Title
Topic
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‘Low dimensionality of Phenotypic Space as an Emergent Property of Coordinated Teams in Biological Regulatory Networks’
“Cell-fate decisions involve coordinated genome-wide expression changes, typically leading to a limited number of phenotypes. Although often modeled as simple toggle switches, these rather simplistic representations often disregard the complexity of regulatory networks governing these changes. Here, we unravel design principles underlying complex cell decision-making networks in multiple contexts.” Find the paper and full list of authors in Cell Press.
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‘Interlayer Dzyaloshinskii-Moriya Interactions Induced via Nonlinear Phononics in Bilayer van der Waals Materials’
“We theoretically study the impact of light-driven structural changes via nonlinear phononics on the magnetic order of untwisted bilayer van der Waals materials. We consider an illustrative example of the AA-stacked bilayer honeycomb lattice and show that high-intensity light in resonance with selected phonons induces large-amplitude phonon displacements that modify the magnetic Hamiltonian of the system. … We find that the structural changes in the strongly driven regime lower the symmetry relative to the equilibrium lattice and produce changes in the magnetic interactions between the local moments.” Find the paper and full list of authors in Physical Review B.
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‘Bundling Effect of Semiconductor-Enriched Single-Walled Carbon Nanotube Networks’
“Despite continual progress in creating semiconductor-enriched single-walled carbon nanotube (SWCNT) networks, significant challenges still remain in achieving electronically homogeneous channels for field-effect transistors (FETs) due to persisting metallic percolation and uncontrollable nanotube bundling. To address this critical issue, we systematically explored the bundling effect of the SWCNTs on the electrical characteristics of SWCNT network-based FETs.” Find the paper and full list of authors in Materials Science in Semiconductor Processing.
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‘Biochemical Characterization of Disease-Associated Variants of Human Ornithine Transcarbamylase’
“Human ornithine transcarbamylase deficiency (OTCD) is the most common ureagenesis disorder in the world. OTCD is an X-linked genetic deficiency in which patients experience hyperammonemia to varying degrees depending on the severity of the genetic mutation. More than two-thirds of the known mutations are caused by single nucleotide substitutions. In this paper, partial order optimum likelihood (POOL), a machine learning method, is used to analyze single nucleotide substitutions in OTC with varying disease phenotypes and predicted catalytic efficiencies.” Find the paper and full list of authors in ACS Chemical Biology.
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‘The Microbiome’s Influence on the Neurobiology of Opioid Addiction and Brain Connectivity’
“Opioids are the most effective and potent analgesics available for acute pain management. With no viable alternative for treating chronic or post operative pain, it is not surprising that over 10 million people misuse opioids. This study explores the developmental influence of the microbiome on resistance to opioid addictive behavior and functional connectivity.” Find the paper and full list of authors in Brain Research Bulletin.
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‘Antibiotic Pretreatment Inhibits White Band Disease Infection by Suppressing the Bacterial Pathobiome’
“Diseases have caused unprecedent mortality in Caribbean coral communities. White band disease (WBD) has killed up to 95% of all endangered Caribbean Acroporids since it was first observed in 1979. … To better understand the disease etiology of WBD, we pretreated corals with antibiotics to determine how prophylactic use of antibiotics impacts the transmission of WBD in a replicated tank-based experiment. We found the prophylactic use of antibiotics led to significantly reduced infection rates in disease exposed corals with a 30-percentage point decrease in the infection rate.” Find the paper and full list of authors in Frontiers in Marine Science.
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‘Root of Unity Quantum Cluster Algebras and Discriminants’
“We describe a connection between the subjects of cluster algebras, polynomial identity algebras, and discriminants. For this, we define the notion of root of unity quantum cluster algebras and prove that they are polynomial identity algebras. Inside each such algebra we construct a (large) canonical central subalgebra, which can be viewed as a far reaching generalization of the central subalgebras of big quantum groups constructed by De Concini, Kac, and Procesi and used in representation theory.” Find the paper and full list of authors in Journal of the London Mathematical Society.
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‘Responses of Littorina spp. Intertidal Snails to Thermal Extremes Indicate Countergradient Variation in Fitness’
“Global change models predict not only a steady increase in temperatures but also an increase in the occurrence of hot and cold extremes. Organisms’ responses to thermal extremes will depend on species-specific traits and the degree of within-species variation (among populations). … The evolution of population-specific responses, however, can be limited by gene flow that homogenises populations. Here, we investigate this relationship with a study of the survival of Littorina littorea, L. obtusata, and L. saxatilis—marine snails with varying dispersal potential—collected on either side of a known biogeographic break.” Find the paper and list of authors in Ecology and Evolution.
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‘A Phosphorylation Signal Activates Genome-Wide Transcriptional Control by BfmR’
“The nosocomial pathogen Acinetobacter baumannii is a major threat to human health. The sensor kinase-response regulator system, BfmS-BfmR, is essential to multidrug resistance and virulence in the bacterium and represents a potential antimicrobial target. Important questions remain about how the system controls resistance and pathogenesis. Although BfmR knockout alters expression of >1000 genes, its direct regulon is undefined. Moreover, how phosphorylation controls the regulator is unclear. Here, we address these problems by combining mutagenesis, ChIP-seq, and in vitro phosphorylation to study the functions of phospho-BfmR.” Find the paper and full list of authors in Nucleic Acids Research.
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‘A Prospective Real-Time Transfer Learning Approach To Estimate Influenza Hospitalizations With Limited Data’
“Accurate, real-time forecasts of influenza hospitalizations would facilitate prospective resource allocation and public health preparedness. State-of-the-art machine learning methods are a promising approach to produce such forecasts, but they require extensive historical data to be properly trained. Unfortunately, data on influenza hospitalizations, for the 50 states in the United States, are only available since the beginning of 2020. In addition, the data are far from perfect as they were under-reported for several months before health systems began consistently submitting their data. To address these issues, we propose a transfer learning approach.” Find the paper and list of authors in Epidemics.
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‘3D Spatial Distribution of Sost mRNA and Sclerostin Protein Expression in Response to In Vivo Tibia Loading in Female Mice’
“Bones adapt to external mechanical loads through a process known as mechanoadaptation. Osteocytes are the bone cells that sense the mechanical environment and initiate a biological response. Investigating the changes in osteocyte molecular expression following mechanical loading has been instrumental in characterizing the regulatory pathways involved in bone adaptation. … In this study, we used WISH-BONE (Whole-mount In Situ Histology of Bone) to investigate the spatial distribution of Sost-mRNA transcripts and its encoded protein, sclerostin, in 3D mouse tibia midshaft following in vivo tibia loading.” Find the paper and full list of authors in Bone.
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‘Human Mobility Is Well Described by Closed-Form Gravity-Like Models Learned Automatically From Data’
“Modeling human mobility is critical to address questions in urban planning, sustainability, public health, and economic development. … At one end of the modeling spectrum we have gravity models, which are easy to interpret but provide modestly accurate predictions of flows. At the other end, we have machine learning models, … which predict mobility more accurately than gravity models but do not provide clear insights on human behavior. Here, we show that simple machine-learned, closed-form models of mobility can predict mobility flows as accurately as complex machine learning models, and extrapolate better.” Find the paper and list of authors in…
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‘Interceptive Abilities in Autism Spectrum Sisorder: Comparing Naturalistic and Virtual Visuomotor Tasks’
“A growing body of research reveals that autistic individuals exhibit motor coordination challenges. Multiple theoretical frameworks propose that the seemingly disparate features of autism may arise from a common underlying process: a diminished ability to make predictions. Sensorimotor skills, such as catching a ball, critically rely on predicting the ball’s trajectory as well as anticipatory coordination of the entire body. Here, we assessed four different naturalistic and virtual interception tasks with 31 neurotypical and 23 autistic children (ages 7–12).” Find the paper and full list of authors in Autism Research.
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‘Spontaneous Anthropocentric Language Use in University Students’ Explanations of Biological Concepts’
“Previous research has shown that students employ intuitive thinking when understanding scientific concepts. Three types of intuitive thinking—essentialist, teleological, and anthropic thinking—are used in biology learning and can lead to misconceptions. … In this study, we examined how frequently undergraduate students across two U.S. universities (N = 807) used construal-consistent language (CCL) to explain in response to open-ended questions related to five core biology concepts (e.g., evolution), how CCL use differed by concept, and how this usage was related to misconceptions agreement.” Find the paper and full list of authors in LSE.
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‘Role of Ryanodine Receptor Cooperativity in Ca 2+ Wave-Mediated Triggered Activity in Cardiomyocytes’
“Ca2+ waves are known to trigger delayed after-depolarizations that can cause malignant cardiac arrhythmias. However, modelling Ca2+ waves using physiologically realistic models has remained a major challenge. Existing models with low Ca 2+ sensitivity of ryanodine receptors(RyRs) necessitate large release currents, leading to an unrealistically large Ca2+ transient amplitude incompatible with the experimental observations. Consequently, current physiologically detailed models of delayed after-depolarizations resort to unrealistic cell architectures. … Here, we address these challenges by incorporatingRyR cooperativity into a physiologically detailed model with a realistic cell architecture.” Find the paper and full list of authors in The Journal of Physiology.
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‘Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands’
“Patchy global data on belowground litter decomposition dynamics limit our capacity to discern the drivers of carbon preservation and storage across inland and coastal wetlands. We performed a global, multiyear study in over 180 wetlands across 28 countries and 8 macroclimates using standardized litter as measures of “recalcitrant” (rooibos tea) and “labile” (green tea) organic matter (OM) decomposition. … Our study highlights the potential for reduction in belowground OM in coastal and inland wetlands under increased warming.” Find the paper and full list of authors in Environmental Science & Technology.
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Sun receives patent for energy-saving material
“Electrical and computer engineering distinguished professor Nian Sun was awarded a patent for ‘Topological insulator/normal metal bilayers as spin hall materials for spin orbit torque devices, and methods of fabrication of same.'”
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Bai receives patent to strengthen soft materials
“Mechanical and industrial engineering assistant professor Ruobing Bai, in collaboration with Michigan State University, is leading a $705,664 NSF grant for the ‘Mechanics of End-Linked Polymer Networks With Strain-Induced Crystallization Regulated by Topological Defects.’ The research will lead to understanding mechanisms and developing new end-linked polymer networks with desired mechanical properties, which can facilitate emerging applications such as soft robotics, medical devices, and wearable electronics.”
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Patent protecting against side-channel attacks
“Electrical and computer engineering professor and associate dean for faculty affairs Yunsi Fei was awarded a patent for ‘Methods and Systems for Protecting Against Memory-Based Side-Channel Attacks.'”
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Melodia, Bonati, D’Oro receive patent for ‘self-optimizing’ cellular network systems
“Electrical and computer engineering William Lincoln Smith professor Tommaso Melodia, associate research scientist Leonardo Bonati and associate research professor Salvatore D’Oro were awarded a patent for ‘Operating System for Software-Defined Cellular Networks.'”
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‘Effects of Lipid Headgroups on the Mechanical Properties and In Vitro Cellular Internalization of Liposomes’
“We performed all-atom and coarse-grained simulations of lipid bilayer mixtures of the unsaturated lipid DOPC, with saturated lipids having the same 18-carbon acyl tails and different headgroups, to understand their mechanical properties.”
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‘DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster’
“Ocean acidification significantly affects marine calcifiers like oysters, warranting the study of molecular mechanisms like DNA methylation that contribute to adaptive plasticity in response to environmental change. However, a consensus has not been reached on the extent to which methylation modules gene expression, and in turn plasticity, in marine invertebrates. In this study, we investigated the impact of pCO2 on gene expression and DNA methylation in the eastern oyster, Crassostrea virginica.” Find the paper and full list of authors in Environmental Epigenetics.
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‘L1-ORF1p Nucleoprotein Can Rapidly Assume Distinct Conformations and… Bind More than One Nucleic Acid’
“LINE-1 (L1) is a parasitic retrotransposable DNA element, active in primates for the last 80–120 Myr. L1 has generated nearly one-third of the human genome by copying its transcripts, and those of other genetic elements. … We used optical tweezers to examine ORF1p binding to individual single-stranded DNA (ssDNA) molecules and found that the arrangement of ORF1p on the ssDNA depends on their molar ratio. … Our results suggest that ORF1p displaced from its RNA template during TPRT could bind and destabilize remaining downstream L1 RNP.”Find the paper and full list of authors in Nucleic Acids Research.
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‘Self-Consistent Evaluation of Proximity and Inverse Proximity Effects With Pair-Breaking in Diffusive Superconducting–Normal Metal Junctions’
“We consider a planar superconducting–normal metal junction with both inelastic and spin-flip scattering processes present. …We use a one-dimensional formulation of the Usadel equation to compute the self-consistent energy dependence of the single-particle density of states as a function of distance from the interface on both the superconducting and metallic sides for various spatial profiles of a pair-breaking spin-flip term. The pair-breaking processes fill in the superconducting gap at zero energy, which is reflected in the zero-bias tunneling conductance in scanning tunneling microscopy/spectroscopy experiments, in the vicinity of the junction.” Find the paper and authors in Physical Review B.