bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forest production efficiency increases with growth temperature
Authors: Collalti A. , Ibrom A. , Stockmarr A. , Cescatti A. , Alkama R. , Fernández-Martínez M. , Matteucci G. , Sitch S. , Friedlingstein P. , Ciais P. , Goll D. S. , Nabel J. E. M. S. , Pongratz J. , Arneth A. , Haverd V. , Prentice I. C. 
Published: October 2020

AbstractForest production efficiency (FPE) metric describes how efficiently the assimilated carbon is partitioned into plants organs (biomass production, BP) or—more generally—for the production of organic matter (net primary production, NPP). We present a global analysis of the relationship of FPE to stand-age and climate, based on a large compilation of data on gross primary production and either BP or NPP. FPE is important for both forest production and atmospheric carbon dioxide uptake. We find that FPE increases with absolute latitude, precipitation and (all else equal) with temperature. Earlier findings—FPE declining with age—are also supported by this analysis. However, the temperature effect is opposite to what would be expected based on the short-term physiological response of respiration rates to temperature, implying a top-down regulation of carbon loss, perhaps reflecting the higher carbon costs of nutrient acquisition in colder climates. Current ecosystem models do not reproduce this phenomenon. They consistently predict lower FPE in warmer climates, and are therefore likely to overestimate carbon losses in a warming climate.
A universal method for depositing patterned materials in situ
Authors: Chen Yifan , Hung Siu Fai , Lo Wing Ki , Chen Yang , Shen Yang , Kafenda Kim , Su Jia , Xia Kangwei , Yang Sen 
Published: October 2020

AbstractCurrent techniques of patterned material deposition require separate steps for patterning and material deposition. The complexity and harsh working conditions post serious limitations for fabrication. Here, we introduce a single-step and easy-to-adapt method that can deposit materials in-situ. Its methodology is based on the semiconductor nanoparticle assisted photon-induced chemical reduction and optical trapping. This universal mechanism can be used for depositing a large selection of materials including metals, insulators and magnets, with quality on par with current technologies. Patterning with several materials together with optical-diffraction-limited resolution and accuracy can be achieved from macroscopic to microscopic scale. Furthermore, the setup is naturally compatible with optical microscopy based measurements, thus sample characterisation and material deposition can be realised in-situ. Various devices fabricated with this method in 2D or 3D show it is ready for deployment in practical applications. This method will provide a distinct tool in material technology.
Biofilm dynamics: linking in situ biofilm biomass and metabolic activity measurements in real-time under continuous flow conditions
Authors: Klopper Kyle B. , de Witt Riaan N. , Bester Elanna , Dicks Leon M. T. , Wolfaardt Gideon M. 
Published: October 2020

AbstractThe tools used to study biofilms generally involve either destructive, end-point analyses or periodic measurements. The advent of the internet of things (IoT) era allows circumvention of these limitations. Here we introduce and detail the development of the BioSpec; a modular, nondestructive, real-time monitoring system, which accurately and reliably track changes in biofilm biomass over time. The performance of the system was validated using a commercial spectrophotometer and produced comparable results for variations in planktonic and sessile biomass. BioSpec was combined with the previously developed carbon dioxide evolution measurement system (CEMS) to allow simultaneous measurement of biofilm biomass and metabolic activity and revealed a differential response of these interrelated parameters to changing environmental conditions. The application of this system can facilitate a greater understanding of biofilm mass–function relationships and aid in the development of biofilm control strategies.
High-throughput computational screening for two-dimensional magnetic materials based on experimental databases of three-dimensional compounds
Authors: Torelli Daniele , Moustafa Hadeel , Jacobsen Karsten W. , Olsen Thomas 
Published: October 2020

AbstractWe perform a computational screening for two-dimensional (2D) magnetic materials based on experimental bulk compounds present in the Inorganic Crystal Structure Database and Crystallography Open Database. A recently proposed geometric descriptor is used to extract materials that are exfoliable into 2D derivatives and we find 85 ferromagnetic and 61 antiferromagnetic materials for which we obtain magnetic exchange and anisotropy parameters using density functional theory. For the easy-axis ferromagnetic insulators we calculate the Curie temperature based on a fit to classical Monte Carlo simulations of anisotropic Heisenberg models. We find good agreement with the experimentally reported Curie temperatures of known 2D ferromagnets and identify 10 potentially exfoliable 2D ferromagnets that have not been reported previously. In addition, we find 18 easy-axis antiferromagnetic insulators with several compounds exhibiting very strong exchange coupling and magnetic anisotropy.
Density functional theory-based electric field gradient database
Authors: Choudhary Kamal , Ansari Jaafar N. , Mazin Igor I. , Sauer Karen L. 
Published: October 2020

AbstractThe deviation of the electron density around the nuclei from spherical symmetry determines the electric field gradient (EFG), which can be measured by various types of spectroscopy. Nuclear Quadrupole Resonance (NQR) is particularly sensitive to the EFG. The EFGs, and by implication NQR frequencies, vary dramatically across materials. Consequently, searching for NQR spectral lines in previously uninvestigated materials represents a major challenge. Calculated EFGs can significantly aid at the search’s inception. To facilitate this task, we have applied high-throughput density functional theory calculations to predict EFGs for 15187 materials in the JARVIS-DFT database. This database, which will include EFG as a standard entry, is continuously increasing. Given the large scope of the database, it is impractical to verify each calculation. However, we assess accuracy by singling out cases for which reliable experimental information is readily available and compare them to the calculations. We further present a statistical analysis of the results. The database and tools associated with our work are made publicly available by JARVIS-DFT (https://www.ctcms.nist.gov/~knc6/JVASP.html) and NIST-JARVIS API (http://jarvis.nist.gov/).
Brain activity and transcriptional profiling in mice under chronic jet lag
Authors: Gao Qian , Khan Suliman , Zhang Luoying 
Published: October 2020

AbstractShift work is known to be associated with an increased risk of neurological and psychiatric diseases, but how it contributes to the development of these diseases remains unclear. Chronic jet lag (CJL) induced by shifting light-dark cycles repeatedly is a commonly used protocol to mimic the environmental light/dark changes encountered by shift workers. Here we subjected wildtype mice to CJL and performed positron emission tomography imaging of glucose metabolism to monitor brain activities. We also conducted RNA sequencing using prefrontal cortex and nucleus accumbens tissues from these animals, which are brain regions strongly implicated in the pathology of various neurological and psychiatric conditions. Our results reveal the alterations of brain activities and systematic reprogramming of gene expression in brain tissues under CJL, building hypothesis for how CJL increases the susceptibility to neurological and psychiatric diseases.
The ontology of the anatomy and development of the solitary ascidian Ciona: the swimming larva and its metamorphosis
Authors: Hotta Kohji , Dauga Delphine , Manni Lucia 
Published: October 2020

AbstractCiona robusta(Ciona intestinalistype A), a model organism for biological studies, belongs to ascidians, the main class of tunicates, which are the closest relatives of vertebrates. InCiona, a project on the ontology of both development and anatomy is ongoing for several years. Its goal is to standardize a resource relating each anatomical structure to developmental stages. Today, the ontology is codified until the hatching larva stage. Here, we present its extension throughout the swimming larva stages, the metamorphosis, until the juvenile stages. For standardizing the developmental ontology, we acquired different time-lapse movies, confocal microscope images and histological serial section images for each developmental event from the hatching larva stage (17.5 h post fertilization) to the juvenile stage (7 days post fertilization). Combining these data, we defined 12 new distinct developmental stages (from Stage 26 to Stage 37), in addition to the previously defined 26 stages, referred to embryonic development. The new stages were grouped into four Periods named: Adhesion, Tail Absorption, Body Axis Rotation, and Juvenile. To build the anatomical ontology, 203 anatomical entities were identified, defined according to the literature, and annotated, taking advantage from the high resolution and the complementary information obtained from confocal microscopy and histology. The ontology describes the anatomical entities in hierarchical levels, from the cell level (cell lineage) to the tissue/organ level. Comparing the number of entities during development, we found two rounds on entity increase: in addition to the one occurring after fertilization, there is a second one during the Body Axis Rotation Period, when juvenile structures appear. Vice versa, one-third of anatomical entities associated with the embryo/larval life were significantly reduced at the beginning of metamorphosis. Data was finally integrated within the web-based resource "TunicAnatO", which includes a number of anatomical images and a dictionary with synonyms. This ontology will allow the standardization of data underpinning an accurate annotation of gene expression and the comprehension of mechanisms of differentiation. It will help in understanding the emergence of elaborated structures during both embryogenesis and metamorphosis, shedding light on tissue degeneration and differentiation occurring at metamorphosis.
Manipulation of the gut microbiota by the use of prebiotic fibre does not override a genetic predisposition to heart failure
Authors: Jama Hamdi A. , Fiedler April , Tsyganov Kirill , Nelson Erin , Horlock Duncan , Nakai Michael E. , Kiriazis Helen , Johnson Chad , Du Xiao-Jun , Mackay Charles R. , Marques Francine Z. , Kaye David M. 
Published: October 2020

AbstractIncreasing evidence supports a role for the gut microbiota in the development of cardiovascular diseases such as hypertension and its progression to heart failure (HF). Dietary fibre has emerged as a modulator of the gut microbiota, resulting in the release of gut metabolites called short-chain fatty acids (SCFAs), such as acetate. We have shown previously that fibre or acetate can protect against hypertension and heart disease in certain models. HF is also commonly caused by genetic disorders. In this study we investigated whether the intake of fibre or direct supplementation with acetate could attenuate the development of HF in a genetic model of dilated cardiomyopathy (DCM) due to overexpression of the cardiac specific mammalian sterile 20-like kinase (Mst1). Seven-week-old male mice DCM mice and littermate controls (wild-type, C57BL/6) were fed a control diet (with or without supplementation with 200 mM magnesium acetate in drinking water), or a high fibre diet for 7 weeks. We obtained hemodynamic, morphological, flow cytometric and gene expression data. The gut microbiome was characterised by 16S rRNA amplicon sequencing. Fibre intake was associated with a significant shift in the gut microbiome irrespective of mouse genotype. However, neither fibre or supplementation with acetate were able to attenuate cardiac remodelling or cardiomyocyte apoptosis in Mst1 mice. Furthermore, fibre and acetate did not improve echocardiographic or hemodynamic parameters in DCM mice. These data suggest that although fibre modulates the gut microbiome, neither fibre nor acetate can override a strong genetic contribution to the development of heart failure in the Mst1 model.
Generation of human induced pluripotent stem cell-derived liver buds with chemically defined and animal origin-free media
Authors: Sekine Keisuke , Ogawa Shimpei , Tsuzuki Syusaku , Kobayashi Tatsuya , Ikeda Kazuki , Nakanishi Noriko , Takeuchi Kenta , Kanai Eriko , Otake Yugo , Okamoto Satoshi , Kobayashi Tsuyoshi , Takebe Takanori , Taniguchi Hideki 
Published: October 2020

AbstractAdvances in organoid technology have broadened the number of target diseases and conditions in which human induced pluripotent stem cell (iPSC)-based regenerative medicine can be applied; however, mass production of organoids and the development of chemically defined, animal origin-free (CD-AOF) media and supplements are unresolved issues that hamper the clinical applicability of these approaches. CD-AOF media and supplements ensure the quality and reproducibility of culture systems by lowering lot-to-lot variations and the risk of contamination with viruses or toxins. We previously generated liver organoids from iPSCs, namely iPSC-liver buds (iPSC-LBs), by mimicking the organogenic interactions among hepatocytes, endothelial cells (ECs), and mesenchymal cells (MCs) and recently reported the mass production of iPSC-LBs derived entirely from iPSCs (all iPSC-LBs), which should facilitate their large-scale production for the treatment of liver failure. However, in previous studies we used media originating from animals for differentiation except for the maintenance of undifferentiated iPSCs. Therefore, we developed a CD-AOF medium to generate all iPSC-LBs. We first developed a CD-AOF medium for hepatocytes, ECs, and stage-matched MCs, i.e., septum transversum mesenchyme (STM), in 2D cultures. We next generated all iPSC-LBs by incubating individual cell types in ultra-low attachment micro-dimple plates. The hepatic functions of all iPSC-LBs generated using the CD-AOF medium were equivalent to those of all iPSC-LBs generated using the conventional medium both in vitro and in vivo. Furthermore, we found that this CD-AOF medium could be used in several cell culture settings. Taken together, these results demonstrate the successful development of a CD-AOF medium suitable for all iPSC-LBs. The protocol developed in this study will facilitate the clinical applicability of all iPSC-LBs in the treatment of liver diseases.
SeMSA: a compact super absorber optimised for broadband, low-frequency noise attenuation
Authors: McKay Andrew , Davis Ian , Killeen Jack , Bennett Gareth J. 
Published: October 2020

AbstractThe attenuation of low-frequency broadband noise in a light, small form-factor is an intractable challenge. In this paper, a new technology is presented which employs the highly efficient visco-thermal loss mechanism of a micro-perforated plate (MPP) and successfully lowers its frequency response by combining it with decorated membrane resonators (DMR). Absorption comes from the membranes but primarily from the MPP, as the motion of the two membranes causes a pressure differential across the MPP creating airflow through the perforations. This combination of DMR and MPP has led to the Segmented Membrane Sound Absorber (SeMSA) design, which is extremely effective at low-frequency broadband sound absorption and which can achieve this at deep sub-wavelength thicknesses. The technology is compared to other absorbers to be found in the literature and the SeMSA outperforms them all in either the 20–1000 Hz or 20–1200 Hz range for depths of up to 120 mm. This was verified through analytical, finite element and experimental analyses.
Late first trimester circulating microparticle proteins predict the risk of preeclampsia < 35 weeks and suggest phenotypic differences among affected cases
Authors: McElrath Thomas F. , Cantonwine David E. , Gray Kathryn J. , Mirzakhani Hooman , Doss Robert C. , Khaja Najmuddin , Khalid Malik , Page Gail , Brohman Brian , Zhang Zhen , Sarracino David , Rosenblatt Kevin P. 
Published: October 2020

AbstractWe hypothesize that first trimester circulating micro particle (CMP) proteins will define preeclampsia risk while identifying clusters of disease subtypes among cases. We performed a nested case–control analysis among women with and without preeclampsia. Cases diagnosed < 34 weeks’ gestation were matched to controls. Plasma CMPs were isolated via size exclusion chromatography and analyzed using global proteome profiling based on HRAM mass spectrometry. Logistic models then determined feature selection with best performing models determined by cross-validation. K-means clustering examined cases for phenotypic subtypes and biological pathway enrichment was examined. Our results indicated that the proteins distinguishing cases from controls were enriched in biological pathways involved in blood coagulation, hemostasis and tissue repair. A panel consisting of C1RL, GP1BA, VTNC, and ZA2G demonstrated the best distinguishing performance (AUC of 0.79). Among the cases of preeclampsia, two phenotypic sub clusters distinguished cases; one enriched for platelet degranulation and blood coagulation pathways and the other for complement and immune response-associated pathways (corrected p < 0.001). Significantly, the second of the two clusters demonstrated lower gestational age at delivery (p = 0.049), increased protein excretion (p = 0.01), more extreme laboratory derangement (p < 0.0001) and marginally increased diastolic pressure (p = 0.09). We conclude that CMP-associated proteins at 12 weeks’ gestation predict the overall risk of developing early preeclampsia and indicate distinct subtypes of pathophysiology and clinical morbidity.
Analysis of vasovagal syncope in the blood collection room in patients undergoing phlebotomy
Authors: Yoshimoto Akira , Yasumoto Atsushi , Kamiichi Yuko , Shibayama Haruna , Sato Masaya , Misawa Yoshiki , Morita Kazuharu , Ono Yoshikazu , Sone Shinji , Satoh Tomoaki , Yatomi Yutaka 
Published: October 2020

AbstractVasovagal syncope (VVS) is well-known to occur in patients undergoing phlebotomy, however, there have been no large-scale studies of the incidence of VVS in the blood collection room. The aim of our present retrospective study was to investigate the conditions of phlebotomy and determine the incidence/factors predisposing to the development of VVS. We investigated 677,956 phlebotomies performed in outpatients in the blood collection room, to explore factors predisposing to the development of VVS. Our analysis revealed an overall incidence of VVS of 0.004% and suggested that use of more than 5 blood collection tubes and a waiting time of more than 15 min were associated with a higher risk of VVS. The odds ratios of these factors were 8.10 (95% CI 3.76–17.50) and 3.69 (95% CI 0.87–15.60), respectively. This is the large-scale study to analyze factors of the development of VVS in the blood collection room, and according to our results, use of a large number of blood collection tubes and a prolonged waiting time for phlebotomy may be risk factors for the development of VVS.
Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction
Authors: Tong Li , Wu Po-Yen , Phan John H. , Hassazadeh Hamid R. ,   SEQC Consortium, Jones Wendell D. , Shi Leming , Fischer Matthias , Mason Christopher E. , Li Sheng , Xu Joshua , Shi Wei , Wang Jian , Thierry-Mieg Jean , Thierry-Mieg Danielle , Hertwig Falk , Berthold Frank , Hero Barbara , Liao Yang , Smyth Gordon K. , Kreil David , Łabaj Paweł P. , Megherbi Dalila , Schroth Gary , Fang Hong , Tong Weida , Wang May D. 
Published: October 2020

AbstractTo use next-generation sequencing technology such as RNA-seq for medical and health applications, choosing proper analysis methods for biomarker identification remains a critical challenge for most users. The US Food and Drug Administration (FDA) has led the Sequencing Quality Control (SEQC) project to conduct a comprehensive investigation of 278 representative RNA-seq data analysis pipelines consisting of 13 sequence mapping, three quantification, and seven normalization methods. In this article, we focused on the impact of the joint effects of RNA-seq pipelines on gene expression estimation as well as the downstream prediction of disease outcomes. First, we developed and applied three metrics (i.e., accuracy, precision, and reliability) to quantitatively evaluate each pipeline’s performance on gene expression estimation. We then investigated the correlation between the proposed metrics and the downstream prediction performance using two real-world cancer datasets (i.e., SEQC neuroblastoma dataset and the NIH/NCI TCGA lung adenocarcinoma dataset). We found that RNA-seq pipeline components jointly and significantly impacted the accuracy of gene expression estimation, and its impact was extended to the downstream prediction of these cancer outcomes. Specifically, RNA-seq pipelines that produced more accurate, precise, and reliable gene expression estimation tended to perform better in the prediction of disease outcome. In the end, we provided scenarios as guidelines for users to use these three metrics to select sensible RNA-seq pipelines for the improved accuracy, precision, and reliability of gene expression estimation, which lead to the improved downstream gene expression-based prediction of disease outcome.
Microbial community dynamics in phyto-thermotherapy baths viewed through next generation sequencing and metabolomics approach
Authors: Franciosi Elena , Narduzzi Luca , Paradiso Antonella , Carlin Silvia , Tuohy Kieran , Beretta Alberto , Mattivi Fulvio 
Published: October 2020

AbstractPhyto-thermotherapy is a treatment consisting in immersing oneself in baths of self-heating alpine grass, to benefit of the heat and rich aromatic components released by the process. The aim of this study was to characterize the bacterial and fungal diversity of three phyto-thermal baths (PTB) performed in three different months, and to compare the data with the profile of the volatile organic compounds (VOCs) of the process. All the data collected showed that PTBs were structured in two stages: the first three days were characterised by an exponential rise of the temperature, a fast bacterial development, higher microbial diversity and higher concentrations of plant aliphatic hydrocarbons. The second stage was characterised by a stable high temperature, shrinkage of the microbial diversity with a predominance of few bacterial and fungi species and higher concentrations of volatiles of microbial origin. Erwinia was the dominant microbial species during the first stage and probably responsible of the self-heating process. In conclusion, PTBs has shown both similarities with common self-heating processes and important peculiarities such as the absence of pathogenic bacteria and the dominance of plant terpenoids with health characteristics among the VOCs confirming the evidence of beneficial effects in particular in the first three days.