Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structure of Rv 2118 c : An AdoMet-dependent Methyltransferase from Mycobacterium tuberculosis H 37 Rv

0022-2836/01/010381±11 $35.00/0 Rv2118c belongs to the class of conserved hypothetical proteins from Mycobacterium tuberculosis H37Rv. The crystal structure of Rv2118c in complex with S-adenosyl-L-methionine (AdoMet) has been determined at 1.98 AÊ resolution. The crystallographic asymmetric unit consists of a monomer, but symmetry-related subunits interact extensively, leading to a tetrameric structure. The structure of the monomer can be divided functionally into two domains: the larger catalytic C-terminal domain that binds the cofactor AdoMet and is involved in the transfer of methyl group from AdoMet to the substrate and a smaller N-terminal domain. The structure of the catalytic domain is very similar to that of other AdoMet-dependent methyltransferases. The N-terminal domain is primarily a b-structure with a fold not found in other methyltransferases of known structure. Database searches reveal a conserved family of Rv2118c-like proteins from various organisms. Multiple sequence alignments show several regions of high sequence similarity (motifs) in this family of proteins. Structure analysis and homology to yeast Gcd14p suggest that Rv2118c could be an RNA methyltransferase, but further studies are required to establish its functional role conclusively. # 2001 Academic Press
Progress in Community Child Health

Smoking, socioeconomic status and child health outcomes - the ongoing controversy, N. Spenser and S. Logan 2005 - why some children will continue to have more accidents than others, V. Nanton child health surveillance - the state of the art, K. Billingham special needs registers - dreams and practicalities, M. Blair and T. Hutchison iron deficiency anaemia - to screen or not to screen, F. Childs maternal depression and child health, A. Pound paediatric home care, M. Tatman and D. Lessing continuing medical education in community child health for general practitioners - the Australian experience, F. Oberklaid new approaches to school health, S. Stewart-Brown.
The GTH-LID System for the Albayzin LRE 12 Evaluation

This paper contains a description of the data-sets, systems and fusion alternatives developed by the Speech Technology Group (GTH) for the Albayzin 2012 Language Recognition Evaluation for the 4 conditions: plenty-closed condition (core), plenty-open, empty-closed, and empty-open. In all cases, the primary system is the fusion of three different i-vector based systems: one acoustic system, a phonotactic system using trigrams of phone-posteriorgram counts, and another acoustic system based on RPLP features instead of the traditional MFCC features. For each plenty condition, a contrastive system was also included where the RPLP features or MFCC features where replaced by a different system based on using glottal source features. We provide results for the plenty conditions using the proposed metrics for the evaluation (i.e. Fact, Fdis, and Fcal), as well the known Cavg metric used on NIST evaluations.
The onset of bubble vibration

textabstractUltrasound contrast agents are used in a diagnostic imaging technique called medical ultrasonography. In this technique, ultrasound is applied to visualize tissue in the human body. It is a popular imaging technique due to a number of advantages, it is (1) a real-time modality (routinely 20-30 frames/s or more), (2) inexpensive, equipment is installed worldwide, (3) portable, equipment can be taken to bedside, ambulance or private practice office, (4) safe, e.g. no ionising radiation is necessary and (5) widely applicable, provided that air (lungs) and bone are avoided, all soft tissue can be imaged.
Diet , Body Composition , and Disease on Bone Health

Aim: To review current medical literature regarding the causes and clinical management options for low bone mineral density (BMD) in adult patients with eating disorders. Background: Low bone mineral density is a common complication of eating disorders with potentially lifelong debilitating consequences. Definitive, rigorous guidelines for screening, prevention and management are lacking. This article intends to provide a review of the literature to date and current options for prevention and treatment. Methods: Current, peer-reviewed literature was reviewed, interpreted and summarized. Conclusion: Any patient with lower than average BMD should weight restore and in premenopausal females, spontaneous menses should resume. Adequate vitamin D and calcium supplementation is important. Weight-bearing exercise should be avoided unless cautiously monitored by a treatment team in the setting of weight restoration. If a patient has a Z-score less than expected for age with a high fracture risk or likelihood of ongoing BMD loss, physiologic transdermal estrogen plus oral progesterone, bisphosphonates (alendronate or risedronate) or teriparatide could be considered. Other agents, such as denosumab and testosterone in men, have not been tested in eating-disordered populations and should only be trialed on an empiric basis if there is a high clinical concern for fractures or worsening bone mineral density. A rigorous peer-based approach to establish guidelines for evaluation and management of low bone mineral density is needed in this neglected subspecialty of eating disorders.
Combating Stagnation in Reinforcement Learning Through ‘ Guided Learning ’ With ‘ Taught-Response Memory ’ ?

We present the concept of Guided Learning, which outlines a framework that allows a Reinforcement Learning agent to effectively ‘ask for help’ as it encounters stagnation. Either a human or expert agent supervisor can then optionally ‘guide’ the agent as to how to progress beyond the point of stagnation. This guidance is encoded in a novel way using a separately trained neural network referred to as a ‘Taught Response Memory’ that can be recalled when another ‘similar’ situation arises in the future. This paper shows how Guided Learning is algorithm independent and can be applied in any Reinforcement Learning context. Our results achieved superior performance over the agents non-guided counterpart with minimal guidance, achieving, on average, increases of 136% and 112% in the rate of progression of the champion and average genomes respectively. This is due to the fact that Guided Learning allows the agent to exploit more information and thus, the agent’s need for exploration is reduced.
A Wide Ranging Comparison of Routing Protocols in Wireless Sensor Network

Topical advances in the field of designing a micro-sensor units lead to design of several novel protocols exclusively for various applications wireless sensor network (WSN). WSN with huge number of sensor nodes used to congregate information from remote location may be an unreached area and then transmits the gathered data to a sink node, which depends on the application being used. Sensor nodes used have limitation in terms of energy expenditure, storage ability and computation. Routing protocol provides efficient route for data to travel from one node to the other. Such passing and processing of information can be distributed, centralized or local. In this paper, detail comparison of diverse routing protocols based on different parameters in different types of challenges is discussed along with constrains in designing a particular routing protocol. Suggestion on suitable routing protocol for specific WSN application is also provided in such comparison.
Supplemental MaterialsS.1 Distribution of indels of different lengths among introns (Table S1

Since long indels are on average more parsimony consistent than short indels, it might therefore seem desirable to use only long indels in phylogenetic analyses. However,we show here that there are too few long indels to produce a sufficient number of well resolved gene trees needed for coalescent analysis. We grouped indels in nested length categories, and report their numbers per intron as well as the number of introns represented by each category (Table S1). Although there are a total of 141,375 intron indels >50bp in length in our dataset, they are spread unequally among 2,452 loci, only 24% of indels are parsimony informative, and they are distributed among lineages in proportion to branch length. Ergo, there are very few, if any, longer indels in the deep short branches of most gene trees. We calculated Bootstrap Support (BS) on Maximum Likelihood (ML) trees using concatenated data in each of the nested length categories (Figure S1). ML trees were calculated using the BINGAMMA model in RAxML [1] starting from 1 (all indels and >1bp indel length categories) to 10 randomized MP trees (all other length categories), depending on computational limitations in relation to dataset size. The number of bootstrap replications was determined by the extended majority-rule boot-stopping criterion in RAxML (50–800 replications for indel classes >10bp), or truncated manually for the larger datasets of more inclusive indel length categories. Not surprisingly, mean nodal BS support is lower in trees generated using longer indel categories due to the relative dearth of long indels.
Assessment Models for the West Greenland Shrimp Stock Using a Bayesian Approach. First Results

This paper presents first results of a Bayesian approach to shrimp stock assessments. Non-age structured models based on the logistic function with and without an explicit term for cod predation, is used to describe shrimp population dynamics. Biomass indices from survey and standardised commercial catch-per-unit -effort series, catch, cod stock size estimates and prior estimates of model parameters provided information to the models. The inadequacy of a model to fully describe population behaviour and the inevitable errors associated with the observed data series, i.e. observation and process error, was incorporated simultaneously using a state-space modelling framework. The models can provide posterior probability distributions of management related parameters as desired. E.g. the model predicts that in the absence of cod predation a fishery of 100 000 tons annually will have 75% probability of being below ‘Maximum sustainable yield’ – or 25% risk of being above. Introduction Annual landings of northern shrimp (Pandalus borealis) in the North Atlantic have increased from about 100000 tons in the early 1980s to more than 350000 tons in 2000 (Skúladóttir, pers. com.). Although shrimp has become one of the most important target species in these waters, little progress has been made in developing a standardised predictive tool for stock assessment (cf. Stefánsson et al., 1994; Cadrin and Clark, 1999; Savard et al., 1991; Hvingel and Kingsley, 2000; Anon., 2000a). Management advice for most shrimp stocks in the North-west Atlantic is formulated by qualitative assessment of recent trends in biomass indices, in the size composition of the stock, and in the catch history (Anon., 2000b; ref Can. assessment etc.), and by a qualitative evaluation of the short-term prospects for recruitment. Advice is given as a Total Allowable Catch (TAC) one year ahead as set by consensus of the assessment board. The method of arriving at a certain TAC value is not explicitly stated and the uncertainty associated with the process is not quantified. Such methods lack predictive rigour, including formal statements of uncertainty, and are therefore unable to satisfy increasing demands for longer-term predictions and for quantitative comparisons between alternative management options. A quantitative assessment may be reached through construction of mathematical models describing stock dynamics and their links to collected data and ancillary information. Each model represents one hypothesis about "the state of nature". From the infinite collection of possible models a subset of the most plausible may be chosen based on expert knowledge. An integrated evaluation of inferences about management options from that subset may be
Performing Identity: Differences between Native and Nonnative Speakers of English in Gatekeeping Encounters

The current study investigates how native and nonnative speakers of English applying for teaching positions performed their identities in job interviews. The data included two teacher job interviews; one was with a native speaker of English, and the other was with a nonnative speaker. Both interviews were transcribed and analyzed in accordance with Pomerantz and Fehr’s (1997) conversation analysis framework and Gee’s (2000) identity framework. Results indicated that miscommunication, feelings of a lack of experience compared to westerners, and unsuccessful co-membership affected the identity performance of the nonnative speaking candidate. The identity performance of the native speaking candidate was characterized by the absence of miscommunication and successful co-membership. The paper recommends that nonnative speaking teachers of English be exposed to the pragmatics of interviews through direct instructions in teacher preparation and professional development programs. This will help in increasing their chances of successful identity performance in teacher job interviews and other forms of gatekeeping encounters.
Modelling Radiative Exchange in a Vegetated Urban Street Canyon Model

One of the key findings of the recent International Urban Energy Balance Models Comparison Project (PILPSurban) was that models do not capture the magnitude and temporal variability of the latent heat flux relative to observations. This is despite many of the schemes including a vegetation component, which is typically represented by separate vegetation tiles or, in a limited number of models, explicitly within the urban scheme. The inability to reproduce the latent heat flux suggests that many schemes do not accurately represent urban vegetation and do not account for the impact of urban surfaces on vegetation physiology. PILPS-urban did however suggest that there was an advantage in using an integrated vegetation scheme as the range in performances of models using the separate tile was larger. This raises the following question; can we improve model accuracy of urban moisture fluxes by including vegetation explicitly within an urban land surface scheme? To address this question an integrated vegetation scheme is being developed for the Met Office – Reading Urban Surface Exchange Scheme (MORUSES) to explicitly include vegetation in the form of urban trees and natural surfaces (e.g. grass). The new vegetation scheme will be tested within a 2D infinitely long street canyon, with the aim of improving urban weather forecasts and to provide a tool to test the mitigation of extreme heat events through urban greening. This study presents the theory and initial results for the first aspect of the new scheme, radiative exchange within a vegetated urban street canyon. An analytical method was developed and applied to determine the view factors for calculation of the longwave radiation budget between the surfaces within a nonturbulent street canyon, with a range of aspect ratios, containing a representation of an urban street tree. Unlike previous methods for modelling radiative exchange, which often assume that the wall and road surface have the same equilibrium temperature, this work investigates the non-trivial radiative exchange problem of vegetated (tree and grass) and urban surfaces that are likely not to be in equilibrium due to the impact of vegetation physiology on canopy temperature.
Accelerated and Accurate Question Answering

To train a model that could have good performance on the SQuAD 2.0 dataset by developing non-PCE model, we combine GloVe embedding and char-CNN embedding and build our model based on BiDAF with Self-Attention. The stretch goal we propose is to improve the running efficiency of our model, we use SRU, an advanced RNN cell, to parallel our computations. At the time of submission, our EM and F1 scores on the dev set are 68.53 and 71.46.
University of Southern Denmark Gestational diabetes and offspring birth size at elevated environmental pollutant exposures Valvi,

• You may download this work for personal use only. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying this open access version If you believe that this document breaches copyright please contact us providing details and we will investigate your claim. Please direct all enquiries to puresupport@bib.sdu. dk
Microseismic event analysis in conjunction with stimulation treatments at the geothermal research well GtGrSk4/05 in Groß Schönebeck/Germany

The technical feasibility of geothermal power production in a low enthalpy environment will be investigated in the geothermal site at Groß Schönebeck, North German Basin, where a borehole doublet was completed in 2007. In order to complete the Enhanced Geothermal System, three massive hydraulic stimulations were performed. To monitor injection-induced seismicity during fluid injection a seismic network was deployed including a single 3-component downhole seismic sensor at only 500 m distance to the injection point. Injection rates reached up to 9 m/min and maximum injection well-head pressure was as high as ~60 MPa. A total of 80 very small (-1.8 <MW< -1.0) induced seismic events were detected only at the deep borehole sensor. The hypocenters were determined for 29 events using P and S wave onset times and polarization analysis. The events show a strong spatial and temporal clustering and a maximum seismicity rate of 22 events per day. Spectral parameters were
A 3 D Numerical Study of Interface Effects Influencing Viscous Gravity Currents in a Parabolic Fissure , with Implications for Modeling with 1 D Nonlinear Diffusion Equations

Although one-dimensional non-linear diffusion equations are commonly used to model flow dynamics in aquifers and fissures, they disregard multiple effects of real-life flows. Similarity analysis may allow further analytical reduction of these equations, but it is often difficult to provide applicable initial and boundary conditions in practice, or know the magnitude of effects neglected by the 1D model. Furthermore, when multiple simplifying assumptions are made, the sources of discrepancy between modeled and observed data are difficult to identify. We derive one such model of viscous flow in a parabolic fissure from first principals. The parabolic fissure is formed by extruding an upward opening parabola in a horizontal direction. In this setting, permeability is a power law function of height, resulting in a generalized Boussinesq equation. To gauge the effects neglected by this model, 3D Navier-Stokes multiphase flow simulations are conducted for the same geometry. Parameter variations are performed to assess the nature of errors induced by applying the 1D model to a realistic scenario, where the initial and boundary conditions can not be matched exactly. Numerical simulations reveal an undercutting effect observed in laboratory experiments, but not modeled when the Dupuit-Forchheimer assumption is applied. By selectively controlling the effects placed on the free surface in 3D simulations, we are able to demonstrate that free surface slope is the primary driver of the undercutting effect. A consistent lag and overshoot flow regime is observed in the 3D simulations as compared to the 1D model, based on the choice of initial condition. This implies that the undercutting effect is partially induced by the initial condition. Additionally, the presented numerical evidence shows that some of the flow behavior unaccounted for in the 1D model scales with the 1D model parameters.
Evaluation of anti-in lammatory activity of Jasminum sessili lorum extracts

Medicinal plants are important resources for the development of novel antiin lammatory agents. Synthetic anti-in lammatory drugs have several adverse effects. Medicinal plants have numerous bioactive phytoconstituents that are safer as well as better substitutes for the prevention and management of various diseases and disorders. The ethanolic and ethyl acetate extracts of Jasminum sessili lorum were evaluated for their potential as anti-in lammatory agents in vivo by inducing paw edema in rats using carrageenan. The antiin lammatory activity of the reference drug was compared with the extracts of Jasminum sessili lorum. The extracts on screening indicated the presence of phyto-constituents such as phenolics, terpenoids, lavonoids, alkaloids, and saponins. The study established signi icant anti-in lammatory nature of the Jasminum sessili lorum extracts in a manner which is dose-dependent. The results indicate that both the extracts of Jasminum sessili lorum possess antiin lammatory activity of signi icance and can be used in the development for novel anti-in lammatory moieties.
Automatic Extraction of Textbook Glossaries Using Deep Learning

Inquire is a research project at Stanford University to design an "intelligent" biology textbook that allows for more advanced interactions with the text by students. Currently, a knowledge base supporting this functionality must be extracted manually, which is prohibitively time-consuming. In this project, we focused on an important initial approximation of the full knowledge base extraction problem: automatically extracting glossaries from a textbook. We scraped a new dataset for this task from open source science textbooks and achieved a corrected F1 score of 0.74 for extracting glossary terms and an F1 score of 0.47 for extracting glossary term definitions. Though these scores are not immediately usable, our work has provided a useful foundation for future work on the Inquire project.
A fibrous stromal component in hepatocellular carcinoma reveals a cholangiocarcinoma-like gene expression trait and EMT

Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC) are the major primary liver cancers in adults. The phenotypic overlap between HCC and CC has been shown to comprise a continuous liver cancer spectrum. As a proof of this concept, a recent study demonstrated a genomic subtype of HCC that expressed CC-like gene expression traits such as CC-like HCC, which revealed the common genomic trait of stem cell-like properties and aggressive clinical outcomes. Scirrhous HCC (S-HCC), a rare variant of HCC, is characterized by abundant fibrous stroma and has been known to express several liver stem/progenitor cell markers. This suggests that S-HCC may harbor common intermediate traits between HCC and CC including stem cell traits, which are similar to those of CC-like HCC. However, the molecular and pathological characteristics of S-HCC have not been fully evaluated. By performing gene expression profiling and immunohistochemical evaluation, we compared the morphological and molecular features of S-HCC with those of CC and HCC. S-HCC expresses both CC-like and stem cell-like genomic traits. In addition, we observed the expression of core epithelial-mesenchymal transition (EMT)-related genes, which may contribute to the aggressive behavior of S-HCC. Over-expression of transforming growth factor β (TGF-β) signaling was also found, implying its regulatory role in the pathobiology of S-HCC. Conclusion: We suggest that the fibrous stromal component in HCC may contribute to the acquisition of CC-like gene expression traits in HCC. The expression of stem cell-like traits and TGF-β/EMT molecules may play a pivotal role in the aggressive phenotyping of SHCC. INTRODUCTION Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC) are the major primary liver cancers in adults. Most HCCs and CCs are derived from hepatocytes and cholangiocytes, respectively. Both hepatocytes and cholangiocytes originate from common liver stem cells with the potential to differentiate into both types of cells (1-2). Thus, the primary liver cancers that arise from different developmental stages of liver stem cells are thought to harbor common genomic traits between HCC and CC. The existence of combined Page 4 of 38 Hepatology Hepatology