bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of endophyte infected tall fescue seed and red clover isoflavones on rumen microbial populations, fiber fermentation, and volatile fatty acidsin vitro
Authors: Melchior Emily A. , Mulliniks J. Travis , Smith Jason K. , Bates Gary E. , Schneider Liesel G. , McFarlane Zachary D. , Flythe Michael D. , Klotz James L. , Goodman Jack P. , Ji Huihua , Myer Phillip R. 
Published: July 2018

AbstractNegative impacts of endophyte-infectedLolium arundinaceum (Darbyshire)(tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found inTrifolium pretense(red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in anin vitrosystem. Using a dose of 1.10 mg × L−1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type(P= 0.003) and isoflavone treatment (P= 0.005), and ADF disappearance values were significantly different in a seed x isoflavone treatment interaction (P≤ 0.05). A seed x isoflavone treatment interaction was also observed with respect to CP disappearance (P≤ 0.05). Seventeen bacterial taxa were significantly altered by seed x isoflavone treatment interaction groups (P≤ 0.05), six bacterial taxa were increased by isoflavones (P≤ 0.05), and eleven bacterial taxa were altered by seed type (P≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changesin vivo.
Compensatory mechanisms render Tcf7l1a dispensable for eye formation despite its cell-autonomous requirement in eye field specification
Authors: Young Rodrigo M. , Cavodeassi Florencia , Hawkins Thomas A. , Stickney Heather L. , Schwarz Quenten , Lawrence Lisa M. , Wierzbicki Claudia , Gestri Gaia , Ambrosio Elizabeth , Klosner Allison , Rowell Jasmine , Bianco Isaac H. , Allende Miguel L. , Wilson Stephen W. 
Published: July 2018

AbstractThe vertebrate eye originates from the eyefield, a domain of cells specified by a small number of transcription factors. In this study, we show that Tcf7la is one such transcription factor that acts cell-autonomously to specify the eye field in zebrafish. Despite the much reduced eyefield intcf7l1amutants, these fish develop normal eyes revealing a striking ability of the eye to recover from a severe early phenotype. This robustness is not mediated through compensation by paralogous genes; instead, the smaller optic vesicle oftcf7l1amutants shows delayed neurogenesis and continues to grow until it achieves approximately normal size. Although the developing eye is robust to the lack of Tcf7l1a function, it is sensitised to the effects of additional mutations. In support of this, a forward genetic screen identified mutations inhesx1, cct5andgdf6a, which give synthetically enhanced eye specification or growth phenotypes when in combination with thetcf7l1amutation.
Substantia nigra dopamine neurons evoke a delayed excitation in lateral dorsal striatal cholinergic interneurons via glutamate cotransmission
Authors: Chuhma Nao , Mingote Susana , Yetnikoff Leora , Kalmbach Abigail , Ma Thong , Ztaou Samira , Siena Anna-Claire , Tepler Sophia , Poulin Jean-Francois , Ansorge Mark , Awatramani Rajeshwar , Kang Un Jung , Rayport Stephen 
Published: July 2018

SummaryDopamine neurons have different synaptic actions in the ventral and dorsal striatum (dStr), but whether this heterogeneity extends to dStr subregions has not been addressed. We have found that optogenetic activation of dStr dopamine neuron terminals in mouse brain slices pauses the firing of cholinergic interneurons in both the medial and lateral subregions, while in the lateral subregion the pause is shorter due to a subsequent excitation. This excitation is mediated mainly by metabotropic glutamate receptor 1 (mGluR1) and partially by dopamine D1-like receptors coupled to transient receptor potential channel 3 and 7. DA neurons do not signal to spiny projection neurons in the medial dStr, while they elicit ionotropic glutamate responses in the lateral dStr. The DA neurons mediating these excitatory signals are in the substantia nigra (SN). Thus, SN dopamine neurons engage different receptors in different postsynaptic neurons in different dStr subregions to convey strikingly different signals.
Fundamental and realized feeding niche breadths of sexual and asexual stick-insects
Authors: Chloé Larose , Parker Darren J. , Tanja Schwander 
Published: July 2018

ABSTRACTThe factors contributing to the maintenance of sex over asexuality in natural populations remain largely unknown. Ecological divergences between lineages with different reproductive modes could help to maintain reproductive polymorphisms, at least transiently, but there is little empirical information on the consequences of asexuality for the evolution of ecological niches. Here, we investigated how niche breadths evolve following transitions from sexual reproduction to asexuality. We estimated and compared the realized feeding niche breadths of five independently derived asexual Timema stick insect species and their sexual relatives. We found that asexual species had a systematically narrower realized niche than sexual species. To investigate how the narrower realized niches of asexual versus sexual species come about, we quantified the breadth of their fundamental niches but found no systematic differences between reproductive modes. The narrow realized niches found in asexuals are therefore likely a consequence of biotic interactions that constrain realized niche size in asexuals more strongly than in sexuals. Interestingly, the fundamental niche was broader in the oldest asexual species compared to its sexual relative. This broad ecological tolerance may help explain how this species has persisted over more than a million years in absence of sex.
PDEδ inhibition impedes the proliferation and survival of human colorectal cancer cell lines harboring oncogenic KRas
Authors: Klein Christian H. , Truxius Dina C. , Vogel Holger A. , Harizanova Jana , Murarka Sandip , Martín-Gago Pablo , Bastiaens Philippe I. H. 
Published: July 2018

Novelty and ImpactThe ‘undruggable’ KRas is a prevalent oncogene in CRC with poor prognosis. In hPDAC cells pharmacological targeting of PDEδ affects oncogenic KRas signaling, but it remained unclear whether this approach is transferable to other cancer cells. Here, we show that genetic and pharmacologic PDEδ inhibition also impedes the proliferation of oncogenic, but not wild-type KRas bearing CRC cells indicating that PDEδ inhibition is a specific tool for targeting growth of oncogenic KRas bearing CRC.AbstractRas proteins, most notably KRas, are prevalent oncogenes in human cancer. Plasma membrane localization and thereby signaling of KRas is regulated by the prenyl-binding protein PDEδ. Recently, we have reported the specific anti-proliferative effects of PDEδ inhibition in KRas-dependent human pancreatic ductal adenocarcinoma cell lines. Here, we investigated the proliferative dependence on the solubilizing activity of PDEδ of human colorectal cancer (CRC) cell lines with or without oncogenic KRas mutations. Our results show that genetic and pharmacologic interference with PDEδ specifically inhibits proliferation and survival of CRC cell lines harboring oncogenic KRas mutations whereas isogenic cell lines in which the KRas oncogene has been removed, or cell lines with oncogenic BRaf mutations or EGFR overexpression are not dependent on PDEδ. Pharmacological PDEδ inhibition is therefore a possible new avenue to target oncogenic KRas bearing CRC.
Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales
Authors: Musser Jacob M. , Wagner Günter P. , Liang Cong , Stabile Frank A. , Cloutier Alison , Baker Allan J. , Prum Richard O. 
Published: July 2018

AbstractBirds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping ‘scutate’ scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate ‘reticulate’ scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many “feather-specific genes” are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers – and may represent an important mechanism for the origin of evolutionary novelties.
Neural Circuit Mechanism of Decision Uncertainty and Change-of-Mind
Authors: Atiya Nadim A A , Rañó Iñaki , Prasad Girijesh , Wong-Lin KongFatt 
Published: July 2018

AbstractDecision-making is often accompanied by a degree of confidence on whether a choice is correct. Decision uncertainty, or lack in confidence, may lead to change-of-mind. Studies have identified the behavioural characteristics associated with decision confidence or change-of-mind, and their neural correlates. Although several theoretical accounts have been proposed, there is no neural model that can compute decision uncertainty and explain its effects on change-of-mind. We propose a neuronal circuit model that computes decision uncertainty while accounting for a variety of behavioural and neural data of decision confidence and change-of-mind, including testable model predictions. Our theoretical analysis suggests that change-of-mind occurs due to the presence of a transient uncertainty-induced choice-neutral stable steady state and noisy fluctuation within the neuronal network. Our distributed network model indicates that the neural basis of change-of-mind is more distinctively identified in motor-based neurons. Overall, our model provides a framework that unifies decision confidence and change-of-mind.
Interaction modifications lead to greater robustness than pairwise non-trophic effects in food webs
Authors: Terry J. Christopher D. , Morris Rebecca J. , Bonsall Michael B. 
Published: July 2018

AbstractConsiderable emphasis has been placed recently on the importance of incorporating non-trophic effects in to our understanding of ecological networks. Interaction modifications are well established as generating strong non-trophic impacts by modulating the strength of inter-specific interactions.For simplicity and comparison with direct interactions within a network context, the consequences of interaction modifications have often been described as direct pairwise interactions. The consequences of this assumption have not been examined in non-equilibrium settings where unexpected consequences of interaction modifications are most likely.To test the distinct dynamic nature of these ‘higher-order’ effects we directly compare, using dynamic simulations, the robustness to extinctions under perturbation of systems where interaction modifications are either explicitly modelled or represented by corresponding equivalent pairwise non-trophic interactions.Full, multi-species representations of interaction modifications resulted in a greater robustness to extinctions compared to equivalent pairwise effects. Explanations for this increased stability despite apparent greater dynamic complexity can be found in additional routes for dynamic feedbacks. Furthermore, interaction modifications changed the relative vulnerability of species to extinction from those trophically connected close to the perturbed species towards those receiving a large number of modifications.Future empirical and theoretical research into non-trophic effects should distinguish interaction modifications from direct pairwise effects in order to maximise information about the system dynamics. Interaction modifications have the potential to shift expectations of species vulnerability based exclusively on trophic networks.
PABA Release from Chitosan-PCL with Induced Electric Current
Authors: Miller Jennifer M. , de Guzman Roche C. 
Published: July 2018

AbstractControlled drug delivery systems such as the stimulation-based biomaterial scaffolds for sequestration and release of drugs offer safety and regulated therapeutic approach. In this study, the drug:para-aminobenzoic acid (PABA) was absorbed into a crosslinked chitosan and poly(caprolactone) (PCL) hydrogel and its release kinetics quantified under different conditions. It was experimentally-observed that the higher the pH (or the more basic the pH), the slower the PABA saturation release trended over time. At the acidic environment of pH 4, PABA was released the fastest, and enhanced by the degradation of chitosan-PCL gel. When a constant electric current of 0.6 mA sa applied, PABA release was induced at pH 10. However, at pH 7, PABA was stably-bound to the chitosan-PCL matrix, with or without the external current. The selective sequestration of PABA at basic pH and its stimulated release via electric current application can be further explored for clinical translatability.
Estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution
Authors: Cameron Christopher JF , Dostie Josée , Blanchette Mathieu 
Published: July 2018

AbstractHi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C’s resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces researchers to artificially reduce the resolution of Hi-C matrices at a loss of biological interpretability. We present the Hi-C Interaction Frequency Inference (HIFI) algorithms that accurately estimate restriction-fragment resolution Hi-C matrices by exploiting dependencies between neighboring fragments. Cross-validation experiments and comparisons to 5C data and known regulatory interactions demonstrate HIFI’s superiority to existing approaches. In addition, HIFI’s restriction-fragment resolution reveals a new role for active regulatory regions in structuring topologically associating domains.Availability:https://github.com/BlanchetteLab/HIFI
Distinct timescales of RNA regulators enable the construction of a genetic pulse generator
Authors: Westbrook Alexandra , Tang Xun , Marshall Ryan , Maxwell Colin S. , Chappell James , Agrawal Deepak K. , Dunlop Mary J. , Noireaux Vincent , Beisel Chase L. , Lucks Julius , Franco Elisa 
Published: July 2018

ABSTRACTTo build complex genetic networks with predictable behaviours, synthetic biologists use libraries of modular parts that can be characterized in isolation and assembled together to create programmable higher-order functions. Characterization experiments and computational models for gene regulatory parts operating in isolation are routinely employed to predict the dynamics of interconnected parts and guide the construction of new synthetic devices. Here, we individually characterize two modes of RNA-based transcriptional regulation, using small transcription activating RNAs (STARs) and CRISPR interference (CRISPRi), and show how their distinct regulatory timescales can be used to engineer a composed feedforward loop that creates a pulse of gene expression. We use a cell-free transcription-translation system (TXTL) to rapidly characterize the system, and we apply Bayesian inference to extract kinetic parameters for an ODE-based mechanistic model. We then demonstrate in simulation and verify with TXTL experiments that the simultaneous regulation of a single gene target with STARs and CRISPRi leads to a pulse of gene expression. Our results suggest the modularity of the two regulators in an integrated genetic circuit, and we anticipate that construction and modeling frameworks that can leverage this modularity will become increasingly important as synthetic circuits increase in complexity.
Assessing sub-cellular resolution in spatial proteomics experiments
Authors: Gatto Laurent , Breckels Lisa M. , Lilley Kathryn S. 
Published: July 2018

AbstractThe sub-cellular localisation of a protein is vital in defining its function, and a protein’s mis-localisation is known to lead to adverse effect. As a result, numerous experimental techniques and datasets have been published, with the aim of deciphering the localisation of proteins at various scales and resolutions, including high profile mass spectrometry-based efforts. Here, we present a meta-analysis assessing and comparing the sub-cellular resolution of 29 such mass spectrometry-based spatial proteomics experiments using a newly developed tool termed QSep. Our goal is to provide a simple quantitative report of how well spatial proteomics resolve the sub-cellular niches they describe to inform and guide developers and users of such methods.
Real exchange rate undervaluation and sectoral growth in South Africa
Authors: Mazorodze Brian Tavonga , Tewari Dev D. 
Published: July 2018

PurposeThe purpose of this paper is to establish the empirical link between real exchange rate (RER) undervaluation and sectoral growth in South Africa between 1984 and 2014.Design/methodology/approachThe study employs a dynamic panel data approach estimated by the system generalised method of moments technique in a bid to control for endogeneity.FindingsThe authors find a significant positive impact of undervaluation on sectoral growth which increases with capital accumulation. Also, the authors confirm that undervaluation promotes sectoral growth up to a point where further increases in undervaluation retards growth.Practical implicationsThe results confirm the importance of policies that keep the domestic currency weaker to foster sectoral growth.Originality/valueThe originality of this paper lies in establishing the impact of exchange rate undervaluation on growth at a sector level in the context of South Africa using a dynamic panel data approach.
Decomposition of efficiency using DEA window analysis
Authors: Shawtari Fekri Ali , Abdelnabi Salem Milad , Bakhit Izzeldin 
Published: July 2018

Purpose
The purpose of this paper is to examine empirically the efficiency types of Islamic and conventional banks. It seeks to show whether the efficiency level of conventional and Islamic banks significantly differs from each other. In addition, it investigates the influential factors on each type of efficiency.

Design/methodology/approach
The paper utilises the data envelopment analysis in its windows version to estimate the efficiency scores reflecting the time variance and compares between banking models. The paper uses pure technical efficiency (TE) and scale efficiency to achieve the objective of the study. In addition, the panel data technique is adopted to assess the determinants of the efficiency of the banks econometrically.

Findings
The findings of panel regression initially indicate that the pure TE is higher for conventional banks compared to Islamic banks. However, the Islamic banks are more scale efficient than their conventional counterpart. Macro and micro indicators have different impacts on the both types of efficiency. However, the unique factors that show consistent influence on the efficiency types were loans/finance, non-interest income/finance/liquidity and GDP. Furthermore, the determinants are shaped differently for Islamic and conventional banks when the banking model is controlled for.

Originality/value
This paper examines the efficiency types using a unique window analysis approach to examine the types of efficiency with a longitudinal set of data from 1996 to 2011.
Developing a safety climate factor model in construction research and practice
Authors: Newaz Mohammad Tanvi , Davis Peter Rex , Jefferies Marcus , Pillay Manikam 
Published: July 2018

PurposeSafety climate and its impact on safety performance is well established; however, researchers in this field suggest that the absence of a common assessment framework is a reflection of the state of development of this concept. The purpose of this paper is to propose a five-factor model that can be used to diagnose and measure safety climate in construction safety research and practice.Design/methodology/approachA systematic review was adopted, and following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, 574 articles were selected at the start of the study based on a developed review protocol for investigating safety climate factors. While examining the factor analysis of different studies, data reliability and data validity of the individual research findings were considered and frequency of factors uploaded was used to determine the significance as a quantitative measure to develop the ranking of safety climate factors.FindingsThe review identified that, from the established measures of safety climate in construction, there is little uniformity on factor importance. However, management commitment safety system role of the supervisor; workers’ involvement and group safety climate were found to be the most common across the studies reviewed. It is proposed these factors are used to inform a five-factor model for investigating safety climate in the construction industry.Originality/valueThe findings of this study will motivate researchers and practitioners in safety to use the five-factor safety climate model presented in this paper and test it to develop a common factor structure for the construction industry. The fact that the model is comprised of five factors makes it easier to be used and implemented by small-to medium-sized construction companies, therefore enhancing its potential use.