Syversen Unni , Reseland Janne Elin 
Published: May 2023

Summary

Objectives
Positive effects of irisin on osteogenic differentiation of periodontal ligament (PDL) cells have been identified previously, this study aims to examine its effect on orthodontic tooth movement (OTM) in vivo.

Materials and methods
The maxillary right first molars of male Wistar rats (n = 21) were moved mesially for 14 days, with submucosal injection of two dosages of irisin (0.1 or 1 μg) or phosphate-buffered saline (control) every third day. OTM was recorded by feeler gauge and micro-computed tomography (μCT). Alveolar bone and root volume were analysed using μCT, and plasma irisin levels by ELISA. Histological characteristics of PDL tissues were examined, and the expression of collagen type I, periostin, osteocalcin (OCN), von Willebrand factor (vWF) and fibronectin type III domain-containing protein 5 (FNDC5) in PDL was evaluated by immunofluorescence staining.

Results
Repeated 1 μg irisin injections suppressed OTM on days 6, 9, and 12. No significant differences were observed in OTM in the 0.1 μg irisin group, or in bone morphometric parameters, root volume or plasma irisin, compared to control. Resorption lacunae and hyalinization were found at the PDL-bone interface on the compression side in the control, whereas they were scarce after irisin administration. The expression of collagen type I, periostin, OCN, vWF, and FNDC5 in PDL was enhanced by irisin administration.

Limitations
The feeler gauge method may overestimate OTM.

Conclusions
Submucosal irisin injection reduced OTM by enhancing osteogenic potential of PDL, and this effect was more significant on the compression side.