bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered functional interactions between neurons in primary visual cortex of macaque monkeys with experimental amblyopia
Authors: Acar Katerina , Kiorpes Lynne , Anthony Movshon J. , Smith Matthew A. 
Published: April 2019

AbstractAmblyopia, a disorder in which vision through one of the eyes is degraded, arises because of defective processing of information by the visual system. Amblyopia often develops in humans after early misalignment of the eyes (strabismus), and can be simulated in macaque monkeys by artificially inducing strabismus. In such amblyopic animals, single-unit responses in primary visual cortex (V1) are appreciably reduced when evoked by the amblyopic eye compared to the other (fellow) eye. However, this degradation in single V1 neuron responsivity is not commensurate with the marked losses in visual sensitivity and resolution measured behaviorally. Here we explored the idea that changes in patterns of coordinated activity across populations of V1 neurons may contribute to degraded visual representations in amblyopia, potentially making it more difficult to read out evoked activity to support perceptual decisions. We studied the visually-evoked activity of V1 neuronal populations in three macaques (M. nemestrina) with strabismic amblyopia and in one control. Activity driven through the amblyopic eye was diminished, and these responses also showed more interneuronal correlation at all stimulus contrasts than responses driven through the fellow eye or responses in the control. A decoding analysis showed that responses driven through the amblyopic eye carried less visual information than other responses. Our results suggest that part of the reduced visual capacity of amblyopes may be due to changes in the patterns of functional interaction among neurons in V1.New and noteworthyAmblyopia is a developmental disorder of visual processing that reduces visual function and changes the visual responses of cortical neurons in macaque monkeys. The neuronal and behavioral changes are not always well correlated. We found that the interactions among neurons in the visual cortex of monkeys with amblyopia are also altered. These changes may contribute to amblyopic visual deficits by diminishing the amount of information relayed by neuronal populations driven by the amblyopic eye.
Poorer auditory sensitivity is related to stronger visual enhancement of the human auditory mismatch negativity (MMNm)
Authors: Møller Cecilie , Højlund Andreas , Bærentsen Klaus B. , Hansen Niels Chr. , Skewes Joshua C. , Vuust Peter 
Published: April 2019

AbstractMultisensory processing facilitates perception of our everyday environment and becomes particularly important when sensory information is degraded or close to the discrimination threshold. Here, we used magnetoencephalography and an audiovisual oddball paradigm to assess the complementary role of visual information in subtle pitch discrimination at the neural level of participants with varying levels of pitch discrimination abilities, i.e., musicians and nonmusicians. The amplitude of the auditory mismatch negativity (MMNm) served as an index of sensitivity. The gain in amplitude resulting from compatible audiovisual information was larger in participants whose MMNm amplitude was smaller in the condition deviating only in the auditory dimension, in accordance with the multisensory principle of inverse effectiveness. These findings show that discrimination of even a sensory-specific feature as pitch is facilitated by multisensory information at a pre-attentive level, and they highlight the importance of considering inter-individual differences in uni-sensory abilities when assessing multisensory processing.
Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines
Authors: Perez-Riverol Yasset , Moreno Pablo 
Published: April 2019

AbstractThe recent improvements in mass spectrometry instruments and new analytical methods are increasing the intersection between proteomics and big data science. In addition, the bioinformatics analysis is becoming an increasingly complex and convoluted process involving multiple algorithms and tools. A wide variety of methods and software tools have been developed for computational proteomics and metabolomics during recent years, and this trend is likely to continue. However, most of the computational proteomics and metabolomics tools are targeted and design for single desktop application limiting the scalability and reproducibility of the data analysis. In this paper we overview the key steps of metabolomic and proteomics data processing including main tools and software use to perform the data analysis. We discuss the combination of software containers with workflows environments for large scale metabolomics and proteomics analysis. Finally, we introduced to the proteomics and metabolomics communities a new approach for reproducible and large-scale data analysis based on BioContainers and two of the most popular workflows environments: Galaxy and Nextflow.
Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom
Authors: Bhatnagar Srijak , Cowley Elise S. , Kopf Sebastian H. , Castro Sherlynette Pérez , Kearney Sean , Dawson Scott C. , Hanselmann Kurt , Ruff S. Emil 
Published: April 2019

AbstractPhototrophic microbial mats commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. Here we show that similar coexistence patterns and ecological niches can occur in suspended phototrophic blooms of an organic-rich estuary. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophicCyanobacteria, the middle and lower parts were dominated by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We found multiple uncultured phototrophic lineages and present metagenome-assembled genomes of two uncultured organisms within theChlorobiales. Apparently, thoseChlorobialespopulations were affected byMicroviridaeviruses. We suggest a sulfur cycle within the bloom in which elemental sulfur produced by phototrophs is reduced to sulfide byDesulfuromonas sp. These findings improve our understanding of the ecology and ecophysiology of phototrophic blooms and their impact on biogeochemical cycles.
Yeast Sup35 prion structure: two types, four parts, many variants
Authors: Dergalev Alexander A. , Alexandrov Alexander I. , Ivannikov Roman I. , Ter-Avanesyan Michael D. , Kushnirov Vitaly V. 
Published: April 2019

AbstractThe yeast [PSI+] prion, formed by the Sup35 (eRF3) protein, can exist as multiple structural variants exhibiting phenotypic variation in the strength of nonsense suppression and mitotic stability. Structure of [PSI+] and its variation is only partly characterized. Here, we mapped the Sup35 proteinase K-resistant amyloid cores of 26 [PSI+] prions of different origin, isolated from yeast cells. In all cases the Sup35 amino acid residues 2-32 were fully resistant and the region up to residue 72 was partially resistant. Proteinase K-resistant structures were also found within regions 73-124, 125-153 and 154-221, but their presence differed between [PSI+] isolates. The [PSI+] phenotype depended mainly, if not solely, on the structure in region 2-72. Structures in region 73-221 were in some cases mitotically unstable and heterogenous. Two distinct digestion patterns were observed for the 2-72 fragment, which correlated with the “strong” and “weak” [PSI+] nonsense-suppressor phenotypes. All [PSI+] with a weak pattern were eliminated by multicopyHSP104gene and were not toxic when combined with multicopySUP35.[PSI+] with a strong pattern showed opposite properties, being resistant to multicopyHSP104and lethal in the presence of multicopySUP35. Thus, our data suggest existence of two distinct and reliably distinguishable structural classes of [PSI+] rather than a continuum of prions with gradually altering phenotype.ImportancePrions and amyloids are relatively novel and incompletely characterized structures. To understand them better, we mapped amyloid cores of 26 isolates of the Sup35 yeast prion using proteinase K digestion and mass spectrometry. We found that these cores are composed of up to four proteinase K-resistant elements spanning almost the whole length of Sup35 region inessential for viability. However, only the N-terminal element was present in all structures. There are many variants of the Sup35 prion, and these are usually roughly combined into two groups, “strong” and “weak”, based on the strength of their nonsense-suppressor phenotype. However, it was not clear whether such groups could be distinguished by any reliable qualitative criteria. Our data indicate that these groups do exist and can be reliably distinguished based on the N-terminal element digestion pattern and the effects of the multicopySUP35andHSP104genes on these prion variants.
Fecal short-chain fatty acids are not predictive of colonic tumor status and cannot be predicted based on bacterial community structure
Authors: Sze Marc A. , Topçuoğlu Begüm D. , Lesniak Nicholas A. , Ruffin Mack T. , Schloss Patrick D. 
Published: April 2019

AbstractColonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others exacerbating inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory properties and are produced in large quantities by colonic bacteria which produce SCFAs by fermenting fiber. We assessed whether there was an association between fecal SCFA concentrations and the presence of colonic adenomas or carcinomas in a cohort of individuals using 16S rRNA gene and metagenomic shotgun sequence data. We measured the fecal concentrations of acetate, propionate, and butyrate within the cohort and found that there were no significant associations between SCFA concentration and tumor status. When we incorporated these concentrations into random forest classification models trained to differentiate between people with normal colons and those with adenomas or carcinomas, we found that they did not significantly improve the ability of 16S rRNA gene or metagenomic gene sequence-based models to classify individuals. Finally, we generated random forest regression models trained to predict the concentration of each SCFA based on 16S rRNA gene or metagenomic gene sequence data from the same samples. These models performed poorly and were able to explain at most 14% of the observed variation in the SCFA concentrations. These results support the broader epidemiological data that questions the value of fiber consumption for reducing the risks of colorectal cancer. Although other bacterial metabolites may serve as biomarkers to detect adenomas or carcinomas, fecal SCFA concentrations have limited predictive power.ImportanceConsidering colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anti-carcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentration of a cohort of individuals with varying colonic tumor burden who were previously analyzed to identify microbiome-based biomarkers of tumors. We were unable to find an association between SCFA concentration and tumor burden or use SCFAs to improve our microbiome-based models of classifying people based on their tumor status. Furthermore, we were unable to find an association between the fecal community structure and SCFA concentrations. Our results indicate that the association between fecal SCFAs, the gut microbiome, and tumor burden is weak.
Sustained visual priming effects can emerge from attentional oscillation and temporal expectation
Authors: Wang Muzhi , Huang Yan , Luo Huan , Zhang Hang 
Published: April 2019

AbstractPriming refers to the influence that a previously encountered object exerts on future responses to similar objects. For many years, visual priming has been known as a facilitation and sometimes an inhibition effect that lasts for an extended period of time. It contrasts with the recent finding of an oscillated priming effect where facilitation and inhibition alternate over time periodically. Here we developed a computational model of visual priming that combines rhythmic sampling of the environment (attentional oscillation) with active preparation for future events (temporal expectation). Counterintuitively, it shows both the sustained and oscillated priming effects can emerge from an interaction between attentional oscillation and temporal expectation. The interaction also leads to novel predictions such as the change of visual priming effects with temporal expectation and attentional oscillation. Reanalysis of two published datasets and the results of two new experiments of visual priming tasks with male and female human participants provide support for the model’s relevance to human behavior. More generally, our model offers a new perspective that may unify the increasing findings of behavioral and neural oscillations with the classic findings in visual perception and attention.Significance StatementThere is increasing behavioral and neural evidence that visual attention is a periodic process that sequentially samples different alternatives in the theta frequency range. It contrasts with the classic findings of sustained facilitatory or inhibitory attention effects. How can an oscillatory perceptual process give rise to sustained attention effects? Here we make this connection by proposing a computational model for a “fruit fly” visual priming task and showing both the sustained and oscillated priming effects can have the same origin: an interaction between rhythmic sampling of the environment and active preparation for future events. One unique contribution of our model is to predict how temporal contexts affects priming. It also opens up the possibility of reinterpreting other attention-related classic phenomena.
The level of workaholism and its relation to positive and negative perfectionism
Authors: Ali Aldahadha Basim Mohammad 
Published: April 2019

AbstractThe present study aimed to test how common workaholism is and which groups are most targeted in the workplace among Jordanian employees. Additionally, the roles of positive and negative perfectionism in workaholism were investigated. The sample consisted of 686 employees. All of them completed the study instruments. The results showed that the mean of workaholism, positive perfectionism, and negative perfectionism were respectively 2.60, 4.04, and 3.53. Additionally, multivariate tests showed that the results of post hoc differences for positive perfectionism were in favor of males, subordinates, those with a bachelor’s degree, those with less than 5 years of experience, and those aged less than 30 years. Furthermore, the differences for negative perfectionism were in favor of those with a bachelor’s degree and subordinates. For workaholism, the differences were in favor of subordinates, public sector employees, married persons, and those with a diploma degree. Finally, the results of hierarchical regression analysis found that positive and negative perfectionism and some demographic variables predicted 129% of the variability in workaholism, and the typical hierarchical regression model included positive and negative perfectionism without other demographic variables.
Measuring the impact of an interdisciplinary learning project on nursing, architecture and landscape design students’ empathy
Authors: Donnelly Samantha , Dean Suzanne J , Razavy Shohreh , Levett-Jones Tracy 
Published: April 2019

AbstractIn Australia and internationally, domestic violence is a major cause of homelessness for women and children. When designing emergency accommodation, the concerns, preferences, and perspectives of individuals who access refuge services must be sought in order to create spaces that are conducive to the needs of this diverse and vulnerable group. An empathic ‘lens’ can provide meaningful insights that can inform the design of refuge services specifically targeted at addressing these needs.This paper describes an authentic interdisciplinary learning experience for nursing, architecture and landscape students’, and presents the results of a study designed to measure the impact of this initiative on participants’ empathy towards women and children who access refuge services as a result of homelessness and/or domestic violence. Empathy levels were measured using the Comprehensive State Empathy Scale.The learning experience consisted of collaborative meetings with stakeholders from the refuge sector, fieldwork, individual research, exchanging ideas and problem-solving in teams. Students then developed design guides for refuges that demonstrated their emerging understanding of the specific needs and perspectives of the issues faced by women and children who were homeless.A convenience sample of 48 students (nursing n = 22; architecture n = 11; and landscape n = 13) participated in the study. Participants were aged from 19 to 37 years with an average of 23.8 years (SD= 3.65). Pre-post Comprehensive State Empathy Scale results indicated that the empathy levels of nursing and landscape students increased and those of architecture students decreased, however, these results were not statistically significant.In Australia, one in six women have experienced domestic violence and domestic violence remains the single largest cause of homelessness for women. Yet reports suggest that these women frequently encounter discrimination, both in the community and when accessing services. As empathy is one of the strongest negative correlates of prejudice, authentic teaching and learning activities, such as the one described in this paper, have the potential to positively impact the lived experience of these women.
Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed
Authors: Ishaq Suzanne L. , Lachman Medora M. , Wenner Benjamin A. , Baeza Amy , Butler Molly , Gates Emily , Olivo Sarah , Geddes Julie Buono , Hatfield Patrick , Yeoman Carl J. 
Published: April 2019

AbstractDiet composed of smaller particles can improve feed intake, digestibility, and animal growth or health, but in ruminant species can reduce rumination and buffering – the loss of which may inhibit fermentation and digestibility. However, the explicit effect of particle size on the rumen microbiota remains untested, despite their crucial role in digestion. We evaluated the effects of reduced particle size on rumen microbiota by feeding long-stem (loose) alfalfa hay compared to a ground and pelleted version of the same alfalfa in yearling sheep wethers.In situdigestibility of the pelleted diet was greater at 48 h compared with loose hay; however, distribution of residual fecal particle sizes in sheep did not differ between the dietary treatments at any time point. Both average daily gain and feed efficiency were greater for the wethers consuming the pelleted diet. Observed bacterial richness was very low at the end of the adaptation period and increased over the course of the study, suggesting the rumen bacterial community was still in flux after two weeks of adaptation. The pelleted-hay diet group had a greater increase in bacterial richness, including common fibrolytic rumen inhabitants. The pelleted diet was positively associated with severalSucciniclasticum, a Prevotella, and uncultured taxa in the Ruminococcaceae and Rickenellaceae families and Bacteroidales order. Pelleting an alfalfa hay diet for sheep does shift the rumen microbiome, though the interplay of diet particle size, retention and GI transit time, microbial fermentative and hydrolytic activity, and host growth or health is still largely unexplored.
Tuberculosis at farmer-cattle interface in the rural villages of South Gondar Zone of northwest Ethiopia
Authors: Alelign Amir , Zewude Aboma , Petros Beyene , Ameni Gobena 
Published: April 2019

AbstractBackgroundTuberculosis (TB) has been an important public health concern in Ethiopia, particularly at areas of human-animal intersection. However, limited epidemiological information is available in this respect in the country. Therefore, the present study was conducted to investigate the transmission of TB at human-cattle interface, associated risk factors and public awareness about the disease at South Gondar Zone, northwest Ethiopia.MethodsA cross sectional study was conducted between March 2015 and April 2018 on 186 farmers and 476 cattle in South Gondar Zone, northwest Ethiopia. Bacteriological examination, region of difference (RD) 9 based polymerase chain reaction (PCR), single intradermal comparative tuberculin test (SIDCTT) and questionnaire were used for undertaking this study.ResultsCulture positivity in farmers was 59.7% (111/186) and all the culture positive isolates wereM. tuberculosis. About 68% (74/111) of culture positive respondents did not know about the transmission of TB from cattle to human or vice versa. The animal and herd prevalence of bovine TB were 1.5% (7/476) and 7.4% (7/95) respectively. The odd of bovine TB in cattle owned by TB positive households was slightly higher than those owned by TB free households (adjusted odds ratio, AOR=1.39; 95% CI: 0.31-7.10; p = 0.76).ConclusionAlthough SIDCTT reactivity was slightly higher in cattle owned by TB positive households, all the human isolates wereM. tuberculosisand noM. boviswas isolated from farmers, which could be due to the low prevalence of bovine TB in the area.
Identification and Characterization of the First Fragment Hits for SETDB1 Tudor Domain
Authors: Mader Pavel , Mendoza-Sanchez Rodrigo , Iqbal Aman , Dong Aiping , Dobrovetsky Elena , Corless Victoria B. , Liew Sean K. , Houliston Scott R. , De Freitas Renato Ferreira , Smil David , Dela Sena Carlo C. , Kennedy Steven , Diaz Diego B. , Wu Hong , Dombrovski Ludmila , Allali-Hassani Abdellah , Min Jinrong , Schapira Matthieu , Vedadi Masoud , Brown Peter J. , Santhakumar Vijayaratnam , Yudin Andrei K. , Arrowsmith Cheryl H. 
Published: April 2019

ABSTRACTSET domain bifurcated protein 1 (SETDB1) is a human histone-lysine methyltransferase, which is amplified in human cancers and was shown to be crucial in the growth of non-small and small cell lung carcinoma. In addition to its catalytic domain, SETDB1 harbors a unique tandem tudor domain which recognizes histone sequences containing both methylated and acetylated lysines, and likely contributes to its localization on chromatin. Using X-ray crystallography and NMR spectroscopy fragment screening approaches, we have identified the first small molecule fragment hits that bind to histone peptide binding groove of the TTD of SETDB1. Herein, we describe the binding modes of these fragments and analogues and the biophysical characterization of key compounds. These confirmed small molecule fragments will inform the development of potent antagonists of SETDB1 interaction with histones.