bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA-assembled superconducting 3D nanoscale architectures
Authors: Shani Lior , Michelson Aaron N. , Minevich Brian , Fleger Yafit , Stern Michael , Shaulov Avner , Yeshurun Yosef , Gang Oleg 
Published: November 2020

AbstractStudies of nanoscale superconducting structures have revealed various physical phenomena and led to the development of a wide range of applications. Most of these studies concentrated on one- and two-dimensional structures due to the lack of approaches for creation of fully engineered three-dimensional (3D) nanostructures. Here, we present a ‘bottom-up’ method to create 3D superconducting nanostructures with prescribed multiscale organization using DNA-based self-assembly methods. We assemble 3D DNA superlattices from octahedral DNA frames with incorporated nanoparticles, through connecting frames at their vertices, which result in cubic superlattices with a 48 nm unit cell. The superconductive superlattice is formed by converting a DNA superlattice first into highly-structured 3D silica scaffold, to turn it from a soft and liquid-environment dependent macromolecular construction into a solid structure, following by its coating with superconducting niobium (Nb). Through low-temperature electrical characterization we demonstrate that this process creates 3D arrays of Josephson junctions. This approach may be utilized in development of a variety of applications such as 3D Superconducting Quantum interference Devices (SQUIDs) for measurement of the magnetic field vector, highly sensitive Superconducting Quantum Interference Filters (SQIFs), and parametric amplifiers for quantum information systems.
A tunable LIC1-adaptor interaction modulates dynein activity in a cargo-specific manner
Authors: Lee In-Gyun , Cason Sydney E. , Alqassim Saif S. , Holzbaur Erika L. F. , Dominguez Roberto 
Published: November 2020

AbstractCytoplasmic dynein-1 (dynein) is the motor responsible for most retrograde transport of cargoes along microtubules in eukaryotic cells, including organelles, mRNA and viruses. Cargo selectivity and activation of processive motility depend on a group of so-called “activating adaptors” that link dynein to its general cofactor, dynactin, and cargoes. The mechanism by which these adaptors regulate dynein transport is poorly understood. Here, based on crystal structures, quantitative binding studies, and in vitro motility assays, we show that BICD2, CRACR2a, and HOOK3, representing three subfamilies of unrelated adaptors, interact with the same amphipathic helix of the dynein light intermediate chain-1 (LIC1). While the hydrophobic character of the interaction is conserved, the three adaptor subfamilies use different folds (coiled-coil, EF-hand, HOOK domain) and different surface contacts to bind the LIC1 helix with affinities ranging from 1.5 to 15.0 μM. We propose that a tunable LIC1-adaptor interaction modulates dynein’s motility in a cargo-specific manner.
Estimation of global tropical cyclone wind speed probabilities using the STORM dataset
Authors: Bloemendaal Nadia , de Moel Hans , Muis Sanne , Haigh Ivan D. , Aerts Jeroen C. J. H. 
Published: November 2020

AbstractTropical cyclones (TC) are one of the deadliest and costliest natural disasters. To mitigate the impact of such disasters, it is essential to know extreme exceedance probabilities, also known as return periods, of TC hazards. In this paper, we demonstrate the use of the STORM dataset, containing synthetic TCs equivalent of 10,000 years under present-day climate conditions, for the calculation of TC wind speed return periods. The temporal length of the STORM dataset allows us to empirically calculate return periods up to 10,000 years without fitting an extreme value distribution. We show that fitting a distribution typically results in higher wind speeds compared to their empirically derived counterparts, especially for return periods exceeding 100-yr. By applying a parametric wind model to the TC tracks, we derive return periods at 10 km resolution in TC-prone regions. The return periods are validated against observations and previous studies, and show a good agreement. The accompanying global-scale wind speed return period dataset is publicly available and can be used for high-resolution TC risk assessments.
3D micro-organisation printing of mammalian cells to generate biological tissues
Authors: Jeffries Gavin D. M. , Xu Shijun , Lobovkina Tatsiana , Kirejev Vladimir , Tusseau Florian , Gyllensten Christoffer , Singh Avadhesh Kumar , Karila Paul , Moll Lydia , Orwar Owe 
Published: November 2020

AbstractSignificant strides have been made in the development of in vitro systems for disease modelling. However, the requirement of microenvironment control has placed limitations on the generation of relevant models. Herein, we present a biological tissue printing approach that employs open-volume microfluidics to position individual cells in complex 2D and 3D patterns, as well as in single cell arrays. The variety of bioprinted cell types employed, including skin epithelial (HaCaT), skin cancer (A431), liver cancer (Hep G2), and fibroblast (3T3-J2) cells, all of which exhibited excellent viability and survivability, allowing printed structures to rapidly develop into confluent tissues. To demonstrate a simple 2D oncology model, A431 and HaCaT cells were printed and grown into tissues. Furthermore, a basic skin model was established to probe drug response. 3D tissue formation was demonstrated by co-printing Hep G2 and 3T3-J2 cells onto an established fibroblast layer, the functionality of which was probed by measuring albumin production, and was found to be higher in comparison to both 2D and monoculture approaches. Bioprinting of primary cells was tested using acutely isolated primary rat dorsal root ganglia neurons, which survived and established processes. The presented technique offers a novel open-volume microfluidics approach to bioprint cells for the generation of biological tissues.
Transcriptome analysis of xa5-mediated resistance to bacterial leaf streak in rice (Oryza sativa L.)
Authors: Xie Xiaofang , Chen Zhiwei , Zhang Binghui , Guan Huazhong , Zheng Yan , Lan Tao , Zhang Jing , Qin Mingyue , Wu Weiren 
Published: November 2020

AbstractBacterial leaf steak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease in rice production. The resistance to BLS in rice is a quantitatively inherited trait, of which the molecular mechanism is still unclear. It has been proved that xa5, a recessive bacterial blast resistance gene, is the most possible candidate gene of the QTL qBlsr5a for BLS resistance. To study the molecular mechanism of xa5 function in BLS resistance, we created transgenic lines with RNAi of Xa5 (LOC_Os05g01710) and used RNA-seq to analyze the transcriptomes of a Xa5-RNAi line and the wild-type line at 9 h after inoculation with Xoc, with the mock inoculation as control. We found that Xa5-RNAi could (1) increase the resistance to BLS as expected from xa5; (2) alter (mainly up-regulate) the expression of hundreds of genes, most of which were related to disease resistance; and (3) greatly enhance the response of thousands of genes to Xoc infection, especially of the genes involved in cell death pathways. The results suggest that xa5 is the cause of BLS-resistance of QTL qBlsr5a and it displays BLS resistance effect probably mainly because of the enhanced response of the cell death-related genes to Xoc infection.
From bridges to cycles in spectroscopic networks
Authors: Árendás P. , Furtenbacher T. , Császár A. G. 
Published: November 2020

AbstractSpectroscopic networks provide a particularly useful representation of observed rovibronic transitions of molecules, as well as of related quantum states, whereby the states form a set of vertices connected by the measured transitions forming a set of edges. Among their several uses, SNs offer a practical framework to assess data in line-by-line spectroscopic databases. They can be utilized to help detect flawed transition entries. Methods which achieve this validation work for transitions taking part in at least one cycle in a measured spectroscopic network but they do not work for bridges. The concept of two-edge-connectivity of graph theory, introduced here to high-resolution spectroscopy, offers an elegant approach that facilitates putting the maximum number of bridges, if not all, into at least one cycle. An algorithmic solution is shown how to augment an existing spectroscopic network with a minimum number of new spectroscopic measurements selected according to well-defined guidelines. In relation to this, two metrics are introduced, ranking measurements based on their utility toward achieving the goal of two-edge-connectivity. Utility of the new concepts are demonstrated on spectroscopic data of $$^{14} {\text {NH}}_3$$

14

NH
3

.
Detection of stratospheric gravity waves induced by the total solar eclipse of July 2, 2019
Authors: Colligan Thomas , Fowler Jennifer , Godfrey Jaxen , Spangrude Carl 
Published: November 2020

AbstractAtmospheric gravity waves generated by an eclipse were first proposed in 1970. Despite numerous efforts since, there has been no definitive evidence for eclipse generated gravity waves in the lower to middle atmosphere. Measuring wave characteristics produced by a definite forcing event such as an eclipse provides crucial knowledge for developing more accurate physical descriptions of gravity waves. These waves are fundamental to the transport of energy and momentum throughout the atmosphere and their parameterization or simulation in numerical models provides increased accuracy to forecasts. Here, we present the findings from a radiosonde field campaign carried out during the total solar eclipse of July 2, 2019 aimed at detecting eclipse-driven gravity waves in the stratosphere. This eclipse was the source of three stratospheric gravity waves. The first wave (eclipse wave #1) was detected 156 min after totality and the other two waves were detected 53 and 62 min after totality (eclipse waves #2 and #3 respectively) using balloon-borne radiosondes. Our results demonstrate both the importance of field campaign design and the limitations of currently accepted balloon-borne analysis techniques for the detection of stratospheric gravity waves.
Assessing the climate suitability and potential economic impacts of Oak wilt in Canada
Authors: Pedlar John H. , McKenney Daniel W. , Hope Emily , Reed Sharon , Sweeney Jon 
Published: November 2020

AbstractWe assess risks posed by oak wilt—a disease caused by the fungal pathogenBretziella fagacearum. Though not currently found in Canada, our distribution models indicate that suitable climate conditions currently occur in southern Ontario forB. fagacearumand two of its main insect dispersal vectors,Colopterus truncatusandCarpophilus sayi.Climate habitat for these species is projected to expand northward under climate change, with much of the oak range in eastern Canada becoming climatically suitable within the next two decades. Potential costs for the removal and replacement of oak street trees ranged from CDN$266 to $420 million, with variation related to uncertainty in costs, rate of tree replacement, and city-level estimates of oak street tree density. The value of standing oak timber in eastern Canada was estimated at CDN$126 million using provincial stumpage fees and as a CDN$24 million annual contribution to national Gross Domestic Product (GDP) when calculated using a combination of economic and forestry product statistics. These values can help inform the scale of eradication and/or management efforts in the event of future oak wilt introductions.
Importance of the pyrolysis for microstructure and superconducting properties of CSD-grown GdBa2Cu3O7−x-HfO2 nanocomposite films by the ex-situ approach
Authors: Cayado Pablo , Rijckaert Hannes , Bruneel Els , Erbe Manuela , Hänisch Jens , Van Driessche Isabel , Holzapfel Bernhard 
Published: November 2020

AbstractFor the first time, GdBa2Cu3O7−x nanocomposites were prepared by chemical solution deposition following the ex-situ approach. In particular, ~ 220 nm GdBa2Cu3O7−x-HfO2 (GdBCO-HfO2) nanocomposite films were fabricated starting from a colloidal solution of 5 mol% HfO2 nanoparticles. Hereby, one of the main challenges is to avoid the accumulation of the nanoparticles at the substrate interface during the pyrolysis, which would later prevent the epitaxial nucleation of the GdBCO grains. Therefore, the effect of pyrolysis processing parameters such as heating ramp and temperature on the homogeneity of the nanoparticle distribution has been investigated. By increasing the heating ramp to 300 °C/h and decreasing the final temperature to 300 °C, a more homogenous nanoparticle distribution was achieved. This translates into improved superconducting properties of the grown films reaching critical temperatures (Tc) of 94.5 K and self-field critical current densities ($${J}_{\mathrm{c}}^{\mathrm{sf}}$$

J

c

sf

) at 77 K of 2.1 MA/cm2 with respect to films pyrolyzed at higher temperatures or lower heating ramps.
Expanded and activated allogeneic NK cells are cytotoxic against B-chronic lymphocytic leukemia (B-CLL) cells with sporadic cases of resistance
Authors: Calvo Tania , Reina-Ortiz Chantal , Giraldos David , Gascón María , Woods Daniel , Asenjo Judit , Marco-Brualla Joaquín , Azaceta Gemma , Izquierdo Isabel , Palomera Luis , Sánchez-Martínez Diego , Marzo Isabel , Naval Javier , Vilches Carlos , Villalba Martín , Anel Alberto 
Published: November 2020

AbstractAdoptive transfer of allogeneic natural killer (NK) cells is becoming a credible immunotherapy for hematological malignancies. In the present work, using an optimized expansion/activation protocol of human NK cells, we generate expanded NK cells (eNK) with increased expression of CD56 and NKp44, while maintaining that of CD16. These eNK cells exerted significant cytotoxicity against cells from 34 B-CLL patients, with only 1 sample exhibiting resistance. This sporadic resistance did not correlate with match between KIR ligands expressed by the eNK cells and the leukemic cells, while cells with match resulted sensitive to eNK cells. This suggests that KIR mismatch is not relevant when expanded NK cells are used as effectors. In addition, we found two examples of de novo resistance to eNK cell cytotoxicity during the clinical course of the disease. Resistance correlated with KIR-ligand match in one of the patients, but not in the other, and was associated with a significant increase in PD-L1 expression in the cells from both patients. Treatment of one of these patients with idelalisib correlated with the loss of PD-L1 expression and with re-sensitization to eNK cytotoxicity. We confirmed the idelalisib-induced decrease in PD-L1 expression in the B-CLL cell line Mec1 and in cultured cells from B-CLL patients. As a main conclusion, our results reinforce the feasibility of using expanded and activated allogeneic NK cells in the treatment of B-CLL.
Single nucleotide polymorphisms in LCAT may contribute to dyslipidaemia in HIV-infected individuals on HAART in a Ghanaian population
Authors: Bani Simon Bannison , Danquah Kwabena Owusu , Obirikorang Christian , Owiredu William K. B. A. , Quaye Lawrence , Muonir Der Edmund , Acheampong Emmanuel , Adams Yussif , Dapare Peter Paul M. , Banyeh Moses , Anto Enoch Odame , Sakyi Samuel Asamoah 
Published: November 2020

AbstractHighly active antiretroviral therapy (HAART) is known to cause lipid abnormalities such as dyslipidaemia in HIV-infected individuals. Yet, dyslipidaemia may not independently occur as it may be worsened by single nucleotide polymorphisms (SNPs) in lecithin cholesterol acyltransferase (LCAT) and lipoprotein lipase (LPL). This case–control study was conducted in three-selected hospitals in the Northern part of Ghana. The study constituted a total of 118 HIV-infected participants aged 19–71 years, who had been on HAART for 6–24 months. Dyslipidaemia was defined based on the NCEP-ATP III criteria. HIV-infected individuals on HAART with dyslipidaemia were classified as cases while those without dyslipidaemia were grouped as controls. Lipid profile was measured using an automatic clinical chemistry analyzer and genomic DNA was extracted for PCR (GeneAmp PCR System 2700). Overall, the prevalence of dyslipidaemia was 39.0% (46/118). High levels of low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and reduced levels of high-density lipoprotein cholesterol (HDL-C) were observed in all cases. A total of 256 selected PCR amplicons comprising 137LPL(exons 3, 5 and 6) and 119LCAT(exons 1, 4, and 6) were sequenced in 46 samples (Inqaba Biotech). Six (6) clinically significant SNPs were identified in exons 1 and 4 forLCATwhereas 25 non-clinically significant SNPs were identified forLPLin exons 5 and 6. At position 97 forLCATexon 1, there was a deletion of the nucleotide, ‘A’ in 32.5% (13/40) of the sampled population while 67.5% (27/40) of the sample population retained the nucleotide, ‘A’ which was significantly associated with dyslipidaemic outcomes in the study population (p = 0.0004). A total of 25 SNPs were identified in exons 5 and 6 ofLPL; 22 were substitutions, and 3 were insertions. However, none of the 25 SNPs identified inLPLexon 5 and 6 were statistically significant. SNPs in LCAT may independently contribute to dyslipidaemia among Ghanaian HIV-infected individuals on HAART, thus, allowing genetic and/or functional differential diagnosis of dyslipidaemia and creating an opportunity for potentially preventive options.
Hik36–Hik43 and Rre6 act as a two-component regulatory system to control cell aggregation in Synechocystis sp. PCC6803
Authors: Kera Kota , Yoshizawa Yuichiro , Shigehara Takehiro , Nagayama Tatsuya , Tsujii Masaru , Tochigi Saeko , Uozumi Nobuyuki 
Published: November 2020

AbstractIn response to environmental stress the model cyanobacterium, Synechocystis sp. PCC6803 can switch from a planktonic state to autoaggregation and biofilm formation. The precise mechanism of this transition remains unknown. Here we investigated the role of a candidate two-component regulatory system (TCS) in controlling morphological changes, as a way to understand the intermediate molecular steps that are part of the signaling pathway. A bacterial two-hybrid assay showed that the response regulator Rre6 formed a TCS together with a split histidine kinase consisting of Hik36 and Hik43. Individual disruption mutants displayed autoaggregation in a static culture. In contrast, unlike in the wild type, high salinity did not induce biofilm formation in Δhik36, Δhik43 and Δrre6. The expression levels of exopolysaccharide (EPS) production genes were higher in Δhik36 and Δhik43, compared with the wild type, but lower in Δrre6, suggesting that the TCS regulated EPS production in Synechocystis. Rre6 interacted physically with the motor protein PilT2, that is a component of the type IV pilus system. This interaction was enhanced in a phosphomimic version of Rre6. Taken together, Hik36–Hik43–Rre6 function as an upstream component of the pili-related signal transduction cascade and control the prevention of cell adhesion and biofilm formation.
Patient-derived ovarian cancer explants: preserved viability and histopathological features in long-term agitation-based cultures
Authors: Abreu Sofia , Silva Fernanda , Mendes Rita , Mendes Teresa F. , Teixeira Marta , Santo Vítor E. , Boghaert Erwin R. , Félix Ana , Brito Catarina 
Published: November 2020

AbstractOvarian carcinoma (OvC) remains a major therapeutic challenge due to its propensity to develop resistance after an initial response to chemotherapy. Interactions of tumour cells with the surrounding microenvironment play a role in tumour survival, invasion capacity and drug resistance. Cancer models that retain tissue architecture and tumour microenvironment components are therefore essential to understand drug response and resistance mechanisms. Herein, our goal was to develop a long-term OvC patient-derived explant (OvC-PDE) culture strategy in which architecture and cell type heterogeneity of the original tumour would be retained. Samples from 25 patients with distinct OvC types and one with a benign tumour, were cultured for 30 days in agitation-based culture systems with 100% success rate. OvC-PDE cultures retained the original tumour architecture and main cellular components: epithelial cells, fibroblasts and immune cells. Epithelial cells kept their original levels of proliferation and apoptosis. Moreover, the major extracellular components, such as collagen-I and -IV, were retained in explants. OvC-PDE cultures were exposed to standard-of-care chemotherapeutics agents for 2 weeks, attesting the ability of the platform for drug assays employing cyclic drug exposure regimens. We established an OvC-PDE dynamic culture in which tumour architecture and cell type heterogeneity were preserved for the different OvC types, replicating features of the original tumour and compatible with long-term drug exposure for drug efficacy and resistance studies.
Raman spectroscopy reveals age- and sex-related differences in cortical bone from people with osteoarthritis
Authors: Nieuwoudt Michel K. , Shahlori Rayomand , Naot Dorit , Patel Rhea , Holtkamp Hannah , Aguergaray Claude , Watson Maureen , Musson David , Brown Cameron , Dalbeth Nicola , Cornish Jillian , Simpson M. Cather 
Published: November 2020

AbstractBone strength in human cortical bone is determined by the composition and structure of both the mineral and collagen matrices and influenced by factors such as age, gender, health, lifestyle and genetic factors. Age-related changes in the bone matrix are known to result in loss of mechanical strength and increased fragility. In this study we show how Raman spectroscopy, with its exquisite sensitivity to the molecular structure of bone, reveals new insights into age- and sex-related differences. Raman analysis of 18 samples of cortical hip bone obtained from people aged between 47–82 years with osteoarthritis (OA) found subtle changes in the lipid and collagen secondary structure, and the carbonate (CO32−) and phosphate (PO43−) mineral ratios in the bone matrix. Significant differences were observed between older and younger bones, and between older female and older male bones; no significant differences were observed between younger male and female bones. Older female bones presented the lowest mineral to matrix ratios (MMR) and highest CO32−/PO43−ratios, and relative to lipid/collagen –CH2deformation modes at 1450 cm−1they had lowest overall mineral content, higher collagen cross linking and lipid content but lower levels of α-helix collagen structures than older male and younger male and female bones. These observations provided further insight on bone composition changes observed in the bone volume fraction (BV/TV) for the older female bones from microCT measurements on the same samples, while tissue mineral density (TMD) measurements had shown no significant differences between the samples.