bluuebunny/crossref_metadata_2025_split huggingface dataset:
A theory of stochastic fluvial landscape evolution
Authors: Roberts G. G. , Wani O. 
Published: February 2024

Geometries of eroding landscapes contain important information about geologic, climatic, biotic and geomorphic processes. They are also characterized by variability, which makes disentangling their origins challenging. Observations and physical models of fluvial processes, which set the pace of erosion on most continents, emphasize complexity and variability. By contrast, the spectral content of longitudinal river profiles and similarity of geometries at scales greater than approximately

100

km

highlight relatively simple emergent properties. A general challenge then, addressed in this manuscript, is development of a theory of landscape evolution that embraces such scale-dependent insights. We do so by incorporating randomness and probability into a theory of fluvial erosion. First, we explore the use of stochastic differential equations of the Langevin type, and the Fokker–Planck equation, for predicting migration of erosional fronts. Second, analytical approaches incorporating distributions of driving forces, critical thresholds and associated proxies are developed. Finally, a linear programming approach is introduced, that, at its core, treats evolution of longitudinal profiles as a Markovian stochastic problem. The theory is developed essentially from first principles and incorporates physics governing fluvial erosion. We explore predictions of this theory, including the natural growth of discontinuities and scale-dependent evolution, including local complexity and emergent simplicity.
Type 1 immunity enables neonatal thymic ILC1 production
Authors: Tougaard Peter , Pérez Mario Ruiz , Steels Wolf , Huysentruyt Jelle , Verstraeten Bruno , Vetters Jessica , Divert Tatyana , Gonçalves Amanda , Roelandt Ria , Takahashi Nozomi , Janssens Sophie , Buus Terkild Brink , Taghon Tom , Leclercq Georges , Vandenabeele Peter 
Published: February 2024

AbstractThymic atrophy occurs following type 1 inflammatory conditions like viral infection and sepsis, resulting in cell death and disruption of T-cell development. However, it remains undetermined whether the thymus actively contributes to the immune response. Thus, we cultured neonatal thymusex vivowith the type 1 cytokines IL-12 plus IL-18, resulting in a rapid shift from steady-state T-cell development to the production, expansion, and thymic exit of CXCR6+CD62L-type 1 innate lymphoid cells (ILC1s). Single-cell RNA-sequencing and functional assays identified these cells as embryonic-wave-derived KLRG1+ILC1s that mainly differentiated from immature neonatal thymic ILC1s. Confocal 3D imaging confirmed neonatal thymic ILC1 expansion during MCMV infection. Furthermore, thymic grafts revealedin vivothymic ILC1 egress and type 1 inflammation-induced homing of thymus-derived KLRG1+ILC1s to the liver and peritoneal cavity. Altogether, our data reveal a novel thymic function where type 1 immunity enables the production and peripheral homing of thymic-derived ILC1s.
MAGIC matrices: freeform bioprinting materials to support complex and reproducible organoid morphogenesis
Authors: Graham Austin J. , Khoo Michelle W.L. , Srivastava Vasudha , Viragova Sara , Kim Honesty , Parekh Kavita , Hennick Kelsey M. , Bird Malia , Goldhammer Nadine , Yu Jie Zeng , Morley Cameron D. , Lebel Paul , Kumar Sanjay , Rosenbluth Jennifer M. , Nowakowski Tomasz J. , Klein Ophir , Gómez-Sjöberg Rafael , Gartner Zev J. 
Published: February 2024

AbstractOrganoids are powerful models of tissue physiology, yet their applications remain limited due to their relatively simple morphology and high organoid-to-organoid structural variability. To address these limitations we developed a soft, composite yield-stress extracellular matrix that supports optimal organoid morphogenesis following freeform 3D bioprinting of cell slurries at tissue-like densities. The material is designed with two temperature regimes: at 4 °C it exhibits reversible yield-stress behavior to support long printing times without compromising cell viability. When transferred to cell culture at 37 °C, the material cross-links and exhibits similar viscoelasticity and plasticity to basement membrane extracts such as Matrigel. We first characterize the rheological properties of MAGIC matrices that optimize organoid morphogenesis, including low stiffness and high stress relaxation. Next, we combine this material with a custom piezoelectric printhead that allows more reproducible and robust self-organization from uniform and spatially organized tissue “seeds.” We apply MAGIC matrix bioprinting for high-throughput generation of intestinal, mammary, vascular, salivary gland, and brain organoid arrays that are structurally similar to those grown in pure Matrigel, but exhibit dramatically improved homogeneity in organoid size, shape, maturation time, and efficiency of morphogenesis. The flexibility of this method and material enabled fabrication of fully 3D microphysiological systems, including perfusable organoid tubes that experience cyclic 3D strain in response to pressurization. Furthermore, the reproducibility of organoid structure increased the statistical power of a drug response assay by up to 8 orders-of-magnitude for a given number of comparisons. Combined, these advances lay the foundation for the efficient fabrication of complex tissue morphologies by canalizing their self-organization in both space and time.
Identification and Structural Characterization of a mutant KRAS-G12V specific TCR restricted by HLA-A3
Authors: Sim Malcolm J. W. , Hanada Ken-ichi , Stotz Zachary , Yu Zhiya , Lu Jinghua , Brennan Paul , Quastel Max , Gillespie Geraldine M. , Long Eric O. , Yang James C. , Sun Peter D. 
Published: February 2024

SummaryMutations in KRAS are some of the most common across multiple cancer types and are thus attractive targets for therapy. Recent studies demonstrated that mutant KRAS generates immunogenic neoantigens that can be targeted in adoptive T cell therapy in metastatic diseases. To expand mutant KRAS specific immunotherapies, it is critical to identify additional HLA-I allotypes that can present KRAS neoantigens and their cognate T cell receptors (TCR). Here, we identified a murine TCR specific to a KRAS-G12V neoantigen (7VVVGAVGVGK16) using a vaccination approach with transgenic mice expressing the common HLA-I allotype, HLA-A*03:01 (HLA-A3). This TCR demonstrated exquisite specificity for mutant G12V and not Wt KRAS peptides. To investigate the molecular basis for neoantigen recognition by This TCR, we determined its structure in complex with HLA-A3(G12V). G12V-TCR CDR3β and CDR1 β formed a hydrophobic pocket to interact with p6 Val of the G12V but not Wt KRAS peptide. To improve the tumor sensitivity of This TCR, we designed rational substitutions to improve TCR:HLA-A3 contacts. Two substitutions exhibited modest improvements in TCR binding to HLA-A3 (G12V), but did not sufficiently improve T cell sensitivity for further clinical development. Our study provides mechanistic insight into how TCRs detect neoantigens and reveals the challenges in targeting KRAS-G12V mutations. [203]
A covariant model of molecular and diversification patterns through time and the history of large clades
Authors: Budd Graham E. , Mann Richard P. 
Published: February 2024

AbstractRate shifts in speciation and extinction have been recognised as important contributors to the creation of evolutionary patterns. In particular, the distribution of modern clade sizes is difficult to reconcile with models that do not include them. Although recent advances have allowed rate shifts to be integrated into evolutionary models, these have largely been for the purpose of inferring historical rate shifts across phylogenetic trees. In addition, these models have typically assumed an independence between patterns of diversification and rates of molecular and morphological evolution, despite there being mounting evidence of a connection between them. Here, we develop a new model with two principal goals: first, to explore the general patterns of diversification implied by constantly changing rates, and secondly to integrate diversification, molecular and morphological evolution into a single coherent framework. We thus develop and analyse a covariant birth-death process in which rates of all evolutionary processes (i.e. speciation, extinction and molecular and morphological change) covary continuously, both for each species and through time. We use this model to show that modern diversity is likely to be dominated by a small number of extremely large clades at any historical epoch; that these large clades are expected to be characterised by explosive early radiations accompanied by elevated rates of molecular evolution; and that extant organisms are likely to have evolved from species with unusually fast evolutionary rates. In addition, we show that under such a model, the amount of molecular change along a particular lineage is essentially independent of its height, which further weakens the molecular clock hypothesis. Finally, our model predicts the existence of “living fossil” sister groups to large clades that are both species poor and have exhibited slow rates of morphological and molecular change. Although our model is highly stochastic, it includes no special evolutionary moments or epochs. Our results thus demonstrate that the observed historical patterns of evolution can be modelled without invoking special evolutionary mechanisms or innovations that are unique to specific times or taxa, even when they are highly non-uniform: instead they could emerge from a process that is fundamentally homogeneous throughout time.
Nestling-Care Decisions by Cooperatively Breeding American Crows
Authors: Caffrey Carolee , Peterson Charles C. , Hackler Tiffany W. 
Published: February 2024

ABSTRACTDuring the nestling stage of breeding seasons in Stillwater, OK, pairs of American Crows (Corvus brachyrhynchos brachyrhynchos) lived alone or in groups of variable composition; auxiliaries included individuals that had delayed dispersal, immigrated into groups, or returned to natal territories after having lived elsewhere. Most, but not all, auxiliaries contributed to feeding nestlings, and their contributions varied considerably. On average, breeders fed nestlings at greater rates than did auxiliaries, and female breeders spent more time at nests than did other group members. Breeders compensated for auxiliary contributions by reducing their own; this and breeder responses to the disappearance of auxiliary feeding group members provide evidence that these long-lived, iteroparous animals were managing energy budgets so as to maximize fitness over the long term. Female breeders in larger groups spent more time at nests than did those in smaller groups, but not for expected reasons and not to any reproductive benefit. A few female auxiliaries spent increasing amounts of time at nests as nestlings aged. No other measured phenotypic characteristic of individuals was found to explain any of the wide variation in the patterns of nestling care exhibited by members of our population.
Nanopore-based DNA long-read sequencing analysis of the aged human brain
Authors: Ramirez Paulino , Sun Wenyan , Kazempour Dehkordi Shiva , Zare Habil , Fongang Bernard , Bieniek Kevin F. , Frost Bess 
Published: February 2024

ABSTRACTAging disrupts cellular processes such as DNA repair and epigenetic control, leading to a gradual buildup of genomic alterations that can have detrimental effects in post-mitotic cells. Genomic alterations in regions of the genome that are rich in repetitive sequences, often termed “dark loci,” are difficult to resolve using traditional sequencing approaches. New long-read technologies offer promising avenues for exploration of previously inaccessible regions of the genome. Using nanopore-based long-read whole-genome sequencing of DNA extracted from aged 18 human brains, we identify previously unreported structural variants and methylation patterns within repetitive DNA, focusing on transposable elements (“jumping genes”) as crucial sources of variation, particularly in dark loci. Our analyses reveal potential somatic insertion variants and provides DNA methylation frequencies for many retrotransposon families. We further demonstrate the utility of this technology for the study of these challenging genomic regions in brains affected by Alzheimer’s disease and identify significant differences in DNA methylation in pathologically normal brains versus those affected by Alzheimer’s disease. Highlighting the power of this approach, we discover specific polymorphic retrotransposons with altered DNA methylation patterns. These retrotransposon loci have the potential to contribute to pathology, warranting further investigation in Alzheimer’s disease research. Taken together, our study provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, structural variants, and DNA methylation in the aging brain affected with Alzheimer’s disease neuropathology.
Individual performance niches may buffer population responses to climate change in estuarine fishes
Authors: Bellotto Clara , Fowler Ashley M. , Booth David J. 
Published: February 2024

AbstractClimate change may impact individual organisms in different ways, a consideration often overshadowed by predominant focus on population effects in studies. We examined three estuarine fish species to determine if individual fish performance, persisted across winter water temperatures. Fish performance at 16°C (current Sydney winter estuarine water temperature) and 20°C (predicted under climate change) with low and high food regimes was assessed using key physiological (growth, aerobic scope, burst speed) and behavioural parameters (foraging activity, boldness, shelter usage, predator escape response). We expected a strong positive relationship between performance at 16°C and 20°C for each parameter, and interactions with food level, however in general this was not found for any species. Relative performance was only maintained across temperatures for a few parameters, such as bite rate, boldness, and shelter response in one species (trumpeterPelates sexlineatus), with aerobic scope in silver biddyGerres subfasciatus, and boldness in fortescueCentropogon australis.Our results suggest that individuals’ fitness (directly via changes in growth, indirectly via behaviours) will be impacted by climate warming due to differences in relative performance among individuals across water temperatures. Changes in relative performance among individuals may initially compensate for a population-level response, thereby buffering the effects of climate change.
Fluctuating salinity during development impacts fish productivity
Authors: Chung Meng-Han Joseph , Noble Daniel W. A. , Fox Rebecca J. , Harrison Lauren M. , Jennions Michael D. 
Published: February 2024

ABSTRACTClimate change is elevating salinity levels in many freshwater systems, and more erratic rainfall is increasing variation in salinity. Consequently, many species now experience more extreme developmental environments. Resultant shifts in developmental trajectories could change key life history traits that persist into adulthood. To date, however, how variation in salinity affects the life histories of freshwater species has been neglected despite its implications for fisheries. We ran a large-scale experiment with a global pest, the mosquitofish (Gambusia holbrooki), and manipulated the salinity experienced by juveniles: freshwater (0‰), stable salinity (10‰) or fluctuating salinity (0-20‰; mean = 10 ‰). Fish developing in stable, high salinity grew faster and matured earlier, albeit with a decline in male telomeres and female gut development. Stable high salinity resulted in larger adult body size in females, but not males, which increased female fecundity. Conversely, fluctuations in salinity induced fish to grow more slowly and lowered female fecundity. Crucially, several of the long-term effects of salinity fluctuations were sex-specific, more adversely affecting females than males. We highlight that environmental variability alters an organism’s vulnerability to stressors, with implications that should be considered if we wish to understand the impact of climate change on population dynamics.
Spatiotemporal profiling defines persistence and resistance dynamics during targeted treatment of melanoma
Authors: Rubinstein Jill C. , Domanskyi Sergii , Sheridan Todd B. , Sanderson Brian , Park SungHee , Kaster Jessica , Li Haiyin , Anczukow Olga , Herlyn Meenhard , Chuang Jeffrey H. 
Published: February 2024

AbstractResistance of BRAF-mutant melanomas to targeted therapy arises from the ability of cells to enter a persister state, evade treatment with relative dormancy, and repopulate the tumor when reactivated. Using spatial transcriptomics in patient derived xenograft models, we capture clonal lineage evolution during treatment, finding the persister state to show increased oxidative phosphorylation, decreased proliferation, and increased invasive capacity, with central-to-peripheral gradients. Phylogenetic tracing identifies intrinsic- and acquired-resistance mechanisms (e.g. dual specific phosphatases, Reticulon-4, CDK2) and suggests specific temporal windows of potential therapeutic efficacy. Using deep learning to analyze histopathological slides, we find morphological features of specific cell states, demonstrating that juxtaposition of transcriptomics and histology data enables identification of phenotypically-distinct populations using imaging data alone. In summary, we define state change and lineage selection during melanoma treatment with spatiotemporal resolution, elucidating how choice and timing of therapeutic agents will impact the ability to eradicate resistant clones.Statement of SignificanceTumor evolution is accelerated by application of anti-cancer therapy, resulting in clonal expansions leading to dormancy and subsequently resistance, but the dynamics of this process are incompletely understood. Tracking clonal progression during treatment, we identify conserved, global transcriptional changes and local clone-clone and spatial patterns underlying the emergence of resistance.
Does method of field preparation affect survival and growth of juvenile Chinook salmon in agricultural floodplains?
Authors: Tallman Rachelle L. , Wampler Alexandra N. , Singer Gabriel P. , Jeffres Carson A. , Cocherell Dennis E. , Colby Jordan , Fangue Nann A. , Lusardi Robert A. , Rypel Andrew L. 
Published: February 2024

AbstractThere is growing interest to integrate conservation initiatives into agricultural practices using a reconciliation ecology framework. In California’s Central Valley, one approach to improving crucial nursery habitat for threatened and endangered fish species is by re-creating floodplain habitats through the inundation of agricultural fields during the non-growing season. We conducted a series of field experiments in agricultural floodplains (winter-flooded rice fields that were once natural floodplains) to explore whether different field preparation methods enhanced growth and survival of floodplain-dependent fish species. Approximately 8,000 juvenile fall-run Chinook Salmon (Oncorhynchus tshawytscha) were reared for at least 28 days on eight, 0.2 ha experimental fields. Each experimental field represented one of four treatments (two replicates per treatment): addition of large wood, addition of in-field canals, addition of both large wood and in-field canals, and control-where no additional field preparations were implemented beyond standard post-growing practices: i.e., chopping rice into stubble, baling and removing excess rice straw, and discing the field with a single pass by plowing rice straw into the ground to promote decomposition. We found no significant difference in water temperature, fish growth or fish survival among habitat treatments. Across treatments, survival ranged from 50.1%-78.3% and averaged 65.75% (⁺/- 7.89% SE). These findings suggest agricultural floodplains require no additional modifications to promote fish growth and survival. Results illustrate the benefits of integrating working landscapes with conservation initiatives by creating more accessible and beneficial habitat for native fishes.
StimulatedProrocentrum donghaiensecell growth byin-situmariculture dissolved organic matter
Authors: Wang Hongwei , Wu Siyang , Ma Jian , Hong Yiting , Guo Chentao , Zhao Jing , Lin Xin 
Published: February 2024

AbstractMixotrophic dinoflagellates frequently cause harmful algal blooms (HAB) in eutrophic mariculture waters that contain diverse excreted dissolved organic matter (DOM). The phagotrophy and the utilization of single organic small molecules have been extensively investigated in the bloom-forming mixotrophic dinoflagellates. However, their ability to utilize thein-situDOM via absorbtrophy still remains unexplored. Here we examined the growth promotion effect of thein-situmariculture DOM onProrocentrum donghaiense, a representative HAB-forming species in coastal waters. Our results showed that the cell growth and photosynthesis ofP. donghaiensewere significantly promoted underin-situDOM culture conditions. Additionally, parallel cultures were set up to disclose the potential role of the bacterioplankton in the free-living community (helper), where they aid in the remineralization of thein-situDOM, and the phycosphere community (competitor), where they compete against the algal host to acquire nutrients from thein-situDOM. Meanwhile, we determined the cellular stoichiometry under different culture conditions, showing that mariculture DOM can shape cellular stoichiometry significantly. Elevated cellular N (84.96%) and P (48.3%) were observed in spring DOM groups compared with the control groups. For the first time, this study quantifies the efficient utilization of thein-situDOM via absorbtrophy, indicating the vital role in the outbreak and maintenance of HAB events.