Miracle-dz/UniFAR-FTUs huggingface dataset:
CHANGES IN THE NESTING POPULATIONS OF COLONIAL WATERBIRDS IN JAMAICA BAY WILDLIFE REFUGE, NEW YORK, 1974–1998

Abstract The Jamaica Bay Wildlife Refuge (JBWR) represents the largest protected area for over 300 species of migratory and resident birds on Long Island (LI), New York, and occupies a key position along the Atlantic flyway. We identified changes in nesting populations for 18 species of colonial waterbirds in JBWR and on LI, during 1974–1998, to provide a basis for future wildlife management decisions in JBWR and also at nearby John F. Kennedy International Airport. None of the populations was stable over the past 25 years in JBWR or on LI. Some populations in JBWR increased (Laughing Gull L. atricilla Linnaeus, Great Black-backed Gull L. marinus Linnaeus, Forster's Tern Sterna forsteri Nuttall) while others decreased (Herring Gull Larus argentatus Coues, Snowy Egret Egretta thula Molina), but only Cattle Egrets (Bubulcus ibis Linnaeus) have disappeared from the refuge. Common Tern (S. hirundo Linnaeus), Least Tern (S. antillarum Lesson), Roseate Tern (S. dougallii Montagu), Black Skimmer (Rynchops niger Linnaeus), Black-crowned Night Heron (Nycticorax nycticorax Linnaeus) and Great Egret (Ardea alba Linnaeus) populations all increased on LI over the sampling period although the Common Tern colonies in JBWR have been declining since 1986. The continued protection of the colony sites, particularly saltmarsh islands, in JBWR will be important to the conservation efforts of many colonial waterbird populations on Long Island. The JBWR colonies may serve as a source of emigrants to other Long Island colonies, and in some cases, act as a “sink” for birds immigrating from New Jersey and elsewhere.
Efficacy of antimicrobial coated orthopaedic implants on the prevention of periprosthetic infections: a systematic review and meta-analysis

Introduction: Implant-associated infections are a major problem in orthopaedic surgery. Local delivery systems of antimicrobial agents on the implant surface have attracted great interest recently. The purpose of this study was to identify antimicrobial coatings currently used in clinical practice, examining their safety and effectiveness in reducing post-operative infection rates. Materials and Methods: A systematic review was conducted in four databases (Medline, Embase, Cochrane, Cinahl) according to the Preferred Reporting Items for Systematic reviews and Meta-analysis (PRISMA) guidelines up to December 2019, using the key words “orthopaedic implant coated”, “coated implant infection”, “silver coating ” and “antibiotic coating”. Results: Seven articles involving 1307 patients (561 with coated implants and 746 controls who were not) comparing the incidence of periprosthetic infections after the application of internal fracture fixation, total arthroplasties and endoprostheses were evaluated. Three different coating technologies were identified: gentamicin coating for tibia nail and total arthroplasties; silver technology and povidone-iodine coating for tumour endoprostheses and titanium implants. Meta-analysis demonstrated that patients who were treated with antimicrobial coated implants presented lower infection rates compared to controls over the seven studies (Q = 6.1232, I2 = 0.00, 95% CI: 1.717 to 4.986, OR: 2.926, Z= 3.949, p<0.001). Subgroup statistical analysis revealed that each coating technique was effective in the prevention of periprosthetic infections (Q = 9.2606, I2 = 78.40%, 95% CI: 1.401 to 4.070, OR: 2.388, Z= 3.200, p<0.001). Conclusion: All technologies were reported to have good biocompatibility and were effective in the reduction of post-operative peri-prosthetic infection rates.
Fracture resistance of single-walled carbon nanotubes through atomistic simulation

The mechanical behavior of Carbon Nanotubes (CNTs) has drawn much attention because of their ultra-high stiffness and strength. From the perspective of durability and reliability of CNT-based materials and devices, fracture of CNTs due to mechanical loading becomes an important issue. Presumably, because of their small size, few experiments are available in the literature to directly investigate the details of fracture process. According to existing studies (most of which are numerical modelings), zigzag tubes generally favor brittle mode, while armchair tubes, under high temperature and high strain, can undergo significant plastic deformation before they break. Nevertheless, brittle fracture could be one of the important failure modes, or even the dominant mode of Single-Walled Nanotube (SWNT) failure due to mechanical loading. However, based on the authors’ knowledge, the fracture resistance of CNTs has not been quantified so far. In this paper, the brittleness of CNTs with preexisting defects is calculated using fracture mechanics concepts. Such mechanistic modeling is an essential ingredient to understanding the stochastic fluctuations in fracture properties. The strain energy release rate, G, is computed through a series of simulated mechanical loading of SWNTs with preexisting cracks of various lengths. Atomistic simulation is used to model the tensile loading of these SWNTs. The interatomic forces are modeled with a modified Morse potential. The loading is displacement controlled, applied through moving the outmost layer of atoms at one end of the SWNT at constant speed. This computation is applied to (35,0) SWNTs with cracks up to 29. 5Å long. A significant dependence of Gc on crack length is observed: Gc increases with crack length at small length, and tends to reach a constant value as crack length is large. For example, at 300 Kelvin, Gc converges to 6 Joule/m as the crack length exceeds 20 Angstrom. This value is comparable with the fracture toughness of graphite and Silicon.
Isolation and characterisation of genes involved in carbon and chlorophyll metabolism in Saccharum species hybrids

viii Samevatting ix References xi Aim xi Layout of thesis xi Acknowledgments xiii List of Figures xiv List of Tables xvii List of Abbreviations xviii Chapter 1: Literature Review 1 1.1 Modification of agricultural traits in sugarcane 2 1.2 Protoporphyrinogen oxidase 3 1.2. 1 Conserved domain and enzyme structure 4 1.2. 2 Protoporphyrinogen oxidase‟s role in heme and chlorophyll synthesis 5 1.2. 3 Diphenylether type herbicides and inhibition of PPO activity 6 1.2. 4 PPO isolation and characterization 7 1.2. 4.1 PPO isolation and characterization in prokaryotes 7 1.2. 4.2 PPO isolation and characterization in eukaryotes 7 1.2. 4.3 PPO isolation and characterization in plants 7 1.2. 5 Natural DPE resistance in plants 10 1.2. 6 Development of DPE resistant crop plants and PPO genes 11 1.2. 7 PPO as an alternative in vitro selection system 13 Stellenbosch University https://scholar.sun.ac.za
Effects of Travel Agent’s Brand Commitment on Seniors’ Satisfaction-Mediation Effect of Word-of-Mouth Behavior

The results of this study are revealing the significant effects that the higher travel agents’ Brand Commitment of the, the higher customer Satisfaction is presented; travel agents’ Brand Commitment to senior customers’ Word-of-mouth Behavior presenting the remarkable effects that the higher travel agents’ Brand Commitment of, the better willingness of customers’ word-of-mouth is shown; senior customers’ Word-of-mouth Behavior to the Satisfaction revealing the notable effects that the higher intention of customers’ Word-of-mouth Behavior, the higher Satisfaction is shown; and the moderating effects of Word-of-mouth Behavior on the relationship between Brand Commitment and Satisfaction.
Capparis spinosa: a comparative study of raw and processed fruits

Abbreviations: DPPH, 2,2-diphenyl-1-picrylhydrazyl; FRAP, ferric reducing ability of plasma, R-HPLC, reverse phase high performance liquid chromatography; TLC, thin layer chromatography; MDBK, madin-darby bovine kidney cells, HepG-2, hepatocellular carcinoma cells; MCF-7, michigan cancer foundation-7 breast cancer cells; MTT, 3-(4,5Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide; TPTZ, (2,4,6-tri-pyridyl-s-triazine); BHT, Butylated hydroxytoluene; ITM, Iranian traditional medicine
ISOLATION AND CHARACTERIZATION OF PARMALES (HETEROKONTAHETEROKONTOPHYTASTRAMENOPILES) FROM THE OYASHIO REGION, WESTERN NORTH PACIFIC1

A small siliceous species of marine phytoplankton, order Parmales (Heterokonta), was isolated and characterized for the first time with the aid of a fluorescent silicon tracer 2-(4-pyridyl)-5-([4-(2-dimethylaminoethylaminocarbamoyl)-methoxy]phenyl) oxazole (PDMPO). This dye was easily detected by clear fluorescence in newly produced silica cell plates. Our isolate was surrounded by eight smooth plates without any ornamentation, suggesting a similarity to Triparma laevis B. C. Booth. TEM observation showed the typical ultrastructure of photosynthetic heterokontophytes; with two chloroplast endoplasmic reticulate membranes, a girdle lamella, three thylakoid lamellae, and mitochondrion with tubular cristae. Molecular phylogenetic analyses of SSU rDNA and rbcL genes showed that the parmalean alga was within the bolidophycean clade of autotrophic naked flagellates and a sister group of diatoms. HPLC analysis detected chl a, c1 + c2, and c3; fucoxanthin; and diadinoxanthin as major photosynthetic pigments, and a composition that is shared with Bolidophyceae and diatoms. Together, these data indicate a close evolutionary relationship between Parmales, Bolidophyceae, and diatoms. The PDMPO-staining procedure should accelerate isolation of other Parmales species, helping to establish their diversity and aiding quantitative study of their role in oceanic processes.
Aquaculture Systems

The worldwide expansion of marine aquaculture industries has caused growing concern regarding their environmental impact. Marine aquaculture is a significant industry that continues to grow more rapidly than all other animal food-producing sectors, with an average annual growth rate worldwide of 8.8% per year since 1970, compared with only 1.2% for capture fisheries and 2.8% for terrestrial farmed meat production systems (FAO 2007). This increase in marine aquaculture activities is thought to be in response to the increase in demand for fish, which cannot be fulfilled by traditional fisheries because of the decline in wild populations. Moreover, marine aquaculture is essentially an economic development within smalland medium-sized enterprises in areas where alternative employment is scarce.
Financial Disruptions and Heightened Uncertainty: A Case for Timely Policy Action

We examine whether the response of the euro area economy to uncertainty shocks depends on the state of financial conditions. We find strong evidence that uncertainty shocks have much more powerful effects on key macroeconomic variables in episodes marked by financial distress than in normal times. We document that the recovery of economic activity is state-dependent following an adverse uncertainty shock. More precisely, it is gradual in normal times, but displays a more accelerated rebound when the shock hits during financial distress. These findings are based on a non-linear data-driven model that accounts for regime switching and time-varying volatility. Finally, from a policy perspective, we argue that whether financial markets are calm or distressed matters when it comes to the appropriate policy responses to uncertainty shocks.
Branching models predict loss of many bird and mammal orders within centuries

Branching (birth–death) models are used to project the time to extinction for bird and mammal orders. While such projections are very coarse, they provide information on how long fundamental units of biodiversity, as represented by such higher taxa as orders, will persist at specified rates of species extinction. The results of a basic decay model indicate that, if all threatened species in each order go extinct within the next 100 years, and this species extinction rate continues indefinitely, then half the species in most orders will disappear in a few hundred years or less. This result is robust and is in agreement with other estimates. A more detailed branching model indicates that most bird and mammal orders will become 100% extinct in a few thousand years if current extinction trends are extrapolated. This projection is also relatively robust, as it is consistently produced using a number of different methods and estimates of future species extinction rates. Mammal orders generally have substantially shorter half‐lives and time to 100% extinction than bird orders because of a combination of fewer species per order and higher species extinction rates.
A new species and new section of Viola (Violaceae) from Guangdong, China

Viola hybanthoides W. B. Liao et Q. Fan (Violaceae), a new species from Mount Danxia of Guangdong province in China, is described and illustrated. The most distinctive characters of Viola hybanthoides are the subshrub habit, the anterior petal with a long stalk-like claw (up to 3.5 mm, ca. 1/3 of the petal’s length), and the very short upper petals (only 2.5–3 mm long, less than 1/2 of the lateral petals’ length), all of which are characters shared with some Hybanthus species. These characters of this species are distinguishable from all other Viola species, which are usually herbs, and have the anterior petal without a long stalk-like claw and much longer upper petals (usually more than 8 mm long). Based on the new species, a new Viola section Danxiaviola W. B. Liao et Q. Fan is described. To distinguish Viola sections in China, an identification key is provided.
Monitoring of process and risk-adjusted medical outcomes using a multi-stage MEWMA chart

Most statistical process control programmes in healthcare focus on surveillance of outcomes at the final stage of a procedure, such as mortality or failure rates. Such an approach ignores the multi-stage nature of these procedures, in which a patient progresses through several stages prior to the final stage. In this paper, we develop a multi-stage control chart based on a multivariate exponentially weighted moving average (EWMA) test statistic derived from score equations. This allows simultaneous monitoring of all intermediate and final stage outcomes of a healthcare process, with adjustment for underlying patient risk factors and dependence between outcome variables. Use of the EWMA test statistics allows quick detection of small gradual changes in any part of the process. Three advantages of the approach are: better understanding of how outcomes at different stages relate to each other, explicit monitoring of upstream stage outcomes may help curtail trends that lead to poorer end-stage outcomes and understanding the impact of each stage can help determine the most effective allocation of quality improvement resources. Simulations are performed to test the control charts under various types of hypothesised shifts, and the results are summarised using out-of-control average run lengths.
Genetic analysis and traits association in two double haploid populations of bread wheat (Triticum aestivum L.)

A study was conducted for genetic analysis and estimating association of the traits in double haploid populations of bread wheat (Triticum aestivum L.). These populations were planted at Directorate of Wheat Research, Karnal during rabi season 2008-09 and 2009-10 in augmented design along with five checks in three blocks, wherein all checks were repeated in each block. The genetic variance and correlation coefficients were carried out for assessment of the performance of double haploid lines derived from the cross (Ducula4/2* Brookton) and (Camm/ HD 2329), through six metric traits, viz. plant height, days to heading, days to maturity, tillers per plot, 1000-grain weight and grain yield. Analysis of variance on the basis of F- values, revealed wide variability for most of the traits over the year and pooled. The phenotypic coefficient of variation (PCV) was higher than genotypic coefficient of variation (GCV) for all traits, while high heritability (<60%) coupled with high genetic advance (<15%) was found for all the traits, excepting the days to maturity and spike length. At phenotypic level, positive and significant correlation coefficients revealed that grain yield is directly influenced by spike length, tillers per plot and thousand grain weight, while significant and negative correlations was found of plant height and days to maturity with grain yield, respectively in both the populations. There is wide genetic diversity available for metric traits, which may be utilized for yield improvement in bread wheat through planned hybridization and selection. The traits plant height, maturity days, tillers per plot, spike length and 1000-grain weight of both populations can be of importance in further yield enhancement.
Twisted quantum affinizations and quantization of extended affine Lie algebras

In this paper, for an arbitrary Kac-Moody Lie algebra $\mathfrak{g}$ and a diagram automorphism $\mu$ of $\mathfrak{g}$ satisfying two linking conditions, we introduce and study a $\mu$-twisted quantum affinization algebra $\mathcal{U}_{\hbar}(\hat{\mathfrak{g}}_\mu)$ of $\mathfrak{g}$. When $\mathfrak{g}$ is of finite type, $\mathcal{U}_{\hbar}(\hat{\mathfrak{g}}_\mu)$ is Drinfeld's current algebra realization of the twisted quantum affine algebra. And, when $\mu=\mathrm{Id}$, $\mathcal{U}_{\hbar}(\hat{\mathfrak{g}}_\mu)$ is the quantum affinization algebra introduced by Ginzburg-Kapranov-Vasserot. As the main results of this paper, we first prove a triangular decomposition of $\mathcal{U}_{\hbar}(\hat{\mathfrak{g}}_\mu)$. Second, we give a simple characterization of the affine quantum Serre relations on restricted $\mathcal{U}_{\hbar}(\hat{\mathfrak{g}}_\mu)$-modules in terms of "normal order products". Third, we prove that the category of restricted $\mathcal{U}_{\hbar}(\hat{\mathfrak{g}}_\mu)$-modules is a monoidal category and hence obtain a topological Hopf algebra structure on the "restricted completion" of $\mathcal{U}_{\hbar}(\hat{\mathfrak{g}}_\mu)$. Fourth, we study the classical limit of $\mathcal{U}_{\hbar}(\hat{\mathfrak{g}}_\mu)$ and abridge it to the quantization theory of extended affine Lie algebras. In particular, based on a classification result of Allison-Berman-Pianzola, we obtain the $\hbar$-deformation of nullity $2$ extended affine Lie algebras.
Tilting instability of magnetically confined spheromaks

We consider the tilting instability of a magnetically confined spheromak using three-dimensional magnetohydrodynamic and relativistic particle-in-cell calculations with an application to astrophysical plasmas, specifically those occurring in magnetar magnetospheres. The instability is driven by the counter-alignment of the spheromak's intrinsic magnetic dipole with the external magnetic field. Initially, the spheromak rotates – tilts – trying to lower its magnetic potential energy. As a result, a current sheet forms between the internal magnetic field of a spheromak and the confining field. Magnetic reconnection sets in; this leads to the annihilation of the newly counter-aligned magnetic flux of the spheromak. This occurs on a few Alfvén time scales. In the case of a higher-order (second-order) spheromak, the internal core is first pushed out of the envelope, resulting in formation of two nearly independent tilting spheromaks. Thus, the magnetically twisted outer shell cannot stabilize the inner core. During dissipation, helicity of the initial spheromak is carried away by torsional Alfvén waves, violating the assumptions of the Taylor relaxation theorem. In applications to magnetar giant flares, fast development of tilting instabilities and no stabilization of the higher-order spheromaks make it unlikely that trapped spheromaks are responsible for the tail emission lasting hundreds of seconds.
Pushing the Limit of Unsupervised Learning for Ultrasound Image Artifact Removal

Ultrasound (US) imaging is a fast and non-invasive imaging modality which is widely used for real-time clinical imaging applications without concerning about radiation hazard. Unfortunately, it often suffers from poor visual quality from various origins, such as speckle noises, blurring, multi-line acquisition (MLA), limited RF channels, small number of view angles for the case of plane wave imaging, etc. Classical methods to deal with these problems include image-domain signal processing approaches using various adaptive filtering and model-based approaches. Recently, deep learning approaches have been successfully used for ultrasound imaging field. However, one of the limitations of these approaches is that paired high quality images for supervised training are difficult to obtain in many practical applications. In this paper, inspired by the recent theory of unsupervised learning using optimal transport driven cycleGAN (OT-cycleGAN), we investigate applicability of unsupervised deep learning for US artifact removal problems without matched reference data. Experimental results for various tasks such as deconvolution, speckle removal, limited data artifact removal, etc. confirmed that our unsupervised learning method provides comparable results to supervised learning for many practical applications.
Not all Failure Modes are Created Equal: Training Deep Neural Networks for Explicable (Mis)Classification

Deep Neural Networks are often brittle on image classification tasks and known to misclassify inputs. While these misclassifications may be inevitable, all failure modes cannot be considered equal. Certain misclassifications (eg. classifying the image of a dog to an airplane) can create surprise and result in the loss of human trust in the system. Even worse, certain errors (eg. a person misclassified as a primate) can have societal impacts. Thus, in this work, we aim to reduce inexplicable errors. To address this challenge, we first discuss how to obtain the class-level semantics that captures the human's expectation ($M^h$) regarding which classes are semantically close vs. ones that are far away. We show that for data-sets like CIFAR-10 and CIFAR-100, class-level semantics can be obtained by leveraging human subject studies (significantly inexpensive compared to existing works) and, whenever possible, by utilizing publicly available human-curated knowledge. Second, we propose the use of Weighted Loss Functions to penalize misclassifications by the weight of their inexplicability. Finally, we show that training (or even fine-tuning) existing classifiers with the two proposed methods lead to Deep Neural Networks that have (1) comparable top-1 accuracy, an important metric in operational contexts, (2) more explicable failure modes and (3) require significantly less cost in teams of additional human labels compared to existing work.
Quantum electronic transport across ‘bite’ defects in graphene nanoribbons

On-surface synthesis has recently emerged as an effective route towards the atomically precise fabrication of graphene nanoribbons (GNRs) of controlled topologies and widths. However, whether and to what degree structural disorder occurs in the resulting samples is a crucial issue for prospective applications that remains to be explored. Here, we experimentally visualize ubiquitous missing benzene rings at the edges of 9-atom wide armchair nanoribbons that form upon cleavage of phenyl groups in the precursor molecules. These defects are referred to as ‘bite’ defects. First, we address their density and spatial distribution on the basis of scanning tunnelling microscopy and find that they exhibit a strong tendency to aggregate. Next, we explore their effect on the quantum charge transport from first-principles calculations, revealing that such imperfections substantially disrupt the conduction properties at the band edges. Finally, we generalize our theoretical findings to wider nanoribbons in a systematic manner, hence establishing practical guidelines to minimize the detrimental role of such defects on the charge transport. Overall, our work portrays a detailed picture of ‘bite’ defects in bottom-up armchair GNRs and assesses their effect on the performance of carbon-based nanoelectronic devices.