We investigate the performance of three statistics, R1, R2 (Glas in Psychometrika 53:525–546, 1988), and M2 (Maydeu-Olivares & Joe in J. Am. Stat. Assoc. 100:1009–1020, 2005, Psychometrika 71:713–732, 2006) to assess the overall fit of a one-parameter logistic model (1PL) estimated by (marginal) maximum likelihood (ML). R1 and R2 were specifically designed to target specific assumptions of Rasch models, whereas M2 is a general purpose test statistic. We report asymptotic power rates under some interesting violations of model assumptions (different item discrimination, presence of guessing, and multidimensionality) as well as empirical rejection rates for correctly specified models and some misspecified models. All three statistics were found to be more powerful than Pearson’s X2 against two- and three-parameter logistic alternatives (2PL and 3PL), and against multidimensional 1PL models. The results suggest that there is no clear advantage in using goodness-of-fit statistics specifically designed for Rasch-type models to test these models when marginal ML estimation is used.

The Cladonia cervicornis group comprises lichen-forming fungi characterized by having scyphi with central proliferations. It includes c. 20 species globally. The taxonomy of this group is poorly resolved, with many species not thoroughly disentangled. The focus of this study is the European species in the C. cervicornis group. In order to estimate the phylogenetic relationships of these species, six loci were used: ITS rDNA, IGS rDNA, RPB1, RPB2, ef1α and cox1. Species delimitation methods (ASAP, PTP and GMYC) were used to infer the species boundaries based on four loci, ITS rDNA, IGS rDNA, cox1 and RPB2. A morphological analysis based on multivariate methods was performed to assess the importance of phenotypic differences among the lineages. The phylogenetic reconstructions placed the species of this group in the subclade Cladonia. Five lineages were recovered, corresponding to C. cervicornis, C. macrophyllodes, C. pulvinata, C. verticillata and a new lineage that we describe here, C. teuvoana. Our analyses revealed that Cladonia cineracea, C. stricta and C. trassii are polyphyletic.

Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.

Clearfield™ (CL) rice (Oryza sativa L.) is a weedy rice (Oryza spp.; synonym = red rice) control tool that has been used in Brazil since 2003. This system includes the use of an imidazolinone (IMI)-tolerant cultivar and the application of IMI herbicides. In this review article, Brazilian weed scientists evaluate the challenges and lessons learned over 18 yr of CL use. CL system benefits include selective weedy rice control, better crop establishment during the most advantageous period of the year, and more efficient fertilizer use. In Rio Grande do Sul state, the CL system, in conjunction with other improvements, has contributed to rice grain yield gains from 5,500 kg ha−1 before 2002 to around 8,400 kg ha−1 currently. In contrast, the main problem that has arisen over this period is the rapid evolution of IMI-resistant weedy rice, caused by gene flow from CL rice cultivars. The off-label use (rate and continuous use) of IMI herbicides has contributed to the evolution of resistance in Echinochloa spp. and other weeds. IMI herbicide carryover has also affected susceptible crops grown after CL rice. Crop rotation with soybean [Glycine max (L.) Merr.] is increasing, ensuring system sustainability. The importance of minimum tillage has also become apparent. Such cultivation includes applying nonselective herbicides before sowing or just before crop emergence (at the spiking stage to eliminate as much weedy rice as possible and other weeds at an early growth stage). It also includes the use of certified seeds free of weedy rice, following label instructions for IMI herbicides, applying the herbicide PRE followed by POST, and complementary weedy rice management practices, such as roguing of surviving weedy rice plants.

Weedy rice (WR) (Oryza spp.) is the most troublesome weed infesting rice paddies in Brazil. Several changes have occurred in this region regarding crop management, especially WR control based on the Clearfield® (CL) rice production system launched in 2003. This survey’s objective was to evaluate the WR infestation status by assessing the producers’ perception and the management practices used in southern Brazil after 18 yr of CL use in Brazil. Rice consultants and extension agents distributed a questionnaire to 213 producers in the Rio Grande do Sul (RS) and Santa Catarina (SC) states in the 2018 to 2019 growing season. In RS, most farms are larger than 150 ha, and farmers have adopted the CL system for more than 2 yr and use minimal or conventional tillage, permanent flooding, clomazone PRE tank-mixed with glyphosate at the rice spiking stage, and crop rotation with soybean [Glycine max (L.) Merr.] or pasture. In SC, rice farms are small, averaging from 20 to 30 ha, farmers predominantly plant pre-germinated rice and do not rotate rice with other crops, and roguing is practiced. Comparing both states, the CL system is used in 99.5% and 69.3% of the total surveyed rice areas in RS and SC, respectively. Imidazolinone-resistant WR is present in 68.4% and 26.6% of rice farms in RS and SC, respectively. Rice cultivation in Brazil is currently coexisting with WR with minimal integration of control methods. However, integrated practices can control this weed and are fundamental to the sustainability of systems based on herbicide-resistant rice cultivars.

Although the population of Griffon Vulture Gyps fulvus is significantly increasing in Europe, in Italy the species is still on the Red List as ‘Critically Endangered’, with the last natural population persisting on the island of Sardinia. Several episodes of poisoning hampered the success of conservation actions implemented in the years 1987–1995. In 2005 there were estimated to be only 31–32 territorial pairs, with the population occupying the territories of Alghero and Bosa. We used a long-term dataset of reproductive records from the Sardinian Griffon Vulture populations to run a population viability analysis (PVA) to evaluate the extinction risk using the Vortex simulation software. The model estimated the probability of extinction over the next five generations (estimated generation time: 11 years, simulation time used: 55 years) as 96.4% for the Alghero population, and near-zero for the Bosa population. We used sensitivity analyses to understand how uncertainty about parameter values affect model outcomes. Population projections were evaluated under different management scenarios tackling the main threats (poisoning and human disturbance) and implementing conservation actions (supplementary feeding and restocking). Our results showed that population size is a critical factor in affecting the projections of population dynamics of Griffon Vultures. Sensitivity analyses highlighted the importance of poisoning events to population persistence and showed that juvenile and adult mortality rates had a secondary impact on population viability. The only conservation measure effective in significantly increasing stochastic growth rates in the Alghero population, whose initial population was set at five individuals, was the complete removal of poisoning events. When targeting the Bosa population (initial population size 94 individuals), supplementary feeding, mitigation of the risk of poisoning episodes, restocking, and mitigation of human disturbance in the reproductive sites significantly increased stochastic growth rate. A cost-effectiveness analysis should be performed to prioritise interventions.

Trichomonas vaginalis induces cellular damage to the host cells (cytotoxicity) through the proteolytic activity of multiple proteinases of the cysteine type (CPs). Some CPs are modulated by environmental factors such as iron, zinc, polyamines, etc. Thus, the goal of this study was to assess the effect of glucose on T. vaginalis cytotoxicity, proteolytic activity and the particular role of TvCP2 (TVAG_057000) during cellular damage. Cytotoxicity assays showed that glucose-restriction (GR) promotes the highest HeLa cell monolayers destruction (~95%) by trichomonads compared to those grown under high glucose (~44%) condition. Zymography and Western blot using different primary antibodies showed that GR increased the proteolytic activity, amount and secretion of certain CPs, including TvCP2. We further characterized the effect of glucose on TvCP2. TvCP2 increases in GR, localized in vesicles close to the plasma membrane and on the surface of T. vaginalis. Furthermore, pretreatment of GR-trichomonads with an anti-TvCP2r polyclonal antibody specifically reduced the levels of cytotoxicity and apoptosis induction to HeLa cells in a concentration-dependent manner. In conclusion, our data show that GR, as a nutritional stress condition, promotes trichomonal cytotoxicity to the host cells, increases trichomonad proteolytic activity and amount of CPs, such as TvCP2 involved in cellular damage.

The implantation and controlled release of growth factors can enhance the proliferation and differentiation of cells that promote new bone formation at defect sites. Therefore, chitosan polymer microspheres were prepared by the water-in-oil emulsion (W/O) method and solvent freeze-drying, using glutaraldehyde as an ionic crosslinker, along with the lyophilization of solvents, to microencapsulate growth factors, preventing denaturation. The microspheres were loaded with recombinant bone morphogenetic protein 2 (Rh-BMP-2). They were spherical in shape, with a rough surface ranging in particle size from 0.4 to 1.6 μm. The yield percentage with respect to the polymer was 70% and the BMP-2 load was regulated by the initial protein dose. BMP-2 release experiments were performed for 7 days in PBS solutions at pH 4 and 7.4. The results showed that the protein release rate was only 2% lower at pH 7.4. BMP-2/chitosan microspheres were compatible with the MG-63 cell line (ATCC®CRL-1427™Homo sapiens bone osteosarcoma) and could be considered drug delivery vehicles in bone tissue engineering applications.