bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical shaping of the polarization anisotropy in a laterally coupled quantum dot dimer
Authors: Kim Heedae , Kyhm Kwangseuk , Taylor Robert A. , Kim Jong Su , Song Jin Dong , Park Sungkyun 
Published: June 2020

AbstractWe find that the emission from laterally coupled quantum dots is strongly polarized along the coupled direction [1$$\bar 1$$

1

¯

0], and its polarization anisotropy can be shaped by changing the orientation of the polarized excitation. When the nonresonant excitation is linearly polarized perpendicular to the coupled direction [110], excitons (X1 and X2) and local biexcitons (X1X1 and X2X2) from the two separate quantum dots (QD1 and QD2) show emission anisotropy with a small degree of polarization (10%). On the other hand, when the excitation polarization is parallel to the coupled direction [1$$\bar 1$$

1

¯

0], the polarization anisotropy of excitons, local biexcitons, and coupled biexcitons (X1X2) is enhanced with a degree of polarization of 74%. We also observed a consistent anisotropy in the time-resolved photoluminescence. The decay rate of the polarized photoluminescence intensity along the coupled direction is relatively high, but the anisotropic decay rate can be modified by changing the orientation of the polarized excitation. An energy difference is also observed between the polarized emission spectra parallel and perpendicular to the coupled direction, and it increases by up to three times by changing the excitation polarization orientation from [110] to [1$$\bar 1$$

1

¯

0]. These results suggest that the dipole–dipole interaction across the two separate quantum dots is mediated and that the anisotropic wavefunctions of the excitons and biexcitons are shaped by the excitation polarization.
A variant in IL6ST with a selective IL-11 signaling defect in human and mouse
Authors: Schwerd Tobias , Krause Freia , Twigg Stephen R. F. , Aschenbrenner Dominik , Chen Yin-Huai , Borgmeyer Uwe , Müller Miryam , Manrique Santiago , Schumacher Neele , Wall Steven A. , Jung Jonathan , Damm Timo , Glüer Claus-Christian , Scheller Jürgen , Rose-John Stefan , Jones E. Yvonne , Laurence Arian , Wilkie Andrew O. M. , Schmidt-Arras Dirk , Uhlig Holm H. 
Published: June 2020

AbstractThe GP130 cytokine receptor subunit encoded by IL6ST is the shared receptor for ten cytokines of the IL-6 family. We describe a homozygous non-synonymous variant in IL6ST (p.R281Q) in a patient with craniosynostosis and retained deciduous teeth. We characterize the impact of the variant on cytokine signaling in vitro using transfected cell lines as well as primary patient-derived cells and support these findings using a mouse model with the corresponding genome-edited variant Il6st p.R279Q. We show that human GP130 p.R281Q is associated with selective loss of IL-11 signaling without affecting IL-6, IL-27, OSM, LIF, CT1, CLC, and CNTF signaling. In mice Il6st p.R279Q lowers litter size and causes facial synostosis and teeth abnormalities. The effect on IL-11 signaling caused by the GP130 variant shows incomplete penetrance but phenocopies aspects of IL11RA deficiency in humans and mice. Our data show that a genetic variant in a pleiotropic cytokine receptor can have remarkably selective defects.
Lin28A promotes IRF6-regulated aerobic glycolysis in glioma cells by stabilizing SNHG14
Authors: Lu Jinjing , Liu Xiaobai , Zheng Jian , Song Jian , Liu Yunhui , Ruan Xuelei , Shen Shuyuan , Shao Lianqi , Yang Chunqing , Wang Di , Cai Heng , Cao Shuo , Xue Yixue 
Published: June 2020

AbstractWarburg effect is a hallmark of cancer cells, wherein glycolysis is preferred over oxidative phosphorylation even in aerobic conditions. Reprogramming of glycometabolism is especially crucial for malignancy in glioma. RNA-binding proteins and long noncoding RNAs are important for aerobic glycolysis during malignant transformation. Thus, we determined the expression and function of RNA-binding protein Lin28A, long noncoding RNA SNHG14, and transcription factor IRF6 in human glioma cells to elucidate the mechanism(s) underlying their role in glycolysis. Quantitative real-time polymerase chain reaction and western blotting showed that Lin28A and SNHG14 were overexpressed and IRF6 was downregulated in glioma. Depleting Lin28A from cells decreased the stability and expression of SNHG14. Furthermore, depleting SNHG14 reduced IRF6 mRNA degradation by targeting its 3′ untranslated region and inhibiting STAU1-mediated degradation, thereby increasing the expression of IRF6. PKM2 is an important enzyme in aerobic glycolysis, and GLUT1 is the primary transporter that facilitates glucose uptake. IRF6 inhibited the transcription of PKM2 and GLUT1, thereby impairing glycolysis and cell proliferation and inducing apoptosis in glioma. Notably, depleting Lin28A and SNHG14 and overexpressing IRF6 reduced the growth of xenograft tumors in vivo and prolonged the survival of nude mice. Taken together, our data revealed that the Lin28A/SNHG14/IRF6 axis is crucial for reprogramming glucose metabolism and stimulating tumorigenesis in glioma cells. Thus, targeting this axis might help in the development of a novel therapeutic strategy for glioma metabolism.
From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses
Authors: Kabiljo Julijan , Laengle Johannes , Bergmann Michael 
Published: June 2020

AbstractOncolytic viruses constitute an emerging strategy in immunomodulatory cancer treatment. The first oncolytic virus, Talimogene laherparepvec (T-VEC), based on herpes simplex virus 1 (HSV-1), was approved by the Food and Drug Administration (FDA) and European Medicines Agency (EMA) in 2015. The field of oncolytic virotherapy is still in its beginnings, since many promising viruses remain only superficially explored. Influenza A virus causes a highly immunogenic acute infection but never leads to a chronic disease. While oncolytic influenza A viruses are in preclinical development, they have not made the transition into clinical practice yet. Recent insights into different types of cell death caused by influenza A virus infection illuminate novel possibilities of enhancing its therapeutic effect. Genetic engineering and experience in influenza A virus vaccine development allow safe application of the virus in patients. In this review we give a summary of efforts undertaken to develop oncolytic influenza A viruses. We discuss strategies for targeting viral replication to cancerous lesions and arming them with immunogenic transgenes. We furthermore describe which modes of cell death are induced by influenza A virus infection and how these insights may be utilized to optimize influenza A virus-based oncolytic virus design.
Metabolic reprogramming by Zika virus provokes inflammation in human placenta
Authors: Chen Qian , Gouilly Jordi , Ferrat Yann J. , Espino Ana , Glaziou Quentin , Cartron Géraldine , El Costa Hicham , Al-Daccak Reem , Jabrane-Ferrat Nabila 
Published: June 2020

AbstractThe recent outbreak of Zika virus (ZIKV) was associated with birth defects and pregnancy loss when maternal infection occurs in early pregnancy, but specific mechanisms driving placental insufficiency and subsequent ZIKV-mediated pathogenesis remain unclear. Here we show, using large scale metabolomics, that ZIKV infection reprograms placental lipidome by impairing the lipogenesis pathways. ZIKV-induced metabolic alterations provide building blocks for lipid droplet biogenesis and intracellular membrane rearrangements to support viral replication. Furthermore, lipidome reprogramming by ZIKV is paralleled by the mitochondrial dysfunction and inflammatory immune imbalance, which contribute to placental damage. In addition, we demonstrate the efficacy of a commercially available inhibitor in limiting ZIKV infection, provides a proof-of-concept for blocking congenital infection by targeting metabolic pathways. Collectively, our study provides mechanistic insights on how ZIKV targets essential hubs of the lipid metabolism that may lead to placental dysfunction and loss of barrier function.
Efficient arbitrary simultaneously entangling gates on a trapped-ion quantum computer
Authors: Grzesiak Nikodem , Blümel Reinhold , Wright Kenneth , Beck Kristin M. , Pisenti Neal C. , Li Ming , Chaplin Vandiver , Amini Jason M. , Debnath Shantanu , Chen Jwo-Sy , Nam Yunseong 
Published: June 2020

AbstractEfficiently entangling pairs of qubits is essential to fully harness the power of quantum computing. Here, we devise an exact protocol that simultaneously entangles arbitrary pairs of qubits on a trapped-ion quantum computer. The protocol requires classical computational resources polynomial in the system size, and very little overhead in the quantum control compared to a single-pair case. We demonstrate an exponential improvement in both classical and quantum resources over the current state of the art. We implement the protocol on a software-defined trapped-ion quantum computer, where we reconfigure the quantum computer architecture on demand. Our protocol may also be extended to a wide variety of other quantum computing platforms.
Assessing the effectiveness of a national protected area network for carnivore conservation
Authors: Terraube J. , Van doninck J. , Helle P. , Cabeza M. 
Published: June 2020

AbstractProtected areas (PAs) are essential to prevent further biodiversity loss yet their effectiveness varies largely with governance and external threats. Although methodological advances have permitted assessments of PA effectiveness in mitigating deforestation, we still lack similar studies for the impact of PAs on wildlife populations. Here we use an innovative combination of matching methods and hurdle-mixed models with a large-scale and long-term dataset for Finland’s large carnivore species. We show that the national PA network does not support higher densities than non-protected habitat for 3 of the 4 species investigated. For some species, PA effects interact with region or time, i.e., wolverine densities decreased inside PAs over the study period and lynx densities increased inside eastern PAs. We support the application of matching methods in combination of additional analytical frameworks for deeper understanding of conservation impacts on wildlife populations. These methodological advances are crucial for preparing ambitious PA targets post-2020.
Poincaré maps for analyzing complex hierarchies in single-cell data
Authors: Klimovskaia Anna , Lopez-Paz David , Bottou Léon , Nickel Maximilian 
Published: June 2020

AbstractThe need to understand cell developmental processes spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry, a suboptimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method that harness the power of hyperbolic geometry into the realm of single-cell data analysis. Often understood as a continuous extension of trees, hyperbolic geometry enables the embedding of complex hierarchical data in only two dimensions while preserving the pairwise distances between points in the hierarchy. This enables the use of our embeddings in a wide variety of downstream data analysis tasks, such as visualization, clustering, lineage detection and pseudotime inference. When compared to existing methods — unable to address all these important tasks using a single embedding — Poincaré maps produce state-of-the-art two-dimensional representations of cell trajectories on multiple scRNAseq datasets.
Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae
Authors: Can Muyou , Wei Wei , Zi Hailing , Bai Magaweng , Liu Yunfei , Gao Dan , Tu Dengqunpei , Bao Yuhong , Wang Li , Chen Shaofeng , Zhao Xing , Qu Guangpeng 
Published: June 2020

AbstractKobresia plants are important forage resources in the Qinghai-Tibet Plateau and are essential in maintaining the ecological balance of grasslands. Therefore, it is beneficial to obtain Kobresia genome resources and study the adaptive characteristics of Kobresia plants in the Qinghai-Tibetan Plateau. We assembled the genome of Kobresia littledalei C. B. Clarke, which was about 373.85 Mb in size. 96.82% of the bases were attached to 29 pseudo-chromosomes, combining PacBio, Illumina and Hi-C sequencing data. Additional investigation of the annotation identified 23,136 protein-coding genes. 98.95% of these were functionally annotated. According to phylogenetic analysis, K. littledalei in Cyperaceae separated from Poaceae about 97.6 million years ago after separating from Ananas comosus in Bromeliaceae about 114.3mya. For K. littledalei, we identified a high-quality genome at the chromosome level. This is the first time a reference genome has been established for a species of Cyperaceae. This genome will help additional studies focusing on the processes of plant adaptation to environments with high altitude and cold weather.
MicroRNA-128-3p Enhances the Chemosensitivity of Temozolomide in Glioblastoma by Targeting c-Met and EMT
Authors: Zhao Chengbin , Guo Ruiming , Guan Fangxia , Ma Shanshan , Li Mu , Wu Junru , Liu Xianzhi , Li Hongwei , Yang Bo 
Published: June 2020

AbstractTemozolomide is a first line anti-tumor drug used for the treatment of patients with Glioblastoma multiforme (GBM). However, the drug resistance to temozolomide limits its clinical application. Therefore, novel strategies to overcome chemoresistance are desperately needed for improved treatment of human GBM. Recent studies have demonstrated that miRNAs are closely related to resistance to cancer chemotherapy. This study aimed to further validate the biological role of miR-128-3p and to investigate whether miR-128-3p can enhance the chemosensitivity of glioblastoma to temozolomide (TMZ) and the underlying mechanisms. The effects of miR-128-3p and TMZ on the proliferation of glioblastoma cells were investigated by cell counting kit-8 (cck8). Transwell and intracerebral invasion assays were applied to determine the effects of the combination of miR-128-3p and TMZ on the invasion and migration of glioblastoma in vitro and in vivo. Flow cytometry was used to detect apoptosis in each group, and immunofluorescence was used to determine the expression levels of EMT-related proteins. RT-PCR and Western-blot were applied to detect EMT-transformed proteins (c-Met, PDGFRα, Notch1, and Slug) and EMT phenotype-associated proteins (Vim, CD44, and E-cadherin) at both mRNA and protein levels. Based on the microRNA.org database, we predicted the target genes of miR-128-3p. The target-relationship between miR-128-3p and c-Met and PDGFRα was verified by dual luciferase reporter gene. The tumor volume, weight and the expression levels of the proteins described above were measured in subcutaneously transplanted tumor model in nude mice. We found that the expression of miR-128-3p was down-regulated in glioblastoma tissue samples and cell lines. miR-128-3p suppressed the proliferation, migration, and invasion of GBM both in vitro and in vivo; miR-128-3p enhanced the therapeutic effect of TMZ via inhibition of proliferation, invasion and migration of glioblastoma cells and induction of apoptosis. Overexpression of miR-128-3p down-regulated the expression levels of EMT-transformed proteins (c-Met, PDGFRα, Notch1 and Slug) to enhance the effect of TMZ. In addition, we found that miR-128-3p targeted and bound c-Met. More importantly, the upregulation of c‐Met significantly prompted U87 and U251 cell proliferation. This effect could be abolished when c‐Met was silenced. The investigation in tumor bearing nude mice showed that miR-128-3p in combination with TMZ reduced tumor volume and the invasion extent, and increased the sensitivity of glioblastoma to TMZ. miR-128-3p is capable of enhancing the sensitivity of glioblastoma to TMZ through regulating c-Met/EMT.
Detection of Hepatocellular Carcinoma in Contrast-Enhanced Magnetic Resonance Imaging Using Deep Learning Classifier: A Multi-Center Retrospective Study
Authors: Kim Junmo , Min Ji Hye , Kim Seon Kyoung , Shin Soo-Yong , Lee Min Woo 
Published: June 2020

AbstractHepatocellular carcinoma (HCC) is one of the most common malignant tumors and a leading cause of cancer-related death worldwide. We propose a fully automated deep learning model to detect HCC using hepatobiliary phase magnetic resonance images from 549 patients who underwent surgical resection. Our model used a fine-tuned convolutional neural network and achieved 87% sensitivity and 93% specificity for the detection of HCCs with an external validation data set (54 patients). We also confirmed whether the lesion detected by our deep learning model is a true lesion using a class activation map.
Trackway evidence for large bipedal crocodylomorphs from the Cretaceous of Korea
Authors: Kim Kyung Soo , Lockley Martin G. , Lim Jong Deock , Bae Seul Mi , Romilio Anthony 
Published: June 2020

AbstractLarge well-preserved crocodylomorph tracks from the Lower Cretaceous (? Aptian) Jinju Formation of South Korea, represent the well-known crocodylomorph ichnogenusBatrachopus. The Korean sample includes multiple, narrow-gauge, pes-only trackways with footprint lengths (FL) 18–24 cm, indicating trackmaker body lengths up to ~3.0 m. Surprisingly, the consistent absence of manus tracks in trackways, with well-preserved digital pad and skin traces, argues for bipedal trackmakers, here assigned toBatrachopus grandisichnosp. nov. No definitive evidence, either from pes-on-manus overprinting or poor track preservation, suggests the trackways where made by quadrupeds that only appear bipedal. This interpretation helps solve previous confusion over interpretation of enigmatic tracks of bipeds from younger (? Albian) Haman Formation sites by showing they are not pterosaurian as previously inferred. Rather, they support the strong consensus that pterosaurs were obligate quadrupeds, not bipeds. Lower JurassicBatrachopuswith foot lengths (FL) in the 2–8 cm range, and CretaceousCrocodylopodus(FL up to ~9.0 cm) known only from Korea and Spain registered narrow gauge trackways indicating semi-terrestrial/terrestrial quadrupedal gaits. Both ichnogenera, from ichnofamily Batrachopodidae, have been attributed toProtosuchus-like semi-terrestrial crocodylomorphs. The occurrence of bipedalB. grandisichnosp. nov. is evidence of such adaptations in the Korean Cretaceous.
A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe
Authors: Giffin Karen , Lankapalli Aditya Kumar , Sabin Susanna , Spyrou Maria A. , Posth Cosimo , Kozakaitė Justina , Friedrich Ronny , Miliauskienė Žydrūnė , Jankauskas Rimantas , Herbig Alexander , Bos Kirsten I. 
Published: June 2020

AbstractDevelopments in techniques for identification of pathogen DNA in archaeological samples can expand our resolution of disease detection. Our application of a non-targeted molecular screening tool for the parallel detection of pathogens in historical plague victims from post-medieval Lithuania revealed the presence of more than one active disease in one individual. In addition to Yersinia pestis, we detected and genomically characterized a septic infection of Treponema pallidum pertenue, a subtype of the treponemal disease family recognised as the cause of the tropical disease yaws. Our finding in northern Europe of a disease that is currently restricted to equatorial regions is interpreted within an historical framework of intercontinental trade and potential disease movements. Through this we offer an alternative hypothesis for the history and evolution of the treponemal diseases, and posit that yaws be considered an important contributor to the sudden epidemic of late 15th century Europe that is widely ascribed to syphilis.
Heat treatment dependent cytotoxicity of silicalite-1 films deposited on Ti-6Al-4V alloy evaluated by bone-derived cells
Authors: Nemcakova Ivana , Jirka Ivan , Doubkova Martina , Bacakova Lucie 
Published: June 2020

AbstractA silicalite-1 film (SF) deposited on Ti-6Al-4V alloy was investigated in this study as a promising coating for metallic implants. Two forms of SFs were prepared: as-synthesized SFs (SF-RT), and SFs heated up to 500 °C (SF-500) to remove the excess of template species from the SF surface. The SFs were characterized in detail by X-ray photoelectron spectroscopy (XPS), by Fourier transform infrared spectroscopy (FTIR), by scanning electron microscopy (SEM) and water contact angle measurements (WCA). Two types of bone-derived cells (hFOB 1.19 non-tumor fetal osteoblast cell line and U-2 OS osteosarcoma cell line) were used for a biocompatibility assessment. The initial adhesion of hFOB 1.19 cells, evaluated by cell numbers and cell spreading area, was better supported by SF-500 than by SF-RT. While no increase in cell membrane damage, in ROS generation and in TNF-alpha secretion of bone-derived cells grown on both SFs was found, gamma H2AX staining revealed an elevated DNA damage response of U-2 OS cells grown on heat-treated samples (SF-500). This study also discusses differences between osteosarcoma cell lines and non-tumor osteoblastic cells, stressing the importance of choosing the right cell type model.
Detachment of cell sheets from clinically ubiquitous cell culture vessels by ultrasonic vibration
Authors: Imashiro Chikahiro , Hirano Makoto , Morikura Takashi , Fukuma Yuki , Ohnuma Kiyoshi , Kurashina Yuta , Miyata Shogo , Takemura Kenjiro 
Published: June 2020

AbstractProteinases that digest the extracellular matrix are usually used to harvest cells from culture vessels in a general culture process, which lowers the initial adhesion rate in regenerative medicine. Cell sheet engineering is one of the most important technologies in this field, especially for transplantation, because fabricated cell sheets have rich extracellular matrixes providing strong initial adhesion. Current cell sheet fabrication relies on temperature-responsive polymer-coated dishes. Cells are cultured on such specialized dishes and subjected to low temperature. Thus, we developed a simple but versatile cell sheet fabrication method using ubiquitous culture dishes/flasks without any coating or temperature modulation. Confluent mouse myoblasts (C2C12 cell line) were exposed to ultrasonic vibration from underneath and detached as cell sheets from entire culture surfaces. Because of the absence of low temperature, cell metabolism was statically increased compared with the conventional method. Furthermore, viability, morphology, protein expression, and mRNA expression were normal. These analyses indicated no side effects of ultrasonic vibration exposure. Therefore, this novel method may become the standard for cell sheet fabrication. Our method can be easily conducted following a general culture procedure with a typical dish/flask, making cell sheets more accessible to medical experts.