A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs.

Fungal specialized metabolites are a major source of beneficial compounds that are routinely isolated, characterized, and manufactured as pharmaceuticals, agrochemical agents, and industrial chemicals. The production of these metabolites is encoded by biosynthetic gene clusters that are often silent under standard growth conditions. There are limited resources for characterizing the direct link between abiotic stimuli and metabolite production. Herein, we introduce a network analysis-based, data-driven algorithm comprising two routes to characterize the production of specialized fungal metabolites triggered by different exogenous compounds: the direct route and the auxiliary route. Both routes elucidate the influence of treatments on the production of specialized metabolites from experimental data. The direct route determines known and putative metabolites induced by treatments and provides additional insight over traditional comparison methods. The auxiliary route is specific for discovering unknown analytes, and further identification can be curated through online bioinformatic resources. We validated our algorithm by applying chitooligosaccharides and lipids at two different temperatures to the fungal pathogen Aspergillus fumigatus. After liquid chromatography-mass spectrometry quantification of significantly produced analytes, we used network centrality measures to rank the treatments' ability to elucidate these analytes and confirmed their identity through fragmentation patterns or in silico spiking with commercially available standards. Later, we examined the transcriptional regulation of these metabolites through real-time quantitative polymerase chain reaction. Our data-driven techniques can complement existing metabolomic network analysis by providing an approach to track the influence of any exogenous stimuli on metabolite production. Our experimental-based algorithm can overcome the bottlenecks in elucidating novel fungal compounds used in drug discovery.

Lupeol acetate isolated from Chrysophyllum cainito L. fruit as a template for the synthesis of N-alkyl-arylsulfonamide derivatives and their synergistic effects with metronidazole against Trichomonas vaginalis.

Pentacyclic triterpenes are found in a great variety of natural products and constitute an organic template for the development of new derivative compounds with therapeutic applications. In the present work, lupeol acetate isolated from Chrysophyllum cainito L. fruit was used as a template for the synthesis of novel N-alkyl-arylsulfonamide derivatives, and their synergistic effects with metronidazole against strains of Trichomonas vaginalis were tested. A library of 18 derivatives was synthesized. Ten compounds exhibited an IC50 < 100 µM against a metronidazole-sensitive strain of T. vaginalis. Only seven of these compounds (12, 15, 18-22) also showed activity against metronidazole-resistant strains. The compounds 20 (N-cyclohexyl-p-chlorobenzenesulfonamidolupeol acetate) and 22 (N-cyclohexyl-p-nitrobenzenesulfonamidolupeol acetate) exhibited a similar IC50 against both susceptible and resistant T. vaginalis strains and enhanced the efficacy of metronidazole in a partial and total synergistic way, respectively. These data provided evidence of the trichomonicidal effect of N-alkyl-arylsulfonamide derivatives of lupeol acetate, representing highly promising novel antiparasitic agents.

Hybridization, ecogeographical displacement and the emergence of new lineages - A genotyping-by-sequencing and ecological niche and species distribution modelling study of Sempervivum tectorum L. (Houseleek).

Ecogeographical displacement of homoploid hybrid lineages from their parents is well documented and considered an important mechanism to achieve reproductive isolation. In this study, we investigated the origin of the flowering plant species Sempervivum tectorum in the Massif Central (France) through homoploid hybridization between lineages of the species from the Rhine Gorge area (Germany) and the Pyrenees (France). We used genotyping-by-sequencing genetic data as evidence for the hybrid origin of the Massif Central lineage, and WorldClim climatic data and soil pH and soil temperature data collected by us for ecological niche and species distribution modelling. We could show that the Massif Central lineage shows hybrid admixture and that the niche of this lineage is significantly different from those of the parental lineages. In comparison with the parental niches, different variables of the niche of the hybrid lineage are intermediate, parental-combined or extreme. The different niche of the Massif Central populations thus can plausibly be interpreted as hybridization-derived. Our species distribution modelling for the Last Glacial Maximum and Mid-Holocene showed that the potential distribution of the hybrid lineage at the likely time of its origin in the Quaternary possibly was parapatric in relation to the largely sympatric distributions of the parental lineages. We hypothesize that reproductive isolation of the hybrid lineage from the parental lineages resulted from the segregation of distribution ranges by a differential response of the three lineages to a warming climate.

Highly Efficient Semitransparent Perovskite Solar Cells for Four Terminal Perovskite-Silicon Tandems.

Tandem solar cells (SCs) based on perovskite and silicon represent an exciting possibility for a breakthrough in photovoltaics, enhancing SC power conversion efficiency (PCE) beyond the single-junction limit while keeping the production cost low. A critical aspect to push the tandem PCE close to its theoretical limit is the development of high-performing semitransparent perovskite top cells, which also allow suitable near-infrared transmission. Here, we have developed highly efficient semitransparent perovskite SCs (PSCs) based on both mesoporous and planar architectures, employing Cs0.05(MA0.17FA0.83)0.95Pb(I0.83Br0.17)3 and FA0.87Cs0.13PbI2Br perovskites with band gaps of 1.58 and 1.72 eV, respectively, which achieved PCEs well above 17 and 14% by detailed control of the deposition methods, thickness, and optical transparency of the interlayers and the semitransparent electrode. By combining our champion 1.58 eV PSCs (PCE of 17.7%) with an industrial-relevant low-cost n-type Si SCs, a four-terminal (4T) tandem efficiency of 25.5% has been achieved. Moreover, for the first time, 4T tandem SCs' performances have been measured in the low light intensity regime, achieving a PCE of 26.6%, corresponding to revealing a relative improvement above 9% compared to the standard 1 sun illumination condition. These results are very promising for their implementation under field-operating conditions.

Optical design considerations of rear-side dielectric for higher efficiency of PERC solar cells.

Higher reflectance of the rear-side dielectric stack, at the wavelength of the laser source used for ablation, reduces laser-induced damage and improves the open-circuit voltage of PERC silicon solar cells. The understanding of this correlation increases the working window of cost-effective nanosecond laser ablation of the rear-side dielectric for higher-efficiency industrial PERC-like solar cells.

Effect of sodium diffusion on the properties of CIGS solar absorbers prepared using elemental Se in a two-step process.

The influence of Na diffusion from various glass substrates during a high-temperature slenization process on the microstructure and morphology of two-step formed CIGS absorber layers is investigated. In order to minimise the CIGS absorber formation time, elemental Se vapour is used to prepare the CIGS absorber. The grain sizes of the CIGS films are found to increase with increasing sodium in the glass substrates (extra clear glass, soda-lime glass, borosilicate glass). TiN and SiN thin films are used as diffusion barrier layers inserted between the glass substrate and the Mo rear conatct to tune the Na diffusion from the soda-lime glass. The interdiffusion between the In-rich CuInSe2 surface layer and the Ga-rich CuGaSe2 layer is promoted by the barrier layer, leading to larger CIGS grains. Efforts are also taken to understand the differences in Na diffusion (from the glass substrates) and their effects on the MoSe2 intermediate layer formation during the high-temperature CIGS absorber formation processes. We find that excess amounts of Na and Se are essential for the MoSe2 growth. The excessive Na in the form of Na2Sex at the CIGS/Mo interface works as a Se source and catalyses the MoSe2 formation. The Se flow in the two-step CIGS formation process must be sufficiently high to obtain high-efficiency CIGS solar cells.

Noise in the intensive care unit and its influence on sleep quality: a multicenter observational study in Dutch intensive care units.

BACKGROUND: High noise levels in the intensive care unit (ICU) are a well-known problem. Little is known about the effect of noise on sleep quality in ICU patients. The study aim is to determine the effect of noise on subjective sleep quality. METHODS: This was a multicenter observational study in six Dutch ICUs. Noise recording equipment was installed in 2-4 rooms per ICU. Adult patients were eligible for the study 48 h after ICU admission and were followed up to maximum of five nights in the ICU. Exclusion criteria were presence of delirium and/or inability to be assessed for sleep quality. Sleep was evaluated using the Richards Campbell Sleep Questionnaire (range 0-100 mm). Noise recordings were used for analysis of various auditory parameters, including the number and duration of restorative periods. Hierarchical mixed model regression analysis was used to determine associations between noise and sleep. RESULTS: In total, 64 patients (68% male), mean age 63.9 (± 11.7) years and mean Acute Physiology And Chronic Health Evaluation (APACHE) II score 21.1 (± 7.1) were included. Average sleep quality score was 56 ± 24 mm. The mean of the 24-h average sound pressure levels (LAeq, 24h) was 54.0 dBA (± 2.4). Mixed-effects regression analyses showed that background noise (ß = - 0.51, p < 0.05) had a negative impact on sleep quality, whereas number of restorative periods (ß = 0.53, p < 0.01) and female sex (ß = 1.25, p < 0.01) were weakly but significantly correlated with sleep. CONCLUSIONS: Noise levels are negatively associated and restorative periods and female gender are positively associated with subjective sleep quality in ICU patients. TRIAL REGISTRATION: www.ClinicalTrials.gov, NCT01826799 . Registered on 9 April 2013.

Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations.

Phylogeographic analyses of the gall fly Urophora cardui have in earlier studies based on allozymes and mtDNA identified small-scale, parapatrically diverged populations within an expanding Western Palearctic population. However, the low polymorphism of these markers prohibited an accurate delimitation of the evolutionary origin of the parapatric divergence. Urophora cardui from the Western Palearctic have been introduced into Canada as biological control agents of the host plant Cirsium arvense. Here, we characterise 12 microsatellite loci with hexa-, penta- and tetra-nucleotide repeat motifs and report a genotyping-by-sequencing SNP protocol. We test the markers for genetic variation among three parapatric U. cardui populations. Microsatellite variability (N = 59 individuals) was high: expected heterozygosity/locus/population (0.60-0.90), allele number/locus/population (5-21). One locus was alternatively sex-linked in males or females. Cross-species amplification in the sister species U. stylata was successful or partially successful for seven loci. For genotyping-by-sequencing (N = 18 individuals), different DNA extraction methods did not affect data quality. Depending on sequence sorting criteria, 1,177-2,347 unlinked SNPs and 1,750-4,469 parsimony informative sites were found in 3,514-5,767 loci recovered after paralog filtering. Both marker systems quantified the same population partitions with high probabilities. Many and highly differentiated loci in both marker systems indicate genome-wide diversification and genetically distinct populations.

Population-specific genotype x genotype x environment interactions in bacterial disease of early life stages of Pacific oyster larvae.

The consequences of emerging marine diseases on the evolutionary trajectories of affected host populations in the marine realm are largely unexplored. Evolution in response to natural selection depends on the genetic variation of the traits under selection and the interaction of these traits with the environment (GxE). However, in the case of diseases, pathogen genotypes add another dimension to this interaction. Therefore, the study of disease resistance needs to be extended to the interaction of host genotype, pathogen genotype and environment (GxGxE). In this study, we used a full-sib breeding design crossing two genetically differentiated populations of the Pacific oyster Crassostrea gigas (Thunberg, 1793), to determine the influence of host genotype, pathogen genotype and temperature on disease resistance. Based on a controlled infection experiment on two early life stages, that is, D-larvae and Pediveliger larvae at elevated and ambient water temperatures, we estimated disease resistance to allopatric and sympatric Vibrio sp. by measuring survival and growth within and between genetically differentiated oyster populations. In both populations, survival was higher upon infection with sympatric Vibrio sp., indicating that disease resistance has a genetic basis and is dependent on host genotype. In addition, we observed a significant GxGxE effect in D-larvae, where contrary to expectations, disease resistance was higher at warm than at cold temperatures. Using thermal reaction norms, we could further show that disease resistance is an environment dependent trait with high plasticity, which indicates the potential for a fast acclimatization to changing environmental conditions. These population-specific reaction norms disappeared in hybrid crosses between both populations which demonstrates that admixture between genetically differentiated populations can influence GxGxE interactions on larger scales.

Optical scattering modeling of etched ZnO:Al superstrates and device simulation studies of a-Si:H solar cells with different texture morphologies.

Transparent conductive oxide (TCO) materials have been widely used as the front electrodes of thin-film amorphous silicon (a-Si:H) solar cells. To improve the performance of solar cells, textured front TCO is required as the optical layer which effectively scatters the incoming light and thus enhances the photon absorption within the device. One promising TCO material is aluminum-doped zinc oxide (AZO), which is most commonly prepared by magnetron sputtering. After deposition, sputtered AZO films are typically wet-chemically etched using diluted hydrochloric (HCl) or hydrofluoric (HF) acid to obtain rough surface morphologies. In this paper, we report the effects of a textured AZO front electrode on the performance of a-Si:H solar cells based on optical scattering modeling and electrical device simulations, involving four different AZO surface morphologies. The simulated light scattering behaviors indicate that a better textured surface not only scatters more light, but also allows more light get transmitted into the absorber (∼90% of visible light), due to greatly reduced front reflection by the rough surface. Device simulation results show that the two-step AZO texturing process should give improved a-Si:H solar cell performance, with an enhanced short-circuit current density of 16.5 mA/cm2, which leads to a high photovoltaic (PV) efficiency of 9.9%.

Primary CNS T-cell Lymphomas: A Clinical, Morphologic, Immunophenotypic, and Molecular Analysis.

Primary central nervous system (CNS) lymphomas are relatively rare with the most common subtype being diffuse large B-cell lymphoma. Primary CNS T-cell lymphomas (PCNSTL) account for <5% of CNS lymphomas. We report the clinical, morphologic, immunophenotypic, and molecular characteristics of 18 PCNSTLs. Fifteen cases were classified as peripheral T-cell lymphoma, not otherwise specified, 2 of which were of γδ T-cell derivation and 1 was TCR silent; there was 1 anaplastic large cell lymphoma, ALK-positive and 2 anaplastic large cell lymphoma, ALK-negative. Median age was 58.5 years (range, 21 to 81 y), with an M:F ratio of 11:7. Imaging results showed that 15 patients had supratentorial lesions. Regardless of subtype, necrosis and perivascular cuffing of tumor cells were frequently observed (11/18 cases). CD3 was positive in all cases but 1; 10/17 were CD8-positive, and 5/17 were CD4-positive. Most cases studied had a cytotoxic phenotype with expression of TIA1 (13/15) and granzyme-B (9/13). Polymerase chain reaction analysis of T-cell receptor γ rearrangement confirmed a T-cell clone in 14 cases with adequate DNA quality. Next-generation sequencing showed somatic mutations in 36% of cases studied; 2 had >1 mutation, and none showed overlapping mutations. These included mutations in DNMT3A, KRAS, JAK3, STAT3, STAT5B, GNB1, and TET2 genes, genes implicated previously in other T-cell neoplasms. The outcome was heterogenous; 2 patients are alive without disease, 4 are alive with disease, and 6 died of disease. In conclusion, PCNSTLs are histologically and genomically heterogenous with frequent phenotypic aberrancy and a cytotoxic phenotype in most cases.

Thin-film a-Si:H solar cells processed on aluminum-induced texture (AIT) glass superstrates: prediction of light absorption enhancement.

Light scattering superstrates are important for thin-film a-Si:H solar cells. In this work, aluminum-induced texture (AIT) glass, covered with nonetched Al-doped ZnO (AZO), is investigated as an alternative to the commonly used planar glass with texture-etched AZO superstrate. Four different AIT glasses with different surface roughnesses and different lateral feature sizes are investigated for their effects on light trapping in a-Si:H solar cells. For comparison, two reference superstrates are investigated as well: planar glass covered with nonetched AZO and planar glass covered with texture-etched AZO. Single-junction a-Si:H solar cells are deposited onto each superstrate, and the scattering properties (haze and angular resolved scattering) as well as the solar cell characteristics (current-voltage and external quantum efficiency) are measured and compared. The results indicate that AIT glass superstrates with nonetched AZO provide similar, or even superior, light trapping than the standard reference superstrate, which is demonstrated by a higher short-circuit current Jsc and a higher external quantum efficiency. Using the trapped light fraction δ, a quantity based on the integrated light scattering at the AZO/a-Si:H interface, we show that Jsc linearly increases with δ in the scattering regime of the samples, regardless of the type of superstrate used.

The realistic energy yield potential of GaAs-on-Si tandem solar cells: a theoretical case study.

Si based tandem solar cells represent an alternative to traditional compound III-V multijunction cells as a promising way to achieve high efficiencies. A theoretical study on the energy yield of GaAs on Si (GaAs/Si) tandem solar cells is performed to assess their energy yield potential under realistic illumination conditions with varying spectrum. We find that the yield of a 4-terminal contact scheme with thick top cell is more than 15% higher than for a 2-terminal scheme. Furthermore, we quantify the main losses that occur for this type of solar cell under varying spectra. Apart from current mismatch, we find that a significant power loss can be attributed to low irradiance seen by the sub-cells. The study shows that despite non-optimal bandgap combination, GaAs/Si tandem solar cells have the potential to surpass 30% energy conversion efficiency.

NOTCH1 intracellular domain immunohistochemistry as a diagnostic tool to distinguish T-lymphoblastic lymphoma from thymoma.

Distinction between lymphocyte-rich thymoma and T-lymphoblastic lymphoma/leukemia (T-LBL) can be problematic because of a predominance of precursor T cells in both, particularly if the epithelial component in a thymoma is undersampled. Because of very different clinical implications, accurate diagnosis is critical. The NOTCH1 signaling pathway is frequently activated in T-LBL and plays a central role in the pathogenesis of this disease. Antibodies to NOTCH1 intracellular domain (N1ICD), recognizing the active form of NOTCH1, have been developed. We hypothesized that detection of N1ICD would be useful in distinguishing T-LBL from thymoma and investigated a series of formalin-fixed, paraffin-embedded tissues for immunoreactivity with an N1ICD antibody using automated immunohistochemistry. Slides were scored using a 25% nuclear reactivity threshold for positivity. Hyperplastic tonsil showed positivity in few scattered interfollicular lymphoid cells, suprabasilar epithelial cells, and endothelial cells. Thymocytes from non-neoplastic thymus were largely negative for N1ICD. All thymomas tested (n=23) were negative for N1ICD, although epithelial cells and a small minority of thymocytes may be positive, requiring careful interpretation. All T-LBL cases (n=16) were scored positive for N1ICD: 8 (50%) of these showed diffuse and mostly strong immunoreactivity, whereas the remaining 8 (50%) had less extensive positivity, but with consistently >25% nuclear staining. In conclusion, normal thymocytes do not express significant levels of N1ICD. In keeping with this pattern, thymomas are negative for N1ICD, whereas a high percentage of T-LBL expresses N1ICD. Thus, N1ICD immunohistochemistry appears to be a useful method in distinguishing T-LBL from thymoma.

Frequency, interobserver reproducibility and clinical significance of equivocal peaks in PCR clonality testing using Euroclonality/BIOMED-2 primers.

AIMS: PCR studies for lymphoid clonality are now widely employed, especially using Euroclonality/BIOMED-2 primers. Criteria for interpretation as a clonal result, however, have proven controversial. This study examines the frequency and clinical significance of equivocal amplification patterns and measures the interobserver reproducibility of clonality interpretations. METHODS: At our institution, results of each primer set are first classified as clonal, non-clonal or abnormal (equivocal peak on polyclonal background). Final results for all primer sets are then collectively reported as positive (≥1 clonal result), negative (non-clonal results) or indeterminate (≥1 abnormal result) for a clonal population. Results of 274 consecutive clonality cases were reviewed, and the interobserver reproducibility of individual primer set reactions and final results was determined in a subset of 30 cases. RESULTS: 44/161 (27%) B-cell and 50/163 (31%) T-cell cases contained at least one abnormal peak. Of these, 29 (64%) and 31 (62%), respectively, showed clonal results in another primer set. Interobserver reproducibility was excellent for most primer sets and for final interpretations, but only fair to good for IGK V-J and TCRB D-J1+2 primer sets. A definitive diagnosis of lymphoma was rendered in 93%, 20% and 6% of B-cell cases and 90%, 42%, and 14% of T-cell cases positive, indeterminate or negative for a clonal population, respectively. CONCLUSIONS: Using a subjective approach, abnormal (equivocal) peaks are frequently observed in routine practice. However, most cases with abnormal peaks contain clonal rearrangements in other primer sets, facilitating overall interpretation of final results with excellent interobserver reproducibility.

Analytical solution for haze values of aluminium-induced texture (AIT) glass superstrates for a-Si:H solar cells.

Light scattering at randomly textured interfaces is essential to improve the absorption of thin-film silicon solar cells. Aluminium-induced texture (AIT) glass provides suitable scattering for amorphous silicon (a-Si:H) solar cells. The scattering properties of textured surfaces are usually characterised by two properties: the angularly resolved intensity distribution and the haze. However, we find that the commonly used haze equations cannot accurately describe the experimentally observed spectral dependence of the haze of AIT glass. This is particularly the case for surface morphologies with a large rms roughness and small lateral feature sizes. In this paper we present an improved method for haze calculation, based on the power spectral density (PSD) function of the randomly textured surface. To better reproduce the measured haze characteristics, we suggest two improvements: i) inclusion of the average lateral feature size of the textured surface into the haze calculation, and ii) considering the opening angle of the haze measurement. We show that with these two improvements an accurate prediction of the haze of AIT glass is possible. Furthermore, we use the new equation to define optimum morphology parameters for AIT glass to be used for a-Si:H solar cell applications. The autocorrelation length is identified as the critical parameter. For the investigated a-Si:H solar cells, the optimum autocorrelation length is shown to be 320 nm.

Follicular lymphomas in children and young adults: a comparison of the pediatric variant with usual follicular lymphoma.

Follicular lymphoma (FL), a common lymphoma in adults, occurs rarely in pediatric and young adult patients. Most pediatric cases have been described as grade 3, but the criteria to distinguish the pediatric variant of FL (PFL) from usual FL (UFL) seen in adults are not well defined. We undertook a study of FL in patients under the age of 30. We identified 63 cases, which were analyzed by morphology, immunohistochemistry, and polymerase chain reaction analysis of IGH@ and IGK@ clonality. These data were correlated with clinical findings including stage, treatment, and outcome. Among the 63 cases, 34 cases were classified as PFL: 22 presenting in lymph nodes, 8 in the Waldeyer ring, and 4 in the testis. Clonal immunoglobulin gene rearrangement was detected in 97% of PFL cases, but fluorescence in situ hybridization analysis showed an absence of the BCL2/IGH@ translocation in all cases tested. Twenty-nine cases were classified as UFL, 28 of which presented in lymph nodes. The nodal PFLs were observed exclusively in male patients in both children and young adults with a median age of 15 years. They showed marked head/neck predilection, blastoid cytologic features with a high proliferation rate, lack of BCL2 protein and t(14;18), low clinical stage at presentation, and good prognosis. PFLs involving the Waldeyer ring were distinguished by MUM1 expression, 50% (3/6) of which carried IRF4 breaks. BCL2 expression was common (63%) in the absence of BCL2/IGH@ translocation. UFLs were more common in female patients, exclusively in young adults (median age, 24 y), with no cases reported in patients under the age of 18. Twenty-five of 29 cases were of grade 1-2, and 4 cases were classified as grade 3A. They exhibited a higher clinical stage at presentation. Eighty-three percent expressed BCL2. Our results indicate that histologic and immunophenotypic criteria can reliably separate PFL and UFL and that UFL is exceptionally rare in the pediatric age group. PFL associated with particular anatomic sites have distinctive features and should be evaluated separately in future clinical and biological studies.

Follicular lymphoma in situ: clinical implications and comparisons with partial involvement by follicular lymphoma.

Follicular lymphoma in situ (FLIS) was first described nearly a decade ago, but its clinical significance remains uncertain. We reevaluated our original series and more recently diagnosed cases to develop criteria for the distinction of FLIS from partial involvement by follicular lymphoma (PFL). A total of 34 cases of FLIS were identified, most often as an incidental finding in a reactive lymph node. Six of 34 patients had prior or concurrent FL, and 5 of 34 had FLIS composite with another lymphoma. Of patients with negative staging at diagnosis and available follow-up (21 patients), only one (5%) developed FL (follow-up: median, 41 months; range, 10-118 months). Follow-up was not available in 2 cases. Fluorescence in situ hybridization for BCL2 gene rearrangement was positive in all 17 cases tested. PFL patients were more likely to develop FL, diagnosed in 9 of 17 (53%) who were untreated. Six patients with PFL were treated with local radiation therapy (4) or rituximab (2) and remained with no evidence of disease. FLIS can be reliably distinguished from PFL and has a very low rate of progression to clinically significant FL. FLIS may represent the tissue counterpart of circulating t(14;18)-positive B cells.