Complementary Functions Research Articles

Genome-wide identification and transcriptional profiling analysis of PIN/PILS auxin transporter gene families in Panax ginseng

ObjectivePlant hormones act as chemical messengers in the regulation of plant development and metabolism. The production of ginsenosides in Panax hybrid is promoted by auxins that are transported and accumulated by PIN-FORMED (PIN) and PIN-LIKES (PILS) auxin transporters. However, genome-wide studies of PIN/PILS of ginseng are still scarce. In current study, identification and transcriptional profiling of PIN/PILS gene families, as well as their potential relationship with ginsenoside biosynthesis in Panax ginseng were investigated. MethodsPIN/PILS genes in P. ginseng was identified via in silico genome-wide analysis, followed by phylogenetic relationships, gene structure, and protein profiles investigation. Moreover, previously reported RNA-sequence data from various tissues and roots after infection were utilized for PIN/PILS genes expression pattern analysis. The Pearson’s correlation analysis of specific PIN/PILS genes expression level and main ginsenoside contents were taken to reveal the potential relationship between auxin transports and ginsenoside biosynthesis in P. ginseng. ResultsA genome-wide search of P. ginseng genome for homologous auxin transporter genes identified a total of 17 PIN and 11 PILS genes. Sequence alignment, putative motif organization, and sub-cellular localization indicated redundant and complementary biological functions of these PIN/PILS genes. Most PIN/PILS genes were differentially expressed in a tissue-specific manner, and showed significant correlations with ginsenoside content correspondingly. Eight auxin transporter genes, including both PIN and PILS subfamily members, were positively correlated with ginsenoside content (cor > 0.60; P-value <0.05). The expression levels of eleven auxin transporter genes were increased dramatically in the early stage (0–0.5 DPI) after Cylindrocarpon destructans infection, accompanied with various overall expression patterns, implying the dynamic auxin transport in response to biotic stress. ConclusionBased on the results, we speculate that the accumulation or depletion in temporal or spatial manner of auxin by PIN/PILS transporters involved in the regulation of HMGR activity and subsequent ginsenoside biosynthesis.

Deterrence and Restraint: Do Joint Military Exercises Escalate Conflict?

Multinational military exercises are among the most notable demonstrations of military cooperation and intent. On average, one is initiated every 8.9 days. But it has often been argued that joint military exercises (JMEs) increase the risk of war. Using a relational contracting approach, we claim that formal military alliances mediate the effect of JMEs. Exercises and alliances serve complementary functions: The former allows targeted responses to military provocations by adversaries, while the latter provides institutional constraints on partners and establishes a partnership’s overall strategic limitations. In combination, alliances dampen the conflict escalation effects of exercises, deterring adversaries while simultaneously restraining partners. We test this theory using a two-stage model on directed dyadic data of JMEs from 1973 through 2003. We find that JMEs in general do not escalate conflict, and that JMEs conducted with allies in particular reduce the probability of conflict escalation.

A Direct Comparison of Afferents to the Rat Anterior Thalamic Nuclei and Nucleus Reuniens: Overlapping But Different.

Both nucleus reuniens and the anterior thalamic nuclei are densely interconnected with medial cortical and hippocampal areas, connections that reflect their respective contributions to learning and memory. To better appreciate their comparative roles, pairs of different retrograde tracers were placed in these two thalamic sites in adult rats. Both thalamic sites receive modest cortical inputs from layer V that contrasted with much denser projections from layer VI. Despite frequent overlap in layer VI, ventral prefrontal and anterior cingulate inputs to nucleus reuniens were concentrated in the deepest sublayer (VIb). Meanwhile, inputs to the anterior thalamic nuclei originated more evenly from both sublayers VIa and VIb, with the result that they were often located more superficially than the projections to nucleus reuniens. Again, while the many hippocampal (subiculum) neurons projecting to nucleus reuniens and the anterior thalamic nuclei were partially intermingled within the deep cellular parts of the subiculum, cells projecting to nucleus reuniens consistently tended to lie even deeper (i.e., immediately adjacent to the alveus). Variable numbers of double-labeled cells were present in those cortical and subicular portions where the two cell populations intermingled, though they remained in a minority. Our data also show how projections to these two thalamic sites are organized in opposing dorsal/ventral and rostral/caudal gradients across both the cortex and hippocampal formation. While the anterior thalamic nuclei are preferentially innervated by dorsal cortical sites, more ventral frontal sites preferentially reach nucleus reuniens. These anatomic differences may underpin the complementary cognitive functions of these two thalamic areas.

Network sensitivity function, optimization and robust performance in dynamic average consensus

AbstractIn this article, a novel sensitivity minimization approach is proposed to optimize the performance of proportional‐integral (PI) dynamic average consensus (DAC) algorithms subject to measurement noises and model uncertainties. Network sensitivity and complementary sensitivity functions are defined to characterize the effects of the reference signals and measurement noises on the tracking error, respectively. Minimization of the norms of network sensitivity and complementary sensitivity functions, describing how large the PI DAC algorithm amplifies the reference and noise signals in the worst case, are conducted to optimize the tracking performance with respect to the reference signals and measurement noises without requiring prior knowledge. Further, by studying the weighted optimization of the network sensitivity functions, necessary and sufficient conditions are provided for the PI DAC algorithm to have a good tracking performance for low‐frequency reference signals and high‐frequency measurement noises. The proposed sensitivity minimization approach is shown to be a robust approach, by considering the PI DAC algorithm in the presence of norm‐bounded additive uncertainties. The robust weighted performance specification is formulated and a sufficient condition is provided, relying on the network topology, the bound of the uncertainties, and the parameters of the DAC algorithms. A tradeoff relationship between the tracking performance and robustness is unveiled. The special case of proportional DAC algorithms is similarly discussed.

Blending the Evaporation Precipitation Ratio With the Complementary Principle Function for the Prediction of Evaporation

AbstractOne class of descriptions of landscape evaporation is based on the principle that actual evaporation E and atmospheric evaporative demand exhibit complementary behavior. A feature of some recent implementations of this approach is the need for the estimation of a free parameter, usually by calibration. In a different class of representations of landscape evaporation, several functional forms have been proposed in the past for the dependency of the mean annual evaporation precipitation ratio (E/P) on the mean annual aridity index —the Schreiber‐Oldekop hypothesis, also known as the Budyko framework. While there is no general agreement in the literature on the optimal formulation of the “maximum possible evaporation” the functional forms of appear to be quite insensitive to its exact nature. This observation allows to be equated with the atmospheric evaporative demand and this immediately leads to a blending of the mean annual evaporation precipitation ratio (E/P) with the complementary evaporation principle, and the prediction of its unknown free parameter. As this free parameter is found to be relatively insensitive to time scale, the complementary functions become not only calibration‐free at the mean annual time scale, but also applicable even at daily time scales. The results are shown to be applicable worldwide with experimental data from 524 catchment water balance set‐ups and 156 high quality eddy covariance flux stations. The present approach offers a practical tool for the prediction of daily evaporation using only routine meteorological inputs including air temperature, humidity, wind speed, net radiation, and long‐term average precipitation.

Solving the Longest Common Subsequence Problem Concerning Non-Uniform Distributions of Letters in Input Strings

The longest common subsequence (LCS) problem is a prominent NP–hard optimization problem where, given an arbitrary set of input strings, the aim is to find a longest subsequence, which is common to all input strings. This problem has a variety of applications in bioinformatics, molecular biology and file plagiarism checking, among others. All previous approaches from the literature are dedicated to solving LCS instances sampled from uniform or near-to-uniform probability distributions of letters in the input strings. In this paper, we introduce an approach that is able to effectively deal with more general cases, where the occurrence of letters in the input strings follows a non-uniform distribution such as a multinomial distribution. The proposed approach makes use of a time-restricted beam search, guided by a novel heuristic named Gmpsum. This heuristic combines two complementary scoring functions in the form of a convex combination. Furthermore, apart from the close-to-uniform benchmark sets from the related literature, we introduce three new benchmark sets that differ in terms of their statistical properties. One of these sets concerns a case study in the context of text analysis. We provide a comprehensive empirical evaluation in two distinctive settings: (1) short-time execution with fixed beam size in order to evaluate the guidance abilities of the compared search heuristics; and (2) long-time executions with fixed target duration times in order to obtain high-quality solutions. In both settings, the newly proposed approach performs comparably to state-of-the-art techniques in the context of close-to-uniform instances and outperforms state-of-the-art approaches for non-uniform instances.

MALAYSIA'S PRIVATE HIGHER EDUCATION SECTOR AS PROVIDER OF ACCESSIBILITY: A WIDER VIEW OF ITS HISTORICAL GROWTH AND ROLES VIS-À-VIS THE PUBLIC HIGHER EDUCATION SECTOR

Existing studies relating to the complementary functions of Malaysia’s private higher education institutions (PHIEs) to public higher education institutions, especially in terms of accessibility to tertiary studies, often suffer from a lack of comprehensiveness. While most of the previous works generally address the subject in a politico-economic and policy-making context, this paper discusses as extensively as possible the role of PHIEs in supplementing public higher education institutions from a historical perspective. The findings show it reconstructs the evolution of PHIE's roles as an alternative-provider from the promulgation of the Private Higher Education Act in 1996 to the first decade of the 2000s, primarily by using government official statistics from 2002 to 2010. Focus is put on the educational opportunities provided by private institutions; opportunities for studying courses not offered by public universities; opportunities for furthering study abroad through twinning programs and; the industrial relevance of the courses. Much of the discussion is in the form of qualitative analyses of statistical data.

PSO 알고리즘을 이용한 트랙킹 진동량 추정과 최적 제어기 설계

This paper presents a method for estimating the vibration quantity and designing a controller using a PSO algorithm for controlling the uncertainties of tracking actuator and disk reflectivity. After estimating the vibration quantity of an actual tracking loop through measurement, the proposed method calibrates the estimated vibration quantity by additionally reflecting the effect of the uncertainties. A minimum tracking loop gain can be appropriately modeled using the estimated vibration quantity. It can be applied to an H<SUB>∞</SUB> objective function to efficiently attenuate the tracking vibration and also to an objective function that prevents the tracking loop gain from becoming larger than necessary. An optimal tracking controller can be designed by minimizing the complementary objective functions using a PSO algorithm. The proposed estimation and design method is applied to a DVD track-following system and verified experimentally.

Stable and EGF-Induced Temporal Interactome Profiling of CBL and CBLB Highlights Their Signaling Complex Diversity.

The epidermal growth factor receptor (EGFR) signal modulates cell proliferation, migration, and survival. Aberrant activation of EGFR constitutes the major cause of various cancers. Receptor ubiquitination and degradation mediated by CBL proteins play negative regulatory roles and control the intensity and duration of the signaling. With the construction of stable cell lines inducibly expressing FLAG-tagged CBL or CBLB, we identified 102 and 82 stable interacting proteins of CBL and CBLB, respectively, through the affinity purification followed by mass spectrometry (AP-MS) approach. Time-resolved profiling at six different time points combined with functional annotations of the temporal interactomes provides insights into the dynamic assembly of signal proteins upon EGFR signaling activation. Comparison between the interactomes of CBL and CBLB indicates their redundant but also complementary functions. Importantly, we validated the stable association of EPS15L1 and ITSN2 and temporal association of TNK2 to both CBL and CBLB through biochemical assays. Collectively, these results offer a useful resource for CBL and CBLB interactomes and highlight their prominent and diverse roles in the EGFR signaling network.

Inflammation‐Instructed Hierarchical Delivery of IL‐4/miR‐21 Orchestrates Osteoimmune Microenvironment toward the Treatment of Rheumatoid Arthritis

AbstractDysregulated inflammation and failure in resolution account for the incidence and deterioration of rheumatoid arthritis (RA). IL‐4 and miR‐21 possess complementary functions in inhibiting inflammation and fostering resolution. Thus, inflammation‐instructed nanocomplexes (NCs) are herein developed to mediate hierarchical co‐delivery of miR‐21 and IL‐4 to orchestrate the osteoimmune microenvironment against RA. The NCs comprise a cationic inner core assembled from the membrane‐penetrating, helical polypeptide (PG) and miR‐21, an outer layer based on the acid‐responsive, charge reversal polymer (PLL‐CA), and surface‐adsorbed IL‐4. The negatively charged NCs enable prolonged blood circulation after systemic administration, and thus passively accumulate in the inflamed joint. In the slightly acidic microenvironment of inflamed synovium, PLL‐CA transforms from negative to positive, which sheds off to liberate IL‐4 extracellularly and facilitate the intracellular delivery of the PG/miR‐21 core into macrophages. Thus, the anti‐inflammatory miR‐21 cooperates with the proresolving IL‐4 to attenuate inflammation via NF‐κB inhibition, promote macrophage polarization to M2a/M2c phenotypes, propel resolution, and promote tissue repair against Zymosan A‐induced arthritis. This study provides an effective strategy toward the programmed delivery of drug/gene cargoes at different extracellular/intracellular locations, and the combined mechanism of anti‐inflammation and proresolution renders insights into the treatment of inflammatory diseases.

Learning from Noisy Labels with Complementary Loss Functions

Recent researches reveal that deep neural networks are sensitive to label noises hence leading to poor generalization performance in some tasks. Although different robust loss functions have been proposed to remedy this issue, they suffer from an underfitting problem, thus are not sufficient to learn accurate models. On the other hand, the commonly used Cross Entropy (CE) loss, which shows high performance in standard supervised learning (with clean supervision), is non-robust to label noise. In this paper, we propose a general framework to learn robust deep neural networks with complementary loss functions. In our framework, CE and robust loss play complementary roles in a joint learning objective as per their learning sufficiency and robustness properties respectively. Specifically, we find that by exploiting the memorization effect of neural networks, we can easily filter out a proportion of hard samples and generate reliable pseudo labels for easy samples, and thus reduce the label noise to a quite low level. Then, we simply learn with CE on pseudo supervision and robust loss on original noisy supervision. In this procedure, CE can guarantee the sufficiency of optimization while the robust loss can be regarded as the supplement. Experimental results on benchmark classification datasets indicate that the proposed method helps achieve robust and sufficient deep neural network training simultaneously.

A powerful numerical approach for the axisymmetric bending response of shear deformable two-directional functionally graded (2D-FG) plates with variable thickness

In the present article, a powerful numerical approach is applied to the axisymmetric bending of 2 D-FG circular and annular plates with variable thickness. The mechanical properties of the materials of the plate are assumed to vary continuously both in the radial and thickness directions. The principle of minimum total potential energy is used to obtain the governing equations. Shear deformation is considered based on the first-order shear deformation theory (FSDT). These ODEs are solved via the Complementary Functions Method (CFM) for the first time. The novelty of this paper is the infusion of the CFM to the axisymmetric bending of a wide range of annular or circular plates, with variable thickness, radially FG (RFG), FG in thickness direction, or 2D-FG. In addition to adopting this effective numerical approach to the present class of problems, various parametric studies are presented to show the influence of material variation parameters and geometric constants on the axisymmetric bending response of the considered structures. Results of the proposed approach are validated with those carried out by FEM and those of the available published literature. An excellent agreement is observed.

An active role of inferior frontal cortex in conscious experience

In the search for the neural correlates of consciousness, it has remained controversial whether prefrontal cortex determines what is consciously experienced or, alternatively, serves only complementary functions, such as introspection or action. Here, we provide converging evidence from computational modeling and two functional magnetic resonance imaging experiments that indicated a key role of inferior frontal cortex in detecting perceptual conflicts caused by ambiguous sensory information. Crucially, the detection of perceptual conflicts by prefrontal cortex turned out to be critical in the process of transforming ambiguous sensory information into unambiguous conscious experiences: in a third experiment, disruption of neural activity in inferior frontal cortex through transcranial magnetic stimulation slowed down the updating of conscious experience that occurs in response to perceptual conflicts. These findings show that inferior frontal cortex actively contributes to the resolution of perceptual ambiguities. Prefrontal cortex is thus causally involved in determining the contents of conscious experience.

Secondary Serpentine Forests of Poland as a Refuge for Vascular Flora

The aim of present study was to determine the role of secondary, serpentine forests in Poland in the protection of rare vascular plant species. On the basis of 95 phytosociological relevés collected between 2009 and 2020, we identified the main types of serpentine forest communities and assessed their diversity indices. Ordination methods were used to determine the relationship between the degree of transformation of forest communities (reflected by the occurrence of alien and nitrophilic species) and the presence of endangered species in their undergrowth including the environmental background. We distinguished four types of communities: thermophilic and mesophilic pine plantations (both secondary in origin) as well as thermophilous oak forest and acidophilous oak–hornbeam forest (semi-natural and close to natural in character, respectively). Rare and endangered species were unevenly distributed and concentrated in oak forest (16 species) and thermophilic pine plantation (nine species). The endangered species mainly preferred sites at higher altitudes and with higher slope inclination, light availability, and soil reaction. We did not confirm that the presence of alien or nitrophilic species negatively influenced the ability of studied forests to preserve rare plants. As secondary forests can still harbor endangered species, they should fulfil complementary functions in the nature protection system.

Evidence Theory Representations for Properties Associated With Weak Link/Strong Link Systems, Part 3: Margins for Failure Time and Failure Temperature

Abstract The use of evidence theory and associated cumulative plausibility functions (CPFs), cumulative belief functions (CBFs), cumulative distribution functions (CDFs), complementary cumulative plausibility functions (CCPFs), complementary cumulative belief functions (CCBFs), and complementary cumulative distribution functions (CCDFs) in the analysis of time and temperature margins associated with loss of assured safety (LOAS) for one weak link (WL)/two strong link (SL) systems is illustrated. Article content includes cumulative and complementary cumulative belief, plausibility, and probability for (i) SL/WL failure time margins defined by (time at which SL failure potentially causes LOAS) − (time at which WL failure potentially prevents LOAS), (ii) SL/WL failure temperature margins defined by (the temperature at which SL failure potentially causes LOAS) − (the temperature at which WL failure potentially prevents LOAS), and (iii) SL/SL failure temperature margins defined by (the temperature at which SL failure potentially causes LOAS) − (the temperature of SL whose failure potentially causes LOAS at the time at which WL failure potentially prevents LOAS).

Evidence Theory Representations for Properties Associated With Weak Link/Strong Link Systems, Part 2: Failure Time and Failure Temperature

Abstract The use of evidence theory and associated cumulative plausibility functions (CPFs), cumulative belief functions (CBFs), cumulative distribution functions (CDFs), complementary cumulative plausibility functions (CCPFs), complementary cumulative belief functions (CCBFs), and complementary cumulative distribution functions (CCDFs) in the analysis of loss of assured safety (LOAS) for weak link (WL)/strong link (SL) systems is introduced and illustrated. Article content includes cumulative and complementary cumulative belief, plausibility, and probability for (i) time at which LOAS occurs for a one WL/two SL system, (ii) time at which a two-link system fails, (iii) temperature at which a two-link system fails, and (iv) temperature at which LOAS occurs for a one WL/two SL system. The presented results can be generalized to systems with more than one WL and two SLs.

IMAP: A Web Server for Metabolomics Data Integrative Analysis

Metabolomics data analysis depends on the utilization of bioinformatics tools. To meet the evolving needs of metabolomics research, several integrated platforms have been developed. Our group has developed a desktop platform IP4M (integrated Platform for Metabolomics Data Analysis) which allows users to perform a nearly complete metabolomics data analysis in one-stop. With the extensive usage of IP4M, more and more demands were raised from users worldwide for a web version and a more customized workflow. Thus, iMAP (integrated Metabolomics Analysis Platform) was developed with extended functions, improved performances, and redesigned structures. Compared with existing platforms, iMAP has more methods and usage modes. A new module was developed with an automatic pipeline for train-test set separation, feature selection, and predictive model construction and validation. A new module was incorporated with sufficient editable parameters for network construction, visualization, and analysis. Moreover, plenty of plotting tools have been upgraded for highly customized publication-ready figures. Overall, iMAP is a good alternative tool with complementary functions to existing metabolomics data analysis platforms. iMAP is freely available for academic usage at https://imap.metaboprofile.cloud/ (License MPL 2.0).

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.

Specialised metabolites from microbial sources are well-known for their wide range of biomedical applications, particularly as antibiotics. When mining paired genomic and metabolomic data sets for novel specialised metabolites, establishing links between Biosynthetic Gene Clusters (BGCs) and metabolites represents a promising way of finding such novel chemistry. However, due to the lack of detailed biosynthetic knowledge for the majority of predicted BGCs, and the large number of possible combinations, this is not a simple task. This problem is becoming ever more pressing with the increased availability of paired omics data sets. Current tools are not effective at identifying valid links automatically, and manual verification is a considerable bottleneck in natural product research. We demonstrate that using multiple link-scoring functions together makes it easier to prioritise true links relative to others. Based on standardising a commonly used score, we introduce a new, more effective score, and introduce a novel score using an Input-Output Kernel Regression approach. Finally, we present NPLinker, a software framework to link genomic and metabolomic data. Results are verified using publicly available data sets that include validated links.

Interactions of the influences of habitat protection, habitat heterogeneity, and periodic flooding on waterbirds of the lower Paraná River, Argentina

AbstractHow waterbirds respond to environmental characteristics of river systems is of interest because of the high biodiversity of waterbirds in these systems, their ecological roles, and the importance of waterbirds in hunting for sport or sustenance. We studied the influence of natural factors (water‐level fluctuations and environmental heterogeneity) and human‐related factors (habitat protection, which primarily excludes cattle grazing and hunting) on waterbirds in the Pre‐Delta region of the Paraná River system during three years. Our objectives were to evaluate the environmental factors that influence the assemblages of waterbirds and whether these variables explain differences in waterbird assemblages between protected and non‐protected areas. Both species richness and abundance of waterbirds per point count increased with the diversity of land cover categories at count spots. Species richness also increased with the surface of open water. The larger surface of open water in the non‐protected area contributed to explaining the higher species richness and abundance of waterbirds, including species with hunting pressure, in this area. During floods, the protected area maintained a high abundance of waterbirds, probably because the higher proportion of trees and aquatic vegetation in this area provided perches and foraging sites. We recommend enlarging protected areas in the Pre‐Delta region because of their role of sheltering waterbirds during floods. Protected and non‐protected areas serve complementary functions in providing habitat for waterbirds; therefore, it is important to maintain both of these management types in the landscape.Abstract in Spanish is available with online material.

In silico analysis of synthetic multispecies biofilms for cellobiose-to-isobutanol conversion reveals design principles for stable and productive communities

Efficient, large-scale conversion of plant-derived feedstocks to commodity chemicals remains a substantial technological challenge with enormous potential for societal benefits. Most research efforts have focused on metabolic engineering of model organisms for planktonic cell cultures in well-mixed suspension bioreactors. We utilized in silico metabolic modeling to explore the potential benefits of an alternative design strategy based on combining bacterial strains with complementary metabolic functions within high density, multispecies biofilms. We simulated four alternative system designs, each of which consisted of an anaerobic cellulolytic bacterium which degraded cellobiose to glucose, an aerobic Escherichia coli strain engineered for glucose-to-isobutanol conversion, and an aerobic or anaerobic byproduct consumer for metabolizing growth-inhibiting organic acids such as acetate secreted by the other two strains. Our simulations predicted dramatically different cellobiose-to-isobutanol conversion capabilities depending on the metabolic compatibility of the three bacteria. Important design considerations included glucose competition between the cellulolytic and isobutanol-producing bacteria, O2 competition between the isobutanol-producing and byproduct-consuming bacteria, organic acid matching between the cellulolytic and byproduct-consuming bacteria and the degree of metabolic redundancy between the community members. We believe that these design principles will be widely applicable to synthetic biofilm communities engineered to perform other bioconversion tasks.