Genome sequence of Soos: a siphovirus of the CP cluster infecting Gordonia rubripertincta  .

Novel actinobacteriophage Soos was isolated and purified from Southern Indiana soil using host Gordonia rubripertincta NRRL B-16540. Sequencing revealed a 57,509 bp circularly permuted genome encoding 87 predicted protein-coding genes. Soos is only the third phage in cluster CP, along with phages Clawz and Sting.

Fragmentomic analysis of circulating tumor DNA-targeted cancer panels.

BACKGROUND: The isolation of cell-free DNA (cfDNA) from the bloodstream can be used to detect and analyze somatic alterations in circulating tumor DNA (ctDNA), and multiple cfDNA-targeted sequencing panels are now commercially available for Food and Drug Administration (FDA)-approved biomarker indications to guide treatment. More recently, cfDNA fragmentation patterns have emerged as a tool to infer epigenomic and transcriptomic information. However, most of these analyses used whole-genome sequencing, which is insufficient to identify FDA-approved biomarker indications in a cost-effective manner. PATIENTS AND METHODS: We used machine learning models of fragmentation patterns at the first coding exon in standard targeted cancer gene cfDNA sequencing panels to distinguish between cancer and non-cancer patients, as well as the specific tumor type and subtype. We assessed this approach in two independent cohorts: a published cohort from GRAIL (breast, lung, and prostate cancers, non-cancer, n = 198) and an institutional cohort from the University of Wisconsin (UW; breast, lung, prostate, bladder cancers, n = 320). Each cohort was split 70%/30% into training and validation sets. RESULTS: In the UW cohort, training cross-validated accuracy was 82.1%, and accuracy in the independent validation cohort was 86.6% despite a median ctDNA fraction of only 0.06. In the GRAIL cohort, to assess how this approach performs in very low ctDNA fractions, training and independent validation were split based on ctDNA fraction. Training cross-validated accuracy was 80.6%, and accuracy in the independent validation cohort was 76.3%. In the validation cohort where the ctDNA fractions were all <0.05 and as low as 0.0003, the cancer versus non-cancer area under the curve was 0.99. CONCLUSIONS: To our knowledge, this is the first study to demonstrate that sequencing from targeted cfDNA panels can be utilized to analyze fragmentation patterns to classify cancer types, dramatically expanding the potential capabilities of existing clinically used panels at minimal additional cost.

Concussion Education for Athletes: Symptom Reporting and Safe Return to Sport.

¼ Educational programs on concussion have been demonstrated to improve knowledge for athletes, families, athletic trainers, and coaches about concussion, with the goal of reducing concussion incidence, duration, severity, and complications.¼ Despite the widespread availability and often mandatory concussion education provided to high school and collegiate athletes, there has not been an adequate change in knowledge, attitudes, and self-reporting behavior in this population.¼ Recently published studies suggest improving concussion education by emphasizing athletes' symptom reporting behavior, to contrast with current emphasis on knowledge-based outcomes.¼ Future educational programs about concussions for athletes, families, athletic trainers, and coaches should aim to emphasize cultural and behavioral changes that demonstrate outcome changes rather than solely evaluating knowledge improvements to determine effective programming.

Exploring the Charge Density Wave Phase of 1T-TaSe_{2}: Mott or Charge-Transfer Gap?

1T-TaSe_{2} is widely believed to host a Mott metal-insulator transition in the charge density wave (CDW) phase according to the spectroscopic observation of a band gap that extends across all momentum space. Previous investigations inferred that the occurrence of the Mott phase is limited to the surface only of bulk specimens, but recent analysis on thin samples revealed that the Mott-like behavior, observed in the monolayer, is rapidly suppressed with increasing thickness. Here, we report combined time- and angle-resolved photoemission spectroscopy and theoretical investigations of the electronic structure of 1T-TaSe_{2}. Our experimental results confirm the existence of a state above E_{F}, previously ascribed to the upper Hubbard band, and an overall band gap of ∼0.7 eV at Γ[over ¯]. However, supported by density functional theory calculations, we demonstrate that the origin of this state and the gap rests on band structure modifications induced by the CDW phase alone, without the need for Mott correlation effects.

Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics.

This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1-0.2 ppt and brackish 0.3-1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10-100 kyr old), MP (105-120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

Imaging the breaking of electrostatic dams in graphene for ballistic and viscous fluids.

The charge carriers in a material can, under special circumstances, behave as a viscous fluid. In this work, we investigated such behavior by using scanning tunneling potentiometry to probe the nanometer-scale flow of electron fluids in graphene as they pass through channels defined by smooth and tunable in-plane p-n junction barriers. We observed that as the sample temperature and channel widths are increased, the electron fluid flow undergoes a Knudsen-to-Gurzhi transition from the ballistic to the viscous regime characterized by a channel conductance that exceeds the ballistic limit, as well as suppressed charge accumulation against the barriers. Our results are well modeled by finite element simulations of two-dimensional viscous current flow, and they illustrate how Fermi liquid flow evolves with carrier density, channel width, and temperature.

Low repetition-rate, high-resolution femtosecond transmission electron microscopy.

The spatial and energy resolutions of state-of-the-art transmission electron microscopes (TEMs) have surpassed 50 pm and 5 meV. However, with respect to the time domain, even the fastest detectors combined with the brightest sources may only be able to reach the microsecond timescale. Thus, conventional methods are incapable of resolving the myriad fundamental ultrafast (i.e., attosecond to picosecond) atomic-scale dynamics. The successful demonstration of femtosecond (fs) laser-based (LB) ultrafast electron microscopy (UEM) nearly 20 years ago provided a means to span this nearly 10-order-of-magnitude temporal gap. While nanometer-picosecond UEM studies of dynamics are now well established, ultrafast Å-scale imaging has gone largely unrealized. Further, while instrument development has rightly been an emphasis, and while new modalities and uses of pulsed-beam TEM continue to emerge, the overall chemical and materials application space has been only modestly explored to date. In this Perspective, we argue that these apparent shortfalls can be attributed to a simple lack of data and detail. We speculate that present work and continued growth of the field will ultimately lead to the realization that Å-scale fs dynamics can indeed be imaged with minimally modified UEM instrumentation and with repetition rates (frep) below-and perhaps even well below-1 MHz. We further argue that the use of low frep, whether for LB UEM or for chopped/bunched beams, significantly expands the accessible application space. This calls for systematically establishing modality-specific limits so that especially promising technologies can be pursued, thus, ultimately facilitating broader adoption as individual instrument capabilities expand.

Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes.

The holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism's microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.

Single-photoelectron collection efficiency in 4D ultrafast electron microscopy.

In femtosecond (fs) 4D ultrafast electron microscopy (UEM), a tradeoff is made between photoelectrons per packet and time resolution. One consequence of this can be longer-than-desirable acquisition times for low-density packets, and particularly for low repetition rates when complete photothermal dissipation is required. Thus, gaining an understanding of photoelectron trajectories in the gun region is important for identifying factors that limit collection efficiency (CE; fraction of photoelectrons that enter the illumination system). Here, we continue our work on the systematic study of photoelectron trajectories in the gun region of a Thermo Fisher/FEI Tecnai Femto UEM, focusing specifically on CE in the single-electron regime. Using General Particle Tracer, calculated field maps, and the exact architecture of the Tecnai Femto UEM, we simulated the effects of fs laser parameters and key gun elements on CE. The results indicate CE strongly depends upon the laser spot size on the source, the (unbiased) Wehnelt aperture diameter, and the incident photon energy. The CE dispersion with laser spot size is found to be strongly dependent on aperture diameter, being nearly dispersionless for the largest apertures. A gun crossover is also observed, with the beam-waist position being dependent on the aperture diameter, further illustrating that the Wehnelt aperture acts as a simple, fixed electrostatic lens in UEM mode. This work provides further insights into the operational aspects of fs 4D UEM.

Social divergence: molecular pathways underlying castes and longevity in a facultatively eusocial small carpenter bee.

Unravelling the evolutionary origins of eusocial life is a longstanding endeavour in the field of evolutionary-developmental biology. Descended from solitary ancestors, eusocial insects such as honeybees have evolved ontogenetic division of labour in which short-lived workers perform age-associated tasks, while a long-lived queen produces brood. It is hypothesized that (i) eusocial caste systems evolved through the co-option of deeply conserved genes and (ii) longevity may be tied to oxidative damage mitigation capacity. To date, however, these hypotheses have been examined primarily among only obligately eusocial corbiculate bees. We present brain transcriptomic data from a Japanese small carpenter bee, Ceratina japonica (Apidae: Xylocopinae), which demonstrates both solitary and eusocial nesting in sympatry and lives 2 or more years in the wild. Our dataset captures gene expression patterns underlying first- and second-year solitary females, queens and workers, providing an unprecedented opportunity to explore the molecular mechanisms underlying caste-antecedent phenotypes in a long-lived and facultatively eusocial bee. We find that C. japonica's queens and workers are underpinned by divergent gene regulatory pathways, involving many differentially expressed genes well-conserved among other primitively eusocial bee lineages. We also find support for oxidative damage reduction as a proximate mechanism of longevity in C. japonica.

Isotope effects on the structural transformation and relaxation of deeply supercooled water.

We have examined the structure of supercooled liquid D2O as a function of temperature between 185 and 255 K using pulsed laser heating to rapidly heat and cool the sample on a nanosecond timescale. The liquid structure can be represented as a linear combination of two structural motifs, with a transition between them described by a logistic function centered at 218 K with a width of 10 K. The relaxation to a metastable state, which occurred prior to crystallization, exhibited nonexponential kinetics with a rate that was dependent on the initial structural configuration. When the temperature is scaled by the temperature of maximum density, which is an isostructural point of the isotopologues, the structural transition and the non-equilibrium relaxation kinetics of D2O agree remarkably well with those for H2O.

Defining a "Safe System of Work".

Providing a "safe system of work" is the essence of the general duties that employers have to their employees under workplace health and safety regulations. Despite this, consistent and appropriate definition of what constitutes a safe system of work is almost non-existent. Available definitions tend to confuse a safe system of work with management practices intended to bring about a safe system, or conflate the broad system suggested in general duties clauses with procedures or work methods that are focused on particular hazards or tasks. This article develops a definition of safe systems of work which recognises the broad scope of the concept and includes psychological health and return to work processes. This definition can be used by a range of stakeholders to better communicate the scope of occupational health and safety duties and more consistently assess whether a safe system has been provided both before and after incidents occur.

Toward Å-fs-meV resolution in electron microscopy: systematic simulation of the temporal spread of single-electron packets.

Though efforts to improve the temporal resolution of transmission electron microscopes (TEMs) have waxed and waned for decades, with relatively recent advances routinely reaching sub-picosecond scales, fundamental and practical challenges have hindered the advance of combined Å-fs-meV resolutions, particularly for core-loss spectroscopy and real-space imaging. This is due in no small part to the complexity of the approach required to access timescales upon which electrons, atoms, molecules, and materials first begin to respond and transform - attoseconds to picoseconds. Here we present part of a larger effort devoted to systematically mapping the instrument parameter space of a TEM modified to reach ultrafast timescales. With General Particle Tracer, we studied the statistical temporal distributions of single-electron packets as a function of various fs pulsed-laser parameters and electron-gun configurations and fields for the exact architecture and dimensions of a Thermo Fisher Tecnai Femto ultrafast electron microscope. We focused on easily-adjustable parameters, such as laser pulse duration, laser spot size, photon energy, Wehnelt aperture diameter, and photocathode size. In addition to establishing trends and dispersion behaviors, we identify regimes within which packet duration can be 100s of fs and approach the 300 fs laser limit employed here. Overall, the results provide a detailed picture of the temporal behavior of single-electron packets in the Tecnai Femto gun region, forming the initial contribution of a larger effort.

Measuring and Tuning the Potential Landscape of Electrostatically Defined Quantum Dots in Graphene.

We use Kelvin probe force microscopy (KPFM) to probe the carrier-dependent potential of an electrostatically defined quantum dot (QD) in a graphene/hexagonal boron nitride (hBN) heterostructure. We show that gate-dependent measurements enable a calibration scheme that corrects for uncertainty inherent in typical KPFM measurements and accurately reconstructs the potential well profile. Our measurements reveal how the well changes with carrier concentration, which we associate with the nonlinear dependence of graphene's work function on carrier density. These changes shift the energy levels of quasi-bound states in the QD which we can measure via scanning tunneling spectroscopy (STS). We show that the experimentally extracted energy levels closely compare with wave functions calculated from the reconstructed KPFM data. This methodology, where KPFM and STS data are simultaneously acquired from 2D materials, allows the quasiparticle response to an electrostatic potential to be determined in a self-consistent way.

Structural relaxation and crystallization in supercooled water from 170 to 260 K.

The origin of water's anomalous properties has been debated for decades. Resolution of the problem is hindered by a lack of experimental data in a crucial region of temperatures, T, and pressures where supercooled water rapidly crystallizes-a region often referred to as "no man's land." A recently developed technique where water is heated and cooled at rates greater than 109 K/s now enables experiments in this region. Here, it is used to investigate the structural relaxation and crystallization of deeply supercooled water for 170 K < T < 260 K. Water's relaxation toward a new equilibrium structure depends on its initial structure with hyperquenched glassy water (HQW) typically relaxing more quickly than low-density amorphous solid water (LDA). For HQW and T > 230 K, simple exponential relaxation kinetics is observed. For HQW at lower temperatures, increasingly nonexponential relaxation is observed, which is consistent with the dynamics expected on a rough potential energy landscape. For LDA, approximately exponential relaxation is observed for T > 230 K and T < 200 K, with nonexponential relaxation only at intermediate temperatures. At all temperatures, water's structure can be reproduced by a linear combination of two, local structural motifs, and we show that a simple model accounts for the complex kinetics within this context. The relaxation time, τ rel , is always shorter than the crystallization time, τ xtal For HQW, the ratio, τ xtal /τ rel , goes through a minimum at ∼198 K where the ratio is about 60.

Cabazitaxel versus abiraterone or enzalutamide in poor prognosis metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase II trial.

BACKGROUND: Treatment of poor prognosis metastatic castration-resistant prostate cancer (mCRPC) includes taxane chemotherapy and androgen receptor pathway inhibitors (ARPI). We sought to determine optimal treatment in this setting. PATIENTS AND METHODS: This multicentre, randomised, open-label, phase II trial recruited patients with ARPI-naive mCRPC and poor prognosis features (presence of liver metastases, progression to mCRPC after <12 months of androgen deprivation therapy, or ≥4 of 6 clinical criteria). Patients were randomly assigned 1 : 1 to receive cabazitaxel plus prednisone (group A) or physician's choice of enzalutamide or abiraterone plus prednisone (group B) at standard doses. Patients could cross over at progression. The primary endpoint was clinical benefit rate for first-line treatment (defined as prostate-specific antigen response ≥50%, radiographic response, or stable disease ≥12 weeks). RESULTS: Ninety-five patients were accrued (median follow-up 21.9 months). First-line clinical benefit rate was greater in group A versus group B (80% versus 62%, P = 0.039). Overall survival was not different between groups A and B (median 37.0 versus 15.5 months, hazard ratio (HR) = 0.58, P = 0.073) nor was time to progression (median 5.3 versus 2.8 months, HR = 0.87, P = 0.52). The most common first-line treatment-related grade ≥3 adverse events were neutropenia (cabazitaxel 32% versus ARPI 0%), diarrhoea (9% versus 0%), infection (9% versus 0%), and fatigue (7% versus 5%). Baseline circulating tumour DNA (ctDNA) fraction above the cohort median and on-treatment ctDNA increase were associated with shorter time to progression (HR = 2.38, P < 0.001; HR = 4.03, P < 0.001). Patients with >30% ctDNA fraction at baseline had markedly shorter overall survival than those with undetectable ctDNA (HR = 38.22, P < 0.001). CONCLUSIONS: Cabazitaxel was associated with a higher clinical benefit rate in patients with ARPI-naive poor prognosis mCRPC. ctDNA abundance was prognostic independent of clinical features, and holds promise as a stratification biomarker.

Sociality sculpts similar patterns of molecular evolution in two independently evolved lineages of eusocial bees.

While it is well known that the genome can affect social behavior, recent models posit that social lifestyles can, in turn, influence genome evolution. Here, we perform the most phylogenetically comprehensive comparative analysis of 16 bee genomes to date: incorporating two published and four new carpenter bee genomes (Apidae: Xylocopinae) for a first-ever genomic comparison with a monophyletic clade containing solitary through advanced eusocial taxa. We find that eusocial lineages have undergone more gene family expansions, feature more signatures of positive selection, and have higher counts of taxonomically restricted genes than solitary and weakly social lineages. Transcriptomic data reveal that caste-affiliated genes are deeply-conserved; gene regulatory and functional elements are more closely tied to social phenotype than phylogenetic lineage; and regulatory complexity increases steadily with social complexity. Overall, our study provides robust empirical evidence that social evolution can act as a major and surprisingly consistent driver of macroevolutionary genomic change.

Reversible structural transformations in supercooled liquid water from 135 to 245 K.

A fundamental understanding of the unusual properties of water remains elusive because of the limited data at the temperatures and pressures needed to decide among competing theories. We investigated the structural transformations of transiently heated supercooled water films, which evolved for several nanoseconds per pulse during fast laser heating before quenching to 70 kelvin (K). Water's structure relaxed from its initial configuration to a steady-state configuration before appreciable crystallization. Over the full temperature range investigated, all structural changes were reversible and reproducible by a linear combination of high- and low-temperature structural motifs. The fraction of the liquid with the high-temperature motif decreased rapidly as the temperature decreased from 245 to 190 K, consistent with the predictions of two-state "mixture" models for supercooled water in the supercritical regime.

Chemiluminescent sensors for quantitation of the bacterial second messenger cyclic di-GMP.

Chemiluminescent biosensors have been developed and broadly applied to mammalian cell systems for studying intracellular signaling networks. For bacteria, biosensors have largely relied on fluorescence-based systems for quantitating signaling molecules, but these designs can encounter issues in complex environments due to their reliance on external illumination. In order to circumvent these issues, we designed the first ratiometric chemiluminescent biosensors for studying a key bacterial second messenger, cyclic di-GMP. We have shown recently that these biosensors function both in vitro and in vivo for detecting changes in cyclic di-GMP levels. In this chapter, we present a practical and broadly applicable method for high-throughput quantitation of cyclic di-GMP in bacterial cell extracts using the high affinity biosensor tVYN-TmΔ that could serve as the "Bradford assay" equivalent for this bacterial signaling molecule.

HSD3B1 (1245A>C) germline variant and clinical outcomes in metastatic castration-resistant prostate cancer patients treated with abiraterone and enzalutamide: results from two prospective studies.

BACKGROUND: A common polymorphism (1245A>C) in the HSD3B1 gene is associated with increased de novo synthesis of androgens and worse outcomes in men treated with androgen-deprivation therapy for metastatic castration-sensitive prostate cancer. The objective of the study was to determine whether this polymorphism is associated with outcomes for metastatic castration-resistant prostate cancer (mCRPC) treated with abiraterone or enzalutamide. PATIENTS AND METHODS: A total of 547 patients treated with abiraterone or enzalutamide from two prospective cohorts were evaluated. The HSD3B1 genotype was determined by targeted sequencing and/or TaqMan single-nucleotide polymorphism genotyping. In cohort 1, patients were randomized to receive abiraterone + prednisone or enzalutamide. In cohort 2, patients received either agent according to investigator's choice. Prostate-specific antigen (PSA) response rate, time to PSA progression (TTPP), time to progression (TTP) and overall survival were determined. Associations between HSD3B1 genotypes and outcomes were evaluated via univariate Cox regression. Multivariable Cox model was used to determine the independent association of each covariate. RESULTS: The HSD3B1 variant genotype (CC) was present in 15% of patients and was associated with worse TTP [hazard ratio (HR) 1.31, 95% confidence interval (CI) 1.02-1.67, P = 0.032] and PSA response rates (48% for CC versus 62% and 65% for AA and AC, respectively [P = 0.019]), with no significant difference in TTPP (HR 1.28, 95% CI 0.99-1.66, P = 0.064). The effect of genotype was similar for treatment with abiraterone or enzalutamide with a negative test for interaction for TTPP (P = 0.997) and TTP (P = 0.749). Multivariable analysis did not show a significant association between genotype and TTP or TTPP. CONCLUSIONS: The HSD3B1 (CC) genotype was associated with shorter TTP and lower PSA response rate in patients with mCRPC treated with abiraterone or enzalutamide. However, the CC genotype did not provide prognostic information beyond that conferred by standard clinical variables, suggesting that it may not be a suitable stand-alone biomarker in mCRPC.