Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproductive state leads to intraspecific habitat partitioning and survival differences in greater sage-grouse: implications for conservation

Abstract Context. Inter- and intraspecific habitat partitioning is widespread across taxa, yet limited information is available on differences in intraspecific habitat selection by same-sex individuals among differing reproductive states. Understanding habitat selection by conspecifics of different reproductive states may help optimise conservation efforts, particularly for gallinaceous bird species such as greater sage-grouse (Centrocercus urophasianus), which are long-lived but have only moderate reproductive rates. Aims. We predicted that habitat use differed between grouse under different reproductive states and that reproductive investment decreased survival of adults in summer. Methods. We compared habitat characteristics used by brood-rearing and broodless female sage-grouse and evaluated the influence of reproductive investment and habitat use on survival of adult females. Key results. We found that brood-rearing and broodless female sage-grouse partitioned habitat at micro- and macrohabitat scales. Broodless females were more likely to survive the summer. Conclusions. Our findings suggest reproductive state variability in habitat selection by female sage-grouse. Broodless females were roosting and foraging in concealed habitats with intermediate visual obstruction and annual vegetation productivity, but less food forb availability compared with early and late brood-rearing females. In contrast, brood-rearing females likely selected more herbaceous understoreys to predictably maximise foraging opportunities and promote growth of their chicks, which appeared to mitigate the influence of reproductive costs on summer survival, particularly during the late brood-rearing period. Implications. Survival of adult females is critical for population persistence of sage-grouse and other long-lived Galliformes, yet conservation efforts generally focus on habitats used during nesting and brood-rearing. Our results suggest that habitat partitioning is a potential risk-aversion strategy where individuals across different reproductive states likely select habitats to maximise their survival. Conservation efforts should focus on conserving habitats used by both brood-rearing and broodless sage-grouse to ensure population persistence.
A NOVEL MULTI-COMBINED METHOD FOR HANDLING MEDICAL DATASET WITH IMBALANCED CLASSES PROBLEM

A BSTRACT . The imbalanced datasets are quite common in medical research, which has impacted on classiﬁcation accuracy. Diseases are always life-threatening, and any small bias may harm the patient; hence the medical ﬁeld has a relatively low tolerance of misjudgment. In order to accurately identify diseased and non-disease individuals, this study proposes a novel multi-combined method to deal with the medical dataset with imbalanced classes problem. The proposed method applies the synthetic minority oversampling technique (SMOTE) to deal with the minority class and then used the particle swarm optimization (PSO) to select important attributes. Finally, the ﬁve cost-sensitive classiﬁers based on the MetaCost method are employed to classify the medical datasets. The experimental results indicate that the random forest can achieve the best accuracy. The best false positive rate is the LibSVM classiﬁer, and the best false-negative rate occurs in the LibSVM classiﬁer combined with the PSO attribute selection, SMOTE, and MetaCost. At last, the results can assist physicians in identifying diseases, and then the patients can be early diagnosed and treated for increasing their chances of survival.
The clonal plant microbiota : assembly rules, heritability and influence on host phenotype

Les plantes vivent en association avec une grande diversite de microorganismes qui forment son microbiota. Ce microbiote fournit des fonctions cles qui influencent tous les aspects de la vie d'une plante, de l'etablissement a la croissance jusqu'a la production. Cette these a pour intention de determiner les reglent d'assemblage du microbiote et ses consequences pour le phenotypel l'adaptation et l'evolution des plantes. Pour atteindre cet objectif nous avont utilise differentes approches experimentales comprenant des plantes clonales comme organismes modeles ainsi que des mesocosmes prairiaux pour analyses a l'echelle des communautes. Nos resultats ont demontre i) que les Champignons Mycohiziens a Arbuscules induisent d'important es variations phenotypiques pour les traits des plantes clonales impliques dans l'exploration de l'espace et l'exploitation des ressources. Ces changements dependent de l'identite des symbiontes et alterent les capacites des plantes a developper des reponses plastiques a l'heterogeneite environnementale. ii) Les plantes ont evolue un mechanisme permettant la transmission d'une partie de leur microbiote a leur descendance, assurant la qualite de leur habitat. iii) Le contexte specifique des communautes de plantes est un facteur majeur structurant l'assemblage du microbiota des plantes a echelle locale. L'abondance de certaines especes de plante dans le voisinage d'une plante cible augmente ou diminue la diversite de son microbiote, determinant in fine ses performances. De maniere generale, cette these demontre l'importance des organismes symbiotiques dans la comprehension de l'adaptation et de l'evolution des plantes.
From evolutionary governance to evolutionary strategies: Standing on the edge of chaos

The perspective of Evolutionary Governance that I have developed since 2012 is part of the emerging evolutionary perspective on the economy. I have proposed a new vision of governance as the function that optimizes the cognitive and behavioral collective intelligence of a firm to make decisions facing risks and uncertainty. The Board of Directors acts to anticipate variations of external conditions and internal routines, select the right orientations (decisions and routines which ensure the sustainability of the firm) and enhance co-evolution. The term "evolutionary" refers to the process of endogenously developing variations, selection and retention on the one hand, and on the co-evolution phenomenon on the other hand. Once limited to paleoanthropology, it has been extended as an abstract process to conceptualize many domains, among which economics. The original process of variation/selection/retention has become a generic concept of evolution as novelty/emergence/dissemination. Why is it necessary to introduce evolutionary concepts into governance research? To answer this question, I review in the first part the succession of influences over governance theories, and the pitfalls of the current framing compared to the objectives I assign to governance, as an internal mechanism of organizations to structure itself to face risks and uncertainty. In the second part, I review the breakthroughs of evolutionary concepts in various domains in close links with governance: strategy and political science and public administration. And in the last part, I explore the interesting properties of evolutionary governance and overview the impacts of this theory over strategy and economics.
Spatial pattern of intraspecific trait variability in Sphagnum fuscum

Recent studies have shown that intraspecific variability is a mechanism by which species respond to environmental heterogeneity, and that intraspecific variation can have large implications for ecological processes. Here, we studied whether there is meaningful intraspecific variation in the ecohydrological traits, biomass allocation, and decomposability in Sphagnum moss, and if so, to explore the spatial pattern of variability. We implemented a hierarchical design in which we quantified traits of S. fuscum at three spatial scales: (i) between individuals within 8 cm2 patches; (ii) between replicate patches located within a single hummock or hollow location; and (iii) between hummocks. Although we focused on S. fuscum, we also compared the variability in some morphological features of S. fuscum and S. magellanicum. If growth is affected by density, we expected variability to be lowest at the patch level. Contrary to our expectation, most of the variability in both species occurred within-patch, which is our smallest sampling unit. Variability was generally higher in the traits for S. magellanicum compared with the variability in the traits for S. fuscum, which was generally negligible. Also, the pattern of variability observed for some of the traits such as the capitulum mass suggests that the mechanisms controlling different traits may be operating at different spatial scales.
Complete chloroplast genome of Ulleung Island endemic basswood, Tilia insularis (Malvaceae), in Korea

Abstract The first complete chloroplast genome sequences of Korean endemic basswood in Ulleung Island, Tilia insularis, were reported in this study. The T. insularis plastome was 162,565 bp long, with the large single-copy (LSC) region of 91,100 bp, the small single-copy (SSC) region of 20,381 bp, and two inverted repeat (IR) regions of 25,542 bp. The plastome contained 131 genes, including 86 protein-coding, eight ribosomal RNA, and 37 transfer RNA genes. The overall GC content was 36.5%. Phylogenetic analysis of 14 representative plastomes within the family Malvaceae suggests that T. insularis is closely related to other congeneric species in subfamily Tilioideae.
Modifying TiO2 Nanoparticles by Atomic Layer Deposition for Enhanced Photocatalytic Water Purification

Photocatalysts, contrary to conventional catalysts, utilize light to drive a reaction. By absorption of photons, electrons are excited and reach higher states to initiate a redox reaction. This principle can be broadly used to produce chemicals such as hydrogen via the reduction of water or transform carbon dioxide into solar fuels, i.e., methane, methanol, and formaldehyde. Besides chemical production, the reductive/oxidative potential of the excited electrons/holes can be utilized to degrade molecules. This is especially useful for self-cleaning materials or for cleaning waste water streams from molecules such as dyes, pesticides, or pharmaceuticals, as water pollution levels increasingly harm human health, especially in developing countries. Despite the great potential and vast research activities over the last decades, the development of cheap and efficient photocatalysts and especially the evaluation of the mechanism of photocatalytic degradation pathways are still lacking, which hampers the translation from lab to application. TiO2 (P25) is a cheap and non-toxic photoactive material, yet too inefficient for water cleaning. This thesis focuses on the surface modification of TiO2 (P25), minimizing various drawbacks of TiO2 (P25) and on the evaluation of the photocatalytic mechanisms. Atomic layer deposition (ALD) allows us to precisely control the deposition of many different materials at the atomic level, an advantage that could improve the photocatalyst design and optimize the activity.
Phenotypic and molecular characterization of the causal agent of chafer beetle mortality in the wheat fields of the Kurdistan province, Iran

We report the first case of chafer beetle [Anisoplia austriaca (Herbst 1783)] mortality caused by Actinomucor elegans var. elegans in wheat fields of the Kurdistan province, Iran. For three years, dead larvae of Anisoplia austriaca were collected from wheat fields of the Kurdistan province. Similar isolates of a fast-growing fungus were recovered from all samples. The fungal isolates were identified as A. elegans var. elegans based on morphological and cultural characteristics. The identity of the species was further confirmed using sequence data of the ITS (Internal Transcribed Spacer) region of ribosomal DNA. Koch’s postulates were fulfilled by the inoculation of the larvae of A. austriaca and Galleria mellonella (Linnaeus, 1758) (as the model insect) using the spore suspension of A. elegans var. elegans. The viability of sporangiospores was evaluated using a spore dilution technique on germination medium. The results on the pathogenicity (100% mortality in A. austriaca larvae) and viability tests (germination: 95.45%) demonstrated that A. elegans var. elegans can be considered as a potential biocontrol agent against the chafer beetle. Field experiments are still required to evaluate the capacity of A. elegans as a biological control agent.
TOMATOD: EVALUATION OF OBJECT DETECTION ALGORITHMS ON A NEW REAL-WORLD TOMATO DATASET

Abstract. The integration of modern technologies in farming poses a challenging task to the research community. In this work, the task of selective cropping and treating is considered, whereas learning algorithms can provide essential assistance on crop growth and disease prediction, species recognition and fruit detection. In this paper, we introduce a highly specialized object detection (OD) and classification dataset of tomato fruits that contains class information for the ripening stage of each tomato fruit apart from its corresponding bounding box. With this dataset we aim to encourage the development of task-specific production ready object detection algorithms, as well as to evaluate and provide a baseline result of common state-of-the-art generic OD algorithms. In detail, a thorough presentation of the most common OD datasets takes place, where we discuss both generic OD and some highly specialized datasets. Our dataset contains more than 250 images and 2400 annotations in total. The dataset contains class information for three ripening stages of a tomato fruit provided by expert agriculturists, while providing views consistent with the targeted real-world use case scenario. Compared to other OD datasets our proposition differs in core areas such as the quality of the annotations, the object size distribution and the public availability. Evaluating the performance in our dataset for six object detection models we draw conclusions about the strength and weaknesses of each one’s performance. Finally, we present a future roadmap of revisions and discuss some future research topics that could improve the performance of OD algorithms in our dataset.
Pin1: WW domain ligands, catalytic inhibitors, and the mechanism

The peptidyl prolyl cis/trans isomerase, PPIase, has been the focus of numerous studies in the field of cell cycle regulation since proline-directed phosphorylation is an essential signaling mechanism that might arrest cancer proliferation. Pin1 is the first phosphorylation-dependent PPIase enzyme to be discovered. The Pin1 regulatory mechanism, acting on other mitotic proteins in vivo and in vitro, remains largely unknown. For the study of Pin1 function, two types of assays were used to identity ligands for Pin1: (1) The Enzyme-Linked Enzyme Binding Assay (ELEBA) for the identification of WW domain ligands, (2) a catalytic assay to identified inhibitors of Pin1 catalytic activity. The ELEBA offers a selective approach for detecting ligands that bind to the Pin1 WW domain from chemical libraries. By using the ELEBA, a pSer-Pro peptidomimetic library of 315 ligands was screened, identifying three promising ligands cis-D2, O2, and M18. Competitive Kd values for cis-D2, O2, and M18 were determined to be 263 ± 6.4, 206 ± 3.4, and 130 ± 3.0 μM, respectively. Furthermore, we screened the pSer-Pro peptidomimetic library using a Pin1 discontinuous-catalytic assay to identify inhibitors of Pin1. Ligands D20 and K7 were identified to decrease more than 90% of the Pin1 catalytic activity. To investigate the nature of the Pin1 interaction with c-Myc, we synthesized and characterized four peptides corresponding to the c-Myc sequence. These peptides were used in NMR isomerization studies of Pin1 by our collaborator Dr. Jeffry Peng (University of Notre Dame). Preliminary work shows that Pin1 binds and isomerizes the Ac–LLPpTPPLSPS–NH2 peptide at the cMyc pThr58 position. Finally, we measured a secondary kinetic isotope effect (2o KIE) to study the Pin1 catalytic mechanism of proline isomerization. The ratio of kH/kD for unlabeled and [d3]Serlabeled substrate gave a SKIE value of 1.34 ± 0.01. The normal 2o KIE value indicates that carbonyl-serine hybridization is not changing from sp 2 to sp 3 . This result supports substrate analogue inhibitor studies, and previous solvent and SKIE results on Pin1, that suggest a twisted amide mechanism assisted by a transient hydrogen bond in the transition state.
Hypoxia-Induced amine secretion from rodent carotid body and adrenal chromaffin cells: Evidence against NADPH oxidase as an 02 sensor

An adequate supply of oxygen (02) is essential to the survival of all higher organisms. The mammalian carotid body, located at the common carotid artery senses blood levels of 0 2, carbon dioxide (C02) and acidity. Glomus cells, or type I cells in the carotid body are the main 0 2-sensors which regulate blood p02 via reflex control of ventilation. The carotid body secretes multiple neurotransmitters including dopamine (DA), which is potentiated during low p02 levels and is thought to modulate sensory signaling by apposing afferent nerve fibers. Catecholamine (CA) release is also critical for the animal's ability to survive hypoxic stress associated with the birthing process and the transition to extrauterine life. However, the source for this CA release (primarily epinephrine; EPI) is from adrenal chromaffin cells. The primary 02-sensor in both adrenal chromaffin cells and carotid body type I cells is unknown. One potential candidate is the cytochrome b55s/NADPH oxidase complex that generates the respiratory burst in phagocytes. To test this hypothesis, cultured adrenal medulla chromaffin cells and intact carotid bodies from wild type (WT) and oxidase deficient (OD) mice (knockout gp91 phox, the glycoprotein subunits in the NADPH oxidase complex) were investigated. High performance liquid chromatography and immunocytochemistry were used to quantify amine release in these two chemoreceptors following exposure to hypoxia. Both WT and OD chromaffin cells and carotid bodies responded to the hypoxic challenge with increased monoamine secretion. Norepinephrine and epinephrine were the principal amines released from chromaffin cells, compared to dopamine and serotonin from carotid bodies. These findings suggest that NADPH oxidase is not the primary 02-
Linking functional diversity and ecosystem processes: A framework for using functional diversity metrics to predict the ecosystem impact of functionally unique species

Functional diversity (FD) metrics are widely used to assess invasion ecosystem impacts, but we have limited theory to predict how FD should respond to invasion. A key challenge to effectively using FD metrics is the complexity of conceptualizing alterations to multidimensional trait space, making it difficult to select a priori the most appropriate metric for specific ecological questions. Here, we provide expectations on how invasion should change four commonly used FD metrics—functional richness (FRic), evenness (FEve), divergence (FDiv) and dispersion (FDis)—and then test these expectations in a laboratory decomposition experiment. We simulate invasion of a forest by understorey plants by adding leaf litter from 18 natives and non‐natives to a representative canopy tree litter mixture to test changes in FD and decomposition. All four metrics changed predictably with invasion. Species that were more functionally unique or when added at greater proportions had larger impacts on FD. Overall, FRic, FEve and FDiv were poor choices for understanding impacts of non‐native species. FDis was the only metric that both changed predictably with addition of understorey litter and correlated intuitively with changes in carbon mineralization. Furthermore, ranking species based upon how much they changed FDis of the litter mixture provided a fair assessment of which species had the largest impact on decomposition. As such, functional dispersion may be a key tool for predicting a priori which non‐natives will have the greatest impact on ecosystem processes. Synthesis. We highlight the need to assess the suitability of each functional diversity metric for the specific ecological question at hand. Our work reveals the pitfalls of considering multiple metrics or randomly choosing a single metric without suitability assessments. At the same time, it suggests a framework for metric assessment that should help lead to selection of a metric or metrics that provide robust a priori insights into how invasion by non‐native species can impact ecosystem processes.
DETERMINATION OF LETHAL CONCENTRATION OF TROPICAL SODA APPLE, SOLANUM VIARUM (DUNAL) AGAINST COMMON CUTWORM, SPODOPTERA LITURA (FABRICIUS) (LEPIDOPTERA: NOCTUIDAE)

Spodotera litura a polyphagous pest on economically important crops such a cotton, groundnut, chilli, tobacco, bhendi and pulses are developing resistant to most of the insecticides available in the market and in order to develop an alternate method. The present study targets to workout determent dose 50 for Solanum viarum fruit extract by following feeding assay against S.litura. Three types of extracts were used in the feeding assay to experiment insecticidal activity of S.vairum fruit extract. In total 10 accessions and one variety of S.viarum fruits were tested for their insecticidal effects. Among the tested accessions kolli hills accessions were found effective in exerting mortality. The LC50 worked out 0.48% for the S.viarum fruits (kolli hills accessions)
In vitro germination of several South African summer rainfall Disa (Orchidaceae) species: is seed testa structure a function of habitat and a determinant of germinability ?

Seed germination is consistently poor for the majority of Disa species, with in vitro culture revealing a decrease in species germinability as one moves from the winter to the summer-rainfall areas of South Africa. In an effort to enhance seed culture as a means of promoting conservation in Disa, the seed testa is highlighted as a regulatory factor in germination. A prominent feature of the mature seed is the variable colour of the testa in the ten species investigated, attributable to different levels of phenolic compounds. Total leachable phenolic content correlates positively with germinability and by inference, with species distribution. NaOCl treatment enhanced germination in certain species by scarifying the testa and enhancing permeability to water. Similarly liquid cultures and culture media containing activated charcoal decrease the time taken to, and result in elevated levels of synchronous germination. Culture of immature seed (before phenolic deposition has occurred) also hastens germination. Scanning electron microscopy has highlighted basic differences between species regarding seed size and testa cell arrangement. All features of the testa and its influence on germinability in the summer-rainfall Disas are explained as adaptations to environmental conditions. The authors speculate on the occurrence of coat-imposed dormancy within Disa species endemic to the summer rainfall areas of South Africa.
The expression tractability of a biological trait

Understanding how gene expression is translated to phenotype is central to modern molecular biology, but the success is contingent on the intrinsic tractability of the specific traits under examination. However, an a priori estimate of trait tractability from the perspective of gene expression is unavailable. Motivated by the concept of entropy in a thermodynamic system, we here propose such an estimate (ST) by gauging the number (N) of different expression states that underlie the same trait abnormality, with large ST corresponding to large N. By analyzing over 200 yeast morphological traits we show that ST is constrained by natural selection, which builds co-regulated gene modules to minimize the total number of possible expression states. We further show that ST is a good measure of the titer of recurrent patterns of an expression-trait relationship, predicting the extent to which the trait could be deterministically understood with gene expression data.