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The Lactobacillales (LB) stand apart among bacterial orders, using manganese (Mn) instead of iron to support their growth and swiftly ferment complex foods while acidifying their environment. The present work investigates whether a shift in the use of Mn could mark the origin of LB. Transmembrane carriers of the ubiquitous Slc11 family play key roles in LB physiology by catalyzing proton-dependent Mn import. In prior studies, the Slc11 clade found in LB (MntH Cb, MCb) showed both remarkable structural plasticity and highly efficient Mn uptake, and another Slc11 clade, MCg1, demonstrated divergent evolution coinciding with emergence of bacterial genera (e.g., Bordetella, Achromobacter). Herein, the Slc11 clade MCb is subdivided in sister groups: MCbie and MCbgut. MCbie derives directly from the Slc11 clade MCa, pointing an intermediate stage in the evolution of MCbgut. MCbie predominates in marine Bacillaceae, is more conserved than MCbgut, lacks the structural plasticity that typify MCbgut carriers, and responds differently to identical mutagenesis. Exchanging MCbie/MCbgut amino acid residues at sites that distinguish these clades showed conformation-dependent effects with both MCbie and MCbgut templates, and the 3D location of the targeted sites in the carrier structure together suggests that the mechanism to open the inner gate, and release Mn into the cytoplasm, differs between MCbie and MCbgut. Building on the established phylogeny for Enterococcus revealed that a pair of genes encoding MCbgut was present in the common ancestor of LB, as MCbgu1 and MCbgu2 templates exhibited distinct structural dynamics properties. These data are discussed when examining whether MCbgut+ LB could emerge in the upper gut of early vertebrates (ca. 540 mya), through genome contraction and evolution toward Mn-centrism, as they specialized as gastric aids favoring stomach establishment in jawed vertebrates through bi-directional communication with host nervous, endocrine and immune systems.

Abstract Purpose To investigate whether the same health state results in the same distribution of responses on the EQ-5D youth and adult descriptive systems. Methods Adolescents aged 13–18 years with a range of health conditions and from the general school going population were recruited in South Africa (ZA) and Ethiopia (ET). In ZA participants completed the English EQ-5D-3L, EQ-5D-Y-3L and EQ-5D-5L in parallel. Whereas in ET participants completed the Amharic EQ-5D-5L and EQ-5D-Y-5L in parallel. Analysis aimed to describe the transition between youth and adult instruments and not differences between countries. Results Data from 592 adolescents completing the EQ-5D-3L, EQ-5D-Y-3L and EQ-5D-5L (ZA) and 693 completing the EQ-5D-5L and EQ-5D-Y-5L (ET) were analysed. Adolescents reported more problems on the youth versions compared to the adult version for the dimension of mental health. 13% and 4% of adolescents who reported no problems on the EQ-5D-3L and EQ-5D-5L reported some problems on the EQ-5D-Y-3L respectively. This was less notable with transition between the five level versions with 4% of adolescents reporting more problems on the EQ-5D-Y-5L than the EQ-5D-5L. Very few adolescents reported severe problems (level 3 on the EQ-5D-3L or EQ-5D-Y-3L and level 4 and level 5 on the EQ-5D-5L or EQ-5D-5L) thus there was little variation between responses between the versions. In ZA, discriminatory power, measured on the Shannon’s Index, was higher for Y-3L compared to 3L for pain/discomfort (ΔH′=0.11) and anxiety/depression (ΔH′=0.04) and across all dimensions for Y-3L compared to 5L. Similarly, in ET discriminatory power was higher for Y-5L than 5L (ΔH′ range 0.05–0.09). Gwet’s AC showed good to very good agreement across all paired (ZA) 3L and (ET) 5L dimensions. The summary score of all EQ-5D versions were able to differentiate between known disease groups. Conclusion Despite the overall high levels of agreement between EQ-5D instruments for youth and for adults, they do not provide identical results in terms of health state, from the same respondent. The differences were most notable for anxiety/depression. These differences in the way individuals respond to the various descriptive systems need to be taken into consideration for descriptive analysis, when transitioning between instruments, and when comparing preference-weighted scores.

Abstract Sjögren syndrome (SS) is an autoimmune disease characterized by chronic inflammatory infiltrates in the salivary and lacrimal glands. Mucosal-associated invariant T (MAIT) cells are a subset of innate-like T-cells, predominantly found in mucosal tissues with crucial role in epithelial homeostasis. Thus, MAIT cells may be implicated in mucosal alterations of SS patients. Activation markers, inflammatory and cytotoxic cytokines were examined in 23 SS patients and compared to 23 healthy controls (HC). Tissular MAIT cells in salivary gland (SG) biopsies were also analyzed. Circulating MAIT cells were decreased in SS patients with a higher expression of CD69 and a higher CD4/CD8 ratio of MAIT cells. MAIT cells showed a higher production of IFNγ, TNFα and GzB in SS compare to HC. Tissular MAIT cells were present within inflamed SG of SS patients, while they were absent in SG of HC. Overall, circulating MAIT cells are decreased in the peripheral blood of SS albeit producing higher amounts of IFNγ, TNFα, and GzB. Tissular MAIT cells are detected in salivary glands from SS with a proinflammatory tissular cytokine environment. MAIT cells with abnormal phenotype, functions and tissular homeostasis may contribute to epithelial damage in SS.

Abstract Agricultural dykelands in Nova Scotia rely heavily on a surface drainage technique called land forming, which is used to alter the topography of fields to improve drainage. The presence of land-formed fields provides useful information to better understand land utilization on these lands vulnerable to rising sea levels. Current field boundaries delineation and classification methods, such as manual digitalization and traditional segmentation techniques, are labour-intensive and often require manual and time-consuming parameter selection. In recent years, deep learning (DL) techniques, including convolutional neural networks and Mask R-CNN, have shown promising results in object recognition, image classification, and segmentation tasks. However, there is a gap in applying these techniques to detecting surface drainage patterns on agricultural fields. This paper develops and tests a Mask R-CNN model for detecting land-formed fields on agricultural dykelands using LiDAR-derived elevation data. Specifically, our approach focuses on identifying groups of pixels as cohesive objects within the imagery, a method that represents a significant advancement over pixel-by-pixel classification techniques. The DL model developed in this study demonstrated a strong overall performance, with a mean Average Precision (mAP) of 0.89 across Intersection over Union (IoU) thresholds from 0.5 to 0.95, indicating its effectiveness in detecting land-formed fields. Results also revealed that 53% of Nova Scotia’s dykelands are being used for agricultural purposes and approximately 75% (6924 hectares) of these fields were land-formed. By applying deep learning techniques to LiDAR-derived elevation data, this study offers novel insights into surface drainage mapping, enhancing the capability for precise and efficient agricultural land management in regions vulnerable to environmental changes.

Mechanical harvesting of wild blueberries on uneven topography is challenging for the operators, emphasizing the need for harvester header automation. This research aims to develop accurate Digital Elevation Models (DEMs) and map plant height using a DJI Matrice-300 RTK Drone equipped with two distinct DJI sensors, Zenmuse P1 and Zenmuse L1. Accuracy assessment involved comparing drone-generated DEMs with elevation data from a Global Navigation Satellite System receiver, Emlid RS2. Results indicate that the P1 camera outperformed the L1 sensor in estimating DEMs within wild blueberry fields, with root mean square error values ranging from 0.36 to 1.04 cm and 1.29 to 1.70 cm for the P1 and L1 sensors, respectively. Furthermore, P1 demonstrated a significantly lower standard deviation than L1 in selected fields. The P1 imagery dataset determined wild blueberry plant heights with standard deviations of 3.66 cm and 4.77 cm for Field-A and Field-B, respectively. The precise DEMs and plant height information can be integrated into the control system of the wild blueberry harvester, facilitating automation that accounts for spatial variations in plant height, slope, and fruit zone within fields. Implementing an automated harvester holds promise for reducing fruit losses, enhancing grower profitability, and alleviating operator stress.

Background: The COVID-19 pandemic has had multiple health and behavioral effects in the general population worldwide, including effects on nutritional and lifestyle behavior such as alcohol consumption. This study aimed to determine the frequency of and predictors for change in alcohol consumption two years after onset of the COVID-19 pandemic among participants from the general population of six countries. Methods: Longitudinal study design with 4999 participants (47% male; aged 18–75 years) from a general population cohort from six countries: Greece, Italy, the Netherlands, Sweden, the United Kingdom (UK) and the United States of America (US). Measurements: Three web-based surveys at different time waves: T1 = 22 April–1 June 2020; T2 = 2 May–29 June 2021 and T3 = 29 April–25 June 2022. The surveys included questions on self-reported retrospective alcohol consumption, demographics, health, anxiety and depression symptoms and recent life events. Results: Of 4999 respondents, most (82.3%) reported no change in drinking habits during the pandemic, whereas 12.5% reported drinking less and 5.1% drinking more. Predictive factors for increased alcohol consumption include age 35–54 years, male gender, high educational level, moderate-severe depression symptoms, excessive drinking before the COVID-19 pandemic, no change in general health status and job loss. Predictive factors for decreased alcohol consumption were age 18–34 years, male gender, having chronic disease(s), moderate-severe depression symptoms, excessive drinking before the pandemic and job loss. Conclusion: The proportion of participants who reported a decrease in alcohol consumption during the COVID-19 pandemic was higher compared to those who reported an increase. Excessive drinking before the pandemic, depression symptoms and job loss were predictors for both drinking more and drinking less alcohol during the COVID-19 pandemic with an stronger association for an increase in alcohol consumption.

Background Standard of care treatment of non-muscle invasive bladder cancer (NMIBC) with intravesical Bacillus Calmette Guérin (BCG) is associated with side effects, disease recurrence/progression and supply shortages. We recently showed in a phase I trial (NCT03421236) that intravesical instillation in patients with NMIBC with the maximal tolerated dose of Ty21a/Vivotif, the oral vaccine against typhoid fever, might have a better safety profile. In the present report, we assessed the immunogenicity of intravesical Ty21a in patients of the clinical trial that had received the maximal tolerated dose and compared it with data obtained in patients that had received standard BCG.Methods Urinary cytokines and immune cells of patients with NMIBC treated with intravesical instillations of Ty21a (n=13, groups A and F in NCT03421236) or with standard BCG in a concomitant observational study (n=12, UROV1) were determined by Luminex and flow cytometry, respectively. Serum anti-lipopolysaccharide Typhi antibodies and circulating Ty21a-specific T-cell responses were also determined in the Ty21a patients. Multiple comparisons of different paired variables were performed with a mixed-effect analysis, followed by Sidak post-test. Single comparisons were performed with a paired or an unpaired Student’s t-test.Results As compared with BCG, Ty21a induced lower levels of inflammatory urinary cytokines, which correlated to the milder adverse events (AEs) observed in Ty21a patients. However, both Ty21a and BCG induced a Th1 tumor environment. Peripheral Ty21a-specific T-cell responses and/or antibodies were observed in most Ty21a patients, pointing the bladder as an efficient local immune inductive site. Besides, Ty21a-mediated stimulation of unconventional Vδ2 T cells was also observed, which turned out more efficient than BCG. Finally, few Ty21a instillations were sufficient for increasing urinary infiltration of dendritic cells and T cells, which were previously associated with therapeutic efficacy in the orthotopic mouse model of NMIBC.Conclusions Ty21a immunotherapy of patient with NMIBC is promising with fewer inflammatory cytokines and mild AE, but induction of immune responses with possible antitumor potentials. Future phase II clinical trials are necessary to explore possible efficacy of intravesical Ty21a.

Abstract Background The EQ-5D-5L and 15D are generic preference-accompanied health status measures with similar dimensions. In this study, we aim to compare the measurement properties of the EQ-5D-5L and 15D descriptive systems and index values in a general population sample. Methods In August 2021, an online cross-sectional survey was conducted in a representative adult general population sample (n = 1887). The EQ-5D-5L and 15D descriptive systems and index values were compared in terms of ceiling and floor, informativity (Shannon’s Evenness index), agreement, convergent and known-groups validity for 41 chronic physical and mental health conditions. Danish value sets were used to compute index values for both instruments. As a sensitivity analysis, index values were also estimated using the Hungarian EQ-5D-5L and Norwegian 15D value sets. Results Overall, 270 (8.6%) and 1030 (3.4*10−6%) unique profiles occurred on the EQ-5D-5L and 15D. The EQ-5D-5L dimensions (0.51–0.70) demonstrated better informativity than those of 15D (0.44–0.69). EQ-5D-5L and 15D dimensions capturing similar areas of health showed moderate or strong correlations (0.558–0.690). The vision, hearing, eating, speech, excretion and mental function 15D dimensions demonstrated very weak or weak correlations with all EQ-5D-5L dimensions, which may indicate potential room for EQ-5D-5L bolt-ons. The 15D index values showed lower ceiling than the EQ-5D-5L (21% vs. 36%). The mean index values were 0.86 for the Danish EQ-5D-5L, 0.87 for the Hungarian EQ-5D-5L, 0.91 for the Danish 15D and 0.81 for the Norwegian 15D. Strong correlations were found between the index values (Danish EQ-5D-5L vs. Danish 15D 0.671, Hungarian EQ-5D-5L vs. Norwegian 15D 0.638). Both instruments were able to discriminate between all chronic condition groups with moderate or large effect sizes (Danish EQ-5D-5L 0.688–3.810, Hungarian EQ-5D-5L 1.233–4.360, Danish 15D 0.623–3.018 and Norwegian 15D 1.064–3.816). Compared to the 15D, effect sizes were larger for the EQ-5D-5L in 88–93% of chronic condition groups. Conclusions This is the first study to compare the measurement properties of the EQ-5D-5L and 15D in a general population sample. Despite having 10 fewer dimensions, the EQ-5D-5L performed better than the 15D in many aspects. Our findings help to understand the differences between generic preference-accompanied measures and support resource allocation decisions.

Background We previously demonstrated that retinal ischemic perivascular lesions (RIPLs), which are indicative of ischemia in the middle retina, may be a biomarker of ischemic cardiovascular disease. In this study, we sought to determine the relationship between RIPLs and atrial fibrillation, a common source of cardiac emboli. Methods and Results In this case‐control study, we identified individuals between the ages of 50 and 90 years who had undergone macular spectral domain optical coherence tomography imaging. Individuals with atrial fibrillation were identified, and age‐ and sex‐matched individuals from the same pool, but without a diagnosis of atrial fibrillation, were selected as controls. Spectral domain optical coherence tomography scans were reviewed by 3 independent and masked observers for presence of RIPLs. The relationship between RIPLs and atrial fibrillation was analyzed using multivariable logistic regression models. There were 106 and 91 subjects with and without atrial fibrillation, respectively. The percentage of subjects with RIPLs was higher in the atrial fibrillation group compared with the control group (57.5% versus 37.4%; P=0.005). After adjusting for age, sex, smoking history, hypertension, diabetes, coronary artery disease, carotid stenosis, stroke, and myocardial infarction, the presence of RIPLs was significantly associated with atrial fibrillation, with an odds ratio of 1.91 (95% CI, 1.01–3.59). Conclusions RIPLs are significantly associated with atrial fibrillation, independent of underlying ischemic heart disease or cardiovascular risk factors. This association may inform the diagnostic cardiovascular workup for individuals with RIPLs incidentally detected on optical coherence tomography scan of the macula.

Abstract Background The COVID-19 pandemic affected the mental health of the general population through multiple pathways. The aim of this study was to examine anxiety, depression, self-confidence, and social connectedness among the general population of eight countries during the COVID-19 pandemic, their underlying factors, and vulnerable groups. Methods A web-based survey was administered to persons from the general population of China, Greece, Italy, Netherlands, Russia, Sweden, the United Kingdom, and the United States. The survey included the Generalized Anxiety Disorder-7 (GAD-7), Patient Health Questionnaire-9 (PHQ-9) and items on self-confidence, social connectedness, and socio-demographics. Data were analyzed with descriptive statistics, exploratory factor analysis and regression analysis. Results Twenty-three thousand six hundred twenty-two respondents completed the survey. Overall, 42% of the total sample had mild to severe anxiety symptoms and 43% had mild to severe depression symptoms. 14% to 38% reported suboptimal ratings in self-confidence, social participation, contact with family and friends, and feeling connected to others. In the exploratory factor analyses, in most countries, one dominant factor had a high influence on GAD-7, PHQ-9 sum scores and self-confidence with eigenvalue (% variance) above 3.2 (53.9%). One less dominant factor had a high influence on social connectedness scores with eigenvalue (% variance) ranging above 0.8 (12.8%). Being younger, female, having chronic conditions, perceived as risky to COVID-19 infection, and feeling not very well protected against COVID-19 were significantly associated with the two underlying factors. Conclusions Anxiety, depression, and problems with self-confidence and social connectedness were highly prevalent in the general population of eight countries during the early phase of the COVID-19 pandemic. This highlights the importance of the allocation of additional resources to implement policies to mitigate the impact of the pandemic on mental health.

BackgroundStill little is known about the impact of post COVID-19 condition (PC) on health-related quality of life (HRQOL) and mental well-being. We compared participants with PC with three groups: an acute COVID-19 infection (AC) only, at least one chronic condition (CC) but no COVID-19, or no condition at all, healthy (PH). Between these disease groups, we also estimated and compared HRQOL and mental well-being change over time.MethodsParticipants from six countries (Greece, Italy, Netherlands, Sweden, United Kingdom and United States) completed two web-based questionnaires (T1 = April–May 2020 and T2 = April–June 2022). Primary outcomes were HRQOL, measured by EQ-5D-5L and EQ VAS, and mental well-being (measured by World Health Organisation-Five (WHO-5) Well-Being Index, Patient Health Questionnaire (PHQ)-9 and General Anxiety Disorder (GAD)-7). All analyses were stratified by the disease groups.ResultsIn total, 4,999 participants filled out both surveys: 240 were in PC, 107 in AC, 1798 in CC and 2,854 in PH. At T2, the mean EQ-5D-5L index values for the PC, AC, CC and PH groups were 0.70, 0.73, 0.75 and 0.92 (p

Hair fescue is a common perennial grass weed in wild blueberry fields in Nova Scotia, Canada and reduces yield if not adequately controlled. Hair fescue is typically managed with a broadcast propyzamide application which is costly for growers. Current research on the management of hair fescue in wild blueberry fields focuses on the development of a precision granular herbicide applicator with individual nozzle control. The integration of aerial images could benefit current work by providing a large-scale perspective on hair fescue location. This research suggests a new strategy to identify infield areas with hair fescue infestation, generate prescription maps, and integrate them into a widely available navigation system of heavy farming equipment to improve the processing workflow of hair fescue detection on a larger scale. This method proposes the integration of multi-resolution segmentation on multispectral (Blue, Green, Red, Red Edge, Near-Infrared) drone images to group hair fescue plants into segments with similar spectral characteristics. The best performing segmentation was classified and tested on wild blueberry fields in Nova Scotia. Results were assessed by comparing classified boundaries to reference data collected with high resolution RGB images. Findings from hair fescue and wild blueberry spectral profiles showed that hair fescue could be identified using blue, green, and red bands and showed no advantages over multispectral cameras. Results from the classification of wild blueberry and hair fescue showed high Kappa coefficient values of 0.90 and 0.94 and overall accuracy of 95 and 97% were achieved for both fields surveyed. Results also demonstrated an average potential cost saving of $CAD1246.43 ha-1 when compared to a broadcast application of granular dichlobenil. This work represents the first attempt to integrate aerial imagery and a precision granular herbicide applicator to manage important weeds in wild blueberry fields.

Transmembrane carriers of the Slc11 family catalyze proton (H+)-dependent uptake of divalent metal ions (Me2+) such as manganese and iron—vital elements coveted during infection. The Slc11 mechanism of high-affinity Me2+ cell import is selective and conserved between prokaryotic (MntH) and eukaryotic (Nramp) homologs, though processes coupling the use of the proton motive force to Me2+ uptake evolved repeatedly. Adding bacterial piracy of Nramp genes spread in distinct environmental niches suggests selective gain of function that may benefit opportunistic pathogens. To better understand Slc11 evolution, Alphafold (AF2)/Colabfold (CF) 3D predictions for bacterial sequences from sister clades of eukaryotic descent (MCb and MCg) were compared using both native and mutant templates. AF2/CF model an array of native MCb intermediates spanning the transition from outwardly open (OO) to inwardly open (IO) carriers. In silico mutagenesis targeting (i) a set of (evolutionarily coupled) sites that may define Slc11 function (putative synapomorphy) and (ii) residues from networked communities evolving during MCb transition indicates that Slc11 synapomorphy primarily instructs a Me2+-selective conformation switch which unlocks carrier inner gate and contributes to Me2+ binding site occlusion and outer gate locking. Inner gate opening apparently proceeds from interaction between transmembrane helix (h) h5, h8 and h1a. MCg1 xenologs revealed marked differences in carrier shape and plasticity, owing partly to an altered intramolecular H+ network. Yet, targeting Slc11 synapomorphy also converted MCg1 IO models to an OO state, apparently mobilizing the same residues to control gates. But MCg1 response to mutagenesis differed, with extensive divergence within this clade correlating with MCb-like modeling properties. Notably, MCg1 divergent epistasis marks the emergence of the genus Bordetella-Achromobacter. Slc11 synapomorphy localizes to the 3D areas that deviate least among MCb and MCg1 models (either IO or OO) implying that it constitutes a 3D network of residues articulating a Me2+-selective carrier conformation switch which is maintained in fast-evolving clades at the cost of divergent epistatic interactions impacting carrier shape and dynamics.

BackgroundGeneric health-related quality of life instruments, such as the EQ-5D, are increasingly used by countries to monitor population health via general population health surveys. Our aim was to demonstrate analytic options to measure socio-demographic differences in self-reported health using the EuroQol Group's archive of EQ-5D-3L population surveys that accumulated over the past two decades.MethodsAnalyses captured self-reported EQ-5D-3L data on over 100,000 individuals from 18 countries with nationally representative population surveys. Socio-demographic indicators employed were age, sex, educational level and income. Logistic regression odds ratios and the health concentration index methodology were used in the socio-demographic analysis of EQ-5D-3L data.ResultsStatistically significant socio-demographic differences existed in all countries (p < 0.01) with the EQ VAS based health concentration index varying from 0.090 to 0.157 across countries. Age had generally the largest contributing share, while educational level also had a consistent role in explaining lower levels of self-reported health. Further analysis in a subset of 7 countries with income data showed that, beyond educational level, income itself had an additional significant impact on self-reported health. Among the 5 dimensions of the EQ-5D-3L descriptive system, problems with usual activities and pain/discomfort had the largest contribution to the concentration of overall self-assessed health measured on the EQ VAS in most countries.ConclusionThe EQ-5D-3L was shown to be a powerful multi-dimensional instrument in the analyses of socio-demographic differences in self-reported health using various analytic methods. It offered a unique insight of inequalities by health dimensions.

Aberrant glycosylation actively contributes to tumor progression and is a key hallmark of cancer. Most of the glycan moieties expressed on the surface of cancer cells are sialic acids that may modulate antitumor immune responses via binding to sialic acid–binding immunoglobulin-like lectins (Siglecs) expressed by immune cells. Here we show that Siglecs may decrease the bladder tumor immune response mediated by natural killer (NK) cells. We observed higher NK cell activity against desialylated bladder tumor cell lines. We therefore determined the expression of nine Siglecs on circulatory NK cells from healthy donors and patients with bladder cancer (BCa). NK cells from blood mainly express Siglec-7, which is highly upregulated in non–muscle-invasive BCa (NMIBC), as well as Siglec-6, albeit at a much lower level. However, both Siglecs are expressed by urinary NK cells from NMIBC patients undergoing bacillus Calmette-Guérin therapy. Ex vivo analysis of Siglec-6 and Siglec-7 expression levels on tumor-infiltrating NK cells (TINKs) from BCa patients showed that only Siglec-7 is expressed by TINKs. Finally, analyses for The Cancer Genome Atlas data set revealed that BCa patients with high expression levels of Siglec-7 have a poor survival rate. This work indicates that Siglec-7 may restrain NK-mediated antitumor immunity in BCa. Patient summary: We investigated the expression of proteins called Siglecs in natural killer (NK) cells from patients with bladder cancer. We showed that levels of the protein Siglec-7 in blood, urine, and tumors from patients with bladder cancer are associated with poor clinical outcomes. Thus, Siglec-7 may be involved in the regulation of antitumor immunity mediated by NK cells in bladder cancer.

It was predicted that in the regime of strong electron-phonon interactions, electrons and phonons can form a coupled non-equilibrium state, characterized by the conservation of the total momentum and by hydrodynamic transport. Here, the authors report experimental evidence for such a coupled electron-phonon liquid in NbGe2.

The molecular underpinnings driving uveal melanoma (UM) progression are unknown. Here the authors show that loss of Polycomb Repressive Complex 1 triggers chromosomal instability, which promotes inflammatory signaling and migration in UM.

Abstract Uveal melanoma, the most common intraocular primary cancer in adults, is characterized by striking variability in metastatic tendencies. BAP1 deletion in the primary tumor is associated with uveal melanoma metastasis, but it cannot always be resolved by bulk DNA sequencing of heterogeneous tumors. Here, we show that assessment of BAP1 methylation is an accurate and readily clinically actionable assay to accurately identify high-risk uveal melanoma patients.

Background Bladder cancer is an important public health concern due to its prevalence, high risk of recurrence and associated cost of management. Although BCG instillation for urothelial cancer treatment is the gold-standard treatment for this indication, repeated BCG treatments are associated with significant toxicity and failure, underlining the necessity for alternative or complementary immunotherapy and overall for better understanding of T-cell responses generated within bladder mucosa. Tumor-infiltrating lymphocytes (TIL) have long been recognized as a crucial component of the tumor microenvironment for the control of tumor. Among TIL, unconventional γδ T cells sparked interest due to their potent antitumor functions. Although preclinical mouse xenograft models demonstrated the relevance of using γδ T cells as a novel therapy for bladder cancer (BCa), the contribution of γδ T cells in BCa patients’ pathology remains unaddressed.Methods Therefore, we first determined the proportion of intratumor γδ T cells in muscle-invasive patients with BCa by deconvoluting data from The Cancer Genome Atlas (TCGA) and the frequency of blood Vδ1, Vδ2, and total γδ T cells, by flow cytometry, from 80 patients with BCa (40 non-muscle and 40 muscle-invasive patients with BCa), as well as from 20 age-matched non-tumor patients. Then we investigated in vitro which treatment may promote BCa tumor cell recognition by γδ T cells.Results We observed a decrease of γδ T-cell abundance in the tumor compared with corresponding normal adjacent tissue, suggesting that the tumor microenvironment may alter γδ T cells. Yet, high intratumor γδ T-cell proportions were significantly associated with better patient survival outcomes, potentially due to Vδ2 T cells. In the blood of patients with BCa, we observed a lower frequency of total γδ, Vδ1, and Vδ2 T cells compared with non-tumor patients, similarly to the TCGA analysis. In addition, a favorable clinical outcome is associated with a high frequency of circulating γδ T cells, which might be mainly attributed to the Vδ2 T-cell subset. Furthermore, in vitro assays revealed that either BCG, Zoledronate, or anti-BTN3 agonistic antibody treatment of bladder tumor cells induced Vδ2 T-cell cytolytic (CD107a+) and cytokine-production (IFN-γ and TNF-α). Strikingly, combining BCG and Zoledronate treatments significantly elicited the most quantitative and qualitative response by increasing the frequency and the polyfunctionality of bladder tumor-reactive Vδ2 T cells.Conclusions Overall, our results suggest that (1) Vδ2 T cells might play a prominent role in bladder tumor control and (2) non-muscle invasive patients with BCa undergoing BCG therapy may benefit from Zoledronate administration by boosting Vδ2 T cells’ antitumor activity.

Abstract Background The EQ-5D instrument is increasingly used in clinical and resource allocation decision making in developed and developing countries. EQ-5D valuation and population norms studies have been undertaken for Trinidad and Tobago, however no population norms or value sets have been generated for the other Caribbean countries. The aims of this study were to provide population norms for Barbados and Jamaica, and to develop a set of population norms that could be used by the other English-speaking Caribbean countries. Methods The EQ-5D-5L self-reported health questionnaire was included in surveys of representative samples of adults in Barbados and adults in Jamaica in 2013. EQ-5D health states, mean EQ VAS scores and mean EQ-5D-5L index values (using the Trinidad and Tobago value set) were calculated for demographic groups in both countries based on 2347 respondents from Barbados and 1423 from Jamaica. A set of ‘Caribbean’ norms were developed by combining the Barbados and Jamaica data with norms recently published for Trinidad and Tobago. Results Data were obtained for 2347 and 1423 respondents in Barbados and Jamaica respectively. The mean index and EQ VAS values were 0.943 and 81.9 for Barbados, and 0.948 and 87.8 for Jamaica. The health states most commonly observed in the two countries were similar. Generally the demographic patterns of self-reported health were consistent with those found in other studies. Some differences between the countries were observed in the patterns of rates of reporting problems on the EQ-5D dimensions among age-gender groups specifically for anxiety/depression and pain/discomfort Conclusion This study has produced a set of EQ-5D population norms that can be used as base-line values in clinical and clinico-economic analyses for Barbados and Jamaica and for the English-Speaking Caribbean region.

Abstract Background The Swedish National Quality Registries (NQRs) contain individual-level health care data for specific patient populations, or patients receiving specific interventions. Approximately 90% of the 105 Swedish NQRs include any patient-reported outcome measure, with EQ-5D being the most common. As there has been no general overview of EQ-5D data within the NQRs, this study fills a knowledge gap by reporting how the data are collected, presented, and used at different levels of the Swedish health care system. Methods All 46 NQRs with a license for the use of EQ-5D were included. Information was retrieved from the registries’ annual reports or from websites, using a template that was subsequently sent to each registry for completion and confirmation. If considered necessary, the contact was followed-up with an interview, either in-person or over the telephone. The uses of EQ-5D were categorised as denoting usage for follow-up, decision-making, or quality improvement in Swedish health care. Results In total, 41 of the 46 licensed registries reported collection of EQ-5D data. EQ-5D is most commonly collected within registries related to the musculoskeletal system, but it has a wide application also in other disease areas. Thirty-six registries provide EQ-5D results to patients, clinicians, or other decision-makers. Twenty-two of the registries reported that EQ-5D data are being used for follow-up, decision-making or quality improvement. The registries most commonly reported use of data for assessing interventions, and in quality indicators to follow-up the quality of care at a national level. Conclusion Collection and use of EQ-5D data vary across the Swedish NQRs, which may partly be accounted for by the different purposes of the registries. The provided examples of use illustrate how EQ-5D data can inform decisions at different levels of the health care system. However, there is potential for improving the use of EQ-5D data.

IntroductionThe effects of the COVID-19 pandemic caused considerable psychological and physical effects in healthy and diseased New Yorkers aside from the effects in those who were infected. We investigated the relationship between known risk-enhancing and health-promoting factors (social and medical), comorbidity indicators, and, as the primary outcome, health-related quality of life (HRQoL).MethodsBetween April 22 and May 5, 2020, a market research agency (Dynata) administered a digital survey including the EQ-5D-5L and items related to individual characteristics, social position, occupational and insurance status, living situation, exposures (smoking and COVID-19), detailed chronic conditions, and experienced access to care to an existing internet panel representative of New Yorkers.Results2684 persons completed the questionnaire. The median age was 48 years old, and most respondents were non-Hispanic white (74%) and reported at least higher vocational training or a university education (83%). During COVID-19, mean HRQoL scores were 0.82 for the EQ-5D-5L index and 79.3 for the EQ VAS. Scores varied for healthy and diseased respondents differently by the above determinants. Lower age, impaired occupational status, loss of health insurance, and limited access to care exerted more influence on EQ-5D-5L scores of diseased persons compared to healthy persons. Among diseased persons, the number of chronic conditions and limited access to health care had the strongest association with EQ-5D-5L scores. While EQ-5D-5L scores improved with increasing age, gender had no noticeable effect. Deprivation factors showed moderate effects, which largely disappeared in (stratified) multivariable analysis, suggesting mediation through excess chronic morbidity and poor healthcare access. Generally, modifying effects were larger in the EQ-5D-5L as compared to the EQ VAS.ConclusionsAlmost all factors relating to a disadvantaged position showed a negative association with HRQoL. In diseased respondents, pre-existing chronic comorbidity and experienced access to health care are key factors.

Objectives: Our study aimed to (1) assess health-related quality of life (HRQoL) and mental well-being of healthy and diseased persons in the general population during the early stage of the COVID-19 pandemic and (2) examine the relationship between HRQoL and mental well-being and individual characteristics and government response against COVID-19, as measured by the stringency index. Methods: A web-based survey was administered to a cohort of persons from the general population of eight countries: Greece, Italy, the Netherlands, Russia, South Africa, Sweden, the United Kingdom (UK) and the United States of America (US) from April 22 to May 5 and May 26 to June 1, 2020. Country-level stringency indices were adopted from the COVID-19 Government Response Tracker. Primary outcomes were HRQoL, measured using the EQ-5D-5L, and mental well-being, measured using the World Health Organization-5 Well-Being (WHO-5). Findings: 21,354 respondents were included in the study. Diseased respondents had lower EQ-5D-5L and WHO-5 scores compared to healthy respondents. Younger respondents had lower WHO-5 scores than older respondents. The stringency index had a stronger association with the EQ-5D-5L and WHO-5 among diseased respondents compared to healthy respondents. Increasing stringency was associated with an increase in EQ-5D-5L scores but a decrease in the WHO-5 index. Conclusion: The stringency of government response is inversely related to HRQoL and mental well-being with a small positive relation with HRQoL and strong negative relation with mental well-being. The magnitude of effects differed for healthy and diseased persons and by age but was most favourable for diseased and older persons.

This study aimed to investigate socioeconomic and health-related determinants and recent life events and their relation to changes in health-related quality of life (HRQoL) and mental well-being during the first year of the COVID-19 pandemic. A web-based survey was administered repeatedly to participants from Greece, Italy, the Netherlands, the United Kingdom, and the United States. Primary outcome measures were HRQoL (measured by EQ-5D-5L) and mental well-being (measured by WHO-5). Linear regression analyses were performed to estimate the impact of determinants on HRQoL and well-being. In total, 6765 respondents completed the questionnaire at T1 (April–May 2020) and T2 (May–June 2021). Regarding results, 33% showed improved HRQoL at T2, whereas 31% deteriorated. In terms of mental well-being, 44% improved and 41% deteriorated. The greatest deterioration in HRQoL and mental well-being from T1 to T2 was observed with an increasing number of chronic conditions. The effect of negative life events on HRQoL and mental well-being was larger than the effect of positive life events. We conclude that slightly more respondents showed improved rather than deteriorated HRQoL and mental well-being, with some variation by outcome measure and country.

Introduction Myasthenia gravis (MG) is a rare, chronic, autoimmune disease, mediated by immunoglobulin G antibodies, which causes debilitating muscle weakness. As with most rare diseases, there is little patient-reported data with which to understand and address patient needs. This study explores the impact of MG in the real world from the patient perspective.Methods and analysis This is a 2-year prospective, observational, digital, longitudinal study of adults with MG, resident in the following countries: the USA, Japan, Germany, France, the UK, Italy, Spain, Canada and Belgium. The planned sample size is 2000. Recruitment will be community based, via patient advocacy groups, social media and word of mouth. Participants will use a smartphone application (app) to check eligibility, provide consent and contribute data. Planned data entry is as follows: (1) personal profile on enrollment—covering demographics, MG characteristics and previous care; (2) monthly event tracker—current treatments, healthcare visits, treatment-related adverse events, productivity losses; (3) monthly selection of validated generic and disease-specific patient-reported outcomes instruments: EQ-5D-5L, Myasthenia Gravis Activities of Daily Living, Myasthenia Gravis Quality of Life 15-item revised scale, Hospital Anxiety and Depression Scale and Health Utilities Index III. Analyses are planned for when the study has been running in most countries for approximately 6, 12, 18 and 24 months.Ethics and dissemination The study protocol has been reviewed and granted ethics approval by Salus IRB for participants resident in the following countries: Germany, the UK and the US. Local ethics approval is being sought for the following study countries: Belgium, Canada, France, Italy, Japan and Spain. Study results will be communicated to the public and participants via conference presentations and journal publications, as well as regular email, social media and in-application communication.Trial registration number NCT04176211.

Land use and land cover (LULC) classification maps help understand the state and trends of agricultural production and provide insights for applications in environmental monitoring. One of the major downfalls of the LULC technique is inherently linked to its need for ground truth data to cross-validate maps. This paper aimed at evaluating the efficiency of machine learning (ML) in limiting the use of ground truth data for LULC maps. This was accomplished by (1) extracting reliable LULC information from Sentinel-2 and Landsat-8 s images, (2) generating remote sensing indices used to train ML algorithms, and (3) comparing the results with ground truth data. The remote sensing indices that were tested include the difference vegetation index (DVI), the normalized difference vegetation index (NDVI), the normalized built-up index (NDBI), the urban index (UI), and the normalized bare land index (NBLI). Extracted vegetation indices were evaluated on three ML algorithms, namely, random forest (RF), k-nearest neighbour (K-NN), and k dimensional-tree (KD-Tree). The accuracy of these algorithms was assessed with standard statistical measures and ground truth data randomly collected in Prince Edward Island, Canada. Results showed that high kappa coefficient values were achieved by K-NN (82% and 74%), KD-Tree (80% and 78%), and RF (83% and 73%) for Sentinel-2A and Landsat-8 imagery, respectively. RF was a better classifier than K-NN and KD-Tree and had the highest overall accuracy with Sentinel-2A satellite images (92%). This approach provides the basis for limiting the collection of ground truth data and thus reduces the labour cost, time, and resources needed to collect ground truth data for LULC maps.

Background: Cardiovascular disease is the leading cause of mortality and disability worldwide. A noninvasive test that can detect underlying cardiovascular disease has the potential to identify patients at risk prior to the occurrence of adverse cardiovascular events. We sought to determine whether an easily observed imaging finding indicative of retinal ischemia, which we term ‘retinal ischemic perivascular lesions’ (RIPLs), could serve as a biomarker for cardiovascular disease. Methods: We reviewed optical coherence tomography (OCT) scans of individuals, with no underlying retinal pathology, obtained at UC San Diego Health from July 2014 to July 2019. We identified 84 patients with documented cardiovascular disease and 76 healthy controls. OCT scans were assessed for evidence of RIPLs. In addition, the 10-year atherosclerotic cardiovascular disease (ASCVD) risk calculator was used to risk-stratify the subjects into four different categories. Findings: Patients with documented cardiovascular disease had higher number of RIPLs compared to healthy controls (2.8 vs 0.8, p 37). The number of RIPLs in individuals with intermediate and high 10-year ASCVD risk scores was higher than in those with low ASCVD risk scores (1.7 vs 0.64, p = 0.02 and 2.9 vs 0.64, p 0.002, respectively). Interpretation: The presence of RIPLs, which are anatomical markers of prior retinal ischemic infarcts, is suggestive of coexisting cardiovascular disease. RIPLs detection, obtained from routine retinal scans, may thus provide an additional biomarker to identify patients at risk of developing adverse cardiovascular events. Funding: None.

Abstract Background It is not clear whether socioeconomic status influences health outcomes among older adults through its effect on physical activity. The aim of this study was to assess the effect of sex and neighborhood socio-economic status on the change in health related quality of life (HR-QOL) as a function of physical activity over a three-year period. Methods This cohort study included French-speaking community-dwelling older adults recruited in primary care practices in the province of Quebec and participating in the ‘Étude sur la Santé des Ainés’ (ESA)-Services study on the health of the elderly. Primary care practices were recruited through participating general practitioners (GPs) working full-time in the health administrative region. A stratified sample was comprised of various types of primary care practices (family medicine group, local community health services centers, primary care practices with less than 3 GPs, and with at least 3 GPs). In this study sample, 967 participants with scores ≥26 on the Mini Mental State Examination (MMSE) were included and followed for 3 years to study HR-QOL as a function of reported exercise at baseline and follow-up, controlling for study variables. Analyses were also carried out to study the effect of change in reported exercise at follow-up with respect to baseline and categorised as follows: no change, decrease in exercise and increase in exercise. The interaction terms area of residence socio-economic status*exercise and sex*exercise, were tested. Results Exercise at baseline did not significantly predict HR-QOL at follow-up when adjusting for all other study variables. Exercise at follow-up was cross-sectionally associated with follow-up HR-QOL. Participants reporting never exercising and those reporting a decrease in exercise reported a lower HR-QOL at follow-up, when controlling for all other study variables. There was no interaction between exercise and sex and socioeconomic status. Conclusions For healthy ageing, maintaining and increasing physical activity throughout the years is necessary for improved HR-QOL. Past physical activity does not confer protection against future decline of HR-QOL. Future research should focus on potential moderating and mediating psycho-social barriers associated with exercising in older age populations.

Abstract Background Insecticide resistance in malaria vectors is an increasing threat to vector control tools currently deployed in endemic countries. Resistance management must be an integral part of National Malaria Control Programmes’ (NMCPs) next strategic plans to alleviate the risk of control failure. This obviously will require a clear database on insecticide resistance to support the development of such a plan. The present work gathers original data on insecticide resistance between 2009 and 2015 across Côte d’Ivoire in West Africa. Methods Two approaches were adopted to build or update the resistance data in the country. Resistance monitoring was conducted between 2013 and 2015 in 35 sentinel sites across the country using the WHO standard procedure of susceptibility test on adult mosquitoes. Four insecticide families (pyrethroids, organochlorides, carbamates and organophosphates) were tested. In addition to this survey, we also reviewed the literature to assemble existing data on resistance between 2009 and 2015. Results High resistance levels to pyrethroids, organochlorides and carbamates were widespread in all study sites whereas some Anopheles populations remained susceptible to organophosphates. Three resistance mechanisms were identified, involving high allelic frequencies of kdr L1014F mutation (range = 0.46–1), relatively low frequencies of ace-1 R (below 0.5) and elevated activity of insecticide detoxifying enzymes, mainly mixed function oxidases (MFO), esterase and glutathione S-transferase (GST) in almost all study sites. Conclusion This detailed map of resistance highlights the urgent need to develop new vector control tools to complement current long-lasting insecticidal nets (LLINs) although it is yet unclear whether these resistance mechanisms will impact malaria transmission control. Researchers, industry, WHO and stakeholders must urgently join forces to develop alternative tools. By then, NMCPs must strive to develop effective tactics or plans to manage resistance keeping in mind country-specific context and feasibility.

Dykelands are agricultural ground protected from coastal inundation by dyke infra-structure and constitute some of the most agriculturally productive lands in Nova Scotia. Between 2015 and 2019, Canada’s Annual Crop Inventory was used to characterize and estimate hectares of agricultural dykelands cultivated in Nova Scotia. The number of hectares of wheat, barley, corn, forages and soybeans were compiled for each year and compared to the previous year. This was accomplished using GIS software, satellite images, and geodata from the Nova Scotia’s Land Property Database. Results revealed that from 2015 to 2019, an average of 56% of the dykelands’ total surface was dedicated to the production of field crops (wheat, barley, corn, soybeans) and forage. Results also highlighted the importance of forage production on the dykelands. Forage was the largest commodity grown, representing around 80% of the total crop land area of the agricultural dykelands. Corn and soybeans were the second and third crops of abundance, constituting 12 and 4% of the total crop land area, respectively. This study represents the first attempt to document the number of hectares of the principal crops grown on Nova Scotia’s dykelands using crop inventory and property boundaries. Given the predictions of rising sea levels and the overtopping risks that the dykelands face, this study will facilitate more suitable land-use policies by providing stakeholders with an accurate quantitative assessment of the utilization of agricultural dykelands.

Group 2 innate lymphoid cells (ILC2s) modulate inflammatory and allergic responses, but their function in cancer immunity is still unclear. Here the authors show that, in acute promyelocytic leukaemia, tumour-activated ILC2s secrete IL-13 to induce myeloid-derived suppressor cells and support tumour growth.

Analysis of single-channel activity provides unparalleled insight into ion channel structure, function, and mechanism. An essential step in the analysis pipeline is the assignment and sorting of bursts of activity that can be attributed to a single ion channel. Here we present scbursts, an R package for the analysis and sorting of single-channel bursts. Using scbursts, idealized data from a variety of single-channel analysis software packages can be read directly into R, and parsed into bursts according to a user-defined critical closed duration. Bursts can be analyzed and sorted based on a variety of parameters, including burst open probability, and the number of openings per burst. Sorted bursts can then be exported in a standard format for downstream kinetic fitting. We provide examples illustrating the implementation and utility of scbursts, as well as how scbursts brings the statistical prowess and versatility of R to single-channel analysis. Keywords: Single-molecule analysis, single-channel analysis, bursts, ion channel, kinetic fitting

The immune system plays a central role in cancer development, showing both anti-tumor and pro-tumor activities depending on the immune cell subsets and the disease context. While CD8 T cells are associated with a favorable outcome in most cancers, only T helper type 1 (Th1) CD4 T cells play a protective role, in contrast to Th2 CD4 T cells. Double positive (DP) CD4+CD8+ T cells remain understudied, although they were already described in human cancers, with conflicting data regarding their role. Here, we quantified and phenotypically/functionally characterized DP T cells in blood from urological cancer patients. We analyzed blood leukocytes of 24 healthy donors (HD) and 114 patients with urological cancers, including bladder (n = 54), prostate (n = 31), and kidney (n = 29) cancer patients using 10-color flow cytometry. As compared to HD, levels of circulating DP T cells were elevated in all urological cancer patients, which could be attributed to increased frequencies of both CD4highCD8low and CD4+CD8high DP T-cell subsets. Of note, most CD4highCD8low DP T cells show a CD8αα phenotype, whereas CD4+CD8high cells express both CD8α and CD8β subunits. Functional properties were investigated using ex-vivo generated DP T-cell clones. DP T cells from patients were skewed toward an effector memory phenotype, along with enhanced Th2 cytokine production. Interestingly, both CD8αα and CD8αβ DP T cells were able to trigger Th2 polarization of naïve CD4 T cells, while restraining Th1 induction. Thus, these data highlight a previously unrecognized immunoregulatory mechanism involving DP CD4+CD8+ T cells in urological cancers.

The EQ-5D instrument is now used in many health systems as a health outcomes measure. Recently an EQ-5D valuation study was conducted for Trinidad and Tobago, but thus far there have been no population norms published for Trinidad and Tobago or for any Caribbean country. The objective of this study is to provide a set of population norms, and to investigate inequalities in health in Trinidad and Tobago. The EQ-5D-5L questionnaire was included in the 2012/2013 Adult Population Survey of the Global Entrepreneurship Monitor for Trinidad and Tobago. This survey covered a representative sample of 2,036 adults aged 18 and over. Demographic data and self-reported health using EQ-5D-5L were collected. The Trinidad and Tobago value set was used to obtain EQ-5D index values. The Kakwani index and logistic regression models were used to evaluate inequalities in health. Mean EQ-5D index values and EQ-VAS values were calculated by age group, ethnicity, gender, income, educational attainment, employment status and place of residence. The 10 most commonly observed EQ-5D-5L states accounted for 90% of the respondents. The mean VAS value for the sample was 83.6 and the mean EQ-5D-5L index value was 0.95. Pain/discomfort was found to be the EQ-5D dimension with the highest prevalence of reported problems with 22% of the population reporting pain at any level. Self-care was the dimension with the lowest prevalence of problems reported at any level (3%). Health declines with increasing age, and men reported fewer problems and higher levels of self-reported health than women. Age, gender and education level were found to be important drivers of health status as measured by the EQ-5D instrument. Being in a very low income group was also observed to affect EQ-VAS values among younger respondents. The population norms provided in this study can be used by clinicians, academics and policy makers in several ways. They can be used in comparing different demographic groups or patient groups, or as a basis for tracking the progress of patients through a treatment regimen. They can also provide a baseline for cost utility analysis of health interventions for Trinidad and Tobago.

Determination of the crystal structure of ScaDMT, a member of the Slc11 family, provided opportunity to advance understanding of proton-dependent metal-ion uptake by interfacing Slc11 molecular evolution and structural biology. Slc11 carriers belong to the ancient and broadly distributed APC superfamily characterized by the pseudo-symmetric LeuT-fold. This fold comprises two topologically inverted repeats (protomers) that exchange alternate configurations during carrier cycling. Examining ScaDMT molecule inserted within a model membrane allowed to pinpoint residues that may interact with surrounding lipid solvent molecules. Three-dimensional mapping of Slc11-specific sites demonstrated they distribute at the protomer interface, along the transmembrane ion-conduction pathway. Functional sites were predicted by modeling hypothetical ScaDMT alternate conformers based on APC templates; these candidate homologous sites were found to co-localize with Slc11-specific sites, a distribution pattern that fits the functional diversity in the APC superfamily. Sites that diverged among eukaryotic Slc11 (Nramp) types were located in transmembrane helices that may participate in discrete steps during co-substrate translocation, suggesting these sites influence transport activity. Adding some functional dimension to Slc11 carrier evolution will inform molecular understanding of metal-ion transport selectivity and regulation, Slc11 physiological roles and contribution to host resistance to microbial infection.

The Cancer Genome Atlas (TCGA) uveal melanoma project was a comprehensive multi-platform deep molecular investigation of 80 uveal melanoma primary tissue samples supported by the National Cancer Institute. In addition to identification of important mutations for the first time, it identified four different clusters (subgroups) of patients paralleling prognosis. The findings of the TCGA marker paper are summarized in this review manuscript and other investigations that have stemmed from the findings of the TCGA project are reviewed.

Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers1-4, but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei5,6 and subsequent rupture of the micronuclear envelope7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer.

The Natural resistance-associated macrophage protein 1 (Nramp1 or Solute carrier 11 member 1, Slc11a1) transports divalent metals across the membrane of late endosomes and lysosomes in professional phagocytes. Nramp1 represents an ancient eukaryotic cell-autonomous defense whereas the gene duplication that yielded Nramp1 and Nramp2 predated the origin of Sarcopterygians (lobe-finned fishes and tetrapods). SLC11A1 genetic polymorphisms associated with human resistance to tuberculosis consist of potential regulatory variants. Herein, current knowledge of the regulation of SLC11A1 gene expression is reviewed and comprehensive analysis of ENCODE data available for hematopoietic cell-types suggests a hypothesis for the regulation of SLC11A1 expression during myeloid development and phagocyte functional polarization. SLC11A1 is part of a 34.6 kb CTCF-insulated locus scattered with predicted regulatory elements: a 3' enhancer, a large 5' enhancer domain and four elements spread around the transcription start site (TSS), including several C/EBP and PU.1 sites. SLC11A1 locus ends appear mobilized by ETS-related factors early during myelopoiesis; activation of both 5' and 3' enhancers in myelo-monocytic cells correlate with transcription factor binding at the TSS. Characterizing the corresponding cis/trans determinants functionally will establish the mechanisms involved and possibly reveal genetic variation that impacts susceptibility to infectious or immune diseases.

Early events during primary HIV infection (PHI) are thought to influence disease outcome. Although a growing body of evidence suggests a beneficial role of HIV-specific CD4 help in HIV infection, it is unclear how early viral replication, systemic immune activation and antiretroviral therapy (ART) may shape CD4 T-cell responses during PHI, and whether HIV-specific CD4 responses contribute to the high immune activation observed in PHI. Twenty-seven patients with early PHI were included in a prospective longitudinal study and twelve of them received ART after enrollment. Fresh PBMC were used for measurement of ex-vivo T-cell activation and of cytokine-producing CD4 T-cells following stimulation with PMA/ionomycin or HIV-1-gag-p24 antigen. Patients were segregated based on CD8 T-cell activation level (i.e. %HLA-DR+CD38+ CD8 T-cells) at baseline. Patients with lower immune activation exhibited higher frequency of bulk CD4 T-cells producing IFN-γ or IL-17, and higher effector-to-regulatory cell ratios. No differences were found in HIV-specific CD4 T-cell frequencies. In contrast, segregation of patients based on plasma-viral load (pVL) revealed that patients with higher pVL showed higher cytokine-producing HIV-specific CD4 responses. Of note, the frequency of IFN-γ+ HIV-specific CD4 T cells significantly diminished between baseline and month-6 only in ART-treated patients. However, early treatment initiation was associated with better maintenance of HIV-specific IFN-γ+ CD4 T-cells. These data suggest that HIV-specific CD4 responses do not fuel systemic T-cell activation, and are driven by viral replication but not able to contribute to its control in the early phase of infection. Moreover, our data also suggest a benefit of early treatment for the maintenance of HIV-specific CD4 T-cell help.