bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transferability of Brain decoding using Graph Convolutional Networks
Authors: Zhang Yu , Bellec Pierre 
Published: June 2020

AbstractTransfer learning has been a very active research topic in natural image processing. But few studies have reported notable benefits of transfer learning on medical imaging. In this study, we sought to investigate the transferability of deep artificial neural networks (DNN) in brain decoding, i.e. inferring brain state using fMRI brain response over a short window. Instead of using pretrained models from ImageNet, we trained our base model on a large-scale neuroimaging dataset using graph convolutional networks (GCN). The transferability of learned graph representations were evaluated under different circumstances, including knowledge transfer across cognitive domains, between different groups of subjects, and among different sites using distinct scanning sequences. We observed a significant performance boost via transfer learning either from the same cognitive domain or from other task domains. But the transferability was highly impacted by the scanner site effect. Specifically, for datasets acquired from the same site using the same scanning sequences, using transferred features highly improved the decoding performance. By contrast, the transferability of representations highly decreased between different sites, with the performance boost reducing from 20% down to 7% for the Motor task and decreasing from 15% to 5% for Working-memory tasks. Our results indicate that in contrast to natural images, the scanning condition, instead of task domain, has a larger impact on feature transfer for medical imaging. With other advanced tools such as layer-wise fine-tuning, the decoding performance can be further improved through learning more site-specific high-level features while retaining the transferred low-level representations of brain dynamics.
microRNA-19b regulates proliferation & patterning in the avian forebrain
Authors: Mishra Archita , Sindhu Suvimal Kumar , Udaykumar Niveda , Sen Jonaki 
Published: June 2020

AbstractUnlike the six-layered organization of neurons in the mammalian neocortex, the avian pallium features spatially-segregated neuronal clusters with partially conserved gene expression. While efforts to uncover similarities between the avian pallium and mammalian neocortex have persisted, the mechanisms of pallial development in birds have not been comprehensively explored. Here, we have established the role of a highly conserved microRNA, miR-19b, in controlling proliferation in the embryonic avian forebrain, by regulating the expression of E2f8, a cell-cycle inhibitor and NeuroD1, a neuronal differentiation factor. Further, investigation revealed that there exists a proliferation-dependent specification of pallial neurons in birds, similar to that in mammals. In summary, these findings suggest a profound role of miR-19b in shaping the avian pallium and indicate a closer resemblance of developmental mechanisms between the avian pallium and the mammalian neocortex.
TMT-Based Quantitative Proteomic Analysis of Intestinal Organoids Infected byListeria monocytogeneswith Different Virulence
Authors: Huang Jie , Zhou Cong , Zhou Guanghong , Ye Keping 
Published: June 2020

AbstractListeria monocytogenes (Lm)is an opportunistic food-borne pathogen that cause listeriosis.L. monocytogenesbelonged to different serovars presents with different virulence in the host and caused different host reactions. To investigate the remodeling of host proteome by differently toxic strains, the cellular protein responses of intestinal organoids were analyzed using TMT labeling and high performance liquid chromatography-mass spectrometry. Quantitative proteomic analysis revealed 6564 differentially expressed proteins, of which 5591 proteins were quantified. The fold-change cutoff was set at 1.3 (Lmvs control), the virulent strain caused 102 up-regulated proteins and 52 down-regulated proteins, while the low virulent strain caused 188 up-regulated proteins and 25 down-regulated proteins. These identified proteins were involved in the regulation of essential processes such as biological metabolism, energy metabolism, and immune system process. Some selected proteins were screened by Real-time PCR and Western blotting. These results revealed that differently toxicL. monocytogenesinduced similar biological functions and immune responses while had different regulation on differential proteins in the pathway.
PRKCA overexpression is frequent in young oral tongue squamous cell carcinoma patients and is associated with poor prognosis
Authors: Parzefall Thomas , Schnoell Julia , Monschein Laura , Foki Elisabeth , Liu David Tianxiang , Frohne Alexandra , Grasl Stefan , Pammer Johannes , Lucas Trevor , Kadletz Lorenz , Brunner Markus 
Published: June 2020

AbstractOral tongue squamous cell carcinoma (OTSCC) have an increasing incidence in young patients and many have an aggressive course of disease. The molecular mechanisms for this increase are unknown and biologic markers to identify high risk patients are lacking.In an unbiased data screening for differential protein expression of younger (≤45 years) and older (>45 years) OTSCC patients in The Cancer Genome Atlas (TCGA) cohort (n=98) we identified Protein kinase C alpha (PRKCA), to be significantly more frequently overexpressed in younger versus older patients (p=0.0001). These results were experimentally validated and confirmed in an independent Austrian OTSCC patient sample (n=34) by immunohistochemistry (p=0.0026). PRKCA upregulation was associated with negative anamnesis for alcohol consumption (p=0.009) and tobacco smoking (p=0.02). Univariate and multivariate analysis of overall survival (OS) and disease-free survival (DFS) showed a significantly worse prognosis in patients with tumors overexpressing PRKCA regarding OS (univariate p= 0.04, multivariate p< 0.01). In the young subgroup both OS and DFS were significantly decreased in PRKCA positive patients (both p< 0.001). TCGA messenger RNA enrichment analysis showed 24 mRNAs with significant differential expression in PRKCA positive OTSCC (all p≤ 0.05 after Benjamini-Hochberg correction).Our findings suggest the potential existence of a distinct molecular subtype of alcohol and tobacco negative, high risk OTSCC in a significant proportion of early onset individuals. Our findings warrant validation in additional OTSCC patient cohorts. Further analysis of the molecular PRKCA interactome may decipher the underlying mechanisms of carcinogenesis and clinicopathological behavior of PRKCA overexpressing OTSCC.
Intrafamilial Exposure to SARS-CoV-2 Induces Cellular Immune Response without Seroconversion
Authors: Gallais Floriane , Velay Aurélie , Wendling Marie-Josée , Nazon Charlotte , Partisani Marialuisa , Sibilia Jean , Candon Sophie , Fafi-Kremer Samira 
Published: June 2020

AbstractBackgroundIn the background of the current COVID-19 pandemic, serological tests are being used to assess past infection and immunity against SARS-CoV-2. This knowledge is paramount to determine the transmission dynamics of SARS-CoV-2 through the post pandemic period. Several individuals belonging to households with an index COVID-19 patient, reported symptoms of COVID-19 but discrepant serology results.MethodsHere we investigated the humoral and cellular immune responses against SARS-CoV-2 in seven families, including nine index patients and eight contacts, who had evidence of serological discordances within the households. Ten unexposed healthy donors were enrolled as controls.ResultsAll index patients recovered from a mild COVID-19. They all developed anti-SARS-CoV-2 antibodies and a significant T cell response detectable up to 69 days after symptom onset. Six of the eight contacts reported COVID-19 symptoms within 1 to 7 days after the index patients but all were SARS-CoV-2 seronegative. Six out of eight contacts developed a SARS-CoV-2-specific T cell response against structural and/or accessory proteins that lasts up to 80 days post symptom onset suggesting a past SARS-CoV-2 infection.ConclusionExposure to SARS-CoV-2 can induce virus-specific T cell responses without seroconversion. T cell responses may be more sensitive indicators of SARS-Co-V-2 exposure than antibodies. Our results indicate that epidemiological data relying only on the detection of SARS-CoV-2 antibodies may lead to a substantial underestimation of prior exposure to the virus.
Bacterial retrons encode tripartite toxin/antitoxin systems
Authors: Bobonis Jacob , Mateus André , Pfalz Birgit , Garcia-Santamarina Sarela , Galardini Marco , Kobayashi Callie , Stein Frank , Savitski Mikhail M. , Elfenbein Johanna R. , Andrews-Polymenis Helene , Typas Athanasios 
Published: June 2020

ABSTRACTRetrons are genetic retroelements, commonly found in bacterial genomes and recently repurposed as genome editing tools. Their encoded reverse transcriptase (RT) produces a multi-copy single-stranded DNA (msDNA). Despite our understanding of their complex biosynthesis, the function of msDNAs and therefore, the physiological role of retrons has remained elusive. We establish that the retron-Sen2 inSalmonellaTyphimurium encodes a toxin, which we have renamed as RcaT (Retron cold-anaerobic Toxin). RcaT is activated when msDNA biosynthesis is perturbed and its toxicity is higher at ambient temperatures or during anaerobiosis. The RT and msDNA form together the antitoxin unit, with the RT binding RcaT, and the msDNA enabling the antitoxin activity. Using anotherE. coliretron, we establish that this toxin/antitoxin function is conserved, and that RT-toxin interactions are cognate. Altogether, retrons constitute a novel family of tripartite toxin/antitoxin systems.
Synergistic epistasis enhances cooperativity of mutualistic interspecies interactions
Authors: Turkarslan Serdar , Stopnisek Nejc , Thompson Anne W , Arens Christina E , Valenzuela Jacob J , Wilson James , Hunt Kristopher A , Hardwicke Jessica , Lim Sujung , Seah Yee Mey , Fu Ying , Wu Liyou , Zhou Jizhong , Hillesland Kristina L , Stahl David A , Baliga Nitin S 
Published: June 2020

SUMMARYFrequent fluctuations in sulfate availability rendered syntrophic interactions between the sulfate reducing bacteriumDesulfovibrio vulgaris(Dv) and the methanogenic archaeonMethanococcus maripaludis(Mm) unsustainable. By contrast, prolonged laboratory evolution in obligate syntrophy conditions improved the productivity of this community but at the expense of erosion of sulfate respiration (SR). Hence, we sought to understand the evolutionary trajectories that could both increase the productivity of syntrophic interactions and sustain SR. We combined a temporal and combinatorial survey of mutations accumulated over 1000 generations of 9 independently-evolved communities with analysis of the genotypic structure for one community down to the single-cell level. We discovered a high level of parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance of a rare SR+Dvlineage within many evolution lines. An in-depth investigation revealed that synergistic epistasis acrossDvandMmgenotypes had enhanced cooperativity within SR- and SR+ assemblages, allowing their co-existence asr- andK-strategists, respectively.
Critical information thresholds underlying concurrent face recognition functions
Authors: Quek Genevieve L. , Rossion Bruno , Liu-Shuang Joan 
Published: June 2020

AbstractHumans rapidly and automatically recognise faces on multiple different levels, yet little is known about how the brain achieves these manifold categorisations concurrently. We bring a new perspective to this emerging issue by probing the relative informational dependencies of two of the most important aspects of human face processing: categorisation of the stimulusas a face(generic face recognition) and categorisation of its familiarity (familiar face recognition). Recording electrophysiological responses to a large set of natural images progressively increasing in image duration (Expt. 1) or spatial frequency content (Expt. 2), we contrasted critical sensory thresholds for these recognition functions as driven by the same face encounters. Across both manipulations, individual observer thresholds were consistently lower for distinguishing faces from other objects than for distinguishing familiar from unfamiliar faces. Moreover, familiar face recognition displayed marked inter-individual variability compared to generic face recognition, with no systematic relationship evident between the two thresholds. Scalp activation was also more strongly right-lateralised at the generic face recognition threshold than at the familiar face recognition threshold. These results suggest that high-level recognition of a faceas a facearises based on minimal sensory input (i.e., very brief exposures/coarse resolutions), predominantly in right hemisphere regions. In contrast, the amount of additional sensory evidence required to access face familiarity is highly idiosyncratic and recruits wider neural networks. These findings underscore the neurofunctional distinctions between these two recognition functions, and constitute an important step forward in understanding how the human brain recognises various dimensions of a face in parallel.Significance StatementThe relational dynamics between different aspects of face recognition are not yet well understood. We report relative informational dependencies for two concurrent, ecologically relevant face recognition functions: distinguishing faces from objects, and recognising people we know. Our electrophysiological data show that for a given face encounter, the human brain requires less sensory input to categorise that stimulus as a face than to recognise whether the face is familiar. Moreover, where sensory thresholds for distinguishing faces from objects are remarkably consistent across observers, they vary widely for familiar face recognition. These findings shed new light on the multifaceted nature of human face recognition by painting a more comprehensive picture of the concurrent evidence accumulation processes initiated by seeing a face.
Flower initiates a positive feedback loop upon PIP2enrichment at periactive zones to control bulk endocytosis
Authors: Li Tsai-Ning , Chen Yu-Jung , Wang You-Tung , Lin Hsin-Chieh , Yao Chi-Kuang 
Published: June 2020

AbstractSynaptic vesicle (SV) endocytosis is coupled to exocytosis to maintain SV pool size and thus neurotransmitter release. Intense stimulation induces activity-dependent bulk endocytosis (ADBE) to recapture large quantities of SV constituents in large endosomes from which SVs reform. How these consecutive processes are spatiotemporally coordinated remains unknown. Here, we show that the Flower Ca2+channel-dependent phosphatidylinositol 4,5-bisphosphate (PIP2) compartmentalization governs such control. Strong stimuli trigger PIP2microdomain formation at periactive zones. Upon exocytosis Flower translocates from SVs to periactive zones, where it increases PIP2levels via Ca2+influxes. Remarkably, PIP2directly enhances Flower channel activity, thereby establishing a positive feedback loop for PIP2microdomain compartmentalization. The PIP2microdomains drive ADBE and SV reformation from bulk endosomes. PIP2further sorts Flower to bulk endosomes, thereby terminating endocytosis. Hence, we propose that the interplay between Flower and PIP2is the crucial spatiotemporal cue that couples exocytosis to ADBE and subsequent SV reformation.
Advancing capacity to adapt to climate change: addressing information needs in the Australian property industry
Authors: Warren-Myers Georgia , Hurlimann Anna , Bush Judy 
Published: June 2020

Purpose
The purpose of this paper is to understand the sources of climate change information used and trusted by key stakeholders in the Australian property industry, their information needs and their capacity to translate that information into decision-making.

Design/methodology/approach
Qualitative research applying in-depth interviews with 24 key stakeholders from a diverse range of property/real estate companies in Australia.

Findings
This research identified a wide range of information types used by key stakeholders, ranging from reliance on unsophisticated mass media reporting to detailed analysis of scientific research. The capacity of stakeholders to translate this information for their organisation was polarised; 11 of the 24 interviewees indicated they had the capacity, while the other 13 indicated they did not, often owing to time horizons or lack of current interest within the organisation or from clients.

Research limitations/implications
This research was limited to 24 in-depth interviews and is not intended to be a representative sample. However, this limitation is offset by the fact that a diverse range of stakeholders were interviewed and an in-depth and rich understanding has been provided about their approach to climate change.

Practical implications
The results can inform the development of better communication channels for climate change for the property industry by supporting science-practice collaborations in the timely and effective dissemination of research. This is important to understand given the identified need to bridge the gap among research, policy and practice.

Social implications
Climate change poses significant challenges and risks for built environments. The property industry, as a key stakeholder, has great potential to influence current practices. The results reported here assist in addressing these challenges.

Originality/value
At present, limited research globally has been conducted about climate change actions in the property industry. This research responds to this gap.
Outcome of slip features on the peristaltic flow of a Rabinowitsch nanofluid in an asymmetric flexible channel
Authors: Imran Naveed , Javed Maryiam , Sohail Muhammad , Farooq S. , Qayyum Mubashir 
Published: June 2020

PurposeNaturally, all the materials are not viscous (i.e. milk, mayonnaise, blood, vaccines, syrups, cosmetics, oil reservoirs, paints, etc.). Here present analysis focuses on the usage of non-Newtonian fluid rheological properties enhancing, damping tools, protection apparatus individuals and in various distinct mechanical procedures. Industrial applications of non-Newtonian liquids include minimum friction, reduction in oil-pipeline friction, scale-up, flow tracers and in several others. The peristaltic mechanism is used as a non-Newtonian material carrier here. This mechanism occurs because of continuous symmetrical and asymmetrical propulsion of smooth channel walls. Peristalsis is a very significant mechanism for carrying drugs and other materials during sensitive diseases treatments.Design/methodology/approachKeeping in mind the considered problem assumptions (Rabinowitsch fluid model, thermal Grashof number, Prandtl number, density Grashof number, wall properties, etc.), it is found that the modeled equations are coupled and nonlinear. Thus here, analytical results are quite challenging to acquire and very limited to extremely venerated circumstances unsettled to their nonlinearity. Hence various developments found in computing proficiencies, numerical procedures that provides accurate, stable and satisfying solutions for non-Newtonian material flows exclusively in complex dimensions play a significant role. Here BVP4C numerical technique is developed to evaluate the nonlinear coupled system of equations with appropriate boundary constraints.FindingsDue to convectively heated surface fluid between the walls having a small temperature. Sherwood and Nusselt numbers both deduce for fixed radiation values and different Rabinowitsch fluid quantity. Skin friction is maximum in the case of Newtonian, while minimum in case of dilatant model and pseudoplastic models. The influence of numerous parameters associated with flow problems such as thermal Grashof number, density Grashof number, Hartman number, Brownian motion, thermophoresis motion factor and slip parameters are also explored in detail and plotted for concentration profile, temperature distribution and velocity. From this analysis, it is concluded that velocity escalates for largerOriginality/valueThe work reported in this manuscript has not been investigated so far by any researcher.
Hall and ion slip current’s impact on magneto-sodium alginate hybrid nanoliquid past a moving vertical plate with ramped heating, velocity slip and Darcy effects
Authors: Ali A. , Banerjee Soma Mitra , Das S. 
Published: June 2020

PurposeThe purpose of this study is to analyze an unsteady MHD Darcy flow of nonNewtonian hybrid nanoliquid past an exponentially accelerated vertical plate under the influence of velocity slip, Hall and ion slip effects in a rotating frame of reference. The fluids in the flow domain are assumed to be viscously incompressible electrically conducting. Sodium alginate (SA) has been taken as a base Casson liquid. A strong uniform magnetic field is applied under the assumption of low magnetic Reynolds number. Effect of Hall and ion-slip currents on the flow field is examined. The ramped heating and time-varying concentration at the plate are taken into consideration. First-order homogeneous chemical reaction and heat absorption are also considered. Copper and alumina nanoparticles are dispersed in base fluid sodium alginate to be formed as hybrid nanoliquid.Design/methodology/approachThe model problem is first formulated in terms of partial differential equations (PDEs) with physical conditions. Laplace transform method (LTM) is used on the nondimensional governing equations for their closed-form solution. Based on these results, expressions for nondimensional shear stresses, rate of heat and mass transfer are also determined. Graphical presentations are chalked out to inspect the impacts of physical parameters on the pertinent physical flow characteristics. Numerical values of the shear stresses, rate of heat and mass transfer at the plate are tabulated for various physical parameters.FindingsNumerical exploration reveals that a significant increase in the secondary flow (i.e. crossflow) near the plate is guaranteed with an augmenting in Hall parameter or ion slip parameter. MHD and porosity have an opposite effect on velocity component profiles for both types of nanoliquids. Result addresses that both shear stresses are strongly enhanced by the Casson effect. Also, hybrid nanosuspension in Casson fluid (sodium alginate) exhibits a lower rate of heat transfer than usual nanoliquid.Social implicationsThis model may be pertinent in cooling processes of metallic infinite plate in bath and hybrid magnetohydrodynamic (MHD) generators, metallurgical process, manufacturing dynamics of nanopolymers, magnetic field control of material processing, synthesis of smart polymers, making of paper and polyethylene, casting of metals, etc.Originality/valueThe originality of this study is to obtain an analytical solution of the modeled problem by using the Laplace transform method (LTM). Such an exact solution of nonNewtonian fluid flow, heat and mass transfer is rare in the literature. It is also worth remarking that the influence of Hall and ion slip effects on the flow of nonNewtonian hybrid nanoliquid is still an open question.