Renewing Felsenstein's phylogenetic bootstrap in the era of big data.

Felsenstein's application of the bootstrap method to evolutionary trees is one of the most cited scientific papers of all time. The bootstrap method, which is based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now available for a wide variety of species, and phylogenies based on hundreds or thousands of taxa are becoming routine. With phylogenies of this size Felsenstein's bootstrap tends to yield very low supports, especially on deep branches. Here we propose a new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual 'transfer' distance rather than the binary presence or absence index used in Felsenstein's original version. The resulting supports are higher and do not induce falsely supported branches. The application of our method to large mammal, HIV and simulated datasets reveals their phylogenetic signals, whereas Felsenstein's bootstrap fails to do so.

Molecular dynamics simulation of thermal transport across a solid/liquid interface created by a meniscus.

Understandings heat transfer across a solid/liquid interface is crucial for establishing novel thermal control pathways in a range of energy applications. One of the major problems raised in this context is the impact of the three-phase contact line between solid, liquid, and gas on heat flux perturbations at the nanoscale. The focus of this research is the thermal transport via nanosized meniscus restricted between two solid walls. The molecular dynamics approach was used to consider different wetting states of the meniscus by varying the interaction potential between atoms of the substrate and the liquid. The influence of the meniscus size on the energy exchange between two solid walls was also studied. It was discovered that possessing a three-phase contact line reduces the interfacial boundary resistance between solid and liquid. Furthermore, the finite element method was employed to connect atomistic simulations with continuum mechanics. We show that the wetting angle and interfacial boundary resistance are essential important parameters for multiscale analysis of thermal engineering issues with precise microscale parametrization.

Gene transfer of two entry inhibitors protects CD4⁺ T cell from HIV-1 infection in humanized mice.

Targeting viral entry is the most likely gene therapy strategy to succeed in protecting the immune system from pathogenic HIV-1 infection. Here, we evaluated the efficacy of a gene transfer lentiviral vector expressing a combination of viral entry inhibitors, the C46 peptide (an inhibitor of viral fusion) and the P2-CCL5 intrakine (a modulator of CCR5 expression), to prevent CD4⁺ T-cell infection in vivo. For this, we used two different models of HIV-1-infected mice, one in which ex vivo genetically modified human T cells were grafted into immunodeficient NOD.SCID.γc⁻/⁻mice before infection and one in which genetically modified T cells were derived from CD34⁺ hematopoietic progenitors grafted few days after birth. Expression of the transgenes conferred a major selective advantage to genetically modified CD4⁺ T cells, the frequency of which could increase from 10 to 90% in the blood following HIV-1 infection. Moreover, these cells resisted HIV-1-induced depletion, contrary to non-modified cells that were depleted in the same mice. Finally, we report lower normalized viral loads in mice having received genetically modified progenitors. Altogether, our study documents that targeting viral entry in vivo is a promising avenue for the future of HIV-1 gene therapy in humans.

Characterization of oral immune cells in birch pollen-allergic patients: impact of the oral allergy syndrome and sublingual allergen immunotherapy on antigen-presenting cells.

BACKGROUND: A detailed characterization of human oral immune cells is needed to better understand local mechanisms associated with allergen capture following oral exposure. METHODS: Oral immune cells were characterized by immunohistology and immunofluorescence in biopsies obtained from three healthy individuals and 23 birch pollen-allergic patients with/without oral allergy syndrome (OAS), at baseline and after 5 months of sublingual allergen immunotherapy (AIT). RESULTS: Similar cell subsets (i.e., dendritic cells, mast cells, and T lymphocytes) were detected in oral tissues from healthy and birch pollen-allergic individuals. CD207+ Langerhans cells (LCs) and CD11c+ myeloid dendritic cells (DCs) were found in both the epithelium and the papillary layer of the Lamina propria (LP), whereas CD68+ macrophages, CD117+ mast cells, and CD4+ /CD8+ T cells were rather located in both the papillary and reticular layers of the LP. Patterns of oral immune cells were identical in patients with/without OAS, except lower numbers of CD207+ LCs found in oral tissues from patients with OAS, when compared to OAS- patients (P < 0.05). A 5-month sublingual AIT had a limited impact on oral immune cells, with only a significant increase in IgE+ cells in patients from the active group. Colocalization experiments confirmed that such IgE-expressing cells mostly encompass CD68+ macrophages located in the LP, and to a lesser extent CD207+ LCs in the epithelium. CONCLUSION: Two cell subsets contribute to antigen/allergen uptake in human oral tissues, including (i) CD207+ LCs possibly involved in the physiopathology of OAS and (ii) CD68+ macrophages likely critical in allergen capture via IgE-facilitated mechanisms during sublingual AIT.

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.

Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available on github.com/evolbioinfo/phylodeep .

Lugol chromo-endoscopy versus narrow band imaging for endoscopic screening of esophageal squamous-cell carcinoma in patients with a history of cured esophageal cancer: a feasibility study.

To date, Lugol chromo-endoscopy is the reference technique to detect an esophageal neoplasia in patients with prior esophageal squamous-cell carcinoma (ESCC), but is not easy to perform without general anesthesia, which can limit its use in routine practice. The objective of this study were to compare the accuracy of white light, narrow band imaging (NBI), and Lugol to detect esophageal neoplasia in patients with a history of cured ESCC, in a prospective study. Thirty patients were prospectively included between June 2006 and June 2009. They all had a history of cured ESCC. Esophageal mucosa was examined first using white light, second NBI, and third after Lugol staining. Histology was obtained in all abnormalities detected by white light, NBI, and/or Lugol. Five neoplastic lesions in five different patients were identified at histology, four cancers, and one high-grade dysplasia. NBI and Lugol both detected all esophageal neoplastic lesions, whereas white light detected the four cancers but missed the high-grade dysplasia. In this feasibility study, NBI and Lugol both detected all identified esophageal neoplasia in very high-risk patients of ESCC. This result suggests that NBI could be used instead of Lugol to detect an esophageal neoplasia in patients with high risk of ESCC, but needs to be confirmed in a larger study.

Optimal treatment with systemic chemotherapy, complete surgical excision and hyperthermic intraperitoneal chemotherapy for a desmoplastic small round cell tumor in an adult male patient.

Desmoplastic small round cell tumor (DSRCT) is a very rare but aggressive malignancy. It is usually observed in males during adolescent and early adulthood. The tumor primarily affects the intra-abdominal serosal and is characterized by distinctive histological and immunophenotypic features and by the specific reciprocal translocation EWS-WT1. Prognosis is mainly poor with a mean survival approximately of 2.5 years. However, long-term survivals have been reported using aggressive multimodal therapy based on complete surgical excision, systemic chemotherapy and radiotherapy. The addition of hyperthermic intraperitoneal chemotherapy in the multimodal approach has been reported in very few cases but no effect on survival has been clearly demonstrated. We report a case of a 51-year old adult patient presenting with a DSRCT treated with aggressive therapy based on systemic chemotherapy, complete cytoreductive surgery associated with hyperthermic intraperitoneal chemotherapy, resulting in a long term survival of 4 years.

Identification of CD8+CD25+Foxp3+ suppressive T cells in colorectal cancer tissue.

BACKGROUND: The antitumoral immune response is one determinant of colorectal cancer (CRC) outcome. Recent work suggests that Foxp3(+)CD25(+)CD4(+) regulatory T cells (T4reg) might hamper effective immunosurveillance of emerging cancer cells and impede effective immune responses to established tumours. In this descriptive study, we analysed blood and tissue regulatory T cell populations in patients with CRC. METHODS: Blood and tissue regulatory Foxp3(+) T cells from 40 patients with CRC were compared to regulatory Foxp3(+) T cells from normal colonic tissue and from blood of 26 healthy volunteers. Flow cytometry was used to quantify and phenotype all Foxp3(+) T cell populations. Correlations were sought with the tumour stage and with micro-invasive status. The suppressive capacity of regulatory Foxp3(+) T cells was assessed by their effect on CD4(+)CD25(-) T cell proliferation in vitro and by their capacity to inhibit cytokine production by conventional T cells. RESULTS: We found a significant increase of CD8(+)CD25(+)Foxp3(+) cells (T8reg) in blood and CRC tissue; their phenotype was close to that of T4reg. T8reg cells infiltrating CRC were activated, as suggested by increased cytoxic T lymphocyte-associated antigen-4, glucocorticoid-induced tumour necrosis factor-related protein, and transforming growth factor (TGF)beta1 expression compared to T8reg from normal autologous colonic tissue. Moreover, T8reg were able to suppress CD4(+)CD25(-) T cell proliferation and Th1 cytokine production ex vivo, demonstrating that tumour-infiltrating T8reg have strong suppressive capacities. T8reg numbers correlated with the tumour stage and with micro-invasive status. Finally, interleukin 6 and TGF beta 1 synergistically induced the generation of CD8(+)CD25(+)Foxp3(+) T cells ex vivo. CONCLUSIONS: We have identified a new regulatory T cell population (CD8(+)Foxp3(+)) in colorectal tumours. After isolation from cancer tissue these CD8(+)Foxp3(+) cells demonstrated strong immunosuppressive properties in vitro. These data suggest that these cells may contribute to tumoral immune escape and disease progression.

The shape and internal structure of the moon from the clementine mission.

Global topographic and gravitational field models derived from data collected by the Clementine spacecraft reveal a new picture of the shape and internal structure of the moon. The moon exhibits a 16-kilometer range of elevation, with the greatest topographic excursions occurring on the far side. Lunar highlands are in a state of near-isostatic compensation, whereas impact basins display a wide range of compensation states that do not correlate simply with basin size or age. A global crustal thickness map reveals crustal thinning under all resolvable lunar basins. The results indicate that the structure and thermal history of the moon are more complex than was previously believed.

The gravity field of Mars: results from Mars Global Surveyor.

Observations of the gravity field of Mars reveal a planet that has responded differently in its northern and southern hemispheres to major impacts and volcanic processes. The rough, elevated southern hemisphere has a relatively featureless gravitational signature indicating a state of near-isostatic compensation, whereas the smooth, low northern plains display a wider range of gravitational anomalies that indicates a thinner but stronger surface layer than in the south. The northern hemisphere shows evidence for buried impact basins, although none large enough to explain the hemispheric elevation difference. The gravitational potential signature of Tharsis is approximately axisymmetric and contains the Tharsis Montes but not the Olympus Mons or Alba Patera volcanoes. The gravity signature of Valles Marineris extends into Chryse and provides an estimate of material removed by early fluvial activity.

Internal structure and early thermal evolution of Mars from Mars Global Surveyor topography and gravity.

Topography and gravity measured by the Mars Global Surveyor have enabled determination of the global crust and upper mantle structure of Mars. The planet displays two distinct crustal zones that do not correlate globally with the geologic dichotomy: a region of crust that thins progressively from south to north and encompasses much of the southern highlands and Tharsis province and a region of approximately uniform crustal thickness that includes the northern lowlands and Arabia Terra. The strength of the lithosphere beneath the ancient southern highlands suggests that the northern hemisphere was a locus of high heat flow early in martian history. The thickness of the elastic lithosphere increases with time of loading in the northern plains and Tharsis. The northern lowlands contain structures interpreted as large buried channels that are consistent with northward transport of water and sediment to the lowlands before the end of northern hemisphere resurfacing.

The global topography of Mars and implications for surface evolution.

Elevations measured by the Mars Orbiter Laser Altimeter have yielded a high-accuracy global map of the topography of Mars. Dominant features include the low northern hemisphere, the Tharsis province, and the Hellas impact basin. The northern hemisphere depression is primarily a long-wavelength effect that has been shaped by an internal mechanism. The topography of Tharsis consists of two broad rises. Material excavated from Hellas contributes to the high elevation of the southern hemisphere and to the scarp along the hemispheric boundary. The present topography has three major drainage centers, with the northern lowlands being the largest. The two polar cap volumes yield an upper limit of the present surface water inventory of 3.2 to 4.7 million cubic kilometers.

Modernizing and Expanding the NASA Space Geodesy Network to Meet Future Geodetic Requirements.

NASA maintains and operates a global network of Very Long Baseline Interferometry (VLBI), Satellite Laser Ranging (SLR), and Global Navigation Satellite System (GNSS) ground stations as part of the NASA Space Geodesy Program. The NASA Space Geodesy Network (NSGN) provides the geodetic products that support Earth observations and the related science requirements as outlined by the US National Research Council (NRC 2010, 2018). The Global Geodetic Observing System (GGOS) and the NRC have set an ambitious goal of improving the Terrestrial Reference Frame (TRF) to have an accuracy of 1 millimeter and stability of 0.1 millimeters per year, an order of magnitude beyond current capabilities. NASA and its partners within GGOS are addressing this challenge by planning and implementing modern geodetic stations co-located at existing and new sites around the world. In 2013, NASA demonstrated the performance of its next-generation systems at the prototype next-generation core site at NASA's Goddard Geophysical and Astronomical Observatory in Greenbelt, Maryland. Implementation of a new broadband VLBI station in Hawaii was completed in 2016. NASA is currently implementing new VLBI and SLR stations in Texas and is planning the replacement of its other aging domestic and international legacy stations. In this article, we describe critical gaps in the current global network and discuss how the new NSGN will expand the global geodetic coverage and ultimately improve the geodetic products. We also describe the characteristics of a modern NSGN site and the capabilities of the next-generation NASA SLR and VLBI systems. Finally, we outline the plans for efficiently operating the NSGN by centralizing and automating the operations of the new geodetic stations.

Preclinical evaluation of mRNA trimannosylated lipopolyplexes as therapeutic cancer vaccines targeting dendritic cells.

Clinical trials with direct administration of synthetic mRNAs encoding tumor antigens demonstrated safety and induction of tumor-specific immune responses. Their proper delivery to dendritic cells (DCs) requires their protection against RNase degradation and more specificity for dose reduction. Lipid-Polymer-RNA lipopolyplexes (LPR) are attractive mRNA delivery systems and their equipment with mannose containing glycolipid, specific of endocytic receptors present on the membrane of DCs is a valuable strategy. In this present work, we evaluated the capacity of LPR functionalized with a tri-antenna of α-d-mannopyranoside (triMN-LPR) concerning (i) their binding to CD209/DC-SIGN and CD207/Langerin expressing cell lines, human and mouse DCs and other hematopoietic cell populations, (ii) the nature of induced immune response after in vivo immunization and (iii) their therapeutic anti-cancer vaccine efficiency. We demonstrated that triMN-LPR provided high induction of a local inflammatory response two days after intradermal injection to C57BL/6 mice, followed by the recruitment and activation of DCs in the corresponding draining lymph nodes. This was associated with skin production of CCR7 and CXCR4 at vaccination sites driving DC migration. High number of E7-specific T cells was detected after E7-encoded mRNA triMN-LPR vaccination. When evaluated in three therapeutic pre-clinical murine tumor models such as E7-expressing TC1 cells, OVA-expressing EG7 cells and MART-1-expressing B16F0 cells, triMN-LPR carrying mRNA encoding the respective antigens significantly exert curative responses in mice vaccinated seven days after initial tumor inoculation. These results provide evidence that triMN-LPR give rise to an efficient stimulatory immune response allowing for therapeutic anti-cancer vaccination in mice. This mRNA formulation should be considered for anti-cancer vaccination in Humans.

Autocrine production of pre-B-cell stimulating activity by a variety of transformed murine pre-B-cell lines.

Current evidence suggests that the proliferation and differentiation of normal pre-B-cells may be regulated by interactions with mesenchymally derived stromal cells. The nature of these cell-cell interactions has not yet been fully elucidated, but the involvement of pre-B-cell stimulating factors produced by various mesenchymal cell lines has recently been demonstrated in the murine system. In this model, transformed pre-B-cells differ from their normal counterparts in their acquisition of autonomous growth potential, as seen by an ability to be maintained in vitro in the absence of mesenchymal cell feeders. To test the hypothesis that autonomy might be associated with autocrine growth factor production, we tested the ability of a spontaneous pre-B-cell transformant (H9 cells) and two independently derived Abelson murine leukemia virus transformed pre-B-cell lines to produce pre-B-cell stimulating factors. All three lines released activities that stimulated the proliferation of themselves or H9 cells when cultured at low cell densities. One of the three transformed pre-B-cell lines could also substitute for mesenchymal feeders to stimulate normal pre-B-cells. Time course studies of an evolving Abelson murine leukemia virus transformant showed that the production of an autocrine pre-B-cell growth factor increased concomitantly with the acquisition of autonomous growth potential suggesting a relationship between these two phenotypic changes. Preliminary characterization of the growth factor responsiveness of H9 cells and the nature of the autostimulatory activity produced by this line suggested its nonidentity with any known hemopoietic growth factor. Activation of autocrine growth factor production appears to be a common event in the evolution of malignant pre-B-cells arising through different oncogenic mechanisms and may therefore be relevant to the pathogenesis of human acute lymphoid leukemia.

Prognostic index for clinical Stage I cutaneous malignant melanoma.

Thirteen variables were evaluated for their significance in predicting the survival of 148 patients in a retrospective study with clinical Stage I cutaneous malignant melanoma. The variables studied were histological type, tumor thickness, level of invasion, mitotic activity, pigmentation type, existence of ulceration, presence of lymphocytic infiltration, cell type, sex and age of the patient, site of melanoma, and wide local excision preceded or not by contact radiotherapy and associated or not with lymphadenectomy. When these variables were individualized, only seven were significantly related to survival: histological type; tumor thickness; level of invasion; mitotic activity; pigmentation type; existence of ulceration; and sex of the patient. Multivariate analysis based on Breslow's version of the Cox proportional-hazards model was performed on a group of 110 patients. This analysis demonstrated that 5 of the original 13 variables (i.e., mitotic activity, tumor thickness, sex, lymphadenectomy, and site of primary melanoma) could be used to develop a prognostic model. A Gompertz distribution which provided for an appropriate smoothing of the Breslow model estimates was used to derive a simple prognostic index and to predict the survival of individual patients. Fifty-four patients in a prospective study were subsequently evaluated with the Gompertz model in order to test the prognostic accuracy of the model for the five variables.

Small-scale density variations in the lunar crust revealed by GRAIL.

Data from the Gravity Recovery and Interior Laboratory (GRAIL) mission have revealed that ~98% of the power of the gravity signal of the Moon at high spherical harmonic degrees correlates with the topography. The remaining 2% of the signal, which cannot be explained by topography, contains information about density variations within the crust. These high-degree Bouguer gravity anomalies are likely caused by small-scale (10's of km) shallow density variations. Here we use gravity inversions to model the small-scale three-dimensional variations in the density of the lunar crust. Inversion results from three non-descript areas yield shallow density variations in the range of 100-200 kg/m3. Three end-member scenarios of variations in porosity, intrusions into the crust, and variations in bulk crustal composition were tested as possible sources of the density variations. We find that the density anomalies can be caused entirely by changes in porosity. Characteristics of density anomalies in the South Pole-Aitken basin also support porosity as a primary source of these variations. Mafic intrusions into the crust could explain many, but not all of the anomalies. Additionally, variations in crustal composition revealed by spectral data could only explain a small fraction of the density anomalies. Nevertheless, all three sources of density variations likely contribute. Collectively, results from this study of GRAIL gravity data, combined with other studies of remote sensing data and lunar samples, show that the lunar crust exhibits variations in density by ±10% over scales ranging from centimeters to 100's of kilometers.

HTLV-1 Tax protein sensitizes cells to apoptotic cell death induced by DNA damaging agents.

Transient HTLV-1 Tax expression suppresses cellular nucleotide excision repair, and this effect correlates with Tax transactivation of the proliferating cell nuclear antigen promoter. The inability to repair DNA damage typically induces apoptotic cell death. Therefore, we investigated the effect of Tax-mediated suppression of DNA repair on apoptosis in stable Tax-expressing cells. Constitutive Tax expression reduced cellular nucleotide excision repair activity compared with parental and control cells. Tax-expressing cells were also more sensitive to apoptosis induced by DNA damaging agents than control cells. Even though Tax-expressing cells displayed reduced DNA repair, they showed increased DNA replication following UV damage. These results suggest that Tax suppresses the cell's ability to repair DNA damage and stimulates DNA replication even in the presence of damage. The inability to repair DNA damage is likely to stimulate apoptotic cell death in the majority of Tax-expressing cells while the ability to promote DNA replication may also allow the survival of a small population of cells. We propose that together these effects contribute to the monoclonal nature and low efficiency of HTLV-1 transformation.

Good correlation between RT-PCR analysis and relapse in Philadelphia (Ph1)-positive acute lymphoblastic leukemia (ALL).

We sequentially performed cytogenetic analysis and RT-PCR analysis of BCR-ABL transcripts in 17 cases of Ph1-positive ALL who had achieved hematological complete remission (CR) with intensive chemotherapy (CT). Sixteen cases were studied prospectively. All but one of the patients had reached cytogenetic CR, but cytogenetic has low sensitivity in predicting relapse. Twelve patients relapsed, three died in first CR and two were alive in first CR. Two of five, two of four, and five of nine patients who were allografted (in first or second CR), autografted and received consolidation CT, respectively, achieved negative two-round PCR in the bone marrow (BM): three died in CR, three remained in CR with negative two-step PCR in the BM and three relapsed after 22 to 28 months. In all cases, relapse was preceded by switch to PCR positivity in the BM by 4 to 6 months. The remaining nine patients remained PCR-positive in the BM and relapsed after 2 to 16 months. In the four autografted cases, PCR was positive at the time of bone marrow harvest. The two patients who received a purged transplant achieved negative PCR and prolonged CR, whereas the two patients who received an unpurged transplant remained PCR positive and relapsed. In 34% of the samples where analysis was concomitant, sensitivity of PCR proved lower in the blood than in the BM. These findings show that RT-PCR is a useful tool in the monitoring of MRD in Ph1 positive ALL.