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The procedure for the energy calibration of the high granularity electromagnetic calorimeter PHOS of the ALICE experiment is presented. The methods used to perform the relative gain calibration, to evaluate the geometrical alignment and the corresponding correction of the absolute energy scale, to obtain the nonlinearity correction coefficients and finally, to calculate the time-dependent calibration corrections, are discussed and illustrated by the PHOS performance in proton-proton (pp) collisions at √s=13 TeV. After applying all corrections, the achieved mass resolutions for π0 and η mesons for pT > 1.7 GeV/c are σmπ0 = 4.56 ± 0.03 MeV/c2 and σmη = 15.3 ± 1.0 MeV/c2, respectively.
Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing.
Nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) can present with different histopathological growth patterns. The impact of these histopathological growth patterns on relapse characteristics is unknown. We therefore analyzed paired biopsies obtained at initial diagnosis and relapse from 33 NLPHL patients who had received first‐line treatment within German Hodgkin Study Group (GHSG) trial protocols, and from a second cohort of 41 relapsed NLPHL patients who had been treated outside GHSG studies. Among the 33 GHSG patients, 21 patients presented with a typical growth pattern at initial diagnosis, whereas 12 patients had a variant histology. The histopathological growth patterns at initial diagnosis and at relapse were consistent in 67% of cases. A variant histology at initial diagnosis was associated with a shorter median time to lymphoma recurrence (2.8 vs 5.2 years; P = .0219). A similar tendency towards a shorter median time to lymphoma recurrence was observed for patients presenting with a variant histology at relapse, irrespective of the growth pattern at initial diagnosis. Results obtained from the 41 NLPHL patients who had been treated outside GHSG studies were comparable (median time to lymphoma recurrence for variant histology vs typical growth pattern at initial diagnosis: 1.5 vs 7.0 years). In conclusion, the histopathological growth pattern remains consistent at relapse in the majority of NLPHL cases, and has major impact on the time of relapse.
The Afrotropical (including Malagasy Subregion) species of the genus Asobara Foerster, 1863, are revised. In addition to the redescribed 15 known species, 25 new species are described and illustrated, viz., Asobara abyssiniensis Peris-Felipo, sp. nov., A. caboverdensis van Achterberg, sp. nov., A. carinata Peris-Felipo, sp. nov., A. cracentis van Achterberg, sp. nov., A. elongitarsis van Achterberg, sp. nov., A. fletcheri Peris-Felipo, sp. nov., A. harrinsmithensis Peris-Felipo, sp. nov., A. kawandensis Peris-Felipo, sp. nov., A. kibalensis van Achterberg, sp. nov., A. laticlypeata van Achterberg, sp. nov., A. mediana van Achterberg, sp. nov., A. mellicephalata van Achterberg, sp. nov., A. natalensis Peris-Felipo, sp. nov., A. notleyi Peris-Felipo, sp. nov., A. robusta van Achterberg, sp. nov., A. sarae Peris-Felipo, sp. nov., A. somersetensis Peris-Felipo, sp. nov., A. stubbsi Peris-Felipo, sp. nov., A. taylori Peris-Felipo, sp. nov., A. vanalpheni van Achterberg, sp. nov., A. vanharteni van Achterberg, sp. nov., A. victoriana Peris-Felipo, sp. nov., A. zaprionae van Achterberg, sp. nov., A. zimbabwana Peris-Felipo, sp. nov., A. zululana Peris-Felipo, sp. nov. Moreover, the following new combination is suggested: Asobara pulchricornis (Szépligeti, 1911) comb. nov. A key to all Afrotropical (including Malagasy) species is provided for the first time.
We consider a simple model of modified gravity interacting with a single scalar field ϕ with weakly coupled exponential potential within the framework of non-Riemannian spacetime volume-form formalism. The specific form of the action is fixed by the requirement of invariance under global Weyl-scale symmetry. Upon passing to the physical Einstein frame we show how the non-Riemannian volume elements create a second canonical scalar field u and dynamically generate a non-trivial two-scalar-field potential Ueff(u,ϕ) with two remarkable features: (i) it possesses a large flat region for large u describing a slow-roll inflation; (ii) it has a stable low-lying minimum w.r.t. (u,ϕ) representing the dark energy density in the “late universe”. We study the corresponding two-field slow-roll inflation and show that the pertinent slow-roll inflationary curve ϕ = ϕ(u) in the two-field space (u,ϕ) has a very small curvature, i.e., ϕ changes very little during the inflationary evolution of u on the flat region of Ueff(u,ϕ). Explicit expressions are found for the slow-roll parameters which differ from those in the single-field inflationary counterpart. Numerical solutions for the scalar spectral index and the tensor-to-scalar ratio are derived agreeing with the observational data.
Background: Germinal center-derived B cell lymphomas are tumors of the lymphoid tissues representing one of the most heterogeneous malignancies. Here we characterize the variety of transcriptomic phenotypes of this disease based on 873 biopsy specimens collected in the German Cancer Aid MMML (Molecular Mechanisms in Malignant Lymphoma) consortium. They include diffuse large B cell lymphoma (DLBCL), follicular lymphoma (FL), Burkitt’s lymphoma, mixed FL/DLBCL lymphomas, primary mediastinal large B cell lymphoma, multiple myeloma, IRF4-rearranged large cell lymphoma, MYC-negative Burkitt-like lymphoma with chr. 11q aberration and mantle cell lymphoma.
Methods: We apply self-organizing map (SOM) machine learning to microarray-derived expression data to generate a holistic view on the transcriptome landscape of lymphomas, to describe the multidimensional nature of gene regulation and to pursue a modular view on co-expression. Expression data were complemented by pathological, genetic and clinical characteristics.
Results: We present a transcriptome map of B cell lymphomas that allows visual comparison between the SOM portraits of different lymphoma strata and individual cases. It decomposes into one dozen modules of co-expressed genes related to different functional categories, to genetic defects and to the pathogenesis of lymphomas. On a molecular level, this disease rather forms a continuum of expression states than clearly separated phenotypes. We introduced the concept of combinatorial pattern types (PATs) that stratifies the lymphomas into nine PAT groups and, on a coarser level, into five prominent cancer hallmark types with proliferation, inflammation and stroma signatures. Inflammation signatures in combination with healthy B cell and tonsil characteristics associate with better overall survival rates, while proliferation in combination with inflammation and plasma cell characteristics worsens it. A phenotypic similarity tree is presented that reveals possible progression paths along the transcriptional dimensions. Our analysis provided a novel look on the transition range between FL and DLBCL, on DLBCL with poor prognosis showing expression patterns resembling that of Burkitt’s lymphoma and particularly on "double-hit" MYC and BCL2 transformed lymphomas.
Conclusions: The transcriptome map provides a tool that aggregates, refines and visualizes the data collected in the MMML study and interprets them in the light of previous knowledge to provide orientation and support in current and future studies on lymphomas and on other cancer entities.
As a cognitively-mediated response, autonomous adaptation at farm-gate levels constitutes reactionary actions by farmers against climate impacts. These actions are shaped by interacting factors such as household characteristics, livelihood scope and resources. It is driven by the goal of adapting cultivated farmlands to climate and for sustaining crop yields. Thus, interest in balancing adaptation goals with protection of vegetation conditions is less of a priority. Lack of research interest in understanding the gap between objectives of reactionary adaptation and protection of surface conditions (vegetation canopies) is a gap in research. In many studies, farm-gate level adaptation is described as a set of zero-feedback actions in response to climate impacts. This perception conceals the stress and impact-engendering attribute of reactionary adaptation. Inspired towards addressing this conceptual gap; this study investigates impact of farmers’ reactionary adaptation on vegetation cover in Keffi, Nasarawa, Nigeria. A twenty-year time-series NDVI and rainfall datasets are linearly regressed to examine the extent of NDVI-rainfall sensitivity. A weak linear relationship between NDVI and rainfall in Keffi for the period, 1999-2018 is observed. At a regression slope of 0.001, R squared, R2=0.129 (implying that only about 13% of the variability in NDVI in Keffi are explained by rainfall amount) and a bivariate regression coefficient, r=0.359; statistical evidence shows that rainfall amount are not significant predictors of NDVI in Keffi. In investigating the possible interference of non-rainfall factors on vegetation productivity (NDVI) in Keffi; a residual trend (RESTREND) analysis was carried out. Regression of residuals from NDVI-Rainfall linear regression produced a R=0.192 with a negative and downwards slope. The downward character of the RESTREND slope is suggestive of non-rainfall factors contained in the residuals. In validating the RESTREND analysis, a comparative analysis between observed and predicted NDVI derived from a reference NDVI value of 0.46 was carried out. The NDVI value of 0.46, is empirically assumed to be average NDVI value expected at a minimum rainfall amount of 850mm/year reported in tropical Savanna ecosystems. Using this empirical relationship, NDVI values were predicted for Keffi. Even at higher rainfall amounts≈1340mm/year, amounts were unable to produce corresponding higher NDVI values; rather a more plausible correlation between reference-derived predicted NDVI values and rainfall was obtained. A further analysis with predicted NDVI values, based on 1999 NDVI value in Keffi returned higher NDVI units than observed NDVI values. This strengthens the attribution of the possible interference of rainfall-NDVI sensitivity by non-rainfall factors like human activities on vegetation productivity. Surface soil analysis to exclude potential impacts of soil nutrients and moisture deficiency on vegetation productivity, showed that soil had insignificant effect on vegetation dynamics. Further inferential analysis, using the inter-annual NDVI and the reclassified bi-decadal NDVI maps showed that spatial vegetation distribution in Keffi were driven by farmers inter-annual rotational cultivation footprints than rainfall variability. With a three-class categorization, “gain, loss and significant loss”, the spatial distribution of vegetation in Keffi between (1999-2008) and (2009-2018) was assessed. Temporal condition (stressed and healthy) across the three classes supports the attribution of farmers’ reactionary adaptation and cultivation practices on the dynamic spatial vegetation distribution. Between 1999 -2018, an increase in areas with significant vegetation loss (42%), so with a decrease of -25% in areas with healthy vegetation was observed. The character of vegetation cover across the two decadal time slices, reflects landuse intensity and unsustainable farming practices. Preferences for modification of cultivation practices and changes in seed by farmers exerts positive feedbacks on vegetation cover. Higher statistical measures, 38.4% (yearly cropping) and 44% (shifting cultivation with less fallow periods) were observed in the chi-square analysis. These measures were higher than 2.0% relating to shifting cultivation with more fallow periods. While 11.6% farmers noted cultural practices as reasons for preferred cultivation methods, 48.4% farmers attributed climate as reason behind cultivation modification. This was higher than 24.4% who linked issues of tenure rights to cultivation practices. With preferences for yield- breaching strategies, the non-receding cultivation and shorter fallow practices in Keffi triggers feedback on vegetation dynamics. Evidence from this study shows that the NDVI-rainfall functional sensitivity in Keffi is plausibly dampened by effects of reactionary farm-gate level adaptation practices.
The present study aims to clarify the confused taxonomy of Z. schaufussi von Frauenfeld, 1862 and Zospeum suarezi Gittenberger, 1980. Revision of Iberian Zospeum micro snails is severely hindered by uncertainties regarding the identity of the oldest Iberian Zospeum species, Z. schaufussi von Frauenfeld, 1862. In this paper, we clarify its taxonomic status by designating a lectotype from the original syntype series and by describing its internal and external shell morphology. Using SEM-EDX, we attempt to identify the area of the type locality cave more precisely than "a cave in Spain". The shell described and illustrated by Gittenberger (1980) as Z. schaufussi appears not to be conspecific with the lectotype shell, and is considered a separate species, Z. gittenbergeri Jochum, Prieto & De Winter, sp. n.
Zospeum suarezi was described from various caves in NW Spain. Study of the type material reveals that these shells are not homogenous in shell morphology. The holotype shell of Z. suarezi is imaged here for the first time. The paratype shell, illustrated by Gittenberger (1980) from a distant, second cave, is described as Zospeum praetermissum Jochum, Prieto & De Winter, sp. n. The shell selected here as lectotype of Z. schaufussi, was also considered a paratype of Z. suarezi by Gittenberger (1980). Since this specimen is morphologically very similar to topotypic shells of Z. suarezi, the latter species is considered a junior synonym of Z. schaufussi (syn. n.). The internal shell morphology of all these taxa is described and illustrated using X-ray Micro Computer Tomography (Micro-CT).
Launching and manipulation of polaritons in van der Waals materials offers novel opportunities for field-enhanced molecular spectroscopy and photodetection, among other applications. Particularly, the highly confined hyperbolic phonon polaritons (HPhPs) in h-BN slabs attract growing interest for their capability of guiding light at the nanoscale. An efficient coupling between free space photons and HPhPs is, however, hampered by their large momentum mismatch. Here, we show —by far-field infrared spectroscopy, infrared nanoimaging and numerical simulations— that resonant metallic antennas can efficiently launch HPhPs in thin h-BN slabs. Despite the strong hybridization of HPhPs in the h-BN slab and Fabry-Pérot plasmonic resonances in the metal antenna, the efficiency of launching propagating HPhPs in h-BN by resonant antennas exceeds significantly that of the non-resonant ones. Our results provide fundamental insights into the launching of HPhPs in thin polar slabs by resonant plasmonic antennas, which will be crucial for phonon-polariton based nanophotonic devices.
Background and aims: Patients with gastric cancer often show signs of malnutrition. We sought to evaluate the influence of sarcopenia in patients with locally advanced, not metastasized, gastric or gastro-esophageal junction (GEJ) cancer undergoing curative treatment (perioperative chemotherapy and surgery) on morbidity and mortality in order to identify patients in need for nutritional intervention.
Patients and methods: Two-centre study, conducted in the Frankfurt University Clinic and Krankenhaus Nordwest (Frankfurt) as part of the University Cancer Center Frankfurt (UCT). 47/83 patients were treated in the FLOT trial (NCT01216644). Patients´ charts were reviewed for clinical data. Two consecutive CT scans were retrospectively analyzed to determine the degree of sarcopenia. Survival was calculated using the Kaplan-Meier method, multivariate analysis was performed using the Cox regression.
Results: 60 patients (72.3%) were male and 23 (27.7%) female. 45 patients (54.2%) had GEJ type 1–3 and 38 (45.8%) gastric tumors, respectively. Sarcopenic patients were significantly older than non-sarcopenic patients (mean age 65.1 years vs. 59.5 years, p = 0.042), terminated the chemotherapy significantly earlier (50% vs. 22.6%, p = 0.037) and showed higher Clavien-Dindo scores, indicating more severe perioperative complications (score ≥3 43.3 vs. 17.0%, p = 0.019). Sarcopenic patients had a significantly shorter survival than non-sarcopenic patients (139.6 ± 19.5 [95% CI, 101.3–177.9] vs. 206.7 ± 13.8 [95% CI, 179.5–233.8] weeks, p = 0.004). Multivariate Cox regression analysis showed that, besides UICC stage, sarcopenia significantly influenced survival.
Conclusion: Sarcopenia is present in a large proportion of patients with locally advanced gastric or GEJ cancer and significantly influences tolerability of chemotherapy, surgical complications and survival.