bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex
Authors: Jessop Matthew , Arragain Benoit , Miras Roger , Fraudeau Angélique , Huard Karine , Bacia-Verloop Maria , Catty Patrice , Felix Jan , Malet Hélène , Gutsche Irina 
Published: January 2020

AbstractThe hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI form a 3.3 MDa cage, proposed to assist assembly of specific respiratory complexes in E. coli. Here, we show that inside the LdcI-RavA cage, RavA hexamers adopt an asymmetric spiral conformation in which the nucleotide-free seam is constrained to two opposite orientations. Cryo-EM reconstructions of free RavA reveal two co-existing structural states: an asymmetric spiral, and a flat C2-symmetric closed ring characterised by two nucleotide-free seams. The closed ring RavA state bears close structural similarity to the pseudo two-fold symmetric crystal structure of the AAA+ unfoldase ClpX, suggesting a common ATPase mechanism. Based on these structures, and in light of the current knowledge regarding AAA+ ATPases, we propose different scenarios for the ATP hydrolysis cycle of free RavA and the LdcI-RavA cage-like complex, and extend the comparison to other AAA+ ATPases of clade 7.
Early prediction of extubation failure in patients with severe pneumonia: a retrospective cohort study
Authors: Yu He , Luo Jian , Ni Yuenan , Hu Yuehong , Liu Dan , Wang Maoyun , Liang Binmiao , Liang Zongan 
Published: January 2020

Abstract
Backgroud: Severe pneumonia is one of the most common causes for mechanical ventilation. We aimed to early identify severe pneumonia patients with high risk of extubation failure in order to improve prognosis.
Methods: From April 2014 to December 2015, medical records of intubated patients with severe pneumonia in intensive care unit were retrieved from database. Patients were divided into extubation success and failure groups, and multivariate logistic regressions were performed to identify independent predictors for extubation failure.
Results: A total of 125 eligible patients were included, of which 82 and 43 patients had extubation success and failure, respectively. APACHE II score (odds ratio (OR) 1.141, 95% confident interval (CI) 1.022–1.273, P = 0.019, cutoff at 17.5), blood glucose (OR 1.122, 95%CI 1.008–1.249, P = 0.035, cutoff at 9.87 mmol/l), dose of fentanyl (OR 3.010, 95%CI 1.100–8.237, P = 0.032, cutoff at 1.135 mg/d), and the need for red blood cell (RBC) transfusion (OR 2.774, 95%CI 1.062–7.252, P = 0.037) were independent risk factors for extubation failure.
Conclusion: In patients with severe pneumonia, APACHE II score &gt; 17.5, blood glucose &gt; 9.87 mmol/l, fentanyl usage &gt; 1.135 mg/d, and the need for RBC transfusion might be associated with higher risk of extubation failure.
Carcinogenesis effects of E2F transcription factor 8 (E2F8) in hepatocellular carcinoma outcomes: an integrated bioinformatic report
Authors: Lü Ying , Zhang Jing , Li Lei , Li Shun , Yang Zongguo 
Published: January 2020

Abstract
This report aimed to investigate the carcinogenesis effects of E2F transcription factor 8 (E2F8) in hepatocellular carcinoma (HCC). E2F8 expression level was compared in Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and Oncomine. Survival analysis of E2F8 for HCC were conducted in Kaplan–Meier plotter. Correlations of E2F8 and clinico-pathological features were performed in TCGA. Enrichment of interacted and similar genes with E2F8 was evaluated in Gene Set Enrichment Analysis (GSEA) and Metascape. We found that E2F8 was significantly up-regulated in tumor tissues compared with nontumor tissues (all P &lt; 0.01). Moreover, E2F8 was significantly overexpressed in peripheral blood mononuclear cell (PBMC) in HCC patients than that in healthy individuals (P &lt; 0.001). Meta-analysis in Oncomine database confirmed that E2F8 was significantly higher in HCC tumors (P = 4.28E-08). Additionally, E2F8 elevation significantly correlated with overall survival (OS), recurrence-free survival (RFS), disease-specific survival (DSS) and progression-free survival (PFS) in HCC patients (all P &lt; 0.01). E2F8 level was significantly higher in HCC patients with advanced neoplasm histologic grade, American Joint Committee on Cancer (AJCC) stage and α-fetoprotein (AFP) elevation (all P &lt; 0.05). Cox regression model demonstrated that high E2F8 was an independent risk factor for OS and DFS in HCC patients (HR = 2.16, P = 0.003 and HR = 1.64, P = 0.002, respectively). Enrichment analysis revealed that genes interacted/similar with E2F8 were mainly enriched in cell cycle pathways/biological process. Conclusively, up-regulated in tumors, E2F8 might accelerate tumor progression and result in unfavorable outcomes in HCC patients.
Effect of system dynamics in multi‐channel 850 nm VCSEL‐based radio‐over‐G.652 fibre
Authors: Nanni J. , Fernandez L. , Hadi M.U. , Viana C. , Tegegne Z.G. , Polleux J.‐L. , Tartarini G. 
Published: January 2020

To decrease cost and consumption of future wireless infrastructures, radio‐over fibre systems utilising 850 nm vertical cavity surface emitting lasers and standard single‐mode fibre (SSMF) are deserving particular attention in replacing the typical use of graded‐index multimode fibre (GI‐MMF). In the present work, a characterisation of noise and non‐linearities of these links is performed, followed by an estimation of their impact on the system dynamics and the quality of the received signal. This allows to show that very good and similar performances can be obtained through the utilisation of SSMF and GI‐MMF for the transmission of five long‐term evolution channels with 20 MHz bandwidth, confirming that the former, by the higher diffusion and lower cost per metre of the SSMF, can be put among the leading candidates for the realisation of fourth‐generation (4G) and 5G wireless networks.
Regularised primal–dual interior‐point method for dynamic optimal power flow with block‐angular structures
Authors: Zhang Chen , Jian Jinbao , Yang Linfeng 
Published: January 2020

To implement privacy protection and high‐efficiency distributed computing of the large‐scale dynamic optimal power flow (DOPF) of the multi‐area interconnected power system, the regularised term (RT) and primal–dual interior‐point method (PDIPM), denoted by R‐PDIPM, is proposed to distribute and parallel such DOPF solutions. First, the DOPF is transformed into a prime block‐angular problem through the replication of the coupling node variables, and the multi‐area decoupling of the power grid is realised. However, it is easier to develop a singular (ill‐conditioned) block matrix of Newton's system under the distributed computing of PDIPM. Second, though introducing the RT into the Lagrangian function of PDIPM based on regular technology, the matrix of Newton's system becomes quasi‐definite and strongly factorisable. The robustness of distributed computing of PDIPM is enhanced, and the convergence speed is also improved. Case studies on the 3012 and 3074 node systems over 2–4 time intervals are presented. The results show that the R‐PDIPM is more robust in efficiently solving the problem than PDIPM in distributed computing, which is suited for distributed calculation of DOPF in a large‐scale multi‐area power system.
La Corée du Sud à la recherche du leadership mondial sur les technologies de l’hydrogène
Authors: Masy Jean-Claude , Guidez Joël 
Published: January 2020

Le développement de l’économie de l’hydrogène est devenu une des priorités des autorités sud-coréennes, avec la publication en janvier 2019 d’une feuille de route ambitieuse : devenir le leader mondial dans le domaine de la voiture à hydrogène. Ce plan est soutenu par un budget conséquent d’aide à la R&D et aux constructeurs nationaux. Cette politique est bien relayée au niveau des villes, qui y voient un moyen d’améliorer la qualité de l’air. Mais à quel prix en termes d’émissions de CO2 ?
Artificial Intelligence in Radiology Residency Training
Authors: Forney Michael C. , McBride Aaron F. 
Published: January 2020

AbstractArtificial intelligence (AI) is an emerging technology that brings a wide array of new tools to the field of radiology. AI will certainly have an impact on the day-to-day work of radiologists in the coming decades, thus training programs must prepare radiology residents adequately for their future careers. Radiology training programs should aim to give residents an understanding of the fundamentals and types of AI in radiology, the broad areas AI can be applied in radiology, how to assess AI applications in radiology, and resources available to build their knowledge in IA applications in radiology.
How Do I Counsel Parents of a Newly Diagnosed Boy with Haemophilia A?
Authors: Kurnik Karin , Bidlingmaier Christoph , Olivieri Martin 
Published: January 2020

AbstractWith the recent approval of improved therapeutic options for patients suffering from haemophilia A such as the extended half-life, recombinant factor concentrates, non-factor VIII replacement therapies like Emicizumab and after consideration of the currently running clinical trials investigating even more advanced approaches, counselling of parents of a newly diagnosed boy with haemophilia A has not become less demanding. Parents need to be informed about the pathophysiology, the chronic nature and the potential risks that are commonly associated with this disease and its treatment, depending on disease severity. Above all, the safety and efficacy of the medicinal drug(s) to be used are of utmost importance, given the impact of non-virus-inactivated plasma-derived factor concentrates in the 1980s. As a consequence, the subsequent development and registration of recombinant clotting factors from mammalian, and recently, even human, cell cultures are seen by many as a breakthrough, although, regarding the product-type-dependent development of inhibitors in previously untreated patients, the discussion is still open. Clinical data for the humanised bispecific antibody Emicizumab in paediatric patients below 2 years of age without inhibitors who suffer from severe haemophilia A are currently limited.
Endothelial sphingosine 1-phosphate receptors promote vascular normalization and antitumor therapy
Authors: Cartier Andreane , Leigh Tani , Liu Catherine H. , Hla Timothy 
Published: January 2020

Significance
Tumor progression is dependent on angiogenesis, which supplies nutrients and enables gas exchange and metastatic dissemination. However, tumor vessels are dysfunctional and immature, which hinders the effectiveness of various therapeutics. Sphingosine 1-phosphate receptors in endothelial cells are essential for developmental angiogenesis and physiological functions such as the maintenance of the vascular barrier and vascular tone. This study shows that endothelial sphingosine 1-phosphate receptors determine the tumor vascular phenotype and maturation and that function of S1P receptor-1 is needed for tumor vascular normalization, which allows better blood circulation and enhances antitumor therapeutic efficacy in mouse models.
Organelle-specific targeting of polymersomes into the cell nucleus
Authors: Zelmer Christina , Zweifel Ludovit P. , Kapinos Larisa E. , Craciun Ioana , Güven Zekiye P. , Palivan Cornelia G. , Lim Roderick Y. H. 
Published: January 2020

Significance
Synthetic nanomaterials are being sought to shuttle therapeutic payloads directly into the cell nucleus as a major target for chemo- and gene-based therapies. However, it remains uncertain whether and how synthetic entities are able to bypass the nuclear pore complexes (NPCs) that regulate transport into and out of the nucleus. We have constructed biocompatible polymer vesicles that infiltrate NPCs and resolved their nuclear uptake mechanism in vitro and in vivo. Their ability to deliver payloads directly into cell nuclei is further validated by transmission electron microscopy.
Control of cellular organization and its coordination with the cell cycle
Authors: Kume Kazunori 
Published: January 2020

AbstractCells organize themselves to maintain proper shape, structure, and size during growth and division for their cellular functions. However, how these cellular organizations coordinate with the cell cycle is not well understood. This review focuses on cell morphogenesis and size of the membrane-bound nucleus in the fission yeast Schizosaccharomyces pombe. Growth polarity, an important factor for cell morphogenesis, in rod-shaped fission yeast is restricted to the cell tips and dynamically changes depending on the cell cycle stage. Furthermore, nuclear size in fission yeast is proportional to the cell size, resulting in a constant ratio between nuclear volume and cellular volume (N/C ratio). This review summarizes the signaling pathway(s) involved in growth polarity control and key factors involved in N/C ratio control and provides their roles in coordination between cell organization and the cell cycle.
Lattice-Boltzmann simulations of the dynamics of liquid barrels
Authors: Ruiz-Gutiérrez Élfego , Ledesma-Aguilar Rodrigo 
Published: January 2020

Abstract
We study the relaxation towards equilibrium of a liquid barrel—a partially wetting droplet in a wedge geometry—using a diffuse-interface approach. We formulate a hydrodynamic model of the motion of the barrel in the framework of the Navier–Stokes and Cahn–Hilliard equations of motion. We present a lattice-Boltzmann method to integrate the diffuse-interface equations, where we introduce an algorithm to model the dynamic wetting of the liquid on smooth solid boundaries. We present simulation results of the over-damped dynamics of the liquid barrel. We find that the relaxation of the droplets is driven by capillary forces and damped by friction forces. We show that the friction is determined by the contribution of the bulk flow, the corner flow near the contact lines and the motion of the contact lines by comparing simulation results for the relaxation time of the barrel. Our results are in broad agreement with previous analytical predictions based on a sharp interface model.
A highly sensitive laser focus positioning method with sub-micrometre accuracy using coherent Fourier scatterometry
Authors: Kolenov Dmytro , Meng Peiwen , Pereira Silvania 
Published: January 2020

Abstract
We report a novel method of focus determination with high sensitivity and submicrometre accuracy. The technique relies on the asymmetry in the scattered far field from a nanosphere located at the surface of interest. The out-of-focus displacement of the probing beam manifests itself in imbalance of the signal of the differential detector located at the far field. Up–down scanning of the focussed field renders an error S-curve with a linear region that is slightly bigger than the corresponding vectorial Rayleigh range. We experimentally show that the focus can be determined not only for a surface with high optical contrast, such as a silicon wafer, but also for a weakly reflecting surface, such as fused silica glass. Further, for the probing wavelength of 405 nm, three sizes of polystyrene latex spheres, namely 200, 100, and 50 nm in diameter, are tested. Higher sensitivity was obtained as the sphere diameter became smaller. However, due to the fact that the scattering cross-section decreases as the sixth power of the nanosphere diameter, we envision that further size reduction of the studied sphere would not contribute to a drastic improvement in sensitivity. We believe that the proposed method can find applications in bio/nano detection, micromachining, and optical disk applications.
A temperature-dependent multilayer model for direct current carrying HTS coated-conductors under perpendicular AC magnetic fields
Authors: Ma Jun , Geng Jianzhao , Chan Wan Kan , Schwartz Justin , Coombs Tim 
Published: January 2020

Abstract
When a type II superconductor carrying a direct current is subjected to a perpendicular oscillating magnetic field, a direct current (DC) voltage will appear. This voltage can either result from dynamic resistance effect or from flux flow effect, or both. The temperature variation in the superconductor plays an important role in the nature of the voltage, and there has been little study of this so far. This paper presents and experimentally verifies a 2D temperature-dependent multilayer model of the second generation (2G) high temperature superconducting (HTS) coated conductors (CC), which is based on H-formulation and a general heat transfer equation. The model has coupled the electromagnetic and thermal physics, and it can simulate the behavior of 2G HTS coated conductors in various working conditions where the temperature rise has a significant impact. Representative electromagnetic phenomena such as the dynamic resistance effect and the flux flow effect, and thermal behavior like quench and recovery have been simulated. This thermal-coupled model is a powerful tool to study the thermal-electromagnetic behaviors of 2G HTS coated conductors in different working conditions, especially when the impact of temperature rise is important. This multilayer model is also very useful in analyzing the impact of different layers in the 2G HTS CCs, especially the metal stabilizer layers. It has been proven to be a very powerful tool to help understand more complicated characteristics in the CCs which could not be accurately measured or simulated by previous numerical models. The work is indicative and very useful in designing ac magnetic field controlled persistent current switches and flux pumps, in terms of increasing the off-state resistance, analyzing different sources of losses, minimizing detrimental losses, and enhancing the safety and stability.
Neutron/gamma pulse discrimination analysis of GS10 lithium glass and EJ-204 plastic scintillators
Authors: Hamrashdi H. Al , Monk S.D. , Cheneler D. 
Published: January 2020

Two radiation sensitive scintillators known for their dual sensitivity to neutron and gamma-ray fields are investigated for their pulse discrimination abilities; a lithium glass GS10 inorganic scintillator and a fast organic plastic scintillator EJ-204. Each of these scintillators are optically coupled with an 8 × 8-silicon photomultiplier array to act as a photodetector. Pulse height analysis, the charge comparison method and pulse gradient analysis have all been applied here on neutron and gamma-ray events generated by a Cf-252 source. The three discrimination methods were evaluated based on the figure of merit of the probability density plots generated. Within a GS10 crystal, it has been deduced that pulse height analysis and pulse gradient analysis possess greater abilities to discriminate between the two radiation fields compared to the charge comparison method with both showing a figure of merit of over one. The charge comparison method indicated a lower discrimination ability with a figure of merit around 0.3. When the EJ-204 detector was used, it was deduced that only pulse height analysis exhibits discrimination abilities with a figure of merit around 0.6, while the other two discrimination methods presented no distinction between the two radiation fields.
Hydrodynamics modeling with MIKE system in the Semak Daun Lagoon, Seribu Islands Indonesia
Authors: Saenuddin  , Nurjaya I W , Bengen D G , Prartono T , Efendi I 
Published: January 2020

Abstract
At low tide condition, the Semak Daun Lagoon (SDL) barrier reef is drowned during high tide and appeared to the surface during low tide. How are hydrodynamics in low tide and tidal conditions? This study aims to examine the pattern and current velocity in the SDL under four tidal conditions. The two-dimension model is built based on two motion generations namely wind pressure and tides. The discretization of the equation uses the finite volume method. Domain discretization is divided into 14,575 triangular elements with a grid area of 1,000 m2. The results of the model, verified with observational data in the field, show the similarity of tidal patterns and current velocity as indicated by the MAPE value of 7.9%, meaning that the model is well constructed. Current patterns generally move from southwest to northeast at high tide to low tide condition and vice versa at low tide to high tide condition. At low tide, there is a buildup of water mass in the lagoon because the only channel north is functioning as an outlet. This causes a slowing of current flow inside the lagoon and acceleration in the northern canal. Current velocity ranges from 0.02-0.51 m.s−1. The pattern and speed of the current in the lagoon are dominantly influenced by tidal dynamics. Residual current velocity varies in the range of 0.01-0.04 m.s−1.
Seasonal variation of the Sunda Shelf Throughflow
Authors: Apriansyah  , Atmadipoera A S 
Published: January 2020

Abstract
The Sunda Shelf Throughflow (SSTF) is defined as a seasonal reversal shallow current system flowing from the South China Sea to the Indonesian Throughflow (ITF) region via the Natuna and Java Seas. This current system plays an important role on transferring heat and freshwater fluxes into the ITF system and vice versa. This paper aims to investigate seasonal changes of transport volume in three sections within the Sunda Shelf region (namely Natuna, Karimata and Java section). We used the validated daily ocean circulation model outputs from INDESO configuration between 2008 and 2014. It is shown that mean transport volume of the SSTF is relatively small on the order of -0.5Sv toward the ITF region (1Sv=106m3/s) due to a strong seasonal reversal flow of the SSTF forced by the monsoonal winds. However, on seasonal scale this transport volume strengthens drastically to about 2-3Sv (1-2 Sv) during the northwest (southeast) monsoon period, which is in good agreement with previous studies. Transport estimate in Java section is reduced to about -0.1Sv may be due to a leakage of the flow via Sunda Strait and also a strong recirculation of Makassar ITF into Java Sea.
Bio-fuel algal waste diet effect on growth and histological structure of Wader Pari (Rasbora lateristriata Bleeker, 1854) intestine
Authors: Manganang Y A P , Hananya A , Pujiyati S , Retnoaji B 
Published: January 2020

Abstract
Sufficient availability of good food quality is important for fish aquaculture in order to increase fish production. Microalga is one of alternative protein sources, and one among those is Chorella sp. Protein content of Chlorella sp. is very high, around 51- 58 % and consists of various kinds of essential fatty acids, which is important for fish nutrition. Recently, Algae also prospective source of ethanol biofuel. Ethanol extraction usually produce waste material, which still consist of high protein content, which valuable for fish feed sources. Therefore, the study aimed to examine the effects of fish food derived from algae biofuel-waste on growth and histological structure of wader pari (Rasbora lateristriata) intestine. Fish were divided into 5 groups of control negative (no additional protein), feed with waste algae, waste + Fresh algae, fresh algae and commercial fish food, respectively. The fish morphometry, weight, and intestine histological structure were examine. The results showed that fish feed treatment gave effect on fish growth and instestine histological structure. Algae waste feed showed similar performance to commercial fish feed on fish growth and showed no negatif effect on intestine villi length and goblet cells number, evidenced good prospect of algae waste as fish feed.