bluuebunny/crossref_metadata_2025_split huggingface dataset:
Power brushing and chemical denture cleansers induced color changes of pre-polymerized CAD/CAM denture acrylic resins
Authors: Alfouzan Afnan F , AlNouwaisar Alhanouf N , AlAzzam Njood F , Al-Otaibi Hanan N , Labban Nawaf , Alswaidan Mashaal H , Al Taweel Sara M , Alshehri Huda A 
Published: August 2021

Abstract
Denture wearers are advised to follow the protocol of using both mechanical and chemical hygiene methods. In this study, the in-vitro color stability of heat-cured, light-cured and newly developed pre-polymerized CAD/CAM acrylic resin base materials were evaluated after exposure to mechanical brushing and chemical denture cleansers. Two polymethyl methacrylate (PMMA) (heat-cured, and pre-polymerised CAD/CAM) and one urethane dimethacrylate based resin denture base material were subjected to mechanical brushing, followed by immersion in chemical denture cleansers (Corega, 5.25% Sodium hypochlorite (NaOCl), and 0.2% chlorhexidine gluconate (CHG)) and thermal-cycling to simulate one-year of normal prosthesis use. Baseline and final color measurements were determined and the difference in color was calculated using bench-top UV light visible spectrophotometer. The highest (29.69 ± 1.84) and lowest (19.03 ± 8.78) mean ΔE was observed with light-cured and CAD/CAM materials immersed in 0.2% CHG, respectively. Tukey’s post-hoc test showed that heat cured and light-cured resins immersed in either of the denture cleansers showed no significant differences (p > 0.05) in the mean ΔE values. On the contrary, CAD/CAM materials immersed in either of the denture cleansers demonstrated significant differences in the mean ΔE values (p ≤ 0.05). A statistically significant interaction between the combination of materials and denture cleansers (F = 4.890; p = 0.001) was observed. The color stability of the pre-polymerized CAD/CAM acrylic discs is comparatively better than the conventional acrylic resin materials. The changes in the color values of all the tested materials were above the clinically acceptable range, regardless of the type of denture cleanser used.
An open-endcap blade trap for radial-2D ion crystals
Authors: Xie Yuanheng , Cui Jiafeng , D’Onofrio Marissa , Rasmusson A J , Howell Stephen W , Richerme Philip 
Published: August 2021

Abstract
We present the design and experimental demonstration of an open-endcap radio frequency trap to confine ion crystals in the radial-two dimensional (2D) structural phase. The central axis of the trap is kept free of obstructions to allow for site-resolved imaging of ions in the 2D crystal plane, and the confining potentials are provided by four segmented blade electrodes. We discuss the design challenges, fabrication techniques, and voltage requirements for implementing this open-endcap trap. Finally, we validate its operation by confining up to 29 ions in a 2D triangular lattice, oriented such that both in-plane principal axes of the 2D crystal lie in the radial direction.
DeepLncLoc: a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding
Authors: Zeng Min , Wu Yifan , Lu Chengqian , Zhang Fuhao , Wu Fang-Xiang , Li Min 
Published: August 2021

AbstractLong non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. A growing amount of evidence reveals that subcellular localization of lncRNAs can provide valuable insights into their biological functions. Existing computational methods for predicting lncRNA subcellular localization use k-mer features to encode lncRNA sequences. However, the sequence order information is lost by using only k-mer features. We proposed a deep learning framework, DeepLncLoc, to predict lncRNA subcellular localization. In DeepLncLoc, we introduced a new subsequence embedding method that keeps the order information of lncRNA sequences. The subsequence embedding method first divides a sequence into some consecutive subsequences and then extracts the patterns of each subsequence, last combines these patterns to obtain a complete representation of the lncRNA sequence. After that, a text convolutional neural network is employed to learn high-level features and perform the prediction task. Compared with traditional machine learning models, popular representation methods and existing predictors, DeepLncLoc achieved better performance, which shows that DeepLncLoc could effectively predict lncRNA subcellular localization. Our study not only presented a novel computational model for predicting lncRNA subcellular localization but also introduced a new subsequence embedding method which is expected to be applied in other sequence-based prediction tasks. The DeepLncLoc web server is freely accessible at http://bioinformatics.csu.edu.cn/DeepLncLoc/, and source code and datasets can be downloaded from https://github.com/CSUBioGroup/DeepLncLoc.
ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data
Authors: Zhang Wei , Xu Hanwen , Qiao Rong , Zhong Bixi , Zhang Xianglin , Gu Jin , Zhang Xuegong , Wei Lei , Wang Xiaowo 
Published: August 2021

Abstract
Quantifying cell proportions, especially for rare cell types in some scenarios, is of great value in tracking signals associated with certain phenotypes or diseases. Although some methods have been proposed to infer cell proportions from multicomponent bulk data, they are substantially less effective for estimating the proportions of rare cell types which are highly sensitive to feature outliers and collinearity. Here we proposed a new deconvolution algorithm named ARIC to estimate cell type proportions from gene expression or DNA methylation data. ARIC employs a novel two-step marker selection strategy, including collinear feature elimination based on the component-wise condition number and adaptive removal of outlier markers. This strategy can systematically obtain effective markers for weighted $\upsilon$-support vector regression to ensure a robust and precise rare proportion prediction. We showed that ARIC can accurately estimate fractions in both DNA methylation and gene expression data from different experiments. We further applied ARIC to the survival prediction of ovarian cancer and the condition monitoring of chronic kidney disease, and the results demonstrate the high accuracy and robustness as well as clinical potentials of ARIC. Taken together, ARIC is a promising tool to solve the deconvolution problem of bulk data where rare components are of vital importance.
The heritable legacy of diethylstilbestrol: a bellwether for endocrine disruption in humans
Authors: Robotti Suzanne 
Published: August 2021

Abstract
Millions of women and their fetuses were exposed to the toxic pregnancy drug diethylstilbestrol (DES) from the 1940s into the 1970s, a time when the medical profession had little knowledge about potential developmental consequences of fetal drug exposures. Pathological consequences of DES exposure to the pregnant mothers and their offspring are well documented, but now generational research is finding that the grandchildren of women given DES in pregnancy are also at risk. This commentary summarizes presentations on this subject from the Beyond Genes panel “Heritable Impacts of Diethylstilbestrol (DES).”
Cloud-Based Environmental Monitoring to Streamline Remote Sensing Analysis for Biologists
Authors: Stahl Amanda T , Fremier Alexander K , Heinse Laura 
Published: August 2021

Abstract
Timely, policy-relevant monitoring data are essential for evaluating the effectiveness of environmental policies and conservation measures. Satellite and aerial imagery can fill data gaps at low cost but are often underused for ongoing environmental monitoring. Barriers include a lack of expertise or computational resources and the lag time between image acquisition and information delivery. Online image repositories and cloud computing platforms are increasingly used by researchers because they offer near-real-time, centralized access to local-to-global-scale data sets and analytics with minimal in-house computational requirements. We aim to broaden knowledge of these open access resources for biologists whose work routinely informs policy and management. To illustrate potential applications of cloud-based environmental monitoring (CBEM), we developed an adaptable approach to detect changes in natural vegetative cover in an agricultural watershed. The steps we describe can be applied to identify opportunities and caveats for applying CBEM in a wide variety of monitoring programs.
Intravenous delivery of adeno-associated viral gene therapy in feline GM1 gangliosidosis
Authors: Gross Amanda L , Gray-Edwards Heather L , Bebout Cassie N , Ta Nathan L , Nielsen Kayly , Brunson Brandon L , Lopez Mercado Kalajan R , Osterhoudt Devin E , Batista Ana Rita , Maitland Stacy , Seyfried Thomas N , Sena-Esteves Miguel , Martin Douglas R 
Published: August 2021

Abstract
GM1 gangliosidosis is a fatal neurodegenerative disease caused by a deficiency of lysosomal β-galactosidase. In its most severe form, GM1 gangliosidosis causes death by 4 years of age, and no effective treatments exist. Previous work has shown that injection of the brain parenchyma with an adeno-associated viral (AAV) vector provides pronounced therapeutic benefit in a feline GM1 model. To develop a less invasive treatment for the brain and increase systemic biodistribution, intravenous injection of AAV9 was evaluated.
AAV9 expressing feline β-galactosidase was intravenously administered at 1.5×1013 vector genomes/kg body weight to six GM1 cats at ∼1 month of age. The animals were divided into two cohorts: (i) a long-term group, which was followed to humane end point; and (ii) a short-term group, which was analysed 16 weeks post-treatment. Clinical assessments included neurological exams, CSF and urine biomarkers, and 7 T MRI and magentic resonance spectroscopy (MRS). Post-mortem analysis included β-galactosidase and virus distribution, histological analysis and ganglioside content.
Untreated GM1 animals survived 8.0 ± 0.6 months while intravenous treatment increased survival to an average of 3.5 years (n = 2) with substantial improvements in quality of life and neurological function. Neurological abnormalities, which in untreated animals progress to the inability to stand and debilitating neurological disease by 8 months of age, were mild in all treated animals. CSF biomarkers were normalized, indicating decreased CNS cell damage in the treated animals. Urinary glycosaminoglycans decreased to normal levels in the long-term cohort. MRI and MRS showed partial preservation of the brain in treated animals, which was supported by post-mortem histological evaluation. β-Galactosidase activity was increased throughout the CNS, reaching carrier levels in much of the cerebrum and normal levels in the cerebellum, spinal cord and CSF. Ganglioside accumulation was significantly reduced by treatment. Peripheral tissues such as heart, skeletal muscle, and sciatic nerve also had normal β-galactosidase activity in treated GM1 cats. GM1 histopathology was largely corrected with treatment. There was no evidence of tumorigenesis or toxicity.
Restoration of β-galactosidase activity in the CNS and peripheral organs by intravenous gene therapy led to profound increases in lifespan and quality of life in GM1 cats. These data support the promise of intravenous gene therapy as a safe, effective treatment for GM1 gangliosidosis.
The contribution of beta-amyloid to dementia in Lewy body diseases: a 1-year follow-up study
Authors: Biundo Roberta , Weis Luca , Fiorenzato Eleonora , Pistonesi Francesca , Cagnin Annachiara , Bertoldo Alessandra , Anglani Mariagiulia , Cecchin Diego , Antonini Angelo 
Published: August 2021

AbstractDementia in Lewy Body Diseases (Parkinson’s disease and dementia with Lewy Bodies) affects progression of disabilities, quality of life and well-being. Understanding its pathogenetic mechanisms is critical to properly implement disease-modifying strategies. It has been hypothesized that synuclein- and amyloid-pathology act synergistically aggravating cognitive decline in elderly patients but their precise contribution to dementia is debated. In this study, we aimed at exploring if presence of amyloid deposits influences clinical, cognitive and neuroanatomical correlates of mental decline in a cohort of 40 Parkinson’s disease patients with normal cognition (n = 5), mild cognitive impairment (n = 22), and dementia (n = 13) as well as in Dementia with Lewy Bodies (n = 10). Patients underwent simultaneous 3 T PET/MRI with [18F]-flutemetamol and were assessed with an extensive baseline motor and neuropsychological examination, which allowed level II diagnosis of mild cognitive impairment and dementia. The role of amyloid positivity on each cognitive domain, and on the rate of conversion to dementia at 1-year follow-up was explored. A Kaplan Meier and the Log Rank (Mantel–Cox) test were used to assess the pairwise differences in time-to-develop dementia in Parkinson’s disease patients with and without significant amyloidosis. Furthermore, the presence of an Alzheimer’s dementia-like morphological pattern was evaluated using visual and automated assessment of T1-weighted and T2-weighted MRI images. We observed similar percentage of amyloid deposits in Parkinson’s disease dementia and dementia with Lewy Bodies cohorts (50% in each group) with an overall prevalence of 34% of significant amyloid depositions in Lewy Body Diseases. PET amyloid positivity was associated with worse global cognition (Montreal Cognitive Assessment and Mini Mental State Examination), executive and language difficulties. At 12-month follow-up, amyloid positive Parkinson’s disease patients were more likely to have become demented than those without amyloidosis. Moreover, there was no difference in the presence of an Alzheimer’s disease-like atrophy pattern and in vascular load (at Fazekas scale) between Lewy Body Diseases with and without significant amyloid deposits. Our findings suggest that in Lewy Body Diseases, amyloid deposition enhances cognitive deficits, particularly attention-executive and language dysfunctions. However, the large number of patients without significant amyloid deposits among our cognitively impaired patients indicates that synuclein pathology itself plays a critical role in the development of dementia in Lewy Body Diseases.
Posterior cortical atrophy phenotypic heterogeneity revealed by decoding 18F-FDG-PET
Authors: Townley Ryan A , Botha Hugo , Graff-Radford Jonathan , Whitwell Jennifer , Boeve Bradley F , Machulda Mary M , Fields Julie A , Drubach Daniel A , Savica Rodolfo , Petersen Ronald C , Senjem Matthew L , Knopman David S , Lowe Val J , Jack Clifford R , Josephs Keith A , Jones David T 
Published: August 2021

Abstract
Posterior cortical atrophy is a neurodegenerative syndrome with a heterogeneous clinical presentation due to variable involvement of the left, right, dorsal and ventral parts of the visual system, as well as inconsistent involvement of other cognitive domains and systems. 18F-fluorodeoxyglucose (FDG)-PET is a sensitive marker for regional brain damage or dysfunction, capable of capturing the pattern of neurodegeneration at the single-participant level. We aimed to leverage these inter-individual differences on FDG-PET imaging to better understand the associations of heterogeneity of posterior cortical atrophy. We identified 91 posterior cortical atrophy participants with FDG-PET data and abstracted demographic, neurologic, neuropsychological and Alzheimer’s disease biomarker data. The mean age at reported symptom onset was 59.3 (range: 45–72 years old), with an average disease duration of 4.2 years prior to FDG-PET scan, and a mean education of 15.0 years. Females were more common than males at 1.6:1. After standard preprocessing steps, the FDG-PET scans for the cohort were entered into an unsupervised machine learning algorithm which first creates a high-dimensional space of inter-individual covariance before performing an eigen-decomposition to arrive at a low-dimensional representation. Participant values (‘eigenbrains’ or latent vectors which represent principle axes of inter-individual variation) were then compared to the clinical and biomarker data. Eight eigenbrains explained over 50% of the inter-individual differences in FDG-PET uptake with left (eigenbrain 1) and right (eigenbrain 2) hemispheric lateralization representing 24% of the variance. Furthermore, eigenbrain-loads mapped onto clinical and neuropsychological data (i.e. aphasia, apraxia and global cognition were associated with the left hemispheric eigenbrain 1 and environmental agnosia and apperceptive prosopagnosia were associated with the right hemispheric eigenbrain 2), suggesting that they captured important axes of normal and abnormal brain function. We used NeuroSynth to characterize the eigenbrains through topic-based decoding, which supported the idea that the eigenbrains map onto a diverse set of cognitive functions. These eigenbrains captured important biological and pathophysiologic data (i.e. limbic predominant eigenbrain 4 patterns being associated with older age of onset compared to frontoparietal eigenbrain 7 patterns being associated with younger age of onset), suggesting that approaches that focus on inter-individual differences may be important to better understand the variability observed within a neurodegenerative syndrome like posterior cortical atrophy.
The geopolitics behind the routes data travel: a case study of Iran
Authors: Salamatian Loqman , Douzet Frédérick , Salamatian Kavé , Limonier Kévin 
Published: August 2021

Abstract
In November 2019, in the wake of political demonstrations against the regime, Iran managed to selectively cut off most traffic from the global Internet while fully operating its own domestic network. It seemingly confirmed the main hypothesis our research had led us to, based on prior observation of data routing: Iran’s architecture of connectivity enables selective censorship of international traffic. This paper examines, through the case of Iran, how states can leverage the Border Gateway Protocol (BGP) as a tool of geopolitical control and what are the trade-offs they face. This question raises a methodological question that we also address: how the analysis of BGP can infer and document these strategies of territorialization of cyberspace. The Internet is a network of networks where each network is an autonomous system. Autonomous systems (ASes) are independent administrative entities controlled by a variety of actors such as governments, companies and universities. Their administrators have to agree and communicate on the path followed by packets travelling across the Internet, which is made possible by BGP. Agreements between ASes are often confidential but BGP requires neighbouring ASes to interact with each other in order to coordinate routing through the constant release of connectivity update messages. These messages announce the availability (or withdrawal) of a sequence of ASes that can be followed to reach an IP address prefix. In our study, we inferred the structure of Iran's connectivity through the capture and analysis of these BGP announcements. We show how the particularities of Iran's BGP and connectivity structure can enable active measures, such as censorship, both internally and externally throughout the network. We argue that Iran has found a way to reconcile a priori conflicting strategic goals: developing a self-sustaining and resilient domestic Internet, but with tight control at its borders. It thus enables the regime to leverage connectivity as a tool of censorship in the face of social instability and as a tool of regional influence in the context of strategic competition.
Laminopathies: should Wenckebach be a cause for concern? A case report
Authors: Sen Gautam , Jackson Tom 
Published: August 2021

Abstract

Background
LMNA cardiomyopathy is a cause of dilated cardiomyopathy (DCM) characterized by aggressive heart failure, high risk of arrhythmias, and sudden cardiac death. We present a case of a male presenting with an LMNA mutation with an aggressive DCM leading to sudden cardiac death (SCD).

Case summary
A 42-year-old male presented with the feeling of lethargy and intermittent dizziness. Electrocardiogram demonstrated atrioventricular block in keeping with Mobitz type 1, at a rate of 40 b.p.m. and cardiac monitoring showed non-sustained ventricular tachycardia. Cardiac magnetic resonance imaging showed preserved left ventricular (LV) ejection function (59%) but features suggesting DCM. These included mild LV dilatation with an end diastolic volume (EDV) of 213 mL and late enhancement showing a single mid myocardial focus of high signal over the distal right ventricular insertion point inferiorly and a linear area of high signal over the basal septum. After discussion at the cardiology multi-disciplinary meeting, a pacemaker was implanted so that beta-blockers could be initiated to suppress the ventricular arrhythmias. A laminopathy was suspected and if this was confirmed from genetic testing the plan was to upgrade to an implantable defibrillator. Due to stability, this was decided to be done in an outpatient setting. He unfortunately had an out-of-hospital VF arrest and died. Post-mortem showed subtle cardiomyopathy in keeping with a DCM. Genetic tests results were returned a few months later which confirmed a pathogenic variant in LMNA.

Discussion
Because of the complexity of LMNA-related cardiac disease, they should be managed and followed up in centres with special expertise in inherited cardiomyopathy.
Fusion cardiac resynchronization therapy in an left ventricular assist device patient from two devices and crossing leads: a case report
Authors: Egorova Anastasia D , van Erven Lieselot , Beeres Saskia L M A , Tops Laurens F 
Published: August 2021

Abstract

Background
Cardiac implanted electronic devices (CIED) have significantly improved the survival and quality of life in heart failure patients. Although implantable cardioverter-defibrillators (ICD) and cardiac resynchronization therapy (CRT) have a major role in patients with moderate to severe heart failure symptoms, the role of these devices in patients with a left ventricular assist device (LVAD) is not yet well defined. The burden of CIED-related procedures in patients with an LVAD is high. The price of lead malfunctions and pocket complications requires creative approaches to tackle CIED-related issues in this patient population.

Case summary
Here, we describe the clinical course of a 67-year-old ventricular pacing dependent LVAD patient with an ICD indication based on recurrent monomorphic ventricular tachycardias and a CRT indication due to previous deterioration of (right-sided) heart failure in the absence of biventricular pacing. We were confronted with impending right ventricular lead failure and bilateral venous access problems due to chronic subclavian vein occlusion in a patient with a total of five transvenous leads, therapeutic anticoagulation, and pronounced thoracic collaterals. We sought for a creative solution to be able to deliver effective biventricular fusion pacing with the existing leads from two contralateral pulse generators resulting in biventricular fusion pacing. This provided the solution to deliver effective CRT.

Discussion
This case illustrates the complexity of care and CIED-related decision-making in pacing dependent LVAD patients, in particularly those with an ICD and CRT indication.