The tuning of the Fermi level in tin telluride, a topological crystalline insulator, is essential for accessing its unique surface states and optimizing its electronic properties for applications such as spintronics and quantum computing. In this study, we demonstrate that the Fermi level in tin telluride can be effectively modulated by controlling the tin concentration during chemical vapor deposition synthesis. By introducing tin-rich conditions, we observed a blue shift in the X-ray photoelectron spectroscopy core-level peaks of both tin and tellurium, indicating an upward shift in the Fermi level. This shift is corroborated by a decrease in work function values measured via ultraviolet photoelectron spectroscopy, confirming the suppression of Sn vacancies. Our findings provide a low-cost, scalable method to achieve tunable Fermi levels in tin telluride, offering a significant advancement in the development of materials with tailored electronic properties for next-generation technological applications. .
Individuals with "agrammatic" receptive aphasia have long been known to rely on semantic plausibility rather than syntactic cues when interpreting sentences. In contrast to early interpretations of this pattern as indicative of a deficit in syntactic knowledge, a recent proposal views agrammatic comprehension as a case of "noisy-channel" language processing with an increased expectation of noise in the input relative to healthy adults. Here, we investigate the nature of the noise model in aphasia and whether it is adapted to the statistics of the environment. We first replicate findings that a) healthy adults (N = 40) make inferences about the intended meaning of a sentence by weighing the prior probability of an intended sentence against the likelihood of a noise corruption and b) their estimate of the probability of noise increases when there are more errors in the input (manipulated via exposure sentences). We then extend prior findings that adults with chronic post-stroke aphasia (N = 28) and healthy age-matched adults (N = 19) similarly engage in noisy-channel inference during comprehension. We use a hierarchical latent mixture modeling approach to account for the fact that rates of guessing are likely to differ between healthy controls and individuals with aphasia and capture individual differences in the tendency to make inferences. We show that individuals with aphasia are more likely than healthy controls to draw noisy-channel inferences when interpreting semantically implausible sentences, even when group differences in the tendency to guess are accounted for. While healthy adults rapidly adapt their inference rates to an increase in noise in their input, whether individuals with aphasia do the same remains equivocal. Further investigation of comprehension through a noisy-channel lens holds promise for a parsimonious understanding of language processing in aphasia and may suggest potential avenues for treatment.
We report the genome sequences of four Endozoicomonas sp. strains isolated from the octocoral Litophyton maintained long term at an aquarium facility. Our analysis reveals the coding potential for versatile polysaccharide metabolism; Type II, III, IV, and VI secretion systems; and the biosynthesis of novel ribosomally synthesized and post-translationally modified peptides.
Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.gov), a database of transgenic enhancer assays conducted in developing mouse embryos in vivo. Since the original publication in 2007, the database grew nearly 20-fold from 250 to over 4500 experiments and currently harbors over 23 500 images. The updated database provides structured information on experiments conducted at different stages of embryonic development, including enhancer activities of human pathogenic and synthetic variants and sequences derived from a variety of species. In addition to manually curated results of thousands of individual experiments, the new database also features hundreds of manually curated comparisons between alleles. The VISTA Enhancer Browser provides a crucial resource for study of human genetic variation, gene regulation and developmental biology.
The Genomes OnLine Database (GOLD; https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute is a comprehensive online metadata repository designed to catalog and manage information related to (meta)genomic sequence projects. GOLD provides a centralized platform where researchers can access a wide array of metadata from its four organization levels namely Study, Organism/Biosample, Sequencing Project and Analysis Project. GOLD continues to serve as a valuable resource and has seen significant growth and expansion since its inception in 1997. With its expanded role as a collaborative platform, it not only actively imports data from other primary repositories like National Center for Biotechnology Information but also supports contributions from researchers worldwide. This collaborative approach has enriched the database with diverse datasets, creating a more integrated resource to enhance scientific insights. As genomic research becomes increasingly integral to various scientific disciplines, more researchers and institutions are turning to GOLD for their metadata needs. To meet this growing demand, GOLD has expanded by adding diverse metadata fields, intuitive features, advanced search capabilities and enhanced data visualization tools, making it easier for users to find and interpret relevant information. This manuscript provides an update and highlights the new features introduced over the last 2 years.
The [PSI+] prion phenotype in yeast manifests as a white, pink, or red color pigment. Experimental manipulations destabilize prion phenotypes, and allow colonies to exhibit [psi-] (red) sectored phenotypes within otherwise completely white colonies. Further investigation of the size and frequency of sectors that emerge as a result of experimental manipulation is capable of providing critical information on mechanisms of prion curing, but we lack a way to reliably extract this information. Images of experimental colonies exhibiting sectored phenotypes offer an abundance of data to help uncover molecular mechanisms of sectoring, yet the structure of sectored colonies is ignored in traditional biological pipelines. In this study, we present [PSI]-CIC, the first computational pipeline designed to identify and characterize features of sectored yeast colonies. To overcome the barrier of a lack of manually annotated data of colonies, we develop a neural network architecture that we train on synthetic images of colonies and apply to real images of [PSI+] , [psi-] , and sectored colonies. In hand-annotated experimental images, our pipeline correctly predicts the state of approximately 95% of colonies detected and frequency of sectors in approximately 89.5% of colonies detected. The scope of our pipeline could be extended to categorizing colonies grown under different experimental conditions, allowing for more meaningful and detailed comparisons between experiments. Our approach streamlines the analysis of sectored yeast colonies providing a rich set of quantitative metrics and provides insight into mechanisms driving the curing of prion phenotypes.
Symbiotic marine bacteria that are transmitted through the environment are susceptible to abiotic factors (salinity, temperature, physical barriers) that can influence their ability to colonize their specific hosts. Given that many symbioses are driven by host specificity, environmentally transmitted symbionts are more susceptible to extrinsic factors depending on conditions over space and time. In order to determine whether the population structure of environmentally transmitted symbionts reflects host specificity or biogeography, we analysed the genetic structure of Sepiola atlantica (Cephalopoda: Sepiolidae) and their Vibrio symbionts (V. fischeri and V. logei) in four Galician Rías (Spain). This geographical location is characterized by a jagged coastline with a deep-sea entrance into the land, ideal for testing whether such population barriers exist due to genetic isolation. We used haplotype estimates combined with nested clade analysis to determine the genetic relatedness for both S. atlantica and Vibrio bacteria. Analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for both host and symbiont genetic data. Our analyses reveal a low percentage of variation among and between host populations, suggesting that these populations are panmictic. In contrast, Vibrio symbiont populations show certain degree of genetic structure, demonstrating that the hydrology of the rías is driving bacterial distribution (and not host specificity). Thus, for environmentally transmitted symbioses such as the sepiolid squid-Vibrio association, abiotic factors can be a major selective force for determining population structure for one of the partners.
