bluuebunny/crossref_metadata_2025 huggingface dataset:
Internal electric field enhanced photoelectrochemical water splitting in direct Z-scheme GeC/HfS2 heterostructure: A first-principles study
Authors: Zhang Yu , Shen Yanqing , Liu Jiajia , Lv Lingling , Zhou Min , Yang Xin , Meng Xianghui , Zhou Zhongxiang
Published: January 2023

Designing direct Z-scheme heterostructure photocatalysts has received enormous attention due to the efficient separation of photo-generated carriers in water splitting. Based on first-principles calculations, electronic properties and a photocatalytic mechanism of a GeC/HfS2 van der Waals (vdW) heterostructure are systematically explored. From the analysis of band arrangement and the built-in electric field, the heterostructure, with an indirect bandgap of 0.40 eV, is demonstrated to be a typical direct Z-scheme system. Remarkably, there is also a 0.40 eV interlayer work function difference in the heterostructure, which is helpful to further drive carrier separation and enhance the water splitting ability by partially bending the redox potential of water. The Gibbs calculation shows that the GeC/HfS2 vdW heterostructure can achieve overall photocatalytic water splitting spontaneously under neutral conditions. Moreover, excellent visible light absorption ability (∼5×105 cm−1) and giant carrier mobilities (5823 cm2 V−1 s−1) also make GeC/HfS2 heterostructure highly competitive in numerous photocatalytic materials and optoelectronic devices. The bandgap can be flexibly adjusted by biaxial strain, enabling a wider application of the heterostructure. All these significant properties not only demonstrate the great application potential of GeC/HfS2 heterostructure as photocatalysis but also provide ideas for designing novel electric field-enhanced heterostructures.
Enhanced photovoltaic effect in graphene–silicon Schottky junction under mechanical manipulation
Authors: Pu Dong , Anwar Muhammad Abid , Zhou Jiachao , Mao Renwei , Pan Xin , Chai Jian , Tian Feng , Wang Hua , Hu Huan , Xu Yang
Published: January 2023

A graphene–silicon Schottky junction (GSJ), which has potentials of large-scale manufacturing and integration, can bring new opportunities to Schottky solar cells for photovoltaic (PV) power conversion. However, the essential power conversion limitation for these devices lies in a small open-circuit voltage (Voc), which depends on the Schottky barrier height. In this study, we introduce an electromechanical method based on a flexoelectric effect to enhance the PV efficiency in GSJ. By atomic force microscope (AFM) tip-based indentation and in situ current measurement, the current–voltage (I–V) responses under a flexoelectric strain gradient are obtained. The Voc is observed to increase for up to 20%, leading to an evident improvement of the power conversion efficiency. Our studies suggest that the strain gradient may offer unprecedented opportunities for the development of GSJ-based flexo-photovoltaic applications.
Structure–transport correlations in Na11Sn2SbSe12 and its sulfide solid solutions
Authors: Ramos Erika P. , Assoud Abdeljalil , Zhou Laidong , Shyamsunder Abhinandan , Rettenwander Daniel , Nazar Linda F.
Published: January 2023

We report a new ion conductor—Na11Sn2SbSe12—as a possible candidate for a solid catholyte in composite cathodes for all-solid state Na-batteries, which exhibits a room temperature ionic conductivity of 0.15 ± 0.03 mS cm−1 and an activation energy of 0.39 ± 0.02 eV. The sulfide solid solutions of Na11Sn2SbSe12, namely, Na11Sn2SbS12−xSex (x = 1 and 6), were also investigated through a combination of Rietveld refinement against powder x-ray diffraction data and electrochemical impedance spectroscopy to reveal the complex structure–property relationships governing ion transport in this class of materials. Meanwhile, broadening of the Na-ion diffusion pathways in Na11Sn2SbSe12 is expected to facilitate Na-ion transport compared to the sulfide-rich member of the solid solution, the opposite holds: increasing the Se fraction in Na11Sn2SbS12−xSex leads to a little change in the activation energy but a reduction in the ionic conductivity. We ascribe this to the lowering of the prefactor, σ0, in the Arrhenius relationship with increasing lattice “softening” as a function of higher Se content.
Structured light signal transmission through clouds
Authors: Wang Tianhong , Ali Reza Saad Bin , Buldt Finn , Bassène Pascal , N’Gom Moussa
Published: January 2023

Dynamic media such as atmospheric clouds and fog form a formidable barrier to light propagation for free-space optical communication (FSO). To overcome such an obstacle, we propose to make use of the acoustic properties of a laser filament coupled together with a donut-shaped signal beam. A filament generated by an ultrafast laser is accompanied by an acoustic wave that clears a cylindrical chamber around the filament’s plasma column that can mimic a transmission channel. We present a method to couple a Laguerre–Gauss beam through the obstacle-free channel. We image and measure the transmitted signal carried by the structured beam to demonstrate an efficient method for FSO through cloudy conditions, which requires low energy, is resilient to noise, and is unaffected by the filament.
Formation of delta shock and vacuum state for the pressureless hydrodynamic model under the small disturbance of traffic pressure
Authors: Wang Yixuan , Sun Meina
Published: January 2023

The formation of delta shock and vacuum state for the pressureless hydrodynamic model is investigated in detail under the small disturbance of traffic pressure. Exact Riemann solutions for the perturbed system can be constructed explicitly for four different possible structures. Asymptotically, the perturbed Riemann solution involving two shocks will collapse to a single delta shock, and the perturbed Riemann solution involving two rarefaction waves will degenerate into a solution containing two contact discontinuities along with the vacuum state between them when the perturbed parameter goes to zero. It should be stressed here that the internal state in each of the two rarefaction wave-fans turns out to be the vacuum state gradually in such a limiting case, which differs obviously from the previous result that each of the two rarefaction wave-fans is compressed globally to be a single contact discontinuity. Additionally, some typical numerical results exhibiting the formation process of delta shock and vacuum state are presented to verify our theoretic results.
Refractive index profile renormalization for a silicon waveguide bend
Authors: Lu Ronger , Wang Jiaying , Zhang Binglin , Di Dongrui , Liu Ang
Published: January 2023

An index profile renormalization method is proposed to study the effective refraction index increase in a high-index contrast waveguide bend such as a silicon waveguide bend. This method transforms a waveguide bend to an equivalent straight waveguide (ESW). The simulation results show that the ESW method can calculate the effective refraction index increase in a three-dimensional (3D) bend, costing much less time than the traditional finite difference time domain method and the index profile renormalization (IPR) method developed for small radius cases. In addition, the field center shift is studied. The relationships are established between the effective refraction index increase and field center shift from the bend axis along the radial direction for estimations based on the approximated IPR method. These results can lead to great convenience in estimating the effective refraction index increase in 3D bend, which could be used in conditions requiring critical phase control.
Non-equilibrium view of the amorphous solidification of liquids with competing interactions
Authors: Carretas-Talamante Ana Gabriela , Zepeda-López Jesús Benigno , Lázaro-Lázaro Edilio , Elizondo-Aguilera Luis Fernando , Medina-Noyola Magdaleno
Published: January 2023

The interplay between short-range attractions and long-range repulsions (SALR) characterizes the so-called liquids with competing interactions, which are known to exhibit a variety of equilibrium and non-equilibrium phases. The theoretical description of the phenomenology associated with glassy or gel states in these systems has to take into account both the presence of thermodynamic instabilities (such as those defining the spinodal line and the so called λ line) and the limited capability to describe genuine non-equilibrium processes from first principles. Here, we report the first application of the non-equilibrium self-consistent generalized Langevin equation theory to the description of the dynamical arrest processes that occur in SALR systems after being instantaneously quenched into a state point in the regions of thermodynamic instability. The physical scenario predicted by this theory reveals an amazing interplay between the thermodynamically driven instabilities, favoring equilibrium macro- and micro-phase separation, and the kinetic arrest mechanisms, favoring non-equilibrium amorphous solidification of the liquid into an unexpected variety of glass and gel states.
Direct bandgaps, Weyl fermions, and strong light absorption ability in Janus Ti2OFCl MOene
Authors: Yan Luo , Zhu Jiaojiao , Li Qiaoqiao , Ku Ruiqi , Huang Xingyong , Wang Bao-Tian , Song Hai-Zhi , Yang Shengyuan A. , Zhou Liujiang
Published: January 2023

Recently, the MXene-like MOenes provide a novel combination of mechanical, electronic, and optical properties attractive for next-generation low-dimensional quantum and optoelectronic devices. The Janus structure induced by asymmetric surfaces could bring about unique features due to the existence of a built-in electric field. In this study, Janus 2H- and 1T-Ti2OFCl monolayers are systematically scrutinized via the first-principle calculations. 2H- and 1T-Ti2OFCl monolayers are direct semiconductors with a bandgap of 0.75 and 1.12 eV, respectively. Intriguingly, biaxial strains can lead to a three-component 2D pseudospin-1 fermion and a two-component 2D double Weyl fermion during the quantum phase transitions. The effective k·p models further help to characterize these emergent fermions. In addition, the light absorbance calculations including the excitonic effect show that Ti2OFCl monolayers can be potentially applied in infrared detectors and exciton solar cells. This work would further understand the inherently chemical and physical features of the MOene family.
Flashover characteristics of a droplet impacting the silicone rubber surface
Authors: Li Zong , Wang Naixiao , Dong Kai , Mu Lei , Cao Bin , Wang Liming
Published: January 2023

The surface discharge of silicone rubber (SIR) is one of the main reasons to accelerate the aging of its surface material in power systems. It is known that static water droplets on the SIR surface can make the flashover voltage substantially fall, while the flashover characteristics of water droplets impacting the SIR surface are unknown. In this work, the dynamic flashover characteristics of the water droplets impacting the SIR surface are studied. When the water droplets impact the SIR surface, they will stretch first and then shrink. The minimum flashover voltage occurs at the moment when the spreading area of the water droplet reaches the maximum, and this flashover voltage drop is nearly 1.8 times that of the static water droplet. When the water droplet begins to shrink, the bright arc first turns into a filament-like arc and then disappears as the water droplet continues to shrink. At the same time, when the droplet falls at a large height, the water droplet will be broken under the action of electric arc force, and the broken water droplet will likely make the static flashover voltage to further fall.
Nucleation enhancement by energy dissipation with the collision of a supercooled water droplet
Authors: Wu Haocheng , Bian Peixiang , Kong Weiliang , Liu Hong
Published: January 2023

Lack of knowledge on nucleation with mechanical disturbances hinders researchers in understanding the anti-icing properties of superhydrophobic surfaces. In this research, experiments are designed to observe the freezing process of a supercooled water droplet at −14 °C with different levels of external disturbances by changing the impact velocity, and the nucleation rates are statistically analyzed. It is found that compared with the static state, the nucleation rates of droplets during the collision increase by three and five orders of magnitude on the hydrophilic epoxy resin and superhydrophobic polytetrafluoroethylene (PTFE) surfaces, respectively, which leads to a much higher instantaneous nucleation rate on the superhydrophobic surface than on the hydrophilic surface. Then, the mechanical energy dissipation during the impact is analyzed. The logarithm of the nucleation rate is approximately linear in relation to the logarithm of the average energy dissipation rate, while the nucleation rate of the rough PTFE surface increases more rapidly than that of the other smooth surface. Finally, the effect of the energy dissipation on the nucleation energy barrier is discussed theoretically and an impact-nucleation model is proposed, which drives the reconsideration of the design of a superhydrophobic anti-icing coating.
Doped umbite materials for selective abatement of cesium radionuclides from nuclear waste streams
Authors: Nearchou Antony , Chen Tzu-Yu , Parsons Daniel S. , O’Brien Luke , Hodge Nicholas A. , Abrahamsen-Mills Liam , Allan Phoebe K. , Hriljac Joseph A.
Published: January 2023

Sb- and Nb-doped Zr and Sn-umbites have been prepared using hydrothermal synthesis with both high purity and yield. All four materials display excellent removal of Cs+ cations from acidic, neutral, and basic solutions, abating at least 80% of the Cs present. This performance is retained in the presence of competing Na+ cations as well as across the pH range. The most sustained selectivity is observed in acidic media, with evidence of a minor reduction in selectivity under basic conditions. The umbites have successfully been shaped into pellets, introducing macroporosity and retaining the selective uptake of Cs in the presence of excess Na. Through thermal treatment, samples of partially Cs-exchanged umbite can be converted into dense silicate phases where radioactive Cs can be immobilized in a potential wasteform for long term storage. These findings present doped umbites as prospective materials for industrial use with selective abatement properties and capabilities for deployment followed by end of life geological disposal.
Direct calculation of the temperature dependence of 2D-IR spectra: Urea in water
Authors: Borkowski Ashley K. , Campbell N. Ian , Thompson Ward H.
Published: January 2023

A method for directly calculating the temperature derivative of two-dimensional infrared (2D-IR) spectra from simulations at a single temperature is presented. The approach is demonstrated by application to the OD stretching spectrum of isotopically dilute aqueous (HOD in H2O) solutions of urea as a function of concentration. Urea is an important osmolyte because of its ability to denature proteins, which has motivated significant interest in its effect on the structure and dynamics of water. The present results show that the temperature dependence of both the linear IR and 2D-IR spectra, which report on the underlying energetic driving forces, is more sensitive to urea concentration than the spectra themselves. Additional physical insight is provided by calculation of the contributions to the temperature derivative from different interactions, e.g., water–water, water–urea, and urea–urea, present in the system. Finally, it is demonstrated how 2D-IR spectra at other temperatures can be obtained from only room temperature simulations.
High pressure behavior of ethylene and water: From clathrate hydrate to polymerization in solid ice mixtures
Authors: Berni S. , Scelta D. , Fanetti S. , Bini R.
Published: January 2023

Among the ice mixtures that can be found in our universe, those involving ethylene are poorly studied even though ethylene reportedly exists in the presence of water in several astrochemical domains. Here, we report on the chemistry of ethylene and water mixtures in both pressure (0–15 GPa) and temperature (300–370 K) ranges relevant to celestial bodies conditions. The behavior of the binary mixture has been tracked, starting from the ethylene clathrate hydrate and following its evolution through two different crystalline phases up to 2.10 GPa, where it decomposes into a solid mixture of water ice and crystalline ethylene. The pressure and temperature evolution of this mixture has been studied up to the complete transformation of ethylene into polyethylene and compared with that of the pure hydrocarbon, reporting here for the first time its spectroscopic features upon compression. The spectroscopic analysis of the recovered polymers from the ice mixtures provided hints about the reactivity of the monomer under the environmental stress exerted by the water network. The results of this study are expected to be significant in a variety of fields ranging from astrochemistry to material science and also to fundamental chemistry, particularly regarding the study and modelization of the behavior of complex mixtures.
Recent and future declines of a historically widespread pollinator linked to climate, land cover, and pesticides
Authors: Janousek William M. , Douglas Margaret R. , Cannings Syd , Clément Marion A. , Delphia Casey M. , Everett Jeffrey G. , Hatfield Richard G. , Keinath Douglas A. , Koch Jonathan B. Uhuad , McCabe Lindsie M. , Mola John M. , Ogilvie Jane E. , Rangwala Imtiaz , Richardson Leif L. , Rohde Ashley T. , Strange James P. , Tronstad Lusha M. , Graves Tabitha A.
Published: January 2023

The acute decline in global biodiversity includes not only the loss of rare species, but also the rapid collapse of common species across many different taxa. The loss of pollinating insects is of particular concern because of the ecological and economic values these species provide. The western bumble bee (
Bombus occidentalis
) was once common in western North America, but this species has become increasingly rare through much of its range. To understand potential mechanisms driving these declines, we used Bayesian occupancy models to investigate the effects of climate and land cover from 1998 to 2020, pesticide use from 2008 to 2014, and projected expected occupancy under three future scenarios. Using 14,457 surveys across 2.8 million km
2
in the western United States, we found strong negative relationships between increasing temperature and drought on occupancy and identified neonicotinoids as the pesticides of greatest negative influence across our study region. The mean predicted occupancy declined by 57% from 1998 to 2020, ranging from 15 to 83% declines across 16 ecoregions. Even under the most optimistic scenario, we found continued declines in nearly half of the ecoregions by the 2050s and mean declines of 93% under the most severe scenario across all ecoregions. This assessment underscores the tenuous future of
B. occidentalis
and demonstrates the scale of stressors likely contributing to rapid loss of related pollinator species throughout the globe. Scaled-up, international species-monitoring schemes and improved integration of data from formal surveys and community science will substantively improve the understanding of stressors and bumble bee population trends.
High-performance infrared photodetection beyond bandgap limitation based on surface plasmon resonance in sub-stoichiometry molybdenum oxide nanostructures
Authors: Yu Yuanfang , Zhong Fan , Li Ruizhi , Cui Yueying , Wu Jianfeng , Zhang Jialin
Published: January 2023

High-performance photodetectors in the near-infrared (NIR) regime are essential for many advanced applications, such as optical communication, intelligent driving, and imaging system. However, conventional photoconductive infrared detectors commonly suffer from slow response speed and narrow spectral response. Here, we demonstrate a high performance NIR photodetector based on plasmonic sub-stoichiometry molybdenum oxide (MoO3−x) nanostructures/graphene heterostructure. Empowered by surface plasmon resonance induced near-field enhancement in MoO3−x
and the subsequent hot-electron injection (HEI), a fast response time (rise time ∼6.7 μs, decay time ∼12.5 μs), high responsivity (3.3 A/W), low noise equivalent power (∼4.9 pW/Hz1/2), as well as wide response range from visible light to NIR is obtained at room temperature. The weak carrier–phonon interaction in graphene prevents the relaxation of injected hot electrons and enables efficient electron extraction. The response speed is nearly four orders of magnitude improved compared with other graphene-based hybrid devices with similar device structures. Moreover, the interfacial HEI breaks the bandgap limits of molybdenum oxide and further extends the response spectrum of the device to conventional band (C-band) of optical communication. Our proposed device architecture offers new strategy for developing high-performance infrared photodetectors.
Evaluation of silicone rubber-lead shield's effectiveness in protecting the breast during thoracic CT
Authors: Lestari Yulianti M , Anam Choirul , Sutanto Heri , Arifin Zaenal , Alkian Ilham , Suyudi Imam , Dougherty Geoff
Published: January 2023

Radiation of thoracic computed tomography (CT) involves the breast although it is not considered an organ of interest. According to the International Commission on Radiological Protection (ICRP) No. 103, the breast is an organ with a high level of sensitivity when interacting with x-rays, increasing the potential risk of breast cancer. Therefore, the radiation dose must be optimized while maintaining image quality. The dose optimization can be accomplished using a radiation shield. This study aims to determine the effect of silicone rubber (SR)-lead (Pb) in various thicknesses as an alternative protective material limiting dose and preserving the image quality of the breast in thoracic CT. SR-Pb was made from SR and Pb by a simple method. The SR-Pb had thicknesses of 3, 6, 9, and 12 mm. The breast dose was measured using a CT dose profiler on the surface of the breast phantom. The CT number and the noise level of the resulting image were determined quantitatively. The dose without the radiation shield was 5.4 mGy. The doses measured using shielding with thicknesses of 3, 6, 9, and 12 mm were 5.2, 4.5, 4.3, and 3.3 mGy, respectively. Radiation shielding with a thickness of 12 mm reduced breast surface dose by up to 38%. The CT numbers and noise levels for the left and right breast phantom images were almost the same as those ​​without radiation shields indicating there were only slight artifacts in the image. Therefore, SR-Pb is considered a good shielding material which can be pplied in a clinical setting by placing it directly on the breast surface for dose optimization.
Tracking the same fast-LGSO crystals by changing surface treatments for better coincidence timing resolution in PET
Authors: Kiyokawa Miho , Kang Han Gyu , Yamaya Taiga
Published: January 2023

Achieving fast coincidence timing resolution (CTR) is an important issue in clinical time-of-flight positron emission tomography (TOF-PET) to improve the reconstructed image quality. One of the major factors affecting the CTR is the crystal surface treatment, which is often parameterized as surface roughness. However, previous studies on the crystal surface treatment optimization had two limitations of crystal-by-crystal variation and worse CTR over 200 ps. Here, we report the effects of the crystal surface treatment on the performance of a 20 mm long fast-LGSO crystal based TOF detector by tracking the same crystals in the sub-180 ps CTR regime. The light collection efficiency (LCE), energy resolution (ER) and CTR of the TOF detector were evaluated with six different crystal surface treatments of chemically polished (C.P), C.P half side roughened (1/2S) treatment, and then the C.P one side roughened (1S) treatment, mechanically polished (M.P) treatment, M.P 1/2S treatment, and M.P 1S treatment. The four lateral surfaces of each crystal were wrapped by using enhanced specular reflector film while the top surface was covered by using Teflon tape. The bottom surface of the crystal was optically coupled to a silicon photomultiplier. The timing and energy signals were extracted by using a custom-made high-frequency readout circuit, and then digitized by using a waveform digitizer. All the experimental conditions were same except the crystal surface treatment. Among the six different crystal surface treatments, the M.P 1S would be the optimal crystal surface treatment which balanced enhancements in the CTR (165 ± 3 ps) and ER (10.5 ± 0.5%). Unlike the M.P 1S, the C.P 1S did not enhance the CTR and ER. Hence, the C.P without roughening would be the second-best optimal crystal surface treatment which balanced the CTR (169 ± 3 ps) and ER (10.5 ± 0.5%).
Doping carbon electrodes with sulfur achieves reversible sodium ion storage
Authors: de Tomas Carla , Alabidun Sarat , Chater Luke , Darby Matthew T , Raffone Federico , Restuccia Paolo , Au Heather , Titirici Magda M , Cucinotta Clotilde S , Crespo-Ribadenyra Maria
Published: January 2023

We present a combination of experiments and theory to study the effect of sulfur doping in hard carbons anodes for sodium-ion batteries. Hard carbons are synthesised through a two step process: hydrothermal carbonisation followed by pyrolysis of a biomass-derived carbon precursor. Subsequent sulfur doping is introduced via chemical-vapour deposition. The resulting sulfur-doped hard carbon shows enhanced sodium storage capacity with respect to the pristine material, with significantly improved cycling reversibility. Atomistic first principles simulations give insight into this behaviour, revealing that sulfur chemisorbed onto the hard carbon increases the sodium adsorption energies and facilitates sodium desorption. This mechanism would increase reversible Na storage, confirming our experimental observations and opening a pathway towards more efficient Na-ion batteries.
On the enumeration of finite 𝐿-algebras
Authors: Dietzel C. , Menchón P. , Vendramin L.
Published: January 2023

We use Constraint Satisfaction Methods to construct and enumerate finite

L
L

-algebras up to isomorphism. These objects were recently introduced by Rump and appear in Garside theory, algebraic logic, and the study of the combinatorial Yang–Baxter equation. There are 377,322,225 isomorphism classes of

L
L

-algebras of size eight. The database constructed suggests the existence of bijections between certain classes of

L
L

-algebras and well-known combinatorial objects. We prove that Bell numbers enumerate isomorphism classes of finite linear

L
L

-algebras. We also prove that finite regular

L
L

-algebras are in bijective correspondence with infinite-dimensional Young diagrams.
CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities
Authors: Oarga Alexandru , Bannerman Bridget P , Júlvez Jorge
Published: January 2023

Motivation

Despite the fact that antimicrobial resistance is an increasing health concern, the pace of production of new drugs is slow due to the high cost and uncertain success of the process. The development of high-throughput technologies has allowed the integration of biological data into detailed genome-scale models of multiple organisms. Such models can be exploited by means of computational methods to identify system vulnerabilities such as chokepoint reactions and essential reactions. These vulnerabilities are appealing drug targets that can lead to novel drug developments. However, the current approach to compute these vulnerabilities is only based on topological data and ignores the dynamic information of the model. This can lead to misidentified drug targets.

Results

This work computes flux constraints that are consistent with a certain growth rate of the modelled organism, and integrates the computed flux constraints into the model to improve the detection of vulnerabilities. By exploiting these flux constraints, we are able to obtain a directionality of the reactions of metabolism consistent with a given growth rate of the model, and consequently, a more realistic detection of vulnerabilities can be performed. Several sets of reactions that are system vulnerabilities are defined and the relationships among them are studied. The approach for the detection of these vulnerabilities has been implemented in the Python tool CONTRABASS. Such tool, for which an online web server has also been implemented, computes flux constraints and generates a report with the detected vulnerabilities.

Availability and implementation

CONTRABASS is available as an open source Python package at https://github.com/openCONTRABASS/CONTRABASS under GPL-3.0 License. An online web server is available at http://contrabass.unizar.es.

Supplementary information

A glossary of terms are available at Bioinformatics online.
An instrumental variable method for point processes: generalized Wald estimation based on deconvolution
Authors: Jiang Zhichao , Chen Shizhe , Ding Peng
Published: January 2023

Point processes are probabilistic tools for modelling event data. While there exists a fast-growing literature on the relationships between point processes, how such relationships connect to causal effects remains unexplored. In the presence of unmeasured confounders, parameters from point process models do not necessarily have causal interpretations. We propose an instrumental variable method for causal inference with point process treatment and outcome. We define causal quantities based on potential outcomes and establish nonparametric identification results with a binary instrumental variable. We extend the traditional Wald estimation to deal with point process treatment and outcome, showing that it should be performed after a Fourier transform of the intention-to-treat effects on the treatment and outcome, and thus takes the form of deconvolution. We refer to this approach as generalized Wald estimation and propose an estimation strategy based on well-established deconvolution methods.
Partial-year continuous light treatment reduces precocious maturation in age 1+ hatchery–reared male spring Chinook Salmon (Oncorhynchus tshawytscha)
Authors: Hoffman Nick F , Medeiros Lea R , Graham Neil D , Nuetzel Hayley M , Pierce Andrew L , Nagler James J
Published: January 2023

Hatchery programs designed to conserve and increase the abundance of natural populations of spring Chinook Salmon Oncorhynchus tshawytscha have reported high proportions of males precociously maturing at age 2, called minijacks. High proportions of minijacks detract from hatchery supplementation, conservation and production goals. This study tested the effects of rearing juvenile Chinook Salmon under continuous light (LL) on minijack maturation in two trials. The controls were maintained on a simulated natural photoperiod for both trials. For trial 1, LL treatment began on the summer solstice 2019 or the autumn equinox 2019 and ended in late March 2020 (LL-Jun-Apr and LL-Sep-Apr, respectively). A significant reduction in the mean percent of minijacks (%MJ) was observed versus control (28.8%MJ) in both LL-Jun-Apr (5.4%MJ) and LL-Sep-Apr (9.3%MJ). Trial 2 was designed to evaluate whether stopping LL treatment sooner was still effective at reducing maturation proportions relative to controls. LL treatments began on the summer solstice 2020 and continued until the winter solstice (LL-Jun-Dec) or the final sampling in April 2021 (LL-June-Apr). LL-Jun-Dec tanks were returned to a simulated natural photoperiod after the winter solstice. Both photoperiod treatments showed a significant reduction in mean %MJ from the control (66%MJ): LL-Jun-Dec (11.6%MJ), LL-Jun-Apr (10.3%MJ). In both trials, minijacks had higher body weights, were longer and had increased condition factor when compared to females and immature males in all treatment groups at the final sampling. In both trials, there was little or no effect of LL treatment on fork length or body weight in immature males and females versus controls, but an increase in condition factor versus controls was observed. This study shows that continuous light treatment reduces minijack maturation in juvenile male spring Chinook Salmon and could provide an effective method for Spring Chinook Salmon hatcheries interested in reducing minijack production.
Context-dependent DNA methylation signatures in animal livestock
Authors: Venkatesh Geetha , Tönges Sina , Hanna Katharina , Ng Yi Long , Whelan Rose , Andriantsoa Ranja , Lingenberg Annika , Roy Suki , Nagarajan Sanjanaa , Fong Steven , Raddatz Günter , Böhl Florian , Lyko Frank
Published: January 2023

DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting.
A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)
Authors: Ludt William B , Corbett Eamon C , Kattawar Jerry , Chakrabarty Prosanta , Faircloth Brant C
Published: January 2023

North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary relationships and species boundaries among members of this group, many of which are known to hybridize. Here, we describe a chromosome-scale genome assembly representing Bluegill (Lepomis macrochirus), one of the most widespread centrarchid species. By combining long-read, Oxford Nanopore sequencing data with short-insert, whole-genome and HiC sequence reads, we produced an assembly (Lm_LA_1.1) having a total length of 889 Mb including 1,841 scaffolds and having a scaffold N50 of 36 Mb, L50 of 12, N90 of 29 Mb, and L90 of 22. We detected 99% (eukaryota_odb10) and 98% (actinopterygii_odb10) universal single-copy orthologs (BUSCOs), and ab initio gene prediction performed using this new assembly identified a set of 17,233 genes that were supported by external (OrthoDB v10) data. This new assembly provides an important addition to the growing set of assemblies already available for spiny-rayed fishes (Acanthomorpha), and it will serve as a resource for future studies that focus on the complex evolutionary history of centrarchids.
Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera
Authors: Tandon Kshitij , Ricci Francesco , Costa Joana , Medina Mónica , Kühl Michael , Blackall Linda L , Verbruggen Heroen
Published: January 2023

At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.
Are Italian Rules on Copyright Collective Management in Line with EU Law?
Authors: Meo Carlo
Published: January 2023

Directive (EU) 2014/26 liberalised the market for collective management of copyright and related rights in Europe. In doing so it distinguished collecting societies into two categories. ‘Collective Management Organisations’ (CMOs) are entities that are either controlled (or owned) by rightholders or organised on a ‘non-profit’ basis. Conversely, ‘Independent Management Entities’ (IMEs) operate ‘for profit’ and are not controlled by rightholders. Prior to the adoption of this Directive, Italian law entrusted SIAE (Italian Society of Authors and Publishers) with a legal monopoly for the collective management of copyright. In 2017 a reform put an end to this system by opening the market to new entrants. However, according to the new rules, an entity can only manage copyright in Italy if it qualifies as a CMO. IMEs are therefore still not allowed to manage copyright in the Italian market. Such a restriction has raised a lively debate in Italy and its compatibility with EU law has recently been the object of a request for a preliminary ruling of the CJEU by the Tribunal of Rome. This work deals with the question of whether the choice of preventing IMEs from entering the Italian market is compatible with the principles of Directive 2014/26 and with general principles of EU law on the Internal Market.
A Multicenter, Controlled Human Infection Study of Influenza A(H1N1)pdm09 in Healthy Adults
Authors: Ortiz Justin R , Bernstein David I , Hoft Daniel F , Woods Christopher W , McClain Micah T , Frey Sharon E , Brady Rebecca C , Bryant Christopher , Wegel Ashley , Frenck Robert W , Walter Emmanuel B , Abate Getahun , Williams Sarah R , Atmar Robert L , Keitel Wendy A , Rouphael Nadine , Memoli Mathew J , Makhene Mamodikoe K , Roberts Paul C , Neuzil Kathleen M
Published: January 2023

Background

We evaluated the associations between baseline influenza virus–specific hemagglutination inhibition (HAI) and microneutralization (MN) titers and subsequent symptomatic influenza virus infection in a controlled human infection study.

Methods

We inoculated unvaccinated healthy adults aged 18–49 years with an influenza A/California/04/2009/H1N1pdm-like virus (NCT04044352). We collected serial safety labs, serum for HAI and MN, and nasopharyngeal swabs for reverse-transcription polymerase chain reaction (RT-PCR) testing. Analyses used the putative seroprotective titer of ≥40 for HAI and MN. The primary clinical outcome was mild-to-moderate influenza disease (MMID), defined as ≥1 postchallenge positive qualitative RT-PCR test with a qualifying symptom/clinical finding.

Results

Of 76 participants given influenza virus challenge, 54 (71.1%) experienced MMID. Clinical illness was generally very mild. MMID attack rates among participants with baseline titers ≥40 by HAI and MN were 64.9% and 67.9%, respectively, while MMID attack rates among participants with baseline titers <40 by HAI and MN were 76.9% and 78.3%, respectively. The estimated odds of developing MMID decreased by 19% (odds ratio, 0.81 [95% confidence interval, .62–1.06]; P = .126) for every 2-fold increase in baseline HAI. There were no significant adverse events.

Conclusions

We achieved a 71.1% attack rate of MMID. High baseline HAI and MN were associated with protection from illness.

Clinical Trials Registration. NCT04044352.
Striking differences in weight gain after cART initiation depending on early or advanced presentation: results from the ANRS CO4 FHDH cohort
Authors: Grabar Sophie , Potard Valérie , Piroth Lionel , Abgrall Sophie , Bernard Louis , Allavena Clotilde , Caby Fabienne , de Truchis Pierre , Duvivier Claudine , Enel Patricia , Katlama Christine , Khuong Marie-Aude , Launay Odile , Matheron Sophie , Melica Giovanna , Melliez Hugues , Meynard Jean-Luc , Pavie Juliette , Slama Laurence , Bregigeon Sylvie , Tattevin Pierre , Capeau Jacqueline , Costagliola Dominique
Published: January 2023

Background

Many studies have reported weight gain in ART-naive people living with HIV (PWH) initiating an integrase strand-transfer inhibitor-based regimen. We studied the impact of early or advanced presentation and that of individual drugs in PWH initiating combined ART (cART) between 2012 and 2018.

Methods

From the French Hospital Database HIV cohort, we assessed factors associated with a weight gain  ≥10%, weight change after cART initiation or BMI increase  ≥5 kg/m2 up to 30 months. The analyses were conducted overall, and among PWH with early (primary infection or CD4 >350/mm3 and viral load  <100 000 copies/mL, without AIDS) and advanced presentation (AIDS or CD4 <200/mm3, not during primary infection).

Results

At 30 months, 34.5% (95% CI: 33.5–35.6) of the 12 773 PWH had a weight gain ≥10%, with 20.9% (95% CI: 19.6–22.2) among the 5794 with early presentation and 63.1% (95% CI: 60.9–65.3) among the 3106 with advanced presentation. Weight gain was 2.8 kg (95% CI: 2.0–3.7) for those with early presentation and 9.7 kg (95% CI: 8.4–11.1) for those with advanced presentation. Most weight gain occurred in the first 12 months. Underweight and obese PWH were at significantly higher risk of a BMI increase  ≥5 kg/m2 than normal-weight PWH. Results differed within classes and by outcome. Raltegravir and dolutegravir were consistently associated with greater weight gain than the other third agents. Tenofovir alafenamide was also associated with higher weight gain than tenofovir disoproxil or abacavir.

Conclusions

After initiating cART, PWH with early presentation exhibited a small weight gain, whereas it was large among those with advanced presentation. The choice of ART should account for the risk of weight gain, especially for PWH who present with advanced disease and/or are obese.
Bayesian multistate modelling of incomplete chronic disease burden data
Authors: Jackson Christopher , Zapata-Diomedi Belen , Woodcock James
Published: January 2023

The ‘multistate lifetable’ is a widely used model for the long-term health impacts of public health interventions. It requires estimates of the incidence, case fatality, and sometimes also remission rates, for multiple diseases by age and gender. The case fatality is the rate of death from a disease for people with a disease, and is commonly not observed directly. Instead, we often observe the mortality in the general population. Similarly, we might know the disease prevalence, but not the incidence. This paper presents Bayesian continuous-time multistate models for estimating transition rates between disease states based on incomplete data. It unifies and extends two previous methods, by using a formal statistical model, with more efficient computational algorithms. This allows rates for different ages, areas, and time periods to be related in more flexible ways, and allows models to be formally checked and compared. The methods are made more widely usable through an R package. The models are used to estimate case fatality for multiple diseases in the city regions of England, based on incidence, prevalence, and mortality data from the Global Burden of Disease study. The estimates can be used to inform health impact models relating to those diseases and areas.
Disease severity and genotype–phenotype correlation in adult patients with familial Mediterranean fever
Authors: Tuncer Kuru Fatma , Gokcen Neslihan , Yazici Ayten , Cefle Ayse
Published: January 2023

Objectives

To assess the relationships of disease severity with genotype and phenotype in adult familial Mediterranean fever patients.

Methods

Two-hundred seventy-five patients included in the study were divided into four groups according to their mutations: Group 1, M694V homozygous; Group 2, M694V–other; Group 3, other–other; and Group 4, no meaningful gene variants. Disease severity was evaluated using the Pras disease severity score. The association between Pras scores and other possible predictors was assessed by the multiple linear regression analysis.

Results

In this study, 12.4% of all patients were in Group 1, 55.3% were in Group 2, 26.5% were in Group 3, and 5.8% were in Group 4. Pras scores were higher in Group 1 than in Groups 2, 3, and 4 (post hoc pairwise comparisons; P = .001, P < .001, and P = .001, respectively). Age at disease onset and age at diagnosis were found moderately and strongly correlated with Pras scores. Patients with moderate and severe disease were intensely involved in Group 1.

Conclusions

Higher Pras scores, earlier age of symptoms and diagnosis, more frequent arthritis and erysipelas-like erythema, and higher colchicine dose are closely associated with M694V homozygous familial Mediterranean fever patients. These patients also have mostly moderate and severe disease severity.
Hyperglobulinemia predicts increased risk of mortality in primary Sjögren’s syndrome: Based on a Chinese multicentre registry
Authors: Zhong Hui , Wang Yanhong , Yang Pingting , Duan Xinwang , Wang Yongfu , Xu Jian , Wu Lijun , Li Qin , Kong Xiaodan , Zhang Liyun , Li Xiaomei , Xu Dong , Li Mengtao , Zhao Yan , Zeng Xiaofeng
Published: January 2023

Objective

To investigate whether primary Sjögren’s syndrome (pSS) patients with hyperglobulinemia have an increased risk of all-cause mortality.

Methods

Patients who registered in the Chinese Rheumatism Data Centre from May 2016 to July 2021 and met the 2002 American European Consensus Group criteria or 2016 American College of Rheumatology /European League Against Rheumatism classification criteria for Sjögren’s syndrome were included. Hyperglobulinemia was defined as any elevated serum levels of immunoglobulin G (IgG), immunoglobulin A (IgA), or immunoglobulin M (IgM). The primary outcome was all-cause death. Data for demographic and clinical characteristics, laboratory results, disease activity, damage scores, and treatments were evaluated.

Results

A total of 9527 pSS patients were included in the analysis, of whom 4236 (44.5%) had at least one kind of elevated immunoglobulin level among IgG, IgA, and IgM. Patients with hyperglobulinemia had a significantly increased risk of death (crude hazard ratio 2.60; 95% confidence interval 1.91–3.55; adjusted hazard ratio 1.90; 95% confidence interval 1.20–3.01). The risk of death was positively correlated with IgG level (P trend <.001). The 5-, 10-, and 15-year survival rates of patients with hyperglobulinemia were 96.9%, 92.3%, and 87.9%, respectively, and significantly lower than the corresponding rates of 98.8%, 97.9%, and 96.4% in patients without hyperglobulinemia.

Conclusions

Hyperglobulinemia is an independent risk factor for increased all-cause mortality in pSS patients. The risk of death is positively correlated with IgG level.
Clinical Correlation of Adenoviral Load in the Respiratory Tract Measured by Digital PCR in Immunocompromised Children
Authors: Hijano Diego R , Ferrolino Jose A , Hidinger Jennifer , Brazelton Jessica N , Gu Zhengming , Suganda Sri , Glasgow Heather L , Allison Kim J , Peterson Megan , Dallas Ronald H , Maron Gabriela , Hayden Randall T
Published: January 2023

Immunocompromised patients can have life-threatening adenoviral infection. Viral load in blood and stool is commonly used to guide antiviral therapy. We developed and evaluated a digital polymerase chain reaction assay to quantify human adenovirus in the respiratory tract and showed that higher peak load correlates with disseminated infection, mechanical ventilation, and death.