Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure/Function Analysis of the Quorum-sensing Regulator EsaR from the Plant Pathogen Pantoea stewartii

Pantoea stewartii subsp. stewarti is the causative agent of Stewart’s wilt disease in maize. Disease symptoms develop after the bacteria grow to high cell densities in the plant xylem and secrete an abundance of exopolysaccharide (EPS). EPS production is regulated by quorum sensing. Two regulatory proteins are key to the process of quorum sensing, the LuxI and LuxR homologues EsaI and EsaR. Most LuxR homologues function as activators of transcription in the presence of their cognate acylated homoserine lactone signal (AHL). EsaR utilizes an AHL-response opposite of the majority of the LuxR homologues. EsaR represses EPS production at low cell densities. However, at high cell densities when high concentrations of AHL are present, EsaR is inactivated and derepression of EPS production occurs. The mechanism that enables EsaR to respond to AHL in a manner opposite to that of most LuxR homologues remains elusive. A comparative study of EsaR and the well characterized quorum-sensing regulators LuxR from Vibrio fischeri and TraR from Agrobacterium tumefaciens was initiated. Previous studies demonstrated that in the absence of AHL, EsaR retains the ability to function as a weak activator of the lux operon in recombinant Escherichia coli. This thesis research further characterized the role of EsaR as an activator. Variant forms of EsaR with deletions or single residue substitutions were generated and their ability to regulate transcription was examined in vivo. Furthermore, a native EsaR-activated promoter has been identified, which controls expression of a putative regulatory sRNA in P. stewartii.
Evaluating forage quality of pastures.

Highlight: Ten irrigated pastures located in northeastern Colorado were evaluated for forage quality during the 1972 growing season. Most of the pastures used the center-pivot type of sprinkler system and consisted mainly of mixtures of alfalfa (Medicago sativa L.), orchardgrass (Dactylis glomerata L.), and smooth bromegrass (Bromus inermis Leyss.) in varying proportions. Thirteen factors for quality were evaluated from each pasture from samples obtained over a j-month period Mg, P, K, crude protein, in vitro digestibility, cell wall constituents, cell contents, hemicellulose, cellulose, lignin, and silica showed significant fluctuations during the growing season, while calcium and ash insoluble in neutral detergent remained fairly constant. Changes that occurred during the growing season could be accounted for by time of harvest, management practices, species, and other environmental factors such as differences in climate and soil. In spite of differences between pastures, satisfactory regression functions were developed to give good estimations of forage quality using in vitro dry matter digestibility as the dependent variable. By submitting the data to the stepwise regression calculation techniques, good predictive equations for IVDMD were developed that can readily be applied to pastures in northeastern Colorado regardless of location, management, or species composition.
Plant species, mycorrhiza, and aphid age influence the performance and behaviour of a generalist

1. Life‐history traits of herbivores are shaped by the combination of various extrinsic and intrinsic variables. However, studies investigating the impact of both variables on insect behavioural phenotypes are rare, and research including the modulation of host plant quality by arbuscular mycorrhiza (AM) (extrinsic variable) and the herbivore developmental stage (intrinsic variable) on aphid behaviour is lacking.
Structural Annotation and Homology Modeling of Protein Kinase 6(PfPK6) from Plasmodium Falciparum

Malaria is a major public health burden in the developing world. Plasmodium falciparum enters in blood stream and replicates in S-phase of cell cycle and releases merozoites. PfPK6, a putative homologue of p34cdc cyclindependent kinase (CDK) required for entry into both S-phase and mitosis. Our work suggests that PfPK6 protein can acts as target for the inhibition of Plasmodium falciparum activity in Malaria disease. The present investigation includes retrieval of amino acid information and sequence analysis of PfPK6 from major protein sequence database and tools. The Physiochemical parameters like amino acid propensity, molecular weight, isoelectric point, aliphatic index, hydropathicity were determined. The secondary structure of PfPK6 was predicted using SOPMA secondary structure method. The 3D structure was predicted using SWISS-MODEL server and model was further validated using PROCHECK analysis tool. The function of PfPK6 was identified by Pfam domain database. In silico structural characterization and homology modeling of PfPK6 can put insight into development of new antimalarial drugs by structure based drug designing.
FIRST REPORT OF BANANA BRACT MOSAIC VIRUS IN BANANA IN ASSAM, INDIA

Banana bract mosaic disease was first recorded in 1966 in a plantain cv. Nendran as Kokkan disease of unknown etiology in Kerala. The casual agent was identified as Banana bract mosaic virus (BBrMV, genus Potyvirus, family Potyviridae) (Rodoni et al., 1997). BBrMV causes major losses to banana growers in four southern states of India (Selvarajan and Jeyabaskaran, 2006), but has not been recorded in north and north east region (NER) of India. In June 2016, banana plants of cv. Chini Champa (Syn: Mysore, AAB) showing spindle shaped pinkish to reddish mosaic and streaks symptoms on pseudostem and bracts were observed in a field located in Kahikuchi, Assam. Initially 15 plants were tested to be positive for BBrMV using antigen-coated plate (ACP)-ELISA with BBrMV-specific polyclonal antiserum developed at Indian Council of Agricultural Research-National Research Centre for Banana, Tiruchirappalli. Total RNA was isolated from the leaves of infected plants and RT-PCR was performed using the coat protein gene specific primers (RSR10FP: 5’- ATAGGATCCTCTGGAACGGAGTCAACC-3’ and RSR10RP: 5’- TTCATGTTTCATCCCAAGCAGAG-3’) (Balasubramanian and Selvarajan, 2014). An expected 900 bp size fragment obtained from infected plant was cloned into TA cloning vector pTZ57R/T and sequenced (GenBank accession No. KY369923). No amplification was obtained from healthy plants. Sequence analysis revealed 80-96% and 84-98% identity at the nucleotide and amino acid level, respectively, with other BBrMV isolates. Previously BBrMV was confined to southern India and was not reported from NER of India where wild progenitors of cultivated banana are believed to be originated. The virus should be contained before it can spread into banana germplasm resources in the NER of India and other bananaproducing-countries in which BBrMV is a quarantine pathogen. To the best of our knowledge, this is the first record of BBrMV infection in the NER of India.
The Utility of Culture Independent Methods to Evaluate the Fecal Microbiome in Overweight Horses Fed Orchard Grass Hay

This dissertation documents efforts to evaluate metabolic variables and the fecal microbiome in adult horses fed grass hay. In the first study, eight Arabian geldings limit-fed an 18% vs. 12% non-structural carbohydrate (NSC) hays in a cross-over design during two 28-day periods were included to evaluate the influence of grass hay NSC on serum insulin and plasma glucose concentrations. Serum insulin concentrations was higher in geldings fed the 18% NSC hay; however, this difference was only detected on day 7 and none of the geldings developed hyperinsulinemia. Blood glucose concentrations did not differ between hay groups. The second and third studies were extensions of the first and were conducted to use denaturing gradient gel electrophoresis (DGGE) and real-time PCR in evaluating the effect of forage carbohydrates on equine fecal bacteria diversity and abundance, respectively. Fecal microbiomes were similar (80.5-87.9%) between geldings. The abundance of bacteria belonging to the Firmicutes phylum increased (p = 0.02) in the feces of geldings fed 12% NSC hay (mean 8.06 range [8.03-8.11] log10 copies/g feces) compared to the feces of the same geldings when fed the 18% NSC hay (7.97 [7.97-7.98] log10 copies/g feces). The Firmicutes (43.7%), Verrucomicrobia (4.1%), Proteobacteria (3.8%), and Bacteroidetes (3.7%) phyla dominated the fecal microbiomes. This work was the first to report the presence of the Actinobacteria, Cyanobacteria, and TM7 phyla in the equine fecal or gut microbiome. There was a high abundance (38%) of unclassified bacterial sequences in the gelding fecal microbiome. In the fourth study, 5 overweight adult mixed-breed mares and 5 adult mixed-breed mares in moderate condition, limit-fed a grass hay, were used to evaluate the effect of body condition
Taxonomy, systematics, and life cycles of Azygiids (Digenea: Azygiidae) of the Southeastern United States

ii ACKNOWLEDGMENTS . iv LIST OF TABLES . ix LIST OF FIGURES . x CHAPTER 1: PROTEROMETRA EPHOLKOS SP. N. (DIGENEA: AZYGIIDAE) FROM TERRAPIN CREEK, ALABAMA, USA: MOLECULAR CHARACTERIZATION OF LIFE CYCLE, REDESCRIPTION OF PROTEROMETRA ALBACAUDA, AND UPDATED LISTS OF HOST AND GEOGRAPHIC LOCALITY RECORDS FOR PROTEROMETRA SPP. IN NORTH AMERICA . 1
Taxonomic revision of Psilorrhynchus Gemminger & Harold, 1869, the neglected replacement name for Psilorhynchus Blanchard, 1844 (Coleoptera: Cantharidae)

Summary Psilorrhynchus Gemminger & Harold, 1869, is revised. The name Psilorrhynchus is reaffirmed as a replacement name for Psilorhynchus Blanchard, 1844, junior homonym of Psilorhynchus McClelland, 1839. Two species are recognized as valid: Psilorrhynchus bifasciatus (Blanchard, 1844) n. comb. and P. abdominalis (Perty, 1830) n. comb. Psilorrhynchus nigrolineatus Pic, 1910 and P. bifasciatus var. inapicalis Pic, 1947 are considered as new synonyms of Psilorrhynchus bifasciatus (Blanchard, 1844) n. comb. , whilst P. abdominalis var. prolongata Pic, 1947 is considered to be a new synonym of Psilorrhynchus abdominalis (Perty, 1830) n. comb. Lectotypes are designated for Psilorhynchus bifasciatus var. inapicalis Pic, 1947, Psilorrhynchus nigrolineatus Pic, 1910, Malthinus abdominalis Perty, 1830, and Psilorhynchus abdominalis var. prolongata Pic, 1947. A distribution map of Psilorrhynchus in South America is provided.
NLO Corrections to Light-Quark Mixed QCD-EW Contributions to Higgs Production

We present for the first time the exact NLO QCD corrections to the light-quark part of the mixed QCD-EW contributions to Higgs production via gluon fusion at LHC13, with exact EW-boson mass dependence. The relevant two-loop real-emission matrix element is computed using a dynamic one-dimensional series expansion strategy whose stability and speed allows for a numerical phase-space integration using local IR subtraction counterterms. For $\mu_R=\mu_F=M_H$, we find: \begin{equation}\sigma^{(\alpha_s^2\alpha^2+\alpha_s^3\alpha^2)}_{g g\rightarrow H+X} = 1.467(2)^{\;+18.7\%}_{\;-14.6\%}\;(\mu_R\;\text{var.})\;\pm 2\%\;(\text{PDF}) \ \textrm{pb},\end{equation} which we use to provide the best result including an estimate of suppressed contributions: \begin{equation}\sigma^{(\text{EW},\textrm{best})}_{p p\rightarrow H+X} = 2.11 \pm 0.28 \ (\textrm{theory}) \ \mathrm{pb}. \end{equation}
Learning Latent Space Energy-Based Prior Model for Molecule Generation

Deep generative models have recently been applied to molecule design. If the molecules are encoded in linear SMILES strings, modeling becomes convenient. However, models relying on string representations tend to generate invalid samples and duplicates. Prior work addressed these issues by building models on chemically-valid fragments or explicitly enforcing chemical rules in the generation process. We argue that an expressive model is sufficient to implicitly and automatically learn the complicated chemical rules from the data, even if molecules are encoded in simple character-level SMILES strings. We propose to learn latent space energy-based prior model with SMILES representation for molecule modeling. Our experiments show that our method is able to generate molecules with validity and uniqueness competitive with state-of-the-art models. Interestingly, generated molecules have structural and chemical features whose distributions almost perfectly match those of the real molecules.
Generating Large Convex Polytopes Directly on Point Clouds

In this paper, we present a method to efficiently generate large, free, and guaranteed convex space among arbitrarily cluttered obstacles. Our method operates directly on point clouds, avoids expensive calculations, and processes thousands of points within a few milliseconds, which extremely suits embedded platforms. The base stone of our method is sphere flipping, a one-one invertible nonlinear transformation, which maps a set of unordered points to a nonlinear space. With these wrapped points, we obtain a collision-free star convex polytope. Then, utilizing the star convexity, we efficiently modify the polytope to convex and guarantee its free of obstacles. Extensive quantitative evaluations show that our method significantly outperforms state-of-the-art works in efficiency. We also present practical applications with our method in 3D, including large-scale deformable topological mapping and quadrotor optimal trajectory planning, to validate its capability and efficiency. The source code of our method will be released for the reference of the community.
C ONVERSATIONAL Q UESTION A

In spoken question answering, QA systems are designed to answer questions from contiguous text spans within the related speech transcripts. However, the most natural way that human seek or test their knowledge is via human conversations. Therefore, we propose a new Spoken Conversational Question Answering task (SCQA), aiming at enabling QA systems to model complex dialogues flow given the speech utterances and text corpora. In this task, our main objective is to build a QA system to deal with conversational questions both in spoken and text forms, and to explore the plausibility of providing more cues in spoken documents with systems in information gathering. To this end, instead of adopting automatically generated speech transcripts with highly noisy data, we propose a novel unified data distillation approach, DDNet, which directly fuse audio-text features to reduce the misalignment between automatic speech recognition hypotheses and the reference transcriptions. In addition, to evaluate the capacity of QA systems in a dialogue-style interaction, we assemble a Spoken Conversational Question Answering (Spoken-CoQA) dataset with more than 120k question-answer pairs. Experiments demonstrate that our proposed method achieves superior performance in spoken conversational question answering.
Induction of NK Cell Reactivity Against Myeloid Leukemia By a Novel Fc-Optimized CD133 Antibody

NK cells largely contribute to the success of monoclonal antibody (mAb) application in cancer due to their ability to mediate antibody-dependent cellular cytotoxicity (ADCC), a feature considered critical for therapeutic success. Up to now, no immunotherapeutic antibodies are available for the treatment of myeloid leukemias. Recently, we reported on the development of mAb targeting CD133, which is expressed on a wide variety of tumor cells (Koerner et al., Blood 2014 124:2309). Here we extend our analyses and provide further data on the preclinical characterization of an Fc-engineered CD133 mAb for the treatment of myeloid leukemia. Compared to two other anti-human CD133 mAb (clones AC133 and W6B3), which both bound to primary AML and CML cells in 15/25 and 7/10 cases, respectively, clone 293C3 recognized the leukemic cells in 22/25 AML cases and 7/10 CML cases. Based on these results, clone 293C3 was chosen to generate chimeric mAb with either a wildtype Fc part (293C3-WT) or a variant containing amino acid exchanges (S239D/I332E) to enhance affinity to the activating Fc receptor CD16 on NK cells (293C3-SDIE). Treatment with 293C3-SDIE resulted in significantly enhanced activation, degranulation and lysis of primary CD133-positive AML cells by NK cells in allogeneic and autologous experimental ex vivo settings as compared to its wildtype counterpart. Considering the expression of CD133 on healthy hematopoietic progenitor cells, we further performed colony forming unit assays with healthy bone marrow (BM) cells. In line with the observed lower expression levels of CD133 on healthy compared to malignant hematopoietic cells no relevant toxicity of 293C3-SDIE at the level of committed hematopoietic progenitor cells was observed. Moreover, 293C3-SDIE did not induce lysis of of healthy BM cells by allogeneic or autologous NK cells. In a NOD.Cg- Prkdc scid IL2rg tmWjl /Sz (NSG) xenotransplantation model, induction of ADCC by treatment with 293C3-SDIE resulted in the elimination of patient AML cells by NK cells from a matched human donor. Thus, 293C3-SDIE constitutes an attractive immunotherapeutic compound, in particular for the elimination of minimal residual disease in CD133 bearing leukemia in the context of allogenic SCT. Disclosures No relevant conflicts of interest to declare.
New Esterases Amplification Involved in Organophosphate Resistance in Culex Pipiens Mosquitoes from Tunisia

In Tunisia, the mosquito Culex pipiens shows various organophosphate resistance alleles at Ester locus. Resistance to the organophosphate chlorpyrifos was investigated in one population of Culex pipiens collected in northwestern Tunisia. High resistance to chlorpyrifos was observed and new esterases were detected. These results must be considered in future mosquito control programs since detected esterases can lead to high resistance to several organophosphorus insecticides. To cite this article [Tabbabi, A. , Daaboub, J., Laamari, A. , & Ben Cheikh, H. (2016). New Esterases Amplification Involved in Organophosphate Resistance in Culex Pipiens Mosquitoes from Tunisia. The Journal of Middle East and North Africa Sciences, 2(12), 1-2]. (P-ISSN 24129763) (e-ISSN 2412-8937). www.jomenas. org. 1
Human fetal, cord blood, and adult lymphocyte progenitors have similar potential for generating B cells with a diverse immunoglobulin repertoire. Running Title: Ig repertoire potential in adult and fetal B cells

Human fetal, cord blood, and adult lymphocyte progenitors have similar potential for generating B cells with a diverse immunoglobulin repertoire. Abstract Several characteristics of the immunoglobulin repertoire in fetuses and adults set them apart from each other. Functionally, this translates into differences in the affinity and effectiveness of the humoral immune response between adults and the very young. At least two possibilities could explain these differences: (1) fetal and adult lymphocyte progenitors differ significantly in their potential to form a diverse repertoire, and (2) factors extrinsic to the immunoglobulin locus are more influential to the character of the repertoire. To address this we used NOD/SCID/ (cid:1) 2 m -/- mice reconstituted with human B cell progenitors to compare the immunoglobulin repertoire potential of human fetal, cord blood and adult sources. We found nearly identical VH and JH gene segment utilization and only modest differences in HCDR3 characteristics. We conclude that the repertoire potential is remarkably similar regardless of the age of the individual from which progenitors are derived. Aging related differences in the immunoglobulin repertoire and variance of B cell responses to immunization appear to arise from selection rather than from changes in recombination of the immunoglobulin locus itself. From the standpoint of the Ig repertoire, an immune system reconstituted from fetal or neonatal stem cells would likely be as diverse as one generated from adult bone marrow.
A Framework to Learn with Interpretation

With increasingly widespread use of deep neural networks in critical decision-making applications, interpretability of these models is becoming imperative. We consider the problem of jointly learning a predictive model and its associated interpretation model. The task of the interpreter is to provide both local and global interpretability about the predictive model in terms of human-understandable high level attribute functions, without any loss of accuracy. This is achieved by a dedicated architecture and well chosen regularization penalties. We seek for a small-size dictionary of attribute functions that take as inputs the outputs of selected hidden layers and whose outputs feed a linear classifier. We impose a high level of conciseness by constraining the activation of a very few attributes for a given input with a real-entropy-based criterion while enforcing fidelity to both inputs and outputs of the predictive model. A major advantage of simultaneous learning is that the predictive neural network benefits from the interpretability constraint as well. We also develop a more detailed pipeline based on some common and novel simple tools to develop understanding about the learnt features. We show on two datasets, MNIST and QuickDraw, their relevance for both global and local interpretability.
Statistics of ash dieback in Latvia

Dieback of the common ash (Fraxinus excelsior L.) has been spreading throughout Europe since the 1990s, causing severe ecological and economical consequences; however, detailed statistics on its dynamics have been published rarely. This paper presents the dynamics of mature ashdominated stands in Latvia for the period 2005–2015. Data from the national forest inventory and a permanent sampling plot network were summarised. According to the official statistics, the dieback has caused a twofold decrease in area of the ash stands (from 21 891 to 13 011 ha, which respectively comprised ca. 0.8 to ca. 0.4% of the total forest area). The official statistics on standing volume appeared biased, as they did not account for increased mortality. According to the permanent sampling plots, standing volume and stand density have been affected even more, having decreased by 53.1 and 69.9%, respectively, compared to 2005 (the stand density and standing volume of ash in 2015 was 77 individuals ha–1 and 151 m3 ha–1, respectively). The mortality of the trees has not been stable. Stand density decreased faster during 2005–2009 compared to 2010–2015, with mortality rates of 9.6 and 8.2% year–1, respectively. In contrast, the decrease in standing volume in 2005–2009 was slower than in 2010–2015 (mortality rates were 4.7 and 7.7% year–1, respectively) because trees with smaller dimensions were more susceptible to the dieback. Nevertheless, the observed mortality rates clearly indicate negative prospects for ash stands in Latvia.
Integrative Studies on the Role of CaMKII in Cardiac Disease and Arrhythmias

ii Acknowledgments. iii Vita . ii List of Tables . ii List of Figures . ii Chapter 1: Introduction . 1 1.1: Objective . 1 1.2: Overview of Cardiac Physiology and Cell Biology . 2 1.3: Cardiac Action Potential . 5 1.4: Sodium Channels . 8 1.5: Causes of Increased Late INa . 13 1.6: Excitation-Contraction Coupling . 15 1.7: Regulation of Excitation-Contraction Coupling in Response to Acute Stress . 16 1.8: CaMKII-dependent regulation of Excitation-contraction coupling . 18 1.9: CaMKII-dependent regulation of Nav1.5 . 20