Tuning the Stability of DNA Tetrahedra with Base Stacking Interactions.

DNA nanotechnology uses the programmable assembly of DNA to create nanoscale objects. Recent work from our laboratory suggested that terminal stacking interactions between adjacent strands could be a design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra with sticky ends containing identical base pairing interactions but different stacking interactions.

Influence of aqueous solutions of 2-(tetrafluoro(trifluoromethyl)-λ-sulfanyl-ethan-1-ol (CFSF-ethanol) on the stabilization of the secondary structure of melittin: comparison with aqueous trifluoroethanol using molecular dynamics simulations and circular dichroism experiments.

The influence of aqueous solutions of 2-(tetrafluoro(trifluoromethyl)-λ-sulfanyl-ethan-1-ol (CFSF-ethanol) and 2,2,2-trifluoroethanol (TFE) on the secondary structure of melittin was studied using circular dichroism (CD) and molecular dynamics (MD) simulations. In water, melittin transitions into a random coil. However, upon addition of even as little as 1% by volume of CFSF-ethanol, the secondary structure of melittin stabilizes as a helix.

Examining the relationship between emotion regulation, sleep quality, and anxiety disorder diagnosis.

Anxiety disorders are highly comorbid with sleep disturbance and have also been associated with deficits in emotion regulation, the ability to control and express emotions. However, the extent to which specific dimensions of sleep disturbance and emotion regulation are associated with anxiety diagnosis is not well-explored. This study examined dimensions of emotion regulation and sleep disturbance that may predict greater likelihood of anxiety diagnosis using novel machine learning techniques.

Estimating the rate of failure to notice function word errors in natural reading.

Skilled readers sometimes fail to notice seemingly obvious errors in text, such as the repetition or omission of a function word or the transposition of two words, suggesting that linguistic knowledge can override bottom-up input at either a perceptual or postperceptual level. The present study investigates the role of this top-down process of error correction in natural reading of extended texts. In previous research, critical sentences have been presented one at a time, and subjects were explicitly tasked with detecting errors.

Emergence of String Monodromy in Effective Field Theory.

We demonstrate that when the field theory Kleiss-Kuijf and Bern-Carrasco-Johansson relations are imposed on one color ordering of general local bi-adjoint scalar effective field theories, the string monodromy relations must be obeyed by the other color ordering. This is a surprising example of an open string world-sheet property appearing in a purely field theoretic context. As part of the derivation, we show that nonlinear relations among the four-point Wilson coefficients arise from imposing linear symmetries on the six-point amplitude via factorization.

Developing an eco-driving strategy in a hybrid traffic network using reinforcement learning.

Eco-driving has garnered considerable research attention owing to its potential socio-economic impact, including enhanced public health and mitigated climate change effects through the reduction of greenhouse gas emissions. With an expectation of more autonomous vehicles (AVs) on the road, an eco-driving strategy in hybrid traffic networks encompassing AV and human-driven vehicles (HDVs) with the coordination of traffic lights is a challenging task. The challenge is partially due to the insufficient infrastructure for collecting, transmitting, and sharing real-time traffic data among vehicles, facilities, and traffic control centers, and the following decision-making of agents involved in traffic control.

Tuning the stability of DNA tetrahedra with base-stacking interactions.

DNA nanotechnology relies on programmable anchoring of regions of single-stranded DNA through base pair hybridization to create nanoscale objects such as polyhedra, tubes, sheets, and other desired shapes. Recent work from our lab measured the energetics of base-stacking interactions and suggested that terminal stacking interactions between two adjacent strands could be an additional design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra held together with sticky ends that contain identical base pairing interactions but different terminal stacking interactions.

The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch.

A central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination of Escherichia coli RNA polymerase in vitro transcription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants.

Elucidating the influence of RNA modifications and Magnesium ions on tRNA conformational dynamics in : Insights from Replica Exchange Molecular Dynamics simulations.

Post-transcriptional modifications in RNA can significantly impact their structure and function. In particular, transfer RNAs (tRNAs) are heavily modified, with around 100 different naturally occurring nucleotide modifications contributing to codon bias and decoding efficiency. Here, we describe our efforts to investigate the impact of RNA modifications on the structure and stability of tRNA Phenylalanine (tRNA ) from S.

Differential roles of normal and lung cancer-associated fibroblasts in microvascular network formation.

Perfusable microvascular networks offer promising three-dimensional models to study normal and compromised vascular tissues as well as phenomena such as cancer cell metastasis. Engineering of these microvascular networks generally involves the use of endothelial cells stabilized by fibroblasts to generate robust and stable vasculature. However, fibroblasts are highly heterogenous and may contribute variably to the microvascular structure.

Mutation of two intronic nucleotides alters RNA structure and dynamics inhibiting MBNL1 and RBFOX1 regulated splicing of the Insulin Receptor.

Alternative splicing (AS) of Exon 11 of the Insulin Receptor ( ) is highly regulated and disrupted in several human disorders. To better understand exon 11 AS regulation, splicing activity of an exon 11 minigene reporter was measured across a gradient of the AS regulator muscleblind-like 1 protein (MBNL1). The RNA-binding protein Fox-1 (RBFOX1) was added to determine its impact on MBNL1-regulated splicing.

Paradoxical Effects of Depression on Psoriatic Arthritis Outcomes in a Combined Psoriasis-Psoriatic Arthritis Center.

Backgroud: Psoriatic arthritis (PsA) is a chronic, inflammatory arthritis that, when left untreated, can lead to erosions, deformities and decrease in quality of life. PsA is known to be associated with multiple comorbidities, including cardiovascular, metabolic and mental health syndromes, all of which can increase its overall morbidity and mortality.

Objective: To characterize a cohort of patients with PsA and understand the impact of depression on PsA outcome measures.

The Effect of Pseudoknot Base Pairing on Cotranscriptional Structural Switching of the Fluoride Riboswitch.

A central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination of RNA polymerase transcription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants.

Dating and Hookup Apps and Websites as Facilitators of Entry into Sex Work.

Introduction: Technological developments, primarily starting with the Internet, have transformed male sex work in fundamental ways including making the meeting of buyers and sellers of sex much more likely to occur virtually rather than on streets or bars. Notably, popular dating and hookup websites and apps not designed for sex work have become a new pathway into such activity. However, because they can blur the line between casual and exchange sex encounters, there may be a growing population of men engaging in exchange sex who do not identify as sex workers.

Systematic comparison of rAAV vectors manufactured using large-scale suspension cultures of Sf9 and HEK293 cells.

Recombinant adeno-associated virus (rAAV) vectors could be manufactured by plasmid transfection into human embryonic kidney 293 (HEK293) cells or baculovirus infection of Spodoptera frugiperda (Sf9) insect cells. However, systematic comparisons between these systems using large-scale, high-quality AAV vectors are lacking. rAAV from Sf9 cells (Sf9-rAAV) at 2-50 L and HEK293 cells (HEK-rAAV) at 2-200 L scales were characterized.

Three-dimensional flat bands in pyrochlore metal CaNi.

Electronic flat-band materials host quantum states characterized by a quenched kinetic energy. These flat bands are often conducive to enhanced electron correlation effects and emergent quantum phases of matter. Long studied in theoretical models, these systems have received renewed interest after their experimental realization in van der Waals heterostructures and quasi-two-dimensional (2D) crystalline materials.

Complex Three-Dimensional Microscale Structures for Quantum Sensing Applications.

We present a novel method for fabricating highly customizable three-dimensional structures hosting quantum sensors based on nitrogen vacancy (NV) centers using two-photon polymerization. This approach overcomes challenges associated with structuring traditional single-crystal quantum sensing platforms and enables the creation of complex, fully three-dimensional, sensor assemblies with submicroscale resolutions (down to 400 nm) and large fields of view (>1 mm). By embedding NV center-containing nanoparticles in exemplary structures, we demonstrate high sensitivity optical sensing of temperature and magnetic fields at the microscale.

Aggregation in Aqueous Solutions of 2-(Tetrafluoro(trifluoromethyl)-λ-sulfanyl-ethan-1-ol (CFSF-ethanol)): A Comparison with Aqueous Trifluoroethanol and Hexafluoroisopropanol Using Molecular Dynamics Simulations and Dynamic Light Scattering Experiments.

2-Tetrafluoro(trifluoromethyl)-λ-sulfanylethan-1-ol (CFSF-ethanol) combines the polar hydrophobicity of tetrafluoro(trifluoromethyl)-λ-sulfanyl (CFSF) group with the polarity of simple alcohols. The properties of aqueous solutions of the well-known fluorinated alcohols 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) were compared with those of aqueous solutions of the novel CFSF-ethanol. Those properties were computed using all atom molecular dynamics simulations with OPLS-compatible parameters.

Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop.

Molecular dynamics (MD) simulations have become increasingly powerful and can now describe the folding/unfolding of small biomolecules in atomic detail. However, a major challenge in MD simulations is to represent the complex energy landscape of biomolecules using a small number of reaction coordinates. In this study, we investigate the folding pathways of an RNA tetraloop, gcGCAAgc, using five classical MD simulations with a combined simulation time of approximately 120 μs.

Bootstrapping the String Kawai-Lewellen-Tye Kernel.

We show that double-copy maps for amplitudes in effective field theory are severely constrained at four points by self-consistency and locality at six points. The resulting double-copy kernel depends only on two parameters as well as a specific symmetric function in s, t, u and interpolates between the original Kawai-Lewellen-Tye (KLT) string double copy and the open and closed string period integrals. Amplitudes double copied with this map must obey either the string monodromy relations or the field theory Kleiss-Kuijf (KK) and Bern, Carrasco, and Johansson (BCJ) relations; there are no other options.

The impacts of the 340B Program on health care quality for low-income patients.

Objective: To assess the effects of hospital 340B eligibility on quality of inpatient care provided to Medicaid and uninsured patients and for all patients.

Data: Agency for Health Care Research and Quality's Healthcare Cost and Utilization Project State Inpatient Data, Hospital Cost Reporting Information System Data, Office of Pharmacy Affairs Information System Data, and American Hospital Association Annual Survey.

Design: Regression discontinuity design comparing hospitals just above the DSH percentage program eligibility threshold to those just below.

Hospital concentration and low-income populations: Evidence from New York State Medicaid.

While a large body of evidence has examined hospital concentration, its effects on health care for low-income populations are less explored. We use comprehensive discharge data from New York State to measure the effects of changes in market concentration on hospital-level inpatient Medicaid volumes. Holding fixed hospital factors constant, a one percent increase in HHI leads to a 0.