Miracle-dz/UniFAR-FTUs huggingface dataset:
Global monitoring of terrestrial chlorophyll fluorescence from moderate-spectral-resolution near-infrared satellite measurements: methodology, simulations, and application to GOME-2

Abstract. Globally mapped terrestrial chlorophyll fluorescence retrievals are of high interest because they can provide information on the functional status of vegetation including light-use efficiency and global primary productivity that can be used for global carbon cycle modeling and agricultural applications. Previous satellite retrievals of fluorescence have relied solely upon the filling-in of solar Fraunhofer lines that are not significantly affected by atmospheric absorption. Although these measurements provide near-global coverage on a monthly basis, they suffer from relatively low precision and sparse spatial sampling. Here, we describe a new methodology to retrieve global far-red fluorescence information; we use hyperspectral data with a simplified radiative transfer model to disentangle the spectral signatures of three basic components: atmospheric absorption, surface reflectance, and fluorescence radiance. An empirically based principal component analysis approach is employed, primarily using cloudy data over ocean, to model and solve for the atmospheric absorption. Through detailed simulations, we demonstrate the feasibility of the approach and show that moderate-spectral-resolution measurements with a relatively high signal-to-noise ratio can be used to retrieve far-red fluorescence information with good precision and accuracy. The method is then applied to data from the Global Ozone Monitoring Instrument 2 (GOME-2). The GOME-2 fluorescence retrievals display similar spatial structure as compared with those from a simpler technique applied to the Greenhouse gases Observing SATellite (GOSAT). GOME-2 enables global mapping of far-red fluorescence with higher precision over smaller spatial and temporal scales than is possible with GOSAT. Near-global coverage is provided within a few days. We are able to show clearly for the first time physically plausible variations in fluorescence over the course of a single month at a spatial resolution of 0.5° × 0.5°. We also show some significant differences between fluorescence and coincident normalized difference vegetation indices (NDVI) retrievals.
Polymerase Chain Reaction-Based Clonality Analysis of Cutaneous B-Cell Lymphoproliferative Processes

INTRODUCTION: The differential diagnosis of B-cell lymphoproliferative processes remains a challenge for pathologists, dermatologists and oncologists, despite advances in histology, immunohistochemistry and molecular biology. OBJECTIVE: Evaluate aid and limitations of clonality analysis in the diagnosis of primary cutaneous B-cell lymphomas and B-cell pseudolymphomas. METHODS: This study included 29 cases of B-cell lymphoproliferative processes classified as primary cutaneous B-cell lymphomas (13), B-cell pseudolymphomas (6) and inconclusive cases (10) using histology and immunohistochemistry. The clonality analysis was performed by polymerase chain reaction analysis of immunoglobulin light chain and heavy chain rearrangements. RESULTS: DNA quality was shown to be generally poor; eight samples were inadequate for polymerase chain reaction analysis. The results showed monoclonality in eight of the primary cutaneous B-cell lymphomas and polyclonality in four of the B-cell pseudolymphomas. In addition, monoclonality was shown in two of the inconclusive cases by histology and immunohistochemistry, demonstrating the utility of polymerase chain reaction as an ancillary diagnostic tool for primary cutaneous B-cell lymphomas. DISCUSSION: The low quality DNA extracted from these cases demanded the use of an IgH protocol that yielded small fragments and IgK. Both methods used together improved detection. CONCLUSION: Use of the two protocols, immunoglobulin heavy chain FR3-trad and immunoglobulin light chain-Kappa Biomed protocols for clonality analysis improved diagnostic accuracy.
Adaptive Capacity of the Habitat Modifying Sea Urchin Centrostephanus rodgersii to Ocean Warming and Ocean Acidification: Performance of Early Embryos

Background Predicting effects of rapid climate change on populations depends on measuring the effects of climate stressors on performance, and potential for adaptation. Adaptation to stressful climatic conditions requires heritable genetic variance for stress tolerance present in populations. Methodology/Principal Findings We quantified genetic variation in tolerance of early development of the ecologically important sea urchin Centrostephanus rodgersii to near-future (2100) ocean conditions projected for the southeast Australian global change hot spot. Multiple dam-sire crosses were used to quantify the interactive effects of warming (+2–4°C) and acidification (−0.3−0.5 pH units) across twenty-seven family lines. Acidification, but not temperature, decreased the percentage of cleavage stage embryos. In contrast, temperature, but not acidification decreased the percentage of gastrulation. Cleavage success in response to both stressors was strongly affected by sire identity. Sire and dam identity significantly affected gastrulation and both interacted with temperature to determine developmental success. Positive genetic correlations for gastrulation indicated that genotypes that did well at lower pH also did well in higher temperatures. Conclusions/Significance Significant genotype (sire) by environment interactions for both stressors at gastrulation indicated the presence of heritable variation in thermal tolerance and the ability of embryos to respond to changing environments. The significant influence of dam may be due to maternal provisioning (maternal genotype or environment) and/or offspring genotype. It appears that early development in this ecologically important sea urchin is not constrained in adapting to the multiple stressors of ocean warming and acidification. The presence of tolerant genotypes indicates the potential to adapt to concurrent warming and acidification, contributing to the resilience of C. rodgersii in a changing ocean.
Excepting Myotis capaccinii, the wings' contribution to take-off performance does not correlate with foraging ecology in six species of insectivorous bat

ABSTRACT Take-off in bats is separated into two distinct phases: an initial jump and a subsequent wing powered acceleration. Here, using footage from a high-speed camera, the first comparative study of the performance during the wing induced phase of take-off in six insectivorous bat species is described. Despite distinct differences in foraging strategy, the mass specific power generated by the bats during wing induced take-off did not differ between species, with the exception of Myotis capaccinii. This suggests that differences in take-off performance may only be evident in bats that exhibit particularly unusual foraging strategies, such as the trawling behaviour of M. capaccinii – with differences in the remaining species only manifesting in subtler aspects of flight performance such as agility or manoeuvrability. The poorer take-off performance of M. capaccinii could be related to either a reduction in wing-stroke amplitude to stop the wings hitting the water's surface during foraging or perhaps an effect of having very large feet. No scaling relationship between body mass and mass-specific take-off power was found, which supports earlier research on birds and insects, suggesting that the mass-specific muscle power available for flight is broadly similar across a large range of body sizes and species.
High‐resolution melting analysis (HRMA): a highly sensitive inexpensive genotyping alternative for population studies

High‐resolution melting analysis (HRMA) is a highly sensitive closed‐tube genotyping method used primarily in clinical studies. As the method is rapid, inexpensive and amenable to high throughput, we decided to investigate its applicability to population studies. Small amplicons and unlabelled probes were used to genotype the nuclear genes, lactate dehydrogenase‐A (ldh‐A), myosin light chain‐2 (mlc‐2), acidic ribosomal phosphoprotein P0 (ARP) and calmodulin (CaM) in populations of swordfish, Xiphias gladius. Results indicate that HRMA is a powerful genotyping tool to study wild populations.
A NOVEL DIFFERENTIAL EVOLUTION BASED ALGORITHM FOR HIGHER ORDER NEURAL NETWORK TRAINING

In this paper, an application of an adaptive differential evolution (DE) algorithm for training higher order neural networks (HONNs), especially the Pi-Sigma Network (PSN) has been introduced. The proposed algorithm is a variant of DE/rand/2/bin and possesses two modifications to avoid the shortcomings of DE/rand/2/bin. The base vector for perturbation is the best vector out of the three randomly selected individuals for mutation, which actually assists intensification keeping the diversification property of DE/rand/2/bin; and novel mutation and crossover strategies are followed considering both exploration and exploitation. The performance of the proposed algorithm for HONN training is evaluated through a wellknown neural network training benchmark i.e. to classify the parity-p problems. The results obtained from the proposed algorithm to train HONN have been compared with solutions from the following algorithms: the basic CRO algorithm, CRO-HONNT and the two most popular variants of the differential evolution algorithm (DE/Rand/1/bin and DE/best/1/bin). It is observed that the application of the proposed algorithm to HONN training (DE-HONNT) performs statistically better than that of other algorithms.
Wiki deployment in corporate settings

Our research question concerns the usefulness of wikis in corporate settings. The answer to this question is not clear. On one hand, business firms are aware of the impact wikis have had on the Internet, and perceive wikis as an up-and-coming technology for supporting collaborative work. On the other hand, the fundamental principles underlying wikis - openness, non-attribution, egalitarianism, and decentralized control - run in contrast to traditional command-and-control management. To date, little information is available regarding wikis' usage in corporate settings. This paper examines the actual use of wikis in a business setting, to identify factors driving user participation, and to assess the extent to which wikis provide value to both individuals and the organization.
Probes and participation

This exploratory paper reflects on the relationship between methodological techniques and forms of user participation. Specifically our concern is to document and describe our experiences with different kinds of participation that different sorts of 'Probes' - 'Cultural Probes', 'Technology Probes' etc - elicit, encourage and provoke. Analysis of the different kinds of participation invoked by Probes - imaginative, investigative, emotional, discursive, reactive, disruptive, reflective, and playful - may prove useful as heuristic devices guiding the selection and deployment of these methodological and design tools. Whilst there are further opportunities for new forms of participation through 'Probing', new concerns, challenges and risks also emerge.
Binding Specificity of the Porphyromonas gingivalis Heme and Hemoglobin Receptor HmuR, Gingipain K, and Gingipain R1 for Heme, Porphyrins, and Metalloporphyrins

ABSTRACT Previous genetic and biochemical studies have confirmed that hemoglobin and hemin utilization in Porphyromonas gingivalis is mediated by the outer membrane hemoglobin and heme receptor HmuR, as well as gingipain K (Kgp), a lysine-specific cysteine protease, and gingipain R1 (HRgpA), one of two arginine-specific cysteine proteases. In this study we report on the binding specificity of the recombinant P. gingivalis HmuR protein and native gingipains for hemoglobin, hemin, various porphyrins, and metalloporphyrins as assessed by spectrophotometric assays, by affinity chromatography, and by enzyme-linked immunosorbent assay. Protoporphyrin, mesoporphyrin, deuteroporphyrin, hematoporphyrin, and some of their iron, copper, and zinc derivatives were examined to evaluate the role of both the central metal ion and the peripheral substituents on binding to recombinant HmuR and soluble gingipains. Scatchard analysis of hemin binding to Escherichia coli cells expressing recombinant membrane-associated six-His-tagged HmuR yielded a linear plot with a binding affinity of 2.4 × 10−5 M. RecombinantE. coli cells bound the iron, copper, and zinc derivatives of protoporphyrin IX (PPIX) with similar affinities, and approximately four times more tightly than PPIX itself, which suggests that the active site of HmuR contains a histidine that binds the metal ion in the porphyrin ring. Furthermore, we found that recombinant HmuR prefers the ethyl and vinyl side chains of the PPIX molecule to either the larger hydroxyethyl or smaller hydrogen side chains. Kgp and HRgpA were demonstrated to bind various porphyrins and metalloporphyrins with affinities similar to those for hemin, indicating that the binding of Kgp and HRgpA to these porphyrins does not require a metal within the porphyrin ring. We did not detect the binding of RgpB, the arginine-specific cysteine protease that lacks a C-terminal hemagglutinin domain, to hemoglobin, porphyrins, or metalloporphyrins. Kgp and HRgpA, but not RgpB, were demonstrated to bind directly to soluble recombinant six-His-tagged HmuR. Several possible mechanisms for the cooperation between outer membrane receptor HmuR and proteases Kgp and HRgpA in hemin and hemoglobin binding and utilization are discussed.
Interacting effects of temperature, habitat and phenotype on predator avoidance behaviour in Diadema antillarum : implications for restorative conservation

Caribbean long-spined sea urchin Diadema antillarum populations crashed following a mass mortality event in 1983-1984 with cascading effects on reef health. Population restoration efforts may be hampered by unknown effects of short- and long-term elevated sea surface temperature (SST). We investigated how a key behavioural trait, predator avoidance behaviour (PAB; percentage of long defensive spines that moved in response to shadow stimuli), was affected by elevated SST in 180 individuals from 2 contrasting Honduran reefs: Utila (flattened reef structure, dearth of predation refugia) and Banco Capiro (complex reef structure, abundant refugia). Initiation of PAB is mediated by melanin, which breaks down at elevated water temperatures; thus, as SST rises, D. antillarum may become vulnerable to predation. We compared local current SST (CSST; 29.7°C) with 2 IPCC predicted long-term climate change scenarios under laboratory conditions. PAB decreased by 13.98-15.37% at CSST +1.4°C and 31.67-42.44% at CSST +3.1°C. Trial temperatures were similar to maxima recorded in the Caribbean during the 2016 El Nino, so our results also represent likely responses to worst-case short-term acute temperature anomalies. Juveniles maintained higher PAB than adults, indicating increased reliance on anti-predation behaviours. White-spined phenotypes from Utila’s flattened reef maintained higher PAB than black-spined counterparts, likely due to increased conspicuousness to visual predators. Habitat complexity may mitigate temperature-driven losses in natural behavioural defences. D. antillarum may be resilient to near-term (<2039) SST increases and periodic temperature stresses but may struggle under long-term, worst-case scenario conditions. Restoration of D. antillarum populations must be coupled to augmented reef complexity to improve future resilience.
A multi-level relational system

A relation can be conceptually viewed as a table of data. The table's heading defines the relation's name, the column headings are the attribute names, and each row corresponds to an n-tuple of data values describing a single entity. The set of values which can be used in a column is called a domain. A relational data base is composed of a set of time varying relations inter-related through common domains.
Four-leg active filter based solution to IT Park's power quality issues

The paper explains the power quality study conducted in an IT Park, to investigate the critical electrical problems caused by the neutral loading, harmonics, unbalance and poor power factor and the development of 500kVAR four-leg full-bridge active filter as solution for PQ issues. The selected control strategy ensures instantaneous control of current through each phase and neutral of the shunt active filter. The experimental results verifying the performance of the active filter are also presented.
Graph-based Sybil Detection in social and information systems

Sybil attacks in social and information systems have serious security implications. Out of many defence schemes, Graph-based Sybil Detection (GSD) had the greatest attention by both academia and industry. Even though many GSD algorithms exist, there is no analytical framework to reason about their design, especially as they make different assumptions about the used adversary and graph models. In this paper, we bridge this knowledge gap and present a unified framework for systematic evaluation of GSD algorithms. We used this framework to show that GSD algorithms should be designed to find local community structures around known non-Sybil identities, while incrementally tracking changes in the graph as it evolves over time.
CORONARY ARTERY DISEASE Original Studies Does Creatine Kinase-MB (CK-MB) Isoenzyme Elevation Following Percutaneous Coronary Intervention With Drug-Eluting Stents Impact Late Clinical Outcome?

Background: The incidence of postprocedural creatine kinase (CK)-MB elevation to>33 the upper limit of normal after percutaneous coronary intervention (PCI) has been reported at rates of up to 18% in the bare metal stent era and is correlated with higher adverse cardiovascular outcomes. This study examined the incidence and prognostic significance of CK-MB elevations after drug-eluting stent (DES) implantation. Methods: The records of 2,537 patients who underwent DES implantation and completed 6 months’ follow-up were evaluated. Patients with acute myocardial infarction and those who presented in cardiogenic shock and had elevated cardiac enzymes at baseline were excluded from the analysis. Of these, 179 patients (7.1%) had 33 postprocedural CK-MB and 2,358 patients had<33 CK-MB elevation. The composite end point of target vessel revascularization-major adverse cardiac events (TVR-MACE) at 6 months was compared between groups. Univariate andmultivariate regression analyses were performed to identify predictors of adverse cardiac outcomes. Results: The patients with CK-MB 33 elevation had a higher number of diseased vessels (2.15 6 0.86 vs. 1.81 6 0.87; P < 0.001), higher prevalence of type C lesions (29.9% vs. 17.7%; P < 0.001), received a higher average number of stents, and total stented length (1.72 6 0.89 vs. 1.49 6 0.83; P < 0.001 and 37.4 6 23.0 mm vs. 30.8 6 20.7 mm; P = 0.0003, respectively), and had lower rates of clinical success (91.9% vs. 99.2%; P < 0.001). The 6-month and 1-year TVR-MACE rates were higher for the elevated CK-MB group (11.9% vs. 7.0%; P = 0.02 and 16.1% vs. 26.6%, respectively; P = 0.005). The rates of subacute thrombosis were also significantly higher in the group with elevated CK-MB (0.4% vs. 3.2%, P < 0.001). Though significant CK-MB release was a predictor of TVR-MACE after univariate analysis, multivessel PCI, subacute stent thrombosis, total stented length, and history of prior PCI were the only predictors after multivariate regression analysis. Conclusions: Postprocedural CK-MB 33 elevation following PCI with DES continues to be a marker for the complexity of coronary disease and lack of clinical success; and correlates with higher rates of subacute thrombosis as well as late adverse events at 6-months and 1-year postprocedure. ' 2007Wiley-Liss, Inc.
On the Application of Automatic Subword Unit Derivation and Pronunciation Generation for Under-Resourced Language ASR: A Study on Scottish Gaelic

Abstract Automatic speech recognition (ASR) systems typically require acoustic and lexical resources (such as a phonetic lexicon) which maynotbeavailable,inparticularforunder-resourcedlanguages. Atypicalapproachtoaddresstheissueoflexicalresourcesintheliteratureistousegraphemesasthesubwordunits. However,thesuccessofgrapheme-basedASRsystemsdependsonthegrapheme-to-phonemerelationshipinthelanguage. Inthispaperweinvestigatethepotentialofusingautomaticallyderivedsubwordunits(ASWUs)forunder-resourced languages that lack lexical resources and have limited acoustic resources. More precisely, we exploit a recently proposedhidden Markov model (HMM) formalism in which the subword units and the associated pronunciations are derived using only targetlanguage transcribed speech data. Our experimental studies on Scottish Gaelic, a minority and under-resourced language, show thatASWUs can lead to signicantly better ASR systems compared to grapheme subword units. Furthermore, the ASWU-based ASRsystems yield comparable performance to the systems using multilingual acoustic and lexical resources.IndexTerms: automaticsubwordunitderivation, pronunciationgeneration, hiddenMarkovmodel, Kullback-Leiblerdivergencebasedhidden Markov model, under-resourced language, automatic speech recognition
U.S. Water Resource System under Climate Change

Water availability is a growing concern globally (UN, 2012). Many countries are affected by water scarcity and quality issues (Postel, 2000). The United States (U.S.) is no exception, with the Colorado and the Rio Grande rivers so severely exploited that they often do not reach the oceans. The exploitation of U.S. water resources is the consequence of growing population and economic activity, and lack of conservation measures. Under the threat of climate change and consequently a change in water resources, water issues are even more pressing. To investigate the issue of water allocation and scarcity for the U.S., we use a computable general equilibrium (CGE) model to drive water requirements in an integrated assessment framework. Specifically, we apply a specially tailored version of the Integrated Global System Model – Water Resource System (IGSM-WRS) model (Strzepek et al., 2012), which draws on the water system module (WSM) developed by the International Food Policy Research Institute (Rosegrant et al. 2008). WRS allows the linkage of WSM with the IGSM (Sokolov et al. 2005). This integrated assessment framework facilitates evaluation of both the direct (via a geophysical model) and indirect (thanks to a CGE model) impacts of climate policy on water scarcity. Taking advantage of data available for the U.S., we model water at a 99-basin level (instead of the 14 regions in the global WRS model). Detailed economic inputs are supplied by the 11-region U.S. Regional Economic Policy (USREP) model (Rausch et al. 2009). This CGE model also provides detailed energy demand which allows a better estimation of water requirements for mining and thermoelectric power generation. WRS-US models water resources and requirements and allocates the available water to different users each month while minimizing annual water deficits (i.e. water requirements that are not met). To do so, the model solves the allocation of water for each ASR simultaneously for all the months of ea.