bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synchronized time tagger for single-photon detection in one- and two-dimension quantum experiments
Authors: Ye Runchuan , Lin Xue , Zhou Feifei , Dai Yulin , Hu Qidi , Li Xining , Xie Guangjun , Xu Nanyang 
Published: June 2022

We report a synchronized time tagger based on a field-programmable-gate-array chip for one- or two-dimensional quantum experiments that require precise single-photon detections. The time tagger has a 9.2 ps single-shot root-mean-square precision and is equipped with a 1 GB dynamic memory for data storage. Because the relationship between the control parameter and acquired data is guaranteed by using hardware synchronization, the experiment can be performed much faster than conventional schemes that are based on software synchronization. With this technique, an improvement of up to 61.3% in efficiency is observed in a typical nitrogen-vacancy center quantum experiment. We further show advanced optical features of the center using the detected high-resolution photon-arrival information and provide detailed electrical benchmarking of the device. This technique could be easily extended to other quantum control systems.
Phonon thermal transport in copper: The effect of size, crystal orientation, and grain boundaries
Authors: Sæther Sandra , Erichsen Merete Falck , Xiao Senbo , Zhang Zhiliang , Lervik Anders , He Jianying 
Published: June 2022

In electronic devices at the micro- and nanoscale, thermal management is vital. At such small sizes, crystal orientation, grain boundaries, and even the size itself can play an important role in the thermal transport and need to be taken into careful consideration when devices are designed. In this article, we perform computational experiments using non-equilibrium molecular dynamics simulations to evaluate the effect of size, orientation, and grain boundaries on the phonon thermal transport of copper. In addition, we compare the results obtained from the rescale and Langevin thermostat procedures. We find that the contribution of phonons to the total thermal conductivity in copper increases as the size decreases. Furthermore, the Σ5(210)[001] twist grain boundary is found to have a significant effect on the thermal transport of a bi-crystalline copper system when the grains are 15 nm. No such effect is found for the Σ3(112)[110] twin boundary. The effect of crystal orientation on the thermal conductivity is also studied, and no discerned effect can be observed. It is found that the Langevin thermostat leads to an over-estimation of the thermal conductivities at smaller scales and should be used with caution.
From the laboratory to the consumer: Innovation, supply chain, and adoption with applications to natural resources
Authors: Zilberman David , Reardon Thomas , Silver Jed , Lu Liang , Heiman Amir 
Published: June 2022

SignificanceResearch on innovation has two strands: institutions undertaking innovation as a research and development process and companies commercializing innovative products. We combine these strands, analyzing a sequence going from an innovation supply chain to a product supply chain from laboratory to market. We argue that these supply chains are symbiotic, and the relationship between entities is affected by economic considerations. Our framework allows an understanding of how research, regulatory policies, and economic conditions affect the emergence of innovations, the creation of institutions (markets, firms, contracts) to carry out these innovations, and the diffusion of the resulting products. Our approach may improve the design of strategies to induce climate change and food security solutions.
Membrane particles evoke a serotype-independent cross-protection against pneumococcal infection that is dependent on the conserved lipoproteins MalX and PrsA
Authors: Narciso Ana Rita , Iovino Federico , Thorsdottir Sigrun , Mellroth Peter , Codemo Mario , Spoerry Christian , Righetti Francesco , Muschiol Sandra , Normark Staffan , Nannapaneni Priyanka , Henriques-Normark Birgitta 
Published: June 2022

Significance
Pneumococcal infections are major contributors to morbidity and mortality worldwide. Introduction of pneumococcal conjugated vaccines (PCVs) into the childhood vaccination program has led to a decrease in invasive pneumococcal disease (IPD) in vaccinated children but concurrently to an increase of nonvaccine-type IPD, also in nonvaccinated age groups such as the elderly. Thus, novel vaccine approaches are urgently needed, especially for the elderly, targeting all pneumococci causing IPD. Here, we show that pneumococcal membrane particles (MPs) evoke a serotype-independent cross-protection against IPD. This protection is dependent on the presence of the two conserved lipoproteins MalX and PrsA. We suggest that MPs can be used for pneumococcal vaccine development.
Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes
Authors: Yu You , Li Shibai , Ser Zheng , Kuang Huihui , Than Thane , Guan Danying , Zhao Xiaolan , Patel Dinshaw J. 
Published: June 2022

Significance
The Smc5/6 complex plays multiple roles in DNA replication and repair. Its genome-protecting functions rely on its interaction with DNA; however, how this complex engages DNA is poorly understood. We report on a cryogenic electron microscopy structure of DNA-bound budding yeast Smc5/6 complex, revealing that its subunits form a clamp to encircle a double-helical DNA. We define the multi-subunit interactions forming the DNA clamp and the DNA binding sites distributed among subunits. We identify subunit transformations upon DNA capture and functional effects conferred by its multiple DNA contact sites. Our findings, in conjunction with studies on other structural maintenance of chromosomes (SMC) complexes, suggest a common SMC DNA-clamp mechanism with individual complex specific features that enable diverse genome organization and protection functions by SMC family complexes.
The nonclassical MHC class I Qa-1 expressed in layer 6 neurons regulates activity-dependent plasticity via microglial CD94/NKG2 in the cortex
Authors: Marin Ioana A. , Gutman-Wei Alan Y. , Chew Kylie S. , Raissi Aram J. , Djurisic Maja , Shatz Carla J. 
Published: June 2022

Significance
Molecules regulated by neuronal activity are necessary for circuits to adapt to changing inputs. Specific classical major histocompatibility class I (MHCI) molecules play roles in circuit and synaptic plasticity, but the function of most members of this family remains unexplored in brain. Here, we show that a nonclassical MHCI molecule, Qa-1 (H2-T23), is expressed in a subset of excitatory neurons and regulated by visually driven activity in the cerebral cortex. Moreover, CD94/NKG2 heterodimers, cognate receptors for Qa-1, are expressed in microglia. A functional interaction between Qa-1 and CD94/NKG2 is necessary for regulating the magnitude of ocular dominance plasticity during the critical period in the visual cortex, implying an interaction in which activity-dependent changes in neurons may be monitored by microglia.
Ion flux–energy distributions across grounded grids in an RF plasma source with DC-grounded electrodes
Authors: Soni Kunal , Antunes Rodrigo , Steiner Roland , Moser Lucas , Marot Laurent , Meyer Ernst 
Published: June 2022

Abstract
We present an experimental investigation of the ion flux–energy distribution functions (IFEDFs) obtained across grounded grids in an asymmetric capacitively coupled RF source using a helium discharge. The powered electrode in the RF source is DC-grounded via a λ/4 filter, which lifts its DC potential to zero. Grids of different dimensions (hole width, thickness, and geometric transparency) were used to confine the plasma, while the IFEDF of the ion beam departing the grid and reaching the reactor walls was studied using a retarding field energy analyser. The IFEDF obtained was double-peaked, indicating the presence of fast ions arriving from the plasma source, and cold ions generated upon charge exchange collisions between the fast ions and neutrals. The flux, as well as the peak energies of the two ion groups, depended significantly on the process parameters: RF power, He pressure, the distance between grids and walls, and the dimensions of the grids. The results indicate that confining plasma with grids can reduce the ion flux at the walls by over 60%, significantly lowering the wall sputtering rate. This was confirmed with a dedicated long-exposure plasma discharge with a gridded plasma reactor, wherein less than 1 nm of Cu deposition was found on the DC-grounded powered electrode, and the surface reflectivity was preserved to pristine values. In contrast, a similar experiment in a gridless reactor resulted in Cu deposition of 35 nm with a drastic drop in surface reflectivity. These studies are of great importance for the application of similar RF plasma sources with in-situ cleaning of diagnostic mirrors in fusion devices, as well as in a variety of plasma processing applications.
Continuous-variable quantum key distribution over a 15 km multi-core fiber
Authors: Sarmiento S , Etcheverry S , Aldama J , López I H , Vidarte L T , Xavier G B , Nolan D A , Stone J S , Li M J , Loeber D , Pruneri V 
Published: June 2022

Abstract
The secure transfer of information is critical to the ever-increasing demands of the digital world. Continuous-variable quantum key distribution (CV-QKD) is a promising technology that can provide high secret key rates over metropolitan areas, using conventional telecom components. In this study, we demonstrate the utilization of CV-QKD over a 15 km multi-core fiber (MCF), in which we take advantage of one core to remotely frequency lock Bob's local oscillator with Alice's transmitter. We also demonstrate the capacity of the MCF to boost the secret key rate by parallelizing CV-QKD across multiple cores. Our results indicate that MCFs are promising for the metropolitan deployment of QKD systems.
Erbium-ytterbium co-doped photonic crystal fiber amplifier supporting amplification for orbital angular momentum
Authors: Zhao Lijuan , Liang Ruoyu , Xu Zhiniu 
Published: June 2022

Abstract
In order to reduce the loss in orbital angular momentum (OAM) long-distance communication systems, an OAM erbium-ytterbium co-doped fiber amplifier (OAM-EYDFA) based on photonic crystal fiber (PCF) is proposed and investigated for the first time in this work. We set up a three-dimensional electromagnetic field model of the PCF in Comsol and solved it by the finite element method. Then, we designed a three-dimensional model of the OAM-EYDFA based on the proposed PCF using Comsol and MATLAB. The results reveal that the proposed OAM-EYDFA has a flat-high gain of about 47 dB, a differential mode gain of lower than 0.3 dB and a noise figure of lower than 3.4 dB. Compared with existing studies, its gain is increased by at least 25 dB, and other properties are also improved. The proposed OAM-EYDFA can provide a reference for OAM-based long-distance communication systems.
A 3 Giga Sample Per Second 14-bit Digital Receiver with 9 GHz Input Bandwidth for Solar Radio Observation
Authors: Zhang Yuanyuan , Zhang Lei , Shang Ziqian , Lu Guang , Wu Zhao , Su Yanrui , Chen Yao , Yan Fabao 
Published: June 2022

Abstract
A new digital receiver with excellent performances has been designed and developed for solar radio observation, which can receive the radio signal from direct current (DC) to 9 GHz in the direct acquisition way. On the digital receiver, the analog-to-digital converter (ADC) with 14-bit, two input channels and 3 Giga Samples per second (Gsps) are used to acquire observed signal, and the field-programmable-gate-array chip XCKU115 acts as the processing module. The new digital receiver can be used to directly sample the solar radio signals of frequency under 9 GHz. When receiving the solar radio signal above 9 GHz, the new digital receiver can save 1–2 stages of frequency down-conversion, and effectively improve many indexes of the solar radio observation system, i.e., the time resolution, analog front-end circuit, weight and volume of the analog circuit system. Compared with the digital receiver with sampling rate below 1 Gsps used in existing solar radio telescope, the new digital receiver reduces the frequency switching times of large bandwidth, which is beneficial to improving the frequency and time resolutions. The ADC sampling resolution of 14 bits, providing a large dynamic range, is very beneficial to observing smaller solar eruptions. This receiver, which would be used in the solar radio observation system, well meets the latest requirements with the resolutions of time (≤1 ms) and frequency (≤0.5 MHz) for fine observation of radio signals.
Integrated modelling and multiscale gyrokinetic validation study of ETG turbulence in a JET hybrid H-mode scenario
Authors: Citrin J. , Maeyama S. , Angioni C. , Bonanomi N. , Bourdelle C. , Casson F.J. , Fable E. , Görler T. , Mantica P. , Mariani A. , Sertoli M. , Staebler G. , Watanabe T. 
Published: June 2022

Abstract
Previous studies with first-principle-based integrated modelling suggested that electron temperature gradient (ETG) turbulence may lead to an anti-gyroBohm isotope scaling in JET high-performance hybrid H-mode scenarios. A dedicated comparison study against higher-fidelity turbulence modelling invalidates this claim. Ion-scale turbulence with magnetic field perturbations included, can match the power balance fluxes within temperature gradient error margins. Multiscale gyrokinetic simulations from two distinct codes produce no significant ETG heat flux, demonstrating that simple rules-of-thumb are insufficient criteria for its onset.
Experimental and theoretical study of weakly coherent mode in I-mode edge plasmas in the EAST tokamak
Authors: Liu Z.X. , Liu Y.J. , Xiao J.Y. , Xia T.Y. , Li Y.L. , Xu X.Q. , Wu M.Q. , Li G.Q. , Wu M.F. , Zhang T. , Gao X. , Gong X.Z. , Liu H.Q. , Zang Q. , Liu A.D. , Zhou C. , Lan T. , Li H. , Xie J.L. , Mao W.Z. , Ding W.X. , Zhuang G. , Li J.G. , Liu W.D. , the EAST Team  
Published: June 2022

Abstract
The I-mode is a promising operation mode for fusion in the future, featuring high-temperature and low-density confinement, but the reason why the temperature and density are decoupled remains an important aspect to be explored. The experimental results from the experimental advanced superconducting tokamak (EAST) showed that the weakly coherent mode (WCM) is directly related to sustaining the I-mode and that the peak amplitude of the WCM is proportional to the temperature in the pedestal. Simulating the experimental data from EAST with the six-field model of BOUT++, we find a density perturbation close to the frequency of the WCM observed in the experiment. By testing all the physical terms in this model, we find that the density perturbation and particle transport are directly related to the drift Alfvén wave (DAW) mode. We also use the SymPIC program (Xiao et al Plasma Sci. Technol.
20 110501; Phys. Plasmas
22 112504; Plasma Sci. Technol.
23 055102) to simulate the same experimental data and find that the frequency range of the WCM is close to both experimental and BOUT++ results. Therefore, the WCM of the I-mode can be considered to be driven by the DAW, which helps improve the transport of the I-mode.
Invited Commentary: Is Bias Towards the Null From Nondifferential Misclassification Wishful Thinking?
Authors: Hamra Ghassan B 
Published: June 2022

Abstract
In their article, Yland et al. (Am J Epidemiol. 2022;191(8):1485–1495) bring renewed attention to the oft-cited heuristic “nondifferential misclassification biases results towards the null.” They make a compelling case, as others have before, that this heuristic is misguided. Herein, I briefly discuss the history of this heuristic, discuss why I believe it became and stayed popular, and note the very limited circumstances for which it may be appropriate.
Pharmacokinetics and tissue distribution of orally administrated imidazole dipeptides in carnosine synthase gene knockout mice
Authors: Sakano Taiken , Egusa Ai Saiga , Kawauchi Yoko , Wu Jiawei , Nishimura Toshihide , Nakao Nobuhiro , Kuramoto Ayumu , Kawashima Takumi , Shiotani Shigenobu , Okada Yukio , Sato Kenichiro , Yanai Nobuya 
Published: June 2022

Abstract
Imidazole dipeptides (ID) are abundant in skeletal muscle and the brain and have various functions, such as antioxidant, pH-buffering, metal-ion chelation. However, the physiological significance of ID has not been fully elucidated. In this study, we orally administered ID to conventional carnosine synthase gene-deficient mice (Carns-KO mice) to investigate the pharmacokinetics. Carnosine or anserine was administered at a dose of 500 mg (approximately 2 mmol) per kilogram of mouse body weight, and ID contents in the tissues were measured. No ID were detected in untreated Carns-KO mice. In the ID treatment groups, the ID concentrations in the tissues increased in a time-dependent manner in the gastrocnemius muscle, soleus muscle, and cerebrum after ID administration. Our findings suggest that the Carns-KO mice are a valuable animal model for directly evaluate the effects of dietary ID and for elucidating the physiological functions of oral ID administration.
Dietary oleamide attenuates obesity induced by housing mice in small cages
Authors: Kobayashi Yasuyuki , Kubota Mai , Sugimoto Keiichiro , Kitakaze Tomoya , Harada Naoki , Yamaji Ryoichi 
Published: June 2022

Abstract
Physical inactivity due to prolonged sedentary behavior induces obesity. Therefore, we investigated whether housing mice in small cages to mimic sedentary behavior induced obesity and whether dietary oleamide (cis-9,10-octadeceneamide) suppressed the induced obesity. A single oral administration of oleamide (50 mg/kg) to mice resulted in the accumulation of the exogenous oleamide in abdominal visceral fat. Next, mice were housed in small cages and oleamide (50 mg/kg/d) was orally administered for 12 weeks. Housing mice in small cages impaired glucose tolerance and increased food efficiency. It also increased body weight and abdominal fat mass. Dietary oleamide improved the impairment and inhibited their increases in mice housed in small cages. Furthermore, dietary oleamide suppressed the mRNA expression of inflammation-related factors in abdominal fat of mice housed in small cages. Hence, these results indicate that although housing mice in small cages induces obesity and increases abdominal fat mass, dietary oleamide suppresses the obesity.
Improving E. coli organic solvent tolerance by 1,4-dihydroxy-2-naphthoic acid
Authors: Doukyu Noriyuki , Fujisawa Hideyuki , Saito Ryota 
Published: June 2022

Abstract
Improving the organic solvent tolerance of bacteria is beneficial for the bioproduction of various valuable chemicals. In this study, we found that 1,4-dihydroxy-2-naphthoic acid (DHNA), known as a prebiotic, increased organic solvent tolerance in Escherichia coli. The AcrAB‒TolC multidrug efflux pump contributes to the intrinsic organic solvent tolerance of E. coli. The addition of DHNA increased this pump's expression level. Transcriptional activators MarA, SoxS, and Rob proteins are known to control the expression of marA/soxS/rob regulon genes, including acrAB and tolC. Evaluation of the organic solvent tolerances of DmarA mutant, DsoxS mutant, and Drob mutant showed that DmarA mutant and DsoxS mutant did not improve organic solvent tolerance by the addition of DHNA. In addition, DHNA increased the promoter activities of both marA and soxS. These results indicated that DHNA induces the AcrAB‒TolC pump through both the marRAB system and the soxRS system.
Palo: spatially aware color palette optimization for single-cell and spatial data
Authors: Hou Wenpin , Ji Zhicheng 
Published: June 2022

AbstractSummaryIn the exploratory data analysis of single-cell or spatial genomic data, single-cells or spatial spots are often visualized using a two-dimensional plot where cell clusters or spot clusters are marked with different colors. With tens of clusters, current visualization methods often assign visually similar colors to spatially neighboring clusters, making it hard to identify the distinction between clusters. To address this issue, we developed Palo that optimizes the color palette assignment for single-cell and spatial data in a spatially aware manner. Palo identifies pairs of clusters that are spatially neighboring to each other and assigns visually distinct colors to those neighboring pairs. We demonstrate that Palo leads to improved visualization in real single-cell and spatial genomic datasets.Availability and implementationPalo R package is freely available at Github (https://github.com/Winnie09/Palo) and Zenodo (https://doi.org/10.5281/zenodo.6562505).Supplementary informationSupplementary data are available at Bioinformatics online.
Effector-GAN: prediction of fungal effector proteins based on pretrained deep representation learning methods and generative adversarial networks
Authors: Wang Yansu , Luo Ximei , Zou Quan 
Published: June 2022

AbstractMotivationPhytopathogenic fungi secrete effector proteins to subvert host defenses and facilitate infection. Systematic analysis and prediction of candidate fungal effector proteins are crucial for experimental validation and biological control of plant disease. However, two problems are still considered intractable to be solved in fungal effector prediction: one is the high-level diversity in effector sequences that increases the difficulty of protein feature learning, and the other is the class imbalance between effector and non-effector samples in the training dataset.ResultsIn our study, pretrained deep representation learning methods are presented to represent multiple characteristics of sequences for predicting fungal effectors and generative adversarial networks are adapted to create synthetic feature samples to address the data imbalance problem. Compared with the state-of-the-art fungal effector prediction methods, Effector-GAN shows an overall improvement in accuracy in the independent test set.Availability and implementationEffector-GAN offers a user-friendly interface to inspect potential fungal effector proteins (http://lab.malab.cn/~wys/webserver/Effector-GAN). The Python script can be downloaded from http://lab.malab.cn/~wys/gitlab/effector-gan.Supplementary informationSupplementary data are available at Bioinformatics online.