bluuebunny/crossref_metadata_2025 huggingface dataset:
Eyasi Plateau Paleontological Expedition, Laetoli, Tanzania, fossil specimen database 1998–2005
Authors: Reed Denné , Harrison Terry , Kwekason Amandus
Published: December 2019

The Eyasi Plateau Paleontological Expedition (EPPE) Laetoli specimen database contains 13716 records of plant and animal fossils (ca. 28248 specimens) collected by EPPE field teams working at Laetoli, Tanzania between 1998 and 2005. This dataset is a digital version of the original hard-copy specimen catalog, and it documents the discovery, stratigraphic provenience and taxonomic diversity of Plio-Pleistocene fauna and flora in northern Tanzania between 4.4 Ma and >200 ka. Laetoli is renowned for the discovery of important hominin fossils, including the lectotype for Australopithecus afarensis, one of our early hominin ancestors, the first record of Paranthropus aethiopicus outside Kenya-Ethiopia, and an early record of our own species Homo sapiens. This database is one of the few publicly available palaeoanthropological fossil datasets and serves as an example for expanding open access to primary fossil occurrence data in palaeoanthropology. The taxonomic identifications appearing in this dataset are the original field identifications and are provisional. Any taxonomic analysis employing this dataset should refer to updated taxonomic identifications published by specialists.
TOFF, a database of traits of fish to promote advances in fish aquaculture
Authors: Lecocq Thomas , Benard Alain , Pasquet Alain , Nahon Sarah , Ducret Alex , Dupont-Marin Kevin , Lang Iris , Thomas Marielle
Published: December 2019

Functional traits can be valuable pieces of information for aquaculture research and management. Although fish traits have been the focus of an abundant research, trait datasets for these organisms are difficult to access and often unpractical to achieve meta-analyses without a time-consuming extensive review. Already available large-scale compilations include trait information for many fish species but not as detailed as required for aquaculture purpose. Here, we introduce the TOFF (i.e. Traits OF Fish), a database focusing on fish functional traits that aims at bringing together behavioral, morphological, phenological, and physiological traits always coupled to environmental measurement context into a single open-source access repository. TOFF hosts data from published field and experimental studies. Here, we release data for 228 traits for 174 species extracted from 165 publications and present a collaborative platform. We ultimately aim at providing an inclusive and accessible data resource to facilitate advances in aquaculture development.
Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta
Authors: Nowak Robert M. , Jastrzębski Jan P. , Kuśmirek Wiktor , Sałamatin Rusłan , Rydzanicz Małgorzata , Sobczyk-Kopcioł Agnieszka , Sulima-Celińska Anna , Paukszto Łukasz , Makowczenko Karol G. , Płoski Rafał , Tkach Vasyl V. , Basałaj Katarzyna , Młocicki Daniel
Published: December 2019

Despite the use of Hymenolepis diminuta as a model organism in experimental parasitology, a full genome description has not yet been published. Here we present a hybrid de novo genome assembly based on complementary sequencing technologies and methods. The combination of Illumina paired-end, Illumina mate-pair and Oxford Nanopore Technology reads greatly improved the assembly of the H. diminuta genome. Our results indicate that the hybrid sequencing approach is the method of choice for obtaining high-quality data. The final genome assembly is 177 Mbp with contig N50 size of 75 kbp and a scaffold N50 size of 2.3 Mbp. We obtained one of the most complete cestode genome assemblies and annotated 15,169 potential protein-coding genes. The obtained data may help explain cestode gene function and better clarify the evolution of its gene families, and thus the adaptive features evolved during millennia of co-evolution with their hosts.
Transcriptome and chromatin accessibility in porcine intestinal epithelial cells upon Zearalenone exposure
Authors: Wang Haifei , Jin Jian , Wu Jiayun , Qu Huan , Wu Shenglong , Bao Wenbin
Published: December 2019

Zearalenone (ZEA) is one of the main mycotoxins widely spread in contaminated cereal crops, which poses a great threat to food safety as well as human and animal health. Biological control strategies are emerging as important solutions to eliminate mycotoxin contaminations. However, molecular mechanisms underlying ZEA cytotoxic effects are only partly understood. Noncoding RNAs and chromatin accessibilities are important regulators of gene expression and implicate in a variety of biological processes. Here, we established a study model of porcine intestinal epithelial cells upon ZEA exposure and presented a RNA-seq dataset for mRNA, microRNA, and lncRNA profiling in 18 experimental samples. In addition, chromatin accessibilities of four samples were also explored by ATAC-seq. This dataset will shed new light on gene expression profiling and transcriptional regulation of animal cells in the response to ZEA exposure, which further contributes to detecting biomarkers and drug targets for predicting and controlling ZEA contamination.
Diversity of Streptomyces spp. from mangrove forest of Sarawak (Malaysia) and screening of their antioxidant and cytotoxic activities
Authors: Law Jodi Woan-Fei , Chan Kok-Gan , He Ya-Wen , Khan Tahir Mehmood , Ab Mutalib Nurul-Syakima , Goh Bey-Hing , Lee Learn-Han
Published: December 2019

Streptomycetes have been the center of attraction within scientific community owing to their capability to produce various bioactive compounds, for instance, with different antimicrobial, anticancer, and antioxidant properties. The search for novel Streptomyces spp. from underexplored area such as mangrove environment has been gaining attention since these microorganisms could produce pharmaceutically important metabolites. The aim of this study is to discover the diversity of Streptomyces spp. from mangrove in Sarawak and their bioactive potentials — in relation to antioxidant and cytotoxic activities. A total of 88 Streptomyces isolates were successfully recovered from the mangrove soil in Kuching, state of Sarawak, Malaysia. Phylogenetic analysis of all the isolates and their closely related type strains using 16S rRNA gene sequences resulted in 7 major clades in the phylogenetic tree reconstructed based on neighbour-joining algorithm. Of the 88 isolates, 18 isolates could be considered as potentially novel species according to the 16S rRNA gene sequence and phylogenetic analyses. Preliminary bioactivity screening conducted on the potential novel Streptomyces isolates revealed significant antioxidant activity and notable cytotoxic effect against tested colon cancer cell lines (HCT-116, HT-29, Caco-2, and SW480), with greater cytotoxicity towards SW480 and HT-29 cells. This study highlighted that the Sarawak mangrove environment is a rich reservoir containing streptomycetes that could produce novel secondary metabolites with antioxidant and cytotoxic activities.
Antioxidant constituents of three selected red and green color Amaranthus leafy vegetable
Authors: Sarker Umakanta , Oba Shinya
Published: December 2019

Red color (A. tricolor) genotypes are an excellent source of pigments, such as betalain (1122.47 ng g−1 FW), β-xanthin (585.22 ng g−1 FW), β-cyanin (624.75 ng g−1 FW), carotenoids (55.55 mg 100 g−1 FW), and antioxidant phytochemicals, such as vitamin C (122.43 mg 100 g−1 FW), TFC (312.64 RE µg g−1 DW), TPC (220.04 GAE µg g−1 DW), TAC (DPPH and ABTS+) (43.81 and 66.59 TEAC µg g−1 DW) compared to green color (A. lividus) genotype. Remarkable phenolic acids, such as salicylic acid, vanillic acid, protocatechuic acid, gallic acid, gentisic acid, β-resorcylic acid, p-hydroxybenzoic acid, syringic acid, ellagic acid, chlorogenic acid, sinapic acids, trans-cinnamic acid, m-coumaric acid, caffeic acid, p-coumaric acid, ferulic acid, and flavonoids, such as rutin, hyperoside, isoquercetin, myricetin, quercetin, apigenin, kaempferol, and catechin were observed in the red color amaranth genotypes, which was much higher compared to the green color amaranth genotype. We newly identified four flavonoids such as quercetin, catechin, myricetin, and apigenin in amaranth. Among the three selected advanced genotypes studied the red color genotype VA13 and VA3 had abundant antioxidant pigments, phytochemicals, phenolic acids, flavonoids, and antioxidant activity could be selected for extracting colorful juice. Correlation study revealed that all antioxidant constituents of red color amaranth had strong antioxidant activity. The present investigation revealed that two red color genotypes had an excellent source of antioxidants that demand detail pharmacological study.
Surface Grafted MSI-78A Antimicrobial Peptide has High Potential for Gastric Infection Management
Authors: Parreira Paula , Monteiro Claudia , Graça Vanessa , Gomes Joana , Maia Sílvia , Gomes Paula , Gonçalves Inês C. , Martins M. Cristina L.
Published: December 2019

As we approach the end of the antibiotic era, newer therapeutic options, such as antimicrobial peptides (AMPs), are in urgent demand. AMP surface grafting onto biomaterials has been described as a good strategy to overcome problems associated with their in vivo stability. Helicobacter pylori is among the bacteria that pose greatest threat to human health, being MSI-78A one of the few bactericidal AMPs against this bacterium. Here, we report that MSI-78A grafted onto model surfaces (Self-Assembled Monolayers –SAMs), in a concentration of 30.3 ± 1.2 ng/cm2 determined by quartz crystal microbalance with dissipation (QCM-D), was able to kill, by contact, 98% of planktonic H. pylori in only 2 h. This fact was not verified against the control bacteria (Staphylococcus epidermidis), although the minimal inhibitory concentration (MIC) of MSI-78A in solution is much lower for S. epidermidis (2 μg/mL) than for H. pylori (64 μg/mL). Our results also demonstrated that, in opposite to other bacteria, H. pylori cells were attracted to ethylene glycol terminated (antiadhesive) surfaces, which can explain the high bactericidal potential of grafted MSI-78A. This proof of concept study establishes the foundations for development of MSI-78A grafted nanoparticles for gastric infection management within a targeted nanomedicine concept.
Diel and tidal pCO2 × O2 fluctuations provide physiological refuge to early life stages of a coastal forage fish
Authors: Cross Emma L. , Murray Christopher S. , Baumann Hannes
Published: December 2019

Coastal ecosystems experience substantial natural fluctuations inpCO2and dissolved oxygen (DO) conditions on diel, tidal, seasonal and interannual timescales. Rising carbon dioxide emissions and anthropogenic nutrient input are expected to increase thesepCO2and DO cycles in severity and duration of acidification and hypoxia. How coastal marine organisms respond to naturalpCO2 × DO variability and future climate change remains largely unknown. Here, we assess the impact of static and cyclingpCO2 × DO conditions of various magnitudes and frequencies on early life survival and growth of an important coastal forage fish,Menidia menidia. Static low DO conditions severely decreased embryo survival, larval survival, time to 50% hatch, size at hatch and post-larval growth rates. Static elevatedpCO2did not affect most response traits, however, a synergistic negative effect did occur on embryo survival under hypoxic conditions (3.0 mg L−1). CyclingpCO2 × DO, however, reduced these negative effects of static conditions on all response traits with the magnitude of fluctuations influencing the extent of this reduction. This indicates that fluctuations inpCO2and DO may benefit coastal organisms by providing periodic physiological refuge from stressful conditions, which could promote species adaptability to climate change.
The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly
Authors: Marchant D. Blaine , Sessa Emily B. , Wolf Paul G. , Heo Kweon , Barbazuk W. Brad , Soltis Pamela S. , Soltis Douglas E.
Published: December 2019

Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern speciesCeratopteris richardiito address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies ofCeratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history ofCeratopterisbased on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.
The Impact of Comorbidity Burden on The Association between Vascular Access Type and Clinical Outcomes among Elderly Patients Undergoing Hemodialysis
Authors: Jhee Jong Hyun , Hwang Seun Deuk , Song Joon Ho , Lee Seoung Woo
Published: December 2019

The optimal vascular access type for elderly hemodialysis patients is controversial. We evaluated the impact of comorbidity burden on the association between vascular access type and mortality risk among 23,100 hemodialysis patients aged ≥65 years from the Korean Society of Nephrology End-Stage Renal Disease registry data. Subjects were stratified into tertiles according to the simplified Charlson comorbidity index (sCCI), and the survival and hospitalization rates were compared with respect to vascular access type: arteriovenous fistula (AVF), arteriovenous graft (AVG), and central venous catheter (CVC). Among all tertiles of sCCI, CVC use showed highest risk of mortality than AVF use. In the lowest to middle tertile, no difference was observed in survival rates between the use of AVF and AVG. However, in the highest tertile, AVG use showed higher risk of mortality than AVF use. When subjects were classified according to a combination of sCCI tertile and access type (AVF vs. AVG), patients with the highest CCI with AVG showed 1.75-folded increased risk of mortality than those with the lowest sCCI with AVF. Hospitalization rates due to access malfunction were highest in patients with CVC in all sCCI tertiles. In the highest tertile, patients with AVG showed increased rates of hospitalization compared to those with AVF due to access malfunction. However, hospitalization rates due to access infection were highest in patients with AVG in all tertiles. The use of AVF may be of benefit and switching to AVF should be considered in elderly hemodialysis patients with a high burden of comorbidity.
Meglumine acridone acetate, the ionic salt of CMA and N-methylglucamine, induces apoptosis in human PBMCs via the mitochondrial pathway
Authors: Plotnikova Marina A. , Klotchenko Sergey A. , Kiselev Artem A. , Gorshkov Andrey N. , Shurygina Anna-Polina S. , Vasilyev Kirill A. , Uciechowska-Kaczmarzyk Urszula , Samsonov Sergey A. , Kovalenko Alexey L. , Vasin Andrey V.
Published: December 2019

Meglumine acridone acetate (MA) is used in Russia for the treatment of influenza and other acute respiratory viral infections. It was assumed, until recently, that its antiviral effect was associated with its potential ability to induce type I interferon. Advanced studies, however, have shown the failure of 10-carboxymethyl-9-acridanone (CMA) to activate human STING. As such, MA’s antiviral properties are still undergoing clarification. To gain insight into MA’s mechanisms of action, we carried out RNA-sequencing analysis of global transcriptomes in MA-treated (MA+) human peripheral blood mononuclear cells (PBMCs). In response to treatment, approximately 1,223 genes were found to be differentially expressed, among which 464 and 759 were identified as either up- or down-regulated, respectively. To clarify the cellular and molecular processes taking place in MA+ cells, we performed a functional analysis of those genes. We have shown that evident MA subcellular localizations are: at the nuclear envelope; inside the nucleus; and diffusely in perinuclear cytoplasm. Postulating that MA may be a nuclear receptor agonist, we carried out docking simulations with PPARα and RORα ligand binding domains including prediction and molecular dynamics-based analysis of potential MA binding poses. Finally, we confirmed that MA treatment enhanced nuclear apoptosis in human PBMCs. The research presented here, in our view, indicates that: (i) MA activity is mediated by nuclear receptors; (ii) MA is a possible PPARα and/or RORα agonist; (iii) MA has an immunosuppressive effect; and (iv) MA induces apoptosis through the mitochondrial signaling pathway.
Modeling and Optimizing Medium Composition for Shoot Regeneration of Chrysanthemum via Radial Basis Function-Non-dominated Sorting Genetic Algorithm-II (RBF-NSGAII)
Authors: Hesami Mohsen , Naderi Roohangiz , Tohidfar Masoud
Published: December 2019

The aim of the current study was modeling and optimizing medium compositions for shoot proliferation of chrysanthemum, as a case study, through radial basis function- non-dominated sorting genetic algorithm-II (RBF-NSGAII). RBF as one of the artificial neural networks (ANNs) was used for modeling four outputs including proliferation rate (PR), shoot number (SN), shoot length (SL), and basal callus weight (BCW) based on four variables including 6-benzylaminopurine (BAP), indole-3-butyric acid (IBA), phloroglucinol (PG), and sucrose. Afterward, models were linked to the optimization algorithm. Also, sensitivity analysis was applied for evaluating the importance of each input. The R2 correlation values of 0.88, 0.91, 0.97, and 0.76 between observed and predicted data were obtained for PR, SN, SL, and BCW, respectively. According to RBF-NSGAII, optimal PR (98.85%), SN (13.32), SL (4.83 cm), and BCW (0.08 g) can be obtained from a medium containing 2.16 µM BAP, 0.14 µM IBA, 0.29 mM PG, and 87.63 mM sucrose. The results of sensitivity analysis indicated that PR, SN, and SL were more sensitive to BAP, followed by sucrose, PG, and IBA. Finally, the performance of predicted and optimized medium compositions were tested, and results showed that the difference between the validation data and RBF-NSGAII predicted and optimized data were negligible. Generally, RBF-NSGAII can be considered as an efficient computational strategy for modeling and optimizing in vitro organogenesis.
Comparability of accelerometer signal aggregation metrics across placements and dominant wrist cut points for the assessment of physical activity in adults
Authors: Migueles Jairo H. , Cadenas-Sanchez Cristina , Rowlands Alex V. , Henriksson Pontus , Shiroma Eric J. , Acosta Francisco M. , Rodriguez-Ayllon Maria , Esteban-Cornejo Irene , Plaza-Florido Abel , Gil-Cosano Jose J. , Ekelund Ulf , van Hees Vincent T. , Ortega Francisco B.
Published: December 2019

Large epidemiological studies that use accelerometers for physical behavior and sleep assessment differ in the location of the accelerometer attachment and the signal aggregation metric chosen. This study aimed to assess the comparability of acceleration metrics between commonly-used body-attachment locations for 24 hours, waking and sleeping hours, and to test comparability of PA cut points between dominant and non-dominant wrist. Forty-five young adults (23 women, 18–41 years) were included and GT3X + accelerometers (ActiGraph, Pensacola, FL, USA) were placed on their right hip, dominant, and non-dominant wrist for 7 days. We derived Euclidean Norm Minus One g (ENMO), Low-pass filtered ENMO (LFENMO), Mean Amplitude Deviation (MAD) and ActiGraph activity counts over 5-second epochs from the raw accelerations. Metric values were compared using a correlation analysis, and by plotting the differences by time of the day. Cut points for the dominant wrist were derived using Lin’s concordance correlation coefficient optimization in a grid of possible thresholds, using the non-dominant wrist estimates as reference. They were cross-validated in a separate sample (N = 36, 10 women, 22–30 years). Shared variances between pairs of acceleration metrics varied across sites and metric pairs (range in r2: 0.19–0.97, all p < 0.01), suggesting that some sites and metrics are associated, and others are not. We observed higher metric values in dominant vs. non-dominant wrist, thus, we developed cut points for dominant wrist based on ENMO to classify sedentary time (<50 mg), light PA (50–110 mg), moderate PA (110–440 mg) and vigorous PA (≥440 mg). Our findings suggest differences between dominant and non-dominant wrist, and we proposed new cut points to attenuate these differences. ENMO and LFENMO were the most similar metrics, and they showed good comparability with MAD. However, counts were not comparable with ENMO, LFENMO and MAD.
Moisture transverse moving mechanism during presteamed oak lumber drying
Authors: Li Chengyuan , Kang Chun-Won , Zhao Xue-Feng
Published: December 2019

Effect of steaming at 100 °C, 80 °C and 60 °C dry-bulb temperature and 0 °C wet-bulb depression for 4 hours prior to drying on the drying rate and drying deformation of 25.4 mm thick oak lumbers during kiln drying was explored in this study. The results showed that presteaming delayed the drying time by at least 19 percent, and increased the crooks and bows of the lumbers. The mechanism that presteaming delayed the drying time is attributed to the smaller and fewer moisture transverse pathways inside the surface layers of presteamed lumbers. These pathways decrease the moving rates of the bound water and the water vapor from the inner part to the surface layers of presteamed lumbers during the middle and last stage of drying because of reduced distance between the microfibrils and increased crystallinity.
Prenatal Glucocorticoid Exposure Results in Changes in Gene Transcription and DNA Methylation in the Female Juvenile Guinea Pig Hippocampus Across Three Generations
Authors: Constantinof Andrea , Boureau Lisa , Moisiadis Vasilis G. , Kostaki Alisa , Szyf Moshe , Matthews Stephen G.
Published: December 2019

Synthetic glucocorticoids (sGC) are administered to women at risk for pre-term delivery, to mature the fetal lung and decrease neonatal morbidity. sGC also profoundly affect the fetal brain. The hippocampus expresses high levels of glucocorticoid (GR) and mineralocorticoid receptor (MR), and its development is affected by elevated fetal glucocorticoid levels. Antenatal sGC results in neuroendocrine and behavioral changes that persist in three generations of female guinea pig offspring of the paternal lineage. We hypothesized that antenatal sGC results in transgenerational changes in gene expression that correlate with changes in DNA methylation. We used RNASeq and capture probe bisulfite sequencing to investigate the transcriptomic and epigenomic effects of antenatal sGC exposure in the hippocampus of three generations of juvenile female offspring from the paternal lineage. Antenatal sGC exposure (F0 pregnancy) resulted in generation-specific changes in hippocampal gene transcription and DNA methylation. Significant changes in individual CpG methylation occurred in RNApol II binding regions of small non-coding RNA (snRNA) genes, which implicates alternative splicing as a mechanism involved in transgenerational transmission of the effects of antenatal sGC. This study provides novel perspectives on the mechanisms involved in transgenerational transmission and highlights the importance of human studies to determine the longer-term effects of antenatal sGC on hippocampal-related function.
Random access to palatable food stimulates similar addiction-like responses as a fixed schedule, but only a fixed schedule elicits anticipatory activation
Authors: Muñoz-Escobar Geovanni , Guerrero-Vargas Natalí N. , Escobar Carolina
Published: December 2019

Restricted intermittent food access to palatable food (PF) induces addiction-like behaviors and plastic changes in corticolimbic brain areas. Intermittent access protocols normally schedule PF to a fixed time, enabling animals to predict the arrival of PF. Because outside the laboratory the presence of PF may occur in a random unpredictable manner, the present study explored whether random access to PF would stimulate similar addiction-like responses as observed under a fixed scheduled. Rats were randomly assigned to a control group without chocolate access, to ad libitum access to chocolate, to fixed intermittent access (CH-F), or to random unpredictable access (CH-R) to chocolate. Only the CH-F group developed behavioral and core temperature anticipation to PF access. Both groups exposed to intermittent access to PF showed binge eating, increased effort behaviors to obtain chocolate, as well as high FosB/ΔFosB in corticolimbic areas. Moreover, FosB/ΔFosB in all areas correlated with the intensity of binge eating and effort behaviors. We conclude that both conditions of intermittent access to PF stimulate addiction-like behaviors and FosB/ΔFosB accumulation in brain reward areas; while only a fixed schedule, which provides a time clue, elicited anticipatory activation, which is strongly associated with craving behaviors and may favor relapse during withdrawal.
A multi-scale approach to study biochemical and biophysical aspects of resveratrol on diesel exhaust particle-human primary lung cell interaction
Authors: Zhang Wei , Li Qifei , Tang Mingjie , Zhang Han , Sun Xiaoping , Zou Sige , Jensen Judy L. , Liou Theodore G. , Zhou Anhong
Published: December 2019

Diesel exhaust particles (DEPs) are major air pollutants that lead to numerous human disorders, especially pulmonary diseases, partly through the induction of oxidative stress. Resveratrol is a polyphenol that ameliorates the production of reactive oxygen species (ROS) and delays aging-related processes. Herein we studied the cytoprotective effect of resveratrol on DEP-exposed human lung cells in a factorial experimental design. This work investigates biophysical features including cellular compositions and biomechanical properties, which were measured at the single-cell level using confocal Raman microspectroscopy (RM) and atomic force microscopy (AFM), respectively. Principal component analysis (PCA), hierarchical cluster analysis (HCA) and partial least square regression (PLS) analysis were applied to analyze Raman spectra with and without resveratrol protection. The health status of individual cells could be effectively predicted using an index derived from characteristic Raman spectral peak (e.g., 1006 cm−1) based on PLS model. AFM measurements indicated that cellular adhesion force was greatly reduced, while Young’s modulus was highly elevated in resveratrol treated DEP-exposed cells. Anti-oxidant resveratrol reduced DEP-induced ROS production and suppressed releases of several cytokines and chemokines. These findings suggest resveratrol may enhance resistance of human lung cells (e.g., SAEC) to air pollutants (e.g. DEPs).
Mapping Knowledge Gaps of Mozambique’s Terrestrial Mammals
Authors: Neves Isabel Queirós , Mathias Maria da Luz , Bastos-Silveira Cristiane
Published: December 2019

A valuable strategy to support conservation planning is to assess knowledge gaps regarding primary species occurrence data to identify and select areas for future biodiversity surveys. Currently, increasing accessibility to these data allows a cost-effective method for boosting knowledge about a country’s biodiversity. For understudied countries where the lack of resources for conservation is more pronounced to resort to primary biodiversity data can be especially beneficial. Here, using a primary species occurrence dataset, we assessed and mapped Mozambique’s knowledge gaps regarding terrestrial mammal species by identifying areas that are geographically distant and environmentally different from well-known sites. By comparing gaps from old and recent primary species occurrence data, we identified: (i) gaps of knowledge over time, (ii) the lesser-known taxa, and (iii) areas with potential for spatiotemporal studies. Our results show that the inventory of Mozambique’s mammal fauna is near-complete in less than 5% of the territory, with broad areas of the country poorly sampled or not sampled at all. The knowledge gap areas are mostly associated with two ecoregions. The provinces lacking documentation coincide with areas over-explored for natural resources, and many such sites may never be documented. It is our understanding that by prioritising the survey of the knowledge-gap areas will likely produce new records for the country and, continuing the study of the well-known regions will guarantee their potential use for spatiotemporal studies. The implemented approach to assess the knowledge gaps from primary species occurrence data proved to be a powerful strategy to generate information that is essential to species conservation and management plan. However, we are aware that the impact of digital and openly available data depends mostly on its completeness and accuracy, and thus we encourage action from the scientific community and government authorities to support and promote data mobilisation.
Cortical neurodynamics changes mediate the efficacy of a personalized neuromodulation against multiple sclerosis fatigue
Authors: Porcaro Camillo , Cottone Carlo , Cancelli Andrea , Rossini Paolo M. , Zito Giancarlo , Tecchio Franca
Published: December 2019

The people with multiple sclerosis (MS) often report that fatigue restricts their life. Nowadays, pharmacological treatments are poorly effective accompanied by relevant side effects. A 5-day transcranial direct current stimulation (tDCS) targeting the somatosensory representation of the whole body (S1) delivered through an electrode personalized based on the brain MRI was efficacious against MS fatigue (FaReMuS treatment). This proof of principle study tested whether possible changes of the functional organization of the primary sensorimotor network induced by FaReMuS partly explained the effected fatigue amelioration. We measured the brain activity at rest through electroencephalography equipped with a Functional Source Separation algorithm and we assessed the neurodynamics state of the primary somatosensory (S1) and motor (M1) cortices via the Fractal Dimension and their functional connectivity via the Mutual Information. The dynamics of the neuronal electric activity, more distorted in S1 than M1 before treatment, as well as the network connectivity, altered maximally between left and right M1 homologs, reverted to normal after FaReMuS. The intervention-related changes explained 48% of variance of fatigue reduction in the regression model. A personalized neuromodulation tuned in on specific anatomo-functional features of the impaired regions can be effective against fatigue.
Acquisition of fluoroquinolone resistance leads to increased biofilm formation and pathogenicity in Campylobacter jejuni
Authors: Whelan Matthew V. X. , Ardill Laura , Koide Kentaro , Nakajima Chie , Suzuki Yasuhiko , Simpson Jeremy C. , Ó Cróinín Tadhg
Published: December 2019

The World Health Organization has listed C. jejuni as one of 12 microorganisms on a global priority list for antibiotic resistance due to a rapid increase in strains resistant to fluoroquinolone antibiotics. This fluoroquinolone resistance is conferred through a single point mutation in the QRDR region within the gyrA gene known to be involved in DNA supercoiling. We have previously revealed that changes in DNA supercoilikng play a major role in the regulation of virulence in C. jejuni with relaxation of DNA supercoiling associated with increased attachment to and invasion of human epithelial cells. The aim of this study was to investigate whether fluoroquinolone resistant strains of C. jejuni displayed altered supercoiling associated phenotypes. A panel of fluoroquinolone resistant mutants were derived and shown to have a greater ability to form viable biofilms under aerobic conditions, invade epithelial cells and promote virulence in the Galleria mellonella model of infection. We thus report for the first time that fluoroquinolone resistance in C. jejuni is associated with an increase in virulence and the ability to form viable biofilms in oxygen rich environments. These altered phenotypes likely play a critical role in the continued increase in fluoroquinolone resistance observed for this important pathogen.
Characterizing temperature-dependent optical properties of (MA0.13FA0.87) PbI3 single crystals using spectroscopic ellipsometry
Authors: Chen Hsiao-Wen , Gulo Desman Perdamaian , Chao Yu-Chiang , Liu Hsiang-Lin
Published: December 2019

In this paper, we present spectroscopic ellipsometry measurements of (MA0.13FA0.87)PbI3 single crystals assessed at photon energies of 0.73–6.42 eV and at temperatures between 4.4 and 400 K. At room temperature, the refractive index was dispersed as a function of frequency, which is typical of a semiconductor. The absorption spectrum exhibited several electronic transitions. We estimated a room temperature direct band gap of 1.66 ± 0.02 eV and exciton binding energy of 40 meV. With decreasing temperature, the refractive index increased. The room-temperature thermo-optic coefficients were −1.7 × 10−4 and −2.5 × 10−4 K−1 at wavelength of 600 and 1200 nm. The exciton peak position and bandgap energy exhibited a redshift, which was attributed to a reverse ordering of the band structures. Additionally, an anomaly in exciton peak position and bandgap occurred at approximately 100–200 K due to the structural phase transition. This phenomenon was associated with the coexistence of MA/FA-disordered and MA/FA-ordered domains. Our results provide a foundation for the technological development of lead halide perovskites-based photonic devices at various temperatures.
Phosphomimetic cardiac myosin-binding protein C partially rescues a cardiomyopathy phenotype in murine engineered heart tissue
Authors: Dutsch Alexander , Wijnker Paul J. M. , Schlossarek Saskia , Friedrich Felix W. , Krämer Elisabeth , Braren Ingke , Hirt Marc N. , Brenière-Letuffe David , Rhoden Alexandra , Mannhardt Ingra , Eschenhagen Thomas , Carrier Lucie , Mearini Giulia
Published: December 2019

Phosphorylation of cardiac myosin-binding protein C (cMyBP-C), encoded by MYBPC3, increases the availability of myosin heads for interaction with actin thus enhancing contraction. cMyBP-C phosphorylation level is lower in septal myectomies of patients with hypertrophic cardiomyopathy (HCM) than in non-failing hearts. Here we compared the effect of phosphomimetic (D282) and wild-type (S282) cMyBP-C gene transfer on the HCM phenotype of engineered heart tissues (EHTs) generated from a mouse model carrying a Mybpc3 mutation (KI). KI EHTs showed lower levels of mutant Mybpc3 mRNA and protein, and altered gene expression compared with wild-type (WT) EHTs. Furthermore, KI EHTs exhibited faster spontaneous contractions and higher maximal force and sensitivity to external [Ca2+] under pacing. Adeno-associated virus-mediated gene transfer of D282 and S282 similarly restored Mybpc3 mRNA and protein levels and suppressed mutant Mybpc3 transcripts. Moreover, both exogenous cMyBP-C proteins were properly incorporated in the sarcomere. KI EHTs hypercontractility was similarly prevented by both treatments, but S282 had a stronger effect than D282 to normalize the force-Ca2+-relationship and the expression of dysregulated genes. These findings in an in vitro model indicate that S282 is a better choice than D282 to restore the HCM EHT phenotype. To which extent the results apply to human HCM remains to be seen.
Silicon confers protective effect against ginseng root rot by regulating sugar efflux into apoplast
Authors: Abbai Ragavendran , Kim Yu-Jin , Mohanan Padmanaban , El-Agamy Farh Mohamed , Mathiyalagan Ramya , Yang Dong-Uk , Rangaraj Suriyaprabha , Venkatachalam Rajendran , Kim Yeon-Ju , Yang Deok-Chun
Published: December 2019

Root rot caused by Ilyonectria mors-panacis is a devastating fungal disease leading to defect in root quality and causes reduced yield during the perennial life cycle of Panax ginseng Meyer. This indicates the imperative need to understand the molecular basis of disease development and also to enhance tolerance against the fungus. With this idea, the protective effect of silicon (supplied as silica nanoparticles) in P. ginseng root rot pathosystem and its molecular mechanism was investigated in the current study. We have tested different concentrations of silicon (Si) to disease-infected ginseng and found that long term analysis (30 dpi) displayed a striking 50% reduction in disease severity index upon the treatment of Si. Expectedly, Si had no direct degradative effect against the pathogen. Instead, in infected roots it resulted in reduced expression of PgSWEET leading to regulated sugar efflux into apoplast and enhanced tolerance against I. mors-panacis. In addition, under diseased condition, both protopanaxadiol (PPD) and protopanaxatriol (PPT) type ginsenoside profile in roots were higher in Si treated plants. This is the first report indicating the protective role of Si in ginseng-root rot pathosystem, thereby uncovering novel features of ginseng mineral physiology and at the same time, enabling its usage to overcome root rot.
Bioprospecting desert plant Bacillus endophytic strains for their potential to enhance plant stress tolerance
Authors: Bokhari Ameerah , Essack Magbubah , Lafi Feras F. , Andres-Barrao Cristina , Jalal Rewaa , Alamoudi Soha , Razali Rozaimi , Alzubaidy Hanin , Shah Kausar H. , Siddique Shahid , Bajic Vladimir B. , Hirt Heribert , Saad Maged M.
Published: December 2019

Plant growth-promoting bacteria (PGPB) are known to increase plant tolerance to several abiotic stresses, specifically those from dry and salty environments. In this study, we examined the endophyte bacterial community of five plant species growing in the Thar desert of Pakistan. Among a total of 368 culturable isolates, 58 Bacillus strains were identified from which the 16 most divergent strains were characterized for salt and heat stress resilience as well as antimicrobial and plant growth-promoting (PGP) activities. When the 16 Bacillus strains were tested on the non-host plant Arabidopsis thaliana, B. cereus PK6-15, B. subtilis PK5-26 and B. circulans PK3-109 significantly enhanced plant growth under salt stress conditions, doubling fresh weight levels when compared to uninoculated plants. B. circulans PK3-15 and PK3-109 did not promote plant growth under normal conditions, but increased plant fresh weight by more than 50% when compared to uninoculated plants under salt stress conditions, suggesting that these salt tolerant Bacillus strains exhibit PGP traits only in the presence of salt. Our data indicate that the collection of 58 plant endophytic Bacillus strains represents an important genomic resource to decipher plant growth promotion at the molecular level.
Neurite regrowth stimulation by a red-light spot focused on the neuronal cell soma following blue light-induced retraction
Authors: Kao Yu-Chiu , Liao Yu-Cing , Cheng Pei-Lin , Lee Chau-Hwang
Published: December 2019

The interaction of light with biological tissues has been considered for various therapeutic applications. Light-induced neurite growth has the potential to be a clinically useful technique for neuron repair. However, most previous studies used either a large illumination area to accelerate overall neurite growth or employed a light spot to guide a growing neurite. It is not clear if optical stimulation can induce the regrowth of a retracted neurite. In the present work, we used blue light (wavelength: 473 nm) to cause neurite retraction, and we proved that using a red-light (wavelength: 650 nm) spot to illuminate the soma near the junction of the retracted neurite could induce neurite regrowth. As a comparison, we found that green light (wavelength 550 nm) had a 62% probability of inducing neurite regrowth, while red light had a 75% probability of inducing neurite regrowth at the same power level. Furthermore, the neurite regrowth length induced by red light was increased by the pre-treatment with inhibitors of myosin functions. We also observed actin propagation from the soma to the tip of the re-growing neurite following red-light stimulation of the soma. The red light-induced extension and regrowth were abrogated in the calcium-free medium. These results suggest that illumination with a red-light spot on the soma may trigger the regrowth of a neurite after the retraction caused by blue-light illumination.
Application of fluorescence spectroscopy using classical right angle technique in white wines classification
Authors: Suciu Ramona-Crina , Zarbo Liviu , Guyon Francois , Magdas Dana Alina
Published: December 2019

The potential of excitation - emission matrices (EEM) measurements using classical right angle technique, in conjunction with chemometrics, was prospected for white wine classification with respect to their cultivar and geographical origin. For this purpose, wines belonging to four cultivars (Chardonnay, Pinot Gris, Riesling and Sauvignon) from two different countries (Romania and France) were investigated. The excitation – emission matrices were statistically processed using parallel factor analysis (PARAFAC). According to Soft Independent Modeling Classification Analogy (SIMCA) model, for cultivar differentiation, only 3 out of 107 wine samples (1 Pinot Gris (Romania); 1 Riesling (Romania) and 1 Sauvignon (France)) were misclassified while for geographical origin assessment, only 2 wines (1 Romania and 1 France) were misclassified. This study  demonstrates the potential of excitation – emission fluorescence matrices spectroscopy using the classical right angle technique in wine authentication, without sample dilution.
Microplastics ingestion and heterotrophy in thermally stressed corals
Authors: Axworthy Jeremy B. , Padilla-Gamiño Jacqueline L.
Published: December 2019

Rising sea temperatures and increasing pollution threaten the fate of coral reefs and millions of people who depend on them. Some reef-building corals respond to thermal stress and subsequent bleaching with increases in heterotrophy, which may increase the risk of ingesting microplastics. Whether this heterotrophic plasticity affects microplastics ingestion or whether ingesting microplastics affects heterotrophic feeding in corals is unknown. To determine this, two coral species, Montipora capitata and Pocillopora damicornis, were exposed to ambient (~27 °C) and increased (~30 °C) temperature and then fed microplastics, Artemia nauplii, or both. Following thermal stress, both species significantly reduced feeding on Artemia but no significant decrease in microplastics ingestion was observed. Interestingly, P. damicornis only ingested microplastics when Artemia were also present, providing evidence that microplastics are not selectively ingested by this species and are only incidentally ingested when food is available. As the first study to examine microplastics ingestion following thermal stress in corals, our results highlight the variability in the risk of microplastics ingestion among species and the importance of considering multiple drivers to project how corals will be affected by global change.
Preferential flow pathways in a deforming granular material: self-organization into functional groups for optimized global transport
Authors: van der Linden Joost H. , Tordesillas Antoinette , Narsilio Guillermo A.
Published: December 2019

Existing definitions of where and why preferential flow in porous media occurs, or will occur, assume a priori knowledge of the fluid flow and do not fully account for the connectivity of available flow paths in the system. Here we propose a method for identifying preferential pathways through a flow network, given its topology and finite link capacities. Using data from a deforming granular medium, we show that the preferential pathways form a set of percolating pathways that is optimized for global transport of interstitial pore fluid in alignment with the applied pressure gradient. Two functional subgroups emerge. The primary subgroup comprises the main arterial paths that transmit the greatest flow through shortest possible routes. The secondary subgroup comprises inter- and intra-connecting bridges that connect the primary paths, provide alternative flow routes, and distribute flow through the system to maximize throughput. We examine the multiscale relationship between functionality and subgroup structure as the sample dilates in the lead up to the failure regime where the global volume then remains constant. Preferential flow pathways chain together large, well-connected pores, reminiscent of force chain structures that transmit the majority of the load in the solid grain phase.
Marked TGF-β-regulated miRNA expression changes in both COPD and control lung fibroblasts
Authors: Ong J. , Faiz A. , Timens W. , van den Berge M. , Terpstra M. M. , Kok K. , van den Berg A. , Kluiver J. , Brandsma C. A.
Published: December 2019

COPD is associated with disturbed tissue repair, possibly due to TGF-β-regulated miRNA changes in fibroblasts. Our aim was to identify TGF-β-regulated miRNAs and their differential regulation and expression in COPD compared to control fibroblasts. Small RNA sequencing was performed on TGF-β-stimulated and unstimulated lung fibroblasts from 15 COPD patients and 15 controls. Linear regression was used to identify TGF-β-regulated and COPD-associated miRNAs. Interaction analysis was performed to compare miRNAs that responded differently to TGF-β in COPD and control. Re-analysis of previously generated Ago2-IP data and Enrichr were used to identify presence and function of potential target genes in the miRNA-targetome of lung fibroblasts. In total, 46 TGF-β-regulated miRNAs were identified in COPD and 86 in control fibroblasts (FDR < 0.05). MiR-27a-5p was the most significantly upregulated miRNA. MiR-148b-3p, miR-589-5p and miR-376b-3p responded differently to TGF-β in COPD compared to control (FDR < 0.25). MiR-660-5p was significantly upregulated in COPD compared to control (FDR < 0.05). Several predicted targets of miR-27a-5p, miR-148b-3p and miR-660-5p were present in the miRNA-targetome, and were mainly involved in the regulation of gene transcription. In conclusion, altered TGF-β-induced miRNA regulation and differential expression of miR-660-5p in COPD fibroblasts, may represent one of the mechanisms underlying aberrant tissue repair and remodelling in COPD.