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Cropland abandonment is a widespread phenomenon with an increasing trend around the world, including China. Cropland abandonment is the result of a multi-scale and multifactor nested structure. In order to comprehensively identify the individual and background effects, this study explores the causes of the differences in farmland abandonment levels at two levels: farm household and village, based on a hierarchical linear model. The results show that (1) 83.63% of the differences in farm abandonment rates are differences in farm households, while 16.37% are differences in their villages; (2) several factors, including whether the head of household is healthier, per capita cropland area, ratio of transferred farmland, possession of large-scale agricultural production machinery or livestock for agricultural production, ratio of agricultural income, and whether there are village cadres, have a significant negative impact on abandonment rates at the farm household level, while at the village level, commuting distance, whether it is a suburb of a large or medium-sized city, topography of the village is plain or not, and the ratio of the number of people in agricultural production in the village have a significant positive impact on abandonment rates. Furthermore, whether it has experienced land expropriation has a significant positive effect on the abandonment rate; (3) commuting distance weakens the negative correlation between the ratio of transferred cropland and the ratio of agricultural income and the abandonment rate. In addition, whether it is a suburb of a large or medium-sized city strengthens the negative correlation between whether it owns large-scale agricultural production machinery or livestock and the abandonment rate, and whether the topography of the village is plain weakens the negative correlation between the possession of large agricultural production machinery or livestock for agricultural production and the agricultural income ratio and the abandonment rate. Furthermore, ratio of the number of people in agricultural production in the village weakens the negative correlation between the ratio of transferred cropland and abandonment rate, and whether the village has experienced land expropriation strengthens the negative correlation between the ratio of agricultural income and abandonment rate. [ABSTRACT FROM AUTHOR]

Cropland abandonment is a widespread phenomenon with an increasing trend around the world, including China. Cropland abandonment is the result of a multi-scale and multifactor nested structure. In order to comprehensively identify the individual and background effects, this study explores the causes of the differences in farmland abandonment levels at two levels: farm household and village, based on a hierarchical linear model. The results show that (1) 83.63% of the differences in farm abandonment rates are differences in farm households, while 16.37% are differences in their villages; (2) several factors, including whether the head of household is healthier, per capita cropland area, ratio of transferred farmland, possession of large-scale agricultural production machinery or livestock for agricultural production, ratio of agricultural income, and whether there are village cadres, have a significant negative impact on abandonment rates at the farm household level, while at the village level, commuting distance, whether it is a suburb of a large or medium-sized city, topography of the village is plain or not, and the ratio of the number of people in agricultural production in the village have a significant positive impact on abandonment rates. Furthermore, whether it has experienced land expropriation has a significant positive effect on the abandonment rate; (3) commuting distance weakens the negative correlation between the ratio of transferred cropland and the ratio of agricultural income and the abandonment rate. In addition, whether it is a suburb of a large or medium-sized city strengthens the negative correlation between whether it owns large-scale agricultural production machinery or livestock and the abandonment rate, and whether the topography of the village is plain weakens the negative correlation between the possession of large agricultural production machinery or livestock for agricultural production and the agricultural income ratio and the abandonment rate. Furthermore, ratio of the number of people in agricultural production in the village weakens the negative correlation between the ratio of transferred cropland and abandonment rate, and whether the village has experienced land expropriation strengthens the negative correlation between the ratio of agricultural income and abandonment rate.

Inbred genetic background significantly influences the expression of phenotypes associated with known genetic perturbations and can underlie variation in disease severity between individuals with the same mutation. However, the effect of epistatic interactions on the development of complex traits, such as craniofacial morphology, is poorly understood. Here, we investigated the effect of three inbred backgrounds (129X1/SvJ, C57BL/6J, and FVB/NJ) on the expression of craniofacial dysmorphology in mice (Mus musculus) with loss of function in three members of the Sprouty family of growth factor negative regulators (Spry1, Spry2, or Spry4) in order to explore the impact of epistatic interactions on skull morphology. We found that the interaction of inbred background and the Sprouty genotype explains as much craniofacial shape variation as the Sprouty genotype alone. The most severely affected genotypes display a relatively short and wide skull, a rounded cranial vault, and a more highly angled inferior profile. Our results suggest that the FVB background is more resilient to Sprouty loss of function than either C57 or 129, and that Spry4 loss is generally less severe than loss of Spry1 or Spry2 While the specific modifier genes responsible for these significant background effects remain unknown, our results highlight the value of intercrossing mice of multiple inbred backgrounds to identify the genes and developmental interactions that modulate the severity of craniofacial dysmorphology. Our quantitative results represent an important first step toward elucidating genetic interactions underlying variation in robustness to known genetic perturbations in mice.

Plant architecture is an accessible approach to achieving high‐yield potential. The DENSE AND ERECT PANICLE 1 (DEP1) gene regulating panicle morphology, grain number per panicle, and nitrogen uptake and metabolism has been widely used for the breeding of high‐yield rice in northern Chinese japonica varieties. However, there has been no consensus on the genetic effects of dep1 on grain yield and quality under different genetic backgrounds and growing environments. In the present study, we developed two sets of near‐isogenic lines (NILs) of DEP1 (AKI‐dep1, AKI‐DEP1, LG5‐dep1 and LG5‐DEP1), each carrying the DEP1 region from either 'Liaogeng5' (LG5) or 'Akitakomachi' (AKI) in the AKI and LG5 backgrounds. Our results demonstrated that AKI‐dep1/LG5‐dep1 exhibited erect panicle and enhanced grain number per panicle, thereby consequently increasing grain yield, whereas they possessed inferior grain appearance compared with AKI‐DEP1/LG5‐DEP1 in the same background. However, the effects of dep1 on grain processing quality and eating and cooking quality varied with the background. These results provide useful information for high‐yield erect panicle rice breeding by marker‐assisted selection. [ABSTRACT FROM AUTHOR]

Inbred genetic background significantly influences the expression of phenotypes associated with known genetic perturbations and can underlie variation in disease severity between individuals with the same mutation. However, the effect of epistatic interactions on the development of complex traits, such as craniofacial morphology, is poorly understood. Here, we investigated the effect of three inbred backgrounds (129X1/SvJ, C57BL/6J, and FVB/NJ) on the expression of craniofacial dysmorphology in mice (Mus musculus) with loss of function in three members of the Sprouty family of growth factor negative regulators (Spry1, Spry2, or Spry4) in order to explore the impact of epistatic interactions on skull morphology. We found that the interaction of inbred background and the Sprouty genotype explains as much craniofacial shape variation as the Sprouty genotype alone. The most severely affected genotypes display a relatively short and wide skull, a rounded cranial vault, and a more highly angled inferior profile. Our results suggest that the FVB background is more resilient to Sprouty loss of function than either C57 or 129, and that Spry4 loss is generally less severe than loss of Spry1 or Spry2. While the specific modifier genes responsible for these significant background effects remain unknown, our results highlight the value of intercrossing mice of multiple inbred backgrounds to identify the genes and developmental interactions that modulate the severity of craniofacial dysmorphology. Our quantitative results represent an important first step toward elucidating genetic interactions underlying variation in robustness to known genetic perturbations in mice.

The phenotypic consequence of a given mutation can be influenced by the genetic background. For example, conditional gene essentiality occurs when the loss of function of a gene causes lethality in one genetic background but not another. Between two individual Saccharomyces cerevisiae strains, S288c and Σ1278b, ~1% of yeast genes were previously identified as "conditional essential." Here, in addition to confirming that some conditional essential genes are modified by a nonchromosomal element, we show that most cases involve a complex set of genomic modifiers. From tetrad analysis of S288C/Σ1278b hybrid strains and wholegenome sequencing of viable hybrid spore progeny, we identified complex sets of multiple genomic regions underlying conditional essentiality. For a smaller subset of genes, including CYS3 and CYS4, each of which encodes components of the cysteine biosynthesis pathway, we observed a segregation pattern consistent with a single modifier associated with conditional essentiality. In natural yeast isolates, we found that the CYS3/CYS4 conditional essentiality can be caused by variation in two independent modifiers, MET1 and OPT1, each with roles associated with cellular cysteine physiology. Interestingly, the OPT1 allelic variation appears to have arisen independently from separate lineages, with rare allele frequencies below 0.5%. Thus, while conditional gene essentiality is usually driven by genetic interactions associated with complex modifier architectures, our analysis also highlights the role of functionally related, genetically independent, and rare variants. [ABSTRACT FROM AUTHOR]

Depth information plays an important role in human vision as it provides additional cues that distinguish objects from their backgrounds. This paper explores depth information for analyzing stereoscopic saliency and presents a computational model that predicts stereoscopic visual saliency based on three aspects of human vision: 1) the pop-out effect; 2) comfort zones; and 3) background effects. Through an analysis of these three phenomena, we find that most of the stereoscopic saliency region can be explained. Our model comprises three modules, each describing one aspect of saliency distribution, and a control function that can be used to adjust the three models independently. The relationship between the three models is not mutually exclusive. One, two, or three phenomena may appear in one image. Therefore, to accurately determine which phenomena the image conforms to, we have devised a selection strategy that chooses the appropriate combination of models based on the content of the image. Our approach is implemented within a framework based on the multifeature analysis. The framework considers surrounding regions, color/depth contrast, and points of interest. The selection strategy can improve the performance of the framework. A series of experiments on two recent eye-tracking datasets shows that our proposed method outperforms several state-of-the-art saliency models. [ABSTRACT FROM AUTHOR]

The phenotypic consequences of a given mutation can vary across individuals. This so-called background effect is widely observed, from mutant fitness of loss-of-function variants in model organisms to variable disease penetrance and expressivity in humans; however, the underlying genetic basis often remains unclear. Taking insights gained from recent large-scale surveys of genetic interaction and suppression analyses in yeast, we propose that the genetic network context for a given mutation may shape its propensity of exhibiting background-dependent phenotypes. We argue that further efforts in systematically mapping the genetic interaction networks beyond yeast will provide not only key insights into the functional properties of genes, but also a better understanding of the background effects and the (un)predictability of traits in a broader context. [ABSTRACT FROM AUTHOR]

Microarray images commonly used in gene expression studies are heavily contaminated by noise and/or outlying values (outliers). Unfortunately, standard methodology for the analysis of Illumina BeadChip microarray images turns out to be too vulnerable to data contamination by outliers. In this paper, an alternative approach to low-level pre-processing of images obtained by the BeadChip microarray technology is proposed. The novel approach robustifies the standard methodology in a complex way and thus ensures a sufficient robustness (resistance) to outliers. A gene expression data set from a cardiovascular genetic study is analyzed and the performance of the novel robust approach is compared with the standard methodology. The robust approach is able to detect and delete a larger percentage of outliers. More importantly, gene expressions are estimated more precisely. As a consequence, also the performance of a subsequently performed classification task to two groups (patients vs. control persons) is improved over the cardiovascular gene expression data set. A further improvement was obtained when considering weighted gene expression values, where the weights correspond to a robust estimate of variability of the measurements for each individual gene transcript. [ABSTRACT FROM AUTHOR]

Inbred genetic background significantly influences the expression of phenotypes associated with known genetic perturbations and can underlie variation in disease severity between individuals with the same mutation. However, the effect of epistatic interactions on the development of complex traits, such as craniofacial morphology, is poorly understood. Here, we investigated the effect of three inbred backgrounds (129X1/SvJ, C57BL/6J, and FVB/NJ) on the expression of craniofacial dysmorphology inmice (Musmusculus) with loss of function in three members of the Sprouty family of growth factor negative regulators (Spry1, Spry2, or Spry4) in order to explore the impact of epistatic interactions on skull morphology.We found that the interaction of inbred background and the Sprouty genotype explains as much craniofacial shape variation as the Sprouty genotype alone. The most severely affected genotypes display a relatively short and wide skull, a rounded cranial vault, and a more highly angled inferior profile. Our results suggest that the FVB background is more resilient to Sprouty loss of function than either C57 or 129, and that Spry4 loss is generally less severe than loss of Spry1 or Spry2. While the specificmodifier genes responsible for these significant background effects remain unknown, our results highlight the value of intercrossing mice of multiple inbred backgrounds to identify the genes and developmental interactions that modulate the severity of craniofacial dysmorphology. Our quantitative results represent an important first step toward elucidating genetic interactions underlying variation in robustness to known genetic perturbations in mice. [ABSTRACT FROM AUTHOR]

The phenotypic effect of any genetic variant can be altered by variation at other genomic loci. Known as epistasis, these genetic interactions shape the genotype-phenotype map of every species, yet their origins remain poorly understood. To investigate this, we employed high-throughput genome editing to measure the fitness effects of 1,826 naturally polymorphic variants in four strains of Saccharomyces cerevisiae . About 31% of variants affect fitness, of which 24% have strain-specific fitness effects indicative of epistasis. We found that beneficial variants are more likely to exhibit genetic interactions and that these interactions can be mediated by specific traits such as flocculation ability. This work suggests that adaptive evolution will often involve trade-offs where a variant is only beneficial in some genetic backgrounds, potentially explaining why many beneficial variants remain polymorphic. In sum, we provide a framework to understand the factors influencing epistasis with single-nucleotide resolution, revealing widespread epistasis among beneficial variants., Competing Interests: H.B.F. is a coinventor of a patent application describing the CRISPEY approach (application number 16/293,550). S.-A.A.C., A.F.K., and H.B.F. are coinventors of a patent application describing the CRISPEY-BAR approach (application number 63/344,470)., (© 2023 The Authors.)

Studies of the perception of motion in three-dimensional scenes have provided extensive information about the effects of changes in the size, speed, and disparity of an object's image on the perception of the object's trajectory. The present study demonstrates that this perception is not determined primarily by the object's motion but by the shape of the background against which this motion is displayed. The effect of a scene background on judgments of the trajectory of a moving object was examined in 2 experiments with 33 observers. In the first experiment, observers judged whether the trajectory was concave or convex. In the second experiment, observers judged which of 2 displays, differing in curvature of the motion path and curvature of the background, depicted the more curved motion path. Judgments of sign of curvature and judgments of relative magnitude of curvature were determined almost entirely by the background curvature. [ABSTRACT FROM AUTHOR]

Gene-background interaction is a commonly observed phenomenon in many species, but the molecular mechanisms of such an interaction is less well understood. Here we report the cloning of a maize mutant gene and its modifier. A recessive mutant with a virescent yellow-like ( vyl) phenotype was identified in an ethyl methanesulfonate-mutagenized population derived from the maize inbred line B73. Homozygous mutant maize plants exhibited a yellow leaf phenotype after emergence but gradually recovered and became indistinguishable from wild-type plants after approximately 2 weeks. Taking the positional cloning approach, the Chr.9_ClpP5 gene, one of the proteolytic subunits of the chloroplast Clp protease complex, was identified and validated as the candidate gene for vyl. When introgressed by backcross into the maize inbred line PH09B, the mutant phenotype of vyl lasted much longer in the greenhouse and was lethal in the field, implying the presence of a modifier(s) for vyl. A major modifier locus was identified on chromosome 1, and a paralogous ClpP5 gene was isolated and confirmed as the candidate for the vyl-modifier. Expression of Chr.1_ClpP5 is induced significantly in B73 by the vyl mutation, while the expression of Chr.1_ClpP5 in PH09B is not responsive to the vyl mutation. Moreover, expression and sequence analysis suggests that the PH09B Chr.1_ClpP5 allele is functionally weaker than the B73 allele. We propose that functional redundancy between duplicated paralogous genes is the molecular mechanism for the interaction between vyl and its modifier. [ABSTRACT FROM AUTHOR]

Background effect is a crucial limitation for the monitoring of leaf nitrogen concentration (LNC) in crops with unmanned aerial vehicle (UAV) multispectral imagery. Some background removal approaches have been developed for improve the estimation of LNC, but their performances are not compared in one study and it is unclear whether they are sensitive to the observation time of UAV imagery. This study evaluated three background removal approaches, i.e., the soil-adjusted vegetation index (SAVI) approach, the green pixel vegetation index approach (GPVI) and abundance adjusted vegetation index (AAVI), for estimating rice LNC from UAV-based multispectral imagery at individual and across growth stages as well as different observation times of the day. The red edge chlorophyll index (CI re) was chosen as the common basis for the last two approaches. In particular, the AAVI approach was refined with a higher number of endmembers and automated endmember extraction, and further evaluated for assessing the effect of separating sunlit components from shaded components of the canopy. Our results demonstrated that the vegetation indices (VIs) for off-noon observation times showed better relationships with LNC than those for noon at individual and across growth stages. Compared to both SAVI and CI re-green , the AACI re for all pixels (AACI re-all) exhibited the weakest sensitivity to observation time and yielded the best relationships for single-stage (jointing: r 2 =0.70, booting: r 2 =0.76, heading: r 2 =0.70) and across-stage (r 2 =0.66) models. Among the AAVIs derived from three categories of pixels, the AACI re-sunlit (R2 =0.90, RMSE=0.17%, Bias=0.03%) outperformed AACI re-all (R2 =0.85, RMSE=0.23%, Bias=0.08%) and then AACI re-shaded (R2 =0.38, RMSE=0.49%, Bias=0.40%) remarkably for the estimation accuracy of LNC. This study suggests that the refined AAVI approach has great value in reducing the background effect for more accurate monitoring of growth parameters and could be extended to other crops and regions for improved precision crop management and field-based high-throughput phenotyping. [Display omitted] • Background effect impacted leaf N concentration (LNC) estimation with UAV imagery. • Background removal weaked sensitivity to observation time in rice LNC estimation. • AACI re from sunlit pixels (AACI re-sunlit) outperformed AACI re from all pixels. • AACI re-sunlit yielded higher accuracies than SAVI and the CI re from green pixels. [ABSTRACT FROM AUTHOR]

Many feature generation methods have been developed for object recognition. Some of these methods succeeded in achieving invariance against object translation, rotation and scaling but faced problems of the bright background effect and non‐uniform light on the quality of the generated features. This problem has hindered recognition systems from working in a free environment. This paper proposes a new method to enhance the feature quality based on pulse‐coupled neural network. An adaptive model that defines continuity factor is proposed as a weight factor of the current pulse in signature generation process. The proposed new method has been employed in a hybrid feature extraction model that is followed by a classifier and was applied and tested in Arabic sign language static hand posture recognition; the superiority of the new method is shown. [ABSTRACT FROM AUTHOR]

In natural populations, the same mutation can lead to different phenotypic outcomes due to the genetic variation that exists among individuals. Such genetic background effects are commonly observed, including in the context of many human diseases. However, systematic characterization of these effects at the species level is still lacking to date. Here, we sought to comprehensively survey background-dependent traits associated with gene loss-of-function (LoF) mutations in 39 natural isolates of Saccharomyces cerevisiae using a transposon saturation strategy. By analyzing the modeled fitness variability of a total of 4,469 genes, we found that 15% of them, when impacted by a LoF mutation, exhibited a significant gain- or loss-of-fitness phenotype in certain natural isolates compared with the reference strain S288C. Out of these 632 genes with predicted background-dependent fitness effects, around 2/3 impact multiple backgrounds with a gradient of predicted fitness change while 1/3 are specific to a single genetic background. Genes related to mitochondrial function are significantly overrepresented in the set of genes showing a continuous variation and display a potential functional rewiring with other genes involved in transcription and chromatin remodeling as well as in nuclear-cytoplasmic transport. Such rewiring effects are likely modulated by both the genetic background and the environment. While background-specific cases are rare and span diverse cellular processes, they can be functionally related at the individual level. All genes with background-dependent fitness effects tend to have an intermediate connectivity in the global genetic interaction network and have shown relaxed selection pressure at the population level, highlighting their potential evolutionary characteristics.

The phenotypic consequence of a given mutation can be influenced by the genetic background. For example, conditional gene essentiality occurs when the loss of function of a gene causes lethality in one genetic background but not another. Between two individual Saccharomyces cerevisiae strains, S288c and Σ1278b, ∼1% of yeast genes were previously identified as "conditional essential." Here, in addition to confirming that some conditional essential genes are modified by a nonchromosomal element, we show that most cases involve a complex set of genomic modifiers. From tetrad analysis of S288C/Σ1278b hybrid strains and whole-genome sequencing of viable hybrid spore progeny, we identified complex sets of multiple genomic regions underlying conditional essentiality. For a smaller subset of genes, including CYS3 and CYS4 , each of which encodes components of the cysteine biosynthesis pathway, we observed a segregation pattern consistent with a single modifier associated with conditional essentiality. In natural yeast isolates, we found that the CYS3 / CYS4 conditional essentiality can be caused by variation in two independent modifiers, MET1 and OPT1 , each with roles associated with cellular cysteine physiology. Interestingly, the OPT1 allelic variation appears to have arisen independently from separate lineages, with rare allele frequencies below 0.5%. Thus, while conditional gene essentiality is usually driven by genetic interactions associated with complex modifier architectures, our analysis also highlights the role of functionally related, genetically independent, and rare variants., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)