A Uniform Approximation for the Fidelity in Chaotic Systems

In quantum/wave systems with chaotic classical analogs, wavefunctions evolve in highly complex, yet deterministic ways. A slight perturbation of the system, though, will cause the evolution to diverge from its original behavior increasingly with time. This divergence can be measured by the fidelity, which is defined as the squared overlap of the two time evolved states. For chaotic systems, two main decay regimes of either Gaussian or exponential behavior have been identified depending on the strength of the perturbation. For perturbation strengths intermediate between the two regimes, the fidelity displays both forms of decay. By applying a complementary combination of random matrix and semiclassical theory, a uniform approximation can be derived that covers the full range of perturbation strengths. The time dependence is entirely fixed by the density of states and the so-called transition parameter, which can be related to the phase space volume of the system and the classical action diffusion constant, respectively. The accuracy of the approximations are illustrated with the standard map.Comment: 16 pages, 4 figures, accepted in J. Phys. A, special edition on Random Matrix Theor

Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotopes

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode

Availability of Family Caregiver Programs in Us Cancer Centers

IMPORTANCE: Family caregivers provide the majority of health care to the 18 million patients with cancer in the US. Yet despite providing complex medical and nursing care, a large proportion of caregivers report no formal support or training. In recognition of this gap, many interventions to support cancer caregivers have been developed and tested over the past 2 decades. However, there are few system-level data on whether US cancer centers have adopted and implemented these interventions. OBJECTIVE: to describe and characterize the availability of family caregiver support programs in US cancer centers. DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional national survey study was conducted between September 1, 2021, and April 30, 2023. Participants comprised clinical and administrative staff of Commission on Cancer-accredited US cancer centers. Data analysis was performed in May and June 2023. MAIN OUTCOMES AND MEASURES: Survey questions about the availability of 11 types of family caregiver programs (eg, peer mentoring, education classes, and psychosocial programs) were developed after literature review, assessment of similar program evaluation surveys, and discussions among a 13-member national expert advisory committee. Family caregiver programs were defined as structured, planned, and coordinated groups of activities and procedures aimed at specifically supporting family caregivers as part of usual care. Survey responses were tabulated using standard descriptive statistics, including means, proportions, and frequencies. RESULTS: Of the surveys sent to potential respondents at 971 adult cancer centers, 238 were completed (response rate, 24.5%). After nonresponse weight adjustment, most cancer centers (75.4%) had at least 1 family caregiver program; 24.6% had none. The most common program type was information and referral services (53.6%). Cancer centers with no programs were more likely to have smaller annual outpatient volumes (χ2 = 11.10; P = .011). Few centers had caregiver programs on training in medical and/or nursing tasks (21.7%), caregiver self-care (20.2%), caregiver-specific distress screening (19.3%), peer mentoring (18.9%), and children caregiving for parents (8.3%). Very few programs were developed from published evidence in a journal (8.1%). The top reason why cancer centers selected their programs was community members requesting the program (26.3%); only 12.3% of centers selected their programs based on scientific evidence. Most programs were funded by the cancer center or hospital (58.6%) or by philanthropy (42.4%). CONCLUSIONS AND RELEVANCE: In this survey study, most cancer centers had family caregiver programs; however, a quarter had none. Furthermore, the scope of programming was limited and rarely evidence based, with few centers offering caregiving education and training. These findings suggest that implementation strategies are critically needed to foster uptake of evidence-based caregiver interventions

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species.

Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present "haplotagging," a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations

Developing a National Implementation Strategy to accelerate Uptake of Evidence-Based Family Caregiver Support in Us Cancer Centers

OBJECTIVE: Characterize key factors and training needs of U.S. cancer centers in implementing family caregiver support services. METHODS: Sequential explanatory mixed methods design consisting of: (1) a national survey of clinicians and administrators from Commission-on-Cancer-accredited cancer centers (N = 238) on factors and training needed for establishing new caregiver programs and (2) qualitative interviews with a subsample of survey respondents (N = 30) to elicit feedback on survey findings and the outline of an implementation strategy to facilitate implementation of evidence-based family caregiver support (the Caregiver Support Accelerator). Survey data was tabulated using descriptive statistics and transcribed interviews were analyzed using thematic analysis. RESULTS: top factors for developing new caregiver programs were that the program be: consistent with the cancer center\u27s mission and strategic plan (87%), supported by clinic leadership (86.5%) and providers and staff (85.7%), and low cost or cost effective (84.9%). top training needs were how to: train staff to implement programs (72.3%), obtain program materials (63.0%), and evaluate program outcomes (62.6%). Only 3.8% reported that no training was needed. Qualitative interviews yielded four main themes: (1) gaining leadership, clinician, and staff buy-in and support is essential; (2) cost and clinician burden are major factors to program implementation; (3) training should help with adapting and marketing programs to local context and culture; and (4) the Accelerator strategy is comprehensive and would benefit from key organizational partnerships and policy standards. CONCLUSION: Findings will be used to inform and refine the Accelerator implementation strategy to facilitate the adoption and growth of evidence-based cancer caregiver support in U.S. cancer centers

Taking the Measure of the Universe: Precision Astrometry with SIM PlanetQuest

Precision astrometry at microarcsecond accuracy has application to a wide range of astrophysical problems. This paper is a study of the science questions that can be addressed using an instrument that delivers parallaxes at about 4 microarcsec on targets as faint as V = 20, differential accuracy of 0.6 microarcsec on bright targets, and with flexible scheduling. The science topics are drawn primarily from the Team Key Projects, selected in 2000, for the Space Interferometry Mission PlanetQuest (SIM PlanetQuest). We use the capabilities of this mission to illustrate the importance of the next level of astrometric precision in modern astrophysics. SIM PlanetQuest is currently in the detailed design phase, having completed all of the enabling technologies needed for the flight instrument in 2005. It will be the first space-based long baseline Michelson interferometer designed for precision astrometry. SIM will contribute strongly to many astronomical fields including stellar and galactic astrophysics, planetary systems around nearby stars, and the study of quasar and AGN nuclei. SIM will search for planets with masses as small as an Earth orbiting in the `habitable zone' around the nearest stars using differential astrometry, and could discover many dozen if Earth-like planets are common. It will be the most capable instrument for detecting planets around young stars, thereby providing insights into how planetary systems are born and how they evolve with time. SIM will observe significant numbers of very high- and low-mass stars, providing stellar masses to 1%, the accuracy needed to challenge physical models. Using precision proper motion measurements, SIM will probe the galactic mass distribution and the formation and evolution of the Galactic halo. (abridged)Comment: 54 pages, 28 figures, uses emulateapj. Submitted to PAS

Toll-Like Receptor Ligands Induce Human T Cell Activation and Death, a Model for HIV Pathogenesis

Background: Recently, heightened systemic translocation of microbial products was found in persons with chronic HIV infection and this was linked to immune activation and CD4 + T cell homeostasis. Methodology: We examined here the effects of microbial Toll-like receptor (TLR) ligands on T cell activation in vitro. Conclusions/Findings: We show that exposure to TLR ligands results in activation of memory and effector CD4 + and CD8 + T cells. After exposure to each of 8 different ligands that activate TLRs 2, 3, 4, 5, 7, 8, and 9, CD8 + T cells are activated and gain expression of the C type lectin CD69 that may promote their retention in lymphoid tissues. In contrast, CD4 + T cells rarely increase CD69 expression but instead enter cell cycle. Despite activation and cell cycle entry, CD4 + T cells divide poorly and instead, disproportionately undergo activation-induced cell death. Systemic exposure to TLR agonists may therefore increase immune activation, effector cell sequestration in lymphoid tissues and T cell turnover. These events may contribute to the pathogenesis of immune dysfunction and CD4+ T cell losses in chronic infection with the human immunodeficiency virus

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin