bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical forces in photonic Weyl system
Authors: Yang Yang , Chan Hsun-Chi , Bi Ke , Duan Gaoyan , Liu Maoxin , Wang Haoyi , Li Liangsheng
Published: March 2022

Topological photonics has attracted extensive attention, since it allows for a platform to explore and exploit versatile nano-optics systems. In particular, the ideal Weyl metamaterials have recently been demonstrated with fascinating phenomena such as chiral zero mode and negative refraction. In this work, we apply the photonic Weyl metamateirals into the optical tweezers. Based on the effective medium approach, the optical force generated by the body state of the Weyl metamaterial is systematically investigated. Interestingly, theoretical results show that for oblique incidence, the optical force spectra present a valley around Weyl frequency with zero magnitude exactly at the Weyl frequency, and the forces show strong optical circular dichroism. In addition, due to the bi-anisotropic properties, transmissions through the Weyl metamaterial exhibit a significant linear-to-circular polarization conversion and the transmitted wavefront acquires spin momenta of photons, which induces abnormal force on chiral particles. Our study may provide potential applications in the optical manipulations, polarization conversions, and wavefront engineering optics.
A comparison of multilayered coordination numbers in FCC and HCP crystals
Authors: Duan Lingjie , Liu Yongchang
Published: March 2022

A comparative study of multilayered coordination numbers between the face center cubic (FCC) and the hexagonal closest packing (HCP) was conducted. First, by the Diophantine equation models, we derived generating functions to calculate the multilayered coordination radii r

k
and coordination numbers N

k
for FCC and HCP, respectively. Calculated results for FCC and HCP were further compared, including their coordination radii, coordination numbers and mean coordination numbers. Finally, we strictly proved that the sequences {N

k
} for both FCC and HCP are unbounded, and for FCC, there is a subsequence

N

k

n

=
6

, while for HCP, there is a subsequence

N

k

n

=
2

.
Simulation study of fast ion losses associated with the rotating n = 1 resonant magnetic perturbations in KSTAR
Authors: Rhee Tongnyeol , Kim Junghee , Kim Kimin , Kang Jisung , Podestà Mario , Park Young-Seok , Park Byoung-Ho
Published: March 2022

This paper describes a simulation framework for testing the fast ion loss mechanism associated with the experimentally observed beam ion losses when an externally applied toroidally rotating perturbed magnetic field is used to control edge localized modes in the KSTAR tokamak. The simulations reproduce the key qualitative features of neutral beam injection (NBI) ion detection by a fast ion loss detector. The NBI ion losses in the simulation mainly occur for passing particles due to orbit stochastization, which is caused by orbit resonance with the 3D field perturbations. The relative toroidal angle of NBI ion deposition to the orbit island determines the radial path of the particles between confinement or loss. The fast ion loss quantity depends on the toroidal angle rotation of the 3D field with respect to the beam deposition position. The averaged transport of toroidal canonical angular momentum reveals that linear and nonlinear resonance of the NBI ions within the 3D field are the main factors determining fast ion transport and loss.
High precision scalable power converter for accelerator magnets
Authors: Haugen K.L. , Papastergiou K. , Asimakopoulos P. , Peftitsis D.
Published: March 2022

The lower conduction power losses and the positive temperature coefficient that favours parallel connections, make Silicon Carbide (SiC) Metal Oxide Semiconductor Field-Effect Transistors (MOSFETs) to be an excellent replacement of existing Silicon Insulated Gate Bipolar Transistors (IGBTs) technology. These characteristics combined with high switching frequency operation, enables the design of high-accuracy DC-DC converters with minimised filtering requirements. This paper investigates the design for a converter with high-accuracy current (0.9 ppm) supplying a 0.05 H electromagnetic load, aiming to achieve the accuracy without the use of active filters, by using SiC MOSFETs and a scalable module-based converter design.
Recent results from the first lpGBT-based prototypes of the end-of-substructure card for the ATLAS Strip Tracker Upgrade
Authors: Boebel A. , Ceslik H. , Dam M. , Diez Cornell S. , Gregor I. , Goettlicher P. , Keaveney J. , Naidoo J. , Nikoi Van Der Merwe M. , Oechsle J. , Schmitt S. , Stanitzki M. , Ström R. , Wyngaard J.
Published: March 2022

The building blocks of the upgraded ATLAS Strip Tracker for HL-LHC are modules that host silicon sensors and front-end ASICs. The modules are mounted on carbon-fibre substructures hosting up to 14 modules per side. An End-of-Substructure (EoS) card on each substructure side connects up to 28 differential data lines at 640 Mbit/s to lpGBT and VTRx+ ASICs that provide data serialisation and 10 Gbit/s optical data transmission to the off-detector systems respectively. Prototype EoS cards have been designed and extensively tested using lpGBT and VTRx+ prototypes. The status of the electronics design and recent test results are presented.
The neutron imaging system for inertial confinement fusion at the 100 kilo-Joule laser facility
Authors: Chen Z. , Zhang X. , Wang F. , Yu B. , Zheng J. , Huang T. , Dong Y. , Yang D. , Yang J.
Published: March 2022

The neutron imaging system based on the penumbral aperture for the inertial confinement fusion research at the 100 kilo-Joule laser facility has been developed. The aperture has been designed with a geometric model and fabricated by machining one half double-tapered cylinder into each of two tungsten slabs. The aperture is mounted into a box which helps to precisely fix two slabs to form a biconic-shaped aperture. The neutron image recording system has been constructed with a capillary-array neutron image detector, and tested with the static accelerator neutron source. The spatial resolution of neutron image detector can be within 1.1 mm. The preliminary results of neutron imaging system in the exploding pusher target experiment at the 100 kilo-Joule laser facility have been presented.
8 b 10 MS/s differential SAR ADC in 28 nm CMOS for precise energy measurement
Authors: Kaczmarczyk P. , Kmon P.
Published: March 2022

In this article an 8-bit differential Successive Approximation Register (SAR) Analog-to-Digital Converter (ADC), designed in the 28 nm CMOS process is presented. It is aimed at pixelated radiation imaging detectors. It allows to distinguish 256 levels of energy and is capable of converting 10 MS/s. The measured INL and DNL are ±0.5 LSB and ±0.3 LSB, respectively. Importantly, the proposed ADC’s comparator offset voltage correction is realized in a time domain allowing to shift the transfer characteristics within the 12 LSB range with no conversion rate degradation. The core of the ADC occupies only 30 µm × 60 µm and the power consumption is 45 µW.
Spectral tracking of energetic charged particles in wide field-of-view with miniaturized telescope MiniPIX Timepix3 1 × 2 stack
Authors: Granja C. , Jakubek J. , Soukup P. , Jakubek M. , Turecek D. , Marek L. , Oancea C. , Vuolo M. , Datkova M. , Zach V. , Stursa J. , Koprda M. , Pacik J.
Published: March 2022

A highly integrated particle telescope is assembled from two MiniPIX Timepix3 detectors in stack configuration to provide time- and spectral-sensitive tracking of energetic charged particles. The telescope architecture, high granularity and per-pixel spectral response of the imaging detectors enable directional mapping of energetic charged particles in wide field-of-view (FoV) with high angular resolution (sub degree) without the need for collimators. The pixel detectors are operated in sync and readout each with separate USB 2.0 cable for integrated control and power supply. Timepix3 two per-pixel signal channels are operated in energy and time mode for detailed spectral- and time-registration of single events in each detector. Events are registered with time stamp resolution at tens of ns level between both detectors. Correlated events between both detector layers are resolved by correlated time stamp with a coincident time window <100 ns. The stack sync configuration allows to perform precise spectrometry (energy loss) and high-resolution tracking over the entire FoV. Particle-event classification is enhanced by spectral and tracking analysis of correlated events in both detectors. The sensors of the detectors can be of different semiconductor material or thickness for selective multiple energy loss ΔE1 + ΔE2 technique. Data products include detailed angular distributions of energetic charged particles with high angular resolution, time stamp, spectral response (energy loss, LET value) and enhanced particle-type resolving power of over 8 event classes. The directional response and angular resolution depend on the spacing gap between the tracker detectors. The resulting field-of-view, geometric factor and angular resolution are evaluated. Results are presented with proof-of-principle of the technique and evaluation of synchronized operation with 31 MeV protons.
Automated firmware generation and continuous testing for the CMS HGCAL trigger primitive generator
Authors: Beaujean F. , Romanteau T. , Sauvan J.-B.
Published: March 2022

The prototype version of the trigger primitive generator firmware for the Phase-2 CMS endcap calorimeter upgrade is being implemented in order to assess the FPGA resource requirements and dimension the system. For the development of some of these blocks, a data-driven design flow based on VHDL and HLS C/C++ templates is used to automate the production of multiple firmware variants. In addition, the design steps are integrated into Gitlab Continuous Integration tools to automatically test and validate every change, and as much as possible avoid repetitive manual tasks and the associated errors.
Effects of loading and unloading control parameters on adhesive performance for biomimetic controllable adhesive with wedge-shaped microstructures
Authors: Wang Wei , Liu Yang , Xie Zongwu
Published: March 2022

The adhesive performance of biomimetic controllable adhesive based on wedge-shaped microstructures is affected by some relevant control parameters in the process of loading and unloading. An appropriate selection of these control parameters is of great significance for its effective application. However, little research has concentratively and comprehensively explored these control parameters. In order to make up for the shortcoming, this study systematically explored the macroscopic adhesive performance of the self-developed wedge-shaped microstructures under different loading and unloading control parameters. The results show that preloading depth and tangential dragging distance have a positive effect on the adhesive performance, while preloading angle and peeling angle have a negative effect on the adhesive performance. Specifically, a low preloading angle can weaken the normal preloading force under the same preloading depth, thereby improving the preloading benefit; the application of tangential dragging distance can also induce the normal preloading force generated in the preloading stage to change the adhesion, so as to stimulate more adhesion. Based on the interactive analysis of these control parameters, it can be sure that applying a moderate normal preloading force and a larger tangential dragging distance to the wedge-shaped microstructures at low preloading angle not only makes the wedge-shaped microstructures possess better adhesive capacity, but also can obtain a good preloading benefit. In addition, the promotion effect of a low peeling angle on the adhesive performance also implies that a higher peeling angle should be used to realize the easy detachment of the adhesive interface. The first concentrative and comprehensive investigation of the relevant control parameters of wedge-shaped microstructures lays the foundation for designing a climbing robot or adhesive gripper based on the wedge-shaped microstructures, and also provides guidance for formulating the corresponding control strategies.
Tau-functions for the Ablowitz–Ladik hierarchy: the matrix-resolvent method
Authors: Cafasso Mattia , Yang Di
Published: March 2022

We extend the matrix-resolvent method for computing logarithmic derivatives of tau-functions to the Ablowitz–Ladik hierarchy. In particular, we derive a formula for the generating series of the logarithmic derivatives of an arbitrary tau-function in terms of matrix resolvents. As an application, we provide a way of computing certain integrals over the unitary group.
The Acceptance of Primary Health Centre Information System Among Health Staff: An extended TAM Model
Authors: Ilmi Laili Rahmatul
Published: March 2022

Ngaglik I Public Health Center in Sleman is one of the health centers that have already applied SIMPUS (an application of management information system for public health center). The implementation of clinical information systems could potentially improve the performance of health care facilities, save operational costs, and increase patient satisfaction. In fact, the clinical information systems applied by public health center vary. One of them is SIMPUS. However until present, there have not been any assessments of the acceptance of the clinical information system, especially SIMPUS, at Ngaglik I Public Health Center. To describe the use of SIMPUS at Ngaglik I Public Health Center and evaluate user understanding in accepting SIMPUS application based on the Technology Acceptance Model (TAM). This was a quantitative study which used a survey method and a cross-sectional design. The research sample consisted of 50 respondents who were selected using a simple random sampling method. The data analysis technique was the SEM-PLS analysis with the TAM model and SmartPLS software. Statistically, the relationship between the Job Relevance and Perceived Ease of Use variables was weak (p-value = 0.818). There was a weak relationship between Output Quality and Perceived Ease of Use (p-value = 0.208). There was a strong relationship between Result Demonstrability and Perceived Ease of Use (0.000). There was a strong relationship between Result Demonstrability and Intention to Use (p-value = 0.011). There was a weak relationship between Screen Design and Intention to Use (p-value = 0.870). There was a weak relationship between Perceived Ease of Use and intention to use. Users’ job relevance to SIMPUS did not have any effect on perceived ease of use. Output quality did not have any effect on perceived ease of use. The screen design of SIMPUS display had no effect on intention to use. Intention to use did not affect system use. Intention to use did not affect system use. Facilitating condition did not have any effect on system use. System use was influenced by perceived ease of use and intention to use. Perceived ease of use and intention to use were influenced by result demonstrability.
Generation, dynamics and bifurcation of high power soliton beams in cubic-quintic nonlocal nonlinear media
Authors: Mishra Manoj , Kajala Sandeep Kumar , Sharma Mohit , Konar Swapan , Jana Soumendu
Published: March 2022

This article presents the generation and propagation dynamics of a high power Gaussian soliton beam through a highly nonlocal nonlinear media having cubic-quintic nonlinearity. Solitons are also generated with lesser explored Hermite super-Gaussian, Hermite cosh-Gaussian and Hermite cosh-super-Gaussian beam profiles. The governing nonlocal nonlinear Schrödinger equation yields matching solitons analytically using variational method as well as numerically using split-step Fourier method. Linear stability analysis identifies the parametric space for stability of the solitons against small perturbation. The variation of the system parameters leads to the bifurcation of the beam beyond a critical point. A parametric zone of bifurcation is identified. Some of the solitons are bistable too. The influence of quintic nonlinearity on generation, propagation and bifurcation is highlighted.
Effect of shock wave formation on propellant ignition in capillary discharge
Authors: ZHANG Jiangbo , GAO Hongxu , XIAO Fei , LIU Wei , LIANG Taixin , MA Zhongliang , WU Jian
Published: March 2022

In order to study the effect of shock wave formation on propellant ignition in capillary discharge, the shock wave formation process was analyzed using experimental and theoretical methods; the plasma jet temperature was measured, and closed bomb and 30 mm gun experiments were carried out. The results show that the first shock wave has a smaller value and larger range of influence, while the second shock wave has a larger value and smaller range of influence. A plasma jet can generate a shock wave at the nozzle according to the calculated plasma pressure and velocity, which is well confirmed by experiments and calculations. The plasma jet temperature is high during the formation of a shock wave and then decreases sharply. Plasma ignition can increase the burning rate of a propellant by about 30% by increasing the burning surface area of the propellant. Compared to conventional ignition, the average maximum chamber pressure and average muzzle velocity of plasma ignition are increased by 9.1 MPa and 29.3 m·s−1 (∼3%), respectively, in a 30 mm gun. Plasma ignition has strong ignition ability and short ignition delay time due to the generation of a shock wave. By increasing the burning rate of the propellant, the muzzle velocity can be greatly improved when the maximum chamber pressure increases a little. The characteristics of the shock wave can be applied in the application of the capillary discharge plasma. For example, it can be applied in fusion, launching and combustion.
Stabilization of ion-temperature-gradient mode by trapped fast ions
Authors: WANG Siqi , CAI Huishan , GAO Baofeng , LI Ding
Published: March 2022

Understanding and modeling fast-ion stabilization of ion-temperature-gradient (ITG) driven microturbulence have profound implications for designing and optimizing future fusion reactors. In this work, an analytic model is presented, which describes the effect of fast ions on ITG mode. This model is derived from a bounce-average gyro-kinetic equation for trapped fast ions and ballooning transformation for ITG mode. In addition to dilution, strong wave-fast-ion resonant interaction is involved in this model. Based on numerical calculations, the effects of the main physical parameters are studied. The increasing density of fast ions will strengthen the effects of fast ions. The effect of wave-particle resonance strongly depends on the temperature of fast ions. Furthermore, both increasing density gradient and the ratio of the temperature and density gradients can strengthen the stabilization of fast ions in ITG mode. Finally, the influence of resonance broadening of wave-particle interaction is discussed.
On the monodromy group of desingularised moduli spaces of sheaves on K3 surfaces
Authors: Onorati Claudio
Published: March 2022

In this paper we prove a conjecture of Markman about the shape of the monodromy group of irreducible holomorphic symplectic manifolds of OG10 type. As a corollary, we also compute the locally trivial monodromy group of the underlying singular symplectic variety.
The projective cover of tableau-cyclic indecomposable 𝐻_{𝑛}(0)-modules
Authors: Choi Seung-Il , Kim Young-Hun , Nam Sun-Young , Oh Young-Tak
Published: March 2022

Let

α
\alpha

be a composition of

n
n

and

σ
\sigma

a permutation in

S

ℓ
(
α
)

\mathfrak {S}_{\ell (\alpha )}

. This paper concerns the projective covers of

H
n

(
0
)

H_n(0)

-modules

V

α

\mathcal {V}_\alpha

,

X
α

X_\alpha

, and

S

α

σ

\mathbf {S}^\sigma _{\alpha }

whose images under the quasisymmetric characteristic are the dual immaculate quasisymmetric function, the extended Schur function, and the quasisymmetric Schur function when

σ
\sigma

is the identity, respectively. First, we show that the projective cover of

V

α

\mathcal {V}_\alpha

is the projective indecomposable module

P

α

\mathbf {P}_\alpha

due to Norton, and

X
α

X_\alpha

and the

ϕ
\phi

-twist of the canonical submodule

S

β
,
C

σ

\mathbf {S}^{\sigma }_{\beta ,C}

of

S

β

σ

\mathbf {S}^\sigma _{\beta }

for

(
β
,
σ
)

(\beta ,\sigma )

’s satisfying suitable conditions appear as homomorphic images of

V

α

\mathcal {V}_\alpha

. Second, we introduce a combinatorial model for the

ϕ
\phi

-twist of

S

α

σ

\mathbf {S}^\sigma _{\alpha }

and derive a series of surjections starting from

P

α

\mathbf {P}_\alpha

to the

ϕ
\phi

-twist of

S

α
,
C

i
d

\mathbf {S}^\mathrm {id}_{\alpha ,C}

. Finally, we construct the projective cover of every indecomposable direct summand

S

α
,
E

σ

\mathbf {S}^\sigma _{\alpha , E}

of

S

α

σ

\mathbf {S}^\sigma _{\alpha }

. As a byproduct, we give a characterization of triples

(
σ
,
α
,
E
)

(\sigma ,\alpha ,E)

such that the projective cover of

S

α
,
E

σ

\mathbf {S}^\sigma _{\alpha ,E}

is indecomposable.
Absolutely continuous spectrum for CMV matrices with small quasi-periodic Verblunsky coefficients
Authors: Li Long , Damanik David , Zhou Qi
Published: March 2022

We consider standard and extended CMV matrices with small quasi-periodic Verblunsky coefficients and show that on their essential spectrum, all spectral measures are purely absolutely continuous. This answers a question of Barry Simon from 2005.
Homogeneous algebras via heat kernel estimates
Authors: Bruno Tommaso
Published: March 2022

We study homogeneous Besov and Triebel–Lizorkin spaces defined on doubling metric measure spaces in terms of a self-adjoint operator whose heat kernel satisfies Gaussian estimates together with its derivatives. When the measure space is a smooth manifold and such operator is a sum of squares of smooth vector fields, we prove that their intersection with

L
∞

L^\infty

is an algebra for pointwise multiplication. Our results apply to nilpotent Lie groups and Grushin settings.
A perinuclear α-helix with amphipathic features in Brl1 promotes NPC assembly
Authors: Vitale Jlenia , Khan Azqa , Neuner Annett , Schiebel Elmar
Published: March 2022

Fusion of the inner and outer nuclear membranes during assembly of nuclear pore complexes (NPCs) is one of cell biology’s outstanding questions. We have identified an integral membrane protein, Brl1, which contains an amphipathic helix that is essential for fusion of the nuclear envelope during NPC biogenesis.
The Purposive Transformation of Corporate Law
Authors: Kershaw David , Schuster Edmund
Published: March 2022

What is the purpose of a corporation? This fundamental question is as old as corporate law itself, and traditionally it is asked with reference to the ultimate beneficiaries of a corporation’s activities. Modern management theory and the current technology-driven transformation of the economy, however, have breathed new life into the question about corporate purpose. Here, purpose is understood as an animated mission-purpose articulation of the reason for a corporation’s existence; an aspirational idea about its existence that has the capacity to bond internal and external stakeholders to the company, inspiring innovation, productivity, and customer loyalty. This understanding of corporate purpose offers a pathway to a more inclusive and interconnected form of modern capitalism.

This approach to purpose is now gaining regulatory traction. In December 2018, the United Kingdom’s “comply or explain” Corporate Governance Code adopted a provision which provides that “the board should establish the company’s purpose.” This Article takes the United Kingdom’s regulatory adoption of mission-purpose as a platform from which we can explore the economic and social benefits of purposeful companies and the legal and non-legal conditions that are necessary to support and nurture such companies. The Article argues that in the absence of purposeful shareholders corporate law must enable companies to construct a zone of insulation which protects its purpose—whatever it may be—from the pressures of immediate shareholder preferences which can compromise mission-purpose. It argues that in jurisdictions where law and market practice prevent the construction of such a zone of insulation, the economic and social benefits of purposeful companies will be unavailable, as mission-purpose disintegrates into the prosaic or a mere marketing device. This claim generates several theoretical and empirical objections, which the Article considers and rejects.
Climate shapes the seed germination niche of temperate flowering plants: a meta-analysis of European seed conservation data
Authors: Carta Angelino , Fernández-Pascual Eduardo , Gioria Margherita , Müller Jonas V , Rivière Stéphane , Rosbakh Sergey , Saatkamp Arne , Vandelook Filip , Mattana Efisio
Published: March 2022

Background and Aims

Interactions between ecological factors and seed physiological responses during the establishment phase shape the distribution of plants. Yet, our understanding of the functions and evolution of early-life traits has been limited by the scarcity of large-scale datasets. Here, we tested the hypothesis that the germination niche of temperate plants is shaped by their climatic requirements and phylogenetic relatedness, using germination data sourced from a comprehensive seed conservation database of the European flora (ENSCOBASE).

Methods

We performed a phylogenetically informed Bayesian meta-analysis of primary data, considering 18 762 germination tests of 2418 species from laboratory experiments conducted across all European geographical regions. We tested for the interaction between species’ climatic requirements and germination responses to experimental conditions including temperature, alternating temperature, light and dormancy-breaking treatments, while accounting for between-study variation related to seed sources and seed lot physiological status.

Key Results

Climate was a strong predictor of germination responses. In warm and seasonally dry climates the seed germination niche includes a cold-cued germination response and an inhibition determined by alternating temperature regimes and cold stratification, while in climates with high temperature seasonality opposite responses can be observed. Germination responses to scarification and light were related to seed mass but not to climate. We also found a significant phylogenetic signal in the response of seeds to experimental conditions, providing evidence that the germination niche is phylogenetically constrained. Nevertheless, phylogenetically distant lineages exhibited common germination responses under similar climates.

Conclusion

This is the first quantitative meta-analysis of the germination niche at a continental scale. Our findings showed that the germination niches of European plants exhibit evolutionary convergence mediated by strong pressures at the macroclimatic level. In addition, our methodological approach highlighted how large datasets generated by conservation seed banking can be valuable sources to address questions in plant macroecology and evolution.
Improved method for preparation and purification of recombinant α-synuclein: high-mannose-type free N-glycan prepared from an edible bean (Vigna angulari, Azuki bean) inhibits α-synuclein aggregation
Authors: Kosaka Shota , Katsube Makoto , Maeda Megumi , Kimura Yoshinobu
Published: March 2022

Parkinson's disease is characterized by the accumulation of amyloid, which consists of α-synuclein (α-Syn). To screen compounds with amyloid aggregation inhibitory activity, an effective method for the preparation of α-Syn is a prerequisite. We established a simpler method for α-Syn preparation using freeze-thaw treatment of transformed Escherichia coli. Furthermore, we found that the high-mannose type free N-glycans could prevent α-Syn aggregation.
Individuals with larger head volume have better learning ability in wild chestnut thrushes
Authors: Lou Yingqiang , Zou Yuqi , Fang Yun , Swenson Jon E , Pape Møller Anders , Sun Yuehua
Published: March 2022

Recent comparative studies on fish and mammals have suggested that brain size is associated with cognitive ability, such as problem solving and self-control; larger-brained individuals are assumed to have better cognitive ability. However, it remains largely unexplored whether larger-brained birds perform better in learning and spatial memory tests. Here, we used two experiments (novel skill learning task and spatial memory task) to examine whether head volume (proxy for brain size) could predict the learning performance and spatial performance in wild chestnut thrushes (Turdus rubrocanus). First, we found that chestnut thrushes with larger head volume were more likely to learn the novel skill than individuals with smaller head volume. Second, individuals with larger head volume relative to their tarsus (relative head volume) learned the novel skill faster. Age, sex, and exploratory tendency of individuals were not related to learning performance or learning speed. Finally, head volume, relative head volume and age was not associated with spatial performance in the spatial memory tasks. Together, these findings provided empirical evidences for the relationship between head volume and the ability of novel skill learning, and also provide a non-invasive method for studying the relationship between cognitive ability and head volume in other bird species.
Loss of mouse Y chromosome geneZfy1andZfy2leads to spermatogenesis impairment, sperm defects, and infertility
Authors: Yamauchi Yasuhiro , Matsumura Takafumi , Bakse Jackson , Holmlund Hayden , Blanchet Genevieve , Carrot Emmaelle , Ikawa Masahito , Ward Monika A
Published: March 2022

Using mice with Y chromosome deficiencies and supplementing Zfy transgenes, we, and others, have previously shown that the loss of Y chromosome Zfy1 and Zfy2 genes is associated with infertility and spermiogenic defects and that the addition of Zfy transgenes rescues these defects. In these past studies, the absence of Zfy was linked to the loss of other Y chromosome genes, which might have contributed to spermiogenic phenotypes. Here, we used CRISPR/Cas9 to specifically remove open reading frame of Zfy1, Zfy2, or both Zfy1 and Zfy2, and generated Zfy knockout (KO) and double knockout (DKO) mice. Zfy1 KO and Zfy2 KO mice were both fertile, but the latter had decreased litters size and sperm number, and sperm headshape abnormalities. Zfy DKO males were infertile and displayed severe spermatogenesis defects. Postmeiotic arrest largely prevented production of sperm and the few sperm that were produced all displayed gross headshape abnormalities and structural defects within head and tail. Infertility of Zfy DKO mice could be overcome by injection of spermatids or sperm directly to oocytes, and the resulting male offspring had the same spermiogenic phenotype as their fathers. The study is the first describing detailed phenotypic characterization of mice with the complete Zfy gene loss. It provides evidence supporting that the presence of at least one Zfy homolog is essential for male fertility and development of normal sperm functional in unassisted fertilization. The data also show that while the loss of Zfy1 is benign, the loss of Zfy2 is mildly detrimental for spermatogenesis.
Protective antibody response to mRNA-1273 and BNT162b2 vaccines in patients on maintenance haemodialysis: a prospective cohort study
Authors: Dimitrov Yves , Krummel Thierry , Chantrel François , Faller Anne-Laure , Ott Julien , David Daniela , Bazin-Kara Dorothée , Hannedouche Thierry , Borni Claire
Published: March 2022

Background

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is more frequent and severe in patients with chronic kidney disease (CKD) on maintenance haemodialysis (HD). Vaccines are now available, but the protective response rates and determinants of humoral response to the vaccine are poorly described.

Methods

This prospective observational study describes the response rates of detectable and protective antibody titres 1 month after each dose of an mRNA vaccine in a cohort of 851 patients on maintenance HD.

Findings

Among naïve SARS-CoV-2 patients, a vast majority produced detectable (95.2%) or protective levels of antibodies (69.6%) 1 month after the second vaccine dose. In addition, the response rate was significantly higher with the mRNA-1273 than with the BNT162b2 vaccine 1 month after the second dose (79.8 versus 59.1%, respectively; P < 0.001). The main determinants for an inadequate humoral response were older age, treatment with immunosuppressants or oral anticoagulants and low serum albumin. All the patients who encountered coronavirus disease 2019 before vaccination also reached a highly protective humoral response.

Interpretation

We found an acceptable humoral response rate in patients on maintenance HD, much higher than in transplant recipients. Therefore the third dose of vaccine may be justified in those patients with an inadequate humoral response, particularly those with a history of organ transplantation or immunosuppressive treatment.
CWSOGG: Catching Web Shell Obfuscation Based on Genetic Algorithm and Generative Adversarial Network
Authors: Pang Bo , Liang Gang , Yang Jin , Chen Yijing , Wang Xinyi , He Wenbo
Published: March 2022

A web shell is a backdoor used by hackers to control Web servers and perform privilege escalation, and thus it is crucial to detect web shells effectively. However, the detection of obfuscated web shells has always been a challenge. Inspired by adversarial training methods in the field of computer vision, this paper proposes a generative adversarial network (GAN)-based web shell detection model training framework. Since there has been no method that can generate obfuscated web shells effectively, a generator based on the genetic algorithm, which combines and optimizes the pre-set obfuscation methods, is used to obtain new obfuscation combinations and generate obfuscated samples. The whole proposed framework is named the CWSOGG. When training the detection model, the generator generates web shells that can bypass the discriminator, and the discriminator catches the features of obfuscated samples. Through the adversarial training of the discriminator and generator, the detection model improves its ability to detect obfuscated web shells. To verify the proposed framework is flexible to different models, the discriminator based on four main neural networks has been implemented. Meanwhile, to build complete feature extraction models, both statistical and semantic features are extracted. Due to the lack of web shell data, a clean dataset containing 4,375 web shells is constructed and used to evaluate the CWSOGG. The results have shown that the detection accuracy of each model increases by 86.71% on the generated obfuscated web shells on average and by 7.50% on the simulated real-world obfuscated web shells on average.
After the Cambridge Controversies: Reflections Old and New
Authors: Gram Harvey
Published: March 2022

Perfect foresight is a consequence of applying the Pontryagin Maximum Principle to the analysis of an intertemporal general equilibrium. For this reason, the capital theory controversy ended in an intellectual impasse. The critique of mainstream theory largely ignored the perfect foresight entailments of intertemporal equilibrium analysis, while its defenders, with notable exceptions, too often failed to acknowledge this implication of the technique of dynamic programming. From this standpoint, the long debate over the existence or non-existence of an aggregate production function is secondary. This leaves open the theoretical question of how to proceed with an analysis of the actual dynamics of capitalist development. The critique of mainstream capital theory remains a ‘prelude’, caught up in an ever deeper analysis of the implications of alternative representations of the technique of production. The first part of this paper deals with the question of how perfect foresight came to infect mainstream theory; the second part turns to a consideration of a weakness in the dual representation of the technique of production in the simplest Sraffian framework. Neither part addresses the bigger questions of how to analyze the process of uneven development under the capitalist rules of the game.
Favourable Tolerability and Drug Survival of Tioguanine Versus Methotrexate After Failure of Conventional Thiopurines in Crohn’s Disease
Authors: Savelkoul E H J , Maas M H J , Bourgonje A R , Crouwel F , Biemans V B C , den Broeder N , Russel M G V M , Römkens T E H , de Boer N K , Dijkstra G , Hoentjen F
Published: March 2022

Background and Aims

Both methotrexate and tioguanine can be considered as treatment options in patients with Crohn’s disease after failure of conventional thiopurines. This study aimed to compare tolerability and drug survival of methotrexate and tioguanine therapy after failure of conventional thiopurines in patients with Crohn’s disease.

Methods

We conducted a retrospective, multicentre study, including patients with Crohn’s disease initiating monotherapy methotrexate or tioguanine after failure [all causes] of conventional thiopurines. Follow-up duration was 104 weeks or until treatment discontinuation. The primary outcome was cumulative therapy discontinuation incidence due to adverse events. Secondary outcomes included total number of [serious] adverse events, and ongoing monotherapy.

Results

In total, 219 patients starting either methotrexate [n = 105] or tioguanine [n = 114] were included. In all 65 [29.7%] patients (methotrexate 43.8% [46/105 people], tioguanine 16.7% [19/114 people], p <0.001) discontinued their treatment due to adverse events during follow-up. Median time until discontinuation due to adverse events was 16 weeks (interquartile range [IQR] 7-38, p = 0.812). Serious adverse events were not significantly different. Patients treated with methotrexate experienced adverse events more often [methotrexate 83%, tioguanine 46%, p <0.001]. Total monotherapy drug survival after 104 weeks was 22% for methotrexate and 46% for tioguanine [p <0.001].

Conclusions

We observed a higher cumulative discontinuation incidence due to adverse events for methotrexate [44%] compared with tioguanine [17%] in Crohn’s disease patients after failure of conventional thiopurines. The total adverse events incidence during methotrexate use was higher, whereas serious adverse events incidence was similar. These favourable results for tioguanine treatment may guide the selection of immunosuppressive therapy after failure of conventional thiopurines.
Alarmist reporting on the pandemic: time to say no!
Authors: Roy Ambuj
Published: March 2022

This commentary refers to ‘Multi-organ assessment in mainly non-hospitalized individuals after SARS-CoV-2 infection: The Hamburg City Health Study COVID programme’ by E.L. Petersen et al., https://doi.org/10.1093/eurheartj/ehab914 and the discussion piece ‘Attentive follow-up to counter alarmism’ by R. Twerenbold et al.’, https://doi.org/10.1093/eurheartj/ehac165.
Bacterial extracellular polymeric substances as potential saliva substitute
Authors: Kardas Piotr , Astasov-Frauenhoffer Monika , Braissant Olivier , Bornstein Michael M , Waltimo Tuomas
Published: March 2022

This proof-of-principle study aims to find commensal oral bacteria that can produce extracellular polymeric substances (EPS), which have similar lubrication properties to saliva and could serve as saliva substitutes. Saliva and plaque samples were collected from 21 generally healthy individuals. Primary screening was done by conventional culturing and Gram-staining; all species selected for further analysis were identified by MALDI-TOF and deposited in DSMZ. Lactobacillus gasseri (DSM32453 and DSM32455), Lactobacillus rhamnosus (DSM32452), Lactobacillus paracasei (DSM32454), and Streptococcus sanguinis (DSM32456) produced 413.6, 415.7, 431.1, 426.8, and 877.6 µg/ml of EPS, respectively. At the same time calcium dissolution could not be detected for both L. gasseri strains, minimal dissolution for the other three: S. sanguinis 0.3 mm, and 3.7 mm for L. rhamnosus and L. paracasei. There were no differences found between the EPS samples and the saliva for the effect of shear rate on the viscosity and for the effect of sliding speed on lubrication properties. In conclusion, five commensal bacterial strains have been isolated, all able to produce EPS and lead to no or to low calcium dissolution. EPS produced exhibits rheological and tribological properties comparable to human saliva. A total of four out of five selected strains are probiotic and, therefore, may exhibit additional beneficial influence within the oral cavity.
Gene Body Methylation in Plants: Mechanisms, Functions, and Important Implications for Understanding Evolutionary Processes
Authors: Muyle Aline M , Seymour Danelle K , Lv Yuanda , Huettel Bruno , Gaut Brandon S
Published: March 2022

Gene body methylation (gbM) is an epigenetic mark where gene exons are methylated in the CG context only, as opposed to CHG and CHH contexts (where H stands for A, C, or T). CG methylation is transmitted transgenerationally in plants, opening the possibility that gbM may be shaped by adaptation. This presupposes, however, that gbM has a function that affects phenotype, which has been a topic of debate in the literature. Here, we review our current knowledge of gbM in plants. We start by presenting the well-elucidated mechanisms of plant gbM establishment and maintenance. We then review more controversial topics: the evolution of gbM and the potential selective pressures that act on it. Finally, we discuss the potential functions of gbM that may affect organismal phenotypes: gene expression stabilization and upregulation, inhibition of aberrant transcription (reverse and internal), prevention of aberrant intron retention, and protection against TE insertions. To bolster the review of these topics, we include novel analyses to assess the effect of gbM on transcripts. Overall, a growing body of literature finds that gbM correlates with levels and patterns of gene expression. It is not clear, however, if this is a causal relationship. Altogether, functional work suggests that the effects of gbM, if any, must be relatively small, but there is nonetheless evidence that it is shaped by natural selection. We conclude by discussing the potential adaptive character of gbM and its implications for an updated view of the mechanisms of adaptation in plants.
Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples
Authors: Biddanda Arjun , Steinrücken Matthias , Novembre John
Published: March 2022

Archeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the nonrandom association of genetic variants at different loci (i.e. linkage disequilibrium). This may be in part because basic properties of linkage disequilibrium in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: (1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; (2) The product of the linkage disequilibrium coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and (3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.
Laterally constrained surface wave inversion
Authors: Cruz-Hernández Favio , Gallardo Luis A , Calò Marco , Castro Raúl R , Romo-Jones José M
Published: March 2022

In the last 15 yr, the use of surface waves retrieved from the cross-correlation of ambient seismic noise has significantly increased its applications to determine or monitor changes in the elastic properties of the Earth's interior. We designed a methodology for laterally constrained surface wave inversion based on a two-stage technique to estimate the 3-D distribution of the S-wave velocity (Vs). The first stage inverts traveltimes to estimate group or phase velocity dispersion maps and their inverse covariance matrix for different periods. The inverse covariance matrix is constructed explicitly using the ray tracing information. The inverse covariance matrix adds the lateral sensitivity of the maps to the structure, whereas the period-dependency provides sensitivity to the structure at depth. The second stage applies a nonlinear conjugate gradient scheme to estimate the 3-D distribution of S-wave velocity using the ensemble of velocity dispersion maps and their estimated inverse covariance matrix. We validate the methodology using a synthetic model. The results show an improved estimation of subsurface S-wave velocity structures compared to conventional point-wise inversion.
Membrane glycome is impacted by the cell culturing mode of neuroblastoma cells with differing migration and invasion potential
Authors: Sumer-Bayraktar Zeynep , Fife Christopher M , Byrne Frances L , Kavallaris Maria , Packer Nicolle H
Published: March 2022

Neuroblastoma is a highly metastatic childhood cancer for which studies indicate an association between protein glycosylation and tumor behavior. However, there is a lack of detailed glycome analysis on neuroblastoma cells that have varying metastatic potential. Furthermore, the impact of the cell culturing mode, i.e. 2-dimensional (2D) versus 3-dimensional (3D) spheroids, on the membrane protein glycome is unknown. To address these gaps in knowledge, we mapped membrane protein N- and O-glycosylation of neuroblastoma cells that have lower invasive and metastatic potential (Stathmin shRNA-expressing cells, StmnSeq2SH, and StmnSeq3SH) compared with control cells (control shRNA-expressing cells, CtrlSH). We showed that the neuroblastoma cells with different migratory and invasive potential underwent drastic changes in their membrane protein N-glycosylation exclusively when cultured in 3D spheroids. We also investigated the impact of 2D and 3D cell culture methods on cellular glycosylation using the neuroblastoma cells and found the cell N-glycome was markedly impacted by the culture method, with the 2D grown cells showing an abundance of oligomannosidic glycans, whereas 3D spheroids expressed more complex type glycans on their membrane proteins. In summary, this study provides the first comprehensive protein glycome profiling of neuroblastoma cells that have varying invasiveness and migratory potential and unravels the distinct membrane glycan features of cells that are grown under 2D versus 3D culture conditions.