bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening marker sensitivity: Optimizing eDNA‐based rare species detection
Authors: Xia Zhiqiang , Zhan Aibin , Johansson Mattias L. , DeRoy Emma , Haffner Gordon Douglas , MacIsaac Hugh J. 
Published: March 2021

AbstractAimEnvironmental DNA (eDNA)‐based techniques are useful tools in disciplines such as conservation biogeography at local to global scales since they provide promising methods to locate organisms at low abundance. Here, we raise a largely overlooked issue that the marker (primer pairs and/or probes) sensitivity of eDNA‐based detection should be optimized and reported to improve detection performance and result interpretation.LocationGlobal.MethodsWe analysed 250 articles published between 2008 and 2019 that sought to detect animals from environmental water samples using species‐specific markers to identify effort required.ResultsMost (66.0%) studies used newly designed markers, and real‐time quantitative PCR dominated the studies (72.4% of articles). The use of quantitative PCR increased significantly over time (p = .016), while conventional PCR decreased significantly (p = .005). In 82.4% of studies using newly designed markers, researchers did not screen their chosen markers for sensitivity, and 46.7% of these studies did not report the limit of detection (LoD). Limited knowledge of sensitivity screening and LoD was also found among aquatic species on the list of the world's worst alien invasive species, and many studies used published markers without such knowledge, potentially propagating errors.Main conclusionsThe rapidly growing use of eDNA‐based detection of low‐abundance species requires well‐designed protocols to improve sensitivity. Knowledge of the limits of eDNA technology is imperative, particularly when applied to conservation biogeography studies for detecting non‐indigenous or endangered species. Our results highlight the currently inadequate sensitivity screening of genetic markers used in most studies, contrasting the transition to highly sensitive PCR methods. Along with ongoing calls for standardization in the eDNA methods, we add that newly designed markers be screened to determine and optimize sensitivity before use to reduce the uncertainty of detection and benefit future applications within or beyond areas of their development.
Effectiveness of two biopesticides against the invasive tomato pest Tuta absoluta
Authors: Sarr Oumar Mal , Bal Amadou Bocar , Fossati‐Gaschignard Odile , Gauthier Nathalie 
Published: March 2021

AbstractTuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) is among the most devastating pests worldwide of solanaceous plants, particularly of tomato (Solanum lycopersicum L.). Since its recent introduction into sub‐Saharan Africa, it has become an additional widespread tomato pest throughout the region. When no control measures are taken, yield losses caused by T. absoluta larvae can reach 100%. Chemical control remains the primary management option despite its many adverse effects and increasing inefficiency due to the species’ endophytic habits and ability to develop insecticide resistance. Safer and more effective alternatives are therefore urgently required. Here, we investigated the effectiveness of two bioinsecticides compared to that of a widely used deltamethrin‐based synthetic insecticide, in preventing damage caused by T. absoluta larvae to tomato leaves and fruits, thereby affecting tomato yield. A field trial was conducted in 2018 and 2019 in northwestern Senegal using a randomized complete block design. Damage caused by T. absoluta affected approximately 65% of total leaf area and 3–24% of the fruits. Damage to the leaves caused by other insect species or other factors was less significant. At the dose applied, the chemical insecticide did not significantly reduce the surface area of leaflets affected by T. absoluta or other causal agents, the number of T. absoluta mines on the leaflets, or the proportion of fruits damaged. In contrast, the azadirachtin and Bacillus thuringiensis (Bt) formulations rapidly and significantly reduced damage to both leaves and fruits. The proportion of fruits damaged was reduced by a factor two and the total tomato yield was improved, particularly when the Bt formulation was used. In addition to their effectiveness in reducing damage caused by T. absoluta larvae to tomato leaves and fruit, and increasing the yield of marketable fruits, the viability of these organic alternatives was shown. The scope of our results is discussed in the context of T. absoluta control, in particular in integrated pest management programmes for tomato crops.
Effects of light and nutrients on intraspecific competition among midges from a shallow eutrophic lake
Authors: Wetzel Rebecca L. , McCormick Amanda R. , Phillips Joseph S. , Ives Anthony R. 
Published: March 2021

1. Intraspecific competition for food may affect the development, survival, and fecundity of organisms. However, environmental variation in abiotic conditions can influence resource quality and/or quantity, thereby modifying the strength of intraspecific competition.2. This study focuses on intraspecific competition among Tanytarsus gracilentus (Chironomidae: Diptera) larvae. In Lake Mývatn, Iceland, T. gracilentus undergoes large population fluctuations, and evidence suggests that these fluctuations are governed by consumer‐resource interactions between the larvae and benthic diatoms. In two experiments, we studied (i) the effects of larval density on individual development and survival, and (ii) how light and nutrients (nitrogen and phosphorus) mediate the strength of intraspecific competition across a density gradient.3. Survival declined with increasing larval density in both experiments, although not significantly in the first experiment in which we manipulated only density. In the second experiment, enhancement of either light or phosphorus mitigated the negative effect of larval density on survival. In both experiments, density had a negative effect on individual development. In the first experiment, fewer larvae progressed to the final fourth instar at higher densities. In the second experiment, larvae were smaller in high density treatments, and this effect was most pronounced in the treatments without light or phosphorus supplementation.4. These results highlight the potential for environmental factors to influence the strength of density‐dependent competition. Environmental variation that affects resource quantity or quality may influence the overall dynamics of our study organism and other populations whose dynamics are controlled by consumer‐resource relationships.
Defibrotide in hematopoietic stem cell transplantation: A multicenter survey study of the Spanish Hematopoietic Stem Cell Transplantation Group (GETH)
Authors: González Vicent Marta , Díaz de Heredia Cristina , González de Pablo Jesús , Molina Blanca , Regueiro Alexandra , Pérez Martinez Antonio , Palomo Pilar , López Corral Lucía , García Estefanía , Fernández José María , Pérez Ariadna , Jiménez María José , Guerreiro Manuel , Vallejo Carlos , Gallardo Ana Isabel , López Oriana , Benito Ana , Marsal Julia , Duarte Mónica , Bento Leyre , Badell Isabel , Pedraza Alexandra , Jiménez Ubieto Ana , González Pedro , Gómez Centurión Ignacio , Costilla Lissette , Beléndez Cristina , Esquirol Albert , Espigado Ildefonso , Lavilla Esperanza , Díaz Miguel Ángel 
Published: March 2021

AbstractBackgroundDefibrotide is approved in European Union for the treatment of severe sinusoidal obstruction syndrome (SOS) after HSCT. However, it has also been used for SOS prophylaxis, moderate SOS and in other complications such as transplant‐associated thrombotic microangiopathy (TAM). The objective of this study was to evaluate current uses, effectiveness and safety of defibrotide in patients with HSCT.MethodsThis multicenter, retrospective study included patients treated with defibrotide for any indication at 28 HSCT centers of the Grupo Español de Trasplante Hematopoyetico (GETH) including the pediatric subgroup Grupo Español de Trasplante de Medula en Niños (GETMON).ResultsThree hundred and eighty eight patients treated with defibrotide between January 2011 and December 2018 were included. 253 patients were children, and 135 patients were adults. In total, 332 transplants were allogeneic, and the remainder were autologous. Main indications for defibrotide use were severe/very severe SOS in 173 patients, SOS prophylaxis in 135 patients, moderate SOS in 41 patients, TAM in six patients and suspected SOS in 33 patients. Overall survival (OS) at day +100 in the SOS prophylaxis group was 89% (95% CI, 87%‐91%). In the group of patients with moderate and severe/very severe SOS, the OS at day +100 was 80% (95% CI, 74%‐86%) and 62% (95% CI, 59%‐65%), respectively (P = .0015). With a longer follow‐up, median of 2 years (4 months–7 years), OS was 63% (95% CI, 59%‐67%) in the SOS prophylaxis patients. OS for patients with moderate and severe/very severe SOS groups was 53% (95% CI, 47%‐61%) and 26% (95% CI, 22%‐30%), respectively (P = .006). 191 patients died, and SOS was the main cause of death in 23 patients (12%).ConclusionsDefibrotide has an acceptable safety profile with an improved response in severe/very severe SOS compared with historical controls, mainly in pediatric patients. Use of defibrotide for prophylaxis may improve prognosis of patients at high risk of complications due to endothelial damage such as those who receive a second transplant. SOS has an important impact on the HSCT long‐term survival, as can be concluded from our study.
Synergistic effect of sleep depth and seizures correlates with postictal heart rate
Authors: Schomer Andrew C. , Lynch Morgan , Lowenhaupt Stephanie , Leonardo Juliana , Baljak Valentina , Clark Matthew , Kapur Jaideep , Quigg Mark 
Published: March 2021

ABSTRACTOur objective was to determine the effect of sleep on heart rate following a recorded seizure. We prospectively acquired heart rate data in hospitalized epilepsy monitoring unit patients. We analyzed heart rate trends for multiple seizures (n = 101) in patients (n = 42) with electroencephalographically confirmed events. The patient's sleep state was scored for the 5 min preceding each seizure and correlated with the postictal nadir heart rate (PINHR). The depth of sleep during the 5 min before a seizure correlated (correlation coefficient [CC] = −.229, p < .05) with PINHR. This result was more significant and strengthened (CC = −.272, 95% confidence interval = −.392 to −.152, p < .001) when adjusted for covariates of age, generalized tonic–clonic seizures, and baseline heart rate. Sleep depth is an independent predictor of the change in heart rate following a seizure. Diminished heart rate following a seizure in the setting of sleep is likely secondary to non‐rapid eye movement sleep's synergistic effect on parasympathetic tone.
Magnetic resonance‐guided laser interstitial thermal therapy: Correlations with seizure outcome
Authors: Kang Joon Y. , Pickard Allyson A. , Bronder Jay , Yenokyan Gayane , Chen Mo , Anderson William S. , Sperling Michael R. , Nei Maromi 
Published: March 2021

SummaryObjectiveThis study was undertaken to identify clinical factors associated with seizure freedom after magnetic resonance‐guided laser interstitial thermal therapy (MRgLiTT) in temporal lobe epilepsy patients with unilateral mesial temporal sclerosis (MTS).MethodsWe identified 56 patients with magnetic resonance imaging‐defined MTS who underwent MRgLiTT with at least 1 year of follow‐up. Primary outcome was seizure freedom at 1 year. We examined the association of seizure freedom and the following clinical factors: age at surgery, gender, history of febrile seizures, history of focal to bilateral tonic–clonic seizures, duration of epilepsy at the time of surgery, frequency of interictal epileptiform discharges (IEDs), seizure frequency, and presence of bilateral IEDs.ResultsThirty‐five (62.5%) patients were seizure‐free at 1 year. The presence of bilateral IEDs and age at surgery were associated with 1‐year seizure freedom after MRgLiTT. The presence of bilateral IEDS was associated with lower odds of seizure freedom (odds ratio [OR] = .05, 95% confidence interval [CI] = .01–.46, p = .008), whereas increasing age at surgery was associated with increased odds of seizure freedom (OR = 1.10, 95% CI = 1.03–1.19, p = .009).SignificanceThis study demonstrates associations between presence of bilateral IEDs and age at surgery and seizure freedom at 1 year after MRgLiTT.
Whole genome genotyping reveals discrete genetic diversity in north‐east Atlantic maerl beds
Authors: Jenkins Tom L. , Guillemin Marie‐Laure , Simon‐Nutbrown Cornelia , Burdett Heidi L. , Stevens Jamie R. , Peña Viviana 
Published: March 2021

AbstractMaerl beds are vital habitats for a diverse array of marine species across trophic levels, but they are increasingly threatened by human activities and climate change. Furthermore, little is known about the genetic diversity of maerl‐forming species and the population structure of maerl beds, both of which are important for understanding the ability of these species to adapt to changing environments and for informing marine reserve planning. In this study, we used a whole genome genotyping approach to explore the population genomics of Phymatolithon calcareum, a maerl‐forming red algal species, whose geographical distribution spans the north‐east Atlantic, from Norway to Portugal. Our results, using 14,150 genome‐wide SNPs (single nucleotide polymorphisms), showed that P. calcareum maerl beds across the north‐east Atlantic are generally structured geographically, a pattern likely explained by low dispersal potential and limited connectivity between regions. Additionally, we found that P. calcareum from the Fal Estuary, south‐west England, is genetically distinct from all other P. calcareum sampled, even from The Manacles, a site located only 13 km away. Further analysis revealed that this finding is not the result of introgression from two closely related species, Phymatolithon purpureum or Lithothamnion corallioides. Instead, this unique diversity may have been shaped over time by geographical isolation of the Fal Estuary maerl bed and a lack of gene flow with other P. calcareum populations. The genomic data presented in this study suggest that P. calcareum genetic diversity has accumulated over large temporal and spatial scales, the preservation of which will be important for maximizing the resilience of this species to changes in climate and the environment. Moreover, our findings underline the importance of managing the conservation of maerl beds across western Europe as distinct units, at a site‐by‐site level.
Conservation insights from wild bee genetic studies: Geographic differences, susceptibility to inbreeding, and signs of local adaptation
Authors: Kelemen Evan P. , Rehan Sandra M. 
Published: March 2021

AbstractConserving bees are critical both ecologically and economically. Genetic tools are valuable for monitoring these vital pollinators since tracking these small, fast‐flying insects by traditional means is difficult. By surveying the current state of the literature, this review discusses how recent advances in landscape genetic and genomic research are elucidating how wild bees respond to anthropogenic threats. Current literature suggests that there may be geographic differences in the vulnerability of bee species to landscape changes. Populations of temperate bee species are becoming more isolated and more genetically depauperate as their landscape becomes more fragmented, but tropical bee species appear unaffected. These differences may be an artifact of historical differences in land‐use, or it suggests that different management plans are needed for temperate and tropical bee species. Encouragingly, genetic studies on invasive bee species indicate that low levels of genetic diversity may not lead to rapid extinction in bees as once predicted. Additionally, next‐generation sequencing has given researchers the power to identify potential genes under selection, which are likely critical to species’ survival in their rapidly changing environment. While genetic studies provide insights into wild bee biology, more studies focusing on a greater phylogenetic and life‐history breadth of species are needed. Therefore, caution should be taken when making broad conservation decisions based on the currently few species examined.
The genic view of hybridization in the Anthropocene
Authors: Ottenburghs Jente 
Published: March 2021

AbstractHuman impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land‐use changes, introduction of non‐native species and rapid climate change, are altering the distributions of countless species, often giving rise to human‐mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016–2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non‐native species (34% intentional and 19% unintentional). These human‐induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre‐Anthropocene hybridization events with current human‐induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
Charting a course for genetic diversity in the UN Decade of Ocean Science
Authors: Thomson Alex Innes , Archer Frederick I. , Coleman Melinda A. , Gajardo Gonzalo , Goodall‐Copestake William P. , Hoban Sean , Laikre Linda , Miller Adam D. , O’Brien David , Pérez‐Espona Sílvia , Segelbacher Gernot , Serrão Ester A. , Sjøtun Kjersti , Stanley Michele S. 
Published: March 2021

AbstractThe health of the world's oceans is intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society's continuing needs. The decade beginning 2021–2030 has additionally been declared as the UN Decade of Ocean Science for Sustainable Development. This program aims to maximize the benefits of ocean science to the management, conservation, and sustainable development of the marine environment by facilitating communication and cooperation at the science–policy interface. A central principle of the program is the conservation of species and ecosystem components of biodiversity. However, a significant omission from the draft version of the Decade of Ocean Science Implementation Plan is the acknowledgment of the importance of monitoring and maintaining genetic biodiversity within species. In this paper, we emphasize the importance of genetic diversity to adaptive capacity, evolutionary potential, community function, and resilience within populations, as well as highlighting some of the major threats to genetic diversity in the marine environment from direct human impacts and the effects of global climate change. We then highlight the significance of ocean genetic diversity to a diverse range of socioeconomic factors in the marine environment, including marine industries, welfare and leisure pursuits, coastal communities, and wider society. Genetic biodiversity in the ocean, and its monitoring and maintenance, is then discussed with respect to its integral role in the successful realization of the 2030 vision for the Decade of Ocean Science. Finally, we suggest how ocean genetic diversity might be better integrated into biodiversity management practices through the continued interaction between environmental managers and scientists, as well as through key leverage points in industry requirements for Blue Capital financing and social responsibility.
The lysosomal endopeptidases Cathepsin D and L are selective and effective proteases for the middle‐down characterization of antibodies
Authors: Čaval Tomislav , Hecht Elizabeth Sara , Tang Wilfred , Uy‐Gomez Maelia , Nichols Andrew , Kil Yong J. , Sandoval Wendy , Bern Marshall , Heck Albert J. R. 
Published: March 2021

Mass spectrometry is gaining momentum as a method of choice to de novo sequence antibodies (Abs). Adequate sequence coverage of the hypervariable regions remains one of the toughest identification challenges by either bottom‐up or top‐down workflows. Methods that efficiently generate mid‐size Ab fragments would further facilitate top‐down MS and decrease data complexity. Here, we explore the proteases Cathepsins L and D for forming protein fragments from three IgG1s, one IgG2, and one bispecific, knob‐and‐hole IgG1. We demonstrate that high‐resolution native MS provides a sensitive method for the detection of clipping sites. Both Cathepsins produced multiple, albeit specific cleavages. The Abs were cleaved immediately after the CDR3 region, yielding ~ 12 kDa fragments, that is, ideal sequencing‐sized. Cathepsin D, but not Cathepsin L, also cleaved directly below the Ab hinge, releasing the F(ab’)2. When constrained by the different disulfide bonds found in the IgG2 subtype or by the tertiary structure of the hole‐containing bispecific IgG1, the hinge region digest product was not produced. The Cathepsin L and Cathepsin D clipping motifs were related to sequences of neutral amino acids and the tertiary structure of the Ab. A single pot (L + D) digestion protocol was optimized to achieve 100% efficiency. Nine protein fragments, corresponding to the VL, VH, CL, CH1, CH2, CH3, CL + CH1, and F(ab')2, constituted ~ 70% of the summed intensities of all deconvolved proteolytic products. Cleavage sites were confirmed by the Edman degradation and validated with top‐down sequencing. The described work offers a complementary method for middle‐down analysis that may be applied to top‐down Ab sequencing.EnzymesCathepsin L—EC 3.4.22.15, Cathepsin D—EC 3.4.23.5.