bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grow with the flow: a latitudinal cline in physiology is associated with more variable precipitation inErythranthe cardinalis
Authors: Muir Christopher D. , Angert Amy L. 
Published: October 2016

AbstractLocal adaptation is commonly observed in nature: organisms perform well in their natal environment, but poorly outside it. Correlations between traits and latitude, or latitudinal clines, are among the most common pieces of evidence for local adaptation, but identifying the traits under selection and the selective agents is challenging. Here, we investigated a latitudinal cline in growth and photosynthesis across 16 populations of the perennial herbErythranthe cardinalis(Phrymaceae). Using machine learning methods, we identify interannual variation in precipitation as a likely selective agent: Southern populations from more variable environments had higher photosynthetic rates and grew faster. We hypothesize that selection may favor a more annualized life history – grow now rather than save for next year – in environments where severe droughts occur more often. Thus our study provides insight into how species may adapt if Mediterranean climates become more variable due to climate change.
Rapid and consistent evolution of colistin resistance inPseudomonas aeruginosaduring morbidostat culture
Authors: Regenbogen Bianca , Willmann Matthias , Steglich Matthias , Bunk Boyke , Nübel Ulrich , Peter Silke , Neher Richard A. 
Published: October 2016

AbstractColistin is a last resort antibiotic commonly used against multidrug-resistant strains ofPseudomonas aeruginosa. To investigate the potential forin-situevolution of resistance against colistin and map the molecular targets of colistin resistance, we exposed twoP. aeruginosaisolates to colistin using a continuous culture device known as morbidostat. Colistin resistance emerged within two weeks along with highly stereotypic yet strain specific mutation patterns. The majority of mutations hit theprmABtwo component signaling system and genes involved in lipopolysaccharide synthesis, includinglpxC,pmrE, andmigA. In seven out of 18 cultures, we observed mutations inmutSalong with a mutator phenotype that seemed to facilitate resistance evolution.
Benchmarking substrate-based kinase activity inference using phosphoproteomic data
Authors: Hernandez-Armenta Claudia , Ochoa David , Gonçalves Emanuel , Saez-Rodriguez Julio , Beltrao Pedro 
Published: October 2016

AbstractMotivationPhosphoproteomic experiments are increasingly used to study the changes in signalling occurring across different conditions. It has been proposed that changes in phosphorylation of kinase target sites can be used to infer when a kinase activity is under regulation. However, these approaches have not yet been benchmarked due to a lack of appropriate benchmarking strategies.ResultsWe curated public phosphoproteomic experiments to identify a gold standard dataset containing a total of 184 kinase-condition pairs where regulation is expected to occur. A list of kinase substrates was compiled and used to estimate changes in kinase activities using the following methods: Z-test, Kolmogorov Smirnov test, Wilcoxon rank sum test, gene set enrichment analysis (GSEA), and a multiple linear regression model (MLR). We also tested weighted variants of the Z-test, and GSEA that include information on kinase sequence specificity as proxy for affinity. Finally, we tested how the number of known substrates and the type of evidence(in vivo, in vitroorin silico)supporting these influence the predictions.ConclusionsMost models performed well with the Z-test and the GSEA performing best as determined by the area under the ROc curve (Mean AUC=0.722). Weighting kinase targets by the kinase target sequence preference improves the results only marginally. However, the number of known substrates and the evidence supporting the interactions has a strong effect on the predictions.
Low plastic ingestion rate in Atlantic Cod (Gadus morhua) from Newfoundland destined for human consumption collected through citizen science methods
Authors: Liboiron Max , Liboiron France , Wells Emily , Richárd Natalie , Zahara Alexander , Mather Charles , Bradshaw Hillary , Murichi Judyannet 
Published: October 2016

AbstractMarine microplastics are a contaminant of concern because their small size allows ingestion by a wide range of marine life. Using citizen science during the Newfoundland recreational cod fishery, we sampled 205 Atlantic cod (Gadus morhua) destined for human consumption and found that 5 had eaten plastic, an ingestion prevalence rate of 2.4%. This ingestion rate for Atlantic cod is the second lowest recorded rate in the reviewed published literature (the lowest is 1.4%), and the lowest for any fish in the North Atlantic. This is the first report for plastic ingestion in fish in Newfoundland, Canada, a province dependent on fish for sustenance and livelihoods.Highlights (3–5 points, 85 char max including spaces)Plastic ingestion rate of 2.4% for Atlantic Cod (n=205)First recorded baseline for fish in Newfoundland, CanadaThis plastic ingestion prevalence rate is among the lowest recorded to dateUsed citizen science to collect GI tracts from fish destined for human consumption
High precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization
Authors: Marquart Gregory D. , Tabor Kathryn M. , Horstick Eric J. , Brown Mary , Burgess Harold A. 
Published: October 2016

AbstractAtlases provide a framework for information from diverse sources to be spatially mapped and integrated into a common reference space. In particular, brain atlases allow regional annotation of gene expression, cell morphology, connectivity and activity. In larval zebrafish, advances in genetics, imaging and computational methods have enabled the collection of large datasets providing such information on a whole-brain scale. However, datasets from different sources may not be aligned to the same spatial coordinate system, because technical considerations may necessitate use of different reference templates. Two recent brain atlases for larval zebrafish exemplify this problem. The Z-Brain atlas contains information on gene expression, neural activity and neuroanatomical segmentation acquired using immunohistochemical staining of fixed tissue. In contrast, the Zebrafish Brain Browser (ZBB) atlas was constructed from live scans of fluorescent reporter genes in transgenic larvae. Although different reference brains were used, the two atlases included several transgene patterns in common that provided potential 'bridges' for transforming each into the other’s coordinate space. We therefore tested multiple bridging channels and registration algorithms. The symmetric diffeomorphic normalization (SyN) algorithm in ANTs improved the precision of live brain registration while better preserving cell morphology than the previously used B-spline elastic registration algorithm. SyN could also be calibrated to correct for tissue distortion introduced during fixation and permeabilization. Finally, multi-reference channel optimization provided a transformation matrix that enabled Z-Brain and ZBB to be co-aligned with acceptable precision and minimal perturbation of cell and tissue morphology. This study demonstrates the feasibility of integrating whole brain datasets, despite disparate acquisition protocols and reference templates, when sufficient information is present for bridging.Anatomical abbreviationsacanterior commissureDTThalamusGTGriseum tectaleHaHabenulaHcHypothalamus caudal zoneHiHypothalamus intermediate zoneMOMedulla oblongataNXmVagus motor neuronsOBOlfactory bulbOEOlfactory epitheliumIOInferior oliveLCLocus coeruleusMNMauthner neuronMOMedulla oblongataPalPalliumpcposterior commissurePrPretectumSRSuperior rapheTegTegmentumTeOnOptic tectum neuropilTGTrigeminal ganglionTLTorus longitudinalis
Discovering event structure in continuous narrative perception and memory
Authors: Baldassano Christopher , Chen Janice , Zadbood Asieh , Pillow Jonathan W , Hasson Uri , Norman Kenneth A 
Published: October 2016

SummaryDuring realistic, continuous perception, humans automatically segment experiences into discrete events. Using a novel model of neural event dynamics, we investigate how cortical structures generate event representations during continuous narratives, and how these events are stored and retrieved from long-term memory. Our data-driven approach enables identification of event boundaries and event correspondences across datasets without human-generated stimulus annotations, and reveals that different regions segment narratives at different timescales. We also provide the first direct evidence that narrative event boundaries in high-order areas (overlapping the default mode network) trigger encoding processes in the hippocampus, and that this encoding activity predicts pattern reinstatement during recall. Finally, we demonstrate that these areas represent abstract, multimodal situation models, and show anticipatory event reinstatement as subjects listen to a familiar narrative. Our results provide strong evidence that brain activity is naturally structured into semantically meaningful events, which are stored in and retrieved from long-term memory.
Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.HttQ111/+model of Huntington’s disease
Authors: Bragg Robert M. , Coffey Sydney R. , Weston Rory M. , Ament Seth A. , Cantle Jeffrey P. , Minnig Shawn , Funk Cory C. , Shuttleworth Dominic D. , Woods Emily L. , Sullivan Bonnie R. , Jones Lindsey , Glickenhaus Anne , Anderson John S. , Anderson Michael D. , Dunnett Stephen B. , Wheeler Vanessa C. , MacDonald Marcy E. , Brooks Simon P. , Price Nathan D. , Carroll Jeffrey B. 
Published: October 2016

AbstractWe investigated the appearance and progression of disease-relevant signs in the B6.HttQ111/+mouse, a genetically precise model of the mutation that causes Huntington’s disease (HD). We find that B6.HttQ111/+mice are healthy, show no overt signs of central or peripheral inflammation, and no gross motor impairment as late as 12 months of age. Behaviorally, we find that 4-9 month old B6.HttQ111/+mice have normal activity levels and show no clear signs of anxiety or depression, but do show clear signs of reduced motivation. The neuronal density, neuronal size, synaptic density and number of glia is normal in B6.HttQ111/+striatum, the most vulnerable brain region in HD, up to 12 months of age. Despite this preservation of the synaptic and cellular composition of the striatum, we observe clear progressive, striatal-specific, transcriptional dysregulation and accumulation of neuronal intranuclear inclusions (NIIs). Simulation studies suggest these molecular endpoints are sufficiently robust for future preclinical studies, and that B6.HttQ111/+mice are a useful tool for modeling disease-modifying or neuroprotective strategies for disease processes before the onset of overt phenotypes.
Maintaining tiger connectivity and minimizing extinction into the next century: Insights from landscape genetics and spatially-explicit simulations
Authors: Thatte Prachi , Joshi Aditya , Vaidyanathan Srinivas , Landguth Erin , Ramakrishnan Uma 
Published: October 2016

AbstractHabitat loss is the greatest threat to large carnivores around the world. Maintenance of functional connectivity in fragmented landscapes will be important for long-term species persistence. Here, we merge landscape genetics analyses and spatially-explicit simulations to understand future persistence and extinction of tigers (Panthera tigris) in Central India. Tigers in this landscape are restricted to Protected Areas (PAs) and forest fragments embedded within a mosaic of agricultural fields and human settlements. We examined current population connectivity of tigers across nine reserves (using 116 non-invasively sampled individuals and 12 microsatellites). Genetic data was used to infer resistance-to-movement. Our results suggest that dense human settlements and roads with high traffic are detrimental to tiger movement. We used landscape genetic simulations to model 86 different scenarios that incorporated impacts of future land-use change on inferred population connectivity and extinction. Our results confirm that genetic variability (heterozygosity) will decrease in the future and small and/or isolated PAs will have a high risk of local extinction. The average extinction risk of small PAs reduced by 23-70% on adding a 5 km buffer around exiting boundaries. Unplanned development results in 35% lower heterozygosity and 56% higher average extinction probability for tigers even within protected areas. Increasing tiger numbers in such a scenario decreases extinction probability just by 12 % (from 56% to 44%). Scenarios where habitat connectivity was enhanced and maintained, stepping-stone populations were introduced/maintained, and tiger numbers were increased, led to low overall extinction probability (between 3-21%). Our simulations provide a means to quantitatively evaluate the effects of different land-use change scenarios on connectivity and extinction, linking basic science to land-use change policy and planned infrastructure development.
Inferring Synaptic Excitation/Inhibition Balance from Field Potentials
Authors: Gao Richard D. , Peterson Erik J. , Voytek Bradley 
Published: October 2016

SUMMARYNeural circuits sit in a dynamic balance between excitation (E) and inhibition (I). Fluctuations in this E:I balance have been shown to influence neural computation, working memory, and information processing. While more drastic shifts and aberrant E:I patterns are implicated in numerous neurological and psychiatric disorders, current methods for measuring E:I dynamics require invasive procedures that are difficult to perform in behaving animals, and nearly impossible in humans. This has limited the ability to examine the full impact that E:I shifts have in neural computation and disease. In this study, we develop a computational model to show that E:I ratio can be estimated from the power law exponent (slope) of the electrophysiological power spectrum, and validate this relationship using previously published datasets from two species (rat local field potential and macaque electrocorticography). This simple method--one that can be applied retrospectively to existing data--removes a major hurdle in understanding a currently difficult to measure, yet fundamental, aspect of neural computation.
Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma
Authors: deCarvalho Ana C. , Kim Hoon , Poisson Laila M. , Winn Mary E. , Mueller Claudius , Cherba David , Koeman Julie , Seth Sahil , Protopopov Alexei , Felicella Michelle , Zheng Siyuan , Multani Asha , Jiang Yongying , Zhang Jianhua , Nam Do-Hyun , Petricoin Emanuel F. , Chin Lynda , Mikkelsen Tom , Verhaak Roel G.W. 
Published: October 2016

ABSTRACTTo understand how genomic heterogeneity of glioblastoma (GBM) contributes to the poor response to therapy, which is characteristic of this disease, we performed DNA and RNA sequencing on GBM tumor samples and the neurospheres and orthotopic xenograft models derived from them. We used the resulting data set to show that somatic driver alterations including single nucleotide variants, focal DNA alterations, and oncogene amplification in extrachromosomal DNA (ecDNA) elements were in majority propagated from tumor to model systems. In several instances, ecDNAs and chromosomal alterations demonstrated divergent inheritance patterns and clonal selection dynamics during cell culture and xenografting. Longitudinal patient tumor profiling showed that oncogenic ecDNAs are frequently retained after disease recurrence. Our analysis shows that extrachromosomal elements increase the genomic heterogeneity during tumor evolution of glioblastoma, independent of chromosomal DNA alterations.
Systemizing and empathy in forensic ASD talk
Authors: Dobbinson Sushie Jayne 
Published: October 2016

Purpose
Since often missed in forensic care settings, little is known about how the autism spectrum disorder (ASD) social and communication deficit impacts on rehabilitation work, particularly when accompanied by intellectual disability. The purpose of this paper is to show how Baron-Cohen’s empathizing – systemizing theory can elucidate common processes in the interaction-based risk-reduction work carried on between ASD forensic patients and their clinicians.

Design/methodology/approach
Conversation analysis (CA) is used to analyse the talk of two ASD men engaged in risk reduction work with their clinicians on a forensic intellectual disability ward in a medium secure psychiatric hospital in the UK. The clinicians include two forensic nurses and a speech and language therapist.

Findings
Clinicians adapt to their patients’ systematic processes particularly with regard to helping them understand complex social phenomena such as others’ emotional displays and their understanding of empathy.

Practical implications
Since ASD in forensic care is poorly researched, clinicians have little in the way of guidance about the interactive strengths and weaknesses of their ASD patients, despite risk reduction work being carried out by means of conversational interactions. This paper demonstrates some key aspects of ASD clinical interactions which may be used to inform treatment strategies elsewhere in the forensic establishment.

Originality/value
By using Baron-Cohen’s empathizing systemizing theory in combination with CA, this paper aims to bring understanding of ASD interaction up to date. This is of particular importance for this poorly researched patient group, who, because of the way in which they differ to standard psychiatric patients, are at risk of being detained for lengthy periods where treatment strategies are not designed to fit their social and communicative profiles.
The prevalence of autistic spectrum conditions in a community offender sample
Authors: Bates Andrew 
Published: October 2016

Purpose
Previous prevalence studies of likely autistic spectrum condition (ASC) within criminal justice settings have focussed on specialist forensic mental health settings. The purpose of this paper is to examine prevalence of autism in a general community forensic sample.

Design/methodology/approach
In total, 336 offenders managed by a probation office were administered with a recognised screening tool to identify likely autism (AQ-10). Screenings were scored and those above the threshold were identified, where possible further diagnostic information was sought on positive-screened cases.

Findings
In total, 4.5 per cent (15 offenders) of the caseload screened positive for autism. Descriptive demographic information such as gender, age and offence type is provided for this group. Further diagnostic information was available on eight of the cases. Three already had an autism diagnosis and further psychometric assessment indicated that a further three cases were 80 per cent likely to be diagnosable with autism.

Research limitations/implications
Demographic information on the sample could not be compared with norms across the whole probation caseload due to limitation of resources for the project. No further diagnostic information was available on six offenders who screened positive for autism.

Practical implications
The research indicates that autism is not substantially over-represented in a large community offender sample although further research is required to identify the full degree of representation.

Social implications
Different kinds of offences are observed to be committed by offenders who do exhibit autism. It would be useful for criminal justice staff to have a general knowledge about autism, also how people with autism might offend and how they might best be supervised by probation services.

Originality/value
This is the first study of its kind internationally to examine prevalence of autism in a general community forensic sample.
Evaluation of automation levels for construction change management
Authors: Karimidorabati Shahin , Haas Carl T. , Gray Joel 
Published: October 2016

Purpose
Current processes to manage changes are subject to failure since they are heavily dependent on human discipline. The purpose of this paper is to evaluate and quantify the difference between levels of automation of change management processes and to provide input for determining the use of automation systems for change management.

Design/methodology/approach
Three generations of change management processes are defined to represent progressive practices used in major capital projects over the past few decades. Discrete event simulation was used to model these processes to capture their behavior and compare their performance according to time and compliance metrics. An oil and gas megaproject served to validate the findings of this modeling and analysis.

Findings
The results showed that automated processes can bring more compliance and real-time traceability, but not a significant time reduction in the change process. This contributes to the understanding of the impact of workflow-based automation on construction process performance. The validity of the conclusions are limited by the breadth of sectors studied and the inability to capture off-line time allocations of the personnel involved. Future research may build on the work presented here by studying additional processes such as requests for information, project change notices, requests for scaffolding, and interface management in various industry sectors.

Originality/value
A new approach for modeling and evaluating construction management process automation is contributed and the specific results of the paper indicate that automated workflow-based change management processes should be implemented in megaprojects.
Principal component analysis of professional competencies of architects in the Ghanaian construction industry
Authors: Kwofie Titus Ebenezer , Amos-Abanyie Samuel , Afram Samuel Owusu 
Published: October 2016

Purpose
The identification and development of appropriate competencies remain very critical and central to performance measures in mainstream human resource management genre towards effective teams. It is posited as a viable means for validating and engendering best practices and developing suitable competencies towards acceptable performance outcome in construction project delivery. The purpose of this paper is to identify the critical professional competencies of an architect in the Ghanaian construction industry (GCI) towards effective performance in the construction project delivery.

Design/methodology/approach
From a mixed method design involving semi-structured qualitative interview and a questionnaire survey of architects in Ghana, 16 professional architectural competencies were identified for respondents to indicate their importance to effective architectural practice and consulting in the GCI on a five-point Likert scale. Factor analysis was used to explore the interrelations among the variables and make possible empirical explanations.

Findings
Factor analysis revealed four underlying clusters named in order of their significance as efficient design response to client needs, legal aspects of practice, sustainable design and construction and efficient project management skills. The study provides insight into the contextual practice, characteristics and the critical professional architectural competencies needed by architects in the construction industry in Ghana.

Originality/value
The findings have rigorously revealed and provided clear understanding and insight into the thematic critical professional competencies of architects important to the construction industry in Ghana which should be the focus of architectural training and practice. It is also very important towards developing and stimulating a continuous professional development agenda, developing a body of knowledge of professional practice in architecture and conducting curriculum review to meet current emerging competency profiles necessary for influencing performance levels in the GCI.