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Surrogate selection is an experimental design that without sequencing any DNA can restrict a sample of cells to those carrying certain genomic mutations. In immunological disease studies, this design may provide a relatively easy approach to enrich a lymphocyte sample with cells relevant to the disease response because the emergence of neutral mutations associates with the proliferation history of clonal subpopulations. A statistical analysis of clonotype sizes provides a structured, quantitative perspective on this useful property of surrogate selection. Our model specification couples within-clonotype birth-death processes with an exchangeable model across clonotypes. Beyond enrichment questions about the surrogate selection design, our framework enables a study of sampling properties of elementary sample diversity statistics; it also points to new statistics that may usefully measure the burden of somatic genomic alterations associated with clonal expansion. We examine statistical properties of immunological samples governed by the coupled model specification, and we illustrate calculations in surrogate selection studies of melanoma and in single-cell genomic studies of T cell repertoires. 

Inocybe is the largest genus in the family Inocybaceae, with approximately 1000 species worldwide. Basic data on the species diversity, geographic distribution, and the infrageneric framework of Inocybe are still incomplete because of the intricate nature of this genus, which includes numerous unrecognized taxa that exist around the world. A multigene phylogeny of the I. umbratica–paludinella group, initially designated as the “I. angustifolia subgroup”, was conducted using the ITS-28S-rpb2 nucleotide datasets. The seven species, I. alabamensis, I. angustifolia, I. argenteolutea, I. olivaceonigra, I. paludinella, I. subangustifolia, and I. umbratica, were confirmed as members of this species group. At the genus level, the I. umbratica–paludinella group is a sister to the lineage of the unifying I. castanea and an undescribed species. Inocybe sect. Umbraticae sect. nov. was proposed to accommodate species in the I. umbratica–paludinella group and the I. castanea lineage. This section now comprises eight documented species and nine new species from China, as described in this paper. Additionally, new geographical distributions of I. angustifolia and I. castanea in China are reported. The nine new species and I. angustifolia, I. castanea, I. olivaceonigra, and I. umbratica are described in detail and illustrated herein with color plates based on Chinese materials. A global key to 17 species in the section Umbraticae is provided. The results of the current study provide a more detailed basis for the accurate identification of species in the I. umbratica-paludinella group and a better understanding of their phylogenetic placement. 

Abstract The brain integrates activity across networks of interconnected neurons to generate behavioral outputs. Several physiological and imaging-based approaches have been previously used to monitor responses of individual neurons. While these techniques can identify cellular responses greater than the neuron’s action potential threshold, less is known about the events that are smaller than this threshold or are localized to subcellular compartments. Here we use NEAs to obtain temporary intracellular access to neurons allowing us to record information-rich data that indicates action potentials, and sub-threshold electrical activity. We demonstrate these recordings from primary hippocampal neurons, induced pluripotent stem cell-derived (iPSC) neurons, and iPSC-derived brain organoids. Moreover, our results show that our arrays can record activity from subcellular compartments of the neuron. We suggest that these data might enable us to correlate activity changes in individual neurons with network behavior, a key goal of systems neuroscience. 

Abstract The factors that control strain partitioning along plate boundaries and within continental interiors remains poorly resolved. Plate convergence may be accommodated via distributed crustal shortening or discrete crustal‐scale strike‐slip faulting, but what controls these differing modes of deformation is debated. Here we address this question by examining the actively deforming regions that surround the Tarim Basin in central Asia, where deformation is uniquely partitioned into predominately strike‐slip faults in the east and distributed fold‐thrust belts in the west to accommodate Cenozoic India‐Asia plate convergence. We present integrated geological and geophysical observations to elucidate patterns in crustal deformation and compositional structure in and around the Tarim Basin. The thrust‐dominated western Tarim Basin correlates with a strongly‐magnetic lower crust, whereas strike‐slip faulting along the eastern margins of the Tarim Basin lack such magnetic signals. We suggest that the lower crust of the western Tarim is more mafic and stronger than in the east, which impacts intra‐plate strain partitioning. A stronger lower crust results in vertical decoupling to drive mid‐crust horizontal detachments and facilitate thrust faulting, whereas a more homogenized crust favored vertical transcrustal strike‐slip faulting. These rheological differences likely originated from the impingement of the Permian Tarim plume focused in the west. A comparison with the Longmen Shan of eastern Tibetan Plateau reveals remarkably similar strain partitioning that correlates with variations in foreland rheology. Our results highlight how variations in lower‐crust viscosity impact strain partitioning in an intra‐plate setting and how plume processes exert a strong control on later continental tectonic processes. 

Deformation-resistant cratons comprise >60% of the continental landmass on Earth. Because they were formed mostly in the Archean to Mesoproterozoic, it remains unclear if cratonization was a process unique to early Earth. We address this question by presenting an integrated geological-geophysical data set from the Tarim region of central Asia. This data set shows that the Tarim region was a deformable domain from the Proterozoic to early Paleozoic, but deformation ceased after the emplacement of a Permian plume despite the fact that deformation continued to the north and south due to the closure of the Paleo-Asian and Tethyan Oceans. We interpret this spatiotemporal correlation to indicate plume-driven welding of the earlier deformable continents and the formation of Tarim’s stable cratonic lithosphere. Our work highlights the Phanerozoic plume-driven cratonization process and implies that mantle plumes may have significantly contributed to the development of cratons on early Earth.