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When a diamagnetic graphite plate is placed on top of a magnet, it is subject to both magnetic levitation and gravitational forces. Computational modeling is used to demonstrate that these forces can balance each other to allow a stable tilt angle θ to be attained when the graphite plate pivots on the magnet surface. θ depends on the magnetic susceptibility χmag, which can be controlled by using laser irradiation to change the temperature of the graphite. Over a limited temperature range, there is a linear relation between the angle change Δθ and the temperature change ΔT. This predicted behavior is confirmed experimentally using a graphite plate (5 × 5 × 0.83 mm) placed on top of a 7.5 cm diameter neodymium iron boride magnet with a surface field strength of ∼5000 G. Using a 532 nm laser, θ could be continuously tuned from 52° to 26° by varying the laser power between 20 and 800 mW. The response time was about 15 s at all powers. Higher laser powers were observed to lead to a complete loss of levitation, followed by recovery and oscillation in and out of the laser beam. The linear dependence of Δθ on power suggests that photothermal tilting of the graphite plate in a magnetic field provides a fatigue resistant way to achieve large angular deviations using an external light source. This effect can be harnessed to function as a laser-controlled beam steering device. [ABSTRACT FROM AUTHOR]

The link between the oral microbiome and neurodevelopmental disorders remains a compelling hypothesis, still requiring confirmation in large-scale datasets. Leveraging over 7000 whole-genome sequenced salivary samples from 2025 US families with children diagnosed with autism spectrum disorders (ASD), our cross-sectional study shows that the oral microbiome composition can discriminate ASD subjects from neurotypical siblings (NTs, AUC = 0.66), with 108 differentiating species (q < 0.005). The relative abundance of these species is highly correlated with cognitive impairment as measured by Full-Scale Intelligence Quotient (IQ). ASD children with IQ < 70 also exhibit lower microbiome strain sharing with parents (p < 10−6) with respect to NTs. A two-pronged functional enrichment analysis suggests the contribution of enzymes from the serotonin, GABA, and dopamine degradation pathways to the distinct microbial community compositions observed between ASD and NT samples. Although measures of restrictive eating diet and proxies of oral hygiene show relatively minor effects on the microbiome composition, the observed associations with ASD and IQ may still represent unaccounted-for underlying differences in lifestyle among groups. While causal relationships could not be established, our study provides substantial support to the investigation of oral microbiome biomarkers in ASD. Here, Manghi et al. identify potential salivary microbial biomarkers for autism through a large-scale metagenomic analysis of 2,000 families, revealing shifts in neurotransmitter-related pathways [ABSTRACT FROM AUTHOR]

Understanding the maintenance and shift in reproductive strategies is a fundamental question in evolutionary research. Although many efforts have been made to compare different reproductive strategies, the association between reproductive strategies and lineage divergence is largely unknown. To explore the impact of different reproductive strategies on lineage divergence, we investigated the evolution of clonality in Saxifraga sect. Irregulares+Heterisia. By integrating several lines of evidence, we found that the loss of clonality in Irregulares+Heterisia was associated with a progressive increase in diversification rate and intraspecific morphological diversity but with a reduction in species distribution range. Our findings provide insights into the ecological and evolutionary effects of different reproductive strategies, suggesting the necessity of integrating clonality into ecological and evolutional research. [ABSTRACT FROM AUTHOR]

Millions of United States (U.S.) troops deployed to the Middle East and Southwest Asia were exposed to toxic airborne hazards and/or open-air burn pits. Burn pit emissions contain particulate matter combined with toxic gasses and heavy metals. Ongoing research has demonstrated that exposures to the airborne hazards from military burn pits have profound and lasting health and wellness consequences. Research on the long-term health consequences of exposure to open burn pits has been limited. Work continues to understand the scope of the health impacts and the underlying pathobiology following exposures and to establish care standards. The U.S. Sergeant First Class Heath Robinson Honoring our Promise to Address Comprehensive Toxics (PACT) Act was signed into law August 2022. This act expands the benefits and services to U.S. Veterans exposed to toxicants, requires the Veterans Health Administration to provide toxic exposure screening, and supports increased research, education, and treatment due to toxic occupational exposures. This review highlights the state of the science related to military burn pit exposures research with an emphasis on pulmonary health. Clinical data demonstrate areas of reduced or delayed pulmonary ventilation and lung pathologies such as small airways scarring, diffuse collagen deposition and focal areas of ossification. Identification and characterization of foreign matter deposition in lung tissues are reported, including particulate matter, silica, titanium oxides, and polycyclic aromatic hydrocarbons. These data are consistent with toxic exposures and with the symptoms reported by post-deployment Veterans despite near-normal non-invasive pulmonary evaluations. On-going work toward new methods for non-invasive pulmonary diagnoses and disease monitoring are described. We propose various studies and databases as resources for clinical and health outcomes research. Pre-clinical research using different burn pit modeling approaches are summarized, including oropharyngeal aspiration, intranasal inhalation, and whole-body exposure chamber inhalation. These studies focus on the impacts of specific toxic substances as well as the effects of short-term and sustained insults over time on the pulmonary systems. [ABSTRACT FROM AUTHOR]

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Natural radiogenic isotopes (primarily 87Sr/86Sr) from hot springs in the Upper Geyser Basin of the Yellowstone Plateau volcanic field and associated rocks were used to evaluate groundwater flow patterns, water‐rock reactions, and the extent of mixing between various groundwater sources. Thermal waters have very low uranium concentrations and 234U/238U activity ratios near 1.0, which limit their utility as tracers in this reducing setting. Thermal waters have higher Sr concentrations (<22 ng/g) and a wide range of 87Sr/86Sr values that vary both temporally at individual discharge sites and between adjacent springs, indicating that conduits tap different subsurface reservoirs to varying degrees. Sr from local rhyolites have 87Sr/86Sr compositions that bound the range of values observed in groundwater throughout the basin. Non‐boiling springs on the west flank of the basin discharge water with low 87Sr/86Sr consistent with flow through young volcanic rocks exposed at the surface. Boiling springs in the central basin have higher 87Sr/86Sr values reflecting interactions with older, more radiogenic volcanic rocks. Variability in upwelling thermal waters requires mixing with a low 87Sr/86Sr component derived from young lava or glacial sediments, or more likely, from deeper sources of hot groundwater circulating through buried Lava Creek Tuff having intermediate 87Sr/86Sr. Isotope data constrain basin‐wide output of thermal water to 110–140 kg·s−1. Results underscore the utility of radiogenic Sr isotopes as valuable tracers of hydrothermal flow patterns and improve the understanding of temperature‐dependent water‐rock reactions in one of the largest continental hydrothermal systems on Earth. Plain Language Summary: Radiogenic isotopes of strontium (87Sr/86Sr) vary widely in rocks and the waters that interact with them. We use 87Sr/86Sr in waters from hot springs in the Upper Geyser Basin of the Yellowstone Plateau volcanic field to help define patterns of groundwater flow through subsurface volcanic rocks. Lava flows and tuffs adjacent to and underlying the basin have different 87Sr/86Sr compositions reflecting different crustal and mantle components incorporated during rhyolite generation. Groundwater interacting with those rocks inherits their 87Sr/86Sr signature, which can then be used to trace subsurface flowpaths. Modern and past hot springs along the basin margin discharge water having low 87Sr/86Sr values that indicate groundwater was restricted to shallow flowpaths through younger volcanic rocks. Hot springs in the central basin have compositions reflecting mixing between groundwater flowing through deeper and older, high‐87Sr/86Sr volcanic rocks and groundwater having lower 87Sr/86Sr values. The low‐87Sr/86Sr component could be derived from shallow sources (young volcanic rocks or glacial sediments) or from more‐deeply buried tuff associated with the most recent collapse of the Yellowstone caldera. The data presented here provide a means of tracing hydrothermal flow patterns in complex volcanic environments and improve the understanding of hydrothermal activity in one of the largest active continental magmatic systems on Earth. Key Points: Water from hot springs in the Upper Geyser Basin has 87Sr/86Sr derived from volcanic rocks flanking and underlying the basinVariable 87Sr/86Sr in water from springs in proximity and over time reflect mixing between groundwater in distinct rock reservoirsReducing conditions along flowpaths yield groundwater with low U concentrations and 234U/238U activities near 1.0 [ABSTRACT FROM AUTHOR]

Simple Summary: The Argentine ant, Linepithema humile (Mayr), was introduced into the United States from South America in the late 1800s. Since its establishment in California and the southeastern U.S., it has become an agricultural pest by interfering with citrus production in California, but it is widely known in most of its range as a major nuisance pest. It commonly establishes nest sites in mulch and leaf litter, where colonies may be populated by hundreds of thousands of worker ants (or more) with a large home range. When searching for food, ants may discover and recruit to sweet foods inside of structures. To alleviate ant pest problems, the structural pest control industry may incorporate EPA-approved baits and residual products that are designed to reduce the ant population. Homeowners experiencing nuisance pests are often motivated to solve their own problem, and they may be susceptible to outlandish, fact-free claims of do-it-yourself "secret" solutions that "they don't want you to know about". In this study, we evaluated several of these recommendations. In two trials designed to evaluate a product's ability to deter Argentine ants from a preferred nest site, we evaluated several common home remedies, namely the use of tansy plant leaves, cucumber peels, and soybean extract. None of these home remedies deterred ants from a preferred harborage. Fresh leaves from rosemary and spearmint plants, however, did deter ants, as do many commercially available essential oils. In two laboratory trials, natural products, including freshly picked leaves from spearmint, rosemary, and tansy plants, a water extract from soybean plants, peels from a common cucumber, and 1% peppermint oil in hexane, were placed in a moist harborage preferred by Argentine ants, Linepithema humile (Mayr), and the number of ants entering the harborage after two and four hours was counted. None of the recommended home remedies (tansy, cucumber, or soybean extract) deterred ants from an attractive, moist harborage in either trial, even when the quantity of these treatments was increased 4- to 10-fold. Freshly picked leaves from rosemary and spearmint plants deterred ants from harboring, and the 1% peppermint oil was the most deterrent of all treatments. [ABSTRACT FROM AUTHOR]

Background: Few validated brief scales are available to measure constructs that may hinder mpox-related prevention and care engagement, such as knowledge and stigma. Both are highly salient barriers to infectious disease care and disease understanding, precursors to evaluating one's risk and need to, for example, accept vaccination. To address this gap, we developed and validated the Mpox Stigma Scale (MSS) and Mpox Knowledge Scale (MKS). Methods: As part of a full-scale clinical trial, we offered an optional mpox survey to participants who self-identified as African American or Black, were 18–29 years old, and lived in Alabama, Georgia, or North Carolina (2023, N = 330). We calculated psychometric properties through confirmatory factor analyses (CFA) and applied Comparative Fit Index (CFI), Goodness of Fit Index (GFI), and Tucker-Lewis Index (TLI) values equal to or exceeding 0.90 and Root Mean Square Error of Approximation (RMSEA) and Standardized Root Mean Square Residual (SRMR) values less than 0.08 to determine adequate model fit. We computed internal reliability using Cronbach's alpha and calculated Pearson or Spearman correlation coefficients between the MSS and MKS and related variables. Results: For the MSS, CFA results showed that the one-factor model fit the data well (χ2(df = 5, N = 330) = 34.962, CFI = 0.97, GFI = 0.99, TLI = 0.94, RMSEA = 0.13, SRMR = 0.03). For the MKS, the one-factor model provided a good fit to the data (χ2(df = 6, N = 330) = 8.44, CFI = 0.99, GFI = 0.99, TLI = 0.95, RMSEA = 0.15, SRMR = 0.02). Cronbach's alphas were MSS = 0.91 and MKS = 0.83, suggesting good to excellent reliability. The MSS was correlated with the MKS (r =.55, p <.001), stigmatizing attitudes (r =.24, p <.001), attitudes towards mpox vaccination (r=-.12, p =.030), and worry about contracting mpox (r =.44, p <.001). The MKS was correlated with worry about contracting mpox (r =.30, p <.001) and mpox disclosure (r=-.16, p =.003). Conclusions: The MSS and MKS are reliable and valid tools for public health practice, treatment and prevention research, and behavioral science. Further validation is warranted across populations and geographic locations. Trial Registration: ClinicalTrials.gov NCT05490329. [ABSTRACT FROM AUTHOR]

The angiosperm family Cactaceae, a member of the Caryophyllales, is a large and diverse group of stem succulents comprising 1,438–1,870 species within approximately 130 genera predominantly distributed from northern Canada to Patagonia. Four centers of diversity from Central and North America (Chihuahua, Puebla‐Oaxaca, Sonora‐Sinaloan, and Jalisco) and three centers of diversity from South America (Southern Central Andes, Caatinga, and Mara Atlantica) have played a pivotal role in disbursing cacti around the globe. Mexico is considered the richest area in cacti species with close to 563 species grouped into 50 genera. Approximately 118 species have been domesticated by Mesoamerican people as food crops and for ornamental purposes. Cacti inhabit a wide range of ecosystems and climate regions, ranging from tropical to subtropical and from arid to semiarid regions. Species belonging to the genus Opuntia are the major food crop producers in the family. Cacti have derived characteristics from familial synapomorphies within the Caryophyllales. Reproduction occurs through pollination facilitated by birds, bats, bees, and other insects. Climate variability, whether natural or human‐induced threatens global crop production including high temperatures, salinity, drought, flood, changes in soil pH, and urbanization. Cacti have several adaptations that are important for coping with abiotic stresses, such as crassulacean acid metabolism (CAM photosynthesis), as well as modifications to root and stem physiological pathways. This review aims to provide a comprehensive view of the fruit crops in Cactaceae, including their evolution, worldwide distribution, and the environmental factors impacting cultivation. [ABSTRACT FROM AUTHOR]

The small subfamily Linnaeoideae of Caprifoliaceae exhibits a disjunct distribution in Eurasia and North America, including Mexico, with most taxa occurring in eastern Asia or Mexico and the monospecific Linnaea Gronov. ex L. having a circumboreal to north temperate distribution. We sampled 17 of the 20 species representing all Linnaeoideae genera and used nuclear (target enrichment) and complete plastome sequence data to reconstruct the phylogeny. Our results show strong topological conflicts between nuclear and plastid data, especially concerning Dipelta Maxim. and Diabelia Landrein, supporting hybridization events complicating the deep diversification. Nuclear data were used for divergence time estimation and ancestral area reconstruction. The divergence time between the Mexican Vesalea M. Martens & Galeotti and the Linnaea clade was dated to 39.5 Ma, with a 95% highest posterior density of 28.2 Ma (mid‐Oligocene) to 45.2 Ma (mid‐Eocene). Reconstructed ancestral areas support a widespread common ancestor of Linnaea plus Vesalea in Mexico and at least another area (eastern Asia, North America, or Europe). The biogeographic analysis, including fossils, supports the ancestral range of Linnaeoideae to be widespread in central and western China + Europe + Mexico, or eastern and northern Asia + central and western China + Mexico, or central and western China + North America + Mexico. The North Atlantic and/or the Bering land bridges may be important in the widespread distribution across continents in the Northern Hemisphere. Our study highlights the importance of utilizing fossils in biogeographic inferences andusing data from different genomes while reconstructing deep and shallow phylogenies of organisms. [ABSTRACT FROM AUTHOR]

This paper focuses on developing a reduction-based algebraic multigrid (AMG) method that is suitable for solving general (non)symmetric linear systems and is naturally robust from pure advection to pure diffusion. Initial motivation comes from a new reduction-based AMG approach, ℓAIR (local approximate ideal restriction), that was developed for solving advection-dominated problems. Though this new solver is very effective in the advection-dominated regime, its performance degrades in cases where diffusion becomes dominant. This is consistent with the fact that in general, reduction-based AMG methods tend to suffer from growth in complexity and/or convergence rates as the problem size is increased, especially for diffusion-dominated problems in two or three dimensions. Motivated by the success of ℓAIR in the advective regime, our aim in this paper is to generalize the AIR framework with the goal of improving the performance of the solver in diffusion-dominated regimes. To do so, we propose a novel way to combine mode constraints as used commonly in energy-minimization AMG methods with the local approximation of ideal operators used in ℓAIR. The resulting constrained ℓAIR algorithm is able to achieve fast scalable convergence on advective and diffusive problems. In addition, it is able to achieve standard low complexity hierarchies in the diffusive regime through aggressive coarsening, something that was previously difficult for reduction-based methods. [ABSTRACT FROM AUTHOR]

Traumatic brain injury (TBI) is one of the foremost causes of disability and mortality globally. While the scientific and medical emphasis is to save lives and avoid disability during acute period of injury, a severe health problem can manifest years after injury. For instance, TBI increases the risk of cognitive impairment in the elderly. Remote TBI history was reported to be a cause of the accelerated clinical trajectory of Alzheimer's disease-related dementia (ADRD) resulting in earlier onset of cognitive impairment and increased AD-associated pathological markers like greater amyloid deposition and cortical thinning. It is not well understood whether a single TBI event may increase the risk of dementia. Moreover, the cellular signaling pathways remain elusive for the chronic effects of TBI on cognition. We have hypothesized that a single TBI induces sustained neuroinflammation and disrupts cellular communication in a way that results later in ADRD pathology. To test this, we induced TBI in young adult CD1 mice and assessed the behavioral outcomes after 11 months followed by pathological, histological, transcriptomic, and MRI assessment. On MRI scans, these mice showed significant loss of tissue, reduced CBF, and higher white matter injury compared to sham mice. We found these brains showed progressive atrophy, markers of ADRD, sustained astrogliosis, loss of neuronal plasticity, and growth factors even after 1-year post-TBI. Because of progressive neurodegeneration, these mice had motor deficits, showed cognitive impairments, and wandered randomly in open field. We, therefore, conclude that progressive pathology after adulthood TBI leads to neurodegenerative conditions such as ADRD and impairs neuronal functions. [ABSTRACT FROM AUTHOR]

Understanding phenology, its genetics and agronomic consequences, is critical for crop adaptation. Here we aim to (i) characterize lentil response to photoperiod with a focus on five loci: the lentil ELF3 orthologue Sn , two loci linked to clusters of lentil FT orthologues, and two loci without candidates in chromosomes 2 and 5 (Experiment 1: 36 lines, short and long days in a phytotron), and (ii) establish the phenology–yield relationship (Experiment 2: 25 lines, 11 field environments). A vintage perspective, where we quantify time trends in phenotype over three decades of breeding, links both experiments. Yield increased linearly from older to newer varieties at 29 kg ha–1 year–1 or 1.5% year–1, correlated negatively with flowering time in both winter- and summer-rainfall regimes, and decoupled from biomass in favourable environments. Time to flowering shortened from older to newer varieties at –0.56% year–1 in the field, and –0.42% year–1 (short days) and –0.99% year–1 (long days) in the phytotron. Early-flowering lines of diverse origin carried multiple early alleles for the five loci, indicating that at least some of these loci affect phenology additively. Current germplasm primarily features the early-flowering haplotype for an FTb cluster region, hence the potential to increase phenological diversity with yield implications. [ABSTRACT FROM AUTHOR]

During the 2021 (n = 15) and 2022 (n = 13) summers, we measured the total and dissolved (<0.45 μm) concentration of 25 elements in Utah Lake using Inductively Coupled Plasma–Optical Emission Spectrometry (ICP-OES) with detection limits in the order of a few parts-per-billion (ppb). This resulted in 1400 measurements, which is a unique dataset in terms of sensitivity and temporal resolution. Regulated elements are not commonly measured at the ppb-level; thus, these data provide insight into both the behavior and existence of these elements in an aquatic environment and have implications for both the management and regulation of the lake. Utah regulates twelve of these elements. While ICP-OES has ppb-level sensitivity, it is not the approved regulatory analysis method for these elements. All regulations are for dissolved concentrations, except aluminum (Al) and phosphorus (P), which are for total recovery. We found total Al above the allowable concentration, but dissolved concentrations were well below allowable concentrations. We attribute high total concentrations to suspended clays. This suggests that regulatory methods should be reviewed for lakes with a high suspended-solid content. Dissolved copper (Cu) concentrations were below regulatory levels in 2021, but some samples were above regulatory levels in 2022. This could be related to the use of Cu-based algaecide treatments, or from other sources. Lead (Pb) data were inconclusive; dissolved Pb concentrations were well below the acute (1 h average) limit, but the chronic concentration limit (4 h average) was below the ICP-OES minimal detection limit. Arsenic (As) concentrations exhibited a seasonal trend that we attribute to groundwater inflows—they were below regulatory levels for aquatic environments but around the levels for drinking water. This ppb-level study with high temporal resolution provides insight into regulated elements in Utah Lake previously not available due to the high sensitivity of the method and measurements of both total and dissolved concentrations. [ABSTRACT FROM AUTHOR]

Niemann–Pick disease type C (NPC) is a rare and fatal neurological disorder caused by mutations in Npc1 or Npc2, with Npc1 accounting for 95% of cases. These mutations result in the functional loss of their respective proteins, causing cellular abnormalities characterized by disrupted lipid dysregulation, calcium dysfunction, elevated damage associated molecular patterns (DAMPs), and a pro-inflammatory environment. This cellular pathology ultimately triggers neurodegeneration, with the cerebellum being the earliest and most affected region. We have recently shown atypical activation of interferon signaling in the presymptomatic Npc1−/− mouse cerebellum and, to a lesser extent, in the cerebral cortex. In addition, we reported that the Amyloid Precursor Protein (APP) is an NPC disease modifier. Loss of APP function leads to widespread neurodegeneration in the NPC brain, including exacerbated interferon signaling in the cerebellum. To better understand the role of APP as a disease modifier throughout the NPC brain, here we carried out a transcriptomic analysis of the cerebral cortex and cerebellum from 3-week-old Npc1−/− mice as well as age-matched controls in the presence and absence of APP. We report differential effects of APP loss of function in the cerebral cortex and cerebellum, including cholesterol and tau dysregulation, in both brain regions. Our findings demonstrate a novel link between APP loss and early pathogenic mechanisms in NPC. [ABSTRACT FROM AUTHOR]

The amount of turbulence in protoplanetary discs around young stars is critical for determining the efficiency, timeline, and outcomes of planet formation. It is also difficult to measure. Observations are still limited, but direct measurements of the non-thermal, turbulent gas motion are possible with the Atacama Large Millimeter/submillimeter Array (ALMA). Using CO(2–1)/ |$^{13}$| CO(2–1)/C |$^{18}$| O(2–1) ALMA observations of the disc around IM Lup at |$\sim 0.4$|  arcsec (⁠|$\sim$| 60 au) resolution we find evidence of significant turbulence, at the level of |$\delta v_{\rm turb}=(0.18-0.30)$| c |$_\mathrm{ s}$|⁠. This result is robust against systematic uncertainties (e.g. amplitude flux calibration, mid-plane gas temperature, disc self-gravity). We find that gravito-turbulence as the source of the gas motion is unlikely based on the lack of an imprint on the rotation curve from a massive disc, while magneto-rotational instabilities and hydrodynamic instabilities are still possible, depending on the unknown magnetic field strength and the cooling time-scale in the outer disc. [ABSTRACT FROM AUTHOR]

Obesity impairs tissue insulin sensitivity and signaling, promoting type-2 diabetes. Although improving insulin signaling is key to reversing diabetes, the multi-organ mechanisms regulating this process are poorly defined. Here, we screen the secretome and receptome in Drosophila to identify the hormonal crosstalk affecting diet-induced insulin resistance and obesity. We discover a complex interplay between muscle, neuronal, and adipose tissues, mediated by Bone Morphogenetic Protein (BMP) signaling and the hormone Bursicon, that enhances insulin signaling and sugar tolerance. Muscle-derived BMP signaling, induced by sugar, governs neuronal Bursicon signaling. Bursicon, through its receptor Rickets, a Leucine-rich-repeat-containing G-protein coupled receptor (LGR), improves insulin secretion and insulin sensitivity in adipose tissue, mitigating hyperglycemia. In mouse adipocytes, loss of the Rickets ortholog LGR4 blunts insulin responses, showing an essential role of LGR4 in adipocyte insulin sensitivity. Our findings reveal a muscle-neuronal-fat-tissue axis driving metabolic adaptation to high-sugar conditions, identifying LGR4 as a critical mediator in this regulatory network. Obesity induces insulin resistance and impairs insulin signaling, causing diabetes. Here, the authors show that BMP and LGR signaling mediate communication between muscle, neuronal, and adipose tissues to enhance insulin signaling, identifying LGR as key in protecting against insulin resistance. [ABSTRACT FROM AUTHOR]

The Yamuna River in India and the Mississippi River in the United States hold significant commercial, cultural, and ecological importance. This preliminary survey compares the bacterial communities sampled in surface waters at 11 sites (Yamuna headwaters, Mississippi headwaters, Yamuna River Yamunotri Town, Mississippi River at Winona, Tons River, Yamuna River at Paonta Sahib, Yamuna River Delhi-1, Yamuna River Delhi-2, Yamuna River before Sangam, Sangam, Ganga River before Sangam). Bacterial 16S rDNA analyses demonstrate dominance of Proteobacteria and Bacteroidetes phyla. Actinobacteria were also dominant at sites near Sangam in India and sites in Minnesota. A dominance of Epsilonbacteraeota were found in Delhi, India. Principal component analysis (PCA) using unique operational taxonomic units (OTUs) resulted in the identification of 3 groups that included the Yamuna River locations in Delhi (Delhi locations), Yamuna headwaters and Yamuna River at Yamunotri (Yamuna River locations below the Glacier) and Mississippi, Ganga, Tons, and other Yamuna River locations. Diversity indices were significantly higher at the Yamuna River locations below the Glacier (Simpson D = 0.986 and Shannon H = 5.06) as compared (p value <0.001) to the Delhi locations (D = 0.951 and H = 4.23) and as compared (p value < 0.001) to Mississippi, Ganga, Tons, and other Yamuna River locations (D = 0.943 and H = 3.96). To our knowledge, this is the first survey to compare Mississippi and Yamuna River bacterial communities. We demonstrate higher diversity in the bacterial communities below the Yamunotri glacier in India. [ABSTRACT FROM AUTHOR]

Glycans, carbohydrates, and glycoconjugates are involved in many crucial biological processes, such as disease development, immune responses, and cell–cell recognition. Glycans and carbohydrates are known for the large number of isomeric features associated with their structures, making analysis challenging compared with other biomolecules. Mass spectrometry has become the primary method of structural characterization for carbohydrates, glycans, and glycoconjugates. Metal adduction is especially important for the mass spectrometric analysis of carbohydrates and glycans. Metal‐ion adduction to carbohydrates and glycoconjugates affects ion formation and the three‐dimensional, gas‐phase structures. Herein, we discuss how metal‐ion adduction impacts ionization, ion mobility, ion activation and dissociation, and hydrogen/deuterium exchange for carbohydrates and glycoconjugates. We also compare the use of different metals for these various techniques and highlight the value in using metals as charge carriers for these analyses. Finally, we provide recommendations for selecting a metal for analysis of carbohydrate adducts and describe areas for continued research. [ABSTRACT FROM AUTHOR]

Premise: Traditional methods of ploidal‐level estimation are tedious; using DNA sequence data for cytotype estimation is an ideal alternative. Multiple statistical approaches to leverage sequence data for ploidy inference based on site‐based heterozygosity have been developed. However, these approaches may require high‐coverage sequence data, use inappropriate probability distributions, or have additional statistical shortcomings that limit inference abilities. We introduce nQuack, an open‐source R package that addresses the main shortcomings of current methods. Methods and Results: nQuack performs model selection for improved ploidy predictions. Here, we implement expectation maximization algorithms with normal, beta, and beta‐binomial distributions. Using extensive computer simulations that account for variability in sequencing depth, as well as real data sets, we demonstrate the utility and limitations of nQuack. Conclusions: Inferring ploidy based on site‐based heterozygosity alone is difficult. Even though nQuack is more accurate than similar methods, we suggest caution when relying on any site‐based heterozygosity method to infer ploidy. [ABSTRACT FROM AUTHOR]

Black‐and‐white snub‐nosed monkeys (Rhinopithecus bieti) rely on behavioral and dietary flexibility to survive in temperate latitudes at high‐elevation habitats characterized by climate and resource seasonality. However, little is known about how elevation influences their behavioral and dietary flexibility at monthly or seasonal scales. We studied an isolated R. bieti population at Mt. Lasha in the Yunling Provincial Nature Reserve, Yunnan, China, between May 2008 and August 2016 to assess the impacts of elevation on feeding behavior and diet. Across our sample, R. bieti occupied elevations between 3031 and 3637 m above mean sea level (amsl), with a 315.1 m amsl range across months and a 247.3 m amsl range across seasons. Contrary to expectations, individuals spent less time feeding when ranging across higher elevations. Lichen consumption correlated with elevation use across months and seasons, with individuals spending more time feeding on this important resource at higher elevations. Leaf consumption only correlated with elevation use during the spring. Our results suggest that R. bieti do not maximize their food intake at higher elevations and that monthly and seasonal changes in lichen and leaf consumption largely explain variation in elevation use. These findings shed light on the responses of R. bieti to environmental change and offer insight into strategies for conserving their habitats in the face of anthropogenic disturbance. Research Highlights: Black‐and‐white snub‐nosed monkeys (Rhinopithecus bieti) spend less time feeding in months and seasons when occupying higher‐elevation habitats.Leaves only comprise a higher percentage of the R. bieti diet when occupying higher‐elevation habitats in the spring.Lichen comprise a higher percentage of the R. bieti diet in months and seasons when occupying higher‐elevation habitats. [ABSTRACT FROM AUTHOR]

Background: Emulation of the "target trial" (TT), a hypothetical pragmatic randomized controlled trial (RCT), using observational data can be used to mitigate issues commonly encountered in comparative effectiveness research (CER) when randomized trials are not logistically, ethically, or financially feasible. However, cardiovascular (CV) health research has been slow to adopt TT emulation. Here, we demonstrate the design and analysis of a TT emulation using electronic health records to study the comparative effectiveness of the addition of a disease-modifying anti-rheumatic drug (DMARD) to a regimen of methotrexate on CV events among rheumatoid arthritis (RA) patients. Methods: We used data from an electronic medical records-based cohort of RA patients from Northwestern Medicine to emulate the TT. Follow-up began 3 months after initial prescription of MTX (2000–2020) and included all available follow-up through June 30, 2020. Weighted pooled logistic regression was used to estimate differences in CVD risk and survival. Cloning was used to handle immortal time bias and weights to improve baseline and time-varying covariate imbalance. Results: We identified 659 eligible people with RA with average follow-up of 46 months and 31 MACE events. The month 24 adjusted risk difference for MACE comparing initiation vs non-initiation of a DMARD was -1.47% (95% confidence interval [CI]: -4.74, 1.95%), and the marginal hazard ratio (HR) was 0.72 (95% CI: 0.71, 1.23). In analyses subject to immortal time bias, the HR was 0.62 (95% CI: 0.29–1.44). Conclusion: In this sample, we did not observe evidence of differences in risk of MACE, a finding that is compatible with previously published meta-analyses of RCTs. Thoughtful application of the TT framework provides opportunities to conduct CER in observational data. Benchmarking results of observational analyses to previously published RCTs can lend credibility to interpretation. [ABSTRACT FROM AUTHOR]

The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change. The high species diversity in this mountain system has long been attributed to a complex set of factors, and recent large‐scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago (Mya) to the present. Despite our increasing understanding of the temporal mode of speciation, finer‐scale population‐level investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation. This is largely due to the dearth of organismal sampling among closely related species and populations, spanning the incredible size and topological heterogeneity of this region. Our study dives into these evolutionary dynamics of speciation using genomic and eco‐morphological data of Stellera chamaejasme L. We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages, suggesting a more recent diversification (~2.67–0.90 Mya), largely influenced by Pleistocene glaciation and biotic factors. These factors likely influenced allopatric speciation and advocated cyclical warming–cooling episodes along elevational gradients during the Pleistocene. The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity, necessitating increased conservation efforts. [ABSTRACT FROM AUTHOR]

Silicon photonic integrated circuit foundries enable wafer-level fabrication of entire electro-optic systems-on-a-chip for applications ranging from datacommunication to lidar to chemical sensing. However, silicon's indirect bandgap has so far prevented its use as an on-chip optical source for these systems. Here, we describe a fullyintegrated broadband silicon waveguide light source fabricated in a state-of-the-art 300-mm foundry. A reverse-biased p-i-n diode in a silicon waveguide emits broadband near-infrared optical radiation directly into the waveguide mode, resulting in nanowatts of guided optical power from a few milliamps of electrical current. We develop a one-dimensional Planck radiation model for intraband emission from hot carriers to theoretically describe the emission. The brightness of this radiation is demonstrated by using it for broadband characterization of photonic components including Mach-Zehnder interferometers and lattice filters, and for waveguide infrared absorption spectroscopy of liquid-phase analytes. This broadband silicon-based source can be directly integrated with waveguides and photodetectors with no change to existing foundry processes and is expected to find immediate application in optical systems-on-a-chip for metrology, spectroscopy, and sensing. On-chip optical sensing and metrology systems are rapidly progressing, but CMOS-compatible silicon light sources remain a challenge. This work demonstrates a broadband, foundry integrated silicon waveguide emitter and the theory that describes it. [ABSTRACT FROM AUTHOR]

Two strategies are central to the debate regarding agricultural development: one integrates farming and conservation (land sharing), and the other separates farming and conservation, intensifying production to allow the offset of natural habitat (land sparing). The role of wildlife‐friendly habitat in the wider surrounding landscape (landscape wildlife friendliness (WF)) in promoting farmland diversity is potentially an unexplored benefit of land sharing.We sampled birds across primary forests and cattle pastures in the western Amazon, where terrestrial biodiversity peaks. We tested the hypothesis that increased landscape WF will lead to increased species richness (SR) on farmland, even at low levels of 'on‐farm' wildlife‐friendly habitat (farm WF).We show that while there is a minor increase in SR linked to increased levels of landscape WF, a large component of the avian community is functionally absent. Most forest‐dependent species are missing from pasture, even at high levels of farm WF. For these species, the preservation of blocks of contiguous forest under land sparing is vastly superior.We modelled both strategies under different levels of production. Land sparing always retained significantly higher SR than land sharing, regardless of the level of landscape WF.Synthesis and applications. Landscape wildlife friendliness (WF) provided through land sharing is of limited benefit to many tropical forest‐dependent species that are unable to move across or utilise pasture, even at high levels of farm and landscape WF. To ensure the persistence of these species, policymakers should urgently implement sustainable intensification mechanisms to increase farmland productivity while enabling the protection of large blocks of spared natural habitat. [ABSTRACT FROM AUTHOR]

Background: Human epidermal growth factor-2 (HER2) overexpression is an oncogenic driver in many solid tumors, including urothelial bladder cancer (UBC). In addition, activating mutations in the ERBB2 gene have been shown to play an oncogenic role similar to ERBB2 amplification. Objective: To describe and compare the frequency and nature of genomic alterations (GA) of ERBB2-altered (mutations, amplification) and ERBB2 wild-type UBC. Patients and Methods: Using a hybrid capture-based comprehensive profiling assay, 9518 UBC cases were grouped by ERBB2 alteration and evaluated for all classes of genomic alterations (GA), tumor mutational burden (TMB), microsatellite instability (MSI), genome-wide loss of heterozygosity (gLOH), and genomic mutational signature. PD-L1 expression was measured by immunohistochemistry (Dako 22C3). Categorical statistical comparisons were performed using Fisher's exact tests. Results: A total of 602 (6.3%) UBC cases featured ERBB2 extracellular domain short variant (SV) GA (ECDmut+), 253 (2.7%) cases featured ERBB2 kinase domain SV GA (KDmut+), 866 (9.1%) cases had ERBB2 amplification (amp+), and 7797 (81.9%) cases were ERBB2 wild-type (wt). European genetic ancestry of ECDmut+ was higher than ERBB2wt. Numerous significant associations were observed when comparing GA by group. Notably among these, CDKN2A/MTAP loss were more frequent in ERBB2wt versus ECDmut+ and amp+. ERBB3 GA were more frequent in ECDmut+ and KDmut+ than ERBB2wt. TERT GA were more frequent in ECDmut+, KDmut+, and amp+ versus ERBB2wt. TOP2A amplification was significantly more common in ECDmut+ and amp+ versus ERBB2wt, and TP53 SV GA were significantly higher in ERBB2 amp+ versus ERBB2wt. Mean TMB levels were significantly higher in ECDmut+, KDmut+, and amp+ than in ERBB2wt. Apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBEC) signature was more frequent in ECDmut+, KDmut+, and amp+ versus ERBB2wt. No significant differences were observed in PD-L1 status between groups, while gLOH-high status was more common in amp+ versus ERBB2wt. MSI-high status was more frequent in KDmut+ versus ERBB2wt, and in ERBB2wt than in amp+. Conclusions: We noted important differences in co-occurring GA in ERBB2-altered (ECDmut+, KDmut+, amp+) versus ERBB2wt UBC, as well as higher mean TMB and higher APOBEC mutational signature in the ERBB2-altered groups. Our results can help refine future clinical trial designs and elucidate possible response and resistance mechanisms for ERBB2-altered UBC. [ABSTRACT FROM AUTHOR]

The discontinuous geographic distribution pattern of plants in the north temperate zone has been a focus of biogeographic research, especially concerning the mechanisms behind the formation of such a pattern and the spatial and temporal evolution of this intermittent distribution pattern. Hypotheses of boreotropical origin, land bridge migration, and out‐of‐Tibet have been proposed to explain the formation of the discontinuous distribution pattern. The distribution of Lonicera shows a typical Europe–Asia–North America discontinuous distribution, which makes for a good case study to investigate the above three hypotheses. In this study, we inferred the phylogeny based on plastid genomes and a nuclear data set with broad taxon sampling, covering 83 species representing two subgenera and four sections. Both nuclear and plastid phylogenetic analyses found section Isika polyphyletic, while sections Nintooa, Isoxylosteum, and Coelxylosteum were monophyletic in subgenus Chamaecerasus. Based on the nuclear and chloroplast phylogeny, we suggest transferring Lonicera maximowiczii and Lonicera tangutica into section Nintooa. Reconstruction of ancestral areas suggests that Lonicera originated in the Qinghai–Tibetan Plateau (QTP) and/or Asia, and subsequently dispersed to other regions. The aridification of the Asian interior may have facilitated the rapid radiation of Lonicera in the region. At the same time, the uplifts of the Tibetan Plateau appear to have triggered the spread and recent rapid diversification of the genus on the QTP and adjacent areas. Overall, our results deepen the understanding of the evolutionary diversification history of Lonicera. [ABSTRACT FROM AUTHOR]

The ability to manipulate the refractive index is a fundamental principle underlying numerous photonic devices. Various techniques exist to modify the refractive index across diverse materials, making performance comparison far from straightforward. In evaluating these methods, power consumption emerges as a key performance characteristic, alongside bandwidth and footprint. Here a comprehensive comparison of the energy and power requirements for the most well‐known index change schemes is undertaken. The findings reveal that while the energy per volume for index change remains within one or two orders of magnitude across different techniques and materials, the power consumption required to achieve switching, 100% modulation, or 100% frequency conversion can differ significantly, spanning many orders of magnitude. As it turns out, the material used has less influence on power reduction than the specific resonant or traveling wave scheme employed to enhance the interaction time between light and matter. Though this work is not intended to serve as a design guide, it does establish the limitations and trade‐offs involved in index modulation, thus providing valuable insights for photonics practitioners. [ABSTRACT FROM AUTHOR]

Utah Lake is unusual due to its large surface area, shallow depth, phosphorus-rich sediments, and well-mixed, unstratified waters. This creates conditions where water column phosphorous concentrations tend toward equilibrium, with lake sediments containing high concentrations of geologic phosphorus. To help understand the potential impact of phosphorous load reductions, we computed a time history of phosphorus mass in the lake using state and federal records of lake volume, dissolved phosphorus concentrations, and outflow. We show that historically, Utah Lake phosphorus concentrations have remained stable over time, in the range of 0.02 to 0.04 mg/L, despite large changes in lake volume and internal phosphorus mass. We performed sorption calculations using data from the literature, demonstrating that it would take unrealistically large load changes to alter water column phosphorus concentrations under sorption processes. The sorption model produces results consistent with historical data that show relatively constant phosphorous concentrations despite large lake volume changes. We show, through several lines of evidence, that water column phosphorus concentrations are insensitive to external loads. Phosphorous load reduction is unlikely to have a significant effect on phosphorus concentrations in Utah Lake and, by extension, in other sorption-dominated shallow lakes with phosphorus-rich sediment. [ABSTRACT FROM AUTHOR]

Background: Prior studies have assessed the impact of the pretransplantation recipient body mass index (BMI) on patient outcomes after lung transplantation (LT), but they have not specifically addressed early postoperative complications. Moreover, the impact of donor BMI on these complications has not been evaluated. The first aim of this study was to assess complications during hospitalization in the ICU after LT according to donor and recipient pretransplantation BMI. Methods: All the recipients who underwent LT at Bichat Claude Bernard Hospital, Paris, between January 2016 and August 2022 were included in this observational retrospective monocentric study. Postoperative complications were analyzed according to recipient and donor BMIs. Univariate and multivariate analyses were also performed. The 90-day and one-year survival rates were studied. P < 0.05 was considered to indicate statistical significance. The Paris-North Hospitals Institutional Review Board approved the study. Results: A total of 304 recipients were analyzed. Being underweight was observed in 41 (13%) recipients, a normal weight in 130 (43%) recipients, and being overweight/obese in 133 (44%) recipients. ECMO support during surgery was significantly more common in the overweight/obese group (p = 0.021), as were respiratory complications (primary graft dysfunction (PGD) (p = 0.006), grade 3 PDG (p = 0.018), neuroblocking agent administration (p = 0.008), prone positioning (p = 0.007)), and KDIGO 3 acute kidney injury (p = 0.036). However, pretransplantation overweight/obese status was not an independent risk factor for 90-day mortality. An overweight or obese donor was associated with a decreased PaO2/FiO2 ratio before organ donation (p < 0.001), without affecting morbidity or mortality after LT. Conclusion: Pretransplantation overweight/obesity in recipients is strongly associated with respiratory and renal complications during hospitalization in the ICU after LT. [ABSTRACT FROM AUTHOR]

Single-limb balance training is integral to preventing and rehabilitating lower extremity injuries. Previous investigations have shown that when using instability devices, differences may or may not exist in the postural sway parameters during use, depending on the specific devices being assessed. Thus, this investigation sought to examine the differences between a commonly used foam pad and a novel instability device (block) in postural sway measures. Twenty-two healthy individuals with no history of lower extremity injury or neurological disorders participated in this investigation. The participants performed three single-limb static balance exercises on a force platform sampling at 120 Hz. Each condition contained three 10-s trials separated by thirty seconds. The mean CoP values of the three trials in each condition were then compared using a within-subjects repeated-measures analysis of variance. Statistically significant differences were seen in the sway area between conditions (p = 0.009), the CoP path length (p = 0.007), the peak medial–lateral CoP displacement (p = 0.004), and the average sway velocity (p = 0.007). All variables displayed similar trends whereby the control condition showed significantly lower values than both instability devices, with no differences between devices. This investigation provides supporting evidence that different instability devices may deliver similar changes to postural sway parameters compared to control conditions. The novel block instability device used in this investigation may be used similarly to the traditional foam pad in prevention and rehabilitation settings based on the absence of differences between the two devices. [ABSTRACT FROM AUTHOR]

Homeologue expression bias occurs when one progenitor copy of a gene is expressed at a higher level than the other in allopolyploids. Morphological variation, including differences in flower colour, exists between natural and synthetic allopolyploids of Nicotiana tabacum and their progenitors. In this study, we use a comparative transcriptomic approach to investigate gene expression differences as well as homeologue bias in the flavonoid biosynthetic pathway (FBP) in these accessions. We do not observe reciprocal homeologue bias between dark and light pink allopolyploids, but the production of light pink flowers is correlated with high FLAVONOL SYNTHASE:DIHYDROFLAVONOL-4-REDUCTASE (FLS:DFR) ratio at 60% of anthesis length due to delayed activation of DFR in these accessions. We do find that natural allopolyploids have stronger homeologue bias than synthetic allopolyploids in both FBP genes and across the transcriptome. While there is no overall subgenome dominance, there is a bias towards expression of N. tomentosiformis homeologues in FBP genes; however, the magnitude of this bias is reduced in allopolyploids compared to the progenitors, suggesting that N. sylvestris homeologues play an active role in the development of flower colour in N. tabacum allopolyploids. In addition, synthetic allopolyploids tend to exhibit trans regulation of homeologues whereas natural allopolyploids often have evolved cis -regulatory differences between homeologues since their origin. [ABSTRACT FROM AUTHOR]

Long-read sequencing offers long contiguous DNA fragments, facilitating diploid genome assembly and structural variant (SV) detection. Efficient and robust algorithms for SV identification are crucial with increasing data availability. Alignment-based methods, favored for their computational efficiency and lower coverage requirements, are prominent. Alternative approaches, relying solely on available reads for de novo genome assembly and employing assembly-based tools for SV detection via comparison to a reference genome, demand significantly more computational resources. However, the lack of comprehensive benchmarking constrains our comprehension and hampers further algorithm development. Here we systematically compare 14 read alignment-based SV calling methods (including 4 deep learning-based methods and 1 hybrid method), and 4 assembly-based SV calling methods, alongside 4 upstream aligners and 7 assemblers. Assembly-based tools excel in detecting large SVs, especially insertions, and exhibit robustness to evaluation parameter changes and coverage fluctuations. Conversely, alignment-based tools demonstrate superior genotyping accuracy at low sequencing coverage (5-10×) and excel in detecting complex SVs, like translocations, inversions, and duplications. Our evaluation provides performance insights, highlighting the absence of a universally superior tool. We furnish guidelines across 31 criteria combinations, aiding users in selecting the most suitable tools for diverse scenarios and offering directions for further method development. Long-read sequencing can greatly improve detection of genomic structural variants (SVs), and numerous methods have been developed to identify SVs using long-read data. Here the authors compare the performance of these methods and provide guidelines to aid users in selecting the most suitable tools for various scenarios. [ABSTRACT FROM AUTHOR]

We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades--inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)--began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence. [ABSTRACT FROM AUTHOR]

Objectives: Evaluate potential effects of calcium channel blockers (CCB) and bisphosphonates (BP) on residual hearing following cochlear implantation. Methods: Medications of 303 adult hearing preservation (HP) candidates (low frequency pure tone average [LFPTA] of 125, 250, and 500 Hz ≤80 dB HL) were reviewed. Postimplantation LFPTA of patients taking CCBs and BPs were compared to controls matched by age and preimplantation LFPTA. Results: Twenty-six HP candidates were taking a CCB (N = 14) or bisphosphonate (N = 12) at implantation. Median follow-up was 1.37 years (range 0.22–4.64y). Among subjects with initial HP, 29% (N = 2 of 7) CCB users compared to 50% (N = 2 of 4) controls subsequently lost residual hearing 3–6 months later (OR = 0.40, 95% CI = 0.04–4.32, p = 0.58). None of the four BP patients with initial HP experienced delayed loss compared to 50% (N = 2 of 4) controls with initial HP (OR = 0.00, 95% CI = 0.00–1.95, P = 0.43). Two CCB and one BP patients improved to a LFPTA <80 dB HL following initial unaided thresholds that suggested loss of residual hearing. Discussion: There were no significant differences in the odds of delayed loss of residual hearing with CCBs or BPs. Conclusion: Further investigation into potential otoprotective adjuvants for maintaining residual hearing following initial successful hearing preservation is warranted, with larger cohorts and additional CCB/BP agents. [ABSTRACT FROM AUTHOR]

The kinetics of fluid-driven metamorphic reactions are challenging to study in nature because of the tendency of metamorphic systems to converge towards chemical equilibrium. However, in cases where mineral textures that reflect incomplete reactions are preserved, kinetic processes may be investigated. Atoll garnet, a texture formed by the dissolution of a garnet's core, has been described in 2D from thin sections of rocks worldwide. Quantifying the extent of this dissolution reaction requires a sample-wide examination of hundreds of individual grains in 3D. In this study, we quantified the distribution of atoll garnet using micro-computed tomography and grain shape analysis. A convolutional neural network was trained on human-labeled garnet grains for automated garnet classification. This approach was applied to a retrogressed mafic eclogite from the Zermatt–Saas Zone (Western Alps). Pervasive atoll-like resorption preferentially affected the larger porphyroblasts, suggesting that compositional zoning patterns exert a first-order control on dissolution rates. A kinetic model shows that the reactivity of metastable garnet to form atolls is favored at pressure–temperature conditions of 560 ± 30°C and 1.6 ± 0.2 GPa. These conditions coincide with the release of water when lawsonite breaks down during the exhumation of mafic eclogites. The model predicts dissolution rates that are three to five times faster for the garnet core than for the rim. This study shows that deep learning algorithms can perform automated textural analysis of crystal shapes in 3D and that these datasets have the potential to elucidate petrological processes, such as the kinetics of fluid-driven metamorphic reactions. [ABSTRACT FROM AUTHOR]

The performance of a recently proposed integrated graphene-bolometric photodetector is assessed. The responsivity of hundreds of A/W and speed on the scale of hundreds of GHz are predicted. The impressive performance is attributed to the small length over which the energy is absorbed by graphene. The short length leads to a highly enhanced energy density, which causes the increase of the electron temperature in graphene. The model has been validated against recently published experimental results from high-speed graphene photodetectors and found to be in good agreement. [ABSTRACT FROM AUTHOR]

Growing concern has been expressed about uranium (U) accumulation in agricultural soils caused by the long-term application of mineral fertilizers. More than 80% of naturally occurring U transfers from phosphate rock (PR), the raw material used in mineral fertilizer production, to phosphorus (P) fertilizers. These fertilizers are then distributed on agricultural soils, where the U could accumulate over time and become a risk to the environment. The objective of this work was to review the reported content of U in P fertilizers, its potential dispersion in soils, and its uptake by plants in different countries in the world as reported in the literature. The articles for this systematic review were selected from the Scopus database published between 2003 and 2022. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) protocol were used. A total of 54 articles were assessed based on the standard inclusion and exclusion criteria. U concentrations in P fertilizers, agricultural soil dissemination, and plant uptake for available data were obtained and assessed. In order to compare a set of related data from the collected articles, box and whisker plots showing the distribution of U in P fertilizers are presented by region. The results from the reviewed articles show that the U concentrations in P fertilizer were in the range of 0.1–653 mg kg−1. Interestingly, Minjingu P fertilizers from Tanzania, which are used in six East African countries, showed the highest U concentrations (159 to 653 mg kg−1, average 390 mg kg−1). The reported U concentrations for these fertilizers are, in fact, comparable to those of conventional low-grade uranium deposits mined in Namibia and elsewhere. Additionally, approximately 96% of the reviewed articles indicate that fertilized soil has higher U concentrations than non-fertilized soils, hinting at a measurable effect of mineral fertilizer use. The review recommends U extraction during mineral fertilizer production so that potential environmental risks can be reduced and U resources that would otherwise be lost can be recovered and used to substitute conventional U mining elsewhere. [ABSTRACT FROM AUTHOR]

Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy's interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy's interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient. Author summary: Foldy is a cloud-based application that enables scientists to use AI-based structural biology tools such as AlphaFold and DiffDock without software expertise. With many different deployment options, it can be set up by individuals, labs, universities, and companies in the cloud with no need for hardware resources. Foldy can predict the structure of proteins and complexes up to 6000 amino acids, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. Some structures are visible to the public on the Lawrence Berkeley Labs Foldy instance, and can be viewed at https://foldy.lbl.gov. Our manuscript highlights the user interface, deployment options, relative strengths of Foldy compared to existing tools, and some past applications of Foldy. It's an accessible solution for researchers who are not software experts. Many deployment options are possible and we highlight two: one of which can be set up in minutes, and the other can handle the traffic of thousands of users and hundreds of thousands of protein structures and docked ligands. This makes advanced AI-based tools more widely available, paving the way for accelerating life science research. By developing an easy-to-use platform, our work demonstrates that even computationally expensive AI-based tools like AlphaFold can be made accessible to a wide audience. Improvements in the accessibility of computational tools will allow more biologists to more easily apply computational tools to more problems. We are hopeful that Foldy addresses the growing need of making revolutionary computational tools accessible to more researchers. [ABSTRACT FROM AUTHOR]

This article discusses the duration and prognostic factors of therapy in skull base osteomyelitis (SBO), a rare infection of the skull base. The traditional treatment for SBO involves antimicrobial therapy (AMT) and surgical debridement. However, the recommended duration of treatment varies, and the study aims to identify factors that may influence outcomes and provide clearer recommendations on the duration of AMT. The study found that an average of 6.8 weeks of intravenous AMT followed by a prolonged course of oral AMT is necessary to treat most cases of SBO. Fungal involvement also significantly impacts the duration of AMT. The authors suggest that clinical guidelines are needed to better manage this complex disease. [Extracted from the article]

This article, published in the Journal of Neurological Surgery, compares the outcomes of cochlear implant (CI) speech perception in 100 patients with sporadic vestibular schwannoma (VS) who were managed with observation, radiosurgery, or microsurgery. The study found that patients who underwent microsurgery had poorer implant outcomes compared to those managed with observation or radiosurgery. Open-set speech perception was achieved in 56% of patients managed with microsurgery, 94% with observation, and 80% with radiosurgery. The data suggest that cochlear implants can benefit selected patients with sporadic VS, and that observation or radiosurgery may be more reliable options for achieving open-set speech perception compared to microsurgical resection. [Extracted from the article]

Targeted degradation regulates the activity of the transcriptional repressor Bcl6 and its ability to suppress oxidative stress and inflammation. Here, we report that abundance of endothelial Bcl6 is determined by its interaction with Golgi-localized pannexin 3 (Panx3) and that Bcl6 transcriptional activity protects against vascular oxidative stress. Consistent with data from obese, hypertensive humans, mice with an endothelial cell–specific deficiency in Panx3 had spontaneous systemic hypertension without obvious changes in channel function, as assessed by Ca2+ handling, ATP amounts, or Golgi luminal pH. Panx3 bound to Bcl6, and its absence reduced Bcl6 protein abundance, suggesting that the interaction with Panx3 stabilized Bcl6 by preventing its degradation. Panx3 deficiency was associated with increased expression of the gene encoding the H2O2-producing enzyme Nox4, which is normally repressed by Bcl6, resulting in H2O2-induced oxidative damage in the vasculature. Catalase rescued impaired vasodilation in mice lacking endothelial Panx3. Administration of a newly developed peptide to inhibit the Panx3-Bcl6 interaction recapitulated the increase in Nox4 expression and in blood pressure seen in mice with endothelial Panx3 deficiency. Panx3-Bcl6-Nox4 dysregulation occurred in obesity-related hypertension, but not when hypertension was induced in the absence of obesity. Our findings provide insight into a channel-independent role of Panx3 wherein its interaction with Bcl6 determines vascular oxidative state, particularly under the adverse conditions of obesity. Editor's summary: Obesity induces endothelial dysfunction that can lead to hypertension. Wolpe et al. uncovered a role for Panx3 as a scaffolding protein that limits oxidative stress in the endothelium and hypertension. Panx3 bound to and stabilized the transcriptional repressor Bcl6, which suppressed the expression of Nox4, the gene encoding a hydrogen peroxide–producing enzyme. Mice lacking Panx3 in endothelial cells or treated with a peptide that disrupted the Panx3-Bcl6 interaction showed greater oxidative stress in the endothelium and developed hypertension. Moreover, Panx3 mRNA expression and Bcl6 protein abundance were decreased and Nox4 mRNA expression was increased in mice with diet-induced obesity, but not in mice with pharmacologically induced hypertension. Endothelial Panx3 and Bcl6 abundance were reduced in hypertensive, obese individuals, suggesting that reductions in endothelial Panx3 may drive obesity-associated hypertension. —Wei Wong [ABSTRACT FROM AUTHOR]

Slope units are terrain partitions bounded by drainage and divide lines. In landslide modeling, including susceptibility modeling and event-specific modeling of landslide occurrence, slope units provide several advantages over gridded units, such as better capturing terrain geometry, improved incorporation of geospatial landslide-occurrence data in different formats (e.g., point and polygon), and better accommodating the varying data accuracy and precision in landslide inventories. However, the use of slope units in regional (> 100 km 2) landslide studies remains limited due, in part, to the large computational costs and/or poor reproducibility with current delineation methods. We introduce a computationally efficient algorithm for the parameter-free delineation of slope units that leverages tools from within TauDEM and GRASS, using an R interface. The algorithm uses geomorphic laws to define the appropriate scaling of the slope units representative of hillslope processes, avoiding the often ambiguous determination of slope unit size. We then demonstrate how slope units enable more robust regional-scale landslide susceptibility and event-specific landslide occurrence maps. [ABSTRACT FROM AUTHOR]