Non-uniform vortex lattices in inhomogeneous rotating Bose-Einstein condensates

We derive a general framework, in terms of elastic theory, for describing the distortion of the vortex lattice in a rotating Bose-Einstein condensate at arbitrary rotation speed and determining the dependence of the distortion on the density inhomogeneity of the system. In the rapidly rotating limit, we derive the energetics in terms of Landau levels, including excitation to higher levels; the distortion depends on the excitation of higher levels as well as on the density gradient. As we show, the dominant effect of higher Landau levels in a distorted lattice in equilibrium is simply to renormalize the frequency entering the lowest Landau level condensate wave function -- from the transverse trap frequency, $\omega$, to the rotational frequency, $\Omega$, of the system. Finally, we show how the equilibrium lattice distortion emerges from elastohydrodynamic theory for inhomogeneous systems.Comment: 6 pages, no figure

Structure of vortices in rotating Bose-Einstein condensates

We calculate the structure of individual vortices in rotating Bose-Einstein condensates in a transverse harmonic trap. Making a Wigner-Seitz approximation for the unit cell of the vortex lattice, we derive the Gross-Pitaevskii equation for the condensate wave function in each cell of the lattice, including effects of varying coarse grained density. We calculate the Abrikosov parameter, the fractional core area, and the energy of individual cells.Comment: 10 pages, 9 figures, published versio

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1

With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this study, we investigate the epidemiological characteristics of 5,675 HIV-1 pol gene sequences sampled from distinct infections in the United Kingdom. These sequences were phylogenetically analyzed in conjunction with 976 complete-genome and 3,201 pol gene reference sequences sampled globally and representing the broad range of HIV-1 genetic diversity, allowing us to estimate the probable geographic origins of the various strains present in the United Kingdom. A statistical analysis of phylogenetic clustering in this data set identified several independent transmission chains within the United Kingdom involving recently introduced strains and indicated that strains more commonly associated with infections acquired heterosexually in East Africa are spreading among men who have sex with men. Coalescent approaches were also used and indicated that the transmission chains that we identify originated in the late 1980s to early 1990s. Similar changes in the epidemiological structuring of HIV epidemics are likely to be taking in place in other industrialized nations with large immigrant populations. The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods

Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses

The host innate immune response mediated by type I interferon (IFN) and the resulting up-regulation of hundreds of interferon-stimulated genes (ISGs) provide an immediate barrier to virus infection. Studies of the type I ‘interferome’ have mainly been carried out at a single species level, often lacking the power necessary to understand key evolutionary features of this pathway. Here, using a single experimental platform, we determined the properties of the interferomes of multiple vertebrate species and developed a webserver to mine the dataset. This approach revealed a conserved ‘core’ of 62 ISGs, including genes not previously associated with IFN, underscoring the ancestral functions associated with this antiviral host response. We show that gene expansion contributes to the evolution of the IFN system and that interferomes are shaped by lineage-specific pressures. Consequently, each mammal possesses a unique repertoire of ISGs, including genes common to all mammals and others unique to their specific species or phylogenetic lineages. An analysis of genes commonly down-regulated by IFN suggests that epigenetic regulation of transcription is a fundamental aspect of the IFN response. Our study provides a resource for the scientific community highlighting key paradigms of the type I IFN response

Telomere length associations with cognition depend on Alzheimer's disease biomarkers

Introduction While telomere shortening, a marker of cellular aging, may impact the progression of age‐related neurodegenerative diseases, its association with cognition is unclear, particularly in the context of Alzheimer's disease (AD) pathology. Methods Telomere, cognitive, and CSF data from 482 participants in the AD Neuroimaging Initiative (148 cognitively normal, 283 mild cognitive impairment, 51 AD) was leveraged to assess telomere length associations with cognition (measured by memory and executive function) and interactions with CSF amyloid‐β, tau, and APOE‐ε4. Secondary analyses assessed brain volume and thickness outcomes. Results Longer telomeres at baseline were associated with faster executive function decline. Amyloid‐β and tau interacted with telomere length on cognition, with longer telomeres related to faster decline among biomarker‐positive individuals. Discussion Telomere associations with cognition shift with AD progression, with longer telomeres related to worse outcomes as pathology increases, highlighting the need for further investigation of telomere length along the AD neuropathological cascade

Exploratory randomised controlled trial of a mindfulness-based weight loss intervention for women

To explore the efficacy of a mindfulness-based weight loss intervention for women. Sixty-two women (ages 19-64; BMI 22.5-52.1) who were attempting to lose weight were randomised to an intervention or control condition. The former were invited to attend four 2-h workshops, the latter were asked to continue with their normal diets. Data were collected at baseline, 4 and 6 months. BMI, physical activity, mental health. At 6 months intervention participants showed significantly greater increases in physical activity compared to controls (p<.05) but no significant differences in weight loss or mental health. However, when intervention participants who reported 'never' applying the workshop principles at 6 months (n=7) were excluded, results showed both significantly greater increases in physical activity (3.1 sessions per week relative to controls, p<.05) and significantly greater reductions in BMI (0.96 relative to controls, equivalent to 2.32 kg, p<0.5). Reductions in BMI were mediated primarily by reductions in binge eating. Despite its brevity, the intervention was successful at bringing about change. Further refinements should increase its efficacy

Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures

The SARS-CoV-2 pandemic, and the likelihood of future coronavirus pandemics, emphasized the urgent need for development of novel antivirals. Small-molecule chemical probes offer both to reveal aspects of virus replication and to serve as leads for antiviral therapeutic development. Here, we report on the identification of amiloride-based small molecules that potently inhibit OC43 and SARS-CoV-2 replication through targeting of conserved structured elements within the viral 5′-end. Nuclear magnetic resonance–based structural studies revealed specific amiloride interactions with stem loops containing bulge like structures and were predicted to be strongly bound by the lead amilorides in retrospective docking studies. Amilorides represent the first antiviral small molecules that target RNA structures within the 5′ untranslated regions and proximal region of the CoV genomes. These molecules will serve as chemical probes to further understand CoV RNA biology and can pave the way for the development of specific CoV RNA–targeted antivirals

ABA-overproduction response under salinity

[SPA] Con el fin de comprender la influencia de la fitohormona ácido abscísico (ABA) en la adaptación al riego salino, dos líneas transgénicas independientes de tomate (Solanum lycopersicum L.), sp12 y sp5, que sobreexpresan constitutivamente el gen NCED1 (codifica para la enzima que cataliza un paso limitante en la biosíntesis de ABA) y la variedad silvestre Ailsa Craig, se han estudiado en experimentos o bien i) como planta entera o ii) como portainjerto bajo condiciones control y de estrés salino. Aunque la expresión constitutiva de NCED disminuye el crecimiento bajo condiciones control, minimiza los efectos producidos por la sal (planta completa) y mejora significativamente el crecimiento cuando se usa como portainjerto. El análisis de la savia xilemática de raíz mostró que los fenotipos resultantes bajo las diferentes condiciones de cultivo eran difíciles de explicar en términos de sobreproducción de ABA. Para intentar explicar estos resultados se llevó a cabo un análisis de expresión de un conjunto de genes relacionados con hormonas y estrés mediante PCR cuantitativa, así como un estudio transcriptómico mediante microarrays en la raíz. Los resultados sugieren que la sobreexpresión de NCED parece alterar diversas rutas de señalización, derivando en una respuesta adaptativa al estrés que podría ayudar a explicar los fenotipos observados. [ENG] With the aim of better understanding the influence of the plan hormone abscisic acid (ABA) in adaptation to saline irrigation, two independent transgenic tomato (Solanum lycopersicum L.) lines, sp12 and sp5, overexpressing constitutively NCED1 (the enzyme that catalyzes a key rate-limiting step in ABA biosynthesis) and the wild type Ailsa Craig, have been studied in experiments either i) as whole plants or ii) as rootstocks under control and salinity conditions. While NCED overexpression penalizes growth under control conditions, it minimized the effect of salinity (whole plants) or significantly improved plant growth and yield when used as rootstocks. The analysis of the root xylem sap revealed that the phenotypes resulting under the different conditions were difficult to explain in terms of ABA overproduction. With the aim of explaining these results, the expression of a set of hormone and stress associated genes (analysed by real time PCR) as well as a transcriptomic analysis (by using one-color microarray) were performed in roots. The results suggest that NCED overexpression seems to alter several signalling pathways leading to stress adaptive responses that could help to explain the observed phenotypes.The authors thank Andrew J. Thompson from Cranfield University, the NCED seeds set. This work was supported by CICYT-FEDER (project AGL2011-27996) and European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 289365(ROOTOPOWER project)

Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom

The heterosexual risk group has become the largest HIV infected group in the United Kingdom during the last 10 years, but little is known of the network structure and dynamics of viral transmission in this group. The overwhelming majority of UK heterosexual infections are of non-B HIV subtypes, indicating viruses originating among immigrants from sub-Saharan Africa. The high rate of HIV evolution, combined with the availability of a very high density sample of viral sequences from routine clinical care has allowed the phylodynamics of the epidemic to be investigated for the first time. Sequences of the viral protease and partial reverse transcriptase coding regions from 11,071 patients infected with HIV of non-B subtypes were studied. Of these, 2774 were closely linked to at least one other sequence by nucleotide distance. Including the closest sequences from the global HIV database identified 296 individuals that were in UK-based groups of 3 or more individuals. There were a total of 8 UK-based clusters of 10 or more, comprising 143/2774 (5%) individuals, much lower than the figure of 25% obtained earlier for men who have sex with men (MSM). Sample dates were incorporated into relaxed clock phylogenetic analyses to estimate the dates of internal nodes. From the resulting time-resolved phylogenies, the internode lengths, used as estimates of maximum transmission intervals, had a median of 27 months overall, over twice as long as obtained for MSM (14 months), with only 2% of transmissions occurring in the first 6 months after infection. This phylodynamic analysis of non-B subtype HIV sequences representing over 40% of the estimated UK HIV-infected heterosexual population has revealed heterosexual HIV transmission in the UK is clustered, but on average in smaller groups and is transmitted with slower dynamics than among MSM. More effective intervention to restrict the epidemic may therefore be feasible, given effective diagnosis programmes

Defining unmet clinical need across the pathway of brain tumor care: a patient and carer perspective.

OBJECTIVE: The aim of this study was to determine the experience of patients with brain tumors and their carers across distinct parts of their treatment pathway and identify their views on potential service gaps in need of addressing. METHODS: A structured survey was administered at patient workshops across the UK and online through a charity newsletter. Answers to closed questions were analyzed using descriptive statistics, and open questions were examined using techniques of inductive content analysis. RESULTS: A total of 136 survey responses were received, representing patients with a variety of diagnoses and geographical locations (30 counties). There was a wide range of opinions on the provision of current neuro-oncology services. Key themes identified included a perceived lack of information provision, a gap in postdischarge psychological and neuropsychological supports, and an unmet willingness for involvement in research. CONCLUSION: This national survey enhances our knowledge of current patient and carer experience within neuro-oncology services. A number of areas of unmet clinical need are highlighted providing a basis for informing future patient-centered service improvements and research