bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular potential energy computation via graph edge aggregate attention neural network
Authors: Chang Jian , Kuai Yiming , Wei Xian , Yu Hui , Lan Hai
Published: February 2023

Accurate potential energy surface (PES) calculation is the basis of molecular dynamics research. Using deep learning (DL) methods can improve the speed of PES calculation while achieving competitive accuracy to ab initio methods. However, the performance of DL model is extremely sensitive to the distribution of training data. Without sufficient training data, the DL model suffers from overfitting issues that lead to catastrophic performance degradation on unseen samples. To solve this problem, based on the message passing paradigm of graph neural networks, we innovatively propose an edge-aggregate-attention mechanism, which specifies the weight based on node and edge information. Experiments on MDI7 and QM9 datasets show that our model not only achieves higher PES calculation accuracy but also has better generalization ability compared with Schnet, which demonstrates that edge-aggregate-attention can better capture the inherent features of equilibrium and non-equilibrium molecular conformations.
Flexible colloidal quantum dot lasers enabled by self-assembly
Authors: Chen Wei-guo , Liu Rui-xiang , Fan Feng-jia
Published: February 2023

Colloidal quantum dot (CQD) lasers show promising applications in flexible optoelectronic devices, due to their tunable emission wavelength, narrow spectrum bandwidth and high power intensity. However, fabricating a flexible CQD laser is challenging because of the difficulties in fabricating optical cavities on flexible substrates using traditional microfabrication technologies. Herein, we propose a one-step self-assembly approach to fabricate flexible CQD supraparticle lasers. The whole assembly approach is processed in a liquid environment without surfactants, and the formed spherical CQD supraparticles are featured with smooth surfaces, serving as high-quality-factor whispering-gallery mode cavities to support laser oscillation. A low lasing threshold of 54 µJ/cm2 is observed while exciting a CQD supraparticle with pulsed femtosecond lasers. The calculated cavity quality factor of 963 for CQD supraparticle lasers is twofold larger than that of CQD lasers assembled with surfactants. Moreover, the CQD supraparticles can serve as free-standing lasers, which allows them to be deposited on flexible substrates such as paper and cloth. Furthermore, our CQD lasers show high stability, after being continuously photoexcited above the threshold for 400 min, their lasing intensity remains at 85.7% of the initial value. As bright, free-standing and long-term stable light sources, the assembled CQD lasers proposed in this work show potential applications in wearable devices and medical diagnosis.
Design strategy of infrared 4-hydroxybenzylidene-imidazolinone-type chromophores based on intramolecular charge transfer: A theoretical perspective
Authors: Song Jian , Liang Wen Long , Yang Shouning , Yang Huayan
Published: February 2023

Partial genetically encoded 4-hydroxybenzylidene-imidazolinone (HBI)-type chromophores are new promising fluorescent probes, which are suitable for imaging and detection of living cells. However, the lack of infrared chromophores hinders the development seriously. Here more than 30 HBI-type chromophores with regular structure modifications were employed and typical spectral redshift change laws and mechanisms were investigated by quantum methods. Results show that both one-photon spectrum (OPS, absorption/emission) and two-photon absorption (TPA) can achieve large redshift via either extending conjugated lengths of frag-3 or enlarging conjugated areas of frag-1 of HBI skeleton. Spectral redshifts of all chromophores are highly related to intramolecular charge transfer (ICT), but neutral ones are closely related to the total ICT or electron-accepting-numbers of frag-3, and the high correlative factor of anions is the aromaticity of frag-2 bridge. The frag-2 bridge with high aromaticity can open a reverse charge transfer channel in anion relative to neutral, obtaining significant redshift. Based on analysis, a new 6-hydroxyl-naphthalene-imidazolinone (HNI) series, which have larger conjugated area in frag-1, are predicted. The OPS and TPA of anionic HNI ones acquire about 76–96 nm and 119–146 nm red-shift relative to traditional HBI series respectively as a whole. The longest emission of anionic HNI-4 realizes more 244 nm redshift relative to HBI-1. Our work clarifies worthy spectral regularities and redshift mechanisms of HBI-type chromophores and provides valuable design strategy for infrared chromophores synthesis in experiment.
Atomistic modeling of lithium materials from deep learning potential with
ab initio
accuracy
Authors: Wang Haidi , Li Tao , Yao Yufan , Liu Xiaofeng , Zhu Weiduo , Chen Zhao , Li Zhongjun , Hu Wei
Published: February 2023

Lithium has been paid great attention in recent years thanks to its significant applications for battery and lightweight alloy. Developing a potential model with high accuracy and efficiency is important for theoretical simulation of lithium materials. Here, we build a deep learning potential (DP) for elemental lithium based on a concurrent-learning scheme and DP representation of the density-functional theory (DFT) potential energy surface (PES), the DP model enables material simulations with close-to DFT accuracy but at much lower computational cost. The simulations show that basic parameters, equation of states, elasticity, defects and surface are consistent with the first principles results. More notably, the liquid radial distribution function based on our DP model is found to match well with experiment data. Our results demonstrate that the developed DP model can be used for the simulation of lithium materials.
Design, material, function, and fabrication of metamaterials
Authors: Zadpoor Amir A. , Mirzaali Mohammad J. , Valdevit Lorenzo , Hopkins Jonathan B.
Published: February 2023

Metamaterials are engineered materials with unusual, unique properties and advanced functionalities that are a direct consequence of their microarchitecture. While initial properties and functionalities were limited to optics and electromagnetism, many novel categories of metamaterials that have applications in many different areas of research and practice, including acoustic, mechanics, biomaterials, and thermal engineering, have appeared in the last decade. This editorial serves as a prelude to the special issue with the same title that presents a number of selected studies in these directions. In particular, we review some of the most important developments in the design and fabrication of metamaterials with an emphasis on the more recent categories. We also suggest some directions for future research.
Corrigendum to: Atmospheric turbulent structures and fire sweeps during shrub fires and implications for flaming zone behaviour
Authors: Katurji Marwan , Noonan Bob , Zhang Jiawei , Valencia Andres , Schumacher Benjamin , Kerr Jessica , Strand Tara , Pearce Grant , Zawar-Reza Peyman
Published: February 2023

 Background Wildfires propagate through vegetation exhibiting complex spread patterns modulated by ambient atmospheric wind turbulence. Wind gusts at the fire-front extend and intensify flames causing direct convective heating towards unburnt fuels resulting in rapid acceleration of spread.

 Aims To characterise ambient and fire turbulence over gorse shrub and explore how this contributes to fire behaviour.

 Methods Six experimental burns were carried out in Rakaia, New Zealand under varying meteorological conditions. The ignition process ensured a fire-line propagating through dense gorse bush (1 m high). Two 30-m sonic anemometer towers measured turbulent wind velocity at six different levels above the ground. Visible imagery was captured by cameras mounted on uncrewed aerial vehicles at 200 m AGL.

 Key results Using wavelet decomposition, we identified different turbulent time scales that varied between 1 and 128 s relative to height above vegetation. Quadrant analysis identified statistical distributions of atmospheric sweeps (downbursts of turbulence towards vegetation) with sustained events emanating from above the vegetation canopy and impinging at the surface with time scales up to 10 s.

 Conclusions Image velocimetry enabled tracking of ‘fire sweeps’ and characterised for the first time their lifetime and dynamics in comparison with overlying atmospheric turbulent structures.

 Implications This methodology can provide a comprehensive toolkit when investigating coupled atmosphere–fire interactions.
The ups and downs of relative particles in German diachrony
Authors: Moser Ann-Marie
Published: February 2023

The aim and scope of this article is to take a closer look at the functions and semantics of the three relative
particles da, so, and wo, and to show that they have developed differently over a period from
1350 to 1800, continuing up to our modern dialects and the standard language. We will focus on wo because it is
the only relativizer which is attested both as locative relative and as general relative clause marker, and we will propose that
wo has extended its functional domain from a locative relative to a general relative marker. We will
furthermore discuss if there has been a grammaticalization path “relative locative > general relative clause marker” in German
diachrony or not. Finally, we will suggest that standardization processes are responsible for the different degrees of functional
extension of wo attested in the historical/modern varieties and the standard language.
A diachronic analysis of Spanish alg- series and n- series items in negated clauses
Authors: Yamada Aaron
Published: February 2023

While previous studies have analyzed the changing nature of polarity items (PIs) in Latin (see Gianollo 2018, 2020) and the licensing conditions of PIs in modern languages (see Homer 2021), less research has analyzed the diachronic behavior of PIs in the development of the Spanish language. The present study takes a quantitative approach to historical corpus data in showing that in older varieties of Spanish, there was an increased degree of competition between items of the alg- series (i.e., alguno ‘some’) and items of the n- series (i.e., ninguno ‘none’) in negated clauses which later decreased as the language entered its modern age. We find that the competition between these items in negated clauses is influenced by factors such as register, the syntactic role of the PI, and activation status (following Larrivée 2012, 2017). These data provide quantitative support for Martins (2000), who suggested that earlier forms of Spanish exhibited more versatile licensing conditions of PIs, and that this variation gradually decreased over time due to a greater salience of the n- series in negated clauses. In total, the present work aims to use corpus data to connect historical linguistic research to theoretical approaches regarding the contemporary usage of PIs.
Study of lead free double perovskites Na2XAgCl6 (X = Ga, In Tl) for solar cells and transport applications
Authors: Zelai Taharh
Published: February 2023

The double perovskites are rich merchant to harvest energy from solar cells and thermoelectric generators to cover up its shortfall. Therefore, in this article, the electronic, optical, and thermoelectric characteristics of Na2XAgCl6 (X = Ga, In Tl) are briefly elaborated. The tolerance and octahedral factors are calculated for structural stability and formations energy for thermodynamically existence. The band structures are show the tuning of band gap from 2.57 eV to 1.30 eV by the changing cations from Ga to Tl. The density of states shows the p-d hybridization among X, Ag and Cl ions is responsible for decreasing band gap. The optical analysis in terms of dielectric constant, absorption and other dependent parameters illustrate broad absorption bands in ultraviolet region (Ga, In) and in visible region (Tl). The shifting of absorption zone to visible region increase their potential for solar cells. Thermoelectric calculations have been performed to evaluate the electrical conductivity, Seebeck coefficient, and thermal conductivity by BoltzTraP code. The large figure of merit and extremely small lattice thermal conductivity at room temperature also make them important for thermoelectric generators fabrication to harvest heat energy.
Complex dynamics of a heterogeneous network of Hindmarsh-Rose neurons
Authors: Njitacke Zeric Tabekoueng , Muni Sishu Shankar , Seth Soumyajit , Awrejcewicz Jan , Kengne Jacques
Published: February 2023

This contribution is devoted to the study of the collective behavior of two HR neurons followed by a network of HR neurons. The collective behavior of the two coupled neuron was obtained from the connection between the traditional 3D HR and a memristive 2D HR neuron via a gap junction. The dynamical properties of this first topology revealed that it is dissipative therefore can support complex phenomena. From numerical simulations, it is found that the coupled neurons display a variety of behaviors just by varying the control parameter. Amongst these behaviors found, we have periodic bursting or spiking, quasi-periodic bursting or spiking, and chaotic bursting or spiking. Non-synchronized motion is observed when the electrical coupling strength is weak. However, synchronized cluster states are observed when the coupling strength is increased. Also varied of cross ring networks made of combination of N = 100 these different HR neurons in the network are also investigated. It is discovered that the spatiotemporal patterns are affected by the network topology. The cluster states are represented in the non- homogenous network’s ring and star structures. The ring and ring-star structures contain single and double-well chimera states. Finally, in the PSIM simulation environment, a comparable electronic circuit for the two coupled heterogeneous neurons is designed and investigated. The results obtained from the designed analog circuit and the mathematical model of the two coupled neurons match perfectly.
>10 kW peak power self-frequency doubling laser
Authors: Zhao Chuanrui , Yu Pingzhang , Wang Zhengping , Liu Yanqing , Yu Fapeng , Xu Xinguang
Published: February 2023

A passively Q-switched self-frequency doubling (SFD) green laser based on quasi-continuous diode-pumped and Nd:Ca3TaGa3Si2O14 crystal was developed for the first time with Cr4+:Y3Al5O12 as the saturation absorber. The output wavelength was 533 nm and the maximum average output power was 57 mW, corresponding to single pulse energy, pulse duration, and peak power of 190 μJ, 14.35 ns, and 13.24 kW, respectively. To our knowledge, this is the best result of diode-pumped, pulsed SFD lasers to date. Its compact components and low cost provide a better way to obtain an all-solid-state, miniaturized green laser with high peak power.
Optimisation criteria for the process electron beam lithography of negative AR-N7520 resists
Authors: Koleva E , Kostic I , Andok R , Vutova K , Bencurova A , Konecnikova A
Published: February 2023

Experimental investigation of negative electron resist AR-N 7520 profiles using an electron beam lithography system ZBA23 (Raith) is performed at variation of the exposure doses and the exposure patterns. The form of the obtained after the exposure resist profiles is investigated and optimized. Artificial neural networks for the dependence of the overall geometry of the obtained resist profiles on process parameters are trained, tested and validated. Several overall geometry quality criteria for the shape of the developed resist profile cross-sections are defined. An approach, based on the defined overall quality characteristics and multicriterial parameter optimization, is proposed and implemented for fulfillment of the technological requirements for the produced resist profile dimensions.
Climate change on extreme winds already affects off-shore wind power availability in Europe
Authors: Rapella Lia , Faranda Davide , Gaetani Marco , Drobinski Philippe , Ginesta Mireia
Published: February 2023

Off-shore wind energy in Europe plays a key role in the transition to renewable energy, and its usage is expected to increase in the next few decades. According to the working regimes of a wind turbine, wind energy production can be disrupted by extreme atmospheric events related to low wind speed below the cut-in wind speed and high wind speed above the cut-out wind speed. The purpose of this work is to estimate the behavior of extreme winds on the European panorama, over the period 1950–2020, in order to investigate the large-scale weather regimes related to them and their impact on off-shore wind energy availability. We detected significant changes in the frequency of high and low extreme wind events, proving that climate change or long-term internal climate variability have already affected the off-shore wind power output. Moreover, the analysis of weather regimes showed that high and low extreme wind events can occur simultaneously over Europe. Our results suggest the necessity to implement efficient European energy management policies, to minimize the deficit in wind power supply.
Determination of ring-level dynamic modulus of elasticity in loblolly pine from measurements of ultrasonic velocity and specific gravity
Authors: Dahlen Joseph , Auty David , Eberhardt Thomas L , Schimleck Laurence , Pokhrel Nawa Raj
Published: February 2023

Wood stiffness (modulus of elasticity, MOE) is an important property for conifer wood, with the variability in MOE largely being a function of both the specific gravity (SG) (wood density) and the angle of the microfibrils within the S2 layer of longitudinal tracheids. Rapid analysis techniques can be used together to quantify MOE; while SG can be determined with relative ease, this is not the case for microfibril angle, requiring expensive X-ray diffraction equipment. An alternative to microfibril angle is to measure longitudinal acoustic velocity. The objective of this study was to measure and then model the within tree variation in dynamic MOE (MOEdyn) by developing the methodology to measure ultrasonic velocity (USV) in radial samples from pith to bark using ultrasonic frequencies (>20 kHz). A total of 419 pith-to-bark radial strips, collected from multiple height levels in 92 loblolly pine (Pinus taeda) trees, were processed to obtain matching SG (2mm longitudinal) and USV (8.2-mm longitudinal) samples. Ring-by-ring SG was measured using X-ray densitometry and time-of-flight USV was measured at a 10-mm radial resolution from pith to bark. A subset of samples was sent to SilviScan to determine microfibril angle using X-ray diffraction. The relationship between microfibril angle and USV was strong (R2 = 0.91, RMSE = 2.6°). Nonlinear mixed-effects models were then developed to predict radial variation in SG, USV and MOEdyn. Fixed effects for the models, which included cambial age and height of disk within tree, had pseudo R2 values of 0.67 for SG (RMSE = 0.051), 0.71 for USV (RMSE = 316 m/s) and 0.69 for MOEdyn (RMSE = 1.9 GPa). When combined with SG measurements from X-ray densitometry, USV measurements from pith to bark are a powerful tool for assessing variability in wood stiffness.
SlZF3 regulates tomato plant height by directly repressing SlGA20ox4 in the gibberellic acid biosynthesis pathway
Authors: Luo Jinying , Tang Yunfei , Chu Zhuannan , Peng Yuxin , Chen Jiawei , Yu Huiyang , Shi Chunmei , Jafar Jahanzeb , Chen Rong , Tang Yaping , Lu Yongen , Ye Zhibiao , Li Ying , Ouyang Bo
Published: February 2023

Plant height is an important target trait for crop genetic improvement. Our previous work has identified a salt-tolerant C2H2 zinc finger, SlZF3, and its overexpression lines also showed a semi-dwarf phenotype, but the molecular mechanism remains to be elucidated. Here, we characterized the dwarf phenotype in detail. The dwarfism is caused by a decrease in stem internode cell elongation and deficiency of bioactive gibberellic acids (GAs), and can be rescued by exogenous GA3 treatment. Gene expression assays detected reduced expression of genes in the GA biosynthesis pathway of the overexpression lines, including SlGA20ox4. Several protein–DNA interaction methods confirmed that SlZF3 can directly bind to the SlGA20ox4 promoter and inhibit its expression, and the interaction can also occur for SlKS and SlKO. Overexpression of SlGA20ox4 in the SlZF3-overexpressing line can recover the dwarf phenotype. Therefore, SlZF3 regulates plant height by directly repressing genes in the tomato GA biosynthesis pathway.
Feeding the world: impacts of elevated [CO2] on nutrient content of greenhouse grown fruit crops and options for future yield gains
Authors: Doddrell Nicholas H , Lawson Tracy , Raines Christine A , Wagstaff Carol , Simkin Andrew J
Published: February 2023

Several long-term studies have provided strong support demonstrating that growing crops under elevated [CO2] can increase photosynthesis and result in an increase in yield, flavour and nutritional content (including but not limited to Vitamins C, E and pro-vitamin A). In the case of tomato, increases in yield by as much as 80% are observed when plants are cultivated at 1000 ppm [CO2], which is consistent with current commercial greenhouse production methods in the tomato fruit industry. These results provide a clear demonstration of the potential for elevating [CO2] for improving yield and quality in greenhouse crops. The major focus of this review is to bring together 50 years of observations evaluating the impact of elevated [CO2] on fruit yield and fruit nutritional quality. In the final section, we consider the need to engineer improvements to photosynthesis and nitrogen assimilation to allow plants to take greater advantage of elevated CO2 growth conditions.
Dual functions of PsmiR172b-PsTOE3 module in dormancy release and flowering in tree peony (Paeonia suffruticosa)
Authors: Zhang Yuxi , Gao Linqiang , Wang Yanyan , Niu Demei , Yuan Yanchao , Liu Chunying , Zhan Xinmei , Gai Shupeng
Published: February 2023

MicroRNAs (miRNAs) are non-coding RNAs that interact with target genes and are involved in many physiological processes in plants. miR172-AP2 mainly plays a role in the regulation of flowering time and floral organ differentiation. Bud dormancy release is necessary for forcing culture of tree peony in winter, but the mechanism of dormancy regulation is unclear. In this study, we found that a miR172 family member, PsmiR172b, was downregulated during chilling-induced bud dormancy release in tree peony, exhibiting a trend opposite to that of PsTOE3. RNA ligase-mediated (RLM) 5′-RACE (rapid amplification of cDNA ends) confirmed that miR172b targeted PsTOE3, and the cleavage site was between bases 12 (T) and 13 (C) within the complementary site to miR172b. The functions of miR172b and PsTOE3 were detected by virus-induced gene silencing (VIGS) and their overexpression in tree peony buds. PsmiR172b negatively regulated bud dormancy release, but PsTOE3 promoted bud dormancy release, and the genes associated with bud dormancy release, including PsEBB1, PsEBB3, PsCYCD, and PsBG6, were upregulated. Further analysis indicated that PsTOE3 directly regulated PsEBB1 by binding to its promoter, and the specific binding site was a C-repeat (ACCGAC). Ectopic expression in Arabidopsis revealed that the PsmiR172b-PsTOE3 module displayed conservative function in regulating flowering. In conclusion, our results provided a novel insight into the functions of PsmiR172-PsTOE3 and possible molecular mechanism underlying bud dormancy release in tree peony.
Nonoverlapping spectral additive Schwarz methods for hybrid discontinuous Galerkin discretizations
Authors: Yu Yi , Dryja Maksymilian , Sarkis Marcus
Published: February 2023

This paper develops exact, inexact and some new variants of nonoverlapping spectral additive Schwarz (NOSAS) methods for hybrid discontinuous Galerkin discretizations. The NOSAS are nonoverlapping preconditioners designed for elliptic problems with highly heterogeneous coefficients, and the subdomain interactions are via the interface problem. The interface problem has two components, a local one with degrees of freedom on the interface of the subdomains and a global one based on a few generalized eigenvectors. These generalized eigenvectors are selected to guarantee the robustness of the NOSAS with respect to heterogeneous diffusion coefficients and the number of subdomains. A unique feature of NOSAS is that the corresponding generalized eigenvalue problems are obtained from the Neumann matrix of the nonoverlapping subdomain separately. Additionally, the number of these few generalized eigenvectors can be characterized by the geometry of the coefficients for the case of two coefficients with high contrast. We prove that the condition number of the NOSAS does not depend on the coefficients. With a specific choice of the threshold for selecting these few eigenvalues, we can recover similar convergence rates as we would have obtained for constant coefficients.
Irrationality of Generic Quotient Varieties via Bogomolov Multipliers
Authors: Jezernik Urban , Sánchez Jonatan
Published: February 2023

The Bogomolov multiplier of a group is the unramified Brauer group associated with the quotient variety of a faithful representation of the group. This object is an obstruction for the quotient variety to be stably rational. The purpose of this paper is to study these multipliers associated with nilpotent pro-$p$ groups by transporting them to their associated Lie algebras. Special focus is set on the case of $p$-adic Lie groups of nilpotency class $2$, where we analyse the moduli space. This is then applied to give information on asymptotic behaviour of multipliers of finite images of such groups of exponent $p$. We show that with fixed $n$ and increasing $p$, a positive proportion of these groups of order $p^n$ have trivial multipliers. On the other hand, we show that by fixing $p$ and increasing $n$, log-generic groups of order $p^n$ have non-trivial multipliers. Whence quotient varieties of faithful representations of log-generic $p$-groups are not stably rational, applications in non-commutative Iwasawa theory are developed.
Beauty, Anger, and Artistic Activism
Authors: Carrasco Barranco Matilde
Published: February 2023

The rejection of beauty from a political standpoint is a significant part of the legacy of avant-gardism in contemporary art. In particular, Arthur Danto signaled that artistic activism should avoid beauty simply because beauty induces the wrong perspective on whatever it is desired to have an impact upon. While artistic beauty’s tendency would be to heal, he claimed, political protest needs anger as its trigger. This article challenges such an argument that opposes beauty’s emotional effects on political action by examining the complex nature of both beauty and anger. I contest a mere contemplative view of beauty and, using Carolyn Korsmeyer’s account of “terrible beauties,” bound up with discomforting emotions, I defend that beauty can be compatible with anger albeit, in order to be politically truly effective, anger must move from the wish to punish toward more productive forward-looking thoughts. Though often being necessary as a source of motivation to fight for justice, I believe, with Martha Nussbaum and Myisha Cherry, that anger is truly politically effective and keeps its noble side when detached from revenge and directed by hope, a value related to beauty.
Furthering the Further Quest for Ugaritic
Authors: Daniels Peter T
Published: February 2023

Emendations to a Festschrift contribution, suggested by the honouree, dealing with the decipherment of the Ugaritic script.
Zeolite-encaged mononuclear copper centers catalyze CO2 selective hydrogenation to methanol
Authors: Chai Yuchao , Qin Bin , Li Bonan , Dai Weili , Wu Guangjun , Guan Naijia , Li Landong
Published: February 2023

The selective hydrogenation of CO2 to methanol by renewable hydrogen source represents an attractive route for CO2 recycling and is carbon neutral. Stable catalysts with high activity and methanol selectivity are being vigorously pursued, and current debates on the active site and reaction pathway need to be clarified. Here, we report a design of faujasite-encaged mononuclear Cu centers, namely Cu@FAU, for this challenging reaction. Stable methanol space-time-yield (STY) of 12.8 mmol gcat-1 h-1 and methanol selectivity of 89.5% are simultaneously achieved at a relatively low reaction temperature of 513 K, making Cu@FAU a potential methanol synthesis catalyst from CO2 hydrogenation. With zeolite-encaged mononuclear Cu centers as the destined active sites, the unique reaction pathway of stepwise CO2 hydrogenation over Cu@FAU is illustrated. This work provides a clear example of catalytic reaction with explicit structure-activity relationship and highlights the power of zeolite catalysis in complex chemical transformations.
Low Kirtland’s Warbler fledgling survival in Wisconsin plantations relative to Michigan plantations
Authors: Olah Ashley , Ribic Christine A , Grveles Kim , Warner Sarah , Lopez Davin , Pidgeon Anna M
Published: February 2023

The Kirtland’s Warbler (Setophaga kirtlandii) is a formerly endangered habitat specialist that breeds mainly in young jack pine (Pinus banksiana) forests in northern Lower Michigan, USA. The species is conservation-reliant and depends on habitat management. Management actions have primarily focused on creating jack pine plantations, but the species also breeds in red pine (Pinus resinosa) plantations in central Wisconsin, USA. However, the plantations were not intended as breeding habitat and have suboptimal pine densities. While nesting success is similar between low-density red pine plantations and optimal jack pine habitat, it is not clear if low-density red pine plantations support high fledging survival. If high-quality nesting and post-fledging habitat are not synonymous, fledgling survival and breeding population recruitment may be low. We characterized survival, habitat use, and movement patterns of dependent Kirtland’s Warbler fledglings in Wisconsin red pine plantations and compared fledgling survival between Wisconsin and Michigan. Mayfield cumulative survival estimates at 30 days post-fledging were 0.20 for Wisconsin fledglings and 0.43–0.78 for Michigan fledglings. Logistic exposure cumulative survival estimates for Wisconsin fledglings were 0.23–0.34 at 30 days post-fledging. Fledglings in Wisconsin used areas where vegetation cover and density of red and jack pine were high relative to available areas but not at greater proportions than what was available. Our findings demonstrate that red pine plantations with low pine densities were not equally suitable as nesting and post-fledging habitat, as fledgling survival rates were low. We hypothesize that reduced habitat structure, and not particular pine species, likely contributed to reduced fledgling survival in Wisconsin. Thus, we recommend including red pine as a component in managed Kirtland’s Warbler habitat only if tree densities approach optimal levels.
Methylation of nonessential genes in cutaneous melanoma – Rule Out hypothesis
Authors: Gorlov Ivan P. , Conway Kathleen , Edmiston Sharon N. , Parrish Eloise A. , Hao Honglin , Amos Christopher I. , Tsavachidis Spiridon , Gorlova Olga Y. , Begg Colin , Hernando Eva , Cheng Chao , Shen Ronglai , Orlow Irene , Luo Li , Ernstoff Marc S. , Kuan Pei Fen , Ollila David W. , Tsai Yihsuan S. , Berwick Marianne , Thomas Nancy E.
Published: February 2023

Differential methylation plays an important role in melanoma development and is associated with survival, progression and response to treatment. However, the mechanisms by which methylation promotes melanoma development are poorly understood. The traditional explanation of selective advantage provided by differential methylation postulates that hypermethylation of regulatory 5’-cytosine-phosphate-guanine-3’ dinucleotides (CpGs) downregulates the expression of tumor suppressor genes and therefore promotes tumorigenesis. We believe that other (not necessarily alternative) explanations of the selective advantages of methylation are also possible. Here, we hypothesize that melanoma cells use methylation to shut down transcription of nonessential genes – those not required for cell survival and proliferation. Suppression of nonessential genes allows tumor cells to be more efficient in terms of energy and resource usage, providing them with a selective advantage over the tumor cells that transcribe and subsequently translate genes they do not need. We named the hypothesis the Rule Out (RO) hypothesis. The RO hypothesis predicts higher methylation of CpGs located in regulatory regions (CpG islands) of nonessential genes. It also predicts the higher methylation of regulatory CpGs linked to nonessential genes in melanomas compared to nevi and lower expression of nonessential genes in malignant (derived from melanoma) versus normal (derived from nonaffected skin) melanocytes. The analyses conducted using in-house and publicly available data found that all predictions derived from the RO hypothesis hold, providing observational support for the hypothesis.
Dexamethasone mitigates remdesivir-induced liver toxicity in human primary hepatocytes and COVID-19 patients
Authors: Liu Kaiyan , Stern Sydney , Heil Emily L. , Li Linhao , Khairi Rula , Heyward Scott , Wang Hongbing
Published: February 2023

Background:

Coronavirus disease 2019 (COVID-19) is a global pandemic that has caused more than 600 million cases and over six million deaths worldwide. Despite the availability of vaccination, COVID-19 cases continue to grow making pharmacological interventions essential. Remdesivir (RDV) is an FDA-approved antiviral drug for treatment of both hospitalized and non-hospitalized COVID-19 patients, albeit with potential for hepatotoxicity. This study characterizes the hepatotoxicity of RDV and its interaction with dexamethasone (DEX), a corticosteroid often co-administered with RDV for inpatient treatment of COVID-19.

Methods:

Human primary hepatocytes and HepG2 cells were used as in vitro models for toxicity and drug-drug interaction studies. Real-world data from hospitalized COVID-19 patients were analyzed for drug-induced elevation of serum ALT and AST.

Results:

In cultured hepatocytes, RDV markedly reduced the hepatocyte viability and albumin synthesis, while it increased the cleavage of caspase-8 and caspase-3, phosphorylation of histone H2AX, and release of ALT and AST in a concentration-dependent manner. Importantly, co-treatment with DEX partially reversed RDV-induced cytotoxic responses in human hepatocytes. Moreover, data from COVID-19 patients treated with RDV with and without DEX co-treatment suggested that among 1037 patients matched by propensity score, receiving the drug combination was less likely to result in elevation of serum AST and ALT levels (≥ 3 × ULN) compared to the RDV alone treated patients (OR = 0.44, 95% CI = 0.22–0.92, p = 0.03).

Conclusion:

Our findings obtained from in vitro cell-based experiments and patient data analysis provide evidence suggesting combination of DEX and RDV holds the potential to reduce the likelihood of RDV-induced liver injury in hospitalized COVID-19 patients.
Eccrine Cyst (Hidrocystoma) of the Inner Canthus: A Rare Entity With Immunohistologic Confirmation
Authors: Charles Norman C. , Kim Eleanore T.
Published: February 2023

A small ruptured cyst was excised from the left inner canthus of a 68-year-old woman. Histopathology displayed a cyst lined by a double layer of cuboidal epithelium and filled with amorphous material. The lining cells were strongly positive for cytokeratins 5/6 and 14, with weak reactivity with cytokeratin 7. These findings were identical to those in a single previous report of an eccrine cyst of the eyelid, making this the second example of a bona fide eccrine hidrocystoma of the eyelid.
Prediction model of the horizontal trabecular iris angle after phakic posterior chamber implantable intraocular lens surgery
Authors: Sánchez-Trancón Angel , Manito Santiago Cerpa , Sierra Oscar Torrado , Baptista António Manuel , Serra Pedro Miguel
Published: February 2023

Purpose:

To determine the predictors of the postoperative horizontal trabecular iris angle (TIA750) after phakic posterior chamber implantable intraocular lens (IOL) surgery.

Setting:

Ophthalmology Clinic Vista Sánchez Trancón, Badajoz, Spain.

Design:

Retrospective case series.

Methods:

330 eyes implanted with spherical/toric implantable collamer lens (ICL) were included in this study. From 230 eyes implanted with 13.2 mm ICL, these were divided in modeling (n = 180) and evaluation group (n = 50). Two groups implanted with 12.6 mm and 13.7 mm (n = 50 each) were also used as evaluation. Anterior-segment optical coherence tomography was used preoperatively to perform anterior chamber biometry (angle-to-angle [ATA] distance, crystalline lens rise, anterior chamber depth [ACD], cornea sagittal depth, pupil diameter, nasal/temporal TIA750); postoperatively for measuring the vault, pupil diameter and nasal/temporal TIA750. Corneal curvature and horizontal visible iris diameter were measured using optical tomography. Bivariate correlation analysis was used to determine associations between preoperative and postoperative horizontal TIA750 with anterior chamber biometry, ICL-related parameters and age. Finally, a multivariate linear regression model was constructed for predicting the postoperative TIA750.

Results:

Horizontal TIA750 reduced from 42.9 ± 8.0 degrees preoperatively to 24.4 ± 5.6 degrees postoperatively. Postoperative TIA750 was positively correlated with the preoperative TIA750, cornea sagittal depth and ACD, and negatively associated with the vault. The main predictors of the postoperative TIA750 were the preoperative parameters, TIA750, ICLsize − ATA and pupil diameter (adjusted-R
2 = 0.39). The limits of agreement between predicted and real TIA750 were close to ±10 degrees.

Conclusions:

Implantation of a phakic posterior chamber implantable IOL leads to a reduction in TIA750 and the main factors contributing for this are the preoperative TIA750 aperture and the vault.
Dengue, chikungunya and zika arbovirus infections in Caribbean children
Authors: Christie Celia D.C. , Lue Aileen M. , Melbourne-Chambers Roxanne H.
Published: February 2023

Purpose of review

Dengue, chikungunya and zika have caused significant epidemics in the Caribbean in recent years. This review highlights their impact in Caribbean children.

Recent findings

Dengue has been increasingly intense and severe, seroprevalence is 80–100% in the Caribbean, children have increased attributable morbidity and mortality. Severe dengue, especially dengue with haemorrhage was significantly associated with haemoglobin SC disease and multiple organ-systems involved. These included the gastrointestinal and haematologic systems with extremely high lactate dehydrogenases and creatinine phosphokinases and severely abnormal bleeding indices. Despite appropriate interventions, mortality was highest within the first 48 h of admission. Chikungunya, a togavirus, affected 80% of some Caribbean populations. Paediatric presentations included high fever, skin, joint and neurological manifestations. Children less than 5 years of age had the highest morbidity and mortality. This maiden chikungunya epidemic was explosive and overwhelmed public health systems. Zika, another flavivirus, has a seroprevalence of 15% in pregnancy, so the Caribbean remains susceptible. Paediatric complications include pregnancy losses, stillbirths, Congenital Zika syndrome, Guillain–Barre syndrome, acute disseminated encephalomyelitis and transverse myelitis. Neurodevelopment stimulation programs for zika-exposed infants have been effective in improving language and positive behaviour scores.

Caribbean children remain at risk for dengue, chikungunya and zika, with high attributable morbidity and mortality.
EFFECTS OF SARS COVID-19 POSITIVITY STATUS ON VENOUS THROMBOSIS AND PULMONARY EMBOLISM RATES IN TRAUMA PATIENTS
Authors: Kenney Connor L. , Nelson Austin R. , Fahey Ryan A. , Roubik Daniel J. , How Remealle A. , Radowsky Jason S. , Sams Valerie G. , Schauer Steven G. , Rizzo Julie A.
Published: February 2023

Introduction: COVID-19–induced coagulopathy (CIC) can increase the risk of thromboembolism without underlying clotting disorders, even when compared with other respiratory viruses. Trauma has a known association with hypercoagulability. Trauma patients with concurrent COVID-19 infection potentially have an even greater risk of thrombotic events. The purpose of this study was to evaluate venous thromboembolism (VTE) rates in trauma patients with COVID-19. Methods: This study reviewed all adult patients (≥18 years of age) admitted to the Trauma Service from April through November 2020 for a minimum of 48 hours. Patients were grouped based off COVID-19 status and compared for inpatient VTE chemoprophylaxis regimen, thrombotic complications defined as deep vein thrombosis, pulmonary embolism, myocardial infarction, and cerebrovascular accident, intensive care unit (ICU) length of stay, hospital length of stay, and mortality. Results: A total of 2,907 patients were reviewed and grouped into COVID-19–positive (n = 110) and COVID-19–negative (n = 2,797) groups. There was no difference in terms of receiving deep vein thrombosis chemoprophylaxis or type, but a longer time to initiation in the positive group (P = 0.0012). VTE occurred in 5 (4.55%) positive and 60 (2.15%) negative patients without a significant difference between the groups, as well as no difference in type of VTE observed. Mortality was higher (P = 0.009) in the positive group (10.91%). Positive patients had longer median ICU LOS (P = 0.0012) and total LOS (P < 0.001). Conclusion: There were no increased rates of VTE complications between COVID-19–positive and –negative trauma patients, despite a longer time to initiation of chemoprophylaxis in the COVID-19–positive group. COVID-19–positive patients had increased ICU LOS, total LOS, and mortality, which are likely due to multifactorial causes but primarily related to their underlying COVID-19 infection.
Ergosterol extraction: A comparison of methodologies
Authors: Wilkes Thomas I
Published: February 2023

Ergosterol is a component of the cell membrane of mycorrhizal fungi and is frequently used to quantify their biomass. Arbuscular mycorrhizal (AM) fungi and ectomycorrhizal (ECM) fungi establish a symbiotic relationship with a respective host plant. Several methods are currently employed for quantification of ergosterol; however, these utilise a series of potentially hazardous chemicals with a varying degree of exposure times to the user. The present method comparative study aims to ascertain the most reliable method to extract ergosterol whilst limiting hazard exposure to the user. Chloroform, cyclohexane, methanol and methanol hydroxide extraction protocols were applied to a total of 300 samples of root samples and a further 300 growth substrate samples across all protocols. Extracts were analysed via HPLC methodologies. Chromagraphic analysis showed chloroform based extraction procedures produced a consistently higher concentration of ergosterol in both root and growth substrate samples. Methanol hydroxide, without the addition of cyclohexane, produced very low concentration of ergosterol, with a reduction of quantified ergosterol of between 80 and 92% compared to chloroform extractions. Hazard exposure was greatly reduced following chloroform extraction protocol when compared with other extraction procedures.
Comprehensive codon usage analyses of the mutations in the Parkin protein leading to Parkinsonism
Authors: Biswas Sima , Ali Ananya , Mort Matthew , Bagchi Angshuman
Published: February 2023

Neurodegenerative diseases typically occur due to the abnormal behavior of the proteins. One of the most prevalent neurodegenerative diseases is the Parkinson’s disease. Parkin protein encoded by PARK2 gene is the central player in the central nervous system. Mutations in Parkin lead to the onset of Parkinsonism. In this work, we made an attempt to decipher the codon usage patterns of the amino acid residues in the different domains of Parkin protein. We observed that mutations at the first two codon positions have statistically significant disease associations. This is the first such report that analyzes the correlation between the disease severity of Parkinsonism and its association with the pattern of codon usages.
Discovery of new deregulated miRNAs in gingivo buccal carcinoma using Group Benjamini Hochberg method: a commentary on “A quest for miRNA bio-marker: a track back approach from gingivo buccal cancer to two different types of precancers”
Authors: Koner Salil , De Sarkar Navonil , Laha Nilanjana
Published: February 2023

This formal comment is in response to “A quest for miRNA bio-marker: a track back approach from gingivo buccal cancer to two different types of precancers” written by De Sarkar and colleagues in 2014. The above-mentioned paper found seven miRNAs to be significantly deregulated in 18 gingivo-buccal cancer samples. However, they suspected more miRNAs to be deregulated based on their exploratory statistical analysis. To control the false discovery rate (FDR), the authors used the Benjamini Hochberg (BH) method, which does not leverage any available biological information on the miRNAs. In this work, we show that some specialized versions of the BH method, which can exploit positional information on the miRNAs, can lead to seven more discoveries with this data. Specifically, we group the closely located miRNAs, and use the group Benjamini Hochberg (GBH) methods (Hu et al., 2010), which reportedly have more statistical power than the BH method (Liu et al., 2019). The whole transcriptome analysis of Sing et al. (2017) and previous literature on the miRNAs suggest that most of the newly discovered miRNAs play a role in oncogenesis. In particular, the newly discovered miRNAs include hsa-miR-1 and hsa-miR-21-5p, whose cancer-related activities are well-established. Our findings indicate that incorporating the GBH method into suitable microarray studies may potentially enhance scientific discoveries via the exploitation of additional biological information.
Three-Dimensional Bioconjugated Liquid-Like Solid (LLS) Enhance Characterization of Solid Tumor - Chimeric Antigen Receptor T cell interactions
Authors: Nguyen Duy T. , Liu Ruixuan , Ogando-Rivas Elizabeth , Pepe Alfonso , Pedro Diego , Qdasait Sadeem , Nguyen Nhi Tran Yen , Lavrador Julia M. , Golde Griffin R. , Smolchek Ryan A. , Ligon John , Jin Linchun , Tao Haipeng , Webber Alex , Phillpot Simon , Mitchell Duane A. , Sayour Elias J , Huang Jianping , Castillo Paul , Sawyer W. Gregory
Published: February 2023

Cancer immunotherapy offers lifesaving treatments for cancers, but the lack of reliable preclinical models that could enable the mechanistic studies of tumor-immune interactions hampers the identification of new therapeutic strategies. We hypothesized 3D confined microchannels, formed by interstitial space between bio-conjugated liquid-like solids (LLS), enable CAR T dynamic locomotion within an immunosuppressive TME to carry out anti-tumor function. Murine CD70-specific CAR T cells cocultured with the CD70-expressing glioblastoma and osteosarcoma demonstrated efficient trafficking, infiltration, and killing of cancer cells. The anti-tumor activity was clearly captured via longterm in situ imaging and supported by upregulation of cytokines and chemokines including IFNg, CXCL9, CXCL10, CCL2, CCL3, and CCL4. Interestingly, target cancer cells, upon an immune attack, initiated an “immune escape” response by frantically invading the surrounding microenvironment. This phenomenon however was not observed for the wild-type tumor samples which remained intact and produced no relevant cytokine response. Single cells collection and transcriptomic profiling of CAR T cells at regions of interest revealed feasibility of identifying differential gene expression amongst the immune subpopulations. Complimentary 3D in vitro platforms are necessary to uncover cancer immune biology mechanisms, as emphasized by the significant roles of the TME and its heterogeneity.