bluuebunny/crossref_metadata_2025 huggingface dataset:
Effective spin dynamic control of CoFeB/Nd heterostructure by matched resistivity
Authors: Liang Jian , Chen Qian , Guo Qingjie , Jiang Wei , Huang Zhaocong , You Biao , Du Jun , Zhai Ya
Published: November 2022

The spin dynamics modulation has attracted extensive attention in the past decades. Rare-earth (RE) metals are essential participants in this context due to the large spin–orbit coupling. Here, with neodymium (Nd) capping, we achieve the enhancement on spin dynamic damping of Co40Fe40B20 (CFB) films by three times larger than that of CFB single layer. Based on the spin pumping theory, the interfacial spin mixing conductance Geff↑↓ is calculated as 7.3 × 1015 cm−2, which is one order larger than that of CFB/Pt. It leads to the large spin current transparency at CFB/Nd interface. By comparing of the resistivity of each layer, we found that the matched resistivity at two sides of the CFB/Nd interface plays an important role in the enhancement of Geff↑↓. As a consequence, a high spin transparency of the CFB/Nd interface is obtained as 82%. In addition, damping enhancement of CFB is not changed promptly by inserting 1–2 nm Cu layer, but it is suppressed when the Cu layer is thicker than 3 nm, which is related to the thickness dependence of the Cu resistivity. Our study broadens the horizon for the application of rare-earth (RE) in spintronics.
A history of CSIRO’S Central Australian Laboratory, 1: 1953–80: pastoral land research
Authors: Friedel Margaret H. , Morton Stephen R.
Published: November 2022

CSIRO’s research in the arid zone was initiated after World War 2 when a strong push to develop the sparsely populated and isolated region of northern Australia was promoted as being in the national interest. This impetus had social and political origins but implementation depended on scientific insights into regional ‘potential’, which was couched at the time in terms of agronomic and pastoral use. Ray Perry was a key figure in early land resource surveys of the region and later a key motivator for, and supporter of, research in the arid and semi-arid rangelands of Australia. His commitment was fundamental to the establishment of CSIRO’s Central Australian Laboratory. Pastoral land use and improving the land for that purpose were the primary concerns when CSIRO’s presence in Alice Springs was established in 1953. From an initial focus on ‘making the desert bloom’, in particular making the vast spinifex grasslands more ‘useful’, the focus of research shifted to maintaining the productivity of country preferred by cattle and establishing methods for monitoring its health. It was not until the 1970s that Aboriginal and conservation land management appeared in the laboratory’s research agenda, somewhat intermittently, in response to important social and political changes in the wider Australian community.
Strengthening learning and research in health equity – opportunities for university departments of primary health care and general practice
Authors: Reath Jennifer , Lau Phyllis , Lo Winston , Trankle Steven , Brooks Miriam , Shahab Yasin , Abbott Penelope
Published: November 2022

This paper explores the roles of university departments of primary health care (PHC) and general practice in promoting health equity. The coronavirus disease 2019 (COVID-19) pandemic has exposed long-standing health and workforce inequities in Australia, as elsewhere. Addressing these inequities will require wide-ranging responses particularly focussed on PHC and the PHC workforce. Well-resourced university departments of PHC and general practice have potential to lead research informing PHC transformation and strategies to reduce health inequity, as well as to train and inspire a future PHC workforce. Examples from such academic departments in Australia and internationally are briefly described, and the experience of a recently established department of general practice is considered, in order to recommend enablers including institutional support, curriculum design, and partnerships with communities and between institutions. Support for community-based clinical schools, practice-based research networks and strengthening PHC research capacity will enable the PHC and general practice academy to engage more effectively in addressing health inequity.
Modes of Pangean lake level cyclicity driven by astronomical climate pacing modulated by continental position and
p
CO2
Authors: Landwehrs Jan , Feulner Georg , Willeit Matteo , Petri Stefan , Sames Benjamin , Wagreich Michael , Whiteside Jessica H. , Olsen Paul E.
Published: November 2022

Orbital cyclicity is a fundamental pacemaker of Earth’s climate system. The Newark–Hartford Basin (NHB) lake sediment record of eastern North America contains compelling geologic expressions of this cyclicity, reflecting variations of climatic conditions in tropical Pangea during the Late Triassic and earliest Jurassic (~233 to 199 Ma). Climate modeling enables a deeper mechanistic understanding of Earth system modulation during this unique greenhouse and supercontinent period. We link major features of the NHB record to the combined climatic effects of orbital forcing, paleogeographic changes, and atmospheric
p
CO

2

variations. An ensemble of transient, orbitally driven climate simulations is assessed for nine time slices, three atmospheric
p
CO

2

values, and two paleogeographic reconstructions. Climatic transitions from tropical humid to more seasonal and ultimately semiarid are associated with tectonic drift of the NHB from

~
5

 
°

N

to

20

 
°

N

. The modeled orbital modulation of the precipitation–evaporation balance is most pronounced during the 220 to 200 Ma interval, whereas it is limited by weak seasonality and increasing aridity before and after this interval. Lower
p
CO

2

at around 205 Ma contributes to drier climates and could have led to the observed damping of sediment cyclicity. Eccentricity-modulated precession dominates the orbitally driven climate response in the NHB region. High obliquity further amplifies summer precipitation through the seasonal shifts in the tropical rainfall belt. Regions with other proxy records are also assessed, providing guidance toward an integrated picture of global astronomical climate forcing in the Late Triassic and ultimately of other periods in Earth history.
Silencing RNAs expressed from W-linked
PxyMasc
“retrocopies” target that gene during female sex determination in
Plutella xylostella
Authors: Harvey-Samuel Tim , Xu Xuejiao , Anderson Michelle. A. E. , Carabajal Paladino Leonela. Z. , Purusothaman Deepak , Norman Victoria. C. , Reitmayer Christine. M. , You Minsheng , Alphey Luke
Published: November 2022

The Lepidoptera are an insect order of cultural, economic, and environmental importance, representing ∼10% of all described living species. Yet, for all but one of these species (silkmoth,
Bombyx mori
), the molecular genetics of how sexual fate is determined remains unknown. We investigated this in the diamondback moth (
Plutella xylostella
), a globally important, highly invasive, and economically damaging pest of cruciferous crops. Our previous work uncovered a regulator of male sex determination in
P. xylostella
—
PxyMasc
, a homolog of
B. mori Masculinizer
—which, although initially expressed in embryos of both sexes, is then reduced in female embryos, leading to female-specific splicing of
doublesex
. Here, through sequencing small RNA libraries generated from early embryos and sexed larval pools, we identified a variety of small silencing RNAs (predominantly Piwi-interacting RNAs [piRNAs]) complementary to
PxyMasc
, whose temporal expression correlated with the reduction in
PxyMasc
transcript observed previously in females. Analysis of these small RNAs showed that they are expressed from tandemly arranged, multicopy arrays found exclusively on the W (female-specific) chromosome, which we term “
Pxyfem
”. Analysis of the
Pxyfem
sequences showed that they are partial complementary DNAs (cDNAs) of
PxyMasc
messenger RNA (mRNA) transcripts, likely integrated into transposable element graveyards by the noncanonical action of retrotransposons (retrocopies), and that their apparent similarity to
B. mori feminizer
more probably represents convergent evolution. Our study helps elucidate the sex determination cascade in this globally important pest and highlights the “shortcuts” that retrotransposition events can facilitate in the evolution of complex molecular cascades, including sex determination.
A tool for monitoring cell type–specific focused ultrasound neuromodulation and control of chronic epilepsy
Authors: Murphy Keith R. , Farrell Jordan S. , Gomez Juan L. , Stedman Quintin G. , Li Ningrui , Leung Steven A. , Good Cameron H. , Qiu Zhihai , Firouzi Kamyar , Butts Pauly Kim , Khuri-Yakub Butrus Pierre T. , Michaelides Michael , Soltesz Ivan , de Lecea Luis
Published: November 2022

Focused ultrasound (FUS) is a powerful tool for noninvasive modulation of deep brain activity with promising therapeutic potential for refractory epilepsy; however, tools for examining FUS effects on specific cell types within the deep brain do not yet exist. Consequently, how cell types within heterogeneous networks can be modulated and whether parameters can be identified to bias these networks in the context of complex behaviors remains unknown. To address this, we developed a fiber Photometry Coupled focused Ultrasound System (PhoCUS) for simultaneously monitoring FUS effects on neural activity of subcortical genetically targeted cell types in freely behaving animals. We identified a parameter set that selectively increases activity of parvalbumin interneurons while suppressing excitatory neurons in the hippocampus. A net inhibitory effect localized to the hippocampus was further confirmed through whole brain metabolic imaging. Finally, these inhibitory selective parameters achieved significant spike suppression in the kainate model of chronic temporal lobe epilepsy, opening the door for future noninvasive therapies.
Environmental drivers of the first major animal extinction across the Ediacaran White Sea-Nama transition
Authors: Evans Scott D. , Tu Chenyi , Rizzo Adriana , Surprenant Rachel L. , Boan Phillip C. , McCandless Heather , Marshall Nathan , Xiao Shuhai , Droser Mary L.
Published: November 2022

The Ediacara Biota—the oldest communities of complex, macroscopic fossils—consists of three temporally distinct assemblages: the Avalon (ca. 575–560 Ma), White Sea (ca. 560–550 Ma), and Nama (ca. 550–539 Ma). Generic diversity varies among assemblages, with a notable decline at the transition from White Sea to Nama. Preservation and sampling biases, biotic replacement, and environmental perturbation have been proposed as potential mechanisms for this drop in diversity. Here, we compile a global database of the Ediacara Biota, specifically targeting taphonomic and paleoecological characters, to test these hypotheses. Major ecological shifts in feeding mode, life habit, and tiering level accompany an increase in generic richness between the Avalon and White Sea assemblages. We find that ∼80% of White Sea taxa are absent from the Nama interval, comparable to loss during Phanerozoic mass extinctions. The paleolatitudes, depositional environments, and preservational modes that characterize the White Sea assemblage are well represented in the Nama, indicating that this decline is not the result of sampling bias. Counter to expectations of the biotic replacement model, there are minimal ecological differences between these two assemblages. However, taxa that disappear exhibit a variety of morphological and behavioral characters consistent with an environmentally driven extinction event. The preferential survival of taxa with high surface area relative to volume may suggest that this was related to reduced global oceanic oxygen availability. Thus, our data support a link between Ediacaran biotic turnover and environmental change, similar to other major mass extinctions in the geologic record.
A new chronology for the Māori settlement of Aotearoa (NZ) and the potential role of climate change in demographic developments
Authors: Bunbury Magdalena M.E. , Petchey Fiona , Bickler Simon H.
Published: November 2022

Understanding the role of climate change, resource availability, and population growth in human mobility remains critically important in anthropology. Researching linkages between climate and demographic changes during the short settlement history of Aotearoa (New Zealand) requires temporal precision equivalent to the period of a single generation. However, current modeling approaches frequently use small terrestrial radiocarbon datasets, a practice that obscures past Māori population patterns and their connection to changing climate. Our systematic analysis of terrestrial and marine
14
C ages has enabled robust assessments of the largest dataset yet collated from island contexts. This analysis has been made possible by the recent development of a temporal marine correction for southern Pacific waters, and our findings show the shortcomings of previous models. We demonstrate that human settlement in the mid to late 13th century AD is unambiguous. We highlight initial (AD 1250 to 1275) settlement in the North Island. The South Island was reached a decade later (AD 1280 to 1295), where the hunting of giant flightless moa commenced (AD 1300 to 1415), and the population grew rapidly. Population growth leveled off around AD 1340 and declined between AD 1380 and 1420, synchronous with the onset of the Little Ice Age and moa loss as an essential food source. The population continued to grow in the more economically stable north, where conditions for horticulture were optimal. The enhanced precision of this research afforded by the robust analysis of marine dates opens up unique opportunities to investigate interconnectivity in Polynesia and inform the patterns seen in other island contexts.
Stage-specific transposon activity in the life cycle of the fairy-ring mushroom
Marasmius oreades
Authors: Hiltunen Markus , Ament-Velásquez Sandra Lorena , Ryberg Martin , Johannesson Hanna
Published: November 2022

Genetic variability can be generated by different mechanisms, and across the life cycle. Many basidiomycete fungi have an extended somatic stage, during which each cell carries two genetically distinct haploid nuclei (dikaryosis), resulting from fusion of two compatible monokaryotic individuals. Recent findings have revealed remarkable genome stability at the nucleotide level during dikaryotic growth in these organisms, but whether this pattern extends to mutations affecting large genomic regions remains unknown. Furthermore, despite high genome integrity during dikaryosis, basidiomycete populations are not devoid of genetic diversity, begging the question of when this diversity is introduced. Here, we used a
Marasmius oreades
fairy ring to investigate the rise of large-scale variants during mono- and dikaryosis. By separating the two nuclear genotypes from four fruiting bodies and generating complete genome assemblies, we gained access to investigate genomic changes of any size. We found that during dikaryotic growth in nature the genome stayed intact, but after separating the nucleotypes into monokaryons, a considerable amount of structural variation started to accumulate, driven to large extent by transposons. Transposon insertions were also found in monokaryotic single-meiospore isolates. Hence, we show that genome integrity in basidiomycetes can be interrupted during monokaryosis, leading to genomic rearrangements and increased activity of transposable elements. We suggest that genetic diversification is disproportionate between life cycle stages in mushroom-forming fungi, so that the short-lived monokaryotic growth stage is more prone to genetic changes than the dikaryotic stage.
Structures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers reveal new dimerization modalities in the bHLH-PAS transcription factor family
Authors: Sun Xiangnan , Jing Linqian , Li Fengwei , Zhang Meina , Diao Xiaotong , Zhuang Jingjing , Rastinejad Fraydoon , Wu Dalei
Published: November 2022

Neuronal PER-ARNT-SIM (PAS) domain protein 4 (NPAS4) is a protective transcriptional regulator whose dysfunction has been linked to a variety of neuropsychiatric and metabolic diseases. As a member of the basic helix–loop–helix PER-ARNT-SIM (bHLH-PAS) transcription factor family, NPAS4 is distinguished by an ability to form functional heterodimers with aryl hydrocarbon receptor nuclear translocator (ARNT) and ARNT2, both of which are also bHLH-PAS family members. Here, we describe the quaternary architectures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers in complexes involving DNA response elements. Our crystallographic studies reveal a uniquely interconnected domain conformation for the NPAS4 protein itself, as well as its differentially configured heterodimeric arrangements with both ARNT and ARNT2. Notably, the PAS-A domains of ARNT and ARNT2 exhibit variable conformations within these two heterodimers. The ARNT PAS-A domain also forms a set of interfaces with the PAS-A and PAS-B domains of NPAS4, different from those previously noted in ARNT heterodimers formed with other class I bHLH-PAS family proteins. Our structural observations together with biochemical and cell-based interrogations of these NPAS4 heterodimers provide molecular glimpses of the NPAS4 protein architecture and extend the known repertoire of heterodimerization patterns within the bHLH-PAS family. The PAS-B domains of NPAS4, ARNT, and ARNT2 all contain ligand-accessible pockets with appropriate volumes required for small-molecule binding. Given NPAS4’s linkage to human diseases, the direct visualization of these PAS domains and the further understanding of their relative positioning and interconnections within the NPAS4-ARNT and NPAS4-ARNT2 heterodimers may provide a road map for therapeutic discovery targeting these complexes.
A neuropeptide signal confers ethanol state dependency during olfactory learning in
Caenorhabditis elegans
Authors: Lindsay Jonathan H. , Mathies Laura D. , Davies Andrew G. , Bettinger Jill C.
Published: November 2022

Alcohol intoxication can impact learning and this may contribute to the development of problematic alcohol use. In alcohol (ethanol)-induced state-dependent learning (SDL), information learned while an animal is intoxicated is recalled more effectively when the subject is tested while similarly intoxicated than if tested while not intoxicated. When
Caenorhabditis elegans
undergoes olfactory learning (OL) while intoxicated, the learning becomes state dependent such that recall of OL is only apparent if the animals are tested while intoxicated. We found that two genes known to be required for signal integration, the secreted peptide HEN-1 and its receptor tyrosine kinase, SCD-2, are required for SDL. Expression of
hen-1
in the ASER neuron and
scd-2
in the AIA neurons was sufficient for their functions in SDL. Optogenetic activation of ASER in the absence of ethanol during learning could confer ethanol state dependency, indicating that ASER activation is sufficient to signal ethanol intoxication to the OL circuit. To our surprise, ASER activation during testing did not substitute for ethanol intoxication, demonstrating that the effects of ethanol on learning and recall rely on distinct signals. Additionally, intoxication-state information could be added to already established OL, but state-dependent OL did not lose state information when the intoxication signal was removed. Finally, dopamine is required for state-dependent OL, and we found that the activation of ASER cannot bypass this requirement. Our findings provide a window into the modulation of learning by ethanol and suggest that ethanol acts to modify learning using mechanisms distinct from those used during memory access.
Switchable targeting of solid tumors by BsCAR T cells
Authors: Stepanov Alexey V. , Kalinin Roman S. , Shipunova Victoria O. , Zhang Ding , Xie Jia , Rubtsov Yuri P. , Ukrainskaya Valeria M. , Schulga Alexey , Konovalova Elena V. , Volkov Dmitry V. , Yaroshevich Igor A. , Moysenovich Anastasiia M. , Belogurov Alexey A. , Zhang Hongkai , Telegin Georgij B. , Chernov Alexandr S. , Maschan Mikhail A. , Terekhov Stanislav S. , Wu Peng , Deyev Sergey M. , Lerner Richard A. , Gabibov Alexander G. , Altman Sidney
Published: November 2022

The development of chimeric antigen receptor (CAR) T cell therapy has become a critical milestone in modern oncotherapy. Despite the remarkable in vitro effectiveness, the problem of safety and efficacy of CAR T cell therapy against solid tumors is challenged by the lack of tumor-specific antigens required to avoid on-target off-tumor effects. Spatially separating the cytotoxic function of CAR T cells from tumor antigen recognition provided by protein mediators allows for the precise control of CAR T cell cytotoxicity. Here, the high affinity and capability of the bacterial toxin-antitoxin barnase-barstar system were adopted to guide CAR T cells to solid tumors. The complementary modules based on (
1
) ankyrin repeat (DARPin)-barnase proteins and (
2
) barstar-based CAR (BsCAR) were designed to provide switchable targeting to tumor cells. The alteration of the DARPin-barnase switches enabled the targeting of different tumor antigens with a single BsCAR. A gradual increase in cytokine release and tunable BsCAR T cell cytotoxicity was achieved by varying DARPin-barnase loads. Switchable BsCAR T cell therapy was able to eradicate the HER2
+
ductal carcinoma in vivo. Guiding BsCAR T cells by DARPin-barnase switches provides a universal approach for a controlled multitargeted adoptive immunotherapy.
Odd–even effect on the thermal conductivity of liquid crystalline epoxy resins
Authors: Lv Guangxin , Shen Chengtian , Shan Naisong , Jensen Elynn , Li Xiaoru , Evans Christopher M. , Cahill David G.
Published: November 2022

Rapid developments in high-performance computing and high-power electronics are driving needs for highly thermal conductive polymers and their composites for encapsulants and interface materials. However, polymers typically have low thermal conductivities of ∼0.2 W/(m K). We studied the thermal conductivity of a series of epoxy resins cured by one diamine hardener and seven diepoxide monomers with different precise ethylene linker lengths (
x
= 2–8). We found pronounced odd–even effects of the ethylene linker length on the liquid crystalline order, mass density, and thermal conductivity. Epoxy resins with even
x
have liquid crystalline structure with the highest density of 1.44 g/cm
3
and highest thermal conductivity of 1.0 W/(m K). Epoxy resins with odd
x
are amorphous with the lowest density of 1.10 g/cm
3
and lowest thermal conductivity of 0.17 W/(m K). These findings indicate that controlling precise linker length in dense networks is a powerful route to molecular design of thermally conductive polymers.
A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions
Authors: Vayena Evangelia , Chiappino-Pepe Anush , MohammadiPeyhani Homa , Francioli Yannick , Hadadi Noushin , Ataman Meriç , Hafner Jasmin , Pavlou Stavros , Hatzimanikatis Vassily
Published: November 2022

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annotations being limited to a set of already known reactions. Here, we introduce
N
etwork
I
ntegrated
C
omputational
E
xplorer for
G
ap
A
nnotation of
Me
tabolism (NICEgame), a workflow to identify and curate nonannotated metabolic functions in genomes using the ATLAS of Biochemistry and genome-scale metabolic models (GEMs). To resolve gaps in GEMs, NICEgame provides alternative sets of known and hypothetical reactions, assesses their thermodynamic feasibility, and suggests candidate genes to catalyze these reactions. We identified metabolic gaps and applied NICEgame in the latest GEM of
Escherichia coli
, iML1515, and enhanced the
E. coli
genome annotation by resolving 47% of these gaps. NICEgame, applicable to any GEM and functioning from open-source software, should thus enhance all GEM-based predictions and subsequent biotechnological and biomedical applications.
Seeing what is not shown
Authors: Hengesbach Nicole , McInerny Greg J. , Albuquerque João Porto de
Published: November 2022

Critical studies of data visualization often highlight how the reductive nature of visualization methods excludes
data limitations and qualities that are crucial to understanding those data. This case study explores how a data visualization
could express contingent, situated, and contextual facets of data. We examine how such data limitations might be surfaced and
represented within visualizations through an interplay between the critique of an existing data visualization and the development
of alternative designs. Based on a case study of urban tree data, we interrogate data limitations in relation to four different
types of missingness: Incompleteness, Emptiness, Absence, and Nothingness. Our study enables reflections on how data limitations
can be investigated using visualizations and considers the development of a critical visualization practice.
Effect of electropulsing intensity on nucleation of TiN in 321 stainless steel
Authors: Huang Dongjian , Zhu Zhenghai , Zheng Xiang , Xiao Zixuan , Xiao Lijun , Yang Chengcheng , Zhao Tengfei
Published: November 2022

In the process of titanium microalloyed steel continuous casting, tiny TiN can refine solidification structures, while thick TiN will affect casting. In this paper, the experimental results showed that electropulsing could refine the size of TiN precipitates and improve the nucleation rate of the TiN precipitates. The larger electropulsing intensity resulted in a better effect. The modelling results showed that electropulsing could reduce the nucleation barrier of TiN in the molten steel and the two-phase region. In addition, the larger the electropulsing intensity and the higher the temperature, the better the promotion effect is. This research is of great significance for solving the problem of nozzle clogging and solidification microstructure refinement of titanium microalloyed steel.
Tunable phase transitions in half-Heusler TbPtBi compound
Authors: Patel Pratik D , Sharma Akariti , Devanarayanan Bharathiganesh , Dutta Paramita , Singh Navinder
Published: November 2022

We report various phase transitions in half-Heusler TbPtBi compound using density functional theory. Specifically, the inclusion of spin–orbit coupling (SOC) leads to the band inversion resulting in the transition from the metallic to the topological semimetallic phase. However, in the presence of SOC, there is a phase transition from the topological semimetal to the trivial semimetal when the material is subjected to compressive strain

−
7

%

. Subsequently, under the further increase of compressive strain

(

⩾
−
7
%

)

, we find an opening of a direct band gap at the point, driving the system from the trivial semimetallic to a semiconducting state with changes in the sequence of the bands. In the absence of SOC, only the transition from the metallic to the semiconducting phase is noticed. Under tensile strain, the TbPtBi compound maintains its phase as in the unstrained condition but with an increase in the hole pocket at the Fermi level, both in the absence and presence of SOC. These tunable phase transitions (especially as a fraction of strain) make this compound very promising for application in various quantum devices, such as highly sensitive strain gauges.
On the effect of forcing on fold bifurcations and early-warning signals in population dynamics
Authors: Remo F , Fuhrmann G , Jäger T
Published: November 2022

The classical fold bifurcation is a paradigmatic example of a critical transition. It has been used in a variety of contexts, including in particular ecology and climate science, to motivate the role of slow recovery rates and increased autocorrelations as early-warning signals of such transitions. We study the influence of external forcing on fold bifurcations and the respective early-warning signals. Thereby, our prime examples are single-species population dynamical models with Allee effect under the influence of either quasiperiodic forcing or bounded random noise. We show that the presence of these external factors may lead to so-called non-smooth fold bifurcations, and thereby has a significant impact on the behaviour of the Lyapunov exponents (and hence the recovery rates). In particular, it may lead to the absence of critical slowing down prior to population collapse. More precisely, unlike in the unforced case, the question whether slow recovery rates can be observed or detected prior to the transition crucially depends on the chosen time-scales and the size of the considered data set.
Measuring the kinematic parameters of a rotating object in circular motion using the magnetometer of a smartphone
Authors: Puttharugsa Chokchai , Khemmani Supitch , Pimanpang Samuk
Published: November 2022

This paper describes a method to measure the kinematic parameters of a rotating object in circular motion using the magnetometer of a smartphone. A wheel with four legs had magnetic buttons attached to the ends of the legs. The smartphone was placed on the ground to measure the magnetic field when the wheel rotated. The experimental data can be calculated to obtain an angular position, an angular velocity, and an angular acceleration. The results show that the smartphone can be a useful tool to determine kinematic parameters in circular motion. The experiment is easy to set up using simple available objects, and students can conduct this experiment at home.
Comparing the performance of 850 GHz integrated bias-tee superconductor-insulator-superconductor (SIS) mixers with single- and parallel-junction tuner
Authors: Tan B-K , Rudakov K , Koshelets V P , Khudchenko A , Baryshev A M , Yassin G
Published: November 2022

We present and compare the design and performance of two 850 GHz radial probe fed superconductor-insulator-superconductor mixers, where the antenna is aligned perpendicular to the E-Plane of the input full-height rectangular waveguide connected to a multiple flare-angles smooth-walled horn. Both designs are comprised of 0.5 µm2 hybrid niobium/aluminium-nitride/niobium-nitride tunnel junction, fabricated on top of a niobium titanium nitride ground plane with an Al wiring layer. The entire superconducting circuit is supported with a 40 µm thick quartz substrate. The major difference between the two designs is the method used to cancel out the parasitic junction capacitance for broadband performance. The first design utilises two identical junctions connected in parallel with a short transmission line to convert the capacitance of one junction into the equivalent inductance of the other junction, commonly known as the twin-junction tuning scheme; whilst the second design employs an end-loaded scheme with only one tunnel junction. We found that both methods offer similar radio frequency performances, with close to 2× the double sideband quantum noise temperature, but the twin-junction design is more resilient to fabrication tolerances. However, the end-loaded design offers a much better intermediate frequency (IF) bandwidth performance, made possible by the sub-micron and high current density tunnel junction technology. The improved IF performance is important for many millimetre (mm) and sub-mm observatories, such as future upgrades of Atacama Large Millimetre/sub-mm Array receivers, as well as forthcoming space-borne far-infrared missions. Therefore, we conclude that the single-junction mixer design is the preferred option for THz applications, as long as the fabrication error can be minimised within a certain limit.
Black hole production, eternal inflation, and information in quasi-de Sitter space
Authors: Seo Min-Seok
Published: November 2022

When the slow-roll parameter ϵHis smaller thanH2/MPl2, the quantum fluctuations of the inflaton after the horizon crossing are large enough to realize eternal inflation. Whereas they do not generate a sufficient amount of density fluctuation of the inflaton to produce the black hole in quasi-de Sitter space, they can also generate the sizeable density fluctuation of the radiation when the number of degrees of freedom increases rapidly in time, as predicted by the distance conjecture. We argue that the condition that the density fluctuation of the radiation is not large enough to produce the black hole until the end of inflation is equivalent to the no eternal inflation condition. When the radiation emitted by the horizon does not produce the black hole, even if the number of degrees of freedom increases in time, the information paradox does not arise for ϵHlarger than 10-7(H2/MPl2) and time scale shorter than 104(MPl/H2). Regardless of the presence of the information paradox, a static observer cannot retrieve a sufficient amount of information, which is consistent with the complementarity.
Singularities of regular black holes and the monodromy method for asymptotic quasinormal modes*
Authors: Lan Chen , Wang Yi-Fan
Published: November 2022

We use the monodromy method to investigate the asymptotic quasinormal modes of regular black holes based on the explicit Stokes portraits. We find that, for regular black holes with spherical symmetry and a single shape function, the analytical forms of the asymptotic frequency spectrum are not universal and do not depend on the multipole number but on the presence of complex singularities and the trajectory of asymptotic solutions along the Stokes lines.
Numerical error analysis of SOLPS-ITER simulations of EAST
Authors: Boeyaert Dieter , Carli Stefano , Ghoos Kristel , Dekeyser Wouter , Wiesen Sven , Baelmans Martine
Published: November 2022

Plasma edge simulations with codes like SOLPS-ITER are widely employed to interpret fusion experiments. However, numerical errors appearing in such simulations are rarely investigated, despite their potential large impact on simulation results. These errors consist of the statistical error and the bias, both resulting from the finite number of employed EIRENE Monte Carlo particles and incomplete convergence, and the discretization error due to the finite resolution of the computational grids. In this contribution, the resulting numerical errors on simulations of pure deuterium and neon seeded H-mode EAST discharges are examined. The statistical error can be kept small compared to other numerical error contributions by averaging the plasma profiles. This allows investigating the bias and discretization errors using Richardson extrapolation. It is shown that grid refinement and the number of employed Monte Carlo particles have the largest influence on the result, in agreement with similar studies of an ITER deuterium case. For the first time, numerical error bars on the entire simulated target profiles are determined showing that the largest numerical error is 17.9%, mainly due to the plasma grid discretization. On top, also numerical errors on simulated neutral pressures are investigated in detail, for which the statistical error is dominant. The analysis demonstrates which setup is needed to keep numerical errors limited: the SOLPS-ITER averaging procedure should be employed including enough EIRENE particles, and the involved grids should be sufficiently refined to reduce discretization errors.
Stability of solitary waves in nonlinear Klein–Gordon equations
Authors: Rabán Pablo , Alvarez-Nodarse Renato , Quintero Niurka R
Published: November 2022

The stability of topological solitary waves and pulses in one-dimensional nonlinear Klein–Gordon systems is revisited. The linearized equation describing small deviations around the static solution leads to a Sturm–Liouville problem, which is solved in a systematic way for the

−
l
(
l
+
1
)

s
e
c
h

2

(
x
)

-potential, showing the orthogonality and completeness relations fulfilled by the set of its solutions for all values

l
∈

N

. This approach enables the linear stability of kinks and pulses of certain nonlinear Klein–Gordon equations to be determined. The inverse problem, which starts from Sturm–Liouville problem and obtains nonlinear Klein–Gordon potentials, is also revisited and solved in a direct way. The exact solutions (kinks and pulses) for these potentials are calculated, even when the nonlinear potential is not explicitly known. The kinks are found to be stable, whereas the pulses are unstable. The stability of the pulses is achieved by introducing certain spatial inhomogeneities.
Realization of divertor configuration discharge in J-TEXT tokamak
Authors: CHEN Zhipeng , ZHU Lizhi , XU Xin , ZHENG Wei , ZHANG Ming , GAO Li , XIA Minghui , YANG Jie , ZHU Mingchong , HAO Zhigang , JIAO Shaodong , CHENG Zhifeng , YANG Zhoujun , ZHANG Xiaoqing , CHEN Zhongyong , WANG Nengchao , DING Yonghua , ZHUANG Ge , GENTLE Kenneth W , LIANG Yunfeng , PAN Yuan
Published: November 2022

To extend the operation region of the Joint-Texas Experimental tokamak (J-TEXT) to the divertor configuration and even the H-mode, the divertor configuration discharge has been realized for the first time in the J-TEXT tokamak. Along with the establishment of a power supply for the divertor configuration, the construction of relevant diagnostics, and the installation of the divertor target on the high-field side, divertor discharge has been tested. Through the equilibrium calculation and position stability analysis, the control strategy has evolved to be more stable. High-density experiments and auxiliary heating experiments have been carried out on the divertor configuration. The special midplane single-null (MSN) divertor configuration is shown to be more stable than the limiter configuration in the density limit condition and can reach a higher density in the experiment. In the ECRH experiment, the power injection enhances the electron temperature and density, while more heat outflux is loaded on the divertor target tiles and causes more intensive recycling and impurity release. The future plan for the divertor configuration operation in the J-TEXT tokamak is also included.
Open Access Academic Lectures as Sources for Incidental Vocabulary Learning: Examining the Role of Input Mode, Frequency, Type of Vocabulary, and Elaboration
Authors: Dang Thi Ngoc Yen , Lu Cailing , Webb Stuart
Published: November 2022

Open access academic lectures are potential sources for incidental vocabulary learning. These lectures are available in various formats (transcripts, audios, videos, and video with captions), but no studies have compared the learning of vocabulary in these lectures through different input modes. This study adopted a pretest–posttest design to compare learning at the meaning recall level of 50 words in the same academic lecture through five input modes: reading, listening, reading while listening, viewing, and viewing with captions. One hundred sixty-five English for Academic Purposes learners in China were assigned to five experimental groups and a control group. The experimental groups received the treatment with the assigned input mode while the control group received no treatment. Results show that although learning occurred through all input modes, only viewing significantly contributed to the learning gains. Frequency of occurrence and type of vocabulary significantly predicted the learning gains, but the type of verbal elaboration and nonverbal elaboration did not. This study provides further insights into the value of academic lectures for incidental vocabulary learning and supports the multimedia learning theory and its principles.
Factors Influencing Trust and Trustworthiness: Cosmetic Injectable Patient Experience Exploratory Study (CIPEES)—Part 3
Authors: McDonald Cara B , Heydenrych Izolda
Published: November 2022

Background

Despite the widely recognized importance of trust in professional relationships, it remains elusive, complex, multidimensional, and difficult to quantify due to the lack of validated tools.

Objectives

The authors sought to explore both the important factors for building trust with cosmetic injectable patients and strategies for improving levels of trustworthiness in aesthetic practitioners.

Methods

In order to explore factors in building trust with cosmetic injectable practitioners, a global study was conducted via an online survey. The Cosmetic Injectable Patient Experience Exploratory Study (CIPEES) survey assessed the relative importance of qualifications and training; reviewing of previous work (before and after photos); reputation; connection; time spent; online presence; and personal appearance of the practitioner in developing trust in a cosmetic practitioner.

Results

The CIPEES survey collected 1488 responses across 75 countries, with 66% of participants completing all 15 questions. The respondents were 95.6% female and 4.4% male, with ages ranging from 18 to >65 years old (median 33 years old). The number 1 ranked reason for being able to trust a cosmetic injector was qualifications and training, followed by the reputation of the practitioner, and time spent by the practitioner with the survey respondent. Practitioner online presence was considered the least important factor in helping develop trust.

Conclusions

The CIPEES survey results support patient trust being built through credibility, reliability, and intimacy, with low levels of practitioner self-orientation. The trustworthiness equation provides a framework for identifying practitioner weaknesses in patient relationships and actionable methods of improving trustworthiness.
sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure
Authors: Yan Ke , Lv Hongwu , Guo Yichen , Peng Wei , Liu Bin
Published: November 2022

Motivation

Antimicrobial peptides (AMPs) are essential components of therapeutic peptides for innate immunity. Researchers have developed several computational methods to predict the potential AMPs from many candidate peptides. With the development of artificial intelligent techniques, the protein structures can be accurately predicted, which are useful for protein sequence and function analysis. Unfortunately, the predicted peptide structure information has not been applied to the field of AMP prediction so as to improve the predictive performance.

Results

In this study, we proposed a computational predictor called sAMPpred-GAT for AMP identification. To the best of our knowledge, sAMPpred-GAT is the first approach based on the predicted peptide structures for AMP prediction. The sAMPpred-GAT predictor constructs the graphs based on the predicted peptide structures, sequence information and evolutionary information. The Graph Attention Network (GAT) is then performed on the graphs to learn the discriminative features. Finally, the full connection networks are utilized as the output module to predict whether the peptides are AMP or not. Experimental results show that sAMPpred-GAT outperforms the other state-of-the-art methods in terms of AUC, and achieves better or highly comparable performance in terms of the other metrics on the eight independent test datasets, demonstrating that the predicted peptide structure information is important for AMP prediction.

Availability and implementation

A user-friendly webserver of sAMPpred-GAT can be accessed at http://bliulab.net/sAMPpred-GAT and the source code is available at https://github.com/HongWuL/sAMPpred-GAT/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Vaeda computationally annotates doublets in single-cell RNA sequencing data
Authors: Schriever Hannah , Kostka Dennis
Published: November 2022

Motivation

Single-cell RNA sequencing (scRNA-seq) continues to expand our knowledge by facilitating the study of transcriptional heterogeneity at the level of single cells. Despite this technology’s utility and success in biomedical research, technical artifacts are present in scRNA-seq data. Doublets/multiplets are a type of artifact that occurs when two or more cells are tagged by the same barcode, and therefore they appear as a single cell. Because this introduces non-existent transcriptional profiles, doublets can bias and mislead downstream analysis. To address this limitation, computational methods to annotate and remove doublets form scRNA-seq datasets are needed.

Results

We introduce vaeda (Variational Auto-Encoder for Doublet Annotation), a new approach for computational annotation of doublets in scRNA-seq data. Vaeda integrates a variational auto-encoder and Positive-Unlabeled learning to produce doublet scores and binary doublet calls. We apply vaeda, along with seven existing doublet annotation methods, to 16 benchmark datasets and find that vaeda performs competitively in terms of doublet scores and doublet calls. Notably, vaeda outperforms other python-based methods for doublet annotation. Altogether, vaeda is a robust and competitive method for scRNA-seq doublet annotation and may be of particular interest in the context of python-based workflows.

Availability and implementation

Vaeda is available at https://github.com/kostkalab/vaeda, and the version used for the results we present here is archived at zenodo (https://doi.org/10.5281/zenodo.7199783).

Supplementary information

Supplementary data are available at Bioinformatics online.
Promoting regeneration while blocking cell death preserves motor neuron function in a model of ALS
Authors: Wlaschin Josette J , Donahue Caroline , Gluski Jacob , Osborne Jennifer F , Ramos Leana M , Silberberg Hanna , Le Pichon Claire E
Published: November 2022

Amyotrophic lateral sclerosis (ALS) is a devastating and fatal neurodegenerative disease of motor neurons with very few treatment options. We had previously found that motor neuron degeneration in a mouse model of ALS can be delayed by deleting the axon damage sensor MAP3K12 or dual leucine zipper kinase (DLK). However, DLK is also involved in axon regeneration, prompting us to ask whether combining DLK deletion with a way to promote axon regeneration would result in greater motor neuron protection. To achieve this, we used a mouse line that constitutively expresses ATF3, a master regulator of regeneration in neurons. Although there is precedence for each individual strategy in the SOD1G93A mouse model of ALS, these have not previously been combined. By several lines of evidence including motor neuron electrophysiology, histology and behaviour, we observed a powerful synergy when combining DLK deletion with ATF3 expression. The combinatorial strategy resulted in significant protection of motor neurons with fewer undergoing cell death, reduced axon degeneration and preservation of motor function and connectivity to muscle. This study provides a demonstration of the power of combinatorial therapy to treat neurodegenerative disease.