Rice University

Social and communicative deficits are defining characteristics of autism spectrum disorder (ASD). Some theories suggest that these challenges, among other autistic traits, may arise from differences in predictive coding, or how the brain uses context to predict and interpret incoming information. This idea has the potential to link symptoms of autism to specific neurocomputational processes, and is especially promising for communication, whose impairment is a hallmark of ASD. Here we leveraged the ability of large language models (LLMs) to quantify semantic contextualization to analyze a unique dataset of responses from hippocampal neurons obtained during language listening in three mild-to-severe autistic individuals with comorbid epilepsy. Key elements of semantic coding were preserved in all three individuals with ASD: single-neuron response dynamics, representation of word-word semantic relationships, and patterns of context-dependent shifts in meaning. However, relative to controls, ASD resulted in reduced neural signatures of contextualization: (1) neuronal responses were aligned with earlier, less contextual layers of GPT-2, (2) ASD patients had lower effective dimensionality of the neural subspace predicting semantics, (3) neural representations of word meaning were less influenced by preceding context, and (4) neural signatures of lexical surprisal were reduced. Together, these results support theories of autism that emphasize impairments in contextualization, and highlight the power of LLMs as a tool for quantifying the computational basis of neurodevelopmental disorders.

Accurately resolving the full spectrum of somatic alterations remains a major barrier in cancer genomics. Current short-read sequencing methods often prioritize SNVs and copy-number changes while overlooking SVs, haplotype-specific events, and epigenetic dysregulation. To bridge this gap, we present TumorLens, the first unified long-read framework that jointly detects SNVs, indels, SVs, large CNVs, loss-of-heterozygosity, and CpG methylation in a single assay. TumorLens introduces purity-aware long-read CNV/LoH modeling and personalized HLA-locus reconstruction, enabling the mechanistic interpretation of immune escape through allele-specific methylation profiling. Benchmarked across GIAB standards and clinical cohorts, TumorLens accurately recovered key somatic events, including interferon locus disruptions and HLA loss. Furthermore, it revealed pervasive global hypomethylation alongside focal hypermethylation in critical oncogenic pathways. By consolidating multi-omic layers into an end-to-end analytic pipeline, TumorLens establishes a new standard for comprehensive tumor profiling, accelerating the translation of long-read sequencing into precision oncology.

Molecular interactions are crucial to improving the efficiency and stability of perovskite solar cells, yet current solution-based approaches relying on molecular incorporation or surface passivation show inherent limitations in separately controlling these interactions. Here we reveal an intrinsic interfacial interaction that arises from simple contact between individually crystallized two-dimensional and three-dimensional perovskites without mixing or permanent bonding. We define this contact-triggered cationic interaction (CCI), which reversibly constrains molecular degrees of freedom, suppresses phase transitions, enhances carrier lifetimes and induces a unique recrystallization of the three-dimensional framework. This CCI-driven recrystallization produces refined FAPbI3 with improved cation homogeneity, reduced lattice disorder and superior optoelectronic properties. Devices using CCI-driven FAPbI3 achieve 26.25% efficiency (25.61% certified) and retain a projected operational lifetime exceeding 20,000 h. Our findings provide the first quantitative evidence that intrinsic interfacial cationic interactions can directly influence perovskite material quality and device performance. Solution processing of 2D/3D perovskite structures for solar cells offers limited control over layer formation. Lee et al. propose a dry approach, bringing the 2D and 3D perovskite layers into physical contact, to enhance the quality of the perovskite film.

Bacteriophages (phages) facilitate gene transfer and microbial evolution in all ecosystems and have applications as tools for engineering microbiomes and as antimicrobials. Historic efforts to map phage hosts, such as plaque assays, are limited to cultured bacteria, are low throughput, and are hard to apply in microbial communities and environmentally-relevant contexts. To overcome these limitations, we integrate a synthetic ribozyme that stores information about participation in horizontal gene transfer in 16S ribosomal RNA (rRNA) into the phage-plasmid P1, and perform targeted 16S rRNA sequencing following transduction to identify phage-host interactions. Experiments in synthetic and wastewater communities reveal Aeromonadales as a previously unreported P1 host order and show P1 transduction into pathogens. In wastewater, host range varies across phagemids having different origins of replication and phage-derived particles having different tail fibers. This work shows how autonomous barcoding can be used in phages to identify the molecular controls on their host range in microbial communities.

Abstract Industrial wastewaters with both high salinity and heavy metals are common, yet no existing process can achieve desalination and metal recovery in integrated technology platform. Conventional desalination processes do not distinguish background electrolyte generate toxic brines with heavy metals and miss the opportunities for resource recovery. In this work, we show that electrochemical ion pumping (EIP) has the unique feature to enable simultaneous desalination and metal recovery through programmable control of electrode potential. Because EIP transfers only a small amount of ions per half-cycle via high-frequency circuit switching, the electrode potential can be maintained within a narrow window throughout operation, which allows redox reactions to be selectively activated or suppressed without interrupting continuous ion transport. At potentials above the Cu²⁺/Cu reduction threshold, the system desalinates only capacitively with no metal deposition. Shifting the potential window below this threshold triggers selective copper electrodeposition on the electrode while performing desalination. In an asymmetric five-electrode EIP stack fed with a mixture of Cu²⁺, Ni²⁺, and Na+, positioning the potential window between the reduction potentials of the two metals yielded selective Cu²⁺ capture on the electrode. These findings establish electrode potential as a controllable operation parameter, providing an integrated platform for coupled water recycling with selective resource recovery from complex industrial brines.