Carolyn J Foley, Zachary S. Feiner, Timothy D. Malinich
et al.
Microplastics are present in aquatic ecosystems the world over and may influence the feeding, growth, reproduction, and survival of freshwater and marine biota; however, the extent and magnitude of potential effects of microplastics on aquatic organisms is poorly understood. In the current study, we conducted a meta-analysis of published literature to examine impacts of exposure to microplastics on consumption (and feeding), growth, reproduction, and survival of fish and aquatic invertebrates. While we did observe within-taxa negative effects for all four categories of responses, many of the effects summarized in our study were neutral, indicating that the effects of exposure to microplastics are highly variable across taxa. The most consistent effect was a reduction in consumption of natural prey when microplastics were present. For some taxa, negative effects on growth, reproduction and even survival were also evident. Organisms that serve as prey to larger predators, e.g., zooplankton, may be particularly susceptible to negative impacts of exposure to microplastic pollution, with potential for ramifications throughout the food web. Future work should focus on whether microplastics may be affecting aquatic organisms more subtly, e.g., by influencing exposure to contaminants and pathogens, or by acting at a molecular level.
The advantages of genome selection (GS) in animal and plant breeding are self-evident. Traditional parametric models have disadvantage in better fit the increasingly large sequencing data and capture complex effects accurately. Machine learning models have demonstrated remarkable potential in addressing these challenges. In this study, we introduced the concept of mixed kernel functions to explore the performance of support vector machine regression (SVR) in GS. Six single kernel functions (SVR_L, SVR_C, SVR_G, SVR_P, SVR_S, SVR_L) and four mixed kernel functions (SVR_GS, SVR_GP, SVR_LS, SVR_LP) were used to predict genome breeding values. The prediction accuracy, mean squared error (MSE) and mean absolute error (MAE) were used as evaluation indicators to compare with two traditional parametric models (GBLUP, BayesB) and two popular machine learning models (RF, KcRR). The results indicate that in most cases, the performance of the mixed kernel function model significantly outperforms that of GBLUP, BayesB and single kernel function. For instance, for T1 in the pig dataset, the predictive accuracy of SVR_GS is improved by 10% compared to GBLUP, and by approximately 4.4 and 18.6% compared to SVR_G and SVR_S respectively. For E1 in the wheat dataset, SVR_GS achieves 13.3% higher prediction accuracy than GBLUP. Among single kernel functions, the Laplacian and Gaussian kernel functions yield similar results, with the Gaussian kernel function performing better. The mixed kernel function notably reduces the MSE and MAE when compared to all single kernel functions. Furthermore, regarding runtime, SVR_GS and SVR_GP mixed kernel functions run approximately three times faster than GBLUP in the pig dataset, with only a slight increase in runtime compared to the single kernel function model. In summary, the mixed kernel function model of SVR demonstrates speed and accuracy competitiveness, and the model such as SVR_GS has important application potential for GS.
This paper presents two types of extended diffeomorphism designs to compensate for spatial placement differences between robot workspaces. Teleoperation of multiple robots is attracting attention to expand the utilization of the robot embodiment. Real-time reproduction of robot motion would facilitate the efficient execution of similar tasks by multiple robots. A challenge in the motion reproduction is compensating for the spatial arrangement errors of target keypoints in robot workspaces. This paper proposes a methodology for smooth mappings that transform primary robot poses into follower robot poses based on the predefined key points in each workspace. Through a picking task experiment using a dual-arm UR5 robot, this study demonstrates that the proposed mapping generation method can balance lower mapping errors for precise operation and lower mapping gradients for smooth replicated movement.
Ambisonics is a method for capturing and rendering a sound field accurately, assuming that the acoustics of the playback room does not significantly influence the sound field. However, in practice, the acoustics of the playback room may lead to a noticeable degradation in sound quality. We propose a recording and rendering method based on Ambisonics that utilizes a perceptually-motivated approach to compensate for the reverberation of the playback room. The recorded direct and reverberant sound field components in the spherical harmonics (SHs) domain are spectrally and spatially compensated to preserve the relevant auditory cues including the direction of arrival of the direct sound, the spectral energy of the direct and reverberant sound components, and the Interaural Coherence (IC) across each auditory band. In contrast to the conventional Ambisonics, a flexible number of Ambisonics channels can be used for audio rendering. Listening test results show that the proposed method provides a perceptually accurate rendering of the originally recorded sound field, outperforming both conventional Ambisonics without compensation and even ideal Ambisonics rendering in a simulated anechoic room. Additionally, subjective evaluations of listeners seated at the center of the loudspeaker array demonstrate that the method remains robust to head rotation and minor displacements.
Moritz Wolter, Lokesh Veeramacheneni, Charles Tapley Hoyt
While experimental reproduction remains a pillar of the scientific method, we observe that the software best practices supporting the reproduction of machine learning ( ML ) research are often undervalued or overlooked, leading both to poor reproducibility and damage to trust in the ML community. We quantify these concerns by surveying the usage of software best practices in software repositories associated with publications at major ML conferences and journals such as NeurIPS, ICML, ICLR, TMLR, and MLOSS within the last decade. We report the results of this survey that identify areas where software best practices are lacking and areas with potential for growth in the ML community. Finally, we discuss the implications and present concrete recommendations on how we, as a community, can improve reproducibility in ML research.
In this paper, we study an integro-differential equation which describes the evolutionary dynamics of a population structured by a phenotypic trait. This population undergoes asexual reproduction, competition, selection, and mutation. We provide an asymptotic analysis of the model, assuming that the mutations have small effects. A standard approach for the analysis of the qualitative properties of the solutions of such an equation is to apply a logarithmic transformation, which yields a Hamilton-Jacobi equation with constraint. When the reproduction term is a concave function of the trait, it has been established that the solution is classical. We rigorously derive a first-order asymptotic expansion of the solution. This expansion allows us to approximate the moments of the phenotypic density. This result establishes a connection between the approximations of the phenotypic density obtained via the Hamilton-Jacobi approach and relevant biological quantities, which are more suitable from a modeling perspective.
marzieh valizadeh, seyed mohamad hoseininasr, hamid jalilvand
et al.
Extended Abstract
Background: It is important to research in the field of germplasm protection of native and medicinal tree species in northern Iran forests, especially blood hawthorn with many medicinal properties. Sexual reproduction of hawthorn is possible with apomixis due to the thick shell and two types of physical and physiological dormancy, and its asexual reproduction by rooting cuttings faces many problems. Bloody hawthorn (Crataegus atrosanguinea from the Rosaceae family) is considered one of the valuable species of the forests of the north and west of the country, which is very important due to its fruitfulness, very strong wood, and numerous medicinal properties. The medicinal properties of hawthorn have been proven in the treatment of blood pressure, arteriosclerosis, heart congestion, heart muscle weakness, and coronary insufficiency. Hawthorn contains many secondary metabolites such as flavonoids proanthocyanidin and glycosides. Optimizing the in vitro cultivation conditions of blood hawthorn as one of the natural species of Iran can be a suitable solution for its propagation. The present research was carried out to control pollution, control browning, and induce the callus of blood hawthorn (C. atrosanguinea) in vitro. Controlling the contamination of explants, seeds, and plant tissues is of great importance for the success of plant tissue culture. Since the enrichment of natural plant explants is a priority for tissue culture, this is usually associated with many problems with browning, especially for woody plants that have a thick and woody stem. Determining the type and concentration of the growth regulator of a variable factor is necessary for the growth of plants under in vitro conditions. After applying the growth regulator to the culture medium, the plant will show different reactions, but one of the appropriate ways to choose the correct path of plant regeneration is to determine the wet and dry weights of the callus, which is widely measured as a standard of callus growth. The callus growth curve can be obtained using the wet and dry weights of the callus. The results of past research indicate a wide range of changes in the type and concentration of growth regulators on callus formation and regeneration of different species of the hawthorn genus. A specific type and concentration of growth regulators should be applied according to the type of plant species.
Methods: Young and healthy stems of blood hawthorn were collected from Larijan in Amol, Mazandaran province, Iran, with geographical coordinates of 38' 58° N and 10' 52° E, at the beginning of the growing season. The collected stems were immediately transferred to the plant tissue culture laboratory of the Faculty of Natural Resources at Sari University of Agriculture and Natural Resources, Iran. Disinfection of natural hawthorn stems is very necessary due to surface and tissue contamination. For this purpose, explants of 0.5-1 cm size were cut from the stems. The infection control treatments included HgCl2, H2O2, NaClO, and AgNO3, and five treatments were designed to control the browning of explants. Browning control treatments included control, running water, ascorbic acid, polyvinyl chloride, and activated charcoal. In general, the culture medium consisted of substances including mineral salts (micro- and macroelements) as providers of maximum growth, amino acids and vitamins as nitrogen sources, sugar as a source of carbon and energy, growth regulators as growth and morphogenesis stimulants, agar as the solidifier of the cultivation medium, and water, which includes 90% of the cultivation medium. In this research, the culture medium was MS, which was first created by Driver and Koniaki (1984) and prepared according to Dufussard (1976). In this study, the pH of the culture medium was set to 5.8. For callus induction, IBA, NAA, 2,4-D, BAP, TDZ, and Kin treatments at three concentration levels of 0.1, 1, and 6 mg/L and a combination of NAA (6 mg-1) + BAP (1 mg-1), and IBA (6 mg l-1) + BAP (1 mg-1) were used in the MS culture medium. Stem explants were placed horizontally on the culture medium. Among different callus treatments, callus percentage, degree of callus, callus fresh and dry weights, and cross-sectional area of callus were measured to investigate callus induction. The best treatment was obtained by calculating the mentioned characteristics and that treatment was used for planting. It was transplanted approximately every 20 days and a total of 5-6 times. After callus cultivation in the reproduction medium, the explants were placed in a culture chamber and adaptation racks under 16 hours of light and 8 hours of dark treatment at 25 ± 2 °C with a humidity of 70%.
Results: HgCl2 (0.5%, 16 minutes) with an average of 100% health was the most appropriate pollution control treatment. The control treatment with 98% health was observed as the most appropriate browning control treatment. Moreover, the type, concentration, and interaction effect of the type and concentration of the growth regulator significantly affected the callus induction characteristics of blood hawthorn (P < 0.01). The highest fresh and dry weights of callus, percentage and degree of callus formation, and cross-sectional area of callus were observed among auxin and cytokinin treatments, respectively, for 6 mg/L of NAA and 1 mg/L of BAP treatments. The highest levels of the studied callus induction characteristics were observed in the culture medium containing the combination of auxin and cytokinin (6 mg-1 of IBA+1 mg-1 of BAP).
Conclusion: In general, the results showed a 90% chance of controlling the browning of the explants of natural blood hawthorn branches in a normal state and without applying any treatment. It is recommended to use 0.5% mercuric chloride for 16 minutes to disinfect the explants. The combination of growth regulators in the culture medium was evaluated as very suitable for the callus induction of bloody hawthorn. The results of this research can provide laboratory instructions for the regeneration and mass reproduction of blood hawthorn.
Abstract Background Cranial radiotherapy (CRT) is recommended to high-risk pediatric patients with acute lymphoblastic leukemia or aggressive non-Hodgkin’s lymphoma (ALL/NHL). However, effects of CRT treatment on the development of metabolic/endocrine disorders remain unclear. This meta-analysis aimed to identify metabolic and endocrine disturbances in survivors of childhood-onset and CRT-treated ALL/NHL. Methods Different online databases were searched using restricted search fields. Follow-up data and outcome measurements, including the prevalence of growth hormone (GH) deficiency, hypothyroidism, vitamin D deficiency, overweight/obesity, and hypogonadism were recorded. The height data was indicated by height-standard deviation score (height-SDS). Statistical estimates such as odds ratio (OR) and weighted standard mean difference (SMD) were compared between additional CRT treatment group and non-CRT treatment group. Study-to-study heterogeneity was calculated by calculating I-squared statistic, and fixed/random effect was applied to synthesize and analyze extracted data. Results Fifteen studies were included (4269 patients in total). Adult height SDS was lower in CRT-treated patients (pooled SMD = -0.581, 95% CI: -0.649–-0.512), and CRT-treated patients were likely to develop short stature (pooled OR = 2.289, 95% CI:1.674–3.130). Regardless of the study year, which potentially reflects the state-of-the-art CRT technique, the prevalence of short stature and GH deficiency was time-independent. Additionally, previous CRT can increase the risk of precocious puberty (pooled OR = 2.937, 95% CI: 1.281–6.736), hypothyroidism (pooled OR = 2.057, 95% CI:1.510–2.801), and hypogonadism (pooled OR = 3.098, 95% CI:2.521–3.807). However, the risk of being overweight/obese was similar between the patients with and without CRT (pooled OR = 1.278, 95% CI: 0.675–2.421). Conclusion Childhood-onset and CRT-treated ALL/NHL survivors are likely to have shorter height, precocious puberty, hypothyroidism, and hypogonadism.
Takuro Fujii, Hayato Nakagawa, Teppei Takeshima
et al.
Infertility is a global health problem, and an increasing number of couples are seeking medical assistance to achieve reproduction, at least half of which are caused by men. The success rate of assisted reproductive technologies depends on sperm assessment, in which experts determine whether sperm can be used for reproduction based on morphology and motility of sperm. Previous sperm assessment studies with deep learning have used datasets comprising images that include only sperm heads, which cannot consider motility and other morphologies of sperm. Furthermore, the labels of the dataset are one-hot, which provides insufficient support for experts, because assessment results are inconsistent between experts, and they have no absolute answer. Therefore, we constructed the video dataset for sperm assessment whose videos include sperm head as well as neck and tail, and its labels were annotated with soft-label. Furthermore, we proposed the sperm assessment framework and the neural network, RoSTFine, for sperm video recognition. Experimental results showed that RoSTFine could improve the sperm assessment performances compared to existing video recognition models and focus strongly on important sperm parts (i.e., head and neck).
This work presents a model combining the simplest communicable and non-communicable disease models. The latter is, by far, the leading cause of sickness and death in the World, and introduces basal heterogeneity in populations where communicable diseases evolve. The model can be interpreted as a risk-structured model, another way of accounting for population heterogeneity. Our results show that considering the non-communicable disease (in the end, heterogeneous populations) allows the communicable disease to become endemic even if the basic reproduction number is less than $1$. This feature is known as subcritical bifurcation. Furthermore, ignoring the non-communicable disease dynamics results in overestimating the reproduction number and, thus, giving wrong information about the actual number of infected individuals. We calculate sensitivity indices and derive interesting epidemic-control information.
Suchismita Prusty, Ranjan Kumar Sahoo, Subhendu Nayak
et al.
Micronutrients are essential for plants. Their growth, productivity and reproduction are directly influenced by the supply of micronutrients. Currently, there are eight trace elements considered to be essential for higher plants: Fe, Zn, Mn, Cu, Ni, B, Mo, and Cl. Possibly, other essential elements could be discovered because of recent advances in nutrient solution culture techniques and in the commercial availability of highly sensitive analytical instrumentation for elemental analysis. Much remains to be learned about the physiology of micronutrient absorption, translocation and deposition in plants, and about the functions they perform in plant growth and development. With the recent advancements in the proteomic and molecular biology tools, researchers have attempted to explore and address some of these questions. In this review, we summarize the current knowledge of micronutrients in plants and the proteomic/genomic approaches used to study plant nutrient deficiency and toxicity.
Yuiko Hirata, Muneyuki Matsuo, Kensuke Kurihara
et al.
The linkage between the self-reproduction of compartments and the replication of DNA in a compartment is a crucial requirement for cellular life. In our giant vesicle (GV)-based model protocell, this linkage is achieved through the action of a supramolecular catalyst composed of membrane-intruded DNA and amphiphilic acid catalysts (<b>C@DNA</b>) in a GV membrane. In this study, we examined colocalization analysis for the formation of the supramolecular catalyst using a confocal laser scanning fluorescence microscope with high sensitivity and resolution. Red fluorescence spots emitted from DNA tagged with Texas Red (Texas Red-DNA) were observed in a GV membrane stained with phospholipid tagged with BODIPY (BODIPY-HPC). To our knowledge, this is the first direct observation of DNA embedded in a GV-based model protocellular membrane containing cationic lipids. Colocalization analysis based on a histogram of frequencies of “normalized mean deviation product” revealed that the frequencies of positively correlated [lipophilic catalyst tagged with BODIPY (BODIPY-<b>C</b>) and Texas Red-DNA] were significantly higher than those of [BODIPY-HPC and Texas Red-DNA]. This result demonstrates the spontaneous formation of <b>C@DNA</b> in the GV membrane, which serves as a lipo-deoxyribozyme for producing membrane lipids from its precursor.
David MARTÍN-HIDALGO, Beatriz MACÍAS-GARCÍA, Lauro GONZÁLEZ-FERNÁNDEZ
We aimed to analyze the influence of different cellular concentrations of boar sperm suspensions on the induction of capacitation and acrosome reaction. When spermatozoa were incubated at 100 or 200 mill/ml, significant increases in protein tyrosine phosphorylation in the p32 protein were observed, compared to those at 50 mill/ml. In addition, sperm concentration-dependent increases were observed in plasma membrane lipid disorganization (50 mill/ml vs. 200 mill/ml), induction of the acrosome reaction (50 mill/ml vs. 100 mill/ml and 200 mill/ml), and sperm viability (50 mill/ml vs. 100 mill/ml and 200 mill/ml). Our data indicate that an increase in sperm concentration stimulates the induction of capacitation and acrosome reaction in boars.
We propose a mathematical model to study coupled epidemic and opinion dynamics in a network of communities. Our model captures SIS epidemic dynamics whose evolution is dependent on the opinions of the communities toward the epidemic, and vice versa. In particular, we allow both cooperative and antagonistic interactions, representing similar and opposing perspectives on the severity of the epidemic, respectively. We propose an Opinion-Dependent Reproduction Number to characterize the mutual influence between epidemic spreading and opinion dissemination over the networks. Through stability analysis of the equilibria, we explore the impact of opinions on both epidemic outbreak and eradication, characterized by bounds on the Opinion-Dependent Reproduction Number. We also show how to eradicate epidemics by reshaping the opinions, offering researchers an approach for designing control strategies to reach target audiences to ensure effective epidemic suppression.
<p>We examine the capability of near-spherical-shaped particles to reproduce the triple-wavelength particle linear depolarization ratio (PLDR) and lidar ratio (LR) values measured over Europe for stratospheric smoke originating from Canadian wildfires. The smoke layers were detected both in the troposphere and the stratosphere, though in the latter case the particles presented PLDR values of almost 18 % at 532 nm as well as a strong spectral dependence from the UV to the near-IR wavelength. Although recent simulation studies of rather complicated smoke particle morphologies have shown that heavily coated smoke aggregates can produce large PLDR, herein we propose a much simpler model of compact near-spherical smoke particles. This assumption allows for the reproduction of the observed intensive optical properties of stratospheric smoke, as well as their spectral dependence. We further examine whether an extension of the current Aerosol Robotic Network (AERONET) scattering model to include the near-spherical shapes could be of benefit to the AERONET retrieval for stratospheric smoke cases associated with enhanced PLDR. Results of our study illustrate the fact that triple-wavelength PLDR and LR lidar measurements can provide us with additional insight when it comes to particle characterization.</p>
Background: Before effective vaccines become widely available, sufficient understanding of the impacts of climate, human movement and non-pharmaceutical interventions on the transmissibility of COVID-19 is needed but still lacking. Methods: We collected by crowdsourcing a database of 11 003 COVID-19 cases from 305 cities outside Hubei Province from December 31, 2019 to April 27, 2020. We estimated the daily effective reproduction numbers (Rt) of COVID-19 in 41 cities where the crowdsourced case data are comparable to the official surveillance data. The impacts of meteorological variables, human movement indices and nonpharmaceutical emergency responses on Rt were evaluated with generalized estimation equation models. Findings: The median Rt was 0•46 (IQR: 0•37–0•87) in the northern cities, higher than 0•20 (IQR: 0•09–0•52) in the southern cities (p=0•004). A higher local transmissibility of COVID-19 was associated with a low temperature, a relative humidity near 70–75%, and higher intracity and intercity human movement. An increase in temperature from 0℃ to 20℃ would reduce Rt by 30% (95 CI 10–46%). A further increase to 30℃ would result in another 17% (95% CI 5–27%) reduction. An increase in relative humidity from 40% to 75% would raise the transmissibility by 47% (95% CI 9–97%), but a further increase to 90% would reduce the transmissibility by 12% (95% CI 4–19%). The decrease in intracity human movement as a part of the highest-level emergency response in China reduced the transmissibility by 36% (95% CI 27–44%), compared to 5% (95% CI 1–9%) for restricting intercity transport. Other nonpharmaceutical interventions further reduced Rt by 39% (95% CI 31–47%). Interpretation: Climate can affect the transmission of COVID-19 where effective interventions are implemented. Restrictions on intracity human movement may be needed in places where other nonpharmaceutical interventions are unable to mitigate local transmission. Funding: China Mega-Project on Infectious Disease Prevention; U.S. National Institutes of Health and National Science Foundation.