Summary
The exponential growth of scientific literature – which we call the ‘big literature’ phenomenon – has created great challenges in literature comprehension and synthesis. The traditional ...manual literature synthesis processes are often unable to take advantage of big literature due to human limitations in time and cognition, creating the need for new literature synthesis methods to address this challenge.
In this paper, we discuss a highly useful literature synthesis approach, automated content analysis (ACA), which has not yet been widely adopted in the fields of ecology and evolutionary biology. ACA is a suite of machine learning tools for the qualitative and quantitative synthesis of big literature commonly used in the social sciences and in medical research.
Our goal is to introduce ecologists and evolutionary biologists to ACA and illustrate its capacity to synthesize overwhelming volumes of literature. First, we provide a brief history of the ACA method and summarize the fundamental process of ACA. Next, we present two ACA studies to illustrate the utility and versatility of ACA in synthesizing ecological and evolutionary literature. Finally, we discuss how to maximize the utility and contributions of ACA, as well as potential research directions that may help to advance the use of ACA in future ecological and evolutionary research.
Unlike manual methods of literature synthesis, ACA is able to process high volumes of literature at substantially shorter time spans, while helping to mitigate human biases. The overall efficiency and versatility of this method allow for a broad range of applications for literature review and synthesis, including both exploratory reviews and systematic reviews aiming to address more targeted research questions. By allowing for more extensive and comprehensive reviews of big literature, ACA has the potential to fill an important methodological gap and therefore contribute to the advancement of ecological and evolutionary research.
Identifying potentially invasive species and preventing their introduction and establishment are of critical importance in invasion ecology and land management. Although an extensive body of research ...has been dedicated to identifying traits that confer invasiveness, our current knowledge is still often inconclusive due to limitations in geographic extent and/or scope of traits analyzed. Here, using a comprehensive set of 45 traits, we performed a case study of invasive traits displayed by exotic woody plants in the United States (U.S.) by comparing 63 invasive and 794 non-invasive exotic woody plant species naturalized across the country. We found that invasive woody species often bear the following two key traits: vegetative reproduction and long-distance seed dispersal (via water, birds or mammals). Boosted classification tree models based on these traits accurately predicted species invasiveness (86% accuracy on average). Presented findings provide a generalized understanding of the relative importance of functional traits in identifying potentially invasive woody species in the U.S. The knowledge generated in this study can be used to improve current classification systems of non-native woody plants used by various U.S. governmental agencies and land managers.
As the threat of antimicrobial-resistant bacteria compromises the safety and efficacy of modern healthcare practices, the search for effective treatments is more urgent than ever. For centuries, ...silver (Ag) has been known to have antibacterial properties and, over the past two decades, Ag-based nanoparticles have gained traction as potential antimicrobials. The antibacterial efficacy of Ag varies with structure, size, and concentration. In the present study, we examined Ag nanoparticles (AgNPs) for their antimicrobial activity and safety. We compared different commercially-available AgNPs against gram-negative
,
,
, and gram-positive
methicillin-resistant and susceptible strains. The most effective formula of AgNPs tested had single-digit (μg/mL) minimum inhibitory concentrations against gram-negative multidrug-resistant clinical bacterial isolates with novel and emerging mechanisms of resistance. The mode of killing was assessed in
and was found to be bactericidal, which is consistent with previous studies using other AgNP formulations. We evaluated cytotoxicity by measuring physiological readouts using the
model and found that motility was affected, but not the lifespan. Furthermore, we found that at their antibacterial concentrations, AgNPs were non-cytotoxic to any of the mammalian cell lines tested, including macrophages, stem cells, and epithelial cells. More interestingly, our experiments revealed synergy with clinically relevant antibiotics. We found that a non-toxic and non-effective concentration of AgNPs reduced the minimum inhibitory concentrations of aminoglycoside by approximately 22-fold. Because both aminoglycosides and Ag are known to target the bacterial ribosome, we tested whether Ag could also target eukaryotic ribosomes. We measured the rate of mistranslation at bactericidal concentration and found no effect, indicating that AgNPs are not proteotoxic to the host at the tested concentrations. Collectively, our results suggest that AgNPs could have a promising clinical application as a potential stand-alone therapy or antibiotic adjuvants.
•Meat species identification is an important issue due to food adulteration.•The cyt b 148 bp universal primer used is capable to identify all the species analized.•Eight meat species have been ...identified by rtPCR and HRM profiles.•Five meat mixtures have been identified and approximate DNA percentages are shown.
Meat adulteration by substitution with lower value products and/or mislabeling involves economic, health, quality and socio-religious issues. Therefore, identification and traceability of meat species has become an important subject to detect possible fraudulent practices. In the present study the development of a high resolution melt (HRM) screening method for the identification of eight common meat species is reported. Samples from Bos taurus, Ovis aries, Sus scrofa domestica, Equus caballus, Oryctolagus cuniculus, Gallus gallus domesticus, Meleagris gallopavo and Coturnix coturnix were analyzed through the amplification of a 148 bp fragment from the cyt b gene with a universal primer pair in HRM analyses. Melting profiles from each species, as well as from several DNA mixtures of these species and blind samples, allowed a successful species differentiation. The results demonstrated that the HRM method here proposed is a fast, reliable, and low-cost screening technique.
Climate change has increased the incidence of coral bleaching events, resulting in the loss of ecosystem function and biodiversity on reefs around the world. As reef degradation accelerates, the need ...for innovative restoration tools has become acute. Despite past successes with ultra-low temperature storage of coral sperm to conserve genetic diversity, cryopreservation of larvae has remained elusive due to their large volume, membrane complexity, and sensitivity to chilling injury. Here we show for the first time that coral larvae can survive cryopreservation and resume swimming after warming. Vitrification in a 3.5 M cryoprotectant solution (10% v/v propylene glycol, 5% v/v dimethyl sulfoxide, and 1 M trehalose in phosphate buffered saline) followed by warming at a rate of approximately 4,500,000 °C/min with an infrared laser resulted in up to 43% survival of Fungia scutaria larvae on day 2 post-fertilization. Surviving larvae swam and continued to develop for at least 12 hours after laser-warming. This technology will enable biobanking of coral larvae to secure biodiversity, and, if managed in a high-throughput manner where millions of larvae in a species are frozen at one time, could become an invaluable research and conservation tool to help restore and diversify wild reef habitats.
The mannose-6-phosphate isomerase (Mpi) locus in Semibalanus balanoides has been studied as a candidate gene for balancing selection for more than two decades. Previous work has shown that Mpi ...allozyme genotypes (fast and slow) have different frequencies across Atlantic intertidal zones due to selection on post-settlement survival (i.e., allele zonation). We present the complete gene sequence of the Mpi locus and quantify nucleotide polymorphism in S. balanoides, as well as divergence to its sister taxon Semibalanus cariosus. We show that the slow allozyme contains a derived charge-altering amino acid polymorphism, and both allozyme classes correspond to two haplogroups with multiple internal haplotypes. The locus shows several footprints of balancing selection around the fast/slow site: an enrichment of positive Tajima’s D for nonsynonymous mutations, an excess of polymorphism, and a spike in the levels of silent polymorphism relative to silent divergence, as well as a site frequency spectrum enriched for midfrequency mutations. We observe other departures from neutrality across the locus in both coding and noncoding regions. These include a nonsynonymous trans-species polymorphism and a recent mutation under selection within the fast haplogroup. The latter suggests ongoing allelic replacement of functionally relevant amino acid variants. Moreover, predicted models of Mpi protein structure provide insight into the functional significance of the putatively selected amino acid polymorphisms. While footprints of selection are widespread across the range of S. balanoides, our data show that intertidal zonation patterns are variable across both spatial and temporal scales. These data provide further evidence for heterogeneous selection on Mpi.
We present a cost-effective approach to sequence whole mitochondrial genomes for hundreds of individuals. Our approach uses small reaction volumes and unmodified (non-phosphorylated) barcoded ...adaptors to minimize reagent costs. We demonstrate our approach by sequencing 383 Fundulus sp. mitochondrial genomes (192 F. heteroclitus and 191 F. majalis). Prior to sequencing, we amplified the mitochondrial genomes using 4-5 custom-made, overlapping primer pairs, and sequencing was performed on an Illumina HiSeq 2500 platform. After removing low quality and short sequences, 2.9 million and 2.8 million reads were generated for F. heteroclitus and F. majalis respectively. Individual genomes were assembled for each species by mapping barcoded reads to a reference genome. For F. majalis, the reference genome was built de novo. On average, individual consensus sequences had high coverage: 61-fold for F. heteroclitus and 57-fold for F. majalis. The approach discussed in this paper is optimized for sequencing mitochondrial genomes on an Illumina platform. However, with the proper modifications, this approach could be easily applied to other small genomes and sequencing platforms.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
To effectively conserve forests and the ecosystem services they provide, mechanisms are needed to promote conservation on private lands that reduce forest fragmentation, secure lands with high ...conservation value, and enhance landscape connectivity. Incentive-based programs like payments for ecosystem services (PES) are important policy tools for attaining conservation on private lands. In 2019, we conducted 81 in-person surveys with private forestland owners, whose properties are located on the border of protected areas and in corridors connecting protected areas in Argentina's Chaco forest. We examined landowners' preferences for alternative conservation incentives, how Argentina's current PES program could be altered to increase landowner enrollment, and the amount of compensation landowners require to enroll in PES. We found that knowledge of Argentina's PES program, motivations for forest ownership, attitudes toward forest conservation policy, and property characteristics influenced landowners' preferences for conservation program design. Although indigenous communities preferred conservation easements, other private landowners were more likely to choose a PES program. Research participants preferred PES programs with shorter contract lengths or that permitted them to engage in silvopasture. The payments research participants required to engage in land uses currently authorized under Argentina's PES program exceed current PES funding. Relying solely on PES to engage landowners in conservation may result in lost opportunities to conserve forest on private lands.
•We examined landowners' preference for forest conservation incentives.•We used a mix of landscape ecology, socio-psychological and economics methods.•PES was often chosen over selling land or property tax reductions.•Respondents preferred shorter conservation contract durations.•Respondents preferred programs which allow them to engage in silvopasture.
Cobalt ferrite, CoFe
2
O
4
, nanoparticles in the size range 2–15 nm have been prepared using a non-aqueous solvothermal method. The magnetic studies indicate a superparamagnetic behavior, showing an ...increase in the blocking temperatures (ranging from 215 to more than 340 K) with the particle size,
D
TEM
. Fitting
M
versus
H
isotherms to the saturation approach law, the anisotropy constant,
K
, and the saturation magnetization,
M
S
, are obtained. For all the samples, it is observed that decreasing the temperature gives rise to an increase in both magnetic properties. These increases are enhanced at low temperatures (below ~160 K) and they are related to surface effects (disordered magnetic moments at the surface). The fit of the saturation magnetization to the
T
2
law gives larger values of the Bloch constant than expected for the bulk, increasing with decreasing the particle size (larger specific surface area). The saturation magnetization shows a linear dependence with the reciprocal particle size, 1/
D
TEM
, and a thickness of 3.7 to 5.1 Å was obtained for the non-magnetic or disordered layer at the surface using the dead layer theory. The hysteresis loops show a complex behavior at low temperatures (
T
≤ 160 K), observing a large hysteresis at magnetic fields
H
> ~1000 Oe compared to smaller ones (
H
≤ ~1000 Oe). From the temperature dependence of the ac magnetic susceptibility, it can be concluded that the nanoparticles are in magnetic interaction with large values of the interaction parameter
T
0
, as deduced by assuming a Vogel–Fulcher dependence of the superparamagnetic relaxation time. Another evidence of the presence of magnetic interactions is the almost nearly constant value below certain temperatures, lower than the blocking temperature
T
b
, observed in the FC magnetization curves.
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