Miracle-dz/UniFAR-FTUs huggingface dataset:
A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota).

Chytridiomycota (chytrids) is the only phylum of true Fungi that reproduces with motile spores (zoospores). Chytrids currently are classified into five orders based on habitat, zoospore characters and life cycles. In this paper we estimate the phylogeny of the chytrids with DNA sequences from the ribosomal RNA operon (18S+5.8S+28S subunits). To our surprise the morphologically reduced parasites Olpidium and Rozella comprise two entirely new, and separate, lineages on the fungal tree. Olpidium brassicae groups among the Zygomycota, and Rozella spp. are the earliest branch to diverge in the fungal kingdom. The phylogeny also suggests that Chytridiomycota is not monophyletic and there are four major lineages of chytrids: Rozella spp. , Olpidium brassicae, the Blastocladiales and a "core chytrid clade" containing the remaining orders and families and the majority of flagellated fungi. Within the core chytrid group 11 subclades can be identified, each of which correlates well with zoospore ultrastructure or morphology. We provide a synopsis of each clade and its morphological circumscription. The Blastocladiales appears to be the sister taxon of most nonflagellated fungi. Based on molecular phylogenetic and ultrastructural characters this order is elevated to a phylum, the Blastocladiomycota.
Anti-Biofilm Drug Susceptibility Testing Methods: Looking for NewStrategies against Resistance Mechanism

Biofilm is a reservoir of drug resistant microorganisms that can increase the failure rate of anti-infective therapy and is a public health concern. Antibiofilm drug discovery is necessary for developing new drugs, biocides and wound management protocols. This makes the standardization and implementation of in vitro antibiofilm screening platforms a challenge in the search for new antibiotics, because current antimicrobials are active against planktonic bacteria and have poor diffusion across biofilm matrix. Usually, based in the research topic, the antibiofilm methods have been classified in static and flow depending of continuous supply of nutrients that affect the microbial growth, the final aim of these assays is obtain Minimal Biofilm Inhibitory Concentration (MBIC) and Minimal Biofilm Eradication Concentration (MBEC) values as efficacy parameter of the compound or procedure evaluated, but is very important correlates data from different models in order to give real results of activity. This review aims at describing the initial tools for to establishing an antibiofilm drug discovery-prospecting program.
The Serotonin 1 A Receptor and its Interaction with the Membrane Environment

Serotonin is a neurotransmitter which signals across the plasma membrane by binding to distinct cell surface receptors which have been classified into many groups. The serotonin1A (5-HT1A) receptor is the most extensively studied of the serotonin receptors and belongs to the large family of seven transmembrane domain G-protein coupled receptors. Although the pharmacological and signaling aspects of the functioning of the 5-HT1A receptor have been well explored, the role of the membrane environment in its function is only beginning to be addressed. This review describes various aspects of the membrane biology of 5-HT1A receptors such as modulation of ligand binding to 5-HT1A receptors under a variety of conditions, and functional solubilization of 5-HT1A receptors using the bovine hippocampal serotonin1A receptor as the model system. Recent developments in membrane organization of the 5-HT1A receptor using the phenomenon of detergent insolubility, and the role of membrane cholesterol in ligand binding and G-protein coupling of the 5-HT1A receptor are summarized.
Idarubicin Plus Behenoyl Cytarabine and 6-thioguanine Compares Favorably with Idarubicin Plus Cytarabine-based Regimen for Children with Previously Untreated Acute Myeloid Leukemia: 10-Year Retrospective, Multicenter Study in Korea

We investigated the outcome of idarubicin plus N4-behenoyl-1-β-D-arabinofuranosyl cytosine (BHAC)-based chemotherapy (BHAC group, n=149) compared to idarubicin plus cytarabine-based chemotherapy (cytarabine group, n=191) for childhood acute myeloid leukemia (AML). Between January 1996 and December 2005, 340 children with AML from 5 university hospitals in Korea received the BHAC-based or cytarabine-based chemotherapy, with or without hematopoietic stem cell transplantation. After induction therapy, 264 (77.6%) of 340 children achieved a complete remission (CR) and 43 (12%) achieved a partial remission (PR). The CR rate in the BHAC group was higher than in the cytarabine group (85.2% vs. 71.7%, P=0.004). However, the overall response rate (CR+PR) was not different between the two groups (93.3% vs. 87.9%, P=0.139). The 5-yr estimates of overall survival (OS) of children in the two groups were similar (54.9% for the BHAC group vs. 52.4% for the cytarabine group, P=0.281). Although the results were analyzed according to the treatment type and cytogenetic risk, the OS showed no significant difference between the BHAC group and the cytarabine group. In the present study, the clinical outcomes of the BHAC-based chemotherapy, consisting of BHAC, idarubicin, and 6-TG, are comparable to that of the cytarabine-based chemotherapy for childhood AML.
Assigning game server roles in mobile ad-hoc networks

Over the last couple of years, multi-player games have become more and more popular. Additionally, new mobile devices now have sufficient resources to play these multi-player games in mobile and wireless networks. As the classic centralised game server design is unsuited for mobile ad-hoc networks, a group of nodes can take the role of a distributed game server. This group of nodes can provide the necessary redundancy which is needed in the dynamic environment of a mobile ad-hoc network. In this paper we present a modified dominating set algorithm for server selection which uses local information to determine well-suited nodes from the group of players. Our algorithm uses three phases (discovery, determination and marking) to calculate an initial server set and adjusts to network changes during the game. We implemented our server selection algorithm in NS-2 and evaluated its behaviour in two different realistic scenarios for mobile games (schoolyard and train) as well as in an artificial stress scenario.
Compression Limits for Random Vectors with Linearly Parameterized Second-Order Statistics

The class of complex random vectors whose covariance matrix is linearly parameterized by a basis of Hermitian Toeplitz (HT) matrices is considered, and the maximum compression ratios that preserve all second-order information are derived-the statistics of the uncompressed vector must be recoverable from a set of linearly compressed observations. This kind of vectors arises naturally when sampling wide-sense stationary random processes and features a number of applications in signal and array processing. Explicit guidelines to design optimal and nearly optimal schemes operating both in a periodic and nonperiodic fashion are provided by considering two of the most common linear compression schemes, which we classify as dense or sparse. It is seen that the maximum compression ratios depend on the structure of the HT subspace containing the covariance matrix of the uncompressed observations. Compression patterns attaining these maximum ratios are found for the case without structure as well as for the cases with circulant or banded structure. Universal samplers are also proposed to compress unknown HT subspaces.
AMPK blocks starvation-inducible transgenerational defects in Caenorhabditis elegans

Significance Following periods of famine, a reproducible spectrum of disorders often manifest long after the period of starvation. Curiously, many of these diseases arise in individuals that have no apparent genetic history of the disorder, although they do correlate with specific epigenetic modifications. We used Caenorhabditis elegans as a model to understand how acute periods of starvation might result in physiological or developmental consequences in a single generation or over multiple generations following the initial period of stress. Our data suggest that the AMP-activated protein kinase, an enzyme that mediates metabolic adjustment during starvation, is required to block germ-line gene expression during these conditions. In its absence the inappropriate activation of germ-line transcription results in sterility and transgenerational reproductive defects. Life history events, such as traumatic stress, illness, or starvation, can influence us through molecular changes that are recorded in a pattern of characteristic chromatin modifications. These modifications are often associated with adaptive adjustments in gene expression that can persist throughout the lifetime of the organism, or even span multiple generations. Although these adaptations may confer some selective advantage, if they are not appropriately regulated they can also be maladaptive in a context-dependent manner. We show here that during periods of acute starvation in Caenorhabditis elegans larvae, the master metabolic regulator AMP-activated protein kinase (AMPK) plays a critical role in blocking modifications to the chromatin landscape. This ensures that gene expression remains inactive in the germ-line precursors during adverse conditions. In its absence, critical chromatin modifications occur in the primordial germ cells (PGCs) of emergent starved L1 larvae that correlate with compromised reproductive fitness of the generation that experienced the stress, but also in the subsequent generations that never experienced the initial event. Our findings suggest that AMPK regulates the activity of the chromatin modifying COMPASS complex (complex proteins associated with Set1) to ensure that chromatin marks are not established until nutrient/energy contingencies are satisfied. Our study provides molecular insight that links metabolic adaptation to transgenerational epigenetic modification in response to acute periods of starvation.
Stochastic Characterization and Update of Fatigue Loading for Mechanical Damage Prognosis

Accurate characterization and prediction of loading, while properly accounting for uncertainty, are essential for probabilistic fatigue damage prognosis. Three different techniques, including rainflow counting, the Markov chain method, and autoregressive moving average (ARMA) method, are reviewed for stochastic characterization and reconstruction of the fatigue load spectrum for prognosis. The ARMA method is extended by introducing random coefficients and probabilistic weights, to account for the uncertainty in the selection of models, inherent variability of loading, and uncertainty due to sparse data. A continuous model updating framework based on usage monitoring data is developed and applied to all the three techniques mentioned above. The relation between prediction accuracy and updating period is evaluated quantitatively. A quantitative model validation metric is proposed for assessing the accuracy of load prediction
Rosiglitazone, a Peroxisome Proliferator-Activated Receptor-γ Agonist, Restores Alveolar and Pulmonary Vascular Development in a Rat Model of Bronchopulmonary Dysplasia

Purpose We tested whether rosiglitazone (RGZ), a peroxisome proliferator-activated receptor-γ agonist, can restore alveolar development and vascular growth in a rat model of bronchopulmonary dysplasia (BPD). Materials and Methods A rat model of BPD was induced through intra-amniotic delivery of lipopolysaccharide (LPS) and postnatal hyperoxia (80% for 7 days). RGZ (3 mg/kg/d, i.p.) or vehicle was given daily to rat pups for 14 days. This model included four experimental groups: No BPD+vehicle (V), No BPD+RGZ, BPD+V, and BPD+RGZ. On D14, alveolarization, lung vascular density, and right ventricular hypertrophy (RVH) were evaluated. Results Morphometric analysis revealed that the BPD+RGZ group had significantly smaller and more complex airspaces and larger alveolar surface area than the BPD+V group. The BPD+RGZ group had significantly greater pulmonary vascular density than the BPD+V group. Western blot analysis revealed that significantly decreased levels of vascular endothelial growth factor (VEGF) and its receptor VEGFR-2 by the combined exposure to intra-amniotic LPS and postnatal hyperoxia were restored by the RGZ treatment. RVH was significantly lesser in the BPD+RGZ group than in the BPD+V group. Conclusion These results suggest that RGZ can restore alveolar and pulmonary vascular development and lessen pulmonary hypertension in a rat model of BPD.
Mechanical systems for a synchrotron X-ray-enhanced scanning tunnelling microscope

Synchrotron X-ray-enhanced scanning tunnelling microscopy (SXSTM) is a novel technique by which materials can be studied with elemental-sensitive and nano-metre-spatial resolution. This poster covers the mechanical engineering design for the prototype SXSTM instrument. System performance and sample handling requirements along with the desire to use existing components constrained the design. The SXSTM needs to be mechanically and acoustically isolated from the environment. In addition, all sample preparations are done in situ , and thus, the sample and SXSTM tips need to be prepared and moved inside the vacuum chamber with a wobble stick. The final design incorporates an Advanced Photon Source-designed vacuum chamber, existing components and commercial parts to provide the user with a robust prototype system to demonstrate the impact of this new technique.
Odor naming is difficult, even for wine and coffee experts

Odor naming is difficult for people, but recent cross-cultural research suggests this difficulty is culture-specific. Jahai speakers (hunter-gatherers from the Malay Peninsula) name odors as consistently as colors, and much better than English speakers (Majid & Burenhult, 2014). In Jahai the linguistic advantage for smells correlates with a cultural interest in odors. Here we ask whether sub-cultures in the West with odor expertise also show superior odor naming. We tested wine and coffee experts (who have specialized odor training) in an odor naming task. Both wine and coffee experts were no more accurate or consistent than novices when naming odors. Although there were small differences in naming strategies, experts and non-experts alike relied overwhelmingly on source-based descriptions. So the specific language experts speak continues to constrain their ability to express odors. This suggests expertise alone is not sufficient to overcome the limits of language in the domain of smell.
Sintering Behavior and Properties of Si3N4 Ceramics with Yttrium Chloride Additive

The big gap between the thermal conductivity of Si3N4 ceramics and the theoretical value of beta-Si3N4 single crystal implies that the low thermal conductive oxide grain-boundary phases in the ceramics possibly have a great influence on the thermal conductivity of the ceramics. In this work, yttrium chloride (YOCl) is introduced as sintering additive instead of the commonly-used Y2O3, in order to decrease the amount of the grain-boundary oxide; and the influence of YOCl on the sintering and the properties of Si3N4 ceramics was studied. Results show that YOCl additive can react with Si3N4 powders to form similar Y-Si-O-N grain-boundary phases just like Y2O3 while the Cl disappears during sintering. The thermal conductivity of the ceramics sintered with YOCl additive (85 W/m•K) increases about 15% as comparing with the ceramics sintered with Y2O3 additive, even though the relative density of the former reaches merely 97%. The microstructure of the sample sintered at different temperatures was investigated in the work, for elucidating the sintering process and the relationship between the properties and the microstructure of the YOCl added ceramics.
Separation of Routing and Scheduling in Backpressure-Based Wireless Networks

Backpressure routing and scheduling, with its throughput-optimal operation guarantee, is a promising technique to improve throughput in wireless multihop networks. Although backpressure is conceptually viewed as layered, the decisions of routing and scheduling are made jointly, which imposes several challenges in practice. In this work, we present Diff-Max, an approach that separates routing and scheduling and has three strengths: 1) Diff-Max improves throughput significantly; 2) the separation of routing and scheduling makes practical implementation easier by minimizing cross-layer operations; i.e., routing is implemented in the network layer and scheduling is implemented in the link layer; and 3) the separation of routing and scheduling leads to modularity; i.e., routing and scheduling are independent modules in Diff-Max, and one can continue to operate even if the other does not. Our approach is grounded in a network utility maximization (NUM) formulation and its solution. Based on the structure of Diff-Max, we propose two practical schemes: Diff-subMax and wDiff-subMax. We demonstrate the benefits of our schemes through simulation in ns-2.
Ocean acidification over the next three centuries using a simple global climate carbon-cycle model: projections and sensitivities

Abstract. Continued oceanic uptake of anthropogenic CO2 is projected to significantly alter the chemistry of the upper oceans over the next three centuries, with potentially serious consequences for marine ecosystems. Relatively few models have the capability to make projections of ocean acidification, limiting our ability to assess the impacts and probabilities of ocean changes. In this study we examine the ability of Hector v1.1, a reduced-form global model, to project changes in the upper ocean carbonate system over the next three centuries, and quantify the model's sensitivity to parametric inputs. Hector is run under prescribed emission pathways from the Representative Concentration Pathways (RCPs) and compared to both observations and a suite of Coupled Model Intercomparison (CMIP5) model outputs. Current observations confirm that ocean acidification is already taking place, and CMIP5 models project significant changes occurring to 2300. Hector is consistent with the observational record within both the high- (> 55°) and low-latitude oceans (
olecular and chemical characterization of a Sphagnum palustre lone : Key steps towards a standardized and sustainable moss bag

This work aimed to define the molecular and chemical signature of a S. palustre clone developed in the framework of the EU-FP7 Mossclone project to improve the standardization and reliability of the mossbag technique. The molecular characterization was performed by a set of DNA molecular markers (RAPD, ISJ, PCR-RFLP, sequencing and microsatellites) to tag the clone produced within the project. Molecular characterization also provided new DNA markers that can be applied in systematic analyses of Sphagnum, and gave new insights to implement well established techniques. The elemental composition of the clone was measured by ICP-MS analysis of 54 major and trace elements, with and without commonly applied pre-exposure treatments (oven devitalization and EDTA washing). Concentrations of almost all analyzed elements were significantly lower (from 10 to 100 times) in the clone than in conspecific field moss, apart from some elements (K, Mo, P and Na) deriving from the culture medium or EDTA treatment. Oven devitalization and EDTA washing did not significantly affect the clone composition. A comparison between the elemental composition of the clone with that of naturally growing Sphagnum species proved the particularly low elemental content of the clone. Therefore, in view of a rigorously standardized moss-bag protocol for the monitoring of persistent atmospheric pollutants, the use of the S. palustre clone, a biomaterial with very low and constant element composition, and homogenous morphological characteristics is strongly recommended.
Clustered networks protect cooperation against catastrophic collapse

Abstract Assuming a society of conditional cooperators (or moody conditional cooperators), this computational study proposes a new perspective on the structural advantage of social network clustering. Previous work focused on how clustered structure might encourage initial outbreaks of cooperation or defend against invasion by a few defectors. Instead, we explore the ability of a societal structure to retain cooperative norms in the face of widespread disturbances. Such disturbances may abstractly describe hardships like famine and economic recession, or the random spatial placement of a substantial numbers of pure defectors (or round-1 defectors) among a spatially structured population of players in a laboratory game, etc. As links in tightly clustered societies are reallocated to distant contacts, we observe that a society becomes increasingly susceptible to catastrophic cascades of defection: mutually-beneficial cooperative norms can be destroyed completely by modest shocks of defection. In contrast, networks with higher clustering coefficients can withstand larger shocks of defection before being forced to catastrophically low levels of cooperation. We observe a remarkably linear protective effect of clustering coefficient that becomes active above a critical level of clustering. Notably, both the critical level and the slope of this dependence is higher for decision-rule parameterizations that correspond to higher costs of cooperation. Our modeling framework provides a simple way to reinterpret the counter-intuitive and widely cited human experiments of Suri and Watts (2011) while also affirming the classical intuition that network clustering and higher levels of cooperation should be positively associated.
Synthesis, Characterisation and Textural Analysis to reduce the Multiplicative Noise in Nano dispersed Liquid Crystalline Compounds using HF Technique

Synthesis and characterisation are carried out on four N-(p-n-decyloxy benzylidene-)p-n-alkoxy anilines 10O.Om Liquid Crystalline compounds( LC ) with n=10 and m=3, 5 and with 1% ZnO nano particle dispersion. Further to reduce the multiplicative noise a component of the image is separated linearly in the frequency domain, Homomorphic Filtering technique is used. This technique provides frequency domain procedure to improve the appearance of an image by gray level range compression and contrast enhancement. Textures of the compounds are recorded with polarising microscope connected with hot stage and camera, the illumination and reflectance combined multiplicatively and the image quality is reduced to identify the exact phase in the compound. The compounds with m=3 exhibits NACB phases and m=5 exhibits NACIG, while with a nano dispersion of ZnO exhibits the same phases with reduced clearing temperature as expected when the doping is done with 1% .
Enrichment of OntoSenseNet: Adding a sense-annotated Telugu lexicon

The paper describes the enrichment of OntoSenseNet- a verb-centric lexical resource for Indian Languages. This resource contains a newly developed Telugu-Telugu dictionary. It is important because native speakers can better annotate the senses when both the word and its meaning are in Telugu. Hence efforts are made to develop a soft copy of Telugu dictionary. Our resource also has manually annotated gold standard corpus consisting 8483 verbs, 253 adverbs and 1673 adjectives. Annotations are done by native speakers according to defined annotation guidelines. In this paper, we provide an overview of the annotation procedure and present the validation of our resource through inter-annotator agreement. Concepts of sense-class and sense-type are discussed. Additionally, we discuss the potential of lexical sense-annotated corpora in improving word sense disambiguation (WSD) tasks. Telugu WordNet is crowd-sourced for annotation of individual words in synsets and is compared with the developed sense-annotated lexicon (OntoSenseNet) to examine the improvement. Also, we present a special categorization (spatio-temporal classification) of adjectives.