Miracle-dz/UniFAR-FTUs huggingface dataset:
Water use and bioenergy potential of subtropical Poaceace species as second generation field crops

i DECLARATION ii ACKNOWLEDGEMENTS 3 LIST OF FIGURES 7 LIST OF TABLES 11 LIST OF ABBREVIATIONS 14 LIST OF UNITS 16 CHAPTER 1 17 GENERAL INTRODUCTION 17 CHAPTER 2 19 LITERATURE REVIEW 19 2.1 Fossil fuels 19 2.2 Energy: current consumption and predictions of future requirements 21 2.3 The gravity of the fossil fuel dilemma 21 2.4 Substituting fossil fuels 23 2.5 Alternative energy forms and sources 23 2.5. 1 Bioenergy: problems and solutions 24 2.5. 2 Bioenergy – a maturing field 27 2.6 Righting the wrongs of energy consumption and production 29 2.7 Important attributes of a bioenergy crop 29 2.8 Currently used feedstocks 30 2.8. 1 First generation feedstocks 31 2.8. 2 Second and third generation feedstocks 32 2.9 Species assessed in this study 37 2.9. 1 First generation feedstocks 37 2.9. 2 Second generation feedstocks 39 2.10 Species summary 43 CHAPTER 3 44 MATERIALS AND METHODS 45 3.1 Site specifications and information 45 3.2 Trial design and layout 45 3.3 Selected trial species 47
Spondyloarthritis Research Consortium of Canada magnetic resonance imaging index for assessment of spinal inflammation in ankylosing spondylitis.

OBJECTIVE To develop a feasible magnetic resonance imaging (MRI)-based scoring system for spinal inflammation in patients with spondylarthropathy that requires minimal scan time, does not require contrast enhancement, evaluates the extent of lesions in 3 dimensional planes, and limits the number of vertebral levels that are scored because MRI demonstrates characteristic inflammatory lesions in the spine of patients with ankylosing spondylitis (AS) prior to the development of typical features on plain radiographic. METHODS Our scoring method was based entirely on the assessment of increased signal denoting bone marrow edema on T2-weighted STIR sequences. Blinded MRI films were assessed in random order at 2 sites by 3 blinded readers at each of the 2 sites (the Universities of Alberta and Toronto). Intra- and interreader reliability was assessed by intraclass correlation coefficient. The 24-week response of patients with AS randomized to infliximab:placebo (8:3) was assessed by effect size and standardized response mean. RESULTS An initial analysis of all discovertebral units (DVUs) in the spine of 11 patients demonstrated a mean of 3.2 (95% confidence interval 3.2, 5.2) affected units, while limiting the scoring to a maximum of 6 units captured most of the affected units. We scanned 11 patients with AS with clinically active disease and 20 additional patients randomized to a 24-week trial of either infliximab or placebo. Intraobserver reproducibility for the 6-DVU STIR score ranged from 0.93 to 0.98 (P < 0.0001). Interobserver reproducibility of scores by readers from both sites was 0.79 (P < 0.0001) for status score and 0.82 (P < 0.0001) for change score. Analysis of pretreatment and posttreatment scores for all 20 patients randomized to infliximab/placebo showed a large degree of responsiveness (standardized response mean = 0.87). Reproducibility and responsiveness were only slightly improved by using contrast enhancement with gadolinium diethylenetriaminepentaacetic acid. CONCLUSION The Spondyloarthritis Research Consortium of Canada MRI index is a feasible, reproducible, and responsive index for measuring spinal inflammation in AS.
Panorama Sketching for PDAs

We present a sketch-based system for creating and modifying 3D scenes on mobile devices (PDAs). The user models the scene by sketching a panoramic image. The process of 2D sketching is aided by underlying simplified 3D model of the scene. The 3D model provides additional information to the system, allowing 3D-like transformations of the scene objects and automatic shading. The user either creates the 3D model by sketching, or uses an existing one. This turns the PDA into a portable 3D notepad, useful especially for 3D scene designers. Compared to existing methods for panoramic sketching, our method is optimised for use on PDAs. Problems with low resolution of PDA screens, low data transfer rates and specific interaction methods are addressed. Limited camera movement enforced by the panorama becomes an advantage, as it helps the users to navigate easier in the scene.
Renaissances and current trends with electrochemical sensors and biosensors

were developed (e.g., differential pulse voltammetry) on one hand in combination with stripping analysis on the other. During that period an immense number of publications appeared dealing mainly with the determination of the four “classical” metals easily accessible by inverse voltammetry on mercury electrodes, i.e., Zn, Cd, Pb and Cu. Along with such prosperity in voltammetry also potentiometry slipped into its golden age with the development of new ion selective membranes for many of the elements of the periodic system. In the nineteen eighties a second renaissance could be noticed due to the chemical modification of amperometric electrodes. Whereas the use of mercury electrodes decreased new electrode materials moved into the focus of interest, such as vitreous carbon (glassy carbon), noble metals, heterogeneous composites (carbon paste,4 screen-printed electrodes) in combination with altered surfaces which facilitated broader applicability of electroanalytical methods. Earlier landmarks of sensor design, such as the first amperometric sensor (oxygen electrode5) and the first biosensor (glucose sensor6), both developed by Leland Clark, contributed to a peak-like increase of electroanalytical studies.
Left ventricular hypertrophy in rats with biliary cirrhosis

Portal hypertension induces neuroendocrine activation and a hyperkinetic circulation state. This study investigated the consequences of portal hypertension on heart structure and function. Intrahepatic portal hypertension was induced in male Sprague‐Dawley rats by chronic bile duct ligation (CBDL). Six weeks later, CBDL rats showed higher plasma angiotensin‐II and endothelin‐1 (P < .01), 56% reduction in peripheral resistance and 73% reduction in pulmonary resistance (P < .01), 87% increase in cardiac index and 30% increase in heart weight (P < .01), and increased myocardial nitric oxide (NO) synthesis. In CBDL rats, macroscopic analysis demonstrated a 30% (P < .01) increase in cross‐sectional area of the left ventricular (LV) wall without changes in the LV cavity or in the right ventricle (RV). Histomorphometric analysis revealed increased cell width (12%, P < .01) of cardiomyocytes from the LV of CBDL rats, but no differences in myocardial collagen content. Myocytes isolated from the LV were wider (12%) and longer (8%) than right ventricular myocytes (P < .01) in CBDL rats but not in controls. CBDL rats showed an increased expression of ANF and CK‐B genes (P < .01). Isolated perfused CBDL hearts showed pressure/end‐diastolic pressure curves and response to isoproterenol identical to sham hearts, although generated wall tension was reduced because of the increased wall thickness. Coronary resistance was markedly reduced. This reduction was abolished by inhibition of NO synthesis with N‐nitro‐L‐arginine. Expression of eNOS was increased in CBDL hearts. In conclusion, portal hypertension associated to biliary cirrhosis induces marked LV hypertrophy and increased myocardial NO synthesis without detectable fibrosis or functional impairment. This observation could be relevant to patients with cirrhosis.
Comparative Life Cycle Carbon Footprint of a Non-Residential Steel and Wooden Building Structures

In the field of construction, wood products are known to have environmental benefits in comparison with materials like steel and concrete, especially to mitigate climate change. Since wood is an anisotropic material, comparisons with other building materials on a volume functional unit basis, such as a cubic meter of product, are not relevant. Wood structures also allow for architectural forms that are not feasible with other building materials. To enable a comparison between wood and steel, we have assessed the Life Cycle Carbon Footprint of complete non-residential building structures. This building frame was initially planned to be made from steel, but the architecture was modified to integrate glued laminated timber beams. The structural engineers provided material balance changes. The results show a significant reduction in reenhouse gas emissions for structures using wood as a building material.
Temporal Variability in Nitrate‐Discharge Relationships in Large Rivers as Revealed by High‐Frequency Data

Little is known about temporal variability in nitrate concentration responses to changes in discharge on intraannual time scales in large rivers. To investigate this knowledge gap, we used a six‐year data set of daily surface water nitrate concentration and discharge averaged from near‐continuous monitoring at U.S. Geological Survey gaging stations on the Connecticut, Potomac, and Mississippi Rivers, three large rivers that contribute substantial nutrient pollution to important estuaries. Interannually, a comparison of nitrate concentration‐discharge (c‐Q) relationships between a traditional discrete grab sample data set and the near‐continuous data set revealed differing c‐Q slopes, which suggests that sample frequency can impact how we ultimately characterize hydrologic systems. Intraannually, we conducted correlation analyses over 30‐day windows to isolate the strength and direction of monthly c‐Q relationships. Monthly c‐Q slopes in the Potomac were positive (enrichment/mobilization response) in summer and fall and negative (dilution response) and weakly chemostatic (nonsignificant near‐zero c‐Q slope) in winter and spring, respectively. The Connecticut displayed a dilution response year‐round, except summer when it was weakly chemostatic. Mississippi c‐Q slopes were weakly chemostatic in all seasons and showed inconsistent responses to discharge fluctuations. The c‐Q dynamics in the Potomac and Connecticut were correlated (R > 0.3) to river temperature, flow percentile, and calendar day. Minimal correlation in the Mississippi suggests that the large basin area coupled with spatiotemporally variable anthropogenic forcings from substantial land use development created stochastic short‐term c‐Q relationships. Additional work using high‐frequency sensors across large river networks can improve our understanding of spatial source input dynamics in these natural‐human coupled systems.
The bonding picture in hypervalent XF3 (X = Cl, Br, I, At) fluorides revisited with quantum chemical topology

Hypervalent XF3 (X = Cl, Br, I, At) fluorides exhibit T‐shaped C2V equilibrium structures with the heavier of them, AtF3, also revealing an almost isoenergetic planar D3h structure. Factors explaining this behavior based on simple “chemical intuition” are currently missing. In this work, we combine non‐relativistic (ClF3), scalar‐relativistic and two‐component (X = Br − At) density functional theory calculations, and bonding analyses based on the electron localization function and the quantum theory of atoms in molecules. Typical signatures of charge‐shift bonding have been identified at the bent T‐shaped structures of ClF3 and BrF3, while the bonds of the other structures exhibit a dominant ionic character. With the aim of explaining the D3h structure of AtF3, we extend the multipole expansion analysis to the framework of two‐component single‐reference calculations. This methodological advance enables us to rationalize the relative stability of the T‐shaped C2v and the planar D3h structures: the Coulomb repulsions between the two lone‐pairs of the central atom and between each lone‐pair and each fluorine ligand are found significantly larger at the D3h structures than at the C2v ones for X = Cl − I, but not with X = At. This comes with the increasing stabilization, along the XF3 series, of the planar D3h structure with respect to the global T‐shaped C2v minima. Hence, we show that the careful use of principles that are at the heart of the valence shell electron pair repulsion model provides reasonable justifications for stable planar D3h structures in AX3E2 systems. © 2017 Wiley Periodicals, Inc.
Characterization of the Adaptor-related Protein Complex, AP-3

We have recently shown that two proteins related to two of the adaptor subunits of clathrincoated vesicles, p47 (μ3) and β-NAP (β3B), are part of an adaptor-like complex not associated with clathrin (Simpson, F., N.A. Bright, M.A. West, L.S. Newman, R.B. Darnell, and M.S. Robinson, 1996. J. Cell Biol. 133:749–760). In the present study we have searched the EST database and have identified, cloned, and sequenced a ubiquitously expressed homologue of β-NAP, β3A, as well as homologues of the α/γ and σ adaptor subunits, δ and σ3, which are also ubiquitously expressed. Antibodies raised against recombinant δ and σ3 show that they are the other two subunits of the adaptor-like complex. We are calling this complex AP-3, a name that has also been used for the neuronalspecific phosphoprotein AP180, but we feel that it is a more appropriate designation for an adaptor-related heterotetramer. Immunofluorescence using anti-δ antibodies reveals that the AP-3 complex is associated with the Golgi region of the cell as well as with more peripheral structures. These peripheral structures show only limited colocalization with endosomal markers and may correspond to a postTGN biosynthetic compartment. The δ subunit is closely related to the protein product of the Drosophila garnet gene, which when mutated results in reduced pigmentation of the eyes and other tissues. Because pigment granules are believed to be similar to lysosomes, this suggests either that the AP-3 complex may be directly involved in trafficking to lysosomes or alternatively that it may be involved in another pathway, but that missorting in that pathway may indirectly lead to defects in pigment granules.
Time trend and clinical pattern of extrapulmonary tuberculosis in Serbia, 1993-2007.

BACKGROUND/AIM Increased incidence of extrapulmonary tuberculosis (XPTB) is reported worldwide. Serbia is a country in socio-economic transition period with low-middle HIV prevalence and intermediate-to-low tuberculosis (TB) incidence rate, 100% directly observed treatment (DOT) coverage, and mandatory BCGC vaccination at birth. The aim of the study was to examine the incidence trend and clinical features of XPTB in Serbia during a 15-year period. METHODS This retrospective observational study included XPTB cases diagnosed in the period between 1st January 1993 and 31st Decembre 2007, according to the reports of the National Referral Institute of Lung Diseases and Tuberculosis in Belgrade and Central Tuberculosis Register. Population estimates with extrapolations were based on 1991 and 2002 census data. RESULTS While the overall TB incidence rate showed a slight, not significant decreasing trend (p = 0.535), a significant increase was found for XPTB (y = 1.7996 + 0.089x; R2 = 0.4141; p = 0.01). A total of 2,858 XPTB cases (newly diagnosed and 10% relapses) gave an average age specific incidence rate of 2.51/100,000 population (95% confidence interval, SD = 0.6182) with 8.9% annual increase. The male-to-female ratio was 0.54. Lymph nodes were most frequently affected site (48.5%) followed by genitourinary (20.5%), pleural (12%), and osseo-arthicular (10.3%) TB. Treatment outcome was successful in 88.29% of patients (cured and completed), 3.64% died, 5.18% interrupted, 0.57% displaced, and 2.3% unknown. CONCLUSION Increasing trend of XPTB incidence rate may be a result of increased morbidity due to still present risk factors, possible higher detection rate in Serbia and better notification. A high coverage of newborns with BCG vaccination at birth might contribute to a decreased number and rare XPTB cases in children.
Methodology to analyse cybersecurity in tourism

Nowadays hyperconnectivity provides an opportunity for tourism industry to benefit from big data analytics as determining competitive factor, for decision making, product design and assertive marketing strategies for target segments; but at the same time, having financial, organizational and personal information stored in cyberspace and available to many users makes vulnerable to security risks like phishing and hacking, both common cybercrimes that affect tourism sector. This paper, introduces representation and model design stages of our own methodology based on self-organization approach that we propose to reinforce cybersecurity in tourism, as part of a research project founded by National Council for Science and Technology postdoctoral scholarship for Mexico.
PCR Detection of Virulence Genes in Yersinia enterocolitica and Yersinia pseudotuberculosis and Investigation of Virulence Gene Distribution

ABSTRACT PCR-based assays were developed for the detection of plasmid- and chromosome-borne virulence genes in Yersinia enterocolitica and Yersinia pseudotuberculosis, to investigate the distribution of these genes in isolates from various sources. The results of PCR genotyping, based on 5 virulence-associated genes of 140 strains of Y. enterocolitica, were compared to phenotypic tests, such as biotyping and serotyping, and to virulence plasmid-associated properties such as calcium-dependent growth at 37°C and Congo red uptake. The specificity of the PCR results was validated by hybridization. Genotyping data correlated well with biotype data, and most biotypes resulted in (nearly) homogeneous genotypes for the chromosomal virulence genes (ystA, ystB, and ail); however, plasmid-borne genes (yadA and virF) were detected with variable efficiency, due to heterogeneity within the bacterial population for the presence of the virulence plasmid. Of the virulence genes, only ystB was present in biotype 1A; however, within this biotype, pathogenic and apathogenic isolates could not be distinguished based on the detection of virulence genes. Forty Y. pseudotuberculosis isolates were tested by PCR for the presence of inv, yadA, and lcrF. All isolates were inv positive, and 88% of the isolates contained the virulence plasmid genes yadA and lcrF. In conclusion, this study shows that genotyping of Yersinia spp. , based on both chromosome- and plasmid-borne virulence genes, is feasible and informative and can provide a rapid and reliable genotypic characterization of field isolates.
In vino veritas? Alcohol, response inhibition and lying.

AIMS Despite the widespread belief that alcohol makes the truth come out more easily, we know very little on how alcohol impacts deception. Given that alcohol impairs response inhibition, and that response inhibition may be critically involved in deception, we expected that alcohol intake would hamper lying. METHODS In total, 104 volunteers were tested at a science festival, where they had the opportunity to drink alcohol. Stop-Signal Reaction Times (SSRTs) served as operationalization of response inhibition. Differences in error rates and reaction times (RTs) between lying and truth telling served as indicators of the cognitive cost of lying. RESULTS Higher blood alcohol concentration was related to longer SSRTs, but unrelated to the cognitive costs of lying. CONCLUSION This study validates previous laboratory research on alcohol and response inhibition in a realistic drinking environment, yet failed to find an effect of alcohol on lying. Implications of these findings and for the role of response inhibition in lying are discussed.
A Reinforcement Learning Based Strategy for the Double-Game Prisoner's Dilemma

The Double-Game Prisoner's Dilemma (DGPD) is a new game that incorporates the standard Prisoner's Dilemma (PD) with the Social Game. DGPD provides a novel approach in modelling economic behaviours: in each round, players not only need to choose to cooperate or defect, but also need to adjust their weights for each basic game. As a result, traditional strategies for PD, e.g. Tit- for-Tat, do not perform well in DGPD. In this paper, we propose a new strategy for the DGPD game, based on a Reinforcement Learning (RL) algorithm, namely SARSA( ) with eligibility traces. This algorithm does not require a model of the player's environment and, therefore, is well suited for use in repeated games against unknown opponents. We empirically analyse the effectiveness of the pro- posed strategy. In addition, we discuss several key points in designing this strat- egy, e.g. the values of parameters, and show how they affect the strategy's per- formance. Our RL-based strategy wins the Material Versus Social Payoff Tour- nament (MVSPT) and significantly outperforms other strategies.
Maximum Likelihood Quantization of Genomic Features Using Dynamic Programming

Dynamic programming is introduced to quantize a continuous random variable into a discrete random variable. Quantization is often useful before statistical analysis or reconstruction of large network models among multiple random variables. The quantization, through dynamic programming, finds the optimal discrete representation of the original probability density function of a random variable by maximizing the likelihood for the observed data. This algorithm is highly applicable to study genomic features such as the recombination rate across the chromosomes and the statistical properties of non-coding elements such as LINE1. In particular, the recombination rate obtained by quantization is studied for LINE1 elements that are grouped also using quantization by length. The exact and density-preserving quantization approach provides an alternative superior to the inexact and distance-based k-means clustering algorithm for discretization of a single variable.
Gas Sensors Based on Polymer Field-Effect Transistors

This review focuses on polymer field-effect transistor (PFET) based gas sensor with polymer as the sensing layer, which interacts with gas analyte and thus induces the change of source-drain current (ΔISD). Dependent on the sensing layer which can be semiconducting polymer, dielectric layer or conducting polymer gate, the PFET sensors can be subdivided into three types. For each type of sensor, we present the molecular structure of sensing polymer, the gas analyte and the sensing performance. Most importantly, we summarize various analyte–polymer interactions, which help to understand the sensing mechanism in the PFET sensors and can provide possible approaches for the sensor fabrication in the future.
XPFS: A new parallel PROSITE profile search algorithm on Xeon Phi

PROSITE provides rich documentation entries describing protein domains, families and functional sites, associated patterns as well as generalized profiles to identify them. Generalized profiles in PROSITE are often used to detect distantly related proteins by doing sequence comparison. The developments of the PROSITE have increased the discriminatory power of generalized profiles. However in practice, comparing PROSITE profiles to large protein databases, such as GenBank, usually requires long runtimes on sequential architectures. Due to the continuing rapid growth of sequence databases, there is a high demand to accelerate this task. In this paper we present XPFS, a new parallel algorithm for searching generalized profiles against protein sequence databases based on Xeon Phi which is Intel's first generation Many Integrated Core product. To our knowledge this is the first reported implementation of the PROSITE profile search algorithm on Xeon Phi. The executable binary code of XPFS is available at http://xpfs.sdu-hpcl.org/.