Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomics and Forest Biology: Populus Emerges as the Perennial Favorite

Forest biologists have developed strong justifications for why trees should be viewed as model systems in plant biology, including the obvious challenges in extrapolating findings from annual, herbaceous plants to organisms that are distinguished by perennial growth, large size, complex crown architecture, extensive secondary xylem, dormancy, and juvenile–mature phase changes (Bradshaw et al., 2000; Taylor, 2002). Similar justification has been used to argue why the genome of a tree should be sequenced. The U.S. Department of Energy (DOE), Office of Science, announced earlier this year plans to sequence the first tree genome, that of the black cottonwood ( Populus trichocarpa ) (Figure 1). In what has emerged as an exciting area in forest biology, two meetings recently convened at which advances in Populus genomics were featured: the International Poplar Symposium III, held August 26 to 29, 2002, in Uppsala, Sweden, and the Populus Functional Genomics Workshop, held August 30, 2002, in Umeå, Sweden. Together, the meetings attracted 200 scientists from 23 countries. Here, we summarize those portions of the symposium and workshop that highlight emerging tools, techniques, and research directions in Populus genomics.
Participatory Assessment and Planning Approach: Conceptual and Process Issues

ABSTRACT Past Rapid Rural Appraisals (RRAs) and Participatory Rural Appraisals (PRAs) have placed emphasis on common appraisal factors such as resource diagnosis and problems and constraints identification, with little attention to the follow-up action element of rural development. In this paper, a new agricultural Research and Development (R & D) approach called Participatory Assessment and Planning (PAP) was introduced. The conceptual and process issues relating to the PAP approach were discussed, using a PAP case experience in the Wusi Village community, Deqing County, China. The success of the case study exercise justified the rationality as well as applicability of the design of the PAP approach, showing its great relevance to agricultural R & D efforts in China.
Zooplanktivory ameliorates the effects of ocean acidification on the reef coral Porites spp

I tested the hypothesis that the effects of high pCO2 and temperature on massive Porites spp. (Scleractinia) are modified by heterotrophic feeding (zooplanktivory). Small colonies of massive Porites spp. from the back reef of Moorea, French Polynesia, were incubated for 1 month under combinations of temperature (29.3°C vs. 25.6°C), pCO2 (41.6 vs. 81.5 Pa), and feeding regimes (none vs. ad libitum access to live Artemia spp.), with the response assessed using calcification and biomass. Area‐normalized calcification was unaffected by pCO2, temperature, and the interaction between the two, although it increased 40% with feeding. Biomass increased 35% with feeding and tended to be higher at 25.6°C compared to 29.3°C, and as a result, biomass‐normalized calcification statistically was unaffected by feeding, but was depressed 12–17% by high pCO2, with the effect accentuated at 25.6°C. These results show that massive Porites spp. has the capacity to resist the effects on calcification of 1 month exposure to 81.5 Pa pCO2 through heterotrophy and changes in biomass. Area‐normalized calcification is sustained at high pCO2 by a greater biomass with a reduced biomass‐normalized rate of calcification. This mechanism may play a role in determining the extent to which corals can resist the long‐term effects of ocean acidification.
INFLUENCE OF DIETARY NUTRIENT DENSITY, LEVEL OF FEED INTAKE AND WEANING AGE ON YOUNG PIGS. II. APPARENT NUTRIENT DIGESTIBILITY AND INCIDENCE AND SEVERITY OF DIARRHEA

One hundred and twenty-eight pigs were allotted to a factorial design involving two weaning ages (3 and 4 wk), two diets (normal density, ND, and high density, HD) and two levels of feed intake (ad libitum and restricted) and fed for 28 d postweaning. Feed restriction increased the digestibility of energy (P < 0.05). Apparent digestibility of energy and protein increased with time postweaning (P < 0.05). Pigs weaned at 4 wk of age had higher nutrient digestibilities than those weaned at 3 wk only in the second week postweaning (P < 0.05), showing that the digestive system of older pigs adapts faster. The apparent digestibility of the HD diet was not different from that of the ND diet. Diarrhea was more severe when pigs were weaned at 4 wk (P < 0.10), or when receiving the HD diet (P < 0.10), or when offered feed ad libitum (P < 0.10), showing that both volume of feed consumed and nutrient intake influence occurrence of diarrhea. Postweaning diarrhea was most severe (P < 0.05) and most frequent (P < 0.05) .
PARALLEL INEXACT NEWTON-TYPE METHODS FOR THE SUPG/PSPG SOLUTION OF STEADY INCOMPRESSIBLE 3D NAVIER-STOKES EQUATIONS IN PC CLUSTERS

The finite element discretization of the three-dimensional incompressible Navier-Stokes yields a non-linear problem due the convective terms in the momentum equation. In this work we describe a parallel MPI-based implementation for PC clusters of inexact Newton-type schemes associated to the SUPG/PSPG stabilized finite element formulation of steady incompressible flows. The resulting linear systems of equations are solved iteratively by an element-by-element preconditioned GMRES solver. Performance of the parallel iterative solver and the nonlinear strategy is evaluated by numerical tests in a benchmark problem.
Real-World Super-Resolution via Kernel Estimation and Noise Injection

Recent state-of-the-art super-resolution methods have achieved impressive performance on ideal datasets regardless of blur and noise. However, these methods always fail in real-world image super-resolution, since most of them adopt simple bicubic downsampling from high-quality images to construct Low-Resolution (LR) and HighResolution (HR) pairs for training which may lose track of frequency-related details. To address this issue, we focus on designing a novel degradation framework for real- world images by estimating various blur kernels as well as real noise distributions. Based on our novel degradation framework, we can acquire LR images sharing a common domain with real-world images. Then, we propose a real- world super-resolution model aiming at better perception. Extensive experiments on synthetic noise data and real- world images demonstrate that our method outperforms the state-of-the-art methods, resulting in lower noise and better visual quality. In addition, our method is the winner of NTIRE 2020 Challenge on both tracks of Real-World Super-Resolution, which significantly outperforms other competitors by large margins.
Machine Learning and Optimization Laboratory Privacy-preserving and Personalized Federated Machine Learning for Medical Data Semester project

The federated learning setting is prone to suﬀering from non-identically distributed data across participating agents. This gives rise to the task of model personalization, where agents collaborate to train several diﬀerent machine learning models instead of training only one global model. The aim of model personalization is to minimize the sum of the generalization error incurred from training on small data sets, and the transfer error incurred from applying a globally-trained model to a speciﬁc local distribution. In this report, two novel approaches to personalized cross-silo federated learning are introduced and discussed from a theoretical perspective: the adapted Ndoye factor, and the Weight Erosion aggregation scheme. The latter is implemented and compared to two baseline aggregation schemes in two case studies: training a diagnostic model on real-world medical data, and predicting the survival of passengers on the publicly available Titanic data set. The models trained using the Weight Erosion aggregation scheme are compared to those trained using the baseline aggregation schemes, both in terms of their classiﬁcation accuracy on the local test set and in terms of the learned parameters. We demonstrate that the novel Weight Erosion scheme can outperform both baseline aggregation schemes for some speciﬁc tasks.
Role of Sialylation in the Nervous System Development of Drosophila melanogaster

Role of Sialylation in the Nervous System Development of Drosophila melanogaster. (August 2009) Elena Aleksandrovna Repnikova, B.S.; M.S., Saint Petersburg State Polytechnical University, Russia Chair of Advisory Committee: Dr. Vladislav M. Panin The sialyltransferase family is a group of enzymes that transfer sialic acid from donor CMP-Neu5Ac onto suitable carbohydrate chains of glycoproteins and glycolipids. In vertebrates, sialylation is implicated in many physiological and pathobiological processes, including nervous and immune system development and functioning, pathogen-host interaction, cancer cell proliferation and apoptosis. However, the complexity of the sialylation pathway and limitation of genetic and in vivo approaches interferes with functional analyses in mammalian organisms. We use Drosophila because of its simplified physiology and reduced genetic redundancy to characterize the evolutionarily conserved function of sialylation and to reveal its relationship to the role of sialic acids in humans. This dissertation focuses primarily on Drosophila sialyltransferase, DSIAT, so far the only sialyltransferase described in protostomes. Gene targeting of the DSIAT endogenous locus with a DSIAT-HA tagged version uncovered its remarkably dynamic stageand cell-specific expression. I found that the expression of DSIAT is developmentally regulated and is restricted to motor neurons and
Copepods (Crustacea, Maxillopoda) from shallow reservoirs

Abstract: Aim: Among the planktonic microcrustaceans, copepods Cyclopoida and Calanoida are the most representative groups, being the largest biomass of the plankton community. The aim of this work is to catalogue and analyze the distribution of copepod species (Crustacea, Maxillopoda) in pelagic and littoral zones from small reservoirs in the northwest of the Sao Paulo State, in dry and rainy seasons (2007 and 2009). Methods: Zooplankton samplings were carried out in littoral and pelagic zones of 13 small shallow reservoirs (mean depth: 2.6 m) using vertical hauls and plankton net (45 µm). Water physical and chemical parameters were also monitored with a multiparameter Horiba ® U10. Results: Eighteen species of copepods were identified, 13 Cyclopoida and 5 Calanoida. There was no statistical difference between the distributions of species from the littoral and pelagic zones and neither between dry and rainy seasons. Three species occurred exclusively in the littoral zone Eucyclops elegans, - Paracyclops chiltoni
The Effect of a Bolus Injection of TNF-α and IL-1β on Hepatic Energy Metabolism in Rats

Abstract The effects of intravenous bolus injection of tumor necrosis factor-alpha (TNF-α) and interleukin-1beta (IL-1β) on hepatic mitochondrial energy metabolism were investigated in rats. The rats were injected with 15 μg/kg body wt of human recombinant TNF-α and IL-1β. The hepatic energy charge decreased to 0.794 ± 0.005 and 0.789 ± 0.006 in comparison with the sham control value of 0.838 ± 0.007 and 0.835 ± 0.011 at 12 and 24 hr after the treatment. The mitochondrial redox state (NAD + /NADH) increased from 17.4 ± 1.9, 16.6 ± 1.4, and 19.2 ± 2.1 to 33.5 ± 3.5, 27.8 ± 2.8, and 30.9 ± 2.6 concomitant with an increase in arterial blood ketone body ratio (acetoacetate/β-hydroxybutyrate) from 0.49 ± 0.04, 0.34 ± 0.04, and 0.44 ± 0.09 to 1.00 ± 0.16, 0.69 ± 0.13, and 0.86 ± 0.15 at 3, 12, and 24 hr after the treatment. Total ketone body concentration in liver tissue and arterial blood was significantly lower at 24 hr after the treatment. State 3 respiration rate of isolated mitochondria increased by 29.2, 30.3, and 19.2% concomitant with an increase in oxidative phosphorylation rate by 26, 33.7, and 24.3% at 3, 12, and 24 hr after the treatment. These results showed that the administration of TNF-α and IL-1β in rats induced a hypermetabolic state in hepatic mitochondrial energy metabolism, which is a pattern similar to sepsis and presumably a compensatory reaction to the increased energy consumption.
Applications of mitochondrial DNA analysis in conservation: a critical review

Patterns of variation in mitochondrial DNA (mtDNA) increasingly are being investigated in threatened or managed species, but not always with clearly defined goals for conservation. In this review I identify uses of mtDNA analysis which fall into two different areas: (i) ‘gene conservation’ ‐ the identification and management of genetic diversity, and (ii) ‘molecular ecology’ ‐ the use of mtDNA variation to guide and assist demographic studies of populations. These two classes of application have different conceptual bases, conservation goals and time‐frames. Gene conservation makes extensive use of phylogenetic information and is, in general, most relevant to long‐term planning. Appropriate uses here include identification of Evolutionarily Significant Units and assessment of conservation priority of taxa or areas from an evolutionary perspective. Less appropriate are inferences about fitness from within‐population diversity and about species boundaries. Molecular ecology makes more use of allele frequencies and provides information useful for short‐term management of populations. Powerful applications are to identify Management Units and to define and use naturally occurring genetic tags. Estimating demographic parameters, e.g migration rate and population size, from patterns of mtDNA diversity is fraught with difficulty, particularly where populations are fluctuating, and is unlikely to produce quantitative estimates sufficiently accurate to be useful for practical management of contemporary populations. However, through comparative studies, mtDNA analysis can provide qualitative signals of population changes, allowing efficient targeting of resource‐intensive ecological studies. Thus, there are some relatively straightforward uses of mtDNA, preferably in conjunction with assays of nuclear variation, that can make a significant contribution to the long‐term planning and short‐term execution of species recovery plans.
Compact InP Wavelength Blocker based on a Single AWG and SOA gates for Metro Networks

We present a novel wavelength blocker (WBL) design with a folded configuration for a modular wavelength selective switch (WSS) within the metro network. The folded design enhances scalability of the WSS due its compactness and modularity. The design is experimentally verified with four channels WBL made of a single AWG, SOA-based gates and 90-waveguide crossing of low loss and low cross-talk (< -65dB). Experimental results show error-free operation with < 1.3dB penalty at 10Gbps NRZ-data.
Mapping of randomly amplified polymorphic DNA primer (RAPD) on chromosome 2A of common wheat

Randomly amplified polymorphic DNA primers (RAPDs) were mapped on chromosomes 2A of wheat genotypes using “Chinese Spring” nullisomic-tetrasomic lines. One particular pair of chromosome was absent and another homologous pair was present in the extra dose. Genomic DNA was isolated from two genetic stocks viz; NT1D1B and NT2A2B. Polymerase chain reaction (PCR) were conducted using RAPD primers GLC-07 and GLB-11. PCR amplification using primer GLC-07 produced single band of approximately 1100 bp in both the genetic stocks, indicating that the primer was annealed to a loci other than chromosome 2A. RAPD primer GLB-11 amplified a polymorphic allele of approximately 500 bp which was present in NT1D1B but was absent in NT2A2B, indicating that the locus was present on chromosome 2A of common wheat. Hence, this marker (GLB-11) can reliably be used to keep track of chromosome 2A of wheat. Key words: Wheat, randomly amplified polymorphic DNA primer (RAPD), mapping, chromosomes, homologous, genomes.
MEETING REVIEW Bacterial Signaling and Motility: Sure Bets

The IX International Conference on Bacterial Locomotion and Signal Transduction (BLAST IX) was held from 14 to 19 January 2007 in Laughlin, NV, a town in the Mojave Desert on the Nevada-Arizona border near old Route 66 and along the banks of the Colorado River. This area is a home to rattle-snakes, sagebrush, abandoned gold mines, and compulsive gamblers. What better venue could scientists possibly dream of for a professional meeting? So there they were, about 190 scientists gathered in the Aquarius Casino Resort, the largest hotel and casino in Laughlin, discussing the latest advances in the ﬁeld. Nothing, not the bustling sounds from countless slot machines and poker tables or the unusually cold and windy weather, dampened the atmosphere of the conference or dis-tracted those zealots from their science. Aside from a brief excursion to an abandoned gold mine and a dinner cruise on the Colorado River, the scientists focused on nothing but their data and hypotheses, in spirited arguments and rebuttals, and outlined their visions and future plans in a friendly and open environment. The BLAST IX program was dense, with nearly 50 talks and over 90 posters. For that reason, this meeting report will not attempt to be comprehensive; instead it will ﬁrst provide general background information on the central topics of the meeting and then highlight only a few talks that were of special interest to us and hopefully to the wider scientiﬁc LOV photosensory histidine kinase that has been impli- cated in the light-mediated regulation of cell attachment.
Valuation of football players in financial statements: the power of the crowd versus transfer fees

The aim of this paper is to analyze the convenience of reflecting football players’ value as intangible assets in financial statements of football clubs from the amounts paid on the transfer rights, or through other techniques, such as the methodologies called “market value”, MV, based on crowdvaluation. The research also incorporates an exhaustive and critical review and analysis of academic literature, and football accounting regulations. The paper is based on a model which included 227 observations of crowd valuation, MV, and 127 transfer value/fees, TF, for the best 76 footballers of the Spanish League, Premier League, and German League over 12 years. This paper analyzes the differences between both models to overcome the limitations of standard accounting and fair play FIFA to reflect all the human capital in financial statement of football clubs. This research provides evidence for accounting regulators, UEFA, and football club managers to understand the power and challenges of crowd valuation of football players comparatively to prices paid in the transactions of them. Finally, focusing on the necessity to provide fair football club reporting, more rational and sustainable to their activities, the article concludes that the criteria of IAS 38 does not allow this task due to the impossibility of reflecting correctly the human intangible capital of clubs. The standard accounting should incorporate a special treatment for the talent in football business through the adoption of a generic process based on data analytics to support the football players’ valuation.
Figures de la plainte : la douleur, la souffrance et la considération

De l'experience et de la parole des malades, il est toujours plus question a mesure que s'est developpee une medecine scientifique pouvant s'en dispenser. Divers lieux et pratiques sont recemment apparus pour faire entendre leur plainte : comites d'ethiques, groupes de paroles, soins palliatifs, comites d'examen des plaintes, notamment. De multiples facons, le malade est aujourd'hui invite a temoigner de son experience, a exprimer le bouleversement vecu et a faire connaitre ses besoins. Trois experiences de la parole sont examinees ici, du point de vue du malade et de leur signification culturelle : la douleur, la souffrance et la consideration. Ce sont trois demandes adressees aux soignants, mais aussi trois experiences par lesquelles le malade est amene a penser son individualite et sa relation aux autres, a faire retour sur son passe et a reflechir sur ce qu'il est et aspire a etre. L'experience de la maladie est ainsi devenue un moment privilegie de la construction de l'identite individuelle.
P2 nucleotide receptors in osteoclasts

Osteoclasts are large, multinucleated cells responsible for the resorption of bone and other mineralized tissues. Whereas low concentrations of extracellular ATP stimulate osteoclast formation and resorptive activity, high concentrations inhibit osteoclast formation. Cell surface receptors for nucleotides are classified into two families—P2X (ligand‐gated channels nonselective for cations) and P2Y (G‐protein‐coupled receptors linked, in most cases, to release of Ca2+ from intracellular stores). Several subtypes of P2 receptors are expressed by mammalian osteoclasts. The P2X4 receptor has been identified at both protein and messenger RNA levels and ATP activates a nonselective cation current with properties similar to that mediated by the cloned P2X4 channel. The P2X2 receptor is also expressed; however, currents with properties of P2X2 have yet to be identified. Functional and expression studies also support the existence of the P2X7 receptor, which is activated by high concentrations of ATP. Application of nucleotides to osteoclasts elicits transient elevation of cytosolic free Ca2+ concentration and activation of Ca2+‐dependent K+ channels. Both these responses are mediated, at least in part, by release of Ca2+ from intracellular stores, consistent with the presence of functional P2Y receptors. Expression of P2Y1 and P2Y2 receptors has been demonstrated in mammalian osteoclasts. The presence of multiple subtypes of P2 receptors may account for the biphasic effects of extracellular nucleotides on osteoclast function. These receptors represent potential targets for the development of novel therapeutics to inhibit bone resorption in diseases such as rheumatoid arthritis, osteoporosis, tumor‐induced osteolysis, and periodontitis. Drug Dev. Res. 53:130–139, 2001. © 2001 Wiley‐Liss, Inc.
PII: S0022-247X(02)00638-8

We consider the multiplicity and stability of subharmonic solutions of discrete dynamic systems with periodic perturbations, whose existence was established in the first part of this series. Under the hypotheses that the perturbation is locally Lipschitz continuous, we determine the precise number of subharmonic solutions, and we also show that these subharmonic solutions are stable (unstable) provide the periodic orbit of the unperturbed system is stable (unstable).  2002 Elsevier Science (USA). All rights reserved. * Corresponding author. E-mail address:wujh@mathstat.yorku. ca (J. Wu). 1 Research partially supported by the National Natural Science Foundations of China. This work was complete while the author visited York University. 2 Research partially supported by the National Natural Science Foundations of China. 3 Research partially supported by the Natural Sciences and Engineering Research Council of Canada, and partially supported by the Canada Research Chairs Program. 0022-247X/02/$ – see front matter  2002 Elsevier Science (USA). All rights reserved. PII: S0022-247X(02)00638-8 478 R. Zhang et al. / J. Math. Anal. Appl. 276 (2002) 477–496