Relative Periodic Solutions of the Complex Ginzburg-Landau Equation

A method of finding relative periodic orbits for differential equations with continuous symmetries is described and its utility demonstrated by computing relative periodic solutions for the one-dimensional complex Ginzburg-Landau equation (CGLE) with periodic boundary conditions. A relative periodic solution is a solution that is periodic in time, up to a transformation by an element of the equation's symmetry group. With the method used, relative periodic solutions are represented by a space-time Fourier series modified to include the symmetry group element and are sought as solutions to a system of nonlinear algebraic equations for the Fourier coefficients, group element, and time period. The 77 relative periodic solutions found for the CGLE exhibit a wide variety of temporal dynamics, with the sum of their positive Lyapunov exponents varying from 5.19 to 60.35 and their unstable dimensions from 3 to 8. Preliminary work indicates that weighted averages over the collection of relative periodic solutions accurately approximate the value of several functionals on typical trajectories.Comment: 32 pages, 12 figure

Association of Progressive CD4+ T Cell Decline in SIV Infection with the Induction of Autoreactive Antibodies

The progressive decline of CD4+ T cells is a hallmark of disease progression in human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infection. Whereas the acute phase of the infection is dominated by virus-mediated depletion of memory CD4+ T cells, chronic infection is often associated with a progressive decline of total CD4+ T cells, including the naïve subset. The mechanism of this second phase of CD4+ T cell loss is unclear and may include immune activation–induced cell death, immune-mediated destruction, and regenerative or homeostatic failure. We studied patterns of CD4+ T cell subset depletion in blood and tissues in a group of 20 rhesus macaques inoculated with derivatives of the pathogenic SIVsmE543-3 or SIVmac239. Phenotypic analysis of CD4+ T cells demonstrated two patterns of CD4+ T cell depletion, primarily affecting either naïve or memory CD4+ T cells. Progressive decline of total CD4+ T cells was observed only in macaques with naïve CD4+ T cell depletion (ND), though the depletion of memory CD4+ T cells was profound in macaques with memory CD4+ T cell depletion (MD). ND macaques exhibited lower viral load and higher SIV-specific antibody responses and greater B cell activation than MD macaques. Depletion of naïve CD4+ T cells was associated with plasma antibodies autoreactive with CD4+ T cells, increasing numbers of IgG-coated CD4+ T cells, and increased incidence of autoreactive antibodies to platelets (GPIIIa), dsDNA, and phospholipid (aPL). Consistent with a biological role of these antibodies, these latter antibodies were accompanied by clinical features associated with autoimmune disorders, thrombocytopenia, and catastrophic thrombotic events. More importantly for AIDS pathogenesis, the level of autoreactive antibodies significantly correlated with the extent of naïve CD4+ T cell depletion. These results suggest an important role of autoreactive antibodies in the CD4+ T cell decline observed during progression to AIDS

Caveats of fungal barcoding: a case study in Trametes s.lat. (Basidiomycota: Polyporales) in Vietnam reveals multiple issues with mislabelled reference sequences and calls for third-party annotations

DNA barcoding using the nuclear internal transcribed spacer (ITS) has become prevalent in surveys of fungal diversity. This approach is, however, associated with numerous caveats, including the desire for speed, rather than accuracy, through the use of automated analytical pipelines, and the shortcomings of reference sequence repositories. Here we use the case of a specimen of the bracket fungus Trametes s.lat. (which includes the common and widespread turkey tail, T. versicolor) to illustrate these problems. The material was collected in Vietnam as part of a biodiversity inventory including DNA barcoding approaches for arthropods, plants and fungi. The ITS barcoding sequence of the query taxon was compared against reference sequences in GenBank and the curated fungal ITS database UNITE, using BLASTn and MegaBLAST, and was subsequently analysed in a multiple alignment-based phylogenetic context through a maximum likelihood tree including related sequences. Our results initially indicated issues with BLAST searches, including the use of Frairwise local alignments and sorting through Total score and E value, rather than Percentage identity, as major shortcomings of the DNA barcoding approach. However, after thorough analysis of the results, we concluded that the single most important problem of this approach was incorrect sequence labelling, calling for the implementation of third-party annotations or analogous approaches in primary sequence repositories. In addition, this particular example revealed problems of improper fungal nomenclature, which required reinstatement of the genus name Cubamyces (= Leioirametes), with three new combinations: C. flavidus, C lactineus and C. menziesii. The latter was revealed as the correct identification of the query taxon, although the name did not appear among the best BLAST hits. While the best BLAST hits did correspond to the target taxon in terms of sequence data, their label names were misleading or unresolved, including [Fungal endophyte], [Uncultured fungus], Basidiomycota, Trametes cf. cubensis, Lenzites elegans and Geotrichum candidum (an unrelated ascomycetous contaminant). Our study demonstrates that accurate identification of fungi through molecular barcoding is currently not a fast-track approach that can be achieved through automated pipelines

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.

As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing

The role of classroom observation in the development and assessment of schoolteachers in Vietnam: a review of national policy and research

This paper focuses on the role of classroom observation in the development and assessment of schoolteachers in Vietnam through a narrative review of current policy and cognate research literature. The overall aim of this review was twofold. Firstly, to contribute to a growing bank of Vietnam-based studies to maximise the value of the insights from this scholarly work into recent policy reforms on teachers’ professional development in Vietnam. Secondly, to widen access and exposure to published work on the topic in Vietnamese that is not readily accessible to English-speaking scholars. This review revealed a long history and engrained culture of using observation as a teacher performance evaluation tool. In recent years, there have been policy reforms and research studies that have repositioned observation as a tool for teacher learning and development. However, the implementation of these reforms has been inconsistent across Vietnam, along with recent reform having encountered resistance from a culture of compliance in schools. This paper identifies some of the key issues that policy makers and educational leaders need to address in practice in order to ensure the effective and meaningful implementation of the reforms relating to the use of observation for learning and developmental purposes

Sorting or supporting teachers? An exploration of the imbalanced role of classroom observation in the development and assessment of Vietnamese secondary schoolteachers

In 2018, Vietnam’s National Teacher Education Programme established a new framework for schoolteachers’ professional development. Classroom observation was the dominant method used for teacher monitoring, assessment and development. This paper explores the use and impact of current classroom observation policy and practice on novice teachers in Vietnamese secondary schools. Our study draws on qualitative data from 35 semi-structured interviews across four provinces. Our findings revealed ongoing policy-practice tensions, with the prioritisation and dominance of classroom observation as an assessment tool for sorting rather than supporting teachers. These tensions were indicative of a wider policy-practice disconnect enshrined in recent reform by the Ministry of Education and Training that advocated the adoption of lesson study as the preferred national approach in schools. However, the experiences of our participants reflected a very different picture in practice that reinforced traditional hierarchies of power associated with evaluative models of observation that are designed to standardise and rank teachers’ classroom performance rather than develop the quality of teaching. Instead of the more collaborative and collegial ethos typically associated with inquiry-based approaches like lesson study, observation was being used largely as a high-stakes assessment, resulting in increased levels of anxiety and stress among teachers

Loss of CD103+ DCs and Mucosal IL-17+ and IL-22+ Lymphocytes is Associated with Mucosal Damage in SIV Infection

HIV/SIV disease progression is associated with multifocal damage to the GI tract epithelial barrier that correlates with microbial translocation and persistent pathological immune activation but the underlying mechanisms remain unclear. Investigating alterations in mucosal immunity during SIV infection, we found that damage to the colonic epithelial barrier was associated with loss of multiple lineages of IL-17-producing lymphocytes, cells that microarray analysis showed express genes important for enterocyte homeostasis, including IL-22. IL-22-producing lymphocytes were also lost after SIV infection. Potentially explaining coordinate loss of these distinct populations, we also observed loss of CD103+ DCs after SIV infection which associated with loss of IL-17 and IL-22-producing lymphocytes. CD103+ DCs expressed genes associated with promotion of IL-17/IL-22+ cells, and co-culture of CD103+ DCs and naïve T-cells led to increased IL17A and RORc expression in differentiating T-cells. These results reveal complex interactions between mucosal immune cell subsets providing potential mechanistic insights into mechanisms of mucosal immune dysregulation during HIV/SIV infection, and offer hints for development of novel therapeutic strategies to address this aspect of AIDS virus pathogenesis

The Roasting Marshmallows Program with IGRINS on Gemini South I: Composition and Climate of the Ultra Hot Jupiter WASP-18 b

We present high-resolution dayside thermal emission observations of the exoplanet WASP-18b using IGRINS on Gemini South. We remove stellar and telluric signatures using standard algorithms, and we extract the planet signal via cross correlation with model spectra. We detect the atmosphere of WASP-18b at a signal-to-noise ratio (SNR) of 5.9 using a full chemistry model, measure H2O (SNR=3.3), CO (SNR=4.0), and OH (SNR=4.8) individually, and confirm previous claims of a thermal inversion layer. The three species are confidently detected (>4$\sigma$) with a Bayesian inference framework, which we also use to retrieve abundance, temperature, and velocity information. For this ultra-hot Jupiter (UHJ), thermal dissociation processes likely play an important role. Retrieving abundances constant with altitude and allowing the temperature-pressure profile to freely adjust results in a moderately super-stellar carbon to oxygen ratio (C/O=0.75^{+0.14}_{-0.17}) and metallicity ([M/H]=1.03^{+0.65}_{-1.01}). Accounting for undetectable oxygen produced by thermal dissociation leads to C/O=0.45^{+0.08}_{-0.10} and [M/H]=1.17^{+0.66}_{-1.01}. A retrieval that assumes radiative-convective-thermochemical-equilibrium and naturally accounts for thermal dissociation constrains C/O<0.34 (2$\sigma$) and [M/H]=0.48^{+0.33}_{-0.29}, in line with the chemistry of the parent star. Looking at the velocity information, we see a tantalising signature of different Doppler shifts at the level of a few km/s for different molecules, which might probe dynamics as a function of altitude and location on the planet disk. Our results demonstrate that ground-based, high-resolution spectroscopy at infrared wavelengths can provide meaningful constraints on the compositions and climate of highly irradiated planets. This work also elucidates potential pitfalls with commonly employed retrieval assumptions when applied to UHJ spectra.Comment: 27 pages, 18 figures, submitted to AAS Journals. Community feedback welcom

HLA B*5701-positive long-term nonprogressors/elite controllers are not distinguished from progressors by the clonal composition of HIV-specific CD8+ T cells

To better understand the qualitative features of effective human immunodeficiency virus (HIV)-specific immunity, we examined the TCR clonal composition of CD8+ T cells recognizing conserved HIV p24-derived epitopes in HLA-B*5701-positive long-term nonprogressors/elite controllers (LTNP/EC) and HLA-matched progressors. Both groups displayed oligoclonal HLA-B5701-restricted p24-specific CD8+ T-cell responses with similar levels of diversity and few public clonotypes. Thus, HIV-specific CD8+ T-cell responses in LTNP/EC are not differentiated from those of progressors on the basis of clonal diversity or TCR sharing