bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of flying cars in sustainable mobility
Authors: Kasliwal Akshat , Furbush Noah J. , Gawron James H. , McBride James R. , Wallington Timothy J. , De Kleine Robert D. , Kim Hyung Chul , Keoleian Gregory A. 
Published: April 2019

AbstractInterest and investment in electric vertical takeoff and landing aircraft (VTOLs), commonly known as flying cars, have grown significantly. However, their sustainability implications are unclear. We report a physics-based analysis of primary energy and greenhouse gas (GHG) emissions of VTOLs vs. ground-based cars. Tilt-rotor/duct/wing VTOLs are efficient when cruising but consume substantial energy for takeoff and climb; hence, their burdens depend critically on trip distance. For our base case, traveling 100 km (point-to-point) with one pilot in a VTOL results in well-to-wing/wheel GHG emissions that are 35% lower but 28% higher than a one-occupant internal combustion engine vehicle (ICEV) and battery electric vehicle (BEV), respectively. Comparing fully loaded VTOLs (three passengers) with ground-based cars with an average occupancy of 1.54, VTOL GHG emissions per passenger-kilometer are 52% lower than ICEVs and 6% lower than BEVs. VTOLs offer fast, predictable transportation and could have a niche role in sustainable mobility.
The sponge microbiome within the greater coral reef microbial metacommunity
Authors: Cleary Daniel F. R. , Swierts Thomas , Coelho Francisco J. R. C. , Polónia Ana R. M. , Huang Yusheng M. , Ferreira Marina R. S. , Putchakarn Sumaitt , Carvalheiro Luis , van der Ent Esther , Ueng Jinn-Pyng , Gomes Newton C. M. , de Voogd Nicole J. 
Published: April 2019

AbstractMuch recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought.
Global identification of functional microRNA-mRNA interactions in Drosophila
Authors: Wessels Hans-Hermann , Lebedeva Svetlana , Hirsekorn Antje , Wurmus Ricardo , Akalin Altuna , Mukherjee Neelanjan , Ohler Uwe 
Published: April 2019

AbstractMicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. Here, we generated a transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data. Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila.
Mapping vaccination coverage to explore the effects of delivery mechanisms and inform vaccination strategies
Authors: Utazi C. Edson , Thorley Julia , Alegana Victor A. , Ferrari Matthew J. , Takahashi Saki , Metcalf C. Jessica E. , Lessler Justin , Cutts Felicity T. , Tatem Andrew J. 
Published: April 2019

AbstractThe success of vaccination programs depends largely on the mechanisms used in vaccine delivery. National immunization programs offer childhood vaccines through fixed and outreach services within the health system and often, additional supplementary immunization activities (SIAs) are undertaken to fill gaps and boost coverage. Here, we map predicted coverage at 1 × 1 km spatial resolution in five low- and middle-income countries to identify areas that are under-vaccinated via each delivery method using Demographic and Health Surveys data. We compare estimates of the coverage of the third dose of diphtheria-tetanus-pertussis-containing vaccine (DTP3), which is typically delivered through routine immunization (RI), with those of measles-containing vaccine (MCV) for which SIAs are also undertaken. We find that SIAs have boosted MCV coverage in some places, but not in others, particularly where RI had been deficient, as depicted by DTP coverage. The modelling approaches outlined here can help to guide geographical prioritization and strategy design.
Gene correction for SCID-X1 in long-term hematopoietic stem cells
Authors: Pavel-Dinu Mara , Wiebking Volker , Dejene Beruh T. , Srifa Waracharee , Mantri Sruthi , Nicolas Carmencita E. , Lee Ciaran , Bao Gang , Kildebeck Eric J. , Punjya Niraj , Sindhu Camille , Inlay Matthew A. , Saxena Nivedita , DeRavin Suk See , Malech Harry , Roncarolo Maria Grazia , Weinberg Kenneth I. , Porteus Matthew H. 
Published: April 2019

AbstractGene correction in human long-term hematopoietic stem cells (LT-HSCs) could be an effective therapy for monogenic diseases of the blood and immune system. Here we describe an approach for X-linked sSevere cCombined iImmunodeficiency (SCID-X1) using targeted integration of a cDNA into the endogenous start codon to functionally correct disease-causing mutations throughout the gene. Using a CRISPR-Cas9/AAV6 based strategy, we achieve up to 20% targeted integration frequencies in LT-HSCs. As measures of the lack of toxicity we observe no evidence of abnormal hematopoiesis following transplantation and no evidence of off-target mutations using a high-fidelity Cas9 as a ribonucleoprotein complex. We achieve high levels of targeting frequencies (median 45%) in CD34+HSPCs from six SCID-X1 patients and demonstrate rescue of lymphopoietic defect in a patient derived HSPC population in vitro and in vivo. In sum, our study provides specificity, toxicity and efficacy data supportive of clinical development of genome editing to treat SCID-Xl.
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture
Authors: Gelali Eleni , Girelli Gabriele , Matsumoto Masahiro , Wernersson Erik , Custodio Joaquin , Mota Ana , Schweitzer Maud , Ferenc Katalin , Li Xinge , Mirzazadeh Reza , Agostini Federico , Schell John P. , Lanner Fredrik , Crosetto Nicola , Bienko Magda 
Published: April 2019

AbstractDNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface (http://ifish4u.org) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.
Recent summer warming in northwestern Canada exceeds the Holocene thermal maximum
Authors: Porter Trevor J. , Schoenemann Spruce W. , Davies Lauren J. , Steig Eric J. , Bandara Sasiri , Froese Duane G. 
Published: April 2019

AbstractEastern Beringia is one of the few Western Arctic regions where full Holocene climate reconstructions are possible. However, most full Holocene reconstructions in Eastern Beringia are based either on pollen or midges, which show conflicting early Holocene summer temperature histories. This discrepancy precludes understanding the factors that drove past (and potentially future) climate change and calls for independent proxies to advance the debate. We present a ~13.6 ka summer temperature reconstruction in central Yukon, part of Eastern Beringia, using precipitation isotopes in syngenetic permafrost. The reconstruction shows that early Holocene summers were consistently warmer than the Holocene mean, as supported by midges, and a thermal maximum at ~7.6–6.6 ka BP. This maximum was followed by a ~6 ka cooling, and later abruptly reversed by industrial-era warming leading to a modern climate that is unprecedented in the Holocene context and exceeds the Holocene thermal maximum by +1.7 ± 0.7 °C.
Defective homologous recombination DNA repair as therapeutic target in advanced chordoma
Authors: Gröschel Stefan , Hübschmann Daniel , Raimondi Francesco , Horak Peter , Warsow Gregor , Fröhlich Martina , Klink Barbara , Gieldon Laura , Hutter Barbara , Kleinheinz Kortine , Bonekamp David , Marschal Oliver , Chudasama Priya , Mika Jagoda , Groth Marie , Uhrig Sebastian , Krämer Stephen , Heining Christoph , Heilig Christoph E. , Richter Daniela , Reisinger Eva , Pfütze Katrin , Eils Roland , Wolf Stephan , von Kalle Christof , Brandts Christian , Scholl Claudia , Weichert Wilko , Richter Stephan , Bauer Sebastian , Penzel Roland , Schröck Evelin , Stenzinger Albrecht , Schlenk Richard F. , Brors Benedikt , Russell Robert B. , Glimm Hanno , Schlesner Matthias , Fröhling Stefan 
Published: April 2019

AbstractChordomas are rare bone tumors with few therapeutic options. Here we show, using whole-exome and genome sequencing within a precision oncology program, that advanced chordomas (n = 11) may be characterized by genomic patterns indicative of defective homologous recombination (HR) DNA repair and alterations affecting HR-related genes, including, for example, deletions and pathogenic germline variants of BRCA2, NBN, and CHEK2. A mutational signature associated with HR deficiency was significantly enriched in 72.7% of samples and co-occurred with genomic instability. The poly(ADP-ribose) polymerase (PARP) inhibitor olaparib, which is preferentially toxic to HR-incompetent cells, led to prolonged clinical benefit in a patient with refractory chordoma, and whole-genome analysis at progression revealed a PARP1 p.T910A mutation predicted to disrupt the autoinhibitory PARP1 helical domain. These findings uncover a therapeutic opportunity in chordoma that warrants further exploration, and provide insight into the mechanisms underlying PARP inhibitor resistance.
Spontaneous current constriction in threshold switching devices
Authors: Goodwill Jonathan M. , Ramer Georg , Li Dasheng , Hoskins Brian D. , Pavlidis Georges , McClelland Jabez J. , Centrone Andrea , Bain James A. , Skowronski Marek 
Published: April 2019

AbstractThreshold switching devices are of increasing importance for a number of applications including solid-state memories and neuromorphic circuits. Their non-linear characteristics are thought to be associated with a spontaneous (occurring without an apparent external stimulus) current flow constriction but the extent and the underlying mechanism are a subject of debate. Here we use Scanning Joule Expansion Microscopy to demonstrate that, in functional layers with thermally activated electrical conductivity, the current spontaneously and gradually constricts when a device is biased into the negative differential resistance region. We also show that the S-type negative differential resistance I–V characteristics are only a subset of possible solutions and it is possible to have multiple current density distributions corresponding to the same value of the device voltage. In materials with steep dependence of current on temperature the current constriction can occur in nanoscale devices, making this effect relevant for computing applications.
Geometric imaging of borophene polymorphs with functionalized probes
Authors: Liu Xiaolong , Wang Luqing , Li Shaowei , Rahn Matthew S. , Yakobson Boris I. , Hersam Mark C. 
Published: April 2019

AbstractA common characteristic of borophene polymorphs is the presence of hollow hexagons (HHs) in an otherwise triangular lattice. The vast number of possible HH arrangements underlies the polymorphic nature of borophene, and necessitates direct HH imaging to definitively identify its atomic structure. While borophene has been imaged with scanning tunneling microscopy using conventional metal probes, the convolution of topographic and electronic features hinders unambiguous identification of the atomic lattice. Here, we overcome these limitations by employing CO-functionalized atomic force microscopy to visualize structures corresponding to boron-boron covalent bonds. Additionally, we show that CO-functionalized scanning tunneling microscopy is an equivalent and more accessible technique for HH imaging, confirming the v1/5 and v1/6 borophene models as unifying structures for all observed phases. Using this methodology, a borophene phase diagram is assembled, including a transition from rotationally commensurate to incommensurate phases at high growth temperatures, thus corroborating the chemically discrete nature of borophene.
Efficient allelic-drive in Drosophila
Authors: Guichard Annabel , Haque Tisha , Bobik Marketta , Xu Xiang-Ru S. , Klanseck Carissa , Kushwah Raja Babu Singh , Berni Mateus , Kaduskar Bhagyashree , Gantz Valentino M. , Bier Ethan 
Published: April 2019

AbstractGene-drive systems developed in several organisms result in super-Mendelian inheritance of transgenic insertions. Here, we generalize this “active genetic” approach to preferentially transmit allelic variants (allelic-drive) resulting from only a single or a few nucleotide alterations. We test two configurations for allelic-drive: one, copy-cutting, in which a non-preferred allele is selectively targeted for Cas9/guide RNA (gRNA) cleavage, and a more general approach, copy-grafting, that permits selective inheritance of a desired allele located in close proximity to the gRNA cut site. We also characterize a phenomenon we refer to as lethal-mosaicism that dominantly eliminates NHEJ-induced mutations and favors inheritance of functional cleavage-resistant alleles. These two efficient allelic-drive methods, enhanced by lethal mosaicism and a trans-generational drive process we refer to as “shadow-drive”, have broad practical applications in improving health and agriculture and greatly extend the active genetics toolbox.
A database seed for a community-driven material intensity research platform
Authors: Heeren Niko , Fishman Tomer 
Published: April 2019

AbstractThe data record contains Material Intensity data for buildings (MI). MI coefficients are often used for different types of analysis of socio-economic systems and in particular for environmental assessments. Until now, MI values were compiled and reported ad-hoc with few cross-study comparisons. We extracted and converted more than 300 material intensity data points from 33 studies and provide the results in a comprehensive and harmonized database. Material intensity is reported as kilograms per gross floor area for 32 materials as primary data points. Furthermore, we augmented the data with secondary attributes for regional information, such as climate and socioeconomic indicators. The data are hosted on the version control platform GitHub using accessible data formats and providing detailed contribution guidelines. This “database seed” facilitates data analysis, accessibility, and future data contributions by the research community. In the Technical Validation we illustrate that consistency of the data and opportunities for further analysis. This database can serve scientists from various disciplines as a benchmark to determine typical ranges and identify outliers.
Therapeutic effects of a single injection of human umbilical mesenchymal stem cells on acute and chronic colitis in mice
Authors: Chang Yu-Lung , Lo Huei-Yu , Cheng Shun-Ping , Chang Kuo-Ting , Lin Xiu-Fang , Lee Sheng-Ping , Hsieh Ming-Fa , Chan Chin-Kan 
Published: April 2019

AbstractMultiple injections of bone marrow mesenchymal stem cells (BMMSCs) have been used for treatment of chronic colitis in mice. We aimed to report the therapeutic effects of a single injection of human umbilical cord mesenchymal stem cells (hUCMSCs) on acute and chronic colitis. Male C57BL/6JNarl mice were divided into control, phosphate-buffered saline (PBS), and hUCMSCs treated groups, respectively. Acute and chronic colitis were induced in the mice (except controls) using 3% dextran sulfate sodium (DSS). The mice in the hUCMSCs group underwent a single injection of hUCMSCs. The disease activity index (DAI), colon length, histology, colon inflammation score, in vivo stem cells images, and blood cytokine levels were recorded. The DAI was significantly higher in the hUCMSCs group than in the control group and lower than in the PBS group on all days. The colon length was significantly longer and the colon inflammation score was significantly lower in the hUCMSCs group than in the PBS group on days 8 and 25. IL17A, Gro-α, MIP-1α, MIP-2, and eotaxin were significantly lower in the hUCMSCs group than in the PBS group on days 8 and 25. Single-injection hUCMSCs improved DSS–induced acute colitis and decreased progression of acute colitis to chronic colitis.
Impact of systemic vascular risk factors on the choriocapillaris using optical coherence tomography angiography in patients with systemic hypertension
Authors: Chua Jacqueline , Chin Calvin Woon Loong , Tan Bingyao , Wong Si Han , Devarajan Kavya , Le Thu-Thao , Ang Marcus , Wong Tien Yin , Schmetterer Leopold 
Published: April 2019

AbstractWe investigated the characteristics of the choriocapillaris flow voids using optical coherence tomography angiography (OCTA) in 85 patients (164 eyes) with hypertension (mean ± SD age, 56 ± 11 years; 45% women; 20% poorly controlled BP; 16% diabetes) who are without ocular diseases and determined possible correlations with systemic vascular risk factors. Data on 24-hour ambulatory blood pressure (BP), serum creatinine, and urine microalbumin/creatinine ratio (MCR) were collected. Estimated glomerular filtration rate (eGFR) was calculated based on CKD-EPI Creatinine Equation. OCTA imaging (6 × 6 mm scans; AngioVue) with quantitative microvascular analysis of the choriocapillaris was performed. Linear regression was used to investigate the association of systemic risk factors with area (percentage), size (pixels) and number of choriocapillaris flow voids. Diabetes (β = 0.33; 95% CI, 0.02 to 0.63) and daytime systolic BP (β = −0.13; 95% CI, −0.24 to −0.02) were associated with areas of flow voids. Age (β = 0.21; 95% CI, 0.06 to 0.36) and daytime diastolic BP (β = −0.18; 95% CI, −0.34 to −0.02) were associated with size of flow voids. Age (β = −21.21; 95% CI, −31.79 to −10.63) and nighttime diastolic BP (β = 13.89; 95% CI, 0.61 to 27.17) were associated with number of flow voids. Kidney parameters were not associated with any features of flow voids. In patients with hypertension, a higher BP appeared to increase blood flow in the choriocapillaris which needs to be considered when using the OCTA to study eye diseases in hypertensives.
The free energy landscape of the oncogene protein E7 of human papillomavirus type 16 reveals a complex interplay between ordered and disordered regions
Authors: Kukic Predrag , Lo Piccolo Giuseppe Mattia , Nogueira Marcela O. , Svergun Dmitri I. , Vendruscolo Michele , Felli Isabella C. , Pierattelli Roberta 
Published: April 2019

AbstractWhen present, structural disorder makes it very challenging to characterise the conformational properties of proteins. This is particularly the case of proteins, such as the oncogene protein E7 of human papillomavirus type 16, which contain both ordered and disordered domains, and that can populate monomeric and oligomeric states under physiological conditions. Nuclear magnetic resonance (NMR) spectroscopy is emerging as a powerful method to study these complex systems, most notably in combination with molecular dynamics simulations. Here we use NMR chemical shifts and residual dipolar couplings as structural restraints in replica-averaged molecular dynamics simulations to determine the free energy landscape of E7. This landscape reveals a complex interplay between a folded but highly dynamical C-terminal domain and a disordered N-terminal domain that forms transient secondary and tertiary structures, as well as an equilibrium between a high-populated (98%) dimeric state and a low-populated (2%) monomeric state. These results provide compelling evidence of the complex conformational heterogeneity associated with the behaviour and interactions of this disordered protein associated with disease.
GCR1 and GPA1 coupling regulates nitrate, cell wall, immunity and light responses in Arabidopsis
Authors: Chakraborty Navjyoti , Kanyuka Kostya , Jaiswal Dinesh Kumar , Kumar Abhineet , Arora Vivek , Malik Aakansha , Gupta Neha , Hooley Richard , Raghuram Nandula 
Published: April 2019

AbstractG-protein signaling components have been attributed many biological roles in plants, but the extent of involvement of G-protein coupled receptor 1 (GCR1) with the Gα (GPA1) remained unknown. To address this, we have performed transcriptomic analyses on Arabidopsis gpa1-5gcr1-5 double mutant and identified 656 differentially expressed genes (DEGs). MapMan and Gene Ontology analyses revealed global transcriptional changes associated with external stimulus, cell wall organization/biogenesis and secondary metabolite process among others. Comparative transcriptomic analyses using the single and double mutants of gcr1-5 and gpa1-5 identified 194, 139 and 391 exclusive DEGs respectively, whereas 64 DEGs were common to all three mutants. Further, pair wise comparison of DEGs of double mutant with single mutants of gcr1-5 or gpa1-5 showed about one-third and over half common DEGs, respectively. Further analysis of the DEGs exclusive to the double mutant using protein-protein interaction networks revealed molecular complexes associated with nitrate and light signaling and plant-pathogen interactions among others. Physiological and molecular validation of nitrate-response revealed the sensitivity of germination to low N in the double mutant and differential expression of nitrate transporter (and nitrate reductase in all three mutants). Taken together, GCR1 and GPA1 work in partnership as well as independently to regulate different pathways.