bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Features of Late-onset Semantic Dementia
Authors: Mendez Mario F. , Chavez Diana , Desarzant Randy E. , Yerstein Oleg 
Published: May 2020

Background:
Semantic dementia (SD) is characterized by progressive semantic anomia extending to a multimodal loss of semantic knowledge. Although often considered an early-onset dementia, SD also occurs in later life, when it may be misdiagnosed as Alzheimer disease (AD).

Objective:
To evaluate late-onset SD in comparison to early-onset SD and to AD.

Methods:
We identified 74 individuals with SD and then compared those with late-onset SD (≥65 years of age) to those with early-onset SD (<65) on demographic and clinical features. We also compared a subgroup of 23 of the late-onset SD individuals with an equal number of individuals with clinically probable AD.

Results:
Twenty-six (35.1%) of the SD individuals were late onset, and 48 (64.9%) were early onset. There were no differences between the two groups on clinical measures, although greater asymmetry of temporal involvement trended to significance in the late-onset SD group. Compared to the 23 AD individuals, the subgroup of 23 late-onset SD individuals had worse performance on confrontational naming, irregular word reading, and face recognition; however, this subgroup displayed better verbal delayed recall and constructions. The late-onset SD individuals also experienced early personality changes at a time when most individuals with AD had not yet developed behavioral changes.

Conclusions:
Approximately one-third of SD individuals may be late onset, and the differentiation of late-onset SD from AD can lead to better disease management, education, and prognosis. SD may be distinguished by screening for disproportionate changes in reading, face recognition, and personality.
Uncertainty quantification and sensitivity analysis of left ventricular function during the full cardiac cycle
Authors: Campos J. O. , Sundnes J. , dos Santos R. W. , Rocha B. M. 
Published: May 2020

Patient-specific computer simulations can be a powerful tool in clinical applications, helping in diagnostics and the development of new treatments. However, its practical use depends on the reliability of the models. The construction of cardiac simulations involves several steps with inherent uncertainties, including model parameters, the generation of personalized geometry and fibre orientation assignment, which are semi-manual processes subject to errors. Thus, it is important to quantify how these uncertainties impact model predictions. The present work performs uncertainty quantification and sensitivity analyses to assess the variability in important quantities of interest (QoI). Clinical quantities are analysed in terms of overall variability and to identify which parameters are the major contributors. The analyses are performed for simulations of the left ventricle function during the entire cardiac cycle. Uncertainties are incorporated in several model parameters, including regional wall thickness, fibre orientation, passive material parameters, active stress and the circulatory model. The results show that the QoI are very sensitive to active stress, wall thickness and fibre direction, where ejection fraction and ventricular torsion are the most impacted outputs. Thus, to improve the precision of models of cardiac mechanics, new methods should be considered to decrease uncertainties associated with geometrical reconstruction, estimation of active stress and of fibre orientation.
This article is part of the theme issue ‘Uncertainty quantification in cardiac and cardiovascular modelling and simulation’.
Combinatorial Polyacrylamide Hydrogels for Preventing Biofouling on Implantable Biosensors
Authors: Chan Doreen , Chien Jun-Chau , Axpe Eneko , Blankemeier Louis , Baker Samuel W. , Swaminathan Sarath , Piunova Victoria A. , Zubarev Dmitry Yu. , Maikawa Caitlin L. , Grosskopf Abigail K. , Mann Joseph L. , Soh H. Tom , Appel Eric A. 
Published: May 2020

ABSTRACTBiofouling on the surface of implanted medical devices severely hinders device functionality and drastically shortens device lifetime. Poly(ethylene glycol) and zwitterionic polymers are currently considered “gold standard” device coatings to reduce biofouling. To discover novel anti-biofouling materials, we created a combinatorial library of polyacrylamide-based copolymer hydrogels and screened their ability to prevent fouling from serum and platelet-rich plasma in a high-throughput parallel assay. We found certain non-intuitive copolymer compositions exhibit superior antibiofouling properties over current gold standard materials, and employed machine learning to identify key molecular features underpinning their performance. For validation, we coated the surfaces of electrochemical biosensors with our hydrogels and evaluated their anti-biofouling performancein vitroandin vivoin rodent models. Our copolymer hydrogels preserved device function and enabled continuous measurements of a small-molecule drugin vivobetter than gold standard coatings. The novel methodology we describe enables the discovery of anti-biofouling materials that can extend the lifetime of real-timein vivosensing devices.
A Critical Interpretive Synthesis to Develop Quality Assessment Tools for E-Cigarette Reviews: Scope and Protocol
Authors: O’Leary R. , Costanzo F. 
Published: May 2020

ABSTRACTOne component of a systematic review is the quality assessment of studies to determine their inclusion or exclusion. Studies on e-cigarettes are conducted in the contentious atmosphere surrounding tobacco harm reduction, which has resulted at times in research bias. Therefore, the quality assessment of studies on e-cigarettes requires more scrutiny than what is provided by generic tools on study design. This topic-specific quality assessment must examine the tests, measurements, and analysis methods used for their adherence to research standards. Furthermore, the studies need to be carefully screened for bias. Because standard quality assessment tools do not provide this topic-specific guidance, we propose to develop quality assessment tools specifically for reviews on e-cigarettes, and for our living systematic reviews on e-cigarettes for tobacco harm reduction.
BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes fromBacillus thuringiensis
Authors: Liu Hualin , Zheng Jinshui , Bo Dexin , Yu Yun , Ye Weixing , Peng Donghai , Sun Ming 
Published: May 2020

SummaryBacillus thuringiensis(Bt) which is a spore-forming gram-positive bacterium, has been used as the most successful microbial pesticide for decades. Its toxin genes (cry) have been successfully used for the development of GM crops against pests. We have previously developed a web-based insecticidal gene mining tool BtToxin_scanner, which has been proved to be the most important method for miningcrygenes from Bt genome sequences. To facilitate efficiently mining major toxin genes and novel virulence factors from large-scale Bt genomic data, we re-design this tool with a new workflow. Here we present BtToxin_Digger, a comprehensive, high-throughput, and easy-to-use Bt toxin mining tool. It runs fast and can get rich, accurate, and useful results for downstream analysis and experiment designs. Moreover, it can also be used to mine other targeting genes from large-scale genome and metagenome data with the addition of other query sequences.Availability and ImplementationThe BtToxin_Digger codes and instructions are freely available athttps://github.com/BMBGenomics/BtToxin_Digger. A web server of BtToxin_Digger can be found athttp://bcam.hzau.edu.cn/BtToxin_Digger.Contactjszheng@mail.hzau.edu.cn;m98sun@mail.hzau.edu.cn.
Sex-biased migration and admixture in macaque species revealed by comparison between autosomal and X-chromosomal genomic sequences
Authors: Osada Naoki , Matsudaira Kazunari , Hamada Yuzuru , Malaivijitnond Suchinda 
Published: May 2020

AbstractThe role of sex-specific demography in hybridization and admixture of genetically diverged species and populations is essential to understand the mechanisms forming the genomic diversity of sexually reproducing organisms. In order to infer how sex-linked genetic loci have been differentiated undergoing frequent hybridization and admixture, we examined 17 whole-genome sequences of seven species of the genusMacaca, which shows frequent inter-specific hybridization and predominantly female philopatry. We found that hybridization and admixture were prevalent within these species. For three cases of suggested hybrid origin of species/subspecies,M. arctoides,M. fascicularis ssp. aurea, and ChineseM. mulatta, we examined the level of admixture of X chromosomes, which is less affected by male-biased migration than that of autosomes. In one case, we were able to determine thatM. cyclopisandM. fuscatawas genetically closer to ChineseM. mulattathan to the IndianM. mulatta, and the admixture level of ChineseM. mulattaandM. fuscata/cyclopiswas more pronounced on the X chromosome than on autosomes. Since the mitochondrial genomes of ChineseM. mulatta,M. cyclopis, andM. fuscatawere found to cluster together, and the mitochondrial genome of IndianM. mulattais more distantly related, the observed pattern of genetic differentiation on X-chromosomal loci is consistent with the nuclear swamping hypothesis, in which strong, continuous male-biased introgression from the ancestral ChineseM. mulattapopulation to a population related toM. fuscataandM. cyclopisgenerated incongruencies between the genealogies of the mitochondrial and autosomal genomes.
Exposure to hypergravity during zebrafish development alters cartilage material properties and strain distribution
Authors: Lawrence Elizabeth A , Aggleton Jessye A , Loon Jack J. W. A. van , Godivier Josepha , Harniman Robert L. , Pei Jiaxin , Nowlan N. C. , Hammond Chrissy L 
Published: May 2020

AbstractTerrestrial vertebrates have adapted to life on Earth and its constant gravitational field, which exerts load on the body and influences the structure and function of tissues. While the effects of microgravity on muscle and bone homeostasis are well described, the effects of shorter exposures to increased gravitational fields are less well characterized. Here, we exposed zebrafish to 3 and 6g hypergravity from 3-5 days post fertilisation, when key events in jaw cartilage morphogenesis occur. We did not observe changes to growth, or morphology of cartilage or muscle. However, we observed altered mechanical properties of jaw cartilages. We model the impact of these material property changes using Finite Element Analysis and show strain distribution in the jaw is altered following hypergravity. In regions of predicted altered strain we observed local changes to chondrocyte morphology, suggesting altered gravity affects chondrocyte maturation, ultimately leading to changes to cartilage structure and function.
Effects of Antipsychotic Drugs and Potassium Channel Modulators on Cognition-related Local Field Potential Spectral Properties in Mouse Hippocampus and Frontal Cortex
Authors: Sun Dechuan , Kermani Mojtaba , Hudson Matt , He Xin , Rajasekharan Unnithan Ranjith , French Chris 
Published: May 2020

AbstractLocal field potentials (LFPs) recorded intracranially display a range of location specific oscillatory spectra which have been related to cognitive processes. Although the exact mechanisms producing LFPs are not completely understood, it is likely that voltage-gated ion channels which produce action potentials and patterned discharges play a significant role. It is also known that antipsychotic drugs (APDs) affect LFPs spectra and a direct inhibitory effect on voltage-gated potassium (Kv) channels has been reported. Additionally,Kvchannels have been implicated in the pathophysiology of schizophrenia, a disorder for which APDs are primary therapies. In this study we sought to: i) better characterise the effects of two APDs on LFPs and connectivity measures and ii) examine the effects of potassium channel modulators on LFPs and potential overlap of effects with APDs. Intracranial electrodes were implanted in the hippocampus (HIP) and pre-frontal cortex (PFC) of C57BL/6 mice; power spectra, coherence and phase-amplitude cross frequency coupling were measured. Drugs tested were the APDs haloperidol and clozapine as well as voltage-gated potassium channel modulators (KVMs) 4-aminopyridine(4AP), tetraethylammonium (TEA), E-4031 and retigabine. All drugs and vehicle controls were administered intraperitoneally. Both APDs and KVMs significantly reduced gamma power with the exception of 4AP, which conversely increased slow-gamma power. Clozapine and retigabine additionally reduced coherence between HIP and PFC. Phase-amplitude coupling between theta and gamma oscillations in HIP was significantly reduced by the administration of haloperidol and retigabine. These results provide previously undescribed effects of APDs on LFP properties and demonstrate novel modulation of LFP characteristics by KVMs that intriguingly overlaps with the effects of APDs. The possibility of a common mechanism of action deserves further study.
Scorepochs: A Computer-Aided Scoring Tool for Resting-State M/EEG Epochs
Authors: Fraschini Matteo , La Cava Simone Maurizio , Rodriguez Giuseppe , Vitale Andrea , Demuru Matteo 
Published: May 2020

AbstractM/EEG resting-state analysis often requires the definition of the epoch length and the criteria to select which epochs to include in the subsequent steps. However, the effects of epoch selection remain scarcely investigated and the procedure used to (visually) inspect, label, and remove bad epochs is often not documented, thus hindering the reproducibility of the reported results. In this study, we present Scorepochs, a simple and freely available tool for the automatic scoring of resting-state M/EEG epochs that aims to provide an objective method to aid M/EEG experts during epoch selection procedure. We tested our approach on a freely available EEG dataset containing recordings from 109 subjects using the BCI2000 64-channel system.
Unique maternal immune and functional microbial profiles during prenatal stress
Authors: Antonson Adrienne M. , Evans Morgan V. , Galley Jeffrey D. , Chen Helen J. , Rajesekera Therese A. , Lammers Sydney M. , Hale Vanessa L. , Bailey Michael T. , Gur Tamar L. 
Published: May 2020

AbstractMaternal stress during pregnancy is widespread and stress-induced fetal neuroinflammation is thought to derive from a disruption in intrauterine immune homeostasis, though the exact origins are incompletely defined. We aimed to identify divergent immune and microbial metagenome profiles of stressed gestating mice that may underlie detrimental inflammatory signaling at the maternal-fetal interface. In response to stress, maternal glucocorticoid circuit activation corresponded with diminished spleen mass and IL-1β production, reflecting systemic immunosuppression. At the maternal-fetal interface, density of placental mononuclear leukocytes decreased with stress. Yet maternal whole blood leukocyte analysis indicated monocytosis and classical M1 phenotypic shifts. Genome-resolved microbial metagenomic analyses revealed reductions in genes, microbial strains, and metabolic pathways in stressed dams that are primarily associated with pro-inflammatory function. Overall, these data indicate that stress disrupts maternal immunological and microbial regulation during pregnancy, characterized by concurrent anti- and pro-inflammatory signatures, which may displace immune equilibrium at the maternal-fetal interface.
Lifestyle Risk Score for aggregating multiple lifestyle factors: Handling missingness of individual lifestyle components in meta-analysis of gene-by-lifestyle interactions
Authors: Xu Hanfei , Schwander Karen , Brown Michael R , Wang Wenyi , Waken RJ , Boerwinkle Eric , Cupples L Adrienne , de las Fuentes Lisa , van Heemst Diana , Osazuwa-Peters Oyomoare , de Vries Paul S , van Dijk Ko Willems , Sung Yun Ju , Zhang Xiaoyu , Morrison Alanna C , Rao DC , Noordam Raymond , Liu Ching-Ti 
Published: May 2020

AbstractRecent studies consider lifestyle risk score (LRS), an aggregation of multiple lifestyle exposures, in identifying association of gene-lifestyle interaction with disease traits. However, not all cohorts have data on all lifestyle factors, leading to increased heterogeneity in the environmental exposure in collaborative meta-analyses. We compared and evaluated four approaches (Naïve, Safe, Complete and Moderator Approaches) to handle the missingness in LRS-stratified meta-analyses under various scenarios. Compared to “benchmark” results with all lifestyle factors available for all cohorts, the Complete Approach, which included only cohorts with all lifestyle components, was underpowered, and the Naïve Approach, which utilized all available data and ignored the missingness, was slightly liberal. The Safe Approach, which used all data in LRS-exposed group and only included cohorts with all lifestyle factors available in the LRS-unexposed group, and the Moderator Approach, which handled missingness via moderator meta-regression, were both slightly conservative and yielded almost identical p-values. We also evaluated the performance of the Safe Approach under different scenarios. We observed that the larger the proportion of cohorts without missingness included, the more accurate the results compared to “benchmark” results. In conclusion, we generally recommend the Safe Approach to handle heterogeneity in the LRS based genome-wide interaction meta-analyses.
Imaging the mechanisms of anti-CD20 therapyin vivouncovers
Authors: Grandjean Capucine L. , Garcia Zacarias , Lemaître Fabrice , Bréart Béatrice , Bousso Philippe 
Published: May 2020

Anti-CD20 monoclonal antibody (mAb) represents an effective strategy for the treatment of B cell malignancies that may involve complement activity, antibody dependent cellular cytotoxicity (ADCC) and phagocytosis (ADP). While ADP mediated by Kupffer cells is essential to deplete circulating tumors, the relative contribution of each mechanism to the elimination of non-circulating targets has yet to be clarified. Using intravital imaging in a model of MYC-driven B cell lymphoma, we establish here the dominance and limitations of ADP in the bone marrow (BM). We found that tumor cells were stably residing in the BM with little evidence for recirculation. To quantify the contribution of different cytotoxic mechanismsin situ, we designed a dual fluorescent reporter to track phagocytosis and apoptosis in real-time. ADP by BM-associated macrophages was the primary mode of tumor elimination but was no longer active after one hour, resulting only in partial depletion. Moreover, macrophage density was strongly reduced in tumor-rich regions. Given their sessile phenotype, macrophages primarily targeted neighboring tumors, resulting in a substantial spatial constraint. Overcoming spatiotemporal bottlenecks in tumor-targeting Ab therapy represents a critical path towards the design of optimized therapies.Key pointsFunctional intravital imaging establishes antibody-dependent phagocytosis as the major mechanism acting at the tumor site during anti-CD20 therapy.A transient wave of phagocytosis and a limited macrophage density restrict the efficiency of anti-CD20 anti-tumor activity.
ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
Authors: García-Castro Helena , Kenny Nathan J , Álvarez-Campos Patricia , Mason Vincent , Schönauer Anna , Sleight Victoria A. , Neiro Jakke , Aboobaker Aziz , Permanyer Jon , Iglesias Marta , Irimia Manuel , Sebé-Pedrós Arnau , Solana Jordi 
Published: May 2020

AbstractSingle-cell sequencing technologies are revolutionizing biology, but are limited by the need to dissociate fresh samples that can only be fixed at later stages. We present ACME (ACetic-MEthanol) dissociation, a cell dissociation approach that fixes cells as they are being dissociated. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, can be sorted by Fluorescence-Activated Cell Sorting (FACS) and are permeable, enabling combinatorial single-cell transcriptomic approaches. As a proof of principle, we have performed SPLiT-seq with ACME cells to obtain around ∼34K single cell transcriptomes from two planarian species and identified all previously described cell types in similar proportions. ACME is based on affordable reagents, can be done in most laboratories and even in the field, and thus will accelerate our knowledge of cell types across the tree of life.
Local sensitivity analysis of the ‘Membrane shape equation’ derived from the Helfrich energy
Authors: Rangamani P. , Behzadan A. , Holst M. 
Published: May 2020

AbstractThe Helfrich energy is commonly used to model the elastic bending energy of lipid bilayers in membrane mechanics. The governing differential equations for certain geometric characteristics of the shape of the membrane can be obtained by applying variational methods (minimization principles) to the Helfrich energy functional and are well-studied in the axisymmetric framework. However, the Helfrich energy functional and the resulting differential equations involve a number of parameters, and there is little explanation of the choice of parameters in the literature, particularly with respect to the choice of the “spontaneous curvature” term that appears in the functional. In this paper, we present a careful analytical and numerical study of certain aspects of parametric sensitivity of Helfrich’s model. Using simulations of specific model systems, we demonstrate the application of our scheme to the formation of spherical buds and pearled shapes in membrane vesicles.
Forecasting COVID-19 pandemic in Poland according to government regulations and people behavior
Authors: Orzechowska Magdalena , Bednarek Andrzej K. 
Published: May 2020

AbstractThe coronavirus disease 2019 (COVID-19) outbreak is a worldwide pandemic problem that started in China in December 2019 and within a few months spread to all continents. Very high infectivity of SARS-CoV-2 virus and substantial disease severity caused medical care capacity shortage in many countries. Therefore, real-time epidemic forecasting of the COVID-19 is useful to plan public health strategies like country lockdown and healthcare reorganization.We used extended susceptible-infected-removed (eSIR) model to predict the epidemic trend of COVID-19 in Poland under different scenarios of the lockdown and lockdown removal. We used time-series data of SARS-CoV-2 infection from March 4 to May 22 2020. Our forecast includes the impact of a timeline of preventive measures introduced in Poland. Using eSIR algorithm we estimated the basic reproductive number and a total number of infections under different epidemic trend scenarios.Using eSIR modeling we estimated that the basic reproductive number in Poland concerning different scenarios of the lockdown removal is in a range of 3.91-4.79. The lowest predicted number of infected cases would be 263 900 (0 - 1 734 200, 95%CI) if the strict protective measures were maintained until the end of September. However, under different scenarios of precautions removal, a total number of infected cases may exceed one million within the next year.Relatively early introduction of strong precautions in Poland significantly slowed down epidemic spread in Poland in comparison with other European countries like Italy or Spain. However, early removal of protective measures may result in a significant increase in infection. Data shows that the number of new COVID-19 cases in Poland beyond May 18 is linear what could be a prognosis of a duration of the epidemic exceeding 300 days.