bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum computation is the unique reversible circuit model for which bits are balls
Authors: Krumm Marius , Müller Markus P. 
Published: January 2019

AbstractThe computational efficiency of quantum mechanics can be characterized in terms of the qubit circuit model, which is defined by a few simple properties: each computational gate is a reversible transformation in a connected matrix group; single wires carry quantum bits, i.e. states of a three-dimensional Bloch ball; states on two or more wires are uniquely determined by local measurement statistics and their correlations. In this paper, we ask whether other types of computation are possible if we relax one of those characteristics (and keep all others), namely, if we allow wires to be described by d-dimensional Bloch balls, where d is different from three. Theories of this kind have previously been proposed as possible generalizations of quantum physics, and it has been conjectured that some of them allow for interesting multipartite reversible transformations that cannot be realized within quantum theory. However, here we show that all such potential beyond-quantum models of computation are trivial: if d is not three, then the set of reversible transformations consists entirely of single-bit gates, and not even classical computation is possible. In this sense, qubit quantum computation is an island in theoryspace.
No Association between staging operation and the 5-Year Risk of Reoperation in Patients with Crohn’s Disease
Authors: Zhou Jiajie , Li Yi , Gong Jianfeng , Zhu Weiming 
Published: January 2019

AbstractThe aim of this study was to investigate the impact of staging operation on the risk of reoperation in patients with CD who underwent primary bowel resection. This was a retrospective study of 980 patients with CD who were hospitalized in Jinling Hospital Affiliated to Nanjing Medical University between January 1, 2001, and October 1, 2016. The patients were grouped according to staging operation (n = 64) and one-stage operation (n = 148). Postoperative intestinal function recovery time, postoperative short-term complications, and reoperation rates were compared between the two groups. There was significant difference in disease behavior between the staging operation group and the one-stage operation group. There was no significant difference in postoperative tolerance of enteral nutrition among groups (P > 0.05). Obvious differences were found in the comparison of the first time of exhaustion, defecation after operation, postoperative length of stay and postoperative complications among groups (all P < 0.05). There was no difference in the 5-year cumulative reoperation-free rates between the two groups (P > 0.05). In conclusion, surgical intervention at proper time and appropriate operation during operation are essential for patients with CD. It is believed that staging operation with ostomy followed by intestinal anastomosis is feasible when there are more than two risk factors for postoperative intra-abdominal infectious complications.
Non-universality of the dynamic exponent in two-dimensional random media
Authors: Cho Hyun Woo , Yethiraj Arun , Sung Bong June 
Published: January 2019

AbstractThe diffusion of solutes in two-dimensional random media is important in diverse physical situations including the dynamics of proteins in crowded cell membranes and the adsorption on nano-structured substrates. It has generally been thought that the diffusion constant,D, should display universal behavior near the percolation threshold, i.e.,D ~ (ϕ − ϕc)μ, whereϕis the area fraction of the matrix,ϕcis the value ofϕat the percolation threshold, andμis the dynamic exponent. The universality ofμis important because it implies that very different processes, such as protein diffusion in membranes and the electrical conductivity in two-dimensional networks, obey similar underlying physical principles. In this work we demonstrate, using computer simulations on a model system, that the exponentμis not universal, but depends on the microscopic nature of the dynamics. We consider a hard disc that moves via random walk in a matrix of fixed hard discs and show thatμdepends on the maximum possible displacement Δ of the mobile hard disc, ranging from 1.31 at Δ ≤ 0.1 to 2.06 for relatively large values of Δ. We also show that this behavior arises from a power-law singularity in the distribution of transition rates due to a failure of the local equilibrium approximation. The non-universal value ofμobeys the prediction of the renormalization group theory. Our simulations do not, however, exclude the possibility that the non-universal values ofμmight be a crossover between two different limiting values at very large and small values of Δ. The results allow one to rationalize experiments on diffusion in two-dimensional systems.
Mechanistic Target of Rapamycin Complex 1 Promotes the Expression of Genes Encoding Electron Transport Chain Proteins and Stimulates Oxidative Phosphorylation in Primary Human Trophoblast Cells by Regulating Mitochondrial Biogenesis
Authors: Rosario Fredrick J. , Gupta Madhulika B. , Myatt Leslie , Powell Theresa L. , Glenn Jeremy P. , Cox Laura , Jansson Thomas 
Published: January 2019

AbstractTrophoblast oxidative phosphorylation provides energy for active transport and protein synthesis, which are critical placental functions influencing fetal growth and long-term health. The molecular mechanisms regulating trophoblast mitochondrial oxidative phosphorylation are largely unknown. We hypothesized that mechanistic Target of Rapamycin Complex 1 (mTORC1) is a positive regulator of key genes encoding Electron Transport Chain (ETC) proteins and stimulates oxidative phosphorylation in trophoblast and that ETC protein expression is down-regulated in placentas of infants with intrauterine growth restriction (IUGR). We silenced raptor (mTORC1 inhibition), rictor (mTORC2 inhibition) or DEPTOR (mTORC1/2 activation) in cultured term primary human trophoblast (PHT) cells. mTORC1 inhibition caused a coordinated down-regulation of 18 genes encoding ETC proteins representing all ETC complexes. Inhibition of mTORC1, but not mTORC2, decreased protein expression of ETC complexes I–IV, mitochondrial basal, ATP coupled and maximal respiration, reserve capacity and proton leak, whereas activation of mTORC1 had the opposite effects. Moreover, placental protein expression of ETC complexes was decreased and positively correlated to mTOR signaling activity in IUGR. By controlling trophoblast ATP production, mTORC1 links nutrient and O2 availability and growth factor signaling to placental function and fetal growth. Reduced placental mTOR activity may impair mitochondrial respiration and contribute to placental insufficiency in IUGR pregnancies.
Thermodynamics of sustaining liquid water within rough icephobic surfaces to achieve ultra-low ice adhesion
Authors: Zhao Tom Y. , Jones Paul R. , Patankar Neelesh A. 
Published: January 2019

AbstractThe build-up of ice on aircraft, bridges, oil rigs, wind turbines, electrical lines, and other surfaces exposed to cold environments diminishes their safe and effective operation. To engineer robust surfaces that reduce ice adhesion, it is necessary to understand the physics of what makes a surface icephobic (“ice-hating”) as well as the relationship between icephobicity and ice adhesion. Here we elucidate the molecular origin of icephobicity based on ice-surface interactions and characterize the correlation between material icephobicity and liquid wettability. This fundamental understanding of icephobic characteristics enables us to propose a robust design for topologically textured, icephobic surfaces. The design identifies the critical confinement length scale to sustain liquid water (as opposed to ice) in between roughness features and can reduce the strength of ice adhesion by over a factor of twenty-seven compared to traditional hydrophobic surfaces. The reduction in ice adhesion is due to the metastability of liquid water; as ambient ice cleaves from the textured surface, liquid water leaves confinement and freezes – a process which takes the system from a local energy minimum to a global energy minimum. This phase transition generates a detachment force that actively propels ambient ice from the surface.
miR-181a modulates circadian rhythm in immortalized bone marrow and adipose derived stromal cells and promotes differentiation through the regulation of PER3
Authors: Knarr Matthew , Nagaraj Anil Belur , Kwiatkowski Lily J. , DiFeo Analisa 
Published: January 2019

AbstractmiRNAs are important regulators of diverse cellular processes including proliferation, apoptosis, and differentiation. In the context of bone marrow derived stromal cell and adipose derived stromal cell differentiation, miRNAs are established regulators of both differentiation or stemness depending on their target. Furthermore, miRNA dysregulation can play a key role in various disease states. Here we show that miR-181a is regulated in a circadian manner and is induced during both immortalized bone marrow derived stromal cell (iBMSC) as well as primary patient adipose derived stromal cell (PASC) adipogenesis. Enhanced expression of miR-181a in iBMSCs and PASCs produced a robust increase in adipogenesis through the direct targeting of the circadian factor period circadian regulator 3 (PER3). Furthermore, we show that knocking down endogenous miR-181a expression in iBMSC has a profound inhibitory effect on iBMSC adipogenesis through its regulation of PER3. Additionally, we found that miR-181a regulates the circadian dependency of the adipogenesis master regulator PPARγ. Taken together, our data identify a previously unknown functional link between miR-181a and the circadian machinery in immortalized bone marrow stromal cells and adipose derived stromal cells highlighting its importance in iBMSC and ASC adipogenesis and circadian biology.
Comprehensive circRNA expression profile during ischemic postconditioning attenuating hepatic ischemia/reperfusion injury
Authors: Zhang Pengpeng , Ming Yingzi , Ye Qifa , Niu Ying 
Published: January 2019

AbstractIschemic postconditioning (IPO) attenuates hepatic ischemia/reperfusion (I/R) injury. The aim of this study was to explore the role of circular RNAs (circRNAs) in the protective mechanism of IPO. In this study, microarray hybridization analysis was performed to determine the circRNA expression profile. Briefly, a total of 1599 dysregulated circRNAs were detected. The competitive endogenous RNA (ceRNA) network, including 6 circRNAs, 47 miRNAs and 90 mRNAs, indicated that the potential “housekeeping” function of circRNAs is dysregulated in hepatic I/R injury. Based on the validation results of selected circRNAs, miRNAs and mRNAs following qRT-PCR amplification, the mmu_circRNA_005186-miR-124-3p-Epha2 pathway was constructed. Dual-luciferase reporter analysis showed that miR-124-3p interacted directly with mmu_circRNA_005186 and Epha2 through the predicted binding sites, which suggested that mmu_circRNA_005186, serving as a miRNA sponge for miR-124-3p, regulated the expression of Epha2. Functionally, we explored the mechanism of mmu_circRNA_005186 in LPS-treated RAW264.7 cells which simulated the inflammation in hepatic I/R injury. We found that mmu_circRNA_005186 silencing attenuated the LPS-induced inflammation and was associated with miR-124-3p upregulation and Epha2 downregulation. Our study is the first to show that circRNAs are closely related to hepatic I/R injury and IPO and suggests that targeting mmu_circRNA_005186-miR-124-3p-Epha2 pathway might attenuate hepatic I/R injury.
High lactose whey cheese consumption and risk of colorectal cancer - The Norwegian Women and Cancer Study
Authors: Barnung Runa Borgund , Jareid Mie , Lukic Marko , Oyeyemi Sunday Oluwafemi , Rudolfsen Jan Håkon , Sovershaeva Evgeniya , Skeie Guri 
Published: January 2019

AbstractThe incidence of colorectal cancer (CRC) has increased among Norwegian women, and is among the highest in the world. In order to understand this increase, country specific dietary exposures have been investigated. The aim of this study was to quantify the association between consumption of brown cheese, a common bread topping in Norway, and colorectal, colon, and rectal cancer in the prospective Norwegian Women and Cancer (NOWAC) Study. Data on brown cheese consumption and adjustment factors was available for 82 527 women. During a mean of 14.6 years of follow-up (1.2 million person-years), there were 1360 cases of colorectal cancer (907 colon; 453 rectal). Multivariable Cox proportional hazards models were used to calculate hazard ratios (HR) with 95% confidence intervals (CI) for colorectal, colon, and rectal cancer sites. We modelled restricted cubic splines with 4 knots, to assess a possible non-linear relationship between brown cheese intake and the investigated cancer sites. In the age-adjusted model, consumption of more than 2 slices (>16 grams) of brown cheese per day was associated with 13% reduced risk of colon cancer (95% CI 4%-21%) compared to women who did not consume brown cheese. The multivariable-adjusted model, however, showed no association between brown cheese consumption and the risk of colorectal, colon, or rectal cancer (colorectal: HR = 0.93, 95% CI 0.76–1.13, p-trend 0.37; colon: HR = 0.83, 95% CI 0.65–1.06; p-trend = 0.10; rectal: HR = 1.16, 95% CI 0.84–1.1.61, p-trend = 0.41). In this large, prospective cohort study of women, consumption of brown cheese was suggestively protective against colon cancer. However, adjustment attenuated the inverse risk association. Brown cheese consumption was not associated with rectal cancer, or colorectal cancer overall.
Comparison of whole-body MRI, bone scan, and radiographic skeletal survey for lesion detection and risk stratification of Langerhans Cell Histiocytosis
Authors: Kim Jeong Rye , Yoon Hee Mang , Jung Ah Young , Cho Young Ah , Seo Jong Jin , Lee Jin Seong 
Published: January 2019

AbstractAccurate risk stratification according to the extent of Langerhans cell histiocytosis (LCH) determined on whole-body evaluation is important for determining the treatment plans and prognosis in patients with LCH. This study aimed to compare the lesion detectability and the accuracy of risk stratification of skeletal survey, bone scan, and whole-body magnetic resonance imaging (WB-MRI) in patients with LCH. Patients with newly-diagnosed LCH who underwent all three imaging modalities were retrospectively included (n = 46). The sensitivity and mean number of false-positives per patient for LCH lesions, and the accuracy of risk stratification of each modality were assessed. WB-MRI had significantly higher sensitivity (99.0%; 95% confidence interval, 93.2–99.9%) than skeletal survey (56.6%; p < 0.0001) and bone scan (38.4%; p < 0.0001) for LCH lesions, and there were no significant differences in the number of false-positives per patient (p > 0.017). WB-MRI tended to have higher accuracy for the risk stratification than skeletal survey and bone scan (concordance rate of 0.98, 0.91, and 0.83, respectively), although the differences were not significant (overall p-value 0.066). In conclusion, WB-MRI had higher detectability for LCH lesions than skeletal survey and bone scan, while the three whole-body imaging modalities had comparable accuracy in the initial risk stratification of LCH.
Contagious yawning in virtual reality is affected by actual, but not simulated, social presence
Authors: Gallup Andrew C. , Vasilyev Daniil , Anderson Nicola , Kingstone Alan 
Published: January 2019

AbstractContagious yawning occurs in humans and a few other highly social animals following the detection of yawns in others, yet the factors influencing the propagation of this response remain largely unknown. Stemming from earlier laboratory research, we conducted five experiments to investigate the effects of social presence on contagious yawning in virtual reality (VR). We show that, similar to a traditional laboratory setting, having a researcher present during testing significantly inhibited contagious yawning in VR, even though participants were viewing a virtual environment and unable to see the researcher. Unlike previous research, however, manipulating the social presence in VR (i.e., embedding recording devices and humanoid avatars within the simulation) did not affect contagious yawning. These experiments provide further evidence that social presence is a powerful deterrent of yawning in humans, which warrants further investigation. More generally, these findings also have important applications for the use of VR in psychological research. While participants were quite sensitive to social stimuli presented in VR, as evidenced by contagious yawning, our results suggest a major difference in the influence of social factors within real-world and virtual environments. That is, social cues in actual reality appear to dominate and supersede those in VR.
Cancer cell migration on elongate protrusions of fibroblasts in collagen matrix
Authors: Miyazaki Kaoru , Oyanagi Jun , Hoshino Daisuke , Togo Shinsaku , Kumagai Hiromichi , Miyagi Yohei 
Published: January 2019

AbstractCancer-associated fibroblasts (CAFs) play critical roles in the tumor progression. However, it remains unclear how cancer cells migrate in the three-dimensional (3D) matrix of cancer tissues and how CAFs support the cancer invasion. Here we propose a novel mechanism of fibroblast-dependent cancer cell invasion in the 3D collagen matrix. Human cancer cell lines from the pancreas (Panc-1), lung (A549) and some other organs actively adhered to normal fibroblasts and primary lung CAFs in cultures. To show its significance in tumor invasion, we designed a new invasion assay in which homogeneous microspheroids consisting of cancer cells and fibroblasts were embedded into collagen gel. Time-lapse experiments showed that cancer cells adhered to and quickly migrated on the long protrusions of fibroblasts in the 3D collagen matrix. Fibroblast-free cancer cells poorly invaded the matrix. Experiments with function-blocking antibodies, siRNAs, and immunocytochemistry demonstrated that cancer cells adhered to fibroblasts through integrin α5β1-mediated binding to fibronectin on the surface of fibroblasts. Immunochemical analyses of the co-cultures and lung cancers suggested that cancer cells could acquire the migratory force by the fibronectin/integrin signaling. Our results also revealed that the fibroblast-bound fibronectin was a preferential substrate for cancer cells to migrate in the collagen matrix.
Piwi-interacting RNA (piRNA) expression patterns in pearl oyster (Pinctada fucata) somatic tissues
Authors: Huang Songqian , Ichikawa Yuki , Igarashi Yoji , Yoshitake Kazutoshi , Kinoshita Shigeharu , Omori Fumito , Maeyama Kaoru , Nagai Kiyohito , Watabe Shugo , Asakawa Shuichi 
Published: January 2019

AbstractPiwi-interacting RNAs (piRNAs) belong to a recently discovered class of small non-coding RNAs whose best-understood function is repressing transposable element activity. Most piRNA studies have been conducted on model organisms and little is known about piRNA expression and function in mollusks. We performed high-throughput sequencing of small RNAs extracted from the mantle, adductor muscle, gill, and ovary tissues of the pearl oyster, Pinctada fucata. RNA species with sequences of approximately 30 nt were widely expressed in all tissues. Uridine at the 5′ terminal and protection from β-elimination at the 3′ terminal suggested that these were putative piRNAs. A total of 18.0 million putative piRNAs were assigned to 2.8 million unique piRNAs, and 35,848 piRNA clusters were identified. Mapping to the reference genome showed that 25% of the unique piRNAs mapped to multiple tandem loci on the scaffold. Expression patterns of the piRNA clusters were similar within the somatic tissues, but differed significantly between the somatic and gonadal tissues. These findings suggest that in pearl oysters piRNAs have important and novel functions beyond those in the germ line.
Targeting HIV-1 Protease Autoprocessing for High-throughput Drug Discovery and Drug Resistance Assessment
Authors: Huang Liangqun , Li Linfeng , Tien ChihFeng , LaBarbera Daniel V. , Chen Chaoping 
Published: January 2019

AbstractHIV-1 protease autoprocessing liberates the free mature protease from its Gag-Pol polyprotein precursor through a series of highly regulated autoproteolysis reactions. Herein, we report the development and validation (Z’ ≥ 0.50) of a cell-based functional assay for high-throughput screening (HTS) of autoprocessing inhibitors using fusion precursors in combination with AlphaLISA (amplified luminescent proximity homogeneous assay ELISA). Through pilot screening of a collection of 130 known protease inhibitors, the AlphaLISA assay confirmed all 11 HIV protease inhibitors in the library capable of suppressing precursor autoprocessing at low micromolar concentrations. Meanwhile, other protease inhibitors had no impact on precursor autoprocessing. We next conducted HTS of ~23,000 compounds but found no positive hits. Such high selectivity is advantageous for large-scale HTS campaigns and as anticipated based on assay design because a positive hit needs simultaneously to be nontoxic, cell permeable, and inhibiting precursor autoprocessing. Furthermore, AlphaLISA quantification of fusion precursors carrying mutations known to cause resistance to HIV protease inhibitors faithfully recapitulated the reported resistance, suggesting that precursor autoprocessing is a critical step contributing to drug resistance. Taken together, this reported AlphaLISA platform will provide a useful tool for drug discovery targeting HIV-1 protease autoprocessing and for quantification of PI resistance.
Computational modeling of RNA 3D structure based on experimental data
Authors: Ponce-Salvatierra Almudena , Astha  , Merdas Katarzyna , Nithin Chandran , Ghosh Pritha , Mukherjee Sunandan , Bujnicki Janusz M. 
Published: January 2019

Abstract
RNA molecules are master regulators of cells. They are involved in a variety of molecular processes: they transmit genetic information, sense cellular signals and communicate responses, and even catalyze chemical reactions. As in the case of proteins, RNA function is dictated by its structure and by its ability to adopt different conformations, which in turn is encoded in the sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore the majority of known RNAs remain structurally uncharacterized. To address this problem, predictive computational methods were developed based on the accumulated knowledge of RNA structures determined so far, the physical basis of the RNA folding, and taking into account evolutionary considerations, such as conservation of functionally important motifs. However, all theoretical methods suffer from various limitations, and they are generally unable to accurately predict structures for RNA sequences longer than 100-nt residues unless aided by additional experimental data. In this article, we review experimental methods that can generate data usable by computational methods, as well as computational approaches for RNA structure prediction that can utilize data from experimental analyses. We outline methods and data types that can be potentially useful for RNA 3D structure modeling but are not commonly used by the existing software, suggesting directions for future development.