Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil, water, nutrients and soil organic matter losses by water erosion as a function of soil management in the Posses sub-watershed, Extrema, Minas Gerais, Brazil

O conhecimento da quantidade e qualidade de material perdido por erosao hidrica em funcao do manejo do solo constitui uma necessidade basica para a definicao de zonas de manejo em areas de recarga de agua. O objetivo desse trabalho foi verificar a influencia do manejo do solo sobre a quantidade e qualidade de material perdido por erosao hidrica na sub-bacia hidrografica das Posses, Extrema-MG. Para isso, foram coletados agua e sedimentos erodidos atraves de parcelas de erosao, instaladas, sob chuva natural, em Argissolo Vermelho-Amarelo (PVA) nos manejos: solo descoberto, rotacao cultural (milho/feijao-de-porco/pousio), pastagens degradada e bem manejada, e reflorestamento implantado em 2013; e em Neossolo Litolico (RL) nos manejos: reflorestamento implantado em 2008, solo descoberto e mata nativa. Nas amostras de sedimentos e de solos (coletadas na profundidade de 0-5 cm) foram determinados os teores de Ca, Mg, K, P, N (NT) e de materia orgânica do solo (MOS) e com isso, calculada a taxa de enriquecimento de enxurrada. O manejo exerce maior influencia nas perdas de solo do que nas perdas de agua. Menores perdas foram encontradas no reflorestamento implantado em 2013 (solo), pasto bem manejado (agua) e reflorestamentos (nutrientes e materia orgânica). Ha uma tendencia de estabilizacao dessas perdas com o tempo de implantacao dos sistemas. A tendencia geral das perdas de nutrientes no PVA foi NT > Ca > Mg > K > P; e no RL foi de NT > Ca > K > Mg > P. As taxas de perdas de MOS e NT seguem a ordem: solo descoberto > rotacao cultural > pasto degradado > pasto bem manejado > reflorestamento, no PVA; e solo descoberto > mata nativa > reflorestamento, no RL. O reflorestamento e o manejo das pastagens sao estrategias conservacionistas que minimizam as perdas por erosao hidrica na sub-bacia das Posses, Extrema-MG. O manejo exerce maior influencia nas perdas de solo e de materiais a ele relacionados do que nas perdas de agua. A manutencao da mata nativa sob Argissolo e essencial para a conservacao deste pedoambiente, sobretudo, em declives acentuados.
Nematus spiraeae Zaddach (Hymenoptera: Tenthredinidae) A Palearctic Sawfly on Aruncus (Rosaceae) New to North America

Abstract. Nematus spiraeae Zaddach, a European sawfly that feeds on Aruncus diocus (Walter) Fernald (Rosaceae), was discovered in Quebec. This probable introduction is the first report of N. spiraeae in North America and the first record of a sawfly feeding on Aruncus in North America. A diagnosis and some life history notes are given for N. spiraeae.
Aporpium miniporum , a new polyporoid species with vertically septate basidia from southern China

Vertically septate basidium is rarely present in polyporoid fungal species. In this study, Aporpium miniporum is newly described from Hainan, southern China based on a combination of morphological and ITS-based phylogenetic evidence. This new species is close to Aporpium dimidiatum and A. efibulatum from both morphological and phylogenetic perspectives. Aporpium miniporum differs from A. dimidiatum by its resupinate, effuse-reflexed to pileate basidiocarps, smaller pores and smaller allantoid basidiospores. Aporpium efibulatum is also known from Hainan, but bears resupinate basidiocarps, larger pores and ellipsoid basidiospores.
DeepFinder: An integration of feature-based and deep learning approach for DNA motif discovery

ABSTRACT We propose an improved solution to the three-stage DNA motif prediction approach. The three-stage approach uses only a subset of input sequences for initial motif prediction, and the initial motifs obtained are employed for site detection in the remaining input subset of non-overlaps. The currently available solution is not robust because motifs obtained from the initial subset are represented as a position weight matrices, which results in high false positives. Our approach, called DeepFinder, employs deep learning neural networks with features associated with binding sites to construct a motif model. Furthermore, multiple prediction tools are used in the initial motif prediction process to obtain a higher number of positive hits. Our features are engineered from the context of binding sites, which are assumed to be enriched with specificity information of sites recognized by transcription factor proteins. DeepFinder is evaluated using several performance metrics on ten chromatin immunoprecipitation (ChIP) datasets. The results show marked improvement of our solution in comparison with the existing solution. This indicates the effectiveness and potential of our proposed DeepFinder for large-scale motif analysis.
Efficient Homology Directed Repair by Cas9:DNA Localization and Cationic Polymeric Transfection in Mammalian Cells

Homology directed repair (HDR) induced by site specific DNA double strand breaks (DSB) with CRISPR/Cas9 is a precision gene editing approach that occurs at low frequency in comparison to indel forming non homologous end joining repair. In order to obtain high HDR frequency in mammalian cells, we delivered donor DNA to a DSB site by engineering a Cas9 protein fused to a high-affinity monoavidin domain to accept biotinylated DNA donors. In addition, we used the cationic polymer, polyethylenimine, to efficiently deliver our Cas9-DNA donor complex into the nucleus, thereby avoiding drawbacks such as cytotoxicity and limited in vivo translation associated with the more commonly used nucleofection technique. Combining these strategies led to an improvement in HDR rates of up to 90% on several test loci (CXCR4, EMX1, TLR). Our approach offers a cost effective, simple and broadly applicable editing method, thereby expanding the CRISPR/Cas9 genome editing toolbox.
Adventures With Rna Fish For Diagnosing Viral Infections And Exploring Single-Cell Heterogeneity In Cancer

ADVENTURES WITH RNA FISH FOR DIAGNOSING VIRAL INFECTIONS AND EXPLORING SINGLE-CELL HETEROGENEITY IN CANCER Sydeny Shaffer Arjun Raj Single-molecule RNA FISH is a robust method for visualizing individual molecules of RNA within intact cells that has been used extensively for describing single-cell heterogeneity in gene expression. In this thesis, we leverage RNA FISH-based technologies for two major problems in biology and medicine: rapid detection of viral infections and understanding mechanisms of resistance to targeted therapy in cancer. Until recently, RNA FISH was not a viable technology for rapid diagnostics, as the hybridization process required a minimum of 6 hours. We start by presenting a modification to the RNA FISH protocol developed by Raj et al. 2008, that enables hybridization in only 5 minutes, and then use these improvements in hybridization time to develop RNA FISH for detection of respiratory viruses. We demonstrate that RNA FISH is capable of detecting influenza, rhinovirus, and adenovirus, and propose two probe design strategies with clinical value for discriminating viral strains and detecting many strains at once. Ultimately, we extend these techniques to discriminate single-base differences in the viral sequences, which is clinically useful as single-base mutations can render viruses resistant to our best antiviral medications. In the next section of this thesis, we use RNA FISH for another application: examining single-cell heterogeneity in cancer cells treated with targeted therapy. We first show that melanoma cells can display profound transcriptional variability at the single cell level that predicts which cells will ultimately resist drug. This variability involves infrequent, semi-coordinated transcription of a number of resistance markers at high levels in a very small percentage of cells. The iv addition of drug then induces an epigenetic reprogramming in these cells, converting the transient transcriptional state to a stably resistant state. This reprogramming is a progressive process consisting of a loss of SOX10-mediated differentiation followed by activation of new signaling pathways, partially mediated by activity of Jun-AP-1 and TEAD. Our work reveals the multistage nature of the acquisition of drug resistance and provides a framework for understanding resistance dynamics. Taken together, these two applications of RNA FISH show its generalizability for exploring many different questions in biology and clinical medicine.
Classes of ITD predict outcomes in patients with AML treated with FLT3 inhibitors

Recurrent internal tandem duplication (ITD) mutations are observed in various cancers including acute myeloid leukemia (AML). ITD mutations of Fms-like tyrosine kinase 3 (FLT3) receptor increase kinase activity, and are associated with poor prognostic outcomes. Currently, several small-molecule FLT3 inhibitors (FLT3i) are in clinical trials for targeted therapy of high-risk FLT3-ITD-positive AML. However, the variability of survival following FLT3i treatment suggests that the mere presence of FLT3-ITD mutations in a patient might not guarantee effective clinical response to targeted inhibition of FLT3 kinase. Motivated by the heterogeneity of FLT3-ITD mutations, we sought to investigate the effects of FLT3-ITD structural features on response to treatment in AML patients. To this end, we developed HeatITup (HEAT diffusion for Internal Tandem dUPlication), an algorithm to efficiently and accurately identify ITDs and classify them based on their nucleotide composition into newly defined categories of “typical” or “atypical”. Typical ITDs insert sequences are entirely endogenous to the FLT3 locus whereas atypical ITDs contain nucleotides exogenous to the wildtype FLT3. We applied HeatITup to our cohort of de novo and relapsed AML patients. Individuals with AML carrying typical ITDs benefited significantly more from FLT3i than patients with atypical ITDs, regardless of whether FLT3i was used after initial induction or at relapse. Furthermore, analysis of the TCGA AML cohort demonstrated improved survival for patients with typical ITDs treated with induction chemotherapy. These results underscore the importance of structural discernment of complex somatic mutations such as ITDs in progressing towards personalized treatment for AML patients.
Screening of lentil genotypes for resistance to Bean yellow mosaic virus and effect of mixed infection on the susceptibility of some resistant lentil genotypes

Kanawaty, A. , S.G. Kumari, J. van Leur and H. Hammadi. 2017. Screening of lentil genotypes for resistance to Bean yellow mosaic virus and effect of mixed infection on the susceptibility of some resistant lentil genotypes. Arab Journal of Plant Protection, 35(3): 171-177. A total of 100 lentil genotypes were evaluated for their reaction to a Syrian isolate (SV205-85) of Bean yellow mosaic virus (BYMV, genus Potyvirus, family Potyviridae) under field conditions during 2010/2011 growing season. All plants were inoculated mechanically before flowering stage and selection of resistance was based on: (i) visual symptoms incidence and severity, and (ii) virus movement in the plant tissues based on tissue-blot immunoassay (TBIA) test. Only one genotype (ILL1949) was highly resistant to BYMV and another three (ILL518, ILL1935 and ILL7470) were found resistant. Sixteen lentil genotypes with different levels of susceptibility to BYMV were selected to study the effect of mixed virus infection of BYMV and Faba bean necrotic yellows virus (FBNYV, genus Nanovirus, family Nanoviridae) under plastic house conditions. All plants studied were inoculated mechanically with BYMV followed by FBNYV using viruliferous pea aphids (Acyrthosiphon pisum Harris), and were tested 28 days after inoculation by TBIA. Serological results showed that inoculation with FBNYV did not alter the resistance to BYMV of two lentil resistant genotypes (ILL518 and ILL5005), whereas inoculation with FBNYV increased the susceptibility to BYMV in three lentil genotypes (ILL336, ILL4736 and ILL1949). Three genotypes (ILL74, ILL75 and ILL213) were found highly resistant to BYMV and FBNYV with single virus infection and became moderately resistant to BYMV and resistant to FBNYV following mixed virus infection.
Intensified environmental and density-dependent regulation of white perch recruitment after an ecosystem shift in the Hudson River Estuary

Long-term monitoring data were used to test whether the invasion of zebra mussels (Dreissena polymorpha) in the Hudson River Estuary in 1991 altered the influence of density dependence and environmental conditions on life-stage transitions, growth, and partial migration in white perch (Morone americana). During the post-invasion period (1992–2013), we estimated standing stocks of white perch eggs, yolk-sac larvae (YSL), post-yolk-sac larvae (PYSL), young-of-the-year (YOY), and adults as well as indices of YOY growth and spatial distribution. A series of linear and nonlinear functions were employed to model life-stage transitions, while the effects of six environmental and density-dependent variables on YOY growth and partial migration were quantified. Comparisons to pre-invasion observations (1974–1991) indicated that egg–YSL, PYSL–YOY, and YOY–yearling transitions changed significantly after the invasion, while PYSL abundance developed a stronger negative effect on YOY growth. The PYSL–YOY transition bec.
Cutting from Campomanesia aurea O. Berg (Myrtaceae): the collection time of propagules and the effects of auxin.

: Campomanesia aurea is a potentially ornamental native species of the Pampa Biome and its vegetative propagation may be an alternative for producing seedlings on a commercial scale. Thus, the goal of this study was to verify the feasibility of vegetative propagation of C. aurea collected at different times under the use of IBA. Cuttings were collected in an in situ in the Municipality of Barão do Triunfo, RS, Brazil, in autumn, winter and spring. IBA at concentrations of zero, 2,000, 4,000, 6,000 and 8,000 mg L -1 were tested. Rooting, callogenesis, leaf retention, mortality and root dry matter were analyzed. There was interaction between the doses of IBA and the collection time of cuttings in relation to rooting. In autumn, there was quadratic behavior with a maximum of 28% rooting with curve inflection at IBA doses above 6,500 mg L -1 . The highest callogenesis and leaf retention rates and the lowest mortality rate have been observed in autumn. However, the highest rooting rate and the best root system quality have been observed in spring. We have therefore concluded that the vegetative propagation of C. aurea is feasible and the effects of IBA are dependent on the collection time of propagules .
Australian native flowering plants enhance the longevity of three parasitoids of brassica pests

Floral resources from native plants that are adapted to the local environment could be more advantageous than the use of nonnative plants. In Australia, there is a dearth of information on the benefits of native plants to natural enemies and their selectivity against pests. Accordingly, we examined the longevity of the parasitoids Diaeretiella rapae (McIntosh) and Cotesia glomerata (L.) (both Hymenoptera: Braconidae), and Diadegma semiclausum (Hellen) (Hymenoptera: Ichneumonidae) exposed to flowering shoots from Australian native plants which was compared with the nonnative buckwheat (Fagopyrum esculentum), often used in conservation biological control. Longevity of parasitoids was significantly enhanced by the Australian natives Westringia fruticosa, Mentha satureioides, Callistemon citrinus, Leptospermum cv. ‘Rudolph’, Grevillea cv. ‘Bronze Rambler’, Myoporum parvifolium, Lotus australis, and nonnative F. esculentum. The highest mean survival by native plant species was 3.4× higher for D. rapae with Leptospermum sp. and 4.3× higher for D. semiclausum with M. parvifolium. For C. glomerata, Grevillea sp. increased longevity by 6.9× compared with water only. Longevity of Plutella xylostella (L.) (Lepidoptera: Plutellidae), a major crop pest, was enhanced by all plants against which it was screened except Acacia baileyana, a species that had no effect on parasitoid longevity. Several Australian native plant species that benefit parasitoids were identified. None of the plant species provided a selective benefit to the parasitoid D. semiclausum compared with its host P. xylostella; however, the benefit of M. parvifolium and Grevillea sp. on the longevity of D. semiclausum was relatively higher compared with the pest. These results suggest the need for field studies to determine whether native Australian plants increase P. xylostella impact in nearby brassica crops.
Quality evaluation of traditional fermented milk "Dahi" in Bangladesh

We evaluated the quality of traditional fermented milk ``Dahi'', collected from four areas (Dhaka, Mymensingh, Jamalpur and Bogra) in Bangladesh. Traditionally made 28 dahi samples were collected randomly from those areas and analyzed for chemical and microbial qualities. Of the four areas samples examined, the Bogra area sample had the highest total solids content (38.24±4.37) and the Mymensigh area sample had the lowest total solids content (29.82± 4.61). Total solids content was markedly aŠected by the sugar value of the dahi samples. The other parameters examined by chemical analysis, namely, fat (4.88±0.99) and protein (4.74±0.73), were the highest in the Mymensingh area sample. On the other hand, the chemical and microbial parameters were very similar between Dhaka and Jamalpur area samples. Microbial analysis revealed that Bogra and Jamalpur area samples were free from molds. The presence of mold and yeast cells in samples might be an indication of contamination due to poor packaging, handling and inadequate transportation system.
The taxonomic status of Cossus cossus afghanistanus (Lepidoptera, Cossidae) from Afghanistan: insights from molecular and morphological data

In our study we use a 658 bp fragment of the COI gene to analyze a taxon from Afghanistan usually treated in literature as Cossus cossus afghanistanus (Daniel, 1953) . The previous conclusions on taxonomy and nomenclature were not supported by molecular data therefore the question of identity of this taxon has remained unverified. Phylogenetic analysis revealed C. c. afghanistanus to be strongly differentiated from nominotypical Cossus cossus (Linnaeus, 1758) (p-distance: 6.7% ± 1.5%). Cossus c. afghanistanus forms a distinct well-supported clade in ML and BI trees. This fact, together with prominent morphological differences (wing color and genitalia structure) shows that C. c. afghanistanus represent a separate species rather than a subspecies of Cossus cossus .
The Drosophila apterous56f mutation impairs circadian locomotor activity

Abstract We investigated effects of apterous mutation ap 56f on circadian locomotor activity, eclosion rhythms, and transcript levels of period and timeless in Drosophila. We investigated circadian locomotor activity and eclosion rhythms in ap 56f and wild-type flies, their F1 and F2 offspring, and wingless vestigial mutants and show that ap 56f disrupts circadian locomotor rhythms in a genetically recessive manner, that is not caused by the absence of wings. The apblt strain also showed impaired circadian activity rhythms, providing independent evidence for a significant role of apterous in circadian locomotor rhythm expression. The ap 56f mutation did not disrupt a circadian eclosion rhythm or rhythmic expression of the period and timeless clock genes, indicating that apterous is not essential for circadian clock function, but is necessary for coupling locomotor activity to a circadian clock. Timeless transcription was reduced in ap 56f flies in 12:12 LD, suggesting that apterous may modulate core clock gene expression.
Chrome, Gold and Silver on the Screen

A plausible rendering of metallic effects on a computer display is of high importance for 3D representations—as used in advertising and sales—and for pre-visualizing print designs that include special inks such as gold and/or silver. A human viewer recognizes these materials by their specific reflection properties. Hence, simulating them requires taking the illumination from the environment and the position of the viewer’s head into account. We demonstrate that this can be achieved in a Web-based application that leverages the webcam installed on the user’s computer. Thus, metallic color effects can be made available almost ubiquitously, in particular in Web shops.
Interspecific Pair-Bonding and Hybridization In Warbling (Vireo gilvus) and Red-Eyed (Vireo olivaceus) Vireos

ABSTRACT We present field observations and genetic evidence of interspecific mate-selection and nesting resulting in successful hybridization between the Warbling Vireo (Vireo gilvus) and the Red-eyed Vireo (V. olivaceus). Two interspecific nesting pairs were found in western North America, each of which produced two fledglings. We examined the DNA of a salvaged fledgling from the nest of a mixed-species pair in Reno, Nevada, using mitochondrial and nuclear DNA analyses. The mitochondrial DNA of this individual indicated a Red-eyed Vireo mother, while its nuclear DNA was heterozygous and consistent with a hybrid origin. Phenotypic traits of the fledglings from the nest of a second mixed-species pair near Juneau, Alaska supported heterospecific parents for those offspring as well. We discuss these findings in the context of reproductive barriers that appear to result in little or no admixture across broad areas of sympatry in these two species.
The complete mitochondrial genome of Gracilaria textorii (Gracilariales, Florideophyceae)

Abstract In this study, we determined the mitochondrial genome sequence of Gracilaria textorii. The mitogenome of G. textorii is 25,743 bp in length, with GC content of 28.2%, and includes 25 protein-coding genes, two rRNA genes (rns and rnl), and 22 tRNA genes. The overall nucleotide composition of G. textorii includes 33.9% A, 14.1% C, 14.1% G, and 28.2% T. The newly sequenced mitogenome data were used for reconstruction of phylogenetic relationships in red algae, and the results suggested that G. textorii was closely related to G. salicornia.