bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of misclassified defective proviruses on HIV reservoir measurements
Authors: Reeves Daniel B. , Gaebler Christian , Oliveira Thiago Y. , Peluso Michael J. , Schiffer Joshua T. , Cohn Lillian B. , Deeks Steven G. , Nussenzweig Michel C. 
Published: July 2023

AbstractMost proviruses persisting in people living with HIV (PWH) on antiretroviral therapy (ART) are defective. However, rarer intact proviruses almost always reinitiate viral rebound if ART stops. Therefore, assessing therapies to prevent viral rebound hinges on specifically quantifying intact proviruses. We evaluated the same samples from 10 male PWH on ART using the two-probe intact proviral DNA assay (IPDA) and near full length (nfl) Q4PCR. Both assays admitted similar ratios of intact to total HIV DNA, but IPDA found ~40-fold more intact proviruses. Neither assay suggested defective proviruses decay over 10 years. However, the mean intact half-lives were different: 108 months for IPDA and 65 months for Q4PCR. To reconcile this difference, we modeled additional longitudinal IPDA data and showed that decelerating intact decay could arise from very long-lived intact proviruses and/or misclassified defective proviruses: slowly decaying defective proviruses that are intact in IPDA probe locations (estimated up to 5%, in agreement with sequence library based predictions). The model also demonstrates how misclassification can lead to underestimated efficacy of therapies that exclusively reduce intact proviruses. We conclude that sensitive multi-probe assays combined with specific nfl-verified assays would be optimal to document absolute and changing levels of intact HIV proviruses.
Discovery and mechanism-guided engineering of BHET hydrolases for improved PET recycling and upcycling
Authors: Li Anni , Sheng Yijie , Cui Haiyang , Wang Minghui , Wu Luxuan , Song Yibo , Yang Rongrong , Li Xiujuan , Huang He 
Published: July 2023

AbstractAlthough considerable research achievements have been made to address the plastic crisis using enzymes, their applications are limited due to incomplete degradation and low efficiency. Herein, we report the identification and subsequent engineering of BHETases, which have the potential to improve the efficiency of PET recycling and upcycling. Two BHETases (ChryBHETase and BsEst) are identified from the environment via enzyme mining. Subsequently, mechanism-guided barrier engineering is employed to yield two robust and thermostable ΔBHETases with up to 3.5-fold enhanced kcat/KM than wild-type, followed by atomic resolution understanding. Coupling ΔBHETase into a two-enzyme system overcomes the challenge of heterogeneous product formation and results in up to 7.0-fold improved TPA production than seven state-of-the-art PET hydrolases, under the conditions used here. Finally, we employ a ΔBHETase-joined tandem chemical-enzymatic approach to valorize 21 commercial post-consumed plastics into virgin PET and an example chemical (p-phthaloyl chloride) for achieving the closed-loop PET recycling and open-loop PET upcycling.
Genes associated with cognitive ability and HAR show overlapping expression patterns in human cortical neuron types
Authors: Driessens Stan L. W. , Galakhova Anna A. , Heyer Djai B. , Pieterse Isabel J. , Wilbers René , Mertens Eline J. , Waleboer Femke , Heistek Tim S. , Coenen Loet , Meijer Julia R. , Idema Sander , de Witt Hamer Philip C. , Noske David P. , de Kock Christiaan P. J. , Lee Brian R. , Smith Kimberly , Ting Jonathan T. , Lein Ed S. , Mansvelder Huibert D. , Goriounova Natalia A. 
Published: July 2023

AbstractGWAS have identified numerous genes associated with human cognition but their cell type expression profiles in the human brain are unknown. These genes overlap with human accelerated regions (HARs) implicated in human brain evolution and might act on the same biological processes. Here, we investigated whether these gene sets are expressed in adult human cortical neurons, and how their expression relates to neuronal function and structure. We find that these gene sets are preferentially expressed in L3 pyramidal neurons in middle temporal gyrus (MTG). Furthermore, neurons with higher expression had larger total dendritic length (TDL) and faster action potential (AP) kinetics, properties previously linked to intelligence. We identify a subset of genes associated with TDL or AP kinetics with predominantly synaptic functions and high abundance of HARs.
The host–guest inclusion driven by host-stabilized charge transfer for construction of sequentially red-shifted mechanochromic system
Authors: Sun Dongdong , Wu Yong , Han Xie , Liu Simin 
Published: July 2023

AbstractDeveloping more extensive methods to understand the underlying structure-property relationship of mechanochromic luminescent molecules is demanding but remains challenging. Herein, the effect of host-guest interaction on the mechanochromic properties of organic molecules is illustrated. A series of pyridinium-functionalized triphenylamine derivatives show bathochromic-shifted emission upon mechanical stimulation. These derivatives bind to cucurbit[8]uril to form homoternary host-guest inclusion complexes through host-stabilized intermolecular charge transfer interactions. Remarkably, the homoternary complexes exhibit longer emission than that of free guests in the solid state (even longer than ground guests), and a further bathochromic-shifted emission is observed upon grinding. Additionally, a heteroternary complex constructed through the encapsulation of pyrene (donor) and pyridinium (acceptor) guest pair in cucurbit[8]uril also displays the mechanochromic luminescent property. This work not only discloses the effect of host-guest inclusion on the mechanochromic property of organic molecules, but also provides a principle and a facile way to design the sequentially red-shifted mechanochromic materials.
High-throughput design of perpendicular magnetic anisotropy at quaternary Heusler and MgO interfaces
Authors: Jiang Sicong , Yang Kesong 
Published: July 2023

AbstractHeusler alloys combined with MgO interfaces exhibit interfacial perpendicular magnetic anisotropy, making them attractive for energy-efficient spintronic technologies. However, finding suitable Heusler/MgO heterostructures with desired properties is challenging due to the vast range of compositions available and the complexity of interfacial structures, particularly for the emerging quaternary Heusler compounds. In this study, we report a high-throughput screening of quaternary-Heusler/MgO heterostructures for spintronic applications. By analyzing various materials descriptors, including formation energy, convex hull distance, magnetic ordering, lattice misfit, magnetic anisotropy constant, tunnel magnetoresistance, Curie temperature, and atomic site disordering, we identified 5 promising compounds out of 27,000 quaternary Heusler compounds. These compounds, namely IrCrAlTi, IrCrGaTi, IrMnZnTi, OsCrAlTa, and TaGaOsCr, show potential for designing energy-efficient perpendicular magnetic tunnel junctions. This work demonstrates an efficient approach using open quantum materials repositories, effective materials descriptors, and high-throughput computational techniques to accelerate the discovery of quaternary-Heusler-based functional materials.
Spectroscopic characterization of the quantum linear-zigzag transition in trapped ions
Authors: Zhang J. , Chow B. T. , Ejtemaee S. , Haljan P. C. 
Published: July 2023

AbstractWhile engineered quantum systems are a general route to the manipulation of multipartite quantum states, access in a physical system to a continuous quantum phase transition under sufficient control offers the possibility of an intrinsic source of entangled states. To this end we realize the quantum version of the linear-zigzag structural transition for arrays of up to five ground state-cooled ions held in a linear Paul trap and we demonstrate several of the control requirements towards entangled-state interferometry near the critical point. Using in situ spectroscopy we probe the energy level structure and occupation of the soft mode associated with the structural transition, and show a stable critical point and majority ground state occupation crossing the transition. We resolve biases arising from trap electrode asymmetries that change the nature of the transition, show that they can be suppressed by varying the ion number, and demonstrate control of the transition bias using optical dipole forces.
Thiophosphate photochemistry enables prebiotic access to sugars and terpenoid precursors
Authors: Ritson Dougal J. , Sutherland John D. 
Published: July 2023

AbstractOver the past few years, evidence has accrued that demonstrates that terrestrial photochemical reactions could have provided numerous (proto)biomolecules with implications for the origin of life. This chemistry simply relies on UV light, inorganic sulfur species and hydrogen cyanide. Recently, we reported that, under the same conditions, reduced phosphorus species, such as those delivered by meteorites, can be oxidized to orthophosphate, generating thiophosphate in the process. Here we describe an investigation of the properties of thiophosphate as well as additional possible means for its formation on primitive Earth. We show that several reported prebiotic reactions, including the photoreduction of thioamides, carbonyl groups and cyanohydrins, can be markedly improved, and that tetroses and pentoses can be accessed from hydrogen cyanide through a Kiliani–Fischer-type process without progressing to higher sugars. We also demonstrate that thiophosphate allows photochemical reductive aminations, and that thiophosphate chemistry allows a plausible prebiotic synthesis of the C5 moieties used in extant terpene and terpenoid biosynthesis, namely dimethylallyl alcohol and isopentenyl alcohol.
Present-day North Atlantic salinity constrains future warming of the Northern Hemisphere
Authors: Park In-Hong , Yeh Sang-Wook , Cai Wenju , Wang Guojian , Min Seung-Ki , Lee Sang-Ki 
Published: July 2023

AbstractEarth system models exhibit considerable intermodel spread in Atlantic Meridional Overturning Circulation intensity and its carbon uptake, resulting in great uncertainty in future climate. Here we show that present-day sea surface salinity (SSS) in the North Atlantic subpolar region modulates anthropogenic carbon uptake in the North Atlantic, and thus can be used to constrain future warming. Specifically, models that generate a present-day higher SSS in the North Atlantic subpolar region generate a greater uptake of anthropogenic carbon in the future, suppressing the greenhouse effect and resulting in slower warming, and vice versa in models with a present-day lower SSS. Emergent constraints based on the observed SSS greatly reduce the uncertainty of the Northern Hemisphere surface temperature warming and accumulative carbon uptake by about 30% and 53%, respectively, by the end of the twenty-first century under the Shared Socioeconomic Pathways 5–8.5 scenario.
Positive and Negative Affect Schedule in early COVID-19 pandemic
Authors: Andreu-Sánchez Celia , Martín-Pascual Miguel Ángel 
Published: July 2023

AbstractThe COVID-19 pandemic is the first pandemic in the Information Age. It started in Asia and spread rapidly around the world. As a consequence, millions of people were subject to lockdowns, and traditional media and social media reached more people. Our study, carried out during the lockdown, asked people about their feelings and emotions and included a Positive and Negative Affect Schedule (PANAS). Here, we present the data resulting from that study, which could potentially be reused by psychologists interested in learning about the emotional effects of the COVID-19 pandemic as well as to make comparisons before and after the lockdown period in 2020.
An extinct deep-snouted Alligator species from the Quaternary of Thailand and comments on the evolution of crushing dentition in alligatorids
Authors: Darlim Gustavo , Suraprasit Kantapon , Chaimanee Yaowalak , Tian Pannipa , Yamee Chotima , Rugbumrung Mana , Kaweera Adulwit , Rabi Márton 
Published: July 2023

AbstractFossil Alligator remains from Asia are critical for tracing the enigmatic evolutionary origin of the Chinese alligator, Alligator sinensis, the only living representative of Alligatoridae outside the New World. The Asian fossil record is extremely scarce and it remains unknown whether A. sinensis is an anagenetic lineage or alternatively, extinct divergent species were once present. We provide a detailed comparative description of a morphologically highly distinct Alligator skull from the Quaternary of Thailand. Several autapomorphic characters warrant the designation of a new species. Alligator munensis sp. nov. shares obvious derived features with A. sinensis but autapomorphies imply a cladogenetic split, possibly driven by the uplift of the southeastern Tibetan plateau. The presence of enlarged posterior alveoli in Alligator munensis is most consistent with a reversal to the alligatorine ancestral condition of having crushing dentition, a morphology strikingly absent among living alligatorids. Crushing dentition has been previously considered to indicate an ecological specialisation in early alligatorines that was subsequently lost in Alligator spp. However, we argue that there is yet no evidence for crushing dentition reflecting an adaptation for a narrower niche, while opportunistic feeding, including seasonal utilisation of hard-shelled preys, is a reasonable alternative interpretation of its function.
Treatment effects of Herbst appliance in skeletal Class II cases during pre-pubertal and post-pubertal periods: a cone-beam computed tomographic study
Authors: Farouk Khaled , Eissa Osama , Ghoneima Ahmed , El-Bedwehi Ashraf , Abdel-Fattah Ezzat , Hussein Farouk , El-Bialy Tarek 
Published: July 2023

AbstractIn the present study, Thirty-six Class patients II (A condition in which the upper jaw is larger than the lower jaw) were randomly selected and assigned to one of two groups based on their maturation stage: the pre-pubertal group (18 patients, mean age 9.15 ± 1.5 years) and post-pubertal group (18 patients, mean age 16.3 ± 1.0 years). All patients were treated with a metallic splint-supported Herbst IV appliance (An appliance that acts like artificial joint working between the upper and power jaws that keeps the lower jaw in a forward position, thus improving the Class II condition). Pretreatment (T1) and post-Herbst IV treatment (T2) scans were obtained for both groups. Dental and skeletal measurements were made on the scans and statistically analyzed using paired and independent t-tests. The study hypothesis was that; the dentoskeletal changes in Class II malocclusion treatment using Herbst appliance in the Pre-pubertal is more than the Post-pubertal growth stage due to the remaining growth potential for the pre-pubertal patients. The comparison between the two groups revealed statistically significant differences in horizontal skeletal parameters in the lower jaw only, while other readings were similar.
Channeling is a distinct class of dissolution in complex porous media
Authors: Menke Hannah P. , Maes Julien , Geiger Sebastian 
Published: July 2023

AbstractThe traditional model of solid dissolution in porous media consists of three dissolution regimes (uniform, compact, wormhole)—or patterns—that are established depending on the relative dominance of reaction rate, flow, and diffusion. In this work, we investigate the evolution of pore structure using numerical simulations during acid injection on two models of increasing complexity. We investigate the boundaries between dissolution regimes and characterize the existence of a fourth dissolution regime called channeling, where initially fast flow pathways are preferentially widened by dissolution. Channeling occurs in cases where the distribution in pore throat size results in orders of magnitude differences in flow rate for different flow pathways. This focusing of dissolution along only dominant flow paths induces an immediate, large change in permeability with a comparatively small change in porosity, resulting in a porosity–permeability relationship unlike any that has been previously seen. This work suggests that the traditional conceptual model of dissolution regimes must be updated to incorporate the channeling regime for reliable forecasting of dissolution in applications like geothermal energy production and geologic carbon storage.
Growth factors and mechano-regulated reciprocal crosstalk with extracellular matrix tune the keratocyte–fibroblast/myofibroblast transition
Authors: Pot Simon A. , Lin Zhe , Shiu Jauye , Benn Mario C. , Vogel Viola 
Published: July 2023

AbstractImproper healing of the cornea after injury, infections or surgery can lead to corneal scar formation, which is associated with the transition of resident corneal keratocytes into activated fibroblasts and myofibroblasts (K–F/M). Myofibroblasts can create an extracellular matrix (ECM) niche in which fibrosis is promoted and perpetuated, resulting in progressive tissue opacification and vision loss. As a reversion back to quiescent keratocytes is essential to restore corneal transparency after injury, we characterized how growth factors with demonstrated profibrotic effects (PDGF, FGF, FBS, TGFβ1) induce the K–F/M transition, and whether their withdrawal can revert it. Indeed, the upregulated expression of αSMA and the associated changes in cytoskeletal architecture correlated with increases in cell contractility, fibronectin (Fn) and collagen matrix density and Fn fiber strain, as revealed by 2D cell culture, nanopillar cellular force mapping and a FRET-labeled Fn tension probe. Substrate mechanosensing drove a more complete K–F/M transition reversal following growth factor withdrawal on nanopillar arrays than on planar glass substrates. Using decellularized ECM scaffolds, we demonstrated that the K–F/M transition was inhibited in keratocytes reseeded onto myofibroblast-assembled, and/or collagen-1-rich ECM. This supports the presence of a myofibroblast-derived ECM niche that contains cues favoring tissue homeostasis rather than fibrosis.
Early Mesozoic burst of morphological disparity in the slow-evolving coelacanth fish lineage
Authors: Ferrante Christophe , Cavin Lionel 
Published: July 2023

AbstractSince the split of the coelacanth lineage from other osteichthyans 420 million years ago, the morphological disparity of this clade has remained remarkably stable. Only few outliers with peculiar body shape stood out over the evolutionary history, but they were phylogenetically and stratigraphically independent of each other. Here, we report the discovery of a new clade of ancient latimeriid coelacanths representing a small flock of species present in the Western Tethys between 242 and 241 million years ago. Among the four species, two show highly derived anatomy. A new genus shows reversal to plesiomorphic conditions in its skull and caudal fin organisation. The new genus and its sister Foreyia have anatomical modules that moved from the general coelacanth Bauplau either in the same direction or in opposite direction that affect proportions of the body, opercle and fins. Comparisons with extant genetic models shows that changes of the regulatory network of the Hedgehog signal gene family may account for most of the altered anatomy. This unexpected, short and confined new clade represents the only known example of a burst of morphological disparity over the long history of coelacanths at a recovery period after the Permian–Triassic Mass Extinction.
9000 years of change in coral community structure and accretion in Belize reefs, western Atlantic
Authors: Gischler Eberhard , Hudson J. Harold , Eisenhauer Anton , Parang Soran , Deveaux Michael 
Published: July 2023

AbstractTropical coral reefs, as prominent marine diversity hotspots, are in decline, and long-term studies help to improve understanding of the effects of global warming, sea-level rise, ocean acidification, deterioration of water quality, and disease. Here, we evaluated relative coral abundance and reef accretion rates over the past 9000 years in Belize barrier and atoll reefs, the largest reef system in the Atlantic Ocean.Acropora palmataandOrbicellaspp. have been the most common corals. The abundance of competitive, fast-growing acroporids was constant over multi-millennial timescales. A decline inA. cervicornisabundance, however, and three centennial-scale gaps inA. palmataoccurrence, suggest that the modern decline in acroporids was not unprecedented. Stress-tolerant corals predominate at the beginning of Holocene successions. Following the improvement of environmental conditions after inundation of the reef pedestal, their abundance has decreased. The abundance of weedy corals has increased during the Holocene underlining the importance of fecundity for the coral community. Reef-accretion rate, as calculated based on 76 new U-series age dates, has decreased over the Holocene and the mean value of 3.36 m kyr−1is at the lower end of global reef growth compilations and predicted future rates of rise in sea level.
Life cycle assessment of microgreen production: effects of indoor vertical farm management on yield and environmental performance
Authors: Parkes Michael G. , Azevedo Duarte Leal , Cavallo Ana Celeste , Domingos Tiago , Teixeira Ricardo F. M. 
Published: July 2023

AbstractThe global production of plant-based foods is a significant contributor to greenhouse gas emissions. Indoor vertical farms (IVFs) have emerged as a promising approach to urban agriculture. However, their environmental performance is not well understood, particularly in relation to operational choices where global warming potentials (GWP) can vary between 0.01–54 kg CO2e/kg−1 of leafy greens produced. We conducted a life cycle assessment (LCA) of a building-integrated IVF for microgreen production to analyse a range of operational conditions for cultivation: air temperature, CO2 concentration, and photoperiod. We analyzed a dynamic LCA inventory that combined a process-based plant growth model and a mass balance model for air and heat exchange between the chamber and the outside. Results showed that the GWP of IVFs can vary greatly depending on the operation conditions set, ranging from 3.3 to 63.3 kg CO2e/kg−1. The optimal conditions for minimizing GWP were identified as 20 ℃, maximum CO2 concentration in the chamber, and maximum photoperiod, which led to a minimum GWP of 3.3 kg CO2e/kg−1 and maximum production of 290.5 kg fresh weight week-1. Intensification of production thus led to lower impacts because the marginal increase in yield due to increased resource use was larger than the marginal increase in impact. Therefore, adjusting growing conditions is essential for the sustainability of urban food production.