bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metasurface interferometry toward quantum sensors
Authors: Georgi Philip , Massaro Marcello , Luo Kai-Hong , Sain Basudeb , Montaut Nicola , Herrmann Harald , Weiss Thomas , Li Guixin , Silberhorn Christine , Zentgraf Thomas 
Published: August 2019

AbstractOptical metasurfaces open new avenues for the precise wavefront control of light for integrated quantum technology. Here, we demonstrate a hybrid integrated quantum photonic system that is capable of entangling and disentangling two-photon spin states at a dielectric metasurface. Via the interference of single-photon pairs at a nanostructured dielectric metasurface, a path-entangled two-photon NOON state with circular polarization that exhibits a quantum HOM interference visibility of 86 ± 4% is generated. Furthermore, we demonstrate nonclassicality andphase sensitivity in a metasurface-based interferometer with a fringe visibility of 86.8 ± 1.1% in the coincidence counts. This high visibility proves the metasurface-induced path entanglement inside the interferometer. Our findings provide a promising way to develop hybrid-integrated quantum technology operating in the high-dimensional mode space in various applications, such as imaging, sensing, and computing.
Novel tumor suppressor role of miRNA-876 in cholangiocarcinoma
Authors: Ursu Sarah , Majid Shahana , Garger Caroline , de Semir David , Bezrookove Vladimir , Desprez Pierre-Yves , McAllister Sean , Soroceanu Liliana , Nosrati Mehdi , Yimam Kidist , Hassoun Assad , Osorio Robert , Kashani-Sabet Mohammed , Dar Altaf A. 
Published: August 2019

AbstractCholangiocarcinoma (CCA) is a rare, highly invasive malignancy, and its incidence is increasing globally. MicroRNAs (miRNAs) mediate a wide array of cellular and biological processes and are dysregulated in various tumors. The functional and biological roles of miRNAs in CCA have not been fully elucidated. In this study, we show that miR-876 expression levels and copy number are significantly attenuated in the TCGA cohort of CCA tissue samples. TCGA expression data was consistent with the observed substantial decrease in miR-876 expression in patient samples and CCA cell lines. In-silico algorithm databases revealed BCL-XL as a potential target of miR-876. We observed miR-876 expression to be downregulated, whereas, BCL-XL upregulated in CCA cell lines. BCL-XL was identified as a direct functional target of miR-876 in CCA. miR-876-mediated reduction of BCL-XL regulated cell survival, induced apoptosis and caspase 3/7 expression in CCA. BCL-XL overexpression reversed the miR-876 mediated effect on CCA cell growth and apoptosis. Stable overexpression of miR-876 produced potent tumor suppressor activity and in vivo tumor cell growth reduction. Overexpression of miR-876 in a patient-derived xenograft (PDX) cell line significantly suppressed BCL-XL expression and spheroid formation with a concomitant induction of caspase 3/7 activity and apoptosis. This study demonstrates a novel tumor suppressor role for miR-876 in CCA, identifies BCL-XL as an actionable target, and suggests a potential therapeutic role for miR-876 in CCA.
mTOR direct crosstalk with STAT5 promotes de novo lipid synthesis and induces hepatocellular carcinoma
Authors: Li Ting , Weng Jun , Zhang Yue , Liang Kangyan , Fu Gongbo , Li Yang , Bai Xiaochun , Gao Yi 
Published: August 2019

AbstractHepatocellular carcinoma (HCC) can be the last step of nonalcoholic fatty liver disease (NAFLD) evolution, and the main characteristic of NAFLD is alteration in lipid metabolism. However, the mechanisms of abnormal lipid metabolism in NAFLD and HCC progression are yet to be identified. Here, we demonstrate that liver-specific activation of mTORC1 promoted the expression of lipid synthesis genes and lead to the development of spontaneous HCC. Genetic mouse models developed spontaneous HCC along with increased expressions of SREBP1, ACC1 and FASN. In addition, high levels of p-STAT5 were observed in the livers and particularly evident in the tumor area. And the synthesis of p-STAT5 was increased in patients along with the increase in SREBP1 synthesis in clinical samples. Moreover, mTORC1 interacts with and phosphorylates the STAT5 in hepatocytes. In conclusion, our data suggested that mTORC1 upregulates SREBP1 transcription via crosstalk with the STAT5 pathway which contributes to the NAFLD-related HCC pathogenesis. And the inhibitor of SREBP1 and mTOR may help to prevent HCC in clinical NAFLD patients.
Circular RNA PRKCI promotes glioma cell progression by inhibiting microRNA-545
Authors: Zhang Xuebang , Yang Han , Zhao Lihao , Li Gang , Duan Yuxia 
Published: August 2019

AbstractWe here tested expression and potential functions of circular RNA PRKCI (circPRKCI) in human glioma. Our results show that circPRKCI is upregulated in human glioma tissues and glioma cells, correlating with downregulation of its potential target, microRNA-545 (miR-545). In A172 and primary human glioma cells, shRNA-mediated silencing of circPRKCI inhibited cancer cell growth, survival, proliferation, and migration. Conversely, ectopic circPRKCI overexpression promoted A172 cell progression. miR-545 is the primary target of circPRKCI in glioma cells. Forced overexpression of miR-545 mimicked circPRKCI shRNA-induced actions, inhibiting glioma cell survival and proliferation. In contrast, miR-545 inhibition, by a lentiviral antagomiR-545 construct, reversed circPRKCI shRNA-induced anti-A172 cell activity. Importantly, neither circPRKCI shRNA nor circPRKCI overexpression was effective in miR-545-knockout (Cas9 method) A172 cells. Importantly, the subcutaneous and orthotopic A172 xenograft growth was significantly inhibited by circPRKCI silencing. Collectively, circPRKCI promotes human glioma cell progression possibly by inhibiting miR-545. Targeting circPRKCI-miR-545 cascade could efficiently inhibit human glioma cells.
Clinical characteristics with long-term follow-up of four Okinawan families with moderate hearing loss caused by an OTOG variant
Authors: Ganaha Akira , Kaname Tadashi , Yanagi Kumiko , Tono Tetsuya , Higa Teruyuki , Suzuki Mikio 
Published: August 2019

AbstractWe describe the clinical features of four Japanese families with moderate sensorineural hearing loss due to the OTOG gene variant. We analyzed 98 hearing loss-related genes in patients with hearing loss originally from the Okinawa Islands using next-generation sequencing. We identified a homozygous variant of the gene encoding otogelin NM_001277269(OTOG): c.330C>G, p.Tyr110* in four families. All patients had moderate hearing loss with a slightly downsloping audiogram, including low frequency hearing loss without equilibrium dysfunction. Progressive hearing loss was not observed over the long-term in any patient. Among the three patients who underwent newborn hearing screening, two patients passed the test. OTOG-associated hearing loss was considered to progress early after birth, leading to moderate hearing loss and the later stable phase of hearing loss. Therefore, there are patients whose hearing loss cannot be detected by NHS, making genetic diagnosis of OTOG variants highly useful for complementing NHS in the clinical setting. Based on the allele frequency results, hearing loss caused by the p.Tyr110* variant in OTOG might be more common than we identified. The p.Tyr110* variant was reported in South Korea, suggesting that this variant is a common cause of moderate hearing loss in Japanese and Korean populations.
Discrepancy in scientific authority and media visibility of climate change scientists and contrarians
Authors: Petersen Alexander Michael , Vincent Emmanuel M. , Westerling Anthony LeRoy 
Published: August 2019

AbstractWe juxtapose 386 prominent contrarians with 386 expert scientists by tracking their digital footprints across ∼200,000 research publications and ∼100,000 English-language digital and print media articles on climate change. Projecting these individuals across the same backdrop facilitates quantifying disparities in media visibility and scientific authority, and identifying organization patterns within their association networks. Here we show via direct comparison that contrarians are featured in 49% more media articles than scientists. Yet when comparing visibility in mainstream media sources only, we observe just a 1% excess visibility, which objectively demonstrates the crowding out of professional mainstream sources by the proliferation of new media sources, many of which contribute to the production and consumption of climate change disinformation at scale. These results demonstrate why climate scientists should increasingly exert their authority in scientific and public discourse, and why professional journalists and editors should adjust the disproportionate attention given to contrarians.
Visualization and design of the functional group distribution during statistical copolymerization
Authors: Van Steenberge Paul H. M. , Sedlacek Ondrej , Hernández-Ortiz Julio C. , Verbraeken Bart , Reyniers Marie-Françoise , Hoogenboom Richard , D’hooge Dagmar R. 
Published: August 2019

AbstractEven though functional copolymers with a low percentage of functional comonomer units (up to 20 mol%) are widely used, for instance for the development of polymer therapeutics and hydrogels, insights in the functional group distribution over the actual chains are lacking and the average composition is conventionally used to describe the functionalization degree. Here we report the visualization of the monomer distribution over the different polymer chains by a synergetic combination of experimental and theoretical analysis aiming at the construction of functionality-chain length distributions (FUNC-CLDs). A successful design of the chemical structure of the comonomer pair, the initial functional comonomer amount (13 mol%), and the temperature (100 °C) is performed to tune the FUNC-CLD of copoly(2-oxazoline)s toward high functionalization degree for both low (100) and high (400) target degrees of polymerization. The proposed research strategy is generic and extendable to a broad range of copolymerization chemistries, including reversible deactivation radical polymerization.
Information-based centralization of locomotion in animals and robots
Authors: Neveln Izaak D. , Tirumalai Amoolya , Sponberg Simon 
Published: August 2019

AbstractThe centralization of locomotor control from weak and local coupling to strong and global is hard to assess outside of particular modeling frameworks. We developed an empirical, model-free measure of centralization that compares information between control signals and both global and local states. A second measure, co-information, quantifies the net redundancy in global and local control. We first validate that our measures predict centralization in simulations of phase-coupled oscillators. We then test how centralization changes with speed in freely running cockroaches. Surprisingly, across all speeds centralization is constant and muscle activity is more informative of the global kinematic state (the averages of all legs) than the local state of that muscle’s leg. Finally we use a legged robot to show that mechanical coupling alone can change the centralization of legged locomotion. The results of these systems span a design space of centralization and co-information for biological and robotic systems.
Bounded rationality in C. elegans is explained by circuit-specific normalization in chemosensory pathways
Authors: Cohen Dror , Teichman Guy , Volovich Meshi , Zeevi Yoav , Elbaum Lilach , Madar Asaf , Louie Kenway , Levy Dino J. , Rechavi Oded 
Published: August 2019

AbstractRational choice theory assumes optimality in decision-making. Violations of a basic axiom of economic rationality known as “Independence of Irrelevant Alternatives” (IIA) have been demonstrated in both humans and animals and could stem from common neuronal constraints. Here we develop tests for IIA in the nematode Caenorhabditis elegans, an animal with only 302 neurons, using olfactory chemotaxis assays. We find that in most cases C. elegans make rational decisions. However, by probing multiple neuronal architectures using various choice sets, we show that violations of rationality arise when the circuit of olfactory sensory neurons is asymmetric. We further show that genetic manipulations of the asymmetry between the AWC neurons can make the worm irrational. Last, a context-dependent normalization-based model of value coding and gain control explains how particular neuronal constraints on information coding give rise to irrationality. Thus, we demonstrate that bounded rationality could arise due to basic neuronal constraints.
Global Assessment of Retinal Arteriolar, Venular and Capillary Microcirculations Using Fundus Photographs and Optical Coherence Tomography Angiography in Diabetic Retinopathy
Authors: Tan Tien-En , Nguyen Quang , Chua Jacqueline , Schmetterer Leopold , Tan Gavin Siew Wei , Wong Chee Wai , Tsai Andrew , Cheung Gemmy Chui Ming , Wong Tien Yin , Ting Daniel Shu Wei 
Published: August 2019

AbstractRetinal arterioles, venules and capillaries are differentially affected in diabetes, and studying vascular alterations may provide information on pathogenesis of diabetic retinopathy (DR). We conducted a cross-sectional study on 49 diabetic patients, who underwent fundus photography and optical coherence tomographic angiography (OCT-A). Fundus photographs were analysed using semi-automated software for arteriolar and venular parameters, including central retinal arteriolar equivalent (CRAE), central retinal venular equivalent (CRVE) and fractal dimension (FD). Capillary parameters were measured using OCT-A, including capillary density index (CDI) and capillary FD of superficial (SVP) and deep (DVP) vascular plexuses. Severe DR was defined as severe non-proliferative DR and proliferative DR. We found that eyes with severe DR had narrower CRAE and sparser SVP CDI than eyes without. In logistic regression analysis, capillary parameters were more associated with severe DR than arteriolar or venular parameters. However, combining arteriolar, venular and capillary parameters provided the strongest association with severe DR. In linear regression analysis, eyes with poorer visual acuity had lower CRAE and FD of arterioles, venules, and DVP capillaries. We concluded that the retinal microvasculature is globally affected in severe DR, reflecting widespread microvascular impairment in perfusion. Arteriolar, venular and capillary parameters provide complementary information in assessment of DR.
Airborne transmission may have played a role in the spread of 2015 highly pathogenic avian influenza outbreaks in the United States
Authors: Zhao Yang , Richardson Brad , Takle Eugene , Chai Lilong , Schmitt David , Xin Hongwei 
Published: August 2019

AbstractThe unprecedented 2015 outbreaks of highly pathogenic avian influenza (HPAI) H5N2 in the U.S. devastated its poultry industry and resulted in over $3 billion economic impacts. Today HPAI continues eroding poultry operations and disrupting animal protein supply chains around the world. Anecdotal evidence in 2015 suggested that in some cases the AI virus was aerially introduced into poultry houses, as abnormal bird mortality started near air inlets of the infected houses. This study modeled air movement trajectories and virus concentrations that were used to assess the probability or risk of airborne transmission for the 77 HPAI cases in Iowa. The results show that majority of the positive cases in Iowa might have received airborne virus, carried by fine particulate matter, from infected farms within the state (i.e., intrastate) and infected farms from the neighboring states (i.e., interstate). The modeled airborne virus concentrations at the Iowa recipient sites never exceeded the minimal infective doses for poultry; however, the continuous exposure might have increased airborne infection risks. In the worst-case scenario (i.e., maximum virus shedding rate, highest emission rate, and longest half-life), 33 Iowa cases had > 10% (three cases > 50%) infection probability, indicating a medium to high risk of airborne transmission for these cases. Probability of airborne HPAI infection could be affected by farm type, flock size, and distance to previously infected farms; and more importantly, it can be markedly reduced by swift depopulation and inlet air filtration. The research results provide insights into the risk of airborne transmission of HPAI virus via fine dust particles and the importance of preventative and containment strategies such as air filtration and quick depopulation of infected flocks.
Defining and detecting links in chromosomes
Authors: Niewieczerzal Szymon , Niemyska Wanda , Sulkowska Joanna I. 
Published: August 2019

AbstractSophisticated methods for mapping chromatin contacts enable to generate data of the genome structure that provide deep insights into the formation of chromatin interactions within cell nuclei. Due to the recent progress in this field, three-dimensional genomic structures of individual haploid mouse embryonic stem cells have been determined. Here, we analyze these data (8 cells) and determine comprehensive landscape of entanglements between interphase chromosomes. We find a significant number of stable links formed by chromosome pairs. Some links are even conserved between cells. Moreover, examples of stable multiple links, with at least three chromosomes engaged, are also identified. Types of links and their location along chromosomes are determined based on computations of HOMFLY-PT polynomials and Gauss Linking Numbers. Furthermore, stability of links is studied between different models, cells, and based on relaxation simulations of the genomic structure in a simplified structure-based representation. Identified links suggest that small fraction of chromosomes are entangled not only locally. How topoisomerases engineer such configurations remains an open question. Furthermore, presented methods can be used as a quantitative assessment – descriptor – to distinguish the quality of modeled data.
Establishment of serine protease htrA mutants in Helicobacter pylori is associated with secA mutations
Authors: Zawilak-Pawlik Anna , Zarzecka Urszula , Żyła-Uklejewicz Dorota , Lach Jakub , Strapagiel Dominik , Tegtmeyer Nicole , Böhm Manja , Backert Steffen , Skorko-Glonek Joanna 
Published: August 2019

AbstractHelicobacter pylori plays an essential role in the pathogenesis of gastritis, peptic ulcer disease, and gastric cancer. The serine protease HtrA, an important secreted virulence factor, disrupts the gastric epithelium, which enables H. pylori to transmigrate across the epithelium and inject the oncogenic CagA protein into host cells. The function of periplasmic HtrA for the H. pylori cell is unknown, mainly due to unavailability of the htrA mutants. In fact, htrA has been described as an essential gene in this bacterium. We have screened 100 worldwide H. pylori isolates and show that only in the N6 strain it was possible to delete htrA or mutate the htrA gene to produce proteolytically inactive HtrA. We have sequenced the wild-type and mutant chromosomes and we found that inactivation of htrA is associated with mutations in SecA – a component of the Sec translocon apparatus used to translocate proteins from the cytoplasm into the periplasm. The cooperation of SecA and HtrA has been already suggested in Streptococcus pneumonia, in which these two proteins co-localize. Hence, our results pinpointing a potential functional relationship between HtrA and the Sec translocon in H. pylori possibly indicate for the more general mechanism responsible to maintain bacterial periplasmic homeostasis.
Amino acid supplementation of a simple inorganic salt solution supports efficient in vitro maturation (IVM) of bovine oocytes
Authors: Bahrami Mohammad , Morris Michael B. , Day Margot L. 
Published: August 2019

AbstractDefining oocyte in vitro maturation (IVM) conditions allows for improved reproducibility and efficiency of bovine embryo production. IVM conditions for bovine oocytes have been extensively studied, but beneficial effects of individual supplements remain controversial. This study compared methods of cumulus oocyte complex (COC) isolation, and culture medium requirements, for IVM in order to define optimal conditions. Antral follicles in ovaries were sliced or aspirated to isolate COCs. Brilliant cresyl blue staining of COCs was used to determine the most effective collection technique and the effect of hormones and groups of amino acids in the culture medium was investigated. Our results showed COCs isolated through aspiration had greater meiotic competency to reach MII. Oocyte maturation was achieved with the addition of 1 µg/mL FSH, while estrogen and human chorionic gonadotrophin did not increase the number of MII oocytes. We also provide novel data, that supplementation of a simple inorganic salt solution with L-proline, L-glutamine and essential amino acids in combination, but not individually, resulted in nuclear maturation comparable to TCM199, a more complex medium containing all 20 common amino acids, vitamins, inorganic salts and FBS. Replacement of FBS with BSA in this simplified medium creates a defined medium which provides conditions for IVM that enable reproducible maturation rates.
Predicting seismic-induced liquefaction through ensemble learning frameworks
Authors: Alobaidi Mohammad H. , Meguid Mohamed A. , Chebana Fateh 
Published: August 2019

AbstractThe regional nature of liquefaction records and limited information available for a certain set of explanatories motivate the development of complex prediction techniques. Indirect methods are commonly applied to incidentally derive a hyperplane to this binary classification problem. Machine learning approaches offer evolutionary prediction models which can be used as direct prediction methods to liquefaction occurrence. Ensemble learning is a recent advancement in this field. According to a predefined ensemble architecture, a number of learners are trained and their inferences are integrated to produce stable and improved generalization ability. However, there is a need to consider several aspects of the ensemble learning frameworks when exploiting them for a particular application; a comprehensive evaluation of an ensemble learner’s generalization ability is required but usually overlooked. Also, the literature falls short on work utilizing ensemble learning in liquefaction prediction. To this extent, this work examines useful ensemble learning approaches for seismic-induced liquefaction prediction. A comprehensive analysis of fifteen ensemble models is performed. The results show improved prediction performance and diminishing uncertainty of ensembles, compared with single machine learning models.