bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal Changes in Diet and Toxicity in the Climbing Mantella Frog (Mantella Laevigata)
Authors: Moskowitz Nora A. , Roland Alexandre B. , Fischer Eva K. , Ranaivorazo Ndimbintsoa , Vidoudez Charles , Aguilar Marianne T. , Caldera Sophia M. , Chea Jacqueline , Cristus Miruna G. , Crowdis Jett P. , DeMessie Bluyé , desJardins-Park Caroline R. , Effenberger Audrey H. , Flores Felipe , Giles Michael , He Emma Y. , Izmaylov Nike S. , Lee ChangWon C. , Pagel Nicholas A. , Phu Krystal K. , Rosen Leah U. , Seda Danielle A. , Shen Yong , Vargas Santiago , Murray Andrew W. , Abebe Eden , Trauger Sunia A. , Donoso David A. , Vences Miguel , O’Connell Lauren A. 
Published: July 2018

AbstractPoison frogs acquire chemical defenses from the environment for protection against potential predators. These defensive chemicals are lipophilic alkaloid toxins that are sequestered by poison frogs from dietary arthropods and stored in skin glands. Despite decades of research focusing on identifying poison frog toxins, we know relatively little about how environmental variation and subsequent arthropod availability impacts toxicity in poison frogs. We investigated how seasonal environmental variation influences poison frog toxin profiles through changes in the diet of the Climbing Mantella (Mantella laevigata). We collected M. laevigata females on the Nosy Mangabe island reserve in Madagascar during the wet and dry seasons and tested the hypothesis that seasonal differences in rainfall is associated with changes in the diet and skin toxin profiles of M. laevigata. The arthropod diet of each frog was characterized into five groups (i.e. ants, termites, mites, insect larvae, or ‘other’) using visual identification and cytochrome oxidase 1 DNA barcoding. We found that frog diet differed between the wet and dry seasons, where frogs had a more diverse diet in the wet season and consumed a higher percentage of ants in the dry season. To determine if seasonality was associated with variation in frog defensive chemical composition, we used gas chromatography / mass spectrometry to quantify toxins from individual skin samples. Although the assortment of identified toxins was similar across seasons, we detected significant differences in the abundance of certain alkaloids, which we hypothesize reflects seasonal variation in the diet of M. laevigata. We suggest that these variations could originate from seasonal changes in either arthropod leaf litter composition or changes in frog behavioral patterns. Although additional studies are needed to understand the consequences of long-term environmental shifts, this work suggests that toxin profiles are relatively robust against short-term environmental perturbations.
Decreased IgG core fucosylation, a player in antibody-dependent cell-mediated cytotoxicity, is associated with autoimmune thyroid diseases
Authors: Martin Tiphaine C. , Šimurina Mirna , Ząbczyńska Marta , Kavur Marina Martinić , Rydlewska Magdalena , Pezer Marija , Kozłowska Kamila , Burri Andrea , Vilaj Marija , Turek-Jabrocka Renata , Krnjajić-Tadijanović Milena , Trofimiuk-Müldner Małgorzata , Lityńska Anna , Hubalewska-Dydejczyk Alicja , Trbojević-Akmačić Irena , Lim Ee Mun , Walsh John P. , Pochec Ewa , Spector Tim D. , Wilson Scott G. , Lauc Gordan 
Published: July 2018

AbstractAutoimmune thyroid diseases (AITD) are the most common group of autoimmune diseases, associated with lymphocyte infiltration and the production of thyroid autoantibodies, like thyroid peroxidase antibodies (TPOAb), in the thyroid gland. Immunoglobulins (Igs) and cell-surface receptors are glycoproteins with distinctive glycosylation patterns that play a structural role in maintaining and modulating their functions. We investigated associations of total circulating IgG and peripheral blood mononuclear cells (PBMCs) glycosylation with AITD and the influence of genetic background. The study revealed an inverse association of IgG core fucosylation with TPOAb and PBMCs antennary α1,2 fucosylation with AITD, but no shared genetic variance between AITD and glycosylation. These data suggest that the decreased level of IgG core fucosylation is a risk factor for AITD that promotes antibody-dependent cell-mediated cytotoxicity (ADCC) associated with TPOAb levels.
Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis
Authors: Fan Guangyi , Fu Yuanyuan , Yang Binrui , Liu Minghua , Zhang He , Liang Xinming , Shi Chengcheng , Ma Kailong , Wang Jiahao , Liu Weiqing , Shao Libin , Huang Chen , Guo Min , Cai Jing , Wong Andrew KC , Li Cheuk-Wing , Zhuang Dennis , Chen Ke-Ji , Cong Wei-Hong , Sun Xiao , Chen Wenbin , Xu Xun , Tsui Stephen Kwok-Wing , Liu Xin , Lee Simon Ming-Yuen 
Published: July 2018

AbstractPanax notoginseng is a traditional Chinese herb with high medicinal and economic value. There has been considerable research on the pharmacological activities of ginsenosides contained in Panax spp.; however, very little is known about the ginsenoside biosynthetic pathway. We reported the first de novo genome of 2.36 Gb of sequences from P. notoginseng with 35,451 protein-encoding genes. Compared to other plants, we found notable gene family contraction of disease-resistance genes in P. notoginseng, but notable expansion for several ATP-binding cassette (ABC) transporter subfamilies, such as the Gpdr subfamily, indicating that ABCs might be an additional mechanism for the plant to cope with biotic stress. Combining eight transcriptomes of roots and aerial parts, we identified several key genes, their transcription factor binding sites and all their family members involved in the synthesis pathway of ginsenosides in P. notoginseng, including dammarenediol synthase, CYP716 and UGT71. The complete genome analysis of P. notoginseng, the first in genus Panax, will serve as an important reference sequence for improving breeding and cultivation of this important nutraceutical and medicinal but vulnerable plant species.
FSTbetween Archaic and Present-Day Samples
Authors: Vecchyo Diego Ortega-Del , Slatkin Montgomery 
Published: July 2018

AbstractThe increasing abundance of DNA sequences obtained from fossils calls for new population genetics theory that takes account of both the temporal and spatial separation of samples. Here we exploit the relationship between Wright’sFSTand average coalescence times to develop an analytic theory describing howFSTdepends on both the distance and time separating pairs of sampled genomes. We apply this theory to several simple models of population history. If there is a time series of samples, partial population replacement creates a discontinuity in pairwiseFSTvalues. The magnitude of the discontinuity depends on the extent of replacement. In stepping-stone models, pairwiseFSTvalues between archaic and present-day samples reflect both the spatial and temporal separation. At long distances, an isolation by distance pattern dominates. At short distances, the time separation dominates. Analytic predictions fit patterns generated by simulations. We illustrate our results with applications to archaic samples from European human populations. We compare present-day samples with a pair of archaic samples taken before and after a replacement event.
Gorilla APOBEC3 restricts SIVcpz and influences lentiviral evolution in great ape cross-species transmissions
Authors: Nakano Yusuke , Yamamoto Keisuke , Soper Andrew , Kumata Ryuichi , Aso Hirofumi , Misawa Naoko , Konno Yoriyuki , Kimura Izumi , Nagaoka Shumpei , Juarez-Fernandez Guillermo , Ito Jumpei , Ikeda Terumasa , Koyanagi Yoshio , Harris Reuben S , Sato Kei 
Published: July 2018

SummaryRestriction factors including APOBEC3 family proteins have the potential prevent cross-species lentivirus transmissions. Such events as well as ensuing pathogenesis require the viral Vif protein to overcome/neutralize/degrade the APOBEC3 enzymes of the new host species. Previous investigations have focused on the molecular interaction between human APOBEC3s and HIV-1 Vif. However, the evolutionary interplay between lentiviruses and great ape (including human, chimpanzee and gorilla) APOBEC3s has not been fully investigated. Here we demonstrate that gorilla APOBEC3G plays a pivotal role in restricting lentiviral transmission from chimpanzee to gorilla. We also reveal that a sole amino acid substitution in Vif is sufficient to overcome the gorilla APOBEC3G-mediated species barrier. Moreover, the antiviral effects of gorilla APOBEC3D and APOBEC3F are considerably weaker than those of human and chimpanzee counterparts, which can result in the skewed evolution of great ape lentiviruses leading to HIV-1.HighlightsSIVcpz requires M16E mutation in Vif to counteract gorilla A3GAcidic residue at position 16 of Vif is crucial to counteract gorilla A3GGorilla A3D and A3F poorly suppress lentiviral infectivitySIVgor and related HIV-1s counteract human A3D and A3F independently of DRMR motif
Predicting Functional Associations using Flanking Genes (FlaGs)
Authors: Saha Chayan Kumar , Pires Rodrigo Sanches , Brolin Harald , Delannoy Maxence , Atkinson Gemma Catherine 
Published: July 2018

AbstractAnalysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (Flanking Genes) takes a list of NCBI protein accessions as in input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin-antitoxin system in prokaryotes and bacteriophages. FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run at www.webflags.se.
ClinPhen extracts and prioritizes patient phenotypes directly from medical records to accelerate genetic disease diagnosis
Authors: Deisseroth Cole A. , Birgmeier Johannes , Bodle Ethan E. , Bernstein Jonathan A. , Bejerano Gill 
Published: July 2018

AbstractPurposeSevere genetic diseases affect 7 million births per year, worldwide. Diagnosing these diseases is necessary for optimal care, but it can involve the manual evaluation of hundreds of genetic variants per case, with many variants taking an hour to evaluate. Automatic gene-ranking approaches shorten this process by reporting which of the genes containing variants are most likely to be causing the patient’s symptoms. To use these tools, busy clinicians must manually encode patient phenotypes, which is a cumbersome and imprecise process. With 60 million patients expected to be sequenced in the next 7 years, a fast alternative to manual phenotype extraction from the clinical notes in patients’ medical records will become necessary.MethodsWe introduce ClinPhen: a fast, high-accuracy tool that automatically converts the clinical notes into a prioritized list of patient symptoms using HPO terms.ResultsClinPhen shows superior accuracy to existing phenotype extractors, and when paired with a gene-ranking tool it significantly improve the latter’s performance.ConclusionCompared to manual phenotype extraction, ClinPhen saves more than 5 hours per case in Mendelian diagnosis alone. Summing over millions of forthcoming cases whose medical notes await phenotype encoding, ClinPhen makes a substantial contribution towards ending all patients’ diagnostic odyssey.
Role ofCnot6lin maternal mRNA turnover
Authors: Horvat Filip , Fulka Helena , Jankele Radek , Malik Radek , Jun Ma , Solcova Katerina , Sedlacek Radislav , Vlahovicek Kristian , Schultz Richard M. , Svoboda Petr 
Published: July 2018

ABSTRACTRemoval of poly(A) tail is an important mechanism controlling eukaryotic mRNA turnover. The major eukaryotic deadenylase complex CCR4-NOT contains two deadenylase components, CCR4 and CAF1 for which mammalian CCR4 is encoded byCnot6orCnot6lparalogs. We show thatCnot6lapparently supplies the majority of CCR4 in the maternal CCR4-NOT complex in mouse, hamster, and bovine oocytes. Deletion ofCnot6lyielded viable mice butCnot6l-/-females exhibited ~40% smaller litter size. The main onset of the phenotype was post-zygotic: fertilizedCnot6l-/-eggs developed slower and arrested more frequently thanCnot6l+/-eggs suggesting that maternal CNOT6L is necessary for accurate oocyte-to-embryo transition (OET). Transcriptome analysis revealed major transcriptome changes inCnot6l-/-ovulated eggs and 1-cell zygotes. In contrast, minimal transcriptome changes in preovulatoryCnot6l-/-oocytes were consistent with reportedCnot6lmRNA dormancy. A minimal overlap between transcripts sensitive to decapping inhibition andCnot6lloss suggests that decapping and CNOT6L-mediated deadenylation selectively target distinct subsets of mRNAs during OET in mouse.
Modulatory effect of Syzygium aromaticum and Pelargonium graveolens on oxidative stress and inflammation
Authors: Marmouzi Ilias , Karym El Mostafa , Alami Rachid , Jemli Meryem El , Kharbach Mourad , Mamouch Fouzia , Faridi Bouchra , Attar Aisha , Cherrah Yahia , Faouzi My El Abbes 
Published: July 2018

AbstractBackgroundTherapy combination is defined as disease treatment with two or more medication to acheive efficacy with lower doses or lower toxicity. Regarding its reported toxicities and efficacy, the Essential Oils (EOs) from Syzygium aromaticum (SA) and Pelargonium graveolens (PG) were combined for in vitro and in vivo assays and toxicities.MethodsThe Essential Oils and mixture were tested for in vivo/in vitro antioxidant and anti-inflammatory activities. The assays included the animal model of acute inflammation (carrageenan model), the protective effect on H2O2/Sodium nitroprissude induced stress in Tetrahymena pyriformis, and the in vitro antioxidant assays.ResultsThe chemical analysis of the investigated Oils has lead to the identification of Eugenol (74.06%), Caryophyllene (11.52%) and Carvacrol acetate (7.82%) as the major element in SA; while PG was much higher in Citronellol (30.77%), 10-epi-γ-Eudesmol (22.59%), and Geraniol (13.95%). In our pharmacological screening of samples, both Oils demonstrated good antioxidant effects. In vivo investigation of the antioxidant activity in the protozoa model (T. pyriformis) demonstrated a lesser toxic effect of EOs mixture with no significant differences when oxidative stress markers and antioxidant enzymes (MDA, SOD and CAT) were evaluated. On the other hand the in vivo model of inflammatory response to carrageenan demonstrated a good inhibitory potential of both EOs. The EOs Mixture demonstrated equivalent bioactivity with lower toxic effect and minimal risk for each compound.ConclusionsThe results from this study indicate that EOs mixture from SA and PG demonstrated promising modulatory antioxidant/anti-inflammatory effect, which suggest an efficient association for therapy.
Super-resolution fight club: A broad assessment of 2D & 3D single-molecule localization microscopy software
Authors: Sage Daniel , Pham Thanh-An , Babcock Hazen , Lukes Tomas , Pengo Thomas , Chao Jerry , Velmurugan Ramraj , Herbert Alex , Agrawal Anurag , Colabrese Silvia , Wheeler Ann , Archetti Anna , Rieger Bernd , Ober Raimund , Hagen Guy M. , Sibarita Jean-Baptiste , Ries Jonas , Henriques Ricardo , Unser Michael , Holden Seamus 
Published: July 2018

ABSTRACTWith the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. To guide researchers on the optimal analytical software for their experiments, we have designed, in a large community effort, a competition to extensively characterise and rank these options. We generated realistic simulated datasets for popular imaging modalities – 2D, astigmatic 3D, biplane 3D, and double helix 3D – and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D single molecule localization microscopy software, provides a holistic view of how the latest 2D and 3D single molecule localization software perform in realistic conditions, and ultimately provides insight into the current limits of the field.
Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline
Authors: Grunwald Hannah A. , Gantz Valentino M. , Poplawski Gunnar , Xu Xiang-ru S. , Bier Ethan , Cooper Kimberly L. 
Published: July 2018

AbstractA gene drive biases the transmission of a particular allele of a gene such that it is inherited at a greater frequency than by random assortment. Recently, a highly efficient gene drive was developed in insects, which leverages the sequence-targeted DNA cleavage activity of CRISPR/Cas9 and endogenous homology directed repair mechanisms to convert heterozygous genotypes to homozygosity. If implemented in laboratory rodents, this powerful system would enable the rapid assembly of genotypes that involve multiple genes (e.g., to model multigenic human diseases). Such complex genetic models are currently precluded by time, cost, and a requirement for a large number of animals to obtain a few individuals of the desired genotype. However, the efficiency of a CRISPR/Cas9 gene drive system in mammals has not yet been determined. Here, we utilize an active genetic “CopyCat” element embedded in the mouse Tyrosinase gene to detect genotype conversions after Cas9 activity in the embryo and in the germline. Although Cas9 efficiently induces double strand DNA breaks in the early embryo and is therefore highly mutagenic, these breaks are not resolved by homology directed repair. However, when Cas9 expression is limited to the developing female germline, resulting double strand breaks are resolved by homology directed repair that copies the CopyCat allele from the donor to the receiver chromosome and leads to its super-Mendelian inheritance. These results demonstrate that the CRISPR/Cas9 gene drive mechanism can be implemented to simplify complex genetic crosses in laboratory mice and also contribute valuable data to the ongoing debate about applications to combat invasive rodent populations in island communities.
What you see depends on what you hear: temporal averaging and crossmodal integration
Authors: Chen Lihan , Zhou Xiaolin , Müller Hermann J. , Shi Zhuanghua 
Published: July 2018

AbstractIn our multisensory world, we often rely more on auditory information than on visual input for temporal processing. One typical demonstration of this is that the rate of auditory flutter assimilates the rate of concurrent visual flicker. To date, however, this auditory dominance effect has largely been studied using regular auditory rhythms. It thus remains unclear whether irregular rhythms would have a similar impact on visual temporal processing; what information is extracted from the auditory sequence that comes to influence visual timing; and how the auditory and visual temporal rates are integrated together in quantitative terms. We investigated these questions by assessing, and modeling, the influence of a task-irrelevant auditory sequence on the type of ‘Ternus apparent motion’: group motion versus element motion. The type of motion seen critically depends on the time interval between the two Ternus display frames. We found that an irrelevant auditory sequence preceding the Ternus display modulates the visual interval, making observers perceive either more group motion or more element motion. This biasing effect manifests whether the auditory sequence is regular or irregular, and it is based on a summary statistic extracted from the sequential intervals: their geometric mean. However, the audiovisual interaction depends on the discrepancy between the mean auditory and visual intervals: if it becomes too large, no interaction occurs – which can be quantitatively described by a partial Bayesian integration model. Overall, our findings reveal a crossmodal perceptual averaging principle that may underlie complex audiovisual interactions in many everyday dynamic situations.Public Significance StatementThe present study shows that auditory rhythms, regardless of their regularity, can influence the way in which the visual system times (subsequently presented) events, thereby altering dynamic visual (motion) perception. This audiovisual temporal interaction is based on a summary statistic derived from the auditory sequence: the geometric mean interval, which is then combined with the visual interval in a process of partial Bayesian integration (where integration is unlikely to occur if the discrepancy between the auditory and visual intervals is too large). We propose that this crossmodal perceptual averaging principle underlies complex audiovisual interactions in many everyday dynamic perception scenarios.Author NoteThis study was supported by grants from the Natural Science Foundation of China (31200760, 61621136008, 61527804), German DFG project SH166 3/1 and “projektbezogener Wissenschaftleraustausch” (proWA). The data, and the source code of statistical analysis and modeling are available at https://github.com/msenselab/temporal_averaging. Part of the study has been presented as a talk in 17th International Multisensory Research Forum (IMRF, June 2016, Suzhou, China).
Going beyond western dualism: towards corporate nature responsibility reporting
Authors: Gallhofer Sonja 
Published: July 2018

PurposeThe purpose of this paper is to outline an ecofeminist lens for the analysis of accounting, which is applied to: first, the critique of corporate social responsibility reporting (CSRR); second, the elaboration of elements of a framework for a new accounting – corporate nature responsibility reporting (CNRR) – as a response to the critique of CSRR; and, third, the consideration of elements of an enabling and emancipatory praxis in the context of CNRR, including a sketch of a research agenda.Design/methodology/approachThe paper presents a critical application of aspects of the ecofeminist critique of Western dualism and its emphasis on wholeness, interconnectedness and relatedness, including its particular delineation of nature, to the critique and design of accounting.FindingsInsights from the application of an ecofeminist lens to the critique of CSRR raise questions about the suitability of the western notion of corporate social responsibility (CSR) and its associated accounting currently in use. In order to go beyond critique, the paper introduces the notions of corporate nature responsibility (CNR) and CNRR and offers an outline of key elements of CNRR and an emancipatory praxis in the context of CNRR, including a sketch of a research agenda. The author’s elaborations suggest that in order to overcome the limitations of CSR and CSRR, a corporation ought to be concerned about its broader and holistic CNR. And, it should provide a CNR report, as part of a holistic CNRR concerned with the performance of the company in the context of CNR.Social implicationsThrough creating new visibilities, CNRR has the potential to enhance the well-being of people and nature more generally.Originality/valueEcofeminism’s critique of western dichotomous thinking has been given little consideration in prior studies of accounting. The paper thus draws attention to the relevance of an ecofeminist theoretical lens for the critique and design of accounting by focussing on CSRR. The paper introduces the concepts of CNR and CNRR to address the limitations of CSRR as currently practiced.