Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrogen rate and landscape impacts on life cycle energy use and emissions from switchgrass‐derived ethanol

Switchgrass‐derived ethanol has been proposed as an alternative to fossil fuels to improve sustainability of the US energy sector. In this study, life cycle analysis (LCA) was used to estimate the environmental benefits of this fuel. To better define the LCA environmental impacts associated with fertilization rates and farm‐landscape topography, results from a controlled experiment were analyzed. Data from switchgrass plots planted in 2008, consistently managed with three nitrogen rates (0, 56, and 112 kg N ha−1), two landscape positions (shoulder and footslope), and harvested annually (starting in 2009, the year after planting) through 2014 were used as input into the Greenhouse gases, Regulated Emissions and Energy use in transportation (GREET) model. Simulations determined nitrogen (N) rate and landscape impacts on the life cycle energy and emissions from switchgrass ethanol used in a passenger car as ethanol–gasoline blends (10% ethanol:E10, 85% ethanol:E85s). Results indicated that E85s may lead to lower fossil fuels use (58 to 77%), greenhouse gas (GHG) emissions (33 to 82%), and particulate matter (PM2.5) emissions (15 to 54%) in comparison with gasoline. However, volatile organic compounds (VOCs) and other criteria pollutants such as nitrogen oxides (NOx), particulate matter (PM10), and sulfur dioxides (SOx) were higher for E85s than those from gasoline. Nitrogen rate above 56 kg N ha−1 yielded no increased biomass production benefits; but did increase (up to twofold) GHG, VOCs, and criteria pollutants. Lower blend (E10) results were closely similar to those from gasoline. The landscape topography also influenced life cycle impacts. Biomass grown at the footslope of fertilized plots led to higher switchgrass biomass yield, lower GHG, VOCs, and criteria pollutants in comparison with those at the shoulder position. Results also showed that replacing switchgrass before maximum stand life (10–20 years.) can further reduce the energy and emissions reduction benefits.
The Method of Identifying the Species of Coniferous Wood Based on GLCM

ABSTRACT Zhao, L. and Wang, J., 2020. The method of identifying the species of coniferous wood based on GLCM. In: Yang, Y. ; Mi, C. ; Zhao, L. , and Lam, S. (eds.), Global Topics and New Trends in Coastal Research: Port, Coastal and Ocean Engineering. Journal of Coastal Research, Special Issue No. 103, pp. 570–574. Coconut Creek (Florida), ISSN 0749-0208. Accurate and efficient identification of sheet materials has an important role in the industrialization of sheet metal. This research put a route for identifying plate species based on a GLCM, and selects parameters such as energy, entropy, uniformity, contrast, and correlation of the plate texture image. Based on the principle of maximum similarity, a texture-based material species determination method is established. The minimum difference method and comprehensive threshold method are used for identification analysis, and the contribution rate of each parameter is considered to be the same. The research data show that the route of this paper has higher identification efficiency and accuracy for the species of softwood sheet material, and the identification algorithm has better performance and good robustness.
Relationship between Price–Earnings Ratios and Stock Value in an Emerging Market

In this article, an attempt was made to determine whether price–earnings (P/E) ratio indicates future prices or yields in Indian capital market. While the efficient market hypothesis negates the possibility of prediction, the P/E ratio supporters argue that due to exaggerated investors’ expectations, P/E ratio may indicate future investment performance. Four major indexes of the Bombay Stock Exchange (BSE) are chosen for the investigation: the S&P BSE SENSEX, S&P BSE 500, S&P BSE MID CAP and S&P BSE SMALL CAP. Using vector error correction model (VECM) and vector autoregression (VAR) estimations, I find that subsequent prices will increase and subsequent yields will decline in response to an increase in the P/E ratio. But the prediction only works with blue-chip firms or firms with large market capitalization and not for mid-size firms or small-size firms. The impact on subsequent yield is very weak even for large-size firms.
Picoplankton in Lake Maggiore, Italy

In 1992 we examined the morphological characteristics and space-time distribution of picoplankton cells in Lake Maggiore, a subalpine lake in which oligotrophication is in progress. We measured by image analyser the biovolume of autotrophic (APP), eukaryotic and prokaryotic, and heterotrophic (HPP) picoplankton. Among the APP < 2 μm the yellow fluoresceing are the dominating cells in the euphotic zone. The red cells, mainly eukaryotic, on average are only 11% of the total abundance of cells < 5 μm. The APP cell numbers range from 9.5 x 10 3 cells ml -1 to 1.3 x 10 5 cells ml -1 (average : 5 x 10 4 cells ml -1 ). Their mean biovolume shows a minimum value of 7.8 mm 3 m -3 in March and a maximum of 186.3 mm 3 m -3 in September. The contribution of biovolume of yellow cells to total phytoplankton biovolume varies between 0.3% and 27%, suggesting that picocyanobacteria, at this stage of lake recovery, are not yet a dominant component. The HPP cell density is two order of magnitude higher than the APP with a mean value of 2.6 x 10 6 cells ml -1 . APP mean cell size fluctuates from a minimum of 0.5 μm to a maximum of 1.4 μm (0.26-1.69 μm 3 volume), while HPP range from 0.4 to 0.7 μm (0.07-0.57 μm 3 volume), making it easier to distinguish them on a dimensional basis for most of the year. During the period of thermal stratification, a peak in abundance was noted in the central part of the metalimnion at depths receiving less than 10% of surface irradiance. The total picoplanktonic carbon fraction (APP and HPP) varied from 38 to 384 μgC l -1 with a mean value of 133 μgC l -1 which represents 42% of POC collected on GF/C filters. Most of the picoplankton carbon is made up of HPP cells (34% of the total POC).
Exploiting CRISPR Cas9 in Three-Dimensional Stem Cell Cultures to Model Disease

Three-dimensional (3D) cell culture methods have been widely used on a range of cell types, including stem cells to modulate precisely the cellular biophysical and biochemical microenvironment and control various cell signaling cues. As a result, more in vivo-like microenvironments are recapitulated, particularly through the formation of multicellular spheroids and organoids, which may yield more valid mechanisms of disease. Recently, genome-engineering tools such as CRISPR Cas9 have expanded the repertoire of techniques to control gene expression, which complements external signaling cues with intracellular control elements. As a result, the combination of CRISPR Cas9 and 3D cell culture methods enhance our understanding of the molecular mechanisms underpinning several disease phenotypes and may lead to developing new therapeutics that may advance more quickly and effectively into clinical candidates. In addition, using CRISPR Cas9 tools to rescue genes brings us one step closer to its use as a gene therapy tool for various degenerative diseases. Herein, we provide an overview of bridging of CRISPR Cas9 genome editing with 3D spheroid and organoid cell culture to better understand disease progression in both patient and non-patient derived cells, and we address potential remaining gaps that must be overcome to gain widespread use.
Occurrence, home range and movement patterns of juvenile bull (Carcharhinus leucas) and lemon (Negaprion brevirostris) sharks within a Florida estuary

The movement patterns of large juveniles are poorly known for many shark species. With increasing pressure on shark populations these data are critical for the management of large coastal species. A series of acoustic receivers were positioned in Pine Island Sound, Florida, USA, to passively track the long-term movements of large juvenile bull (Carcharhinus leucas) and lemon (Negaprion brevirostris) sharks. Nineteen C. leucas and five N. brevirostris were monitored during 2003 and 2004. Individual C. leucas were present for 8 to 89 days, while N. brevirostris were present for 12 to 83 days. Weekly minimum convex polygons and kernel utilisation distributions were calculated to demonstrate the home range and core areas of use of both species. Spectral analysis demonstrated that several N. brevirostris showed repetitive diel north–south movement patterns over periods of up to 28 consecutive days. C. leucas demonstrated regular use of backwater habitats. Long-term use of estuarine areas by these large juvenile sharks suggests that estuarine coastal lagoons provide an important habitat for this portion of their life history and as such, protection of these habitats may assist in shark management and conservation.
Facile and ultraclean graphene-on-glass nanopores by controlled electrochemical etching.

A wide range of approaches have been explored to meet the challenges of graphene nanostructure fabrication, all requiring complex and high-end nanofabrication platform and currently suffering from surface contaminations, which not only give rise to potential electrical noise but also hinder its ideally atomic spatial resolution. Here, with the use of an electrical pulse on a low-capacitance graphene-on-glass (GOG) membrane, we fabricated ultraclean graphene nanopores on a commercially available glass substrate with exceptionally low electrical noise. In-situ liquid AFM studies and electrochemical measurements revealed that both graphene nanopore nucleation and growth are stemming from the electrochemical attack on carbon atoms at defect sites, ensuring an inherently ultraclean graphene nanopore. Strikingly, compared to conventional TEM drilled graphene nanopores on SiN supporting membranes, our developed GOG nanopores featured with an order-of-magnitude lowered broadband noise, which we ascribed to the electrochemical refreshing of graphene nanopore on mechanically stable glass chips with negligible parasitic capacitance (~1 pF). Further experiments on double-stranded DNA translocations not only demonstrated the greatly reduced current noise, but also confirmed the formation of single GOG nanopores. Therefore, the exceptionally low noise and ease of ultraclean GOG nanopore platform will facilitate innovative researches to understand the fundamental property and application of such atomically thin nanopore sensors.
The bacterioplankton community composition and a host genotype dependent occurrence of taxa shape the Daphnia magna gut bacterial community

ABSTRACT The assembly of host-associated bacterial communities is influenced by a multitude of biotic and abiotic factors. It is essential to gain insight in the impact and relative strength of these factors if we want to be able to predict the effects of environmental change on the assembly of host-associated bacterial communities, or deliberately modify them. The environmental pool of bacteria, from which the host is colonized, and the genetic background of the host are both considered to be important in determining the composition of host-associated bacterial communities. We experimentally assessed the relative importance of these two factors and their interaction on the composition of Daphnia magna gut bacterial communities. Bacterioplankton originating from natural ponds or a laboratory culture were used to inoculate germ-free Daphnia of different genotypes. We found that the composition of the environmental bacterial community has a major influence on the Daphnia gut bacterial community, both reflected by the presence or absence of specific taxa as well as by a correlation between abundances in the environment and on the host. Our data also indicate a consistent effect of host genotype on the occurrence of specific bacterial taxa in the gut of Daphnia over different environments.
Development of transgenic cotton pure lines harboring a pesticidal gene (cry1Ab).

Each transgenic plant has its unique genetic architecture and level of expression. The present study was conducted to study each transgenic plant separately in order to develop pure transgenic lines to be further used in efficient cotton breeding programme. Earlier MNH-93 cultivar was transformed with the Bacillus thuringiensis (Bt) gene cry1Ab through Agrobacterium-mediated transformation method using mature cotton embryos as explants. Transformed plants obtained out of this transformation event were used to develop pure lines for five consecutive generations. The selection criteria contained confirmation of transgene through PCR and western dot blot, boll damage percentage, insect mortality percentage in lab bioassay with heliothis larvae, seed cotton yield (g), plant height (cm), number of monopodial branches per plant and number of sympodial branches per plant. All the characters were stably inherited in further generations. The expression of introduced genes was found to be variable; however it conferred protection against targeted insect pests. It was concluded that the transgenic pure lines are an excellent source of germplasm to be used in conventional breeding programme.
Actual evapotranspiration and deficit: biologically meaningful correlates of vegetation distribution across spatial scales

Correlative approaches to understanding the climatic controls of vegetation distribution have exhibited at least two important weaknesses: they have been conceptually divorced across spatial scales, and their climatic parameters have not necessarily represented aspects of climate of broad physiological importance to plants. Using examples from the literature and from the Sierra Nevada of California, I argue that two water balance parameters—actual evapotranspiration (AET) and deficit (D)—are biologically meaningful, are well correlated with the distribution of vegetation types, and exhibit these qualities over several orders of magnitude of spatial scale (continental to local). I reach four additional conclusions. (1) Some pairs of climatic parameters presently in use are functionally similar to AET and D; however, AET and D may be easier to interpret biologically. (2) Several well‐known climatic parameters are biologically less meaningful or less important than AET and D, and consequently are poorer correlates of the distribution of vegetation types. Of particular interest, AET is a much better correlate of the distributions of coniferous and deciduous forests than minimum temperature. (3) The effects of evaporative demand and water availability on a site's water balance are intrinsically different. For example, the ‘dry’ experienced by plants on sunward slopes (high evaporative demand) is not comparable to the ‘dry’ experienced by plants on soils with low water‐holding capacities (low water availability), and these differences are reflected in vegetation patterns. (4) Many traditional topographic moisture scalars—those that additively combine measures related to evaporative demand and water availability—are not necessarily meaningful for describing site conditions as sensed by plants; the same holds for measured soil moisture. However, using AET and D in place of moisture scalars and measured soil moisture can solve these problems.
Lethal and Sublethal Effects of Methyl Benzoate on the Predatory Bug Nesidiocoris tenuis

Benzoates (naturally occurring plant toxins) produce pesticidal effects on various pest insects and mites, but their effects on non-target insects are poorly understood. In this study, we evaluate the lethal and sublethal toxicity of methyl benzoate (MB) to adults of the generalist predatory bug Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae). To assess lethal effects, N. tenuis was exposed to plant surfaces treated with 0.25%, 0.5% and 1% MB, as well as negative and positive controls (water and the neonicotinoid acetamiprid, respectively). Exposure to 1% MB resulted in the highest corrected mortality of 17.8% and 13.3% under laboratory and greenhouse conditions, respectively. Thus, 1% MB can be classified as harmless to N. tenuis according to the International Organization for Biological Control rating scheme. At the sublethal level, MB exposure did not significantly affect the consumption of eggs of the whitefly Bemisia tabaci by N. tenuis relative to negative control feeding rates. In contrast, acetamiprid at the manufacturer’s recommended concentration reduced N. tenuis feeding activity by 45.4%. Furthermore, in a Y-tube olfactometer assay, there were no significant differences between the olfactory responses of N. tenuis to MB concentrations and the negative control (water). This study therefore suggests that MB could be used safely for pest control in combination with N. tenuis.
Regulation of Tissue Factor Expression in Myeloid and Monocytic Leukaemia Cells

Tissue factor (TF) is a transmembrane glycoprotein that initiates the blood coagulation cascade and is also involved in cell migration, tumour metastasis and angiogenesis. Pathologic expression of tissue factor by monocytes contributes to several thrombotic complications like acute coronary artery disease and disseminated intravascular coagulation. The aim of this thesis was to investigate the clinically important pathologic expression of TF in myelo-monocytic leukaemia cells and reveal the cellular signals leading to the suppression of TF expression. The studies in this thesis indicate that TF is a marker of immature myelo-monocytic cells. Markedly higher levels of TF were expressed in immature myelo-monocytic cell lines compared to mature monocyte-like cells. Induction of terminal differentiation in immature cells resulted in down-regulation of TF expression, irrespective of the specific phenotypes induced by retinoic acid (RA) or vitamin D3 in monoblastic U-937 cells. TF suppression was also found independent of differentiation pathways, i.e. monocytic or granulocytic. The nuclear receptor activation requirements for transcriptional suppression of TF by retinoic acid (RA) were shown to differ between acute promyelocytic leukaemia (APL) NB4 and U-937 cells. In NB4 cells the binding of the agonist to the RA receptor (RAR)α alone is needed for down-regulation of TF, whereas ligand binding to both RARαand retinoic X receptor was necessary for efficient suppression of TF expression in U-937 cells. To analyse the transcriptional regulation of TF, stable NB4 and U-937 clones expressing the luciferase gene under the control of various 5' flanking regions of the TF gene were selected. Different promoter regions were found to control the basal TF transcriptional activity. Analysis of protein binding to the 140 bp promoter region, responsible for basal TF activity in NB4 cells, revealed binding of RFX-1. RA suppressed the promoter activity in NB4, but not in U-937 cells. The ectopic expression of the APL fusion proteins PML/RARα or PLZF/RARα in U-937 reporter clones were shown to confer sensitivity to RA-induced suppression of TF promoter activity. These results provide a more detailed picture of TF regulation in leukaemic and haematopoietic cells and may have a bearing on new clinical treatment strategies in APL and other leukaemias.
Low Winter Temperatures and the European Pine Shoot Moth, Rhyacionia buoliana (Schiff.) in Ontario.

The European pine shoot moth, Rhyacionia buoliana (Schiff.), was first discovered in North America on Long Island, New York, in 1914 (Busck, 1914). Since that time it has spread throughout most of the northeastern United States, becoming one of the most important insect pests of pine plantations. In Ontario, it was first discovered in the Toronto area (McLaine, 1926) and since that time has dispersed throughout southern Ontario, appearing regvlarly south of a line from the southern end of Gcorgian Bay to a point just east of Lake Ontario (Fig. 1). Isolated occurrences of the shoot moth have been reported north of this line but these have been short-lived on small plantation trees, or have persisted in cities and towns on ornamentals protected by snow cover during the winter. The continuous distribution of the insect has remained relatively static since 1951, and it appears that the northern limit of its range in Ontario has been reached.
Origin of ubiquitous stripes at the graphite-water interface.

The investigation of solid-liquid interfaces is pivotal for understanding processes like wetting, corrosion and mineral dissolution and growth. The graphite-water interface constitutes a prime example for studying the water structure at a seemingly hydrophobic surface. Surprisingly, in a large number of atomic force microscopy (AFM) experiments, well-ordered stripes have been observed at the graphite-water interface. Although many groups have reported about the observation of stripes at this interface, fundamental properties and, in particular, the origin of the stripes are still under debate. Proposed origins include contamination, interplanar stacking of graphene layers, formation of methanol-water nanostructures and the adsorption of nitrogen molecules. Especially the latter interpretation has received considerable attention due to its potential impact for explaining the long-range nature of the hydrophobic interaction. In this study, we demonstrate that these stripes readily form when using standard plastic syringes to insert the water into the AFM instrument. In contrast, when clean glass syringes are used instead, no such stripes form even so nitrogen was present. We, therefore, conclude that contaminations from the plastic syringe rather than nitrogen constitute the origin of the stripes we observe. We provide high-resolution AFM data that reveal detailed structural insights into the arrangement of the stripes. The rich variability of our data suggests that the stripes might be composed of several different chemical species. Even so we cannot rule out that the stripes observed in the literature might originate from other sources, our study offers a rather straightforward explanation for the origin of the stripes. In the view of these results, we propose to carefully reconsider former assignments.
Towards in silico Organogenesis: A Data-based Computational Model for Limb Bud Patterning

The mechanism that controls digit formation has long intrigued developmental and theoretical biologists, and many different models and mechanisms have been proposed. Here we review models of limb development with a specific focus on digit and long bone formation. Decades of experiments have revealed the basic signaling circuits that control limb development, and recent advances in imaging and molecular technologies provide us with unprecedented spatial detail and a broader view on the regulatory networks. Computational approaches are important to integrate the available information into a consistent framework that will allow us to achieve a deeper level of understanding and that will help with the future planning and interpretation of complex experiments, paving the way to in silico genetics. Previous models of development had to be focused on very few, simple regulatory interactions. Algorithmic developments and increasing computing power now enable the generation and validation of increasingly realistic models that can be used to test old theories and uncover new mechanisms.
Clinical Abbreviation Disambiguation Using Deep Contextualized Representation

The objective of this study is to develop a method for clinical abbreviation disambiguation using deep contextualized representation and cluster analysis. We employed the pre-trained BioELMo language model to generate the contextualized word vector for abbreviations within each instance. Then principal component analysis was conducted on word vectors to reduce the dimension. K-Means cluster analysis was conducted for each abbreviation and the sense for a cluster was assigned based on the majority vote of annotations. Our method achieved an average accuracy of around 95% in 74 abbreviations. Simulation showed that each cluster required the annotation of 5 samples to determine its sense.