Bayesian Analysis of Nonnegative Data Using Dependency-Extended Two-Part Models

This article is motivated by the challenge of analysing an agricultural field experiment with observations that are positive on a continuous scale or zero. Such data can be analysed using two-part models, where the distribution is a mixture of a positive distribution and a Bernoulli distribution. However, traditional two-part models do not include any dependencies between the two parts of the model. Since the probability of zero is anticipated to be high when the expected value of the positive part is low, and the other way around, this article introduces dependency-extended two-part models. In addition, these extensions allow for modelling the median instead of the mean, which has advantages when distributions are skewed. The motivating example is an incomplete block trial comparing ten treatments against weed. Gamma and lognormal distributions were used for the positive response, although any density on the support of real numbers can be accommodated. In a cross-validation study, the proposed new models were compared with each other and with a baseline model without dependencies. Model performance and sensitivity to choice of priors were investigated through simulation. A dependency-extended two-part model for the median of the lognormal distribution performed best with regard to mean square error in prediction. Supplementary materials accompanying this paper appear online.

Pain-Induced Impact on Movement: Motor Coordination Variability and Accuracy-Based Skill

Studies on pain are generally conducted for two purposes: first, to study patients with pain who have physical changes due to nerve and muscle lesions, and second, to regain the appropriate kinematic post-pain pattern. The present study aimed to investigate the effect of pain on the coordination variability pattern and throw accuracy. Participants included 30 people with a mean age of 18-25 years who volunteered to participate in the study. Individuals were randomly divided into three groups of local pain, remote pain, and control group. Without pain, participants practiced and acquired skills in 10 blocks of 15 trials. In the retention and transition phase, which were associated with pain, in their respective groups, included 1 hour, 24- hour, and 1- week acquisition; they were re-tested twice in a 15-block trial, which was once with and without pain. The results revealed that pain did not affect the throwing accuracy (p = 0.469). Besides, in the phase of decreasing acceleration in throwing, movement variability pattern in the pain-related groups in the shoulder and elbow joints (p = 0.000), elbow and wrist (p = 0.000), were more than the painless groups. Based on the results, it can be said that the increase in variability in pain-related groups is due to the different strategies and patterns that individuals use to avoid pain. Also, despite the pain, the nervous system attempts to increase the variability find the least painful pattern of movement and reduces this variability over time and using a repetitive pattern.

Attrition Rate in Infant fNIRS Research: A Meta-Analysis

Understanding the trends and predictors of attrition rate, or the proportion of collected data that is excluded from the final analyses, is important for accurate research planning, assessing data integrity, and ensuring generalizability. In this pre-registered meta-analysis, we reviewed 182 publications in infant (0-24 months) functional near-infrared spectroscopy (fNIRS) research published from 1998 to April 9, 2020 and investigated the trends and predictors of attrition. The average attrition rate was 34.23% among 272 experiments across all 182 publications. Among a subset of 136 experiments which reported the specific reasons of subject exclusion, 21.50% of the attrition were infant-driven while 14.21% were signal-driven. Subject characteristics (e.g., age) and study design (e.g., fNIRS cap configuration, block/trial design, and stimulus type) predicted the total and subject-driven attrition rates, suggesting that modifying the recruitment pool or the study design can meaningfully reduce the attrition rate in infant fNIRS research. Based on the findings, we established guidelines on reporting the attrition rate for scientific transparency and made recommendations to minimize the attrition rates. We also launched an attrition rate calculator (LINK) to aid with research planning. This research can facilitate developmental cognitive neuroscientists in their quest toward increasingly rigorous and representative research.

Pain-Induced Impact on Movement: Motor Coordination Variability and Accuracy-Based Skill

Studies on pain are generally conducted for two purposes: first, to study patients with pain who have physical changes due to nerve and muscle lesions, and second, to regain the appropriate kinematic post-pain pattern. The present study aimed to investigate the effect of pain on the coordination variability pattern and throw accuracy. Participants included 30 people with a mean age of 18-25 years who volunteered to participate in the study. Individuals were randomly divided into three groups of local pain, remote pain, and control group. Without pain, participants practiced and acquired skills in 10 blocks of 15 trials. In the retention and transition phase, which were associated with pain, in their respective groups, included 1 hour, 24- hour, and 1- week acquisition; they were re-tested twice in a 15-block trial, which was once with and without pain. The results revealed that pain did not affect the throwing accuracy (p = 0.469). Besides, in the phase of decreasing acceleration in throwing, movement variability pattern in the pain-related groups in the shoulder and elbow joints (p = 0.000), elbow and wrist (p = 0.000), were more than the painless groups. Based on the results, it can be said that the increase in variability in pain-related groups is due to the different strategies and patterns that individuals use to avoid pain. Also, despite the pain, the nervous system attempts to increase the variability find the least painful pattern of movement and reduces this variability over time and using a repetitive pattern.

PRODUTIVIDADE DO MILHO COM A APLICAÇÃO DE Azospirillum spp. DIRETAMENTE NA CAIXA SEMEADORA

RESUMO - A inoculação das sementes com Azospirillum spp. é uma prática que tem sido rotineiramente realizada no milho, sobretudo via formulação líquida. Todavia, as respostas relativas a outros modos de inoculação com diferentes formulações são, ainda, pouco conhecidas. Desta forma, objetivou-se com este trabalho avaliar a eficiência agronômica de doses de A. brasilense em formulação polimérica em pó, aplicada diretamente na caixa semeadora, sobre os componentes da produtividade do milho. Para tanto, foi conduzido um ensaio em blocos casualisados, com quatro repetições. Os tratamentos consistiram de uma testemunha, dose total de N, ½ dose de N; ½ dose de N + inoculação comercial padrão e ½ dose de N + quatro doses de inoculante em pó (1, 2, 4 e 8 g kg-1), aplicado na caixa semeadora. Foram avaliados os caracteres produtividade, números de fileira por espiga e de grãos por fileira, massa de mil grãos, matéria seca da parte aérea e teores de N nos grãos e na parte aérea. Nas condições testadas, a dose de 2 g kg-1 de sementes do inoculante, quando associada à adubação nitrogenada de 90 kg ha-1, apresentou superioridade no rendimento da cultura, ultrapassando, inclusive, a inoculação comercial com produto líquido.Palavras-chave: Zea mays, fixação biológica, inoculante, rendimento. MAIZE YIELD IN RESPONSE TO THE APLICATION OF Azospirillum spp. INTO THE SEED TANK ABSTRACT - Seed inoculation with Azospirillum spp. is a practice that has been routinely carried out in maize crop, especially via liquid formulation. However, responses concerning other methods of inoculation of different formulations are still poorly understood. The objective of this work was to evaluate the agronomic efficiency of the application of powder formulation of Azospirillum brasilense directly into the sowing box. For this purpose, a randomized block trial with 4 replications was carried out. The treatments tested consisted of absence of N fertilizer, the full N recommendation and a combination of the half of recommended N associated with the inoculation of four doses of A. brasilense (1, 2, 4 and 8 g kg-1) in powder formulation. The following variables were evaluated: number of kernel per row, number of row per ear, shoot dry biomass, thousand seed weight, grain N content, shoot N content and grain yield. All treatments submitted to inoculation with the powder formulation showed higher yields than the treatment in which the total dose of N was applied. However, superior results were obtained for the treatment in which ½ dose of N was associated with the powder inoculant in the proportion of 2 g kg-1 of seed.Keywords: Zea mays, biological fixation, inoculant, productivity.

Dissemination of Goss’s Wilt of Corn and Epiphytic Clavibacter michiganensis subsp. nebraskensis from Inoculum Point Sources

Goss’s wilt of corn, caused by Clavibacter michiganensis subsp. nebraskensis, has reemerged since 2006 as an economically important disease of corn in in the Midwestern United States. In 2012 and 2013, field plot studies were conducted with a pathogenic, rifampicin-resistant C. michiganensis subsp. nebraskensis isolate and a Goss’s wilt-susceptible corn hybrid to monitor epiphytic C. michiganensis subsp. nebraskensis population densities and the temporal and spatial spread of Goss’s wilt incidence originating from inoculum point sources. The randomized complete block trial included three treatments: noninoculated control, inoculum point sources established by wound inoculation, and inoculum point sources consisting of C. michiganensis subsp. nebraskensis-infested corn residue. Epiphytic C. michiganensis subsp. nebraskensis was detected on asymptomatic corn leaves collected up to 2.5 m away from inoculum sources at 15 days after inoculation in both years. The percentage of asymptomatic leaf samples on which epiphytic C. michiganensis subsp. nebraskensis was detected increased until mid-August in both years, and reached 90, 55, and 35% in wound-, residue-, and noninoculated plots, respectively, in 2012; and 50, 11, and 2%, respectively, in 2013. Although both growing seasons were drier than normal, Goss’s wilt incidence increased over time and space from all C. michiganensis subsp. nebraskensis point sources. Plots infested with C. michiganensis subsp. nebraskensis residue had final Goss’s wilt incidence of 7.5 and 1.8% in 2012 and 2013, respectively; plots with a wound-inoculated source had final Goss’s wilt incidence of 16.6 and 14.0% in 2012 and 2013, respectively. Our findings suggest that relatively recent outbreaks of Goss’s wilt in new regions of the United States may be the result of a gradual, nondetected buildup of C. michiganensis subsp. nebraskensis inoculum in fields.

Modulation of error-sensitivity during a prism adaptation task in people with cerebellar degeneration

Cerebellar damage can profoundly impair human motor adaptation. For example, if reaching movements are perturbed abruptly, cerebellar damage impairs the ability to learn from the perturbation-induced errors. Interestingly, if the perturbation is imposed gradually over many trials, people with cerebellar damage may exhibit improved adaptation. However, this result is controversial, since the differential effects of gradual vs. abrupt protocols have not been observed in all studies. To examine this question, we recruited patients with pure cerebellar ataxia due to cerebellar cortical atrophy ( n = 13) and asked them to reach to a target while viewing the scene through wedge prisms. The prisms were computer controlled, making it possible to impose the full perturbation abruptly in one trial, or build up the perturbation gradually over many trials. To control visual feedback, we employed shutter glasses that removed visual feedback during the reach, allowing us to measure trial-by-trial learning from error (termed error-sensitivity), and trial-by-trial decay of motor memory (termed forgetting). We found that the patients benefited significantly from the gradual protocol, improving their performance with respect to the abrupt protocol by exhibiting smaller errors during the exposure block, and producing larger aftereffects during the postexposure block. Trial-by-trial analysis suggested that this improvement was due to increased error-sensitivity in the gradual protocol. Therefore, cerebellar patients exhibited an improved ability to learn from error if they experienced those errors gradually. This improvement coincided with increased error-sensitivity and was present in both groups of subjects, suggesting that control of error-sensitivity may be spared despite cerebellar damage.

Soil CO₂ CH₄ and N₂O fluxes from an afforested lowland raised peatbog in Scotland: implications for drainage and restoration

The effect of tree (lodgepole pine) planting with and without intensive drainage on soil greenhouse gas (GHG) fluxes was assessed after 45 yr at a raised peatbog in West Flanders Moss, central Scotland. Fluxes of CO2 CH4 and N2O from the soil were monitored over a 2-yr period every 2 to 4 weeks using the static opaque chamber method in a randomised experimental block trial with the following treatments: drained and planted (DP), undrained and planted (uDP), undrained and unplanted (uDuP) and for reference also from an adjoining near-pristine area of bog at East Flanders Moss (n-pris). There was a strong seasonal pattern in both CO2 and CH4 effluxes which were significantly higher in late spring and summer months because of warmer temperatures. Effluxes of N2O were low and no significant differences were observed between the treatments. Annual CH4 emissions increased with the proximity of the water table to the soil surface across treatments in the order: DP < uDP < uDuP < n-pris with mean annual effluxes over the 2-yr monitoring period of 0.15, 0.64, 7.70 and 22.63 g CH4 m−2 yr−1, respectively. For CO2, effluxes increased in the order uDP < DP< n-pris < uDuP, with mean annual effluxes of 1.23, 1.66, 1.82 and 2.55 kg CO2 m−2 yr−1, respectively. CO2 effluxes dominated the total net GHG emission, calculated using the global warming potential (GWP) of the three GHGs for each treatment (76–98%), and only in the n-pris site was CH4 a substantial contribution (23%). Based on soil effluxes only, the near pristine (n-pris) peatbog had 43% higher total net GHG emission compared with the DP treatment because of high CH4 effluxes and the DP treatment had 33% higher total net emission compared with the uDP because drainage increased CO2 effluxes. Restoration is likely to increase CH4 emissions, but reduce CO2 effluxes. Our study suggests that if estimates of CO2 uptake by vegetation from similar peatbog sites were included, the total net GHG emission of restored peatbog would still be higher than that of the peatbog with trees.