Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein domain of unknown function DUF1023 is an α/β hydrolase

Pfam family DUF1023 consists entirely of uncharacterized proteins generated by sequencing the genomes of Actinobacteria (Bateman A., et al., Nucleic Acids Res. 2004;32 Database issue:D138–141.) Utilizing sequence similarity detection methods, we infer homology between DUF1023 and α/β hydrolases. DUF1023 proteins conserve the core secondary structures in α/β hydrolase fold, and share similar catalytic machinery as that of α/β hydrolases. We predict DUF1023 spatial structure and deduce that they function as hydrolases utilizing catalytic Ser‐His‐Asp triad with the serine as a nucleophile. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Leaf Respiration in Light and Darkness

We investigated whether leaf dark respiration (nonphotorespiratory mitochondrial CO, release) is inhibited by light in several Poa species, and whether differences in light inhibition between the species are related to differences in the rate of leaf net photosynthesis. Four lowland (Poa annua L., Poa compressa L., Poa pratensis L., and Poa trivialis L.), one subalpine (Poa alpina l.), and two alpine (Poa costiniana Vick. and Poa fawcettiae Vick.) Poa species differing in whole plant relative growth rates were grown under identical controlled conditions. Nonphotorespiratory mitochondrial CO, release in the light (R,) was estimated according to the Laisk method. Photosynthesis was measured at ambient CO, partial pressure (35 Pa) and 500 pmol photons m-’s-’. The rate of photosynthesis per unit leaf mass was positively correlated with the relative growth rate, with the slow-growing alpine Poa species exhibiting the lowest photosynthetic rates. Rates of both Rd and respiration in darkness were also substantially lower in the alpine species. Nonphotorespiratory CO, release in darkness was higher than Rd in all species. However, despite some variation between the species in the level of light inhibition of respiration, no relationship was observed between the level of inhibition and the rate of photosynthesis. Similarly, the level of inhibition was not correlated with the relative growth rate. Our results support the suggestion that rates of leaf respiration in the light are closely associated with rates in darkness.
EnsembleSync: Reliable Distributed SGD with Less Communication

Traditionally, distributed large scale training of neural networks splits data across workers. Every step of training requires communicating model parameters to and from a central parameter server, which may be very expensive for modern models. Our insight is that in machine learning, we can relax the conditions for consensus. Different parameters can be reconciled by ensembling rather than requiring a majority to agree on a value. Speciﬁcally, we consider EnsembleSync, a synchronous distributed training algorithm where each worker computes T steps of local training before sending updates to the parameter server, which then reconciles the updates by ensembling (averaging) the parameters. To avoid being bottlenecked by slow/faulty workers during synchronization, we dynamically reallocate more compute (GPUs) for a slower worker under a ﬁxed budget. We ensure progress even with faults on up to M − 1 workers by reallocating resources when workers fail. On top of computation and reliability gains, EnsembleSync increases the model performance with respect to base distributed training algorithms.
DELTA TYPING AND ANALYSIS OF ALCOHOL TOLERANCE GENES (erg2, hsp104, sod2 ) IN SIX LOCAL WINE STRAINS OF Saccharomyces cerevisiae

desirable wine strains of Saccharomyces cerevisiae are maintained is valuable for wine producers to ensure the quantity and quality of wines produced. Random Amplification of Polymorphic DNA (RAPD) in a previous study, generated Polymerase Chain Reaction (PCR) profiles that could distinguish S. cerevisiae wine strains (that exhibited growth in 10% and 15% ethanol) from a non-wine strain (that exhibited growth inhibition in 10 and 15% ethanol) and wine strains from one another. In this study, delta (δ) typing and sequence analysis of three specific genes (erg2, hsp104 and sod2) implicated in alcohol tolerance were T performed in search of a faster and cheaper procedure to distinguish strains of S. cerevisiae. The use of delta primer pair, δ12 / δ2, resulted in a distinct profile for each of yeast strains studied. Compared to RAPD, which makes use of several random primers and several PCR runs, delta typing involves one PCR run and uses a single δ primer pair. Sequence analysis of three S. cerevisiae genes that code for proteins involved in major mechanisms proposed for alcohol tolerance of the species, revealed single (for the erg2 and hsp104 genes) to multiple (for the sod2 gene) nucleotide variations. The nucleotide polymorphisms observed for the erg2 and sod2 genes are not expected to result in amino acid variation while the polymorphisms found in the amplified fragments of the hsp104 gene resulted in amino acid variation at position 236. Nucleotide and protein polymorphisms in these genes, however, could not discriminate the yeast strains studied and the variation did not correlate with the reported strain differences in alcohol tolerance. Results of this study suggest that delta (δ) typing with primers δ12 and δ2, is more discriminatory, faster, and less expensive than RAPD and is recommended to be the first procedure to perform in trying to discriminate wine strains of S. cerevisiae. Polymorphisms observed in the three genes, erg2, hsp104 and sod2, cannot be used as a basis for designing PCR
Evaluation of Potential DNA Barcodes for Identifying Thunbergia spp.

Introduction: A number of Thunbergia species are widely used as medicinal plants. Identifi - cation by traditional morphological methods is diffi cult especially when specimens are commercial herbal products, which morphology is unattainable. To facilitate the identifi cation process, this study searched for potential DNA barcodes by evaluating three DNA loci, the chloroplast psbA-trnH and trnL-trnF intergenic spacers and the second nuclear internal transcribed spacer (ITS2), among eight species of Thunbergia. Methods: Plant samples were collected and fresh leaves were used for genomic DNA extractions. Polymerase chain reaction amplifi cations of the psbA-trnH, trnL-trnF and ITS2 regions were performed. The PCR products were sequenced and verifi ed by BioEdit v7.0. 8 and Clustal W programs. Kimura 2-Parameter (K2P) were computed via MEGA 6.06 to reveal the genetic divergence. Results: Three candidate regions of all Thunbergia DNA samples were successfully amplifi ed with the rate of 100 %. These amplifi ed products were also successfully sequenced (100%) in both directions. The average interspecifi c divergence values calculated from K2P for psbA-trnH, trnL-trnF, and ITS2 were 0.088, 0.054 and 0.121, respectively, implying that each Thunbergia spp. could be discriminated from one another. Conclusion: This study confi rmed the universality of the primers used for psbA-trnH, trnL-trnF and ITS2 PCR amplifi cation and sequencing. The K2P results showed that each locus could individually differentiate between Thunbergia spp. under studied while the most variable region that can make a distinction effectively was ITS2. The combination of ITS2 with psbA-trnH and/or trnL-trnF sequences was proposed as a potential barcode for identifying Thunbergia species.
Endo-β-mannanase activity is associated with the completion of embryogenesis in imbibed carrot (Daucus carota L.) seeds

Abstract Development of the rudimentary embryo in mature carrot (Daucus carota) seed during imbibition was characterized. The small embryo in the carrot seed, located in the micropylar region, elongated into the lateral part during imbibition and attained about two-thirds the length of the seed before radicle protrusion. Developing embryos excised from imbibed seeds were only capable of germinating in both water and Murashige–Skoog (MS) medium when they reached maximum size. The corrosion cavity into which the embryo grew enlarged concomitantly with endosperm degradation. The expression of endo-β-mannanase (EC 3.2.1.78), which is assumed to be involved in endosperm degradation, was characterized. A cDNA encoding an endo-β-mannanase was obtained by reverse transcription polymerase chain reaction (RT-PCR) using total RNA extracted from 24-h-imbibed carrot seeds. The full-length cDNA (DcMAN1) exhibited 64% deduced amino acid sequence identity with tomato (Lycopersicon esculentum) seed germination-associated mannanase (LeMAN2). DcMAN1 mRNA and endo-β-mannanase activity were first detected in the micropylar-half seed and then in the lateral-half seed. The timing of the appearance of DcMAN1 mRNA and endo-β-mannanase activity in the lateral-half seed corresponded with that of embryo development into this region. These results suggest that the expression of DcMAN1 and endo-β-mannanase activity in imbibed carrot seeds is associated with the enlargement of the corrosion cavity, which accompanies embryogenesis.
Gene flowanalysis of anopheles arabiensis (Diptera:culicidae) populations in southern africa using microsatellite DNA markers

Anopheles arabiensis is considered an important vector of human malaria in the southern African region where the disease is the major cause of morbidity and mortality. Gene flow plays an important role in malaria control with the spread of insecticide resistance. The main objectives of this study were to (i) measure the genetic variability within and between five populations (Botswana, Namibia, South Africa, Swaziland and Zimbabwe) of wild An. arabiensis and (ii) estimate the level of gene flow between natural populations across the Southern-limits of An. arabiensis. A total of 1225 An. arabiensis specimens were identified out of 1300 mosquitoes collected from 2000-2003 with the sample sizes ranging from 180-292 per country. Variation at four microsatellite markers was investigated on non-denaturing polyacrylamide gels. The results showed fewer variations between populations (2.96%) than within populations (82.60%) suggesting considerable homogeneity. However, estimates of gene flow (Nm) calculated from mean FST and RST statistics were relatively low, 1.14 and 1.19 respectively, suggesting somewhat restricted gene flow between populations. The occurrence of gene flow within subpopulations of An. arabiensis in Zimbabwe but not in South Africa is interesting with regard to the spread of insecticide resistance in Zimbabwe. The results presented here are obviously subject to the limitations inherent in manual, silver staining method of analysing microsatellite DNA markers. It is possible that a different set of results would be obtained if an Automated Sequencing Analyzer were used.
Determinants of Mallard and Gadwall Nesting on Constructed Islands in North Dakota

Abstract Constructed islands with adequate nesting cover provide secure nesting sites for ducks because islands restrict access by mammalian predators. These islands are costly to construct and should be placed in areas that ensure the greatest use by nesting ducks. We studied mallard (Anas platyrhynchos) and gadwall (A. strepera) nesting on constructed islands in North Dakota in 1996 (n = 20) and 1997 (n = 22) to evaluate factors—particularly amount of perennial grass cover in the surrounding landscape and density of breeding pairs—that possibly influence numbers of initiated nests. We also examined effects of island characteristics, such as island vegetation, on numbers of nests. Numbers of mallard and gadwall nests on islands were negatively related to amounts of perennial grass cover in the surrounding uplands. Numbers of mallard nests were positively related to percentages of tall dense cover on islands. We found no effects of breeding-pair density on numbers of nests initiated by either species, possibly because breeding pairs were abundant on all study sites. Percent shrub cover on islands was a better predictor of island use than was percent tall dense cover. Island use by these species increased with island age and distance from mainland shore. Amounts of perennial cover in landscapes should be primary considerations in determining where to build islands. Our data suggest that use of islands by nesting mallards and gadwalls is greatest in landscapes with little perennial grass cover (i.e., high amounts of cropland). Other researchers documented a positive relation between nest success in upland covers and amount of perennial grass cover in the landscape. Therefore, islands constructed in landscapes with little perennial cover should provide greater gains in duck recruitment rates than islands constructed in landscapes with greater amounts of perennial grass cover.
White butterfly (Pieris rapae) and the white rust Albugo candida on Cook's scurvy grass (Lepidium oleraceum).

Once widespread, Cook's scurvy grass (or nau, Lepidium oleraceum) is now confined to a few offshore populations. Classed as nationally endangered by the New Zealand Department of Conservation, populations of Cook's scurvy grass are threatened by a number of factors, including introduced herbivorous insect species such as the white butterfly (Pieris rapae) and white rust infection caused by the oomycete Albugo candida. In this paper, we investigate the occurrence of white butterfly on Cook's scurvy grass and possible interactions with the white rust infection on the northernmost of the Matariki Islands in the Firth of Thames, New Zealand. We found that larger host plants were more likely to be infested with white butterfly. The occurrence of white butterfly eggs and larvae also decreased as levels of white rust increased. Twenty-eight percent of the white butterfly larvae collected and reared in the laboratory were parasitised by the braconid wasp species Cotesia rubecula. We also reared a hyperparasitoid belonging to the super-family Chalcidoidea from one of the parasitoid cocoons. Further studies on the trophic interactions between Cook's scurvy grass, Albugo candida and white butterfly and its parasitoids could improve the understanding of the threats posed by plant pathogens and insect herbivores to populations of Cook's scurvy grass, which in turn may lead to new management strategies for conservation.
A comparison of the flagellar apparatus in Phytophthora, Saprolegnia, Thraustochytrium, and Rhizidiomyces

The rootlet systems, kinetosomes, and transition zones in zoospores of Phytophthora parasitica, Thraustochytrium aureum, and Rhizidiomyces apophysatus and secondary zoospores of Saprolegnia diclina are compared. Rootlet systems in P. parasitica and S. diclina are very similar and there are only minor differences between these taxa in morphology of their transition zones. In P. parasitica and T. aureum a number of differences exist in the rootlet systems, but the position and orientation of individual rootlets are similar. There are also differences between these taxa in the alignment of their kinetosomes, the morphology of their kinetosome cores, and transition zones. Rhizidiomyces apophysatus has rootlets that correspond in position and orientation to P. parasitica, but there are not as many rootlets and these are morphologically distinctive. However, R. apophysatus and S. diclina have flagellar transition zones that are morphologically alike. Thus, probably the Hyphochytriomycetes are phylogenetically q.
A New Species of Melanophryniscus Gallardo, 1961 (Anura: Bufonidae), with Comments on the Species of the Genus Reported for Misiones, Northeastern Argentina

Abstract A new species of bufonid toad in the genus Melanophryniscus, from the province of Misiones, northeastern Argentina, is described. It is included in the stelzneri group and is most similar to Melanophryniscus atroluteus than to any other species. Melanophryniscus sp. nov. is distinguished, by having a uniformly brown dorsal coloration, numerous white spots along the mandibular arch; the pupil surrounded by a golden ring; the iris gold, finely spotted with dark brown; and the frontoparietal fontanelle widely exposed anteriorly. Moreover, the advertisement call of the new species is noticeable longer than the call of M. atroluteus and has a higher dominant frequency. The Melanophryniscus species present in Misiones are discussed and several areas of syntopy are reported.
Bulbothrix asiatica sp. nov., and other new records of Parmeliaceae with bulbate cilia from Cambodia

Abstract Bulbothrix asiatica Y. Y. Zhang & Li S. Wang sp. nov. is proposed to accommodate specimens with a black lower surface, an emaculate and cracked upper surface and salazinic acid in the medulla. The species is currently known only from Cambodia and southwestern China. Other Parmeliaceae with bulbate cilia here newly reported from Cambodia are: Bulbothrix lyngei, B. subscortea, Relicina abstrusa and R. circumnodata. Phylogenetic trees for Bulbothrix are established to assess the affinities of the new species and test for a differentiation of saxicolous and epiphytic populations of B. subscortea. A key to these species is presented.
Survey and DNA Barcoding of Poaceae in Flat Rock Cedar Glades and Barrens State Natural Area, Murfreesboro, Tennessee

Abstract A survey of grasses from the Flat Rock Cedar Glades and Barrens State Natural Area in Murfreesboro, Tennessee was undertaken during the 2008 growing season with the goal of creating a comprehensive list of grass species living in a single glade environment. Twenty four different species were identified during the survey. All had been previously recorded in Tennessee but two had not been noted in cedar glades, Sprorobilus clandestinus and Elymus hystrix, and one, Dichanthelium scoparium, had not been demonstrated in Rutherford County. The survey also provides information on species distribution within the glade, amount of sunlight exposure, and flowering time within the growing season. The plastid matK and rbcL genes and the trnH-psbA intergenic spacer region were sequenced from the specimens and are cataloged in GenBank. Variance analysis of matK and rbcL loci was conducted with the sequences produced in this study as well as GenBank archived sequences from other grasses. Our data conservatively suggest that the Consortium for the Barcode of Life (CBOL) recommended loci, matK and rbcL, should enable Poaceae species identification with 95% accuracy.
Detection of Distributed Cyber Attacks Based on Weighted Ensembles of Classifiers and Big Data Processing Architecture

Distributed cyber attacks represent a special class of attacks on computer networks and systems which is rather difficult to detect. In many respects it is explained by the complexity of such detection demanding joint implementation of procedures of data analysis and technologies of Big Data processing. For this reason the development of new methods for detection of distributed cyber attacks is of great interest to specialists in the field of cyber security. The paper offers a new approach to detection of such cyber attacks. The approach is based on sharing of the weighted ensembles of different classifiers (Decision trees, Logistic regression, Support vector machines) and the Big Data processing architecture. Results of comparative analysis of three different types of the weighted ensembles (weighted voting, soft voting, and adaboost) integrating basic classifiers are evaluated. Experiments, made with use of the CICIDS2017 data set, demonstrated a rather high effectiveness of cyber attack detection and the acceptable level of consumption of the system and time resources. The approach suggested can be used for other related information assurance tasks, for example, detection and counteraction of inappropriate, dubious and harmful information.
Training needs for a PhD programme in Engineering Education

The field of Engineering Education (EngEd) is a relatively new discipline that is attracting a growing interest all around the world. Despite this interest in research in EngEd, there are still only a few PhD programmes in the area, the oldest being that established in 2004 at Purdue University. Although some research groups exist in Europe, to our knowledge there are only three PhD programmes: those in Aalborg, Chalmers and Uppsala. The Universitat Politècnica de Catalunya – Barcelona Tech is a technical University providing degrees only in engineering, sciences and architecture. We have a strong commitment to high-quality education and face the same problems as other technical universities, such as the need to increase student attraction and retention, the development of an engineering identity and the acquisition of the professional competencies required in a global world. While we have been developing research in all those subjects, our next goal is to create a new PhD programme in Engineering, Science and Technology Education, with the first cohort due to begin in September, 2020. The structure of an EngEd PhD programme consists of a unique combination of engineering and education requirements. In order to design our program, we analysed the training courses offered by five programs (at Aalborg, Chalmers, Purdue, Uppsala, and Virginia Tech). This paper presents what we have learnt about the courses and learning objectives of those programmes.
A Hybrid Modulation Method for Two-stage Grid-tied PV Inverter with Leakage Current Suppression and Efficiency Improvement

Photovoltaic (PV) generation system has attracted wide attention in recent years to convert the solar energy into electricity in a clean way. Two-stage grid-tied single-phase inverters with a Boost stage and an H-bridge stage are potential for PV generation system with simple structure, high extensibility and wide Maximum Power Point Tracking (MPPT) range. Besides, the two stages can be optimized individually to achieve the best performance. However, applying unipolar modulation on the H-bridge may introduce large leakage current so bipolar modulation had to be chosen, resulting in large magnetic hysteresis loss and switching loss. To reduce these losses, a hybrid modulation method for the H-bridge stage combining both the features of bipolar and unipolar modulation is proposed in this paper. With the proposed modulation method, the H-bridge stage is modulated to cooperate with the Boost stage. The overall efficiency can be optimized and meanwhile the leakage current can be well suppressed. The design consideration of the proposed method is presented and the validity is verified by experimental results from a 1kW prototype.
Integrated Dual-Mode 3-dB Power Splitter Based on Multimode Interference Coupler

We design and experimentally demonstrate a dual-mode 3 dB power splitter based on the self-imaging effect in a taper-assisted multimode interference (MMI) coupler. The quality reduction of the two mirrored half-power images of the input field due to accumulated high-order eigenmodes phase error will degrade the performance of dual-mode power splitter. We propose an eigenmode-selective-excitation method to suppress the excitation of high-order eigenmodes in the MMI. By optimizing the geometric parameters and injection position of the input taper waveguide, we realize power ratios of 95.9 % and 94.2 % for the lowest three and five eigenmodes when input TE<sub>0</sub> and TE<sub>1</sub> modes, respectively. The fabricated device occupies a footprint of <inline-formula> <tex-math notation="LaTeX">$5\,\,\mu \text{m}\,\,\times 86.5\,\,\mu \text{m}$ </tex-math></inline-formula> with <inline-formula> <tex-math notation="LaTeX">$5.2~\mu \text{m}$ </tex-math></inline-formula> assisted tapers. The measured excess losses and crosstalks for both modes are less than 0.76 dB and–20.5 dB, on average, over the observable 60 nm bandwidth, respectively, which are consistent with the numerical simulations.