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.

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}.

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.

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.

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.

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.

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.

Radiosensitivity of skin fibroblasts from atomic bomb survivors with and without breast cancer.

Fibroblasts were established in vitro from skin biopsies obtained from 55 women and 1 man with or without breast cancer and with or without exposure to radiation from the atomic bomb explosion in Hiroshima. The radiosensitivity of these cells was evaluated by clonogenic assays after exposure to X-rays or to fission neutrons from a 252Cf source. Data were fitted to a multitarget model, S/S0 = A [1 - (1 - ekD)N], for both X-ray and neutron dose-survival curves. A single hit model, S/S0 = AekD, fits the neutron dose-survival responses as well. There were no differences in the means or variances of radiosensitivity between exposed and nonexposed groups or between patients with or without breast cancer. Hence, although the sample is not large, it provides no support for the hypothesis that atomic bomb radiation preferentially induces breast cancer in women whose cells in vitro are sensitive to cell killing by radiation.

Chromosomal instability and radiosensitivity in myelodysplastic syndrome cells.

Myelodysplastic syndrome (MDS) is a clonal disorder of hematopoietic stem cells. To investigate whether chromosomal instability and/or DNA repair defects are involved in the development of MDS, we measured the micronucleus (MN) frequency in peripheral blood lymphocytes exposed to various doses of X-rays, using a cytokinesis-block micronucleus assay. The spontaneous MN frequencies in RAEB and RAEB-T patients were significantly higher than those in normal individuals (P = 0.0224, P = 0.008, respectively). Also, the X-ray-induced MN frequencies in RA/RARS, RAEB, and RAEB-T patients were significantly higher than those in normal individuals (P = 0.007, P = 0.003, P = 0.003, respectively, at 2 Gy). In order to elucidate the cause of unusual radiosensitivity, we measured the expression levels of nucleotide excision repair (NER) genes in peripheral blood mononuclear cells using a RT-PCR method. Reduction of NER gene expression was found in only one of 10 patients with low risk MDS, but in four of 11 patients with high risk MDS. Our data suggest that chromosomal instability and DNA repair defects may be involved in the pathophysiology of disease progression of MDS.

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.

Tissue-specificity of reactivity to concanavalin-A of human cells in culture.

Concanavalin-A (Con-A) reactivity was studied to identify the tissue-specificity of cells established from various normal human tissues. Cells were treated with Con-A-labelled human red blood cells (C-RBC). C-RBC was not absorbed on the cells derived from the bone marrow, skin and liver. Lung-derived fibroblast cells showed weak C-RBC adsorption. Kidney-derived cells showed epithelial morphology and easily adsorbed C-RBC. These suggest that a large number of Con-A receptors exists on the membrane surface of kidney cells.

Usefulness of the high-frequency ultrasound probe in pretherapeutic staging of superficial-type colorectal tumors.

We evaluated the usefulness of the high-frequency ultrasound probe (HFUP, 20 MHz) to determine the depth of tumor invasion in 45 patients with superficial colorectal tumors. The correct diagnostic rate was 66% (30/45) when the depth of tumor invasion was classified into the following 6 layers: mucosa (m), upper 1/3 (sm1), middle 1/3 (sm2), and lower 1/3 (sm3) areas of the submucosa, muscularis propria (mp), and the subserosa or deeper areas (s). However, when the depth of tumor invasion was evaluated in 3 layers (m-sm1, sm2-sm3, and mp-deeper layer), which is the classification used to select cases for endoscopic mucosal resection, the correct diagnostic rate was 88.9% (40/45). These results suggest that the HFUP is useful to determine the depth of invasion to select treatment for superficial colorectal tumors.

Morphology and microstructure of electrochemically deposited calcium phosphates in a modified simulated body fluid.

Calcium phosphates were deposited on a pure titanium plate for various loading times under 1.3 and 12.9 mA/cm2 in a modified simulated body fluid at 52-92 degrees C. The plate-like crystals formed under 1.3 mA/cm2 were identified to be octacalcium phosphate (OCP) and/or carbonate-containing apatite. OCP converted to carbonate-containing apatite with the elapsing time of the loading current. The needle-like precipitates formed under 12.9 mA/cm2 were identified to be carbonate-containing apatite crystals elongated parallel to the c-axis direction. The degrees of crystallinity of the deposits formed under 1.3 mA/cm2 showed the highest value around 72 degrees C, whereas those under 12.9 mA/cm2 increased with the electrolyte temperature. The carbonate content of the deposits decreased with the electrolyte temperature and the flow current. The degree of crystallinity of the electrochemically deposited calcium phosphates decreased with the carbonate content.

Effect of temperature on electrochemical deposition of calcium phosphate coatings in a simulated body fluid.

Calcium phosphate coatings were deposited on titanium plate by an electrochemical method in simulated body fluid at 5-62 degrees C. X-ray diffractometry and FTIR studies demonstrated that the deposits at 5, 22 and 37 degrees C were amorphous and those at 52 and 62 degrees C contained Mg(OH)2, CaCO3 and carbonate apatite of low crystallinity. The calcium, magnesium and phosphorus contents of deposit increased in direct proportion to the square root of loading time of cathodic potential. Induction periods, which might be thought to be the time required to decrease the pH of the electrolyte around the cathode by the formation of H2 gas and to start deposition of calcium phosphate, were observed on all the regression lines. It is concluded that in the electrochemical synthesis of calcium phosphate in this temperature range the diffusion process is a rate-determining step.