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We present an extension of the massively parallel, GPU native, astrophysical hydrodynamics code Cholla to magnetohydrodynamics (MHD). Cholla solves the ideal MHD equations in their Eulerian form on a static Cartesian mesh utilizing the Van Leer + Constrained Transport integrator, the HLLD Riemann solver, and reconstruction methods at second and third order. Cholla's MHD module can perform over 200 million cell updates per GPU-second while using the HLLD Riemann solver and second order reconstruction. The inherently parallel nature of GPUs combined with increased memory in new hardware allows Cholla's MHD module to perform simulation with resolutions of $>450^3$ cells on a single GPU. We employ GPU direct MPI to attain nearly perfect weak scaling on the exascale supercomputer \textit{Frontier}, while using up to 74,000 GPUs and simulating a total grid size of over 1.2 trillion cells. A suite of test problems highlights the accuracy of Cholla's MHD module and demonstrates that zero magnetic divergence in solutions is maintained to round off error. We also present new testing and continuous integration tools using GoogleTest, GitHub Actions, and Jenkins that have made development more robust and accurate and ensure reliability in the future.

Background: Cerebrospinal fluid (CSF) dynamics are increasingly studied in aging and neurological disorders. Models of CSF-mediated waste clearance suggest that altered CSF dynamics could play a role in the accumulation of toxic waste in the CNS, with implications for Alzheimer’s disease and other proteinopathies. Therefore, approaches that enable quantitative and volumetric assessment of CSF flow velocities could be of value. In this study we demonstrate the feasibility of 4D flow MRI for simultaneous assessment of CSF dynamics throughout the ventricular system, and evaluate associations to arterial pulsatility, ventricular volumes, and age. Methods: In a cognitively unimpaired cohort (N = 43; age 41–83 years), cardiac-resolved 4D flow MRI CSF velocities were obtained in the lateral ventricles (LV), foramens of Monro, third and fourth ventricles (V3 and V4), the cerebral aqueduct (CA) and the spinal canal (SC), using a velocity encoding (venc) of 5 cm/s. Cerebral blood flow pulsatility was also assessed with 4D flow (venc = 80 cm/s), and CSF volumes were obtained from T1- and T2-weighted MRI. Multiple linear regression was used to assess effects of age, ventricular volumes, and arterial pulsatility on CSF velocities. Results: Cardiac-driven CSF dynamics were observed in all CSF spaces, with region-averaged velocity range and root-mean-square (RMS) velocity encompassing from very low in the LVs (RMS 0.25 ± 0.08; range 0.85 ± 0.28 mm/s) to relatively high in the CA (RMS 6.29 ± 2.87; range 18.6 ± 15.2 mm/s). In the regression models, CSF velocity was significantly related to age in 5/6 regions, to CSF space volume in 2/3 regions, and to arterial pulsatility in 3/6 regions. Group-averaged waveforms indicated distinct CSF flow propagation delays throughout CSF spaces, particularly between the SC and LVs. Conclusions: Our findings show that 4D flow MRI enables assessment of CSF dynamics throughout the ventricular system, and captures independent effects of age, CSF space

The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research.

In a previous paper, we reported evidence for quasi-periodicities in the \textsl{TESS} light curves of BL Lacerate and two other blazars found serendipitously in the SDSS AGN catalog. In this work, we find tentative evidence for quasi-periodic features in the \textsl{TESS} observations of five sources in the fourth catalog of the Fermi--LAT (4FGL) sources: J090453.4$-$573503, J2345$-$1555, B0422+004, J002159.2$-$514028, and B0537$-$441. We analysed the \textsl{TESS} light curves of these blazars that we extracted using a customized approach. The quasi-periodic oscillations (QPOs) are searched for using two timing analysis techniques: generalized Lomb-Scargle periodogram and weighted wavelet Z-transform. Their apparent periods lie in the range of 2.8--6.5 days and have at least 3$\sigma$ significance in both of these methods. QPOs at such timescales can originate from the kink instability model which relates the quasi-periodic feature with the growth of kinks in the magnetized relativistic jets. We performed MCMC simulations to obtain the posterior distribution of parameters associated with this model and found the kink period consistent with previous studies., Comment: 12 pages, 4 figures. Accepted for publication in MNRAS main journal

SignificanceGrowing levels of obesity and metabolic syndrome have driven demand for more advanced forms of body composition assessment. While various techniques exist to measure body composition, devices are typically expensive and not portable, involve radiation [in the case of dual-energy x-ray absorptiometry (DXA)], and are limited to analysis of adiposity while metabolic information from blood supply and oxygenation are not considered.AimWe evaluate whether diffuse optical spectroscopic imaging (DOSI) can be used to predict site-specific adiposity and percent fat (whole body) while simultaneously providing information about local tissue hemoglobin levels and oxygenation.ApproachDOSI measures of tissue composition in gastrocnemius, quadriceps, abdomen, and biceps, DXA whole-body composition, and ultrasound-derived skin and adipose tissue thickness (SATT) in the quadriceps were obtained from 99 individuals aged 7 to 34 years old.ResultsVarious DOSI-derived parameters were correlated with SATT and an optical method is proposed for estimating SATT using a newly defined parameter, the optical fat fraction (OFF), which considers all parameters that correlate with SATT. Broadband absorption and scattering spectra from study participants with the thinnest (SATT ≈ 0.25 ± 0.02 cm) and thickest SATT (SATT ≈ 1.55 ± 0.14 cm), representing best estimates for pure in vivo lean and fatty tissue, respectively, are reported. Finally, a trained prediction model is developed which allows DOSI assessment of OFF to predict DXA body-fat percentage, demonstrating that DOSI can be used to quantify body composition.ConclusionsThis study shows that DOSI can be used to assess the adiposity of specific tissues or the entire human body, and the OFF parameter is defined for corroboration and further evaluation in future research.

Nearly half a century ago, two papers postulated the likelihood of lunar lava tube caves using mathematical models. Today, armed with an array of orbiting and fly-by satellites and survey instrumentation, we have now acquired cave data across our solar system-including the identification of potential cave entrances on the Moon, Mars, and at least nine other planetary bodies. These discoveries gave rise to the study of planetary caves. To help advance this field, we leveraged the expertise of an interdisciplinary group to identify a strategy to explore caves beyond Earth. Focusing primarily on astrobiology, the cave environment, geology, robotics, instrumentation, and human exploration, our goal was to produce a framework to guide this subdiscipline through at least the next decade. To do this, we first assembled a list of 198 science and engineering questions. Then, through a series of social surveys, 114 scientists and engineers winnowed down the list to the top 53 highest priority questions. This exercise resulted in identifying emerging and crucial research areas that require robust development to ultimately support a robotic mission to a planetary cave-principally the Moon and/or Mars. With the necessary financial investment and institutional support, the research and technological development required to achieve these necessary advancements over the next decade are attainable. Subsequently, we will be positioned to robotically examine lunar caves and search for evidence of life within Martian caves; in turn, this will set the stage for human exploration and potential habitation of both the lunar and Martian subsurface.

The program AutoEFT is described. It allows one to generate Effective Field Theories (EFTs) from a given set of fields and symmetries. Allowed fields include scalars, spinors, gauge bosons, and gravitons. The symmetries can be local or global Lie groups based on U(1) and SU(N). The mass dimension of the EFT is limited only by the available computing resources. The operators are stored in a compact, human and machine-readable format. Aside from the program itself, we provide input files for EFTs based on the Standard Model and a number of its extensions. These include additional particles and symmetries, EFTs with minimal flavor violation, and gravitons., Comment: 65 pages, 2 ancillary files; published version; the source code is available at https://gitlab.com/auto_eft/autoeft

The gradient-flow formalism proves to be a useful tool in lattice calculations of quantum chromodynamics. For example, it can be used as a scheme to renormalize composite operators by inverting the short-flow-time expansion of the corresponding flowed operators. In this paper, we consider the short-flow-time expansion of five quark bilinear operators, the scalar, pseudoscalar, vector, axialvector, and tensor currents, and compute the matching coefficients through next-to-next-to-leading order QCD. Among other applications, our results constitute one ingredient for calculating bag parameters of mesons within the gradient-flow formalism on the lattice., Comment: 27 pages, 5 figures, 1 ancillary file

Rosemary Bassey, Robert V Hill, Zeinab Nassrallah, Shannon Knutson, Brian Pinard, Doreen M Olvet, William P Rennie Department of Science Education, Donald and Barbara Zucker School of Medicine at Hofstra/ Northwell, Hempstead, NY, USACorrespondence: Rosemary Bassey, Department of Science Education, Donald and Barbara Zucker School of Medicine at Hofstra/ Northwell, Hempstead, NY, 11549, USA, Tel +1 516 463-7504, Email Rosemary.bassey@hofstra.eduIntroduction: Recent changes in undergraduate medical curricula have resulted in time constraints that are particularly challenging, especially when students must learn large blocks of musculoskeletal anatomy content. Consequently, students have resorted to rote memorization to cope, which counteracts our established collaborative self-directed learning model.Methods: For a 6-week musculoskeletal anatomy course, two structured case-based review sessions are described, each following the completion of two five-hour lab sessions, two on the upper extremities and two on the lower extremities. These largely self-directed review sessions consisted of 6 students rotating through 7 to 8 stations every 10 minutes where clinical cases with follow-up questions were projected on large screens. The students were expected to work collaboratively to solve the cases utilizing the prosected specimens provided and discuss the accompanying answers at the end of each case.Results: Ninety-four per cent of the students who participated in this study agreed that the case-based review sessions provided a helpful overview of musculoskeletal anatomy content. Student performance on the open-ended, case-based musculoskeletal examination questions showed no significant difference in performance on shoulder, hand, hip, thigh, and leg questions. There was, however, a statistically significant decrease in the students’ scores on a forearm question in 2021 compared to 2019.Conclusion: This paper describes our integrated, collaborative musculoskeletal cour

Growing global demand for sustainable development places immense pressure on the construction industry to select and promote sustainable construction practices. The selection of sustainable construction practices is a challenging task, as there are numerous variables and uncertainties involved in the concept of sustainability and a consistent and widely accepted framework for assessment and evaluation seems to be lacking. Based on an extensive literature review on sustainability, sustainable construction was redefined and evaluation frameworks were identified for comparison. Furthermore, a conceptual framework is proposed by identifying specific indicators and criteria relating to the objectives of sustainable construction (sociocultural, economic, technical and environmental) to evaluate the sustainability of construction practices. Recommendations for the application of the proposed framework is also presented., Policy Analysis

Chlamydia trachomatis and Neisseria gonorrhoeae are the most frequently reported agents of bacterial sexually transmitted disease worldwide. Nonetheless, C. trachomatis/N. gonorrhoeae coinfection remains understudied. C. trachomatis/N. gonorrhoeae coinfections are more common than expected by chance, suggesting C. trachomatis/N. gonorrhoeae interaction, and N. gonorrhoeae infection may reactivate genital chlamydial shedding in women with latent (quiescent) chlamydial infection. We hypothesized that N. gonorrhoeae would reactivate latent genital Chlamydia muridarum infection in mice. Two groups of C. muridarum-infected mice were allowed to transition into genital latency. One group was then vaginally inoculated with N. gonorrhoeae; a third group received N. gonorrhoeae alone. C. muridarum and N. gonorrhoeae vaginal shedding was measured over time in the coinfected and singly infected groups. Viable C. muridarum was absent from vaginal swabs but detected in rectal swabs, confirming C. muridarum genital latency and consistent with the intestinal tract as a C. muridarum reservoir. C. muridarum inclusions were observed in large intestinal, but not genital, tissues during latency. Oviduct dilation was associated with C. muridarum infection, as expected. Contradicting our hypothesis, N. gonorrhoeae coinfection did not reactivate latent C. muridarum vaginal shedding. In addition, latent C. muridarum infection did not modulate recovery of vaginal viable N. gonorrhoeae. Evidence for N. gonorrhoeae-dependent increased C. muridarum infectivity has thus not been demonstrated in murine coinfection, and the ability of C. muridarum coinfection to potentiate N. gonorrhoeae infectivity may depend on actively replicating vaginal C. muridarum. The proportion of mice with increased vaginal neutrophils (PMNs) was higher in N. gonorrhoeae-infected than in C. muridarum-infected mice, as expected, while that of C. muridarum/N. gonorrhoeae-coinfected mice was intermediate to the singly infec

We report the time series analysis of TESS light curves of three blazars, BL Lacertae, 1RXS J111741.0+254858, and 1RXS J004519.6+212735, obtained using a customized approach for extracting AGN light curves. We find tentative evidence for quasi-periodic oscillations (QPOs) in these light curves that range from 2 to 6 days. Two methods of analysis are used for assessing their significance: generalized Lomb-Scargle periodograms and weighted wavelet Z-transforms. The different approaches of these methods together ensure a robust measurement of the significance of the claimed periodicities. We can attribute the apparent QPOs to the kink instability model which postulates that the observed QPOs are related to the temporal growth of kinks in the magnetized relativistic jet. We confirm the application of this model to BL Lacertae and extend the kink instability model to the other two BL Lac objects., Comment: Accepted for publication in MNRAS

Thirty-six years after the first edition of IEEE standard 982.1, Measures of the Software Aspects of Dependability, the third edition focuses on the measurement of in-service software dependability. This article explains how this new point of view evolved and shaped the third edition's guidance for software dependability measurement., Comment: 18 pages, 4 figures. Accepted for publication in IEEE Computer, April 2024

IntroductionPatients who sustain orthopaedic trauma are at an increased risk of venous thromboembolism (VTE), including fatal pulmonary embolism (PE). Current guidelines recommend low-molecular-weight heparin (LMWH) for VTE prophylaxis in orthopaedic trauma patients. However, emerging literature in total joint arthroplasty patients suggests the potential clinical benefits of VTE prophylaxis with aspirin. The primary aim of this trial is to compare aspirin with LMWH as a thromboprophylaxis in fracture patients.Methods and analysisPREVENT CLOT is a multicentre, randomised, pragmatic trial that aims to enrol 12 200 adult patients admitted to 1 of 21 participating centres with an operative extremity fracture, or any pelvis or acetabular fracture. The primary outcome is all-cause mortality. We will evaluate non-inferiority by testing whether the intention-to-treat difference in the probability of dying within 90 days of randomisation between aspirin and LMWH is less than our non-inferiority margin of 0.75%. Secondary efficacy outcomes include cause-specific mortality, non-fatal PE and deep vein thrombosis. Safety outcomes include bleeding complications, wound complications and deep surgical site infections.Ethics and disseminationThe PREVENT CLOT trial has been approved by the ethics board at the coordinating centre (Johns Hopkins Bloomberg School of Public Health) and all participating sites. Recruitment began in April 2017 and will continue through 2021. As both study medications are currently in clinical use for VTE prophylaxis for orthopaedic trauma patients, the findings of this trial can be easily adopted into clinical practice. The results of this large, patient-centred pragmatic trial will help guide treatment choices to prevent VTE in fracture patients.Trial registration numberNCT02984384.

To the Editor — 2021 is the International Year of Caves and Karst. To honour this occasion, we wish to emphasize the vast potential embodied in planetary subsurfaces. While researchers have pondered the possibility of extraterrestrial caves for more than 50 years, we have now entered the incipient phase of planetary caves exploration....

The effective electroweak Hamiltonian in the gradient-flow formalism is constructed for the current-current operators through next-to-next-to-leading order QCD. The results are presented for two common choices of the operator basis. This paves the way for a consistent matching of perturbatively evaluated Wilson coefficients and non-perturbative matrix elements evaluated by lattice simulations., Comment: 5 pages, 1 figure, 1 ancillary file

Level of evidencePrognostic Level II.

Lipid droplets (LDs) are organelles of cellular lipid storage with fundamental roles in energy metabolism and cell membrane homeostasis. There has been an explosion of research into the biology of LDs, in part due to their relevance in diseases of lipid storage, such as atherosclerosis, obesity, type 2 diabetes, and hepatic steatosis. Consequently, there is an increasing need for a resource that combines datasets from systematic analyses of LD biology. Here, we integrate high-confidence, systematically generated human, mouse, and fly data from studies on LDs in the framework of an online platform named the "Lipid Droplet Knowledge Portal" (https://lipiddroplet.org/). This scalable and interactive portal includes comprehensive datasets, across a variety of cell types, for LD biology, including transcriptional profiles of induced lipid storage, organellar proteomics, genome-wide screen phenotypes, and ties to human genetics. This resource is a powerful platform that can be utilized to identify determinants of lipid storage.

Haploinsufficiency of GRN causes frontotemporal dementia (FTD). The GRN locus produces progranulin (PGRN), which is cleaved to lysosomal granulin polypeptides. The function of lysosomal granulins and why their absence causes neurodegeneration are unclear. Here we discover that PGRN-deficient human cells and murine brains, as well as human frontal lobes from GRN-mutation FTD patients have increased levels of gangliosides, glycosphingolipids that contain sialic acid. In these cells and tissues, levels of lysosomal enzymes that catabolize gangliosides were normal, but levels of bis(monoacylglycero)phosphates (BMP), lipids required for ganglioside catabolism, were reduced with PGRN deficiency. Our findings indicate that granulins are required to maintain BMP levels to support ganglioside catabolism, and that PGRN deficiency in lysosomes leads to gangliosidosis. Lysosomal ganglioside accumulation may contribute to neuroinflammation and neurodegeneration susceptibility observed in FTD due to PGRN deficiency and other neurodegenerative diseases.

BACKGROUND AND AIMS: No consensus exists on defining intestinal ultrasound response, transmural healing, or transmural remission in inflammatory bowel disease, nor clear guidance for optimal timing of assessment during treatment. This systematic review and expert consensus study aimed to define such recommendations, along with key parameters included in response reporting.METHODS: Electronic databases were searched from inception to July 26, 2021, using pre-defined terms. Studies were eligible if at least two intestinal ultrasound assessments at different time points during treatment were reported, along with an appropriate reference standard. The QUADAS-2 tool was used to examine study-level risk of bias. An international panel of experts (n=18) rated an initial 196 statements (RAND/UCLA process, scale 1-9). Two videoconferences were conducted, resulting in additional ratings of 149 and 13 statements, respectively.RESULTS: Out of 5826 records, 31 full-text articles, 16 abstracts, and one research letter were included. 83% (40/48) of included studies showed a low concern of applicability, while 96% (46/48) had a high risk of bias. A consensus was reached on 41 statements, with clear definitions of IUS treatment response, transmural healing, transmural remission, timing of assessment, and general considerations when using intestinal ultrasound in inflammatory bowel disease.CONCLUSIONS: Response criteria and time-points of response assessment varied between studies complicating direct comparison of parameter changes and their relation to treatment outcomes. To ensure a unified approach in routine care and clinical trials, we provide recommendations and definitions for key parameters for intestinal ultrasound response to incorporate into future prospective studies.

Background & Aims: End points to determine the efficacy and safety of medical therapies for Crohn's disease (CD) and ulcerative colitis (UC) are evolving. Given the heterogeneity in current outcome measures, harmonizing end points in a core outcome set for randomized controlled trials is a priority for drug development in inflammatory bowel disease. Methods: Candidate outcome domains and outcome measures were generated from systematic literature reviews and patient engagement surveys and interviews. An iterative Delphi process was conducted to establish consensus: panelists anonymously voted on items using a 9-point Likert scale, and feedback was incorporated between rounds to refine statements. Consensus meetings were held to ratify the outcome domains and core outcome measures. Stakeholders were recruited internationally, and included gastroenterologists, colorectal surgeons, methodologists, and clinical trialists. Results: A total of 235 patients and 53 experts participated. Patient-reported outcomes, quality of life, endoscopy, biomarkers, and safety were considered core domains; histopathology was an additional domain for UC. In CD, there was consensus to use the 2-item patient-reported outcome (ie, abdominal pain and stool frequency), Crohn's Disease Activity Index, Simple Endoscopic Score for Crohn's Disease, C-reactive protein, fecal calprotectin, and co-primary end points of symptomatic remission and endoscopic response. In UC, there was consensus to use the 9-point Mayo Clinic Score, fecal urgency, Robarts Histopathology Index or Geboes Score, fecal calprotectin, and a composite primary end point including both symptomatic and endoscopic remission. Safety outcomes should be reported using the Medical Dictionary for Regulatory Activities. Conclusions: This multidisciplinary collaboration involving patients and clinical experts has produced the first core outcome set that can be applied to randomized controlled trials of CD and UC.

We develop a new approach to drifting games, a class of two-person games with many applications to boosting and online learning settings. Our approach involves (a) guessing an asymptotically optimal potential by solving an associated partial differential equation (PDE); then (b) justifying the guess, by proving upper and lower bounds on the final-time loss whose difference scales like a negative power of the number of time steps. The proofs of our potential-based upper bounds are elementary, using little more than Taylor expansion. The proofs of our potential-based lower bounds are also elementary, combining Taylor expansion with probabilistic or combinatorial arguments. Not only is our approach more elementary, but we give new potentials and derive corresponding upper and lower bounds that match each other in the asymptotic regime.

This work addresses a version of the two-armed Bernoulli bandit problem where the sum of the means of the arms is one (the symmetric two-armed Bernoulli bandit). In a regime where the gap between these means goes to zero as the number of prediction periods approaches infinity, i.e., the difficulty of detecting the gap increases as the sample size increases, we obtain the leading order terms of the minmax optimal regret and pseudoregret for this problem by associating each of them with a solution of a linear heat equation. Our results improve upon the previously known results; specifically, we explicitly compute these leading order terms in three different scaling regimes for the gap. Additionally, we obtain new non-asymptotic bounds for any given time horizon. Although optimal player strategies are not known for more general bandit problems, there is significant interest in considering how regret accumulates under specific player strategies, even when they are not known to be optimal. We expect that the methods of this paper should be useful in settings of that type., Comment: Improved results in the large gap regime

We present time-series CCD photometry in the $BVRI$ passbands of the recently identified symbiotic nova V1835 Aquilae (NSV 11749) over an interval of 5.1 years with 7-14 day cadence, observed during its quiescence. We find slow light variations with a range of $\sim$0.9 mag in $V$ and $\sim$0.3 mag in $I$. Analysis of these data show strong periodicity at $419 \pm 10$ days, which we interpret to be the system's orbital period. A dip in the otherwise-sinusoidal phased light curve suggests a weak ellipsoidal effect due to tidal distortion of the giant star, which in turn opens the possibility that V1835 Aql transfers some of its mass to the hot component via Roche lobe overflow rather than via a stellar wind. We also find evidence that V1835 Aql is an S-type symbiotic star, relatively free of circumstellar dust, and include it among the nuclear burning group of symbiotics. Finally, we provide photometry, periods, and light curve classifications for 22 variable stars in the field around V1835 Aql, about half of which are newly identified., Comment: Main Paper: 28 pages, 5 figures, 5 tables. Supplement: 15 pages, 4 figures, 1 table. To be published in Publications of the Astronomical Society of the Pacific

Training computer-vision related algorithms on medical images for disease diagnosis or image segmentation is difficult in large part due to privacy concerns. For this reason, generative image models are highly sought after to facilitate data sharing. However, 3-D generative models are understudied, and investigation of their privacy leakage is needed. We introduce our 3-D generative model, Transversal GAN (TrGAN), using head & neck PET images which are conditioned on tumour masks as a case study. We define quantitative measures of image fidelity, utility and privacy for our model. These metrics are evaluated in the course of training to identify ideal fidelity, utility and privacy trade-offs and establish the relationships between these parameters. We show that the discriminator of the TrGAN is vulnerable to attack, and that an attacker can identify which samples were used in training with almost perfect accuracy (AUC = 0.99). We also show that an attacker with access to only the generator cannot reliably classify whether a sample had been used for training (AUC = 0.51). This suggests that TrGAN generators, but not discriminators, may be used for sharing synthetic 3-D PET data with minimal privacy risk while maintaining good utility and fidelity., Comment: arXiv admin note: text overlap with arXiv:2111.01866

The effective electroweak Hamiltonian in the gradient-flow formalism is constructed for the current-current operators through next-to-next-to-leading order QCD. The results are presented for two common choices of the operator basis. This paves the way for a consistent matching of perturbatively evaluated Wilson coefficients and non-perturbative matrix elements evaluated by lattice simulations., Comment: 6 pages, 1 figure, 1 ancillary file. v2: minor clarifications, matches published version

Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) are the most common bacterial sexually transmitted infections (STIs) worldwide. The primary site of infection for both bacteria is the epithelium of the endocervix in women and the urethra in men; both can also infect the rectum, pharynx and conjunctiva. Ct/Ng co-infections are more common than expected by chance, suggesting Ct/Ng interactions increase susceptibility and/or transmissibility. To date, studies have largely focused on each pathogen individually and models exploring co-infection are limited. We aimed to determine if Ng co-infection influences chlamydial infection and development and we hypothesized that Ng-infected cells are more susceptible to chlamydial infection than uninfected cells. To address this hypothesis, we established an in vitro model of Ct/Ng co-infection in cultured human cervical epithelial cells. Our data show that Ng co-infection elicits an anti-chlamydial effect by reducing chlamydial infection, inclusion size, and subsequent infectivity. Notably, the anti-chlamydial effect is dependent on Ng viability but not extracellular nutrient depletion or pH modulation. Though this finding is not consistent with our hypothesis, it provides evidence that interaction of these bacteria in vitro influences chlamydial infection and development. This Ct/Ng co-infection model, established in an epithelial cell line, will facilitate further exploration into the pathogenic interplay between Ct and Ng.

The present purposes of teacher evaluation commonly include: (1) professional growth for improvement of instruction; (2) clarifying goals and objectives; (3) measuring progress toward those goals; (4) clarifying inservice needs; (5) judging the contribution of the teacher to pupil progress; (6) determining salary; and (7) determining employment status. Three conceptual frameworks of teacher evaluation are discussed: appraisal based on mutually derived objectives; appraisal based on student learnings; and appraisal based on teacher behavior. The question is which approach or combination of approaches should be used. Several factors are discussed which must be considered in designing a "new" teacher evaluation system: baseline assessment; definition of a decision-making process; clarification of purposes of the evaluation system; identification of alternative approaches; identification of type of data needed; information sources; data collection methods; management structures; selection of plausible design features. Various implementation stages for a teacher evaluation system are outlined, and a model for evaluating the new evaluation system is presented. (JMF)

To investigate the affective and cognitive gains produced in an auto-tutorial world civilizations course, two groups of students were compared. A traditionally-taught (TT) section of 145 students and an auto-tutorially (AT) taught section of 140 were given pre- and posttests and used the same text and Modular Learning Program. The TT section achieved a higher pre-test mean score and showed a more positive attitude to the subject of history than the AT group. The TT section met three times weekly; the AT group met three times during the semester and were given a choice of three options for individual study. At the end of the experiment, the AT section had a higher mean score on the post-test and gave more positive evaluation of the course than those in the TT section. (SK)

Guidelines of a four-phase model for conducting leadership conferences are outlined. Phase I focuses on initial conference planning, including (1) identifying need and purpose for the conference; (2) selecting a conference chairperson; (3) forming the conference planning committee, listing suggested committees and their responsibilities (program, brochure and application, participant selection, registration, publicity, finance, vendors, facilities, and evaluation committees); and (4) convening the conference planning meeting, including reviewing the purpose of the conference, identifying clientele, selecting conference dates and facility (advantages and disadvantages of hotels/motels; convention/conference centers; resorts, retreats, lodges, and parks; schools, colleges, and community centers), developing conference objectives, conducting a needs assessment, formulating a conference program, setting committee assignments, establishing a time line, and wrapping up the session. Phase II focuses on interim conference planning, providing guidelines related to the 9 previously named committees. Activities during the conference itself are discussed in Phase III and Phase IV and post-conference activities in Phase IV. A list of additional resources, sample planning checklist, session evaluation form, and conference evaluation form are provided. (SK)

This guide for graduate students in the sciences focuses on the conduct of research, especially impediments involving approaches, perceptions, and self-initiating efforts. The book is developed in chronological fashion for the beginning graduate student. The first chapter contains an orientation to graduate research departments. It is followed by chapters on commitments and creativity, making choices (e.g., research problems and an advisor), and managing time. These are followed by chapters on the principles of scientific research and ethics in science. Subsequent chapters are devoted to library research, writing skills, preparing theses and dissertations, and presenting and publishing papers. The book continues with chapters on research with human subjects, animals, and biohazards; and on writing and applying for grants. A concluding chapter provides suggestions for getting a job in higher education, government, or industry. (Individual chapters contain references.) (DB)

This teacher's guide suggests activities that provide opportunities for upper elementary students to explore, by direct experiment, many of the properties of light. Equipment is listed and construction of a light source is detailed. Instructions are given for setting up a classroom with electrical equipment. Activities are described in units dealing with mirrors, colored light, and refraction. (CS)

Discusses whether the discovery in 1956 that humans have a chromosome number of 46, as opposed to 47 or 48 as previously thought, fits into a paradigm shift of the Kuhnian type. Concludes that Kuhn probably would not have considered the chromosome number shift to be large enough to be a focus for one of his paradigms. (AIM)

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systemati

IntroductionCluster randomized crossover trials are often faced with a dilemma when selecting an optimal model of consent, as the traditional model of obtaining informed consent from participant's before initiating any trial related activities may not be suitable. We describe our experience of engaging patient advisors to identify an optimal model of consent for the PREP-IT trials. This paper also examines surrogate measures of success for the selected model of consent.MethodsThe PREP-IT program consists of two multi-center cluster randomized crossover trials that engaged patient advisors to determine an optimal model of consent. Patient advisors and stakeholders met regularly and reached consensus on decisions related to the trial design including the model for consent. Patient advisors provided valuable insight on how key decisions on trial design and conduct would be received by participants and the impact these decisions will have.ResultsPatient advisors, together with stakeholders, reviewed the pros and cons and the requirements for the traditional model of consent, deferred consent, and waiver of consent. Collectively, they agreed upon a deferred consent model, in which patients may be approached for consent after their fracture surgery and prior to data collection. The consent rate in PREP-IT is 80.7%, and 0.67% of participants have withdrawn consent for participation.DiscussionInvolvement of patient advisors in the development of an optimal model of consent has been successful. Engagement of patient advisors is recommended for other large trials where the traditional model of consent may not be optimal.

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera).

We compare some predictions of Wagoner & Tandon (2021) with the results of the hydrodynamic and magnetohydrodynamic (MHD) simulations of Reynolds & Miller (2009). It appears that the MHD simulations were not run for long enough and the numerical damping was not small enough to produce the observed high-frequency QPOs (and the g-mode seen in the hydro simulations)., Comment: 2 pages

We investigate the effects of subsonic turbulence on a normal mode of oscillation [a possible origin of the high-frequency quasi-periodic oscillations (HFQPOs) within some black hole accretion disks]. We consider perturbations of a time-dependent background (steady state disk plus turbulence), obtaining an oscillator equation with stochastic damping, (mildly) nonlinear restoring, and stochastic driving forces. The (long-term) mean values of our turbulent functions vanish. In particular, turbulence does not damp the oscillation modes, so `turbulent viscosity' is not operative. However, the frequency components of the turbulent driving force near that of the mode can produce significant changes in the amplitude of the mode. Even with an additional (phenomenological constant) source of damping, this leads to an eventual `blowout' (onset of effects of nonlinearity) if the turbulence is sufficiently strong or the damping constant is sufficiently small. The infrequent large increases in the energy of the mode could be related to the observed low duty cycles of the HFQPOs. The width of the peak in the power spectral density (PSD) is proportional to the amount of nonlinearity. A comparison with observed continuum PSDs indicates the conditions required for visibility of the mode., Comment: 14 pages, 9 figures. To be published in the The Astrophysical Journal