Fungal Planet description sheets: 951-1041

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Apenidiella antarctica from permafrost, Cladosporium fildesense from an unidentified marine sponge. Argentina, Geastrum wrightii on humus in mixed forest. Australia, Golovinomyces glandulariae on Glandularia aristigera, Neoanungitea eucalyptorum on leaves of Eucalyptus grandis, Teratosphaeria corymbiicola on leaves of Corymbia ficifolia, Xylaria eucalypti on leaves of Eucalyptus radiata. Brazil, Bovista psammophila on soil, Fusarium awaxy on rotten stalks of Zea mays, Geastrum lanuginosum on leaf litter covered soil, Hermetothecium mikaniae-micranthae (incl. Hermetothecium gen. nov.) on Mikania micrantha, Penicillium reconvexovelosoi in soil, Stagonosporopsis vannaccii from pod of Glycine max. British Virgin Isles, Lactifluus guanensis on soil. Canada, Sorocybe oblongispora on resin of Picea rubens. Chile, Colletotrichum roseum on leaves of Lapageria rosea. China, Setophoma caverna from carbonatite in Karst cave. Colombia, Lareunionomyces eucalypticola on leaves of Eucalyptus grandis. Costa Rica, Psathyrella pivae on wood. Cyprus, Clavulina iris on calcareous substrate. France, Chromosera ambigua and Clavulina iris var. occidentalis on soil. French West Indies, Helminthosphaeria hispidissima on dead wood. Guatemala, Talaromyces guatemalensis in soil. Malaysia, Neotracylla pini (incl. Tracyllales ord. nov. and Neotracylla gen. nov.) and Vermiculariopsiella pini on needles of Pinus tecunumanii. New Zealand, Neoconiothyrium viticola on stems of Vitis vinifera, Parafenestella pittospori on Pittosporum tenuifolium, Pilidium novae-zelandiae on Phoenix sp. Pakistan, Russula quercus-floribundae on forest floor. Portugal, Trichoderma aestuarinum from saline water. Russia, Pluteus liliputianus on fallen branch of deciduous tree, Pluteus spurius on decaying deciduous wood or soil. South Africa, Alloconiothyrium encephalarti, Phyllosticta encephalarticola and Neothyrostroma encephalarti (incl. Neothyrostroma gen. nov.) on leaves of Encephalartos sp., Chalara eucalypticola on leaf spots of Eucalyptus grandis × urophylla, Clypeosphaeria oleae on leaves of Olea capensis, Cylindrocladiella postalofficium on leaf litter of Sideroxylon inerme, Cylindromonium eugeniicola (incl. Cylindromonium gen. nov.) on leaf litter of Eugenia capensis, Cyphellophora goniomatis on leaves of Gonioma kamassi, Nothodactylaria nephrolepidis (incl. Nothodactylaria gen. nov. and Nothodactylariaceae fam. nov.) on leaves of Nephrolepis exaltata, Falcocladium eucalypti and Gyrothrix eucalypti on leaves of Eucalyptus sp., Gyrothrix oleae on leaves of Olea capensis subsp. macrocarpa, Harzia metrosideri on leaf litter of Metrosideros sp., Hippopotamyces phragmitis (incl. Hippopotamyces gen. nov.) on leaves of Phragmites australis, Lectera philenopterae on Philenoptera violacea, Leptosillia mayteni on leaves of Maytenus heterophylla, Lithohypha aloicola and Neoplatysporoides aloes on leaves of Aloe sp., Millesimomyces rhoicissi (incl. Millesimomyces gen. nov.) on leaves of Rhoicissus digitata, Neodevriesia strelitziicola on leaf litter of Strelitzia nicolai, Neokirramyces syzygii (incl. Neokirramyces gen. nov.) on leaf spots of Syzygium sp., Nothoramichloridium perseae (incl. Nothoramichloridium gen. nov. and Anungitiomycetaceae fam. nov.) on leaves of Persea americana, Paramycosphaerella watsoniae on leaf spots of Watsonia sp., Penicillium cuddlyae from dog food, Podocarpomyces knysnanus (incl. Podocarpomyces gen. nov.) on leaves of Podocarpus falcatus, Pseudocercospora heteropyxidicola on leaf spots of Heteropyxis natalensis, Pseudopenidiella podocarpi, Scolecobasidium podocarpi and Ceramothyrium podocarpicola on leaves of Podocarpus latifolius, Scolecobasidium blechni on leaves of Blechnum capense, Stomiopeltis syzygii on leaves of Syzygium chordatum, Strelitziomyces knysnanus (incl. Strelitziomyces gen. nov.) on leaves of Strelitzia alba, Talaromyces clemensii from rotting wood in goldmine, Verrucocladosporium visseri on Carpobrotus edulis. Spain, Boletopsis mediterraneensis on soil, Calycina cortegadensisi on a living twig of Castanea sativa, Emmonsiellopsis tuberculata in fluvial sediments, Mollisia cortegadensis on dead attached twig of Quercus robur, Psathyrella ovispora on soil, Pseudobeltrania lauri on leaf litter of Laurus azorica, Terfezia dunensis in soil, Tuber lucentum in soil, Venturia submersa on submerged plant debris. Thailand, Cordyceps jakajanicola on cicada nymph, Cordyceps kuiburiensis on spider, Distoseptispora caricis on leaves of Carex sp., Ophiocordyceps khonkaenensis on cicada nymph. USA, Cytosporella juncicola and Davidiellomyces juncicola on culms of Juncus effusus, Monochaetia massachusettsianum from air sample, Neohelicomyces melaleucae and Periconia neobrittanica on leaves of Melaleuca styphelioides × lanceolata, Pseudocamarosporium eucalypti on leaves of Eucalyptus sp., Pseudogymnoascus lindneri from sediment in a mine, Pseudogymnoascus turneri from sediment in a railroad tunnel, Pulchroboletus sclerotiorum on soil, Zygosporium pseudomasonii on leaf of Serenoa repens. Vietnam, Boletus candidissimus and Veloporphyrellus vulpinus on soil. Morphological and culture characteristics are supported by DNA barcodes.

Association between PD1 mRNA and response to anti-PD1 monotherapy across multiple cancer types

Background

We hypothesized that the abundance of PD1 mRNA in tumor samples might explain the differences in overall response rates (ORR) observed following anti-PD1 monotherapy across cancer types.

Patients and methods

RNASeqv2 data from 10 078 tumor samples representing 34 different cancer types was analyzed from TCGA. Eighteen immune-related gene signatures and 547 immune-related genes, including PD1, were explored. Correlations between each gene/signature and ORRs reported in the literature following anti-PD1 monotherapy were calculated. To translate the in silico findings to the clinical setting, we analyzed the expression of PD1 mRNA using the nCounter platform in 773 formalin-fixed paraffin embedded (FFPE) tumor samples across 17 cancer types. To test the direct relationship between PD1 mRNA, PDL1 immunohistochemistry (IHC), stromal tumor-infiltrating lymphocytes (sTILs) and ORR, we evaluated an independent FFPE-based dataset of 117 patients with advanced disease treated with anti-PD1 monotherapy.

Results

In pan-cancer TCGA, PD1 mRNA expression was found strongly correlated (r > 0.80) with CD8 T-cell genes and signatures and the proportion of PD1 mRNA-high tumors (80th percentile) within a given cancer type was variable (0%-84%). Strikingly, the PD1-high proportions across cancer types were found strongly correlated (r = 0.91) with the ORR following anti-PD1 monotherapy reported in the literature. Lower correlations were found with other immune-related genes/signatures, including PDL1. Using the same population-based cutoff (80th percentile), similar proportions of PD1-high disease in a given cancer type were identified in our in-house 773 tumor dataset as compared with TCGA. Finally, the pre-established PD1 mRNA FFPE-based cutoff was found significantly associated with anti-PD1 response in 117 patients with advanced disease (PD1-high 51.5%, PD1-intermediate 26.6% and PD1-low 15.0%; odds ratio between PD1-high and PD1-intermediate/low = 8.31; P < 0.001). In this same dataset, PDL1 tumor expression by IHC or percentage of sTILs was not found associated with response.

Conclusions

Our study provides a clinically applicable assay that links PD1 mRNA abundance, activated CD8 T-cells and anti-PD1 efficacy.

Interhospital Sepsis Code in Catalonia (Spain): Territorial model for initial care of patients with sepsis

Sepsis is a syndromic entity with high prevalence and mortality. The management of sepsis is standardized and exhibits time-dependent efficiency. However, the management of patients with sepsis is complex. The heterogeneity of the forms of presentation can make it difficult to detect and manage such cases, in the same way as differences in training, professional competences or the availability of health resources. The Advisory Commission for Patient Care with Sepsis (CAAPAS), comprising 7 scientific societies, the Emergency Medical System (SEM) and the Catalan Health Service (CatSalut), have developed the Interhospital Sepsis Code (CSI) in Catalonia (Spain). The general objective of the CSI is to increase awareness, promote early detection and facilitate initial care and interhospital coordination to attend septic patients in a homogeneous manner throughout Catalonia.

Could fertility clinics offer a sizable improvement of live birth rates by maturing post-GVBD oocytes in vitro?

PURPOSE

The objective of this study is to analyze the potential of immature, denuded, post-GVBD (germinal vesicle breakdown) oocytes (including prometaphase I, metaphase I, and prometaphase II stages) to result live birth after in vitro maturation. Furthermore, we compared two culture media to identify which of them provides better reproductive outcomes when used for in vitro maturation.

METHODS

We performed a retrospective cohort study including 4022 IVF-ICSI (in vitro fertilization-intracytoplasmic sperm injection) cycles between 2011 and 2015. A total of 4450 immature post-GVBD oocytes from 1442 cycles were cultured in vitro; of these, 2364 oocytes reached MII (metaphase II) stage (IVMC oocytes, in vitro meiotic completion) and were fertilized. Overall, 3933 embryo transfers were performed: 3579 were embryos derived from MII oocytes (ET-MII); 264 were embryos derived from MII + IVMC oocytes (ET-MIX), and 90 embryos from IVMC oocytes (ET-IVMC). In total, 399 IVMC embryos were transferred.

RESULTS

Maturation rate for immature post-GVBD oocytes was 54.1%. G-2™PLUS (Vitrolife) medium provided significantly higher maturation rate (p < 0.001) than G-IVF™PLUS (Vitrolife) (65.7% vs. 42.5%, p < 0.001). Embryos in ET-IVMC in cleavage stage had an average morphological score of 6.8/10 (7.7 in ET-MII; p < 0.001). Regarding reproductive outcomes, ET-IVMC gave 11.1% biochemical pregnancy rate, 10.0% clinical pregnancy rate, 7.8% ongoing pregnancy rate, and 5.6% live birth rate.

CONCLUSIONS

Embryos arising from IVMC oocytes resulted in a live birth rate of 5.6%. We suggest that in vitro maturation of denuded immature post-GVBD oocytes should be performed at the very least when few MII are collected, and likely in all patients, as they provide acceptable maturation and fertilization rates, and a sizeable increase in live birth.

Inaccessible rocky cliffs: An optimized method for plant data collection in extreme environments

Counts are normally used to assess the densities of plants. However, due to the physical characteristics of these sites, habitats and species associated with inaccessible rocky cliffs and other extreme environments pose additional challenges. It is therefore necessary to apply changes to the usual data collection methods. This system allows population sizes to be estimated from an incomplete data collection. This is important because when data collection sites are inaccessible, the fieldwork cannot be carried out within the time that is normally allocated. Furthermore, the minimum sampling effort involved enables economic resources to be saved. This method allows the time spent and the material, methodological and human resources used to be reduced while simultaneously allowing the highest level of accuracy to be maintained. •The minimum effort needed to carry out data collection of plants on vertical walls and other difficult-to-access environments is calculated.•The proposed method is based on the search for the theoretical distribution function with a better adjustment to the actual distribution of the studied species.•This system allows to reduce the necessary resources, while the maximum accuracy is maintained in the calculations.

Injection risk norms and practices among migrant Puerto Rican people who inject drugs in New York City: The limits of acculturation theory

BACKGROUND

Among people who inject drugs (PWID) in New York City (NYC), racial minorities are disproportionately infected with HIV and hepatitis C (HCV). Prior research has shown that PWID who started injecting drugs in Puerto Rico (P.R.) tend to maintain the risky injection behaviors learned there. This study identifies the P.R.-native norms supporting the continued injection risk behavior of migrant Puerto Rican PWID in NYC to inform a culturally appropriate risk-reduction intervention.

METHODS

40 migrant Puerto Rican PWID were recruited in NYC for a longitudinal qualitative study. The sample was stratified to include 20 migrants with <3 years in NYC and 20 migrants with >3-6 years in NYC. Time-location sampling was used to curb possible network bias in recruitment. Over 12 months, migrants completed semi-structured interviews at baseline, monthly follow-ups, and study exit. Analyses were guided by grounded theory.

RESULTS

Most participants (90%) reported having had chronic HCV, and 22.5% reported being HIV-positive. Syringe- and cooker-/cotton-sharing were widespread in both P.R. and NYC. The ubiquitous practice of cleaning used syringes by "water-rinsing and air-blowing" was guided by a normative belief, learned in P.R., that "water and air kill HIV." Sterile syringe use was not a priority. HCV was not a concern. P.R.-native abstinence-only narratives discouraged opioid agonist treatment (OAT) enrollment among recent migrants (≤3 years). Experiences with drug dealers, prison-power groups, and injection doctors ("Gancheros") in P.R. influenced migrants' injection risk behavior in NYC. Those who were Gancheros in P.R. continued working as Gancheros in NYC.

CONCLUSIONS

Injection risks make migrant Puerto Rican PWID in NYC vulnerable to HIV/HCV. Harm reduction programs should pay closer attention to the rationales behind these injection risks. A risk-reduction intervention that incorporates the Ganchero figure may be a credible way to help migrants reduce injection risk and accept OAT and syringe exchange programs (SEP).

Influence of Pre-renal Transplant Secondary Hyperparathyroidism on Later Evolution After Transplantation

Persistence of secondary hyperparathyroidism (SHPT) is common after renal transplantation. Good diagnosis and treatment are important to avoid complications. The objective of our work was to perform a retrospective analysis of the evolution of SHPT after renal transplantation. We selected patients who had received a kidney transplant at our hospital between 2000 and 2014. The biochemical variables of chronic kidney disease-metabolic bone disorders (CKD-MBD) were collected at pretransplantation and at 3, 6, 12, and 24 months post-transplantation. Treatments related to SHPT were also analyzed. Five hundred forty-three renal transplants were included. The average preoperative parathyroid hormone (PTH) was 241.14 pg/mL, 115.7 pg/mL at 3 months, and at 12 and 24 months postoperatively, PTH levels stabilized to 112 pg/mL. Treatment related to SHPT was present in 27.3% of patients during the preoperative period, 40.4% at 3 months postoperatively, 24.2% at 12 months postoperatively, and 23.2% at 24 months postoperatively. There was a significant association between requiring some type of treatment preoperatively and the rest of the postoperative periods (P < .005). The sample was later divided into 3 groups based on preoperative PTH (1: <150 pg/mL, n = 223 [41.1%]; 2: 150-300 pg/mL, n = 173 [31.9%]; 3: >300 pg/mL, n = 147 [27.1%]) and their evolutions were compared. Higher levels of postoperative PTH in group pre-PTH 3 were observed. Group 3 also presented with greater need for treatment in the postoperative periods, with significant association (P < .05). A regression analysis was performed and found that postoperative PTH were dependent on preoperative PTH adjusted by glomerular filtration. In conclusion, parameters related to CKD-MBD (mainly PTH) after kidney transplant, dependent on preoperative levels and glomerular filtration. Patients with a greater grade of SHPT presented with higher levels of postoperative PTH despite receiving more intensive treatment.

Many-Body Multifractality throughout Bosonic Superfluid and Mott Insulator Phases

We demonstrate many-body multifractality of the Bose-Hubbard Hamiltonian's ground state in Fock space, for arbitrary values of the interparticle interaction. Generalized fractal dimensions unambiguously signal, even for small system sizes, the emergence of a Mott insulator that cannot, however, be naively identified with a localized phase in Fock space. We show that the scaling of the derivative of any generalized fractal dimension with respect to the interaction strength encodes the critical point of the superfluid to the Mott insulator transition, and provides an efficient way to accurately estimate its position. We further establish that the transition can be quantitatively characterized by one single wave function amplitude from the exponentially large Fock space.

Implications of crop model ensemble size and composition for estimates of adaptation effects and agreement of recommendations

Climate change is expected to severely affect cropping systems and food production in many parts of the world unless local adaptation can ameliorate these impacts. Ensembles of crop simulation models can be useful tools for assessing if proposed adaptation options are capable of achieving target yields, whilst also quantifying the share of uncertainty in the simulated crop impact resulting from the crop models themselves. Although some studies have analysed the influence of ensemble size on model outcomes, the effect of ensemble composition has not yet been properly appraised. Moreover, results and derived recommendations typically rely on averaged ensemble simulation results without accounting sufficiently for the spread of model outcomes. Therefore, we developed an Ensemble Outcome Agreement (EOA) index, which analyses the effect of changes in composition and size of a multi-model ensemble (MME) to evaluate the level of agreement between MME outcomes with respect to a given hypothesis (e.g. that adaptation measures result in positive crop responses). We analysed the recommendations of a previous study performed with an ensemble of 17 crop models and testing 54 adaptation options for rainfed winter wheat (Triticum aestivum L.) at Lleida (NE Spain) under perturbed conditions of temperature, precipitation and atmospheric CO2 concentration. Our results confirmed that most adaptations recommended in the previous study have a positive effect. However, we also showed that some options did not remain recommendable in specific conditions if different ensembles were considered. Using EOA, we were able to identify the adaptation options for which there is high confidence in their effectiveness at enhancing yields, even under severe climate perturbations. These include substituting spring wheat for winter wheat combined with earlier sowing dates and standard or longer duration cultivars, or introducing supplementary irrigation, the latter increasing EOA values in all cases. There is low confidence in recovering yields to baseline levels, although this target could be attained for some adaptation options under moderate climate perturbations. Recommendations derived from such robust results may provide crucial information for stakeholders seeking to implement adaptation measures.

Adjustable transobturator male system (ATOMS®) as treatment of stress urinary incontinence secondary to transurethral resection of the prostate

OBJECTIVES

Feasibility study to evaluate efficacy and safety of Adjustable Transobturator Male System (ATOMS^®) for male stress urinary incontinence (SUI) after transurethral resection of the prostate.

MATERIALS AND METHODS

Twenty patients were implanted ATOMS^® for SUI caused by transurethral resection of the prostate with or without radiotherapy. Incontinence severity was evaluated as mild (2 pads/day), moderate (3-5 pads/day) or severe (≥6pads/day), and dryness as none or one security pad/day. Changes in pad-test and pad-count after adjustment were investigated, together with operative parameters, patient satisfaction with the procedure, and number and grade of complications (Clavien-Dindo).

RESULTS

Median age was 76.5years. Five patients received previous pelvic radiation (3 prostate, 2 rectal cancer) and 2 (10%) previous failed artificial urinary sphincter with urethral erosion and mechanical failure, respectively. Preoperative SUI was mild in 4 (20%), moderate in 7 (35%) and severe in 9 (45%). Median filling of the system was 13.5ml. Median pad-test decreased from 375±855ml baseline to 10±31.5ml and pad-count from 4±3 to 0±1.5 after adjustment (1±3fillings). Postoperative SUI distribution was mild in 2 (10%), moderate in one (5%) and severe in 2 (10%). Satisfaction rate was 80%, equal for transurethral resection of the prostate with/without previous radiotherapy. No patient had urinary retention after catheter removal. Complications presented in 3 (15%) patients, all minor. After median 38.5mo follow-up no system has been removed, 19 (95%) self-considered better than before and 11 (55%) very much better.

CONCLUSION

Based on short-term efficacy and patient satisfaction ATOMS^® can be considered a realistic alternative for SUI after transurethral resection of the prostate, even after irradiation. Absence of urethral erosion and very limited problems make this alternative especially attractive for cases with diminished dexterity, advanced age and previous failed treatments.

Tailoring diamond's optical properties via direct femtosecond laser nanostructuring

We demonstrate a rapid, accurate, and convenient method for tailoring the optical properties of diamond surfaces by employing laser induced periodic surface structuring (LIPSSs). The characteristics of the fabricated photonic surfaces were adjusted by tuning the laser wavelength, number of impinging pulses, angle of incidence and polarization state. Using Finite Difference Time Domain (FDTD) modeling, the optical transmissivity and bandwidth was calculated for each fabricated LIPSSs morphology. The highest transmission of ~99.5% was obtained in the near-IR for LIPSSs structures with aspect ratios of the order of ~0.65. The present technique enabled us to identify the main laser parameters involved in the machining process, and to control it with a high degree of accuracy in terms of structure periodicity, morphology and aspect ratio. We also demonstrate and study the conditions for fabricating spatially coherent nanostructures over large areas maintaining a high degree of nanostructure repeatability and optical performance. While our experimental demonstrations have been mainly focused on diamond anti-reflection coatings and gratings, the technique can be easily extended to other materials and applications, such as integrated photonic devices, high power diamond optics, or the construction of photonic surfaces with tailored characteristics in general.