Search for: All records

This commentary examines existing challenges in biomedical research and clinical trials that lead to gaps in our understanding of how diseases and treatments impact precision medicine. 

Humility, the organizing virtue of multicultural frameworks in counseling psychology, has traditionally been framed to be positively associated with health and well-being and negatively associated with mental illness. Despite lauded benefits, however, scholars have cautioned that humility may not always be of benefit. To examine these associations, we conducted a meta-analysis to clarify the magnitude of the associations between humility and physical health, mental illness (i.e., depression, anxiety), life satisfaction, and eudaimonic well-being (i.e., meaning in life, purpose in life), in addition to testing moderators. The final sample included 65 studies, with results yielding small to medium associations (rs ranged from −.06 to .20) between humility and examined outcomes. Results suggest that the size and direction of associations depend on methodological choices and cultural contexts. Implications for studying the cultural context of humility are discussed. 

A<sc>bstract</sc> We study (multi) fermion - monopole bound states, many of which are the states that dyons adiabatically transition into as fermions become light. The properties of these bound states depend critically on the UV symmetries preserved by the fermion mass terms, their relative size, and the value ofθ. Depending on the relative size of the mass terms and the value ofθ, the bound states can undergo phase transitions as well as transition from being stable to unstable. In some simple situations, the bound state solution can be related to the Witten effect of another theory with fewer fermions and larger gauge coupling. These bound states are a result of mass terms and symmetry breaking boundary conditions at the monopole core and, consequently, these bound states do not necessarily have definite quantum numbers under accidental IR symmetries. Additionally, they have binding energies that are$$ \mathcal{O}(1) $$ $O\left(1\right)$times the fermion mass and bound state radii of order their inverse mass. As the massless limit is approached, the bound state radii approach infinity, and they become new asymptotic states with odd quantum numbers giving a dynamical understanding to the origin of semitons. 

A<sc>bstract</sc> We introduce a mechanism by which a misaligned ALP can be dynamically converted into a dark photon in the presence of a background magnetic field. An abundance of non-relativistic ALPs will convert to dark photons with momentum of order the inhomogeneities in the background field; therefore a highly homogeneous field will produce non-relativistic dark photons without relying on any redshifting of their momenta. Taking hidden sector magnetic fields produced by a first order phase transition, the mechanism can reproduce the relic abundance of dark matter for a wide range of dark photon masses down to 10⁻¹³eV. 

Abstract Nanopore signal analysis enables detection of nucleotide modifications from native DNA and RNA sequencing, providing both accurate genetic or transcriptomic and epigenetic information without additional library preparation. At present, only a limited set of modifications can be directly basecalled (for example, 5-methylcytosine), while most others require exploratory methods that often begin with alignment of nanopore signal to a nucleotide reference. We present Uncalled4, a toolkit for nanopore signal alignment, analysis and visualization. Uncalled4 features an efficient banded signal alignment algorithm, BAM signal alignment file format, statistics for comparing signal alignment methods and a reproducible de novo training method fork-mer-based pore models, revealing potential errors in Oxford Nanopore Technologies’ state-of-the-art DNA model. We apply Uncalled4 to RNA 6-methyladenine (m6A) detection in seven human cell lines, identifying 26% more modifications than Nanopolish using m6Anet, including in several genes where m6A has known implications in cancer. Uncalled4 is available open source atgithub.com/skovaka/uncalled4. 

Abstract MotivationAs nanopore technology reaches ever higher throughput and accuracy, it becomes an increasingly viable candidate for reading out DNA data storage. Nanopore sequencing offers considerable flexibility by allowing long reads, real-time signal analysis, and the ability to read both DNA and RNA. We need flexible and efficient designs that match nanopore’s capabilities, but relatively few designs have been explored and many have significant inefficiency in read density, error rate, or compute time. To address these problems, we designed a new single-read per-strand decoder that achieves low byte error rates, offers high throughput, scales to long reads, and works well for both DNA and RNA molecules. We achieve these results through a novel soft decoding algorithm that can be effectively parallelized on a GPU. Our faster decoder allows us to study a wider range of system designs. ResultsWe demonstrate our approach on HEDGES, a state-of-the-art DNA-constrained convolutional code. We implement one hard decoder that runs serially and two soft decoders that run on GPUs. Our evaluation for each decoder is applied to the same population of nanopore reads collected from a synthesized library of strands. These same strands are synthesized with a T7 promoter to enable RNA transcription and decoding. Our results show that the hard decoder has a byte error rate over 25%, while the prior state of the art soft decoder can achieve error rates of 2.25%. However, that design also suffers a low throughput of 183 s/read. Our new Alignment Matrix Trellis soft decoder improves throughput by 257× with the trade-off of a higher byte error rate of 3.52% compared to the state of the art. Furthermore, we use the faster speed of our algorithm to explore more design options. We show that read densities of 0.33 bits/base can be achieved, which is 4× larger than prior MSA-based decoders. We also compare RNA to DNA, and find that RNA has 85% as many error-free reads when compared to DNA. Availability and implementationSource code for our soft decoder and data used to generate figures is available publicly in the Github repository https://github.com/dna-storage/hedges-soft-decoder (10.5281/zenodo.11454877). All raw FAST5/FASTQ data are available at 10.5281/zenodo.11985454 and 10.5281/zenodo.12014515. 

The near equality of the dark matter and baryon energy densities is a remarkable coincidence, especially when one realizes that the baryon mass is exponentially sensitive to UV parameters in the form of dimensional transmutation. We explore a new dynamical mechanism, where in the presence of an arbitrary number density of baryons and dark matter, a scalar adjusts the masses of dark matter and baryons until the two energy densities are comparable. In this manner, the coincidence is explained regardless of the microscopic identity of dark matter and how it was produced. This new scalar causes a variety of experimental effects such as a new force and a (dark) matter density-dependent proton mass. Published by the American Physical Society2024 

A<sc>bstract</sc> The presence of a plethora of light spin 0 and spin 1 fields is motivated in a number of BSM scenarios, such as the axiverse. The study of the interactions of such light bosonic fields with the Standard Model has focused mostly on interactions involving only one such field, such as the axion (ϕ) coupling to photons,$$\phi F\widetilde{F}$$, or the kinetic mixing between photon and the dark photon,FF_D. In this work, we continue the exploration of interactions involving two light BSM fields and the standard model, focusing on the mixed axion-photon-dark-photon interaction$$\phi F{\widetilde{F}}_{D}$$. If either the axion or dark photon are dark matter, we show that this interaction leads to conversion of the CMB photons into a dark sector particle, leading to a distortion in the CMB spectrum. We present the details of these unique distortion signatures and the resulting constraints on the$$\phi F{\widetilde{F}}_{D}$$coupling. In particular, we find that for a wide range of masses, the constraints from these effect are stronger than on the more widely studied axion-photon coupling. 

A<sc>bstract</sc> We argue that the striking similarity between the cosmic abundances of baryons and dark matter, despite their very different astrophysical behavior, strongly motivates the scenario in which dark matter resides within a rich dark sector parallel in structure to that of the standard model. The near cosmic coincidence is then explained by an approximateℤ₂exchange symmetry between the two sectors, where dark matter consists of stable dark neutrons, with matter and dark matter asymmetries arising via parallel WIMP baryogenesis mechanisms. Taking a top-down perspective, we point out that an adequateℤ₂symmetry necessitates solving the electroweak hierarchy problem in each sector, without our committing to a specific implementation. A higher-dimensional realization in the far UV is presented, in which the hierarchical couplings of the two sectors and the requisiteℤ₂-breaking structure arise naturally from extra-dimensional localization and gauge symmetries. We trace the cosmic history, paying attention to potential pitfalls not fully considered in previous literature. Residualℤ₂-breaking can very plausibly give rise to the asymmetric reheating of the two sectors, needed to keep the cosmological abundance of relativistic dark particles below tight bounds. We show that, despite the need to keep inter-sector couplings highly suppressed after asymmetric reheating, there can naturally be order-one couplings mediated by TeV scale particles which can allow experimental probes of the dark sector at high energy colliders. Massive mediators can also induce dark matter direct detection signals, but likely at or below the neutrino floor.