bluuebunny/crossref_metadata_2025_split huggingface dataset:
Material-dependent submicrometer particle trapping in capacitively-coupled plasma sheaths in an intermediate collision regime
Authors: Ono Toshisato , Kortshagen Uwe R , Hogan Christopher J 
Published: August 2021

Abstract
Understanding submicrometer particle behavior in non-thermal capacitively coupled plasmas (CCPs) is important in the application of CCP reactors in thin-film vapor deposition; nucleated and resuspended particles can deposit on thin films, forming defects. Prior studies of supermicrometer particle behavior in CCP reactors have revealed that particles are trapped in the pre-sheath or sheath regions near electrodes, but have examined in detail neither the trapping of submicrometer particles, nor the influence of particle material properties on trapping. Using laser light scattering (LLS), we examined trapping of submicrometer metal oxide particles (radii in the 211 nm–565?nm range) of 6 distinct material compositions in the pre-sheath/sheath region of a CCP reactor operated at pressures in the 0.5–2.0 Torr range. We specifically focus on trapping near the upper electrode of a horizontally-oriented reactor. In this instance, trapping is brought about by a balance between electrostatic forces and gravitational forces driving particles away from the electrode, with ion drag forces driving particles toward the electrode. LLS measurements reveal that submicrometer particles are trapped near the upper electrode for all particle sizes, types, and operating pressures, with the trapping location at an increased distance away from the electrode with decreased CCP reactor pressure. Interestingly, we find the trapping location shifts slightly farther from the top electrode with increasing material dielectric constant. This suggests that the ion drag force is influenced by particle material properties, though in an unclarified manner. Measured trapping locations are also compared to model predictions where particle charge levels and the ion drag force are calculated using expressions based on ion trajectory calculations in a plasma sheath accounting for ion–neutral collisions. Predicted ion densities required for trapping are a factor of 6–16 higher than calculated at the observed particle trapping locations when applying a dissipative ion–particle encounter model, with more substantial disagreement found when considering a non-dissipative encounter model. In total, our results confirm that submicrometer particle trapping occurs at the upper electrode of CCP reactors, which must be facilitated by a balance largely between electrostatic and gravitational forces opposed by ion drag forces, but suggest future studies will be required to understand how particle material properties affect forces on particles on the plasma volume boundary, and how the ion drag force is sufficiently high to facilitate trapping.
Vacuum birefringence at x-ray free-electron lasers
Authors: Karbstein Felix , Sundqvist Chantal , Schulze Kai S , Uschmann Ingo , Gies Holger , Paulus Gerhard G 
Published: August 2021

Abstract
We study the perspectives of measuring the phenomenon of vacuum birefringence predicted by quantum electrodynamics using an x-ray free-electron laser (XFEL) alone. We devise an experimental scheme allowing two consecutive XFEL pulses to collide under a finite angle, and thus act as both pump and probe field for the effect. The signature of vacuum birefringence is encoded in polarization-flipped signal photons to be detected with high-purity x-ray polarimetry. Our findings for idealized scenarios underline that the discovery potential of solely XFEL-based setups can be comparable to those involving optical high-intensity lasers. For currently achievable scenarios, we identify several key details of the x-ray optical ingredients that exert a strong influence on the magnitude of the desired signatures.
Quantum brachistochrone for multiple qubits
Authors: Wang Ding , Shi Haowei , Lan Yueheng 
Published: August 2021

Abstract
Efficient control of qubits plays a key role in quantum information processing. In the current work, an alternative set of differential equations are derived for an optimal quantum control of single or multiple qubits with or without interaction. The new formulation enables a great reduction of the computation load by eliminating possible redundant complexity involved in previous algorithms. A relaxation technique is designed for numerically detecting optimal paths involving entanglement. Interesting continuous symmetries are identified in the Lagrangian, which indicates the existence of physically equivalent classes of paths and may be utilized to remove neutral directions in the Jacobian of the evolution. In the ‘ground state’ solution among the set of optimal paths, the time-reversal symmetry of the system shows up, which is expected to be universal for the symmetry-related initial and final state.
Creep feed grinding induced gradient microstructures in the superficial layer of turbine blade root of single crystal nickel-based superalloy
Authors: Miao Qing , Ding Wenfeng , Xu Jiuhua , Cao Lijie , Wang Hongcai , Yin Zhen , Dai Chenwei , Kuang Weijie 
Published: August 2021

Abstract
The service performance of the turbine blade root of an aero-engine depends on the microstructures in its superficial layer. This work investigated the surface deformation structures of turbine blade root of single crystal nickel-based superalloy produced under different creep feed grinding conditions. Gradient microstructures in the superficial layer were clarified and composed of a severely deformed layer (DFL) with nano-sized grains (48–67 nm) at the topmost surface, a DFL with submicron-sized grains (66–158 nm) and micron-sized laminated structures at the subsurface, and a dislocation accumulated layer extending to the bulk material. The formation of such gradient microstructures was found to be related to the graded variations in the plastic strain and strain rate induced in the creep feed grinding process, which were as high as 6.67 and 8.17 × 107 s−1, respectively. In the current study, the evolution of surface gradient microstructures was essentially a transition process from a coarse single crystal to nano-sized grains and, simultaneously, from one orientation of a single crystal to random orientations of polycrystals, during which the dislocation slips dominated the creep feed grinding induced microstructure deformation of single crystal nickel-based superalloy.
Performance Evaluation of Parametric and Nonparametric Methods When Assessing Effect Measure Modification
Authors: Conzuelo Rodriguez Gabriel , Bodnar Lisa M , Brooks Maria M , Wahed Abdus , Kennedy Edward H , Schisterman Enrique , Naimi Ashley I 
Published: August 2021

AbstractEffect measure modification is often evaluated using parametric models. These models, although efficient when correctly specified, make strong parametric assumptions. While nonparametric models avoid important functional form assumptions, they often require larger samples to achieve a given accuracy. We conducted a simulation study to evaluate performance tradeoffs between correctly specified parametric and nonparametric models to detect effect modification of a binary exposure by both binary and continuous modifiers. We evaluated generalized linear models and doubly robust (DR) estimators, with and without sample splitting. Continuous modifiers were modeled with cubic splines, fractional polynomials, and nonparametric DR-learner. For binary modifiers, generalized linear models showed the greatest power to detect effect modification, ranging from 0.42 to 1.00 in the worst and best scenario, respectively. Augmented inverse probability weighting had the lowest power, with an increase of 23% when using sample splitting. For continuous modifiers, the DR-learner was comparable to flexible parametric models in capturing quadratic and nonlinear monotonic functions. However, for nonlinear, nonmonotonic functions, the DR-learner had lower integrated bias than splines and fractional polynomials, with values of 141.3, 251.7, and 209.0, respectively. Our findings suggest comparable performance between nonparametric and correctly specified parametric models in evaluating effect modification.
BIONDA: a free database for a fast information on published biomarkers
Authors: Turewicz Michael , Frericks-Zipper Anika , Stepath Markus , Schork Karin , Ramesh Spoorti , Marcus Katrin , Eisenacher Martin 
Published: August 2021

AbstractSummaryBecause of the steadily increasing and already manually unmanageable total number of biomarker-related articles in biomedical research, there is a need for intelligent systems that extract all relevant information from biomedical texts and provide it as structured information to researchers in a user-friendly way. To address this, BIONDA was implemented as a free text mining-based online database for molecular biomarkers including genes, proteins and miRNAs and for all kinds of diseases. The contained structured information on published biomarkers is extracted automatically from Europe PMC publication abstracts and high-quality sources like UniProt and Disease Ontology. This allows frequent content updates.Availability and implementationBIONDA is freely accessible via a user-friendly web application at http://bionda.mpc.ruhr-uni-bochum.de. The current BIONDA code is available at GitHub via https://github.com/mpc-bioinformatics/bionda.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
Identifying anti-TNF response biomarkers in ulcerative colitis using a diffusion-based signalling model
Authors: Singh Amrinder , Anderssen Endre , Fenton Christopher G , Paulssen Ruth H 
Published: August 2021

AbstractMotivationResistance to anti-TNF therapy in subgroups of ulcerative colitis (UC) patients is a major challenge and incurs significant treatment costs. Identification of patients at risk of nonresponse to anti-TNF is of major clinical importance. To date, no quantitative computational framework exists to develop a complex biomarker for the prognosis of UC treatment. Modelling patient-wise receptor to transcription factor (TF) network connectivity may enable personalized treatment.ResultsWe present an approach for quantitative diffusion analysis between receptors and TFs using gene expression data. Key TFs were identified using pandaR. Network connectivities between immune-specific receptor-TF pairs were quantified using network diffusion in UC patients and controls. The patient-specific network could be considered a complex biomarker that separates anti-TNF treatment-resistant and responder patients both in the gene expression dataset used for model development and separate independent test datasets. The model was further validated in rheumatoid arthritis where it successfully discriminated resistant and responder patients to tocilizumab treatment. Our model may contribute to prognostic biomarkers that may identify treatment-resistant and responder subpopulations of UC patients.Availability and implementationSoftware is available at https://github.com/Amy3100/receptor2tfDiffusion.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies
Authors: Meleshko Dmitry , Hajirasouliha Iman , Korobeynikov Anton 
Published: August 2021

AbstractMotivationThe COVID-19 pandemic has ignited a broad scientific interest in viral research in general and coronavirus research in particular. The identification and characterization of viral species in natural reservoirs typically involves de novo assembly. However, existing genome, metagenome and transcriptome assemblers often are not able to assemble many viruses (including coronaviruses) into a single contig. Coverage variation between datasets and within dataset, presence of close strains, splice variants and contamination set a high bar for assemblers to process viral datasets with diverse properties.ResultsWe developed coronaSPAdes, a novel assembler for RNA viral species recovery in general and coronaviruses in particular. coronaSPAdes leverages the knowledge about viral genome structures to improve assembly extending ideas initially implemented in biosyntheticSPAdes. We have shown that coronaSPAdes outperforms existing SPAdes modes and other popular short-read metagenome and viral assemblers in the recovery of full-length RNA viral genomes.Availability and implementationcoronaSPAdes version used in this article is a part of SPAdes 3.15 release and is freely available at http://cab.spbu.ru/software/spades.Supplementary informationSupplementary data are available at Bioinformatics online.
De novo protein design by an energy function based on series expansion in distance and orientation dependence
Authors: Liang Shide , Li Zhixiu , Zhan Jian , Zhou Yaoqi 
Published: August 2021

Abstract

Motivation
Despite many successes, de novo protein design is not yet a solved problem as its success rate remains low. The low success rate is largely because we do not yet have an accurate energy function for describing the solvent-mediated interaction between amino acid residues in a protein chain. Previous studies showed that an energy function based on series expansions with its parameters optimized for side-chain and loop conformations can lead to one of the most accurate methods for side chain (OSCAR) and loop prediction (LEAP). Following the same strategy, we developed an energy function based on series expansions with the parameters optimized in four separate stages (recovering single-residue types without and with orientation dependence, selecting loop decoys and maintaining the composition of amino acids). We tested the energy function for de novo design by using Monte Carlo simulated annealing.

Results
The method for protein design (OSCAR-Design) is found to be as accurate as OSCAR and LEAP for side-chain and loop prediction, respectively. In de novo design, it can recover native residue types ranging from 38% to 43% depending on test sets, conserve hydrophobic/hydrophilic residues at ∼75%, and yield the overall similarity in amino acid compositions at more than 90%. These performance measures are all statistically significantly better than several protein design programs compared. Moreover, the largest hydrophobic patch areas in designed proteins are near or smaller than those in native proteins. Thus, an energy function based on series expansion can be made useful for protein design.

Availability and implementation
The Linux executable version is freely available for academic users at http://zhouyq-lab.szbl.ac.cn/resources/.
The Invisible Frontier: Practitioner Perspectives on the Privacy Implications of Utilising Social Media in Mental Health Social Work Practice
Authors: Thornton-Rice Arnold , Moran Nicola 
Published: August 2021

AbstractIn the digital age, traditional approaches to accessing information are disrupted by the ‘public’ nature of social media. The notion of accessing service users’ social media in social work practice is fraught with ethical issues around privacy and boundaries, yet lacks clear guidance from existing law and policy. This qualitative study sought to identify how mental health social workers were navigating these issues and how they thought practice could be developed. Ten mental health social workers, from one NHS Trust in England, were interviewed about their views and experiences around accessing service users’ social media without express permission. Semi-structured interviews were analysed using thematic analysis. Practitioners shared a variety of justifications for utilising social media, based upon statutory responsibility and professional values, but felt direct guidance/legislation and training would be helpful. A process of ‘digital reflexivity’ was outlined, which balanced reasons to access social media against considerations of privacy and the potential effects on the therapeutic relationship. Implications include the need for definitive guidance and training around if, when and how to access service users’ social media; inclusion of digital reflexivity in supervision and multidisciplinary meetings; educating service users about privacy controls; and a potential reconfiguration of theoretical boundaries to include the ‘public’ domain.
Tackling the content of a course for academic legal purposes
Authors: Kampouri Smaragda 
Published: August 2021

Abstract
This article addresses the practices that English for academic legal purposes (EALP) teachers employ to tackle law subject content. It draws on research that took place in a British university pre-sessional course for third-year undergraduate and postgraduate law students. The data come from tutorials, legal skills classroom observations and semi-structured interviews. The original study examined four EALP teachers; here I focus on the findings regarding one EALP teacher with sound experience of teaching EAP but no specific law background. The results of the study show that in EALP, as well as wider English for specific academic purposes (ESAP) contexts, limited subject-content knowledge (SCK) can lead to the frustration and lack of confidence of the ESAP teacher, and suggest utilizing the SCK of experienced colleagues and students to address this.
Perturbation of kinetochore function using GFP-binding protein in fission yeast
Authors: Deng Da-Jie , Xia Qian-Cheng , Jia Guo-Song , Suo Fang , Chen Jia-Li , Sun Li , Wang Jin-Qing , Wang Shuang-Min , Du Li-Lin , Wang Yamei , Jin Quan-Wen 
Published: August 2021

AbstractUsing genetic mutations to study protein functions in vivo is a central paradigm of modern biology. Single-domain camelid antibodies generated against GFP have been engineered as nanobodies or GFP-binding proteins (GBPs) that can bind GFP as well as some GFP variants with high affinity and selectivity. In this study, we have used GBP-mCherry fusion protein as a tool to perturb the natural functions of a few kinetochore proteins in the fission yeast Schizosaccharomyces pombe. We found that cells simultaneously expressing GBP-mCherry and the GFP-tagged inner kinetochore protein Cnp1 are sensitive to high temperature and microtubule drug thiabendazole (TBZ). In addition, kinetochore-targeted GBP-mCherry by a few major kinetochore proteins with GFP tags causes defects in faithful chromosome segregation. Thus, this setting compromises the functions of kinetochores and renders cells to behave like conditional mutants. Our study highlights the potential of using GBP as a general tool to perturb the function of some GFP-tagged proteins in vivo with the objective of understanding their functional relevance to certain physiological processes, not only in yeasts, but also potentially in other model systems.
Heat sensitivity of mariculture species in China
Authors: Ma Chao-yi , Zhu Xiao-lu , Liao Ming-ling , Dong Shuang-lin , Dong Yun-wei 
Published: August 2021

Abstract
China's mariculture is an indispensable part of the world's aquaculture and helps address food security issues in China and around the globe. However, this industry is facing a grand challenge from global warming. Therefore, it is urgent to assess the sensitivity of the main mariculture species and production modes to the increasing temperature. Here, we first extracted the coastal temperature data from 1465 grid cells (0.25 × 0.25 arcdegree) in the mariculture regions, and then compiled an upper thermal limit as well as culturing modes dataset of forty-two commercially important mariculture species. With these two datasets, we calculated the thermal safety margin (TSM) for each species across its aquaculture regions. Our results showed that several species with low TSMs were particularly sensitive to the current conditions and future warming, and some culturing regions face catastrophic consequences caused by high temperature and potential heatwaves. It is also noted that several mariculture modes like pond farming and mudflat ranching were more vulnerable compared to other mariculture modes. In summary, China's mariculture industry is sensitive to global warming at present and in the future. Our present study also provided tools to assess the risks in mariculture production and suggested solutions for future mitigation and adaptations.
Utah prairie dog population dynamics on the Awapa Plateau: precipitation, elevation, and plague
Authors: Eads David A , Biggins Dean E 
Published: August 2021

AbstractUtah prairie dogs (UPDs, Cynomys parvidens) are colonial, herbivorous rodents listed under the Endangered Species Act as threatened. Little is known about UPD population dynamics at higher elevations in the species’ range. From 2013 through 2016, we studied UPDs on five colonies at 2,645 to 2,873 m elevation on the Awapa Plateau, Utah, USA. Primary production increases with precipitation and precipitation increases with elevation on the plateau. We hypothesized that UPD body condition, reproduction, survival, and population growth all would vary directly with precipitation and elevation. Each year, we live-trapped UPDs from late-Jun through Aug, weighing each UPD, aging it as adult or pup, measuring its right hind foot, marking it for unique identification, and releasing it at point of capture. Fleas from live-trapped UPDs and opportunistically collected rodent carcasses, and rodent carcasses themselves, were tested for the agent of sylvatic plague (Yersinia pestis), a lethal invasive pathogen. Adult UPD body condition (mass:foot) increased with elevation. In addition, UPD reproduction (pups:adults) and population growth (λ) increased with precipitation. Annual survival declined from 0.49 in 2013–2014 to 0.24 in 2015–2016. We captured 421 UPDs in 2013 but only 149 in 2016. Sylvatic plague may have contributed to population declines. Notwithstanding, plague detection (yes/no by colony and year) had no statistical effect on population growth or annual survival, raising suspicion about the predictive value of binary plague detection variables. Generally speaking, efforts to conserve UPDs may benefit from the restoration and preservation of large colonies at mesic sites.
The C4 cycle and beyond: diverse metabolic adaptations accompany dual-cell photosynthetic functions in Setaria
Authors: Calace Paula , Tonetti Tomás , Margarit Ezequiel , Figueroa Carlos M , Lobertti Carlos , Andreo Carlos S , Gerrard Wheeler Mariel C , Saigo Mariana 
Published: August 2021

AbstractC4 photosynthesis is typically characterized by the spatial compartmentalization of the photosynthetic reactions into mesophyll (M) and bundle sheath (BS) cells. Initial carbon fixation within M cells gives rise to C4 acids, which are transported to the BS cells. There, C4 acids are decarboxylated so that the resulting CO2 is incorporated into the Calvin cycle. This work is focused on the study of Setaria viridis, a C4 model plant, closely related to several major feed and bioenergy grasses. First, we performed the heterologous expression and biochemical characterization of Setaria isoforms for chloroplastic NADP-malic enzyme (NADP-ME) and mitochondrial NAD-malic enzyme (NAD-ME). The kinetic parameters obtained agree with a major role for NADP-ME in the decarboxylation of the C4 acid malate in the chloroplasts of BS cells. In addition, mitochondria-located NAD-ME showed regulatory properties that could be important in the context of the operation of the C4 carbon shuttle. Secondly, we compared the proteomes of M and BS compartments and found 825 differentially accumulated proteins that could support different metabolic scenarios. Most interestingly, we found evidence of metabolic strategies to insulate the C4 core avoiding the leakage of intermediates by either up-regulation or down-regulation of chloroplastic, mitochondrial, and peroxisomal proteins. Overall, the results presented in this work provide novel data concerning the complexity of C4 metabolism, uncovering future lines of research that will undoubtedly contribute to the expansion of knowledge on this topic.