bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Landsat predictions of rangeland fractional cover with multitask learning and uncertainty
Authors: Allred Brady W. , Bestelmeyer Brandon T. , Boyd Chad S. , Brown Christopher , Davies Kirk W. , Ellsworth Lisa M. , Erickson Tyler A. , Fuhlendorf Samuel D. , Griffiths Timothy V. , Jansen Vincent , Jones Matthew O. , Karl Jason , Maestas Jeremy D. , Maynard Jonathan J. , McCord Sarah E. , Naugle David E. , Starns Heath D. , Twidwell Dirac , Uden Daniel R. 
Published: June 2020

AbstractOperational satellite remote sensing products are transforming rangeland management and science. Advancements in computation, data storage, and processing have removed barriers that previously blocked or hindered the development and use of remote sensing products. When combined with local data and knowledge, remote sensing products can inform decision making at multiple scales.We used temporal convolutional networks to produce a fractional cover product that spans western United States rangelands. We trained the model with 52,012 on-the-ground vegetation plots to simultaneously predict fractional cover for annual forbs and grasses, perennial forbs and grasses, shrubs, trees, litter, and bare ground. To assist interpretation and to provide a measure of prediction confidence, we also produced spatiotemporal-explicit, pixel-level estimates of uncertainty. We evaluated the model with 5,780 on-the-ground vegetation plots removed from the training data.Model evaluation averaged 6.3% mean absolute error and 9.6% root mean squared error. Evaluation with additional datasets that were not part of the training dataset, and that varied in geographic range, method of collection, scope, and size, revealed similar metrics. Model performance increased across all functional groups compared to the previously produced fractional product.The advancements achieved with the new rangeland fractional cover product expand the management toolbox with improved predictions of fractional cover and pixel-level uncertainty. The new product is available on the Rangeland Analysis Platform (https://rangelands.app/), an interactive web application that tracks rangeland vegetation through time. This product is intended to be used alongside local on-the-ground data, expert knowledge, land use history, scientific literature, and other sources of information when making interpretations. When being used to inform decision-making, remotely sensed products should be evaluated and utilized according to the context of the decision and not be used in isolation.
Contribution of odorant binding proteins to olfactory detection of (Z)-11-hexadecenal inHelicoverpa armigera
Authors: Guo Hao , Guo Ping-Ping , Sun Ya-Lan , Huang Ling-Qiao , Wang Chen-Zhu 
Published: June 2020

AbstractHelicoverpa armigerautilizes (Z)-11-hexadecenal (Z11-16:Ald) as its major sex pheromone component. Three pheromone binding proteins (PBPs) and two general odorant binding proteins (GOBPs) are abundantly expressed in male antennae ofH. armigera. However, their precise roles in the olfactory detection of Z11-16:Ald remain enigmatic. To answer this question, we first synthesized the antibody against HarmOR13, a pheromone receptor (PR) primarily responding to Z11-16:Ald and mapped the local associations between PBPs / GOBPs and HarmOR13. Immunostaining showed that HarmPBPs and HarmGOBPs were localized in the supporting cells of sensilla trichodea and sensilla basiconica respectively. In particular, HarmPBP1 and HarmPBP2 were colocalized in the cells surrounding the olfactory receptor neurons (ORNs) expressing HarmOR13. Next, using two noninterfering binary expression tools, we heterologously expressed HarmPBP1, HarmPBP2 and HarmOR13 inDrosophilaT1 sensilla to validate the functional interplay between PBPs and HarmOR13. We found that the addition of HarmPBP1 or HarmPBP2 significantly increased the sensitivity of HarmOR13 to Z11-16:Ald. However, the presence of either HarmPBP1 or HarmPBP2 was ineffective to change the tuning breadth of HarmOR13. Taken together, our results support the idea that PBPs are contributors to the peripheral olfactory sensitivity but do not affect the selectivity. Lastly, we discovered that HarmOR13 and theDrosophilaOR67d employed a similar coding mechanism to detect pheromones, suggesting that pheromone detection across different insect orders appears to co-opt a conserved molecular principle to recognize pheromone ligands.
Identification of a lymphocyte minor histocompatibility antigen in Mauritian cynomolgus macaques
Authors: Weinfurter Jason T. , Graham Michael E. , Ericsen Adam J. , Matschke Lea M. , Llewellyn-Lacey Sian , Price David A. , Wiseman Roger W. , Reynolds Matthew R. 
Published: June 2020

AbstractAllogeneic hematopoietic stem cell transplantation can lead to dramatic reductions in human immunodeficiency virus (HIV) reservoirs. This effect is mediated in part by donor T cells that recognize lymphocyte-expressed minor histocompatibility antigens (mHAgs). The potential to mark malignant and latently infected cells for destruction makes mHAgs attractive targets for cellular immunotherapies. However, testing such HIV reservoir reduction strategies will likely require preclinical studies in nonhuman primates (NHPs). In this study, we used a combination of alloimmunization, whole exome sequencing, and bioinformatics to identify a mHAg in Mauritian cynomolgus macaques (MCMs). We mapped the minimal optimal epitope to a 10-mer peptide (SW10) in apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3C (APOBEC3) and determined the major histocompatibility complex class I restriction element as Mafa-A1*063, which is expressed in almost 90% of MCMs. APOBEC3C SW10-specific CD8+ T cells recognized immortalized B cells but not fibroblasts from a mHAg positive MCM. These results collectively provide a framework for identifying mHAgs in a nontransplant setting and suggest that APOBEC3C SW10 could be used as a lymphocyte-restricted model antigen in NHPs to test various mHAg-targeted immunotherapies.ImportanceCellular immunotherapies developed to treat blood cancers may also be effective against latent HIV. Preclinical studies of such immunotherapies are hindered by a lack of known target antigens. We used a combination of alloimmunization, basic immune assays, whole exome sequencing, and bioinformatics to identify a lymphocyte-restricted minor histocompatibility antigen in a genetically related population of nonhuman primates. This minor histocompatibility antigen provides an actionable target for piloting cellular immunotherapies designed to reduce or eliminate latent reservoirs of HIV.
Preserved efficacy and reduced toxicity with intermittent linezolid dosing in combination with bedaquiline and pretomanid in a murine TB model
Authors: Bigelow Kristina M. , Tasneen Rokeya , Chang Yong S. , Dooley Kelly E. , Nuermberger Eric L. 
Published: June 2020

AbstractThe novel regimen of bedaquiline, pretomanid, and linezolid (BPaL) is highly effective against drug resistant tuberculosis, but linezolid toxicities are frequent. We hypothesized that, for a similar total weekly cumulative dose, thrice-weekly administration of linezolid would preserve efficacy while reducing toxicity compared to daily dosing, in the context of the BPaL regimen.Using C3HeB/FeJ and BALB/c mouse models of tuberculosis disease, thrice-weekly linezolid dosing was compared to daily dosing, with intermittent dosing introduced (a) from treatment initiation or (b) following an initial period of daily dosing. In all animals, BPa was dosed daily throughout treatment. Blood counts were used to assess hematologic toxicity. Following unexpected findings of apparent antagonism, we conducted additional experiments to investigate strain-to-strain differences in the contribution of linezolid to regimen efficacy comparing each 1- and 2-drug component to the BPaL regimen in BALB/c mice infected withMycobacterium tuberculosisH37Rv or HN878.Giving linezolid daily for 1-2 months achieved the greatest efficacy, but following that, results were similar if the drug was stopped, dosed thrice-weekly, or continued daily. Erythrocyte counts were lower with daily than thrice-weekly dosing. Linezolid had additive effects with BPa againstM. tuberculosisH37Rv but antagonistic effects with BPa againstM. tuberculosisHN878. However, overall efficacy of BPaL was high and similar against both strains.Dosing linezolid daily for the first two months, then less frequently thereafter, may optimize its therapeutic margin. Linezolid’s contribution to BPaL regimens may depend onM. tuberculosisstrain.
Evolutionary heritage shapes tree distributions along an Amazon-to-Andes elevation gradient
Authors: Griffiths Andy R. , Silman Miles R. , Rios William Farfán , Feeley Kenneth J. , Cabrera Karina García , Meir Patrick , Salinas Norma , Dexter Kyle G. 
Published: June 2020

ABSTRACTUnderstanding how evolutionary constraints shape the elevational distributions of tree lineages provides valuable insight into the future of tropical montane forests under global change. With narrow elevational ranges, high taxonomic turnover, frequent habitat specialisation, and exceptional levels of endemism, tropical montane forests and trees are predicted to be highly sensitive to environmental change. Using plot census data from a gradient traversing >3000 m in elevation on the Amazonian flank of the Peruvian Andes, we employ phylogenetic approaches to assess the influence of evolutionary heritage on distribution trends of trees at the genus level. We find that closely related lineages tend to occur at similar mean elevations, with sister genera pairs occurring a mean 254 m in elevation closer to each other than the mean elevational difference for all genera pairs. We also demonstrate phylogenetic clustering both above and below 1750 m a.s.l, corresponding roughly to the cloud-base ecotone. Belying these general trends, some lineages occur across many different elevations. However, these highly plastic lineages are not phylogenetically clustered. Overall, our findings suggest that tropical montane forests are home to unique tree lineage diversity, constrained by their evolutionary heritage and vulnerable to substantial losses under environmental changes, such as rising temperatures or an upward shift of the cloud base.
Rapid ageing and species identification of natural mosquitoes for malaria surveillance
Authors: Siria Doreen J. , Sanou Roger , Mitton Joshua , Mwanga Emmanuel P. , Niang Abdoulaye , Sare Issiaka , Johnson Paul C.D. , Foster Geraldine , Belem Adrien M.G. , Wynne Klaas , Murray-Smith Roderick , Ferguson Heather M. , González-Jiménez Mario , Babayan Simon A. , Diabaté Abdoulaye , Okumu Fredros O. , Baldini Francesco 
Published: June 2020

AbstractThe malaria parasite, which is transmitted by severalAnophelesmosquito species, requires more time to reach its human-transmissible stage than the average lifespan of a mosquito. Monitoring the species-specific age structure of mosquito populations is critical to evaluating the impact of vector control interventions on malaria risk. We developed a rapid, cost-effective surveillance method based on deep learning of mid-infrared spectra of mosquitoes’ cuticle that simultaneously identifies the species and the age of three main malaria vectors, in natural populations. Using over 40,000 ecologically and genetically diverse females, we could speciate and age gradeAn. gambiae, An. arabiensis, andAn. coluzziiwith up to 95% accuracy. Further, our model learned the age of new populations with minimal sampling effort and detected the impact of control interventions on simulated mosquito populations, measured as a shift in their age structures. We anticipate our method to be applied to other arthropod vector-borne diseases.
Extracellular histones trigger disseminated intravascular coagulation by lytic cell death
Authors: Wu Congqing , Zhang Yan , Li Lan , Pandeya Ankit , Zhang Guoying , Cui Jian , Kirchhofer Daniel , Wood Jeremy P. , Smyth Susan S. , Wei Yinan , Li Zhenyu 
Published: June 2020

AbstractHistones are cationic nuclear proteins that are essential for the structure and functions of eukaryotic chromatin. However, extracellular histones trigger inflammatory responses and contribute to death in sepsis by unknown mechanisms. We recently reported that inflammasome activation and pyroptosis trigger coagulation activation through a tissue factor (TF)-dependent mechanism. Here, we show that histones trigger coagulation activationin vivoas evidenced by coagulation parameters and fibrin deposition in tissues. However, histone-induced coagulopathy was neither dependent on caspase 1/11 and gasdermin D (GSDMD), nor on TLR2 and TLR4, as deficiency of these genes in mice did not protect against histone-induced coagulopathy. Incubation of histones with macrophages induced lytic cell death and phosphatidylserine (PS) exposure, which is required for TF activity, a key initiator of coagulation. Neutralization of TF diminished histone-induced coagulation. Our findings reveal lytic cell death as a novel mechanism of histone-induce coagulation activation and thrombosis.Key PointsHistones trigger DIC in a tissue factor dependent mechanismHistones induce tissue factor activation through lytic cell death
Increasing glucose uptake into neurons antagonizes brain aging and promotes health and life span under dietary restriction inDrosophila
Authors: Oka Mikiko , Suzuki Emiko , Asada Akiko , Saito Taro , Iijima Koichi M. , Ando Kanae 
Published: June 2020

SummaryBrain neurons play a central role in organismal aging, but there is conflicting evidence about the roles of neuronal glucose availability, glucose uptake and metabolism in aging and extended lifespan. Here, we analyzed metabolic changes in the brain neurons ofDrosophiladuring aging. Using a genetically-encoded fluorescent ATP biosensor, we found decreased ATP concentration in the neuronal somata of aged flies, which was correlated with decreased glucose content, expression of glucose transporter and glycolytic enzymes and mitochondrial quality. The age-associated reduction in ATP concentration did not occur in brain neurons with suppressed glycolysis or enhanced glucose uptake, suggesting these pathways contribute to reductions in ATP. Despite age-associated mitochondrial damage, increasing glucose uptake maintained ATP levels, suppressed age-dependent locomotor deficits and extended the life span. Increasing neuronal glucose uptake during dietary restriction resulted in the longest lifespans, suggesting an additive effect of enhancing glucose availability during a bioenergetic challenge on aging.
Factors influencing riverine utilization patterns in two sympatric macaques
Authors: Otani Yosuke , Bernard Henry , Wong Anna , Tangah Joseph , Tuuga Augustine , Hanya Goro , Matsuda Ikki 
Published: June 2020

AbstractMany species of terrestrial animals, including primates, live in varied association with the aquatic (e.g., riverine or coastal) environment. However, the benefits that each species receive from the aquatic environment are thought to vary depending on their social and ecological characteristics, and thus, elucidating those benefits to each species is important for understanding the principles of wild animal behaviour. In the present study, to gain a more complete picture of aquatic environment use, including social and ecological factors in primates, factors affecting riverine habitat utilization of two macaque species(Macaca nemestrinaandM. fascicularis)were identified and qualitative comparisons were made with sympatric proboscis monkeys(Nasalis larvatus), which have different social and ecological characteristics. Temporal variation in sighting frequency of macaques at the riverbanks was positively related to the fruit availability of a dominant riparian plant species and negatively related to the river water level which affects the extent of predation pressure. Riverine utilization of macaques was greatly influenced by distribution and abundance of food (especially fruit) resources, possibly in association with predation pressure. Additionally, qualitative ecological comparisons with sympatric proboscis monkeys suggest that the drivers of riverine utilization depend on the feeding niches of the species, and different anti-predator strategies resulting from their differing social structures.
Opponent intracerebral signals for reward and punishment prediction errors in humans
Authors: Gueguen Maëlle CM , Billeke Pablo , Lachaux Jean-Philippe , Rheims Sylvain , Kahane Philippe , Minotti Lorella , David Olivier , Pessiglione Mathias , Bastin Julien 
Published: June 2020

SummaryWhether maximizing rewards and minimizing punishments rely on distinct brain systems remains debated, inconsistent results coming from human neuroimaging and animal electrophysiology studies. Bridging the gap across species and techniques, we recorded intracerebral activity from twenty patients with epilepsy while they performed an instrumental learning task. We found that both reward and punishment prediction errors (PE), estimated from computational modeling of choice behavior, correlated positively with broadband gamma activity (BGA) in several brain regions. In all cases, BGA increased with both outcome (reward or punishment versus nothing) and surprise (how unexpected the outcome is). However, some regions (such as the ventromedial prefrontal and lateral orbitofrontal cortex) were more sensitive to reward PE, whereas others (such as the anterior insula and dorsolateral prefrontal cortex) were more sensitive to punishment PE. Thus, opponent systems in the human brain might mediate the repetition of rewarded choices and the avoidance of punished choices.
Ancient DNA Insights into Aboriginal Australian Mortuary Practices
Authors: Wasef Sally , Wright Joanne L , Adams Shaun , Westaway Michael C , Flinders Clarence , Willerslev Eske , Lambert David 
Published: June 2020

AbstractPaleogenetics is a relatively new and promising field that has the potential to provide new information about past Indigenous social systems, including insights into the complexity of burial practices. We present results of the first ancient DNA (aDNA) investigation into traditional mortuary practices among Australian Aboriginal people with a focus on North-East Australia. We recovered mitochondrial and Y chromosome sequences from five ancestral Aboriginal Australian remains that were excavated from the Flinders Island group in Cape York, Queensland. Two of these individuals were sampled from disturbed beach burials, while the other three were from bundle burials located in rock shelters. Genomic analyses showed that individuals from all three rock shelter burials and one of the two beach burials had a close genealogical relationship to contemporary individuals from communities from Cape York. In contrast the remaining male individual, found buried on the beach, had a mitochondrial DNA sequence that suggested that he was not from this location but that he was closely related to people from central Queensland or New South Wales. In addition, this individual was associated with a distinctive burial practice to the other four people. It has been suggested that traditionally non-locals or lower status individuals were buried on beaches. Our findings suggest that theories put forward about beach burials being non-local, or less esteemed members of the community, can potentially be resolved through analyses of uniparental genomic data. Generally, these results support the suggestion often derived from ethnohistoric accounts that inequality in Indigenous Australian mortuary practices might be based on the status, sex, and/or age of individuals and may instead relate to place of geographic origin. There is, however, some departure from the traditional ethnohistoric account in that complex mortuary internments were also offered to female individuals of the community, with genomic analyses helping to confirm that the gender of one of the rockshelter internments was that of a young female.
Herkogamy but not reciprocity is a better predictor of legitimate pollen transfer and fruit set inJasminum malabaricum, a self-compatible species with stigma-height dimorphism
Authors: Ganguly Shatarupa , Barua Deepak 
Published: June 2020

AbstractPremiseReciprocity and herkogamy, morphological traits that define style length polymorphisms, are thought to be critical in determining legitimate inter-morph pollen transfer in plants with style length polymorphism. However, the consequences of individual-level variation in these traits for pollen transfer and reproductive success have rarely been examined, and the relationship between these two fundamental traits remains unexplored.MethodsWe quantified individual-level estimates of herkogamy and reciprocity and tested the assumption that higher herkogamy and reciprocity result in higher legitimate pollen transfer and reproductive success in natural populations ofJasminum malabaricum, a species that exhibits stigma-height dimorphism. Additionally, we examined the relationship between herkogamy and reciprocity to understand potential consequences for avoiding self-pollination and encouraging legitimate pollen deposition.ResultsSurprisingly, reciprocity was not related to pollen load, legitimate pollen fraction or reproductive success. In contrast, herkogamy was positively associated with legitimate pollen fraction and fruit set in the long-styled morph. Interestingly, we observed a negative relationship between herkogamy and reciprocity in the long-styled morph.ConclusionsHerkogamy was more important than reciprocity in increasing legitimate pollen transfer and reproductive success inJ. malabaricum. Herkogamy might be particularly important in stabilising species with stigma-height dimorphism and other such polymorphic intermediates with low reciprocity, and this may allow the evolution of reciprocal arrangement of sex organs at a later stage in the pathway towards distyly. The negative relationship between herkogamy and reciprocity suggests a trade-off between avoidance of self-pollen deposition and promotion of legitimate pollen deposition.
Automated conservation assessment of the orchid family using deep learning
Authors: Zizka Alexander , Silvestro Daniele , Vitt Pati , Knight Tiffany M. 
Published: June 2020

AbstractIUCN Red List assessments are essential for prioritizing conservation needs but are resource-intensive and therefore only available for a fraction of global species richness. Tropical plant species are particularly under-represented on the IUCN Red List. Automated conservation assessments based on digitally available geographic occurrence records can be a rapid alternative, but it is unclear how reliable these assessments are. Here, we present automated conservation assessments for 13,910 species of the diverse and globally distributed Orchid family (Orchidaceae), based on a novel method using a deep neural network (IUC-NN), most of which (13,049) were previously unassessed by the IUCN Red List. We identified 4,342 (31.2 % of the evaluated orchid species) asPossibly Threatenedwith extinction (equivalent to the IUCN categories CR, EN, or VU) and point to Madagascar, East Africa, south-east Asia, and several oceanic islands as priority areas for orchid conservation. Furthermore, the Orchid family provides a model, to test the sensitivity of automated assessment methods to issues with data availability, data quality and geographic sampling bias. IUC-NN identified threat-ened species with an accuracy of 84.3%, with significantly lower geographic evaluation bias compared to the IUCN Red List, and was robust against low data availability and geographic errors in the input data. Overall, our results demonstrate that automated assessments have an important role to play in achieving goals of identifying the species that are at greatest risk of extinction.