Miracle-dz/UniFAR-FTUs huggingface dataset:
enhanced Reference Guided Assembly of Complex Genomes

de novo assembly using NGS data have been proposed. Among the most popular, we mention SOAPdenovo [6] and ABySS [7] (see [8] for an updated list). The assemblies produced by tools designed for NGS data are, in general, not comparable in quality with the assemblies produced by instruments like Arachne [9] and those designed for capillary sequencing data. The reason for this is that while, with NGS instruments, coverage is no more a bottleneck, read length, as well as the reduced size of the insertion between paired reads, makes correct assembly and positioning of repeats much more of an issue. De novo assembly with short reads is still very difficult [5] and, when assembling complex and repeated genomes, reasonably conservative de novo assembly programs are likely to produce collections of highly fragmented contigs. An interesting strategy to improve de novo assemblies has been termed “assembly reconciliation”. The goal of assembly reconciliation is to merge the assemblies produced by different tools and to detect possible mis-assemblies [10]. The number of organisms whose genomes have been completely sequenced has been increasing rapidly each year and, for this reason, it is becoming viable to sequence an organism and then to align the sequence against a closely related genome. This strategy goes by the name of Reference Guided Assembly (RGA), its main advantage being the fact that, in general, even low coverage is sufficient to yield useful results. RGA consists of two phases: first, all the reads are aligned against the reference genome; then, a consensus sequence is extrapolated. Everywhere the coverage drops to zero, a sequence of Ns is placed. This problem has already been studied in the context of Sanger sequencing. In [11] and [12], two methods were proposed that use reference sequences to assist the assembly of new organisms. The challenge is becoming even more interesting with the advent of next generation sequencers, beginning with the technicalities and the practical considerations involved in the alignment phase. As a matter of fact, many tools capable of rapidly aligning millions of short reads against a reference genome have been proposed recently. Tools like SOAP2 [13] and rNA [14] are essential for performing reference-guided assembly. The main problem with RGA and NGS is that (essentially for efficiency reasons) mapping ale-RGA: enhanced Reference Guided Assembly of Complex Genomes
Primary evaluation of selected steroid containing herbs for their corticoid potential in rats by Freund ’ s adjuvant arthritis

499 Abstract: Many pharmacologic activities of steroid containing plants like Wildyam, Kanthkari, Agave spices, Indian Sarsaparilla and Fenugreek have been reported. In order to find a safer alternate steroid treatment for management of various ailments, we have resolved to investigate corticoid potential of herbal steroids by freund’s adjuvant arthritis. Anti-inflammatory compounds do not inhibit secondary lesions, which are prevented or diminished by immunosuppressive agents and both anti-inflammatory and Immunomodulatory action suggest test drug’s corticoid potential. In present study Albino Wistar Male rats with an initial body weight of 150 to 200 g was injected into the sub plantar region of the left hind paw with 0.1 ml of heat-killed Mycobacterium tuberculosis (H37Ra) suspended in incomplete freund’s adjuvant (4mg/ml). All ethanolic extract of test drugs Trigonella foenum graecum (ETF), Dioscorea alata (EDA), Hemidesmus indicus (EHI), Agave americana (EAA) and Solanum xanthocarpum (ESX) 300mg/kg per rat and the standard (Hydrocortisone-Primacort200) 10 mg per rat administered orally for 12 days. Purposely, from day 13 to 21, the animals received neither test compound nor the standard. Paw volumes of both sides and body weight were recorded on the day of injection, day 5, day 12, day 17 and day 21 whereby paw volume is measured plethysmographically. The severity of the secondary lesions on day 12 is evaluated visually and graded according scheme. The %inhibition of paw volume and suppression of arthritic lesion on day 21 for HC, EHI, EAA and ESX found highly significant while ETF and EDA showed significant result (p<0.05).
Estimating rock compressive strength from Rock Abrasion Tool (RAT) grinds

Each Mars Exploration Rover carries a Rock Abrasion Tool (RAT) whose intended use was to abrade the outer surfaces of rocks to expose more pristine material. Motor currents drawn by the RAT motors are related to the strength and hardness of rock surfaces undergoing abrasion, and these data can be used to infer more about a target rock's physical properties. However, no calibration of the RAT exists. Here, we attempt to derive an empirical correlation using an assemblage of terrestrial rocks and apply this correlation to data returned by the rover Spirit. The results demonstrate a positive correlation between rock strength and RAT grind energy for rocks with compressive strengths less than about 150 MPa, a category that includes all but the strongest intact rocks. Applying this correlation to rocks abraded by Spirit's RAT, the results indicate a large divide in strength between more competent basaltic rocks encountered in the plains of Gusev crater (Adirondack‐class rocks) and the weaker variety of rock types measured in the Columbia Hills. Adirondack‐class rocks have estimated compressive strengths in the range of 70–130 MPa and are significantly less strong than fresh terrestrial basalts; this may be indicative of a degree of weathering‐induced weakening. Rock types in the Columbia Hills (Wishstone, Watchtower, Clovis, and Peace class) all have compressive strengths <50 MPa and are consistent with impactites or volcanoclastic materials. In general, when considered alongside chemical, spectral, and rock textural data, these inferred compressive strength results help inform our understanding of rock origins and modification history.
Assessment of Forest Aboveground Biomass Stocks and Dynamics with Inventory Data, Remotely Sensed Imagery and Geostatistics

Several issues, related with forest fires, forest disturbances (Garcia-Martin et al., 2008), forest productivity (Chirici et al., 2007; Palmer et al., 2009), forest changes over time (Hu & Wang, 2008), or the role of forests in the global carbon balance cycle (Hese et al., 2005) are, nowadays, the focus of numerous studies and investigations. All these subjects demand the knowledge about aboveground biomass (AGB) stocks and/or its dynamics. Besides the availability of biomass, the information about the growth of forests is of increasing importance. This variable, which is related with the total biomass growth in a specific ecosystem, is called Net Primary Production (NPP). Annual NPP represents the net amount of carbon captured by plants through photosynthesis each year (Melillo et al., 1993; Cao & Woodward, 1998). In practice, NPP can be defined and measured in terms of either biomass or CO2 exchange (Field et al., 1995). Waring et al. (1998) define NPP as the sum of live biomass periodic increment (ΔB) and dead biomass (losses, e.g. broken branches, fallen leaves) [NPP = ΔB + losses]. NPP is an important ecological variable due to its relevance for accurate ecosystem management and for monitoring the impact of human activity on ecosystems vegetation at a range of spatial scales: local, regional and global (Melillo et al., 1993). It is one of the most complete and complex variables, since it reflects the growth of the entire ecosystem thus avoiding the analysis of only part of its components. NPP provides a complete view of the ecosystem including information, not only from the arboreal stratum, but also from the shrubs and all the litter produced from each stratum. Thus, the significance of NPP not only reflects the complexity of its measurement or estimation, but also its integrative ecological perspective ecosystems. Mapping AGB stocks or NPP with the utmost accuracy and expedite methodologies is therefore a challenge. The need of continuous maps where the phenomenon under study can be individually analysed or used as auxiliary variable in a specific model requires that the spatial predictions are represented in the most accurate way. Over the years different spatial prediction methods have been explored in diverse data type (Isaaks & Srivastava, 1989; Goovaerts, 1997; Labrecque et al., 2006; Sales et al., 2007; Meng et al., 2009). Some approaches have a simple application methodology however others are sometimes complex in what concerns to their implementation, or the selection of the variables to be used.
Economic Incentives of the Olympic Games

We provide a game-theoretic analysis of countries strategic allocations of resources among different sports and athletes performance at the Olympic Games. Individuals face opportunity costs of spending efforts and countries maximize their expected number of medals. We suggest several proxy variables for country-specific costs and test the predictions of the model using the summer Olympic Games data for 1960-2004.
Interactive Simulation Software for MultiRegional Model of Freight Transportation

The paper develops a know mathematical model of multiregional flows of goods. We determine the most probable spatial distribution of flows. Transportation costs depend on the distance between the regions within the “gravity model” approach. We use the shortest way length in a transportation network as a measure of these distances. The underlying mathematics of the model is a convex mathematical programming. The problem is represented as nonlinear minimization of a function with linear constraints which is solved numerically. Developed software is implemented for interactive modeling and visualization of the problem solution. The code is implemented on a high-performance cloudserver platform and consist of modules for simulation, visualization and control. Asynchronous http-queries are used for interaction between the platforms. For the data exchange between these modules a declarative model in the JSON format is implemented. The paper demonstrates a practical problem solution for the gasoline freight transportation for Pacific Russia region and the simulation software usage.
Hydraulic Properties and Microgeometry Evolution Accompanying Limestone Dissolution by Acidic Water

A reactive flow-through experiment by carbon dioxide-saturated water at the partial pressure of 0.1 MPa and room temperature was conducted on a porous limestone in order to identify the relationships between fluid chemistry, hydrodynamics and structural properties. Periodic imaging by non destructive X-ray microtomography allowed following the evolution of the core micro-geometry and fluid-rock interface in detail while its porosity and permeability increased due to dissolution. Several mechanisms were successively involved in the rapid permeability increase. Early in the experiment, the permeability increase was related to concomitant particle dissolution and displacement. Later on, permeability continued to rise due to solid-fluid interface smoothing and to pore connectivity increase.
Serum Omentin-1 Concentrations and Biochemical Markers of Chronic Subclinical Inflammation in Obese Subjects

C l i n M e d International Library Citation: Alissa EM, Al-Salmi MM, Alama N, Ferns GA (2015) Serum Omentin-1 Concentrations and Biochemical Markers of Chronic Subclinical Inflammation in Obese Subjects. Int J Clin Cardiol 2:061 Received: September 17, 2015: Accepted: November 18, 2015: Published: November 21, 2015 Copyright: © 2015 Alissa EM, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Alissa et al. Int J Clin Cardiol 2015, 2:6 ISSN: 2378-2951
Balancing Costs and Patients' Health: Dental Students’ Perception of Economics in Dentistry

One aim of higher education is to develop professional identities in students to equip them for future working life. Health professional students will work under financial pressures in a market-based environment, which can lead to conflicts with professional ethical values. This study explores how Swedish dental students perceive economic aspects of dentistry. The article is based on a study of undergraduate research projects. In the analysis of the projects, two themes were identified: (1) cost-effective organizing of dentistry and (2) costs and benefits of interventions. The students displayed socially responsible values by emphasizing the need for dentists to utilize resources effectively, which implies that professional education can support the development of the perception that economic values can be compatible with professional ethical values. Keywords : cost-effectiveness, ethics, healthcare, higher education, social responsibility
A Modified TV Tuner for Spectrum Sensing in TV UHF Bands

A novel system containing low cost TV box has been designed to sense the UHF TV band spectrum. Microcontroller chip is programmed using micro Pascal software to control the TV tuner for scanning the TV band. The implemented system has been used to measure the utilization of the UHF TV band covering the frequency range from 470 to 860 MHz in Cairo (EGYPT). The sensing output data has been recorded and analyzed using suitable software. The obtained results demonstrate significant amount of spectrum available for deployment of cognitive radio systems and IEEE 802.22 WRAN standard in the UHF TV broadcasting band General Terms A new methodology for detecting UHF TV broadcasting band, TV tuner, UHF TV Spectrum usage.
Uncertainties in seawater thermometry deriving from intratest and intertest Mg/Ca variability in Globigerinoides ruber

intertest Mg/Ca variability within these deep-sea core top samples is a source of significant uncertainty in Mg/Ca seawater temperature estimates and is notable for being site specific. Our results indicate that widely assumed uncertainties in Mg/Ca thermometry may be underestimated. We show that statistical power analysis can be used to evaluate the number of tests needed to achieve a target level of uncertainty on a sample by sample case. A varying bias also arises from the presence and varying mix of two morphotypes (G. ruber ruber and G. ruber pyramidalis), which have different mean Mg/Ca values. Estimated calcification temperature differences between these morphotypes range up to 5C and are notable for correlating with the seasonal range in seawater temperature at different sites.
GaIn: Human Gait Inference for Lower Limbic Prostheses for Patients Suffering from Double Trans-Femoral Amputation

Several studies have analyzed human gait data obtained from inertial gyroscope and accelerometer sensors mounted on different parts of the body. In this article, we take a step further in gait analysis and provide a methodology for predicting the movements of the legs, which can be applied in prosthesis to imitate the missing part of the leg in walking. In particular, we propose a method, called GaIn, to control non-invasive, robotic, prosthetic legs. GaIn can infer the movements of both missing shanks and feet for humans suffering from double trans-femoral amputation using biologically inspired recurrent neural networks. Predictions are performed for casual walking related activities such as walking, taking stairs, and running based on thigh movement. In our experimental tests, GaIn achieved a 4.55° prediction error for shank movements on average. However, a patient’s intention to stand up and sit down cannot be inferred from thigh movements. In fact, intention causes thigh movements while the shanks and feet remain roughly still. The GaIn system can be triggered by thigh muscle activities measured with electromyography (EMG) sensors to make robotic prosthetic legs perform standing up and sitting down actions. The GaIn system has low prediction latency and is fast and computationally inexpensive to be deployed on mobile platforms and portable devices.
Thermomonas haemolytica gen. nov., sp. nov., a γ-proteobacterium from kaolin slurry

Four aerobic, Gram-negative bacterial strains isolated from kaolin slurry used in the production of paper were subjected to a polyphasic analysis and characterization to determine their taxonomic position. Analysis of the 16S rDNA sequences of the four strains revealed that they represent a new lineage within the γ-Proteobacteria, related to the genera Xanthomonas, Pseudoxanthomonas, Stenotrophomonas, Luteimonas, Xylella and Rhodanobacter. Analysis of the quinone system, the polyamines, the fatty acids and the polar lipids revealed a combination of characteristics that is unique and not described for the phylogenetic relatives. The four strains contain a ubiquinone Q-8, spermidine as the major polyamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the predominant polar lipids, and a fatty acid profile with predominantly iso-branched fatty acids. The GMC content of the genomic DNA was determined to be within the narrow range 67<1–68<7 mol%. Determination of DNA relatedness, as well as riboprint band patterns and amplified fragment length polymorphism profiles, clearly demonstrated that the four strains are members of a single species. Antibiotic-susceptibility patterns were identical for the four strains. Although showing a high degree of similarites in physiological and biochemical patterns, each of the four strains could be distinguished from the others on the basis of a few biochemical characteristics. On the basis of the estimates of phylogenetic relationships derived from the 16S rDNA sequence analyses, the observed chemotaxonomic characteristics and other phenotypic traits, a new genus, Thermomonas gen. nov., and species, Thermomonas haemolytica sp. nov., are proposed for the strains A50-7-3T ( ̄DSM 13605T ̄LMG 19653T), B 50-7-1 ( ̄DSM 13598 ̄LMG 19655), D50-7-1 ( ̄DSM 13610 ̄LMG 19656) and B50-8-1 ( ̄DSM 13599 ̄LMG 19654), with strain A50-7-3T as the type strain.
Nonlinear Optical Crystals Designed with 4-Nitrophenolate Chromophores: An Engineering Route using a Multidipolar Chromophore, 3-Hydroxy-2,4,6-Trinitrophenolate

Abstract 4-Nitrophenol derivatives are interesting chromophores for nonlinear optics (NLO), being typical donor-acceptor system connected by π conjugation. Due to the presence of the acidic phenolic proton, they also readily form salts with suitably selected organic and metallic bases. The so-formed 4-nitrophenolates have increased molecular hyperpolarizabilities (β). The phenolate and nitro oxygens are strong hydrogen bond acceptors and the nitro group has a tendency to coordinate with metal centers. This opens up two different engineering routes to build NLO materials from these chromophores: (a) organic-organic and (b) metal-organic salts. This paper reviews the crystal packing and nonlinear optical (NLO) efficiency in nitrophenolate crystals engineered through these routes and presents the crystal structure of a new NLO efficient organic-organic salt, 1-hydroxy-4-methylpyridinium 3-hydroxy-2,4,6-trinitrophenolate (P21). In this crystal both the multidipolar anion and dipolar cation are NLO chromophores. The anions form herringbone mediated chain with intra and intermolecular O-H…O hydrogen bonds and the cations are attached to them through strong O-H…O− hydrogen bonds.
Latest inflation model constraints from cosmic microwave background measurements : Addendum

In this addendum to Phys. Rev. D 74, 023502 (2006), we present an update of cosmological constraints on single-field inflation in light of the Wilkinson Microwave Ansiotropy Probe satellite mission five-year results (WMAP5). We find that the cosmic microwave background data are quite consistent with a Harrison-Zel'dovich primordial spectrum with no running and zero tensor amplitude. We find that the three main conclusions of our analysis of the WMAP three-year data (WMAP3) are consistent with the WMAP5 data: (1) the Harrison-Zel'dovich model is within the 95% confidence level contours; (2) there is no evidence for running of the spectral index of scalar perturbations; (3) from the WMAP 5 data alone, potentials of the form V{proportional_to}{phi}{sup p} are consistent with the data for p=2 and are ruled out for p=4. Furthermore, consistent with our WMAP3 analysis, we find no evidence for primordial tensor perturbations, this time with a 95% confidence upper limit of r<0.4 for the WMAP5 data alone, and r<0.35 for the WMAP5 data taken in combination with the Arcminute Cosmology Bolometer Array (ACBAR)
The effect of coriander seed (Coriandrum sativum L.) as diet ingredient on the performance of Japanese quail

This study was conducted to determine the potential of coriander seed as a natural growth promoting substance in quail nutrition. Five hundred and ninety four 3-day old Japanese quails were divided into six groups of 99 birds each and randomly assigned to six treatment diets. Four of the diets contained coriander seed at 0.5%, 1%, 2% or 4% levels of inclusion, one contained 10 mg of the antibiotic, avilamycin, per kg and a control group received no supplement. Effects on feed intake, daily live weight gain, feed conversion ratio and carcass characteristics of the birds were measured over a period of 42 days. After 42 days the highest feed intake was observed in the 4% coriander group. Birds receiving the diet containing 2% coriander seed showed the highest weight gain, followed by those receiving the diets containing 1% coriander seed, the antibiotic, the 4% and the 0.5% coriander seed. The control had the lowest weight gain. The feed conversion ratio over the experimental period was significantly better in the group receiving 2% coriander seed than in the other treatments. The highest carcass yield and liver weights were also recorded in the 2% coriander group, while the lowest abdominal fat percentages were present in the 1%, 2% and 4% coriander groups. These results suggested that coriander seeds could be considered a potential natural growth promoter for poultry, and showed the best responses at a 2% level of inclusion.
The Science behind Weaning from Mechanical Ventilation

Weaning from mechanical ventilation is defi ned as the transition from the ventilatory dependence of the patient to a spontaneous breathing status. Recognizing when a patient is ready to be weaned from mechanical ventilation is greatly infl uences the outcome, and may prevent compromising a patient. Weaning indices were developed to help the physician predict the outcome of weaning trials, a common concern in the intensive care unit (ICU) setting. Many physiological mechanisms explain the
FAMILY CONSTELLATIONS OF THE PARTNERS IN DIVORCED AND MARRIED COUPLES

The general hypothesis has been advanced and tested previously by the writer that later extra-familial relationships have a better chance of happiness and lasting success, the more closely they duplicate the partners' early intra-familial relationships (1-5). Factors of the early relationship with which we have been concerned are birthorder rank, sex distribution of the siblings, and decimation of the family through loss. The present study continues this research by comparing marriages that end in divorce with those that last and are therefore assumed to be the happier. Three specific hypotheses are examined: In divorced couples, (a) older siblings are married more frequently to older siblings and younger siblings to younger siblings; (b) a larger number of partners come from like-sexed sibling configurations; (c) early loss of family members is more prevalent. The underlying assumptions for these hypotheses are, other things being equal: (a) The optimal situation is one in which partners are unlikely to get into conflict over their seniority rights, etc. (b) Individuals having opposite-sex siblings are used to the other sex, and have less difficulty accepting the woman or man who is their marriage partner. (c) The death of a parent or sibling makes an individual slightly more ready to discontinue relationships of his own accord, or to choose, in the first place, those that would not last.