bluuebunny/crossref_metadata_2025 huggingface dataset:
A clash of Umwelts: Anthropomorphism in behavioral neuroscience
Authors: Gomez-Marin Alex
Published: November 2019

Brains enjoy a bodily life. Therefore animals are subjects with a point of view. Yet, coding betrays an anthropomorphic bias: we can, therefore they must. Here I propose a reformulation of Brette's question that emphasizes organismic perception, cautioning for misinterpretations based on external ideal-observer accounts. Theoretical ethology allows computational neuroscience to understand brains from the perspective of their owners.
Relationship between working memory and complex syntax in children with Developmental Language Disorder
Authors: DELAGE Hélène , FRAUENFELDER Ulrich Hans
Published: November 2019

Some theories of Developmental Language Disorder (DLD) explain the linguistic deficits observed in terms of limitations in non-linguistic cognitive systems such as working memory. The goal of this research is to clarify the relationship between working memory and the processing of complex sentences by exploring the performance of 28 French-speaking children with DLD aged five to fourteen years and 48 typically developing children of the same age in memory and linguistic tasks. We identified predictive relationships between working memory and the comprehension and repetition of complex sentences in both groups. As for syntactic measures in spontaneous language, it is the complex spans that explain the major part of the variance in the control children. In children with DLD, however, simple spans are predictive of these syntactic measures. Our results thus reveal a robust relationship between working memory and syntactic complexity, with clinical implications for the treatment of children with DLD.
COMPLEX DYNAMICS IN LUCAS’ TREE ASSET PRICING MODEL WITH DYNAMIC SELF-CONTROL PREFERENCES
Authors: Airaudo Marco
Published: November 2019

This paper studies the global equilibrium dynamics implied by a Lucas’ tree asset pricing model where the representative agent is subject to temptation in consumption choices, and displays dynamic self-control preferences, as defined by Gul and Pesendorfer [(2004) Econometrica 72, 119–158.]. It shows that endogenous cycles of period 2 and higher, as well as chaotic dynamics exist provided temptation utility is sufficiently important (with respect to standard commitment utility) and sufficiently convex. For parameterizations leading to complex deterministic dynamics, a stochastic version of the model admits rational expectations equilibria displaying excess volatility with respect to the underlying fundamentals.
Achieving the 17 Sustainable Development Goals within 9 planetary boundaries
Authors: Randers Jorgen , Rockström Johan , Stoknes Per-Espen , Goluke Ulrich , Collste David , Cornell Sarah E. , Donges Jonathan
Published: November 2019

Non-technical abstract

The world agreed to achieve 17 Sustainable Development Goals by 2030. Nine planetary boundaries set an upper limit to Earth system impacts of human activity in the long run. Conventional efforts to achieve the 14 socio-economic goals will raise pressure on planetary boundaries, moving the world away from the three environmental SDGs. We have created a simple model,Earth3, to measure how much environmental damage follows from achievement of the 14 socio-economic goals, and we propose an index to track effects on people's wellbeing. Extraordinary efforts will be needed to achieve all SDGswithinplanetary boundaries.
The Factor Structure of the 4-Item Perceived Stress Scale in English	Adolescents
Authors: Demkowicz Ola , Panayiotou Margarita , Ashworth Emma , Humphrey Neil , Deighton Jessica
Published: December 2019

Abstract. This study investigated the factor structure, internal consistency, and known-groups validity of the 4-item Perceived Stress Scale in a large sample of 29,388 English adolescents. Results indicated that the original unidimensional structure was not viable and instead provided support for a two-factor structure. Examination of a bifactor-( S − 1) model indicated that this multidimensionality can be attributed to reverse-worded items; however, beyond method effects, these factors appear to capture distinct, though inter-related, constructs. As this multidimensional structure relies on 2-item factors, we advise use of longer versions of this measure where possible.
An Earthquake Early Warning Method Based on Huygens Principle: Robust Ground Motion Prediction Using Various Localized Distance‐Attenuation Models
Authors: Kodera Yuki
Published: November 2019

For the stable operation of earthquake early warning systems under complex earthquake scenarios such as large earthquakes with complicated rupture processes and multiple simultaneous events during intense aftershock activity, wavefield‐based ground motion prediction approaches that can predict shaking directly from the observed shaking, without source parameter characterization, have been proposed. These existing algorithms, however, have weak points, including the employment of inflexible wave propagation models and limited available lead times for sites that have a potential to obtain long lead times. To address these shortcomings, I developed the Approximation by Local Pseudo‐Hypocenter Attenuation (ALPHA) method, a new wavefield‐based algorithm that predicts ground motion by estimating the distance‐attenuation relation from direct observations of the ongoing wavefield in real time. For this estimation, ALPHA uses multiple point‐source models located below each observation station to simulate elementary wave propagation in accordance with Huygens principle. Application to the 2011 Mw9.0 Tohoku‐Oki and 2016 M7.3 Kumamoto earthquakes and 21 additional earthquakes with M ≥ 7 showed that ALPHA stably calculated accurate ground motion predictions for those events and provided long lead times for sites with an intensity threshold on bedrock of three on the Japan Meteorological Agency scale (~IV–VI on the modified Mercalli intensity scale). These findings indicate that ALPHA would enable early warning systems to issue accurate warnings to wider areas at an early stage than existing algorithms.
Pore‐Scale 3D Dynamic Modeling and Characterization of Shale Samples: Considering the Effects of Thermal Maturation
Authors: Wu Yuqi , Tahmasebi Pejman , Yu Hao , Lin Chengyan , Wu HengAn , Dong Chunmei
Published: November 2019

The development of shale gas necessitates accurate modeling and characterization of these complicated formations, at both small and large scales. At the small scale, the studies based on experimental techniques have uncovered that the components and pore types in shales vary dramatically. Several pore types are identified and varied when the thermal maturation of shales changes. Therefore, accurate modeling and characterization of shale samples require taking such dynamic variations into consideration. This study presents a novel, dynamic, and three‐dimensional (3D) modeling technique considering pore‐system variation when the thermal maturation changes. The technique can construct dynamic shale models based on quartet structure generation set algorithm and morphological operation. This method can include various elements available in the shale samples in a very accurate way when the dynamic processes are reproduced. To evaluate the performance of the presented technique, 12 dynamic 3D shale models of three cases are constructed. These models are then characterized by analyzing the fractions of components and pores, pore and throat size distributions, coordination number distribution, fractal dimension, and tortuosity. Besides, gas transport in these dynamic 3D shale models is also simulated using pore network modeling to demonstrate the permeability variation of these models. Moreover, the fractions of interparticle and intraparticle pores and cementation degree are changed to further illustrate the capability of the developed algorithm. This study reveals such a dynamic modeling technique is a robust tool to construct various porous media with complicated elements and pores, which is not limited to shale samples.
Deformation of Intrasalt Beds Recorded by Magnetic Fabrics
Authors: Issachar R. , Weinberger R. , Alsop G. I. , Levi T.
Published: November 2019

Key Points

Magnetic fabrics are used to study the deformation and kinematics of thick intrasalt beds within the Sedom salt wall in the Dead Sea Basin

Magnetic fabrics show tectonic imprints due to folding associated with passive diapirism

Thick intrasalt beds are mechanically distinct from the flowing salt and preserve information on salt tectonic processes operating at depth
Multisatellite Analyses of Spatiotemporal Variability in Photosynthetic Activity Over the Tibetan Plateau
Authors: Wang Xiaoyi , Wang Tao , Liu Dan , Zhang Taotao , Xu Jinfeng , Cui Guishan , Lv Guanting , Huang Huabing
Published: November 2019

Ecosystems on the Tibetan Plateau are particularly sensitive to climate change. Significant advances have been made toward understanding the effects of climate change on the vegetation productivity of the plateau by using satellite observations, but a comprehensive study including various satellite measurements has yet to be presented. Here, we analyze the spatiotemporal variability in Tibetan vegetation productivity using a variety of proxies, including the Normalized Difference Vegetation Index, Enhanced Vegetation Index, Near‐Infrared Reflectance of vegetation, and Solar‐Induced chlorophyll Fluorescence. First, in terms of productivity responses to seasonal climate variation, Near‐Infrared Reflectance of vegetation‐ and Solar‐Induced chlorophyll Fluorescence‐based growing season length had better correlation with eddy covariance site measurements and was ~50 days shorter than those of the other proxies. Second, all proxies, except the Normalized Difference Vegetation Index derived from Système Probatoire d'Observation de la Terre, displayed a dipole‐like trend pattern, similar to the observed north‐south dipole pattern of precipitation change. This result is explained by the finding that moisture is a dominant driver controlling the interannual variation in productivity. Third, we analyzed the long‐term responses of vegetation productivity to the precipitation regime and found four distinct productivity regimes, desert steppe, alpine steppe, meadow, and shrub/forests, indicating that Tibetan productivity varies with precipitation in a nonlinear way. The result offers insights into how Tibetan vegetation will respond to future climate change. Our results provide a multisatellite perspective on the impacts of climate change on spatiotemporal variation in productivity and suggest an urgent need to improve Tibetan productivity simulation.
Synaptic deficits in iPSC-derived cortical interneurons in schizophrenia are mediated by NLGN2 and rescued by N-acetylcysteine
Authors: Kathuria Annie , Lopez-Lengowski Kara , Watmuff Bradley , McPhie Donna , Cohen Bruce M. , Karmacharya Rakesh
Published: November 2019

Human postmortem studies suggest a major role for abnormalities in GABAergic interneurons in the prefrontal cortex in schizophrenia. Cortical interneurons differentiated from induced pluripotent stem cells (iPSCs) of schizophrenia subjects showed significantly lower levels of glutamate decarboxylase 67 (GAD67), replicating findings from multiple postmortem studies, as well as reduced levels of synaptic proteins gehpyrin and NLGN2. Co-cultures of the interneurons with excitatory cortical pyramidal neurons from schizophrenia iPSCs showed reduced synaptic puncta density and lower action potential frequency. NLGN2 overexpression in schizophrenia neurons rescued synaptic puncta deficits while NLGN2 knockdown in healthy neurons resulted in reduced synaptic puncta density. Schizophrenia interneurons also had significantly smaller nuclear area, suggesting an innate oxidative stressed state. The antioxidant N-acetylcysteine increased the nuclear area in schizophrenia interneurons, increased NLGN2 expression and rescued synaptic deficits. These results implicate specific deficiencies in the synaptic machinery in cortical interneurons as critical regulators of synaptic connections in schizophrenia and point to a nexus between oxidative stress and NLGN2 expression in mediating synaptic deficits in schizophrenia.
Effectiveness of the adjunctive use of ozone and chlorhexidine in patients with chronic periodontitis
Authors: Gandhi Kaveri Kranti , Cappetta Emil G. , Pavaskar Rajdeep
Published: November 2019

Background

Scaling and root planning (SRP) is the gold standard approach for treatment of chronic periodontitis but used alone it may not be effective in removing periodontal pathogens from sites where access is poor.

Objective

To evaluate and compare the clinical and microbiological efficacy of ozone and chlorhexidine (CHX) as an adjunct to SRP in patients with chronic periodontitis.

Methods

Twenty-five patients with generalized moderate to severe chronic periodontitis with presence of at least one site in each quadrant with a probing depth ≥5 mm were recruited. In a split mouth study design, two quadrants were randomly allocated to the SRP and ozone therapy and the remaining two quadrants to SRP and CHX therapy. Plaque index (PI), Gingival index (GI), probing depth (PD), clinical attachment loss (CAL) were assessed. Subgingival plaque samples were obtained for assessment of Aggregatibacter actinomycetemcomitans (Aa) and Porphyromonas gingivalis (Pg).

Results

Both groups demonstrated significant intragroup reduction in PI, GI, PD, CAL, Pg count and Aa count from baseline to 3 months follow-up. There were no significant differences between two groups for any of the parameters.

Conclusion

Ozonated olive oil can be used as an adjunctive subgingival irrigant in patients with chronic periodontitis.
Coordinated targeting of CK2 and KIT in gastrointestinal stromal tumours
Authors: Huang Mengyuan , Yang Wenyu , Zhu Jiaqing , Mariño-Enríquez Adrián , Zhu Chennianci , Chen Jiaming , Wu Yuehong , Quan Yanping , Qiu Haibo , Li Xuhui , Chai Li , Fletcher Jonathan A. , Ou Wen-Bin
Published: November 2019

Background

Most gastrointestinal stromal tumours (GIST) are driven by activating oncogenic mutations of KIT/PDGFRA, which provide a compelling therapeutic target. Our previous studies showed that CDC37, regulated by casein kinase 2 (CK2), is a crucial HSP90 cofactor for KIT oncogenic function and a promising and more selective therapeutic target in GIST.

Methods

Biologic mechanisms of CK2-mediated CDC37 regulation were assessed in GISTs by immunoblotting, immunoprecipitations, knockdown and inactivation assays. The effects of a combination of KIT and CK2 inhibition were assessed by immunoblotting, cell viability, colony growth, cell cycle analysis, apoptosis, migration and invasiveness.

Results

CK2 overexpression was demonstrated by immunoblotting in GIST cell lines and patient biopsies. Treatment with a specific CK2 inhibitor, CX4945, leads to CDC37 dephosphorylation and inhibits KIT signalling in imatinib-sensitive and in imatinib-resistant GIST cell lines. Immunoprecipitation demonstrated that CK2 inhibition blocks KIT:HSP90:CDC37 interaction in GIST cells. Coordinated inhibition of CK2 and KIT by CX4945 (or CK2 shRNA) and imatinib, respectively, leads to increased apoptosis, anti-proliferative effects and cell cycle arrest and decreased p-AKT and p-S6 expression, migration and invasiveness in all GIST cell lines compared with either intervention alone, indicating additive effects of inhibiting these two important regulators of GIST biology.

Conclusion

Our findings suggest that combinatorial inhibition of CK2 and KIT warrants evaluation as a novel therapeutic strategy in GIST, especially in imatinib-resistant GIST.
Advanced maternal age compromises fetal growth and induces sex-specific changes in placental phenotype in rats
Authors: Napso Tina , Hung Yin-Po , Davidge Sandra T. , Care Alison S. , Sferruzzi-Perri Amanda N.
Published: November 2019

Advanced maternal age is associated with an increased risk of pregnancy complications. It programmes sex-specific cardiovascular dysfunction in rat offspring, however the intrauterine mechanisms involved remain unknown. This study in the rat assessed the impact of advanced maternal age on placental phenotype in relation to the growth of female and male fetuses. We show that relative to young (3–4 months) dams, advanced maternal age (9.5–10 months) compromises growth of both female and male fetuses but affects the placental phenotype sex-specifically. In placentas from aged versus young dams, the size of the placental transport and endocrine zones were increased and expression of Igf2 (+41%) and placental lactogen (Prl3b1: +59%) genes were upregulated in female, but not male fetuses. Placental abundance of IGF2 protein also decreased in the placenta of males only (−95%). Moreover, in placentas from aged versus young dams, glucocorticoid metabolism (11β-hsd2: +63% and 11β-hsd1: −33%) was higher in females, but lower in males (11β-hsd2: −50% and 11β-hsd1: unaltered). There was however, no change in the placental abundance of 11β-HSD2 protein in aged versus young dams regardless of fetal sex. Levels of oxidative stress in the placenta were increased in female and male fetuses (+57% and +90%, respectively) and apoptosis increased specifically in the placenta of males from aged rat dams (+700%). Thus, advanced maternal age alters placental phenotype in a sex-specific fashion. These sexually-divergent changes may play a role in determining health outcomes of female and male offspring of aged mothers.
Individual Differences in Serial Dependence of Facial Identity are Associated with Face Recognition Abilities
Authors: Turbett Kaitlyn , Palermo Romina , Bell Jason , Burton Jessamy , Jeffery Linda
Published: December 2019

Serial dependence is a perceptual bias where current perception is biased towards prior visual input. This bias occurs when perceiving visual attributes, such as facial identity, and has been argued to play an important functional role in vision, stabilising the perception of objects through integration. In face identity recognition, this bias could assist in building stable representations of facial identity. If so, then individual variation in serial dependence could contribute to face recognition ability. To investigate this possibility, we measured both the strength of serial dependence and the range over which individuals showed this bias (the tuning) in 219 adults, using a new measure of serial dependence of facial identity. We found that better face recognition was associated with stronger serial dependence and narrower tuning, that is, showing serial dependence primarily when sequential faces were highly similar. Serial dependence tuning was further found to be a significant predictor of face recognition abilities independently of both object recognition and face identity aftereffects. These findings suggest that the extent to which serial dependence is used selectively for similar faces is important to face recognition. Our results are consistent with the view that serial dependence plays a functional role in face recognition.
Correcting Artifacts in Single Molecule Localization Microscopy Analysis Arising from Pixel Quantum Efficiency Differences in sCMOS Cameras
Authors: Babcock Hazen P. , Huang Fang , Speer Colenso M.
Published: December 2019

Optimal analysis of single molecule localization microscopy (SMLM) data acquired with a scientific Complementary Metal-Oxide-Semiconductor (sCMOS) camera relies on statistical compensation for its pixel-dependent gain, offset and readout noise. In this work we show that it is also necessary to compensate for differences in the relative quantum efficiency (RQE) of each pixel. We found differences in RQE on the order of 4% in our tested sCMOS sensors. These differences were large enough to have a noticeable effect on analysis algorithm results, as seen both in simulations and biological imaging data. We discuss how the RQE differences manifest themselves in the analysis results and present the modifications to the Poisson maximum likelihood estimation (MLE) sCMOS analysis algorithm that are needed to correct for the RQE differences.
Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania
Authors: Katani Robab , Schilling Megan A. , Lyimo Beatus , Tonui Triza , Cattadori Isabella M. , Eblate Ernest , Martin Andimile , Estes Anna B. , Buza Teresia , Rentsch Dennis , Davenport Karen W. , Hovde Blake T. , Lyimo Samson , Munuo Lydia , Stomeo Francesca , Tiambo Christian , Radzio-Basu Jessica , Mosha Fausta , Hudson Peter J. , Buza Joram J. , Kapur Vivek
Published: December 2019

Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.
Organ Dynamics and Hemodynamic of the Whole HH25 Avian Embryonic Heart, Revealed by Ultrasound Biomicroscopy, Boundary Tracking, and Flow Simulations
Authors: Ho Sheldon , Chan Wei Xuan , Phan-Thien Nhan , Yap Choon Hwai
Published: December 2019

Congenital heart malformations occur to substantial number of pregnancies. Studies showed that abnormal flow biomechanical environments could lead to malformations, making it important to understand the biomechanical environment of the developing heart. We performed 4D high-frequency ultrasound scans of chick embryonic hearts at HH25 to study the biomechanics of the whole heart (atria and ventricle). A novel and high-fidelity motion estimation technique, based on temporal motion model and non-rigid image registration algorithm, allowed automatic tracking of fluid-structure boundaries from scan images, and supported flow simulations. Results demonstrated that atrial appendages were the most contractile portion of the atria, having disproportionately high contribution to atrial blood pumping for its volume in the atria. However, the atria played a small role in blood pumping compared to the ventricle, as it had much lower ejection energy expenditure, and as the ventricle appeared to be able to draw inflow from the veins directly during late diastole. Spatially and temporally averaged wall shear stresses (WSS) for various cardiac structures were 0.062–0.068 Pa, but spatial-averaged WSS could be as high as 0.54 Pa in the RV. WSS was especially elevated at the atrial inlet, atrioventricular junction, regions near to the outflow tract, and at dividing lines between the left and right atrium and left and right side of the ventricle, where septation had begun and the lumen had narrowed. Elevated WSS could serve as biomechanics stimulation for proper growth and development.
The bears from Dmanisi and the first dispersal of early Homo out of Africa
Authors: Medin Tsegai , Martínez-Navarro Bienvenido , Madurell-Malapeira Joan , Figueirido Borja , Kopaliani Giorgi , Rivals Florent , Kiladze Gocha , Palmqvist Paul , Lordkipanidze David
Published: November 2019

We report on the taxonomy and paleodiet of the bear population that inhabited the emblematic palaeoanthropological Early Pleistocene (1.8 Ma) site of Dmanisi (Georgia), based on a dual approach combining morphometrics and microwear of upper and lower teeth. Given that the teeth of Ursus etruscus Cuvier, 1823 from Dmanisi show considerable size variability, their systematic position has been debated. However, a comparative study of the coefficients of variation for tooth size measurements in several modern bear species shows that the variability in tooth size of the ursid population from Dmanisi could result from sexual dimorphism. The analysis of tooth microwear indicates that these bears inhabited a mixed environment of open plain with forest patches, where they had a browsing diet with a substantial contribution of meat and/or fish. Comparative tooth morphometric analyses of modern ursids and fossil U. etruscus indicate that this extinct species had an omnivorous behavior similar to that of extant brown bears. The ecological interactions of the Dmanisi bears with other members of the large mammals community, including the first hominins that dispersed out of Africa, are discussed in the light of this new evidence.
Associations between cognitive impairment at onset and disability accrual in young people with multiple sclerosis
Authors: Carotenuto Antonio , Moccia Marcello , Costabile Teresa , Signoriello Elisabetta , Paolicelli Damiano , Simone Marta , Lus Giacomo , Brescia Morra Vincenzo , Lanzillo Roberta ,   Cogniped study group, Rosa Laura , Barbarulo Anna Maria , Falco Fabrizia , Viterbo Rosa Gemma , Lauro Francesca
Published: December 2019

Differently from the adult multiple sclerosis (MS) population, the predictive value of cognitive impairment in early-onset MS is still unknown. We aim to evaluate whether cognitive performances at disease onset predict disease progression in young people with MS. This is a retrospective study on early onset (<25 years) MS patients, who had a baseline cognitive evaluation at disease onset. Demographic and longitudinal clinical data were collected up to 7 years follow up. Cognitive abilities were assessed at baseline through the Brief Repeatable Battery. Associations between cognitive abilities and clinical outcomes (occurrence of a relapse, and 1-point EDSS progression) were evaluated with stepwise logistic and Cox regression models. We included 51 patients (26 females), with a mean age at MS onset of 17.2 ± 3.9 years, and an EDSS of 2.5 (1.0–6.0). Over the follow-up, twenty-five patients had at least one relapse, and 7 patients had 1-point EDSS progression. Relapse occurrence was associated with lower 10/36 SPART scores (HR = 0.92; p = 0.002) and higher WLG scores (HR = 1.05; p = 0.01). EDSS progression was associated with lower SDMT score (OR: 0.70; p = 0.04). Worse visual memory and attention/information processing were associated with relapses and with increased motor disability after up to 7-years follow-up. Therefor, specific cognitive subdomains might better predict clinical outcomes than the overall cognitive impairment in early-onset MS.
Oscillations in the near-field feeding current of a calanoid copepod are useful for particle sensing
Authors: Giuffre Carl , Hinow Peter , Jiang Houshuo , Strickler J. Rudi
Published: November 2019

Calanoid copepods are small crustaceans that constitute a major element of aquatic ecosystems. Key to their success is their feeding apparatus consisting of sensor-studded mouth appendages that are in constant motion. These appendages generate a feeding current to enhance the encounter probability with food items. Additionally, sensing enables the organism to determine the position and quality of food particles, and to alter the near-field flow to capture and manipulate the particles for ingestion or rejection. Here we observe a freely swimming copepod Leptodiaptomus sicilis in multiple perspectives together with suspended particles that allow us to analyse the flow field created by the animal. We observe a highly periodic motion of the mouth appendages that is mirrored in oscillations of nearby tracer particles. We propose that the phase shift between the fluid and the particle velocities is sufficient for mechanical detection of the particles entrained in the feeding current. Moreover, we propose that an immersed algal cell may benefit from the excitation by increased uptake of dissolved inorganic compounds.
A New Index of Coordinated Posterior and Anterior Evoked EEG to Detect Recall Under Sedation – A Pilot Study
Authors: Baron Shahaf Dana , Hare Gregory M. T. , Baker Andrew J. , Chenosia Violina , Priven Leonid , Mistry Nikhil , Shahaf Goded
Published: November 2019

EEG-based technologies may be limited in identifying recall under sedation (RUS). We developed a novel index, posteriorization/anteriorization (P/A) index, based on auditory evoked EEG signal and assessed whether it could differentiate between patients with or without RUS. Methods: EEG and BIS were sampled from 3 groups: 1. Patients undergoing sedation (n = 26); 2. Awake volunteers (n = 13, positive control for recall) 3. Patients undergoing general anesthesia (GA, n = 12, negative control for recall). In recovery, recall was assessed using the BRICE questionnaire. Of the 26 sedated patients, 12 experienced recall. Both The P/A index and BIS differentiated between patients with recall and no recall. However, BIS differentiation may have been sensitive to the main drug used for sedation (midazolam vs. propofol) and the P/A index did not show similar drug-based sensitivity. Furthermore, only BIS results were correlated with EMG. Conclusion: This pilot study provided support for the association between P/A index and recall after sedation. Further research is needed in integrating the index into clinical use: (1) it should be derived by an easy-to-use EEG system with a better signal-to-noise ratio; (2) its applicability to other drugs must be shown.
The integrative knowledge base for miRNA-mRNA expression in colorectal cancer
Authors: Jevšinek Skok Daša , Hauptman Nina , Boštjančič Emanuela , Zidar Nina
Published: December 2019

“miRNA colorectal cancer” (https://mirna-coadread.omics.si/) is a freely available web application for studying microRNA and mRNA expression and their correlation in colorectal cancer. To the best of our knowledge, “miRNA colorectal cancer” has the largest knowledge base of miRNA-target gene expressions and correlations in colorectal cancer, based on the largest available sample size from the same source of data. Data from high-throughput molecular profiling of 295 colon and rectum adenocarcinoma samples from The Cancer Genome Atlas was analyzed and integrated into our knowledge base. The objective of developing this web application was to help researchers to discover the behavior and role of miRNA-target gene interactions in colorectal cancer. For this purpose, results of differential expression and correlation analyses of miRNA and mRNA data collected in our knowledge base are available through web forms. To validate our knowledge base experimentally, we selected genesFN1,TGFB2,RND3,ZEB1andZEB2and miRNAshsa-miR-200a/b/c-3p,hsa-miR-141-3pandhsa-miR-429. Both approaches revealed a negative correlation between miRNAhsa-miR-200b/c-3pand its target geneFN1and betweenhsa-miR-200a-3pand its targetTGFB2, thus supporting the usefulness of the developed knowledge base.
Crude Oil Sensing using Carbon Nano Structures Synthetized from Phoenix Dactylifera L. Cellulose
Authors: Fethiza Tedjani Chouaib , Ben Mya Omar , Rebiai Abdelkrim , Khachkhouche Abdelhamid , Dehbi Abdelhakim , Méchara Nacer Eddine
Published: November 2019

This study reports on the crude oil-sensing using carbon nano structures (CNSs). A mixture of CNSs was obtained by a simple method of preparation using palm cellulose ash and nitric acid as precursors, the powder was characterized by x-ray diffraction and infrared spectroscopy. The optical density of crude oil from Rhoud El-Baguel area (Southeast of Algeria) studied using UV-Vis spectroscopy, before and after adding an amount of CNSs powder to view the CNSs crude oil sensing and therefore a new method to determine the quality of crude oils and the comparison between them. Results show that CNSs prepared from palm cellulose ash have a good crystallinity and it is formed mainly from carbon nano dots (CNDs) with 4.32 Å in layers spacing and 7.4 Å in crystallite size, indicate that CNSs can be used as an excellent crude oil sensor.
Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics
Authors: Han Jie , Meng Jun , Chen Shuya , Li Chuang
Published: November 2019

The intestinal microbiota contributes to host metabolism and health. This study aimed to assess the effects of biochar on cecal microbiome-related metabolic changes in rats. Rats were orally administered rice straw biochar (RSB) at 1120 mg/kg body weight for 5 weeks. Cecal samples were analyzed to perform metabolic and microbial profiling via a combination of 16S rRNA gene sequencing and LC/MS techniques. We observed a significant influence of RSB in shaping the cecal bacterial community, including some potentially beneficial members of phylum Firmicutes belonging to unclassified Lachnospiraceae, Oscillibacter, and Clostridium XlVa and IV, as well as the depletion of some opportunistic pathogens belonging to Prevotella, Bacteroides and Paraprevotella. The metabolomic analysis revealed distinct changes in the cecal metabolic phenotype, including lower levels of L-isoleucine, indole-3-acetic acid, benzoic acid, and tetradecanoic acid as well as higher levels of L-phenylalanine, L-glutamate, 3-phenylpropanoic acid, chenodeoxycholic acid, cholic acid, 7-dehydrocholesterol, (5Z, 8Z, 11Z, 14Z, 17Z)-eicosapentaenoic acid, 11-deoxycorticosterone and retinol, which are mainly involved in the metabolic pathways of linoleic acid, amino acid and steroid hormone biosynthesis. Correlation analysis revealed a positive association of unclassified Lachnospiraceae, Oscillibacter and Clostridium IV with 3-phenylpropanoic acid, L-phenylalanine, L-glutamate, 11-deoxycorticosterone and 7-dehydrocholesterol. These results confirm that the gut microbiome is altered and may be critical for good performance under RSB application by interacting with metabolism.
Aging, sex and cognitive Theory of Mind: a transcranial direct current stimulation study
Authors: Adenzato Mauro , Manenti Rosa , Gobbi Elena , Enrici Ivan , Rusich Danila , Cotelli Maria
Published: December 2019

Aging is accompanied by changes in cognitive abilities and a great interest is spreading among researchers about aging impact on social cognition skills, such as the Theory of Mind (ToM). Transcranial direct current stimulation (tDCS) has been used in social cognition studies founding evidence of sex-related different effects on cognitive ToM task in a young people sample. In this randomized, double-blind, sham-controlled study, we applied one active and one sham tDCS session on the medial prefrontal cortex (mPFC) during a cognitive ToM task, including both social (i.e., communicative) and nonsocial (i.e., private) intention attribution conditions, in sixty healthy aging individuals (30 males and 30 females). In half of the participants the anode was positioned over the mPFC, whereas in the other half the cathode was positioned over the mPFC. The results showed that: (i) anodal tDCS over the mPFC led to significant slower reaction times (vs. sham) for social intention attribution task only in female participants; (ii) No effects were found in both females and males during cathodal stimulation. We show for the first time sex-related differences in cognitive ToM abilities in healthy aging, extending previous findings concerning young participants.
Gate-tunable graphene-based Hall sensors on flexible substrates with increased sensitivity
Authors: Uzlu Burkay , Wang Zhenxing , Lukas Sebastian , Otto Martin , Lemme Max C. , Neumaier Daniel
Published: December 2019

We demonstrate a novel concept for operating graphene-based Hall sensors using an alternating current (AC) modulated gate voltage, which provides three important advantages compared to Hall sensors under static operation: (1) The sensor sensitivity can be doubled by utilizing both n- and p-type conductance. (2) A static magnetic field can be read out at frequencies in the kHz range, where the 1/f noise is lower compared to the static case. (3) The off-set voltage in the Hall signal can be reduced. This significantly increases the signal-to-noise ratio compared to Hall sensors without a gate electrode. A minimal detectable magnetic field Bmin down to $$290\,{\rm{nT}}/\surd {\rm{Hz}}$$290nT/√Hz and sensitivity up to 0.55 V/VT was found for Hall sensors working on flexible polyimide (PI) substrates. This clearly outperforms state-of-the-art flexible Hall sensors and is comparable to the values obtained by the best rigid III/V semiconductor Hall sensors.
Predicting the spatial abundance of Ixodes ricinus ticks in southern Scandinavia using environmental and climatic data
Authors: Jung Kjær Lene , Soleng Arnulf , Edgar Kristin Skarsfjord , Lindstedt Heidi Elisabeth H. , Paulsen Katrine Mørk , Andreassen Åshild Kristine , Korslund Lars , Kjelland Vivian , Slettan Audun , Stuen Snorre , Kjellander Petter , Christensson Madeleine , Teräväinen Malin , Baum Andreas , Klitgaard Kirstine , Bødker René
Published: December 2019

Recently, focus on tick-borne diseases has increased as ticks and their pathogens have become widespread and represent a health problem in Europe. Understanding the epidemiology of tick-borne infections requires the ability to predict and map tick abundance. We measured Ixodes ricinus abundance at 159 sites in southern Scandinavia from August-September, 2016. We used field data and environmental variables to develop predictive abundance models using machine learning algorithms, and also tested these models on 2017 data. Larva and nymph abundance models had relatively high predictive power (normalized RMSE from 0.65–0.69, R2 from 0.52–0.58) whereas adult tick models performed poorly (normalized RMSE from 0.94–0.96, R2 from 0.04–0.10). Testing the models on 2017 data produced good results with normalized RMSE values from 0.59–1.13 and R2 from 0.18–0.69. The resulting 2016 maps corresponded well with known tick abundance and distribution in Scandinavia. The models were highly influenced by temperature and vegetation, indicating that climate may be an important driver of I. ricinus distribution and abundance in Scandinavia. Despite varying results, the models predicted abundance in 2017 with high accuracy. The models are a first step towards environmentally driven tick abundance models that can assist in determining risk areas and interpreting human incidence data.
Role of the I16-D194 ionic interaction in the trypsin fold
Authors: Stojanovski Bosko M. , Chen Zhiwei , Koester Sarah K. , Pelc Leslie A. , Di Cera Enrico
Published: December 2019

Activity in trypsin-like proteases is the result of proteolytic cleavage at R15 followed by an ionic interaction that ensues between the new N terminus of I16 and the side chain of the highly conserved D194. This mechanism of activation, first proposed by Huber and Bode, organizes the oxyanion hole and primary specificity pocket for substrate binding and catalysis. Using the clotting protease thrombin as a relevant model, we unravel contributions of the I16-D194 ionic interaction to Na+ binding, stability of the transition state and the allosteric E*-E equilibrium of the trypsin fold. The I16T mutation abolishes the I16-D194 interaction and compromises the architecture of the oxyanion hole. The D194A mutation also abrogates the I16-D194 interaction but, surprisingly, has no effect on the architecture of the oxyanion hole that remains intact through a new H-bond established between G43 and G193. In both mutants, loss of the I16-D194 ionic interaction compromises Na+ binding, reduces stability of the transition state, collapses the 215–217 segment into the primary specific pocket and abrogates the allosteric E*-E equilibrium in favor of a rigid conformation that binds ligand at the active site according to a simple lock-and-key mechanism. These findings refine the structural role of the I16-D194 ionic interaction in the Huber-Bode mechanism of activation and reveal a functional linkage with the allosteric properties of the trypsin fold like Na+ binding and the E*-E equilibrium.
Upregulation of vitamin D-binding protein is associated with changes in insulin production in pancreatic beta-cells exposed to p,p′-DDT and p,p′-DDE
Authors: Pavlíková Nela , Daniel Petr , Šrámek Jan , Jelínek Michael , Šrámková Veronika , Němcová Vlasta , Balušíková Kamila , Halada Petr , Kovář Jan
Published: December 2019

Persistent organochlorine pollutants (POPs) gradually accumulate in the human organism due to their presence in the environment. Some studies have described a correlation between the level of POPs in the human body and the incidence of diabetes, but we know little about the direct effect of POPs on pancreatic beta-cells. We exposed pancreatic beta-cells INS1E to non-lethal concentrations of p,p′-DDT (1,1′-(2,2,2-Trichloroethane-1,1-diyl)bis(4-chlorobenzene)) and p,p′-DDE (1,1′-(2,2-dichloroethene-1,1-diyl)bis(4-chlorobenzene)) for 1 month, and assessed changes in protein expression and the intracellular insulin level. 2-D electrophoresis revealed 6 proteins with changed expression in cells exposed to p,p′-DDT or p,p′-DDE. One of the detected proteins – vitamin D-binding protein (VDBP) – was upregulated in both cells exposed to p,p′-DDT, and cells exposed to p,p′-DDE. Both exposures to pollutants reduced the intracellular level of insulin mRNA, proinsulin, and insulin monomer; p,p′-DDT also slightly reduced the level of hexameric insulin. Overexpression of VDBP caused by the stable transfection of beta-cells with the gene for VDBP decreased both the proinsulin and hexameric insulin level in beta-cells similarly to the reduction detected in cells exposed to p,p′-DDT. Our data suggest that in the cells exposed to p,p′-DDT and p,p′-DDE, the increased VDBP protein level decreased the proinsulin expression in an unknown mechanism.
Acyl ethanolamides in Diabetes and Diabetic Nephropathy: Novel targets from untargeted plasma metabolomic profiles of South Asian Indian men
Authors: Devi Sarita , Nongkhlaw Bajanai , Limesh M. , Pasanna Roshni M. , Thomas Tinku , Kuriyan Rebecca , Kurpad Anura V. , Mukhopadhyay Arpita
Published: December 2019

The pathophysiology of diabetic nephropathy (DN) in type 2 diabetes (T2D) patients is minimally understood. We compared untargeted high-resolution accurate mass (HRAM) orbitrap-based plasma metabolomic profiles of 31 T2D-DN (with estimated glomerular filtration rate ≤80 mL/min/1.73 m2), 29 T2D and 30 normal glucose tolerance (NGT) Indian men. Of the 939 plasma metabolites that were differentially abundant amongst the NGT, T2D and T2D-DN (ANOVA, False Discovery Rate – FDR adjusted p-value < 0.05), 48 were associated with T2D irrespective of the renal function of the subjects. Acyl ethanolamides and acetylcholine were decreased while monoacylglycerols (MAGs) and cortisol were elevated in both T2D and T2D-DN. Sixteen metabolites, including amino acid metabolites Imidazolelactate and N-Acetylornithine, changed significantly between NGT, T2D and T2D-DN. 192 metabolites were specifically dysregulated in T2D-DN (ratio ≥2 or ≤0.5 between T2D-DN and T2D, similar abundance in NGT and T2D). These included increased levels of multiple acylcarnitine and amino acid metabolites. We observed a significant dysregulation of amino acid and fatty acid metabolism in South Asian Indian male T2D-DN subjects. Unique to this study, we report a reduction in acyl ethanolamide levels in both T2D and T2D-DN males. Those with dysregulation in acyl ethanolamides, which are endogenous agonists of GPR119, are likely to exhibit improved glycemic control with GPR119 agonists.
Short-term depression shapes information transmission in a constitutively active GABAergic synapse
Authors: Lavian Hagar , Korngreen Alon
Published: December 2019

Short-term depression is a low-pass filter of synaptic information, reducing synaptic information transfer at high presynaptic firing frequencies. Consequently, during elevated presynaptic firing, little information passes to the postsynaptic neuron. However, many neurons fire at relatively high frequencies all the time. Does depression silence their synapses? We tested this apparent contradiction in the indirect pathway of the basal ganglia. Using numerical modeling and whole-cell recordings from single entopeduncular nucleus (EP) neurons in rat brain slices, we investigated how different firing rates of globus pallidus (GP) neurons affect information transmission to the EP. Whole-cell recordings showed significant variability in steady-state depression, which decreased as stimulation frequency increased. Modeling predicted that this variability would translate into different postsynaptic noise levels during constitutive presynaptic activity. Our simulations further predicted that individual GP-EP synapses mediate gain control. However, when we consider the integration of multiple inputs, the broad range of GP firing rates would enable different modes of information transmission. Finally, we predict that changes in dopamine levels can shift the action of GP neurons from rate coding to gain modulation. Our results thus demonstrate how short-term depression shapes information transmission in the basal ganglia in particular and via GABAergic synapses in general.
Imaging of intermittent lipid-receptor interactions reflects changes in live cell membranes upon agonist-receptor binding
Authors: Tornmalm Johan , Piguet Joachim , Chmyrov Volodymyr , Widengren Jerker
Published: December 2019

Protein-lipid interactions in cellular membranes modulate central cellular functions, are often transient in character, but occur too intermittently to be readily observable. We introduce transient state imaging (TRAST), combining sensitive fluorescence detection of fluorophore markers with monitoring of their dark triplet state transitions, allowing imaging of such protein-lipid interactions. We first determined the dark state kinetics of the biomembrane fluorophore 7-nitrobenz-2-oxa-1,3-diazole-4-yl (NBD) in lipid vesicles, and how its triplet state is quenched by spin-labels in the same membranes. We then monitored collisional quenching of NBD-lipid derivatives by spin-labelled stearic acids in live cell plasma membranes, and of NBD-lipid derivatives by spin-labelled G-Protein Coupled Receptors (GPCRs). We could then resolve transient interactions between the GPCRs and different lipids, how these interactions changed upon GPCR activation, thereby demonstrating a widely applicable means to image and characterize transient molecular interactions in live cell membranes in general, not within reach via traditional fluorescence readouts.