Miracle-dz/UniFAR-FTUs huggingface dataset:
Two short-striated species of Staurosirella [Bacillariophyceae] from Indonesia and the United States

The paper presents a detailed morphological analyses by light (LM) and scanning electron microscopy (SEM) of two short-striated diatoms of the genus Staurosirella D. M. Williams & Round. The fi rst was encountered in the periphyton of a river in Oregon (U.S.A.) and is described here as a new species, S. krammeri sp. nov. The second diatom was found in a lake plankton collection made during the Wallacea-Expedition in the early 1930s; it was originally described as Fragilaria lapponica f. lanceolata Hustedt, but based on its ultrastructure we propose its transfer to Staurosirella at species level as S. lanceolata comb. nov. et stat. nov. These two taxa are compared by LM and SEM with the generitype Staurosirella lapponica (Grunow) D. M. Williams & Round as well as other morphologically related species in the light of available published material.
Leaf area, chlorophyll content, and relative growth rate of grass on different shading and fertilization

Plant morphology and physiology such as leaf area, total chlorophyll, and chlorophyll a/b ratio were affected by shading and fertilization. An experiment was conducted in Indonesian Research Institute for Animal Production (IRIAP) Ciawi, West Java. The objective of this study was to determine the morphology and physiology adaptation of three short grasses species for grazing namely Paspalum notatum, Brachiaria humidicola, Stenotaphrum secundatum on different shading and fertilization level. The experiment was arranged in split-split plot design. The main plot was shading level (0, 38, 56%); sub-plot was fertilizer dosage (0, 100, and 200 kg N/ha) while sub-sub plot was grass species. The results showed that leaf area were significantly different on different grass species, and there was interaction between shading and species on total leaf area. P. notatum on 38% shading level has the highest total leaf area (240.2 cm 2 ). S. secundatum and P. notatum had a better adaptation in shading area compared to B. humidicola by increasing of total chlorophyll and decreasing of chlorophyll a/b ratio. Relative growth rate (RGR) of P. notatum and S. secundatum were increased by the increasing shading level. On the other hand relative growth rate of B. humidicola was decreased by the increasing shading level. Leaf area, chlorophyll content, and RGR were not significantly affected by fertilization dosage. Key Words : Shading, Fertilization, Adaptation, Growth, Chlorophyll
COMBINED REUSE OF WASTEWATER AND DESALINATION FOR THE MANAGEMENT OF WATER SYSTEMS IN CONDITIONS OF SCARCITY

The occurrence of problems related to the shortage of water resources and the consequent higher difficulties in meeting the needs of users, require studies aimed at identifying possible interventions for the increase in water availability. They are mainly the large drinking water infrastructure for multiple purposes that are in crisis in meeting the needs on a local basis. In such circumstances, rationalization and integration of water resources should be sought through the use of unconventional supply systems. This is the case of the Alto Ionio Cosentino (Region Calabria, Southern Italy), a territory characterized by a significant water deficit, competition between drinking and irrigation use and an inefficient water supply system in terms of satisfying demand. Through the optimization of the allocation of water resources, to overcome the problems of the territory, this paper assesses the possibility of a combined use between desalination of sea water and reuse of wastewater to meet the drinking needs and to increase irrigation requirements.
Molecular and cellular basis of the internalization of "Bartonella henselae" by human endothelial cells

The facultative intracellular bacterium Bartonella henselae enters human endothelial cells either passively by conventional phagocytosis or actively by a pathogen-triggered process known as invasome-mediated internalization. The latter involves the formation of a cell-surface-associated bacterial aggregate, which is subsequently engulfed by host cell membranes eventually resulting in its complete internalization. Recent work indicated that invasome formation of B. henselae depends on its VirB/VirD4 T4SS. This work describes that the VirB/VirD4 T4SS of B. henselae injects a cocktail of seven effector proteins into endothelial host cells to subvert cellular functions and that one of these translocated effector proteins, BepG, mediates the sustained cytoskeletal changes leading to invasome formation. Moreover, this work indicates the existence of two non-redundant pathways to promote invasome formation, one of which is governed by the action of BepG and another one, involving further Bep proteins, which is BepG-independent. On the host cell side, Rho-family small GTPases Cdc42 and Rac1, but not RhoA are shown to be required for invasome-mediated internalization. Furthermore, it is shown that invasome formation leads both to the rearrangement of pre-existing F-actin fibers and to localized actin polymerization enriched for Arp2/3, which occurs in a Scar1/WAVE-dependent manner. Finally, this work provides evidence that after complete internalization the invasome membranes do not fuse with Lamp-1 positive lysosomes, indicating that invasome-mediated invasion represents a novel mechanism allowing the uptake of bacteria without entering the endocytic-lysosomal pathway. Importantly, this is the first report, which attributes the orchestrated action of more than one effector protein of B. henselae to a known VirB/VirD4 T4SS-dependent phenotype, namely invasome formation, which represents a multifacetted example for the complexity of host cell subversion by a bacterial pathogen.
Ecophysiological responses of Araucaria angustifolia (Araucariaceae) seedlings to different irradiance levels.

Brazilian pine (Araucaria angustifolia [Bert.] O.Ktze.) is an indigenous conifer of the southern region of South America, typically regarded as a sun-loving species. However, there is insufficient information on the species’ behaviour under different irradiances to characterise its plasticity to light. The purpose of this work was to measure some ecophysiological responses of Brazilian pine seedlings to three irradiance levels: 100, 45 and 10% full sunlight. Thirty seedlings were grown under each of the irradiance treatments and, after 5 months, growth parameters, leaf chlorophyll concentration and in vivo nitrate reductase activity, in both leaves and roots, were analysed. There was no increase in shoot biomass allocation in response to shading, in contrast to results from other experiments. Only low-light seedlings showed significant increase in specific leaf area, as well as in the ratio of height to shoot biomass. Chlorophyll content and the ratio of chlorophyll a to chlorophyll b did not vary among treatments. Nitrate reductase activity was detected only in roots and was reduced in the low-light treatment. An overall analysis of the results points to a normal growth of Brazilian pine seedlings at both high- and medium-light sites, at least in their initial stages of development.
Isolation and Identification of Escherichia Coli (E. coli) From Children Suspecting Urinary Tract Infection (UTI)

Urinary Tract infection is the second most common bacterial infection in children. Classic symptoms and signs ware poor feeding irritability or fever combined with emesis and apparent abdominal pain. The most frequent etiology continues to be Escherichia coli (E. coli). The present study was undertaken to isolate the E coli from children suspecting urinary tract infection of different age groups and sex. Identification and conformation of these bacteria was done based on microscopic, cultural and biochemical characteristics and we also studied their antimicrobial susceptibility patterns. The study was conducted at department of Medical Laboratory Technology, Doon (PG) paramedical college, HNB Garhwal University, Dehradun, India between October and November 2011. The study encompassed of 83 subjects. The children, aged 11-15 were selected for study in absence of clinical sign and symptoms of UTI. Urines samples were collected and examined and organisms were identified by conventional methods and antimicrobial testing was done according to Kirby Bauer's method on all isolates. Specific morphological characteristic of E coli strains were gram negative and rod shaped. E coli strains showed pink colored colonies on MacConkey’s agar medium while white creamy color colonies on the nutrient agar medium. Specific biochemical characteristic of strains were oxidase negative, H2S positive, nitrate-reduction positive, phenylalanine-deaminase negative, malonate negative, β-galactosidase positive, Methyl-Red positive and Voges-Proskauer negative. Thirty seven strains showed more than 105cfu/ml urine sample on MacConkey agar medium and EMB agar medium. E. coli strains showed specific morphological, cultural and biochemical characteristic of E. coli. The increase in incidence of bacteriuria in female subjects was observed in all three age groups (60.00%), (66.66%), (62.50%) as compared with male subjects were (40.00%), (33.33%), (37.50%) respectively. All E. coli strains were sensitive to Norfloxacin, Roxithromycin, Chloramphenicol, Amikacin, Gentamicin, Azithromycin, Ciprofloxacin but the strains were resistant against Tetracycline (TE/30μg), Erythromycin (E/15μg).
Interactions of Eukaryotic Translation Initiation Factors and 3' Untranslated Region of Barley Yellow Dwarf Virus Mrna During Protein Synthesis: A Study of Equilibrium Binding, Kinetics and Thermodynamics

Eukaryotic initiation factor (eIF) 4F binding to mRNA is the first committed step in capdependent protein synthesis. Barley Yellow Dwarf Virus (BYDV) employs a cap-independent mechanism of translation initiation which is mediated by a structural element BTE (BYDV translation element) located in the 3’ UTR of its mRNA. eIF4F bound the BTE and a translational inactive mutant with high affinity; thus questioning the role of eIF4F in translation of BYDV. To examine the effects of eIF4F in BYDV translation initiation, BTE mutants with widely different in vitro translation efficiencies ranging from 5-164% compared to WT were studied. Using fluorescence anisotropy to obtain quantitative data, we show 1) the equilibrium binding affinity (complex stability) correlated well with translation efficiency, whereas the “on” rate of binding did not. 2) other unidentified proteins or small molecules in wheat germ extract (WGE) prevented eIF4F binding to mutant BTE but not WT BTE. 3) BTE mutants-eIF4F interactions were found to be both enthalpically and entropically favorable with an enthalpic contribution of 52-90% to ∆G° at 25°C suggesting hydrogen bonding contributes to stability and 4) in contrast to cap-dependent and tobacco etch virus (TEV) Internal Ribosome Entry Site (IRES) interaction with eIF4F, PABP did not increase eIF4F binding. Further, the eIF4F bound to the 3’ BTE with higher affinity than for either m7G cap or TEV IRES, suggesting that the 3’
Regulation of mTOR complex 1 in response to growth factors and nutrients

In multicellular organisms, cells ensure the simultaneous availability of growth factors and nutrients before they invest in cellular processes that lead to growth. The TOR kinase is a master regulator of cellular growth and nucleates two distinct protein complexes known as TOR complex 1 and 2 (TORC1 and 2). The activity of TORC2 is mainly regulated by growth factors, whereas TORC1 activity is responsive to both growth factors and nutrients, and thus acts as a detector of favorable growth conditions. The consequence of TORC1 activation is increased protein translation through its substrates S6K and 4E-BP1. Many of the upstream signals that lead to activation of TOR pathway are tumor suppressors and deregulation of the pathway leads to disease. We aim to better understand the regulation of mammalian TORC1 (mTORC1) by upstream signals. In the work described here, we identified PRAS40 as a new component of mTORC1. PRAS40 is phosphorylated in response to growth factors and this phosphorylation event leads to mTORC1 activation. We also showed that the small GTPase Rheb, a major upstream activator of mTORC1, activates it by directly interacting with mTORC1. Both PRAS40 and Rheb relay information from growth factors to mTORC1, and do not seem to be regulated by nutrients, particularly amino acids. In this work, we also investigated how amino acids lead to mTORC1 activation. We showed that amino acids activate mTORC1 by recruiting the complex to lysosomal surface through the action of evolutionarily conserved Rag GTPases. We also indentified a complex of three proteins (p14, p18 and MP1), that we call the “Ragulator” complex, as Rag GTPase interacting proteins. The Ragulator itself localizes to lysosomes through lipid modifications on p18, and tethers the Rag GTPases on the lysosomal surface. We speculate that amino acid-induced lysosomal localization of mTORC1 enables its encounter with Rheb. Through this work, we propose a model for growth factor and amino acid-induced mTORC1 activation. Thesis Supervisor: David M. Sabatini Title: Associate Professor of Biology, MIT; Member, Whitehead Institute for Biomedical Research
The Genes of the Isometric Phages and Their Functions

The small isometric DNA phages ϕ X174 and S13 are currently believed to encode nine genes, which specify at least 16 gene products (Fig. 1). The concept that each gene on a DNA molecule is physically distinct from every other gene has been shattered for this class of phages. The production of two proteins from one DNA sequence was reported by Linney et al. (1972), who found that translation of the gene- A region was initiated at two different sites in the same reading frame. The spectacular finding by Barrell et al. (1976), Sanger et al. (1977), and Weisbeek et al. (1977) of overlapping sequences that are translated in different reading frames, yielding functional proteins, provided an entirely new view of gene topology. By the criteria of complementation tests, which measure units of genetic function, there are at least eight genes in these phages (Jeng et al. 1970), designated A through H . To these must be added gene J , which specifies a major capsid component but is not yet represented by any known mutation. The “one gene-one protein” hypothesis can be converted into a definition of a gene and used as a biochemical method of counting genes. Any stretch of DNA that codes for a protein is counted as one gene, whether or not some other protein is coded for somewhere in that same stretch of DNA. This method of identifying genes is implicit in current research. We are faced with a plethora of gene products, only some of whose functions have.
Housing, breeding and management practices of Mahabubnagar goats

A study on Mahabubnagar goats of Andhra Pradesh was carried out in 150 households of 56 villages in Mahabubnagar, Nalgonda and Ranga Reddy districts with the objective of cataloguing management practices of Mahabubnagar goats. The study revealed that closed type of housing system was adopted by 60 percent of farmers with thatched roof and kutcha floor. The common feeding practice was grazing (72%), while 27.33% farmers supplemented their animals with concentrates, crop byproducts, etc. during lean periods. The overall flock size was 43.69 ± 1.70 and 58% farmers maintained 26 to 50 goats per flock under field conditions. Majority of the farmers followed 1 : 21 to 30 sex ratio in their flocks and they did not rotate the breeding bucks as well as did not select breeding males and females. Deworming (82.08%), deticking (6.67%) and vaccination (18.67%) schedules were followed as preventive health measures. Most of the goats were disposed off at villages as per the wishes of butcher, middlemen and traders based on the animal size and shape.
The amo operon in marine, ammoniaoxidizingγ-proteobacteria

While there is an extensive database of genes encoding ammonia monooxygenase (amo) found in the ammonia-oxidizing β-proteobacteria, few amo sequences are available representing the γ-proteobacteria. We sequenced the complete amo operon (amoCAB) for Nitrosococcus oceani (ATCC 19707), a marine, autotrophic, ammonia-oxidizing bacterium belonging to the γ-subdivision of the proteobacteria. An additional autotrophic, ammonia-oxidizing bacterium isolated from a marine environment (strain C-113) was identified as belonging to the Nitrosococcus genus by 16S rDNA analysis and its amo operon was sequenced. This is the first report of a full-length sequence for the amo operon from a γ-subdivision autotrophic ammonia-oxidizing bacterium. The N. oceani and C-113 amo genes were 88–90% identical to each other, 49–53% identical to the pmo genes encoding the related particulate methane monooxygenase of Methylococcus capsulatus (Bath), and 39–42% identical to the amo genes of the β-subdivision autotrophic ammonia-oxidizing bacteria. In both Nitrosococcus strains, the amo operon was found as a single copy and contained three genes, amoC, amoA, amoB, with intergenic spacer regions between amoC and amoA (286 bp) and between amoA and amoB (65 bp). We conclude that the amo genes will allow for a finer scale phylogenetic differentiation than 16S rDNA within the γ-subdivision AOB.
Gender Stereotypes in Halloween Costumes

approved:_____________________________________________________ Aurora Sherman Previous research has shown that gender stereotypes are present in advertisements and in popular culture items. We conducted a content analysis of Halloween costumes to examine the presence of gender stereotypes in the poses of the models, weapons, and costume role (e.g. hero, counter authority, mythical creature, royalty). A sample of 990 costumes was randomly selected from a larger pool of costumes from four different U.S. costume retailers. An exploratory analysis for Spanish costumes was also conducted with a sample of 100 randomly selected costumes from the Spanish website Party Fiesta. Chisquare analyses revealed that in both datasets, men were more frequently posed actively, had active hands, stable/grounded stance, and stable/grounded feet. Women were more frequently posed with decorative hands, with a curved spine, off-balanced or displayed stance, and off-balanced or displayed feet. Male models were twice as likely to be pictured with a weapon as female models, though this did not reach significance in the Spanish dataset. Female models were more likely to take on costume roles of princess and mythical creature, while male models were more likely to take on costume roles of heroes and counter authorities. The results of this study indicate that gender stereotypes are present in Halloween costumes. Gender socialization consequences are discussed.
Decorated Dyck paths and the Delta conjecture

We discuss the combinatorics of the decorated Dyck paths appearing in the Delta conjecture framework in (Haglund et al 2015) and (Zabrocki 2016), by introducing two new statistics, bounce and bounce (cid:48) . We then provide plethystic formulae for their q , t -enumerators, by proving in this way a decorated version of Haglund’s q , t -Schröder theorem, answering a question in (Haglund et al 2015). In particular we provide both an algebraic and a combinatorial explanation of a symmetry conjecture in (Haglund et al 2015) and (Zabrocki 2016). This is an extended abstract of (D’Adderio, Vanden Wyngaerd 2017).
Novel fibrin clot components : identification, characterization and function

textabstractThe main goal of blood coagulation is to diminish blood loss and to support vessel damage repair. The initial step in primary hemostasis is the adhesion of platelets to the exposed subendothelial extracellular matrix which contains several adhesive macromolecules such as collagen, von Willebrand factor (vWF), laminin, fibronectin and thrombospondin. These adhesive macromolecules are ligands for different platelet-surface receptors. Upon binding, platelets can be activated by different signal transduction pathways. Platelet adhesion and activation is followed by platelet aggregation, which involves fibrinogen binding to an integrin on the surface of the activated platelet. Secondary hemostasis is initiated by exposure of tissue factor (TF) to blood by endothelial damage. TF forms a complex with coagulation factor VII which activates factor IX and factor X. Activated factor X (FXa) forms the prothrombinase complex together with activated factor V (FVa) on a phospholipid membrane surface, which is provided by, for example, activated platelets and microparticles, and which converts prothrombin into thrombin. Thrombin can amplify its own generation by activating FXI, and FXIa activates FIX, that together with activated FVIII forms more FX. Thrombin is an important enzyme that cleaves fibrinogen into fibrin monomer. Fibrin monomers polymerize and the resulting network is stabilized by factor XIIIa-catalyzed cross-linking. This tight fibrin network together with activated platelets occludes the site of vascular injury. After its formation, the clot will retract. The speed and degree of clot retraction are proportional to the number of platelets. Neither the significance of in vivo clot retraction for hemostasis as well as the mechanism of clot retraction are well understood. Retraction may improve the mechanical stability of clots. To maintain a balance, the coagulation pathway is inhibited by several inhibitors. Tissue factor pathway inhibitor (TFPI) inhibits the TF-induced coagulation firstly by binding to FXa. Secondly, this TFPI-FXa complex binds to the TF-FVIIa complex resulting in the formation of an inactive quaternary complex. TFPI can also inhibit the initiation phase of coagulation in one step by binding to activated FX that is not yet released from its complex with TF-FVIIa. Thrombin is directly inhibited by the serine protease inhibitor antithrombin as well as heparin cofactor II. Thrombin can also bind to thrombomodulin and form a complex that activates protein C. Activated protein C (APC), with its cofactor protein S, has anticoagulant properties through proteolytic inactivation of factors Va and VIIIa.
Corporate governance and intellectual capital disclosure : evidence from the Scandinavian countries

In the modern society intellectual capital (IC) disclosure offers valuable insights on the information transparency between the organisation and its stakeholders. The purpose of the present study is to analyse the determinants of IC disclosure based on the firm data collected from the Scandinavian countries. We have chosen to analyse 123 annual reports in the local language for the period of 2008 to 2012. The annual reports act as one of the best sources of data revealing important information about firms that are beyond the reporting requirements of the accounting regulations. This paper combines the empirical research of IC disclosure with the previous literature to identify its strategic implications on corporate governance. The aim is to examine the relationship between firm size, leverage ratio, information asymmetry and industry-specific factors on the level of IC disclosure. Our results call the potential need for more IC disclosure.