Augmenting astrophysical scaling relations with machine learning: Application to reducing the Sunyaev-Zeldovich flux-mass scatter.

Complex astrophysical systems often exhibit low-scatter relations between observable properties (e.g., luminosity, velocity dispersion, oscillation period). These scaling relations illuminate the underlying physics, and can provide observational tools for estimating masses and distances. Machine learning can provide a fast and systematic way to search for new scaling relations (or for simple extensions to existing relations) in abstract high-dimensional parameter spaces. We use a machine learning tool called symbolic regression (SR), which models patterns in a dataset in the form of analytic equations. We focus on the Sunyaev-Zeldovich flux-cluster mass relation (YSZ - M), the scatter in which affects inference of cosmological parameters from cluster abundance data. Using SR on the data from the IllustrisTNG hydrodynamical simulation, we find a new proxy for cluster mass which combines YSZ and concentration of ionized gas (cgas): M ∝ Yconc3/5 ≡ YSZ3/5(1 - A cgas). Yconc reduces the scatter in the predicted M by ∼20 - 30% for large clusters (M ≳ 1014 h-1 M⊙), as compared to using just YSZ. We show that the dependence on cgas is linked to cores of clusters exhibiting larger scatter than their outskirts. Finally, we test Yconc on clusters from CAMELS simulations and show that Yconc is robust against variations in cosmology, subgrid physics, and cosmic variance. Our results and methodology can be useful for accurate multiwavelength cluster mass estimation from upcoming CMB and X-ray surveys like ACT, SO, eROSITA and CMB-S4.

Transcriptome and TCR Repertoire Measurements of CXCR3+ T Follicular Helper Cells Within HIV-Infected Human Lymph Nodes.

Follicular-helper T cells (TFH) are an essential arm of the adaptive immune system. Although TFH were first discovered through their ability to contribute to antibody affinity maturation through co-stimulatory interactions with B cells, new light has been shed on their ability to remain a complex and functionally plastic cell type. Due to a lack sample availability, however, many studies have been limited to characterizing TFH in mice or non-canonical tissue types, such as peripheral blood. Such constraints have resulted in a limited, and sometimes contradictory, understanding of this fundamental cell type. One subset of TFH receiving attention in chronic infection are CXCR3-expressing TFH cells (CXCR3+TFH) due to their abnormal accumulation in secondary lymphoid tissues. Their function and clonal relationship with other TFH subsets in lymphoid tissues during infection, however, remains largely unclear. We thus systematically investigated this and other subsets of TFH within untreated HIV-infected human lymph nodes using Mass CyTOF and a combination of RNA and TCR repertoire sequencing. We show an inflation of the CXCR3+TFH compartment during HIV infection that correlates with a lower HIV burden. Deeper analysis into this population revealed a functional shift of CXCR3+TFH away from germinal center TFH (GC-TFH), including the altered expression of several important transcription factors and cytokines. CXCR3+TFH also upregulated cell migration transcriptional programs and were clonally related to peripheral TFH populations. In combination, these data suggest that CXCR3+TFH have a greater tendency to enter circulation than their CXCR3- counterparts, potentially functioning through distinct modalities that may lead to enhanced defense.

Mapping the Lineage Relationship between CXCR5+ and CXCR5- CD4+ T Cells in HIV-Infected Human Lymph Nodes.

CXCR5 is a key marker of follicular helper T (TFH) cells. Using primary lymph nodes (LNs) from HIV-infected patients, we identified a population of CXCR5- CD4+ T cells with TFH-cell-like features. This CXCR5- subset becomes expanded in severe HIV infection and is characterized by the upregulation of activation markers and high PD-1 and ICOS surface expression. Integrated analyses on the phenotypic heterogeneity, functional capacity, T cell receptor (TCR) repertoire, transcriptional profile, and epigenetic state of CXCR5-PD-1+ICOS+ T cells revealed a shared clonal relationship with TFH cells. CXCR5-PD-1+ICOS+ T cells retained a poised state for CXCR5 expression and exhibited a migratory transcriptional program. TCR sequence overlap revealed a contribution of LN-derived CXCR5-PD-1+ICOS+ T cells to circulating CXCR5- CD4+ T cells with B cell help function. These data link LN pathology to circulating T cells and expand the current understanding on the diversity of T cells that regulate B cell responses during chronic inflammation.

Genetic diversity and differentiation among Prosopis alba (Leguminosae) populations from dry valleys of Bolivia with different levels of human disturbance and altitude.

The fast expansion of human population around La Paz, Bolivia (3,200-4,100 m.a.s.l.) triggered new suburban settlements in nearby areas in valleys and mountain feet. The white mesquite, Prosopis alba Griseb. (Leguminosae), is a resource (originally used by native communities) that is strongly affected by changes in land use. A gradient in the level of disturbance is found moving away from the La Paz city toward less altitude areas. The main objective of this study was to characterize genetically three P. alba populations with different levels of human disturbance located at different altitudes in Bolivia, in order to provide some guidelines for management and conservation of these species. Based on 10 SSR loci, the populations showed high level of genetic diversity in comparison with other forest species. The population less disturbed and situated at the lowest altitude was the most variable (H e  = 0.51-0.42), whereas the less variable was the most disturbed and situated at the highest altitude. Heterozygote excess was observed in all populations. Most of genetic diversity (99%) is contained within populations. Genetic differentiation among populations is low (1%), suggesting low gene flow among populations. No evidence of recent bottlenecks events was detected. The estimates of the effective population size were low in all populations. The results are in agreement with the hypothesis that genetic diversity is reduced by the impact of anthropic disturbance in the population located at higher altitude in comparison with the lightly disturbed situated at lower altitude and farther from urban settlements.

Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue.

Current paradigms of CD8+ T cell-mediated protection in HIV infection center almost exclusively on studies of peripheral blood, which is thought to provide a window into immune activity at the predominant sites of viral replication in lymphoid tissues (LTs). Through extensive comparison of blood, thoracic duct lymph (TDL), and LTs in different species, we show that many LT memory CD8+ T cells bear phenotypic, transcriptional, and epigenetic signatures of resident memory T cells (TRMs). Unlike their circulating counterparts in blood or TDL, most of the total and follicular HIV-specific CD8+ T cells in LTs also resemble TRMs Moreover, high frequencies of HIV-specific CD8+ TRMs with skewed clonotypic profiles relative to matched blood samples are present in LTs of individuals who spontaneously control HIV replication in the absence of antiretroviral therapy (elite controllers). Single-cell RNA sequencing analysis confirmed that HIV-specific TRMs are enriched for effector-related immune genes and signatures compared with HIV-specific non-TRMs in elite controllers. Together, these data indicate that previous studies in blood have largely failed to capture the major component of HIV-specific CD8+ T cell responses resident within LTs.

The receptor repertoire and functional profile of follicular T cells in HIV-infected lymph nodes.

Follicular helper CD4+ T cells (TFH) play an integral role in promoting B cell differentiation and affinity maturation. Whereas TFH cell frequencies are increased in lymph nodes (LNs) from individuals infected with HIV, humoral immunity remains impaired during chronic HIV infection. Whether HIV inhibits TFH responses in LNs remains unclear. Advances in this area have been limited by the difficulty of accessing human lymphoid tissues. Here, we combined high-dimensional mass cytometry with T cell receptor repertoire sequencing to interrogate the composition of TFH cells in primary human LNs. We found evidence for intact antigen-driven clonal expansion of TFH cells and selective utilization of specific complementarity-determining region 3 (CDR3) motifs during chronic HIV infection, but the resulting TFH cells acquired an activation-related TFH cell signature characterized by interleukin-21 (IL-21) dominance. These IL-21+ TFH cells contained an oligoclonal HIV-reactive population that preferentially accumulated in patients with severe HIV infection and was associated with aberrant B cell distribution in the same LN. These data indicate that TFH cells remain capable of responding to HIV antigens during chronic HIV infection but become functionally skewed and oligoclonally restricted under persistent antigen stimulation.

Successive annual influenza vaccination induces a recurrent oligoclonotypic memory response in circulating T follicular helper cells.

T follicular helper (Tfh) CD4 cells are crucial providers of B cell help during adaptive immune responses. A circulating population of CD4 T cells, termed cTfh, have similarity to lymphoid Tfh, can provide B cell help, and responded to influenza vaccination. However, it is unclear whether human vaccination-induced cTfh respond in an antigen-specific manner and whether they form long-lasting memory. Here, we identified a cTfh population that expressed multiple T cell activation markers and could be readily identified by coexpression of ICOS and CD38. This subset expressed more Bcl-6, c-Maf, and IL-21 than other blood CD4 subsets. Influenza vaccination induced a strong response in the ICOS+CD38+ cTfh at day 7, and this population included hemagglutinin-specific cells by tetramer staining and antigen-stimulated Activation Induced Marker (AIM) expression. Moreover, TCRB sequencing identified a clonal response in ICOS+CD38+ cTfh that correlated strongly with the increased circulating ICOS+CD38+ cTfh frequency and the circulating plasmablast response. In subjects who received successive annual vaccinations, a recurrent oligoclonal response was identified in the ICOS+CD38+ cTfh subset at 7 days after every vaccination. These oligoclonal responses in ICOS+CD38+ cTfh after vaccination persisted in the ICOS-CD38- cTfh repertoire in subsequent years, suggesting clonal maintenance in a memory reservoir in the more-stable ICOS-CD38- cTfh subset. These data highlight the antigen-specificity, lineage relationships and memory properties of human cTfh responses to vaccination, providing new avenues for tracking and monitoring cTfh responses during infection and vaccination in humans.

Identification of non-coding genetic variants in samples from hypoxemic respiratory disease patients that affect the transcriptional response to hypoxia.

A wide range of diseases course with an unbalance between the consumption of oxygen by tissues and its supply. This situation triggers a transcriptional response, mediated by the hypoxia inducible factors (HIFs), that aims to restore oxygen homeostasis. Little is known about the inter-individual variation in this response and its role in the progression of disease. Herein, we sought to identify common genetic variants mapping to hypoxia response elements (HREs) and characterize their effect on transcription. To this end, we constructed a list of genome-wide HIF-binding regions from publicly available experimental datasets and studied the genetic variability in these regions by targeted re-sequencing of genomic samples from 96 chronic obstructive pulmonary disease and 144 obstructive sleep apnea patients. This study identified 14 frequent variants disrupting potential HREs. The analysis of the genomic regions containing these variants by means of reporter assays revealed that variants rs1009329, rs6593210 and rs150921338 impaired the transcriptional response to hypoxia. Finally, using genome editing we confirmed the functional role of rs6593210 in the transcriptional regulation of EGFR. In summary, we found that inter-individual variability in non-coding regions affect the response to hypoxia and could potentially impact on the progression of pulmonary diseases.

Antigen exposure shapes the ratio between antigen-specific Tregs and conventional T cells in human peripheral blood.

The T-cell receptor (TCR) is required for maturation and function of regulatory T cells (Tregs), but the ligand specificities of Tregs outside the context of transgenic TCRs are largely unknown. Using peptide-MHC tetramers, we isolated rare specific Foxp3+ cells directly ex vivo from adult peripheral blood and defined their frequency and phenotype. We find that a proportion of circulating Tregs recognize foreign antigens and the frequency of these cells are similar to that of self-reactive Tregs in the absence of cognate infection. In contrast, the frequencies of Tregs that recognize some common microbial antigens are significantly reduced in the blood of most adults. Exposure to peripheral antigens likely has a major influence on the balance between Tregs and conventional T-cell subsets because a larger proportion of flu-specific T cells has a regulatory cell phenotype in the cord blood. Consistent with this finding, we show that lymphocytic choriomeningitis virus infection can directly modulate the ratio of virus-specific effectors and Tregs in mice. The resulting change in the balance within an antigen-specific T-cell population further correlates with the magnitude of effector response and the chronicity of infection. Taken together, our data highlight the importance of antigen specificity in the functional dynamics of the T-cell repertoire. Each specific population of CD4+ T cells in human peripheral blood contains a subset of Tregs at birth, but the balance between regulatory and effector subsets changes in response to peripheral antigen exposure and this could impact the robustness of antipathogen immunity.

Riesgos para la salud y recomendaciones en el manejo de nanopartículas en entornos laborales / Health risks and recommendations on handling nanoparticles at workplaces

El incremento de la producción de nanomateriales en estos últimos años ha originado la aparición de patologías, frecuentemente pulmonares, asociadas a la exposición a nanopartículas (NPs), ya sean liberadas de forma natural o en procesos industriales. Estas pueden penetrar sobre todo por el sistema respiratorio y depositarse en los alvéolos, difundiéndose a través del sistema circulatorio hasta alcanzar diversos órganos, induciendo enfermedades. El principal mecanismo involucrado en la aparición de patología está relacionado con la producción de radicales libres e interferencia de las NPs con el metabolismo celular. Es necesario desarrollar mayor número de estudios orientados a determinar posibles efectos nocivos sobre la salud y herramientas que permitan establecer valores límites fiables, tanto para las exposiciones laborales como para la población general. Actualmente se utilizan modelos simplificados de evaluación cualitativa para evaluación de riegos, tanto inespecíficos para nanomateriales (ConsExpo) como específicos (herramientas de control banding). Las recomendaciones y medidas preventivas establecidas para la manipulación y gestión de residuos de sustancias químicas, humos y aerosoles, se presentan útiles en el manejo de nanopartículas

The increasing production of nanomaterials in recent years has led to the appearance of pathologies, often lung diseases, associated with the exposure to nanoparticles (NPs), released naturally or during industrial processes. These ones can penetrate the respiratory system and deposit in the alveoli. Thus they spread through the circulatory system and reach various organs, inducing diseases. The main mechanism involved in the pathology appearance is related to the production of free radicals and interference of NPs with cell metabolism. It is necessary to develop more studies aimed to determine possible adverse health effects as well as tools for establishing reliable limit’s values for both occupational and general population exposure. Currently, simplified models of qualitative risk evaluation are used, both non-specific for nanomaterials (ConsExpo) as well as specific (control banding tools). The recommendations and preventive measures established for handling and managing chemical waste, fumes, aerosols and sprays, appear to be helpful in handling nanoparticles

Los priones, un nuevo desafío evolutivo / Prions: a new evolutionary defiance

El objetivo de esta reseña es actualizar información ya publicada sobre los priones y las patologías que éstos transmiten. La existencia de una nueva variante de la enfermedad de Creutzfeld-Jakob y la confirmación experimental de que es causada por la misma cepa de priones que la encefalopatía espongiforme bovina (BSE), ha incrementado dramáticamente la necesidad de una precisa comprensión de las bases moleculares de la propagación priónica. El agente infeccioso es una proteína cuya conformación se encuentra alterada, que se reproduce a sí misma convirtiendo una proteína normal en una proteína con conformación priónica. La observación de que los priones se replican en los órganos linfoides en estadios muy tempranos de la infección lleva a cuestionar sobre cuáles son los requerimientos de tipo celular a ser infectado en el sistema linforreticular. Las células dendríticas foliculares serían el sitio de elección para la replicación y el reservorio de priores. El diagnóstico de las enfermedades producidas por priones presenta una serie de problemas debido a las peculiaridades de este tipo de patologías. Considerando que los priones se replican en el sistema linforreticular y posteriormente migran al sistema nervioso central, existe un lapso durante el cual podría propagarse este agente infeccioso por medio de la sangre, sus componentes o sus derivados. De esta forma representaría una nueva patología con la potencial capacidad de transmisión transfusional. Esta nueva forma de herencia independiente de los ácidos nucleicos obliga a replantear el axioma de transferencia de la información genética, hasta el momento, y con concordancia con la teoría evolutiva de Darwin, sólo pensando mediante moléculas constituidas por nucleótidos. ¿Será tiempo de cambiar el paradigma?

Los priones, un nuevo desafío evolutivo / Prions: a new evolutionary defiance

El objetivo de esta reseña es actualizar información ya publicada sobre los priones y las patologías que éstos transmiten. La existencia de una nueva variante de la enfermedad de Creutzfeld-Jakob y la confirmación experimental de que es causada por la misma cepa de priones que la encefalopatía espongiforme bovina (BSE), ha incrementado dramáticamente la necesidad de una precisa comprensión de las bases moleculares de la propagación priónica. El agente infeccioso es una proteína cuya conformación se encuentra alterada, que se reproduce a sí misma convirtiendo una proteína normal en una proteína con conformación priónica. La observación de que los priones se replican en los órganos linfoides en estadios muy tempranos de la infección lleva a cuestionar sobre cuáles son los requerimientos de tipo celular a ser infectado en el sistema linforreticular. Las células dendríticas foliculares serían el sitio de elección para la replicación y el reservorio de priores. El diagnóstico de las enfermedades producidas por priones presenta una serie de problemas debido a las peculiaridades de este tipo de patologías. Considerando que los priones se replican en el sistema linforreticular y posteriormente migran al sistema nervioso central, existe un lapso durante el cual podría propagarse este agente infeccioso por medio de la sangre, sus componentes o sus derivados. De esta forma representaría una nueva patología con la potencial capacidad de transmisión transfusional. Esta nueva forma de herencia independiente de los ácidos nucleicos obliga a replantear el axioma de transferencia de la información genética, hasta el momento, y con concordancia con la teoría evolutiva de Darwin, sólo pensando mediante moléculas constituidas por nucleótidos. ¿Será tiempo de cambiar el paradigma?