Reducing the number of accepted species in Aspergillus series Nigri.

The Aspergillus series Nigri contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (benA, CaM and RPB2) for 276 strains from series Nigri and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: A. niger, A. tubingensis and A. brasiliensis. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on benA, CaM and RPB2 is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the A. niger and A. brasiliensis lineages, while one to four species were inconsistently delimited in the A. tubingensis lineage. After considering all of these results and their practical implications, we propose that the revised series Nigri includes six species: A. brasiliensis, A. eucalypticola, A. luchuensis (syn. A. piperis), A. niger (syn. A. vinaceus and A. welwitschiae), A. tubingensis (syn. A. chiangmaiensis, A. costaricensis, A. neoniger and A. pseudopiperis) and A. vadensis. We also showed that the intraspecific genetic variability in the redefined A. niger and A. tubingensis does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy. Citation: Bian C, Kusuya Y, Sklenár F, D'hooge E, Yaguchi T, Ban S, Visagie CM, Houbraken J, Takahashi H, Hubka V (2022). Reducing the number of accepted species in Aspergillus series Nigri. Studies in Mycology 102: 95-132. doi: 10.3114/sim.2022.102.03.

Search for Electron Antineutrino Appearance in a Long-Baseline Muon Antineutrino Beam.

Electron antineutrino appearance is measured by the T2K experiment in an accelerator-produced antineutrino beam, using additional neutrino beam operation to constrain parameters of the Pontecorvo-Maki-Nakagawa-Sakata (PMNS) mixing matrix. T2K observes 15 candidate electron antineutrino events with a background expectation of 9.3 events. Including information from the kinematic distribution of observed events, the hypothesis of no electron antineutrino appearance is disfavored with a significance of 2.40σ and no discrepancy between data and PMNS predictions is found. A complementary analysis that introduces an additional free parameter which allows non-PMNS values of electron neutrino and antineutrino appearance also finds no discrepancy between data and PMNS predictions.

Predicting the Debonding of CAD/CAM Composite Resin Crowns with AI.

A preventive measure for debonding has not been established and is highly desirable to improve the survival rate of computer-aided design/computer-aided manufacturing (CAD/CAM) composite resin (CR) crowns. The aim of this study was to assess the usefulness of deep learning with a convolution neural network (CNN) method to predict the debonding probability of CAD/CAM CR crowns from 2-dimensional images captured from 3-dimensional (3D) stereolithography models of a die scanned by a 3D oral scanner. All cases of CAD/CAM CR crowns were manufactured from April 2014 to November 2015 at the Division of Prosthodontics, Osaka University Dental Hospital (Ethical Review Board at Osaka University, approval H27-E11). The data set consisted of a total of 24 cases: 12 trouble-free and 12 debonding as known labels. A total of 8,640 images were randomly divided into 6,480 training and validation images and 2,160 test images. Deep learning with a CNN method was conducted to develop a learning model to predict the debonding probability. The prediction accuracy, precision, recall, F-measure, receiver operating characteristic, and area under the curve of the learning model were assessed for the test images. Also, the mean calculation time was measured during the prediction for the test images. The prediction accuracy, precision, recall, and F-measure values of deep learning with a CNN method for the prediction of the debonding probability were 98.5%, 97.0%, 100%, and 0.985, respectively. The mean calculation time was 2 ms/step for 2,160 test images. The area under the curve was 0.998. Artificial intelligence (AI) technology-that is, the deep learning with a CNN method established in this study-demonstrated considerably good performance in terms of predicting the debonding probability of a CAD/CAM CR crown with 3D stereolithography models of a die scanned from patients.

Search for CP Violation in Neutrino and Antineutrino Oscillations by the T2K Experiment with 2.2×10

The T2K experiment measures muon neutrino disappearance and electron neutrino appearance in accelerator-produced neutrino and antineutrino beams. With an exposure of 14.7(7.6)×10^{20} protons on target in the neutrino (antineutrino) mode, 89 ν_{e} candidates and seven anti-ν_{e} candidates are observed, while 67.5 and 9.0 are expected for δ_{CP}=0 and normal mass ordering. The obtained 2σ confidence interval for the CP-violating phase, δ_{CP}, does not include the CP-conserving cases (δ_{CP}=0, π). The best-fit values of other parameters are sin^{2}θ_{23}=0.526_{-0.036}^{+0.032} and Δm_{32}^{2}=2.463_{-0.070}^{+0.071}×10^{-3} eV^{2}/c^{4}.

Long-Term Outcomes of Patients with Stent Tips Embedded into Internal Carotid Artery Branches during Aneurysm Coiling.

BACKGROUND AND PURPOSE: During stent-assisted coiling of ICA aneurysms, stent tips are sometimes unintentionally embedded into ICA branches. Stent tips can be visualized because they have radiopaque markers. Concerns regarding stent tip misplacement include risks of artery perforation and occlusion. The aim of this study was to evaluate the long-term outcomes of ICA branches with embedded stent tips. MATERIALS AND METHODS: ICA branches with embedded stent tips were identified among 35 patients with unruptured ICA aneurysms treated with stent-assisted coiling between November 2003 and November 2014. Patient clinical and angiographic outcomes associated with the embedded stent tip were analyzed. RESULTS: Most of the 35 studied aneurysms were paraclinoid ICA aneurysms (n = 30). The most commonly involved ICA branch was the posterior communicating artery (26 patients, 74.3%), followed by the anterior choroidal artery (8 patients, 22.9%) and ophthalmic artery (1 patient, 2.9%). During the follow-up period (38.6 ± 17.9 months), no new neurologic deficits developed. Neither hemorrhagic nor thromboembolic events occurred. Angiography was performed during the final follow-up evaluation at a mean of 32.7 ± 18.0 months, and all ICA branches with embedded stent tips showed patent blood flow without severe luminal narrowing. CONCLUSIONS: In our experience, placement of a stent tip into ICA branches during stent-assisted coiling was not associated with any major adverse events.

Combined Analysis of Neutrino and Antineutrino Oscillations at T2K.

T2K reports its first results in the search for CP violation in neutrino oscillations using appearance and disappearance channels for neutrino- and antineutrino-mode beams. The data include all runs from January 2010 to May 2016 and comprise 7.482×10^{20} protons on target in neutrino mode, which yielded in the far detector 32 e-like and 135 µ-like events, and 7.471×10^{20} protons on target in antineutrino mode, which yielded 4 e-like and 66 µ-like events. Reactor measurements of sin^{2}2θ_{13} have been used as an additional constraint. The one-dimensional confidence interval at 90% for the phase δ_{CP} spans the range (-3.13, -0.39) for normal mass ordering. The CP conservation hypothesis (δ_{CP}=0, π) is excluded at 90% C.L.

Measurement of Coherent π

We report the first measurement of the flux-averaged cross section for charged current coherent π^{+} production on carbon for neutrino energies less than 1.5 GeV, and with a restriction on the final state phase space volume in the T2K near detector, ND280. Comparisons are made with predictions from the Rein-Sehgal coherent production model and the model by Alvarez-Ruso et al., the latter representing the first implementation of an instance of the new class of microscopic coherent models in a neutrino interaction Monte Carlo event generator. We observe a clear event excess above background, disagreeing with the null results reported by K2K and SciBooNE in a similar neutrino energy region. The measured flux-averaged cross sections are below those predicted by both the Rein-Sehgal and Alvarez-Ruso et al.

Assessment of apple core collections constructed using phenotypic and genotypic data.

Several types of information can be used to select core collections, including passport data, agronomic data, and molecular data. However, little is known about the ability of core collections to retain the genetic diversity and structure of the whole collection for characters that were not considered during the selection, particularly when molecular markers are used. In this study, two core subsets were established for the apple (Malus spp) germplasm bank curated at the Apple Research Station, National Institute of Horticultural and Herbal Science, Korea, based upon genetic diversity estimated with 14 simple sequence repeat markers, and phenotypic diversity based on 23 traits. Comparisons between these two subsets and with the whole collection were used to determine the effect of the data used in the selection on phenotypic and genetic diversity, and population structure. The two subsets had a similar diversity and did not differ from the original collection, according to the Nei and Shannon diversity indices. Allele and class frequencies were also maintained in the two subsets. Overall, the type of data used to construct the core collection had little influence on the phenotypic and genetic diversity retained. Therefore, in the case of apple collections, the use of molecular markers is preferable, because they allow rapid and reliable characterization.

Older adults with biliary tract cancer: treatment and prognosis.

OBJECTIVES: To compare survival in older (≥65) and younger (<65) individuals with biliary tract cancer (BTC) and to determine whether treatment efficacy varies according to age. DESIGN: Retrospective cohort study and nested case-control study. SETTING: Tertiary referral center in Korea. PARTICIPANTS: Five hundred thirty-one individuals diagnosed with BTC from 2003 to 2011. MEASUREMENTS: Demographic and clinical characteristics of 326 older (≥65) and 205 younger (<65) individuals with BTC were compared. Differences in survival were also assessed after matching according to propensity score. RESULTS: There were no significant differences in sex, symptoms and signs, tumor histology, stage, or surgery between the two groups, but older participants had more comorbidities and poorer performance status and underwent less chemotherapy and radiotherapy (P < .05). Survival of the two groups was compared. After adjustment for baseline characteristics using the propensity score method, survival was still comparable (P = .72). When survival of older participants in the treatment group (TG, those who underwent surgery, chemotherapy, or radiotherapy) was compared with that of those in the supportive care group (SCG, those who received only supportive care), those in the TG had a longer survival time than those in the SCG (P < .001). This result was confirmed in the propensity analysis (including individuals undergoing surgery, P < .001; excluding individuals undergoing surgery, P < .001). In the multivariable Cox analysis, surgical resection and chemotherapy were significantly associated with longer survival, and advanced tumor stage, lower baseline serum albumin level, and greater comorbidity were found to significantly predict poor survival. Age was not associated with survival in individuals with BTC (P = .33). CONCLUSION: Older age was not associated with poor survival in BTC, and treated individuals had longer survival in the older BTC population. Therefore, treatment should not be restricted on the basis of age.

New teleomorph combinations in the entomopathogenic genus Metacordyceps.

The genus Metacordyceps contains arthropod pathogens in Clavicipitaceae (Hypocreales) that formerly were classified in Cordyceps sensu Kobayasi et Mains. Of the current arthropod pathogenic genera of Hypocreales, the genus Metacordyceps remains one of the most poorly understood and contains a number of teleomorphic morphologies convergent with species of Cordyceps s.s. (Cordycipitaceae) and Ophiocordyceps (Ophiocordycipitaceae). Of note, the anamorph genera Metarhizium and Pochonia were found to be associated only with Metacordyceps and demonstrated to be phylogenetically informative for the clade. Several species of Cordyceps considered to have uncertain placements (incertae sedis) in the current taxonomic framework of clavicipitoid fungi were collected during field expeditions mostly in eastern Asia. Species reclassified here in Metacordyceps include Cordyceps atrovirens Kobayasi & Shimizu, Cordyceps indigotica Kobayasi & Shimizu, Cordyceps khaoyaiensis Hywel-Jones, Cordyceps kusanagiensis Kobayasi & Shimizu, Cordyceps martialis Speg., Ophiocordyceps owariensis Kobayasi, Cordyceps pseudoatrovirens Kobayasi & Shimizu and Ophicordyceps owariensis f. viridescens (Uchiy. & Udagawa) G.H. Sung, J.M. Sung, Hywel-Jones & Spatafora. Incorporation of these species in a multigene phylogenetic framework of the major clades of clavicipitoid fungi more than doubled the number of species in Metacordyceps and allowed for refinement of morphological concepts for the genus consistent with the phylogenetic structure. Based on these findings we then discuss evolution of this genus, subgeneric relationships, anamorph connections, and suggest additional species that should be confirmed for possible inclusion in Metacordyceps.

Analysis of the effect of structural materials in a wall-less tissue-equivalent proportional counter irradiated by 290 MeV u(-1) carbon beam.

Effects of structural materials in a wall-less tissue-equivalent proportional counter were evaluated based on the calculation of energy deposits by EGS5 and the measurement of lineal energy distributions using 290 MeV u(-1) carbon beams. It is found that the correction of measured data based on simulation is necessary for understanding the energy deposition spectra in the homogeneous condition in tissues.

Caudal midazolam does not affect sevoflurane requirements and recovery in pediatric day-case hernioplasty.

BACKGROUND: This prospective, randomized, double-blind study aimed to determine whether caudal midazolam combined with ropivacaine affects anesthetic requirements, recovery profiles, and post-operative analgesia compared with ropivacaine alone in pediatric day-case hernioplasty. METHODS: Sixty boys (2-5 years old) received caudal injections of 0.2% ropivacaine 1 ml/kg and epinephrine 1 : 200,000 with (RM group) or without (R group) 50 microg/kg of midazolam under sevoflurane anesthesia. The sevoflurane requirement was determined by adjusting to a bispectral index score=50. RESULTS: Concentrations of end-tidal sevoflurane (ETsevo%) after induction were similar in both groups. After caudal block, ETsevo% before and after surgical stimuli did not show significant intra- or intergroup differences. Recovery characteristics, including post-operative sedations, were similar in both groups. Post-operative pain scores were significantly lower in the RM group than the R group. CONCLUSIONS: Caudal midazolam (50 microg/kg) added to 2% ropivacaine did not influence sevoflurane requirement or recovery but improved post-operative analgesia compared with ropivacaine alone in pediatric day-case hernioplasty.

Computing the Heat of Adsorption using Molecular Simulations: The Effect of Strong Coulombic Interactions.

Molecular simulations are an important tool for the study of adsorption of hydrocarbons in nanoporous materials such as zeolites. The heat of adsorption is an important thermodynamic quantity that can be measured both in experiments and molecular simulations, and therefore it is often used to investigate the quality of a force field for a certain guest-host (g - h) system. In molecular simulations, the heat of adsorption in zeolites is often computed using either of the following methods: (1) using the Clausius-Clapeyron equation, which requires the partial derivative of the pressure with respect to temperature at constant loading, (2) using the energy difference between the host with and without a single guest molecule present, and (3) from energy/particle fluctuations in the grand-canonical ensemble. To calculate the heat of adsorption from experiments (besides direct calorimetry), only the first method is usually applicable. Although the computation of the heat of adsorption is straightforward for all-silica zeolites, severe difficulties arise when applying the conventional methods to systems with nonframework cations present. The reason for this is that these nonframework cations have very strong Coulombic interactions with the zeolite. We will present an alternative method based on biased interactions of guest molecules that suffers less from these difficulties. This method requires only a single simulation of the host structure. In addition, we will review some of the other important issues concerning the handling of these strong Coulombic interactions in simulating the adsorption of guest molecules. It turns out that the recently proposed Wolf method ( J. Chem. Phys. 1999, 110 , 8254 ) performs poorly for zeolites as a large cutoff radius is needed for convergence.

Competitive coexistence of superconductivity with antiferromagnetism in CeRhIn5.

We carried out ac magnetic susceptibility measurements under pressures P on the heavy fermion antiferromagnet CeRhIn5. We report bulk superconductivity (SC) at ambient pressure with a transition temperature Tc approximately or equal to 90 mK. The degraded SC in a powdered or polished sample was restored by annealing, showing that the SC state is sensitive to inhomogeneity. In a coexistence region of the SC with antiferromagnetism (AF), we find that Tc(P)(n)TN(P)(1-n) = const where TN indicates a Néel temperature and n denotes a ratio of electronic specific heat coefficients below and above TN, indicating the competition of the SC and the AF for states at the Fermi surface.

The effect of epidural sufentanil in ropivacaine on urinary retention in patients undergoing gastrectomy.

BACKGROUND: Although epidural opioids have excellent analgesic property, their side-effects limit its use in patient-controlled epidural analgesia (PCEA). This study was designed to compare side-effects of epidural sufentanil in ropivacaine with that of morphine in ropivacaine focusing on lower urinary tract function after major abdominal surgery. METHODS: In total 60 patients undergoing gastrectomy were randomly allocated to receive either sufentanil in ropivacaine (Group S, n=30) or morphine in ropivacaine (Group M, n=30) for their PCEA. Epidural catheter was inserted between the 7th and 8th thoracic spine. Visual analogue pain score and side-effects such as nausea, vomiting, pruritus, hypotension and urinary retention were evaluated during postoperative days (PODs) 1 and 2 in the postanaesthetic care unit. RESULTS: The incidence of serious to major micturition problem in Group S was lower than that in Group M (P<0.001). The incidence of pruritus, nausea and vomiting was also lower in Group S than in Group M on POD 1. CONCLUSIONS: The lower incidence of major/serious micturition problem in patients receiving sufentanil in ropivacaine thoracic epidural analgesia suggests that continuation of urinary drainage may not be necessary from POD 1 onwards.

Venepuncture is preferable to heel lance for blood sampling in term neonates.

BACKGROUND: The analgesic effect of oral sucrose in newborn infants undergoing painful procedures is generally accepted. For blood sampling, some studies have shown that venepuncture (VP) is less painful than heel lance (HL). OBJECTIVE: To determine the least painful and most effective method among blood sampling by VP or HL with or without sucrose. DESIGN: Randomised, double blind, placebo controlled trial. SUBJECTS: A total of 100 healthy, full term newborn infants being screened for inborn errors of metabolism were randomly allocated to one of four experimental groups (25 infants in each). Intervention and OUTCOME MEASURE: Seven specially trained nurses took turns to carry out blood sampling two minutes after administration of oral sucrose or water. Neonatal pain was assessed by the neonatal facial coding system (NFCS), as well as by crying. RESULTS: Without sucrose, the NFCS score was higher in the HL group than the VP group during blood sampling (median 58 v 23, p<0.001). Oral sucrose significantly reduced the score of the HL group (58 v 47, p<0.01) and also tended to reduce the score of the VP group (23 v 2, p<0.1). However, the HL with sucrose group still had a higher score than the VP without sucrose group (47 v 23, p<0.01). Crying and the total procedure time showed the same trends as the NFCS score. CONCLUSIONS: VP is less painful and more effective than HL for blood sampling in newborn infants. Although oral sucrose may have an additive analgesic effect, it is not necessarily required if VP is used for blood sampling.

Arrangement of high-energy neutron irradiation field and shielding experiment using 4 m concrete at KENS.

An irradiation field of high-energy neutrons produced in the forward direction from a thick tungsten target bombarded by 500 MeV protons was arranged at the KENS spallation neutron source facility. In this facility, shielding experiment was performed with an ordinary concrete shield of 4 m thickness assembled in the irradiation room, 2.5 m downstream from the target centre. Activation detectors of bismuth, aluminium, indium and gold were inserted into eight slots inside the shield and attenuations of neutron reaction rates were obtained by measurements of gamma-rays from the activation detectors. A MARS14 Monte Carlo simulation was also performed down to thermal energy, and comparisons between the calculations and measurements show agreements within a factor of 3. This neutron field is useful for studies of shielding, activation and radiation damage of materials for high-energy neutrons, and experimental data are useful to check the accuracies of the transmission and activation calculation codes.

Taxonomic discrimination of flowering plants by multivariate analysis of Fourier transform infrared spectroscopy data.

Fourier transform infrared spectroscopy (FTIR) provides biochemical profiles containing overlapping signals from a majority of the compounds that are present when whole cells are analyzed. Leaf samples of seven higher plant species and varieties were subjected to FTIR to determine whether plants can be discriminated phylogenetically on the basis of biochemical profiles. A hierarchical dendrogram based on principal component analysis (PCA) of FTIR data showed relationships between plants that were in agreement with known plant taxonomy. Genetic programming (GP) analysis determined the top three to five biomarkers from FTIR data that discriminated plants at each hierarchical level of the dendrogram. Most biomarkers determined by GP analysis at each hierarchical level were specific to the carbohydrate fingerprint region (1,200-800 cm(-1)) of the FTIR spectrum. Our results indicate that differences in cell-wall composition and structure can provide the basis for chemotaxonomy of flowering plants.