bluuebunny/crossref_metadata_2025_split huggingface dataset:
Element banding and organic linings within chamber walls of two benthic foraminifera
Authors: Geerken E. , de Nooijer L. J. , Roepert A. , Polerecky L. , King H. E. , Reichart G. J. 
Published: March 2019

AbstractTrace and minor elements incorporated in foraminiferal shells are among the most used proxies for reconstructing past environmental conditions. A prominent issue concerning these proxies is that the inter-specimen variability in element composition is often considerably larger than the variability associated with the environmental conditions for which the proxy is used. Within a shell of an individual specimen the trace and minor elements are distributed in the form of bands of higher and lower concentrations. It has been hypothesized that differences in specimen-specific element banding patterns cause the inter-specimen and inter-species variability observed in average element composition, thereby reducing the reliability of proxies. To test this hypothesis, we compared spatial distributions of Mg, Na, Sr, K, S, P and N within chamber walls of two benthic foraminiferal species (Amphistegina lessonii and Ammonia tepida) with largely different average Mg content. For both species the selected specimens were grown at different temperatures and salinities to additionally assess how these parameters influence the element concentrations within the shell wall. Our results show that Mg, Na, Sr and K are co-located within shells, and occur in bands that coincide with organic linings but extend further into the calcite lamella. Changes in temperature or salinity modulate the element-banding pattern as a whole, with peak and trough heights co-varying rather than independently affected by these two environmental parameters. This means that independent changes in peak or trough height do not explain differences in average El/Ca between specimens. These results are used to evaluate and synthesize models of underlying mechanisms responsible for trace and minor element partitioning during calcification in foraminifera.
DESTINI: A deep-learning approach to contact-driven protein structure prediction
Authors: Gao Mu , Zhou Hongyi , Skolnick Jeffrey 
Published: March 2019

AbstractThe amino acid sequence of a protein encodes the blueprint of its native structure. To predict the corresponding structural fold from the protein’s sequence is one of most challenging problems in computational biology. In this work, we introduce DESTINI (deep structural inference for proteins), a novel computational approach that combines a deep-learning algorithm for protein residue/residue contact prediction with template-based structural modelling. For the first time, the significantly improved predictive ability is demonstrated in the large-scale tertiary structure prediction of over 1,200 single-domain proteins. DESTINI successfully predicts the tertiary structure of four times the number of “hard” targets (those with poor quality templates) that were previously intractable, viz, a “glass-ceiling” for previous template-based approaches, and also improves model quality for “easy” targets (those with good quality templates). The significantly better performance by DESTINI is largely due to the incorporation of better contact prediction into template modelling. To understand why deep-learning accomplishes more accurate contact prediction, systematic clustering reveals that deep-learning predicts coherent, native-like contact patterns compared to co-evolutionary analysis. Taken together, this work presents a promising strategy towards solving the protein structure prediction problem.
The NADPH oxidase 4 is a major source of hydrogen peroxide in human granulosa-lutein and granulosa tumor cells
Authors: Buck Theresa , Hack Carsten Theo , Berg Dieter , Berg Ulrike , Kunz Lars , Mayerhofer Artur 
Published: March 2019

AbstractH2O2 is a reactive oxygen species (ROS), which can diffuse away from its site of generation and may act as a cell-to-cell signaling factor. The mechanisms responsible for the generation of H2O2 in human ovarian follicles and possible signaling role(s) of H2O2 are not well known. We identified a source of H2O2, the enzyme NADPH oxidase (NOX) 4, in isolated differentiated, in-vitro fertilisation-derived human granulosa-lutein cells (GCs), in proliferating human granulosa tumour cells (KGN), as well as in situ in cells of growing ovarian follicles. H2O2 was readily detected in the supernatant of cultured GCs and KGN cells. H2O2 levels were significantly lowered by the NOX4 blocker GKT137831, indicating a pronounced contribution of NOX4 to overall H2O2 generation by these cells. We provide evidence that extracellular H2O2 is taken up by GCs, which is facilitated by aquaporins (peroxiporins). We thus conclude that GC-derived H2O2 might act as autocrine/paracrine factor. Addition of H2O2 increased MAPK-phosphorylation in GCs. Moreover, reducing H2O2 production with GKT137831 slowed proliferation of KGN cells. Our results pinpoint NOX4 and H2O2 as physiological players in the regulation of GC functions.
Minimum viable population size and population growth rate of freshwater fishes and their relationships with life history traits
Authors: Wang Teng , Fujiwara Masami , Gao Xin , Liu Huanzhang 
Published: March 2019

AbstractThe minimum viable population (MVP) size has been compared for a wide range of organisms in conservation biology, but a limited number of studies investigated it for freshwater fishes, which exhibit diverse life history strategies. In this study, the MVP size and population growth rate of 36 fish species in the Yangtze River were estimated and compared with their life-history traits. The results indicated that the MVP size ranged from 42 to 320 individuals, and instantaneous per-capita population growth rate ranged from 0.009 to 0.188 per year. MVP size and population growth rate were significantly associated with three life history traits: the age at maturity, generation time, and fecundity. Long-lived species with delayed maturation, long generation time, and high fecundity had a greater MVP size and a lower population growth rate than short-lived species. Therefore, our results emphasize a need for prioritizing our conservation effort more on long-lived species.
TMEM10 Promotes Oligodendrocyte Differentiation and is Expressed by Oligodendrocytes in Human Remyelinating Multiple Sclerosis Plaques
Authors: de Faria Omar , Dhaunchak Ajit S. , Kamen Yasmine , Roth Alejandro D. , Kuhlmann Tanja , Colman David R. , Kennedy Timothy E. 
Published: March 2019

AbstractOligodendrocyte precursor cells (OPCs) differentiate during postnatal development into myelin-forming oligodendrocytes, in a process distinguished by substantial changes in morphology and the onset of myelin gene expression. A mammalian-specific CNS myelin gene, tmem10, also called Opalin, encodes a type 1 transmembrane protein that is highly upregulated during early stages of OPC differentiation; however, a function for TMEM10 has not yet been identified. Here, consistent with previous studies, we detect TMEM10 protein in mouse brain beginning at ~P10 and show that protein levels continue to increase as oligodendrocytes differentiate and myelinate axons in vivo. We show that constitutive TMEM10 overexpression in the Oli-neu oligodendroglial cell line promotes the expression of the myelin-associated genes MAG, CNP and CGT, whereas TMEM10 knock down in primary OPCs reduces CNP mRNA expression and decreases the percentage of MBP-positive oligodendrocytes that differentiate in vitro. Ectopic TMEM10 expression evokes an increase in process extension and branching, and blocking endogenous TMEM10 expression results in oligodendrocytes with abnormal cell morphology. These findings may have implications for human demyelinating disorders, as oligodendrocytes expressing TMEM10 are detected in human remyelinating multiple sclerosis lesions. Together, our findings provide evidence that TMEM10 promotes oligodendrocyte terminal differentiation and may represent a novel target to promote remyelination in demyelinating disorders.
New insights into the relationship between taste perception and oral microbiota composition
Authors: Cattaneo Camilla , Gargari Giorgio , Koirala Ranjan , Laureati Monica , Riso Patrizia , Guglielmetti Simone , Pagliarini Ella 
Published: March 2019

AbstractFairly poor data are available on the relationship between taste perception, food preferences and oral microbiota. In the present study, we investigated the hypothesis that subjects with higher responsiveness to 6-n-propylthiuracil (PROP) might be characterized by a different taste sensitivity and tongue microbiota composition. Indeed, the bacterial metabolism may modulate/enhance the concentration of tastants near the taste receptors, modifying taste perception through a sensorial adaptation mechanism or by a broad range of microbial metabolic pathways. The detection thresholds of sweet, sour, salty and bitter, the Fungiform Papillae Density (FPD) and the composition of bacteria lining the tongue were determined in Supertasters (high PROP responsiveness, ST) and Non-tasters (low PROP responsiveness, NT). An important inter-individual variability was found for all taste stimuli and FPD between the two groups, with NT subjects showing significant higher threshold values and a lower FPD than with STs. We found five bacterial genera whose relative abundances were significantly higher in STs than NTs. This study opens new avenues of research by highlighting associations between parameters usually studied independently.
Temporal changes in cell division rate and genotoxic stress tolerance in quiescent center cells of Arabidopsis primary root apical meristem
Authors: Timilsina Rupak , Kim Jin Hee , Nam Hong Gil , Woo Hye Ryun 
Published: March 2019

AbstractPlant roots provide structural support and absorb nutrients and water; therefore, their proper development and function are critical for plant survival. Extensive studies on the early stage of ontogenesis of the primary root have revealed that the root apical meristem (RAM) undergoes dynamic structural and organizational changes during early germination. Quiescent center (QC) cells, a group of slowly dividing cells at the center of the stem-cell niche, are vital for proper function and maintenance of the RAM. However, temporal aspects of molecular and cellular changes in QC cells and their regulatory mechanisms have not been well studied. In the present study, we investigated temporal changes in QC cell size, expression of QC cell-specific markers (WOX5 and QC25), and genotoxic tolerance and division rate of QC cells in the Arabidopsis primary root. Our data revealed the decreased size of QC cells and the decreased expression of the QC cell-specific markers with root age. We also found that QC cell division frequency increased with root age. Furthermore, our study provides evidence supporting the link between the transition of QC cells from a mitotically quiescent state to the frequently dividing state and the decrease in tolerance to genotoxic stress.
A novel echocardiographic method closely agrees with cardiac magnetic resonance in the assessment of left ventricular function in infarcted mice
Authors: Russo Ilaria , Micotti Edoardo , Fumagalli Francesca , Magnoli Michela , Ristagno Giuseppe , Latini Roberto , Staszewsky Lidia 
Published: March 2019

AbstractCardiac Magnetic Resonance (CMR) is the gold standard for left ventricular (LV) function assessment in small rodents and, though echocardiography (ECHO) has been proposed as an alternative method, LV volumes may be underestimated when marked eccentric remodeling is present. In the present study we described a novel echocardiographic method and we tested the agreement with CMR for LV volumes and ejection fraction calculation in mice with experimental myocardial infarction. Sham-operated and infarcted mice, subjected to Coronary Artery Ligation, underwent ECHO and CMR. Volumes and ejection fraction were calculated by ECHO using a standard Simpson’s modified method (ECHO pLAX) or a method from sequential parasternal short axis (ECHO pSAX) acquired mechanically by translating the probe every 1 mm along the left ventricle. The mean differences ±1.96 standard deviation near to zero suggested close agreement between ECHO pSAX and CMR; contrarily ECHO pLAX agreement with CMR was lower. In addition, ECHO was three times shorter and cheaper (Relative cost difference: pLAX: −66% and pSAX −57%) than CMR. In conclusion, ECHO pSAX is a new, fast, cheap and accurate method for LV function assessment in mice.
Thalamic Reticular Nucleus Parvalbumin Neurons Regulate Sleep Spindles and Electrophysiological Aspects of Schizophrenia in Mice
Authors: Thankachan Stephen , Katsuki Fumi , McKenna James T. , Yang Chun , Shukla Charu , Deisseroth Karl , Uygun David S. , Strecker Robert E. , Brown Ritchie E. , McNally James M. , Basheer Radhika 
Published: March 2019

AbstractThe thalamic reticular nucleus (TRN) is implicated in schizophrenia pathology. However, it remains unclear whether alterations of TRN activity can account for abnormal electroencephalographic activity observed in patients, namely reduced spindles (10–15 Hz) during sleep and increased delta (0.5–4 Hz) and gamma-band activity (30–80 Hz) during wakefulness. Here, we utilized optogenetic and reverse-microdialysis approaches to modulate activity of the major subpopulation of TRN GABAergic neurons, which express the calcium-binding protein parvalbumin (PV), and are implicated in schizophrenia dysfunction. An automated algorithm with enhanced efficiency and reproducibility compared to manual detection was used for sleep spindle assessment. A novel, low power, waxing-and-waning optogenetic stimulation paradigm preferentially induced spindles that were indistinguishable from spontaneously occurring sleep spindles without altering the behavioral state, when compared to a single pulse laser stimulation used by us and others. Direct optogenetic inhibition of TRN-PV neurons was ineffective in blocking spindles but increased both wakefulness and cortical delta/gamma activity, as well as impaired the 40 Hz auditory steady-state response. For the first time we demonstrate that spindle density is markedly reduced by (i) optogenetic stimulation of a major GABA/PV inhibitory input to TRN arising from basal forebrain parvalbumin neurons (BF-PV) and; (ii) localized pharmacological inhibition of low-threshold calcium channels, implicated as a genetic risk factor for schizophrenia. Together with clinical findings, our results support impaired TRN-PV neuron activity as a potential cause of schizophrenia-linked abnormalities in cortical delta, gamma, and spindle activity. Modulation of the BF-PV input to TRN may improve these neural abnormalities.
A multimodal approach to cardiovascular risk stratification in patients with type 2 diabetes incorporating retinal, genomic and clinical features
Authors: Fetit Ahmed E. , Doney Alexander S. , Hogg Stephen , Wang Ruixuan , MacGillivray Tom , Wardlaw Joanna M. , Doubal Fergus N. , McKay Gareth J. , McKenna Stephen , Trucco Emanuele 
Published: March 2019

AbstractCardiovascular diseases are a public health concern; they remain the leading cause of morbidity and mortality in patients with type 2 diabetes. Phenotypic information available from retinal fundus images and clinical measurements, in addition to genomic data, can identify relevant biomarkers of cardiovascular health. In this study, we assessed whether such biomarkers stratified risks of major adverse cardiac events (MACE). A retrospective analysis was carried out on an extract from the Tayside GoDARTS bioresource of participants with type 2 diabetes (n = 3,891). A total of 519 features were incorporated, summarising morphometric properties of the retinal vasculature, various single nucleotide polymorphisms (SNPs), as well as routine clinical measurements. After imputing missing features, a predictive model was developed on a randomly sampled set (n = 2,918) using L1-regularised logistic regression (lasso). The model was evaluated on an independent set (n = 973) and its performance associated with overall hazard rate after censoring (log-rankp < 0.0001), suggesting that multimodal features were able to capture important knowledge for MACE risk assessment. We further showed through a bootstrap analysis that all three sources of information (retinal, genetic, routine clinical) offer robust signal. Particularly robust features included: tortuousity, width gradient, and branching point retinal groupings; SNPs known to be associated with blood pressure and cardiovascular phenotypic traits; age at imaging; clinical measurements such as blood pressure and high density lipoprotein. This novel approach could be used for fast and sensitive determination of future risks associated with MACE.
Dual role of the Anopheles coluzzii Venus Kinase Receptor in both larval growth and immunity
Authors: Gouignard Nadège , Cherrier Floriane , Brito-Fravallo Emma , Pain Adrien , Zmarlak Natalia Marta , Cailliau Katia , Genève Corinne , Vernick Kenneth D. , Dissous Colette , Mitri Christian 
Published: March 2019

AbstractVector-borne diseases and especially malaria are responsible for more than half million deaths annually. The increase of insecticide resistance in wild populations of Anopheles malaria vectors emphasises the need for novel vector control strategies as well as for identifying novel vector targets. Venus kinase receptors (VKRs) constitute a Receptor Tyrosine Kinase (RTK) family only found in invertebrates. In this study we functionally characterized Anopheles VKR in the Gambiae complex member, Anophelescoluzzii. Results showed that Anopheles VKR can be activated by L-amino acids, with L-arginine as the most potent agonist. VKR was not required for the fecundity of A. coluzzii, in contrast to reports from other insects, but VKR function is required in both Anopheles males and females for development of larval progeny. Anopheles VKR function is also required for protection against infection by Plasmodium parasites, thus identifying a novel linkage between reproduction and immunity in Anopheles. The insect specificity of VKRs as well as the essential function for reproduction and immunity suggest that Anopheles VKR could be a potentially druggable target for novel vector control strategies.
Performance of 24-hour urinary creatinine excretion-estimating equations in relation to measured 24-hour urinary creatinine excretion in hospitalized hypertensive patients
Authors: Jędrusik Piotr , Symonides Bartosz , Gaciong Zbigniew 
Published: March 2019

AbstractEstimated 24-hour urinary creatinine excretion (24 hrUCr) may be useful for converting spot urine analyte/creatinine ratio into estimated 24-hour urinary excretion of the evaluated analyte, and for verifying completeness of 24-hour urinary collections. We compared various published 24 hrUCr-estimating equations against measured 24 hrUCr in hospitalized hypertensive patients. 24 hrUCr was measured in 293 patients and estimated using eight formulas (CKD-EPI, Cockcroft-Gault, Walser, Goldwasser, Rule, Gerber-Mann, Kawasaki, Tanaka). We used the Pearson correlation coefficient, the Bland-Altman method, and the percentage of estimated 24 hrUCr within 15%, 30% (P30), and 50% of measured 24hUCr to compare estimated and measured 24 hrUCr. Differences between the mean bias by eight formulas were evaluated using the Friedman rank sum test. Overall, the best formulas were CKD-EPI (mean bias 0.002 g/d, P30 86%) and Rule (mean bias 0.022 g/d, P30 89%), although both tended to underestimate 24 hrUCr with higher excretion values. The Gerber-Mann formula and the Asian formulas (Tanaka, Kawasaki) were less precise in our study population but superior in an analysis restricted to subjects with highest measured 24 hrUCr per body weight. We found significant differences between 24 hrUCr-estimating equations in hypertensive patients. In addition, formula performance was critically affected by inclusion criteria based on measured 24 hrUCr per body weight.
Dissolution behaviour of radiocaesium-bearing microparticles released from the Fukushima nuclear plant
Authors: Okumura Taiga , Yamaguchi Noriko , Dohi Terumi , Iijima Kazuki , Kogure Toshihiro 
Published: March 2019

AbstractRadiocaesium-bearing microparticles (CsMPs) composed of silicate glass were released by the Fukushima Daiichi Nuclear Power Plant accident in March 2011. Since CsMPs contain a high concentration of radiocaesium, their dynamics and fate in the environment are urgent issues to be investigated. Here, we show that CsMPs are dissolved by weathering in the environment and that their radioactivity is more rapidly decreased by dissolution than the physical decay of radiocaesium. We conducted dissolution experiments with CsMPs in pure water that absorbed CO2 from the atmosphere and in artificial seawater at several temperatures. The dissolution progress was monitored by the decrease in the 137Cs radioactivity in CsMPs, and the dissolution rate was estimated. The activation energy for the dissolution of CsMPs was estimated to be 65 and 88 kJ/mol and the dissolution rate at 13 °C (approximate annual mean temperature in Fukushima City) was 0.014 and 0.140 μm/y for pure water and seawater, respectively, assuming that radiocaesium is uniformly distributed in spherical CsMPs. The shapes of the CsMPs dissolved in pure water were considerably altered, suggesting that the dissolution proceeded without maintaining the geometry. Tin oxide and iron oxide nanoparticulates formed on the surfaces. Such features were similar to those observed in CsMPs recently collected in Fukushima Prefecture, indicating that weathering dissolution of CsMPs is also occurring in the environment. For the CsMPs dissolved in seawater, a crust of secondary Mg- and Fe-rich minerals was formed, and the glass matrix inside the crust decreased, creating space between the crust and the glass matrix.
Spatio-temporal variations and factors of a provincial PM2.5 pollution in eastern China during 2013–2017 by geostatistics
Authors: Sun Xue , Luo Xiao-San , Xu Jiangbing , Zhao Zhen , Chen Yan , Wu Lichun , Chen Qi , Zhang Dan 
Published: March 2019

AbstractFine particulate matter (PM2.5) is a typical air pollutant and has adverse health effects across the world, especially in the rapidly developing China due to significant air pollution. The PM2.5 pollution varies with time and space, and is dominated by the locations owing to the differences in geographical conditions including topography and meteorology, the land use and the characteristics of urbanization and industrialization, all of which control the pollution formation by influencing the various sources and transport of PM2.5. To characterize these parameters and mechanisms, the 5-year PM2.5 pollution patterns of Jiangsu province in eastern China with high-resolution was investigated. The Kriging interpolation method of geostatistical analysis (GIS) and the HYbrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model were conducted to study the spatial and temporal distribution of air pollution at 110 sites from national air quality monitoring network covering 13 cities. The PM2.5 pollution of the studied region was obvious, although the annual average concentration decreased from previous 72 to recent 50 μg m−3. Evident temporal variations showed high PM2.5 level in winter and low in summer. Spatially, PM2.5 level was higher in northern (inland, heavy industry) than that in eastern (costal, plain) regions. Industrial sources contributed highest to the air pollution. Backward trajectory clustering and potential source contribution factor (PSCF) analysis indicated that the typical monsoon climate played an important role in the aerosol transport. In summer, the air mass in Jiangsu was mainly affected by the updraft from near region, which accounted for about 60% of the total number of trajectories, while in winter, the long-distance transport from the northwest had a significant impact on air pollution.