bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic predictive ability for foliar nutritive traits in perennial ryegrass
Authors: Arojju Sai Krishna , Cao Mingshu , Jahufer M. Z. Zulfi , Barrett Brent A , Faville Marty J 
Published: August 2019

AbstractForage nutritive value impacts animal nutrition, which underpins livestock productivity, reproduction and health. Genetic improvement for nutritive traits has been limited, as they are typically expensive and time-consuming to measure through conventional methods. Genomic selection is appropriate for such complex and expensive traits, enabling cost-effective prediction of breeding values using genome-wide markers. The aims of the present study were to assess the potential of genomic selection for a range of nutritive traits in a multi-population training set, and to quantify contributions of genotypic, environmental and genotype-by-environment (G × E) variance components to trait variation and heritability for nutritive traits. The training set consisted of a total of 517 half-sibling (half-sib) families, from five advanced breeding populations, evaluated in two distinct New Zealand grazing environments. Autumn-harvested samples were analyzed for 18 nutritive traits and maternal parents of the half-sib families were genotyped using genotyping-by-sequencing. Significant (P<0.05) genotypic variation was detected for all nutritive traits and genomic heritability (h2g) was moderate to high (0.20 to 0.74). G × E interactions were significant and particularly large for water soluble carbohydrate (WSC), crude fat, phosphorus (P) and crude protein. GBLUP, KGD-GBLUP and BayesC genomic prediction models displayed similar predictive ability, estimated by 10-fold cross validation, for all nutritive traits with values ranging fromr= 0.16 to 0.45 using phenotypes from across two environments. High predictive ability was observed for the mineral traits sulphur (0.44), sodium (0.45) and magnesium (0.45) and the lowest values were observed for P (0.16), digestibility (0.22) and high molecular weight WSC (0.23). Predictive ability estimates for most nutritive traits were retained when marker number was reduced from 1 million to as few as 50,000. The moderate to high predictive abilities observed suggests implementation of genomic selection is feasible for most of the nutritive traits examined. For traits with lower predictive ability, multi-trait genomic prediction approaches that exploit the strong genetic correlations observed amongst some nutritive traits may be useful. This appears to be particularly important for WSC, considered one of the primary constituent of nutritive value for forages.
24-hour multi-omics analysis of residential sewage reflects human activity and informs public health
Authors: Matus Mariana , Duvallet Claire , Soule Melissa Kido , Kearney Sean M. , Endo Noriko , Ghaeli Newsha , Brito Ilana , Ratti Carlo , Kujawinski Elizabeth B. , Alm Eric J. 
Published: August 2019

AbstractHigh-throughput molecular analysis of sewage is a promising tool for precision public health. Here, we combine sewer network and demographic data to identify a residential catchment for sampling, and explore the potential of applying untargeted genomics and metabolomics to sewage to collect actionable public health data. We find that wastewater sampled upstream in a residential catchment is representative of the human microbiome and metabolome, and we are able to identify glucuronidated compounds indicative of direct human excretion, which are typically degraded too quickly to be detected at treatment plants. We show that diurnal variations during 24-hour sampling can be leveraged to discriminate between biomarkers in sewage that are associated with human activity from those related to the environmental background. Finally, we putatively annotate a suite of human-associated metabolites, including pharmaceuticals, food metabolites, and biomarkers of human health and activity, suggesting that mining untargeted data derived from residential sewage can expand currently-used biomarkers with direct public health or policy relevance.
bioPROTACs as versatile modulators of intracellular therapeutic targets: Application to proliferating cell nuclear antigen (PCNA)
Authors: Lim Shuhui , Khoo Regina , Peh Khong Ming , Teo Jinkai , Chang Shih Chieh , Ng Simon , Beilhartz Greg L. , Melnyk Roman A. , Johannes Charles W. , Brown Christopher J. , Lane David P. , Henry Brian , Partridge Anthony W. 
Published: August 2019

ABSTRACTTargeted degradation approaches have recently generated much excitement as a paradigm shift to address human disease in unprecedented ways. Amongst these, small molecule based approaches such as Proteolysis targeting chimeras (PROTACs) have attracted the lion’s share of attention due to their potential to tackle historically intractable targets and achieve greater potency, efficacy, and specificity over traditional small molecule inhibitors. Despite their promise, the identification of high-affinity ligands that can serve as starting points for PROTAC strategies remains challenging. As a complementary approach, we describe herein a class of intracellular biologics termed bioPROTACs. The substrate binding component of these fusion proteins consists of a peptide or an antibody-mimetic which allows for an unprecedented diversity of protein targets that can be addressed. The high-affinity binder is linked directly to an E3 ubiquitin ligase to harness the power of targeted degradation. Using GFP-tagged proteins as model substrates, we show that there is considerable flexibility in both the choice of substrate binders (binding positions, scaffold-class) and the E3 ligases. Indeed, 9 out of 16 binder-E3 combinations tested resulted in greater than 70% target clearance. Through a systematic approach, we then identified a highly effective bioPROTAC against an oncology target, proliferating cell nuclear antigen (PCNA), a sliding DNA clamp with critical roles in DNA replication and repair. The bioPROTAC, termed Con1-SPOP, elicited rapid and robust PCNA degradation and associated effects on DNA synthesis and cell cycle progression. Compared to RNAi-based approaches which typically take days to manifest, PCNA knockdown using Con1-SPOP was evident within 4 h. The advantage of degradation versus stoichiometric inhibition was also clearly demonstrated with bioPROTAC strategies. Combining superior pharmacological inhibition and relative ease of development, bioPROTACs are powerful tools for interrogating the degradability of a substrate, for guiding the identification of the fittest E3 ligase, for studying the functional consequences associated with target protein down-regulation, and potentially for making therapeutic impacts.
C. difficile-associated antibiotics prime the host for infection by a microbiome-independent mechanism
Authors: Kester Jemila C. , Brubaker Douglas K. , Velazquez Jason , Wright Charles , Lauffenburger Douglas A. , Griffith Linda G. 
Published: August 2019

AbstractThe most clinically relevant risk factor for Clostridioides difficile-associated disease (CDAD) is recent antibiotic treatment. Though most broad-spectrum antibiotics significantly disrupt the structure of the gut microbiota, only particular ones increase CDAD risk, suggesting additional factors might increase the risk from certain antibiotics. Here we show that commensal-independent effects of antibiotics collectively prime an in vitro germ-free human gut for CDAD. We found a marked loss of mucosal barrier and immune function with CDAD-associated antibiotic pretreatment distinct from pretreatment with an antibiotic unassociated with CDAD, which did not reduce innate immune or mucosal barrier functions. Importantly, pretreatment with CDAD-associated antibiotics sensitized mucosal barriers to C. difficile toxin activity in primary cell-derived enteroid monolayers. These data implicate commensal-independent host changes in the increased risk of CDAD with specific antibiotics. Our findings are contrary to the previously held belief that antibiotics allow for CDAD solely through disruption of the microbiome. We anticipate this work to suggest potential avenues of research for host-directed treatment and preventive therapies for CDAD, and to impact human tissue culturing protocols.
Gamma oscillations during episodic memory processing reveal reversal of information flow between the hippocampus and prefrontal cortex
Authors: Seger Sarah , Rugg Michael D. , Lega Bradley C. 
Published: August 2019

AbstractA critical and emerging question in human episodic memory is how the hippocampus interacts with the prefrontal cortex during the encoding and retrieval of items and their contexts. In the present study, participants performed an episodic memory task (free recall) while intracranial electrodes were simultaneously inserted into the hippocampus and multiple prefrontal locations, allowing the quantification of relative onset times of gamma band activity in the cortex and the hippocampus in the same individual. We observed that in left anterior ventrolateral prefrontal cortex (aVLPFC) gamma band activity onset was significantly later than in the hippocampus during memory encoding, whereas its activity significantly preceded that in the hippocampus during memory retrieval. These findings provide direct evidence to support models of prefrontal-hippocampal interactions derived from studies of rodents, but suggest that in humans, it is the aVLPFC rather than medial prefrontal cortex that demonstrate these reciprocal interactions.
Modulation of articulation muscles during listening and reading: a matter of intention to speak out loud
Authors: Zur Naama , Eviatar Zohar , Karni Avi 
Published: August 2019

AbstractThe articulation of speech sounds is often contingent on the intention to subsequently produce other sounds (co-articulation). Thus, intended acts affect the way current acts are executed. We show that the intention to subsequently repeat a short sentence, overtly or covertly, significantly modulated articulatory muscle activity already during speech perception or reading (input interval) and when delaying response (i.e., prior to production). Young adults were instructed to read (whole sentences or word-by-word) or listen to recordings of sentences to be repeated afterwards, either covertly or overtly. Surface electromyography (sEMG) recordings showed different patterns of articulatory muscle modulation in the two articulatory muscles measured – orbicularis oris inferior (OOI) and sternohyoid (STH). In the OOI, activity increased relative to baseline during speech perception or reading in both intended output conditions (overt and covert); in the STH, articulatory muscle activity decreased, during the input intervals, in both intended output conditions. However, the modulations in EMG activity were contingent on the intention to subsequently repeat the input overtly or covertly, so that activation in the OOI, and inhibition in the STH, were significantly more pronounced when overt responses were intended. Input modality was also a factor; immediately before overt responses, activity in the OOI muscle increased for listening and word-by-word reading, but not in reading whole sentences. The current results suggest that speech perception and articulation interact already during the input phase, listening or reading, reflecting the intended responses. However, this interaction may differentially affect facial-articulatory and laryngeal control mechanisms of speech production.
Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping
Authors: Young Eleanor , Abid Heba Z. , Kwok Pui-Yan , Riethman Harold , Xiao Ming 
Published: August 2019

AbstractDetailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (HG38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends we estimate a timeline for the spread of these duplication blocks.Author SummaryThe ends of human chromosomes have caps called telomeres that are essential. These telomeres are influenced by the portions of DNA next to them, a region known as the subtelomere. We need to better understand the subtelomeric region to understand how it impacts the telomeres. This subtelomeric region is not well described in the current references. This is due to large variations in this region and portions that are repeated many times, making current sequencing technologies struggle to capture these regions. Many of these variations are evolutionary recent. Here we use 154 different samples from the 26 geographic regions of the world to gain a better understanding of the variation in these regions. We found many new haplotypes and clarified the haplotypes existing in the current reference. We then examined population and chromosome specific trends.
Growth behavior and glyphosate resistance level in 10 biotypes ofEchinochloa colonain Australia
Authors: Mahajan Gulshan , Kaur Vishavdeep , Thompson Michael , Chauhan Bhagirath S. 
Published: August 2019

AbstractRecently, poor control ofEchinochloa colonawith glyphosate has been reported in no-till agriculture systems of the northern grain region (NGR) of Australia. Two experiments were conducted using 10 biotypes ofE. colonaselected from the NGR of Australia to understand differences in their growth behavior and resistance pattern. Growth studies revealed that these biotypes differed in plant height (53-70 cm plant−1), tiller production (30-52 tillers plant−1), leaf production (124-186 leaves plant−1) and seed head production (37-65 seed heads plant−1). Days taken to seed heads and shoot biomass in these biotypes ranged between 40-48 d and 21-27 g plant−1, respectively. Seed production in these biotypes ranged between 5380 and 10244 seeds plant−1; lowest for biotype B17/25 and highest for biotype B17/13. Correlation studies revealed that seed number plant−1had a positive correlation with plant height (r= 0.67), tiller number plant−1(r= 0.89), leaf number plant−1(r= 0.73), seed heads plant−1(r= 0.78), seed head weight (r= 0.79), shoot biomass (r= 0.77) and root biomass (r= 0.46). The glyphosate dose-response study showed a wide range of responses in these biotypes and the glyphosate dose required to reduce 50% biomass (GR50values) was estimated between 217 to 2159 g a.e. glyphosate ha−1. GR50values of biotypes B17/16, B 17/34 and B17/35 were 719, 2159 and 884 g ha−1, respectively, making them 3, 10 and 4-fold resistant to glyphosate compared with the susceptible biotype B17/37. Growth behavior and seed production potential in these biotypes had no correlation with the resistance index. These results suggest that some biotypes ofE. colonaare highly problematic; for example, biotype B17/34 was not only highly glyphosate-resistant, but also produced a high seed number (9300 seeds plant−1). This study demonstrated that there is a possibility of great risk with the increased use of glyphosate for managingE. colonain the NGR of Australia. The results warrant integrated weed management strategies and improved stewardship guidelines are required for managing glyphosate-resistant biotypes ofE. colonaand to restrict further movement of resistant biotypes to other regions of Australia.
Futures of new post-truth: new research frontiers on disturbingly fascinating pathologies affecting information dissemination and knowledge production
Authors: Ahen Frederick 
Published: August 2019

Purpose
The purpose of this study is to explore in depth the anatomy of post-truth in the quest to set a new research agenda. The author interrogates knowledge production/dissemination and the political positions of those behind them. This study diagnoses and challenges existing claims of supremacy of certain hegemonic epistemological and ontological orthodoxies that have been weaponized.

Design/methodology/approach
This study philosophically engages with different worlds of credible ‘pluriversal’ knowledge(s) and leads to the exposure of historically ‘taken-for-granted’ definitions of the nature and composition of acceptable truth and how it is deeply entrenched in interest group politics.

Findings
Each generation in different contexts has had to battle with specific troubling forces of deception and organized hypocrisy. Here, both new social actors and incumbents influence the disgruntled, deceive the gullible or connect with the enlightened masses at the emotional level whilst strongly undermining the rules-of-logic and fact-based discourses using disruptive social media technologies. The author specifies how the five P’s: political power, profits, populism, politics and the private visions of technologists and scientists will continue to play very influential roles in how knowledge production will affect future policies and global governance.

Social implications
Based on historicized explanations, the author argues that deception and mass ignorance as weaponized features of global governance and its capitalist order are typical Machiavellian strategies for gaining control over knowledge production/information dissemination. Massive changes are not expected in the future unless society and academia introduce novel science, technology and political platforms for engaging society and policy-makers.

Originality/value
The author provides ample historical illustrations to support the claims made in this study that public insights into the postulated structures of post-truth remain extremely superficial, making people insufficiently informed to engage in crucial discourses about knowledge production and dissemination that affect their futures. This study provides several ingredients for stimulating further debate.
Thermal analysis and post construction verification
Authors: Flood Cormac , Scott Lloyd 
Published: August 2019

Purpose
The residential sector in Ireland accounted for 25 per cent of energy related CO2 emissions in 2016 through burning fossil fuels, a major contributor to climate change. In support of Ireland’s CO2 reduction targets, the existing housing stock could contribute greatly to the reduction of space-heating energy demand through retrofit. Approximately 50 per cent of Ireland’s 2m dwellings pre-date building regulations and are predominantly of cavity and solid wall construction, the performance of which has not been extensively investigated at present. Although commitment to thermal upgrade/retrofit of existing buildings may increase under future government policies, the poor characterisation of actual thermal performance of external walls may hinder the realisation of these targets. Thermal transmittance (U-values) of exterior walls represents a source of uncertainty when estimating the energy performance of dwellings. It has been noted in research that the standard calculation methodology for thermal transmittance should be improved. Implementing current U-value calculation methods may result in misguided retrofit strategies due to the considerable discrepancies between in situ measurements and calculated wall U-values as documented in the case studies carried out in this research. If the method of hygrothermal analysis were to be employed as a replacement for the current standard calculation, it could have significant implications for policy and retrofit decision making. The paper aims to discuss this issue.

Design/methodology/approach
This research project analysed a case study situated in Dublin, Ireland. The case studies offer an account of the in situ thermal transmittance of exterior walls and link these to hygrothermally simulated comparisons along with more traditional design U-values.

Findings
The findings of this research identify discrepancies between in situ and design U-values, using measurement, hygrothermal simulation and standard method U-value calculations. The outcomes of the research serve as an introduction to issues emanating from a larger research project in order to encourage researchers to understand and further explore the topic.

Originality/value
It has previously been highlighted that moisture content is linked to the increase in thermal conductivity of building materials, thus reducing the thermal effectiveness and increasing the elemental U-value. Therefore, it is vital to implement reliable prediction tools to assess potential thermal performance values. This paper presents the findings of a critical instance case study in Dublin, Ireland in which an existing west facing external wall in a semi-detached dwelling was analysed, simulated and measured to verify the elemental wall assembly and quantify thermal transmittance (U-value) incorporating the major criteria required for building performance simulation.
Barriers to low-carbon warehousing and the link to carbon abatement
Authors: Goh Shao Hung 
Published: August 2019

Purpose
Warehouses are large emitters of greenhouse gases and their impact on climate change is under increasing focus. The purpose of this paper is to investigate the barriers that inhibit the adoption of low-carbon warehousing in Asia-Pacific and their links to carbon abatement performance.

Design/methodology/approach
An exploratory conceptual model was first developed from a literature review of the general barriers to sustainable supply chain practices and hence potentially in low-carbon warehousing. A large contract logistics services provider in the Asia-Pacific served as the subject of a case study. The perceived barriers to low-carbon warehousing were derived from an internal survey of respondents from the case company and regressed against carbon abatement outcomes at that organization’s operations across the region.

Findings
Results show that the case company reduced carbon emissions by 36 percent on a revenue-normalized basis between 2008 and 2014, but with relatively lower success in emerging markets vs mature markets. An Elastic Net regression analysis confirms that technology and government-related factors are the most important barriers in the case company’s efforts to “decarbonize” its local warehousing operations. However, results suggest that the customer-related barrier, which is highly correlated with the government barrier, is in part driven by the latter.

Research limitations/implications
This case study is based on a single multinational company in Asia-Pacific, but nonetheless serves as an impetus for more cross-sectional studies to form an industry-wide view.

Originality/value
An extended stewardship framework based on the natural resource-based view has been proposed, in which logistics services providers take on a proactive boundary-spanning role to lower the external barriers to low-carbon warehousing.