Table Of Contents Page, PNAS Volume 121, Number 37

PNAS September 10, 2024

This Week in PNAS

Inner Workings

QnAs

Retrospective

Commentaries

Perspective

Mechanical force has repeatedly been highlighted to be involved in T cell activation. However, the biological significance of mechanical force for T cell receptor signaling remains under active consideration. Here, guided by theoretical analysis, we ...

Letters

Brief Report

Humans explore visual scenes by alternating short fixations with saccades directing the fovea to points of interest. During fixation, the visual system not only examines the foveal stimulus at high resolution, but it also processes the extrafoveal input ...

Physical Sciences

Biophysics and Computational Biology

Utilizing molecular dynamics and free energy perturbation, we examine the relative binding affinity of several covalent polycyclic aromatic hydrocarbon - DNA (PAH-DNA) adducts at the central adenine of NRAS codon-61, a mutational hotspot implicated in ...
The Caenorhabditis elegans HMP-2/HMP-1 complex, akin to the mammalian β-catenin- α-catenin complex, serves as a critical mechanosensor at cell–cell adherens junctions, transducing tension between HMR-1 (also known as cadherin in mammals) and the actin ...
Collective cell migration is crucial in various physiological processes, including wound healing, morphogenesis, and cancer metastasis. Adherens Junctions (AJs) play a pivotal role in regulating cell cohesion and migration dynamics during tissue ...

Chemistry

Oral delivery of proteins faces challenges due to the harsh conditions of the gastrointestinal (GI) tract, including gastric acid and intestinal enzyme degradation. Permeation enhancers are limited in their ability to deliver proteins with high molecular ...
The nature of interchain π-system contacts, and their relationship to hole transport, are elucidated for the high-mobility, noncrystalline conjugated polymer C16-IDTBT by the application of scanning tunneling microscopy, molecular dynamics, and quantum ...
We present Einstein coefficient spectra and a detailed-balance derivation of generalized Einstein relations between them that is based on the connection between spontaneous and stimulated emission. If two broadened levels or bands overlap in energy, ...
Catalytic hydrogenation of CO2 to value-added fuels and chemicals is of great importance to carbon neutrality but suffers from an activity–selectivity trade-off, leading to limited catalytic performance. Herein, the ZnFeAlO4 + SAPO-34 composite catalyst ...
Transition metal oxides ion diffusion channels have been developed for ammonium-ion batteries (AIBs). However, the influence of microstructural features of diffusion channels on the storage and diffusion behavior of NH4+ is not fully unveiled. In this ...
Free of posttransfer, on-surface synthesis (OSS) of single-atomic-layer nanostructures directly on semiconductors holds considerable potential for next-generation devices. However, due to the high diffusion barrier and abundant defects on semiconductor ...
Bacterial evolution, particularly in hospital settings, is leading to an increase in multidrug resistance. Understanding the basis for this resistance is critical as it can drive discovery of new antibiotics while allowing the clinical use of known ...

Computer Sciences

Finding optimal bipartite matchings—e.g., matching medical students to hospitals for residency, items to buyers in an auction, or papers to reviewers for peer review—is a fundamental combinatorial optimization problem. We found a distributed algorithm for ...
The rapid growth of large-scale spatial gene expression data demands efficient and reliable computational tools to extract major trends of gene expression in their native spatial context. Here, we used stability-driven unsupervised learning (i.e., staNMF) ...

Engineering

Stereolithography enables the fabrication of three-dimensional (3D) freeform structures via light-induced polymerization. However, the accumulation of ultraviolet dose within resin trapped in negative spaces, such as microfluidic channels or voids, can ...

Environmental Sciences

High forest low deforestation jurisdictions (HFLDs) contain many of the world’s last intact forests with historically low deforestation. Since carbon financing typically uses historical deforestation rates as baselines, HFLDs facing the prospect of future ...
Homogenous advanced oxidation processes (AOPs) based on transition metal catalysts toward the activation of H2O2 to hydroxyl radical (•OH) have been widely applied to organic pollutants removal, such as Fenton and Fenton-like processes. These transition ...
Electrochemical ammonia (NH3) synthesis from nitrate reduction (NITRR) offers an appealing solution for addressing environmental concerns and the energy crisis. However, most of the developed electrocatalysts reduce NO3 to NH3 via a hydrogen (H*)-...
Peroxymonosulfate-based electrochemical advanced oxidation processes (PMS-EAOPs) have great potential for sustainable water purification, so an in-depth understanding of its catalytic mechanism is imperative to facilitate its practical application. Herein,...

Physics

Entanglement in a soft condensed matter system is enabled in the form of entangled disclination lines by using colloidal particles in nematic liquid crystals. These topological excitations are manifested as colloidal entanglement at equilibrium. How to ...
The unconventional superconductor UTe 2 exhibits numerous signatures of spin-triplet superconductivity—a rare state of matter which could enable quantum computation protected against decoherence. UTe 2 possesses a complex phase landscape comprising two ...

Statistics

Trajectory inference methods are essential for analyzing the developmental paths of cells in single-cell sequencing datasets. It provides insights into cellular differentiation, transitions, and lineage hierarchies, helping unravel the dynamic processes ...
Single-cell RNA sequencing (scRNA-seq) data, susceptible to noise arising from biological variability and technical errors, can distort gene expression analysis and impact cell similarity assessments, particularly in heterogeneous populations. Current ...

Sustainability Science

High forest low deforestation jurisdictions (HFLDs) contain many of the world’s last intact forests with historically low deforestation. Since carbon financing typically uses historical deforestation rates as baselines, HFLDs facing the prospect of future ...
The outstanding mechanical properties, light weight, and biodegradability of cellulose nanofibrils (CNFs) make them promising components of renewable and sustainable next-generation reinforced composite biomaterials and bioplastics. Manufacturing CNFs at ...

Social Sciences

Anthropology

This study reports the earliest directly dated occurrence of archaeological wheat and cotton in the humid forests of West Africa. These are the first archaeobotanical results from the medieval urban center of Ile-Ife, southwestern Nigeria, best known for ...

Political Sciences

States have long used economic sanctions in response to violations of international law as a strategy to restore order. Increasingly, firms also reject doing business with violators. In response to the war in Ukraine, hundreds of multinational ...

Psychological and Cognitive Sciences

Creating opportunities for people to achieve socioeconomic mobility is a widely shared societal goal. Paradoxically, however, achieving this goal can pose a threat to high-socioeconomic-status (SES) people as they look to maintain their privileged ...
The presaccadic preview of a peripheral target enhances the efficiency of its postsaccadic processing, termed the extrafoveal preview effect. Peripheral visual performance—and thus the quality of the preview—varies around the visual field, even at ...

Social Sciences

Immigrants are highly entrepreneurial. But, what is the broader relationship between high-skilled immigration and regional entrepreneurship activity beyond the ventures that immigrants establish themselves? Using administrative data on newly awarded H-1B ...
The transition to adolescence is a critical period for mental health development. Socio-experiential environments play an important role in the emergence of depressive symptoms with some adolescents showing more sensitivity to social contexts than others. ...

Biological Sciences

Applied Biological Sciences

Succinic acid (SA), a dicarboxylic acid of industrial importance, can be efficiently produced by metabolically engineered Mannheimia succiniciproducens. Although the importance of magnesium (Mg2+) ion on SA production has been evident from our previous ...
Droplet microfluidics has become a very powerful tool in high-throughput screening, including antibody discovery. Screens are usually carried out by physically sorting droplets hosting cells of the desired phenotype, breaking them, recovering the ...

Biochemistry

Drug-resistant Tuberculosis (TB) is a global public health problem. Resistance to rifampicin, the most effective drug for TB treatment, is a major growing concern. The etiological agent, Mycobacterium tuberculosis (Mtb), has a cluster of ATP-binding ...
Alzheimer’s disease (AD) is a prevalent neurodegenerative disease characterized by cognitive decline and learning/memory impairment associated with neuronal cell loss. Estrogen-related receptor α (ERRα) and ERRγ, which are highly expressed in the brain, ...
The ubiquitin ligase Anaphase-Promoting Complex/Cyclosome (APC/C) and its regulatory protein Cdc20 play important roles in the control of different stages of mitosis. APC/C associated with Cdc20 is active and promotes metaphase–anaphase transition by ...

Biophysics and Computational Biology

Trajectory inference methods are essential for analyzing the developmental paths of cells in single-cell sequencing datasets. It provides insights into cellular differentiation, transitions, and lineage hierarchies, helping unravel the dynamic processes ...
The rapid growth of large-scale spatial gene expression data demands efficient and reliable computational tools to extract major trends of gene expression in their native spatial context. Here, we used stability-driven unsupervised learning (i.e., staNMF) ...
The Caenorhabditis elegans HMP-2/HMP-1 complex, akin to the mammalian β-catenin- α-catenin complex, serves as a critical mechanosensor at cell–cell adherens junctions, transducing tension between HMR-1 (also known as cadherin in mammals) and the actin ...
Prolyl-hydroxylation is an oxygen-dependent posttranslational modification (PTM) that is known to regulate fibril formation of collagenous proteins and modulate cellular expression of hypoxia-inducible factor (HIF) α subunits. However, our understanding ...
Autophagy of glycogen (glycophagy) is crucial for the maintenance of cellular glucose homeostasis and physiology in mammals. STBD1 can serve as an autophagy receptor to mediate glycophagy by specifically recognizing glycogen and relevant key autophagic ...

Cell Biology

Collective cell migration is crucial in various physiological processes, including wound healing, morphogenesis, and cancer metastasis. Adherens Junctions (AJs) play a pivotal role in regulating cell cohesion and migration dynamics during tissue ...
Proteostasis and genomic integrity are respectively regulated by the endoplasmic reticulum–associated protein degradation (ERAD) and DNA damage repair signaling pathways, with both pathways essential for carcinogenesis and drug resistance. How these ...

Developmental Biology

Ovarian development was traditionally recognized as a “default” sexual outcome and therefore received much less scientific attention than testis development. In turtles with temperature-dependent sex determination (TSD), how the female pathway is ...

Ecology

Anthropogenic habitat destruction and climate change are reshaping the geographic distribution of plants worldwide. However, we are still unable to map species shifts at high spatial, temporal, and taxonomic resolution. Here, we develop a deep learning ...

Evolution

A central goal in evolutionary biology is to understand how different evolutionary processes cause trait change in wild populations. However, quantifying evolutionary change in the wild requires linking trait change to shifts in allele frequencies at ...

Genetics

Immunology and Inflammation

While the acute inflammatory response to harmful stimuli is protective, unrestrained neutrophil swarming drives collateral tissue damage and inflammation. Biosynthesized from omega-3 essential polyunsaturated fatty acids, resolvins are a family of ...
Human C-reactive protein (CRP) is a pentameric complex involved in immune defense and regulation of autoimmunity. CRP is also a therapeutic target, with both administration and depletion of serum CRP being pursued as a possible treatment for autoimmune ...

Medical Sciences

Stereolithography enables the fabrication of three-dimensional (3D) freeform structures via light-induced polymerization. However, the accumulation of ultraviolet dose within resin trapped in negative spaces, such as microfluidic channels or voids, can ...
Epidemiological studies have revealed an inverse relationship between the incidence of Alzheimer’s disease (AD) and various cancers, including colorectal cancer (CRC). We aimed to determine whether the incidence of CRC is reduced in AD-like mice and ...
Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating ...
Residual nonvisible bladder cancer after proper treatment caused by technological and therapeutic limitations is responsible for tumor relapse and progression. This study aimed to demonstrate the feasibility of a solution for simultaneous detection and ...

Microbiology

We generated SARS-CoV-2 variants resistant to three SARS-CoV-2 main protease (Mpro) inhibitors (nirmatrelvir, TKB245, and 5h), by propagating the ancestral SARS-CoV-2WK521WT in VeroE6TMPRSS2 cells with increasing concentrations of each inhibitor and ...
Organisms display an immense variety of shapes, sizes, and reproductive strategies. At microscopic scales, bacterial cell morphology and growth dynamics are adaptive traits that influence the spatial organization of microbial communities. In one such ...

Neuroscience

Finding optimal bipartite matchings—e.g., matching medical students to hospitals for residency, items to buyers in an auction, or papers to reviewers for peer review—is a fundamental combinatorial optimization problem. We found a distributed algorithm for ...
Variations in interoceptive signals from the baroreceptors (BRs) across the cardiac and respiratory cycle can modulate cortical excitability and so affect awareness. It remains debated at what stages of processing they affect awareness-related event-...
Many RNA-binding proteins (RBPs) are linked to the dysregulation of RNA metabolism in motor neuron diseases (MNDs). However, the molecular mechanisms underlying MN vulnerability have yet to be elucidated. Here, we found that such an RBP, Quaking5 (Qki5), ...
In the brain, a microvascular sensory web coordinates oxygen delivery to regions of neuronal activity. This involves a dense network of capillaries that send conductive signals upstream to feeding arterioles to promote vasodilation and blood flow. ...
The retinal fovea in human and nonhuman primates is essential for high acuity and color vision. Within the fovea lies specialized circuitry in which signals from a single cone photoreceptor are largely conveyed to one ON and one OFF type midget bipolar ...

Physiology

The factors that contribute to pain after nerve injury remain incompletely understood. Laser-assisted in situ keratomileusis (LASIK) and photorefractive keratectomy (PRK) are common surgical techniques to correct refractive errors. After LASIK or PRK, a ...

Plant Biology

Root exudates are known signaling agents that influence legume root nodulation, but the molecular mechanisms for nonflavonoid molecules remain largely unexplored. The number of soybean root nodules during the initial growth phase shows substantial ...
In plants, development of all above-ground tissues relies on the shoot apical meristem (SAM) which balances cell proliferation and differentiation to allow life-long growth. To maximize fitness and survival, meristem activity is adjusted to the prevailing ...

Psychological and Cognitive Sciences

The transition to adolescence is a critical period for mental health development. Socio-experiential environments play an important role in the emergence of depressive symptoms with some adolescents showing more sensitivity to social contexts than others. ...

Corrections

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