Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust Nonlocal Low-Rank SAR Time Series Despeckling Considering Speckle Correlation by Total Variation Regularization

Outliers and speckle both corrupt time series of synthetic aperture radar (SAR) acquisitions. Owing to the coherence between SAR acquisitions, their speckle can no longer be regarded as independent. In this study, we propose an algorithm for nonlocal low-rank time series despeckling, which is robust against outliers and also specifically addresses speckle correlation between acquisitions. By imposing total variation regularization on the signal’s speckle component, the correlation between acquisitions can be identified, facilitating the extraction of outliers from unfiltered signals and the correlated speckle. This robustness against outliers also addresses matching errors and inaccuracies in the nonlocal similarity search. Such errors include mismatched data in the nonlocal estimation process, which degrade the denoising performance of conventional similarity-based filtering approaches. Multiple experiments on real and synthetic data assess the performance of the approach by comparing it with state-of-the-art methods. It provides filtering results of comparable quality but is not adversely affected by outliers. The source code is available at https://github.com/gbaier/nllrtv.
Recombinant Escherichia coli cells immobilized in Ca-alginate beads for metabolite production

Milligram amounts of metabolites of drug candidates are required to identify toxic products. Human drug metabolites are currently produced selectively in a time- and cost-efficient manner in bioreactor systems containing recombinant Escherichia coli co-expressing a human cytochrome P450 isoenzyme/NADPH cytochrome P450 reductase (hCYP/HR) complex. For further optimization, immobilization of the catalytic system in Ca-alginate microbeads was considered. This new concept was designed for CYP3A4 with testosterone as substrate. Immobilized E. coli cells had a high maximal and homogeneously distributed biomass. Viability was stable over at least 1 week of culture and even longer during storage. Gene expression was ideally initiated 6 h after immobilization. Although immobilized E. coli cells expressed a highly functional enzyme system after 2 days, they did not metabolize testosterone, probably due to cell permeability problems resulting from immobilization. Therefore, immobilized cell membranes displaying testosterone bioconversion activity, even after long-term storage, will be used in bioreactors with high organic solvent content.
Analysis of sequence patterns proximal to the stop codons in Oryza sativa

Abstract A comprehensive analysis of sequence patterns around the stop codons was performed, by using more than 26,000 rice full-length cDNA sequences. Here it is shown that the bias was most outstanding at the position immediately before the stop codons (−1 codon), where the AAC codon was strongly preferred among ANC codons. Compared with other positions, the codon immediately after the stop codons (+1 codon) also displayed an apparent difference, and had a strong consensus for base A at the first, C at the second, and A at the third letters, respectively. Notably, the base biases at the positions directly downstream of the stop codons, such as the +4, +5 and +6 positions, were much stronger than other positions in the 3′-UTR region, suggesting that those base positions might act as an extended stop signal in the process of protein synthesis. Examination of the relationship between sequence pattern and gene expression level, assessed by CAI values and EST counting, revealed a tendency towards bigger base biases for highly expressed genes. It could be inferred that the translation stop signal is possibly involved in many sequence recognition elements other than the stop codons; highly expressed genes should hold strong sequence consensus around the stop codons for efficient translation termination.
Recent Development of Machine Learning Methods in Microbial Phosphorylation Sites

A variety of protein post-translational modifications has been identified that control many cellular functions. Phosphorylation studies in mycobacterial organisms have shown critical importance in diverse biological processes, such as intercellular communication and cell division. Recent technical advances in high-precision mass spectrometry have determined a large number of microbial phosphorylated proteins and phosphorylation sites throughout the proteome analysis. Identification of phosphorylated proteins with specific modified residues through experimentation is often labor-intensive, costly and time-consuming. All these limitations could be overcome through the application of machine learning (ML) approaches. However, only a limited number of computational phosphorylation site prediction tools have been developed so far. This work aims to present a complete survey of the existing ML-predictors for microbial phosphorylation. We cover a variety of important aspects for developing a successful predictor, including operating ML algorithms, feature selection methods, window size, and software utility. Initially, we review the currently available phosphorylation site databases of the microbiome, the state-of-the-art ML approaches, working principles, and their performances. Lastly, we discuss the limitations and future directions of the computational ML methods for the prediction of phosphorylation.
The influence of lean management and environmental practices on relative competitive quality advantage and performance

Firms are adopting strategies to advance product quality and environmental sustainability to achieve improved profitability and shareholders’ wealth. The study investigates strategies that create a superior quality performance to competitors and improve both environmental and business performances. This paper explores the direct and indirect influence of lean management and environmental practices on relative competitive quality advantage, environmental performance and business performance. ,The study uses a quantitative method where data is gathered from 259 manufacturing firms in Ghana. The data is gathered through customized questionnaires. The partial least squares structural equation modeling (SmartPLS 3.2.8) is used to analyze the data. Firm size, industry type and importance of environmental issues are used as control variables in this study. ,The findings of the study indicate that both lean management and environmental practices create relative competitive quality advantage and improve environmental performance and business performance. Environmental performance and relative competitive quality advantage mediate the influence of lean management and environmental practices on business performance. The results further indicate that lean management creates a higher relative competitive quality advantage than environmental practices, while environmental practices have more potency to enhance environmental performance than lean management. ,The study develops and proposes a comprehensive theoretical framework that examines the potency of environmental practices and lean management in creating a relative competitive quality advantage and improving environmental performance and business performance from a Ghanaian perspective, which is an emerging economy in Africa. Lean management and environmental practices may jointly help firms create relative competitive advantage and improve environmental performance to enhance business performance.
Contribution of the Leigh Marine Laboratory to knowledge of marine species diversity

Abstract We review the contribution of the Leigh Marine Laboratory, as an extension of the University of Auckland campus, to knowledge of marine taxonomic diversity, particularly in New Zealand. Increase in knowledge of the marine biota of the Hauraki Gulf region (and beyond) in the 1960s–2010s was achieved through targeted taxonomic studies and indirectly in the course of other research and fieldwork by staff, students and visitors. The Cape Rodney to Okakari Point Marine Reserve is the type locality for 46 species and the area including Leigh harbour, Matheson Bay and Whangateau Harbour includes the type localities for 21 additional species. Altogether, University of Auckland staff and their students, throughout their professional careers, have described 570 new species of New Zealand marine life, c. 3.2% of the known marine biota of the exclusive economic zone. The laboratory has had an immeasurable influence as a training ground for field work and experimentation and from decades of oral instruction, published books, monographs and papers, and the examples and inspiration of the key personalities. Current informatics activities at the laboratory, facilitating syntheses of biodiversity data in a global context, continue that legacy.
Changes in diets of river otters in Prince William Sound, Alaska: effects of the Exxon Valdez oil spill

We studied the effects of the Exxon Valdez oil spill on the diets of river otters (Lutra canadensis) from oiled and nonoiled areas of Prince William Sound, Alaska, U.S.A. , in 1989 and 1990. On the basis of identification of prey remains in their feces, otters fed principally on marine, bottom-dwelling fishes. Marine gastropods, bivalves, and crustaceans composed most of the invertebrates in the diet of otters; freshwater and terrestrial food items seldom occurred in their feces. The diets of otters included 149 different taxa, most of which rarely occurred in their feces. Sixty-five taxa occurred ≥ 5 times in our combined data set. Species richness and diversity of prey remains in otter feces were similar on oiled and nonoiled study areas in late winter (April) 1989 (before the oil spill) and during summer (June–October) 1989 following the spill. By summer (July–September) 1990, however, there were significant declines in the richness and diversity of species (mostly bony fish, molluscs, and bivalves) in .
Genetic dissection of the developmental behaviour of total starch content and its components in wheat grain

Abstract. Starch in wheat is an important component of flour and is related to grain yield and wheat end-products. In this study, a doubled haploid (DH) population with 168 lines derived from a cross of elite Chinese wheat (Triticum aestivum L.) cultivars Huapei 3 and Yumai 57 was used to identify dynamic quantitative trait loci (QTLs) for total starch content (TSC), amylose (AMS) and amylopectin (AMP) in wheat grain. Traits were measured at stages, grown under three treatments in two seasons, and were assessed by unconditional and conditional QTL analyses. Thirty-three additive QTLs and 21 pairs of epistatic QTLs for TSC, AMS and AMP were detected by unconditional mapping, whereas 19 additive QTLs and 15 pairs of epistatic QTLs were identified by conditional mapping. Of these, QTsc4A.1 and QAms4A.1 were detected continuously at five stages under three treatments in two seasons by unconditional mapping, indicating that the accumulated effects of these QTLs were expressed stably from 12 days after flowering (DAF) and were little affected by nitrogen and water agronomic treatment. These two QTLs also showed net expression from 12 to 22 DAF by conditional mapping. The results indicate that the two loci play an important role in starch synthesis. Most of the epistatic QTLs belonged to a minor QTL, but played an important role in the target traits. Therefore, the development of starch is mainly affected by additive effects besides the epistasis effect. The data are useful for potential marker-assisted selection and cloning of the target gene in further fine mapping, and provide a foundation to understand the genetic mechanism underlying the development of starch in wheat and to increase yield.
Construct-Related Validity of the Emotional Skills and Competence Questionnaire – Children’s Form (ESCQ-C)

Social and emotional skills have an important role in children’s general functioning and social relationships (e.g., with peers, and family). Questionnaires measuring these competencies should be carefully developed and validated and be in accordance with the developmental stage of children. The Emotional Skills and Competence Questionnaire – Children’s form (ESCQ-C) is a self-report measure of one’s ability to perceive and understand emotions, to express and label emotions, and to manage and regulate emotions. It was developed within the theoretical framework from the Mayer and Salovey (1997) emotional intelligence model. Structural validity of the ESCQ-C was assessed in a sample of preadolescent children (N = 639, 53% girls, Mage = 11.24, SDage = 0.71), and convergent validity was tested by correlating ESCQ-C subscales scores with the social, emotional and academic self-efficacy (The Self-Efficacy Questionnaire for Children, Muris, 2001). Our results suggest the four-factor structure for the ESCQ-C. Manage and regulate emotions subscale was divided into two subscales: the self-perceived ability to regulate one’s own emotions and other’s emotions. Correlations with the self-efficacy scales were moderate, suggesting good convergent validity. The ESCQ-C can be considered a valid measure of the emotional skills and competences for children.
Evaluation of mustard (Brassica compestris Var. Toria) and legume intercropping under 1:1 and 2:1 row-replacement series systems.

Field experiments were conducted at Agricultural Experimental Farm, Giridih, Bihar during the winter seasons of 1992–93 and 1993–94 to compare 1 : 1 and 2 : 1 row-replacement series intercropping of mustard (Brassica campestris Var. Toria) with pea (Pisum sativum), with lentil (Lens culinaris) and with gram (Cicer areitinum L.). Intercropping systems were assessed on the basis of new indices termed ‘actual yield loss’ (AYL) and ‘intercropping advantage’ (IA), as well as several existing intercropping indices such as LER, RCC and aggressivity. Intercropping reduced the yield of component crops, compared with respective pure stands. Mustard + pea in 1 : 1 row-replacement series gave the highest mustard yield equivalent value (1.00 t/ha). When the actual sown proportion was considered, mustard + lentil (1 : 1) resulted in maximum AYL (+0.438) and IA (+2.889) values. We conclude that AYL and IA are more appropriate, particularly when per plant yield is considered.
Can C4 plants contribute to aquatic food webs of subtropical streams

1. Recent stable isotope studies have revealed that C4 plants play a minor role in aquatic food webs, despite their often widespread distribution and production. We compared the breakdown of C3 (Eucalyptus) and C4 (Saccharum and Urochloa) plant litter in a small rain forest stream and used laboratory feeding experiments to determine their potential contribution to the aquatic food web. 2. All species of litter broke down at a fast rate in the stream, although Urochloa was significantly faster than Eucalyptus and Saccharum. This was consistent with the observed higher total organic nitrogen of Urochloa compared with the other two species. 3. The breakdown of Urochloa and Saccharum was, however, not associated with shredding invertebrates, which were poorly represented in leaf packs compared with the native Eucalyptus. The composition of the invertebrate fauna in packs of Urochloa quickly diverged from that of the other two species. 4. Feeding experiments using a common shredding aquatic insect Anisocentropus kirramus showed a distinct preference for Eucalyptus over both C4 species. Anisocentropus was observed to ingest C4 plant litter, particularly in the absence of other choices, and faecal material collected was clearly of C4 origin, as determined by stable isotope analysis. However, the stable carbon isotope values of the larvae did not shift away from their C3 signature in any of the feeding trials. 5. These data suggest that shredders avoid the consumption of C4 plants, in favour of native C3 species that appear to be of lower food quality (based on C : N ratios). Lower rates of consumption and lack of assimilation of C4 carbon also suggest that shredders may have a limited ability to process this material, even in the absence of alternative litter sources. Large scale clearing of forest and vegetation for C4 crops such as sugarcane will undoubtedly have important consequences for stream ecosystem function.
Vocal production in nonhuman primates: Acoustics, physiology, and functional constraints on “honest” advertisement

The physiological mechanisms and acoustic principles underlying sound production in primates are important for analyzing and synthesizing primate vocalizations, for determining the range of calls that are physically producible, and for understanding primate communication in the broader comparative context of what is known about communication in other vertebrates. In this paper we discuss what is known about vocal production in nonhuman primates, relying heavily on models from speech and musical acoustics. We first describe the role of the lungs and larynx in generating the sound source, and then discuss the effects of the supralaryngeal vocal tract in modifying this source. We conclude that more research is needed to resolve several important questions about the acoustics of primate calls, including the nature of the vocal tract's contribution to call production. Nonetheless, enough is known to explore the implications of call acoustics for the evolution of primate communication. In particular, we discuss how anatomy and physiology may provide constraints resulting in “honest” acoustic indicators of body size. © 1995 Wiley‐Liss, Inc.
Complementary fruiting phenologies facilitate sharing of one pollinator fig wasp by two fig trees

Aims Most pollinator fig wasps are host plant specific, with each species only breeding in the figs of one fig tree species, but increasing numbers of species are known to be pollinated by more than one fig wasp, and in rare instances host switching can result in Ficus species sharing pollinators. In this study, we examined factors facilitating observed host switching at Xishuangbanna in Southwestern (SW) China, where Ficus squamosa is at the northern edge of its range and lacks the fig wasps that pollinate it elsewhere, and its figs are colonized by a Ceratosolen pollinator that routinely breeds in figs of F. heterostyla. Methods We recorded the habitat preferences of F. squamosa and F. heterostyla at Xishuangbanna, and compared characteristics such as fig size, location and colour at receptive phase. Furthermore, the vegetative and reproductive phenologies in the populations of F. squamosa and F. heterostyla were recorded weekly at Xishuangbanna Tropical Botanical Garden for 1 year. Important Findings Ficus squamosa is a shrub found near fast-flowing rivers, F. heterostyla is a small tree of disturbed forest edges. Although preferring different habitats, they can be found growing close together. Both species have figs located at or near ground level, but they differ in size when pollinated. Fig production in F. squamosa was concentrated in the colder months. F. heterostyla produced more figs in summer but had some throughout the year. The absence of its normal pollinators, in combination with similarly located figs and partially complementary fruiting patterns appear to have facilitated colonization of F. squamosa by the routine pollinator of F. heterostyla. The figs probably also share similar attractant volatiles. This host switching suggests one mechanism whereby fig trees can acquire new pollinators and emphasizes the likely significance of edges of ranges in the genesis of novel fig tree-fig wasp relationships.
A QUESTÃO ÉTICA NO ABATE DE ANIMAIS: UM ESTUDO CRÍTICO

Neste artigo apresentamos os resultados de uma pesquisa sobre a etica no abate de animais. O foco foi estudar fatos que ocorrem com os animais, fatos estes, que podem ferir a sensibilidade animal, com posterior morte. O objetivo foi avaliar como se efetiva o abate, identificando se existe, ou nao, maus tratos para com os animais, se sofrem nos abatedouros, antes de uma morte anunciada, e como esta acao e realiza em relacao aos animais de rua. Esclarecemos que o presente texto nao tem o intuito de apoiar qualquer causa da populacao vegana, mas debater cientificamente sobre o ambiente em que os animais foram e, continuam sendo, considerados como bens no ordenamento juridico brasileiro, apesar dos avancos que este obteve ao longo dos anos. Para alcancar tais objetivos realizamos uma pesquisa qualitativa e bibliografica (SEVERINO, 2001; GIL, 2002; ALMEIDA ET ALL, 2017; MIRANDA E SILVA, 2019). Outro procedimento foi uma pesquisa do tipo internetnografica (ALMEIDA ET ALL, 2017a), quando utilizamos a internet, seus bancos de dados e bibliotecas virtuais para gerar os dados que foram analisados a luz da analise de conteudo (CAMPOS, 2004). Os resultados permitem afirmar que os animais continuam sofrendo atos de maus-tratos e crueldade, e que a Jurisprudencia atua como uma via de mao dupla, ora agindo favoravelmente a Etica dos Animais, ora se posicionando contra a dignidade animal.
Superpixel-based imaging for residential area detection of high spatial resolution remote sensing imagery

Abstract. The precise and efficient location of residential areas using high spatial resolution remote sensing imagery is a popular research area in the field of Earth observation. Most of the existing approaches are supervised or semisupervised and use data training. Among the unsupervised approaches, corner density-based mapping using kernel density estimate has been widely employed to predict the presence of built-up areas. However, it is computationally time-consuming and the statistical threshold segmentation makes it difficult to obtain a stable and accurate output. To overcome this deficiency, a new two-stage object-oriented residential area extraction scheme was designed. First, a set of corners was extracted using the Gabor filter bank with structural tensor analysis to indicate candidate buildings. Then, instead of pixel units, our method takes superpixel-based image partitions as the primary calculation elements, and an object-oriented weighted sparse spatial voting technique was proposed to accelerate the generation of a residential area presence index. It was demonstrated that the superpixel-based voting strategy was not only efficient in accelerating the calculation process, but it also reduced the false negative rate in the final detection result. Second, a graph-cut method was employed to address the residential area segmentation by integrating a density map as a prior cue that preserves the boundary accuracy better than traditional statistical threshold methods. The effectiveness of the proposed method was evaluated using a series of experiments on the sets of high-resolution Google Earth, IKONOS, and GaoFen-2 (GF2) satellite imagery. The results showed that the proposed approach outperforms the existing algorithms in terms of computational speed and accuracy.