bluuebunny/crossref_metadata_2025_split huggingface dataset:
Materials Cloud, a platform for open computational science
Authors: Talirz Leopold , Kumbhar Snehal , Passaro Elsa , Yakutovich Aliaksandr V. , Granata Valeria , Gargiulo Fernando , Borelli Marco , Uhrin Martin , Huber Sebastiaan P. , Zoupanos Spyros , Adorf Carl S. , Andersen Casper Welzel , Schütt Ole , Pignedoli Carlo A. , Passerone Daniele , VandeVondele Joost , Schulthess Thomas C. , Smit Berend , Pizzi Giovanni , Marzari Nicola 
Published: September 2020

AbstractMaterials Cloud is a platform designed to enable open and seamless sharing of resources for computational science, driven by applications in materials modelling. It hosts (1) archival and dissemination services for raw and curated data, together with their provenance graph, (2) modelling services and virtual machines, (3) tools for data analytics, and pre-/post-processing, and (4) educational materials. Data is citable and archived persistently, providing a comprehensive embodiment of entire simulation pipelines (calculations performed, codes used, data generated) in the form of graphs that allow retracing and reproducing any computed result. When an AiiDA database is shared on Materials Cloud, peers can browse the interconnected record of simulations, download individual files or the full database, and start their research from the results of the original authors. The infrastructure is agnostic to the specific simulation codes used and can support diverse applications in computational science that transcend its initial materials domain.
Comparing the visual outcome, visual quality, and satisfaction among three types of multi-focal intraocular lenses
Authors: Paik Dong Won , Park Jun Sang , Yang Chan Min , Lim Dong Hui , Chung Tae-Young 
Published: September 2020

AbstractThis study compared the visual outcome, visual quality, and satisfaction following implantation of the Mix-and-Match bifocal IOLs (+ 2.75 D and + 3.25 D add power Tecnis Multifocal Model), EDOF IOL (Tecnis Symfony IOL), and Trifocal IOL (FineVision PodFT, PhysIOL). All outcomes were compared among the three groups. The manifest refraction indicated that the EDOF group had significantly higher myopic spherical equivalent values than did the others. In the terms of visual acuity, there were no significant differences in far or intermediate visual acuity among the three groups. Only in near (33 cm), the EDOF group had significantly worse binocular visual acuity than did the Trifocal group (p = 0.002). Regarding to defocus curve, the Trifocal group had better defocus curves at near distances (− 2.0 to − 3.5 D; p = 0.001 vs. EDOF) than did the other two groups. In contrast sensitivity test, the EDOF group had relatively lower value than did the other two groups. In reading speed, only at 0.3 logMAR (6.5-point font), Mix-and-Match group had a significantly higher reading speed than did the other two groups (p =  < 0.001 vs. EDOF, p = 0.007 vs. Trifocal). also Mix-and-Match group showed significantly fewer visual artifacts. There were no differences between the three groups in terms of patient satisfaction.ClinicalTrials.gov number: NCT04019691.
Evolution of isoprenyl diphosphate synthase-like terpene synthases in fungi
Authors: Wei Guo , Eberl Franziska , Chen Xinlu , Zhang Chi , Unsicker Sybille B. , Köllner Tobias G. , Gershenzon Jonathan , Chen Feng 
Published: September 2020

AbstractTerpene synthases (TPSs) and trans-isoprenyl diphosphate synthases (IDSs) are among the core enzymes for creating the enormous diversity of terpenoids. Despite having no sequence homology, TPSs and IDSs share a conserved “α terpenoid synthase fold” and a trinuclear metal cluster for catalysis, implying a common ancestry with TPSs hypothesized to evolve from IDSs anciently. Here we report on the identification and functional characterization of novel IDS-like TPSs (ILTPSs) in fungi that evolved from IDS relatively recently, indicating recurrent evolution of TPSs from IDSs. Through large-scale bioinformatic analyses of fungal IDSs, putative ILTPSs that belong to the geranylgeranyl diphosphate synthase (GGDPS) family of IDSs were identified in three species of Melampsora. Among the GGDPS family of the two Melampsora species experimentally characterized, one enzyme was verified to be bona fide GGDPS and all others were demonstrated to function as TPSs. Melampsora ILTPSs displayed kinetic parameters similar to those of classic TPSs. Key residues underlying the determination of GGDPS versus ILTPS activity and functional divergence of ILTPSs were identified. Phylogenetic analysis implies a recent origination of these ILTPSs from a GGDPS progenitor in fungi, after the split of Melampsora from other genera within the class of Pucciniomycetes. For the poplar leaf rust fungus Melampsora larici-populina, the transcripts of its ILTPS genes were detected in infected poplar leaves, suggesting possible involvement of these recently evolved ILTPS genes in the infection process. This study reveals the recurrent evolution of TPSs from IDSs since their ancient occurrence and points to the possibility of a wide distribution of ILTPS genes in three domains of life.
Assessing the effect of wind farms in fauna with a mathematical model
Authors: Refoyo Román Pablo , Olmedo Salinas Cristina , Muñoz Araújo Benito 
Published: September 2020

AbstractEnergy production by wind turbines has many advantages. The wind is a renewable energy that does not emit greenhouse gases and has caused a considerable increase in wind farms around the world. However, this type of energy is not completely free of impact. In particular, wind turbines displace and kill a wide variety of wild species what forces us to plan their location well. In any case, the determination of the effects of wind farms on fauna, especially the flying one, is difficult to determine and depends on several factors. In this work, we will try to establish a mathematical algorithm that allows us to combine all variables that affect the species with the idea of quantifying the effect that can cause the installation of a wind farm with certain characteristics in a given place. We have considered specific parameters of wind farms, the most relevant environmental characteristics related to the location of the wind farm, and morphological, ethological and legal characteristics in the species. Two types of assessment are established for the definitive valuation. Total Assessment and Weighted Assessment. Total Valuation is established based on a reference scale that will allow us to establish categories of affection for the different species while Weighted valuation allows us to establish which species are most affected.
Effects of time and temperature during melanging on the volatile profile of dark chocolate
Authors: Clark Caitlin , Bettenhausen Harmonie M. , Heuberger Adam L. , Miller Jeffrey , Yao Linxing , Stone Martha 
Published: September 2020

AbstractChocolate made from small-batch production is known for distinct sensory properties that differentiate its products from large-scale production. Specifically, small-batch processing includes a melanging step, a chocolate refining (a process involving time and temperature to refine texture and flavor) process that occurs in a stone wet-grinder. Chocolatiers understand that melanging is essential to flavor and overall quality, however the influence of melanging on the aroma chemistry of the finished chocolate is anecdotal and largely uncharacterized. Here, we evaluated the effects of time and temperature of melanging on the volatile chemistry of the finished chocolate. Specifically, chocolate aroma was profiled using HS/SPME–GC–MS for three different time and temperature combinations. A total of 88 compounds were annotated by mass spectrometry and included a diverse set of chemical classes such as pyrazines, aldehydes, terpenes, alcohols, esters, and ketones. Analysis of variance (ANOVA), principal component analysis (PCA), and partial least squares analysis (PLS) revealed that the overall aroma profile was influenced by the type of melanging, and time had a greater effect than temperature. Example compounds affected by time include 2-methylpropanal, dimethyl sulfide, and benzaldehyde. Particle size was also measured for each sample. Majority particle size was found to be below 25 microns generally at all time points beyond 8 h. Analysis showed significantp-values for the temperature variable for several compounds, but significantp-values for the time variable were apparent for a greater number of compounds. For compounds which showed dependency on both time and temperature, thep-value for the time variable was much smaller in most cases. Both PCA and OPLS analyses suggested the same trends. These data support that time is a critical factor in determining the aroma chemistry of chocolate and affects a diverse set of known flavor active compounds.
In vivo non-invasive staining-free visualization of dermal mast cells in healthy, allergy and mastocytosis humans using two-photon fluorescence lifetime imaging
Authors: Kröger Marius , Scheffel Jörg , Nikolaev Viktor V. , Shirshin Evgeny A. , Siebenhaar Frank , Schleusener Johannes , Lademann Jürgen , Maurer Marcus , Darvin Maxim E. 
Published: September 2020

AbstractMast cells (MCs) are multifunctional cells of the immune system and are found in skin and all major tissues of the body. They contribute to the pathology of several diseases including urticaria, psoriasis, atopic dermatitis and mastocytosis where they are increased at lesional sites. Histomorphometric analysis of skin biopsies serves as a routine method for the assessment of MC numbers and their activation status, which comes with major limitations. As of now, non-invasive techniques to study MCs in vivo are not available. Here, we describe a label-free imaging technique to visualize MCs and their activation status in the human papillary dermis in vivo. This technique uses two-photon excited fluorescence lifetime imaging (TPE-FLIM) signatures, which are different for MCs and other dermal components. TPE-FLIM allows for the visualization and quantification of dermal MCs in healthy subjects and patients with skin diseases. Moreover, TPE-FLIM can differentiate between two MC populations in the papillary dermis in vivo—resting and activated MCs with a sensitivity of 0.81 and 0.87 and a specificity of 0.85 and 0.84, respectively. Results obtained on healthy volunteers and allergy and mastocytosis patients indicate the existence of other MC subpopulations within known resting and activated MC populations. The developed method may become an important tool for non-invasive in vivo diagnostics and therapy control in dermatology and immunology, which will help to better understand pathomechanisms involving MC accumulation, activation and degranulation and to characterize the effects of therapies that target MCs.
Poor prognosis of NSCLC located in lower lobe is partly mediated by lower frequency of EGFR mutations
Authors: Lee Hyun Woo , Park Young Sik , Park Sangshin , Lee Chang-Hoon 
Published: September 2020

AbstractIt is controversial whether a tumor located in the lower lobe is related with worse outcome of non-small cell lung cancer (NSCLC). This study aimed to clarify the prognostic role of primary tumor location in NSCLC. Patients newly diagnosed with NSCLC in a tertiary referral hospital from January 2011 to December 2014 were followed up for 5 years. Of the 2,289 NSCLC cases, 911 (39.8%) cases pertained to lower lobe cancers. Patients with lower lobe cancer showed a higher all-cause mortality rate than those with non-lower lobe cancer (48.6% vs. 40.3%, p < 0.001). Patients with lower lobe cancer had a lower proportion of adenocarcinoma histology and epidermal growth factor receptor (EGFR) mutations. Furthermore, compared to patients with non-lower lobe cancer, those with lower lobe cancer had a higher level of tumor markers (neuron-specific enolase and cytokeratin fragment 21-1). Mediation analysis revealed that the association between lower lobe cancer and higher all-cause mortality could be explained by an indirect pathway through EGFR mutations (percent mediated = 17.3%, p = 0.005). The sensitivity analysis for adenocarcinoma patients showed similar results (percent mediated = 18.8%, p = 0.021). Lower lobe cancer is associated with a higher all-cause mortality risk in patients with NSCLC, which is partly mediated by a lower proportion of EGFR mutations.
A digital health intervention for cardiovascular disease management in primary care (CONNECT) randomized controlled trial
Authors: Redfern Julie , Coorey Genevieve , Mulley John , Scaria Anish , Neubeck Lis , Hafiz Nashid , Pitt Chris , Weir Kristie , Forbes Joanna , Parker Sharon , Bampi Fiona , Coenen Alison , Enright Gemma , Wong Annette , Nguyen Theresa , Harris Mark , Zwar Nick , Chow Clara K. , Rodgers Anthony , Heeley Emma , Panaretto Katie , Lau Annie , Hayman Noel , Usherwood Tim , Peiris David 
Published: September 2020

AbstractDigital health applications (apps) have the potential to improve health behaviors and outcomes. We aimed to examine the effectiveness of a consumer web-based app linked to primary care electronic health records (EHRs). CONNECT was a multicenter randomized controlled trial involving patients with or at risk of cardiovascular disease (CVD) recruited from primary care (Clinical Trial registration ACTRN12613000715774). Intervention participants received an interactive app which was pre-populated and refreshed with EHR risk factor data, diagnoses and, medications. Interactive risk calculators, motivational messages and lifestyle goal tracking were also included. Control group received usual health care. Primary outcome was adherence to guideline-recommended medications (≥80% of days covered for blood pressure (BP) and statin medications). Secondary outcomes included attainment of risk factor targets and eHealth literacy. In total, 934 patients were recruited; mean age 67.6 (±8.1) years. At 12 months, the proportion with >80% days covered with recommended medicines was low overall and there was no difference between the groups (32.8% vs. 29.9%; relative risk [RR] 1.07 [95% CI, 0.88–1.20] p = 0.49). There was borderline improvement in the proportion meeting BP and LDL targets in intervention vs. control (17.1% vs. 12.1% RR 1.40 [95% CI, 0.97–2.03] p = 0.07). The intervention was associated with increased attainment of physical activity targets (87.0% intervention vs. 79.7% control, p = 0.02) and e-health literacy scores (72.6% intervention vs. 64.0% control, p = 0.02). In conclusion, a consumer app integrated with primary health care EHRs was not effective in increasing medication adherence. Borderline improvements in risk factors and modest behavior changes were observed.
Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor
Authors: Olson Linda J. , Misra Sandeep K. , Ishihara Mayumi , Battaile Kevin P. , Grant Oliver C. , Sood Amika , Woods Robert J. , Kim Jung-Ja P. , Tiemeyer Michael , Ren Gang , Sharp Joshua S. , Dahms Nancy M. 
Published: September 2020

AbstractThe cation-independent mannose 6-phosphate receptor (CI-MPR, IGF2 receptor or CD222), is a multifunctional glycoprotein required for normal development. Through the receptor’s ability to bind unrelated extracellular and intracellular ligands, it participates in numerous functions including protein trafficking, lysosomal biogenesis, and regulation of cell growth. Clinically, endogenous CI-MPR delivers infused recombinant enzymes to lysosomes in the treatment of lysosomal storage diseases. Although four of the 15 domains comprising CI-MPR’s extracellular region bind phosphorylated glycans on lysosomal enzymes, knowledge of how CI-MPR interacts with ~60 different lysosomal enzymes is limited. Here, we show by electron microscopy and hydroxyl radical protein footprinting that the N-terminal region of CI-MPR undergoes dynamic conformational changes as a consequence of ligand binding and different pH conditions. These data, coupled with X-ray crystallography, surface plasmon resonance and molecular modeling, allow us to propose a model explaining how high-affinity carbohydrate binding is achieved through allosteric domain cooperativity.
A neoceratopsian dinosaur from the early Cretaceous of Mongolia and the early evolution of ceratopsia
Authors: Yu Congyu , Prieto-Marquez Albert , Chinzorig Tsogtbaatar , Badamkhatan Zorigt , Norell Mark 
Published: September 2020

AbstractCeratopsia is a diverse dinosaur clade from the Middle Jurassic to Late Cretaceous with early diversification in East Asia. However, the phylogeny of basal ceratopsians remains unclear. Here we report a new basal neoceratopsian dinosaurBeg tsebased on a partial skull from Baruunbayan, Ömnögovi aimag, Mongolia.Begis diagnosed by a unique combination of primitive and derived characters including a primitively deep premaxilla with four premaxillary teeth, a trapezoidal antorbital fossa with a poorly delineated anterior margin, very short dentary with an expanded and shallow groove on lateral surface, the derived presence of a robust jugal having a foramen on its anteromedial surface, and five equally spaced tubercles on the lateral ridge of the surangular. This is to our knowledge the earliest known occurrence of basal neoceratopsian in Mongolia, where this group was previously only known from Late Cretaceous strata. Phylogenetic analysis indicates that it is sister to all other neoceratopsian dinosaurs.
L-Arginine prevents cereblon-mediated ubiquitination of glucokinase and stimulates glucose-6-phosphate production in pancreatic β-cells
Authors: Cho Jaeyong , Horikawa Yukio , Enya Mayumi , Takeda Jun , Imai Yoichi , Imai Yumi , Handa Hiroshi , Imai Takeshi 
Published: September 2020

AbstractWe sought to determine a mechanism by which L-arginine increases glucose-stimulated insulin secretion (GSIS) in β-cells by finding a protein with affinity to L-arginine using arginine-immobilized magnetic nanobeads technology. Glucokinase (GCK), the key regulator of GSIS and a disease-causing gene of maturity-onset diabetes of the young type 2 (MODY2), was found to bind L-arginine. L-Arginine stimulated production of glucose-6-phosphate (G6P) and induced insulin secretion. We analyzed glucokinase mutants and identified three glutamate residues that mediate binding to L-arginine. One MODY2 patient with GCKE442* demonstrated lower C-peptide-to-glucose ratio after arginine administration. In β-cell line, GCKE442* reduced L-arginine-induced insulin secretion compared with GCKWT. In addition, we elucidated that the binding of arginine protects glucokinase from degradation by E3 ubiquitin ligase cereblon mediated ubiquitination. We conclude that L-arginine induces insulin secretion by increasing G6P production by glucokinase through direct stimulation and by prevention of degradation.
Structure of an anti-PEG antibody reveals an open ring that captures highly flexible PEG polymers
Authors: Huckaby Justin T. , Jacobs Tim M. , Li Zhongbo , Perna Robert J. , Wang Anting , Nicely Nathan I. , Lai Samuel K. 
Published: September 2020

AbstractPolyethylene glycol (PEG) is a polymer routinely used to modify biologics and nanoparticles to prolong blood circulation and reduce immunogenicity of the underlying therapeutic. However, several PEGylated therapeutics induce the development of anti-PEG antibodies (APA), leading to reduced efficacy and increased adverse events. Given the highly flexible structure of PEG, how APA specifically bind PEG remains poorly understood. Here, we report a crystal structure illustrating the structural properties and conformation of the APA 6-3 Fab bound to the backbone of PEG. The structure reveals an open ring-like sub-structure in the Fab paratope, whereby PEG backbone is captured and then stabilized via Van der Waals interactions along the interior and exterior of the ring paratope surface. Our finding illustrates a strategy by which antibodies can bind highly flexible repeated structures that lack fixed conformations, such as polymers. This also substantially advances our understanding of the humoral immune response generated against PEG.
Creating and using large grids of precalculated model atmospheres for a rapid analysis of stellar spectra
Authors: Zsargó J. , Fierro-Santillán C. R. , Klapp J. , Arrieta A. , Arias L. , Valencia J. M. , Sigalotti L. Di G. , Hareter M. , Puebla R. E. 
Published: September 2020

Aims. We present a database of 43 340 atmospheric models (∼80 000 models at the conclusion of the project) for stars with stellar masses between 9 and 120 M⊙, covering the region of the OB main-sequence and Wolf-Rayet stars in the Hertzsprung-Russell diagram.
Methods. The models were calculated using the ABACUS I supercomputer and the stellar atmosphere code CMFGEN.
Results. The parameter space has six dimensions: the effective temperature Teff, the luminosity L, the metallicity Z, and three stellar wind parameters: the exponent β, the terminal velocity V∞, and the volume filling factor Fcl. For each model, we also calculate synthetic spectra in the UV (900−2000 Å), optical (3500−7000 Å), and near-IR (10 000−40 000 Å) regions. To facilitate comparison with observations, the synthetic spectra can be rotationally broadened using ROTIN3, by covering v sin i velocities between 10 and 350 km s−1 with steps of 10 km s−1.
Conclusions. We also present the results of the reanalysis of ϵ Ori using our grid to demonstrate the benefits of databases of precalculated models. Our analysis succeeded in reproducing the best-fit parameter ranges of the original study, although our results favor the higher end of the mass-loss range and a lower level of clumping. Our results indirectly suggest that the resonance lines in the UV range are strongly affected by the velocity-space porosity, as has been suggested by recent theoretical calculations and numerical simulations.
The TUDID Study – Background and Design of a Prospective
Cohort
Authors: Jaghutriz Benjamin Assad , Wagner Robert , Kullmann Stephanie , Fritsche Louise , Eckstein Sabine S. , Dannecker Corinna , Willmann Caroline , Randrianarisoa Elko , Lehn-Stefan Angela , Hieronimus Anja , Hudak Sarah , Vosseler Dorothea , Lamprinou Apostolia , Huber Philipp , Vosseler Andreas , Willmann Gabriel , Heyne Nils , Wolff Diana , Stefan Norbert , Häring Hans-Ulrich , Birkenfeld Andreas L. , Peter Andreas , Fritsche Andreas , Heni Martin 
Published: September 2020

AbstractPrevalence of both type 1 and type 2 diabetes mellitus is growing worldwide and
one major cause for morbidity and mortality. However, not every patient develops
diabetes-related complications, but causes for the individual susceptibility are
still not fully understood. As a platform to address this, we initiated the
TUDID (TUebingen DIabetes Database) study, a prospective, monocentric,
observational study that includes adults with diabetes mellitus who are treated
in the inpatient clinic of a University Hospital in southern Germany. Besides a
thorough clinical examination and extensive laboratory tests (with integrated
biobanking), major study focuses are the kidneys, the eyes, the vasculature as
well as cognition and mood where standardized investigations for early stages
for diabetes complications are performed. Analyses of the data generated by this
precise characterization of diabetes-related complications will contribute to
our understanding of the development and course of such complications, and thus
facilitate the implementation of tailored treatment options that can reduce the
risk and severity of diabetes-related complications.