bluuebunny/crossref_metadata_2025 huggingface dataset:
An ab initio study for the photodissociation of HCl and HF
Authors: Qin Zhi , Bai Tianrui , Liu Linhua
Published: August 2022

Detailed studies of HCl and HF photodissociation are required for an in-depth understanding the chlorine and fluorine chemistry in Venus and exoplanets. Here, we present an ab initio study of photodissociation of HCl and HF. Except for the widely studied A 1Π←X 1Σ+ photodissociation process, the ground-state photodissociation processes for HCl and HF via higher excited states are considered. State-resolved cross-sections are computed for nine photodissociation processes of HCl from a total of 871 ground rovibrational levels. For HF, seven photodissociation processes are considered for the computation of state-resolved cross-sections from all the rovibrational levels in the ground state. Subsequently, temperature-dependent cross-sections for the considered transition processes of HCl and HF are estimated from 0 to 10 000 K with a grid of 34 temperatures. Careful comparisons with the recent ExoMol study and the Leiden Observatory database are made. The photodissociation rates in the interstellar and blackbody radiation fields are also discussed.
Chaotic diffusion of asteroids in the exterior 1:2 mean motion resonance with Mars
Authors: Christou Apostolos A , Dermott Stanley F , Li Dan
Published: August 2022

The inner asteroid belt between 2.1 and 2.5 au is of particular dynamical significance because it is the dominant source of both chondritic meteorites and near-Earth asteroids. This inner belt is bounded by an eccentricity-type secular resonance and by the 1:3 mean motion resonance with Jupiter. Unless asteroid perihelia are low enough to allow scattering by Mars, escape requires transport to one of the bounding resonances. In addition Yarkovsky forces are generally ineffective in changing either the eccentricity and/or inclination for asteroids with diameter ≳30 km. Thus, large asteroids with pericentres far from Mars may only escape from the inner belt through large changes in their eccentricities. In this paper, we study chaotic diffusion of orbits near the 1:2 mean motion resonance with Mars in a systematic way. We show that, while chaotic orbital evolution in both resonant and non-resonant orbits increase the dispersion of the inclinations and eccentricities, it does not significantly change their mean values. We show further that, while the dispersive growth is greatest for resonant orbits, at high e the resonance acts to mitigate asteroid scattering by Mars - making the asteroid lifetime in the belt longer than it would have been for a non-resonant orbit. For asteroids of all sizes in both resonant and non-resonant orbits, the changes in eccentricity needed to account for the observations cannot be achieved by gravitational forces alone. The role of resonant trapping in protecting asteroids from encounters with Mars is also analysed.
Formation of black holes in the pair-instability mass gap: Evolution of a post-collision star
Authors: Costa Guglielmo , Ballone Alessandro , Mapelli Michela , Bressan Alessandro
Published: August 2022

The detection of GW190521 by the LIGO–Virgo collaboration has revealed the existence of black holes (BHs) in the pair-instability (PI) mass gap. Here, we investigate the formation of BHs in the PI mass gap via star–star collisions in young stellar clusters. To avoid PI, the stellar-collision product must have a relatively small core and a massive envelope. We generate our initial conditions from the outputs of a hydrodynamical simulation of the collision between a core helium burning star (∼58 M⊙) and a main-sequence star (∼42 M⊙). The hydrodynamical simulation allows us to take into account the mass lost during the collision (∼12 M⊙) and to build the chemical composition profile of the post-collision star. We then evolve the collision product with the stellar evolution codes parsec and mesa. We find that the post-collision star evolves through all the stellar burning phases until core collapse, avoiding PI. At the onset of core collapse, the post-collision product is a blue supergiant star. We estimate a total mass-loss of about 1 M⊙ during the post-collision evolution, due to stellar winds and shocks induced by neutrino emission in a failed supernova. The final BH mass is ≈87 M⊙. Therefore, we confirm that the collision scenario is a suitable formation channel to populate the PI mass gap.
Metalation calculators for E. coli strain JM109 (DE3): aerobic, anaerobic, and hydrogen peroxide exposed cells cultured in LB media
Authors: Foster Andrew W , Clough Sophie E , Aki Zeynep , Young Tessa R , Clarke Alison R , Robinson Nigel J
Published: August 2022

Three Web-based calculators, and three analogous spreadsheets, have been generated that predict in vivo metal occupancies of proteins based on known metal affinities. The calculations exploit estimates of the availabilities of the labile buffered pools of different metals inside a cell. Here, metal availabilities have been estimated for a strain of Escherichia coli that is commonly used in molecular biology and biochemistry research, e.g. in the production of recombinant proteins. Metal availabilities have been examined for cells grown in Luria-Bertani (LB) medium aerobically, anaerobically, and in response to H2O2 by monitoring the abundance of a selected set of metal-responsive transcripts by quantitative polymerase chain reaction (qPCR). The selected genes are regulated by DNA-binding metal sensors that have been thermodynamically characterized in related bacterial cells enabling gene expression to be read out as a function of intracellular metal availabilities expressed as free energies for forming metal complexes. The calculators compare these values with the free energies for forming complexes with the protein of interest, derived from metal affinities, to estimate how effectively the protein can compete with exchangeable binding sites in the intracellular milieu. The calculators then inter-compete the different metals, limiting total occupancy of the site to a maximum stoichiometry of 1, to output percentage occupancies with each metal. In addition to making these new and conditional calculators available, an original purpose of this article was to provide a tutorial that discusses constraints of this approach and presents ways in which such calculators might be exploited in basic and applied research, and in next-generation manufacturing.
Layer Hall effect induced by hidden Berry curvature in antiferromagnetic insulators
Authors: Chen Rui , Sun Hai-Peng , Gu Mingqiang , Hua Chun-Bo , Liu Qihang , Lu Hai-Zhou , Xie X C
Published: August 2022

The layer Hall effect describes electrons spontaneously deflected to opposite sides at different layers, which has been experimentally reported in the MnBi2Te4 thin films under perpendicular electric fields. Here, we reveal a universal origin of the layer Hall effect in terms of the so-called hidden Berry curvature, as well as material design principles. Hence, it gives rise to zero Berry curvature in momentum space but non-zero layer-locked hidden Berry curvature in real space. We show that, compared to that of a trivial insulator, the layer Hall effect is significantly enhanced in antiferromagnetic topological insulators. Our universal picture provides a paradigm for revealing the hidden physics as a result of the interplay between the global and local symmetries, and can be generalized in various scenarios.
Cavitation in a soft porous material
Authors: Leng Yu , Vlachos Pavlos P , Juanes Ruben , Gomez Hector
Published: August 2022

We study the collapse and expansion of a cavitation bubble in a deformable porous medium. We develop a continuum-scale model that couples compressible fluid flow in the pore network with the elastic response of a solid skeleton. Under the assumption of spherical symmetry, our model can be reduced to an ordinary differential equation that extends the Rayleigh–Plesset equation to bubbles in soft porous media. The extended Rayleigh–Plesset equation reveals that finite-size effects lead to the breakdown of the universal scaling relation between bubble radius and time that holds in the infinite-size limit. Our data indicate that the deformability of the porous medium slows down the collapse and expansion processes, a result with important consequences for wide-ranging phenomena, from drug delivery to spore dispersion.
Mass-selective and ice-free electron cryomicroscopy protein sample preparation via native electrospray ion-beam deposition
Authors: Esser Tim K , Böhning Jan , Fremdling Paul , Agasid Mark T , Costin Adam , Fort Kyle , Konijnenberg Albert , Gilbert Joshua D , Bahm Alan , Makarov Alexander , Robinson Carol V , Benesch Justin L P , Baker Lindsay , Bharat Tanmay A M , Gault Joseph , Rauschenbach Stephan
Published: August 2022

Despite tremendous advances in sample preparation and classification algorithms for electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA), sample heterogeneity remains a major challenge and can prevent access to high-resolution structures. In addition, optimization of preparation conditions for a given sample can be time-consuming. In the current work, it is demonstrated that native electrospray ion-beam deposition (native ES-IBD) is an alternative, reliable approach for the preparation of extremely high-purity samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, separated from other proteins, contaminants, aggregates, and fragments, gently deposited on cryo-EM grids, frozen in liquid nitrogen, and subsequently imaged by cryo-EM. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected protein complexes. SPA reveals that the complexes remain folded and assembled, but variations in secondary and tertiary structures are currently limiting information in 2D classes and 3D EM density maps. We identify and discuss challenges that need to be addressed to obtain a resolution comparable to that of the established cryo-EM workflow. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM for protein structure determination and provide an essential link between gas-phase and solution-phase protein structures.
Comment on the subtlety of defining a real-time path integral in lattice gauge theories
Authors: Matsumoto Nobuyuki
Published: August 2022

Recently, Hoshina, Fujii, and Kikukawa pointed out that the naive lattice gauge theory action in the Minkowski signature does not result in a unitary theory in the continuum limit, and Kanwar and Wagman proposed alternative lattice actions to the Wilson action without divergences. We show here that the subtlety can be understood from the asymptotic expansion of the modified Bessel function, which has been discussed for the path integral of compact variables in nonrelativistic quantum mechanics. The essential ingredient for defining the appropriate continuum theory is the iε prescription, and with the proper implementation of this we show that the Wilson action can be used for real-time path integrals. It is important that iε should be implemented for both timelike and spacelike plaquettes. We also suggest why iε is required for the Wilson action from the Hamiltonian formalism: it is needed to manifestly suppress the contributions from singular paths, for which the Wilson action can give different values from those of the actual continuum action.
Sequence Dependent UV Damage of Complete Pools of Oligonucleotides
Authors: Kufner Corinna L. , Krebs Stefan , Fischaleck Marlis , Philippou-Massier Julia , Blum Helmut , Bucher Dominik B. , Braun Dieter , Zinth Wolfgang , Mast Christof B.
Published: August 2022

Understanding the sequence-dependent DNA damage formation requires to probe a complete pool of sequences over a wide dose range of the damage causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA with ultraviolet radiation at 266 nm and doses of up to 500 photons per base. At the dimer level our results confirm existing literature values, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow to predict their survival chances in high-UV environments.
They call me the wanderer – Neurovascular anatomy of dwarfed dinosaur implies precociality in sauropods
Authors: Schade Marco , Knötschke Nils , Hörnig Marie K. , Paetzel Carina , Stumpf Sebastian
Published: August 2022

Macronaria, a group of mostly colossal sauropod dinosaurs, comprised the largest terrestrial vertebrates of Earth’s history. However, some of the smallest sauropods belong to this group as well. The Late Jurassic macronarianEuropasaurus holgeriis one of the best-known sauropods worldwide. So far, the braincase material of this taxon from Germany pended greater attention. With the aid of microCT, we report on the neuroanatomy of the almost complete braincase of an adult individual, as well as the inner ears of one other adult and several juveniles (also containing so far unknown vascular cavities). The presence of large and morphologically adult inner ears in juvenile material suggests precociality. Our findings add to the diversity of neurovascular anatomy in sauropod braincases and buttress the perception of sauropods as fast-growing and autonomous giants with manifold facets of reproductive and social behavior. This suggests that – apart from sheer size – little separated the island dwarfEuropasaurusfrom its large-bodied relatives.
Soluble amyloid-β precursor peptide does not regulate GABAB receptor activity
Authors: Rem Pascal Dominic , Sereikaite Vita , Fernandez-Fernandez Diego , Reinartz Sebastian , Ulrich Daniel , Fritzius Thorsten , Trovò Luca , Roux Salome , Chen Ziyang , Rondard Philippe , Pin Jean-Philippe , Schwenk Jochen , Fakler Bernd , Gassmann Martin , Barkat Tania R. , Strømgaard Kristian , Bettler Bernhard
Published: August 2022

Amyloid-β precursor protein (APP) regulates neuronal activity through the release of secreted APP (sAPP) acting at cell-surface receptors. APP and sAPP were reported to bind to the extracellular sushi domain 1 (SD1) of GABAB receptors (GBRs). A 17 amino-acid peptide (APP17) derived from APP was sufficient for SD1 binding and shown to mimic the inhibitory effect of sAPP on neurotransmitter release and neuronal activity. The functional effects of APP17 and sAPP were similar to those of the GBR agonist baclofen and blocked by a GBR antagonist. These experiments led to the proposal that sAPP activates GBRs to exert its neuronal effects. However, whether APP17 and sAPP indeed influence classical GBR signaling pathways in heterologous cells was not analyzed. Here, we confirm that APP17 binds to GBRs with nanomolar affinity. However, biochemical and electrophysiological assays indicate that APP17 does not influence GBR activity in heterologous cells. Moreover, we found no evidence for APP17 regulating K+ currents in cultured neurons, neurotransmitter release in brain slices, or neuronal activity in vivo. Our results show that APP17 is not a functional GBR ligand and indicate that sAPP exerts neuronal effects through receptors other than GBRs.
Alternative promoters in CpG depleted regions pervasively account for epigenetic misregulation of cancer transcriptomes
Authors: Nepal Chirag , Andersen Jesper B.
Published: August 2022

Eukaryotic genes are regulated by multiple alternative promoters with distinct expression patterns. In cancer, alternative promoters are pervasively utilized, but our understanding of the mechanism of activation and how their regulatory architecture differs from reference promoters remains elusive. We analyzed 100 CAGE-seq libraries from HCC patients and annotated 4083 alternative promoters in 2926 multi-promoter genes that are known genes involved in hepatocarcinogenesis. Many alternative promoters are undetected in the normal liver. We find that multi-promoter genes are enriched among genes downregulated in the tumor, highlighting alternative promoters’ impact in global transcription changes in cancer. Alternative promoters are depleted for CpG islands, have narrow nucleosome depleted regions, and are enriched for sharp promoters as well as tissue-specific transcription factors. Alternative promoters have high DNA methylation levels around transcription start sites. Tumor cells globally lose DNA methylation, but there exists a hierarchical retention of intragenic DNA methylation, which is dictated by the genomic CG content. As such, intragenic CG-poor regions lose methylation, while CG-rich regions retain it, a phenomenon caused by differential binding of H3K36me3,DNMT3B, TET1andSETD2.Thus, the selective loss of DNA methylation in CG-poor regions opens the chromatin and makes these regions accessible for transcription. Upon transcription factors availability, alternative transcription can pervasively occur in cancer. These results provide a framework for understanding the importance of alternative promoters in controlling the tumor transcriptomes, highlighting their architecture and role in regulatory mechanism(s).
Lung Tumor Microphysiological System with 3D Endothelium to Evaluate Modulators of T-Cell Infiltration
Authors: Wisdom Katrina M. , Suijker Johnny , van den Broek Lenie , Sridharan BanuPriya , Grandhi Taraka Sai Pavan , Cheng Aaron , Lamb Mahdi , Titus Steven A. , Gehman Andrew , Poore Derek , Shah Niyant , Cheng Shih-Hsun , Kim Edward , Griffin Sue , Ekert Jason
Published: August 2022

Lung cancer is a leading cause of death worldwide, with only a fraction of patients responding to immunotherapy. The correlation between increased T-cell infiltration and positive patient outcomes has motivated the search for therapeutics promoting T-cell infiltration. While transwell and spheroid platforms have been employed, these models lack flow and endothelial barriers, and cannot faithfully model T-cell adhesion, extravasation and migration through 3D tissue. Presented here is a 3D chemotaxis assay, in a lung tumor on chip model with 3D endothelium (LToC-Endo), to address this need. The described assay consists of a vascular tubule cultured under rocking flow, through which T-cells are added; a collagenous stromal barrier, through which T-cells infiltrate; and a chemoattractant/tumor compartment. Here, activated T-cells extravasate and infiltrate in response to gradients of rhCXCL11 and rhCXCL12. Adopting a T-cell activation protocol with a rest period enables proliferative burst prior to introducing T-cells into chips, increases T-cell expression of CXCR3 and CXCR4 receptors, and enhances assay sensitivity. In addition, incorporating this rest recovers endothelial activation in response to rhCXCL12. As a final control, we show that blocking ICAM-1 interferes with T-cell adhesion and chemotaxis. This microphysiological system, which mimics in vivo stromal and vascular barriers, can be used to evaluate potentiation of immune chemotaxis into tumors while probing for vascular responses to potential therapeutics. Finally, we propose a translational strategy by which this assay could be linked to preclinical and clinical models to support human dose prediction, personalized medicine, and the reduction, refinement, and replacement of animal models.
MOSQUITO MICROBIOMES OF RWANDA: CHARACTERIZING MOSQUITO HOST AND MICROBIAL COMMUNITIES IN THE LAND OF A THOUSAND HILLS
Authors: Tokash-Peters Amanda G. , Niyonzima Jean Damascene , Kayirangwa Mirielle , Muhayimana Simon , Tokash Ivan W. , Jabon Jaimy D. , Lopez Sergio G. , Woodhams Douglas C.
Published: August 2022

Mosquitoes are a complex nuisance around the world, and tropical countries bear the greatest brunt of the burden of mosquito-borne diseases. Rwanda has had success in reducing malaria and some arboviral diseases over the last few years, but still faces challenges to elimination. By building our understanding ofin situmosquito communities in Rwanda at a disturbed, human-occupied site and at a natural, preserved site, we can build our understanding of natural mosquito microbiomes toward the goal of implementing novel microbial control methods. Here, we examined the composition of collected mosquitoes and their microbiomes at two diverse sites using Cytochrome c Oxidase I sequencing and 16S V4 barcode sequencing. The majority of mosquitoes captured and characterized in this study are the first-known record of their species for Rwanda but have been characterized in other nations in East Africa. Beta diversity metrics were significantly different between sampling sites, mosquito genera, and mosquito species, but not between mosquito sexes, catch method, or presumed bloodfed status. Bacteria of interest for arbovirus control,Asaia, Serratia, andWolbachia, were found in abundance at both sites, but were more prevalent at the disturbed site and varied greatly by species. Additional studies to build our understanding of naturally-formed microbial communities are essential to safely employing microbial control methods and further reducing the burden of mosquito-borne diseases.
Resource asynchrony and landscape homogenization as drivers of virulence evolution
Authors: Kürschner Tobias , Scherer Cédric , Radchuk Viktoriia , Blaum Niels , Kramer-Schadt Stephanie
Published: August 2022

In the last years, the emergence of zoonotic diseases and the frequency of disease outbreaks have increased substantially, fuelled by habitat encroachment and asynchrony of biological cycles due to global change. The virulence of these diseases is a key aspect for their success. In order to understand the complex processes of pathogen virulence evolution in the global change context, we adapted an established individual-based model of host-pathogen dynamics. Our model simulates a population of social hosts affected by an evolving pathogen in a dynamic landscape. Pathogen virulence evolution is explored by the inclusion of multiple strains in the model that differ in their transmission capability and lethality. Simultaneously, the host’s resource landscape is subjected to spatial and temporal dynamics, emulating effects of global change.

We found an increase in pathogenic virulence and a shift in strain dominance with increasing landscape homogenisation. Our model further shows a trend to lower virulence pathogens being dominant in fragmented landscapes, although pulses of highly virulent strains are expected under resource asynchrony. While all landscape scenarios favour coexistence of low and high virulent strains, when host density increases, the high virulence strains capitalize on the high possibility for transmission and are likely to become dominant.

Author Summary

Disease outbreaks primarily caused by contact with animals are increasing in recent years, related to habitat destruction and altered biological cycles due to climate change. Pathogens associated with such outbreaks will be more successful the more effectively they can spread in a population. Thus, understanding the conditions over which those pathogens evolve will help us to limit the impact of disease outbreaks in the future. To this end, we used an individual based model that allowed us to study different scenarios. Our model had three main components: a host-pathogen system, a dynamic resource landscape with different degrees of fragmentation and temporal resource mismatches. We used dynamic landscapes with varying resource amounts over the years and consisting of multiple large or smaller habitat clusters. Our simulations showed that homogenous landscapes resulted in higher virulent pathogens and fragmented landscapes in lesser virulent pathogens. However, across all scenarios, high and low virulent pathogen strains were able to coexist.
Persistent Hypersomnia Following Repetitive Mild Experimental Traumatic Brain Injury: Roles of Chronic Stress and Sex Differences
Authors: Portillo Edwin , Zi Xiaomei , Kim Yeonho , Tucker Laura B. , Fu Amanda , Miller Lauren A. , Valenzuela Krystal S. , Sullivan Genevieve M. , Gauff Amina K. , Yu Fengshan , Radomski Kryslaine L. , McCabe Joseph T. , Armstrong Regina C.
Published: August 2022

Traumatic brain injury (TBI) is often more complicated than a single head injury. An extreme example of this point may be military service members who experience a spectrum of exposures over a prolonged period under stressful conditions. Understanding the effects of complex exposures can support proper evaluation and care for patients experiencing persistent symptoms. We designed a longitudinal series of non-invasive procedures in adult mice to evaluate the effects of prolonged mild exposures. We assessed anxiety, depression, and sleep-wake dysfunction as symptoms that can impact long term outcomes after mild TBI. Unpredictable chronic mild stress (UCMS) was generated from a variable sequence of environmental stressors distributed within each of 21 days. Subsequently, mice received a mild blast combined with closed-head mild TBI on five days at 24-hour intervals. TBI components were either five linear force impacts, or a novel alternating repetitive mild TBI (Ar-mTBI) model of linear and rotational (CHIMERA) impacts over five days to produce diffuse pathology. In males and females, UCMS induced anxiety without depressive behavior. Persistent hypersomnia, specifically increased sleep during the active dark period, was found through 6-12 month time points in male mice receiving UCMS with repetitive blast plus TBI events, or surprisingly after UCMS alone. Sleep-wake dysfunction was not found with TBI events alone and was not found in females under any conditions. These results identify prolonged stress and sex differences as important considerations for sleep-wake dysfunction. Furthermore, this reproducible hypersomnia is similar to excessive daytime sleepiness reported in patients, which may inform treatments.
Distributed cortical regions for the recall of people, places and objects
Authors: Kidder Alexis , Silson Edward H , Nau Matthias , Baker Chris I
Published: August 2022

Human medial parietal cortex (MPC) is recruited during multiple cognitive processes. Previously, we demonstrated regions specific to recall of people or places and proposed that the functional organization of MPC mirrors the category selectivity defining the medial-lateral axis of ventral temporal cortex (VTC). However, prior work considered recall of people and places only and VTC also shows object-selectivity sandwiched between face- and scene-selective regions. Here, we tested a strong prediction of our proposal: like VTC, MPC should show a region specifically recruited during object recall, and its relative cortical position should mirror the one of VTC. While responses during people and place recall showed a striking replication of prior findings, we did not observe any evidence for object-recall effects within MPC, which differentiates it from the spatial organization in VTC. Importantly, beyond MPC, robust recall-effects were observed for people, places, and objects on the lateral surface of the brain. Place-recall effects were present in the angular gyrus, frontal eye fields and peripheral portions of early visual cortex, whereas people-recall selectively drove response in the right posterior superior temporal sulcus. Object-recall effects were largely restricted to a region posterior to left somatosensory cortex, in the vicinity of the supramarginal gyrus. Taken together, these data demonstrate that while there are distributed regions active during recall of people, places and objects, the functional organization of MPC does not mirror the medial-lateral axis of VTC but reflects only the most salient features of that axis - namely representations of people and places.

Significance statement

Human medial parietal cortex (MPC) is recruited during multiple cognitive processes. Recently, we proposed a framework for interpreting the functional organization of MPC by suggesting that it reflects the categorical preferences for people and places that is evident also in ventral temporal cortex (VTC). Because VTC also exhibits selectivity for objects, we here extend this framework to test whether MPC also shows object selectivity during recall. Robust people and place recall effects were evident in MPC, but we found no evidence for object-recall within MPC, suggesting that MPC and VTC are not mirror-copies of each other. Together, these data suggest that the functional organization of MPC reflects the most salient categorical representations within VTC for people and places.
A novel subtype of reactive astrocytes critical for HIV associated pain pathogenesis
Authors: Zheng Junying , Spurgat Michael , Tang Shao-Jun
Published: August 2022

Pathological pain is common in HIV patients, but the underlying mechanism remains elusive and therapeutic targets for effective treatment have not been identified. Reactive astrocytes are specifically activated in the spinal dorsal horn (SDH) of HIV patients with pathological pain and required for the development of HIV-associated pain in mouse models. These findings suggest a key role of reactive astrocytes in HIV-associated pain pathogenesis. However, due to the heterogeneity of reactive astrocytes, the pathogenic subtype is unknown. Using single-nucleus RNA-seq (snRNA-seq) transcriptomic analysis, we identified a novel subtype of HIV-pain associated astrocytes (HIPAs) in the lumbar spinal cord of the HIV -1 gp120 transgenic model. HIPAs were galectin 3 (Gal3)-positive and had transcriptomic signatures of phagocytosis and inflammation; they were also induced in the spinal cord of HIV patients. We showed HIPAs phagocytosed neuronal and synaptic components and were associated with neuronal degeneration. We found that knockout (KO) of Gal3 in gp120 transgenic mice severely diminished HIPAs. Interestingly, the activation of other astrocytes (e.g., homeostatic astrocytes) were also diminished in the Gla3 KO/gp120 transgenic mice. These results indicate that Gal3 is critical for gp120 to induce HIPAs, and that Gal3 may directly or via HIPAs to control the activation of other subtypes of astrocytes. Finally, we showed that the loss of HIPAs caused by Gal3 KO was associated with attenuated neuronal degeneration, neuroinflammation, and pain in gp120 transgenic mice. Collectively, our data suggest that HIPAs are a Gal3-expressing astrocytic subtype that mediates gp120-induced neurodegeneration and neuroinflammation in the spinal pain neural circuit during pain pathogenesis and is a potential cell target for treating HIV-associated pain.
Crosslinker Structure Modulates Bulk Mechanical Properties and Dictates hMSC Behavior on Hyaluronic Acid Hydrogels
Authors: Morton Logan D. , Castilla-Casadiego David A. , Palmer Ajay C. , Rosales Adrianne M.
Published: August 2022

Synthetic hydrogels are attractive platforms due in part to their highly tunable mechanics, which impact cell behavior and secretory profile. These mechanics are often controlled by altering the number of crosslinks or the total polymer concentration in the gel, leading to structure-property relationships that inherently couple network connectivity to the overall modulus. In contrast, the native extracellular matrix (ECM) contains structured biopolymers that enable stiff gels even at low polymer content, facilitating 3D cell culture and permeability of soluble factors. To mimic the hierarchical order of natural ECM, this work describes a synthetic hydrogel system in which mechanics are tuned using the structure of sequence-defined peptoid crosslinkers, while fixing network connectivity. Peptoid crosslinkers with different secondary structures are investigated: 1) a helical, molecularly stiff peptoid, 2) a non-helical, less stiff peptoid, and 3) an unstructured, relatively flexible peptoid. Bulk hydrogel storage modulus increases when crosslinkers of higher chain stiffness are used. In-vitro studies assess the viability, proliferation, cell morphology, and immunomodulatory activity of human mesenchymal stem cells (hMSCs) on each hydrogel substrate. Matrix mechanics regulate the morphology of hMSCs on the developed substrates, and all of the hydrogels studied upregulate IDO production over culture on TCP. Softer substrates further this upregulation to a plateau. Overall, this system offers a biomimetic strategy for decoupling hydrogel storage modulus from network connectivity, enabling systematic study of biomaterial properties on hMSC behavior and enhancement of cellular functionality for therapeutic applications.

Graphical Abstract
Genomics highlight an underestimation of the urban heat island effect on red oak phenology
Authors: Blumstein M. , Webster S. , Hopkins R. , Basler D. , Des Marais D. L
Published: August 2022

The phenological timing of leaf-out in temperate forests is a critical transition point each year, altering the global climate system via changes to carbon and hydrologic cycles and land-surface albedo. In turn, climate is impacting phenology by advancing leaf-out an average of 2.8 +/-0.35 days per decade as the planet warms. Thus, understanding the relationship between warming and leaf-out is critical for understanding future global change. Rural-to-urban gradients in temperature, which result in clines over which urban areas are up to 4°C warmer than their surrounding countryside (dubbed the urban heat island – UHI – effect), may be used as a space-for-time substitution in studies of response to climate change. However, studies have recently highlighted that using the UHI effect over space rather than measurements at the same site through time results in consistently weaker relationships between temperature and leaf-out date in spring (i.e., urban-to-rural gradients underpredict the impact of warming on leaf-out). While such studies suggest many potential environmental explanations, the effect of genetic diversity is often neglected. While sensitive to environmental warming, leaf-out phenology is also highly heritable. Given that rural areas are largely natural sites, they likely have higher intraspecific genetic diversity than urban sites, where plants are selected by land managers for a narrow set of resilience traits. Here we measured the environment, genomic background, and phenological timing of northern red oak (Q. rubra) over several years between an urban and rural site to demonstrate how genetic background explains why the UHI effect leads to an underprediction of plant response to warming. Using a space-for-time substitution, we found that the date of leaf-out at our sites is predicted to advance approximately 20 days over the next 80 years. However, if we further account for the genomic background at the two sites, leaf-out, phenology is predicted to advance 22 days; a 10% difference between the two models. We demonstrate that this stronger relationship is because urban trees are largely a monoculture and, moreover, are most closely related to individuals at the rural site that leaf out latest. We highlight the critical need to consider genetic background, particularly in studies examining highly heritable traits, because both environmentandgenetics are changing across rural-to-urban gradients.
Clarifying the role of an unavailable distractor in human multiattribute choice
Authors: Cao Yinan , Tsetsos Konstantinos
Published: August 2022

Decisions between two economic goods can be swayed by a thirdunavailable‘decoy’ alternative, which does not compete for choice, notoriously violating the principles of rational choice theory. Although decoy effects typically depend on the decoy’s position in a multiattribute choice space, recent studies using risky prospects (i.e., varying in reward and probability) reported a novel ‘positive’ decoy effect operating on a single ‘value’ dimension: the higher the ‘expected value’ of an unavailable (distractor) prospect was, the easier the discrimination between two available target prospects became, especially when their expected-value difference was small. Here we show that this unidimensional distractor effect affords alternative interpretations: it occurred because the distractor’s expected value covaried positively with the subjective utility difference between the two targets. Looking beyond this covariation, we report a modest ‘negative’ distractor effect operating on subjective utility, as well as classic multiattribute decoy effects. A normatively meaningful model (selective integration), in which subjective utilities are shaped by ‘intra-attribute’ information distortion, reproduces the multiattribute decoy effects, and as an epiphenomenon, the negative unidimensional distractor effect. These findings clarify the modulatory role of an unavailable distracting option, shedding fresh light on the mechanisms that govern multiattribute decisions.
A circuit mechanism for the coordinated actions of opposing neuropeptide and neurotransmitter signals
Authors: Soden Marta E. , Yee Joshua X. , Zweifel Larry S.
Published: August 2022

Fast-acting neurotransmitters and slow, modulatory neuropeptides are commonly co-released from neurons in the central nervous system (CNS), albeit from distinct synaptic vesicles1. The mechanisms of how co-released neurotransmitters and neuropeptides that have opposing actions, e.g., stimulatory versus inhibitory, work together to exert control of neural circuit output remain unclear. This question has been difficult to resolve due to the inability to selectively isolate these signaling pathways in a cell- and circuit-specific manner. To overcome these barriers, we developed a genetic-based anatomical disconnect procedure that utilizes distinct DNA recombinases to independently facilitate conditional in vivo CRISPR/Cas9 mutagenesis2 of neurotransmitter- and neuropeptide-related genes in distinct cell types in two different brain regions simultaneously. With this approach we demonstrate that the stimulatory neuropeptide neurotensin (Nts) and the inhibitory neurotransmitter γ-aminobutyric acid (GABA), which are co-released from neurons in the lateral hypothalamus (LH), work coordinately to activate dopamine neurons of the ventral tegmental area (VTA-DA). We show that GABA release from LH-Nts neurons acts on GABA neurons within the VTA to rapidly disinhibit VTA-DA neurons, while Nts signals through the Nts receptor 1 (Ntsr1) on VTA-DA neurons to promote a slow depolarization of these cells. Thus, these two signals act on distinct time scales through different cell types to enhance mesolimbic dopamine neuron activation, which optimizes behavioral reinforcement. These data demonstrate a circuit-based mechanism for the coordinated action of a neurotransmitter and neuropeptide with opposing effects on cell physiology.
Characterizing the genetic polymorphisms in 370 challenging medically relevant genes using long-read sequencing data from 41 human individuals among 19 global populations
Authors: Ji Yanfeng , Gong Jiao , Sedlazeck Fritz J , Fan Shaohua
Published: August 2022

Numerous challenging medically relevant genes (CMRGs) cannot be adequately investigated using next-generation sequencing, hindering the detection of functional variation among these genes. In this study, long-read sequencing data from 41 human individuals across 19 populations were analyzed using the current version of the human reference genome assembly (GRCh38) and a telomere-to-telomere assembly of the human genome (T2T-CHM13). After excluding 142 CMRGs containing windows with a depth of coverage (DoC) significantly deviating from the average DoC value of proteincoding regions in the GRCh38 (138) or T2T-CHM13 (47) assemblies, 179 and 263 CMRGs exhibited copy number variation (CNV) signal in GRCh38 and T2T-CHM13, respectively. In addition, 451 high-impact short variants were detected in 188 CMRGs. Further, some genetic alterations were individual- or continental-superpopulation-specific, suggesting a strong need to consider genetic background differences in future genetic testing and drug design studies. Finally, side-by-side comparisons of short variant calls in CMRGs using NGS and LRS data from 13 samples indicated that 15.79% to 33.96% of high-impact short variants in different individuals could only be detected using LRS data. The results described herein will be an important reference for future clinical and pharmacogenetic studies to further improve precision medicine.
Evaluation of a process to implement advance care planning conversations in primary care: uptake and patient experience
Authors: Arora Neha , Guenter Dale , Hafid Abe , Elston Dawn , Gallagher Erin , Winemaker Samantha , Hansen Nicolle , Waters Heather , Howard Michelle
Published: August 2022

Objective

Advance care planning (ACP) can support patients in achieving current and future medical care that aligns with their values and goals. In primary care, a lack of standardized processes hinders implementation of ACP conversations. This study reports a quality improvement process to identify and engage patients and clinicians in ACP.

Methods

Primary care clinicians received training in conversations based on the Serious Illness Conversation Guide and tools to support ACP. In December 2019, patients 65 years of age and older with chronic obstructive pulmonary disease were systematically identified, mailed ACP resources and telephoned by the clinic to invite them to an ACP appointment. We tracked the attendance of the patients and evaluated patient experience using a survey.

Results

Of the 91 patients telephoned, 50 were reached, and 27 attended the appointment. Further efforts were suspended in March 2020 due to the COVID-19 pandemic. Thirteen patients completed the survey. There were statistically significant increases in the patient’s perception of being heard and understood by their physician, feeling hopeful about quality of life and feeling peaceful.

Conclusion

This study provides evidence that with training, tools and processes, patients and primary care clinicians can be effectively engaged in ACP conversations.

KEY MESSAGES

What was already known?

Training resources exist for help clinicians enhance their advance care planning communication skills

Besides a need for skills, other practical challenges exist in implementing advance care planning in family practice

What are the new findings?

Structured patient identification and preparation can facilitate advance care planning conversations in family practice

Patients reported positive experiences of the conversations

What is their significance?

Clinical: It is important to move beyond clinician training alone to implement processes in family practice to trigger advance care planning conversations

Research: Further research to identify effective scalable approaches to triggering and implementing advance care planning conversations in family practice would be beneficial
A County-level Analysis of the Association Between Medicaid Expansion and Medicare Spending
Authors: El-Nahal Walid G. , Eisenberg Mattew D.
Published: August 2022

Background

If access to Medicaid improves health outcomes, it may also result in lower long-term spending, however the association between Medicaid expansion and Medicare spending is unknown. In this analysis we sought to investigate the association between Medicaid expansion and per capita Medicare spending at the county level.

Methods

This is an observational analysis of all U.S. counties in the ten years from 2010 to 2019. We used a difference-in-difference event study to investigate the difference in per capita Medicare spending between counties in states that expanded Medicaid and counties in states that did not expand Medicaid. The exposure was treatment year, which characterized whether a county was in an expansion state and when expansion occurred. In non-expansion counties, treatment year was assigned 0 for all observations. In expansion counties, treatment year ranged from -3 to +6, with treatment year 1 corresponding to the first full year of expansion. The primary outcome was fee-for-service Medicare spending per capita in each county. A secondary analysis investigated subcategories of per capita spending including inpatient, outpatient, skilled nursing care, inpatient rehabilitation, home health, and hospice care.

Results

We analyzed 1,648 expansion and 1,494 non-expansion counties, with ten observations per county, one for each year between 2010 and 2019. In the adjusted event study analysis, the difference between expansion and non-expansion counties in expansion year 5 compared to pre-expansion was -200 [95% Confidence Interval (CI): -406, 6] dollars. In the subcategory analysis, the difference in inpatient care, skilled nursing care, outpatient care, and home health spending were -46 [95% CI: -103, 12], -92 [95% CI: -194, 11], 57 [95% CI: -67, 181], and 55 [95% CI: -17, 126] dollars per capita respectively.

Conclusions

Medicaid expansion is not consistently significantly associated with lower Medicare spending compared to pre-expansion. However, observed trends towards lower spending and cost-shifting from inpatient to outpatient settings in expansion counties warrant additional investigation.
Circulating tumor DNA profiling approach based on in silico background elimination guides patient classification of multiple cancers
Authors: Li Ming , Xie Sisi , Hou Tao , Shao Tong , Kuang Jingyu , Lu Chenyu , Liu Xianling , Zhu Lingyun , Zhu Lvyun
Published: August 2022

Circulating tumor DNA (ctDNA) analysis is increasingly providing a promising minimally invasive alternative to tissue biopsies in precision oncology. However, current methods of ctDNA mutation profiling have limited resolution because of the high background noise and false-positive rate caused by benign variants in plasma cell-free DNA (cfDNA), majorly generated during clonal hematopoiesis. Although personalized parallel white blood cell (WBC) genome sequencing suppresses the noise of clonal hematopoiesis variances observed in ctDNA based liquid biopsy, the system cost and complexity restrict its extensive application in clinical settings. To address this challenge, we describe a Matched WBC Genome sequencing Independent CtDNA profiling (MaGIC) approach, which enables the sensitive detection of recurrent tumor mutant information harbored by ctDNA from a bulk cfDNA background based on hybrid capture cfDNA deep sequencing, in silico background elimination, and a reliable readout measurement by the calculation the number of key mutated exons. Leveraging somatic mutation data from 10163 patients across 24 cancer types obtained from The Cancer Genome Atlas, we confirm that the MaGIC approaches are of ideal performance in prediction of prognosis by tissue biopsy samples of patients across multiple cancers. Meanwhile, MaGIC approaches enable the classification of prostate cancer patients from heathy cohorts by ctDNA sequencing data. We further profiled the ctDNAs of 80 plasma samples from 40 patients with nasopharyngeal carcinoma before and during chemotherapy by MaGIC approaches. The MaGICv2 can predict the chemosensitivity with high accuracy by simply using one liquid biopsy sample of each patient before a stereotypical treatment course. We anticipate that this new approach has the potential utility of ctDNA detection in multiple clinical cancer contexts, thus facilitating precise cancer therapy.

Teaser

A liquid biopsy analysis method for multifunctional patient classification such as diagnosis and chemosensitivity prediction.