bluuebunny/crossref_metadata_2025_split huggingface dataset:
A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task
Authors: Chandravadia N. , Liang D. , Schjetnan A. G. P. , Carlson A. , Faraut M. , Chung J. M. , Reed C. M. , Dichter B. , Maoz U. , Kalia S. K. , Valiante T. A. , Mamelak A. N. , Rutishauser U. 
Published: March 2020

AbstractA challenge for data sharing in systems neuroscience is the multitude of different data formats used. Neurodata Without Borders: Neurophysiology 2.0 (NWB:N) has emerged as a standardized data format for the storage of cellular-level data together with meta-data, stimulus information, and behavior. A key next step to facilitate NWB:N adoption is to provide easy to use processing pipelines to import/export data from/to NWB:N. Here, we present a NWB-formatted dataset of 1863 single neurons recorded from the medial temporal lobes of 59 human subjects undergoing intracranial monitoring while they performed a recognition memory task. We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. This combined data and code release is a case study for how to utilize NWB:N for human single-neuron recordings and enables easy re-use of this hard-to-obtain data for both teaching and research on the mechanisms of human memory.
Transcriptomic response to soybean meal-based diets as the first formulated feed in juvenile yellow perch (Perca flavescens)
Authors: Kemski Megan M. , Rappleye Chad A. , Dabrowski Konrad , Bruno Richard S. , Wick Macdonald 
Published: March 2020

AbstractWith increasing levels of fish meal (FM) protein in aquafeeds being replaced with soybean meal (SBM) protein, understanding the molecular mechanisms involved in response to alternative diets has become a critical concern. Thus, the goal of this study was to examine transcriptional differences in the intestine of juvenile yellow perch through RNA-sequencing (RNA-seq), after their initial introduction to a formulated diet with 75% SBM protein inclusion for 61 days, compared to those fed a traditional FM-based diet. Transcriptomic analysis revealed a concise set of differentially expressed genes in juveniles fed the SBM-based diet, the majority of which were intrinsic to the cholesterol biosynthesis pathway. Analysis of total body lipid and cholesterol levels were also investigated, with no between-treatment differences detected. Results of this study demonstrate that in response to SBM-based diets, yellow perch juveniles up-regulate the cholesterol biosynthesis pathway in order to maintain homeostasis. These findings suggest that the upregulation of the cholesterol biosynthesis pathway may negatively impact fish growth due to its large energy expenditure, and future studies are warranted.
Bacterial chemotaxis towards polysaccharide pectin by pectin-binding protein
Authors: Konishi Hidenori , Hio Mamoru , Kobayashi Masahiro , Takase Ryuichi , Hashimoto Wataru 
Published: March 2020

AbstractAs opposed to typical bacteria exhibiting chemotaxis towards low-molecular-weight substances, such as amino acids and mono/oligosaccharides, gram-negative Sphingomonas sp. strain A1 shows chemotaxis towards alginate and pectin polysaccharides. To identify the mechanism of chemotaxis towards macromolecules, a genomic fragment was isolated from the wild-type strain A1 through complementation with the mutant strain A1-M5 lacking chemotaxis towards pectin. This fragment contained several genes including sph1118. Through whole-genome sequencing of strain A1-M5, sph1118 was found to harbour a mutation. In fact, sph1118 disruptant lost chemotaxis towards pectin, and this deficiency was recovered by complementation with wild-type sph1118. Interestingly, the gene disruptant also exhibited decreased pectin assimilation. Furthermore, the gene product SPH1118 was expressed in recombinant E. coli cells, purified and characterised. Differential scanning fluorimetry and UV absorption spectroscopy revealed that SPH1118 specifically binds to pectin with a dissociation constant of 8.5 μM. Using binding assay and primary structure analysis, SPH1118 was predicted to be a periplasmic pectin-binding protein associated with an ATP-binding cassette transporter. This is the first report on the identification and characterisation of a protein triggering chemotaxis towards the macromolecule pectin as well as its assimilation.
Divergent mammalian body size in a stable Eocene greenhouse climate
Authors: Ring Simon J. , Bocherens Hervé , Wings Oliver , Rabi Márton 
Published: March 2020

AbstractA negative correlation between body size and the latitudinal temperature gradient is well established for extant terrestrial endotherms but less so in the fossil record. Here we analyze the middle Eocene site of Geiseltal (Germany), whose record is considered to span ca. 5 Myrs of gradual global cooling, and generate one of the most extensive mammalian Paleogene body size datasets outside North America. The δ18O and δ13C isotopic analysis of bioapatite reveals signatures indicative of a humid, subtropical forest with no apparent climatic change across Geiseltal. Yet, body mass of hippomorphs and tapiromorphs diverges rapidly from a respective median body size of 39 kg and 124 kg at the base of the succession to 26 kg and 223 kg at the top. We attribute the divergent body mass evolution to a disparity in lifestyle, in which both taxa maximize their body size-related selective advantages. Our results therefore support the view that intrinsic biotic processes are an important driver of body mass outside of abrupt climate events. Moreover, the taxonomy previously used to infer the duration of the Geiseltal biota is not reproducible, which precludes chronological correlation with Eocene marine temperature curves.
Periodic Fractal-Growth Branching to Nano-Structured Grating Aggregation in Phthalic Acid
Authors: Chen Tzu-Yu , Woo Eamor M. , Nagarajan Selvaraj 
Published: March 2020

AbstractSmall-molecule phthalic acid (PA), confined in micrometer thin films, was crystallized in the presence of strongly interacting tannic acid (TA) to investigate crystal assembly and correlation between banded patterns and branching structures. Several compositions of the mixture of ethanol/water solutions and evaporation temperatures were also manipulated to investigate the kinetic effects on the morphology of PA crystals. With increasing evaporation rate, the morphology of PA crystals systematically changes from circular-banded spherulites to highly ordered grating-banded patterns. A unique periodic fractal-branch pattern with contrasted birefringent bands exists at intermediate evaporation rate, and this unique grating architecture has never been found in other banded crystals. Crystal assembly of these three periodic morphologies was analyzed by utilizing atomic-force microscopy (AFM) and scanning electron microscopy (SEM) to reveal the mechanisms of formation of hierarchical structures of PA. The detailed growth mechanisms of the novel fractal-branching assembly into circular- or grating-banded patterns are analyzed in this work.
Food additives: distribution and co-occurrence in 126,000 food products of the French market
Authors: Chazelas Eloi , Deschasaux Mélanie , Srour Bernard , Kesse-Guyot Emmanuelle , Julia Chantal , Alles Benjamin , Druesne-Pecollo Nathalie , Galan Pilar , Hercberg Serge , Latino-Martel Paule , Esseddik Younes , Szabo Fabien , Slamich Pierre , Gigandet Stephane , Touvier Mathilde 
Published: March 2020

AbstractBackground. More than 330 food additives (e.g. artificial sweeteners, emulsifiers, dyes) are authorized in Europe, with a great variability of use across food products. Objective. The objective of this study was to investigate the distribution and co-occurrence of food additives in a large-scale database of foods and beverages available on the French market. Design. The open access crowdsourced Open Food Facts database (https://world.openfoodfacts.org/) was used to retrieve the composition of food and beverage products commonly marketed on the French market (n = 126,556), based on the ingredients list. Clustering of food additive variables was used in order to determine groups of additives frequently co-occurring in food products. The clusters were confirmed by network analysis, using theeLassomethod. Results. Fifty-three-point eight percent of food products contained at least 1 food additive and 11.3% at least 5. Food categories most likely to contain food additives (in more than 85% of food items) were artificially sweetened beverages, ice creams, industrial sandwiches, biscuits and cakes. The most frequently used food additives were citric acid, lecithins and modified starches (>10,000 products each). Some food additives with suspected health effects also pertained to the top 50: sodium nitrite, potassium nitrate, carrageenan, monosodium glutamate, sulfite ammonia caramel, acesulfame K, sucralose, (di/tri/poly) phosphates, mono- and diglycerides of fatty acids, potassium sorbate, cochineal, potassium metabisulphite, sodium alginate, and bixin (>800 food products each). We identified 6 clusters of food additives frequently co-occurring in food products. Conclusions. Food additives are widespread in industrial French products and some clusters of additives frequently co-occurring in food products were identified. These results pave the way to future etiological studies merging composition data to food consumption data to investigate their association with chronic disease risk, in particular potential ‘cocktail effects’.
Purification, Characterization and Mechanistic Evaluation of Angiotensin Converting Enzyme Inhibitory Peptides Derived from Zizyphus Jujuba Fruit
Authors: Memarpoor-Yazdi Mina , Zare-Zardini Hadi , Mogharrab Navid , Navapour Leila 
Published: March 2020

AbstractThe synthetic Angiotensin Converting Enzyme (ACE) inhibitors have side effects and hence demands for natural ACE inhibitors have been rising. The aim of this study is to purify and introduce natural ACE inhibitors extracted from Zizyphus jujuba fruits. Proteins from Zizyphus jujuba were lysed by trypsin, papain and their combination. Acquired peptides were purified and evaluated for ACE inhibitory activity. Peptide fractions with inhibitory activity were sequenced using tandem mass spectrometry. To elucidate the mode of peptide binding to ACE, homology modeling, molecular docking and molecular dynamics simulation were performed. Amino acid sequence of F2 and F4 peptides, which were the most active hydrolysates, were determined to be IER and IGK with the IC50 values of 0.060 and 0.072 mg/ml, respectively. Results obtained by computational analysis revealed that similar to the common ACE competitive inhibitors such as captopril, IER tripeptide binds to the enzyme active site, in vicinity of the zinc binding site, and occupies the S1 and S2’ subsites. Binding occurs through hydrogen bonding with Gln293, Lys522, His524, Tyr531 and also several hydrophobic interactions. Collectively, these findings indicate that IER tripeptide inhibits the rabbit ACE enzyme through a competitive mechanism of inhibition with IC50 values in the millimolar range.
In silico simulation of future hybrid performance to evaluate heterotic pool formation in a self-pollinating crop
Authors: Cowling Wallace A. , Gaynor R. Chris , Antolín Roberto , Gorjanc Gregor , Edwards Stefan M. , Powell Owen , Hickey John M. 
Published: March 2020

AbstractHybrid vigour has the potential to substantially increase the yield of self-pollinating crops such as wheat and rice, but future hybrid performance may depend on the initial strategy to form heterotic pools. We used in silico stochastic simulation of future hybrid performance in a self-pollinating crop to evaluate three strategies of forming heterotic pools in the founder population. The model included either 500, 2000 or 8000 quantitative trait nucleotides (QTN) across 10 chromosomes that contributed to a quantitative trait with population mean 100 and variance 10. The average degree of dominance at each QTN was either 0.2, 0.4 or 0.8 with variance 0.2. Three strategies for splitting the founder population into two heterotic pools were compared: (i) random split; (ii) split based on genetic distance according to principal component analysis of SNP genotypes; and (iii) optimized split based on F1 hybrid performance in a diallel cross among the founders. Future hybrid performance was stochastically simulated over 30 cycles of reciprocal recurrent selection based on true genetic values for additive and dominance effects. The three strategies of forming heterotic pools produced similar future hybrid performance, and superior future hybrids to a control population selected on inbred line performance when the number of quantitative trait nucleotides was ≥2000 and/or the average degree of dominance was ≥0.4.
Shoreline Erosion Assessment Modelling for Sohar Region: Measurements, Analysis, and Scenario
Authors: Abushandi E. , Abualkishik A. 
Published: March 2020

AbstractThe extended coastlines of Oman have been forced to change in the last few decades because of urbanization development or by natural disasters. Recently, Oman has suffered from a couple of tornados and cyclones, e.g. Cyclone Gonu on June 1, 2007, making the changes even much more dynamic. In order to protect the coastal regions infrastructure, an accurate estimation of shoreline erosion is required. This research paper presents an assessment of shoreline erosion magnitudes using field measurements coupled with Multiple Linear Regressions Models (MLR) to predict future changes. Inverse Distance Weighing and Kriging interpolation methods have been applied in order to visualize shoreline variations from gathered data prospective. The field measurements for the shoreline were taken at 19 different points, the space between the points in a range of 500–700 m approximately. The first field measurements were taken on 19th 20th 21st of June, 2016 while the second field measurements were taken on 14th 15th 16th of November 2016. Pearson correlation shows a strong relationship between the first and the second field trips with an average of 0.83. This significant relationship ensures the applicability of MLRs to project future changes on the shorelines. The results of the MLRs showed severe negative volumetric shoreline erosion with an average of 5.2 m/year with some exceptions at the catchment outlets.
Statistical Learning and Social Competency: The Mediating Role of Language
Authors: Parks Kaitlyn M. A. , Griffith Laura A. , Armstrong Nicolette B. , Stevenson Ryan A. 
Published: March 2020

AbstractThe current study sought to examine the contribution of auditory and visual statistical learning on language and social competency abilities as well as whether decreased statistical learning abilities are related to increased autistic traits. To answer these questions, participants’ (N = 95) auditory and visual statistical learning abilities, language, social competency, and level of autistic traits were assessed. Although the relationships observed were relatively small in magnitude, our results demonstrated that visual statistical learning related to language and social competency abilities and that auditory learning was more related to autism symptomatology than visual statistical learning. Furthermore, the relationship between visual statistical learning and social competency was mediated by language comprehension abilities, suggesting that impairments in statistical learning may cascade into impairments in language and social abilities.
Disentangling sensorimotor and cognitive cardioafferent effects: A cardiac-cycle-time study on spatial stimulus-response compatibility
Authors: Larra Mauro F. , Finke Johannes B. , Wascher Edmund , Schächinger Hartmut 
Published: March 2020

AbstractCardiac-cycle-time effects are attributed to variations in baroreceptor (BR) activity and have been shown to impinge on subcortical as well as cortical processes. However, cognitive and sensorimotor processes mediating voluntary responses seem to be differentially affected. We sought to disentangle cardiac-cycle-time effects on subcortical and cortical levels as well as sensorimotor and cognitive processes within a spatial stimulus-response-compatibility paradigm employing startling stimuli of different modalities. Air-puffs and white noise-bursts were presented unilaterally during either cardiac systole or diastole while bilateral startle EMG responses were recorded. Modality, laterality and cardiac-cycle-time were randomly varied within-subjects. Cognitive and sensorimotor stimulus-response-compatibility was orthogonally varied between-subjects: Participants (N = 80) responded to the stimuli via left/right button-push made with either the contra- or ipsilateral hand (sensorimotor compatibility) on either the ipsi- or contralateral button (cognitive compatibility). We found that sensorimotor compatible reactions were speeded during systole whereas sensorimotor incompatible ones were prolonged. This effect was independent of cognitive compatibility and restricted to auditory stimuli. Startle was inhibited during systole irrespective of modality or compatibility. Our results demonstrate how differential cardiac-cycle-time effects influence performance in conflict tasks and further suggest that stimulus-response-compatibility paradigms offer a viable method to uncover the complex interactions underlying behavioral BR effects.
Virus Like Particles (VLP) as multivalent vaccine candidate against Chikungunya, Japanese Encephalitis, Yellow Fever and Zika Virus
Authors: Garg Himanshu , Mehmetoglu-Gurbuz Tugba , Joshi Anjali 
Published: March 2020

AbstractMosquito borne viral diseases are an emerging threat as evident from the recent outbreak of Zika virus (ZIKV) as well as repeated outbreaks of Chikungunya (CHIKV), Yellow fever (YFV) and Japanese encephalitis (JEV) virus in different geographical regions. These four arboviruses are endemic in overlapping regions due to the co-prevalence of the transmitting mosquito vector species Aedes and Culex. Thus, a multivalent vaccine that targets all four viruses would be of benefit to regions of the world where these diseases are endemic. We developed a potential Virus Like Particle (VLP) based multivalent vaccine candidate to target these diseases by using stable cell lines that continuously secrete VLPs in the culture supernatants. Moreover, inclusion of Capsid in the VLPs provides an additional viral protein leading to an enhanced immune response as evident from our previous studies with ZIKV. Immunization of Balb/c mice with different combinations of Capsid protein containing VLPs either as monovalent, bivalent or tetravalent formulation resulted in generation of high levels of neutralizing antibodies. Interestingly, the potential tetravalent VLP vaccine candidate provided strong neutralizing antibody titers against all four viruses. The 293 T stable cell lines secreting VLPs were adapted to grow in suspension cultures to facilitate vaccine scale up. Our stable cell lines secreting individual VLPs provide a flexible yet scalable platform conveniently adaptable to different geographical regions as per the need. Further studies in appropriate animal models will be needed to define the efficacy of the multivalent vaccine candidate to protect against lethal virus challenge.
A novel histidine–tryptophan–ketoglutarate formulation ameliorates intestinal injury in a cold storage and ex vivo warm oxygenated reperfusion model in rats
Authors: Chen Zhiquan , Kebschull Linus , Föll Daniel Arno , Rauen Ursula , Hansen Uwe , Heitplatz Barbara , Hessler Michael , Senninger Norbert , Vogel Thomas , Mohr Annika , Becker Felix 
Published: March 2020

Abstract
Aim: The present study aims to evaluate protective effects of a novel histidine–tryptophan–ketoglutarate solution (HTK-N) and to investigate positive impacts of an additional luminal preservation route in cold storage-induced injury on rat small bowels.
Methods: Male Lewis rats were utilized as donors of small bowel grafts. Vascular or vascular plus luminal preservation were conducted with HTK or HTK-N and grafts were stored at 4°C for 8 h followed by ex vivo warm oxygenated reperfusion with Krebs–Henseleit buffer for 30 min. Afterwards, intestinal tissue and portal vein effluent samples were collected for evaluation of morphological alterations, mucosal permeability and graft vitality.
Results: The novel HTK-N decreased ultrastructural alterations but otherwise presented limited effect on protecting small bowel from ischemia–reperfusion injury in vascular route. However, the additional luminal preservation led to positive impacts on the integrity of intestinal mucosa and vitality of goblet cells. In addition, vascular plus luminal preservation route with HTK significantly protected the intestinal tissue from edema.
Conclusion: HTK-N protected the intestinal mucosal structure and graft vitality as a luminal preservation solution. Additional luminal preservation route in cold storage was shown to be promising.
Association between serum adiponectin concentrations and chronic obstructive pulmonary disease: a meta-analysis
Authors: Lin Yi-Hua , Jiang Tian-Xiang , Hu Su-Xian , Shi Yong-Hong 
Published: March 2020

AbstractBackground: Adiponectin has been implicated to play a role in the pathophysiology of chronic obstructive pulmonary disease (COPD). Many studies have assessed serum adiponectin concentrations in COPD patients. However, results from different reports were not consistent. To assess the association of serum adiponectin concentrations and COPD, a meta-analysis was performed.Methods: PubMed, Embase, Web of Science and Cochrane Library were searched for eligible studies. Data were extracted, and then standard mean differences (SMDs) and 95% confidence intervals (CI) were calculated.Results: Thirteen studies involving a total of 1131 cases and 689 controls were included in this meta-analysis. Combined data indicated that the serum adiponectin levels were higher in COPD patients than those in controls (SMD: 1.09, 95% CI [0.73–1.45], P &lt; 0.001). In the subgroup analyses by disease period, there were similar results in stable COPD patients (SMD: 0.77, 95% CI [0.47–1.07], p &lt;0.001; I2 = 83.9%, P &lt; 0.001), AECOPD patients (SMD: 2.51, 95% CI [0.71–4.30], P = 0.006; I2 = 95.2%, P &lt; 0.001) and mixed COPD patients (SMD: 1.21, 95% CI [0.67–1.75], P &lt; 0.001). Furthermore, the serum adiponectin levels were higher in AECOPD patients than those in stable COPD patients (SMD: 1.06, 95% CI [0.13–1.99], P = 0.026).Conclusions: This meta-analysis indicates that patients with COPD have higher serum adiponectin concentration than healthy controls.