bluuebunny/crossref_metadata_2025 huggingface dataset:
Superconductivity and density-wave fluctuations in an extended triangular Hubbard model: an application to SnSe2
Authors: Li Yun-Xiao , Yao Zi-Jian , Yu Shun-Li , Li Jian-Xin
Published: December 2022

We employ the fluctuation-exchange approximation to study the relation of superconducting pairing symmetries and density-wave fluctuations based on the extended triangular Hubbard model upon electron doping and interactions, with an possible application to the layered metal dichalcogenide SnSe2. For the case where the interactions between electrons contain only the on-site Hubbard term, the superconducting pairings are mainly mediated by spin fluctuations, and the spin-singlet pairing with the d-wave symmetry robustly dominates in the low and moderate doping levels, and a d-wave to extended s-wave transition is observed as the electron doping reaches n = 1. When the near-neighbor site Coulomb interactions are also included, the charge fluctuations are enhanced, and the spin-triplet pairings with the p-wave and f-wave symmetries can be realized in the high and low doping levels, respectively.
3D optical measurement techniques
Authors: Engel Thomas
Published: December 2022

The field of optical 3D metrology is gaining significant interest in the past years. Optical sensors can probe the geometry of workpieces and biological samples very fast, highly accurate and without any tactile physical contact to the object’s surface. In this respect, optical sensors are a pre-requisite for many applications in the big trends like Industrial Internet of Things, Industry 4.0 or Medicine 4.0. The interest for optical 3D metrology is shifting from a metrology for quality assurance in industrial production to “digitize the real world” to facilitate a precise digital representation of an object or an environment for documentation or as input data for virtual applications like digital fab or augmented reality. The aspiration to digitize the world necessitates fast and efficient contact free sensing principles of appropriate accuracy for solid and even soft objects with a variety of colour, surface texture and lighting conditions. This review article tries to give a concise conceptual overview about the evolution of a broad variety of optical measurement principles that evolved and gained some importance in the field of 3D metrology for industrial 3D applications and their related technological enablers.
BDS-3 RDSS two-way time transfer with asymmetric delay compensation model
Authors: Ren Zhiling , Huang Xinming , Gong Hang , Peng Jing , Sun Guangfu
Published: December 2022

In the BeiDou navigation satellite system-3 (BDS-3) radio determination satellite service (RDSS), there exists a natural two-way link between the center station and the user site that can be used to achieve time transfer. Traditionally, RDSS two-way time transfer is realized by analogy with the two-way satellite time and frequency transfer (TWSTFT) technique. However, unlike TWSTFT, the signal propagation delays are not completely symmetrical in the RDSS two-way link because of the differences in signal emission time. In this study, a model of two-way time transfer with BDS-3 RDSS is presented. An asymmetric delay compensation method is introduced to solve the asymmetry of RDSS signals and improve the accuracy of two-way time transfer. In addition, BDS-3 RDSS common clock difference experiments are designed to test the performance of two-way time transfer with an asymmetric delay compensation model. Based on analyses of the experimental results, three conclusions can be drawn. First, the accuracy of RDSS two-way time transfer is improved when the asymmetric delay compensation model is applied. Second, BDS-3 RDSS two-way time transfers in different in-station beams and subbands do not show many discrepancies on the whole, and the standard deviation values of the BDS-3 RDSS time transfer results range from 1.7 ns to 2.6 ns for the test signals. Third, the two-way time transfer results are not generally affected by receiver coordinate errors.
Graphene nano-sieves by femtosecond laser irradiation
Authors: Katsiaounis S , Chourdakis N , Michail E , Fakis M , Polyzos I , Parthenios J , Papagelis K
Published: December 2022

The formation of nano-pores in graphene crystal structure is alternative way to engineer its electronic properties, chemical reactivity, and surface interactions, enabling applications in technological fields such as sensing, energy and separation. The past few years, nano-perforation of graphene sheets has been accomplished by a variety of different methods suffering mainly from poor scalability and cost efficiency issues. In this work, we introduce an experimental protocol to engineer nanometer scale pores in CVD graphene membranes under ambient conditions, using low power ultra-short laser pulses and overcoming the drawbacks of other perforation techniques. Using Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM) we visualized and quantified the nanopore network while Raman spectroscopy is utilized to correlate the nano-perforated area with the nanotopographic imaging. We suggest that Raman imaging provides the identification of nanoporous area and, in combination with AFM, we provide solid evidence for the reproducibility of the method, since under these experimental conditions, nanopores of a certain size distribution are formed.
Uncertainty-driven determination of target measurement times for indirect tracking validation in adaptive radiotherapy
Authors: Remy Charlotte , Bouchard Hugo
Published: December 2022

Objective. Hybrid indirect tumor tracking strategies combine continuous monitoring of surrogate signals with episodic radiographic imaging of the target to check and update their models during the treatment. This validation process is traditionally performed at predetermined and fixed-rate time intervals. This study investigates a new validation procedure based on the real-time uncertainty associated with the predicted target positions. Approach. An adaptive version of a Bayesian method for indirect tracking is developed to simulate different validation processes within a single framework: no validation, regular validation and uncertainty-based validation. While regular validation involves measuring targets at fixed intervals, uncertainty-based validation takes advantage of a key Bayesian feature, which is the real-time confidence information associated with predictions. The validation processes are applied to ground truth breathing signals consisting of a lung target and two different surrogates (one internal, one external). Their impact on prediction accuracy is evaluated with root-mean-square error (RMSE) and incidence of large errors. The number of validation measurements triggered is also examined. Main results. When using the internal surrogate and compared to regular validation, uncertainty-based validation results in significantly better prediction accuracy while using fewer validation measurements: RMSE and fraction of large errors are reduced on average by 12% and 26% respectively, with 36% fewer validation measurements. With the external surrogate, whose correlation with the target is less stable over time, more validation measurements are automatically triggered, which leads to a substantial reduction of prediction errors: RMSE and fraction of large errors are reduced on average by 17% and 28% respectively compared to regular validation. It is also observed that depending on the initial instant, regular validation can result in worse prediction accuracy compared to no validation. Significance. Uncertainty-based validation has the potential to be more efficient and effective than a validation process performed at prescheduled and fixed-rate time intervals.
A temporo-spatial description of moving tumor and organs by the probability of presence time proportion: concept and implementation for 4D dose calculation and optimization
Authors: Ren Qing , Niu Tianye
Published: December 2022

Objective. The binary definition of the internal target volume (ITV) artificially separates tumor from healthy organs at motion overlapping area for dose evaluation and optimization, bringing confusion about taking partial organs as tumor or adversely. In this work, the probability of presence time (PPT) proportion of a moving anatomic voxel at a geometric voxel is defined to construct a temporo-spatial description of moving objects. The geometric overlapping of tumor and organs in 3D space is distinguished by individual residence time proportion. The dose deposition at a geometric voxel is decomposed into individual dose delivered to tumor and organs for accumulative dose calculation and optimization. Approach. A novel PPT-based plan optimization strategy is proposed to generate an optimized non-uniform dose distribution based on the temporo-spatial relationship between tumor and organs. Main results. Results from a simulation study on phantoms show that the proposed method provides promising performance for surrounding organs at risk (OAR) avoidance with a reduction of mean and maximum dose at a range of 22.6%–23.1% and 23.6%–28.3% compared with ITV-based plans under different geometric conditions, while keeping the clinical target volume dose as prescription. Significance. The PPT definition constructs a unified framework to deal with the 4D temporo-spatial distribution, accumulative dose calculation and optimization of moving tumor and organs. The advantages of the PPT-based dose calculation and optimization approach are demonstrated by simulation study with significant reduction of OARs dose level compared with conventional ITV-based plan.
Plasma shape effects on the Alfvén eigenmode spectrum through Alfvén slow-magnetosonic wave coupling
Authors: Kramer G J , Cheng C Z
Published: December 2022

The effect of the plasma shaping (triangularity and elongation) on the continuous spectrum, frequency gaps, and number of eigenmodes is studied. The plasma shaping affects the coupling between Alfvén and slow magnetosonic waves via the geodesic magnetic curvature and the plasma pressure. The Alfvén-slow coupling creates a large number of new gaps in the continuous spectrum below the Alfvén frequency where discrete modes can reside. In ideal magnetohydrodynamic simulations a large number (a few hundred or more) of potential eigenmodes are found. The number of eigenmodes is correlated with the maximum geodesic curvature and a minimum number of possible discrete eigenmodes is found at a negative triangularity of −0.3. It is hypothesized that these possible eigenmodes form a low amplitude and dense discrete spectrum, which can be studied experimentally.
Dependence of reverse leakage on the edge termination process in vertical GaN power device
Authors: Xie Tailang , da Silva Cláudia , Szabó Nadine , Mikolajick Thomas , Wachowiak Andre
Published: December 2022

The trench gate metal oxide semiconductor field effect transistor (MOSFET) represents a prominent device architecture among the Gallium Nitride (GaN) based vertical devices currently investigated for the next generation of power electronics. A low leakage current level in off-state under high drain bias is of great importance for vertical transistors since it is a crucial feature for high breakdown voltage and device reliability. The off-state drain leakage originates from different sources in the vertical trench gate MOSFET. Besides the trench gate module, the leakage paths at the dry-etched sidewall of the lateral edge termination can also significantly contribute to the off-state drain-current. In this report, the influence of each relevant process step on the drain leakage current in off-state that is related to the lateral edge termination is investigated utilizing specific test structures on high-quality GaN epitaxial material which mimic the lateral edge termination of the MOSFET. Electrical characterization reveals the sensitivity of the leakage current to plasma-related processes. A termination technology is presented that results in low leakage current while including thick dielectric layers from plasma-assisted deposition as intended for fabrication of a field plate structure over the edge termination.
Magnetization loss and transport current loss in ReBCO racetrack coils carrying stationary current in time-varying magnetic field at 4.2 K
Authors: ter Harmsel Jeroen , Otten Simon , Dhallé Marc , ten Kate Herman
Published: December 2022

ReBCO racetrack coils may be used in high-dynamic superconducting linear motor systems, typically replacing either permanent- or electromagnets in the DC stator. Even so, in order to achieve a significant increase in force density, the superconductor needs to carry a high transport current while simultaneously experiencing the time-varying magnetic field from the copper mover coils. To aid with the design of such devices, a 2D numerical model has been developed that predicts the AC loss under motor-relevant conditions, i.e. under the combined influence of a stationary transport current and an alternating external magnetic field. The main aim of the experiments described in this paper is to validate this model with dedicated AC loss measurements. To this end, we constructed a set-up that simultaneously measures magnetization-, transport current- and overall AC loss. Two identical insulated sub-scale ReBCO racetrack coils were tested at 4.2 K while carrying a stationary transport current of up to 700 A in a sinusoidal, alternating magnetic field up to 1.5 T, applied perpendicular to the broad face of the windings. Just like with metallic superconductors, the transport current significantly increases the AC loss level and lowers the penetration field. The inductive, electric and calorimetric data were found to be consistent with each other, validating the experimental calibration methods involved. Furthermore, the numerical model accurately predicted all AC loss components in the coils without any fitting to the data and can thus reliably be used in the design of superconducting machines.
Entanglement in a qubit-qubit-tardigrade system
Authors: Lee K S , Tan Y P , Nguyen L H , Budoyo R P , Park K H , Hufnagel C , Yap Y S , Møbjerg N , Vedral V , Paterek T , Dumke R
Published: December 2022

Quantum and biological systems are seldom discussed together as they seemingly demand opposing conditions. Life is complex, ‘hot and wet’ whereas quantum objects are small, cold and well controlled. Here, we overcome this barrier with a tardigrade—a microscopic multicellular organism known to tolerate extreme physicochemical conditions via a latent state of life known as cryptobiosis. We observe coupling between the animal in cryptobiosis and a superconducting quantum bit and prepare a highly entangled state between this combined system and another qubit. The tomographic data shows entanglement in the qubit-qubit-tardigrade system, with the tardigrade modelled as an ensemble of harmonic oscillators or collection of electric dipoles. The animal is then observed to return to its active form after 420 h at sub 10 mK temperatures and pressures below

6
×

10

−
6

 mbar, setting a new record for the conditions that a complex form of life can survive.
Transition of turbulence regime during neutral beam injection on EAST
Authors: Ma Longhao , Xiang Nong , Hu Yemin , Huang Yueheng , Chen Jiale , Zhai Xuemei , Qian Zehua , Gong Xianzu , Ye Kaixuan , Wang Fudi , Jin Yifei , Qian Jinping , Zang Qing , Liu Haiqing
Published: December 2022

In recent experiments on EAST with neutral beam injection (NBI) and radio frequency (RF) waves (lower hybrid wave (LHW) and electron cyclotron waves) heating, it was observed that an increase in the line-averaged electron density and a decrease in the plasma internal inductance occurred in the duration of NBI. To explain the experimental observation, the simulations are conducted by using the equilibrium code EFIT and the transport codes ONETWO and TGYRO. It is shown that L-H transition is triggered right after neutral beam is injected, leading to the formation of density pedestal, the plasma density gradient in the outer region (0.4 < ρ < 0.75) is thus changed, which leads to an increase in η
i (

η

i

=

L

n

i

/

L

T

i

, where

1

/

L

n

i

=
∣
d

lnn

i

/

dr
∣

and

1

/

L

T

i

=
∣
d
ln

T

i

/

dr
∣

), where ρ is the normalized square root of the toroidal magnetic flux. A transition from a trapped electron modes (TEM) to an ion temperature gradient (ITG) modes dominant turbulence regime then happens due to the increase of η
i in the region (0.4 < ρ < 0.75), which results in an inward particle pinch. As a result of the rise of plasma density, the parallel refractive index and ray trajectories of the LHW are affected and more power is deposited outside ρ > 0.6, which drives more off-axis current and therefore the internal inductance is reduced.
Investigating the slow light in a 2D heterostructure photonic crystal composed of circular rods and holes in the square lattices
Authors: Zeinalvand Farzin Behnam , Seyedein Ardebili S Bahareh , Kim Jong Su , Kang Tae In
Published: December 2022

This theoretical work proposed a two-dimensional heterostructure of photonic crystal and investigated it for slow light applications. The structure includes two photonic crystals: circular Ge rods in the air background and circular holes in the Ge background. It is assumed that both of the crystals have square lattices. The band structures of the individual photonic crystals were studied to choose appropriate rod and hole radii to achieve common photonic band gaps. The effect of the possible combinations of the rod and hole radii was investigated on the group indices, bandwidths, and group index-bandwidth products. The optimum rod and hole radii were achieved. Moreover, the effect of displacements of the rods relative to the hole cylinders was studied, and the optimum displacement was calculated to achieve a high group index-bandwidth product value.
Carbon monoxide gas sensor based on Co/Ni-MOF-74 coated no-core-fiber Michelson interferometer
Authors: Zhou Juncheng , Huang Xinyue , Feng Wenlin
Published: December 2022

A Michelson interferometric carbon monoxide (CO) fiber-optic sensor based on Co/Ni-MOF-74 is proposed and fabricated. The bimetallic-ion-coordination MOFs material Co/Ni-MOF-74 was prepared by solvothermal method. Through XRD and XPS characterizations, the results show that Co/Ni-MOF-74 and Ni-MOF-74 have the same crystal structure. Co/Ni-MOF-74 has a good adsorption effect on CO, and it is integrated into the optical fiber sensing structure for CO detection. In the CO concentration range of 0–35 ppm, the sensitivity and linearity are 0.022 35 dB/ppm and 0.999 36, respectively. The detection limit of the sensor is about 1.990 46 ppm. The presented fiber-optic sensor has excellent selectivity, resistance to temperature interference and good time stability, and it is expected to be applied to the detection of trace CO.
Quantum consciousness put in doubt
Authors: Cartlidge Edwin
Published: December 2022

An underground experiment at the Gran Sasso National Laboratory casts doubt on Roger Penrose’s ideas on the role of coherent superpositions in the brain, as Edwin Cartlidge reports
Friction plays crucial role in how dominoes topple in waves
Authors: Jarman Sam
Published: December 2022

Researchers in Canada have used computer simulations to uncover new insights into the physics of toppling dominoes.
UK science in limbo over Horizon
Authors: Allen Michael
Published: December 2022

With the UK still wrangling over joining the €95bn Horizon Europe programme, researchers are warning that the impasse is accelerating the brain drain, as Michael Allen finds out.
Visualizing physics: IUPAP100 photo contest showcases stunning images
Authors: Hiscott Laura
Published: December 2022

An image of the starry sky and the Aurora Australis has bagged one of the main prizes in a photography competition organized by the International Union of Pure and Applied Physics (IUPAP).
The power of photonics
Authors: McKenzie James
Published: December 2022

James McKenzie marvels at the wonders of photonics, which is so much more crucial to everyday life than it first appears.
IOP and investment in defence and fossil fuel
Authors: Tsoumpas Charalampos , Povey Megan , Barnham Keith , Bassant Martin , Eisenhandler Eric , Tibbits Tom , Watson-Parris Duncan
Published: December 2022

Letters criticising the Institute of Physics (IOP) for holding investments in arms companies involved in the nuclear weapons industry, and in fossil fuels.
Fusion and reality
Authors: Kirby Peter
Published: December 2022

A response to the letter by Guy Matthews in July 2022 about commercial investment in fusion.
Direct ink write 3D printing of wave propagation sensor
Authors: Hassan Md Sahid , Zaman Saqlain , Rodriguez Aaron , Molina Laura , Dominguez Cesar Enrique , Morgan Robert , Bernardin John , Lin Yirong
Published: December 2022

The ability to detect impact waves and their propagation across materials is the key to structural health monitoring and defect detection of materials. To detect impact waves from a certain type of structures, it is important for a sensor to be highly flexible and complex in shape. Direct ink write (DIW) allows for the manufacturing of complex sensors. This article presents the fabrication of a flexible impact wave propagation sensor (IWPS) through the DIW technique. The dispersion of a ferroelectric ceramic material barium titanate (BaTiO3, or BTO) in polydimethylsiloxane (PDMS), not only enhances the flexibility of the 3D (three-dimensional) printed sensor but also ensures the uniform piezoelectric response throughout the whole sensor. This research explored the impact load generated impact wave in the flexible sensor and sensing response. The capability of DIW for multi-material printing was utilized to print multi-walled carbon nanotube based electrodes on BTO/PDMS stretchable composites. A total of 50 wt% of BTO in the PDMS matrix resulted in a piezoelectric coefficient of 20 pC N−1 after contact poling of IWPS. Upon applying impact loading at the center of the sensor, an impact wave was generated which gradually diminished with the distance from the origin of the applied impact load. The impact wave propagation was quantitatively characterized by measuring output voltage from different nodes of IWPS. Additionally, from the voltage response time difference at different locations of the sensor, the particle-wave velocity of a certain material attached to IWPS was determined in this research. Using the custom-designed IWPS, it was found that the particle-wave velocity of stainless steel and low-density polyethylene were 5625 m s−1 and 2000 m s−1 respectively, which are consistent with their theoretical values.
Binary operations on neuromorphic hardware with application to linear algebraic operations and stochastic equations
Authors: Iaroshenko Oleksandr , Sornborger Andrew T , Chavez Arana Diego
Published: December 2022

Non-von Neumann computational hardware, based on neuron-inspired, non-linear elements connected via linear, weighted synapses—so-called neuromorphic systems—is a viable computational substrate. Since neuromorphic systems have been shown to use less power than CPUs for many applications, they are of potential use in autonomous systems such as robots, drones, and satellites, for which power resources are at a premium. The power used by neuromorphic systems is approximately proportional to the number of spiking events produced by neurons on-chip. However, typical information encoding on these chips is in the form of firing rates that unarily encode information. That is, the number of spikes generated by a neuron is meant to be proportional to an encoded value used in a computation or algorithm. Unary encoding is less efficient (produces more spikes) than binary encoding. For this reason, here we present neuromorphic computational mechanisms for implementing binary two’s complement operations. We use the mechanisms to construct a neuromorphic, binary matrix multiplication algorithm that may be used as a primitive for linear differential equation integration, deep networks, and other standard calculations. We also construct a random walk circuit and apply it in Brownian motion simulations. We study how both algorithms scale in circuit size and iteration time.
Air quality and health co-benefits of climate change mitigation and adaptation actions by 2030: an interdisciplinary modeling study in Ahmedabad, India
Authors: Limaye Vijay S , Magal Akhilesh , Joshi Jaykumar , Maji Sujit , Dutta Priya , Rajput Prashant , Pingle Shyam , Madan Prima , Mukerjee Polash , Bano Shahana , Beig Gufran , Mavalankar Dileep , Jaiswal Anjali , Knowlton Kim
Published: December 2022

Climate change-driven temperature increases worsen air quality in places where coal combustion powers electricity for air conditioning. Climate solutions that substitute clean and renewable energy in place of polluting coal and promote adaptation to warming through reflective cool roofs can reduce cooling energy demand in buildings, lower power sector carbon emissions, and improve air quality and health. We investigate the air quality and health co-benefits of climate solutions in Ahmedabad, India—a city where air pollution levels exceed national health-based standards—through an interdisciplinary modeling approach. Using a 2018 baseline, we quantify changes in fine particulate matter (PM2.5) air pollution and all-cause mortality in 2030 from increasing renewable energy use (mitigation) and expanding Ahmedabad’s cool roofs heat resilience program (adaptation). We apply local demographic and health data and compare a 2030 mitigation and adaptation (M&A) scenario to a 2030 business-as-usual (BAU) scenario (without climate change response actions), each relative to 2018 pollution levels. We estimate that the 2030 BAU scenario results in an increase of PM2.5 air pollution of 4.13 µg m−3 from 2018 compared to a 0.11 µg m−3 decline from 2018 under the 2030 M&A scenario. Reduced PM2.5 air pollution under 2030 M&A results in 1216–1414 fewer premature all-cause deaths annually compared to 2030 BAU. Achievement of National Clean Air Programme, National Ambient Air Quality Standards, or World Health Organization annual PM2.5 Air Quality Guideline targets in 2030 results in up to 6510, 9047, or 17 369 fewer annual deaths, respectively, relative to 2030 BAU. This comprehensive modeling method is adaptable to estimate local air quality and health co-benefits in other settings by integrating climate, energy, cooling, land cover, air pollution, and health data. Our findings demonstrate that city-level climate change response policies can achieve substantial air quality and health co-benefits. Such work can inform public discourse on the near-term health benefits of mitigation and adaptation.
Symmetry-enforced two-dimensional Dirac node-line semimetals
Authors: Guo Peng-Jie , Peng Chen , Liu Zheng-Xin , Liu Kai , Lu Zhong-Yi
Published: December 2022

Based on symmetry analysis and lattice model calculations, we demonstrate that Dirac nodal line (DNL) can stably exist in two-dimensional (2D) nonmagnetic as well as antiferromagnetic systems. We focus on the situations where the DNLs are enforced by certain symmetries and the degeneracies on the DNLs are inevitable even if spin–orbit coupling is strong. After thorough analysis, we find that five space groups, namely 51, 54, 55, 57 and 127, can enforce the DNLs in 2D nonmagnetic semimetals, and four type-III magnetic space groups (51.293, 54.341, 55.355, 57.380) plus eight type-IV magnetic space groups (51.299, 51.300, 51.302, 54.348, 55.360, 55.361, 57.387 and 127.396) can enforce the DNLs in 2D antiferromagnetic semimetals. By breaking these symmetries, the different 2D topological phases can be obtained. Furthermore, by the first-principles electronic structure calculations, we predict that monolayer YB4C4 is a good material platform for studying the exotic properties of 2D symmetry-enforced Dirac node-line semimetals.
Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES
Authors: Raredon Micha Sam Brickman , Yang Junchen , Kothapalli Neeharika , Lewis Wesley , Kaminski Naftali , Niklason Laura E , Kluger Yuval
Published: December 2022

Motivation

Recent years have seen the release of several toolsets that reveal cell–cell interactions from single-cell data. However, all existing approaches leverage mean celltype gene expression values, and do not preserve the single-cell fidelity of the original data. Here, we present NICHES (Niche Interactions and Communication Heterogeneity in Extracellular Signaling), a tool to explore extracellular signaling at the truly single-cell level.

Results

NICHES allows embedding of ligand–receptor signal proxies to visualize heterogeneous signaling archetypes within cell clusters, between cell clusters and across experimental conditions. When applied to spatial transcriptomic data, NICHES can be used to reflect local cellular microenvironment. NICHES can operate with any list of ligand–receptor signaling mechanisms, is compatible with existing single-cell packages, and allows rapid, flexible analysis of cell–cell signaling at single-cell resolution.

Availability and implementation

NICHES is an open-source software implemented in R under academic free license v3.0 and it is available at http://github.com/msraredon/NICHES. Use-case vignettes are available at https://msraredon.github.io/NICHES/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Phenotypic plasticity in the monoclonal marbled crayfish is associated with very low genetic diversity but pronounced epigenetic diversity
Authors: Vogt Günter
Published: December 2022

Clonal organisms are particularly useful to investigate the contribution of epigenetics to phenotypic plasticity, because confounding effects of genetic variation are negligible. In the last decade, the apomictic parthenogenetic marbled crayfish, Procambarus virginalis, has been developed as a model to investigate the relationships between phenotypic plasticity and genetic and epigenetic diversity in detail. This crayfish originated about 30 years ago by autotriploidy from a single slough crayfish Procambarus fallax. As the result of human releases and active spreading, marbled crayfish has established numerous populations in very diverse habitats in 22 countries from the tropics to cold temperate regions. Studies in the laboratory and field revealed considerable plasticity in coloration, spination, morphometric parameters, growth, food preference, population structure, trophic position, and niche width. Illumina and PacBio whole-genome sequencing of marbled crayfish from representatives of 19 populations in Europe and Madagascar demonstrated extremely low genetic diversity within and among populations, indicating that the observed phenotypic diversity and ability to live in strikingly different environments are not due to adaptation by selection on genetic variation. In contrast, considerable differences were found between populations in the DNA methylation patterns of hundreds of genes, suggesting that the environmentally induced phenotypic plasticity is mediated by epigenetic mechanisms and corresponding changes in gene expression. Specific DNA methylation fingerprints persisted in local populations over successive years indicating the existence of epigenetic ecotypes, but there is presently no information as to whether these epigenetic signatures are transgenerationally inherited or established anew in each generation and whether the recorded phenotypic plasticity is adaptive or nonadaptive.
Late outcomes of ST-elevation myocardial infarction treated by pharmaco-invasive or primary percutaneous coronary intervention
Authors: Jamal Javeria , Idris Hanan , Faour Amir , Yang Wesley , McLean Alison , Burgess Sonya , Shugman Ibrahim , Wales Kathryn , O’Loughlin Aiden , Leung Dominic , Mussap Christian Julian , Juergens Craig Phillip , Lo Sidney , French John Kerswell
Published: December 2022

Aims

Pharmaco-invasive percutaneous coronary intervention (PI-PCI) is recommended for patients with ST-elevation myocardial infarction (STEMI)who are unable to undergo timely primary PCI (pPCI). The present study examined late outcomes after PI-PCI (successful reperfusion followed by scheduled PCI or failed reperfusion and rescue PCI)compared with timely and late pPCI (>120 min from first medical contact).

Methods and results

All patients with STEMI presenting within 12 h of symptom onset, who underwent PCI during their initial hospitalization at Liverpool Hospital (Sydney), from October 2003 to March 2014, were included. Amongst 2091 STEMI patients (80% male), 1077 (52%)underwent pPCI (68% timely, 32% late), and 1014 (48%)received PI-PCI (33% rescue, 67% scheduled). Mortality at 3 years was 11.1% after pPCI (6.7% timely, 20.2% late) and 6.2% after PI-PCI (9.4% rescue, 4.8% scheduled); P < 0.01. After propensity matching, the adjusted mortality hazard ratio (HR) for timely pPCI compared with scheduled PCI was 0.9 (95% CIs 0.4–2.0) and compared with rescue PCI was 0.5 (95% CIs 0.2–0.9). The adjusted mortality HR for late pPCI, compared with scheduled PCI was 2.2 (95% CIs 1.2–3.1)and compared with rescue PCI, it was 1.5 (95% CIs 0.7–2.0).

Conclusion

Patients who underwent late pPCI had higher mortality rates than those undergoing a pharmaco-invasive strategy. Despite rescue PCI being required in a third of patients, a pharmaco-invasive approach should be considered when delays to PCI are anticipated, as it achieves better outcomes than late pPCI.
Transfemoral aortic valve implantation: procedural hospital volume and mortality in Germany
Authors: Bestehorn Kurt , Bestehorn Maike , Zahn Ralf , Perings Christian , Stellbrink Christoph , Schächinger Volker
Published: December 2022

Aims

Studies assessing transfemoral transcatheter aortic valve implantation (TF-TAVI) showed lower rates of in-hospital mortality at high-volume hospitals and minimum caseloads were recommended to assure quality standards.

Methods and results

All patients in the German mandatory quality assurance registry with elective or urgent TF-TAVI procedures in 2018 and 2019 at 81 and 82 hospitals, respectively, were analysed. Observed in-hospital mortality was adjusted to expected mortality by the German AKL-KATH score (O/E) as well as by the EuroScore II (O/E2). Hospital volume and O/E were correlated by regression analyses and volume quartiles. 18 763 patients (age: 81.1 ± 1.0 years, mean EuroSCORE II: 6.9 ± 1.8%) and 22 137 patients (mean age: 80.7 ± 3.5 years, mean EuroSCORE II: 6.5 ± 1.6%) were analysed in 2018 and 2019, respectively. The average observed in-hospital mortality was 2.57 ± 1.83% and 2.36 ± 1.60%, respectively. Unadjusted in-hospital mortality was significantly inversely related to hospital volume by linear regression in both years. After risk adjustment, the association between hospital volume and O/E was statistically significant in 2019 (R2 = 0.049; P = 0.046), but not in 2018 (R2 = 0.027; P = 0.14). The variance of O/E explained by the number of cases in 2019 was low (4.9%). Differences in O/E outcome between the first and the fourth quartile were not statistically significant in both years (1.10 ± 1.02 vs. 0.82 ± 0.46; P = 0.26 in 2018; 1.16 0 .97 vs. 0.74 ± 0.39; P = 0.084 in 2019). Any chosen volume cut-off could not precisely differentiate between hospitals with not acceptable quality (>95th percentile O/E of all hospitals) and those with acceptable (O/E ≤95th percentile) or above-average (O/E < 1) quality. For example, in 2019 a cut-off value of 150 would only exclude one of two hospitals with not acceptable quality, while 20 hospitals with acceptable or above-average quality (25% of all hospitals) would be excluded.

Conclusion

The association between hospital volume and in-hospital mortality in patients undergoing elective TF-TAVI in Germany in 2018 and 2019 was weak and not consistent throughout various analytical approaches, indicating no clinical relevance of hospital volume for the outcome. However, these data were derived from a healthcare system with restricted access to hospitals to perform TAVI and overall high TAVI volumes. Instead of the unprecise surrogate hospital volume, the quality of hospitals performing TF-TAVI should be directly assessed by real achieved risk-adjusted mortality.
Versatile Lactococcus lactis strains improve texture in both fermented milk and soybean matrices
Authors: Poulsen Vera Kuzina , Moghadam Elahe Ghanei , Kračun Stjepan Krešimir , Svendsen Birgit Albrecht , Nielsen Wioleta Marta , Oregaard Gunnar , Krarup Anders
Published: December 2022

Lactic acid bacteria (LAB) have long been used to extend the shelf life and improve the taste and texture of fermented milk. In this study, we investigated the texturing potential of LAB in plant-based fermentation by high-throughput screening of 1232 Lactococcus lactis strains for texture in milk and liquid soybean matrices. We found that most strains with texturing abilities in fermented milk were also capable of enhancing the texture in fermented soybean, despite the large differences in composition of the two matrices. Exocellular polysaccharide production is believed to contribute positively to fermented milk and plant-base texture. It appeared as if it was the properties of the polysaccharides rather than their protein interaction partners that were responsible for the enhanced texture in both matrices. We mined whole genome sequences of texturing strains for polysaccharide biosynthesis (eps) gene clusters. The comparative genomics approach revealed 10 texturing strains with novel eps gene clusters. Currently, the relationship between the novel genes and their functionality in milk and plant matrices is unknown.
Multiflavour SMBH seeding and evolution in cosmological environments
Authors: Spinoso D , Bonoli S , Valiante R , Schneider R , Izquierdo-Villalba D
Published: December 2022

We study the genesis and evolution of supermassive black hole (SMBH) seeds through different formation channels, from PopIII remnants to massive seeds, modelled within the L-Galaxies semi-analytic code. We run the model on the Millennium-II simulation (MR-II) merger trees, as their halo-mass resolution ($M_{\rm vir,res} \sim 10^7\, \mathrm{M}_\odot \, h^{-1}$) allows to study in a cosmological volume ($L_{\rm box}=100\, \mathrm{Mpc}\, h^{-1}$) the evolution of atomic-cooling haloes ($T_{\rm vir} \gtrsim 10^4\, \mathrm{K}$) where intermediate-mass and heavy seeds are expected to form. We track the formation of these seeds according to spatial variations of the chemical and radiative feedback of star formation. Not being able to resolve the first mini-haloes ($T_{\rm vir} \sim 10^3\, \mathrm{K}$), we inherit evolved PopIII remnants in a sub-grid fashion, using the results of the GQd model. We also include the formation of heavy seeds in gas-rich massive mergers, which are very rare in the MR-II volume. The descendants of light seeds numerically prevail among our SMBHs population at all masses and z. Heavier seeds form in dense environments where close neighbours provide the required UV illumination. Overall, our model produces a z = 0 SMBHs population whose statistical properties meet current constraints. We find that the BH occupation fraction highly depends on the seeding efficiency and that the scaling relation between BH and stellar mass, in the dwarf-mass regime, is flatter than in the high-mass range. Finally, a fraction of BHs hosted in local dwarf galaxies never grow since they form at z > 6.
How close dark matter haloes and MOND are to each other: three-dimensional tests based on Gaia DR2
Authors: Zhu Yongda , Ma Hai-Xia , Dong Xiao-Bo , Huang Yang , Mistele Tobias , Peng Bo , Long Qian , Wang Tianqi , Chang Liang , Jin Xi
Published: December 2022

Aiming at discriminating different gravitational potential models of the Milky Way, we perform tests based on the kinematic data powered by the Gaia DR2 astrometry over a large range of (R, z) locations. Invoking the complete form of Jeans equations that admit three integrals of motion, we use the independent R- and z-directional equations  as two discriminators (TR and Tz). We apply the formula for spatial distributions of radial and vertical velocity dispersions proposed by Binney et al., and successfully extend it to azimuthal components, σθ(R, z) and Vθ(R, z); the analytic form avoids the numerical artifacts caused by numerical differentiation in Jeans-equations calculation given the limited spatial resolutions of observations, and more importantly reduces the impact of kinematic substructures in the Galactic disc. It turns out that whereas the current kinematic data are able to reject Moffat’s Modified Gravity (let alone the Newtonian baryon-only model), Milgrom’s MOND is still not rejected. In fact, both the carefully calibrated fiducial model invoking a spherical dark matter (DM) halo and MOND are equally consistent with the data at almost all spatial locations (except that probably both have respective problems at low-|z| locations), no matter which tracer population or which meaningful density profile is used. Since there is no free parameter at all in the quasi-linear MOND model we use, and the baryonic parameters are actually fine-tuned in the DM context, such an effective equivalence is surprising, and might be calling forth a transcending synthesis of the two paradigms.
Multiphase magnetic fields in the galaxy NGC 3627
Authors: Liu Mingrui , Hu Yue , Lazarian A , Xu Siyao , Soida Marian
Published: December 2022

Magnetic fields play an important role in the formation and evolution of a galaxy, but it is challenging to measure them by observation. Here, we study the Seyfert galaxy NGC 3627’s magnetic field orientations measured from the synchrotron polarization observed with the Very Large Array and from the Velocity Gradient Technique (VGT) using spectroscopic data. The latter employs the magnetohydrodynamical turbulence’s anisotropy to probe the magnetic fields. Being applied to the CO (2–1) and H α emission lines obtained from the PHANGS-ALMA and PHANGS-MUSE surveys, it reveals the magnetic field orientation globally consistent with the polarization. The agreement of the VGT-CO and polarization suggests that the magnetic fields associated with synchrotron emission also percolate through star-forming regions. The VGT-H α measurement reveals the magnetic fields in the warm ionized medium that permeates the disc and disc’s vicinity so that it exhibits less agreement with polarization. We find prominent radial fields measured by synchrotron polarization appear in the transition regions from the spiral arms to the galactic bar, while such morphology is less apparent in the VGT-CO and VGT-H α measured magnetic fields. The radial fields suggest that the magnetic torque is important in removing orbiting gas’ angular momentum. We notice that magnetic fields inferred from the dust polarization, VGT-CO, and synchrotron polarization are different in the east arm. We interpret this difference as arising from the fact that the three measurements are tracing the magnetic fields associated with pre-collision, the mixture of pre-collision and post-collision, and post-collision flows, respectively.
Endemism and Reemergence Potential of the Ipomovirus Sweet Potato Mild Mottle Virus (FamilyPotyviridae) in Eastern Africa: Half a Century of Mystery
Authors: Tugume Arthur K. , Mbanzibwa Deusdedith R. , Alicai Titus , Omongo Christopher A. , Maruthi M. N.
Published: December 2022

Viruses have the ability to frequently colonize new hosts and ecological niches because of their inherently high genetic and evolutionary plasticity. However, a virus may emerge and remain of no or less economic importance until changes in viral or environmental factors dictate its epidemiological status. An example is sweet potato mild mottle virus (SPMMV), which was first reported in the 1970s on sweetpotato in eastern Africa. SPMMV has remained endemic in the region and poorly understood, yet accounting for 60 to 95% of losses, especially in mixed infections. Unlike other sweetpotato viruses which have global incidences, SPMMV has never been confirmed outside eastern Africa. This implicates the region as its center of origin but does not fully account for SPMMV's exclusive geographic delimitation to eastern Africa. Despite its importance, several mysteries and research gaps surround SPMMV, which decelerate efforts for effective virus disease management in sweetpotato. The aim of this review is to articulate research gaps, propose pivotal scientific directions, and stimulate knowledge generation for better management of virus diseases in sweetpotato. Vector-mediated transmission of SPMMV remains enigmatic. Here, we postulate testable hypotheses to explain SPMMV transmission. Comparisons between SPMMV and cassava brown streak ipomoviruses demonstrate epidemiological “hallmarks” for monitoring SPMMV. Evolutionary forces on SPMMV coupled with the virus' broad host range imply a “silent build up” of more fit variants in a changing climate, and this could explode into a worse disease conundrum. These information gaps need urgent filling to ease future management of virus disease emergences in sweetpotato.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Ligneous Conjunctivitis Secondary to Viral Conjunctivitis
Authors: Quintero-Estades Jose A. , Iacob Codrin E. , Donnenfeld Eric D. , Perry Henry D.
Published: December 2022

Ligneous conjunctivitis is a rare cause of chronic conjunctivitis that may be triggered by ocular insults such as trauma or infections. We present an interesting case of ligneous conjunctivitis caused by a viral infection that responded well to conservative management. Topical cyclosporine and heparin are a good treatment regimen that caused resolution of lesions and prevented recurrences.
Outbreak of KPC-producing Klebsiella pneumoniae at a Portuguese university hospital: Epidemiological characterization and containment measures
Authors: Peres David , Figueiredo Paulo , Andrade Paulo , Rocha-Pereira Nuno , Carvalho Cláudia , Ferraz Rita , Duro Raquel , Dias Arnaldo , Gomes Abel , Pereira Cláudia , Braga Gisélia , Pereira Virginia , Azevedo Lino , Moniz Edgar , Ribeiro Manuela , Ferreira Eugénia , Manageiro Vera , Teixeira José , Guimarães Tiago , Caniça Manuela , Alves Carlos
Published: December 2022

Background:

KPC-producing K pneumoniae (KPC-Kp) is a public health problem with important clinical and epidemiological implications. We describe an outbreak of KPC-Kp at vascular surgery and neurosurgery wards in a central hospital in Porto, Portugal.

Methods:

A case of KPC-Kp was considered to be a patient positive for KPC-Kp with strong epidemiological plausibility of having acquired this microorganism in the affected wards and/or with genetic relationship ≥92% between KPC-Kp isolates. Active surveillance cultures (ASCs) and real-time polymerase chain reaction were used for the detection of carbapenemase genes through rectal swab in a selected population. Molecular analysis was performed using pulsed-field gel electrophoresis at the National Reference Laboratory. Patient risk factors were collected from the electronic medical record system. Information regarding outbreak containment strategy was collected from the Infection Control Unit records.

Results:

Of the 16 cases, 11 (69%) were identified through active screening, representing 1.4% of the total 766 ASCs collected. The most frequent risk factors identified were previous admission (63%), antibiotic exposure in the past 6 months (50%), and immunodepression (44%). The length of stay until KPC-Kp detection was high (0–121 days, mean 35.6), as was the total length of stay (5–173 days, mean 56.6). Three patients (19%) were infected by KPC-Kp, 2 of whom died. One previously colonized patient died later because of KPC-Kp infection.

Conclusions:

Multifactorial strategy based on contact precautions (with patient and healthcare professional cohorts) and ASC, as well as Antibiotic Stewardship Program reinforcement, allowed to contain this KPC-Kp outbreak.