bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ex vivo rescue of recombinant very virulent IBDV using a RNA polymerase II driven system and primary chicken bursal cells
Authors: Cubas-Gaona Liliana L. , Trombetta Romane , Courtillon Céline , Li Kai , Qi Xiaole , Wang Xiaomei , Lotmani Sofiane , Keita Alassane , Amelot Michel , Eterradossi Nicolas , Soubies Sébastien Mathieu 
Published: August 2020

AbstractInfectious Bursal Disease Virus (IBDV), a member of the Birnaviridae family, causes an immunosuppressive disease in young chickens. Although several reverse genetics systems are available for IBDV, the isolation of most field-derived strains, such as very virulent IBDV (vvIBDV) and their subsequent rescue, has remained challenging due to the lack of replication of those viruses in vitro. Such rescue required either the inoculation of animals, embryonated eggs, or the introduction of mutations in the capsid protein (VP2) hypervariable region (HVR) to adapt the virus to cell culture, the latter option concomitantly altering its virulence in vivo. We describe an improved ex vivo IBDV rescue system based on the transfection of an avian cell line with RNA polymerase II-based expression vectors, combined with replication on primary chicken bursal cells, the main cell type targeted in vivo of IBDV. We validated this system by rescuing to high titers two recombinant IBDV strains: a cell-culture adapted attenuated strain and a vvIBDV. Sequencing of VP2 HVR confirmed the absence of unwanted mutations that may alter the biological properties of the recombinant viruses. Therefore, this approach is efficient, economical, time-saving, reduces animal suffering and can be used to rescue other non-cell culture adapted IBDV strains.
Transglutaminase-2 regulates Wnt and FoxO3a signaling to determine the severity of osteoarthritis
Authors: Han Min-Su , Jung Youn-Kwan , Kim Gun-Woo , Han Seungwoo 
Published: August 2020

AbstractTransglutaminase 2 (TG2), also known as tissue transglutaminase, is a calcium-dependent enzyme that has a variety of intracellular and extracellular substrates. TG2 not only increases in osteoarthritis (OA) tissue but also affects the progression of OA. However, it is still unclear how TG2 affects cartilage degradation in OA at the molecular level. Surgically induced OA lead to an increase of TG2 in the articular cartilage and growth plate, and it was dependent on TGFβ1 in primary chondrocytes. The inhibition of TG2 enzymatic activity with intra-articular injection of ZDON, the peptide-based specific TG2 inhibitor, ameliorated the severity of surgically induced OA as well as the expression of MMP-3 and MMP-13. ZDON attenuated MMP-3 and MMP-13 expression in TGFβ- and calcium ionophore-treated chondrocytes in a Runx2-independent manner. TG2 inhibition with ZDON suppressed canonical Wnt signaling through a reduction of β-catenin, which was mediated by ubiquitination-dependent proteasomal degradation. In addition, TG2 activation by a calcium ionophore enhanced the phosphorylation of AMPK and FoxO3a and the nuclear translocation of FoxO3a, which was responsible for the increase in MMP-13. In conclusion, TG2 plays an important role in the pathogenesis of OA as a major catabolic mediator that affects the stability of β-catenin and FoxO3a-mediated MMP-13 production.
ATIP3 deficiency facilitates intracellular accumulation of paclitaxel to reduce cancer cell migration and lymph node metastasis in breast cancer patients
Authors: Rodrigues-Ferreira Sylvie , Nehlig Anne , Kacem Mariem , Nahmias Clara 
Published: August 2020

AbstractTaxane-based chemotherapy is frequently used in neoadjuvant treatment of breast cancer patients to reduce tumor growth and lymph node metastasis. However, few patients benefit from chemotherapy and predictive biomarkers of chemoresistance are needed. The microtubule-associated protein ATIP3 has recently been identified as a predictive biomarker whose low levels in breast tumors are associated with increased sensitivity to chemotherapy. In this study, we investigated whether ATIP3 deficiency may impact the effects of paclitaxel on cancer cell migration and lymph node metastasis. Expression levels of ATIP3 were analyzed in a cohort of 133 breast cancer patients and classified according to lymph node positivity following neoadjuvant chemotherapy. Results showed that low ATIP3 levels are associated with reduced axillary lymph node metastasis. At the functional level, ATIP3 depletion increases cell migration, front-rear polarity and microtubule dynamics at the plus ends, but paradoxically sensitizes cancer cells to the inhibitory effects of paclitaxel on these processes. ATIP3 silencing concomitantly increases the incorporation of fluorescent derivative of Taxol along the microtubule lattice. Together our results support a model in which alterations of microtubule plus ends dynamics in ATIP3-deficient cells may favor intracellular accumulation of paclitaxel, thereby accounting for increased breast tumor sensitivity to chemotherapy.
Deep learning for synthetic microstructure generation in a materials-by-design framework for heterogeneous energetic materials
Authors: Chun Sehyun , Roy Sidhartha , Nguyen Yen Thi , Choi Joseph B. , Udaykumar H. S. , Baek Stephen S. 
Published: August 2020

AbstractThe sensitivity of heterogeneous energetic (HE) materials (propellants, explosives, and pyrotechnics) is critically dependent on their microstructure. Initiation of chemical reactions occurs at hot spots due to energy localization at sites of porosities and other defects. Emerging multi-scale predictive models of HE response to loads account for the physics at the meso-scale, i.e. at the scale of statistically representative clusters of particles and other features in the microstructure. Meso-scale physics is infused in machine-learned closure models informed by resolved meso-scale simulations. Since microstructures are stochastic, ensembles of meso-scale simulations are required to quantify hot spot ignition and growth and to develop models for microstructure-dependent energy deposition rates. We propose utilizing generative adversarial networks (GAN) to spawn ensembles of synthetic heterogeneous energetic material microstructures. The method generates qualitatively and quantitatively realistic microstructures by learning from images of HE microstructures. We show that the proposed GAN method also permits the generation of new morphologies, where the porosity distribution can be controlled and spatially manipulated. Such control paves the way for the design of novel microstructures to engineer HE materials for targeted performance in a materials-by-design framework.
Comparison of double-layer large-diameter and conventional small-diameter plastic stents for preoperative biliary drainage in resectable distal malignant biliary obstruction
Authors: Matsubara Tokuhiro , Nishida Tsutomu , Hayashi Shiro , Shimakoshi Hiromi , Tomimaru Yoshito , Takahashi Kei , Nakamatsu Dai , Matsumoto Kengo , Yamamoto Masashi , Inada Masami 
Published: August 2020

AbstractThe use of a plastic stent (PS) in resectable patients with distal malignant biliary obstruction (DMBO) is uncommon due to the high failure rate of this method. This study evaluated the efficacy and safety of a double-layer, large-diameter PS as a bridge to surgery compared with a conventional PS. This was a single-center retrospective cohort study. In total, 129 consecutive patients with DMBO underwent pancreaticoduodenectomy between January 2011 and March 2018. Fifty-five patients who preoperatively underwent plastic biliary drainage were enrolled. The patients were divided into two groups based on stent diameter: a large-diameter plastic stent (LPS) group and a small-diameter plastic stent (SPS) group. The primary endpoint was the stent patency period, and the secondary endpoint was the medical cost. Thirty-six patients received SPSs; 19 patients received LPSs. The patency rate until surgery was significantly higher in the LPS group than in the SPS group (89.5% vs. 41.7%, P = 0.0006). Multivariate analysis revealed that LPS use was significantly associated with sufficient stent patency. The total cost of LPS use was significantly lower than that of SPS use. LPSs had longer patency and reduced medical costs than SPSs. LPSs may be suitable for patients with DMBO who are scheduled to undergo surgery.
Plasma half-life and tissue distribution of leukocyte cell-derived chemotaxin 2 in mice
Authors: Kikuchi Akihiro , Takayama Hiroaki , Tsugane Hirohiko , Shiba Kazuhiro , Chikamoto Keita , Yamamoto Tatsuya , Matsugo Seiichi , Ishii Kiyo-aki , Misu Hirofumi , Takamura Toshinari 
Published: August 2020

AbstractLeukocyte cell-derived chemotaxin 2 (LECT2) is a hepatokine that causes skeletal muscle insulin resistance. The circulating levels of LECT2 are a possible biomarker that can predict weight cycling because they reflect liver fat and precede the onset of weight loss or gain. Herein, to clarify the dynamics of this rapid change in serum LECT2 levels, we investigated the in vivo kinetics of LECT2, including its plasma half-life and tissue distribution, by injecting 125I-labelled LECT2 into ICR mice and radioactivity tracing. The injected LECT2 was eliminated from the bloodstream within 10 min (approximate half-life, 5 min). In the kidneys, the radioactivity accumulated within 10 min after injection and declined thereafter. Conversely, the radioactivity in urine increased after 30 min of injection, indicating that LECT2 is mainly excreted by the kidneys into the urine. Finally, LECT2 accumulated in the skeletal muscle and liver until 30 min and 2 min after injection, respectively. LECT2 accumulation was not observed in the adipose tissue. These findings are in agreement with LECT2 action on the skeletal muscle. The present study indicates that LECT2 is a rapid-turnover protein, which renders the circulating level of LECT2 a useful rapid-response biomarker to predict body weight alterations.
Computational flow cytometry of planktonic populations for the evaluation of microbiological-control programs in district cooling plants
Authors: McElhinney J. M. W. R. , Mawart A. , Alkaabi R. S. S. M. , Abdelsamad H. S. S. , Mansour A. M. , Hasan A. 
Published: August 2020

AbstractBiofouling poses a serious concern for the district cooling (DC) industry. Current industry practises for monitoring biofouling continue to rely on culture-based methods for microbial enumeration, which are ultimately flawed. Computational flow cytometric (cFCM) analyses, which offer enhanced reproducibility and streamlined analytics versus conventional flow cytometry were applied to samples taken from 3 sites in each of 3 plants over a 5-week sampling program. We asked whether the application of cFCM to monitoring planktonic community dynamics in DC plants could be able to provide sufficient information to enhance microbiological-control strategies at site and inform about plant performance impacts. The use of cFCM enabled the evaluation of biocide dosing, deep cleaning treatment efficiencies and routes of microbial ingress into the studied systems. Additionally, inherent risks arising from the reintroduction of microbiological communities into recently cleaned WCT basins from contaminated cooling waters were identified. However, short-term dynamics did not relate with plant performance metrics. In summary, the insights offered by this approach can inform on plant status, enable evaluations of microbial loads during biofouling mitigation programs and, ultimately, enhance industry management of the biofouling process.
Mitochondrial DNA enhance innate immune responses in neuromyelitis optica by monocyte recruitment and activation
Authors: Shimizu Mikito , Okuno Tatsusada , Kinoshita Makoto , Sumi Hisae , Fujimura Harutoshi , Yamashita Kazuya , Sugimoto Tomoyuki , Sakakibara Shuhei , Sakakibara Kaori , Koda Toru , Tada Satoru , Ishikura Teruyuki , Murata Hisashi , Beppu Shohei , Shiraishi Naoyuki , Sugiyama Yasuko , Nakatsuji Yuji , Kumanogoh Atsushi , Mochizuki Hideki 
Published: August 2020

AbstractAlthough recent studies indicate the involvement of monocytes in accelerating the lesion formation of neuromyelitis optica spectrum disorder (NMOSD), the precise mechanism of the innate immune system activation remains elusive. Thus, in this study, we aimed to clarify the mechanisms of NMOSD pathogenesis from the viewpoint of innate immunity activation. We established anti-AQP4 recombinant autoantibodies (Ab) from plasmablasts in NMOSD patient’s CSF. Human astrocytes treated with anti-AQP4 Ab produced a significant amount of CCL2 and contributed to the efficient recruitment of monocytes. Moreover, mitochondrial DNA (mtDNA), which activated monocytes via Toll-like receptor 9 (TLR9), was released from astrocytes treated with anti-AQP4 Ab. MtDNA further enhanced CCL2 production by monocytes, and it was demonstrated that mtDNA concentration correlated with the efficiency of monocyte recruitment in the CSF of NMOSD patients. In conclusion, these observations highlight that mtDNA which was released from astrocytes damaged by anti-AQP4 Ab has a central role in establishing the inflammatory loop of monocyte recruitment and activation via an innate immunity pathway.
Remote, autonomous real-time monitoring of environmental DNA from commercial fish
Authors: Hansen Brian K. , Jacobsen Magnus W. , Middelboe Anne Lise , Preston Christina M. , Marin Roman , Bekkevold Dorte , Knudsen Steen W. , Møller Peter R. , Nielsen Einar E. 
Published: August 2020

AbstractEnvironmental DNA (eDNA) is increasingly used for monitoring marine organisms; however, offshore sampling and time lag from sampling to results remain problematic. In order to overcome these challenges a robotic sampler, a 2nd generation Environmental Sample Processor (ESP), was tested for autonomous analysis of eDNA from four commercial fish species in a 4.5 million liter mesocosm. The ESP enabled in situ analysis, consisting of water collection, filtration, DNA extraction and qPCR analysis, which allowed for real-time remote reporting and archival sample collection, consisting of water collection, filtration and chemical preservation followed by post-deployment laboratory analysis. The results demonstrate that the 2G ESP was able to consistently detect and quantify target molecules from the most abundant species (Atlantic mackerel) both in real-time and from the archived samples. In contrast, detection of low abundant species was challenged by both biological and technical aspects coupled to the ecology of eDNA and the 2G ESP instrumentation. Comparison of the in situ analysis and archival samples demonstrated variance, which potentially was linked to diel migration patterns of the Atlantic mackerel. The study demonstrates strong potential for remote autonomous in situ monitoring which open new possibilities for the field of eDNA and marine monitoring.
Evolutionary rearrangements of X chromosomes in voles (Arvicolinae, Rodentia)
Authors: Romanenko Svetlana A. , Fedorova Yulia E. , Serdyukova Natalya A. , Zaccaroni Marco , Stanyon Roscoe , Graphodatsky Alexander S. 
Published: August 2020

AbstractEuchromatic segments of the X chromosomes of placental mammals are the most conservative elements of the karyotype, only rarely subjected to either inter- or intrachromosomal rearrangements. Here, using microdissection-derived set of region-specific probes of Terricola savii we detailed the evolutionary rearrangements found in X chromosomes in 20 vole species (Arvicolinae, Rodentia). We show that the evolution of X chromosomes in this taxon was accompanied by multiple para- and pericentric inversions and centromere shifts. The contribution of intrachromosomal rearrangements to the karyotype evolution of Arvicolinae species was approximately equivalent in both the separate autosomal conserved segments and the X chromosomes. Intrachromosmal rearrangements and structural reorganization of the X chromosomes was likely accompanied by an accumulation, distribution, and evolution of repeated sequences.
Dynamic control of tumor vasculature improves antitumor responses in a regional model of melanoma
Authors: Gabriel Emmanuel M. , Kim Minhyung , Fisher Daniel T. , Powers Colin , Attwood Kristopher , Bagaria Sanjay P. , Knutson Keith L. , Skitzki Joseph J. 
Published: August 2020

AbstractDespite advances in therapy for melanoma, heterogeneous responses with limited durability represent a major gap in treatment outcomes. The purpose of this study was to determine whether alteration in tumor blood flow could augment drug delivery and improve antitumor responses in a regional model of melanoma. This approach to altering tumor blood flow was termed “dynamic control.” Dynamic control of tumor vessels in C57BL/6 mice bearing B16 melanoma was performed using volume expansion (saline bolus) followed by phenylephrine. Intravital microscopy (IVM) was used to observe changes directly in real time. Our approach restored blood flow in non-functional tumor vessels. It also resulted in increased chemotherapy (melphalan) activity, as measured by formation of DNA adducts. The combination of dynamic control and melphalan resulted in superior outcomes compared to melphalan alone (median time to event 40.0 vs 25.0 days, respectively, p = 0.041). Moreover, 25% (3/12) of the mice treated with the combination approach showed complete tumor response. Importantly, dynamic control plus melphalan did not result in increased adverse events. In summary, we showed that dynamic control was feasible, directly observable, and augmented antitumor responses in a regional model of melanoma. Early clinical trials to determine the translational feasibility of dynamic control are ongoing.
D2 dopamine receptor gene (DRD2) Taq1A (rs1800497) affects bone density
Authors: Chiang Ting-I. , Lane Hsien-Yuan , Lin Chieh-Hsin 
Published: August 2020

AbstractSchizophrenia patients are susceptible to lower bone mineral density (BMD). However, studies exploring the genetic effects are lacking. Genes that affect the activity of antipsychotics may be associated with BMD, particularly in patients receiving long-term antipsychotic treatment. We aimed to explore the relationship between the dopamine receptor D2 (DRD2) gene Taq1A (rs1800497) polymorphism and BMD in chronic schizophrenia patients. We recruited schizophrenia patients (n = 47) and healthy controls (n = 39) from a medical center in Taiwan and collected data that may affect BMD. Patients’ BMD was measured by dual-energy X-ray absorptiometer (DEXA). DRD2 rs1800497 was genotyped through polymerase chain reaction–Restriction Fragment Length Polymorphism (PCR–RFLP). Among all participants, subjects with DRD2 rs1800497(T;T) allele had lower DEXA T score and DEXA Z score compared to those with rs1800497(C;T) and rs1800497(C;C) alleles (p = 0.008, 0.003, respectively). In schizophrenia patients, subjects with rs1800497(T;T) allele also had lower DEXA Z score compared to the other two alleles (p = 0.045). Our findings suggest that individuals with the DRD2 rs1800497(T;T) had lower BMD than those with the rs1800497(C;T) and rs1800497(C;C) genotypes. Therefore, genes should be considered as one of the risk factors of lower BMD.
High-temperature differences in plasmonic broadband absorber on PET and Si substrates
Authors: Kim Jin Hee , Lee Sung-Gyu , Kim Teun-Teun , Ha Taewoo , Lee Sang Hyup , Kim Ji-Hee , Lee Young Hee 
Published: August 2020

AbstractThe characteristics of a plasmonic resonator with a metal–dielectric–metal structure is influenced by the size, shape, and spacing of the nanostructure. The plasmonic resonators can be used in various applications such as color filters, light emitting diodes, photodetectors, and broadband absorbers. In particular, broadband absorbers are widely used in thermophotovoltaics and thermoelectrics. To achieve a higher photothermal conversion efficiency, it is important to provoke a larger temperature difference in the absorber. The absorption and thermal conductance of the absorber has a great impact on the temperature difference, but in order to further improve the temperature difference of the absorber, the thermal conductivity of the substrate should be considered carefully. In this study, we designed Cr/SiO2/Cr absorbers on different substrates, i.e., polyethylene terephthalate (PET) and silicon. Although their optical properties do not change significantly, the temperature difference of the absorber on the PET substrate is considerably higher than that on the Si substrate under laser illumination, i.e., 164 K for ΔTPET and 3.7 K for ΔTSi, respectively. This is attributed to the thermal conductance of the substrate materials, which is confirmed by the thermal relaxation time. Moreover, the Seebeck coefficient of graphene on the absorber, 9.8 μV/K, is obtained by photothermoelectrics. The proposed Cr/SiO2/Cr structure provides a clear scheme to achieve high performance in photothermoelectric devices.
Viscoelasticity in simple indentation-cycle experiments: a computational study
Authors: Efremov Yu. M. , Kotova S. L. , Timashev P. S. 
Published: August 2020

AbstractInstrumented indentation has become an indispensable tool for quantitative analysis of the mechanical properties of soft polymers and biological samples at different length scales. These types of samples are known for their prominent viscoelastic behavior, and attempts to calculate such properties from the indentation data are constantly made. The simplest indentation experiment presents a cycle of approach (deepening into the sample) and retraction of the indenter, with the output of the force and indentation depth as functions of time and a force versus indentation dependency (force curve). The linear viscoelastic theory based on the elastic–viscoelastic correspondence principle might predict the shape of force curves based on the experimental conditions and underlying relaxation function of the sample. Here, we conducted a computational analysis based on this theory and studied how the force curves were affected by the indenter geometry, type of indentation (triangular or sinusoidal ramp), and the relaxation functions. The relaxation functions of both traditional and fractional viscoelastic models were considered. The curves obtained from the analytical solutions, numerical algorithm and finite element simulations matched each other well. Common trends for the curve-related parameters (apparent Young’s modulus, normalized hysteresis area, and curve exponent) were revealed. Importantly, the apparent Young’s modulus, obtained by fitting the approach curve to the elastic model, demonstrated a direct relation to the relaxation function for all the tested cases. The study will help researchers to verify which model is more appropriate for the sample description without extensive calculations from the basic curve parameters and their dependency on the indentation rate.
Bulk and local structures of metal–organic frameworks unravelled by high-resolution electron microscopy
Authors: Liu Lingmei , Zhang Daliang , Zhu Yihan , Han Yu 
Published: August 2020

AbstractThe periodic bulk structures of metal–organic frameworks (MOFs) can be solved by diffraction-based techniques; however, their non-periodic local structures—such as crystal surfaces, grain boundaries, defects, and guest molecules—have long been elusive due to a lack of suitable characterization tools. Recent advances in (scanning) transmission electron microscopy ((S)TEM) has made it possible to probe the local structures of MOFs at atomic resolution. In this article, we discuss why high-resolution (S)TEM of MOFs is challenging and how the new low-dose techniques overcome this challenge, and we review various MOF structural features observed by (S)TEM and important insights gained from these observations. Our discussions focus on real-space imaging, excluding other TEM-related characterization techniques (e.g. electron diffraction and spectroscopy).