Miracle-dz/UniFAR-FTUs huggingface dataset:
AMMI analysis of grain yield in rice genotypes across environments

The identification of the highest yielding cultivar for a specific environment on the basis of both genotype (G) and genotype x environment (GE) interaction would be useful to breeders and producers since yield estimates based only on G and environment (E) effects are insufficient. The objective of this study was to demonstrate the usefulness of additive main effects and multiplicative interactions (AMMI) model analysis. Replicated grain yield data of rice (Oryza sativa L.) genotypes at three locations in Coimbatore (E1), Bhavanisagar (E2) and Aliyar Nagar (E3) were obtained and used for this purpose. Through AMMI model analysis, the magnitude and significance of the effects of GE interaction and its interaction principal components relative to the effects of G and E were estimated. Among the three, E3 environment was far away from the origin. The environments E2 and E3 condition were exhibiting high interaction effect, whereas the environment E1 had moderate interaction effect with the other two environments. The parent TP 1021 R and the hybrids viz., IR 80559 A X RR 286 R, APMS 6 A X IR 62037 R, IR 75601 A X IR 72865 R, IR 75601 A X RR 347 R, IR 75596 A X MDU 5 R, IR 75596 A X ASD 06-8 R, CRMS 32 A X IR 62037 R, CRMS 32 A X TP 1021 R and IR 75608 A X ASD 06-8 R showed IPCA 1 score close to zero with high main effects indicating that these varieties were less influenced by environments. Hence, the above said hybrids were stable and had general adaptability for all the environments. Since, the environments E3 had positive IPCA 1 score and high mean, it had positive interaction with these genotypes and this environment was considered as the stable environment for these hybrids.
Identification of Lactic Acid Bacteria from Spontaneous Rye Sourdough and Determination of Their Functional Characteristics

ABSTRACT This study aimed to identify Lactic Acid Bacteria (LAB) present in rye and rye bran sourdoughs that were prepared spontaneously and determine their functional characteristics. Genotypic characterization of the isolates revealed the presence of 15 distinct LAB strains belonging to 6 different species; Leuconostoc citreum, Lactobacillus plantarum, Lactobacillus graminis, Lactococcus lactis subsp. cremoris, Weissella confusa, and Weissella cibaria in rye sourdoughs. PCR screening of eps genes required for exopolysaccharide (EPS) production revealed that all strains possessed at least one gene required for EPS production and all strains produced homopolymeric EPS comprised of glucose or fructose two Lactobacillus plantarum strains produced both glucan and fructan type EPS. Antifungal activity of these strains was tested against Aspergillus niger and Penicillium chrysogenum identified in this study and several patterns were observed. The phytase activity of these strains was also determined and all strains showed phytase activity with varying degrees.
Spatiotemporal expression of FRIGIDA modulate flowering time in Arabidopsis thaliana

FRIGIDA (FRI) as the major regulator of flowering time in Arabidopsis accessions can activate its target FLOWERING LOCUS C (FLC) to delay flowering before vernalization. Besides FLC, other FRI targets also exist in Arabidopsis. Although leaves sense environmental cues to modulate flowering time, it is not known if roots also regulate the floral transition. In this study, we investigated the spatiotemporal effect of FRI on flowering time. Local expression of FRI in the phloem and leaves activated FLC to delay flowering. Furthermore, we found that local expression of FRI in the roots also delayed flowering by activating other targets MADS AFFECTING FLOWERING4 (MAF4) and MAF5 in the roots. Graft and genetic experiments revealed that the spatial expression of FRI in the root might generate a mobile signal, which is transmitted from roots to shoot and antagonizes the FT signal to delay flowering. Specifically expressing FRI in the embryo efficiently delayed flowering, even expressing FRI as early as pro-embryo stage is enough to upregulate FLC expression to delay flowering. Together, our findings confirm the spatiotemporal effect of FRI on delaying flowering, and propose that root tissue also perceives the flowering signal to fine-tune the flowering time through MAF4/5 as novel targets of FRI. Highlight Root FRIDIGA activated the novel targets MAF4/5 to delay flowering; Temporal expressing FRIGIDA at as early as pro-embryo stage is efficient to delay flowering.
Evaluation of the spoilage potential ofShewanella putrefaciens,Aeromonas hydrophila, andAeromonas sobriaisolated from spoiled Pacific white shrimp (Litopenaeus vannamei) during cold storage

The spoilage potential and their interactions of Shewanella putrefaciens, Aeromonas hydrophila, and Aeromonas sobria isolated from spoiled Pacific white shrimp (Litopenaeus vannamei) were evaluated by inoculation into sterile shrimp juice during 12 days at 4 °C. Based on the microbiological analysis, A. sobria was identified as non‐spoilage bacteria, and S. putrefaciens and A. hydrophila developed very rapidly as well as with a high maximum cell density in shrimp juice (up to 8.79 log cfu/g and 7.81 log cfu/g after 12 days at 4 °C, respectively). The higher total volatile basic nitrogen and putrescine productions were observed in coculture with S. putrefaciens and A. sobria compared with single culture of A. sobria, suggesting that the growth and spoilage activity of A. sobria were enhanced with S. putrefaciens. Conversely, A. hydrophila was weakly inhibited by S. putrefaciens. It is concluded that the spoilage behavior of microorganisms in mixed culture is significantly different from pure culture. PRACTICAL APPLICATIONS: We believe that the article may be of particular interest to the readers of this journal as it is the first time investigating the interactions of S. putrefaciens, A. hydrophila, and A. sobria by inoculated in Pacific white shrimp juice. This study could help to reveal the microbial interactions in spoilage food.
A Novel Way of Assessing Plant Vitality in Urban Trees

The assessment of mature urban tree vitality using physiological measurements is still in its infancy. Chlorophyll fluorescence is a method for assessing tree vitality that has potential for use in urban environments, particularly on trunk bark, which is easy to access from the ground. Here we describe how we compared bark and leaf fluorescence in a variety of street and park trees (Ficus macrophylla Pers., Platanus × acerifolia (Aiton) Willd. , and Ulmus parvifolia Jacq. ) with pre-dawn water potential as a way of determining the cause of potential physiological stress in the summer of 2012. Statistical relationships were observed between bark chlorophyll fluorescence and pre-dawn water potential in Ficus macrophylla and Platanus × acerifolia, but were not as consistent in Ulmus parvifolia. In addition, bark and leaf chlorophyll fluorescence were compared with an urban visual vitality index both in autumn 2011 and summer 2012. In this case statistical relationships between bark chlorophyll fluorescence values and urban tree visual vitality were almost non-existent in the Ficus macrophylla and Platanus × acerifolia trees, however, statistical relationships were significant between bark chlorophyll fluorescence and the urban tree vitality index in Ulmus parvifolia. Bark chlorophyll fluorescence may become a useful tool for measuring physiological stress in trees, but further work needs to be undertaken to clarify and better understand the varying responses of different tree species.
The Prediction of Vocabulary Level by Early Declarative and Imperative Communication Acts in Young Children with Autism Spectrum Disorders

screening level was 88.2%. When screening full texts for inclusion, there was 100% agreement. Agreement at the study coding level was 95.4%. See Table 1 for the study-level associations in the meta-analysis. The weighted mean effect size for the correlation of declarative ICAs and language was moderate and significant (r = .42; 95% CI [.34, .50]). Because the confidence interval does not include zero, we rejected the null hypothesis that declarative ICAs and language are not associated in this population. The
Chronic inflammation and immune activation in HIV disease

Chronic activation of the immune system and related tissues is a pervasive characteristic of HIV infection at all stages of disease progression. It is well established that measures of immune activation are strong independent predictors of CD4 T cell depletion and immune suppression. Mechanistic insights of its role in immune pathogenesis are emerging, which point to a direct participation of chronic activation in the development of immune suppression, as well as in other inflammation-related pathologies that accompany HIV infection. Extensive further research has found that activation spans a broad range of cells and functions of the immune system, and is present at all stages of HIV disease, even under control of viral replication. Important advances in the mechanisms underlying immune activation have been made in the last years, revealing diverse triggers ranging from HIV itself to toll-like receptor ligands. Of particular importance, the passage of bacterial products to the blood of HIV-infected patients is a cause of immune activation that has greatly influenced the study and management of HIV pathogenesis. This chapter reviews the evidence for the central pathogenic role of activation, the mechanisms that cause it, its role in immune Correspondence/Reprint request: Dr. Enrique Espinosa, Department for Immunology Research, National Institute for Respiratory Diseases Ismael Cosío Villegas (Instituto Nacional de Enfermedades Respiratorias), Mexico, Calzada de Tlalpan 4502, 14080 México, D.F. , México. E-mail: espinosa@iner.gob. mx Enrique Espinosa 100 suppression, and the consequences of chronic inflammation. Attention is made on non-AIDS-defining illnesses, which have emerged with the control of immunodeficiency by highly active antiretroviral therapy. Recent findings support current efforts to control activation/inflammation as part of effective treatment of HIV infection.
Graph neural networks for multimodal learning and representation

Recently, several deep learning models are proposed that operate on graph-structured data. These models, which are known as graph neural networks, emphasize on methods for reasoning about non-Euclidean data. By combining end-to-end and handcrafted learning, graph neural networks can supply both relational reasoning and compositionality which are extremely important in many emerging tasks. This new paradigm is also consistent with the attributes of human intelligence: a human represents complicated systems as compositions of simple units and their interactions. Another important feature of graph neural networks is that they can often support complex attention mechanisms, and learn rich contextual representations by sending messages across different components of the input data. The main focus of this thesis is to solve some multimodal learning tasks by either introducing new graph neural network architectures or extending the existing graph neural network models and applying them to solve the tasks. I address three tasks: visual question answering (VQA), scene graph generation, and automatic image caption generation. I show that graph neural networks are effective tools to achieve better performance on these tasks. Despite all the hype and excitements about the future influence of graph neural networks, an open question about graph neural networks remains: how can we obtain the (structure of) the graphs that graph neural networks perform on? That is, how can we transform sensory input data such as images and text into graphs. A second main emphasis of this thesis is, therefore, to introduce new techniques and algorithms to address this issue. We introduce a generative graph neural network model based on reinforcement learning and recurrent neural networks (RNNs) to extract a structured representation from sensory data. The specific contributions are the following: We introduce a new neural network architecture, Multimodal Neural Graph Memory Networks (MN-GMN), for the VQA task. A key issue for VQA is how to reason about information from different image regions that is relevant for answering the question. Our novel approach uses graph structure with different region features as node attributes and applies a recently proposed powerful graph neural network model, Graph Network (GN), to reason about objects and their interactions in the scene context. The flexibility of GNs allows us to integrate bimodal sources of local information, text and visual, both within and across
Antidiabetic Potential of Alkaloid Extracts from Vitex doniana and Ficus thonningii Leaves on Alloxan-induced Diabetic Rats

Background: The growing number of diabetes coupled with the harsh side effects of some synthetic drugs has led to the increasing search for alternatives which are relatively cheap with minimal side effects. Aim: This study sought to investigate the antidiabetic potential of alkaloid extracts from Vitex doniana and Ficus thonningii leaves on alloxan-induced diabetic rats. Methods: Fresh leaves of V. doniana and F. thonningii were obtained from a local market Nkwagu in Abakaliki local government area of Ebonyi State. They were washed thoroughly in running water to remove contaminants. They were separately air-dried at room temperature for two weeks. The dried leaves were pulverized to fine granules using manual grinder. Crude alkaloid was extracted using standard method. The acute oral toxicity of both plants was determined. Diabetes was induced in forty male rats intra peritoneally with alloxan at a dose of 120 mg/kg body weight. The rats were grouped into eight groups of five animals per group: Groups 1 and 2 were treated with 200 and 400 mg/kg body weight of V. doniana respectively, groups 3 and 4 were treated with 200 and 400 mg/kg body weight of F. thonningii respectively, group 5 was treated with 100 mg/kg of V. doniana + 100 mg/kg of F. thonningii , group 6 was treated with 200 mg/kg of V. doniana + 200 mg/kg of F. thonningii , group 7 animals were not induced with alloxan and untreated (normal control) while group 8 were induced with alloxan but not treated (diabetic control). The extracts were administered to the animals orally for 30 days. The animal’s blood sugar levels and lipid profile were assayed using standard methods. Results: Both extracts significantly reduced blood glucose level when compared with those of diabetic control at p<0.05. The extracts also favourably perturbed the lipid profile of animals. Conclusion: The present study suggests that both V. doniana and F. thonningii leaves be potent antidiabetic property. They could also reduce the risk of obesity and hypertension due to its hypolipidemic effect.
The mechanism of cross-talk between histone H2B ubiquitination and H3 methylation by Dot1L

Methylation of histone H3, lysine 79 (H3K79), by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B at lysine 120 (H2B-Ub), and is a well-characterized example of histone modification cross-talk that is conserved from yeast to humans. The mechanism by which H2B-Ub stimulates Dot1L to methylate the relatively inaccessible histone core H3K79 residue is unknown. The 3.0 Å resolution cryo-EM structure of Dot1L bound to ubiquitinated nucleosome reveals that Dot1L contains binding sites for both ubiquitin and the histone H4 tail, which establish two regions of contact that stabilize a catalytically competent state and positions the Dot1L active site over H3K79. We unexpectedly find that contacts mediated by both Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to project deep into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals an unexpected structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core.
Roles of Basigin in structure and function of the Drosophila peripheral nerve

iii LAY SUMMARY . v PREFACE . vi TABLE OF CONTENTS . vii LIST OF TABLES . ix LIST OF FIGURES . x LIST OF ABBREVIATIONS . x ACKNOWLEDGMENTS . xiv DEDICATION . xv CHAPTER 1: INTRODUCTION . 1 1.1 Glia and the Drosophila peripheral nervous system . 2 1.2 The axon initial segment . 4 1.2.1 The vertebrate AIS . 5 1.2.2 The invertebrate AIS . 7 1.3 Basigin . 8 1.3. 1 Basigin and integrins . 10 1.3. 2 Basigin and PMCA . 11 1.3. 3 Basigin and monocarboxylate transporters . 12 1.4 Thesis questions . 13 CHAPTER 2: BASIGIN IS ESSENTIAL FOR STRUCTURAL INTEGRITY OF THE PERIPHERAL NERVES. 21 2.1 Synopsis . 21 2.2 Introduction . 21 2.3 Materials and Methods . 24 2.3. 1 Fly strains and genetics . 24 2.3. 2 Immunolabeling and image processing . 24 2.3. 3 Statistical analyses . 25 2.4 Results . 25 2.4. 1 Knockdown of Bsg in the perineurial glia causes glial/ECM constriction . 25 2.4. 2 Constriction of the PG and ECM affects underlying septate junctions . 26 2.4. 3 Glial constriction is limited to the nerve extension region . 27 2.4. 4 Glial constriction does not affect the length of the nerve . 28 2.4. 5 Glial constriction is associated with cytoskeleton disruption . 29 2.4. 6 Bsg knockdown in an integrin mutant background rescues constriction phenotype . 30 2.5 Discussion . 31
Traditional, complementary and integrative medicines in the Brazilian health primary care

Abbreviations: SUS, brazilian unified health system; TCIM, traditional, complementary, and integrative medicine; PHC, primary health care; PNPIC, brazilian national policy of integrative and complementary practices; PMAQ, brazilian national program for access and quality improvement of Primary Care; MS, brazilian ministry of health; CNPq, national council for scientific and technological development of brazil; BIREME, latin american and caribbean center on health sciences information
Scheduling of Physicians with Time‐Varying Productivity Levels in Emergency Departments

Emergency department (ED) overcrowding and long patient wait times have become a worldwide problem. We propose a novel approach to assigning physicians to shifts such that ED wait times are reduced without adding new physicians. In particular, we extend the physician rostering problem (PRP) by including heterogeneity among emergency physicians in terms of their productivity (measured by the number of new patients seen in 1 hour) and by considering the stochastic nature of patient arrivals and physician productivity. We formulate the PRP as a two‐stage stochastic program and solve it with a sample average approximation and the L‐shaped method. To formulate the problem, we perform a data analysis to investigate the major drivers of physician productivity using patient visit data from our partner ED, and we find that the individual physician, shift hour, and shift type (e.g., day or night) are the determining factors of ED productivity. A simulation study calibrated using real data shows that the new scheduling method can reduce patient wait times by as much as 13% compared to the current scheduling system at our study ED. We also demonstrate how to incorporate physician preference in scheduling through physician clustering based on productivity. Our simulation results show that EDs can receive almost the full benefit of the new scheduling method even when the number of clusters is small.
Hybrid finite element methods for seismic wave simulation : coupling of discontinuous Galerkin and spectral element discretizations

Pour resoudre des equations d’ondes posees dans des milieux heterogenes avec des elements finis et un cout numerique raisonnable, nous couplons la methode Discontinue de Galerkine (DGm) avec des elements finis spectraux (SEm). Nous utilisons des maillages hybrides composes de tetraedres et d’hexaedres structures. Le couplage est realise en partant d’une formulation DG mixte primale posee dans un maillage hybride compose d’un macro-element hexaedrique et d’un sous-maillage compose de tetraedres. La SEm est appliquee dans le macro-element decoupe en hexaedres structures et le couplage est assure par les flux numeriques de la DGm appliques sur les faces internes du macro-element communes avec le maillage tetraedrique. La stabilite de la methode couplee est demontree quand l’integration en temps est effectuee avec un schema Saute-Mouton. Les performances de la methode couplee sont etudiees numeriquement et on montre que le couplage permet de reduire les couts numeriques avec un tres bon niveau de precision. On montre aussi que la formulation couplee peut stabiliser la methode DG appliquee dans des domaines incluant des couches parfaitement adaptees.
Exploring the Role of Mesenchymal Stem Cells During Normothermic Organ Perfusion: A New Paradigm to Enhance Outcome Following Allograft Transplantation

Normothermic Machine Perfusion (NMP) has been established in the field of solid organ transplantation for both liver and kidney allografts. The ability to perfuse organs at body temperature enables viability assessment as well as optimisation prior to implantation. A recent in vitro report of the use of Mesenchymal Stem Cells (MSCs) in the use of a normothermic lung perfusion circuit has raised the possibility of their use in solid organ transplantation. The aim of this short review is to outline the potential uses of bone marrow derived MSCs for their use in renal allograft ex vivo NMP. An overview is provided of current literature of NMP as well as theorised uses for MSCs.
Modal analysis of time-dependent structures using Derictional Derivatives

Dans un grand nombre de domaines, l'analyse modale de structures est une composante capitale du dimensionnement. Pour l'identification des frequences et modes propres, les logiciels de calcul elements finis sont maintenant souvent utilises et offrent des reponses rapides et satisfaisantes dans une grande majorite de cas. Cependant, lorsqu'une structure possede une geometrie qui varie au cours du temps ou alors lorsqu'une fissure se propage dans cette structure, les methodes classiques employees peuvent etre contraignantes et consommatrice de temps CPU (remaillage, resolution iterative de problemes aux valeurs propres.), surtout si l'on veut suivre l'evolution des solutions propres.Dans ces travaux de doctorat, une methode originale est proposee afin d’ameliorer la gestion de l’analyse modale de structures subissant des changements de forme au cours du temps. Celle-ci est basee sur les derivees directionnelles et sur la methode X-FEM. En effet, les derivees directionnelles permettent de predire l’evolution des solutions propres entre deux configurations temporelles de la structure et X-FEM permet de s’affranchir des contraintes liees au maillage de chacune des configurations. Grâce a des criteres specifiquement developpes, la methodologie a ete testee pour des cas de problemes plans et axysymetrique. Les resultats obtenus en regard des methodes classiques et les conclusions qu’elles peuvent amener, permettent de voir les nombreux avantages de l’outil que nous avons propose.