bluuebunny/crossref_metadata_2025 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

Animals 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

Because 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

Background

Evaluation 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.

Method

Single-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.

Findings

45 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).

Conclusions

HTB 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 registration

German 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

Phytoplasmas 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

Motivation

3D 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.

Results

In 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.

Availability

Easybiotics and Simbiotics are free to use under the GPL3.0 license, and can be found at: https://bitbucket.org/simbiotics/simbiotics/wiki/Home

Contact

natalio.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

Metaproteomics 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

The 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

Cells 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

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

Osteogenesis 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

Dispersal 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

A 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

Stringent 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

We 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.
Symbolic labelling in 5-month-old human infants
Authors: Kabdebon Claire , Dehaene-Lambertz Ghislaine
Published: September 2018

Humans naturally entertain complex representations of the world based on various symbolic systems, from natural language to mathematical or musical notation. Above and beyond mere perceptual representations, the adult human mind can recode sensory inputs into abstract symbolic representations that can be internally manipulated and projected back onto the external world. However, the ontogeny of this striking ability remains controversial: Are children progressively acquiring symbolic representations through language acquisition, or are mental representations symbolic from the very beginning, language learning consisting in mapping mental symbols onto public symbols? Using high-density electroencephalography, we show here that preverbal infants can form mental representations that feature symbolic attributes. In three experiments, a total of 150 five month-olds were exposed to triplet words characterized by their abstract syllabic structure (AAB/ABA/ABB) consistently followed by an arbitrary label. Subsequently, incongruent structure-label pairings evoked a late violation-of-expectations signal, whereas congruent pairings induced an early priming effect. Importantly, the late surprise response was recorded for incongruent pairs even when the pairing order was reversed at test (i.e. labels preceding structure). Our results indicate that first, far beyond habituation/dishabituation, preverbal infants are able to recode sensory inputs, into abstract mental representations to which arbitrary labels can be flexibly assigned. Second, we demonstrate that, beyond conditioned associations, this mapping is instantly bidirectional. These findings buttress the hypothesis of symbolic representations in preverbal infants, which may serve as a foundation for our distinctively human learning abilities.

Significance Statement

Symbolic systems provide a powerful tool for efficiently re-describing the world into operable mental variables that, in turn, become objects of cognitive manipulation. However, is this ability tied to mastering language? Using an associative learning task in preverbal infants, we show that 5 month-olds can re-describe percepts into abstract mental variables that can be associated with arbitrary labels, well before they produce their first words. Importantly, we show that, beyond associative learning, they readily inferred a bidirectional mapping between the re-described representations and the associated labels, a capacity that animals do not spontaneously exhibit. Human cognitive success might be rooted in such abstract recoding which is no longer sensitive to local variations, thus alleviating cognitive load, and ultimately facilitating learning.
Dioecy in plants: an evolutionary dead end? Insights from a population genomics study in the Silene genus
Authors: Muyle Aline , Martin Hélène , Zemp Niklaus , Mollion Maéva , Gallina Sophie , Tavares Raquel , Silva Alexandre , Bataillon Thomas , Widmer Alex , Glémin Sylvain , Touzet Pascal , Marais Gabriel AB
Published: September 2018

About 15,000 angiosperm species (∼6%) have separate sexes, a phenomenon known as dioecy. Early work reported a lower species richness in dioecious compared to non-dioecious sister clades, which was taken to suggest that dioecy might be an evolutionary dead end. More recently, phylogenetic analyses using different methodologies have challenged this conclusion. Here, we used a population genomics approach to look for evidence of evolutionary handicaps of dioecy in the Silene genus at the molecular level. We obtained RNA-seq data of individuals from several populations in 13 closely related species with different breeding systems: seven dioecious, three hermaphroditic and three gynodioecious species. We show that dioecy is associated with increased genetic diversity and a higher selection efficacy both against deleterious and for beneficial mutations while controlling for differences in population size. We conclude that, in the Silene genus, dioecious species bear no sign of mutational burden or upcoming extinction. On the contrary, dioecious species harbor a higher potential for adaptation than their non-dioecious relatives. Our results do not support the evolutionary dead end hypothesis and re-open the question why dioecy is rare in angiosperms.

Significance statement

Dioecy (=separate sexes) is much rarer in flowering plants compared to animals and other organisms. The “dead-end hypothesis” states that dioecious plant populations might experience evolutionary handicaps such as low seed dispersal (as only 50% of the individuals, the females, contribute), which might cause high genetic drift, low adaptation and ultimately extinction. Here we tested this hypothesis by focusing on the genus Silene and by comparing the population genetics of 13 dioecious and non-dioecious species. We found that dioecious Silene species exhibit lower genetic drift and more adaptation compared to their non-dioecious relatives. Our results thus reject the dead-end hypothesis and re-open the question of why dioecy is rare in flowering plants.
Carbohydrate activity regulation of floral quantity during the juvenile phase in black pepper (Piper nigrumL.)
Authors: Zu Chao , Yang Jianfeng , Li Zhigang , Wang Can , Yu Huan
Published: September 2018

Black pepper plants maintain synchronous vegetative growth and flowering during their lifetimes, even in the juvenile phase. How to limit the duration of flowering, facilitate a return to vegetative development should be studied. Light intensity has been reported to affect the levels of stored carbohydrates in some horticultural trees. However, it is unclear whether increased flowering intensity in adaptable light intensity is due to the regulation of carbohydrates in black pepper. Here, we report the characterization of carbohydrates and enzyme turnover in major source leaves under shading treatments during the juvenile phase of pepper. In addition to the previous finding that carbohydrate levels are correlated with flowering time, we report the novel finding that carbohydrate contents in the leaves control floral quantity. To gain insights into the underlying physiological mechanisms, we analyzed the effect of shading on sugar contents and floral transition, which revealed that shading regulated carbohydrate levels, an increase in starch accumulation improved floral quantity, and sucrose-starch ratio played a negative role in inflorescence quantity. Based on this analysis, we characterized the changes in enzyme activities in the leaves that affect carbohydrate dynamics and identified the key indicator enzymes and optimal shading intensity for the five developmental periods.

Highlight

We identified the key carbohydrates, indicator enzymes and optimal shading intensity to control inflorescence quantity during the juvenile phase in black pepper for labor-saving.
Metabolic adaptations underlying genome flexibility in prokaryotes
Authors: Goyal Akshit
Published: September 2018

Even across genomes of the same species, prokaryotes exhibit remarkable flexibility in gene content. We do not know whether this flexible or “accessory” content is mostly neutral or adaptive, largely due to the lack of explicit analyses of accessory gene function. Here, across 96 diverse prokaryotic species, I show that a considerable fraction (~40%) of accessory genomes harbours beneficial metabolic functions. These functions take two forms: (1) they significantly expand the biosynthetic potential of individual strains, and (2) they help reduce strain-specific metabolic auxotrophies via intra-species metabolic exchanges. I find that the potential of both these functions increases with increasing genome flexibility. Together, these results are consistent with a significant adaptive role for prokaryotic pangenomes.

Author Summary

Recent and rapid advancements in genome sequencing technologies have revealed key insights into the world of bacteria and archaea. One puzzling aspect uncovered by these studies is the following: genomes of the same species can often look very different. Specifically, some “core” genes are maintained across all intraspecies genomes, but many “accessory” genes differ between strains. A major ongoing debate thus asks: do most of these accessory genes provide a benefit to different strains, and if so, in what form? In this study, I suggest that the answer is “yes, through metabolic interactions”. I show that many accessory genes provide significant metabolic advantages to different strains in different conditions. I achieve this by explicitly conducting a large-scale systematic analysis of 1,339 genomes across 96 diverse species of bacteria and archaea. A surprising prediction of this study that in many ecological niches, co-occurring strains of the same species may help each other survive by exchanging metabolites exclusively produced by these different accessory genes. More pronounced gene differences lead to more underlying metabolic advantages.
NEMO: Cancer subtyping by integration of partial multi-omic data
Authors: Rappoport Nimrod , Shamir Ron
Published: September 2018

Motivation:Cancer subtypes were usually defined based on molecular characterization of single omic data. Increasingly, measurements of multiple omic profiles for the same cohort are available. Defining cancer subtypes using multi-omic data may improve our understanding of cancer, and suggest more precise treatment for patients.

Results:We present NEMO (NEighborhood based Multi-Omics clustering), a novel algorithm for multiomics clustering. Importantly, NEMO can be applied to partial datasets in which some patients have data for only a subset of the omics, without performing data imputation. In extensive testing on ten cancer datasets spanning 3168 patients, NEMO outperformed nine state-of-the-art multi-omics clustering algorithms on full data and on imputed partial data. On some of the partial data tests, PVC, a multiview algorithm, performed better, but it is limited to two omics and to positive partial data. Finally, we demonstrate the advantage of NEMO in detailed analysis of partial data of AML patients. NEMO is fast and much simpler than existing multi-omics clustering algorithms, and avoids iterative optimization.

Availability:Code for NEMO and for reproducing all NEMO results in this paper is in github.

Contact:rshamir@tau.ac.il

Supplementary information:Supplementary data are available online.
Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models
Authors: Mollinari Marcelo , Garcia Antonio Augusto Franco
Published: September 2018

Modern SNP genotyping technologies allow to measure the relative abundance of different alleles for a given locus and consequently to estimate their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels in a sequence of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters using the maximum-likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results demonstrate the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations.

Author summary

In this paper, we present a complete multilocus solution based on hidden Markov models to estimate recombination fractions and infer the linkage phase configuration in full-sib mapping populations with even ploidy levels under random chromosome segregation. We also present an efficient pairwise loci analysis to be used in cases were the multilocus analysis becomes compute-intensive.
The sensation of groove is affected by the interaction of rhythmic and harmonic complexity
Authors: Matthews Tomas E. , Witek Maria A. G. , Heggli Ole A. , Penhune Virginia B. , Vuust Peter
Published: September 2018

Groove is defined as the pleasurable desire to move to music. Research has shown that rhythmic complexity modulates the sensation of groove but how other musical features, such as harmony, influence groove is less clear. To address this, we asked people with a range of musical experience to rate stimuli that varied in both rhythmic and harmonic complexity. Rhythm showed an inverted U-shaped relationship with ratings of pleasure and wanting to move, whereas medium and low complexity chords were rated similarly. Pleasure mediated the effect of harmony on wanting to move and high complexity chords attenuated the effect of rhythm. While rhythmic complexity is the primary driver, harmony both modulates the effect of rhythm and makes a unique contribution via its effect on pleasure. These results may be accounted for by predictive processes based on rhythmic and harmonic expectancies that are known to contribute to musical pleasure or reward.
The molecular structure of plant sporopollenin
Authors: Li Fu-Shuang , Phyo Pyae , Jacobowitz Joseph , Hong Mei , Weng Jing-Ke
Published: September 2018

Sporopollenin is a ubiquitous and extremely chemically inert biopolymer that constitutes the outer wall of all land-plant spores and pollen grains. Sporopollenin protects the vulnerable plant gametes against a wide range of environmental assaults, and is considered as a prerequisite for the migration of early plants onto land. Despite its importance, the chemical structure of plant sporopollenin has remained elusive. Using a newly developed thioacidolysis degradative method together with state-of-the-art solid-state NMR techniques, we determined the detailed molecular structure of pine sporopollenin. We show that pine sporopollenin is primarily composed of aliphatic-polyketide-derived polyvinyl alcohol units and 7-O-p-coumaroylated C16 aliphatic units, crosslinked through a distinctive m-dioxane moiety featuring an acetal. Naringenin was also identified as a minor component of pine sporopollenin. This discovery answers the long-standing question about the chemical makeup of plant sporopollenin, laying the foundation for future investigations of sporopollenin biosynthesis and for design of new biomimetic polymers with desirable inert properties.
Effect of intracerebroventricular epinephrine microinjection on blood pressure and urinary sodium handling in gestational protein-restricted rat adult male offspring
Authors: Cardoso Bárbara Vaccari , Custódio Augusto Henrique , Boer Patrícia Aline , Rocha Gontijo José Antonio
Published: September 2018

Background

In this study, we hypothesized that blunting of the natriuresis response to intracerebroventricularly (i.c.v.) microinjected adrenergic agonists are involved in the development of hypertension in maternal low-protein (LP) intake offspring.Methods.Stainless steel cannula was stereotaxically implanted into the right lateral ventricle, by use of techniques reported elsewhere and after that, was evaluated the effect of i.c.v. injection of adrenergic agonists, at increasing concentrations, and of α1 and α2-adrenoceptor antagonists on blood pressure and urinary sodium handling in LP offspring relative to age-matched, normal (NP) protein intake group.

Results

We confirmed that epinephrine (Epi) microinjected into the lateral ventricle (LV) of conscious NP rats leads to enhanced natriuresis followed by a reduction in arterial pressure. This response was associated with increased proximal and post-proximal sodium excretion accompanied by an unchanged glomerular filtration rate. The current study showed in both, NP and LP offspring that natriuretic effect of Epi injection into the LV was abolished by prior local microinjection of an α1-adrenoceptor antagonist (prazosin). Conversely, LV α2-adrenoceptor antagonist (yohimbine) administration potentiated the action of epinephrine. The LV yohimbine pretreatment normalized urinary sodium excretion and reduced the blood pressure in LP compared with age-matched NP offspring.

Conclusion

These are, as far as we are aware, the first results showing the role of central adrenergic receptors interaction on hypertension pathogenesis in maternal protein-restricted fetal programming offspring. The study also provides good evidence of the existence of central nervous system adrenergic mechanisms consisting of α1 and α2-adrenoceptors, which works reciprocally on the control of renal sodium excretion and blood pressure. Although the precise mechanism of the different natriuretic response of NP and LP rats is still uncertain, these results led us to speculate that inappropriate neural adrenergic pathways might have significant effects on tubule sodium transport, resulting in the inability of the kidneys to control hydrosaline balance, and, consequently, an increase in blood pressure.
Major barriers in Lean health care: an exploratory study in Uruguay
Authors: Escuder Matias , Tanco Martin , Santoro Anabella
Published: September 2018

Purpose

This paper aims to outline the barriers in introducing Lean in health care and to asses which of these have a greater impact in the Uruguayan health-care sector.

Design/methodology/approach

To uncover the barriers hindering Lean health-care implementation, a literature review was undertaken. Once identified, first-hand information was obtained from managers and professionals involved in managerial activities who evaluated each of the difficulties using a Likert scale.

Findings

In total, 17 barriers to the implementation of Lean health care were identified. Survey results show that the highest scores correspond to “controllable” barriers, those which can be overcome, almost exclusively, by the organization willing to implement the program.

Practical implications

Managers need to understand and ascertain the existing barriers before implementing Lean if they want to develop strategies to mitigate them. Although the exploratory study was conducted in the Uruguayan health-care sector, it could be replicated elsewhere.

Originality/value

An exhaustive list of barriers was synthesized and was later assessed by managers in the Uruguayan context. This is an important first step that could help foresee obstacles and develop strategies prior future implementation.
Implementing air cargo halal warehouse: insight from Malaysia
Authors: Abdul Rahman Nor Aida , Mohammad Mohammad Fakhrulnizam , Abdul Rahim Suzari , Mohd Noh Hazariah
Published: September 2018

Purpose

This study aims to discuss the challenges in implementing halal warehouse in the air cargo context along with the standard handling process for the storage of halal product for import and export purposes. This is vital to ensure that halal products do not get contaminated and should comply to halal logistics standard throughout the supply chain process.

Design/methodology/approach

This exploratory study adopts single case study to better understand the definition of halal warehouse, the challenges in implementing halal warehouse and also the standard handling process for the storage at the warehouse for import and export purposes. A well-guided case study protocol is followed.

Findings

Five categories have found to be the main challenges in implementing halal warehouse. They are coded as halal product trade, halal asset and facility, halal standard of procedure, human factor and perspectives between logistics provider and halal agencies. With regard to standard handling process for import and export purposes in airgo context with compliance to Shariah at the halal warehouse, there are seven main steps involved for import and nine steps involved for export.

Research limitations/implications

As this paper is among the pioneer study that looks into halal warehouse implementation, it has some limitations. Further empirical study in a bigger context may be performed quantitatively, and multiple case study approach may also be adopted to get deeper insight in understanding halal warehouse implementation domain of study.

Practical implications

This study contributes to the understanding on the gap in the field with adhering or complying with the practice. It will provide input to the authority in understanding the current limitation and suggestion by the practicing companies.

Social implications

Halal requirement in non-Muslim countries are not very well implemented and understood, whereby the understanding of the concept of Halalal Toyyiban throughout the supply chain process is critical. The main aim of halal logistics is to avoid cross contamination between halal and non-halal product during the transport, at the storage in warehouse and also in handling. This study contributes to the understanding of halal warehouse implementation.

Originality/value

There is a critical dearth of academic study that focuses on halal logistics specifically in transport and warehouse. This empirical case study provides basic understanding of implementing halal warehouse and presents the challenges and also required guidelines in handling halal product at the warehouse for both import and export purposes.
Reweaving the rainbow: qualitative color in business education
Authors: Starr-Glass David
Published: September 2018

Purpose

This study aims to reflect on the dominance of a narrowly focused analytical approach within business schools, which provides an artificially fractured and disjointed understanding of the contextual complexities and interconnectedness that students will encounter in the future. This approach unnecessarily constrains sensemaking and inhibits creative response to future social and organizational complexity. As business schools and their graduates come under sustained scrutiny and criticism, it perhaps appropriate to reexamine and reframe their analytical bias.

Design/methodology/approach

The central direction taken in this study is that of critical reflection on the present author’s practice and experience in teaching undergraduate economics and accounting. Although the analysis may have limited generalizability, it is hoped that it may prove of interest and value to business school educators.

Findings

The preferential business school reliance on analytical perspectives suggest that they fail to appreciate the nature of business, its embeddedness in broader society and the competencies required by undergraduates and graduates. This study argues that an emphasis on holistic systems, synthetic fusion and an appreciation of complexity – rather than a reductive analytical agenda – might benefit business schools, their graduates and society at large.

Originality/value

This study provides an original, albeit personal, insight into a significant problem in business education. It offers original perspectives on the problem and presents faculty-centered suggestions on how business students might be encouraged and empowered to see quality as well as quantitative perspectives in their first-year courses.
Building a world class HR department
Authors: Ulrich Dave , Grochowski Joe
Published: September 2018

Purpose

This paper aims to define and clarify the nine criteria of an effective HR department, and it illustrates how these nine criteria deliver value across four distinct stages of an HR department.

Design/methodology/approach

This research is based on over 100,000 respondents from the HR competency study along with interviews and discussions with senior HR professionals in over 100 global 500 organizations across all industry sectors.

Findings

Many HR transformation efforts exclusively focus on how to organize the HR department. This paper argues that organizing and designing the right HR department is an important part of HR transformation, but focusing only on the HR department is a narrow focus of the overall effectiveness of HR. The overall effectiveness of the HR department consists of nine criteria that deliver value across four stages.

Originality/value

This paper provides HR professionals with a simple and practical framework to audit the overall effectiveness of the HR department by clarifying the nine criteria of an effective HR department that deliver value across four stages.