bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lipidomics analysis of juveniles’ blue mussels (Mytilus edulisL. 1758), a key economic and ecological species
Authors: Laudicella Vincenzo Alessandro , Beveridge Christine , Carboni Stefano , Franco Sofia Cota , Doherty Mary K. , Long Nina , Mitchell Elaine , Stanley Michelle S. , Whitfield Philip D. , Hughes Adam D. 
Published: September 2019

AbstractBlue mussels (Mytilus edulisL.) are important components of coastal ecosystems functioning through benthopelagic coupling and ecosystem engineering. At the same time, mussel production is central in the economy of coastal areas. Therefore, understanding their nutritional, physiological and metabolic processes at key life stages is important for their management, both within food production systems and in wild populations.Lipids are crucial molecules for bivalve growth, but their diversity and roles have been considered from fatty acid (FA) perspective. In this paper, we applied lipidomics to bivalve nutrition. Lipidomics provides a holistic perspective on lipid patterns; by examining the lipidome, important physiological information can be acquired. Here, we use controlled laboratory experiments to elucidate the responses to changes in the diet of newly settled mussels juveniles, one of the most critical life stages. The diets considered in this study are single strains diet ofCylindrotheca fusiformisCCAP 1017/2 – CYL,Isochrysis galbanaCCAP 927/1– ISO,Monodopsis subterraneanCCAP 848/1 – MONO,Nannochloropsis oceanicaCCAP 849/10– NANNO and a commercial algae paste –SP.The diets had a significant effect on spat GR and WI, and according to their efficacy resulted ranked as follows: ISO>NANNO/CYL>SP>MONO. Spat FA composition and neutral lipid content (principally triacylglycerols - TG), were influenced by the diets. Furthermore, untargeted lipidomics also showed shifts in several phospholipid species, with changes related to the essential PUFA available from the diet. TG content, neutral lipids and several TG and FA species were correlated (Spearman R2>0.8 FDR p<0.05) with spat WI, suggesting their possible application as markers of mussel juvenile condition. The availability of dietary essential PUFA deeply modified the spat lipidome both for neutral and for polar lipids. This change in the lipidome could have major impacts on their ecology and their production for food.
ML-morph: A Fast, Accurate and General Approach for Automated Detection and Landmarking of Biological Structures in Images
Authors: Porto Arthur , Voje Kjetil L. 
Published: September 2019

ABSTRACTMorphometrics has become an indispensable component of the statistical analysis of size and shape variation in biological structures. Morphometric data has traditionally been gathered through low-throughput manual landmark annotation, which represents a significant bottleneck for morphometric-based phenomics. Here we propose a machine-learning-based high-throughput pipeline to collect high-dimensional morphometric data in images of semi rigid biological structures.The proposed framework has four main strengths. First, it allows for dense phenotyping with minimal impact on specimens. Second, it presents landmarking accuracy comparable to manual annotators, when applied to standardized datasets. Third, it performs data collection at speeds several orders of magnitude higher than manual annotators. And finally, it is of general applicability (i.e., not tied to a specific study system).State-of-the-art validation procedures show that the method achieves low error levels when applied to three morphometric datasets of increasing complexity, with error varying from 0.5% to 2% of the structure’s length in the automated placement of landmarks. As a benchmark for the speed of the entire automated landmarking pipeline, our framework places 23 landmarks on 13,686 objects (zooids) detected in 1684 pictures of fossil bryozoans in 3.12 minutes using a personal computer.The proposed machine-learning-based phenotyping pipeline can greatly increase the scale, reproducibility and speed of data collection within biological research. To aid the use of the framework, we have developed a file conversion algorithm that can be used to leverage current morphometric datasets for automation, allowing the entire procedure, from model training all the way to prediction, to be performed in a matter of hours.
Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence
Authors: Cordero Paul R.F. , Grinter Rhys , Hards Kiel , Cryle Max J. , Warr Coral G. , Cook Gregory M. , Greening Chris 
Published: September 2019

AbstractAerobic soil bacteria metabolize atmospheric hydrogen (H2) to persist when nutrient sources are limited. This process is the primary sink in the global H2cycle and supports the productivity of microbes in oligotrophic environments. To mediate this function, bacteria possess [NiFe]-hydrogenases capable of oxidising H2to subatmospheric concentrations. The soil saprophyteMycobacterium smegmatishas two such [NiFe]-hydrogenases, designated Huc and Hhy, which belong to different phylogenetic subgroups. Huc and Hhy exhibit similar characteristics: both are oxygen-tolerant, oxidise H2to subatmospheric concentrations, and enhance survival during hypoxia and carbon limitation. These shared characteristics pose the question: Why doesM. smegmatisrequire two hydrogenases mediating a seemingly similar function? In this work we resolve this question by showing that Huc and Hhy are differentially expressed, localised, and integrated into the respiratory chain. Huc is active in late exponential and early stationary phase, supporting energy conservation during mixotrophic growth and the transition into dormancy. In contrast, Hhy is most active during long-term persistence, providing energy for maintenance processes when carbon sources are depleted. We show that Huc and Hhy are obligately linked to the aerobic respiratory chain via the menaquinone pool and are differentially affected by respiratory uncouplers. Consistent with their distinct expression profiles, Huc and Hhy interact differentially with the terminal oxidases of the respiratory chain. Huc exclusively donates electrons to, and possibly physically associates with, the proton pumping cytochromebcc-aa3supercomplex. In contrast, the more promiscuous Hhy can also provide electrons to the cytochromebdoxidase complex. These data demonstrate that, despite their similar characteristics, Huc and Hhy perform distinct functions during mycobacterial growth and survival.
Decoding the transcriptional response to ischemic stroke in young and aged mouse brain
Authors: Androvic Peter , Kirdajova Denisa Belov , Tureckova Jana , Zucha Daniel , Rohlova Eva , Abaffy Pavel , Kriska Jan , Anderova Miroslava , Kubista Mikael , Valihrach Lukas 
Published: September 2019

AbstractIschemic stroke is one of the leading causes of mortality and major healthcare and economic burden. It is a well-recognized disease of aging, yet it is unclear how the age-dependent vulnerability occurs and what are the underlying mechanisms. To address these issues, we performed a comprehensive RNA-Seq analysis of aging, ischemic stroke and their interaction using a model of permanent middle cerebral artery occlusion (MCAO) in 3 and 18 month old female mice. We assessed differential gene expression across injury status and age, estimated cell type proportion changes, assayed the results against a range of transcriptional signatures from the literature and performed unsupervised co-expression analysis, identifying modules of genes with varying response to injury. We uncovered selective vulnerability of neuronal populations and increased activation of type-I interferon (IFN-I) signaling and several other inflammatory pathways in aged mice. We extended these findings via targeted expression analysis in tissue as well as acutely purified cellular populations to show differential temporal dynamics of IFN-I signaling between age groups and contribution of individual cell types. Together, these results paint a picture of ischemic stroke as a complex age-related disease and provide insights into interaction of aging and stroke on cellular and molecular level.Graphical summary
Copy number motifs expose genome instability type and predict driver events and disease outcome in breast cancer
Authors: Pladsen Arne V. , Nilsen Gro , Rueda Oscar M. , Aure Miriam R. , Borgan Ørnulf , Liestøl Knut , Vitelli Valeria , Frigessi Arnoldo , Langerød Anita ,   OSBREAC, Mathelier Anthony , Engebråten Olav , Wedge David C. , Van Loo Peter , Caldas Carlos , Børresen-Dale Anne-Lise , Russnes Hege G. , Lingjærde Ole Christian 
Published: September 2019

AbstractTumor evolution is dependent on and constrained by the genotypes emerging from genome instability. We hypothesized that non-site-specific copy number motifs would correlate with underlying replication defects and also with tumor and patient fate. Six feature detectors were defined to characterize and score the local spatial behaviour of a copy number profile. By accumulating scores across genomic regions, a low-dimensional representation of the tumor genome was obtained. The proposed Copy Aberration Regional Mapping Analysis (CARMA) algorithm was applied to 2384 breast tumors from three breast cancer cohorts, revealing distinct copy number motifs in established molecular subtypes. A prognostic index combining the features predicted breast cancer specific survival better than both the genomic instability index (GII) and all commonly used clinical stratifications. CARMA offers effective comparison of tumor subgroups and extracts biologically and clinically relevant features from allele-specific copy number profiles.
The effect of wrist posture on extrinsic finger muscle activity during single joint movements
Authors: Beringer Carl R. , Mansouri Misagh , Fisher Lee E. , Collinger Jennifer L. , Munin Michael C. , Boninger Michael L. , Gaunt Robert A. 
Published: September 2019

AbstractWrist posture impacts the muscle lengths and moment arms of the extrinsic finger muscles that cross the wrist. As a result, the electromyographic (EMG) activity associated with digit movement at different wrist postures may also change. Therefore, we sought to quantify the posture-dependence of extrinsic finger muscle activity. Fine-wire bipolar electrodes were inserted in the extrinsic hand muscles of able-bodied subjects to record EMG activity during wrist and finger movements in various postures. EMG activity of all the recorded finger muscles were significantly different (p<.05, ANOVA) when performing the same movement in five different wrist postures. EMG activity varied by up to 70%, with the highest levels of activity observed in finger extensors when the wrist was extended. Similarly, finger flexors were most active when the wrist was flexed. For the finger flexors, EMG variations with wrist posture were most prominent for index finger muscles, while the EMG activity of all finger extensor muscles were similarly modulated. The extrinsic finger muscles also showed significant activity during wrist movements with the digits held still regardless of finger posture, suggesting that they may play a role in generating torque during wrist movements. Finally, we developed a pair of generalized classifiers that show that finger muscle EMG can be used to predict wrist posture. These results may impact the design of biomimetic control algorithms for myoelectric prosthetic hands, but further work in transradial amputees is necessary to determine whether this phenomenon persists after amputation.
MetroNome — a visual data exploration platform for integrating human genotypic and phenotypic data across diseases
Authors: Stolte Christian , Shi Kevin , Lapchyk Nina , Novod Nathaniel , Abhyankar Avinash , Ostrow Lyle W. , Phatnani Hemali , Bloom Toby 
Published: September 2019

AbstractMetroNome is a web-based visual data exploration platform which integrates de-identified genomic, transcriptomic, and phenotypic data sets. Users can define and compare cohorts constructed from multimodal data and share the data and analyses with outside tools. MetroNome’s interactive visualization and analysis tools allow researchers to quickly form and explore novel hypotheses. The deidentified data is linked back to the source biosample inventories in multiple biobanks, enabling researchers to further investigate new ideas using the most relevant samples.
The tempo and mode of angiosperm mitochondrial genome divergence inferred from intraspecific variation in Arabidopsis thaliana
Authors: Wu Zhiqiang , Waneka Gus , Sloan Daniel B. 
Published: September 2019

ABSTRACTThe mechanisms of sequence divergence in angiosperm mitochondrial genomes have long been enigmatic. In particular, it is difficult to reconcile the rapid divergence of intergenic regions that can make non-coding sequences almost unrecognizable even among close relatives with the unusually high levels of sequence conservation found in genic regions. It has been hypothesized that different mutation/repair mechanisms act on genic and intergenic sequences or alternatively that mutational input is relatively constant but that selection has strikingly different effects on these respective regions. To test these alternative possibilities, we analyzed mtDNA divergence within Arabidopsis thaliana, including variants from the 1001 Genomes Project and changes accrued in published mutation accumulation (MA) lines. We found that base-substitution frequencies are relatively similar for intergenic regions and synonymous sites in coding regions, whereas indel and nonsynonymous substitutions rates are greatly depressed in coding regions, supporting a conventional model in which mutation/repair mechanisms are consistent throughout the genome but differentially filtered by selection. Most types of sequence and structural changes were undetectable in 10-generation MA lines, but we found significant shifts in relative copy number across mtDNA regions for lines grown under stressed vs. benign conditions. We confirmed quantitative variation in copy number across the A. thaliana mitogenome using both whole-genome sequencing and droplet digital PCR, further undermining the classic but oversimplified model of a circular angiosperm mtDNA structure. Our results suggest that copy number variation is one of the most rapidly evolving features in angiosperm mtDNA, even outpacing rearrangements in these notoriously structurally diverse genomes.
SimBSI: An open-source Simulink library for developing closed-loop brain signal interfaces in animals and humans
Authors: Ojeda Alejandro , Buscher Nathalie , Balasubramani Pragathi , Maric Vojislav , Ramanathan Dhakshin , Mishra Jyoti 
Published: September 2019

AbstractObjectiveA promising application of BCI technology is in the development of personalized therapies that can target neural circuits linked to mental or physical disabilities. Typical BCIs, however, offer limited value due to simplistic designs and poor understanding of the conditions being treated. Building BCIs on more solid grounds may require the characterization of the brain dynamics supporting cognition and behavior at multiple scales, from single-cell and local field potential (LFP) recordings in animals to non-invasive electroencephalography (EEG) in humans. Despite recent efforts, a unifying software framework to support closed-loop studies in both animals and humans, is still lacking. The objective of this paper is to develop such a neurotechnology software framework.ApproachHere we develop the Simulink for Brain Signal Interfaces library (SimBSI). Simulink is a mature graphical programming environment within MATLAB that has gained traction for processing electrophysiological data. SimBSI adds to this ecosystem: 1) advanced human EEG source imaging, 2) cross-species multimodal data acquisition based on the Lab Streaming Layer library, and 3) a graphical experimental design platform.Main resultsWe used several examples to demonstrate the capabilities of the library, ranging from simple signal processing, to online EEG source imaging, cognitive task design, and closed-loop neuromodulation. We further demonstrate the simplicity of developing a sophisticated experimental environment for rodents within this environment.SignificanceWith the SimBSI library we hope to aid BCI practitioners of dissimilar backgrounds in the development of, much needed, single and cross-species closed-loop neuroscientific experiments. These experiments may provide the necessary mechanistic data for BCIs to become effective therapeutic tools.
What about the environment?
Authors: Nesselhauf Lucas , Fleuchaus Ruth , Theuvsen Ludwig 
Published: September 2019

Purpose
Fungus-resistant grape varieties (FRGVs) are the key to more environment-friendly wine growing. This paper aims to examine whether German consumers are willing to buy environment-friendly wines. The study focuses on reducing the amount of fungicides applied and the improvement of the carbon footprint, which are both related to the FRGVs . Furthermore, a cluster analysis leads to more insights into the consumer groups that are open to environment-friendly wine.

Design/methodology/approach
A choice experiment was conducted among 1,500 German wine drinkers with the following attributes: “reduction of pesticides”, “reduction of carbon emissions”,“familiarity with the grape variety”,“organic certification”, the slogan “better for the environment” and“price”. The individual-level, part-worth utilities were estimated using the Hierarchical Bayes method. The Ward’s method was used to cluster the individual-level, part-worth utilities. The participants’ wine involvement and environmentalism are used to further analyse the sample.

Findings
The most important attribute is “price”, followed by the “familiarity with the grape variety” and the “reduction of pesticides” and of “carbon emissions”. The least important attribute is “better for the environment”. The cluster analysis results in three clusters: the green-minded, the traditionalists and the price-minded.

Practical implications
The insights about the consumer acceptance of environment-friendly wines can be used to market these wines more effectively to consumers.

Originality/value
This is the first study that combines a choice experiment with attributes that are derived from the benefits of fungus-resistant grape varieties.
Comparing “parallel passages” in digital archives
Authors: Harris Martyn , Levene Mark , Zhang Dell , Levene Dan 
Published: September 2019

PurposeThe purpose of this paper is to present a language-agnostic approach to facilitate the discovery of “parallel passages” stored in historic and cultural heritage digital archives.Design/methodology/approachThe authors explore a novel, and relatively simple approach, using a character-based statistical language model combined with a tailored version of the Basic Local Alignment Tool to extract exact and approximate string patterns shared between groups of documents.FindingsThe approach is applicable to a wide range of languages, and compensates for variability in the text of the documents as a result of differences in dialect, authorship, language change over time and errors due to inaccurate transcriptions and optical character recognition errors as a result of the digitisation process.Research limitations/implicationsA number of case studies demonstrate that the approach is practical and generalisable to a wide range of archives with documents in different languages, domains and of varying quality.Practical implicationsThe approach described can be applied to any digital archive of modern and contemporary texts. This makes the approach applicable to digital archives recording historic texts, but also those composed of more recent news articles, for example.Social implicationsThe analysis of “parallel passages” enables researchers to quantify the presence and extent of text-reuse in a collection of documents, which can provide useful data on author style, text genres and cultural contexts.Originality/valueThe approach is novel and addresses a need by humanities researchers for tools that can identify similar documents and local similarities represented by shared text sequences in a potentially vast large archive of documents. As far as the authors are aware, there are no tools currently exist that provide the same level of tolerance to the language of the documents.
Competences desired among educational leaders of technical education degree institutions
Authors: Sharma Payal , Pandher Jagwinder Singh 
Published: September 2019

Purpose
This study aims to identify and classify various competences and competencies that educational leaders should essentially possess.

Design/methodology/approach
The systematic review of the literature was conducted to identify various competences of educational leaders in the institutions. Later, an empirical research was conducted. The data were analyzed through confirmatory factor analysis (CFA) using AMOS 20.0 to classify these competences according to their relative importance considering natural gaps in standardized beta (ß) values. In all, 96 administrators of 35 technical institutions of Punjab (India) offering engineering and management programs and 93 veteran educational experts had responded in a survey.

Findings
The results of the study identified five competences: pedagogical, leadership, innovative, research and evaluation competences. The competencies “help others in improvement and not blame circumstances”, “set high benchmarks” and “align class activities with learning objectives” have qualified among the “most important” competencies for the educational leaders.

Research limitations/implications
The sample was specific to one state. There may be the chances of response bias in a few situations. Therefore, there are few reservations in generalizing the findings.

Practical implications
The study has several implications for both the faculty and the technical education degree institutes. The study provides a link between the characteristics and competencies of educational leaders. This study also contributes in terms of mapping of these competencies while recruitment of the faculty to test whether the candidates possess the potential of becoming educational leaders.

Originality/value
The administrators can test these competencies in their faculty for the purpose of identifying both the educational leaders within their institutes and the potential educational leaders in future by assessing “requisite” and “important” competencies.