bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neurogenetic dissection of the Drosophila innate olfactory processing center
Authors: Dolan Michael-John , Frechter Shahar , Bates Alexander Shakeel , Dan Chuntao , Huoviala Paavo , Roberts Ruairí J.V. , Schlegel Philipp , Dhawan Serene , Tabano Remy , Dionne Heather , Christoforou Christina , Close Kari , Sutcliffe Ben , Giuliani Bianca , Feng Li , Costa Marta , Ihrke Gudrun , Meissner Geoffrey , Bock Davi , Aso Yoshinori , Rubin Gerald M. , Jefferis Gregory S.X.E. 
Published: September 2018

AbstractAnimals exhibit innate behaviours in response to a variety of sensory stimuli such as olfactory cues. In Drosophila, a higher olfactory centre called the lateral horn (LH) is implicated in innate behaviour. However, our knowledge of the structure and function of the LH is scant, due to the lack of sparse neurogenetic tools for this brain region. Here we generate a collection of split-GAL4 driver lines providing genetic access to 82 LH cell-types. We identify the neurotransmitter and axo-dendritic polarity for each cell-type. Using these lines were create an anatomical map of the LH. We found that ∼30% of LH projections converge with outputs from the mushroom body, the site of olfactory learning and memory. Finally, using optogenetic activation of small groups of LH neurons. We identify cell-types that drive changes in either valence or specific motor programs, such as turning and locomotion. In summary we have generated a resource for manipulating and mapping LH neurons in both light and electron microscopy and generated insights into the anatomy and function of the LH.
Investigating the probability of establishment of Zika virus and detection through mosquito surveillance under different temperature conditions
Authors: Christofferson Rebecca C. 
Published: September 2018

AbstractBecause of the increasing threat that Zika virus (ZIKV) poses to extra-tropical regions due to increased global travel, there is a need for better understanding of the effect(s) of temperature on the establishment potential of ZIKV within these subtropical, temperate, and/or seasonal Ae. aegypti populations. The first step to determining risk establishment of ZIKV in these regions is to assess ZIKV’s ability to infect mosquitoes at less tropical temperatures, and thus be detected through common surveillance programs. To that end, the effect of two rearing temperatures (RT) and extrinsic incubation temperatures (EIT) on infection and dissemination rates was evaluated, as well as the interactions of such. Total, there were four combinations (RT24-EIT24, RT24-DEI28, RT28-EIT24, RT28- EIT28). Further, a stochastic SEIR framework was adapted to determine whether observed data could lead to differential success of establishment of ZIKV in naive mosquito populations. There was no consistent pattern in significant differences found across treatments for either infection or dissemination rates (p>0.05), where only a significant difference was found in infection rates between RT24- EIT24 (44%) and RT28-EIT24(82.6%). Across all temperature conditions, the model predicted between a 77.3% and 93.1% chance of successful establishment of ZIKV in naive mosquito populations under model assumptions. Further, the model predicted between 4.1% and 46.7% chance of at least one mosquito developing a disseminated infection, depending on temperature conditions, despite no significant differences in the experimental data. These results indicate that 1) there is no straightforward relationship between RT, EIT, and infection/dissemination rates for ZIKV, similar to what has been reported for DENV, 2) in more temperate climates, ZIKV may still have the ability to establish in populations of Ae. aegypti, and 3) despite a lack of statistical differences in observed experimental data, model predictions indicate that the interplay of rearing and extrinsic incubation temperatures may still alter the kinetics of ZIKV within the mosquito enough to affect numbers of infected/disseminated mosquitoes and the associated probability of detection through surveillance programs.
Effects and Feasibility of Hyperthermic Baths for Patients with Depressive Disorder: A Randomized Controlled Clinical Pilot Trial
Authors: Naumann Johannes , Sadaghiani Catharina , Kruza Iris , Denkel Luisa , Kienle Gunver , Huber Roman 
Published: September 2018

AbstractBackgroundEvaluation of efficacy, safety and feasibility of hyperthermic baths (HTB; head-out-of-water-immersion in 40°C), twice a week, compared to a physical exercise program (PEP; moderate intensity aerobic exercises) in moderate to severe depression.MethodSingle-site, open-label randomized controlled 8-week parallel-group pilot study at an university outpatient clinic as part of usual depression care. Medically stable outpatients with depressive disorder (ICD-10: F32/F33) as determined by the 17-item Hamilton Depression Rating Scale (HAM-D) score ≥18 and a score ≥2 on item 1 (Depressed Mood) were randomly assigned to receive either two sessions of HTB or PEP per week (40-45 min) provided by two trained doctoral students. An independent biometric center used computer-generated tables to allocate treatments. Primary outcome measure was the change in HAM-D total score from baseline (T0) to the 2-week time point (T1). Linear regression analyses, adjusted for baseline values, were performed to estimate intervention effects on an intention-to-treat (ITT) principle.Findings45 patients (HTBn= 22; PEPn= 23) were randomized and analyzed according to ITT (mean age = 48.4 years, SD = 11.3, mean HAM-D score = 21.7, SD = 3.2). Baseline-adjusted mean difference was 4.3 points in the HAM-D score in favor of HTB (p<0.001). This improvement was achieved after two weeks. Compliance with the intervention and follow-up was far better in the HTB group (2 vs 13 dropouts). There were no treatment-related serious adverse events. Main limitation: the number of dropouts in the PEP group (13 of 23) was far higher than in other trials investigating exercise in depression (18.1 % dropouts).ConclusionsHTB seems to be a fast-acting, safe and easy accessible method leading to clinically relevant improvement in depressive disorder after two weeks; it is also suitable for persons who have problems performing exercise training.Trial registrationGerman Clinical Trials Register (DRKS) with the registration numberDRKS00011013(registration date 2016-09-19) before onset of the study.
Molecular characterization of effector protein SAP54 inBellis Virescence Phytoplasma(16SrIII-J)
Authors: Fernández Franco D , Debat Humberto J , Conci Luis R 
Published: September 2018

AbstractPhytoplasmas are wall-less bacteria, with a parasitic life style responsible for numerous plant diseases worldwide. The genomic landscape of phytoplasmas has been scarcely studied. Nevertheless, since the introduction of next generation sequencing technologies, genome wide studies of these pathogens are flourishing and a handful of phytoplasmas genomes are available in public databases. In South America, phytoplasmas from 16SrIII group (X-disease) are the most widely distributed, and only a draft genome from a phytoplasmas 16SrIII-J infected periwinkle from Chile has been generated (Phytoplasma Vc33). Here, in grafting experiments we characterized the phenotypic signatures of an Argentinian daisy derived isolate of a 16SrIII-J phytoplasma (Bellis VirescencePhytoplasma) infecting periwinkle. Moreover, we applied a pipeline for genome wide annotation of the Vc33 genome and identified the effector protein SAP54. We then employed the obtained data to amplify, clone, sequence and characterize a SAP54 orthologue protein ofBellis VirescencePhytoplasma. Structural and phylogenetic analyses suggested that the identified SAP54 is highly conserved, and that its co-divergence among phytoplasma is not directly consistent with the evolutionary trajectories derived from rRNA analyses. The results gathered here could provide the basis for reverse genetics experiments using 16SrIII-J SAP54 proteins to assess their eventual influence in pathogenesis.
Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations
Authors: Naylor Jonathan , Fellermann Harold , Krasnogor Natalio 
Published: September 2018

AbstractMotivation3D physical modelling is a powerful computational technique which allows for the simulation of complex systems such as consortia of mixed bacterial species. The complexities in physical modelling reside in the knowledge intensive model building process and the computational expense in calculating their numerical solutions. These models can offer insights into microbiology, both in understanding natural systems and as design tools for developing novel synthetic bacteria. Developing a robust synthetic system typically requires multiple iterations around the specify->design->build->test cycle to meet specifications. This process is laborious and expensive for both the computational and laboratory aspects, hence any improvement in any of the workflow steps would be welcomed. We have previously introduced Simbiotics (Naylor, 2017) a powerful and flexible platform for designing and analysing three-dimensional simulations of mixed species bacterial populations. Simbiotics requires programming experience to use which creates barriers to entry for use of the tool.ResultsIn the spirit of enabling biologists who may not have programming skills to install and utilise Simbiotics, we present in this application note Easybiotics, a user-friendly graphical user interface for Simbiotics. Users may design, simulate and analyse models from within the GUI, with features such as live graph plotting and parameter sweeps. Easybiotics provides full access to all of Simbiotics simulation features, such as cell growth, motility and gene regulation.AvailabilityEasybiotics and Simbiotics are free to use under the GPL3.0 license, and can be found at: https://bitbucket.org/simbiotics/simbiotics/wiki/HomeContactnatalio.krasnogor@newcastle.ac.uk
Data-independent acquisition mass spectrometry enables reproducible characterization of microbiota function
Authors: Aakko Juhani , Pietilä Sami , Suomi Tomi , Mahmoudian Mehrad , Toivonen Raine , Kouvonen Petri , Rokka Anne , Hänninen Arno , Elo Laura L 
Published: September 2018

AbstractMetaproteomics is an emerging research area which aims to reveal the functionality of microbial communities – unlike the increasingly popular metagenomics providing insights only on the functional potential. So far, the common approach in metaproteomics has been data-dependent acquisition mass spectrometry (DDA). However, DDA is known to have limited reproducibility and dynamic range with samples of complex microbial composition. To overcome these limitations, we introduce here a novel approach utilizing data-independent acquisition (DIA) mass spectrometry, which has not been applied in metaproteomics of complex samples before. For robust analysis of the data, we introduce an open-source software package diatools, which is freely available at Docker Hub and runs on various operating systems. Our highly reproducible results on laboratory-assembled microbial mixtures and human fecal samples support the utility of our approach for functional characterization of complex microbiota. Hence, the approach is expected to dramatically improve our understanding on the role of microbiota in health and disease.
Multiple Introductions of the Mycobacterium tuberculosis Lineage 2–Beijing into Africa over centuries
Authors: Rutaihwa Liliana K. , Menardo Fabrizio , Stucki David , Gygli Sebastian M. , Ley Serej D , Malla Bijaya , Feldmann Julia , Borrell Sonia , Beisel Christian , Middelkoop Kerren , Carter E Jane , Diero Lameck , Ballif Marie , Jugheli Levan , Reither Klaus , Fenner Lukas , Brites Daniela , Gagneux Sebastien 
Published: September 2018

AbstractThe Lineage 2–Beijing (L2–Beijing) sub-lineage of Mycobacterium tuberculosis has received much attention due to its high virulence, fast disease progression, and association with antibiotic resistance. Despite several reports of the recent emergence of L2–Beijing in Africa, no study has investigated the evolutionary history of this sub-lineage on the continent. In this study, we used whole genome sequences of 817 L2 clinical strains from 14 geographical regions globally distributed to investigate the origins and onward spread of this lineage in Africa. Our results reveal multiple introductions of L2–Beijing into Africa linked to independent bacterial populations from East-and Southeast Asia. Bayesian analyses further indicate that these introductions occurred during the past 300 years, with most of these events pre-dating the antibiotic era. Hence, the success of L2–Beijing in Africa is most likely due to its hypervirulence and high transmissibility rather than drug resistance.
Phage Mediate Bacterial Self Recognition
Authors: Song Sooyeon , Guo Yunxue , Kim Jun-Seob , Wang Xiaoxue , Wood Thomas K. 
Published: September 2018

AbstractCells are social, and self-recognition is an important and conserved aspect of group behavior where cells assist kin and antagonize non-kin to conduct group behavior such as foraging for food and biofilm formation. However, the role of the common bacterial cohabitant, phage, in kin recognition, has not been explored. Here we find that a boundary (demarcation line) is formed between different swimmingEscherichia colistrains but not between identical clones; hence, motile bacterial cells discriminate between self and non-self. The basis for this self-recognition is a novel, 49 kb, T1-type, lytic phage of the family siphoviridae (named here SW1) that controls formation of the demarcation line by utilizing one of the host’s cryptic prophage proteins, YfdM, to propagate. Critically, SW1 increases the fitness ofE. coliK-12 compared to the identical strain that lacks the phage. Therefore, bacteria use phage to recognize kin.
Tibetan antelope rests like a Puppet
Authors: Luo Yunchao , Wang Lin , Yang Le , Tan Ming , Wu Yiqian , Li Yuhang , Li Zhongqiu 
Published: September 2018

Abstract:Rest contributes to a large part of animals’ daily life, and animals usually rest in two ways, standing or in recumbence. For small or medium sized ungulates, they bed to rest in most cases, and standing rest is very rare and hardly seen. Here we described a standing rest behaviour of medium sized Tibetan antelopes (Pantholops hodgsonii) living on the roof of the world, Tibet Plateau, which has not been reported before. We named the standing rest behaviour here as Puppet behaviour, since the antelope can stand still for a certain time just like a Puppet. Of the total 304 focal individuals, 48.3% (98/203) of adult and sub-adult males expressed the Puppet behaviour, whereas only 6.3% (6/96) of females did, indicating an obvious sexual difference. Puppet behaviour occurred more frequently at noon and in the afternoon on sunny and cloudy days, meaning that day time and weather were both influential factors. Puppet behaviour was usually accompanied with rumination and sometimes ended with leg-shaking. Our results suggest that Puppet behaviour is probably an adaptive form of rest, which serves a thermoregulatory and anti-predation function, and is much simpler and safer than recumbent rest.
Dental and facial characteristics of osteogenesis imperfecta type V
Authors: Retrouvey Jean-Marc , Taqi Doaa , Tamimi Faleh , Dagdeviren Didem , Glorieux Francis H. , Lee Brendan , Hazboun Renna , Krakow Deborah , Sutton V. Reid ,   Members of the BBD Consortium, Bober Michael , Esposito Paul , Eyre David R , Gomez Danielle , Harris Gerald , Hart Tracy , Jain Mahim , Krisher Jeffrey , Nagamani Sandesh CS , Orwoll Eric S , Raggio Cathleen L , Rush Eric , Smith Peter , Tosi Laura , Rauch Frank 
Published: September 2018

AbstractOsteogenesis imperfecta (OI) type V is an ultrarare heritable bone disorder caused by the heterozygous c.-14C>T mutation in IFITM5. The dental and craniofacial phenotype has not been described in detail. In the present multicenter study (Brittle Bone Disease Consortium) 14 individuals with OI type V (age 3 to 50 years; 10 females, 4 males) underwent dental and craniofacial assessment. None of the individuals had dentinogenesis imperfecta. Six of the 9 study participants (66%) for whom panoramic radiographs were obtained had at least one missing tooth (range 1 to 9). Class II molar occlusion was present in 8 (57%) of the 14 study participants. The facial profile was retrusive and lower face height was decreased in 8 (57%) individuals. Cephalometry, performed in three study participants, revealed a severely retrusive maxilla and mandible, and poorly angulated incisors in a 14-year old girl, a protrusive maxilla and a retrusive mandible in a 14-year old boy. Cone beam computed tomograpy scans were obtained from two study participants and demonstrated intervertebral disc calcification at the C2-C3 level in one individual. Our study observed that OI type V is associated with missing permanent teeth, especially permanent premolar, but not with dentinogenesis imperfecta. The pattern of craniofacial abnormalities in OI type V thus differs from that in other severe OI types, such as OI type III and IV, and could be described as a bimaxillary retrusive malocclusion with reduced lower face height and multiple missing teeth.
Dispersal limitations of early life stages and sibling aggregations in a broadcastingMilleporahydrocoral, as revealed by parentage analysis
Authors: Dubé Caroline E. , Boissin Emilie , Mercière Alexandre , Planes Serge 
Published: September 2018

AbstractDispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of local dispersal and self-recruitment in a broadcasting reef-builder, the hydrocoralMillepora platyphylla. Using microsatellite markers, we gathered genotypic information from 3160 georeferenced colonies collected over 9000 m2of reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope and back reef. Our parentage analysis revealed a predominance of self-recruitment with 58% of sexual propagules produced locally. Sexual propagules often settled at less than 10 meters from their parents and dispersal events decrease with increasing geographic distance. Limited dispersal among adjacent habitats via cross-reef transport was also detected. Sibship analysis showed that both full and half siblings recruit together on the reef, resulting in sibling aggregations. The identification of local families revealed discrepancies between dispersal patterns of sexual and asexual propagules. Self-recruits are dispersed with along-reef currents and settled in alignment with the location of their parents, while the dispersal of asexual fragments is heavily influenced by wave-driven cross-reef currents. Our findings highlight the importance of self-recruitment together with clonality in stabilising population dynamics, as it can enhance local sustainability and resilience to disturbance, but also raise uncertainties on the widely accepted high dispersal ability of broadcasting reef species.
Improved consistency in estimates of conditional false discovery rates increases power relative to both existing methods and parametric estimators
Authors: Liley James , Wallace Chris 
Published: September 2018

AbstractA common aim in high-dimensional association studies is the identification of the subset of investigated variables associated with a trait of interest. Using association statistics on the same variables for a second related trait can improve power. An important quantity in such analyses is the conditional false-discovery rate (cFDR), the probability of non-association with the trait of interest given p-value thresholds for both traits. The cFDR can be used for hypothesis testing and as a posterior probability in its own right. In this paper, we propose new estimators for the cFDR based on kernel density estimates and mixture-Gaussian models of effect sizes, the latter also allowing estimation of a ‘local’ form of cFDR (cfdr). We also propose a general non-parametric improvement to existing estimators based on estimating a posterior probability previously estimated at 1. We find that new estimators have the desirable property of smooth rejection regions, but, unexpectedly, do not improve the power of the method, even when distributional assumptions are true. Furthermore, we find that although the local cfdr represents a theoretically optimal decision boundary, noisiness in its estimation means it is less powerful than corresponding cFDR estimates. We find, however, that the non-parametric adjustment increases power for every estimator. We demonstrate the best method on transcriptome-wide association study datasets for breast and ovarian cancers. The findings from this analysis are of both theoretical and pragmatic interest, giving insight into the nature of cFDR and the behaviour of false-discovery rates in a two-dimensional setting. Our methods allow improved control over the behaviour of the cFDR estimator and improved power in high-dimensional hypothesis testing.
Immune differentiation regulator p100 tunes NF-κB responses to TNF
Authors: Chatterjee Budhaditya , Roy Payel , Sarkar Uday Aditya , Ratra Yashika , Chawla Meenakshi , Gomes James , Basak Soumen 
Published: September 2018

SummaryStringent regulation of TNF signaling prevents aberrant inflammation. TNF engages the canonical NF-κB pathway for activating the RelA:p50 heterodimer, which mediates specific expressions of pro-inflammatory and immune response genes. Importantly, the NF-κB system discriminates between time-varied TNF inputs. Negative feedback regulators of the canonical pathway, including IκBα, are thought to ensure transient RelA:p50 responses to brief TNF stimulations. The noncanonical NF-κB pathway controls a separate RelB activity associated with immune differentiation. In a systems modeling approach, we uncovered an unexpected role of p100, a constituent of the noncanonical pathway, in TNF signaling. Brief TNF stimulation of p100-deficient cells produced an additional late NF-κB activity consisted of the RelB:p50 heterodimer, which distorted the TNF-induced gene-expression program. Periodic TNF pulses augmented this RelB:p50 activity, which was reinforced by NF-κB-dependent RelB synthesis. In sum, the NF-κB system seems to engage distantly related molecules for enforcing dynamical and gene controls of immune-activating TNF signaling.
Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data
Authors: de Souza Camila P.E. , Andronescu Mirela , Masud Tehmina , Kabeer Farhia , Biele Justina , Laks Emma , Lai Daniel , Ye Patricia , Brimhall Jazmine , Wang Beixi , Su Edmund , Hui Tony , Cao Qi , Wong Marcus , Moksa Michelle , Moore Richard A. , Hirst Martin , Aparicio Samuel , Shah Sohrab P. 
Published: September 2018

AbstractWe present Epiclomal, a probabilistic clustering method arising from a hierarchical mixture model to simultaneously cluster sparse single-cell DNA methylation data and impute missing values. Using synthetic and published single-cell CpG datasets we show that Epiclomal outperforms non-probabilistic methods and is able to handle the inherent missing data feature which dominates single-cell CpG genome sequences. Using a recently published single-cell 5mCpG sequencing method (PBAL), we show that Epiclomal discovers sub-clonal patterns of methylation in aneuploid tumour genomes, thus defining epiclones. We show that epiclones may transcend copy number determined clonal lineages, thus opening this important form of clonal analysis in cancer. Epiclomal is written in R and Python and is available at https://github.com/shahcompbio/Epiclomal.