bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutral excitation density-functional theory: an efficient and variational first-principles method for simulating neutral excitations in molecules
Authors: Roychoudhury Subhayan , Sanvito Stefano , O’Regan David D. 
Published: June 2020

AbstractWe introduce neutral excitation density-functional theory (XDFT), a computationally light, generally applicable, first-principles technique for calculating neutral electronic excitations. The concept is to generalise constrained density functional theory to free it from any assumptions about the spatial confinement of electrons and holes, but to maintain all the advantages of a variational method. The task of calculating the lowest excited state of a given symmetry is thereby simplified to one of performing a simple, low-cost sequence of coupled DFT calculations. We demonstrate the efficacy of the method by calculating the lowest single-particle singlet and triplet excitation energies in the well-known Thiel molecular test set, with results which are in good agreement with linear-response time-dependent density functional theory (LR-TDDFT). Furthermore, we show that XDFT can successfully capture two-electron excitations, in principle, offering a flexible approach to target specific effects beyond state-of-the-art adiabatic-kernel LR-TDDFT. Overall the method makes optical gaps and electron-hole binding energies readily accessible at a computational cost and scaling comparable to that of standard density functional theory. Owing to its multiple qualities beneficial to high-throughput studies where the optical gap is of particular interest; namely broad applicability, low computational demand, and ease of implementation and automation, XDFT presents as a viable candidate for research within materials discovery and informatics frameworks.
Fine-tuning of Genome-Wide Polygenic Risk Scores and Prediction of Gestational Diabetes in South Asian Women
Authors: Lamri Amel , Mao Shihong , Desai Dipika , Gupta Milan , Paré Guillaume , Anand Sonia S. 
Published: June 2020

AbstractGestational diabetes Mellitus (GDM) affects 1 in 7 births and is associated with numerous adverse health outcomes for both mother and child. GDM is suspected to share a large common genetic background with type 2 diabetes (T2D). The aim of our study was to characterize different GDM polygenic risk scores (PRSs) and test their association with GDM using data from the South Asian Birth Cohort (START). PRSs were derived for 832 South Asian women from START using the pruning and thresholding (P + T), LDpred, and GraBLD methods. Weights were derived from a multi-ethnic and a white Caucasian study of the DIAGRAM consortium. GDM status was defined using South Asian-specific glucose values in response to an oral glucose tolerance test. Association with GDM was tested using logistic regression. Results were replicated in South Asian women from the UK Biobank (UKB) study. The top ranking P + T, LDpred and GraBLD PRSs were all based on DIAGRAM’s multi-ethnic study. The best PRS was highly associated with GDM in START (AUC = 0.62, OR = 1.60 [95% CI = 1.44–1.69]), and in South Asian women from UKB (AUC = 0.65, OR = 1.69 [95% CI = 1.28–2.24]). Our results highlight the importance of combining genome-wide genotypes and summary statistics from large multi-ethnic studies to optimize PRSs in South Asians.
Palynological Age Control and Paleoenvironments of the Paleogene Strata in Eastern Dahomey Basin, Southwestern Nigeria
Authors: Bolaji Taiwo A. , Ndukwe Otobong S. , Oyebamiji Ajibola R. , Ikegwuonu Okechukwu N. 
Published: June 2020

AbstractPaleogene deposits are extensively exposed in the Eastern Dahomey (Benin) sedimentary Basin in southwestern Nigeria. Outcrop logging and sampling of lithological sections were systematically carried out at the Ibese Quarry, in order to re-establish the age of sediments and reconstruct their depositional environment using samples rich in organic-walled microfossils. Two formations were recognized; the Ewekoro and Akinbo Formations. Two main lithological units were identified; limestones and carbonaceous shales. Minor lithologies include ferrugineous sandstones and glauconite. Results from the palynological examination show that terrestrial palynomorphs (spores and pollen) dominate over the marine dinoflagellates cyst species in the samples recovered from the Ewekoro Formation, while samples from the Akinbo Formation recorded high abundance with less diversity of the marine dinoflagellates cysts over the terrestrial sporomorph. Age determination/correlation was achieved based on selected stratigraphic index taxa recovered. The samples from Ewekoro Formation were dated as late Early Paleocene to early Middle Paleocene, based on the presence of the following pollen key-taxa: Proxapertites operculatus, Retidiporites magdalenensis, Spinizonocolpites baculatus, Mauritidiites crassiexinus, Scabratriporites simpliformis, and Echitriporites trianguliformis. The samples from the Akinbo Formation were assigned late Middle Paleocene to late Paleocene, based on the presence of the following pollen key-taxa: Proxapertites operculatus/cursus, Grimsdalea polygonalis, Retibrevitricolpites triangulatus, Psilatricolporites operculatus, Retistephanocolpites williamsi, Bombacidites sp., Apectodinium homomorphum, and Apectodinium quinquelatum. The environmentally significant palynomorph species indicated differences in paleodepositional environments, ranging from shallow marine in the Ewekoro Formation at the base, up the stratigraphic sequence, to marginal marine (estuarine) depositional environment in the overlying Akinbo Formation.
Liver colour scoring index, carotenoids and lipid content assessment as a proxy for lumpfish (Cyclopterus lumpus L.) health and welfare condition
Authors: Eliasen Kirstin , Patursson Esbern J. , McAdam Bruce J. , Pino Enrique , Morro Bernat , Betancor Monica , Baily Johanna , Rey Sonia 
Published: June 2020

AbstractEnsuring lumpfish health and welfare in salmon farms is vital to reduce the high mortality rates reported and to guarantee a high delousing efficiency. Recent observations of farmed lumpfish livers have shown colours ranging from pale (colours 1 and 2), through bright orange (colours 3 and 4), to dark reddish-brown (colours 5 and 6), some of which may be related to welfare condition. To characterize the status of lumpfish deployed in four Faroese salmon farms, several welfare indicators were assessed: a weight-length relationship, scoring of external physical damage, and after dissection, stomach content and liver colour scoring. Liver samples were weighed, stored and analysed for lipid content, lipid classes, total pigments, fatty acid profile and histopathology to explain the differences between the mentioned liver colours. Bright orange livers, liver colours 3 and 4, were related to increased levels of carotenoid pigments rather than levels of lipids and appear to reflect good fish welfare. However, dark reddish-brown colours, liver colours 5 and 6, were associated with very low levels of triacyl glycerides in the liver, indicating use of lipid reserves and poor welfare condition. Histopathology confirmed that the dark reddish-brown livers, liver colours 5 and 6, formed a distinct group. Thus, liver colour was shown to be a good welfare indicator and should be monitored in farms.
Comparative Effects of Alpha- and Gamma-Tocopherol on Mitochondrial Functions in Alzheimer’s Disease In Vitro Model
Authors: Pahrudin Arrozi Aslina , Shukri Siti Nur Syazwani , Wan Ngah Wan Zurinah , Mohd Yusof Yasmin Anum , Ahmad Damanhuri Mohd Hanafi , Jaafar Faizul , Makpol Suzana 
Published: June 2020

AbstractVitamin E acts as an antioxidant and reduces the level of reactive oxygen species (ROS) in Alzheimer’s disease (AD). Alpha-tocopherol (ATF) is the most widely studied form of vitamin E besides gamma-tocopherol (GTF) which also shows beneficial effects in AD. The levels of amyloid-beta (Aβ) and amyloid precursor protein (APP) increased in the brains of AD patients, and mutations in the APP gene are known to enhance the production of Aβ. Mitochondrial function was shown to be affected by the increased level of Aβ and may induce cell death. Here, we aimed to compare the effects of ATF and GTF on their ability to reduce Aβ level, modulate mitochondrial function and reduce the apoptosis marker in SH-SY5Y cells stably transfected with the wild-type or mutant form of the APP gene. The Aβ level was measured by ELISA, the mitochondrial ROS and ATP level were quantified by fluorescence and luciferase assay respectively whereas the complex V enzyme activity was measured by spectrophotometry. The expressions of genes involved in the regulation of mitochondrial membrane permeability such as voltage dependent anion channel (VDAC1), adenine nucleotide translocase (ANT), and cyclophilin D (CYPD) were determined by quantitative real-time polymerase chain reaction (qRT-PCR), while the expressions of cyclophilin D (CypD), cytochrome c, Bcl2 associated X (BAX), B cell lymphoma-2 (Bcl-2), and pro-caspase-3 were determined by western blot. Our results showed that mitochondrial ROS level was elevated accompanied by decreased ATP level and complex V enzyme activity in SH-SY5Y cells expressing the mutant APP gene (p < 0.05). Treatment with both ATF and GTF reduced the mitochondrial ROS level with maximum reduction was observed in the cells treated with high concentrations of ATF and GTF (p < 0.05). However, only GTF at 80 µM significantly increase the ATP level and complex V enzyme activity (p < 0.05). VDAC1 and CYPD were downregulated and CypD protein was significantly overexpressed in cells transfected with the wild-type (WT) and mutant APP gene (p < 0.05). Cytochrome c release, the ratio of BAX/Bcl-2, and pro-caspase-3 expression increased in cells expressing mutated APP gene (p < 0.05). The expression of CypD and pro-caspase 3 protein, and the ratio of BAX/Bcl-2 were increased in the following order; SH-SY5Y-APP-WT < SH-SY5Y-APP Swe <SH-SY5Y-APP Swe/Ind. Treatment with both ATF and GTF reduced the release of cytochrome c and the ratio of BAX/Bcl-2. However, only GTF significantly reduced the expression of CypD and pro-caspase-3, suggestive of its unique role in AD. In conclusion, GTF has an effect that was not shown by ATF and thus suggest its potential role in the development of therapeutic agents for AD.
Ultra-rapid glutathionylation of chymotrypsinogen in its molten globule-like conformation: A comparison to archaeal proteins
Authors: Bocedi Alessio , Gambardella Giorgia , Cattani Giada , Bartolucci Simonetta , Limauro Danila , Pedone Emilia , Iavarone Federica , Castagnola Massimo , Ricci Giorgio 
Published: June 2020

AbstractChymotrypsinogen, when reduced and taken to its molten globule-like conformation, displays a single cysteine with an unusual kinetic propensity toward oxidized glutathione (GSSG) and other organic thiol reagents. A single residue, identified by mass spectrometry like Cys1, reacts with GSSG about 1400 times faster than an unperturbed protein cysteine. A reversible protein-GSSG complex and a low pKa (8.1 ± 0.1) make possible such astonishing kinetic property which is absent toward other natural disulfides like cystine, homocystine and cystamine. An evident hyper-reactivity toward 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB) and 1-chloro-2,4-dinitrobenzene (CDNB) was also found for this specific residue. The extraordinary reactivity toward GSSG is absent in two proteins of the thermophilic archaeon Sulfolobus solfataricus, an organism lacking glutathione: the Protein Disulphide Oxidoreductase (SsPDO) and the Bacterioferritin Comigratory Protein 1 (Bcp1) that displays Cys residues with an even lower pKa value (7.5 ± 0.1) compared to chymotrypsinogen. This study, which also uses single mutants in Cys residues for Bcp1, proposes that this hyper-reactivity of a single cysteine, similar to that found in serum albumin, lysozyme, ribonuclease, may have relevance to drive the “incipit” of the oxidative folding of proteins from organisms where the glutathione/oxidized glutathione (GSH/GSSG) system is present.
Parthenium hysterophorus steps up Ca-regulatory pathway in defence against highlight intensities
Authors: Ahmad Javed , Baig M. Affan , Amna  , Alaraidh Ibrahim A. , Alsahli Abdulaziz A. , Qureshi M. Irfan 
Published: June 2020

AbstractParthenium hysterophorus exhibits tolerance to a great extent against abiotic stresses including high light intensities. In this study, P. hysterophorus was subjected to three different light intensities viz. control (CL, 250 µmol photons m−2 s−1), moderately high (ML, 500 µmol photons m−2 s−1) and high (HL, 1000 µmol photons m−2 s−1) for assessment of biochemical and physiological responses at 3 and 5 days after treatment (DAT). Proteomic responses were also observed at 5 DAT. Level of oxidative stress marker, abundance of H2O2 and O2− was highest in leaves exposed to HL followed by ML treatment. Biomass accumulation, photosynthetic parameters, chloroplast and mitochondrial integrity were also affected by both ML and HL treatments. Differential protein expression data showed modulation of thirty-eight proteins in ML and HL intensities. P. hysterophorus exhibited good ability to survive in ML then HL treatment as demonstrated by enhancement of the antioxidant system and photosynthesis. Furthermore, P. hysterophorus mobilized some key proteins related to calcium signaling, which in turn coordinate physiological homeostasis under stress. Proline and total soluble sugar content were high under stress; however, results of simulated experiment of our study indicate such accumulation of osmolytes may inhibit photon-availability to chloroplast. These results clarify our understanding of the mechanisms underlying the light stress tolerance of P. hysterophorus.
Biochar and fulvic acid amendments mitigate negative effects of coastal saline soil and improve crop yields in a three year field trial
Authors: Sun Yun-peng , Yang Jing-song , Yao Rong-jiang , Chen Xiao-bing , Wang Xiang-ping 
Published: June 2020

AbstractChina with large area of land planted with crops are suffering secondary salinization in coastal area for the lack of fresh water and saltwater intrusion to the groundwater. The purpose of this study was to investigate the effects of biochar (BC) and fulvic acid (FA) on the amelioration of coastal saline soil and their impact on crop yields under maize-barley rotation system. A three year field experiment was conducted in a saline soil on a farm in coastal area of east Jiangsu Province, China. A maize-barley rotation system had been carried out for ten years with local conventional management before the experiment. The saline soil was amended with BC at rates of 0, 7.5 t ha−1 (BC1), 15 t ha−1 (BC2) and 30 t ha−1 (BC3) alone or combined with fulvic acid (1.5 t ha−1) compared with control. Fertilizers were applied under normal planting strategies. The BC was added only once during the four growing seasons, and the FA was applied before each sowing. Soil salinity changed significantly during the three year field experiment. This was mainly due to the great quantity of rain during the period of maize cultivation. Although Na+, Cl− and SO42− in BC and /or FA treatments significantly decreased, the pH value increased up to 9.0 as the CO32− + HCO3−content increased. Total organic carbon (TOC) and phosphorus (TP) responded positively to biochar addition rate. BC applied with appropriate rate at 15 t ha−1 (BC2) in combination with FA showed optimal effects on soil salinity amelioration, soil physics properties regulation, soil nutrition improvement and crop yields increase. The TOC and TP was 5.2 g kg−1 and 507 mg kg−1 in BC2 + FA treatment, which were lower than BC3 and BC3 + FA treatments. However, the highest total grain yield was obtained in the BC2 + FA treatment, and the total yield was increased by 62.9% over the CK. This study emphasizes that using combined organic amendment of BC with FA for profitable and sustainable use of salt-affected soils would be practicable.
Sad mood and poor sleep are related to task-unrelated thoughts and experience of diminished cognitive control
Authors: Marcusson-Clavertz David , Kjell Oscar N. E. , Kim Jinhyuk , Persson Stefan D. , Cardeña Etzel 
Published: June 2020

AbstractPrevious studies have indicated that a sad mood and sleep deprivation increase mind wandering, but it is unclear whether these associations reflect reduced effort in concentrating on the task at hand or diminished cognitive control. In an internet-based experiment, participants completed a sleep disturbance questionnaire followed by a complex span task and a 2-back task with thought-sampling probes. Subsequently, participants underwent a positive, neutral, or negative mood induction prior to repeating the 2-back. The results (N = 504) replicated the finding of increased task-unrelated thoughts following sad mood induction, B = 0.56 (SE = 0.14), p < 0.01, d = 0.31. Unguided thoughts were increased following sad mood induction, B = 0.31 (0.13), p = 0.02, but working memory did not significantly moderate this association (p = 0.31). People reported a lower degree of trying to concentrate on the 2-back after the sad mood induction, B = −0.07 (0.04), p = 0.04, but actual performance was not affected (p = 0.46). Sleep disturbances showed small associations with task-unrelated, B = 0.23 (0.08), p < 0.01, and unguided thoughts, B = 0.32 (0.08), p < 0.01. This study strengthens the evidence that a sad mood and poor sleep relate to mind wandering.
Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system
Authors: Dowden R. A. , McGuinness L. R. , Wisniewski P. J. , Campbell S. C. , Guers J. J. , Oydanich M. , Vatner S. F. , Häggblom M. M. , Kerkhof L. J. 
Published: June 2020

AbstractThe mammalian gut microbiome can potentially impact host health and disease state. It is known that the mouse-genome, eating-behavior, and exercise-status promotes higher taxonomic rank-level alterations (e.g. family to phyla-level) of the gut microbiota. Here, host genotype or activity status was investigated to determine if selection of individual bacterial species or strains could be discerned within the murine digestive system. For this study, the fecal bacterial community of adenylyl cyclase 5 knock-out (AC5KO, n = 7) mice or their wild-type (WT, n = 10) littermates under exercise or sedentary conditions were profiled by sequencing rRNA operons. AC5KO mice were chosen since this genotype displays enhanced longevity/exercise capacity and protects against cardiovascular/metabolic disease. Profiling of rRNA operons using the Oxford MinION yielded 65,706 2-D sequences (after size selection of 3.7–5.7 kb) which were screened against an NCBI 16S rRNA gene database. These sequences were binned into 1,566 different best BLAST hits (BBHs) and counted for each mouse sample. Non-metric multidimensional scaling (NMDS) of the gut microbial community demonstrated clustering by physical activity (p = 0.001) but not by host genotype. Additionally, sequence similarity and phylogenetic analysis demonstrated that different bacterial species (closely related to Muribaculum intestinale and Parasutterella excrementihominis) inhabit AC5KO or WT mice depending on activity status. Other bacterial species of the gut microbiota did not follow such patterning (e.g. Turicibacter sanguinis and Turicimonas muris). Our results support the need of improved taxonomic resolution for better characterization of bacterial communities to deepen our understanding of the role of the gut microbiome on host health.
Up regulation of the Hippo signalling effector YAP1 is linked to early biochemical recurrence in prostate cancers
Authors: Marx Andreas , Schumann Aljoscha , Höflmayer Doris , Bady Elena , Hube-Magg Claudia , Möller Katharina , Tsourlakis Maria Christina , Steurer Stefan , Büscheck Franziska , Eichenauer Till , Clauditz Till S. , Graefen Markus , Simon Ronald , Sauter Guido , Izbicki Jakob R. , Huland Hartwig , Heinzer Hans , Haese Alexander , Schlomm Thorsten , Bernreuther Christian , Lebok Patrick , Polonski Adam 
Published: June 2020

AbstractThe transcriptional coactivator YAP1 controls the balance between cell proliferation and apoptosis. YAP1 overexpression is linked to poor prognosis in many cancer types, yet its role in prostate cancer is unknown. Here, we applied YAP1 immunohistochemistry to a tissue microarray containing 17,747 clinical prostate cancer specimens. Cytoplasmic and nuclear YAP1 staining was seen in 81% and 63% of tumours. For both cytoplasmic and nuclear YAP1 staining, high levels were associated with advanced tumour stage, classical and quantitative Gleason grade, positive nodal stage, positive surgical margin, high KI67 labelling index, and early biochemical recurrence (p < 0.0001 each). The prognostic role of YAP1 staining was independent of established prognostic features in multivariate models (p < 0.001). Comparison with previously studied molecular markers identified associations between high YAP1 staining, TMPRSS2:ERG fusion (p < 0.0001), high androgen receptor (AR) expression (p < 0.0001), high Ki67 labelling index (p < 0.0001), and PTEN and 8p deletions (p < 0.0001 each). In conclusion, high YAP1 protein expression is an independent predictor of unfavourable disease course in prostate cancer. That cytoplasmic and nuclear YAP1 staining is equally linked to phenotype and prognosis fits well to a model where YAP1 activation during tumour progression includes up regulation, cytoplasmic accumulation and subsequent translocation to the nucleus.