Miracle-dz/UniFAR-FTUs huggingface dataset:
The Viable but Non-culturable State in Xanthomonas citri subsp. citri is a Reversible State Induced by Low Nutrient Availability and Copper Stress Conditions

Xcc (Xanthomonas citri subsp. citri) causes citrus bacterial canker, a leaf, stem and fruit spotting disease that affects most commercial citrus species and cultivars. Copper compounds, widely used for management of this pathogen, have been reported as inducers of a VBNC (viable but non-culturable state) in plant pathogenic bacteria. VBNC may be considered as a state preceding bacterial death or as a survival mechanism under adverse conditions. Several experiments were performed to characterize the reversibility and persistence of the VBNC state in Xcc. VBNC was induced in low nutrient medium or with amendment of copper at concentrations used for field disease control. The VBNC condition was demonstrated to persist up to 150 days after copper treatment and was reversed after the addition of culture media without copper or amendment with citrus leaf extract. Xcc viability was evaluated by recovery of colonies on culture media, confirmed by membrane integrity, respiratory activity and by real-time RT-PCR targeting a sequence from the gumD gene. Besides, the colonies recovered were pathogenic on citrus leaves. These results confirm that the VBNC state in Xcc is inducible and reversible and therefore may occur in the phyllosphere when Xcc is under copper stress or starvation.
Inferring Transcription Factors and microRNAs Associated with Elevated Expression of the Oncogenic B-Cell Lymphoma 11A in Triple Negative Breast Cancer

Citation Laqtom NN, Algothmi KM, Bakhribah AH. Inferring transcription factors and microRNAs associated with elevated expression of the Oncogenic B-Cell Lymphoma 11A in Triple Negative Breast Cancer. JKAU Med Sci 2016; 23 (3): 9-21. DOI: 10.4197/Med. 23.3. 2 Abstract B-cell lymphoma 11A, a transcriptional repressor, is highly expressed in triple negative breast cancer. The in vitro studies and animal models provide initial evidence suggesting that the knockdown of B-cell lymphoma 11A has a therapeutic eff ect on breast cancer. Defi ning the regulators driving the high expression of B-cell lymphoma 11A is important to understand its cancer-related functions. Among these regulators, transcription factors and microRNAs are critical for gene expression and associated with expression perturbations. Firstly, we identifi ed the transcription factors that potentially interact with B-cell lymphoma 11A promoter. Based on bioinformatics prediction and multiple Omics datasets, two upregulated transcriptional activators Zinc Finger BED-Type Containing 4 and E2F Transcription Factor 1 in triple negative breast cancer were found to have seven sites within B-cell lymphoma 11A promoter. Secondly, we aimed to determine a putative set of microRNA that can mediate the post-transcriptional repression of B-cell lymphoma 11A. miR-513a-5p, miR-139-5p, miR1179, miR-140-5p, and miR-542-3p, harboring at least one site of interaction with B-cell lymphoma 11A 3' untranslated region, were found inhibited in triple negative breast cancer. Taken together, the combinatorial regulation by transcription factors and microRNAs provide valuable information for further investigation on controlling the expression level of B-cell lymphoma 11A in triple negative breast cancer.
Micro RNAs: a Revolutionary Discovery in Biology

MicroRNAs (miRNAs) are endogenous, single-stranded, short, noncoding ribonucleic acids (RNAs), which can bind to their target messenger RNAs (mRNAs), leading to the inhibition of translation or degradation of the mRNA. Only recently have scientists discovered the important role that miRNAs play in gene regulation. To date, more than 700 miRNAs have been identified from the human genome. Malfunctioning miRNAs have been implicated in a number of diseases, due to their regulatory functions in transcription, signal transduction, cell cycle regulation, proliferation, cell growth and metabolism, cell apoptosis, and neurogenesis. Absence of miRNAs or their mutations, detected by genetic analysis, has been associated with a broad spectrum of disease processes, such as various cancers and autoimmune, cardiovascular, infectious, metabolic, neurodegenerative, skin, and psychiatric diseases. The large progress made in understanding miRNAs also points to their great potential as new biomarkers in the diagnosis and early detection of various diseases, as well as their promising role in future therapeutics.
The effect of coterie relocation on release-site retention and behavior of Utah prairie dogs

Utah prairie dogs (Cynomys parvidens) have been extirpated in 90% of their historical range. Because most populations in Utah occur on private land, this threatened species is continually in conflict with landowners. The Utah Division of Wildlife Resources has been relocating Utah prairie dogs from private to public land since the 1970s, but relocations have been largely unsuccessful because of high mortality. Utah prairie dogs are highly social animals, but they are usually relocated without regard to their family group, or coterie. We predicted that relocating Utah prairie dogs with other coterie members would improve their survival rate and result in post-release behavior similar to non-relocated animals. We chose to investigate release-site retention as a measure of relocation success because we were unable to separate emigration from mortality. We relocated Utah prairie dogs from the Cedar Ridge Golf Course in Cedar City, Utah to 2 prepared sites near Bryce Canyon National Park, Utah in 2010 and 2011. We relocated prairie dogs as groups of coterie members or in a control group of individuals trapped with no regard to relatedness. Two months after relocation, we set traps to recapture animals to estimate release-site retention. We quantified activity budgets prior to and following relocation on study animals as well as from a previously established relocated prairie dog population on public land. The best predictor of release-site retention and recapture rate was the animal's weight at initial capture. Larger animals had high retention but low recapture rates. We found no differences in site retention or behavior between prairie dogs relocated with coteries and controls. Relocated individuals behaved more like prairie dogs on public lands than animals in the urban source population, but behaviors were still different from prairie dogs on public lands. We recommend relocating large, adult Utah prairie dogs rather than juveniles or relocating juveniles later in the trapping season to increase relocation success rate. We also suggest that future research should focus on developing additional release methods to reduce dispersal and increase site retention. © 2014 The Wildlife Society.
Antioxidative Activity and Antimutagenicity of Three Plants in Annonaceae in Plant Genetics Conservation at Khok Phutaka, Amphur Phuwiang, Khon Kaen

This study aimed to investigate the antioxidative activity and antimutagenicity of six extracts of three plants in Annonaceae, collected from Khok Phutaka area, Amphur Phuwiang, Khon Kaen. The results showed the strong antioxidative activities of the extracts from stem-root of Ellipeiopsis cherrevensis and leaf of Polyalthia evecta with EC ₅₀ at 14.3 and 14.7 µg/ml, respectively. The other extracts with relative order of activity were leaf of E. cherrevensis > leaf of P. debilis > stem-root of P. evecta > stem-root of P. debilis (EC ₅₀ = 17.9, 22.8, 46.3 and 177.9 µg/ml, respectively). The plant total phenolic contents are well correlated with their antioxidative activities. For pre-incubation bacterial mutation test, the extracts from leaf and stem-root of E. cherrevensis showed mutagenic effect on Salmonella typhimurium TA98 and TA100 in the absence of S-9 mix. Whereas in the presence of S-9 mix, the mutagenicity was found in the extracts from leaf of E. cherrevensis, leaf and stem-root of P. debilis and leaf of P. evecta. The antimutagenicity was detected in both TA98 and TA100 in all extracts in the presence of S-9 mix. In contrast, in the absence of S-9 mix only the extracts from stem-root and leaf of P. debilis; and leaf of P. evecta showed the antimutagenicity to TA98. Therefore, these three plants are interesting to be further studied on their anticancer activity.
Germination Characteristics of Italian Thistle (Carduus pycnocephalus) and Slenderflower Thistle (Carduus tenuiflorus)

Seed germination of Italian thistle (Carduus pycnocephalus L.) and slenderflower thistle (Carduus tenuiflorus Curt.) was rapid and high, with no strong requirements for afterripening. Both species germinated at a wide range of alternating temperatures from −2 to 40 C. Their germination-temperature profiles were similar, with Italian thistle germinating over a slightly wider range of temperatures. The achenes of both species have abundant mucilage. This mucilage, by improving water retention, tended to increase germination on the surface of clay soil.
Time Span of the Subadult Stage in Female Reeves' Pond Turtles Mauremys reevesii (Reptilia: Geoemydidae)

Abstract: Using 55 wild-caught turtles of various sizes [straight carapace length (SCL): 35–227 mm], we estimated a time span of the subadult stage extending from the onset to completion of sexual maturation in female Mauremys reevesii from central Japan. We examined serum vitellogenin (VTG, a yolk-precursor protein) levels of the 55 turtles and thereby determined the size at the onset of sexual maturation. We also sacrificed nine of these turtles (SCL: 143–180 mm) and made anatomical observations focusing on their ovaries and oviducts in order to determine size at the completion of sexual maturation. Serum VTG was detected in all females with SCL ≥155 mm but not in any female with SCL <145 mm, thus indicating that the first vitellogenesis in M. reevesii occurs when SCL has reached around 150 mm. Of the nine turtles dissected, three (SCL: 172–180 mm) had oviductal eggs, corpora lutea, and/or enlarged follicles that would be ovulated in the next breeding season, while the other turtles (SCL: 143–168 mm) did not show any anatomical evidence of full maturity. It is therefore considered that the sexual maturation of female M. reevesii is complete when SCL has reached around 170 mm. A growth curve based on the age and SCL data of the wild-caught turtles indicated that SCLs at the onset and completion of sexual maturation (150 and 170 mm, respectively) corresponded to the ages of five and seven years, respectively. The time span of the subadult stage was therefore estimated to be two years in female M. reevesii.
On Polynomials and Their Polar Derivative

Let P (z) be a polynomial of degree n and for any complex number α, let DαP (z) = nP (z) + (α− z)P ′(z) denote the polar derivative of P (z) with respect to α. Here, we consider the class of polynomials P (z) = anz n + n ∑ ν=μ an−νz n−ν , 1 ≤ μ ≤ n, having all zeros in |z| ≤ k, k ≤ 1 and thereby establish several interesting results regarding the integral mean estimates for the polar derivative of P (z). Our results not only generalize and refine some known polynomial inequalities, but also a variety of interesting results can be deduced from these by a fairly uniform procedure.
Improving quality and safety of hen eggs in new production system by reinforcing the antimicrobial natural defence and by developing tools for grading eggs (Eggdefence QLRT-2001-01606).

Station de recherches avicoles, INRA, 37380 Nouzilly, France Federal Research Centre for Nutrition and Food (BFEL) – Kulmbach, Germany Katholieke Universiteit Leuven, K.U. L, Belgium Ministry of Small Enterprises, Traders and Agriculture Agricultural Research Centre, CLODVK, Belgium Roslin Institute (Edinburgh) ROSLIN, United-Kingdom University of Glasgow, UnivGla, United-Kingdom Consejo Superior de Investigaciones Cientificas, CSIC, Spain Sveriges LantbruksUniversitet, SLU, Sweden Ecole Nationale Superieure Agronomique de Rennes, ENSAR, France Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa K1H 8M5, Canada Institut de selection Animale, ISA, France Lohman Tierzucht GmbH, LTZ, Germany *nys@tours.inra. fr
ABA contents in the guard-cell symplast and guard-cell apoplast are not correlated with stomatal aperture size under three conditions of water sufficiency

ix INTRODUCTION . 1 ABA CONTENTS IN THE GUARD-CELL SYMPLAST AND GUARD-CELL APOPLAST ARE NOT CORRELATED WITH STOMATAL APERTURE SIZE UNDER TWO WELL-WATERED CONDITIONS . 5 Introduction . 5 Materials and Methods. 8 Results . 14 Discussion . 23 IS ABA INVOLVED IN INITIATING STOMATAL CLOSURE UNDER FLOODING IN VICIA FABA? 3
Sampling Based Motion Planning with Reachable Volumes

Motion planning for constrained systems is a version of the motion planning problem in which the motion of a robot is limited by constraints. For example, one can require that a humanoid robot such as a PR2 remain upright by constraining its torso to be above its base or require that an object such as a bucket of water remain upright by constraining the vertices of the object to be parallel to the robots base. Such problems are particularly difficult because the constraints form a manifold in C-space, and planning must be restricted to this manifold. We introduce a new concept, reachable volumes, that are a geometric representation of the regions the joints and end effectors of a robot can reach, and use it to define a new planning space called RV-space where all points automatically satisfy a problems constraints. Samples and paths generated in RV-space naturally conform to constraints, making planning for constrained systems no more difficult than planning for unconstrained systems. Consequently, constrained motion planning problems that were previously difficult or unsolvable become manageable and in many cases trivial. We introduce tools and techniques to extend the state of the art sampling based motion planning algorithms to RV-space. We define a reachable volume sampler, a reachable volume local planner and a reachable volume distance metric. We show that RV-based planners are more efficient than existing methods, particularly for higher dimensional problems, solving problems with 1000+ degrees of freedom for multi-loop, and tree-like linkages. Bio Troy McMahon is a PhD student in the Parasol Lab in the Department of Computer Science and Engineering at Texas A&M University advised by Professor Nancy M. Amato. He received a B.S. from the University of Massachusetts in 2005 where he graduated with a double major in Computer Science and Physics. His research interests include motion planning, robotics, computational biology, computational geometry, artificial intelligence, machine learning, parallel algorithms and graphics. Faculty Host: Kostas Bekris
Dynamic Style Allocation Under the Regime Shifts : Value vs Growth

2) Following Fama and French’s (1992, 1993) findings that firm characteristics or factors such as size and value have forecasting power for excess returns, academics and the financial industry are investigating and investing in styles of value and growth. The literature examining the value premium (the excess performance of value portfolio over growth portfolio) typically focuses on long-term performances in international stock markets, including the Korean stock market. In addition, according to the literature, participants such as institutional investors avoid investing in growth stocks. However, many empirical studies indicate that the value premium is related to the current state of the economy. They argue that value premiums are time-variant. Therefore, we analyze the existence of value premiums and the performance of style allocation strategies across different regimes in Korean stock market. We use style indices data for the Korean stock market developed by three indices companies, FnGuide, WISEfn, and MSCI, comprising three value indices and three growth indices from 2001 to 2014. Although value indices outperform growth indices for three indices companies during the total sample period, the outperforming of styles is not stable over time. That is, the sign and degree of the value premium varies each year. This time-varying value premium suggests that style allocation strategies to spread investment across value and growth stocks outperform strategies * Corresponding Author. Address: Business School, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; E-mail: atsam6@snu.ac. kr; Tel: 82-2-880-6855. This research is financially supported by Seoul Women’s University in 2017.
Ecological paradigms lost : routes of theory change

1. Why a History of Ecology: An Introduction Beatrix E. Beisner and Kim Cuddington Part I POPULATION ECOLOGY 2. Unstructured Models in Ecology: Past, Present and Future 3.Unstructured population models: Do population-level assumptions yield general theory? 4. The Structure of Population Ecology: Philosophical Reflections on Unstructured and Structured Models Part II EPIDEMIOLOGICAL ECOLOGY 5. The Law of Mass Action in Epidemiology: A Historical Perspective 6. Extensions to Mass Action Mixing 7. Mass Action and System Analysis of Infection Transmission Part III COMMUNITY ECOLOGY 8. Community Diversity and Stability: Changing Perspectives and Changing Definitions 9. Perspectives on Diversity, Structure and Stability 10. Diversity and Stability: Theories, Models and Data Part IV EVOLUTIONARY ECOLOGY 11. On the Integration of Community Ecology and Evolutionary Biology: Historical Perspectives and Current Prospects 12. Modeling the ecological context of evolutionary change: deja vu or something new? 13. The Elusive Synthesis Part V ECOSYSTEM ECOLOGY 14. The Loss of Narrative 15. Ecological Management: Control, Uncertainty and Understanding 16. Is Ecosystem Management a Postmodern Science? Kevin de Laplante Part VI CONCLUSION 17. Kuhnian Paradigms Lost: Embracing the pluralism of ecological theory
Is a Long-Chain Fatty Acid omega-Hydroxylase Essential for Sporopollenin Synthesis in Pollen of Arabidopsis. Plant Physiology

Sporopollenin is the major component of the outer pollen wall (exine). Fatty acid derivatives and phenolics are thought to be its monomeric building blocks, but the precise structure, biosynthetic route, and genetics of sporopollenin are poorly understood. Based on a phenotypic mutant screen in Arabidopsis ( Arabidopsis thaliana ), we identiﬁed a cytochrome P450, designated CYP704B1, as being essential for exine development. CYP704B1 is expressed in the developing anthers. Mutations in CYP704B1 result in impaired pollen walls that lack a normal exine layer and exhibit a characteristic striped surface, termed zebra phenotype. Heterologous expression of CYP704B1 in yeast cells demonstrated that it catalyzes v -hydroxylation of long-chain fatty acids, implicating these molecules in sporopollenin synthesis. Recently, an anther-speciﬁc cytochrome P450, denoted CYP703A2, that catalyzes in-chain hydroxylation of lauric acid was also shown to be involved in sporopollenin synthesis. This shows that different classes of hydroxylated fatty acids serve as essential compounds for sporopollenin formation. The genetic relationships between CYP704B1 , CYP703A2 , and another exine gene, MALE STERILITY2 , which encodes a fatty acyl reductase, were explored. Mutations in all three genes resulted in pollen with remarkably similar zebra phenotypes, distinct from those of other known exine mutants. The double and triple mutant combinations did not result in the appearance of novel phenotypes or enhancement of single mutant phenotypes. This implies that each of the three genes is required to provide an indispensable subset of fatty acid-derived components within the sporopollenin biosynthesis framework. of commercially available radiolabeled fatty acids of different chain length (Perkin-Elmer Life Sciences). The standard assay (100 m L) contained 20 m M Na-phosphate buffer (pH 7.4), a radiolabeled substrate (100 m M , 54 Ci mol 2 1 ), plus a NADPH regenerating system (6.7 m M Glc-6-P and 0.4 units of Glc-6-dehydrogenase). The reaction was initiated by the addition of NADPH (to 1 m M ), carried out for 20 min at 27 (cid:4) C, and stopped by the addition of 20 m L of acetonitrile (containing 0.2% [v/v] acetic acid). Reaction mixtures were applied to TLC plates (Silica Gel G60 F254; 0.25 mm; Merck). For separation of hydroxylated fatty acids from the residual substrate, TLC plates were devel- oped with a mixture of diethyl ether:light petroleum:formic acid (50:50:1, v/v/v). Experiments were performed in triplicate. The plates were scanned with a radioactivity detector (Raytest Rita Star). The silica gel area corresponding to the metabolites was scraped into counting vials, and the radio- activity was quantiﬁed by liquid scintillation counting. The radioactivity detected in the absence of NADPH was subtracted from the radioactivity N -methyl- N -triﬂuoroacetamide.
Fibre intake and faeces quality in leaf-eating primates

A high incidence of gastrointestinal disorders as diarrhea, phytobezoars, bloated conditions and weight loss have been observed in captive langurs. This thesis focuses on the effect of the food intake in captive langurs in relation to the quality of faeces and its implications for langurs kept in captivity. According to the literature colobines have a compartmentalized stomach in which food is fermented. The structure and size of the hindgut suggests that fermentation also can take place there. Comparing the digestive tract of langurs with ruminants showed a lot of similarities. Results of a nutrition questionnaire sent to North American and European facilities showed that currently there is no standardized diet fed to Southeast Asian colobines kept in captivity. Chemical analyses of wild fruits, seeds and leaves showed high levels of NDF and indigestible fibre. Langurs prefer a diet containing carbohydrates which are easily digested, but when such a diet is not available, langurs consume diets with more fibre and less digestible carbohydrates. A study showed an improvement of stool quality when a high fiber pellet was fed to Francois langurs (Trachypithecus francoisi) Feeding a high fibre pellet resulted in less distinct feeding peaks and eating was distributed over the whole day in a group of Francois langurs Experiments with captive black and white colobus (Colobus guereza)and spectacled leaf monkeys (Trachypithecus obscurus) showed that faeces quality improved for these foregut fermenting primates when feeding more crude fiber and cellulose. In two groups of Javan langurs (Trachypithecus auratus auratus) in two facilities the effect of removal of produce from the diet was tested. Results in both facilities showed that the faeces quality improved when the diet consisted only of browse and a high fiber pellet. Exclusion of feeds rich in soluble carbohydrates in the diet of Javan langurs caused an increased intake of high fiber pellets and browse. This resulted in a higher fiber intake and a lower dietary water intake and an improvement of the faeces quality. Mean Retention Time (MRT) was calculated by analysing the amount of cobalt-EDTA and chromium oxide in the consumed food and produced faeces in Javan Langurs. No significant differences were found between the retention time of the fluid and particle part in two different diets. After feeding to Javan langurs a diet rich in alpha-linolenic acid instead of that rich in linoleic, a clear increase was shown in the content of alpha-linolenic acid in both plasma and erythrocytes. It indicates that dietary polyunsaturated fatty acids are hydrogenated in the stomach. Comparison of 11 diets fed in Dutch zoos showed that faeces consistency depends on dietary water, protein content and fibre content. High water and protein intakes were associated with deteriorated faeces consistency, where as high fibre intake was associated with improved faeces quality. In relation to the faeces quality, captive langur diets should have a higher dry matter and fibre content and a lower protein content when compared to free-ranging diets.