bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced interlayer adhesion of wetted graphene oxide by confined water bridge
Authors: Zhao Yanyan , Zhou Ke , Liu Yilun
Published: July 2023

Graphene oxide (GO) sheets are widely used as building blocks in flexible electronic devices, structural materials, and energy storage technology owing to physicochemical flexibility and remarkable mechanical properties. GO exists as lamellar structures in these applications and, thus, it urges to enhance interface interaction to prevent interfacial failure. This study explores the adhesion of GO with and without intercalated water utilizing steered molecular dynamics (SMD) simulations. We find the interfacial adhesion energy (γ) depends on the synergistic effect of the types of functional groups, the degree of oxidation (c), and water content (wt). The intercalated monolayer water confined within GO flakes can improve the γ by more than 50% whereas the interlayer spacing is enlarged. The enhancement of adhesion is from the cooperative hydrogen bonding bridges between confined water and functional group on GO. Furthermore, the optimal water content wt = 20% and oxidation degree c = 20% are obtained. Our findings provide an experimentally available way to improve interlayer adhesion through molecular intercalation, which opens the possibility of high-performance laminate nanomaterial-based films for versatile applications.
The multichannel i-propyl + O2 reaction system: A model of secondary alkyl radical oxidation
Authors: Lahm Mitchell E. , Bartlett Marcus A. , Liang Tao , Pu Liang , Allen Wesley D. , Schaefer Henry F.
Published: July 2023

The i-propyl + O2 reaction mechanism has been investigated by definitive quantum chemical methods to establish this system as a benchmark for the combustion of secondary alkyl radicals. Focal point analyses extrapolating to the ab initio limit were performed based on explicit computations with electron correlation treatments through coupled cluster single, double, triple, and quadruple excitations and basis sets up to cc-pV5Z. The rigorous coupled cluster single, double, and triple excitations/cc-pVTZ level of theory was used to fully optimize all reaction species and transition states, thus, removing some substantial flaws in reference geometries existing in the literature. The vital i-propylperoxy radical (MIN1) and its concerted elimination transition state (TS1) were found 34.8 and 4.4 kcal mol−1 below the reactants, respectively. Two β-hydrogen transfer transition states (TS2, TS2′) lie above the reactants by (1.4, 2.5) kcal mol−1 and display large Born–Oppenheimer diagonal corrections indicative of nearby surface crossings. An α-hydrogen transfer transition state (TS5) is discovered 5.7 kcal mol−1 above the reactants that bifurcates into equivalent α-peroxy radical hanging wells (MIN3) prior to a highly exothermic dissociation into acetone + OH. The reverse TS5 → MIN1 intrinsic reaction path also displays fascinating features, including another bifurcation and a conical intersection of potential energy surfaces. An exhaustive conformational search of two hydroperoxypropyl (QOOH) intermediates (MIN2 and MIN3) of the i-propyl + O2 system located nine rotamers within 0.9 kcal mol−1 of the corresponding lowest-energy minima.
High power GaSb-based superluminescent diode with cascade cavity suppression waveguide geometry and ultra-low antireflection coating
Authors: Wang Tianfang , Yang Chengao , Chen Yihang , Shi Jianmei , Yu Hongguang , Su Xiangbin , Zhang Yu , Zhao Youwen , Tong Cunzhu , Wu Donghai , Xu Yingqiang , Ni Haiqiao , Niu Zhichuan
Published: July 2023

We report on a GaSb-based superluminescent diode optimized for high-power broadband operation around a wavelength of 2 μm. The high optical power was achieved by the high-quality epitaxial InGaSb/AlGaAsSb type-I quantum well gain material, which was processed into a double-pass amplification configuration. To prevent lasing at high current injection while enabling strong amplified spontaneous emission, a cascade cavity suppression waveguide geometry was designed to connect the vertical rear facet with the reflectivity-suppressed angled front facet. A Ta2O5/SiO2 ultra-low antireflection coating with a minimum reflectivity of 0.04% was applied to the front facet for further cavity suppression. This combination allowed the superluminescent diodes to demonstrate a record high single-transverse-mode output power of up to 152 mW under continuous-wave operation at room temperature, with a broad spectral band of 42 nm full width at half maximum. A 25% promotion in optical power has been realized compared to current state-of-the-art devices in this wavelength range, without sacrificing spectral bandwidth. The high-power spectral density characteristics, along with a good beam quality, are well suited for absorption spectroscopy applications and hybrid integration with silicon technology.
Liquid thread breakup and the formation of satellite droplets
Authors: Carnevale Luís H. , Deuar Piotr , Che Zhizhao , Theodorakis Panagiotis E.
Published: July 2023

The breakup of liquid threads into smaller droplets is a fundamental problem in fluid dynamics. In this study, we estimate the characteristic wavelength of the breakup process by means of many-body dissipative particle dynamics. This wavelength shows a power-law dependence on the Ohnesorge number in line with results from stability analysis. We also discover that the number of satellite droplets exhibits a power-law decay with exponent 0.72 ± 0.04 in the product of the Ohnesorge and thermal capillary numbers, while the overall size of main droplets is larger than that based on the characteristic wavelength thanks to the asynchronous breakup of the thread. Finally, we show that the formation of satellite droplets is the result of the advection of pinching points toward the main droplets in a remaining thinning neck, when the velocity gradient of the fluid exhibits two symmetric maxima.
Computational pulmonary edema: A microvascular model of alveolar capillary and interstitial flow
Authors: Grotberg James B. , Romanò Francesco
Published: July 2023

We present a microvascular model of fluid transport in the alveolar septa related to pulmonary edema. It consists of a two-dimensional capillary sheet coursing by several alveoli. The alveolar epithelial membrane runs parallel to the capillary endothelial membrane with an interstitial layer in between, making one long septal tract. A coupled system of equations uses lubrication theory for the capillary blood, Darcy flow for the porous media of the interstitium, a passive alveolus, and the Starling equation at both membranes. Case examples include normal physiology, cardiogenic pulmonary edema, acute respiratory distress syndrome (ARDS), hypoalbuminemia, and effects of PEEP. COVID-19 has dramatically increased ARDS in the world population, raising the urgency for such a model to create an analytical framework. Under normal conditions fluid exits the alveolus, crosses the interstitium, and enters the capillary. For edema, this crossflow is reversed with fluid leaving the capillary and entering the alveolus. Because both the interstitial and capillary pressures decrease downstream, the reversal can occur within a single septal tract, with edema upstream and clearance downstream. Clinically useful solution forms are provided allowing calculation of interstitial fluid pressure, crossflows, and critical capillary pressures. Overall, the interstitial pressures are found to be significantly more positive than values used in the traditional physiological literature. That creates steep gradients near the upstream and downstream end outlets, driving significant flows toward the distant lymphatics. This new physiological flow provides an explanation to the puzzle, noted since 1896, of how pulmonary lymphatics can function so far from the alveoli: the interstitium is self-clearing.
Structural transformations in single-crystalline AgPd nanoalloys from multiscale deep potential molecular dynamics
Authors: Guo Longfei , Jin Tao , Shan Shuang , Tang Quan , Li Zhen , Wang Chongyang , Wang Junpeng , Pan Bowei , Wang Qiao , Chen Fuyi
Published: July 2023

AgPd nanoalloys often undergo structural evolution during catalytic reactions; the mechanism underlying such restructuring remains largely unknown due to the use of oversimplified interatomic potentials in simulations. Herein, a deep-learning potential is developed for AgPd nanoalloys based on a multiscale dataset spanning from nanoclusters to bulk configurations, exhibits precise predictions of mechanical properties and formation energies with near-density functional theory accuracy, calculates the surface energies closer to experimental values compared to those obtained by Gupta potentials, and is applied to investigate the shape reconstruction of single-crystalline AgPd nanoalloys from cuboctahedron (Oh) to icosahedron (Ih) geometries. The Oh to Ih shape restructuring is thermodynamically favorable and occurs at 11 and 92 ps for Pd55@Ag254 and Ag147@Pd162 nanoalloys, respectively. During the shape reconstruction of Pd@Ag nanoalloys, concurrent surface restructuring of the (100) facet and internal multi-twinned phase change are observed with collaborative displacive characters. The presence of vacancies can influence the final product and reconstructing rate of Pd@Ag core–shell nanoalloys. The Ag outward diffusion on Ag@Pd nanoalloys is more pronounced in Ih geometry compared to Oh geometry and can be further accelerated by the Oh to Ih deformation. The deformation of single-crystalline Pd@Ag nanoalloys is characterized by a displacive transformation involving the collaborative displacement of a large number of atoms, distinguishing it from the diffusion-coupled transformation of Ag@Pd nanoalloys.
Introduction to the chemistry and pharmacology of psychedelic drugs
Authors: Walker Scott R. , Pullella Glenn A. , Piggott Matthew J. , Duggan Peter J.
Published: July 2023

The science of psychedelics is an intriguing, multi-disciplinary field that has recently been the subject of heightened public interest. This has mainly resulted from publicity associated with a number of high-profile investigations into psychedelic-assisted therapy for a range of difficult-to-treat mental health conditions. With many psychedelic substances known, including natural, semi-synthetic and fully synthetic, and a rangeof receptors, enzymes and transporters implicated in their modes of action, although very interesting, the field can appear daunting to newcomers to the area. This Primer Review is designed to give an overview of the chemistry and pharmacology of psychedelics. It is hoped that it will provide a useful resource for science undergraduates, postgraduates and their instructors, and experienced scientists who require a comprehensive and up-to-date summary of the field. The Review begins with a summary of the important classes of psychedelics and then goes on to summarise the known history of their traditional human use, dating back to prehistoric times. Following that, important classes of psychedelics are examined in more detail, namely the ergolines, such as lysergic acid diethylamide (LSD), tryptamines like psilocybin and N,N-dimethyltryptamine, phenethylamines typified by mescaline and 3,4-methylenedioxymethamphetamine (MDMA), arylcyclohexylamines including ketamine and phenylcyclohexylpiperidine (PCP), and a group of naturally occurring drugs that do not belong to any of these three classes, examples being muscimol and salvinorin A. The contributions made by early pioneers like Albert Hofmann and Alexander Shulgin are briefly summarised. References to primary literature and more specialised reviews are provided throughout.
Comb-structured mRNA vaccine tethered with short double-stranded RNA adjuvants maximizes cellular immunity for cancer treatment
Authors: Tockary Theofilus A. , Abbasi Saed , Matsui-Masai Miki , Hayashi Akimasa , Yoshinaga Naoto , Boonstra Eger , Wang Zheng , Fukushima Shigeto , Kataoka Kazunori , Uchida Satoshi
Published: July 2023

Integrating antigen-encoding mRNA (Messenger RNA) and immunostimulatory adjuvant into a single formulation is a promising approach to potentiating the efficacy of mRNA vaccines. Here, we developed a scheme based on RNA engineering to integrate adjuvancy directly into antigen-encoding mRNA strands without hampering the ability to express antigen proteins. Short double-stranded RNA (dsRNA) was designed to target retinoic acid-inducible gene-I (RIG-I), an innate immune receptor, for effective cancer vaccination and then tethered onto the mRNA strand via hybridization. Tuning the dsRNA structure and microenvironment by changing its length and sequence enabled the determination of the structure of dsRNA-tethered mRNA efficiently stimulating RIG-I. Eventually, the formulation loaded with dsRNA-tethered mRNA of the optimal structure effectively activated mouse and human dendritic cells and drove them to secrete a broad spectrum of proinflammatory cytokines without increasing the secretion of anti-inflammatory cytokines. Notably, the immunostimulating intensity was tunable by modulating the number of dsRNA along the mRNA strand, which prevents excessive immunostimulation. Versatility in the applicable formulation is a practical advantage of the dsRNA-tethered mRNA. Its formulation with three existing systems, i.e., anionic lipoplex, ionizable lipid–based lipid nanoparticles, and polyplex micelles, induced appreciable cellular immunity in the mice model. Of particular interest, dsRNA-tethered mRNA encoding ovalbumin (OVA) formulated in anionic lipoplex used in clinical trials exerted a significant therapeutic effect in the mouse lymphoma (E.G7-OVA) model. In conclusion, the system developed here provides a simple and robust platform to supply the desired intensity of immunostimulation in various formulations of mRNA cancer vaccines.
Crystal structures of multidrug efflux transporters from
Burkholderia pseudomallei
suggest details of transport mechanism
Authors: Kato Takaaki , Okada Ui , Hung Li-Wei , Yamashita Eiki , Kim Heung-Bok , Kim Chang-Yub , Terwilliger Thomas C. , Schweizer Herbert P. , Murakami Satoshi
Published: July 2023

BpeB and BpeF are multidrug efflux transporters from
Burkholderia pseudomallei
that enable multidrug resistance. Here, we report the crystal structures of BpeB and BpeF at 2.94 Å and 3.0 Å resolution, respectively. BpeB was found as an asymmetric trimer, consistent with the widely-accepted functional rotation mechanism for this type of transporter. One of the monomers has a distinct structure that we interpret as an intermediate along this functional cycle. Additionally, a detergent molecule bound in a previously undescribed binding site provides insights into substrate translocation through the pathway. BpeF shares structural similarities with the crystal structure of OqxB from
Klebsiella pneumoniae
, where both are symmetric trimers composed of three “binding”-state monomers. The structures of BpeB and BpeF further our understanding of the functional mechanisms of transporters belonging to the HAE1-RND superfamily.
Radiative controls by clouds and thermodynamics shape surface temperatures and turbulent fluxes over land
Authors: Ghausi Sarosh Alam , Tian Yinglin , Zehe Erwin , Kleidon Axel
Published: July 2023

Land surface temperatures (LSTs) are strongly shaped by radiation but are modulated by turbulent fluxes and hydrologic cycling as the presence of water vapor in the atmosphere (clouds) and at the surface (evaporation) affects temperatures across regions. Here, we used a thermodynamic systems framework forced with independent observations to show that the climatological variations in LSTs across dry and humid regions are mainly mediated through radiative effects. We first show that the turbulent fluxes of sensible and latent heat are constrained by thermodynamics and the local radiative conditions. This constraint arises from the ability of radiative heating at the surface to perform work to maintain turbulent fluxes and sustain vertical mixing within the convective boundary layer. This implies that reduced evaporative cooling in dry regions is then compensated for by an increased sensible heat flux and buoyancy, which is consistent with observations. We show that the mean temperature variation across dry and humid regions is mainly controlled by clouds that reduce surface heating by solar radiation. Using satellite observations for cloudy and clear-sky conditions, we show that clouds cool the land surface over humid regions by up to 7 K, while in arid regions, this effect is absent due to the lack of clouds. We conclude that radiation and thermodynamic limits are the primary controls on LSTs and turbulent flux exchange which leads to an emergent simplicity in the observed climatological patterns within the complex climate system.
Earth’s interior dynamics drive marine fossil diversity cycles of tens of millions of years
Authors: Boulila Slah , Peters Shanan E. , Müller R. Dietmar , Haq Bilal U. , Hara Nathan
Published: July 2023

The fossil record reveals that biotic diversity has fluctuated quasi-cyclically through geological time. However, the causal mechanisms of biotic diversity cycles remain unexplained. Here, we highlight a common, correlatable 36 ± 1 Myr (million years) cycle in the diversity of marine genera as well as in tectonic, sea-level, and macrostratigraphic data over the past 250 Myr of Earth history. The prominence of the 36 ± 1 Myr cycle in tectonic data favors a common-cause mechanism, wherein geological forcing mechanisms drive patterns in both biological diversity and the preserved rock record. In particular, our results suggest that a 36 ± 1 Myr tectono-eustatically driven sea-level cycle may originate from the interaction between the convecting mantle and subducting slabs, thereby pacing mantle-lithospheric deep-water recycling. The 36 ± 1 Myr tectono-eustatic driver of biodiversity is likely related to cyclic continental inundations, with expanding and contracting ecological niches on shelves and in epeiric seas.
Regulation of replication origin licensing by ORC phosphorylation reveals a two-step mechanism for Mcm2-7 ring closing
Authors: Amasino Audra L. , Gupta Shalini , Friedman Larry J. , Gelles Jeff , Bell Stephen P.
Published: July 2023

Eukaryotic DNA replication must occur exactly once per cell cycle to maintain cell ploidy. This outcome is ensured by temporally separating replicative helicase loading (G1 phase) and activation (S phase). In budding yeast, helicase loading is prevented outside of G1 by cyclin-dependent kinase (CDK) phosphorylation of three helicase-loading proteins: Cdc6, the Mcm2-7 helicase, and the origin recognition complex (ORC). CDK inhibition of Cdc6 and Mcm2-7 is well understood. Here we use single-molecule assays for multiple events during origin licensing to determine how CDK phosphorylation of ORC suppresses helicase loading. We find that phosphorylated ORC recruits a first Mcm2-7 to origins but prevents second Mcm2-7 recruitment. The phosphorylation of the Orc6, but not of the Orc2 subunit, increases the fraction of first Mcm2-7 recruitment events that are unsuccessful due to the rapid and simultaneous release of the helicase and its associated Cdt1 helicase-loading protein. Real-time monitoring of first Mcm2-7 ring closing reveals that either Orc2 or Orc6 phosphorylation prevents Mcm2-7 from stably encircling origin DNA. Consequently, we assessed formation of the MO complex, an intermediate that requires the closed-ring form of Mcm2-7. We found that ORC phosphorylation fully inhibits MO complex formation and we provide evidence that this event is required for stable closing of the first Mcm2-7. Our studies show that multiple steps of helicase loading are impacted by ORC phosphorylation and reveal that closing of the first Mcm2-7 ring is a two-step process started by Cdt1 release and completed by MO complex formation.
Cyclin-G-associated kinase GAK/dAux regulates autophagy initiation via ULK1/Atg1 in glia
Authors: Zhang Shiping , Yi Shuanglong , Wang Linfang , Li Shuhua , Wang Honglei , Song Li , Ou Jiayao , Zhang Min , Wang Ruiqi , Wang Mengxiao , Zheng Yuchen , Yang Kai , Liu Tong , Ho Margaret S.
Published: July 2023

Autophagy is a major means for the elimination of protein inclusions in neurons in neurodegenerative diseases such as Parkinson’s disease (PD). Yet, the mechanism of autophagy in the other brain cell type, glia, is less well characterized and remains largely unknown. Here, we present evidence that the PD risk factor, Cyclin-G-associated kinase (GAK)/
Drosophila
homolog Auxilin (dAux), is a component in glial autophagy. The lack of GAK/dAux increases the autophagosome number and size in adult fly glia and mouse microglia, and generally up-regulates levels of components in the initiation and PI3K class III complexes. GAK/dAux interacts with the master initiation regulator UNC-51like autophagy activating kinase 1/Atg1 via its uncoating domain and regulates the trafficking of Atg1 and Atg9 to autophagosomes, hence controlling the onset of glial autophagy. On the other hand, lack of GAK/dAux impairs the autophagic flux and blocks substrate degradation, suggesting that GAK/dAux might play additional roles. Importantly, dAux contributes to PD-like symptoms including dopaminergic neurodegeneration and locomotor function in flies. Our findings identify an autophagy factor in glia; considering the pivotal role of glia under pathological conditions, targeting glial autophagy is potentially a therapeutic strategy for PD.
How reputation does (and does not) drive people to punish without looking
Authors: Jordan Jillian J. , Kteily Nour S.
Published: July 2023

Punishing wrongdoers can confer reputational benefits, and people sometimes punish without careful consideration. But are these observations related? Does reputation drive people to people to “punish without looking”? And if so, is this because
unquestioning
punishment looks particularly virtuous? To investigate, we assigned “Actors” to decide whether to sign punitive petitions about politicized issues (“punishment”), after first deciding whether to read articles opposing these petitions (“looking”). To manipulate reputation, we matched Actors with copartisan “Evaluators,” varying whether Evaluators observed i) nothing about Actors’ behavior, ii) whether Actors punished, or iii) whether Actors punished and whether they looked. Across four studies of Americans (total
n
= 10,343), Evaluators rated Actors more positively, and financially rewarded them, if they chose to (vs. not to) punish. Correspondingly, making
punishment
observable to Evaluators (i.e., moving from our first to second condition) drove Actors to punish more overall. Furthermore, because some of these individuals did not look, making punishment observable increased rates of punishment without looking. Yet punishers who eschewed opposing perspectives did not appear
particularly
virtuous. In fact, Evaluators preferred Actors who punished with (vs. without) looking. Correspondingly, making
looking
observable (i.e., moving from our second to third condition) drove Actors to look
more
overall—and to punish without looking at comparable or
diminished
rates. We thus find that reputation can encourage reflexive punishment—but simply as a byproduct of generally encouraging punishment, and not as a specific reputational strategy. Indeed, rather than fueling unquestioning decisions, spotlighting punishers’ decision-making processes may encourage reflection.
Increased neutralization potency and breadth elicited by a SARS-CoV-2 mRNA vaccine forming virus-like particles
Authors: Zhang Peng , Falcone Samantha , Tsybovsky Yaroslav , Singh Mamta , Gopan Vinay , Miao Huiyi , Seo Yuna , Rogers Denise , Renzi Isabella , Lai Yen-Ting , Narayanan Elisabeth , Stewart-Jones Guillaume , Himansu Sunny , Carfi Andrea , Fauci Anthony S. , Lusso Paolo
Published: July 2023

Vaccines have played a fundamental role in the control of infectious diseases. We previously developed a messenger RNA (mRNA) vaccine against HIV-1 that forms virus-like particles (VLPs) through coexpression of the viral envelope with Gag. Here, we applied the same principle to the design of a VLP-forming mRNA vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To promote cognate interaction with simian immunodeficiency virus (SIV) Gag, we engineered different chimeric proteins encompassing the ectodomain and the transmembrane region of the SARS-CoV-2 Spike protein from the Wuhan-Hu-1 strain fused to the gp41 cytoplasmic tail of either HIV-1 (strain WITO) or SIV (strain mac239) with or without a partial truncation at amino acid 745 to enhance membrane expression. Upon cotransfection with SIV
gag
mRNA, the Spike-SIV
CT.745
(SSt) chimera yielded the highest level of cell-surface expression and extracellular VLP release. Immunization of BALB/c mice with
SSt+gag
mRNA at 0, 4, and 16 wk induced higher titers of Spike-binding and autologous neutralizing antibodies at all time points compared to
SSt
mRNA alone. Furthermore, mice immunized with
SSt+gag
mRNA developed neutralizing antibodies effective against different variants of concern. These data demonstrate that the Gag/VLP mRNA platform can be successfully applied to vaccines against different agents for the prevention of infectious diseases of global relevance.
Cored dark matter halos in the cosmic neutrino background
Authors: Cho Wonsub , Choi Ki-Young , Kim Hee Jung
Published: July 2023

We study the impact of the interaction between DM and the cosmic neutrino background on
the evolution of galactic dark matter halos. The energy transfer from the cosmic background
neutrinos to galactic dark matter can heat the center of the galaxy and make it cored. The core
formation is efficient for the small galaxies such as the satellite galaxies of the Milky Way and
we can put a conservative constraint on the non-relativistic elastic scattering cross section as
 σχν
≲ 10-31 cm2 for 0.1 keV dark matter.
Exploring muonphilic ALPs at muon colliders
Authors: Lu Chih-Ting , Luo Xiaoyi , Wei Xinqi
Published: July 2023

Axion-like particles (ALPs) are new particles that extend beyond the standard model (SM) and are extensively investigated. When considering ALPs within an effective field theory framework, their couplings with SM particles can be studied independently. It is a daunting task to search for GeV-scale ALPs coupled to muons in collider experiments because their coupling is proportional to the muon mass. However, a recent study by Altmannshofer, Dror, and Gori (2022) highlighted the importance of a four-point interaction, W-μ-

-a, as well as interactions from the chiral anomaly, whose couplings are not dependent on the muon mass. These interactions provide a new opportunity to explore muonphilic ALPs (μALPs) at the GeV scale. We explore various μALP production channels at muon colliders with μALPs decaying into a pair of muons. In particular, we find that a pair of neutrinos accompanied by a μALP is the most effective channel to search for μALPs in the electrowek violating (EWV) scenario. In contrast, a photon plus a μALP becomes a better channel to search for μALPs in the electroweak preserving (EWP) scenario because there is no W-μ-

-a interaction in this situation. Most importantly, we find that the future bounds for μALPs in the EWV scenario are considerably stronger than those in the EWP scenario and the existing bounds for exploring μALPs with

GeV

.
Markers of economic activity in satellite aerosol optical depth data
Authors: Kondragunta Shobha , Wei Zigang , Zhang Hai , Liu Hongqing , Laszlo Istvan , Zhang Bin , Cao Changyong , Ciren Pubu
Published: July 2023

This study investigated the impact of COVID-19 lockdowns on satellite aerosol optical depth (AOD), to explore the hypothesis that if changes in economic activity are seen in emissions of NO2, an aerosol precursor, then AOD should change commensurably. We developed a technique to filter AOD data to isolate changes associated with anthropogenic emissions. Overall, in 37 of the 43 cities that were identified as top oxides of nitrogen (NO
x
) emitters from their transportation sectors, AODs decreased by 21.2% ± 7.8%, 18.9% ± 11.7%, 27% ± 12.4%, 22.9% ± 7.6% in the United States, India, western Europe, and China, respectively—an average of 22.4% ± 7.4%. In contrast, AODs increased on average by 11.7% ± 8.4% in Taiwan, where economic stimulus was used as a strategy during the pandemic. This analysis implies NO
x
and volatile organic compounds emissions reductions from the transportation sector can be targeted, and by transitioning 6 million light duty vehicles from gasoline to electricity, the US can achieve 21% improvement in AOD.
Measurement-device-independent nonlinear entanglement witnesses
Authors: Sen Kornikar , Srivastava Chirag , Sen Ujjwal
Published: July 2023

Entanglement witnesses (EWs) are one of the most effective methods to detect entanglement. It is known that nonlinear EW provide better entanglement detection than their linear counterparts, in that the former detect a strictly larger subset of entangled states than the latter. Whether linear or nonlinear, the method is measurement-device dependent, so that imperfect measurements may cause false certification of entanglement in a shared state. Measurement-device-independent EW provide an escape from such measurement dependence of the entanglement detection for linear EW. Here we present measurement-device-independent nonlinear EW for non-positive partial transpose entangled states as well as for bound entangled states with positive partial transpose. Although the witness considered herein does not detect a larger set of entangled states than other nonlinear EW, it is more efficient in that it never leads to a false detection corresponding to wrong measurements. The constructed measurement-device-independent nonlinear EW certify the entanglement of the same sets of entangled states as their device-dependent parents do, and therefore are better than the linear EW, device-independent or otherwise.
On Benford’s law for multiplicative functions
Authors: Chandee Vorrapan , Li Xiannan , Pollack Paul , Singha Roy Akash
Published: July 2023

We provide a criterion to determine whether a real multiplicative function is a strong Benford sequence. The criterion implies that the

k
k

-divisor functions, where

k
≠

10
j

k \neq 10^j

, and Hecke eigenvalues of newforms, such as Ramanujan tau function, are strong Benford. In contrast to some earlier work, our approach is based on Halász’s Theorem.
Global behavior of small data solutions for the 2D Dirac–Klein-Gordon system
Authors: Dong Shijie , Li Kuijie , Ma Yue , Yuan Xu
Published: July 2023

In this paper, we are interested in the two-dimensional Dirac–Klein-Gordon system, which is a basic model in particle physics. We investigate the global behavior of small data solutions to this system in the case of a massive scalar field and a massless Dirac field. More precisely, our main result is twofold: (1) we show sharp time decay for the pointwise estimates of the solutions, which implies the asymptotic stability of this system; (2) we show the linear scattering result of this system which is a fundamental problem when it is viewed as dispersive equations. Our result is valid for general small, high-regular initial data, and in particular, there is no restriction on the support of the initial data.
From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA)
Authors: Ruiz José Luis , Reimering Susanne , Escobar-Prieto Juan David , Brancucci Nicolas M B , Echeverry Diego F , Abdi Abdirahman I , Marti Matthias , Gómez-Díaz Elena , Otto Thomas D
Published: July 2023

Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Long read technologies embody the promise of overcoming scaffolding problems associated with repeats and low complexity sequences, but the number of contigs often far exceeds the number of chromosomes and they may contain many insertion and deletion errors around homopolymer tracts. To overcome these issues, we have implemented the ILRA pipeline to correct long read-based assemblies. Contigs are first reordered, renamed, merged, circularized, or filtered if erroneous or contaminated. Illumina short reads are used subsequently to correct homopolymer errors. We successfully tested our approach by improving the genome sequences of Homo sapiens, Trypanosoma brucei, and Leptosphaeria spp., and by generating four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracts reduced the number of genes incorrectly annotated as pseudogenes, but an iterative approach seems to be required to correct more sequencing errors. In summary, we describe and benchmark the performance of our new tool, which improved the quality of novel long read assemblies up to 1 Gbp. The pipeline is available at GitHub: https://github.com/ThomasDOtto/ILRA.
RegCFinder: targeted discovery of genomic subregions with differential read density
Authors: Weiß Elena , Friedel Caroline C
Published: July 2023

Motivation

To date, no methods are available for the targeted identification of genomic subregions with differences in sequencing read distributions between two conditions. Existing approaches either only determine absolute read number changes, require predefined subdivisions of input windows or average across multiple genes.

Results

Here, we present RegCFinder, which automatically identifies subregions of input windows with differences in read density between two conditions. For this purpose, the problem is defined as an instance of the all maximum scoring subsequences problem, which can be solved in linear time. Subsequently, statistical significance and differential usage of identified subregions are determined with DEXSeq. RegCFinder allows flexible definition of input windows to target the analysis to any regions of interests, e.g. promoters, gene bodies, peak regions and more. Furthermore, any type of sequencing assay can be used as input; thus, RegCFinder lends itself to a wide range of applications. We illustrate the usefulness of RegCFinder on two applications, where we can both confirm previous results and identify interesting gene subgroups with distinctive changes in read distributions.

Availability and implementation

RegCFinder is implemented as a workflow for the workflow management system Watchdog and available at: https://github.com/watchdog-wms/watchdog-wms-workflows/

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Lifetime risk, life expectancy, loss-of-life expectancy and lifetime healthcare expenditure for Stevens–Johnson syndrome/toxic epidermal necrolysis in Taiwan: follow-up of a nationwide cohort from 2008 to 2019
Authors: Chiu Ying-Ming , Chiu Hsien-Yi
Published: July 2023

Background

Stevens–Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) not only cause acute, devastating mucocutaneous reactions but also have long-lasting implications on survivors’ lives.

Objectives

To quantify the lifetime burden of SJS/TEN.

Methods

The cumulative incidence rate (CIR), life expectancy (LE), loss-of-life expectancy (LoLE) and lifetime healthcare expenditure (HE) for SJS/TEN were estimated over the period from 2008 to 2019 using data from the National Health Insurance Research Database of Taiwan and life tables of vital statistics.

Results

In this nationwide cohort of 6552 incident SJS/TEN cases, a trend towards a decrease in the CIR was observed between 2008 and 2019. Compared with the general population, patients with SJS/TEN experience a tremendous loss of 9.43 (1.06) [mean (SEM)] years of LE after diagnosis of SJS/TEN. Male patients with SJS/TEN had higher LoLE [10.74 (1.22) vs. 7.69 (1.43) years] and annual HE than females. Younger age at diagnosis of SJS/TEN was associated with longer LE but greater LoLE and higher lifetime HE. Patients with intensive care unit admission on diagnosis, malignancy, diabetes mellitus, end-stage renal disease and SJS/TEN-associated sequelae experienced substantially greater LoLE and HE per life year.

Conclusions

Patients with SJS/TEN suffer substantial loss-of-LE and HE, particularly young patients, compared with the general population. These data provide a reference estimate of the lifetime burden of SJS/TEN to help health authorities evaluate the cost-effectiveness of future preventive and treatment strategies to minimize the burden of SJS/TEN.
Successful treatment of Bowen disease with 1% tirbanibulin ointment
Authors: Blaya Imbernón Daniel , Finello Malena , Labrandero Hoyos Carolina , Lorca Spröhnle Javier , Casanova Esquembre Andrés , Peñuelas Leal Rodrigo , Grau Echevarría Andrés , Hernández Bel Pablo
Published: July 2023

We report, to the best of our knowledge, the first case of Bowen disease treated with tirbanibulin. In addition to the successful treatment of the malignant lesions, the improvement in skin texture and photodamage is remarkable. With a good safety profile, tolerability and the dosing convenience of this new drug, we believe that its use in pathologies beyond Olsen grade 1 actinic keratoses is promising, but further studies are required.
Focal segmental glomerulosclerosis associated with the use of the IL-23 inhibitor guselkumab
Authors: Stryckers Marijke , Van Oevelen Stefaan , Koshy Priyanka , Sprangers Ben , Van Craenenbroeck Amaryllis H
Published: July 2023

We report a case of a 38-year-old man who developed a nephrotic syndrome shortly after the start of guselkumab for the treatment of plaque psoriasis. Renal biopsy showed focal segmental glomerulosclerosis (FSGS). The clinical course of our case is highly suspect for drug-induced FSGS since the nephrotic syndrome resolved after cessation of the drug without relapse (2 years of follow-up). To the best of our knowledge, this is the first case describing FSGS lesions associated with the use of an interleukin-23 inhibitor.
Determinants of depressive symptoms in patients with heart failure based on the hopelessness theory of depression
Authors: Zhang Yilin , Hou Danhua , Dong Xiaoyu , Zhao Qiuge , Zhang Xiuting , Fan Xiuzhen
Published: July 2023

Aims

Depressive symptoms are common in patients with heart failure (HF) and are associated with adverse outcomes in this group. This study examined depressive symptoms and associated determinants in patients with HF based on the hopelessness theory of depression.

Methods and results

In this cross-sectional study, a total of 282 patients with HF were recruited from 3 cardiovascular units of a university hospital. Symptom burden, optimism, maladaptive cognitive emotion regulation strategies (MCERSs), hopelessness, and depressive symptoms were assessed using self-reported questionnaires. A path analysis model was established to evaluate the direct and indirect effects. The prevalence of depressive symptoms was 13.8% in the patients. Symptom burden had the greatest direct effect on depressive symptoms (β = 0.406; P < 0.001), optimism affected depressive symptoms both directly and indirectly with hopelessness as the mediator (direct: β = −0.360; P = 0.001; indirect: β = −0.169; P < 0.001), and MCERSs only had an indirect effect on depressive symptoms with hopelessness as the mediator (β = 0.035; P < 0.001).

Conclusion

In patients with HF, symptom burden, decreased optimism, and hopelessness contribute to depressive symptoms directly. What is more, decreased optimism and MCERS lead to depressive symptoms indirectly via hopelessness. Accordingly, interventions aimed at decreasing symptom burden, enhancing optimism, and reducing the use of MCERSs, while declining hopelessness, may be conducive to relieving depressive symptoms in patients with HF.
Driver Mutations of Pancreatic Cancer Affect Ca2+ Signaling and ATP Production
Authors: Stopa Kinga B , Łoziński Filip , Kusiak Agnieszka A , Litewka Jacek , Krzysztofik Daria , Mosiołek Sylwester , Morys Jan , Ferdek Paweł E , Jakubowska Monika A
Published: July 2023

Glandular pancreatic epithelia of the acinar or ductal phenotype may seem terminally differentiated, but they are characterized by remarkable cell plasticity. Stress-induced trans-differentiation of these cells has been implicated in the mechanisms of carcinogenesis. Current consensus links pancreatic ductal adenocarcinoma with onco-transformation of ductal epithelia, but under the presence of driver mutations in Kras and Trp53, also with trans-differentiation of pancreatic acini. However, we do not know when, in the course of cancer progression, physiological functions are lost by mutant acinar cells, nor can we assess their capacity for the production of pancreatic juice components. Here, we investigated whether two mutations—KrasG12D and Trp53R172H—present simultaneously in acinar cells of KPC mice (model of oncogenesis) influence cytosolic Ca2+ signals. Since Ca2+ signals control the cellular handling of digestive hydrolases, any changes that affect intracellular signaling events and cell bioenergetics might have an impact on the physiology of the pancreas. Our results showed that physiological doses of acetylcholine evoked less regular Ca2+ oscillations in KPC acinar cells compared to the control, whereas responses to supramaximal concentrations were markedly reduced. Menadione elicited Ca2+ signals of different frequencies in KPC cells compared to control cells. Finally, Ca2+ extrusion rates were significantly inhibited in KPC cells, likely due to the lower basal respiration and ATP production. Cumulatively, these findings suggest that driver mutations affect the signaling capacity of pancreatic acinar cells even before the changes in the epithelial cell morphology become apparent.
Compound heterozygous IFT81 variations in a skeletal ciliopathy patient cause Bardet–Biedl syndrome-like ciliary defects
Authors: Tasaki Koshi , Zhou Zhuang , Ishida Yamato , Katoh Yohei , Nakayama Kazuhisa
Published: July 2023

Owing to their crucial roles in development and homeostasis, defects in cilia cause ciliopathies with diverse clinical manifestations. The intraflagellar transport (IFT) machinery, containing the IFT-A and IFT-B complexes, mediates not only the intraciliary bidirectional trafficking but also import and export of ciliary proteins together with the kinesin-2 and dynein-2 motor complexes. The BBSome, containing eight subunits encoded by causative genes of Bardet–Biedl syndrome (BBS), connects the IFT machinery to ciliary membrane proteins to mediate their export from cilia. Although mutations in subunits of the IFT-A and dynein-2 complexes cause skeletal ciliopathies, mutations in some IFT-B subunits are also known to cause skeletal ciliopathies. We here show that compound heterozygous variations of an IFT-B subunit, IFT81, found in a patient with skeletal ciliopathy cause defects in its interactions with other IFT-B subunits, and in ciliogenesis and ciliary protein trafficking when one of the two variants was expressed in IFT81-knockout (KO) cells. Notably, we found that IFT81-KO cells expressing IFT81(Δ490–519), which lacks the binding site for the IFT25-IFT27 dimer, causes ciliary defects reminiscent of those found in BBS cells and those in IFT74-KO cells expressing a BBS variant of IFT74, which forms a heterodimer with IFT81. In addition, IFT81-KO cells expressing IFT81(Δ490–519) in combination with the other variant, IFT81 (L645*), which mimics the cellular conditions of the above skeletal ciliopathy patient, demonstrated essentially the same phenotype as those expressing only IFT81(Δ490–519). Thus, our data indicate that BBS-like defects can be caused by skeletal ciliopathy variants of IFT81.
Association of patient experience and the quality of hospital care
Authors: Abdalla Rawia , Pavlova Milena , Groot Wim
Published: July 2023

The association between patient experience and the quality of hospital care is controversial. We assess the association between clinical outcomes and patient-reported experience measures (PREMs) in hospitals in Saudi Arabia. Knowledge on this issue informs value-based health-care reforms. A retrospective observational study was conducted in 17 hospitals in Saudi Arabia during the period of 2019–22. Hospital data were collected on PREMs, mortality, readmission, length of stay (LOS), central line–associated bloodstream infection (CLABSI), catheter-associated urinary tract infection (CAUTI), and surgical site infection. Descriptive analysis was used to describe hospital characteristics. Spearman’s rho correlation tests were used to assess the correlation between these measures, and multivariate generalized linear mixed model regression analysis was used to study associations while controlling for hospital characteristics and year. Our analysis showed that PREMs were negatively correlated with hospital readmission rate (r = −0.332, P ≤ .01), LOS (r = −0.299, P ≤ .01), CLABSI (r = −0.297, P ≤ .01), CAUTI (r = −0.393, P ≤ .01), and surgical site infection (r = −0.298, P ≤ .01). The results indicated that CAUTI and LOS converged negatively with PREMs (β = −0.548, P = .005; β = −0.873, P = .008, respectively) and that larger hospitals tended to have better patient experience scores (β =0.009, P = .003). Our findings suggest that better performance in clinical outcomes is associated with higher PREM scores. PREMs are not a substitute or surrogate for clinical quality. Yet, PREMs are complementary to other objective measures of patient-reported outcomes, the process of care, and clinical outcomes.
Development of economic thresholds for pea aphid (Hemiptera: Aphididae) management in lentil (Fabaceae) based on in-field insecticide efficacy trials
Authors: Zhou Ningxing , Wist Tyler , Prager Sean M
Published: July 2023

Pea aphid (Acyrthosiphom pisum Harris, Hemiptera: Aphididae) presents a significant economic challenge to lentil (Lens culinaris Medik.) production in the major growing region of Saskatchewan, Canada. During 2019–2020, field experiments were conducted to optimize the management tools for pea aphid control on lentils. A randomized split-plot design was used with main plots consisting of different pea aphid pressures and subplots consisting of different insecticide treatments. The main plot design was aimed to assess the impact of A. pisum feeding on lentil yields during the late vegetative to early reproductive stages. Subplots of the study evaluated the efficacy of 3 insecticides in suppressing pea aphid populations on lentils. Lentil is susceptible to A. pisum feeding and requires management at low pest densities. The economic threshold for pea aphids on lentil crops varied depending on environmental conditions, ranging from 20 to 66 aphids per sweep, calculated using a discrete daily growth rate of 1.116. The estimated economic thresholds provided a 7-day lead time before aphid populations achieved the economic injury level (EIL). The EIL was defined as 78 ± 14 aphids per sweep net sample or 743 ± 137 cumulative aphid days from the first aphid present in the field. In addition, the results of the study found that, on average, foliar applications of insecticides containing the pyrethroid active ingredient lambda-cyhalothrin (IRAC group: 3A) reduced pea aphid populations by 83% compared with untreated control.