pyResearchInsights—An open‐source Python package for scientific text analysis

1. With an increasing number of scientific articles published each year, there is a need to synthesize and obtain insights across ever‐growing volumes of literature. Here, we present pyResearchInsights, a novel open‐source automated content analysis package that can be used to analyze scientific abstracts within a natural language processing framework.
2. The package collects abstracts from scientific repositories, identifies topics of research discussed in these abstracts, and presents interactive concept maps to visualize these research topics. To showcase the utilities of this package, we present two examples, specific to the field of ecology and conservation biology.
3. First, we demonstrate the end‐to‐end functionality of the package by presenting topics of research discussed in 1,131 abstracts pertaining to birds of the Tropical Andes. Our results suggest that a large proportion of avian research in this biodiversity hotspot pertains to species distributions, climate change, and plant ecology.
4. Second, we retrieved and analyzed 22,561 abstracts across eight journals in the field of conservation biology to identify twelve global topics of conservation research. Our analysis shows that conservation policy and landscape ecology are focal topics of research. We further examined how these conservation‐associated research topics varied across five biodiversity hotspots.
5. Lastly, we compared the utilities of this package with existing tools that carry out automated content analysis, and we show that our open‐source package has wider functionality and provides end‐to‐end utilities that seldom exist across other tools.

     

The effect of a short heat treatment on the <Emphasis Type="Italic">in vitro</Emphasis> induced androgenesis in <Emphasis Type="Italic">Silene latifolia</Emphasis> ssp. <Emphasis Type="Italic">alba</Emphasis>

The effect of a short heat treatment in combination with different culture medium composition on the efficiency of in vitro induced androgenesis in Silene latifolia ssp. alba was studied. The heat shocks (33 and 37°C) were applied for 1, 3, and 5 d. The best androgenic response was observed at 25°C and after a one-day treatment at 33°C. All other treatments reduced androgenic response. Among different media compositions tested, the most satisfactory results were obtained on BMS medium supplemented with 6-benzylaminopurine (0.5 mg dm^–3) and sucrose. The green, albino and chimeric, only female, plants were regenerated. Flow cytometry of 110 regenerants identified haploids, mixoploids (n+2n and 2n+4n) and dihaploids.     

Bonding analysis and stability on alternant B<Subscript>16</Subscript>N<Subscript>16</Subscript> cage and its dimers

Bonding analysis is performed on alternant B₁₆N₁₆ cage based on a combined study of DFT with NBO method. The main feature of such analysis is the separation of bonding structure into two components: σ skeleton and π bond system. Each component is further decomposed into contributions from various NBOs, thus we obtain the details of bonding interactions of every BN unit. Based on these results, relative stability of four covalent dimers of B₁₆N₁₆ is predicted and this prediction is verified by DFT calculations. So the possibility of forecasting properties of oligomers just from analysis on monomer is highlighted in this way.     

<Emphasis Type="Italic">MDM</Emphasis>-1 and <Emphasis Type="Italic">MDM</Emphasis>-2: Two <Emphasis Type="Italic">Mutator</Emphasis>-Derived MITE Families in Rice

Abstract Numerous miniature inverted repeat transposable elements (MITEs) are present in the rice genome but their transposition mechanisms are unknown. In this report, we present evidence that two novel MITE families may have arisen from Mutator-related transposable elements and thus may use a transposition mechanism similar to that of Mutator elements. Two families of novel MITEs, namely, MDM-1 and MDM-2, were identified by searching for MITEs nested with Kiddo, a previously identified MITE family. MDM-1 and MDM-2 bear hallmarks of Mutator elements, such as long terminal inverted repeats (LTIRs), 9-bp target-site duplications (TSDs), and putative transposase binding sites. Strikingly, the MDM-1 family has a 9-bp terminus identical to that of a rice Mutator-like element (MULE-9) and the MDM-2 family has an 8-bp terminus identical to that of the maize autonomous Mutator element MuDR. A putative transposase homologous to MURA protein is identified for the MDM-2 family. Thus, these two novel MITE families, with a total copy number of several hundred in rice, are designated Mutator-derived MITEs (MDMs). Interestingly, sequence decay analysis of MDM families revealed a number of insertion site duplications (ISDs) in the alignment gaps, and widespread historical nesting events are proposed to account for the existence of these ISDs. In addition to its value for discovering new MITEs, the nesting analysis approach used in this study simultaneously identifies MITE insertion polymorphisms.     

Errors in Conventional and Input-Output—based Life—Cycle Inventories

Conventional process-analysis-type techniques for compiling life-cycle inventories suffer from a truncation error, which is caused by the omission of resource requirements or pollutant releases of higher-order upstream stages of the production process. The magnitude of this truncation error varies with the type of product or process considered, but can be on the order of 50%. One way to avoid such significant errors is to incorporate input-output analysis into the assessment framework, resulting in a hybrid life-cycle inventory method. Using Monte-Carlo simulations, it can be shown that uncertainties of input-output– based life-cycle assessments are often lower than truncation errors in even extensive, third-order process analyses.     

A systematic assessment of Ophionella (Apocynaceae; Asclepiadoideae; Stapelieae)

An assessment of characters is carried out for Ophionella Bruyns to establish that it is monophyletic. It is also shown that Pectinaria sensu lata is paraphyletic. Two species are recognized: O. arcuata (N.E. Br.) Bruyns and O. willowmorensis Bruyns sp. nov. The status of O. arcuata var. mirkinii (Piians) Bruyns is changed to O. arcuata subsp. mirkinii (Pillans) Bruyns stat. nov.     

Large‐depth‐of‐field full‐field optical angiography

A large‐depth‐of‐field full‐field optical angiography (LD‐FFOA) method is developed to expand the depth‐of‐field (DOF) using a contrast pyramid fusion algorithm (CPFA). The absorption intensity fluctuation modulation effect is utilized to obtain full‐field optical angiography (FFOA) images at different focus positions. The CPFA is used to process these FFOA images with different focuses. By selecting high‐contrast areas, the CPFA can highlight the characteristics and details of blood vessels to obtain LD‐FFOA images. In the optimal case of the proposed method, the DOF for FFOA is more than tripled using 10 differently focused FFOA images. Both the phantom and animal experimental results show that the LD‐FFOA resolves FFOA defocusing issues induced by surface and thickness inhomogeneities in biological samples. The proposed method can be potentially applied to practical biological experiments.      

Variability of the <Emphasis Type="Italic">Molinion</Emphasis> meadows in Slovakia

Nine vegetation types were distinguished using cluster analysis within Molinion meadows in Slovakia. Vegetation of cluster 1 occurs on most acidic soils and is characterized by the occurrence of species of the Caricion fuscae alliance and of the Nardus grasslands. Vegetation of cluster 2 is also found on rather acidic soils but in contrast to cluster 1 vegetation it contains species of base-rich sites, such as Betonica officinalis, Galium boreale or Serratula tinctoria. Vegetation of cluster 3 occurs in wet base-rich habitats and often contains species of the Caricion davallianae alliance. Species of dry and Nardus grasslands are typical for vegetation of cluster 4, which is found at the driest sites and is confined to oligotrophic sandy soils. Vegetation of clusters 5 and 6 occurs on moist mesotrophic soils. Their species composition is quite similar, the main difference being that the former includes species-poor relevés and the latter includes species-rich relevés. Relevés of cluster 7 include species of dry grasslands and some ruderal species and represent degraded types of inundated floodplain meadows of the Deschampsion alliance. Vegetation of clusters 8 is characterized by species of the Phragmito-Magnocaricetea class and of the Deschampsion alliance, and occurs in wet nutrient-rich habitats. Vegetation of cluster 9, which usually develops from vegetation of cluster 8 due to decrease in the ground-water table, often contains species of dry grasslands and mesic meadows. Except for relevés of clusters 1 and 7, all others can be assigned to the Molinietum caeruleae Koch 1926 association. Cluster 1 corresponds to the Junco effusi-Molinietum caeruleae Tüxen 1954 association. Average Ellenberg indicator values for relevés, which were passively projected on the ordination biplot of detrended correspondence analysis, showed that the first ordination axis correlates with nutrients, soil base status and temperature, and second axis with moisture.     

Cloning of the promoter region of plasma membrane aquaporin<Emphasis Type="Italic">BnPIP1</Emphasis> from<Emphasis Type="Italic">Brassica napus</Emphasis> and its functional analysis

A 1.6 kb upstream regulatory sequence (GenBank accession no. AF472487) of plasma membrane aquaporinBnPIP1 gene fromBrassica napus was obtained by genomic walking based on ligation-mediated PCR method. Sequence analysis indicated that this fragment contained seed germination specific and vascular specific sequences. The 1.6 kb upstream sequence and various 5′ end deleted sequences were fused withuidA gene and constructed into plant expression vectors which were used for tobacco transformation. GUS histochemical assay showed that the 1.6 kb fragment had high levels of promoter activity and the GUS staining was mainly distributed in vascular systems and tissues with rapid expanding and proliferating cells. Promoter deletion analysis showed that the deletion of -1610 — -1030 bp resulted in a dramatic reduction in GUS activity. It was assumed that there might be cis-acting element(s) existing in this region. Whereas, the region located at -1030 — -902 bp strongly inhibited the expression ofgus and probably contained negative regulatory element(s). The fragment of -902 — -19 bp could also directgus expression at high level.     

Morphological and molecular characterisation and differentiation of <Emphasis Type="Italic">Sargassum baccularia</Emphasis> and <Emphasis Type="Italic">S. polycystum</Emphasis> (Phaeophyta)

Two Sargassum species (S. baccularia and S. polycystum) collected from Teluk Kemang and Cape Rachado, Port Dickson, Negeri Sembilan, Malaysia, which are alike in morphology except for the rhizoidal system and vesicles, were characterised using random amplified polymorphism DNA (RAPD). The genomic DNA of both species was isolated from the leaves using a modified CTAB method. Four random primers, that is, OPA2, OPA3, OPA4 and OPA13, successfully amplified the DNA. The polymorphisms generated by these four primers were analysed using the Dice Coefficient of Similarity and cluster analysis was carried out using GelCompar II Version 2.0 (Applied Maths, Kortrijk, Belgium) based on UPGMA. DNA analysis showed that three primers were able to differentiate the two species. Morphological analysis using Principal Components Analysis (PCA) and discriminant function analysis supported the molecular data. Both species are characterised by heavily muricate main branches, oblong-lanceolate leaves with dentate margins and discoid holdfasts and spherical vesicles; both are dioecious. The only difference is that S. polycystum has secondary holdfasts transformed into stolons. This last characteristic is therefore a very important criterion and may contribute to the difference shown by DNA analysis.     

Non‐invasive quantification of ethylene in attached fruit headspace at 1 p.p.b. by gas chromatography–mass spectrometry

Ethylene is a gaseous plant hormone involved in defense, adaptations to environmental stress and fruit ripening. Its relevance to the latter makes its detection highly useful for physiologists interested in the onset of ripening. Produced as a sharp peak during the respiratory burst, ethylene is biologically active at tens of nl L^?1. Reliable quantification at such concentrations generally requires specialized instrumentation. Here we present a rapid, high‐sensitivity method for detecting ethylene in attached fruit using a conventional gas chromatography–mass spectrometry (GC‐MS) system and in situ headspace collection chambers. We apply this method to melon (Cucumis melo L.), a unique species consisting of climacteric and non‐climacteric varieties, with a high variation in the climacteric phenotype among climacteric types. Using a population of recombinant inbred lines (RILs) derived from highly climacteric (‘Védrantais’, cantalupensis type) and non‐climacteric (‘Piel de Sapo’, inodorus type) parental lines, we observed a significant variation for the intensity, onset and duration of the ethylene burst during fruit ripening. Our method does not require concentration, sampling times over 1 h or fruit harvest. We achieved a limit of detection of 0.41 ± 0.04 nl L^?1 and a limit of quantification of 1.37 ± 0.13 nl L^?1 with an analysis time per sample of 2.6 min. Validation of the analytical method indicated that linearity (>98%), precision (coefficient of variation ≤2%) and sensitivity compared favorably with dedicated optical sensors. This study adds to evidence of the characteristic climacteric ethylene burst as a complex trait whose intensity in our RIL population lies along a continuum in addition to two extremes.     

Distinguishing tracks of mink <Emphasis Type="Italic">Mustela vison</Emphasis> and polecat <Emphasis Type="Italic">M. putorius</Emphasis>

Targeted trapping and monitoring methods for mink rely on the correct identification of mink tracks on tracking plates. Previously, there has been no reliable method by which mink tracks can be distinguished from polecat tracks. We present a simple discriminant function based on three measurements that can be used to distinguish the tracks of mink and polecats on clay-based tracking plates with classification success greater than 90%. The method could potentially be used in other circumstances.     

The identity of <Emphasis Type="Italic">Zamia katzeriana</Emphasis> and <Emphasis Type="Italic">Z. verschaffeltii</Emphasis> (Zamiaceae)

The morphological variation of recently described species (also the older taxa) of Zamia distributed within southeastern Mexico that have wide, coriaceous leaflets is analyzed. The complex is designated as the Z. katzeriana species complex in reference to an historic collection of this name, which is also the earliest named species in the complex. The complex consists of Z. cremnophila, Z. lacandona, Z. splendens and Z. purpurea. During the 1990’s, Z. splendens was separately synonymized under Z. katzeriana and Z. verschaffeltii, both collected in Mexico by German collectors during the 18th century, but the precise locality is unknown. Information concerning the incomplete holotype of Z. verschaffeltii is particularly ambiguous, and the possible type locality suggested by Schuster, Socorro, is imprecise, thus generating taxonomic confusion. Morphometric characterization and discriminant analysis of the contemporary and historic collections (i.e., Z. katzeriana and Z. verschaffeltii) included all the known populations (11) and individuals (115) of the complex throughout its range. The results show that Z. verschaffeltii is not morphometrically related to any of the species in the complex and that Z. splendens should be considered a synonym of Z. katzeriana.

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Resumen  En este artículo se caracteriza la variación morfológica de las especies de un complejo de Zamia, que presentan folíolos anchos y coriáceos con distribución en el sureste de México, la mayoría de reciente descripción. El complejo es denominado Z. katzeriana, por una colección histórica de este nombre, y consiste de Z. cremnophila, Z. lacandona, Z. splendens y Z. purpurea. Zamia splendens fue sinonimizada separadamente bajo dos colecciones históricas Z. katzeriana y Z. verschaffeltii, de las cuales se desconoce con exactitud su lugar de procedencia, excepto que fueron colectadas en México por botánicos alemanes del siglo XVIII. La información, en especial sobre el holotipo incompleto de Z. verschaffeltii es muy ambigua y la posible localidad tipo mencionada por Schuster, Socorro, es imprecisa, lo cual ha generado confusiones taxonómicas. La caracterización de la variación morfométrica incluyó a todas las poblaciones (11) e individuos (115) conocidas actualmente para el complejo en todo su rango de distribución en México. El análisis discriminante incluyendo a las colecciones históricas, determina que Z. verschaffeltii no está relacionado morfométricamente con ninguna especie del complejo y Z. katzeriana está estrechamente correlacionada con Z. splendens.

     

The Use of Two‐Way Linear Mixed Models in Multitreatment Meta‐Analysis

Summary Meta‐analysis summarizes the results of a series of trials. When more than two treatments are included in the trials and when the set of treatments tested differs between trials, the combination of results across trials requires some care. Several methods have been proposed for this purpose, which feature under different labels, such as network meta‐analysis or mixed treatment comparisons. Two types of linear mixed model can be used for meta‐analysis. The one expresses the expected outcome of treatments as a contrast to a baseline treatment. The other uses a classical two‐way linear predictor with main effects for treatment and trial. In this article, we compare both types of model and explore under which conditions they give equivalent results. We illustrate practical advantages of the two‐way model using two published datasets. In particular, it is shown that between‐trial heterogeneity as well as inconsistency between different types of trial is straightforward to account for.     

<Emphasis Type="Italic">Aspergillus vadensis</Emphasis>, a new species of the group of black Aspergilli

A strain from the group of black Aspergilli was analysed in detail to determine the species to which it belongs. A detailed analysis of morphology, RFLP patterns and metabolite profiles was carried out. In addition, a phylogenetic tree was constructed for the black Aspergilli using the ITS and the -tubulin sequences of the individual strains. The new species differs by its poor growth on glycerol and galacturonate and its unique extrolite profile consisting of aurasperone B, nigragillin, asperazine and kotanins. RFLP analysis using three genes as probes also resulted in a unique pattern. These data indicate that the strain was closely related but not identical to Aspergillus foetidus, Aspergillus niger and Aspergillus tubingensis. It was therefore designated as a novel species and named Aspergillus vadensis.