bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three stages in the development of the cyst wall of the eye pathogen Acanthamoeba castellanii
Authors: Magistrado-Coxen Pamela , Aqeel Yousuf , Lopez A , Samuelson John 
Published: January 2019

AbstractWhen deprived of nutrients, trophozoites of the eye pathogen Acanthamoeba castellanii make a cyst wall, which contains cellulose and has two layers connected by cone-shaped ostioles. We recently showed chitin is also present and identified three sets of lectins, which localize to the ectocyst layer (Jonah lectin) or the endocyst layer and ostioles (Luke and Leo lectins). To determine how the cyst wall is made, we examined encysting protists using structured illumination microscopy, probes for glycopolymers, and tags for lectins. In the first stage (3 to 9 hr), cellulose, chitin, and a Jonah lectin were each made in dozens of encystation-specific vesicles. In the second stage (12 to 18 hr), a primordial wall contained both glycopolymers and Jonah lectin, while small, flat ostioles were outlined by a Luke lectin. In the third stage (24 to 36 hr), an ectocyst layer enriched in Jonah lectin was connected to an endocyst layer enriched in Luke and Leo lectins by large, conical ostioles. Jonah and Luke lectins localized to the same places in mature cyst walls (72 hr) independent of the timing of expression. The Jonah lectin and the glycopolymer bound by the lectin were accessible in the ectocyst layer of mature walls. In contrast, Luke and Leo lectins and glycopolymers bound by the lectins were mostly inaccessible in the endocyst layer and ostioles. These results show that cyst wall formation is a tightly choreographed event, in which glycopolymers and lectins combine to form a mature wall with a protected endocyst layer.ImportanceWhile the cyst wall of Acanthamoeba castellanii, cause of eye infections, contains cellulose like plants and chitin like fungi, it is a temporary, protective structure, analogous to spore coats of bacteria. We showed here that, unlike plants and fungi, A. castellanii makes cellulose and chitin in encystation-specific vesicles. The outer and inner layers of cyst walls, which resemble the primary and secondary walls of plant cells, respectively, are connected by unique structures (ostioles) that synchronously develop from small, flat circles to large, conical structures. Cyst wall proteins, which are lectins that bind cellulose and chitin, localize to inner or outer layers independent of the timing of expression. Because of its abundance and accessibility in the outer layer, the Jonah lectin is an excellent target for diagnostic antibodies. A description of the sequence of events during cyst wall development is a starting point for mechanistic studies of its assembly.
Spectral tuning of adaptation supports coding of sensory context in auditory cortex
Authors: Espejo Mateo Lopez , Schwartz Zachary P. , David Stephen V. 
Published: January 2019

AbstractPerception of vocalizations and other behaviorally relevant sounds requires integrating acoustic information over hundreds of milliseconds, but the latency of sound-evoked activity in auditory cortex typically has much shorter latency. It has been observed that the acoustic context, i.e., sound history, can modulate sound evoked activity. Contextual effects are attributed to modulatory phenomena, such as stimulus-specific adaption and contrast gain control. However, an encoding model that links context to natural sound processing has yet to be established. We tested whether a model in which spectrally tuned inputs undergo adaptation mimicking short-term synaptic plasticity can account for contextual effects during natural sound processing. Single-unit activity was recorded from primary auditory cortex of awake ferrets during presentation of noise with natural temporal dynamics and fully natural sounds. Encoding properties were characterized by a standard linear-nonlinear spectro-temporal receptive field model (LN STRF) and STRF variants that incorporated STP-like adaptation. In two models, STP was applied either globally across all spectral channels or locally to subsets of channels. For most neurons, STRFs incorporating locally tuned STP predicted neural activity as well or better than the LN and global STP STRF. The strength of nonlinear adaptation varied across neurons. Within neurons, adaptation was generally stronger for activation with excitatory than inhibitory gain. Neurons showing improved STP model performance also tended to undergo stimulus-specific adaptation, suggesting a common mechanism for these phenomena. When STP STRFs were compared between passive and active behavior conditions, response gain often changed, but average STP parameters were stable. Thus, spectrally and temporally heterogeneous adaptation, subserved by a mechanism with STP-like dynamics, may support representation of the diverse spectro-temporal patterns that comprise natural sounds.Author summarySuccessfully discriminating between behaviorally relevant sounds such as vocalizations and environmental noise requires processing how acoustic information changes over many tens to hundreds of milliseconds. The sound-evoked activity measured for most auditory cortical neurons is relatively short (< 50 ms), so it is not clear how the auditory cortex encodes sound information over longer periods. In this study, we propose that nonlinear adaptation, mimicking the effects of short-term synaptic plasticity (STP), enables auditory neurons to encode longer and more complex spectro-temporal patterns. A model in which sound history is stored in the latent state of plastic synapses is able to describe responses of single cortical neurons to natural sounds better than a standard encoding model that does not include nonlinear adaptation. Moreover, STP-like adaptation can account for contextual effects on sound evoked activity that cannot be accounted for by standard encoding models.
Characterizing and comparing missense variants in monogenic disease and in cancer
Authors: Yin Yizhou , Moult John 
Published: January 2019

AbstractIn both monogenic disease and cancer a large fraction of causative mutations are missense, even though these are very different types of disease. Here we examine and compare a number of properties of these mutations in the two classes of disease to determine the extent to which the properties of the mutations are similar or different. Analysis of cancer mutations is complicated by the problem of distinguishing between drivers and passengers. After controlling for this factor in three different ways, we find the following: (1) A very high and similar fraction (~90%) of causal mutations in both diseases are at positions under strong selection pressure. (2) Mutations in structurally disordered regions play a minor role in monogenic disease (only about 10% of mutations are in those regions), but a larger role (about 25%) in cancer, largely because of the higher fraction of disordered regions in cancer driver proteins. (3) A large (~75%) and similar fraction of causal mutations in protein cores in both diseases act by significantly destabilizing three-dimensional structure, implying a large impact on protein function. (4) Cancer oncogene mutations tend to be on the protein surface whereas tumor suppressor and monogenic disease mutations are more common in the core. (5) A surprisingly high fraction (~50%) of mutations in cancer passenger genes are at positions under strong selection pressure.
Structural basis for transcription initiation by bacterial ECF σ factors
Authors: Li Lingting , Fang Chengli , Zhuang Ningning , Wang Tiantian , Zhang Yu 
Published: January 2019

AbstractBacterial RNA polymerase employs extra-cytoplasmic function (ECF) σ factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent σ factor class, the structural basis of ECF σ factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF σ factor σH (σH-RNAP) at 2.7 Å, and solve another crystal structure of a transcription initiation complex of Mtb σH-RNAP (σH-RPo) comprising promoter DNA and an RNA primer at 2.8 Å. The two structures together reveal the interactions between σH and RNAP that are essential for σH-RNAP holoenzyme assembly as well as the interactions between σH-RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF σ factors and primary σ factors employ distinct mechanisms for promoter recognition and for promoter unwinding.
Dissociating neural activity associated with the subjective phenomenology of monocular stereopsis: an EEG study
Authors: Uji Makoto , Jentzsch Ines , Redburn James , Vishwanath Dhanraj 
Published: January 2019

AbstractsThe subjective phenomenology associated with stereopsis, of solid tangible objects separated by a palpable negative space, is conventionally thought to be a by-product of the derivation of depth from binocular disparity. However, the same qualitative impression has been reported in the absence of disparity, e.g., when viewing pictorial images monocularly through an aperture. Here we aimed to explore if we could identify dissociable neural activity associated with the qualitative impression of stereopsis, in the absence of the processing of binocular disparities. We measured EEG activity while subjects viewed pictorial (non-stereoscopic) images of 2D and 3D geometric forms under four different viewing conditions (Binocular, Monocular, Binocular aperture, Monocular aperture). EEG activity was analysed by oscillatory source localization (beamformer technique) to examine power change in occipital and parietal regions across viewing and stimulus conditions in targeted frequency bands (alpha: 8-13Hz & gamma: 60-90Hz). We observed expected event-related gamma synchronization and alpha desynchronization in occipital cortex and predominant gamma synchronization in parietal cortex across viewing and stimulus conditions. However, only the viewing condition predicted to generate the strongest impression of stereopsis (monocular aperture) revealed significantly elevated gamma synchronization within the parietal cortex for the critical contrasts (3D vs. 2D form). These findings suggest dissociable neural processes specific to the qualitative impression of stereopsis as distinguished from disparity processing.
Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow
Authors: Ghashghavi Mohammad , Hester Eric R. , Oliver Viktoria , Lüke Claudia , Jetten Mike S. M. , Lücker Sebastian 
Published: January 2019

AbstractMethane is a potent greenhouse gas that contributes to global warming. However, under certain conditions, its release into the atmosphere can be mitigated by methane-oxidizing microorganisms. Typically, cultivated wetlands (i.e., paddy fields) are a major source of methane (CH4) while forests and meadow uplands are considered to be CH4 sinks. As the global need for rice production increases each year, more uplands are converted to inundated paddy fields. To investigate soils that may be converted into productive land for rice production, we investigated a paddy field and adjacent meadow in Northern Italy. Using a combination of 16S rRNA gene amplicon sequencing to analyze the bacterial community, and gas flux measurements to quantify CH4 emissions, we looked for differences between classically defined CH4 sinks (meadow soils) and CH4 sources (paddy fields). Analysis of the total bacterial community revealed that the family Fimbriimonadaceae, which belongs to the phylum Armatimonadetes, was significantly higher in paddy field soils driving the difference between paddy and meadow soils. Whereas, we found that the methylotrophic families Methyloligellaceae and Methylomirabilaceae were also present in higher relative abundance in the paddy field. Despite these major differences, CH4 fluxes were highly variable between the two sites with no significant differences observed. Furthermore, we found the Methylomonaceae family to be more abundant at the center of a neighboring paddy field compared to the edge of the paddy field from the current study, hinting at methanotrophic variation based on location. Taking these results into account, we propose a conceptual model to explain possible scenarios that may result in paddy and meadow fields not exhibiting classical source/sink properties. These findings call for caution when including paddy and meadow areas separately into global CH4 flux calculations, and urge further research to discern drivers of CH4 cycling under a range of environmental conditions rather than relying on assumptions.
A cross-sectional study to assess the magnitude of Hypertension and Type 2 Diabetes Mellitus in Hatcliffe, Harare
Authors: Gonde Lonestar Lazarus , Chimbari Moses John , Manyangadze Tawanda 
Published: January 2019

AbstractBackgroundHypertension (HTN) and type 2 diabetes mellitus (T2DM) are reported to be on the increase in developing countries. In this study we investigated the epidemiology of the prevalence of HTN and T2DM and its correlates in a high density area. We carried out this study to assess the magnitude of the prevalence of HTN and T2DM so that we can query the drivers that are causing an increase conditions in these conditions.MethodsWe conducted a cross-sectional study in Hatcliffe, a high density area (HDA) in Harare. We interviewed, bled, took anthropometric and measured blood pressure of 381 participants. We investigated HbA1c, blood pressure, BMI and prevalence of prehypertension, prediabetes, co-existence of HTN and T2DM. A geospatial analysis was carried out to ascertain distribution patterns of HTN and T2DM in Hatcliffe.ResultsThe prevalence for prehypertension and prediabetes is higher than it is for full blown conditions of the HTN and T2DM. The prevalence of prehypertension was 35.4% and prediabetes was 29%. The prevalence of HTN in this study was 14.4% whilst that of T2DM was 3.93%. Out of the 55 participants that had developed HTN five had developed T2DM. There was no significant difference in the HTN and T2DM clusters.ConclusionsThe prevalence for prehypertension and prediabetes is higher than it is for full blown conditions of the HTN and T2DM. This indicates the importance of having a strategy for reducing the number of prediabetes and prehypertensive cases so that cases of full blown T2DM and HTN remain low.
Convolutional and Recurrent Neural Network for Human Action Recognition: application on American Sign Language
Authors: Vincent Hernandez , Tomoya Suzuki , Gentiane Venture 
Published: January 2019

AbstractHuman Action Recognition (HAR) is an important and difficult topic because of the important variability between tasks repeated several times by a subject and between subjects. This work is motivated by providing time-series signal classification and a robust validation and test approaches. This study proposes to classify 60 American Sign Language signs from data provided by the LeapMotion sensor by using a combined approach with Convolutional Neural Network (ConvNet) and Recurrent Neural Network with Long-Short Term Memory cells (LSTM) called ConvNet-LSTM. Moreover, a complete kinematic model of the right and left forearm/hand/fingers/thumb is proposed as well as the use of a simple data augmentation technique to improve the generalization of neural networks. Results showed an accuracy of 89.3% on a user-independent test set with data augmentation when using the ConvNet-LSTM, while LSTM alone provided an accuracy of 85.0% on the same test set. The result dropped respectively to 85.9% and 81.4% without data augmentation.
Epigenetic Profiling Provides Insights into AIDS Resistance in African Green Monkey
Authors: Yuan Zheng , Zhou Xiao-jun 
Published: January 2019

AbstractAs a natural host of simian immunodeficiency virus (SIV), African green monkeys (AGM) do not develop AIDS although high levels of SIV replication were maintained. Low frequencies of CD4+ T cells and high frequencies of CD8dim T cells were observed in healthy adult AGM, which may partially explain the absence of SIV-induced disease progression. Elucidating the mechanisms that allow this natural host co-exist with SIV without progressive disease may facilitate knowledge of AIDS pathogenesis. Here we show: (1) Compared with junior AGM, 3 miRNA were up-regulated in adult AGM in which hsa-miR-151a-3p was shown to target both CD4 and MAZR; 15 miRNAs were down-regulated in adult AGM in which hsa-miR-140-5p, hsa-miR-126-3p and hsa-miR-194-5p were shown to target CD8α; (2) MeDIP sequencing analysis of adult AGM samples revealed that hypermethylation exists in the promoter region of CD4, CXCR6, CCR5, while hypomethylation exists in the promoter region of RUNX3, ICAM2; (3) Hypomethylation in the promoter region of PTK2 contributes to up-regulated expression of hsa-miR-151a-3p in adult AGM, while hypermethylation in the promoter region of WWP2 contributes to down-regulated expression of hsa-miR-140-5p. Our data for the first time demonstrates the link between miRNA and DNA methylation expression profile, which may together contribute to the phenotype of AIDS resistance in AGM.Author SummaryAfrican green monkeys (AGM) do not develop AIDS although high levels of SIV replication were maintained. Elucidating the mechanisms that allow this natural host co-exist with SIV without progressive disease may facilitate knowledge of AIDS pathogenesis. In this study, the miRNA expression patterns were found to be associated with the switch from CD4+ to CD4−CD8adim in adult AGM. The up-regulated hsa-miR-151a-3p was shown to target both AGM CD4 and MAZR, while the down-regulated hsa-miR-140-5p, hsa-miR-126-3p and hsa-miR-194-5p were shown to target AGM CD8α. And none of these miRNAs possess target sites in cynomolgus macaque (CM) CD4, CD8α and MAZR reflecting differences in AIDS resistance between these two species. Our data also demonstrates the link between miRNA and DNA methylation expression profile, indicating that multiple distinct mechanisms may contribute to AIDS resistance in AGM. Knowledge of the non-pathogenic nature of SIV infection in AGM may provide insight into development of new therapeutic strategies.
VisualCOBie for facilities management
Authors: Yalcinkaya Mehmet , Singh Vishal 
Published: January 2019

Purpose
The purpose of this paper is to describe the technical features, underlying concepts and implementation details of a novel Building Information Modeling (BIM)-integrated, graph-based platform developed to support BIM for facilities management through a usability driven visual representation of the construction operations building information exchange (COBie) spreadsheet data.

Design/methodology/approach
This paper is based on the iterative steps of design thinking and agile software development methodology. The conceptual development of the VisualCOBie platform is based on Gestalt’s principles of visual perception to facilitate usability and comprehension of the COBie data.

Findings
The paper demonstrates that Gestalt’s principles of visual perception provide a suitable conceptual as well as implementable basis for improving the usability and comprehension of COBie spreadsheets. The implemented BIM-integrated, graph-based VisualCOBie platform supports visual navigation and dynamic search, reducing the cognitive load of large spreadsheets that are common in facilities management software.

Research limitations/implications
The usability, visual search and dependencies-based search of VisualCOBie can potentially transform how we implement and use facilities and information management systems in construction, where large spreadsheets are frequently used in conjunction with BIM and other tools. VisualCOBie also provides usability-based step towards BIM for facilities management.

Originality/value
The VisualCOBie approach provides a novel user interface and information management platform. This paper may also foster a potential paradigm shift in our approach to the representation and use of information exchange standards such as COBie, which are required to facilitate the research and practice on BIM for facilities management.
Differences in management styles, levels of profitability, and performance across generations, and the development of the Family Business Success Model
Authors: Sreih Josiane Fahed , Lussier Robert N. , Sonfield Matthew C. 
Published: January 2019

PurposeThe purpose of this paper is to, first, investigate the differences between generations in family businesses and, second, develop and verify the Family Business Success Model ability to improve the probability of business success measured by perceived profits, growth and meeting the owners’ expectations.Design/methodology/approachData were collected through questionnaires and personal interviews. Overall, 98 usable questionnaires were collected for statistical analysis with a response rate of 82 percent.FindingsOne-way ANOVA hypotheses testing of the variables found four significant differences between generations. Regression analysis found the Family Business Success Model to be significant. Family business owners can improve the probability of success by utilizing a team-management decision-making approach, effectively handling conflict effectively, formulating specific succession plans, developing strategic plans, using sophisticated financial management methods, dealing effectively with the founder’s influence and if they seek to grow, they should consider going public.Practical implicationsThis study provides family business owners, managers, educators and public policy makers with the means to help family businesses survive and grow effectively throughout generations by using the Family Business Success Model. In addition, this study can help consultants and advisors of family businesses to understand the differences between the first, second and third generation family businesses from a holistic perspective and help them implement the family business model.Originality/valueThis study contributes to the literature as one of the few studies in the Lebanese emerging market that examines how the first, second and third generations of family businesses differ. More importantly, it develops a Family Business Success Model that improves the probability of success.
Towards a framework for innovation orientation within business and management studies
Authors: Norris David , Ciesielska Malgorzata 
Published: January 2019

PurposeThe innovation orientation theory has emerged within the literature in the last 40 years particular within the development of other strategic orientations, but the bulk of seminal literature in the area has been developed in the past 11 years. The purpose of this paper is to revisit the concept innovation orientation in the light of recent research.Design/methodology/approachThis paper presents a systematic review of this literature, covering 74 scholarly articles published between 1982 and 2017.FindingsInnovation orientation is a sub-construct positioned within the wider field of innovation and relates to an innovation-based strategic orientation, where orientation is used to describe the overall dominant approach that represents an organisation’s competitive posture and strategic focus. It is a multifaceted construct that includes a range of core common variables innovation culture, competition-based understanding, organisational flexibility and specific capital and knowledge capabilities and is particular relevant for that managers and executives to understand how to manage innovation at the firm level. Literature also reports links between innovation orientation and organisational performance.Originality/valueOn the basis of these analyses, a comprehensive innovation orientation framework is developed including key antecedents and key outcomes in terms of performance enhancement and capabilities development. Suggestions for future research are also presented.