bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast and multiplexed superresolution imaging with DNA-PAINT-ERS
Authors: Civitci Fehmi , Shangguan Julia , Zheng Ting , Tao Kai , Rames Matthew , Kenison John , Zhang Ying , Wu Lei , Phelps Carey , Esener Sadik , Nan Xiaolin 
Published: August 2020

AbstractDNA points accumulation for imaging in nanoscale topography (DNA-PAINT) facilitates multiplexing in superresolution microscopy but is practically limited by slow imaging speed. To address this issue, we propose the additions of ethylene carbonate (EC) to the imaging buffer, sequence repeats to the docking strand, and a spacer between the docking strand and the affinity agent. Collectively termed DNA-PAINT-ERS (E = EC, R = Repeating sequence, and S = Spacer), these strategies can be easily integrated into current DNA-PAINT workflows for both accelerated imaging speed and improved image quality through optimized DNA hybridization kinetics and efficiency. We demonstrate the general applicability of DNA-PAINT-ERS for fast, multiplexed superresolution imaging using previously validated oligonucleotide constructs with slight modifications.
Dual-mode solid-state thermal rectification
Authors: Shrestha Ramesh , Luan Yuxuan , Luo Xiao , Shin Sunmi , Zhang Teng , Smith Phil , Gong Wei , Bockstaller Michael , Luo Tengfei , Chen Renkun , Hippalgaonkar Kedar , Shen Sheng 
Published: August 2020

AbstractThermal rectification is an exotic thermal transport phenomenon which allows heat to transfer in one direction but block the other. We demonstrate an unusual dual-mode solid-state thermal rectification effect using a heterogeneous “irradiated-pristine” polyethylene nanofiber junction as a nanoscale thermal diode, in which heat flow can be rectified in both directions by changing the working temperature. For the nanofiber samples measured here, we observe a maximum thermal rectification factor as large as ~50%, which only requires a small temperature bias of <10 K. The tunable nanoscale thermal diodes with large rectification and narrow temperature bias open up new possibilities for developing advanced thermal management, energy conversion and, potentially thermophononic technologies.
X-ray radiation excited ultralong (>20,000 seconds) intrinsic phosphorescence in aluminum nitride single-crystal scintillators
Authors: Lin Richeng , Zheng Wei , Chen Liang , Zhu Yanming , Xu MengXuan , Ouyang Xiaoping , Huang Feng 
Published: August 2020

AbstractPhosphorescence is a fascinating photoelectronic phenomenon usually observed in rare-earth-doped inorganic crystals and organic molecular crystals, owning great potential in optical information storage, color display and biological dosimetry. Here, we present an ultralong intrinsic phosphorescence (>20,000 seconds) in AlN single-crystal scintillator through X-ray excitation. We suggest that the long afterglow emission originates from the intra-band transition related to native nitrogen vacancy. Some excited states formed by absorbing X-ray photons cannot satisfy the parity difference between initial and final states required by transition selection rule, so they cannot return to the ground state directly through radiation transitions but through several phonon-assisted intra-band transitions slowly. During this process, a long-term broad-spectra phosphorescence emission is formed. Investigating the X-ray excited phosphorescence emission in the AlN is of great significance to understanding the mechanism of phosphorescence in inorganic materials, and to realizing the practical applications in high-energy ray dosimetry.
Incorporating hydrology into climate suitability models changes projections of malaria transmission in Africa
Authors: Smith M. W. , Willis T. , Alfieri L. , James W. H. M. , Trigg M. A. , Yamazaki D. , Hardy A. J. , Bisselink B. , De Roo A. , Macklin M. G. , Thomas C. J. 
Published: August 2020

AbstractContinental-scale models of malaria climate suitability typically couple well-established temperature-response models with basic estimates of vector habitat availability using rainfall as a proxy. Here we show that across continental Africa, the estimated geographic range of climatic suitability for malaria transmission is more sensitive to the precipitation threshold than the thermal response curve applied. To address this problem we use downscaled daily climate predictions from seven GCMs to run a continental-scale hydrological model for a process-based representation of mosquito breeding habitat availability. A more complex pattern of malaria suitability emerges as water is routed through drainage networks and river corridors serve as year-round transmission foci. The estimated hydro-climatically suitable area for stable malaria transmission is smaller than previous models suggest and shows only a very small increase in state-of-the-art future climate scenarios. However, bigger geographical shifts are observed than with most rainfall threshold models and the pattern of that shift is very different when using a hydrological model to estimate surface water availability for vector breeding.
Mitigating the risk of cytokine release syndrome in a Phase I trial of CD20/CD3 bispecific antibody mosunetuzumab in NHL: impact of translational system modeling
Authors: Hosseini Iraj , Gadkar Kapil , Stefanich Eric , Li Chi-Chung , Sun Liping L. , Chu Yu-Waye , Ramanujan Saroja 
Published: August 2020

AbstractMosunetuzumab, a T-cell dependent bispecific antibody that binds CD3 and CD20 to drive T-cell mediated B-cell killing, is currently being tested in non-Hodgkin lymphoma. However, potent immune stimulation with T-cell directed therapies poses the risk of cytokine release syndrome, potentially limiting dose and utility. To understand mechanisms behind safety and efficacy and explore safety mitigation strategies, we developed a novel mechanistic model of immune and antitumor responses to the T-cell bispecifics (mosunetuzumab and blinatumomab), including the dynamics of B- and T-lymphocytes in circulation, lymphoid tissues, and tumor. The model was developed and validated using mosunetuzumab nonclinical and blinatumomab clinical data. Simulations delineated mechanisms contributing to observed cell and cytokine (IL6) dynamics and predicted that initial step-fractionated dosing limits systemic T-cell activation and cytokine release without compromising tumor response. These results supported a change to a step-fractionated treatment schedule of mosunetuzumab in the ongoing Phase I clinical trial, enabling safer administration of higher doses.
A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions
Authors: Gabriel Michael , Fey Vidal , Heinosalo Taija , Adhikari Prem , Rytkönen Kalle , Komulainen Tuomo , Huhtinen Kaisa , Laajala Teemu Daniel , Siitari Harri , Virkki Arho , Suvitie Pia , Kujari Harry , Aittokallio Tero , Perheentupa Antti , Poutanen Matti 
Published: August 2020

AbstractEndometriosis is a common inflammatory estrogen-dependent gynecological disorder, associated with pelvic pain and reduced fertility in women. Several aspects of this disorder and its cellular and molecular etiology remain unresolved. We have analyzed the global gene expression patterns in the endometrium, peritoneum and in endometriosis lesions of endometriosis patients and in the endometrium and peritoneum of healthy women. In this report, we present the EndometDB, an interactive web-based user interface for browsing the gene expression database of collected samples without the need for computational skills. The EndometDB incorporates the expression data from 115 patients and 53 controls, with over 24000 genes and clinical features, such as their age, disease stages, hormonal medication, menstrual cycle phase, and the different endometriosis lesion types. Using the web-tool, the end-user can easily generate various plot outputs and projections, including boxplots, and heatmaps and the generated outputs can be downloaded in pdf-format.Availability and implementationThe web-based user interface is implemented using HTML5, JavaScript, CSS, Plotly and R. It is freely available from https://endometdb.utu.fi/.
Uncovering a high-performance bio-mimetic cellular structure from trabecular bone
Authors: Ghazlan Abdallah , Ngo Tuan , Nguyen Tuan , Linforth Steven , Van Le Tu 
Published: August 2020

AbstractThe complex cellular structure of trabecular bone possesses lightweight and superior energy absorption capabilities. By mimicking this novel high-performance structure, engineered cellular structures can be advanced into a new generation of protective systems. The goal of this research is to develop an analytical framework for predicting the critical buckling load, Young’s modulus and energy absorption of a 3D printed bone-like cellular structure. This is achieved by conducting extensive analytical simulations of the bone-inspired unit cell in parallel to traverse every possible combination of its key design parameters. The analytical framework is validated using experimental data and used to evolve the most optimal cellular structure, with the maximum energy absorption as the key performance criterion. The design charts developed in this work can be used to guide the development of a futuristic engineered cellular structure with superior performance and protective capabilities against extreme loads.
Knowledge and social relatedness shape research portfolio diversification
Authors: Tripodi Giorgio , Chiaromonte Francesca , Lillo Fabrizio 
Published: August 2020

AbstractScientific discovery is shaped by scientists’ choices and thus by their career patterns. The increasing knowledge required to work at the frontier of science makes it harder for an individual to embark on unexplored paths. Yet collaborations can reduce learning costs—albeit at the expense of increased coordination costs. In this article, we use data on the publication histories of a very large sample of physicists to measure the effects of knowledge and social relatedness on their diversification strategies. Using bipartite networks, we compute a measure of topic similarity and a measure of social proximity. We find that scientists’ strategies are not random, and that they are significantly affected by both. Knowledge relatedness across topics explains $$\approx 10\%$$

≈
10
%

of logistic regression deviances and social relatedness as much as $$\approx 30\%$$

≈
30
%

, suggesting that science is an eminently social enterprise: when scientists move out of their core specialization, they do so through collaborations. Interestingly, we also find a significant negative interaction between knowledge and social relatedness, suggesting that the farther scientists move from their specialization, the more they rely on collaborations. Our results provide a starting point for broader quantitative analyses of scientific diversification strategies, which could also be extended to the domain of technological innovation—offering insights from a comparative and policy perspective.
High-precision speckle-tracking X-ray imaging with adaptive subset size choices
Authors: Tian Naxi , Jiang Hui , Li Aiguo , Liang Dongxu , Yu Fucheng 
Published: August 2020

AbstractSpeckle-tracking imaging has the advantages of simple setup and high-sensitivity to slowly varying phase gradients. Subset size choice is regarded as a trade-off problem for speckle-tracking X-ray imaging where one needs to balance the spatial resolution and accuracy, where the subset was defined as the region of interest of windowing choice for digital image correlation algorithm. An adaptive subset size choice method based on a Fourier transform for effectively detecting sample phase information without foreknowledge of the sample structure is presented in this study. The speckle-tracking phase-contrast and the form of dark-field imaging based on this method have the advantages of (i) high resolution and time saving compared to large subset choice and (ii) partially improvement the influence from experimental noises, background fluctuations, and false signals compared to small subset choice at the same time. This method has proven to be particularly robust in the experimental condition of poor signal-to-noise ratio. The proposed method may be expanded to all speckle-based imaging methods and other imaging techniques based on the subset or window matching.
Optimized protocol for twin-field quantum key distribution
Authors: Wang Rong , Yin Zhen-Qiang , Lu Feng-Yu , Wang Shuang , Chen Wei , Zhang Chun-Mei , Huang Wei , Xu Bing-Jie , Guo Guang-Can , Han Zheng-Fu 
Published: August 2020

AbstractTwin-field quantum key distribution (TF-QKD) and its variant protocols are highly attractive due to the advantage of overcoming the rate-loss limit for secret key rates of point-to-point QKD protocols. For variations of TF-QKD, the key point to ensure security is switching randomly between a code mode and a test mode. Among all TF-QKD protocols, their code modes are very different, e.g. modulating continuous phases, modulating only two opposite phases, and sending or not sending signal pulses. Here we show that, by discretizing the number of global phases in the code mode, we can give a unified view on the first two types of TF-QKD protocols, and demonstrate that increasing the number of discrete phases extends the achievable distance, and as a trade-off, lowers the secret key rate at short distances due to the phase post-selection.
Use of n-Butyl 2 Cyanoacrylate without Lipiodol, Using a Modified Protocol in Gastric Variceal Bleed Management: Retrospective Analysis of 2299 Patients
Authors: Desai Pankaj N. , Patel Chintan N. , Kabrawala Mayank V. , Mehta Rajiv M. , Nandwani Subhash K. , Prajapati Ritesh , Patel Nisharg , Parekh Krishna K. 
Published: August 2020

Abstract
Aim To assess the feasibility and amount of cyanoacrylate glue that can be injected safely per session, complications, and long-term results in GOV1, GOV2 and IGV1 varices, using a modified method.
Method All patients from October 2008 to December 2019 presenting to us with variceal bleeding were included. We injected 0.5 mL of cyanoacrylate glue followed by 1.5 mL to 3 mL distilled water in all GOV 1, GOV 2 and IGV varices. Number of glues used were not restricted. Esophageal variceal ligation (EVL) was done for esophageal varices. Follow-up was done at 4 weeks and 3 to 6 months and analyzed.
Results 2299 patients received therapy. Male:female, 69%:31%. Causes of varices–cirrhosis (84.9%) and extrahepatic portal vein obstruction (EHPVO) (15.1%). Causes of cirrhosis–alcohol (38.4%), nonalcoholic fatty liver disease (NAFLD) (29%), hepatitis B (19.9%), hepatitis C (10.1%), Wilson’s disease (1.8%), and autoimmune diseases (0.9%). As much as 41.1% had blood in stomach and 10.2% had active spurt on index endoscopy. As much as 14.5% required endotracheal intubation (active bleed [53.1%], encephalopathy [40.5%], respiratory distress [6.6%]). As much as 30.9% had GOV1 + GOV2, 1.5% had GOV2 + IGV1, 21.3% had GOV1 + IGV1 and 16.4% had GOV1 + GOV2 + IGV1. Hemostasis could be achieved in 99.2% on index endoscopy. A total of 18 (0.8%) patients had uncontrolled bleed of whom 10 (55.6%) had hepatocellular carcinoma. Ongoing bleed was treated with transjugular intrahepatic portosystemic shunt (TIPSS) (61.1%) and endoscopic ultrasound (EUS)-guided coiling (38.8%). Amount of glue required for gastric variceal obturation was 3.6 on index endoscopy, 1.6 on follow-up at 4 to 6 weeks, and 1.2 at 3 months follow up. Glue extrusion with ulcers were seen in 6.4% at 4 to 6 weeks and 4.3% at 3 months. Rebleed occurred in 2.1% and 0.7% patients before 4 weeks and 3 months follow-up, respectively. As much as 1.3% and 1.2% patients were lost to follow-up before 4 weeks and 3 months follow-up sessions, respectively. Complications include pulmonary aspiration in 0.9% and bleeding from ulcers 2.8%. No evidence of pulmonary embolism was seen. In two endoscopic procedures, glue splashing into operator’s eyes occurred. Incidents of needle getting stuck in the varix occurred in three patients.
Conclusions Our modified protocol for glue in gastric varices is safe and feasible, as it has less rebleed, no pulmonary embolism and less ulcers with glue extrusion as compared with available literature.
A chemical dynamics study on the gas phase formation of thioformaldehyde (H2CS) and its thiohydroxycarbene isomer (HCSH)
Authors: Doddipatla Srinivas , He Chao , Kaiser Ralf I. , Luo Yuheng , Sun Rui , Galimova Galiya R. , Mebel Alexander M. , Millar Tom J. 
Published: August 2020

SignificanceSince the detection of carbonyl monosulfide (CS) in star-forming regions, about 200 molecules as complex as fullerenes have been detected in interstellar and circumstellar environments, but the formation routes to organosulfur molecules have remained essentially elusive. Exploiting thioformaldehyde (H2CS) and its thiohydroxycarbene isomer (HCSH), we deliver compelling testimony via laboratory experiments, electronic-structure theory, astrochemical modeling, and quasi-classical trajectory studies that these organosulfur species can be efficiently formed in star-forming regions such as Sagittarius B2 through bimolecular reactions involving hydrogen sulfide and methylidyne radicals. These elementary mechanisms are of fundamental importance to aid our understanding of how carbon and sulfur chemistries are connected in deep space, thus expanding our view on the sulfur cycle in the Galaxy.
Modulational instability and soliton control in a cubic–quintic dissipative Gross–Pitaevskii equation with distributed coefficients*
Authors: Kengne Emmanuel , Liu WuMing 
Published: August 2020

Abstract
In this work, we consider the generalized cubic–quintic dissipative Gross–Pitaevskii equation, which governs the dynamics of matter wave solitons in Bose–Einstein condensates with two- and three-body interatomic interactions in a spatiotemporal-dependent dissipative potential consisting of parabolic, linear, and complex terms. By using the ansatz method, the modulational instability and gray, kink, and bright soliton solutions are presented under certain parametric conditions. We found that the complex potential, related to the feeding or the loss of atoms by the condensates seriously modifies the instability and stability domain, while the linear potential has not effect on the stability of the system. With the use of exact analytical soliton-like solutions, we investigate analytically the solitons control system, and the results show that the soliton control system may relax the limitations to parametric conditions. We found that the motion of matter wave solitons in the systems can be manipulated by controlling both the external harmonic and linear trapping potentials. We have established that the amplitude of the matter wave solitons keep no change in propagating in the system though the total number of the condensate atoms decreases (increases) when the condensate losses (gains) atoms. We also showed that the three-body interatomic interactions is responsible of the soliton compression. Our results also revealed that the found exact soliton-like solutions can be used to describe the compression of matter wave solitons in BEC system with loss of atoms.
Bandwidth limit and synthesis approach for single resonance ultrathin metasurfaces
Authors: Fathnan Ashif A , Olk Andreas E , Powell David A 
Published: August 2020

Abstract
Metasurfaces have emerged as a promising technology for the manipulation of electromagnetic waves within a thin layer. In planar ultrathin metasurfaces, there exist rigorous design methods, based on the equivalent surface impedance of patterned metallic layers on dielectric substrates. In this work, we derive a limit on bandwidth achievable in these metasurfaces, based on constraints that their meta-atoms should be passive, causal and lossless and that they should obey the time-bandwidth product rules of a single resonance structure. The results show that in addition to elementary design parameters involving variation of the surface impedance, the bandwidth is critically limited by the dielectric substrate thickness and permittivity. We then propose a synthesis method for broadband ultrathin metasurfaces, based on an LC resonance fit of the required surface impedance and experimentally verify a broadband dispersive structure at millimeter-wave frequencies. This results in a bandwidth enhancement of over 90%, relative to a reference metasurface created with the narrowband design process.
DNA origami-based microtubule analogue
Authors: Zhang Tao 
Published: August 2020

Abstract
A microtubule hollow structure is one type of cytoskeletons which directs a number of important cellular functions. When recapitulating biological events in a cell-free system, artificial frames are often required to execute similar cytoskeletal functions in synthetic systems. Here, I report a prototypical microtubular assembly using a DNA origami nanostructuring method. Through structural design at the molecular level, 32HB (helices bundle)-based DNA origami objects can form micrometers long tubular structures via shape-complementary side patterns engagement and head-to-tail blunt-end stacking. Multiple parameters have been investigated to gain optimized polymerization conditions. Conformational change with an open vs closed hinge is also included, rendering conformational changes for a dynamic assembly. When implementing further improved external regulation with DNA dynamics (DNA strand displacement reactions or using other switchable non-canonical DNA secondary structures) or chemical stimuli, the DNA origami-based microtubule analogue will have great potential to assemble and disassemble on purpose and conduct significantly complicated cytoskeletal tasks in vitro.
Magnetron sputtering: determining scaling relations towards real power discharges using 3D particle-in-cell Monte Carlo models
Authors: Tonneau R , Pflug A , Lucas S 
Published: August 2020

Abstract
Plasma simulation of glow-magnetized discharges with the particle-in-cell Monte Carlo (PICMC) method is constraint to low current densities because of otherwise huge computational requirements. The present work aims to show, how it is nevertheless possible to extrapolate information for higher current densities similar to realistic lab or industrial conditions by applying a scaling strategy on the simulation. This is demonstrated for a DC magnetron sputtering (DCMS) case study involving the following species: Ar, Ar+, Ti, Ti+ and electrons. The evolution of the electron density is extracted from the simulation and compared with experimental values obtained with a Langmuir probe. A linear relationship between the electron density and the discharge current is highlighted and explained by studying the reaction rates of both ionization and excitation collisions. This allows to scale the reaction rates with the discharge parameters: the Ar-electron impact ionization and excitation rates scale linearly with the discharge current, while the electron impact ionization rate of sputtered species scales quadratically with the discharge current. The simulations also feature propagating plasma instabilities, so-called spokes, but in average, the above-mentioned scaling laws hold. Consequently, the flux of particles at the substrate during a plasma deposition process at realistic power density can be extrapolated from a 3D PICMC simulation at lower power density. Finally, the validity domain of the scaling strategy is discussed in the light of the model constraints.