bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of palmitoylation on the dimer formation of the human dopamine transporter
Authors: Zeppelin Talia , Pedersen Kasper B. , Berglund Nils A. , Periole Xavier , Schiøtt Birgit 
Published: February 2021

AbstractThe human dopamine transporter (hDAT) is one in three members of the monoamine transporter family (MAT). hDAT is essential for regulating the dopamine concentration in the synaptic cleft through dopamine reuptake into the presynaptic neuron; thereby controlling hDAT dopamine signaling. Dysfunction of the transporter is linked to several psychiatric disorders. hDAT and the other MATs have been shown to form oligomers in the plasma membrane, but only limited data exists on which dimeric and higher order oligomeric states are accessible and energetically favorable. In this work, we present several probable dimer conformations using computational coarse-grained self-assembly simulations and assess the relative stability of the different dimer conformations using umbrella sampling replica exchange molecular dynamics. Overall, the dimer conformations primarily involve TM9 and/or TM11 and/or TM12 at the interface. Furthermore, we show that a palmitoyl group (palm) attached to hDAT on TM12 modifies the free energy of separation for interfaces involving TM12, suggesting that S-palmitoylation may change the relative abundance of dimers involving TM12 in a biological context. Finally, a comparison of the identified interfaces of hDAT and palmitoylated hDAT to the human serotonin transporter interfaces and the leucine transporter interface, suggests similar dimer conformations across these protein family.
Competing effects of spreading rate, crystal fractionation and source variability on Fe isotope systematics in mid-ocean ridge lavas
Authors: Richter Marianne , Nebel Oliver , Schwindinger Martin , Nebel-Jacobsen Yona , Dick Henry J. B. 
Published: February 2021

AbstractTwo-thirds of the Earth is covered by mid-ocean ridge basalts, which form along a network of divergent plate margins. Basalts along these margins display a chemical diversity, which is consequent to a complex interplay of partial mantle melting in the upper mantle and magmatic differentiation processes in lower crustal levels. Igneous differentiation (crystal fractionation, partial melting) and source heterogeneity, in general, are key drivers creating variable chemistry in mid-ocean ridge basalts. This variability is reflected in iron isotope systematics (expressed as δ57Fe), showing a total range of 0.2 ‰ from δ57Fe =  + 0.05 to + 0.25 ‰. Respective contributions of source heterogeneity and magma differentiation leading to this diversity, however, remain elusive. This study investigates the iron isotope systematics in basalts from the ultraslow spreading Gakkel Ridge in the Arctic Ocean and compares them to existing data from the fast spreading East Pacific Rise ridge. Results indicate that Gakkel lavas are driven to heavier iron isotope compositions through partial melting processes, whereas effects of igneous differentiation are minor. This is in stark contrast to fast spreading ridges showing reversed effects of near negligible partial melting effects followed by large isotope fractionation along the liquid line of descent. Gakkel lavas further reveal mantle heterogeneity that is superimposed on the igneous differentiation effects, showing that upper mantle Fe isotope heterogeneity can be transmitted into erupting basalts in the absence of homogenisation processes in sub-oceanic magma chambers.
Loss of primary cilia promotes mitochondria-dependent apoptosis in thyroid cancer
Authors: Lee Junguee , Park Ki Cheol , Sul Hae Joung , Hong Hyun Jung , Kim Kun-Ho , Kero Jukka , Shong Minho 
Published: February 2021

AbstractThe primary cilium is well-preserved in human differentiated thyroid cancers such as papillary and follicular carcinoma. Specific thyroid cancers such as Hürthle cell carcinoma, oncocytic variant of papillary thyroid carcinoma (PTC), and PTC with Hashimoto’s thyroiditis show reduced biogenesis of primary cilia; these cancers are often associated the abnormalities in mitochondrial function. Here, we examined the association between primary cilia and the mitochondria-dependent apoptosis pathway. Tg-Cre;Ift88flox/flox mice (in which thyroid follicles lacked primary cilia) showed irregularly dilated follicles and increased apoptosis of thyrocytes. Defective ciliogenesis caused by deleting the IFT88 and KIF3A genes from thyroid cancer cell lines increased VDAC1 oligomerization following VDAC1 overexpression, thereby facilitating upregulation of mitochondria-dependent apoptosis. Furthermore, VDAC1 localized with the basal bodies of primary cilia in thyroid cancer cells. These results demonstrate that loss-of-function of primary cilia results in apoptogenic stimuli, which are responsible for mitochondrial-dependent apoptotic cell death in differentiated thyroid cancers. Therefore, regulating primary ciliogenesis might be a therapeutic approach to targeting differentiated thyroid cancers.
Mining Google and Apple mobility data: temporal anatomy for COVID-19 social distancing
Authors: Cot Corentin , Cacciapaglia Giacomo , Sannino Francesco 
Published: February 2021

AbstractWe employ the Google and Apple mobility data to identify, quantify and classify different degrees of social distancing and characterise their imprint on the first wave of the COVID-19 pandemic in Europe and in the United States. We identify the period of enacted social distancing via Google and Apple data, independently from the political decisions. Our analysis allows us to classify different shades of social distancing measures for the first wave of the pandemic. We observe a strong decrease in the infection rate occurring two to five weeks after the onset of mobility reduction. A universal time scale emerges, after which social distancing shows its impact. We further provide an actual measure of the impact of social distancing for each region, showing that the effect amounts to a reduction by 20–40% in the infection rate in Europe and 30–70% in the US.
Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB
Authors: Sharma Mridula , Kundu Indra , Barai Ram Shankar , Bhaye Sameeksha , Desai Karishma , Pokar Khushal , Idicula-Thomas Susan 
Published: February 2021

AbstractPrecocious puberty (PP) is an important endocrine disorder affecting children globally. Several genes, SNPs and comorbidities are reported to be associated with PP; however, this data is scattered across scientific literature and has not been systematically collated and analysed. In this study, we present PrecocityDB as the first manually curated online database on genes and their ontology terms, SNPs, and pathways associated with PP. A tool for visualizing SNP coordinates and allelic variation on each chromosome, for genes associated with PP is also incorporated in PrecocityDB. Pathway enrichment analysis of PP-associated genes revealed that endocrine and cancer-related pathways are highly enriched. Disease enrichment analysis indicated that individuals with PP seem to be highly likely to suffer from reproductive and metabolic disorders such as PCOS, hypogonadism, and insulin resistance. PrecocityDB is a useful resource for identification of comorbid conditions and disease risks due to shared genes in PP. PrecocityDB is freely accessible at http://www.precocity.bicnirrh.res.in. The database source code and content can be downloaded through GitHub (https://github.com/bic-nirrh/precocity).
Enhancing learning in a perceptual-cognitive training paradigm using EEG-neurofeedback
Authors: Parsons Brendan , Faubert Jocelyn 
Published: February 2021

AbstractThis paper provides the framework and supporting evidence for a highly efficient closed-loop paradigm that modifies a classic learning scenario using real-time brain activity in order to improve learning performance in a perceptual-cognitive training paradigm known as 3-dimensional multiple object tracking, or 3D-MOT. Results demonstrate that, over 10 sessions, when manipulating this novel task by using real-time brain signals, speed and degree of learning can be substantially improved compared with a classic learning system or an active sham-control group. Superior performance persists even once the feedback signal is removed, which suggests that the effects of enhanced training are consolidated and do not rely on continued feedback. This type of learning paradigm could contribute to overcoming one of the fundamental limitations of neurofeedback and other cognitive enhancement techniques, a lack of observable transfer effects, by utilizing a method that can be directly integrated into the context in which improved performance is sought.
Performance of high resolution (400 m) PM2.5 forecast over Delhi
Authors: Jena Chinmay , Ghude Sachin D. , Kumar Rajesh , Debnath Sreyashi , Govardhan Gaurav , Soni Vijay K. , Kulkarni Santosh H. , Beig G. , Nanjundiah Ravi S. , Rajeevan M. 
Published: February 2021

AbstractThis study reports a very high-resolution (400 m grid-spacing) operational air quality forecasting system developed to alert residents of Delhi and the National Capital Region (NCR) about forthcoming acute air pollution episodes. Such a high-resolution system has been developed for the first time and is evaluated during October 2019-February 2020. The system assimilates near real-time aerosol observations from in situ and space-borne platform in the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) to produce a 72-h forecast daily in a dynamical downscaling framework. The assimilation of aerosol optical depth and surface PM2.5 observations improves the initial condition for surface PM2.5 by about 45 µg/m3 (about 50%).The accuracy of the forecast degrades slightly with lead time as mean bias increase from + 2.5 µg/m3 on the first day to − 17 µg/m3 on the third day of forecast. Our forecast is found to be very skillful both for PM2.5 concentration and unhealthy/ very unhealthy air quality index categories, and has been helping the decision-makers in Delhi make informed decisions.
Plasma lipocalin-2/NGAL is stable over 12 weeks and is not modulated by exercise or dieting
Authors: Nakai Michael E. , Denham Joshua , Prestes Priscilla R. , Eikelis Nina , Lambert Elisabeth A. , Straznicky Nora E. , Schlaich Markus P. , Esler Murray D. , O’Brien Brendan J. , Charchar Fadi J. , Lambert Gavin W. , Marques Francine Z. 
Published: February 2021

AbstractAmongst other immune cells, neutrophils play a key role in systemic inflammation leading to cardiovascular disease and can release inflammatory factors, including lipocalin-2 (LCN2). LCN2 drives cardiac hypertrophy and plays a role in maladaptive remodelling of the heart and has been associated with renal injury. While lifestyle factors such as diet and exercise are known to attenuate low-grade inflammation, their ability to modulate plasma LCN2 levels is unknown. Forty-eight endurance athletes and 52 controls (18–55 years) underwent measurement for various cardiovascular health indicators, along with plasma LCN2 concentration. No significant difference in LCN2 concentration was seen between the two groups. LCN2 was a very weak predictor or absent from models describing blood pressures or predicting athlete status. In another cohort, 57 non-diabetic overweight or obese men and post-menopausal women who fulfilled Adult Treatment Panel III metabolic syndrome criteria were randomly allocated into either a control, modified Dietary Approaches to Stop Hypertension (DASH) diet, or DASH and exercise group. Pre- and post-intervention demographic, cardiovascular health indicators, and plasma LCN2 expression were measured in each individual. While BMI fell in intervention groups, LCN2 levels remained unchanged within and between all groups, as illustrated by strong correlations between LCN2 concentrations pre- and 12 weeks post-intervention (r = 0.743, P < 0.0001). This suggests that circulating LCN2 expression are stable over a period of at least 12 weeks and is not modifiable by diet and exercise.
Feeding efficiency gains can increase the greenhouse gas mitigation potential of the Tanzanian dairy sector
Authors: Hawkins James , Yesuf Gabriel , Zijlstra Mink , Schoneveld George C. , Rufino Mariana C. 
Published: February 2021

AbstractWe use an attributional life cycle assessment (LCA) and simulation modelling to assess the effect of improved feeding practices and increased yields of feed crops on milk productivity and GHG emissions from the dairy sector of Tanzania’s southern highlands region. We calculated direct non-CO2 emissions from dairy production and the CO2 emissions resulting from the demand for croplands and grasslands using a land footprint indicator. Baseline GHG emissions intensities ranged between 19.8 and 27.8 and 5.8–5.9 kg CO2eq kg−1 fat and protein corrected milk for the Traditional (local cattle) and Modern (improved cattle) sectors. Land use change contributed 45.8–65.8% of the total carbon footprint of dairy. Better feeding increased milk yields by up to 60.1% and reduced emissions intensities by up to 52.4 and 38.0% for the Traditional and Modern sectors, respectively. Avoided land use change was the predominant cause of reductions in GHG emissions under all the scenarios. Reducing yield gaps of concentrate feed crops lowered emissions further by 11.4–34.9% despite increasing N2O and CO2 emissions from soils management and input use. This study demonstrates that feed intensification has potential to increase LUC emissions from dairy production, but that fertilizer-dependent yield gains can offset this increase in emissions through avoided emissions from land use change.
An in vitro study on factors affecting endotoxin neutralization in human plasma using the Limulus amebocyte lysate test
Authors: Harm Stephan , Schildböck Claudia , Strobl Karin , Hartmann Jens 
Published: February 2021

AbstractEndotoxin neutralization, caused by plasma components, makes it difficult to detect endotoxins in human blood. In this study, we investigated which factors influence the recovery of endotoxins using limulus ameobocyte lysate (LAL)-based assays. The individual factors that were examined in more detail were lipoprotein content, type of blood anticoagulation, kinetics and serum levels of divalent cations. Furthermore, it was investigated whether there is a direct correlation between LAL activity and monocyte activation. We could show that polyanionic heparin increases endotoxin recovery in blood, while citrate anticoagulation promotes endotoxin neutralization. Furthermore, we could show that the endotoxin activity in human plasma and serum decreases strongly over time. Time-dependent endotoxin neutralization reaches its maximum after 4–6 h incubation. By means of filtration tests we could determine that endotoxins in the plasma bind to lipoproteins but do not influence their activity. Comparative measurements have shown that high LAL activity of endotoxins in plasma simultaneously possesses high monocyte activating properties in whole blood. For the maximum recovery of endotoxins in human blood the physiological calcium and magnesium concentrations are sufficient. In this study, it was shown that the endotoxin neutralizing plasma components have a molecular weight similar to β2-microglobulin (11.7 kDa). For the exact identification of the endotoxin neutralizing plasma components, which caused a modulation of the immunostimulating endotoxin activity, further investigations have to be carried out in the future.
Cellular correlates of gray matter volume changes in magnetic resonance morphometry identified by two-photon microscopy
Authors: Asan Livia , Falfán-Melgoza Claudia , Beretta Carlo A. , Sack Markus , Zheng Lei , Weber-Fahr Wolfgang , Kuner Thomas , Knabbe Johannes 
Published: February 2021

AbstractMagnetic resonance imaging (MRI) of the brain combined with voxel-based morphometry (VBM) revealed changes in gray matter volume (GMV) in various disorders. However, the cellular basis of GMV changes has remained largely unclear. We correlated changes in GMV with cellular metrics by imaging mice with MRI and two-photon in vivo microscopy at three time points within 12 weeks, taking advantage of age-dependent changes in brain structure. Imaging fluorescent cell nuclei allowed inferences on (i) physical tissue volume as determined from reference spaces outlined by nuclei, (ii) cell density, (iii) the extent of cell clustering, and (iv) the volume of cell nuclei. Our data indicate that physical tissue volume alterations only account for 13.0% of the variance in GMV change. However, when including comprehensive measurements of nucleus volume and cell density, 35.6% of the GMV variance could be explained, highlighting the influence of distinct cellular mechanisms on VBM results.
Radon degassing triggered by tidal loading before an earthquake
Authors: Omori Yasutaka , Nagahama Hiroyuki , Yasuoka Yumi , Muto Jun 
Published: February 2021

AbstractThe presence of anomalous geochemical changes related to earthquakes has been controversial despite widespread, long time challenges for earthquake prediction. Establishing a quantitative relationship among geochemical changes and geodetical and seismological changes can clarify their hidden connection. Here we determined the response of atmospheric radon (222Rn) to diurnal tidal (K1 constituent) loading in the reported 11-year-long variation in the atmospheric radon concentration, including its anomalous evolution for 2 months before the devastating 1995 Kobe earthquake in Japan. The response to the tidal loading had been identified for 5 years before the occurrence of the earthquake. Comparison between these radon responses relative to crustal strain revealed that the response efficiency for the diurnal K1 tide was larger than that for the earthquake by a factor of 21–33, implying the involvement of crustal fluid movement. The radon responses occurred when compressional crustal stress decreased or changed to extension. These findings suggest that changes in radon exhaled from the ground were induced by ascent flow of soil gas acting as a radon carrier and degassed from mantle-derived crustal fluid upwelling due to modulation of the crustal stress regime.
Effect of temperature, CO2 and O2 on motility and mobility of Anisakidae larvae
Authors: Guan Aiyan , Van Damme Inge , Devlieghere Frank , Gabriël Sarah 
Published: February 2021

AbstractAnisakidae, marine nematodes, are underrecognized fish-borne zoonotic parasites. Studies on factors that could trigger parasites to actively migrate out of the fish are very limited. The objective of this study was to assess the impact of different environmental conditions (temperature, CO2 and O2) on larval motility (in situ movement) and mobility (migration) in vitro. Larvae were collected by candling or enzymatic digestion from infected fish, identified morphologically and confirmed molecularly. Individual larvae were transferred to a semi-solid Phosphate Buffered Saline agar, and subjected to different temperatures (6 ℃, 12 ℃, 22 ℃, 37 ℃) at air conditions. Moreover, different combinations of CO2 and O2 with N2 as filler were tested, at both 6 °C and 12 °C. Video recordings of larvae were translated into scores for larval motility and mobility. Results showed that temperature had significant influence on larval movements, with the highest motility and mobility observed at 22 ℃ for Anisakis spp. larvae and 37 ℃ for Pseudoterranova spp. larvae. During the first 10 min, the median migration of Anisakis spp. larvae was 10 cm at 22 ℃, and the median migration of Pseudoterranova spp. larvae was 3 cm at 37 ℃. Larval mobility was not significantly different under the different CO2 or O2 conditions at 6 °C and 12 ℃. It was concluded that temperature significantly facilitated larval movement with the optimum temperature being different for Anisakis spp. and Pseudoterranova spp., while CO2 and O2 did not on the short term. This should be further validated in parasite-infected/spiked fish fillets.
Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
Authors: Chialva Constanza , Blein Thomas , Crespi Martin , Lijavetzky Diego 
Published: February 2021

AbstractCarrot (Daucus carota L.) is one of the most cultivated vegetable in the world and of great importance in the human diet. Its storage organs can accumulate large quantities of anthocyanins, metabolites that confer the purple pigmentation to carrot tissues and whose biosynthesis is well characterized. Long non-coding RNAs (lncRNAs) play critical roles in regulating gene expression of various biological processes in plants. In this study, we used a high throughput stranded RNA-seq to identify and analyze the expression profiles of lncRNAs in phloem and xylem root samples using two genotypes with a strong difference in anthocyanin production. We discovered and annotated 8484 new genes, including 2095 new protein-coding and 6373 non-coding transcripts. Moreover, we identified 639 differentially expressed lncRNAs between the phenotypically contrasted genotypes, including certain only detected in a particular tissue. We then established correlations between lncRNAs and anthocyanin biosynthesis genes in order to identify a molecular framework for the differential expression of the pathway between genotypes. A specific natural antisense transcript linked to the DcMYB7 key anthocyanin biosynthetic transcription factor suggested how the regulation of this pathway may have evolved between genotypes.
Elevated inflammatory responses and targeted therapeutic intervention in a preclinical mouse model of ataxia-telangiectasia lung disease
Authors: Saunders Rudel A. , Michniacki Thomas F. , Hames Courtney , Moale Hilary A. , Wilke Carol , Kuo Molly E. , Nguyen Johnathan , Hartlerode Andrea J. , Moore Bethany B. , Sekiguchi JoAnn M. 
Published: February 2021

AbstractAtaxia-telangiectasia (A-T) is an autosomal recessive, multisystem disorder characterized by cerebellar degeneration, cancer predisposition, and immune system defects. A major cause of mortality in A-T patients is severe pulmonary disease; however, the underlying causes of the lung complications are poorly understood, and there are currently no curative therapeutic interventions. In this study, we examined the lung phenotypes caused by ATM-deficient immune cells using a mouse model of A-T pulmonary disease. In response to acute lung injury, ATM-deficiency causes decreased survival, reduced blood oxygen saturation, elevated neutrophil recruitment, exaggerated and prolonged inflammatory responses and excessive lung injury compared to controls. We found thatATMnull bone marrow adoptively transferred to WT recipients induces similar phenotypes that culminate in impaired lung function. Moreover, we demonstrated that activated ATM-deficient macrophages exhibit significantly elevated production of harmful reactive oxygen and nitrogen species and pro-inflammatory cytokines. These findings indicate that ATM-deficient immune cells play major roles in causing the lung pathologies in A-T. Based on these results, we examined the impact of inhibiting the aberrant inflammatory responses caused by ATM-deficiency with reparixin, a CXCR1/CXCR2 chemokine receptor antagonist. We demonstrated that reparixin treatment reduces neutrophil recruitment, edema and tissue damage inATMmutant lungs. Thus, our findings indicate that targeted inhibition of CXCR1/CXCR2 attenuates pulmonary phenotypes caused by ATM-deficiency and suggest that this treatment approach represents a viable therapeutic strategy for A-T lung disease.