bluuebunny/crossref_metadata_2025 huggingface dataset:
A compact gain-enhanced microwave helical antenna for 87Rb atomic experiments
Authors: Zheng Yong-Guang , Jiang Lei , Zhu Zi-Hang , Zhang Wei-Yong , Zhou Zhao-Yu , Xiao Bo , Yuan Zhen-Sheng
Published: June 2022

We present a compact and gain-enhanced microwave helical antenna for manipulating ultracold 87Rb atoms coherently. By replacing the reflecting plate with an enhancing cup, the voltage standing wave ratio is reduced by 0.5 in the frequency range of 6.73–6.93 GHz, which covers the resonant frequency between the ground-state hyperfine levels of the 87Rb atom. The gain of the helical antenna is increased by 1.25–1.63 dBi, whose length is 89 mm. Applying the antenna to ultracold 87Rb atomic experiments, we achieve a Rabi frequency of 60(1) ×2π kHz of the oscillation between the hyperfine levels.
Double-server blind quantum computation based on the GHZ state
Authors: Zhou Yi , Wang Yuqi , Jian Liya , Chen Geng , Liu Shiming
Published: June 2022

We propose a new double-server blind quantum computation protocol based on the Greenberger–Horne–Zeilinger (GHZ) state. In this protocol, the correlation of the GHZ triplets has been utilized to deal with the existing double-server blind quantum computation protocol’s limitation, in which two servers cannot communicate with each other. Moreover, although the two servers in this protocol can obtain different parts of the particles in different GHZ states, they cannot match every GHZ state particle correctly, and this is because the positions of the particles are kept secret. Therefore, the protocol is still secure, in which two servers can communicate with each other. Furthermore, the client can make authentication requests to the trusted center, determining if the first server is honest or not by calculating measurements of part of the GHZ particles. After analyzing the security of the protocol, the protocol is found to be unconditionally secure.
A tensor norm approach to quantum compatibility
Authors: Bluhm Andreas , Nechita Ion
Published: June 2022

Measurement incompatibility is one of the most striking examples of how quantum physics is different from classical physics. Two measurements are incompatible if they cannot arise via classical post-processing from a third one. A natural way to quantify incompatibility is in terms of noise robustness. In the present article, we review recent results on the maximal noise robustness of incompatible measurements, which have been obtained by the present authors using free spectrahedra, and rederive them using tensor norms. In this way, we make them accessible to a broader audience from quantum information theory and mathematical physics and contribute to the fruitful interactions between Banach space theory and quantum information theory. We also describe incompatibility witnesses using the tensor norm and matrix convex set duality, emphasizing the relation between the different notions of witnesses.
Fabrication of polydimethylsiloxane/graphene flexible strain sensors by using the scraping and coating method
Authors: Zhang Zhou Q. , Zhang Xue L. , Xu Guang S. , Liu Xue J. , Guo Q. , Feng Z. , Jia Jiang T. , Ku Peng T.
Published: June 2022

Production of flexible strain sensors is complex, time-consuming, and expensive. In this study, a novel fabrication method of polydimethylsiloxane/graphene nanocomposite conductive materials was proposed by using the scraping and coating method for manufacturing sandwich-shape flexible strain sensors. A ZQ-60B tensile testing machine was employed to test the mechanical properties of flexible sensors with 1%, 3%, and 5% graphene content. The results revealed that the stress and strain of the flexible strain sensor exhibited a linear relationship, and the linear correlation coefficients were 0.99706, 0.99819, and 0.99826, respectively. The concentration of graphene was 1%, 3%, and 5%, and the gauge factors (GFs) of the sensor were 24, 6, and 3, respectively. With the increase in the graphene content, the GF decreased gradually. This phenomenon could be attributed to tunneling, which increased the number of conductive pathways with an increase in the graphene content. Furthermore, the sensor exhibited excellent stability after 100 cycles of stretching/scaling. The finger joint bending test revealed that the flexible strain sensor is reproducible and exhibits excellent application prospects in monitoring human movement and health.
Multi-scale modeling of shock initiation of a pressed energetic material. II. Effect of void–void interactions on energy localization
Authors: Nguyen Yen T. , Seshadri Pradeep K. , Sen Oishik , Hardin David B. , Molek Christopher D. , Udaykumar H. S.
Published: June 2022

Heterogeneous energetic materials (EMs) contain microstructural defects such as voids, cracks, interfaces, and delaminated zones. Under shock loading, these defects offer potential sites for energy localization, i.e., hotspot formation. In a porous EM, the collapse of one void can generate propagating blast waves and hotspots that can influence the hotspot phenomena at neighboring voids. Such void–void interactions must be accounted for in predictive multi-scale models for the reactive response of a porous EM. To infuse such meso-scale phenomena into a multi-scale framework, a meso-informed ignition and growth model (MES-IG) has been developed, where the influence of void–void interactions is incorporated into the overall reaction rate through a function, fv−v. Previously, MES-IG was applied to predict the sensitivity and reactive response of EM, where fv−v was assumed to be a function of the overall sample porosity alone. This paper performs a deeper analysis to model the strong dependency of fv−v on other factors, such as void size and shock strength. The improved model for void–void interactions produces good agreement with direct numerical simulations of the HE microstructures and, thus, advances the predictive capability of multi-scale models of the shock response and sensitivity of EM.
Stewartson layer instability and triadic resonances in rotating sphere with oscillating inner core
Authors: Subbotin Stanislav , Shmakova Natalia , Ermanyuk Evgeny , Kozlov Victor
Published: June 2022

This work is devoted to an experimental study of the stability of a steady flow in a rotating spherical cavity with an oscillating core. The case of circular core oscillations in a plane perpendicular to the rotation axis is considered. The steady flow structure strongly depends on the dimensionless oscillation frequency. In the frequency range where there are no inertial waves, the flow resembles a classical Taylor column with an almost uniform distribution of the angular velocity. With an increase in the oscillation amplitude above a certain threshold level, a two-dimensional azimuthal wave is excited at the column boundary. The wave velocity is determined by the intensity of the liquid differential rotation and does not depend on the Ekman number. In the case of oscillation with a frequency less than twice the rotation rate, the inertial waves propagate in fluid bulk and introduce a significant correction to the steady velocity profile. At high amplitudes, the triadic subharmonic resonance of inertial waves is excited. The triadic interactions simultaneously manifest themselves in two regions of the spherical shell, generating secondary waves with the same frequencies, but different wavenumbers: subharmonic waves with shorter (respectively, longer) wavelengths are observed in outer (respectively, inner) regions of the shell. In some cases, the third (intermediate) region with subharmonic waves of intermediate wavelength can be observed. The development of the triadic resonance leads to a strongly nonlinear response in the form of a system of steady vortices with well-defined azimuthal periodicity.
A compound pendulum for thrust measurement of micro-Newton thruster
Authors: Xu Hao , Gao Yong , Mao Qiang-Bing , Ye Liang-Wen , Hu Zhong-Kun , Zhang Kai , Song Peiyi , Li Qing
Published: June 2022

A thrust stand is developed for testing micro-Newton level thrusters on the ground. The stand is composed of a compound pendulum that is symmetrically suspended by two thin beryllium copper strips, and it is precisely calibrated by gravity. The stiffness of the stand can be adjusted in 3 orders of magnitude by a counterweight. When the stiffness is larger than 1 Nm/rad, the stand demonstrates a fast response to thrust. The measured range of the stand reaches 1000 μN, and the noise is less than 0.1 μN/Hz within 1 mHz–1 Hz. To calibrate the resolution of the stand, an electrostatic force is applied to the stand with an actuator. The equivalent thrust is determined to be 0.09 μN with a standard uncertainty of 0.02 μN. Using the stand, a micro-Newton colloid thruster is tested. The output of the colloid thruster changes with the applied voltage as 0.015(1) μN/V. When changing the voltage by 50 V, the change in thrust is measured to be 0.7 μN with a standard uncertainty of 0.1 μN.
Quantum thermal transport beyond second order with the reaction coordinate mapping
Authors: Anto-Sztrikacs Nicholas , Ivander Felix , Segal Dvira
Published: June 2022

Standard quantum master equation techniques, such as the Redfield or Lindblad equations, are perturbative to second order in the microscopic system–reservoir coupling parameter λ. As a result, the characteristics of dissipative systems, which are beyond second order in λ, are not captured by such tools. Moreover, if the leading order in the studied effect is higher-than-quadratic in λ, a second-order description fundamentally fails even at weak coupling. Here, using the reaction coordinate (RC) quantum master equation framework, we are able to investigate and classify higher-than-second-order transport mechanisms. This technique, which relies on the redefinition of the system–environment boundary, allows for the effects of system–bath coupling to be included to high orders. We study steady-state heat current beyond second-order in two models: The generalized spin-boson model with non-commuting system–bath operators and a three-level ladder system. In the latter model, heat enters in one transition and is extracted from a different one. Crucially, we identify two transport pathways: (i) System’s current, where heat conduction is mediated by transitions in the system, with the heat current scaling as jq ∝ λ2 to the lowest order in λ. (ii) Inter-bath current, with the thermal baths directly exchanging energy between them, facilitated by the bridging quantum system. To the lowest order in λ, this current scales as jq ∝ λ4. These mechanisms are uncovered and examined using numerical and analytical tools. We contend that the RC mapping brings, already at the level of the mapped Hamiltonian, much insight into transport characteristics.
Understanding the performance differences between solution and vacuum deposited OLEDs: A computational approach
Authors: Sanderson Stephen , Vamvounis George , Mark Alan E. , Burn Paul L. , White Ronald D. , Philippa Bronson W.
Published: June 2022

Solution-processing of organic light-emitting diode films has potential advantages in terms of cost and scalability over vacuum-deposition for large area applications. However, solution processed small molecule films can have lower overall device performance. Here, novel molecular dynamics techniques are developed to enable faster simulation of solvent evaporation that occurs during solution processing and give films of thicknesses relevant to real devices. All-atom molecular dynamics simulations are then used in combination with kinetic Monte Carlo transport modeling to examine how differences in morphology stemming from solution or vacuum film deposition affect charge transport and exciton dynamics in films consisting of light-emitting bis(2-phenylpyridine)(acetylacetonate)iridium(III) [Ir(ppy)2(acac)] guest molecules in a 4,4′-bis(N-carbazolyl)biphenyl host. While the structures of the films deposited from vacuum and solution were found to differ, critically, only minor variations in the transport properties were predicted by the simulations even if trapped solvent was present.
Acoustic and vibration isolation for a gravity gradiometer
Authors: Sunderland A. , Naveh Y. , Ju L. , Blair D. G. , Lockwood R. , Anderson B. , Dransfield M.
Published: June 2022

Vibration in the audio frequency band affects the performance of rotating gravity gradiometers used for airborne mineral exploration. This is probably due to translation to rotation coupling inside the gradiometer platform. It was found that the DC gravity gradient signal was proportional to the square of the third time derivative of position, or jerk squared. The demanding airborne environment for such instrumentation demands a light weight broadband acoustic shield and vibration isolator. This paper presents the design principles for such an isolator, based on vibration isolated spherical shell structures. Performance data are presented as well as flight test data that demonstrated a 14% gravity gradient noise reduction compared with an unshielded instrument.
There is no quantum measurement problem
Authors: Mermin N. David
Published: June 2022

The idea that the collapse of a quantum state is a physical process stems from a misunderstanding of probability and the role it plays in quantum mechanics.
One Antarctic slug to confuse them all: the underestimated diversity of
Authors: Maroni Paige J. , Baker Bill J. , Moran Amy L. , Woods H. Arthur , Avila Conxita , Johnstone Glenn J. , Stark Jonathan S. , Kocot Kevin M. , Lockhart Susanne , Saucède Thomas , Rouse Greg W. , Wilson Nerida G.
Published: June 2022

The Antarctic marine environment, although rich in life, is predicted to experience rapid and significant effects from climate change. Despite a revolution in the approaches used to document biodiversity, less than one percent of Antarctic marine invertebrates are represented by DNA barcodes and we are at risk of losing biodiversity before discovery. The ease of sequencing mitochondrial DNA barcodes has promoted this relatively ‘universal’ species identification system across most metazoan phyla and barcode datasets are currently readily used for exploring questions of species-level taxonomy. Here we present the most well-sampled phylogeny of the direct-developing, Southern Ocean nudibranch mollusc, Doris kerguelenensis to date. This study sampled over 1000 new Doris kerguelenensis specimens spanning the Southern Ocean and sequenced the mitochondrial COI gene. Results of a maximum likelihood phylogeny and multiple subsequent species delimitation analyses identified 27 new species in this complex (now 59 in total). Using rarefaction techniques, we infer more species are yet to be discovered. Some species were only collected from southern South America or the sub-Antarctic islands, while at least four species were found spanning the Polar Front. This is contrary to dispersal predictions for species without a larval stage such as Doris kerguelenensis. Our work demonstrates the value of increasing geographic scope in sampling and highlights what could be lost given the current global biodiversity crisis.
A broadly applicable, stress-mediated bacterial death pathway regulated by the phosphotransferase system (PTS) and the cAMP-Crp cascade
Authors: Zeng Jie , Hong Yuzhi , Zhao Ningqiu , Liu Qianyu , Zhu Weiwei , Xiao Lisheng , Wang Weijie , Chen Miaomiao , Hong Shouqiang , Wu Liwen , Xue Yunxin , Wang Dai , Niu Jianjun , Drlica Karl , Zhao Xilin
Published: June 2022

Significance

Finding that pan-tolerance derives from defects in carbohydrate regulation connects stress-mediated lesions with metabolic change, identifies a stable type of tolerance, and demonstrates a widely shared death response. Manipulation of the response should improve antimicrobial efficacy, preserve beneficial bacteria during antimicrobial use, and protect industrial bacteria from toxic products. Mutations in many genes can interfere with stress-mediated metabolism; thus, mutation to pan-tolerance could be a high-probability event. Finding that selection of tolerance to one lethal stressor confers tolerance to many, if not all, indicates that massive disinfectant consumption potentially undermines antimicrobial efficacy and immune defenses against pathogenic bacteria. Since pan-tolerance is hidden from current surveillance of resistance, the work indicates a need for facile methods to measure tolerance.
Revealing synergetic structural activation of a CuAu surface during water–gas shift reaction
Authors: Dong Zejian , Nian Yao , Liu Hongpeng , Chen Jiacheng , Wang Yan , Wang Shuangbao , Xu Jing , Han You , Luo Langli
Published: June 2022

Significance

Atomic-level in situ environmental transmission electron microscopy observation of the dynamic activation process on a low-indexed CuAu surface under water–gas shift reaction (WGSR) condition has been revealed. The atomic-scale structural activation of a CuAu surface features a gas-dependent periodic surface restructuring and elemental ordering, explaining the “synergy effect” from the structural point of view. These real-time changes under relevant reactant gases and temperature are correlated with the reaction route of WGSR corroborated by density functional theory–based calculation and ab initio molecular dynamics simulation and can provide insights for atom-precision catalyst design.
Molecular determinants of inhibition of the human proton channel hHv1 by the designer peptide C6 and a bivalent derivative
Authors: Zhao Ruiming , Shen Rong , Dai Hui , Perozo Eduardo , Goldstein Steve A. N.
Published: June 2022

Significance

We designed C6 peptide to address the absence of specific inhibitors of human voltage-gated proton channels (hHv1). Two C6 bind to the two hHv1 voltage sensors at the resting state, inhibiting activation on depolarization. Here, we identify the C6–hHv1 binding interface using tethered-toxin variants and channel mutants, unveil an important role for negatively charged lipids, and present a model of the C6–hHv1 complex. Inspired by nature, we create a peptide with two C6 epitopes (C6
2
) that binds to both channel subunits simultaneously, yielding picomolar affinity and significantly improved inhibition at high potentials. C6 and C6
2
are peptides designed to regulate hHv1, a channel involved in innate immune-system inflammatory pathophysiology, sperm capacitation, cancer-cell proliferation, and tissue damage in ischemic stroke.
Co-component signal transduction systems: Fast-evolving virulence regulation cassettes discovered in enteric bacteria
Authors: Kinch Lisa N. , Cong Qian , Jaishankar Jananee , Orth Kim
Published: June 2022

Significance

Using the domain and operon organization of VtrA/VtrC, combined with fold predictions, we identify co-component signal transduction systems in enteric bacteria that likely regulate virulence. We observe that the heterodimeric VtrA/VtrC periplasmic bile acid receptor controlling the
Vibrio parahaemolyticus
type 3 secretion system 2 is a distant homolog of the ToxR/ToxS master regulator of virulence and has evolved beyond confident sequence recognition. Exploiting the newly developed machine learning methods for structure prediction, we observe a VtrC-like lipocalin fold for both the ToxS periplasmic domain and other detected periplasmic sensor components. This structure prediction supports the divergent evolution of VtrA/VtrC-like co-component signal transduction systems and suggests a role for lipid sensing in regulating virulence in enteric bacteria.
Jelou pipol
Authors: Cotelo García Rosalía
Published: June 2022

This study explores the characteristics of the language used in Twitch, one of the most popular streaming platforms worldwide, as an example of computer-mediated communication (CMC). Some of the most salient traits used to describe CMC are found in Twitch chat messages, as the paper will show, confirming that the communicative interaction that takes place among users of this platform matches the features of CMC described in the academic literature. Additionally, the synchronous and multimodal nature of this platform, as well as the pragmatic implications of the use of subscriber-exclusive emotes are peculiarities that must be considered for a comprehensive description of the language that takes place on Twitch. Lastly, in the case of the videogame chats in Spanish studied, the paper introduces as a key factor in the description of this language the characteristics of the lexicon: its foreign origin, its neological nature and its high level of terminological specialisation.
Features of resonant and non-resonant slab ion-temperature-gradient instabilities in weakly reversed magnetic shear configurations
Authors: Ren Guangzhi , Wei Lai , Li Jiquan , Wang Zheng-Xiong
Published: June 2022

Linear eigenmode analysis of slab ion-temperature-gradient (ITG) instabilities in weakly reversed magnetic shear configurations is performed based on a Gyro-Landau-Fluid model. Numerical results show that the linear features of the ITG instabilities are different in weakly reversed shear plasmas with double, single and non-rational surfaces, respectively. For the case with double rational surfaces separated far away, mode structures exhibit a global symmetry or antisymmetry versus the minimum of the safety factor q

min
with locally odd or even parity around each resonant surface. Linear properties are mainly determined by local magnetic shear as in normal magnetic shear case. With the distance between two surfaces decreasing, linear instability properties vary non-monotonically. Various high order eigenmodes are driven unstable with a moderate distance. The mode structures are eventually localized around q

min
surface in the single rational surface case, even nonresonant one. When there is no rational surface, the nonresonant modes are strongly driven unstable with growth rates even larger than the resonant modes. In addition, similar results in a cylinder plasma indicate the importance of non-resonant ITG instability in the short wavelength regime with weakly reversed magnetic shear.
Quantum speed limits for information and coherence
Authors: Mohan Brij , Das Siddhartha , Pati Arun Kumar
Published: June 2022

The quantum speed limit indicates the maximal evolution speed of the quantum system. In this work, we determine speed limits on the informational measures, namely the von Neumann entropy, maximal information, and coherence of quantum systems evolving under dynamical processes. These speed limits ascertain the fundamental limitations on the evolution time required by the quantum systems for the changes in their informational measures. Erasing of quantum information to reset the memory for future use is crucial for quantum computing devices. We use the speed limit on the maximal information to obtain the minimum time required to erase the information of quantum systems via some quantum processes of interest.
Communicability in time-varying networks with memory
Authors: Estrada Ernesto
Published: June 2022

We develop a first-principles approach to define the communicability between two nodes in a time-varying network with memory. The formulation is based on the time-fractional Schrödinger equation, where the fractional (of Caputo type) derivative accounts for the memory of the system. Using a time-varying Hamiltonian in the tight-binding formalism we propose the temporal communicability as the product of Mittag–Leffer functions of the adjacency matrices of the temporal snapshots. We then show that the resolvent- and exponential-communicabilities of a network are special cases of the proposed temporal communicability when perfect (resolvent) or imperfect (exponential) memory are considered for the system. By using theoretical and empirical evidence we show that real-world systems work out of perfect memory, and with an interrelation between memory-dependent temporal communication and imperfect memory spatial transmission of information. We illustrate our results with the study of trophallaxis interactions in two ant colonies.
Stress accumulation versus shape flattening in frustrated, warped-jigsaw particle assemblies
Authors: Spivack Isaac R , Hall Douglas M , Grason Gregory M
Published: June 2022

Geometrically frustrated assembly has emerged as an attractive paradigm for understanding and engineering assemblies with self-limiting, finite equilibrium dimensions. We propose and study a novel 2D particle based on a so-called ‘warped jigsaw’ (WJ) shape design: directional bonds in a tapered particle favor curvature along multi-particle rows that frustrate 2D lattice order. We investigate how large-scale intra-assembly stress gradients emerge from the microscopic properties of the particles using a combination of numerical simulation and continuum elasticity. WJ particles can favor anisotropic ribbon assemblies, whose lateral width may be self-limiting depending on the relative strength of cohesive to elastic forces in the assembly, which we show to be controlled by the range of interactions and degree of shape misfit. The upper limits of self-limited size are controlled by the crossover between two elastic modes in assembly: the accumulation of shear with increasing width at small widths giving way to unbending of preferred row curvature, permitting assembly to grow to unlimited sizes. We show that the stiffness controlling distinct elastic modes is governed by combination and placement of repulsive and attractive binding regions, providing a means to extend the range of accumulating stress to sizes that are far in excess of the single particle size, which we corroborate via numerical studies of discrete particles of variable interactions. Lastly, we relate the ground-state energetics of the model to lower and upper limits on equilibrium assembly size control set by the fluctuations of width along the ribbon boundary.
Fast capillary discharge device for soft x-ray generation in the “carbon-window” and “water-window” spectral regions
Authors: Samokhvalov A.A. , Sergushichev K.A. , Eliseev S.I. , Smirnov A.A. , Bronzov T.P. , Getman D.V. , Bolshakov E.P. , Timshina M.V. , Burtsev V.A.
Published: June 2022

The paper presents a compact source of soft X-ray radiation
based on a fast capillary discharge developed for “water window”
microscopy methods. The central part of the source is the specially
designed nanosecond voltage pulse generator capable of operating at
a frequency of 600 Hz, with 100 ns pulse duration and energy per
pulse 5 J. The discharge is created in a borosilicate capillary
non-uniformly filled with gas. The plasma emission spectra obtained
for the case of source operation in argon-helium mixture demonstrate
well-pronounced lines in the “carbon window” range, in carbon
dioxide-lines in the “water window” range. An analysis of the
emission spectra in the range of 2–9 nm in cases of different
inlet gas pressures made it possible to estimate the degree of
ablation of the inner wall of the capillary and to determine the
suitable operating pressure range.
Scenarios for future Indian HFC demand compared to the Kigali Amendment
Authors: Hillbrand Alex , Madan Prima , Singh Manjeet , McNamara Marie , Andersen Stephen O , Mathur Ajay , Shende Rajendra , Jaiswal Anjali
Published: June 2022

Demand for hydrofluorocarbon (HFC) refrigerants used as substitutes for ozone-depleting substances is growing in India and is estimated to continue growing at a high rate through the middle of this century. HFCs, although not directly ozone-depleting, are highly potent greenhouse gases subject to a global phasedown under the 2016 Kigali Amendment to the Montreal Protocol on Substances that Deplete the Ozone Layer. As of 20 January 2022, 130 Parties have ratified the Kigali Amendment, including India. This analysis evaluates scenarios for India’s HFC demand trajectory compared to likely control obligations under the Kigali Amendment. It is based on current and projected markets for HFC-using equipment and types of refrigerants utilized now and likely to be used in the future. Sectors considered in this work include mobile air conditioning, stationary air conditioning, refrigeration, and foam blowing agents. Results suggest that India’s annual HFC demand under current market trends could reach 76 MMT CO2-equivalent (CO2e) in 2030 and 197 MMT CO2e in 2050, from 23 MMT CO2e in 2020, making no changes to the current mix of HFCs in use. The Kigali Amendment requires for compliance that India freeze its HFC consumption in 2028 at a projected level of 59–65 MMT CO2e and phase down progressively over the following 29 years; in that case, annual Indian HFC demand would peak in 2030 at a projected 57 MMT CO2e and fall to 8 MMT CO2e by 2050. This trajectory would avoid cumulative HFC use of 2.2 GT CO2e through 2050 versus the current market trends. If actions are taken to accelerate the refrigerant transition in stationary air conditioning by five years, India could peak its annual HFC demand by 2028 at 40 MMT CO2e and avoid additional cumulative HFC demand of 337 MMT CO2e between 2025 and 2050, exceeding its obligations under the Kigali Amendment.
Evidence of regional sea-level rise acceleration for the North Sea
Authors: Steffelbauer David B , Riva Riccardo E M , Timmermans Jos S , Kwakkel Jan H , Bakker Mark
Published: June 2022

Global mean sea-level rise (SLR) has accelerated since 1900 from less than 2 mm yr−1 during most of the century to more than 3 mm yr−1 since 1993. Decision-makers in coastal countries, however, require information on SLR at the regional scale, where detection of an acceleration in SLR is difficult, because the long-term sea-level signal is obscured by large inter-annual variations with multi-year trends that are easily one order of magnitude larger than global mean values. Here, we developed a time series approach to determine whether regional SLR is accelerating based on tide gauge data. We applied the approach to eight 100-year records in the southern North Sea and detected, for the first time, a common breakpoint in the early 1990s. The mean SLR rate at the eight stations increases from 1.7 ± 0.3 mm yr−1 before the breakpoint to 2.7 ± 0.4 mm yr−1 after the breakpoint (95% confidence interval), which is unprecedented in the regional instrumental record. These findings are robust provided that the record starts before 1970 and ends after 2015. Our method may be applied to any coastal region with tidal records spanning at least 40 years, which means that vulnerable coastal communities still have time to accumulate the required time series as a basis for adaptation decisions in the second half of this century.
On Floer minimal knots in sutured manifolds
Authors: Li Zhenkun , Xie Yi , Zhang Boyu
Published: June 2022

Suppose

(
M
,
γ
)

(M, \gamma )

is a balanced sutured manifold and

K
K

is a rationally null-homologous knot in

M
M

. It is known that the rank of the sutured Floer homology of

M
∖
N
(
K
)

M\backslash N(K)

is at least twice the rank of the sutured Floer homology of

M
M

. This paper studies the properties of

K
K

when the equality is achieved for instanton homology. As an application, we show that if

L
⊂

S
3

L\subset S^3

is a fixed link and

K
K

is a knot in the complement of

L
L

, then the instanton link Floer homology of

L
∪
K

L\cup K

achieves the minimum rank if and only if

K
K

is the unknot in

S
3

∖
L

S^3\backslash L

.
Genotypic variation rather than ploidy level determines functional trait expression in a foundation tree species in the presence and absence of environmental stress
Authors: Eisenring Michael , Lindroth Richard L , Flansburg Amy , Giezendanner Noreen , Mock Karen E , Kruger Eric L
Published: June 2022

Background and Aims

At the population level, genetic diversity is a key determinant of a tree species’ capacity to cope with stress. However, little is known about the relative importance of the different components of genetic diversity for tree stress responses. We compared how two sources of genetic diversity, genotype and cytotype (i.e. differences in ploidy levels), influence growth, phytochemical and physiological traits of Populus tremuloides in the presence and absence of environmental stress.

Methods

In a series of field studies, we first assessed variation in traits across diploid and triploid aspen genotypes from Utah and Wisconsin under non-stressed conditions. In two follow-up experiments, we exposed diploid and triploid aspen genotypes from Wisconsin to individual and interactive drought stress and defoliation treatments and quantified trait variations under stress.

Key Results

We found that (1) tree growth and associated traits did not differ significantly between ploidy levels under non-stressed conditions. Instead, variation in tree growth and most other traits was driven by genotypic and population differences. (2) Genotypic differences were critical for explaining variation of most functional traits and their responses to stress. (3) Ploidy level played a subtle role in shaping traits and trait stress responses, as its influence was typically obscured by genotypic differences. (4) As an exception to the third conclusion, we showed that triploid trees expressed 17 % higher foliar defence (tremulacin) levels, 11 % higher photosynthesis levels and 23 % higher rubisco activity under well-watered conditions. Moreover, triploid trees displayed greater drought resilience than diploids as they produced 35 % more new tissue than diploids when recovering from drought stress.

Conclusion

Although ploidy level can strongly influence the ecology of tree species, those effects may be relatively small in contrast to the effects of genotypic variation in highly diverse species.
Trying out a million genes to find the perfect pair withRTIST
Authors: Zhelezov Gleb , Degnan James H
Published: June 2022

Motivation

Consensus methods can be used for reconstructing a species tree from several gene trees, which exhibit incompatible topologies due to incomplete lineage sorting. Motivated by the fact that there are no anomalous rooted gene trees with three taxa and no anomalous unrooted gene trees with four taxa in the multispecies coalescent model, several contemporary methods form the gene tree consensus by finding the median tree with respect to the triplet or quartet distance—i.e. estimate the species tree as the tree which minimizes the sum of triplet or quartet distances to the input gene trees. These methods reformulate the solution to the consensus problem as the solution to a recursively solved dynamic programming (DP) problem. We present an iterative, easily parallelizable approach to finding the exact median triplet tree and implement it as an open source software package that can also find suboptimal consensus trees within a specified triplet distance to the gene trees. The most time-consuming step for methods of this type is the creation of a weights array for all possible subtree bipartitions. By grouping the relevant calculations and array update operations of different bipartitions of the same subtree together, this implementation finds the exact median tree of many gene trees faster than comparable methods, has better scaling properties with respect to the number of gene trees and has a smaller memory footprint.

Results

RTIST (Rooted Triple Inference of Species Trees) finds the exact median triplet tree of a set of gene trees. Its runtime and memory footprints scale better than existing algorithms. RTIST can resolve all the non-unique median trees, as well as sub-optimal consensus trees within a user-specified triplet distance to the median. Although it is limited in the number of taxa (≤20), its runtime changes little when the number of gene trees is changed by several orders of magnitude.

Availability and implementation

RTIST is written in C and Python. It is freely available at https://github.com/glebzhelezov/rtist
MIO: microRNA target analysis system for immuno-oncology
Authors: Monfort-Lanzas Pablo , Gronauer Raphael , Madersbacher Leonie , Schatz Christoph , Rieder Dietmar , Hackl Hubert
Published: June 2022

MicroRNAs have been shown to be able to modulate the tumor microenvironment and the immune response and hence could be interesting biomarkers and therapeutic targets in immuno-oncology; however, dedicated analysis tools are missing. Here, we present a user-friendly web platform MIO and a Python toolkit miopy integrating various methods for visualization and analysis of provided or custom bulk microRNA and gene expression data. We include regularized regression and survival analysis and provide information of 40 microRNA target prediction tools as well as a collection of curated immune related gene and microRNA signatures and processed TCGA data including estimations of infiltrated immune cells and the immunophenoscore. The integration of several machine learning methods enables the selection of prognostic and predictive microRNAs and gene interaction network biomarkers.

Availability and implementation

https://mio.icbi.at, https://github.com/icbi-lab/mio and https://github.com/icbi-lab/miopy.

Supplementary information

Supplementary data are available at Bioinformatics online.
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors
Authors: Zheng Lily , Niknafs Noushin , Wood Laura D , Karchin Rachel , Scharpf Robert B
Published: June 2022

Motivation

Multi-region sequencing of solid tumors can improve our understanding of intratumor subclonal diversity and the evolutionary history of mutational events. Due to uncertainty in clonal composition and the multitude of possible ancestral relationships between clones, elucidating the most probable relationships from bulk tumor sequencing poses statistical and computational challenges.

Results

We developed a Bayesian hierarchical model called PICTograph to model uncertainty in assigning mutations to subclones, to enable posterior distributions of cancer cell fractions (CCFs) and to visualize the most probable ancestral relationships between subclones. Compared with available methods, PICTograph provided more consistent and accurate estimates of CCFs and improved tree inference over a range of simulated clonal diversity. Application of PICTograph to multi-region whole-exome sequencing of tumors from individuals with pancreatic cancer precursor lesions confirmed known early-occurring mutations and indicated substantial molecular diversity, including 6–12 distinct subclones and intra-sample mixing of subclones. Using ensemble-based visualizations, we highlight highly probable evolutionary relationships recovered in multiple models. PICTograph provides a useful approximation to evolutionary inference from cross-sectional multi-region sequencing, particularly for complex cases.

Availability and implementation

https://github.com/KarchinLab/pictograph. The data underlying this article will be shared on reasonable request to the corresponding author.

Supplementary information

Supplementary data are available at Bioinformatics online.
VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern
Authors: Zhao Hongyu , Han Kun , Gao Chao , Madhira Vithal , Topaloglu Umit , Lu Yong , Jin Guangxu
Published: June 2022

Mutation is the key for a variant of concern (VOC) to overcome selective pressures, but this process is still unclear. Understanding the association of the mutational process with VOCs is an unmet need. Motivation: Here, we developed VOC-alarm, a method to predict VOCs and their caused COVID surges, using mutations of about 5.7 million SARS-CoV-2 complete sequences. We found that VOCs rely on lineage-level entropy value of mutation numbers to compete with other variants, suggestive of the importance of population-level mutations in the virus evolution. Thus, we hypothesized that VOCs are a result of a mutational process across the globe. Results: Analyzing the mutations from January 2020 to December 2021, we simulated the mutational process by estimating the pace of evolution, and thus divided the time period, January 2020—March 2022, into eight stages. We predicted Alpha, Delta, Delta Plus (AY.4.2) and Omicron (B.1.1.529) by their mutational entropy values in the Stages I, III, V and VII with accelerated paces, respectively. In late November 2021, VOC-alarm alerted that Omicron strongly competed with Delta and Delta plus to become a highly transmissible variant. Using simulated data, VOC-alarm also predicted that Omicron could lead to another COVID surge from January 2022 to March 2022.

Availability and implementation

Our software implementation is available at https://github.com/guangxujin/VOC-alarm.

Supplementary information

Supplementary data are available at Bioinformatics online.
CNpare: matching DNA copy number profiles
Authors: Chaves-Urbano Blas , Hernando Barbara , Garcia Maria J , Macintyre Geoff
Published: June 2022

Selecting the optimal cancer cell line for an experiment can be challenging given the diversity of lines available. Here, we present CNpare, which identifies similar cell line models based on genome-wide DNA copy number.

Availability and implementation

CNpare is available as an R package at https://github.com/macintyrelab/CNpare. All analysis performed in the manuscript can be reproduced via the code found at https://github.com/macintyrelab/CNpare_analyses.

Supplementary information

Supplementary data are available at Bioinformatics online.
gcFront: a tool for determining a Pareto front of growth-coupled cell factory designs
Authors: Legon Laurence , Corre Christophe , Bates Declan G , Mannan Ahmad A
Published: June 2022

Motivation

A widely applicable strategy to create cell factories is to knockout (KO) genes or reactions to redirect cell metabolism so that chemical synthesis is made obligatory when the cell grows at its maximum rate. Synthesis is thus growth-coupled, and the stronger the coupling the more deleterious any impediments in synthesis are to cell growth, making high producer phenotypes evolutionarily robust. Additionally, we desire that these strains grow and synthesize at high rates. Genome-scale metabolic models can be used to explore and identify KOs that growth-couple synthesis, but these are rare in an immense design space, making the search difficult and slow.

Results

To address this multi-objective optimization problem, we developed a software tool named gcFront—using a genetic algorithm it explores KOs that maximize cell growth, product synthesis and coupling strength. Moreover, our measure of coupling strength facilitates the search so that gcFront not only finds a growth-coupled design in minutes but also outputs many alternative Pareto optimal designs from a single run—granting users flexibility in selecting designs to take to the lab.

Availability and implementation

gcFront, with documentation and a workable tutorial, is freely available at GitHub: https://github.com/lLegon/gcFront and archived at Zenodo, DOI: 10.5281/zenodo.5557755.

Supplementary information

Supplementary data are available at Bioinformatics online.
Outcomes of bariatric surgery in elderly patients: A registry-based cohort study with 3-year follow-up
Authors: Iranmanesh P , Boudreau V , Anvari M
Published: June 2022

Objective

Elderly patients undergo bariatric surgery less frequently than younger patients. Short- and medium-term outcomes after bariatric surgery in the elderly population remain largely unknown. The objective of the present retrospective, registry-based cohort study was to compare short- and medium-term outcomes between patients <65 and ≥65 years undergoing bariatric surgery, hypothesizing similar outcomes between groups.

Methods

In this retrospective, registry-based cohort study, the Ontario Bariatric Registry was used to compare data of patients <65 and ≥65 years who underwent Roux-en-Y gastric bypass and sleeve gastrectomy between January 2010 and August 2019 in all accredited bariatric centers of excellence in Ontario, Canada. Primary outcomes were overall postoperative complications. Secondary outcomes included early (<30 days) complications, readmissions, reoperations, mortality, weight loss and comorbidities improvement at 1 and 3 year after surgery.

Results

Data of 22,981 patients <65 and 532 patients ≥65 years were analyzed. Overall postoperative complications were similar between patients <65 and ≥65 years (3388/22,981 [14.7%] vs. 73/532 [13.7%], p = 0.537). Early (<30 days) postoperative complications, readmissions, reoperations, and mortality rates were also similar between groups. Both groups had significant weight loss and comorbidities improvement at 1- and 3-year follow-up. Patients <65 years had superior weight loss (+3.5%, 95% CI: 1.6–5.4, p < 0.001) and higher rates of remission for diabetes mellitus (63.8% vs. 39.3%, p < 0.001), hypertension (37.9% vs. 14.5%, p < 0.001), dyslipidemia (28.2% vs. 9.5%, p < 0.001) and gastroesophageal reflux (65.1% vs. 24.0%, p < 0.001) compared to patients ≥65 years at 3 year.

Conclusion

Patients <65 and ≥65 years had similar perioperative morbidity and mortality after bariatric surgery. Even though patients <65 years had overall better medium-term outcomes, bariatric surgery is safe and yields significant weight loss and comorbidities improvement in patients ≥65 years.
Long-term outcome after biliopancreatic diversion type duodenal switch: A single-center experience with up to 20 years follow-up
Authors: Süsstrunk J , Kraljević M , Schneider R , Peterli R
Published: June 2022

Objective

Biliopancreatic diversion type duodenal switch (BPD-DS) is the most effective bariatric procedure in terms of weight loss and remission of comorbidities but carries the risk of severe long-term side effects. The aim of this study was to analyze the long-term effects of BPD-DS on weight loss, comorbidities and reoperation rate.

Methods

This is a retrospective single-center study of prospectively collected data of all patients who underwent BPD-DS from 1999 to 2011 at a single institution.

Results

116 patients (83.6% female) underwent BPD-DS with a mean initial body mass index (BMI) of 47 ± 6.5 kg/m2. 68% of the procedures were performed in open technique and 32% laparoscopically. Common channel length was routinely 1  m, mean alimentary limb length (AL) was 1.8 ± 0.6  m and mean bilio-pancreatic limb length (BPL) was 4.9 ± 1.6  m. 76.7% of patients had laparoscopic adjustable gastric banding (LAGB) prior to BPD-DS. Mean follow-up time was 14 ± 4.4 years and follow-up rate at 5, 10 and 14 years was 95.6% (n = 108), 90% (n = 98) and 75.3% (n = 70). Mean excess BMI loss (%EBMIL) at 5, 10 and 14 years was 78% ± 24.1, 76.5% ± 26.7 and 77.8% ± 33.8, respectively. The highest %EBMIL was reached two years postoperatively with 84% ± 23.6. Complete (n = 22) or partial remission (n = 4) of type 2 diabetes mellitus was observed in 92.8% of patients. Reoperation was necessary in 33 patients (28.4%) due to malnutrition or refractory diarrhea (10), excessive weight loss (1), insufficient weight loss or weight rebound (7), reflux or stenosis (7), oxalate nephropathy (2), liver cirrhosis (1) and various/combined indications (5). Mean time to reoperation was 7.7 ± 5 years. The predominant deficiencies were vitamin D (99.1%), zinc (86.9%), iron (83.5%) and calcium (71.3%). The were no procedure-related deaths in the short- or long-term.

Conclusion

BPD-DS leads to sustainable long-term weight loss with an acceptable reoperation rate. Nevertheless, regular follow-up is necessary to detect and treat malnutrition and vitamin deficiencies.