bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk to North American Birds from Climate Change-Related Threats
Authors: Bateman Brooke L. , Taylor Lotem , Wilsey Chad , Wu Joanna , LeBaron Geoffrey S. , Langham Gary 
Published: October 2019

AbstractClimate change is a significant threat to biodiversity globally, compounded by threats that could hinder species’ ability to respond through range shifts. However, little research has examined how future bird ranges may coincide with multiple stressors at a broad scale. Here, we assess the risk to 544 birds in the United States from future climate change threats under a mitigation-dependent global warming scenario of 1.5°C and an unmitigated scenario of 3.0°C. Threats considered included sea level rise, lake level change, human land cover conversion, and extreme weather events. We developed a gridded index of risk based on coincident threats, species richness, and richness of vulnerable species. To assign risk to individual species and habitat groups, we overlaid future bird ranges with threats to calculate the proportion of species’ ranges affected in both the breeding and non-breeding seasons. Nearly all species will face at least one new climate-related threat in each season and scenario analyzed. Even with lower species richness, the 3.0°C scenario had higher risk for species and groups in both seasons. With unmitigated climate change, multiple coincident threats will affect over 88% of the conterminous United States, and 97% of species could be affected by two or more climate-related threats. Some habitat groups will see up to 96% species facing three or more threats. However, climate change mitigation would reduce risk to birds from climate change-related threats across over 90% of the US. Across the threats included here, extreme weather events have the most significant influence on risk and the most extensive spatial coverage. Urbanization and sea level rise will also have disproportionate impacts on species relative to the area they cover. By incorporating threats into predictions of climate change impacts, this assessment provides a comprehensive picture of how climate change will affect birds and the places they need.
Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs
Authors: Murugan Rajagopal , Scally Stephen W. , Costa Giulia , Mustafa Ghulam , Thai Elaine , Decker Tizian , Bosch Alexandre , Prieto Katherine , Levashina Elena A. , Julien Jean-Philippe , Wardemann Hedda 
Published: October 2019

SUMMARYCircumsporozoite protein of the human malaria parasite Plasmodium falciparum (PfCSP) is the main target of antibodies that prevent the infection and disease. Protective antibodies recognize the central PfCSP domain, but our understanding of how parasite inhibition is associated with recognition of this domain and with the evolution of potent antibodies remains scattered. Here, we characterized the epitope specificity of 200 human monoclonal PfCSP antibodies. We show that the majority of PfCSP antibodies bind to NANP and NANP-like motifs with different preferences and define the molecular basis for recognition. Epitope cross-reactivity evolved with increasing antibody affinity around a conserved (N/D)P-NANP-N(V/A) core. High affinity to this motif, but not binding to NANP-like motifs, was associated with parasite inhibition and protection. Thus, NANP drives the development of potent PfCSP antibodies independently of their cross-reactivity profile, a finding with direct implications for the design of a second-generation PfCSP-based malaria vaccine.HIGHLIGHTSThe majority of human PfCSP antibodies recognize multiple epitopesNANP affinity maturation drives the evolution of cross-reactive PfCSP antibodiesPreferential PfCSP antibody binding to a conserved core motifHigh affinity not epitope specificity is associated with PfCSP antibody potency
DNA Barcoding of fogged caterpillars in Peru: A novel approach for unveiling host-plant relationships of tropical moths (Insecta, Lepidoptera)
Authors: Hausmann Axel , Diller Juliane , Moriniere Jerome , Höcherl Amelie , Floren Andreas , Haszprunar Gerhard 
Published: October 2019

AbstractA total of 130 lepidopteran larvae were selected from 37 fogging samples at the Panguana station, district Yuyapichis, province Puerto Inca, department Huánuco, Peru. Target trees were pre-identified and subsequently submitted to molecular confirmation of identity with three markers (rbcL, psbA and trnL-F). Identification of 119 lepidopteran larvae (92 species) was successful through DNA barcoding: Comparison of COI barcodes with the reference database of adult moths resulted in 65 (55%) matches at species level, 32 (27%) at genus level and 19 (16%) at subfamily or family level. Three larvae could not be assigned to a family. For these larvae the fogged target tree now suggests a potential host-plant relationship. Molecular gut content analysis, based on High-Throughput-Sequencing was successfully tested for ten larvae corroborating feeding on the target plant in some cases but elucidating several other cases of potential ‘alternative feeding’. We propose a larger-scale approach using this rapid and efficient method including molecular gut-content analyses for comprehensively testing the ratio of ‘alternative feeders’ and pitfalls caused by collateral fogging of larvae from neighboring trees.
Asamataxis: A cooperative relayed migration in response to subsurface inhomogeneity leads to long-range self-patterning of cells
Authors: Khadpekar Akshada , Mistry Kanksha , Dwivedi Nehal , Paspunurwar Aditya , Tandaiya Parag , Majumder Abhijit 
Published: October 2019

AbstractCells self-organize to give patterns that are essential for tissue functioning. While the effects of biochemical and mechanical cues are relatively well studied, the role of stiffness inhomogeneity on cellular patterning is unexplored. Using a rigid structure embedded in soft polyacrylamide (PAA) gel, we show that such mechanical inhomogeneity leads to long-range self-organized cellular patterns. Our results reveal that this patterning depends on cellular traction and cell morphology. Depending on a suitable combination of cellular morphology and traction, the information about the presence of embedded structure gets relayed outward. In response to this relay, the cells reorient their axis and migrate towards the embedded structure leading to the observed long-range (20-35 cell length) patterning. To predict the possibility of pattern formation, we present a dimensionless number ‘f’ combining the governing parameters. We have also shown that the pattern can be tailor-made by pre-designing sub-surface structures, a potential tool for tissue engineering. This mechanism of directed migration driven long-range pattern formation in response to mechanical inhomogeneity may be involved during several pathophysiological conditions, a proposition that needs further investigation.One Sentence SummarySubstrate inhomogeneity and cooperative cellular traction together lead to cellular migration and long-range pattern formation.
Random Parametric Perturbations of Gene Regulatory Circuit Uncover State Transitions in Cell Cycle
Authors: Katebi Ataur , Kohar Vivek , Lu Mingyang 
Published: October 2019

AbstractMany biological processes involve precise cellular state transitions controlled by complex gene regulation. Here, we use budding yeast cell cycle as a model system and explore how a gene regulatory circuit encodes essential information of state transitions. We present a generalized random circuit perturbation (RACIPE) method, specifically for circuits containing heterogeneous regulation types, and its usage to analyze both stable steady states and oscillatory states from an ensemble of circuit models with random kinetic parameters. The stable steady states form robust clusters with a circular structure that are associated with cell cycle phases. We show that this circular structure in the clusters is consistent with single cell RNA-seq data. The oscillatory states specify irreversible state transitions along cell cycle progression. Furthermore, we identify possible mechanisms to understand irreversible state transitions from steady states of random models. We expect this approach to be robust and generally applicable to unbiasedly predict dynamical transitions of a gene regulatory circuit.
Trans-NanoSim characterizes and simulates nanopore RNA-seq data
Authors: Hafezqorani Saber , Yang Chen , Nip Ka Ming , Warren René L , Birol Inanc 
Published: October 2019

AbstractWe introduce Trans-NanoSim, the first tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-seq data. Through benchmarking on sets of nanopore reads from human and mouse reference transcriptomes, we show the robustness of Trans-NanoSim in capturing the characteristics of nanopore cDNA and direct RNA reads. As a cost-effective alternative to sequencing real transcriptomes, Trans-NanoSim would facilitate the rapid development of analytical tools for nanopore RNA-seq data. Trans-NanoSim is freely accessible at https://github.com/bcgsc/NanoSim
The effects of modified sialic acids on mucus and erythrocytes on influenza A virus HA and NA functions
Authors: Barnard Karen N. , Alford-Lawrence Brynn K. , Buchholz David W. , Wasik Brian R. , LaClair Justin R. , Yu Hai , Honce Rebekah , Ruhl Stefan , Pajic Petar , Daugherity Erin K. , Chen Xi , Schultz-Cherry Stacey L. , Aguilar Hector C. , Varki Ajit , Parrish Colin R. 
Published: October 2019

ABSTRACTSialic acids (Sia) are the primary receptors for influenza viruses, and are widely displayed on cell surfaces and in secreted mucus. Sia may be present in variant forms that includeO-acetyl modifications at C4, C7, C8, and C9 positions, andN-acetyl orN-glycolyl at C5. They can also vary in their linkages, including α2-3 or α2-6-linkages. Here, we analyzed the distribution of modified Sia in cells and tissues of wild-type mice, or in mice lacking cytidine 5’-monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) enzyme that synthesizesN-glycolyl modifications (Neu5Gc). We also examined the variation of Sia forms on erythrocytes and saliva from different animals. To determine the effect of Sia modifications on influenza A virus (IAV) infection, we tested for effects on hemagglutinin (HA) binding and neuraminidase (NA) cleavage. We confirmed that 9-O-acetyl, 7,9-O-acetyl, 4-O-acetyl, and Neu5Gc modifications are widely but variably expressed in mouse tissues, with the highest levels detected in the respiratory and gastrointestinal tracts. Secreted mucins in saliva and surface proteins of erythrocytes showed a great degree of variability in display of modified Sia between different species. IAV HA from different virus strains showed consistently reduced binding to both Neu5Gc andO-acetyl modified Sia; however, while IAV NA were inhibited by Neu5Gc andO-acetyl modifications, there was significant variability between NA types. The modifications of Sia in mucus may therefore have potent effects on the functions of IAV, and may affect both pathogens and the normal flora of different mucosal sites.IMPORTANCESialic acids (Sia) are involved in many different cellular functions and are receptors for many pathogens. Sia come in many chemically modified forms but we lack a clear understanding of how they alter the interactions with microbes. Here we examine the expression of modified Sia in mouse tissues, on secreted mucus in saliva, and on erythrocytes, including those from IAV host species and animals used in IAV research. These Sia forms varied considerably between different animals, and their inhibitory effects on IAV NA and HA activities and on bacterial sialidases (neuraminidases) suggest a host-variable protective role in secreted mucus.
Bats use social information within and across species
Authors: Culina Antica , Garroway Colin J. 
Published: October 2019

AbstractIn Focus: Lewanzik, D., Sundaramurthy, A. K., Goerlitz, H. R. (2019). . Journal of Animal Ecology, 88, 1462–1473.Social interactions can generate social structures that shape the fate of individuals and populations. A key feature of social environments is the information produced by others. Whether actively shared or obtained via ‘eavesdropping’, individuals of many species use publically available information to guide their decision making in important ways. Lewanzik et al. (2019) explore social information use within and across several echolocating bat species. They experimentally manipulated the content of social information about prey abundance with playback experiments of echolocation calls. All species were found to use heterospecific and conspecific social information about conspecific activity levels and prey abundance. This is a rare experimental confirmation of social information use at a community level.
The Neurospora RNA polymerase II kinase CTK negatively regulates catalase expression in a chromatin context‐dependent manner
Authors: Duan Jiabin , Liu Qingqing , Su Sodgerel , Cha Joonseok , Zhou Yike , Tang Ruiqi , Liu Xiao , Wang Ying , Liu Yi , He Qun 
Published: October 2019

SummaryClearance and adaptation to reactive oxygen species (ROS) are crucial for cell survival. As in other eukaryotes, the Neurospora catalases are the main enzymes responsible for ROS clearance and their expression are tightly regulated by the growth and environmental conditions. The RNA polymerase II carboxyl terminal domain (RNAPII CTD) kinase complex (CTK complex) is known as a positive elongation factor for many inducible genes by releasing paused RNAPII near the transcription start site and promoting transcription elongation. However, here we show that deletion of CTK complex components in Neurospora led to high CAT‐3 expression level and resistance to H2O2‐induced ROS stress. The catalytic activity of CTK‐1 is required for such a response. On the other hand, CTK‐1 overexpression led to decreased expression of CAT‐3. ChIP assays shows that CTK‐1 phosphorylates the RNAPII CTD at Ser2 residues in the cat‐3 ORF region during transcription elongation and deletion of CTK‐1 led to dramatic decreases of SET‐2 recruitment and H3K36me3 modification. As a result, histones at the cat‐3 locus become hyperacetylated to promote its transcription. Together, these results demonstrate that the CTK complex is negative regulator of cat‐3 expression by affecting its chromatin structure.
Plant Extracts Inhibit the Formation of Hydroperoxides and Help Maintain Vitamin E Levels and Omega‐3 Fatty Acids During High Temperature Processing and Storage of Hempseed and Soybean Oils
Authors: Kitts David D. , Singh Anika , Fathordoobady Farahnaz , Doi Brenda , Pratap Singh Anubhav 
Published: October 2019

AbstractOxidative stability of hempseed and soybean oils, was evaluated after heating at 180 °C, followed by a subsequent 14‐day storage at 38 °C. Natural plant extracts (Rosemary, Sage, and Thyme) were added to oils, to evaluate the carry‐over stabilizing potential. Heated oils exhibited a relatively faster (P < 0.05) onset of lipid oxidation, as depicted by the analysis of the peroxides and aldehydes formed during the lipid oxidation process, with hempseed oil being more susceptible to lipid oxidation than soybean oil. There were notable losses in ω‐3 PUFA and ω−6‐GLA during storage of heat treated hempseed oil (P < 0.05). Moreover, peroxide values measured from hempseed oil remained low after high‐temperature heating but progressed at a relatively greater rate than that observed in soybean during storage (P < 0.05). The addition of different plant extracts to oils did not prevent oxidation due to heating, but effectively inhibited the generation of hydroperoxides during subsequent storage (P < 0.05). This stabilizing effect was attributed to retention of tocopherols, in particular, γ‐tocopherol.Practical ApplicationThis research demonstrates the use of plant extracts like rosemary, sage and thyme, for improving the shelf‐life and nutritional stability of hempseed and soybean oil. We demonstrate the deterioration of fatty acid profiles and vitamin E levels in the oil on heating and subsequent storage, and show the efficacy of using plant extracts in slowing down these deteriorations. This research will be applicable in food industries using or producing oils for use in food during cooking, and also as dressing on already processed food products.
Investigating Antibiotic Resistance Genes in Marketed Ready‐to‐Eat Small Crickets (Acheta domesticus)
Authors: Roncolini Andrea , Cardinali Federica , Aquilanti Lucia , Milanović Vesna , Garofalo Cristiana , Sabbatini Riccardo , Abaker Mahasin Salih Suliman , Pandolfi Matteo , Pasquini Marina , Tavoletti Stefano , Clementi Francesca , Osimani Andrea 
Published: October 2019

AbstractThe present investigation was aimed at evaluating the occurrence of transferable genes conferring resistance to tetracyclines, macrolide‐lincosamide‐streptogramin B (MLSB), vancomycin, beta‐lactams, and aminoglycosides in 32 samples from eight batches of ready‐to‐eat crickets (Acheta domesticus) commercialized by four European Union producers (two batches per producer). Bacterial DNA extracted directly from the insects was subjected to optimized polymerase chain reaction (PCR) and nested‐PCR assays for the qualitative detection of 12 selected antibiotic resistance (AR) genes. Microbial enumeration demonstrated high counts of spore‐forming bacteria and total mesophilic aerobes. Statistical analyses revealed significant differences between different producers and insect batches. Regarding AR genes, a high prevalence of genes conferring resistance to tetracycline [tet(M), tet(O), tet(K), tet(S)] was observed, together with the presence of genes conferring resistance to erythromycin [erm(B), erm(C)], beta‐lactams (blaZ and mecA), and aminoglycosides [aac(6’)‐Ie aph(2”)‐Ia]. We performed a principal component analysis based on the AR gene frequencies that differentiated samples of batch 1 from those of batch 2. This analysis provided evidence for a difference between the producer from France and all the other producers among the batch 1 samples.Practical applicationOverall, an intrabatch variation was seen in the transferable resistances among different producers. This evidence, coupled with the observed differences in the viable counts, suggests a low standardization of the production processes. Hence, a prudent use of antimicrobials during the rearing of insects destined for human consumption is strongly recommended, as well as a need for a full standardization of production technologies.
Metabarcoding of eukaryotic parasite communities describes diverse parasite assemblages spanning the primate phylogeny
Authors: Gogarten Jan F. , Calvignac‐Spencer Sébastien , Nunn Charles L. , Ulrich Markus , Saiepour Nasrin , Nielsen Henrik Vedel , Deschner Tobias , Fichtel Claudia , Kappeler Peter M. , Knauf Sascha , Müller‐Klein Nadine , Ostner Julia , Robbins Martha M. , Sangmaneedet Somboon , Schülke Oliver , Surbeck Martin , Wittig Roman M. , Sliwa Alexander , Strube Christina , Leendertz Fabian H. , Roos Christian , Noll Angela 
Published: October 2019

AbstractDespite their ubiquity, in most cases little is known about the impact of eukaryotic parasites on their mammalian hosts. Comparative approaches provide a powerful method to investigate the impact of parasites on host ecology and evolution, though two issues are critical for such efforts: controlling for variation in methods of identifying parasites and incorporating heterogeneity in sampling effort across host species. To address these issues, there is a need for standardized methods to catalogue eukaryotic parasite diversity across broad phylogenetic host ranges. We demonstrate the feasibility of a metabarcoding approach for describing parasite communities by analysing faecal samples from 11 nonhuman primate species representing divergent lineages of the primate phylogeny and the full range of sampling effort (i.e. from no parasites reported in the literature to the best‐studied primates). We detected a number of parasite families and regardless of prior sampling effort, metabarcoding of only ten faecal samples identified parasite families previously undescribed in each host (x̅ = 8.5 new families per species). We found more overlap between parasite families detected with metabarcoding and published literature when more research effort—measured as the number of publications—had been conducted on the host species' parasites. More closely related primates and those from the same continent had more similar parasite communities, highlighting the biological relevance of sampling even a small number of hosts. Collectively, results demonstrate that metabarcoding methods are sensitive and powerful enough to standardize studies of eukaryotic parasite communities across host species, providing essential new tools for macroecological studies of parasitism.
Comparing Changes in Controlled Substance Prescribing Trends by Provider Type
Authors: Meadows Amy L. , Strickland Justin C. , Qalbani Shiraz , Conner Kailyn L. , Su Amanda , Rush Craig R. 
Published: October 2019

Background and ObjectivesForty‐nine out of 50 states have implemented Prescription Drug Monitoring Programs (PDMPs) to monitor controlled substance (CS) prescribing. PDMPs change health care provider behavior, but few studies have examined changes in CS prescription by health care provider type.MethodsAggregated yearly data, including number of CS prescriptions, doses, and doses per prescription by health care provider type (physician, advanced practice registered nurse [APRN], and dentist) for each year from 2011 to 2017 was provided by the state PDMP, Kentucky All Schedule Prescription Electronic Reporting System (KASPER). In aggregate, this data set included 64,578,307 total prescriptions and 3,982,130,994 total doses of Schedule II–V medications.ResultsPhysicians and dentists showed a trend of decreasing prescriptions and doses for Schedule II opioids from 2012 to 2017 (27‐32% reduction in 2017 compared to 2011). APRNs showed a substantive increase in the number of doses and prescriptions (121‐204% increase in 2017 compared to 2011), with increases remaining when controlling for number of providers. Physicians increased doses and prescriptions of Schedule II stimulants (37% increase for both doses and prescriptions), but by a smaller magnitude than APRN increases in stimulants (334‐360% increase). Dentists showed decreases in Schedule II stimulants prescribed (69‐80% reduction). Similar trends, but more modest in magnitude, were observed for Schedule III–IV.Discussion and ConclusionsAlthough monitoring and continuing education requirements are similar across all providers in Kentucky, differences in prescription trends for Schedule II opioids and stimulants were noted for physicians, APRNs, and dentists.Scientific SignificanceChanges in prescribing following introduction of mandatory use of KASPER markedly differed based on provider type, with increases observed for APRNs compared with physicians and dentists. These findings advance prior research by providing a detailed examination of prescribing trends by provider type subsequent to a PDMPs mandatory use law. (Am J Addict 2019;00:00–00)
The missed period
Authors: MANKEKAR PURNIMA , GUPTA AKHIL 
Published: October 2019

ABSTRACTBusiness process outsourcing (BPO) industries providing customer service are characterized by three features: the product of labor is affect; affect is central to the labor process; and affect constitutes a crucial modality for the workers’ subject formation. This affective labor is distinctive in that workers’ connections to their customers are live, transnational, and interactive. Such BPOs constitute a form of capitalist production in which profits are based on the management and monetization of affect, including brand loyalty and customer satisfaction. Affective labor generates disjunctive temporalities that are coimplicated with those of family life and with routines of schooling, ritual, and religion. These disjunctive temporalities engender modes of embodiment that are crucial to how BPO workers are constituted as specific kinds of laboring subjects. [affective labor, temporality, business process outsourcing, digital capitalism, Bengaluru, India]