bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishing correlation of axial and vertical force of cardiac artificial tissue using a novel micromachined sensor
Authors: Gaitas Angelo , Stillitano Francesca , Turnbull Irene 
Published: September 2020

AbstractCardiomyocytes iPSC (iPSC-CMs) have great potential for cell therapy, drug assessment, and for understanding the pathophysiology and genetic underpinnings of cardiac diseases. Contraction forces are one of the most important characteristics of cardiac function and are predictors of healthy and diseased states. Cantilever techniques, such as atomic force microscopy, measure the vertical force of a single cell, while systems designed to more closely resemble the physical heart function, such as cardiac tissue on posts, measure the axial force. One important question is how do these two force measurements correlate? By establishing a correlation of the axial and vertical force we will be one step closer in being able to use single cell iPSC instead of more elaborate human engineered tissue or animal heart tissue as models. A novel micromachined sensor for measuring force contractions of artificial tissue has been developed. Using this novel sensor a correlation between axial force and vertical force is experimentally established. This finding supports the use of vertical measurements as an alternative to tissue measurements.
Long-term (1990-2019) monitoring of tropical moist forests dynamics
Authors: Vancutsem C. , Achard F. , Pekel J.-F. , Vieilledent G. , Carboni S. , Simonetti D. , Gallego J. , Aragao L. , Nasi R. 
Published: September 2020

ABSTRACTAccurate characterization of the tropical moist forests changes is needed to support conservation policies and to better quantify their contribution to global carbon fluxes. We document - at pantropical scale - the extent of these forests and their changes (degradation, deforestation and recovery) over the last three decades. We estimate that 17% of the tropical moist forests have disappeared since 1990 with a remaining area of 1060 million ha in 2019, from which 8.5% are degraded. Our study underlines the importance of the degradation process in such ecosystems, in particular as precursor of deforestation and in the recent increase of the tropical moist forest disturbances. Without reduction of the present disturbance rates, undisturbed forests will disappear entirely in large tropical humid regions by 2050. Our study suggests reinforcing actions to prevent the first disturbance scar that leads to forest clearance in 45% of the cases.
Applying Machine Learning Technology in the Prediction of Crop Infestation with Cotton Leafworm in Greenhouse
Authors: Tageldin Ahmed , Adly Dalia , Mostafa Hassan , Mohammed Haitham S 
Published: September 2020

AbstractThe use of technology in agriculture has grown in recent years with the era of data analytics affecting every industry. The main challenge in using technology in agriculture is identification of effectiveness of big data analytics algorithms and their application methods. Pest management is one of the most important problems facing farmers. The cotton leafworm,Spodoptera littoralis(Boisd.) (CLW) is one of the major polyphagous key pests attacking plants includes 73 species recorded at Egypt. In the present study, several machine learning algorithms have been implemented to predict plant infestation with CLW. The moth of CLW data was weekly collected for two years in a commercial hydroponic greenhouse. Furthermore, among other features temperature and relative humidity were recorded over the total period of the study. It was proven that the XGBoost algorithm is the most effective algorithm applied in this study. Prediction accuracy of 84 % has been achieved using this algorithm. The impact of environmental features on the prediction accuracy was compared with each other to ensure a complete dataset for future results. In conclusion, the present study provided a framework for applying machine learning in the prediction of plant infestation with the CLW in the greenhouses. Based on this framework, further studies with continuous measurements are warranted to achieve greater accuracy.
A bioelectric neural interface towards intuitive prosthetic control for amputees
Authors: Nguyen Anh Tuan , Xu Jian , Jiang Ming , Luu Diu Khue , Wu Tong , Tam Wing-kin , Zhao Wenfeng , Drealan Markus W. , Overstreet Cynthia K. , Zhao Qi , Cheng Jonathan , Keefer Edward W. , Yang Zhi 
Published: September 2020

AbstractObjectiveWhile prosthetic hands with independently actuated digits have become commercially available, state-of-the-art human-machine interfaces (HMI) only permit control over a limited set of grasp patterns, which does not enable amputees to experience sufficient improvement in their daily activities to make an active prosthesis useful.ApproachHere we present a technology platform combining fully-integrated bioelectronics, implantable intrafascicular microelectrodes and deep learning-based artificial intelligence (AI) to facilitate this missing bridge by tapping into the intricate motor control signals of peripheral nerves. The bioelectric neural interface includes an ultra-low-noise neural recording system to sense electroneurography (ENG) signals from microelectrode arrays implanted in the residual nerves, and AI models employing the recurrent neural network (RNN) architecture to decode the subject’s motor intention.Main resultsA pilot human study has been carried out on a transradial amputee. We demonstrate that the information channel established by the proposed neural interface is sufficient to provide high accuracy control of a prosthetic hand up to 15 degrees of freedom (DOF). The interface is intuitive as it directly maps complex prosthesis movements to the patient’s true intention.SignificanceOur study layouts the foundation towards not only a robust and dexterous control strategy for modern neuroprostheses at a near-natural level approaching that of the able hand, but also an intuitive conduit for connecting human minds and machines through the peripheral neural pathways.Clinical trialDExterous Hand Control Through Fascicular Targeting (DEFT). Identifier:NCT02994160.
Prey-Driven Behavioral Habitat Use in a Low-Energy Ambush Predator
Authors: Tutterow Annalee M. , Hoffman Andrew S. , Buffington John L. , Truelock Zachary T. , Peterman William E. 
Published: September 2020

AbstractFood acquisition is an important modulator of animal behavior and habitat selection that can affect fitness. Optimal foraging theory predicts that predators should select habitat patches to maximize their foraging success and net energy gain, which predators can achieve by targeting spaces with high prey availability. However, it is debated whether prey availability drives fine-scale habitat selection for predators.We assessed whether an ambush predator, the timber rattlesnake (Crotalus horridus), exhibits optimal foraging site selection based on the spatial distribution and availability of prey.We evaluated the spatial concordance of radio-telemetered timber rattlesnake foraging locations and passive infrared game camera trap detections of potential small mammal prey (Peromyscusspp.,Tamias striatus,andSciurusspp.) in a mixed-use forest in southeastern Ohio from 2016–2019. We replicated a characteristic timber rattlesnake ambush position by focusing cameras over logs and modeled small mammal encounters across the landscape in relation to remotely-sensed forest and landscape structural features. To determine whether snakes selectively forage in areas with higher prey availability, we projected the estimated prey spatial relationships across the landscape and modeled their overlap of occurrence with observed timber rattlesnake foraging locations.We broadly predicted that prey availability was greatest in mature deciduous forests, butT.striatusandSciurusspp. exhibited greater spatial heterogeneity compared toPeromyscusspp. We also combined predicted species encounter rates to encompass a body size gradient in potential prey. The spatial distribution of cumulative small mammal encounters (i.e. overall prey availability), rather than the distribution of any one species, was highly predictive of snake foraging.Timber rattlesnakes appear to select foraging locations where the probability of encountering prey is greatest. Our study provides evidence for fine-scale optimal foraging in a low-energy, ambush predator and offers new insights into drivers of snake foraging and habitat selection.
An accurate aging clock developed from the largest dataset of microbial and human gene expression reveals molecular mechanisms of aging
Authors: Gopu Vishakh , Cai Ying , Krishnan Subha , Rajagopal Sathyapriya , Camacho Francine R. , Toma Ryan , Torres Pedro J. , Vuyisich Momchilo , Perlina Ally , Banavar Guruduth , Tily Hal 
Published: September 2020

AbstractAccurate measurement of the biological markers of the aging process could provide an “aging clock” measuring predicted longevity and allow for the quantification of the effects of specific lifestyle choices on healthy aging. Using modern machine learning techniques, we demonstrate that chronological age can be predicted accurately from (a) the expression level of human genes in capillary blood, and (b) the expression level of microbial genes in stool samples. The latter uses the largest existing metatranscriptomic dataset, stool samples from 90,303 individuals, and is the highest-performing gut microbiome-based aging model reported to date. Our analysis suggests associations between biological age and lifestyle/health factors, e.g., people on a paleo diet or with IBS tend to be biologically older, and people on a vegetarian diet tend to be biologically younger. We delineate the key pathways of systems-level biological decline based on the age-specific features of our model; targeting these mechanisms can aid in development of new anti-aging therapeutic strategies.
GREEN-DB: A framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data
Authors: Giacopuzzi E , Popitsch N , Taylor JC 
Published: September 2020

AbstractNon-coding variants have emerged as important contributors to the pathogenesis of human diseases, not only as common susceptibility alleles but also as rare high-impact variants. Despite recent advances in the study of regulatory elements and the availability of specialized data collections, the systematic annotation of non-coding variants from genome sequencing remains challenging. Here, we propose a new framework for the prioritization of non-coding regulatory variants that integrates information about regulatory regions with prediction scores and HPO-based prioritization. Firstly, we created a comprehensive collection of annotations for regulatory regions including a curated database of 2.4 million regulatory elements (GREEN-DB) annotated with controlled gene(s), tissue(s) and associated phenotype(s) where available. Secondly, we calculated a variation constraint metric and showed that constrained regulatory regions associate with disease-associated genes and essential genes from mouse knock-out screens. Thirdly, we compared 19 non-coding impact prediction scores providing suggestions for variant prioritization. Finally, we developed a VCF annotation tool (GREEN-VARAN) that can integrate all these elements to annotate variants for their potential regulatory impact. In our evaluation, we show that GREEN-DB can capture previously published disease-associated non-coding variants as well as identify additional candidate disease genes in WGS trio analyses.
Autophagy inhibition rescues structural and functional defects caused by the loss of mitochondrial chaperoneHsc70-5/mortalininDrosophila
Authors: Zhu Jun-yi , Hannan Shabab B. , Dräger Nina M. , Vereshchagina Natalia , Krahl Ann-Christin , Fu Yulong , Elliott Christopher J.H. , Han Zhe , Jahn Thomas R. , Rasse Tobias M. 
Published: September 2020

AbstractWe investigate in larval and adultDrosophilamodels whether loss of the mitochondrial chaperoneHsc70-5/mortalinis sufficient to cause pathological alterations commonly observed in Parkinson disease. At affected larval neuromuscular junctions, no effects on terminal size, bouton size or number, synapse size, or number were observed, suggesting that we study an early stage of pathogenesis. At this stage, we noted a loss of synaptic vesicle proteins and active zone components, delayed synapse maturation, reduced evoked and spontaneous excitatory junctional potentials, increased synaptic fatigue, and cytoskeleton rearrangements. The adult model displays ATP depletion, altered body posture, and susceptibility to heat-induced paralysis. Adult phenotypes could be suppressed by knockdown ofDJ-1b, LRRK, p50, p150, Atg1, Atg101, Atg5, Atg7, andAtg12. The knockdown of components of the autophagy machinery or overexpression of humanmortalinbroadly rescued larval and adult phenotypes, while disease-associatedHSPA9variants did not. Overexpression ofPink1or promotion of autophagy exacerbated defects.
Utilization of Epigenome-wide DNA Methylation for Longitudinal Comparison of White Blood Cell Proportions Across Preeclamptic and Normotensive Pregnancy by Self-Reported Race
Authors: Ray Mitali , Heinsberg Lacey W. , Conley Yvette P. , Roberts James M. , Jeyabalan Arun , Hubel Carl A. , Weeks Daniel E. , Schmella Mandy J. 
Published: September 2020

AbstractObjectiveWe utilized epigenome-wide DNA methylation data to estimate/compare white blood cell (WBC) proportions in plasma across preeclamptic (case) and uncomplicated, normotensive (control) pregnancy.MethodsWe previously collected methylation data using Infinium® MethylationEPIC Beadchips during the three trimesters in 28 cases and 28 controls (21 Black, 7 White participants/group). We employed Houseman’s regression calibration method to estimate and compare neutrophil, monocyte, B cell, NK cell, CD4+ T and CD8+ T cell proportions across pregnancy and between cases and controls.ResultsWe observed changes in WBC proportions across pregnancy within cases and controls that varied by cell type and race. Neutrophils represented the largest WBC mean proportion in all three trimesters for cases (Mean±SD: 67.2±9.6% – 74.4±12%) and controls (64.2±11% – 74.0±7.9%). Mean B cell proportions were significantly lower in cases than controls in Trimester 1 (5.25±0.02% versus 6.30±0.02%, p=0.02). The remaining mean cell proportions did not significantly differ in the overall sample. Stratified analyses revealed race-specific differences. In White participants (n=14): (1) neutrophil proportions were significantly higher in cases in Trimester 1 (p=0.04), but significantly lower in Trimester 2 (p=0.02), (2) B cell proportions were significantly lower in cases in Trimester 1 (p=0.001). No significant differences were detected among Black participants (n=42).ConclusionsAlthough chronic inflammation characterizes preeclampsia, few studies have investigated WBCs across pregnancy. We report differences between cases and controls across pregnancy. Our findings in a small sample demonstrate the need for additional studies investigating the relationship between race and WBCs in pregnancy, which could provide insight into preeclampsia pathophysiology.
Digital Speech Analysis in Progressive Supranuclear Palsy and Corticobasal Syndromes
Authors: Parjane Natalia , Cho Sunghye , Ash Sharon , Shellikeri Sanjana , Liberman Mark , Shaw Leslie M. , Irwin David J. , Grossman Murray , Nevler Naomi 
Published: September 2020

ABSTRACTBackgroundProgressive supranuclear palsy and corticobasal syndromes (PSPS-CBS) as well as nonfluent/agrammatic primary progressive aphasia (naPPA) are often due to misfolded 4-repeat Tau, but the diversity of the associated speech disorders beyond Apraxia of Speech (AoS) is poorly understood.ObjectiveInvestigate the full range of acoustic and lexical properties of speech to test the hypothesis that PSPS-CBS show a subset of speech impairments found in naPPA.MethodsAcoustic and lexical measures, extracted from natural, digitized semi-structured speech samples using novel, automated methods, were compared in PSPS-CBS (n=87), naPPA (n=25) and healthy controls (HC, n=41). We also explored speech in a group of PSPS-CBS patients with concomitant naPPA (PSPS-CBS+naPPA, n=8). We related these measures to grammatical performance and speech fluency, core features of naPPA, and to cerebrospinal fluid (CSF) phosphorylated tau (pTau) in patients with available biofluid.ResultsBoth naPPA and PSPS-CBS speech had shorter speech segments, longer pauses, higher pause rate, reduced fundamental frequency (f0) range, and slower speech rate compared to HC. naPPA speech was distinct from PSPS-CBS with shorter speech segments, more frequent pauses, slower speech rate, and reduced verb production. In both groups, acoustic duration measures generally correlated with speech fluency and grammatical performance. PSPS-CBS+naPPA resembled naPPA in most speech measures and had the narrowest f0 range. CSF pTau levels correlated with f0 range and verb production in PSPS-CBS and naPPA.ConclusionThe speech pattern of PSPS-CBS overlaps that of naPPA apart from AoS, and may be related to CSF pTau.
Bronchus-associated macrophages efficiently capture and present soluble inhaled antigens and are capable of local Th2 cell activation
Authors: Tang Xin-Zi , Kreuk Lieselotte S. M. , Cho Cynthia , Metzger Ross J. , Allen Christopher D. C. 
Published: September 2020

AbstractIn allergic asthma, allergen inhalation leads to local Th2 cell activation and peribronchial inflammation. However, the mechanisms for local antigen capture and presentation remain unclear. By two-photon microscopy, we established that soluble antigens in the bronchial airway lumen were efficiently captured and presented by a population of CD11c+interstitial macrophages with high CX3CR1-GFP and MHC class II expression. We refer to these cells as Bronchus-Associated Macrophages (BAMs) based on their localization underneath the bronchial epithelium. BAMs were enriched in collagen-rich regions near some airway branchpoints, where inhaled antigens are likely to deposit. BAMs engaged in extended interactions with effector Th2 cells and promoted Th2 cytokine production. BAMs were also often in contact with dendritic cells (DCs). After exposure to inflammatory stimuli, DCs migrated to draining lymph nodes, whereas BAMs remained lung resident. We propose that BAMs act as local antigen presenting cells in the lung and also transfer antigen to DCs.
The CD28-transmembrane domain mediates chimeric antigen receptor heterodimerization with CD28
Authors: Muller Yannick D. , Nguyen Duy P. , Ferreira Leonardo M.R. , Ho Patrick , Raffin Caroline , Valencia Roxxana Beltran , Congrave-Wilson Zion , Roth Theodore , Eyquem Justin , Van Gool Frederic , Marson Alexander , Wells James A. , Bluestone Jeffrey A. , Tang Qizhi 
Published: September 2020

AbstractAnti-CD19 chimeric antigen receptor (CD19-CAR)-engineered T cells are approved therapeutics for malignancies. The impact of the hinge (HD) and transmembrane (TMD) domains between the extracellular antigen-targeting and the intracellular signaling modalities of CARs has not been systemically studied. Here, a series of CD19-CARs differing only by their HD (CD8/CD28/IgG4) and TMD (CD8/CD28) was generated. CARs containing a CD28-TMD, but not a CD8-TMD, formed heterodimers with the endogenous CD28 in human T cells, as shown by co-immunoprecipitation and CAR-dependent proliferation to anti-CD28 stimulation. This dimerization depended on polar amino-acids in the CD28-TMD. CD28-CAR heterodimerization was more efficient in CARs containing a CD8-HD or CD28-HD as compared to an IgG4-HD. CD28-CAR heterodimers did not respond to CD80 and CD86 stimulation but led to a significant reduction of CD28 cell-surface expression. These data unveil a new property of the CD28-TMD and suggest that TMDs can modulate CAR T-cell activities by engaging endogenous partners.Abstract Figure
“The anti-angiogenic compound axitinib demonstrates low toxicity and anti-tumoral effects against medulloblastoma”
Authors: Pagnuzzi-Boncompagni Marina , Picco Vincent , Vial Valérie , Planas-Bielsa Victor , Vandenberghe Ashaina , Grépin Renaud , Durivault Jérôme , Montemagno Christopher , Martial Sonia , Doyen Jérôme , Gavard Julie , Pagès Gilles 
Published: September 2020

ABSTRACTEvolution of medulloblastoma (MB) treatments has increased the 5-year overall survival of to more than 70%. However, an increasing number of survivors face severe long-term adverse effects and associated morbidity due to multimodal treatments particularly harsh for the younger patients. Chemotherapeutic compounds inducing less adverse effects are key to improving the care of MB patients. The preclinical relevance of last generation anti-angiogenic compounds deserves to be fully assessed. Among these, axitinib showed the highest selectivity index for MB cells, efficiently reduced the growth rate of experimental tumors and led to less toxicity towards normal cells than did a reference treatment. In vivo, axitinib did not lead to acute toxicity in very young rats and was able to cross the blood brain barrier. Analysis of public databases shows that high expression of axitinib targets are of poor prognosis. Altogether, our results suggest that axitinib is a compelling candidate for MB treatment.
Consistent ultra-long DNA sequencing with automated slow pipetting
Authors: Prall Trent M. , Neumann Emma K. , Karl Julie A. , Shortreed Cecilia G. , Baker David A. , Bussan Hailey E. , Wiseman Roger W. , O’Connor David H. 
Published: September 2020

AbstractBackgroundOxford Nanopore Technologies instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome. Sequencing reads of significant length requires the preservation of long DNA template molecules through library preparation by pipetting reagents as slowly as possible to minimize shearing. This process is time-consuming and inconsistent at preserving read length as even small changes in volumetric flow rate can result in template shearing.ResultsWe have designed SNAILS (Slow Nucleic Acid Instrument for Long Sequences), a 3D-printable instrument that automates slow pipetting of reagents used in long read library preparation for Oxford Nanopore sequencing. Across six sequencing libraries, SNAILS preserved more reads exceeding one hundred kilobases in length and increased its libraries’ average read length over manual slow pipetting.ConclusionsSNAILS is a low-cost, easily deployable solution for improving sequencing projects that require reads of significant length. By automating the slow pipetting of library preparation reagents, SNAILS increases the consistency and throughput of long read Nanopore sequencing.