bluuebunny/crossref_metadata_2025 huggingface dataset:
Δ-Learning applied to coarse-grained homogeneous liquids
Authors: Khot Aditi , Savoie Brett M.
Published: August 2023

Coarse-grained molecular dynamics (CGMD) simulations address lengthscales and timescales that are critical to many chemical and material applications. Nevertheless, contemporary CGMD modeling is relatively bespoke and there are no black-box CGMD methodologies available that could play a comparable role in discovery applications that density functional theory plays for electronic structure. This gap might be filled by machine learning (ML)-based CGMD potentials that simplify model development, but these methods are still in their early stages and have yet to demonstrate a significant advantage over existing physics-based CGMD methods. Here, we explore the potential of Δ-learning models to leverage the advantages of these two approaches. This is implemented by using ML-based potentials to learn the difference between the target CGMD variable and the predictions of physics-based potentials. The Δ-models are benchmarked against the baseline models in reproducing on-target and off-target atomistic properties as a function of CG resolution, mapping operator, and system topology. The Δ-models outperform the reference ML-only CGMD models in nearly all scenarios. In several cases, the ML-only models manage to minimize training errors while still producing qualitatively incorrect dynamics, which is corrected by the Δ-models. Given their negligible added cost, Δ-models provide essentially free gains over their ML-only counterparts. Nevertheless, an unexpected finding is that neither the Δ-learning models nor the ML-only models significantly outperform the elementary pairwise models in reproducing atomistic properties. This fundamental failure is attributed to the relatively large irreducible force errors associated with coarse-graining that produces little benefit from using more complex potentials.
Heat capacity changes associated with G-quadruplex unfolding
Authors: Garabet Arees , Liu Lutan , Chalikian Tigran V.
Published: August 2023

G-quadruplexes are four-stranded DNA structures that have been found in the cell and are thought to act as elements of control in genomic events. The measurements of the thermodynamic stability, ΔG, of G-quadruplexes shed light on the molecular forces involved in the stabilization of these structures. In thermodynamic studies, the differential heat capacity, ΔCP, of the folded and unfolded states of a G-quadruplex is a fundamental property that describes the temperature dependences of the differential enthalpy, ΔH, entropy, ΔS, and free energy, ΔG. Despite its recognized importance, the ΔCP of G-quadruplex unfolding has not been measured directly. Here, we use differential scanning calorimetry to evaluate changes in heat capacity, ΔCP, accompanying the unfolding transitions of G-quadruplexes formed by modified DNA sequences from the promoter regions of the c-MYC, VEGF, and Bcl-2 oncogenes. The average value of ΔCP is 0.49 ± 0.12 kcal mol−1 K−1. Our analysis revealed that disregarding ΔCP leads to significant errors in extrapolated values of the differential enthalpy, ΔH, and entropy, ΔS, of the folded and unfolded DNA conformations. Although the compensation between ΔH and ΔS weakens the effect of ΔCP on the differential free energy, ΔG, neglecting ΔCP may still result in relative errors in ΔG extrapolated to room temperature as great as 140%. We emphasize the importance of proper consideration of the effect of ΔCP in conformational studies of guanine-rich DNA molecules.
A stretchable slippery surface fabricated by femtosecond laser direct writing
Authors: Zhang Jialiang , Yang Qing , Ma Qingyun , Ren Fangzheng , Li Haoyu , Zhang Chengjun , Cheng Yang , Chen Feng
Published: August 2023

Surface conditions of flexible electronic devices can affect their accuracy, so it is necessary to keep surfaces clean and stable to ensure their correct-long-term operation. The Nepenthes-inspired slippery surface has excellent self-cleaning, stability, and self-healing properties. A slippery surface with stretching durability is significant for application to a flexible sensors surface. As an advanced micro-nanomanufacturing method, femtosecond laser has become an effective method for preparing porous structures to process a slippery surface. In this study, a femtosecond laser was used to prepare an interconnected porous structure on pre-stretched polydimethylsiloxane in one step. The slippery surface was prepared after being infused with lubricant, which maintained the slippery performance under tensile conditions and after hundreds of stretch cycles. Moreover, it exhibits remarkable self-cleaning and chemical stability. This stretchable slippery surface prepared by femtosecond laser direct writing presents good prospects for flexible electronic devices that require a stable surface in various extreme environmental applications.
Particle migration behavior of fractured lost circulation control: Numerical simulation
Authors: Liu Qinglin , Xu Peng , Wen Fei , Xu Mingbiao , Pu Lei , Dai Baimei , Xu Lin
Published: August 2023

Fracture loss is the most common type of leakage in petroleum drilling engineering. The existing numerical simulation of the particle transport process is relatively simplified. In order to clarify the dynamic behavior characteristics of bridging particles in fractures, this paper adopts the discrete element and computational fluid dynamics coupling numerical simulation methods to establish a bidirectional coupling numerical model of bridging particles and drilling fluid to simulate the dynamic evolution process of bridging plugging particles, such as migration, bridging, and accumulation. The results show that the main factors affecting the transport pattern of plugging particles in the fracture are differential pressure, particle size, drilling fluid viscosity, drilling fluid density, fracture width, and fracture length. The drilling fluid density has a small effect on the inter-particle force in the fracture; the drilling fluid viscosity mainly affects the resistance of the particles, and the pressure difference between the inlet and outlet of the fracture mainly affects the transport speed of the particles. The particle size determines whether a plugging layer can be formed, and the best plugging effect is achieved when the particle size is 1/2 of the fracture width.
Numerical study of the hydrodynamic stability of a wind-turbine airfoil with a laminar separation bubble under free-stream turbulence
Authors: Fava T. C. L. , Lobo B. A. , Nogueira P. A. S. , Schaffarczyk A. P. , Breuer M. , Henningson D. S. , Hanifi A.
Published: August 2023

The interaction of several instabilities and the influence of free-stream turbulence on laminar-turbulent transition on a 20% thick wind-turbine blade section with a laminar separation bubble (LSB) are investigated with wall-resolved large-eddy simulations (LES). Turbulence intensities (TI) of 0%, 2.2%, 4.5%, 8.6%, and 15.6% at chord Reynolds number 105 are considered. Linear receptivity occurs for the most energetic disturbances; high-frequency perturbations are excited via non-linear mechanisms for TI≥8.6%. Unstable Tollmien–Schlichting (TS) waves appear in the inflectional flow region for TI≤4.5%, shifting to inviscid Kelvin–Helmholtz (KH) modes upon separation and forming spanwise rolls. Sub-harmonic secondary instability occurs for TI=0%, with rolls intertwining before transition. Streaks spanwise modulate the rolls and increase their growth rates with TI for TI≤4.5%, reducing separation and shifting transition upstream. The TI=4.5% case presents the highest perturbations, leading to the smallest LSB and most upstream transition. Earlier inception of TS/KH modes occurs on low-speed streaks, inducing premature transition. However, for TI=8.6%, the effect of the streaks is to stabilize the attached mean flow and front part of the LSB. This occurs due to the near-wall momentum deficit alleviation, leading to the transition delay and larger LSB than TI=4.5%. This also suppresses separation and completely stabilizes TS/KH modes for TI=15.6%. Linear stability theory predicts well the modal evolution for TI≤8.6%. Optimal perturbation analysis accurately computes the streak development upstream of the inflectional flow region but indicates higher amplification than LES downstream due to the capture of low-frequency, oblique modal instabilities from the LSB. Only low-amplitude [O(1%)] streaks displayed exponential growth in the LES since non-linearity precludes the appearance of these modes.
Enhanced tunneling electroresistance in multiferroic tunnel junctions through the barrier insulating-metallic transition: A first-principles study
Authors: Chi Boyuan , Jiang Leina , Zhu Yu , Tao Lingling , Han Xiufeng
Published: August 2023

The tunneling electroresistance (TER) ratio is an important device merit of ferroelectric tunnel junction (FTJ) and multiferroic tunnel junction (MFTJ) devices. Here, through first-principles calculations, we propose an efficient way to achieve a sizable TER effect through the interface engineering in both SrRuO3/PbTiO3/FeO/Fe and SrRuO3/PbTiO3/CoO/Co MFTJs. It is found that the interfacial FeO or CoO layer can significantly modify the band alignment between PbTiO3 barrier and electrodes through its large depolarization field, causing the insulating–metallic transition of PbTiO3 barrier upon polarization reversal. As a result, the tunneling resistance changes significantly, leading to a giant TER effect of 105%. Our results suggest a practical way to enhance the TER effect in MFTJs.
Tidal turbine development ebbs and flows
Authors: Berkowitz Rachel
Published: August 2023

The renewable energy technology can benefit remote coastal communities that want to reduce carbon emissions.
Electrons see the guiding light
Authors: Miao Bo , Shrock Jaron , Milchberg Howard
Published: August 2023

To accelerate electrons to multi-GeV energies with lasers, keep the bright light tight.
Optogenetic clustering and membrane translocation of the BcLOV4 photoreceptor
Authors: Pal Ayush Aditya , Benman William , Mumford Thomas R. , Huang Zikang , Chow Brian Y. , Bugaj Lukasz J.
Published: August 2023

Optogenetic tools respond to light through one of a small number of behaviors including allosteric changes, dimerization, clustering, or membrane translocation. Here, we describe a new class of optogenetic actuator that simultaneously clusters and translocates to the plasma membrane in response to blue light. We demonstrate that dual translocation and clustering of the BcLOV4 photoreceptor can be harnessed for novel single-component optogenetic tools, including for control of the entire family of epidermal growth factor receptor (ErbB1-4) tyrosine kinases. We further find that clustering and membrane translocation are mechanistically linked. Stronger clustering increased the magnitude of translocation and downstream signaling, increased sensitivity to light by ~threefold-to-fourfold, and decreased the expression levels needed for strong signal activation. Thus light-induced clustering of BcLOV4 provides a strategy to generate a new class of optogenetic tools and to enhance existing ones.
A Mediator subunit imparts robustness to a polyphenism decision
Authors: Casasa Sofia , Katsougia Eleni , Ragsdale Erik J.
Published: August 2023

Polyphenism is a type of developmental plasticity that translates continuous environmental variability into discontinuous phenotypes. Such discontinuity likely requires a switch between alternative gene-regulatory networks, a principle that has been borne out by mechanisms found to promote morph-specific gene expression. However, whether robustness is required to execute a polyphenism decision has awaited testing at the molecular level. Here, we used a nematode model for polyphenism,
Pristionchus pacificus
, to identify the molecular regulatory factors that ensure the development of alternative forms. This species has a dimorphism in its adult feeding structures, specifically teeth, which are a morphological novelty that allows predation on other nematodes. Through a forward genetic screen, we determined that a duplicate homolog of the Mediator subunit MDT-15/MED15,
P. pacificus
MDT-15.1, is necessary for the polyphenism and the robustness of the resulting phenotypes. This transcriptional coregulator, which has a conserved role in metabolic responses to nutritional stress, coordinates these processes with its effects on this diet-induced polyphenism. Moreover, this MED15 homolog genetically interacts with two nuclear receptors, NHR-1 and NHR-40, to achieve dimorphism: Single and double mutants for these three factors result in morphologies that together produce a continuum of forms between the extremes of the polyphenism. In summary, we have identified a molecular regulator that confers discontinuity to a morphological polyphenism, while also identifying a role for MED15 as a plasticity effector.
Recent advances on low-Co and Co-free high entropy layered oxide cathodes for lithium-ion batteries
Authors: Yu Binkai , Wang Yuqiu , Li Jiaqi , Jin Yuqin , Liang Zixin , Zhou Limin , Chen Mingzhe
Published: August 2023

As the price of the precious metal cobalt continues to rise, there is an urgent need for a cobalt-free or low-cobalt electrode material to reduce the cost of lithium-ion batteries, which are widely used commercially, while maintaining their performance as much as possible. With the introduction of the new concept of high entropy (HE) materials into the battery field, low cobalt and cobalt free HE novel lithium-ion batteries have attracted great attention. It possesses important research value to use HE materials to reduce the use of cobalt metal in electrode materials. In this perspective, the comparison between the new cathode materials of low cobalt and cobalt-free HE lithium-ion battery and traditional cathode materials and the latest progress in maintaining structural stability and conductivity are introduced. It is believed that low cobalt and cobalt-free and HE layered oxides can be used to replace the function of cobalt in the cathode materials of lithium-ion batteries. Finally, the future research directions and the synthesis method of HE cathode materials for lithium-ion batteries are also discussed.
Novel synthetic approach of 2D-metal–organic frameworks (MOF) for wastewater treatment
Authors: Nath Nibedita , Chakroborty Subhendu , Pal Kaushik , Barik Arundhati , Soren Siba
Published: August 2023

In addition to their adjustable functionality, structural tunability, and compositional tunability, metal–organic frameworks (MOFs), often known as MOFs, are a distinct form of crystalline porous material. When reduced to two dimensions, ultrathin layers of MOF retain more of its fantastic external features, which is beneficial for a variety of technological applications. Due to their ultrathin atomic-level thickness, easily modifiable structure, and huge surface area, 2D MOF nanosheets and nanocomposites have been the subject of significant research. MOFs are considered intriguing materials for removing toxic contaminants among the novel technologies taken into account in water remediation processes because they exhibit numerous qualities that make them advantageous in water treatment: large surface area, easily functionalizable cavities, a few stable in water, large-scale synthesis, etc Nowadays, water pollution is a rising environmental concern that must be addressed. Due to their special qualities, which include chemical activities, a variety of functionalities, excellent stability, and the ability to be modified for the detection or adsorption of particular molecules, MOFs are widely used in detecting and removing contaminants from water. This review explores most recent wastewater treatment advancements (WWT) using the 2D MOFs mechanism.
Introducing chaos theory with Arduinos and sounds
Authors: Perea Martins J E M
Published: August 2023

This work aims to create a motivational environment to introduce basic principles of chaos theory, using an Arduino to simultaneously generate a graph and sounds associated with the logistic map behaviour. It presents a basic theory review, and the hardware and software aspects required for a pragmatic approach in the classroom.
Barometric characterization of a draining container
Authors: Salinas Isabel , Muñoz-Pérez Francisco M , Castro-Palacio Juan C , Velazquez Luisberis , Monsoriu Juan A
Published: August 2023

A characterization of a draining container is performed by measuring the pressure change at its bottom while the container drains through a small orifice. The Physics model is based on the continuity equation and Bernoulli’s principle. The pressure is measured with the barometer of the smartphone which is placed inside a hermetically sealed bag and laid at the bottom of the container. The expected theoretical relationship between the pressure at the bottom of the container and time was observed. The value for the coefficient of discharge is also estimated. The results of a survey applied to students and teachers at secondary school level indicate that the use of the pressure sensor of the smartphones helped the students to understand the basic concepts of hydrostatics and hydrodynamics at the same time their motivation for physics was increased.
A review on transport characteristics and bio-sensing applications of silicene
Authors: Ghosal Supriya , Bandyopadhyay Arka , Chowdhury Suman , Jana Debnarayan
Published: August 2023

Silicene, a silicon counterpart of graphene, has been predicted to possess Dirac fermions. The effective spin–orbit interaction in silicene is quite significant compared to graphene; as a result, buckled silicene exhibits a finite band gap of a few meV at the Dirac point. This band gap can be further tailored by applying in plane strain, an external electric field, chemical functionalization and defects. This special feature allows silicene and its various derivatives as potential candidates for device applications. In this topical review, we would like to explore the transport features of the pristine silicene and its possible nano derivatives. As a part of it, Thermoelectric properties as well as several routes for thermoelectric enhancement in silicene are investigated. Besides, the recent progress in biosensing applications of silicene and its hetero-structures will be highlighted. We hope the results obtained from recent experimental and theoretical studies in silicene will setup a benchmark in diverse applications such as in spintronics, bio-sensing and opto-electronic devices.
Constraining study of circular orbits and accretion disk around nonlinear electrodynamics black hole
Authors: Ditta A. , Mustafa G. , Abbas G. , Atamurotov Farruh , Jusufi Kimet
Published: August 2023

The very latest observation of M87 supermassive black hole (BH) by the Event Horizon Telescope (EHT) provides the accretion onto BHs is an interesting study in the theory of gravity. We study the geodesics structure and accretion near a nonlinear electrodynamics BH in strong and weak field approximations. These approximations provide the disc-like structure under the geodesic motion and accretion around the BH. Near the equatorial plane, we provide some new reasons to make circular orbits and accretion of test particles around the BH. Then we investigate perturbations, the critical speed of the fluid and the mass accretion rate of particles around the central object. The physical validity of this study shows that the parameter β and Q play an important role in the circular orbits and the mass accretion rate in strong and weak field approximations.
JWST MIRI Flight Performance: Detector Effects and Data Reduction Algorithms
Authors: Morrison Jane E. , Dicken Daniel , Argyriou Ioannis , Ressler Michael E. , Gordon Karl D. , Regan Michael W. , Cracraft Misty , Rieke George H. , Engesser Michael , Alberts Stacey , Alvarez-Marquez Javier , Colbert James W. , Fox Ori D. , Gasman Danny , Law David R. , Garcia Marin Macarena , Gáspár András , Guillard Pierre , Kendrew Sarah , Labiano A. , Laine Seppo , Noriega-Crespo A. , Shivaei Irene , Sloan G. C.
Published: August 2023

The detectors in the Mid-Infrared Instrument (MIRI) of the James Webb Space Telescope (JWST) are arsenic-doped silicon impurity band conduction (Si:As IBC) devices and are direct descendants of the Spitzer IRAC long wavelength arrays (channels 3 and 4). With appropriate data processing, they can provide excellent performance. In this paper we discuss the various non-ideal behaviors of these detectors that need to be addressed to realize their potential. We have developed a set of algorithms toward this goal, building on experience with previous similar detector arrays. The MIRI-specific stage 1 pipeline algorithms, of a three stage JWST calibration pipeline, were developed using pre-flight tests on the flight detectors and flight spares and have been refined using flight data. This paper describes these algorithms, which are included in the first stage of the JWST Calibration Pipeline for the MIRI instrument.
The MPI + CUDA Gaia AVU–GSR Parallel Solver Toward Next-generation Exascale Infrastructures
Authors: Cesare Valentina , Becciani Ugo , Vecchiato Alberto , Lattanzi Mario Gilberto , Pitari Fabio , Aldinucci Marco , Bucciarelli Beatrice
Published: August 2023

We ported to the GPU with CUDA the Astrometric Verification Unit–Global Sphere Reconstruction (AVU–GSR) Parallel Solver developed for the ESA Gaia mission, by optimizing a previous OpenACC porting of this application. The code aims to find, with a [10, 100] μarcsec precision, the astrometric parameters of ∼108 stars, the attitude and instrumental settings of the Gaia satellite, and the global parameter γ of the parametrized Post-Newtonian formalism, by solving a system of linear equations, A ×
x
=
b
, with the LSQR iterative algorithm. The coefficient matrix A of the final Gaia data set is large, with ∼1011 × 108 elements, and sparse, reaching a size of ∼10–100 TB, typical for the Big Data analysis, which requires an efficient parallelization to obtain scientific results in reasonable timescales. The speedup of the CUDA code over the original AVU–GSR solver, parallelized on the CPU with MPI + OpenMP, increases with the system size and the number of resources, reaching a maximum of ∼14×, >9× over the OpenACC application. This result is obtained by comparing the two codes on the CINECA cluster Marconi100, with 4 V100 GPUs per node. After verifying the agreement between the solutions of a set of systems with different sizes computed with the CUDA and the OpenMP codes and that the solutions showed the required precision, the CUDA code was put in production on Marconi100, essential for an optimal AVU–GSR pipeline and the successive Gaia Data Releases. This analysis represents a first step to understand the (pre-)Exascale behavior of a class of applications that follow the same structure of this code. In the next months, we plan to run this code on the pre-Exascale platform Leonardo of CINECA, with 4 next-generation A200 GPUs per node, toward a porting on this infrastructure, where we expect to obtain even higher performances.
Satellite NO2 trends reveal pervasive impacts of wildfire and soil emissions across California landscapes
Authors: Wang Yurun , Faloona Ian C , Houlton Benjamin Z
Published: August 2023

Nitrogen dioxide (NO2) plays a pivotal role in the production of secondary pollutants, most importantly ozone (O3) and particulate matter. Regulatory controls have greatly reduced NO2 in cities, where most of the surface monitoring occurs, but the change in rural environments is less certain. Here, we present summertime (June–September) spatio-temporal patterns of NO2 concentrations using satellite and ground observations across California from 2009–2020, quantifying the differences in NO2 trends for five distinct land cover classes: urban, forests, croplands, scrublands (shrublands, savannas, and grasslands), and barren (minimally vegetated) lands. Over urban environments, NO2 columns exhibited continued but weakening downward trends (−3.7 ± 0.3%a−1), which agree fairly well with contemporaneous trends estimated from the surface air quality network (−4.5 ± 0.5%a−1). In rural (i.e., non-urban) parts of the state, however, secular trends are insignificant (0.0–0.4 ± 0.4%a−1) or in the case of remote forests are rapidly on the rise (+4.2 ± 1.2%a−1). Sorting the NO2 columns by air temperature and soil moisture reveals relationships that are commensurate with extant parameterizations but do indicate a stronger temperature dependence. We further find that rapidly rising temperatures and, to a lesser extent, decreasing precipitation in response to climate change are acting to increase soil NO
x
emissions, explaining about one-third of the observed NO2 rise in non-urban regions across California. Finally, we show that these trends, or their absence, can be attributed predominantly to the dramatic rise in wildfire frequency, especially since the turn of the 21st century.
Low flow sensitivity to water withdrawals in Central and Southwestern Europe under 2 K global warming
Authors: Greve Peter , Burek Peter , Guillaumot Luca , van Meijgaard Erik , Aalbers Emma , Smilovic Mikhail M , Sperna-Weiland Frederiek , Kahil Taher , Wada Yoshihide
Published: August 2023

A sufficient freshwater supply is vital for humans, ecosystems, and economies, but anticipated climate and socio-economic change are expected to substantially alter water availability. Across Europe, about two-third of the abstracted freshwater comes from rivers and streams. Various hydrological studies address the resulting need for projections on changes in river discharge. However, those assessments rarely specifically account for the impact of various water withdrawal scenarios during low flow periods. We present here a novel, high-resolution hydrological modeling experiment using pseudo-global warming climate data to investigate the effects of changing water withdrawals under 2 K global warming. Especially in Western and Central Europe the projected impacts on low flows highly depend on the chosen water withdrawal assumption and can severely decrease under the worst case assumptions. Our results highlight the importance of accounting for future water withdrawals in low flow projections, showing that climate-focused impact assessments in near-natural catchments provide only one piece of the anticipated response and do not necessarily reflect changes in heavily managed river basins.
Fire, frost, and drought constrain the structural diversity of wood within southern African Erica (Ericaceae)
Authors: Akinlabi F M , Pirie M D , Oskolski A A
Published: August 2023

Erica comprises ~860 species of evergreen shrubs and trees ranged from Europe to southern Africa and Madagascar. Wood structure of the around 20 European species is well studied, but despite its relevance to adaptation across the wider geographic range, it has not yet been explored across the much greater diversity, particularly of southern African lineages. In this study, we examine wood structure of 28 Erica species from southern Africa. In the African Erica clade, loss of scalariform perforation plates could be driven by increased aridity and seasonality in the mid-Miocene, and its re-gain can represent an adaptation to freezing in the high elevation species E. nubigena. As vessels in Erica are mostly solitary, imperforate tracheary elements probably form a subsidiary conduit network instead of vessel groups. Increase of ray frequency in habitats with a prominent dry and hot season probably facilitates refilling of vessels after embolism caused by water stress. Wider rays are ancestral for the lineage comprising African Erica and the Mediterranean E. australis. The negative correlation between ray width and expression of summer drought is consistent with Ojeda’s model explaining the diversification of seeders and resprouters among southern African Erica.
Gender-specific resting-state rDMPFC-centric functional connectivity underpinnings of intertemporal choice
Authors: Lv Chenyu , Xiao Zhibing , Sun Yachen , Zhang Rong , Feng Tingyong , Turel Ofir , He Qinghua
Published: August 2023

Although studies have observed gender differences in intertemporal choice, the neural bases of these differences require further research. The current study used resting state functional connectivity (rsFC) to explore the gender-specific neural basis of intertemporal choice in three independent samples (n1 = 86, n2 = 297, n3 = 172). Behaviorally, three samples (S1, S2, and S3) consistently demonstrated that men had larger delay discounting rate (log k) than women. Then, whole-brain functional connectivity analyses were performed for different genders in S2 and S3 using the right dorsomedial prefrontal cortex (rDMPFC) as a region of interest. By subtracting the common rsFC patterns of different genders, we identified gender-specific log k-related rsFC patterns with significant gender differences in S2. This was verified in an independent sample (S3). Specifically, in women, log k was found to be positively correlated with the rsFC between rDMPFC and anterior cingulate cortex/right orbitofrontal cortex. In contrast, in men, log k was negatively correlated with rsFC between rDMPFC and left orbitofrontal cortex/right precuneus. These gender differences were confirmed by slope tests. The findings highlight how gender may differ when engaging in intertemporal choice. They improve the understanding of gender differences in decision impulsivity and its underlying neural bases.
Neural retrieval processes occur more rapidly for visual mental images that were previously encoded with high-vividness
Authors: Gjorgieva Eva , Morales-Torres Ricardo , Cabeza Roberto , Woldorff Marty G
Published: August 2023

Visual mental imagery refers to our ability to experience visual images in the absence of sensory stimulation. Studies have shown that visual mental imagery can improve episodic memory. However, we have limited understanding of the neural mechanisms underlying this improvement. Using electroencephalography, we examined the neural processes associated with the retrieval of previously generated visual mental images, focusing on how the vividness at generation can modulate retrieval processes. Participants viewed word stimuli referring to common objects, forming a visual mental image of each word and rating the vividness of the mental image. This was followed by a surprise old/new recognition task. We compared retrieval performance for items rated as high- versus low-vividness at encoding. High-vividness items were retrieved with faster reaction times and higher confidence ratings in the memory judgment. While controlling for confidence, neural measures indicated that high-vividness items produced an earlier decrease in alpha-band activity at retrieval compared with low-vividness items, suggesting an earlier memory reinstatement. Even when low-vividness items were remembered with high confidence, they were not retrieved as quickly as high-vividness items. These results indicate that when highly vivid mental images are encoded, the speed of their retrieval occurs more rapidly, relative to low-vivid items.
Personalized and Population-Based Reference Intervals for 48 Common Clinical Chemistry and Hematology Measurands: A Comparative Study
Authors: Coşkun Abdurrahman , Sandberg Sverre , Unsal Ibrahim , Cavusoglu Coskun , Serteser Mustafa , Kilercik Meltem , Aarsand Aasne K
Published: August 2023

Background

Personalized reference intervals (prRIs) have the potential to improve individual patient follow-up as compared to population-based reference intervals (popRI). In this study, we estimated popRI and prRIs for 48 clinical chemistry and hematology measurands using samples from the same reference individuals and explored the effect of using group-based and individually based biological variation (BV) estimates to derive prRIs.

Methods

143 individuals (median age 28 years) were included in the study and had fasting blood samples collected once. From this population, 41 randomly selected subjects had samples collected weekly for 5 weeks. PopRIs were estimated according to Clinical Laboratory Standards Institute EP28 and within-subject BV (CVI) were estimated by CV-ANOVA. Data were assessed for trends and outliers prior to calculation of individual prRIs, based on estimates of (a) within-person BV (CVP), (b) CVI derived in this study, and (c) publically available CVI estimates.

Results

For most measurands, the individual prRI ranges were smaller than the popRI range, but overall about half the study participants had a prRI wider than the popRI for 5 or more out of 48 measurands. The dispersion of prRIs based on CVP was wider than that of prRIs based on CVI.

Conclusion

The prRIs derived in our study varied significantly between different individuals, especially if based on CVP. Our results highlight the limitations of popRIs in interpreting test results of individual patients. If sufficient data from a steady-state situation are available, using prRI based on CVP estimates will provide a RI most specific for an individual patient.
Long-term neurodevelopmental outcome and serial cerebral magnetic resonance imaging assessment in Fontan patients at school age
Authors: Reich Bettina , Schwan Sabrina , Heye Kristina , Logeswaran Thushiha , Hahn Andreas , Götschi Andrea , Held Ulrike , Wetterling Kristina , Steger Celine , Kottke Raimund , Latal Beatrice , Knirsch Walter
Published: August 2023

OBJECTIVES

Children with univentricular congenital heart disease undergoing staged surgical palliation are at risk for impaired neurodevelopmental (ND) outcome. Little is known about the long-term effects on brain growth until school age.

METHODS

In a prospective two-centre study, consecutive patients undergoing stage I (Hybrid or Norwood) to stage III (Fontan procedure) were evaluated by 2 serial cerebral magnetic resonance imaging examinations, somatic growth and ND testing before Fontan procedure at 2 years of age (Bayley-III) and after Fontan at 6–8 years of age (Wechsler Intelligence Scale for Children-third edition). Magnetic resonance imaging findings were compared with 8 healthy controls. Medical and sociodemographic characteristics were documented and related to cerebral and ND findings.

RESULTS

We examined 33 children (16 female) at a mean age of 2.3 (0.35) and 6.8 (± 0.7) years. The mean Bayley-III cognitive scales were 99.1 (9.9), language scales 98.4 (11.9) and motor scales 98.5 (13.8) at the first examination. Follow-up at school age showed a mean total IQ of 86.7 (13.6). The rate of structural brain lesions increased from 39% at 2 years to 58% at school age. Bayley-III language scale (P = 0.021) and mean Wechsler Intelligence Scale for Children-third edition (P = 0.019) were lower in children with pathological MR findings. Total brain volume (P < 0.001), total grey matter volume (P = 0.002), deep grey matter volume (P = 0.001) and white matter volume (P < 0.001) were smaller in patients compared to age- and gender-matched healthy controls.

CONCLUSIONS

Smaller brain volumes and structural brain lesions in complex congenital heart defect patients at school age are associated with impaired ND outcome. For the evaluation of predictive surgical or clinical factors, larger multicentre studies are needed.
Sex differences in cause-specific mortality: regional trends in seven European countries, 1996–2019
Authors: Sauerberg Markus , Klüsener Sebastian , Mühlichen Michael , Grigoriev Pavel
Published: July 2023

Background

Male excess mortality is mostly related to non-biological factors, and is thus of high social- and health-policy concern. Previous research has mainly focused on national patterns, while subnational disparities have been less in the focus. This study takes a spatial perspective on subnational patterns, covering seven European countries at the crossroad between Eastern and Western Europe.

Methods

We analyze a newly gathered spatially detailed data resource comprising 228 regions with well-established demographic methods to assess the contribution of specific causes of death to the evolution of sex mortality differentials (SMDs) since the mid-1990s.

Results

Our results show that declines in SMDs were mostly driven by a reduction of male excess mortality from cardiovascular diseases and neoplasms (about 50–60% and 20–30%, respectively). In Western Europe, trends in deaths from neoplasms contributed more to the reduction of SMDs, while among regions located in Eastern-Central Europe narrowing SMDs were mostly driven by changes in cardiovascular disease-related deaths. Moreover, men show up to three times higher mortality levels from external causes as compared to women in several analyzed regions. But in absolute terms, external deaths play only a minor role in explaining SMDs due to their small contribution to overall mortality.

Conclusions

We conclude that examining the regional development of SMDs is useful for introducing targeted social and health policies in order to reduce and prevent mortality inequalities between women and men.
Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages
Authors: Gangwal Aakriti , Kumar Nishant , Sangwan Nitika , Dhasmana Neha , Dhawan Uma , Sajid Andaleeb , Arora Gunjan , Singh Yogendra
Published: August 2023

Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein–protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
Zuo1, a ribosome-associated J protein, is involved in glucose repression in Saccharomyces cerevisiae
Authors: Yamada Yoichi , Shiroma Atsuki , Hirai Suguru , Iwasaki Jun
Published: August 2023

In Saccharomyces cerevisiae, the J-protein Zuo1 and the nonconventional Hsp70 homologue Ssz1 stimulate the ATPase activity of the chaperone proteins Ssb1 and Ssb2 (Ssb1/2), which are associated with the ribosomes. The dephosphorylation of sucrose nonfermenting 1 (Snf1) on Thr210 is required for glucose repression. The Ssb1/2 and 14–3-3 proteins Bmh1 and Bmh2 appear to be responsible for the dephosphorylation of Snf1 on Thr210 and glucose repression. Here, we investigated the role of Zuo1 in glucose repression. The zuo1∆ strain as well as the ssb1∆ssb2∆ strain exhibited a glucose-specific growth defect during logarithmic growth on glucose. Many of the respiratory chain genes examined were statistically significantly upregulated, but less than 2-fold, in the zuo1∆ strain as well as in the ssb1∆ssb2∆ strain on glucose. In addition, excessive phosphorylation of Snf1 on Thr210 was observed in the zuo1∆ strain as well as in the ssb1∆ssb2∆ strain in the presence of glucose. The mRNA levels of SSB1/2 and BMH1 were statistically significantly reduced by approximately 0.5- to 0.8-fold relative to the wild-type level in the zuo1∆ strain on glucose. These results suggest that Zuo1 is responsible for glucose repression, possibly by increasing the mRNA levels of SSB1/2 and BMH1 during growth on glucose.
Routine nasogastric tube placement in patients with small esophageal perforation after endoscopic foreign body removal may be unnecessary: a propensity score matching analysis
Authors: Liao Foqiang , Yang Qinyu , Zhan Zhenyi , Zhu Zhenhua , Pan Xiaolin , Wang Chong , Li Bimin , Zhu Yin , Chen Youxiang , Shu Xu
Published: July 2023

Background

Nasogastric tube (NGT) placement is part of the post-operative management of upper gastrointestinal perforation, but its routine use in esophageal perforation (EP) caused by foreign bodies remains unclear. The purpose of this research was to investigate the necessity for routine NGT placement in patients with EP after endoscopic foreign body removal.

Methods

A total of 323 patients diagnosed with EP caused by foreign bodies at the First Affiliated Hospital of Nanchang University between January 2012 and December 2021 were included in this retrospective study. Patients were divided into the NGT group and the non-NGT group according to whether or not NGT placement was performed. The perforation healing rate, post-operative adverse events, hospital stay, and death rate were analysed using a 1:1 propensity score matching model.

Results

Before matching, there were 263 patients in the NGT group and 60 patients in the non-NGT group. There were significant differences in the time to treatment, infection, albumin, and types of endoscopy between the two groups, while the length of hospital stay in the NGT group was significantly longer than that in the non-NGT group. After 1:1 propensity score matching, 48 pairs of patients were matched between the two groups. The perforation healing rate, post-operative adverse events, length of hospital stay, and death rate did not show significant differences between the two groups.

Conclusions

For patients with small EP caused by foreign bodies, routine NGT placement after endoscopic foreign body removal may be unnecessary.
Influence of partial saturation on bulk modulus and attenuation: the experiment and the theoretical model
Authors: He Lingyi , Ding Pinbo , Di Bangrang , Zhang Feng
Published: July 2023

Modelling the dispersion and attenuation of seismic waves in partially saturated rocks is important for quantitative interpretation of seismic data. To observe the partial saturation effects on modulus and attenuation, three sandstone samples with different porosities were used in the laboratory experiment. The samples were measured by ultrasonic testing system under different water saturation using drainage process. The experimental results show that the bulk modulus more rapidly increased at higher saturations (>80 per cent), and attenuation peaks could be observed. Then we develop a new partial saturation model based on Chapman’s theory and poroelastic theory. The new model is consistent with the Gassmann equation when the water saturation is 0 or 100 per cent. By analysing the characteristic frequency, the new model can be concluded in the form of a standard linear solid model. A comparison of the new model with the White model and the measured data is conducted. The results show that the model performed well at predicting the effective bulk modulus and attenuation of the rock with different water saturation. Finally, we discussed the impact of frequency, fluids and pore structures on the new model. The results reveal that the new model will be helpful in discussing partial saturation in rocks.
The Gaussian wave packet transform via quadrature rules
Authors: Bergold Paul , Lasser Caroline
Published: July 2023

We analyse the Gaussian wave packet transform. Based on the Fourier inversion formula and a partition of unity, which is formed by a collection of Gaussian basis functions, a new representation of square-integrable functions is presented. Including a rigorous error analysis, the variants of the wave packet transform are then derived by a discretization of the Fourier integral via different quadrature rules. Based on Gauss–Hermite quadrature, we introduce a new representation of Gaussian wave packets in which the number of basis functions is significantly reduced. Numerical experiments in 1D illustrate the theoretical results.
A matrix algebra approach to approximate Hessians
Authors: Hare Warren , Jarry-Bolduc Gabriel , Planiden Chayne
Published: July 2023

This work presents a novel matrix-based method for constructing an approximation Hessian using only function evaluations. The method requires less computational power than interpolation-based methods and is easy to implement in matrix-based programming languages such as MATLAB. As only function evaluations are required, the method is suitable for use in derivative-free algorithms. For reasonably structured sample sets, the method is proven to create an order-$1$ accurate approximation of the full Hessian. Under more specialized structures, the method is proved to yield order-$2$ accuracy. The underdetermined case, where the number of sample points is fewer than required for full interpolation, is studied and error bounds are developed for the resulting partial Hessians.
Decay of HIV RNA in Seminal Plasma and Rectal Fluid in Treatment-Naive Adults Starting Antiretroviral Therapy With Dolutegravir Plus Lamivudine or Bictegravir/Emtricitabine/Tenofovir Alafenamide
Authors: Scévola Sofía , Niubó Jordi , Domingo Pere , Verdejo Guillermo , Curran Adrian , Diaz-Brito Vicens , Peñafiel Judith , Tiraboschi Juan , Morenilla Sandra , Garcia Benito , Soriano Irene , Podzamczer Daniel , Imaz Arkaitz
Published: August 2023

Background

Decay of HIV in seminal plasma (SP) and rectal fluid (RF) has not yet been described for the antiretroviral combination of dolutegravir (DTG) + lamivudine (3TC).

Methods

In this randomized multicenter pilot trial, males who were antiretroviral naive were randomized (2:1) to DTG + 3TC or bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF). HIV-1 RNA was measured in blood plasma (BP), SP, and RF at baseline; days 3, 7, 14, and 28; and weeks 12 and 24.

Results

Of 25 individuals enrolled, 24 completed the study (DTG + 3TC, n = 16; BIC/FTC/TAF, n = 8). No significant differences were observed between groups for median decline in HIV-1 RNA from baseline at each time point or median time to achieve HIV-1 RNA <20 copies/mL in BP and SP and <20 copies/swab in RF. HIV-1 RNA decay patterns were compared in individuals receiving DTG + 3TC. Despite significantly higher percentages for changes from baseline in BP, median (IQR) times to HIV-1 RNA suppression were shorter in SP (7 days; 0–8.75) and RF (10.5 days; 3–17.5) than in BP (28 days; 14–84; P < .001).

Conclusions

Comparable HIV-1 RNA decay in BP, SP, and RF was observed between DTG + 3TC and BIC/FTC/TAF. As shown with triple-drug integrase inhibitor–based regimens, rapid HIV-1 RNA suppression in SP and RF is achieved with DTG + 3TC, despite decay patterns differing from those of BP.

Clinical Trials Registration

EudraCT 2019-004109-28.