bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visual Field Analysis: a reliable method to score left- and right eye-use using automated tracking
Authors: Josserand Mathilde , Rosa-Salva Orsola , Versace Elisabetta , Lemaire Bastien S. 
Published: May 2021

AbstractBrain and behavioural asymmetries have been documented in various taxa. Many of these asymmetries involve preferential left- and right-eye use. However, measuring eye use through manual frame-by-frame analyses from video recordings is laborious and may lead to biases. Recent progress in technology allowed the development of accurate tracking techniques for measuring animal behaviour. Amongst these techniques, DeepLabCut, a python-based tracking toolbox using transfer learning with deep neural networks, offers the possibility to track different body parts with unprecedented accuracy. Exploiting the potentialities of DeepLabCut, we developed ‘Visual Field Analysis’, an additional open-source application for extracting eye-use data. To our knowledge, this is the first application that can automatically quantify left-right preferences in eye use. Here we test the performance of our application in measuring preferential eye-use in young domestic chicks. The comparison with manual scoring methods revealed a perfect correlation in the measures of eye-use obtained by ‘Visual Field Analysis’. With our application, eye-use can be analysed reliably, objectively and at a fine scale in different experimental paradigms.
Oligomannosylation and MAN1A1 expression associate strongly with a subset of human cancer types
Authors: Chatterjee Sayantani , Kawahara Rebeca , Ugonotti Julian , Lee Ling Y. , Everest-Dass Arun , Thaysen-Andersen Morten 
Published: May 2021

AbstractAberrant protein glycosylation is a prominent cancer feature. While many tumour-associated glycoepitopes have been reported, advances in glycoanalytics continue to uncover new associations between glycoproteins and cancer. Guided by a comprehensive literature survey suggesting that oligomannosylation (Man5-9GlcNAc2, M5-M9) is a widespread albeit poorly studied glyco-signature in human cancers, we here re-visit a valuable compilation of nearly 500 LC-MS/MSN-glycomics datasets acquired across 11 human cancer types to systematically test for oligomannose-cancer associations. Firstly, our quantitative glycomics data obtained across 34 cancerous cell lines demonstrated that oligomannosylation, particularly the under-processed M7-M9, is a strong pan-cancer feature. We then showed cell surface expression of oligomannosidic epitopes in the promyelocytic leukemic HL-60 cell line using concanavalin A-based flow cytometry. In keeping with literature, our quantitative glycomics data of tumour and matching control tissues and new MALDI-MS imaging data of tissue microarrays showed a strong cancer-associated elevation of oligomannosylation in both basal cell (p= 1.78 x 10-12) and squamous cell (p= 1.23 x 10-11) skin cancer and colorectal cancer (p= 8.0 x 10-4). The glycomics data also indicated that few cancer types including gastric and liver cancer exhibit unchanged or reduced oligomannose levels, observations also supported by literature and MALDI-MSI. Finally, data from cancer repositories indicated that three α1,2-mannosidases dictate oligomannose expression in cancer cells, and further suggested that deleterious mutations and reduced expression of MAN1A1 are key contributors to the cancer-associated oligomannose elevation. Collectively, these findings open hitherto unexplored avenues for the development of new cancer biomarkers and therapeutic targets.
Live imaging of delamination inDrosophilashows epithelial cell motility and invasiveness are independently regulated
Authors: Inaki Mikiko , Matsuno Kenji 
Published: May 2021

AbstractDelaminating cells undergo complex, precisely regulated changes in cell-cell adhesion, motility, polarity, invasiveness, and other cellular properties. Delamination occurs during development and in pathogenic conditions such as cancer metastasis. We analyzed the requirements for epithelial delamination inDrosophilaovary border cells, which detach from the structured epithelial layer and begin to migrate collectively. We used live imaging to examine cellular dynamics, particularly epithelial cells’ acquisition of motility and invasiveness, in delamination-defective mutants during the time period in which delamination occurs in the wild-type ovary. We found that border cells inslow border cells(slbo), a delamination-defective mutant, lacked invasive cellular protrusions but acquired motility, while JAK/STAT-inhibited border cells lost both invasiveness and motility. Our results indicate that invasiveness and motility, which are cooperatively required for delamination, are regulated independently. Our reconstruction experiments also showed that motility is not a prerequisite for acquiring invasiveness.Summary statementLive imaging of epithelial delamination reveals that cell motility and invasiveness, both of which are required for delamination, are regulated independently and that motility is not a prerequisite for invasiveness.
Comparing the effectiveness of secondary distribution of HIV self-testing to testing card referral in promoting HIV testing among men who have sex with men in China: A quasi-experimental study
Authors: Sha Yongjie , Xiong Yuan , Wang Yehua , Ong Jason , Ni Yuxin , Lu Ying , Cheng Mengyuan , Tucker Joseph , Tang Weiming 
Published: May 2021

AbstractBackgroundSocial network-based HIV self-testing (HIVST) is useful to promote HIV testing. Secondary distribution is one social network-based method whereby individuals (indexes) access multiple HIVST kits and distribute them to their social networks (alters). This quasi-experimental study compared the effectiveness and cost of two social network-based HIV testing strategies (HIVST secondary distribution and HIV testing card referral) in promoting HIV testing among Chinese men who have sex with men (MSM).MethodsMSM aged 18 years or older were recruited in Guangzhou, Guangdong Province. From May to September 2019, indexes recruited during that period could distribute HIVST kits to people within their social network. Indexes recruited from October 2019 to January 2020 could refer HIV testing cards to people within their social network for free facility-based tests. Participants could access 1-5 HIVST kits or testing referral cards for distribution. Alters were encouraged to upload a picture of their test results and complete an online survey. Indexes and alters received an incentive to report test results.ResultsTwo hundred thirty-nine potential participants were assessed for eligibility and 208/245 (84.9%) were eligible. Among those who completed baseline assessment, 154/208 (74.0%) completed one month of follow-up. Overall,106 indexes were recruited in the HIVST arm and 102 in the testing card arm. The two arms had similar socio-demographic characteristics. At the one-month follow-up, 92 indexes in the HIVST arm self-reported having distributed self-test kits to 179 unique alters, and 62 in the testing card arm self-reported having distributed testing referral cards to 26 unique alters. Additionally, 69/92 (75%) in the HIVST arm distributed any test to friends or sexual partners compared to 18/62 (29%) in the testing card arm, with a risk difference of 46% (95% CI 31%, 61%). Indexes in the HIVST arm distributed an average of 1.95 (SD=1.90) tests, compared to 0.42 (SD=0.78) in the testing card arm, with a risk difference of 1.53 (95% CI 1.09, 1.96). Subgroup analysis suggested that indexes in the HIVST arm who self-identified as gay (p = 0.007) or were previously tested for HIV (p = 0.02) were more likely to distribute. The HIVST arm had a higher total cost and higher testing coverage compared to the testing card referral arm. The ICER per alter tested was $52.78.ConclusionsSecondary distribution of HIVST engaged more MSM to distribute tests to their social network and reached more MSM for test. MSM who self-identify as gay or who have previously tested for HIV were more effective in distributing tests. Future testing approaches should include HIVST kits in voluntary counselling and testing settings and incorporate digital strategies for secondary distribution.
Two functionally distinct Purkinje cell populations implement an internal model within a single olivo-cerebellar loop
Authors: Angelaki Dora E. , Laurens Jean 
Published: May 2021

AbstractOlivo-cerebellar loops, where anatomical patches of the cerebellar cortex and inferior olive project one onto the other, form an anatomical unit of cerebellar computation. Here, we investigated how successive computational steps map onto olivo-cerebellar loops. Lobules IX-X of the cerebellar vermis, i.e. the nodulus and uvula, implement an internal model of the inner ear’s graviceptor, the otolith organs. We have previously identified two populations of Purkinje cells that participate in this computation: Tilt-selective cells transform egocentric rotation signals into allocentric tilt velocity signals, to track head motion relative to gravity, and translation-selective cells encode otolith prediction error. Here we show that, despite very distinct simple spike response properties, both types of Purkinje cells emit complex spikes that are proportional to sensory prediction error. This indicates that both cell populations comprise a single olivo-cerebellar loop, in which only translation-selective cells project to the inferior olive. We propose a neural network model where sensory prediction errors computed by translation-selective cells are used as a teaching signal for both populations, and demonstrate that this network can learn to implement an internal model of the otoliths.
Meiofauna is an important, yet neglected, component of biodiversity ofPosidonia oceanica
Authors: García-Gómez Guillermo , García-Herrero Álvaro , Sánchez Nuria , Pardos Fernando , Izquierdo-Muñoz Andrés , Fontaneto Diego , Martínez Alejandro 
Published: May 2021

ABSTRACTPosidonia oceanicameadows are biodiversity reservoirs and provide many ecosystem services in coastal Mediterranean regions. Marine meiofauna, on the other hand, not only represents a major component of regional marine biodiversity, but also a useful tool to address both theoretical and applied questions in ecology, evolution, and conservation. We review the meiofaunal diversity in theP. oceanicaecosystem combining a literature review and a case study. First, we gathered records of 664 species from 69 published studies as well as unpublished sources, including few species exclusive from this ecosystem. Eighteen of those studies quantified the spatial and temporal changes of species composition, highlighting habitat-specific assemblages that fluctuate following the annual changes experienced byP. oceanica. Hydrodynamics, habitat complexity, and food availability, all three inherently linked to the seagrass phenology, are recognised as the main factors at shaping the complex distribution patterns of meiofauna in the meadows. These drivers have been identified mainly from Copepoda and Nematoda, and depend ultimately on species-specific preferences. Second, we tested the generality of these observations using marine mites as a model group, showing that the same processes might be in place also for other less abundant meiofaunal groups. Overall, our study highlights an outstanding diversity of meiofauna inP. oceanicaand shows its potential for future research, not only focused on exploring and describing new species of neglected meiofaunal organisms, but also providing a more complete understanding on the functioning of the iconic Mediterranean ecosystem created byP. oceanica.
Protein phosphatase 1 regulatory inhibitor subunit 14C promotes triple-negative breast cancer progression via sustaining inactive glycogen synthase kinase 3 beta
Authors: Jian Yunting , Kong Lingzhi , Xu Hongyi , Huang Xinjian , Li Yue , Shi Dongni , Xiao Yunyun , Yang Muwen , Li Siqi , Chen Xiangfu , Ouyang Ying , Hu Yameng , Chen Xin , Liu Pian , Wei Weidong 
Published: May 2021

AbstractThe majority of clinical deaths among patients with triple-negative breast cancer (TNBC) are caused by uncontrolled cell proliferation and aggressive metastases, which is regulated by hyperactive glycogen synthase kinase 3 beta (GSK3β); however, the underlying mechanisms remain largely unknown. In the present study, we found that protein phosphatase 1 regulatory inhibitor subunit 14C (PPP1R14C) was specifically upregulated in TNBC, compared with that in normal tissues and non-TNBC. High PPP1R14C expression correlated significantly with shorter 5-year relapse-free survival and overall survival in patients with TNBC. Overexpressing PPP1R14C promoted, while suppression of PPP1R14C decreased the cell proliferation and the aggressive phenotype of TNBC cells, in vitro and in vivo. Importantly, we revealed that PPP1R14C interacted with and inactivated type 1 Ser/Thr protein phosphatase (PP1) to sustain GSK3β phosphorylation at S9, and induced the ubiquitylation and degradation of non-phosphorylated GSK3β (S9A) via recruiting E3 ligase, TRIM25. Furthermore, treating with C2 ceramide (C2), which recovered kinase activity of GSK3β, resulted in tumor growth inhibition in PPP1R14C-overexpressing TNBC cells. Our findings reveal a novel mechanism whereby PPP1R14C sustains inactive GSK3β, which might lead to targeted therapy for TNBC.
Transcriptomic Insights into the Responses in Leaves Storing Lipid Organelles under Different Irradiances
Authors: Winichayakul Somrutai , Macknight Richard , Beechey-Gradwell Zac , Lee Robyn , Xue Hong , Crowther Tracey , Anderson Philip , Richardson Kim , Zou Xiuying , Maher Dorothy , Brock Shona , Cooney Luke , Bryan Gregory , Roberts Nick 
Published: May 2021

ABSTRACTTo increase the nutritional value of forage, transgenic ryegrass known asHighMetabolizableEnergy (HME) were previously generated that co-express cysteine-oleosin and diacylglycerol O-acyltransferase. HME not only accumulate lipids in the leaf but also has elevated CO2assimilation and increased biomass. Shading is one of the most influencing factors for ryegrass growth environments particularly in swards. The aim of this study, therefore, was to determine the influence of irradiance levels on photosynthesis and gene expression in the HME leaves when compared with their corresponding non-transformant (NT). Under low light (150-250 µmol m-2s-1) and standard light (600-1000 µmol m-2s-1), the HME accumulated more lipid than NT. The previously reported elevated photosynthesis and increased biomass was observed when the HME were grown under standard light but not under low light. Under both light conditions, compared to NT, the HME had upregulated a number of transcripts involved in lipid metabolism, light capturing, photosynthesis, and sugar signalling network while downregulated genes participated in sugar and fructan biosynthesis. We further discuss how the HME differentially manipulated several genes other metabolic pathways including maintenance of redox homeostasis. Combined, the data suggests that the increased photosynthesis capacity in the HME likely corresponds to an increase of micro-lipid sink strength; these are influenced by available light energy and may be related to diffusional and biochemical activities of stomata. Overall, this work provides a clearly understanding of the changes in molecular and biochemical mechanisms underlying the carbon storing as leaf lipid sink of the HME ryegrass.One sentence summaryShading led to increase leaf lipid accumulation but limit the greater photosynthesis trait of high lipid ryegrass which may be related to limitation of biochemical activities of stomata.
RNA virome diversity andWolbachiainfection in individualDrosophila simulansflies
Authors: Ortiz-Baez Ayda Susana , Shi Mang , Hoffmann Ary A. , Holmes Edward C. 
Published: May 2021

AbstractThe endosymbiont bacteriumWolbachiais associated with multiple mutualistic effects on insect biology, including nutritional and antiviral properties.Wolbachianaturally occurs inDrosophilafly species, providing an operational model host to study how virome composition may be impacted by its presence.Drosophila simulanspopulations can carry a variety ofWolbachiastrains. In particular, thewAu strain ofWolbachiahas been associated with strong antiviral protection under experimental conditions. We usedD. simulanssampled from the Perth Hills, Western Australia, to investigate the potential virus protective effect of thewAu strain on individual wild-caught flies. Our data revealed no appreciable variation in virus composition and abundance betweenWolbachiainfected/uninfected individuals associated with the presence/absence ofwAu. However, it remains unclear whetherwAu might impact viral infection and host survival by increasing tolerance rather than inducing complete resistance. These data also provide new insights into the natural virome diversity ofD. simulans. Despite the small number of individuals sampled, we identified a repertoire of RNA viruses, including Nora virus, Galbut virus, Chaq virus, Thika virus and La Jolla virus, that have been identified in otherDrosophilaspecies. In addition, we identified five novel viruses from the familiesReoviridae,Tombusviridae,MitoviridaeandBunyaviridae.Overall, this study highlights the complex interaction betweenWolbachiaand RNA virus infections and provides a baseline description of the natural virome ofD. simulans.
An Artificial Neural-Network Approach for Motor Hotspot Identification Based on Electroencephalography: A Proof-of-Concept Study
Authors: Choi Ga-Young , Han Chang-Hee , Lee Hyung-Tak , Paik Nam-Jong , Kim Won-Seok , Hwang Han-Jeong 
Published: May 2021

AbstractBackgroundTo apply transcranial electrical stimulation (tES) to the motor cortex, motor hotspots are generally identified using motor evoked potentials by transcranial magnetic stimulation (TMS). The objective of this study is to validate the feasibility of a novel electroencephalography (EEG)-based motor-hotspot-identification approach using a machine learning technique as a potential alternative to TMS.MethodsEEG data were measured using 63 channels from thirty subjects as they performed a simple finger tapping task. Power spectral densities of the EEG data were extracted from six frequency bands (delta, theta, alpha, beta, gamma, and full) and were independently used to train and test an artificial neural network for motor hotspot identification. The 3D coordinate information of individual motor hotspots identified by TMS were quantitatively compared with those estimated by our EEG-based motor-hotspot-identification approach to assess its feasibility.ResultsThe minimum mean error distance between the motor hotspot locations identified by TMS and our proposed motor-hotspot-identification approach was 0.22 ± 0.03 cm, demonstrating the proof-of-concept of our proposed EEG-based approach. A mean error distance of 1.32 ± 0.15 cm was measured when using only nine channels attached to the middle of the motor cortex, showing the possibility of practically using the proposed motor-hotspot-identification approach based on a relatively small number of EEG channels.ConclusionWe demonstrated the feasibility of our novel EEG-based motor-hotspot-identification method. It is expected that our approach can be used as an alternative to TMS for motor hotspot identification. In particular, its usability would significantly increase when using a recently developed portable tES device integrated with an EEG device.
TAP: Targeting and analysis pipeline for optimization and verification of coil placement in transcranial magnetic stimulation
Authors: Dannhauer Moritz , Huang Ziping , Beynel Lysianne , Wood Eleanor , Bukhari-Parlakturk Noreen , Peterchev Angel V. 
Published: May 2021

AbstractObjectiveTranscranial magnetic stimulation (TMS) can modulate brain function via an electric field (E-field) induced in a brain region of interest (ROI). The ROI E-field can be computationally maximized and set to match a specific reference using individualized head models to find the optimal coil placement and stimulus intensity. However, the available software lacks many practical features for prospective planning of TMS interventions and retrospective evaluation of the experimental targeting accuracy.ApproachThe TMS targeting and analysis pipeline (TAP) software uses an MRI/fMRI-derived brain target to optimize coil placement considering experimental parameters such as the subject’s hair thickness and coil placement restrictions. The coil placement optimization is implemented in SimNIBS 3.2, for which an additional graphical user interface (TargetingNavigator) is provided to visualize/adjust procedural parameters. The coil optimization process also computes the E-field at the target, allowing the selection of the TMS device intensity setting to achieve specific E-field strengths. The optimized coil placement information is prepared for neuronavigation software, which supports targeting during the TMS procedure. The neuronavigation system can record the coil placement during the experiment, and these data can be processed in TAP to quantify the accuracy of the experimental TMS coil placement and induced E-field.Main resultsTAP was demonstrated in a study consisting of three repetitive TMS sessions in five subjects. TMS was delivered by an experienced operator under neuronavigation with the computationally optimized coil placement. Analysis of the experimental accuracy from the recorded neuronavigation data indicated coil location and orientation deviations up to about 2 mm and 2°, respectively, resulting in an 8% median decrease in the target E-field magnitude compared to the optimal placement.SignificanceTAP supports navigated TMS with a variety of features for rigorous and reproducible stimulation delivery, including planning and evaluation of coil placement and intensity selection for E-field-based dosing.
Can charge-reversal be considered as a strategy for attaining thermal stability in proteins?
Authors: Hait Suman , Basu Sudipto , Kundu Sudip 
Published: May 2021

ABSTRACTDo charge reversal mutations (CRM) naturally occur in mesophilic-thermophilic/hyperthermophilic (M-T/HT) orthologous proteins? Do they contribute to thermal stability by altering charge-charge interactions? A careful investigation on 1550 M-T/HT orthologous protein pairs with remarkable structural and topological similarity extracts the role of buried and partially exposed CRMs in enhancing thermal stability. Our findings could assist in engineering thermo-stable variants of proteins.SIGNIFICANCEProtein engineering is one of the hot topics for decades specifically for its applications in different fields like de-novo protein design, directed evolution, making highly stable variants for food and drug industry etc. Proteins from organisms living in extreme environments are therefore a matter of common interest for scientists from different disciplines. Over three decades of study has already found several sequence and structural adaptations related to thermal stability, while charge reversal study remains ignored to a large extent. Influenced by nature’s strategy, our study provides a systemic understanding of how proper designing of few partially exposed and buried CRMs significantly contributes to thermal stability by altering the short distance electrostatic interactions.