Thymic output and functionality of the IL-7/IL-7 receptor system in centenarians: implications for the neolymphogenesis at the limit of human life

During aging, the thymus undergoes a marked involution that is responsible for profound changes in the T-cell compartment. To investigate the capacity of the thymus to produce new cells at the limit of human lifespan, we analyzed some basic mechanisms responsible for the renewal and maintenance of peripheral T lymphocytes in 44 centenarians. Thymic functionality was analyzed by the quantification of cells presenting the T-cell receptor rearrangement excision circles (TREC). A new method based upon real-time PCR was used, and we found that most centenarians (84%) had undetectable levels of TREC+ cells. Six-color cytofluorimetric analysis revealed that centenarians had an extremely low number of naive T cells; central memory and effector memory T cells were greatly increased, while terminally differentiated cells were as numerous as in young (aged 20-45) or middle-aged (aged 58-62) donors. Interleukin (IL)-7 and IL-7 receptor alpha-chain (CD127) levels were the same at all ages, as shown by ELISA, flow cytometry and real-time PCR. However, IL-7 plasma levels were higher in centenarian females than males. The presence of TREC+ cells and of very few naive T lymphocytes suggests that in centenarians such cells could either derive from residues of thymic lymphopoietic islets, or even represent long-living lymphocytes that have not yet encountered their antigen. IL-7 could be one of the components responsible, among others, for the higher probability of reaching extreme ages typical of females

Immune senescence and immune activation in elderly colorectal cancer patients

In our previous study, we found that low thymic output and short telomere length were associated with a higher risk of tumor in elderly cancer patients. Here, we aimed to examine in depth the impact of immunological and biological senescence and immune activation on disease outcome in elderly patients with colorectal cancer (CRC).Peripheral blood samples from 81 CRC patients were studied for immune activation, immune senescence and recent thymic emigrant (RTE) CD4 and CD8 cells by flow cytometry. T-cell receptor rearrangement excision circle (TREC) levels and telomere lengths were measured by real-time PCR. Plasma levels of microbial translocation markers, LPS and sCD14, were quantified by ELISA. While TREC levels and telomere length were not prognostic of disease outcome, high percentages of immune senescent and immune activated CD8 cells were associated with a higher risk of a negative event (relapse, progression, or death) in all studied patients and disease relapse in I-Ill staged patients. Levels of sCD14 and LPS were higher in patients who will experience a negative event than in patients who will not. In conclusion, in elderly CRC patients higher immunological senescence and immune activation negatively impact the disease outcome; how these characteristics influence the antineoplastic treatments remains to be investigated

Tackling Sequence to Sequence Mapping Problems with Neural Networks

In Natural Language Processing (NLP), it is important to detect the relationship between two sequences or to generate a sequence of tokens given another observed sequence. We call the type of problems on modelling sequence pairs as sequence to sequence (seq2seq) mapping problems. A lot of research has been devoted to finding ways of tackling these problems, with traditional approaches relying on a combination of hand-crafted features, alignment models, segmentation heuristics, and external linguistic resources. Although great progress has been made, these traditional approaches suffer from various drawbacks, such as complicated pipeline, laborious feature engineering, and the difficulty for domain adaptation. Recently, neural networks emerged as a promising solution to many problems in NLP, speech recognition, and computer vision. Neural models are powerful because they can be trained end to end, generalise well to unseen examples, and the same framework can be easily adapted to a new domain. The aim of this thesis is to advance the state-of-the-art in seq2seq mapping problems with neural networks. We explore solutions from three major aspects: investigating neural models for representing sequences, modelling interactions between sequences, and using unpaired data to boost the performance of neural models. For each aspect, we propose novel models and evaluate their efficacy on various tasks of seq2seq mapping.Comment: PhD thesi

T cell phenotype in paediatric heart transplant recipients

Paediatric heart transplantation recipients suffer an increased incidence of infectious, autoimmune and allergic problems. The relative roles of thymus excision and immunosuppressive treatments in contributing to these sequelae are not clear. We compared the immunological phenotypes of 25 heart transplant recipients (Tx), 10 children who underwent thymus excision during non-transplantation cardiac surgery (TE) and 25 age range–matched controls, in two age bands: 1-9 and 10-16 years. Significant differences from controls were seen mainly in the younger age band with Tx showing lower CD3 and CD4 cell counts whilst TE showed lower CD8 cell counts. Naïve T cell and recent thymic emigrant proportions and counts were significantly lower than controls in both groups in the lower age band. T cell recombination excision circle (TREC) levels were lower than controls in both groups in both age bands. There were no differences in regulatory T cells, but in those undergoing thymus excision in infancy, their proportions were higher in TE than Tx, a possible direct effect of immunosuppression. T cell receptor V beta spectratyping showed fewer peaks in both groups than in controls (predominantly in the older age band). Thymus excision in infancy was associated with lower CD8 cell counts and higher proportions of Tregs in TE compared to Tx. These data are consistent with thymus excision, particularly in infancy, being the most important influence on immunological phenotype after heart transplantation

Intermediate resolution H-beta spectroscopy and photometric monitoring of 3C 390.3 I. Further evidence of a nuclear accretion disk

We have monitored the AGN 3C390.3 between 1995 and 2000.Two large amplitude outbursts, of different duration, in continuum and H beta light were observed ie.: in October 1994 a brighter flare that lasted about 1000 days and in July 1997 another one that lasted about 700 days were detected. The flux in the H beta wings and line core vary simultaneously, a behavior indicative of predominantly circular motions in the BLR.Important changes of the Hbeta emission profiles were detected: at times, we found profiles with prominent asymmetric wings, as those normaly seen in Sy1s, while at other times, we observe profiles with weak almost symmetrical wings, similar to those seen in Sy1.8s. We found that the radial velocity difference between the red and blue bumps is anticorrelated with the light curves of H beta and continuum radiation.e found that the radial velocity difference between the red and blue bumps is anticorrelated with the light curves of H-beta and continuum radiation. Theoretical H-beta profiles were computed for an accretion disk, the observed profiles are best reproduced by an inclined disk (25 deg) whose region of maximum emission is located roughly at 200 Rg. The mass of the black hole in 3C 390.3, estimated from the reverberation analysis is Mrev = 2.1 x 10^9 Msun, ie. 5 times larger than previous estimatesComment: 18 pages, 13 figures, 4 tables. to appear in Astronomy and Astrophysic

CD4+ T Cell Depletion, Immune Activation and Increased Production of Regulatory T Cells in the Thymus of HIV-Infected Individuals

Mechanisms by which HIV affects the thymus are multiple and only partially known, and the role of thymic dysfunction in HIV/AIDS immunopathogenesis remains poorly understood. To evaluate the effects of HIV infection on intra-thymic precursors of T cells in HIV-infected adults, we conducted a detailed immunophenotypic study of thymic tissue isolated from 7 HIV-infected and 10 HIV-negative adults who were to undergo heart surgery. We found that thymuses of HIV-infected individuals were characterized by a relative depletion of CD4+ single positive T cells and a corresponding enrichment of CD8+ single positive T cells. In addition, thymocytes derived from HIV-infected subjects showed increased levels of activated and proliferating cells. Our analysis also revealed a decreased expression of interleukin-7 receptor in early thymocytes from HIV-infected individuals, along with an increase in this same expression in mature double- and single-positive cells. Frequency of regulatory T cells (CD25+FoxP3+) was significantly increased in HIV-infected thymuses, particularly in priorly-committed CD4 single positive cells. Our data suggest that HIV infection is associated with a complex set of changes in the immunophenotype of thymocytes, including a reduction of intrathymic CD4+ T cell precursors, increased expression of activation markers, changes in the expression pattern of IL-7R and enrichment of T regulatory cells generation

Characterization of human gamma delta T cells in allogeneic hematopoietic stem cell transplantation

Over the last five decades, allogeneic hematopoietic stem cell transplantation (HSCT) has evolved rapidly, continuing to offer a cure for several hematological diseases. Nevertheless, associated life-threatening complications remain an obstacle against exploiting its full therapeutic benefit. Among these complications, infection, relapse, and graft-versus-host disease (GVHD) represent not only the most common but also the most serious ones. Though commonly regarded as distinct clinical events, their underlying pathophysiology is firmly related from an immunological perspective. T lymphocytes are key players in HSCT complications and their proper reconstitution following allogeneic HSCT is central for beneficial clinical outcome. The last two decades have witnessed a growing interest in a subset of T cells known as gamma delta (γδ) T cells. The immunological capabilities of these unconventional cells have been intensively explored. However, more efforts aimed at unraveling the immunobiological features of different γδ subsets are warranted to effectively exploit their full immunotherapeutic potential. In the present work, I tried to tackle several immune-related aspects that directly influence allogeneic HSCT outcome with a special focus on γδ T cells. In paper I, the main objective was to address the impact of different GVHD prophylaxis regimens on de novo generation of T and B lymphocytes. Using PCR methods, T cell receptor recombination excision circle (TREC), kappa deleting recombination excision circle (KREC), and telomere length (TL) were quantified in the peripheral blood (PB) of transplanted patients at several time intervals. Although there was no significant difference between the two GVHD prophylaxis groups, we identified other transplant related factors that were associated with reduced TREC and/or KREC levels after HSCT. Furthermore, we showed that high levels of these excision circles correlated with favorable outcome post HSCT. In paper II-IV, more attention was paid to explore the role of γδ T cells in donor grafts. Using multicolor flow cytometry together with other molecular and functional assays, we found a significant association between graft frequencies of CD8+γδ T cells and acute GVHD (aGVHD) grade II-III in Paper II. Additionally, we showed that higher frequencies of CD27+ γδ T cells in the stem cell grafts were correlated with both less relapse and CMV incidences. The results from paper II highlighting a potential role of CD8+γδ T cells in donor grafts raised our interest to further investigate this subset to elucidate their immunological characteristics. In paper III we thoroughly analysed γδ T cells in BM grafts using multicolor flow cytometry and TCR repertoire analysis using next generation sequencing (NGS). We showed that grafts from CMV+ donors contained higher proportions of CD8+γδ T that preferentially expressed Vγ9- and differentiated towards terminal effector memory phenotype. Additionally, analysis of TCRγ chain revealed a clonally focused repertoire in CMV+ donor grafts. We also showed that CD8+γδ T cells differentially respond to TCR stimuli suggesting adaptive-like phenotype In paper IV, we sought to address whether allogeneic HSCT outcome is influenced by γδ TCR repertoire composition in donor grafts. Immunosequencing of TCRγ chain by NGS revealed a more public repertoire and increased presence of long sequence clonotypes in graft given to non-relapsed patients. Further analysis of the amino acid sequences identified 12 public and 4 private sequences that were exclusively found in high frequencies in grafts given to nonrelapsed patients. Finally, in paper V we aimed to optimize a protocol for efficient in-vitro expansion of Vγ9Vδ2 T cells from umbilical cord blood (UCB). Phenotypical and functional characterization of expanded cells was comparable to PB and suggests that UCB can be a reliable source for Vγ9Vδ2 T cell expansion

Whatever Happened to 1845 - The Missing Decisions of the Texas Supreme Court

Have you ever noticed a gap in the publication of Texas Supreme Court decisions? Both the Harvard Blue Book and the University of Texas Green Book inform readers that opinions of the court from 1840 to 1844 (the Republic period) can be found in Dallam\u27s Decisions, while decisions from 1846 on (statehood) are available in Texas Reports or the Southwestern Reporter. That\u27s all very clear, but whatever happened to 1845? This article will supply half an answer to this question; perhaps some reader can provide the other half. Three questions arise. The first, and simplest: Are there any 1845 opinions? The answer is Yes. The Supreme Court of the Republic of Texas met in December of 1845, had a perfectly ordinary session, wrote more than 30 opinions, and adjourned on Jan. 5, 1846, to reconvene in the fall as the Supreme Court of the State of Texas. That was the easy question. The second one is harder. Why weren\u27t the opinions printed? The last question is the hardest: Where are the 1845 decisions today? It appears that opinions at this time were initially written in longhand by the judges or their clerks, then copied by the court clerk into a bound opinion book. This book is preserved in the State Archives, and does contain the full text, sometimes faint and faded, of 16 opinions. As we said at the beginning, this article provides only half an answer to the question of what happened to the missing year of the Texas Supreme Court. Efforts are underway to arrange publication of all available opinions as a Texas Sesquicentennial project. If any reader has an idea or suggestion as to where the remaining opinions might be found, information would be gratefully received by James Hambleton, Director, State Law Library, Box 12367, Capitol Station, Austin 78711. Naturally, any confidences will be respected. A list of the missing opinions follows [.

A scheme for radiation pressure and photon diffusion with the M1 closure in RAMSES-RT

We describe and test an updated version of radiation-hydrodynamics (RHD) in the RAMSES code, that includes three new features: i) radiation pressure on gas, ii) accurate treatment of radiation diffusion in an unresolved optically thick medium, and iii) relativistic corrections that account for Doppler effects and work done by the radiation to first order in v/c. We validate the implementation in a series of tests, which include a morphological assessment of the M1 closure for the Eddington tensor in an astronomically relevant setting, dust absorption in a optically semi-thick medium, direct pressure on gas from ionising radiation, convergence of our radiation diffusion scheme towards resolved optical depths, correct diffusion of a radiation flash and a constant luminosity radiation, and finally, an experiment from Davis et al. of the competition between gravity and radiation pressure in a dusty atmosphere, and the formation of radiative Rayleigh-Taylor instabilities. With the new features, RAMSES-RT can be used for state-of-the-art simulations of radiation feedback from first principles, on galactic and cosmological scales, including not only direct radiation pressure from ionising photons, but also indirect pressure via dust from multi-scattered IR photons reprocessed from higher-energy radiation, both in the optically thin and thick limits.Comment: 25 pages, 13 figures, accepted for publication in MNRAS. Revised to match published versio

EuroFlow Standardized Approach to Diagnostic Immunopheneotyping of Severe PID in Newborns and Young Children

The EuroFlow PID consortium developed a set of flow cytometry tests for evaluation of patients with suspicion of primary immunodeficiency (PID). In this technical report we evaluate the performance of the SCID-RTE tube that explores the presence of recent thymic emigrants (RTE) together with T-cell activation status and maturation stages and discuss its applicability in the context of the broader EuroFlow PID flow cytometry testing algorithm for diagnostic orientation of PID of the lymphoid system. We have analyzed peripheral blood cells of 26 patients diagnosed between birth and 2 years of age with a genetically defined primary immunodeficiency disorder: 1