bluuebunny/crossref_metadata_2025 huggingface dataset:
Care for Dying Children and Their Families in the PICU: Promoting Clinician Education, Support, and Resilience
Authors: Dryden-Palmer Karen , Garros Daniel , Meyer Elaine C. , Farrell Catherine , Parshuram Christopher S.
Published: August 2018

Objectives:

To describe the consequences of workplace stressors on healthcare clinicians in PICU, and strategies for personal well-being, and professional effectiveness in providing high-quality end-of-life care.

Data Sources:

Literature review, clinical experience, and expert opinion.

Study Selection:

A sampling of foundational and current evidence was accessed.

Data Synthesis:

Narrative review and experiential reflection.

Conclusions:

The well-being of healthcare clinicians in the PICU influences the day-to-day quality and effectiveness of patient care, team functioning, and the retention of skilled individuals in the PICU workforce. End-of-life care, including decision making, can be complicated. Both are major stressors for PICU staff that can lead to adverse personal and professional consequences. Overresponsiveness to routine stressors may be seen in those with moral distress, and underresponsiveness may be seen in those with compassion fatigue or burnout. Ideally, all healthcare professionals in PICU can rise to the day-to-day workplace challenges—responding in an adaptive, effective manner. Strategies to proactively increase resilience and well-being include self-awareness, self-care, situational awareness, and education to increase confidence and skills for providing end-of-life care. Reactive strategies include case conferences, prebriefings in ongoing preidentified situations, debriefings, and other postevent meetings. Nurturing a culture of practice that acknowledges the emotional impacts of pediatric critical care work and celebrates the shared experiences of families and clinicians to build resilient, effective, and professionally fulfilled healthcare professionals thus enabling the provision of high-quality end-of-life care for children and their families.
Should Patients With NAFLD/NASH Be Surveyed for HCC?
Authors: Reig Maria , Gambato Martina , Man Nancy Kwan , Roberts John P. , Victor David , Orci Lorenzo A. , Toso Christian
Published: August 2018

Background

Patients with nonalcoholic fatty liver disease (NAFLD) are at risk of developing hepatocellular carcinoma (HCC), but the magnitude of the association still needs to be determined to define the need for a specific surveillance strategy.

Methods

We based our assessment on a previously published review by White et al (1992-2011) and on a systematic review(2012-2017).

Results

The new search identified 328 abstracts. Combining both eras (1992-2011 and 2012-2017), 25 studies were included in the analysis. Four were prospective, 2 described a retrospective analysis of a prospective database, and the others were retrospective. All studies were published after 2004, but the inclusion period of half of them ended before the year 2000. Studies showed variation in the definition of NAFLD, in the incidence of fibrosis/cirrhosis, in the presence of comorbidities (potentially affecting HCC incidence), and in the type and duration of screening. Considering only studies strictly including patients with or without cirrhosis, the reported incidence of HCC in NAFLD patients with cirrhosis was between 6.7 and 15% at 5 to 10 years, whereas the incidence in NAFLD patients without cirrhosis was 2.7% at 10 years and 23 per 100 000 person-years.

Conclusions

Hepatocellular carcinoma screening in NAFLD patients with cirrhosis is mandatory. However, the currently observed low (and insufficiently documented) incidence of HCC in NAFLD patients without cirrhosis does not justify a systematic surveillance. Research efforts should focus on developing a score, which could aid the clinician in identifying NAFLD patients without cirrhosis who are at higher risk of developing HCC.
Toxic myopathies
Authors: Pasnoor Mamatha , Barohn Richard J. , Dimachkie Mazen M.
Published: August 2018

Purpose of review

Our aim is to highlight major advances reported in the last few years in drug-induced muscle toxicity.

Recent findings

Our focus is on myopathies induced by statins and immune checkpoint inhibitors with a brief overview of rare steroid myopathies. Statin muscle injury is frequently because of direct toxicity rather than an autoimmune mechanism. Laboratory testing and muscle pathologic features distinguish these two conditions. Statin-associated necrotizing autoimmune myopathy (SANAM) is associated with an autoantibody in 66% of cases targeting the HMGCR enzyme. The later autoantibody is a marker for necrotizing autoimmune myopathy, regardless of statin exposure. In SANAM, MHC-I antigens are expressed on the surface of intact muscle fibers. Genetic HLA loci predispose patients exposed to statins to immunologic toxicity. SANAM requires long-term therapy with multiple immunosuppressive therapies. Immune checkpoint inhibitors are powerful emerging therapies for advanced cancer that pause a novel therapeutic challenge.

This review is focused on statins, the most prevalent myotoxic drug class. In addition, we examine the accumulating body of evidence of muscle injury and its management with immune checkpoint inhibitors. We anticipate the reader to become more knowledgeable in recent discoveries related to these myotoxic drugs, and their mechanisms of action and management.
Algorithms: transparency and accountability
Authors: Blacklaws Christina
Published: August 2018

This opinion piece explores the issues of accountability and transparency in relation to the growing use of machine learning algorithms. Citing the recent work of the Royal Society and the British Academy, it looks at the legal protections for individuals afforded by the EU General Data Protection Regulation and asks whether the legal system will be able to adapt to rapid technological change. It concludes by calling for continuing debate that is itself accountable, transparent and public.

This article is part of a discussion meeting issue ‘The growing ubiquity of algorithms in society: implications, impacts and innovations'.
Improving reproducibility by using high-throughput observational studies with empirical calibration
Authors: Schuemie Martijn J. , Ryan Patrick B. , Hripcsak George , Madigan David , Suchard Marc A.
Published: August 2018

Concerns over reproducibility in science extend to research using existing healthcare data; many observational studies investigating the same topic produce conflicting results, even when using the same data. To address this problem, we propose a paradigm shift. The current paradigm centres on generating one estimate at a time using a unique study design with unknown reliability and publishing (or not) one estimate at a time. The new paradigm advocates for high-throughput observational studies using consistent and standardized methods, allowing evaluation, calibration and unbiased dissemination to generate a more reliable and complete evidence base. We demonstrate this new paradigm by comparing all depression treatments for a set of outcomes, producing 17 718 hazard ratios, each using methodology on par with current best practice. We furthermore include control hypotheses to evaluate and calibrate our evidence generation process. Results show good transitivity and consistency between databases, and agree with four out of the five findings from clinical trials. The distribution of effect size estimates reported in the literature reveals an absence of small or null effects, with a sharp cut-off at
p
 = 0.05. No such phenomena were observed in our results, suggesting more complete and more reliable evidence.

This article is part of a discussion meeting issue ‘The growing ubiquity of algorithms in society: implications, impacts and innovations’.
Algorithm-assisted decision-making in the public sector: framing the issues using administrative law rules governing discretionary power
Authors: Oswald Marion
Published: August 2018

This article considers some of the risks and challenges raised by the use of algorithm-assisted decision-making and predictive tools by the public sector. Alongside, it reviews a number of long-standing English administrative law rules designed to regulate the discretionary power of the state. The principles of administrative law are concerned with human decisions involved in the exercise of state power and discretion, thus offering a promising avenue for the regulation of the growing number of algorithm-assisted decisions within the public sector. This article attempts to re-frame key rules for the new algorithmic environment and argues that ‘old’ law—interpreted for a new context—can help guide lawyers, scientists and public sector practitioners alike when considering the development and deployment of new algorithmic tools.

This article is part of a discussion meeting issue ‘The growing ubiquity of algorithms in society: implications, impacts and innovations'.
Humanitarian applications of machine learning with remote-sensing data: review and case study in refugee settlement mapping
Authors: Quinn John A. , Nyhan Marguerite M. , Navarro Celia , Coluccia Davide , Bromley Lars , Luengo-Oroz Miguel
Published: August 2018

The coordination of humanitarian relief, e.g. in a natural disaster or a conflict situation, is often complicated by a scarcity of data to inform planning. Remote sensing imagery, from satellites or drones, can give important insights into conditions on the ground, including in areas which are difficult to access. Applications include situation awareness after natural disasters, structural damage assessment in conflict, monitoring human rights violations or population estimation in settlements. We review machine learning approaches for automating these problems, and discuss their potential and limitations. We also provide a case study of experiments using deep learning methods to count the numbers of structures in multiple refugee settlements in Africa and the Middle East. We find that while high levels of accuracy are possible, there is considerable variation in the characteristics of imagery collected from different sensors and regions. In this, as in the other applications discussed in the paper, critical inferences must be made from a relatively small amount of pixel data. We, therefore, consider that using machine learning systems as an augmentation of human analysts is a reasonable strategy to transition from current fully manual operational pipelines to ones which are both more efficient and have the necessary levels of quality control.

This article is part of a discussion meeting issue ‘The growing ubiquity of algorithms in society: implications, impacts and innovations’.
Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins
Authors: Branger Catherine , Ledda Alice , Billard-Pomares Typhaine , Doublet Benoît , Fouteau Stéphanie , Barbe Valérie , Roche David , Cruveiller Stéphane , Médigue Claudine , Castellanos Miguel , Decré Dominique , Drieux-Rouze Laurence , Clermont Olivier , Glodt Jérémy , Tenaillon Olivier , Cloeckaert Axel , Arlet Guillaume , Denamur Erick
Published: August 2018

To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic history of the parental strains. Finer scale analysis of the more abundant clusters IncF and IncI1 showed that ESBL-encoding plasmids and plasmids isolated before the use of 3GCs had the same diversity and phylogenetic history, and that acquisition of ESBL-encoding genes had occurred during multiple independent events. Moreover, the bla
CTX-M-15 gene, unlike other CTX-M genes, was inserted at a hot spot in a bla
TEM-1-Tn2 transposon. These findings showed that ESBL-encoding genes have arrived on wide range of pre-existing plasmids and that the successful spread of bla
CTX-M-15 seems to be favoured by the presence of well-adapted IncF plasmids that carry a Tn2-bla
TEM-1 transposon.
Cortical Microcircuits from a Generative Vision Model
Authors: George Dileep , Lavin Alexander , Guntupalli J. Swaroop , Mely David , Hay Nick , Lázaro-Gredilla Miguel
Published: August 2018

Understanding the information processing roles of cortical circuits is an outstanding problem in neuroscience and artificial intelligence. The theoretical setting of Bayesian inference has been suggested as a framework for understanding cortical computation. Based on a recently published generative model for visual inference (George et al., 2017), we derive a family of anatomically instantiated and functional cortical circuit models. In contrast to simplistic models of Bayesian inference, the underlying generative model’s representational choices are validated with real-world tasks that required efficient inference and strong generalization. The cortical circuit model is derived by systematically comparing the computational requirements of this model with known anatomical constraints. The derived model suggests precise functional roles for the feedforward, feedback and lateral connections observed in different laminae and columns, and assigns a computational role for the path through the thalamus.
Effects of cochlear synaptopathy on spontaneous and sound-evoked activity in the mouse inferior colliculus
Authors: Shaheen Luke A. , Liberman M. Charles
Published: August 2018

Tinnitus and hyperacusis are life-disrupting perceptual abnormalities that are often preceded by acoustic overexposure. Animal models of overexposure have suggested a link between these phenomena and neural hyperactivity, i.e. elevated spontaneous rates (SRs) and sound-evoked responses. Prior work has focused on changes in central auditory responses, with less attention paid to the exact nature of the associated peripheral damage. The demonstration that acoustic overexposure can cause cochlear nerve damage without permanent threshold elevation suggests this type of peripheral damage may be a key elicitor of tinnitus and hyperacusis in humans with normal audiograms. We addressed this idea by recording responses in the mouse inferior colliculus (IC) following a bilateral, neuropathic noise exposure. Two wks post-exposure, mean SRs were unchanged in mice recorded while awake, or under anesthesia. SRs were also unaffected by more intense, or unilateral exposures. These results suggest that neither neuropathy nor hair cell loss are sufficient to raise SRs in the IC, at least in mice. However, it’s not clear whether our mice had tinnitus. Tone-evoked rate-level functions at the CF were steeper following exposure, specifically in the region of maximal neuropathy. Furthermore, suppression driven by off-CF tones and by ipsilateral noise were also reduced. Both changes were especially pronounced in neurons of awake mice. These findings align with prior reports of elevated acoustic startle in neuropathic mice, and indicate that neuropathy may initiate a compensatory response in the central auditory system leading to the genesis of hyperacusis.
Focus of attention modulates the heartbeat evoked potential
Authors: Petzschner Frederike H. , Weber Lilian A. , Wellstein Katharina V. , Paolini Gina , Tri Do Cao , Stephan Klaas E.
Published: August 2018

Theoretical frameworks such as predictive coding suggest that the perception of the body and world – interoception and exteroception – involve intertwined processes of inference, learning, and prediction. In this framework, attention is thought to gate the influence of sensory information on perception. In contrast to exteroception, there is limited evidence for purely attentional effects on interoception. Here, we empirically tested if attentional focus modulates cortical processing of single heartbeats, using a newly-developed experimental paradigm to probe purely attentional differences between exteroceptive and interoceptive conditions in the heartbeat evoked potential (HEP). We found that the HEP is significantly higher during interoceptive compared to exteroceptive attention, in a time window of 520-580ms after the R-peak. Furthermore, this effect predicted self-report measures of autonomic system reactivity. This study thus provides direct evidence that the HEP is modulated by attention and supports recent interpretations of the HEP as a neural correlate of interoceptive prediction errors.
Pathogens, parasites, and parasitoids of ants: a synthesis of parasite biodiversity and epidemiological traits
Authors: Quevillon Lauren E. , Hughes David P.
Published: August 2018

1.

Ants are among the most ecologically successful organisms on Earth, with a global distribution and diverse nesting and foraging ecologies. Ants are also social organisms, living in crowded, dense colonies that can range up to millions of individuals. Understanding the ecological success of the ants requires understanding how they have mitigated one of the major costs of social living-infection by parasitic organisms. Additionally, the ecological diversity of ants suggests that they may themselves harbor a diverse, and largely unknown, assemblage of parasites. As a first step, we need to know the taxonomic and functional diversity of the parasitic organisms infecting ants. To that end, we provide a comprehensive review of the parasitic organisms infecting ants by collecting all extant records. We synthesize major patterns in parasite ecology by categorizing how parasites encounter their ant hosts, whether they require host death as a developmental necessity, and how they transmit to future hosts.

We report 1,415 records of parasitic organisms infecting ants, the majority of which come from order Diptera (34.8%), phylum Fungi (25.6%), and order Hymenoptera (25.1%). Most parasitic organisms infecting ants are parasitoids (89.6%), requiring the death of their host as developmental necessity and most initially encounter their hosts in the extranidal environment (68.6%). Importantly, though most parasitic organisms infecting ants only need a single host to complete their life cycle (89.2%), the vast majority need to leave the nest before transmission to the next ant host can occur (88.3%), precluding ant-to-ant transmission within the nest. With respect to the host, we only found records for 9 out of 17 extant ant sub-families, and for 82 out of the currently recognized 334 ant genera. Though there is likely bias in the records reported, both host and parasite ecological traits and evolutionary histories underlie the pattern of ant-parasite association reported here. This work provides a foundation for future work that will begin to untangle the ecological drivers of ant-parasite relationships and the evolutionary implications thereof.
Conserved cell types with divergent features between human and mouse cortex
Authors: Hodge Rebecca D , Bakken Trygve E , Miller Jeremy A , Smith Kimberly A , Barkan Eliza R , Graybuck Lucas T , Close Jennie L , Long Brian , Penn Osnat , Yao Zizhen , Eggermont Jeroen , Hollt Thomas , Levi Boaz P , Shehata Soraya I , Aevermann Brian , Beller Allison , Bertagnolli Darren , Brouner Krissy , Casper Tamara , Cobbs Charles , Dalley Rachel , Dee Nick , Ding Song-Lin , Ellenbogen Richard G , Fong Olivia , Garren Emma , Goldy Jeff , Gwinn Ryder P , Hirschstein Daniel , Keene C Dirk , Keshk Mohamed , Ko Andrew L , Lathia Kanan , Mahfouz Ahmed , Maltzer Zoe , McGraw Medea , Nguyen Thuc Nghi , Nyhus Julie , Ojemann Jeffrey G , Oldre Aaron , Parry Sheana , Reynolds Shannon , Rimorin Christine , Shapovalova Nadiya V , Somasundaram Saroja , Szafer Aaron , Thomsen Elliot R , Tieu Michael , Scheuermann Richard H , Yuste Rafael , Sunkin Susan M , Lelieveldt Boudewijn , Feng David , Ng Lydia , Bernard Amy , Hawrylycz Michael , Phillips John W. , Tasic Bosiljka , Zeng Hongkui , Jones Allan R , Koch Christof , Lein Ed S
Published: August 2018

Elucidating the cellular architecture of the human neocortex is central to understanding our cognitive abilities and susceptibility to disease. Here we applied single nucleus RNA-sequencing to perform a comprehensive analysis of cell types in the middle temporal gyrus of human cerebral cortex. We identify a highly diverse set of excitatory and inhibitory neuronal types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to a similar mouse cortex single cell RNA-sequencing dataset revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of human cell type properties. Despite this general conservation, we also find extensive differences between homologous human and mouse cell types, including dramatic alterations in proportions, laminar distributions, gene expression, and morphology. These species-specific features emphasize the importance of directly studying human brain.
MEMS-Actuated Carbon Fiber Microelectrode for Neural Recording
Authors: Zoll Rachel S. , Schindler Craig B. , Massey Travis L. , Drew Daniel S. , Maharbiz Michel M. , Pister Kristofer S. J.
Published: August 2018

Microwire and microelectrode arrays used for cortical neural recording typically consist of tens to hundreds of recording sites, but often only a fraction of these sites are in close enough proximity to firing neurons to record single-unit activity. Recent work has demonstrated precise, depth-controllable mechanisms for the insertion of single neural recording electrodes, but these methods are mostly only capable of inserting electrodes which elicit adverse biological response. We present an electrostatic-based actuator capable of inserting individual carbon fiber microelectrodes which elicit minimal to no adverse biological response. The device is shown to insert a carbon fiber recording electrode into an agar brain phantom and can record an artificial neural signal in saline. This technique provides a platform generalizable to many microwire-style recording electrodes.
Test-retest reliability of functional brain network characteristics using resting-state EEG and graph theory
Authors: Moezzi Bahar , Hordacre Brenton , Berryman Carolyn , Ridding Michael C. , Goldsworthy Mitchell R.
Published: August 2018

Metrics of brain network organization can be derived from neuroimaging data using graph theory. We explored the test-retest reliability of graph metrics of functional networks derived from resting-state electroencephalogram (EEG) recordings. Data were collected within two designs: (1) within sessions (WS) design where EEG data were collected from 18 healthy participants in four trials within a few hours and (2) between sessions (BS) design where EEG data were collected from 19 healthy participants in three trials on three different days at least one week apart. Electrophysiological source activity was reconstructed and functional connectivity between pairs of sensors or brain regions was determined in different frequency bands. We generated undirected binary graphs and used intra-class correlation coefficient (ICC) to estimate reliability. We showed that reliabilities ranged from poor to good. Reliability at the sensor-level was significantly higher than source-level. The most reliable graph metric at the sensor-level was cost efficiency and at the source-level was global efficiency. At the sensor-level: WS reliability was significantly higher than BS reliability; high beta band in WS design had the highest reliability; in WS design reliability in gamma band was significantly lower than reliability in low and high beta bands. At the source-level: low beta band in BS design had the highest reliability; there was no significant main effect of frequency band on reliability; reliabilities of WS and BS designs were not significantly different. These results suggest that these graph metrics can provide reliable outcomes, depending on how the data were collected and analysed.
Evolutionary inference fromQST-FSTcomparisons: disentangling local adaptation from altitudinal gradient selection in snapdragon plants
Authors: Marin Sara , Archambeau Juliette , Bonhomme Vincent , Lascoste Mylène , Pujol Benoit
Published: August 2018

Phenotypic differentiation among natural populations can be explained by natural selection or by neutral processes such as drift. There are many examples in the literature where comparing the effects of these processes on multiple populations has allowed the detection of local adaptation. However, these studies rarely identify the agents of selection. Whether population adaptive divergence is caused by local features of the environment, or by the environmental demand emerging at a more global scale, for example along altitudinal gradients, is a question that remains poorly investigated. Here, we measured neutral genetic (FST) and quantitative genetic (QST) differentiation among 13 populations of snapdragon plants (Antirrhinum majus) in a common garden experiment. We found low but significant genetic differentiation at putatively neutral markers, which supports the hypothesis of either ongoing pervasive homogenisation via gene flow between diverged populations or reproductive isolation between disconnected populations. Our results also support the hypothesis of local adaptation involving phenological, morphological, reproductive and functional traits. They also showed that phenotypic differentiation increased with altitude for traits reflecting the reproduction and the phenology of plants, thereby confirming the role of such traits in their adaptation to environmental differences associated with altitude. Our approach allowed us to identify candidate traits for the adaptation to climate change in snapdragon plants. Our findings imply that environmental conditions changing with altitude, such as the climatic envelope, influenced the adaptation of multiple populations of snapdragon plants on the top of their adaptation to local environmental features. They also have implications for the study of adaptive evolution in structured populations because they highlight the need to disentangle the adaptation of plant populations to climate envelopes and altitude from the confounding effects of selective pressures acting specifically at the local scale of a population.
Analysis and Prediction of Unplanned Intensive Care Unit Readmission using Recurrent Neural Networks with Long Short-Term Memory
Authors: Lin Yu-Wei , Zhou Yuqian , Faghri Faraz , Shaw Michael J. , Campbell Roy H.
Published: August 2018

Background

Unplanned readmission of a hospitalized patient is an extremely undesirable outcome as the patient may have been exposed to additional risks. The rates of unplanned readmission are, therefore, regarded as an important performance indicator for the medical quality of a hospital and healthcare system. Identifying high-risk patients likely to suffer from readmission before release benefits both the patients and the medical providers. The emergence of machine learning to detect hidden patterns in complex, multi-dimensional datasets provides unparalleled opportunities to develop efficient discharge decision-making support system for physicians.

Methods and Findings

We used supervised machine learning approaches for ICU readmission prediction. We used machine learning methods on comprehensive, longitudinal clinical data from the MIMIC-III to predict the ICU readmission of patients within 30 days of their discharge. We have utilized recent machine learning techniques such as Recurrent Neural Networks (RNN) with Long Short-Term Memory (LSTM), by this we have been able incorporate the multivariate features of EHRs and capture sudden fluctuations in chart event features (e.g. glucose and heart rate) that are significant in time series with temporal dependencies, which cannot be properly captured by traditional static models, but can be captured by our proposed deep neural network based model. We incorporate multiple types of features including chart events, demographic, and ICD9 embeddings. Our machine learning models identifies ICU readmissions at a higher sensitivity rate (0.742) and an improved Area Under the Curve (0.791) compared with traditional methods. We also illustrate the importance of each portion of the features and different combinations of the models to verify the effectiveness of the proposed model.

Conclusion

Our manuscript highlights the ability of machine learning models to improve our ICU decision making accuracy, and is a real-world example of precision medicine in hospitals. These data-driven results enable clinicians to make assisted decisions within their patient cohorts. This knowledge could have immediate implications for hospitals by improving the detection of possible readmission. We anticipate that machine learning models will improve patient counseling, hospital administration, allocation of healthcare resources and ultimately individualized clinical care.
CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination
Authors: Perfetto L. , Acencio M.L. , Bradley G. , Cesareni G. , Toro N.Del , Fazekas D. , Hermjakob H. , Korcsmaros T. , Kuiper M. , Lægreid A. , Surdo P. Lo , Lovering R.C. , Orchard S. , Porras P. , Thomas PD. , Touré V. , Zobolas J. , Licata L.
Published: August 2018

Combining multiple layers of information underlying biological complexity into a structured framework, and in particular deciphering the molecular mechanisms behind cellular phenotypes, represent two challenges in systems biology. A key task is the formalisation of such information in models describing how biological entities interact to mediate the response to external and internal signals. Several databases with signaling information, such as SIGNOR, SignaLink and IntAct, focus on capturing, organising and displaying signaling interactions by representing them as binary, causal relationships between biological entities. The curation efforts that build these individual databases demand a concerted effort to ensure interoperability among resources, through the development of a standardized exchange format, ontologies and controlled vocabularies supporting the domain of causal interactions. Aware of the enormous benefits of standardization efforts in the molecular interaction research field, representatives of the signalling network community agreed to extend the PSI-MI controlled vocabulary to include additional terms representing aspects of causal interactions. Here, we present a common standard for the representation and dissemination of signaling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI tab-delimited format, now designated MITAB2.8. We define the new term “causal interaction”, and related child terms, which are children of the PSI-MI “molecular interaction” term. The new vocabulary terms in this extended PSI-MI format will enable systems biologists to model large-scale signaling networks more precisely and with higher coverage than before.
Combining 3D single molecule localization strategies for reproducible bioimaging
Authors: Cabriel Clément , Bourg Nicolas , Jouchet Pierre , Dupuis Guillaume , Leterrier Christophe , Baron Aurélie , Badet-Denisot Marie-Ange , Vauzeilles Boris , Fort Emmanuel , Lévêque-Fort Sandrine
Published: August 2018

We developed a 3D localization-based super-resolution technique providing a slowly varying localization precision over a 1 μm range with precisions down to 15 nm. The axial localization is performed through a combination of point spread function (PSF) shaping and supercritical angle fluorescence (SAF), which yields absolute axial information. Using a dual-view scheme, the axial detection is decoupled from the lateral detection and optimized independently to provide a weakly anisotropic 3D resolution over the imaging range. This method can be readily implemented on most homemade PSF shaping setups and provides drift-free, tilt-insensitive and achromatic results. Its insensitivity to these unavoidable experimental biases is especially adapted for multicolor 3D super-resolution microscopy, as we demonstrate by imaging cell cytoskeleton, living bacteria membranes and axon periodic submembrane scaffolds. We further illustrate the interest of the technique for biological multicolor imaging over a several-μm range by direct merging of multiple acquisitions at different depths.
How much fear is in anxiety?
Authors: Genewsky Andreas J. , Albrecht Nina , Bura Simona A. , Kaplick Paul M. , Heinz Daniel E. , Nußbaumer Markus , Engel Mareen , Grünecker Barbara , Kaltwasser Sebastian F. , Riebe Caitlin J. , Bedenk Benedikt T. , Czisch Michael , Wotjak Carsten T.
Published: August 2018

The selective breeding for extreme behavior on the elevated plus-maze (EPM) resulted in two mouse lines namely high-anxiety behaving (HAB) and low-anxiety behaving (LAB) mice. Using novel behavioral tests we demonstrate that HAB animals additionally exhibit maladaptive escape behavior and defensive vocalizations, whereas LAB mice show profound deficits in escaping from approaching threats which partially results from sensory deficits. We could relate these behavioral distortions to tonic changes in brain activity within the periaqueductal gray (PAG) in HAB mice and the superior colliculus (SC) in LAB mice, using in vivo manganese-enhanced MRI (MEMRI) followed by pharmacological or chemogenetic interventions. Therefore, midbrain-tectal structures govern the expression of both anxiety-like behavior and defensive responses. Our results challenge the uncritical use of the anthropomorphic termsanxietyoranxiety-likefor the description of mouse behavior, as they imply higher cognitive processes, which are not necessarily in place.
DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning
Authors: Ni Peng , Huang Neng , Luo Feng , Wang Jianxin
Published: August 2018

The Oxford Nanopore sequencing enables to directly detect methylation sites in DNA from reads without extra laboratory techniques. In this study, we develop DeepSignal, a deep learning method to detect DNA methylated sites from Nanopore sequencing reads. DeepSignal construct features from both raw electrical signals and signal sequences in Nanopore reads. Testing on Nanopore reads of pUC19, E. coli and human, we show that DeepSignal can achieve both higher read level and genome level accuracy on detecting 6mA and 5mC methylation comparing to previous HMM based methods. Moreover, DeepSignal achieves similar performance cross different methylation bases and different methylation motifs. Furthermore, DeepSignal can detect 5mC and 6mA methylation states of genome sites with above 90% genome level accuracy under just 5X coverage using controlled methylation data.
Altered microRNA expression profles are involved in Storage Lesions of Apheresis Platelet
Authors: Yuan Zhaohu , Wu Qianyu , Chen Xiaojie , Wei Yaming
Published: August 2018

Although platelet is anucleate cell, it contains a large amount miRNAs. This study aims to explore the relationship between miRNAs expression profles and platelets function, as well as miRNAs potential roles during platelet storage lesions. Platelets were collected from 15 healthy men with O blood types. MiRNAs profiles in platelets were detected by Agilent Human miRNA Array Differential miRNA levels were studied using human platelets after apheresis and stored for 2, 5 and 8 days using microarray. There were 167 and 230 altered miRNAs during the 5 and 8 day storage, respectively. In addition, the number of reduced miRNAs was much greater than that of increased. And many of them are involved in functions of platelet activation, degranulation, PDGF receptor signaling pathway and cell differentiation. The results of RT-PCR showed that the expression of miR-21-5p, miR-21-3p and miR-155 decreased on the 5th day, while miR-223, miR-3162 and let-7b increased. Flow cytometry results revealed that with increase of storage time, the expression of P2Y12 increased and phosphorylation level of VASP reduced. Meanwhile, the platelet reactivity index (PRI) decreased from 72.7% to 18.2%, while the apoptotic percentage of platelet significantly increased. For the first time, we found altered miRNAs are closely related to platelet aggregation, including P2Y12, VASP and GPⅡb/Ⅲa. Through KEGG database prediction, we verified there were many miRNAs impacting the pathway of platelet aggregation, such as miR-223, miR-21 and let-7b, which indicated miRNAs might serve as potential biomarkers of storage lesion in platelet. These target miRNAs are related to activation, degranulation and PDGF receptor signaling pathway of platelet.
Tb3Pd2, Er3Pd2 and Er6Co5–x
: structural variations and bonding in rare-earth-richer binary intermetallics
Authors: Bell Thomas , Celania Chris R. , Smetana Volodymyr , Mudring Anja-Verena , Meyer Gerd
Published: August 2018

The three binary Tb/Er-rich transition metal compounds Tb3Pd2 (triterbium dipalladium), Er3Pd2 (trierbium dipalladium) and Er6Co5–x
(hexaerbium pentacobalt) crystallize in the space groups Pbam (Pearson symbol oP20), P4/mbm (tP10) and P63/m (hP22), respectively. Single crystals of Tb3Pd2 and Er6Co5–x
suitable for X-ray structure analysis were obtained using rare-earth halides as a flux. Tb3Pd2 adopts its own structure type, which can be described as a superstructural derivative of the U3Si2 type, which is the type adopted by Er3Pd2. Compound Er6Co5–x
belongs to the Ce6Co2–x
Si3 family. All three compounds feature fused tricapped {TR
6} (R = rare-earth metal and T = transition metal) trigonal prismatic heterometallic clusters. R
3Pd2 is reported to crystallize in the U3Si2 type; however, our more detailed structure analysis reveals that deviations occur with heavier R elements. Similarly, Er6Co5–x
was assumed to be stoichiometric Er4Co3 = Er6Co4.5. Our studies reveal that it has a single defective transition-metal site leading to the composition Er6Co4.72(2). LMTO (linear muffin-tin orbital)-based electronic structure calculations suggest the strong domination of heteroatomic bonding in all three structures.
Supramolecular structures of rhenium(I) complexes mediated by ligand planarity via the interplay of substituents
Authors: Mark-Lee Wun Fui , Chong Yan Yi , Kassim Mohammad B.
Published: August 2018

The crystal and molecular structures of two ReI tricarbonyl complexes, namely fac-tricarbonylchlorido[1-(4-fluorocinnamoyl)-3-(pyridin-2-yl-κN)pyrazole-κN
2]rhenium(I), [ReCl(C17H12FN3O)(CO)3], (I), and fac-tricarbonylchlorido[1-(4-nitrocinnamoyl)-3-(pyridin-2-yl-κN)pyrazole-κN
2]rhenium(I) acetone monosolvate, [ReCl(C17H12ClN4O3)(CO)3]·C3H6O, (II), are reported. The complexes form centrosymmetric dimers that are linked into one-dimensional columns by C—H...Cl and N—O...H interactions in (I) and (II), respectively. C—H...Cl interactions in (II) generate two R
2
1(7) loops that merge into a single R
2
1(10) loop. These interactions involve the alkene, pyrazole and benzene rings, hence restricting the ligand rotation and giving rise to a planar conformation. Unlike (II), complex (I) exhibits a twisted conformation of the ligand and a pair of molecules forms a centrosymmetric dimer with an R
2
2(10) loop via C—H...O interactions. The unique supramolecular structures of (I) and (II) are determined by their planarity and weak interactions. The planar conformation of (II) provides a base for appreciable π–π stacking interactions compared to (I). In addition, an N—O...π interaction stabilizes the supramolecular structure of (II). We report herein the first n→π* interactions of ReI tricarbonyl complexes, which account for 0.33 kJ mol−1. Intermolecular C—H...Cl and C—H...O interactions are present in both complexes, with (II) showing a greater preference for these interactions compared to (I), with cumulative contributions of 48.7 and 41.5%, respectively. The influence of inductive (fluoro) and/or resonance (nitro) effects on the π-stacking ability was further supported by LOLIPOP (localized orbital locator-integrated π over plane) analysis. The benzene ring of (II) demonstrated a higher π-stacking ability compared to that of (I), which is supported by the intrinsic planar geometry. The HOMA (harmonic oscillator model of aromaticity) index of (I) revealed more aromaticity with respect to (II), suggesting that NO2 greatly perturbed the aromaticity. The Hirshfeld fingerprint (FP) plots revealed the preference of (II) over (I) for π–π contacts, with contributions of 6.8 and 4.4%, respectively.
Management accounting change in developing countries: evidence from Libya
Authors: Lasyoud Alhashmi Aboubaker , Haslam Jim , Roslender Robin
Published: August 2018

Purpose

The purpose of this paper is to investigate the change in management accounting and control systems (MACSs) within two large public manufacturing companies in Libya so-called Trucks and Buses Company (TBC) and National Trailers Company (NTC).

Design/methodology/approach

The paper is based on semi-structured interviews, an analysis of documents and observations. It draws on New Institutional Sociology (NIS) perspective (DiMaggio and Powell’s 1983) as theoretical framework to provide explanations regarding how the MACS in the two companies were shaped by various factors.

Findings

The main factors identified in shaping the operations of the MACS were the need to comply with the political pressures, the Libyan Government’s laws and regulations, the instructions imposed by the management committee in both companies, leading organizations’ pressures (ISO), customer satisfaction (coercive isomorphism), the influence of professional associations (normative isomorphism) and the need to imitate efficient organizations in order to be more legitimate and successful (mimetic isomorphism).

Research limitations/implications

The findings of the study have implications for understanding the operations of MACS in developing countries. Future research could focus on alternative theoretical perspectives for the investigation of the process of change in MACS such as structuration theory, agency theory and actor-network theory.

Originality/value

The proposed theoretical framework provides insights into the process of change by focusing on the interplay between the institutional forces, market forces and intra – organizational power relationships to overcome the criticism of NIS that it downplays the role of market forces and intra – organizational power relations.
Corporate social responsibility (CSR) practices by SIN firms
Authors: Sharma Zenu , Song Liang
Published: August 2018

Purpose

The purpose of this paper is to examine corporate social responsibility (CSR) practices of SIN firms. SIN firms are firms from controversial sectors such as tobacco, alcohol, gambling and firearms.

Design/methodology/approach

This paper explains contrasts CSR practices of SIN firms with similar size and industry non-SIN counterparts.

Findings

This paper shows that SIN firms conduct more CSR practices than non-SIN firms. This paper also finds that CSR practices of SIN firms are value relevant only when these firms are performing below their peers.

Originality/value

The motivation for SIN firms to engage in higher CSR is the competitive advantage hypothesis and not moral rebalancing.
Marginal abatement cost of agricultural carbon emissions in China: 1993-2015
Authors: Wu Xianrong , Zhang Junbiao , You Liangzhi
Published: August 2018

Purpose

The purpose of this paper is to estimate shadow prices of agricultural carbon emissions produced by agricultural inputs, rice paddy and burning crop residue, and to explore the impact of cropping pattern on marginal abatement cost (MAC).

Design/methodology/approach

The shadow price of agricultural carbon emissions is estimated by applying directional distance function and non-parametric methods.

Findings

The estimated shadow price of agricultural carbon emissions ranges from 6.78 to 557.83 yuan/ton, and the average value is 62.50 yuan/ton (or $10.18/ton). The MAC value varies in different provinces and years. The regional difference of MAC shows a decreasing trend during the investigation period. Cropping pattern shows a significant negative impact on agricultural MAC. A 1 percent decrease of rice proportion leads to a 0.31 percent increase in MAC value. This implies that the higher the proportion of rice is, the lower the economic cost to reduce agricultural carbon emissions would be.

Practical implications

It is feasible to draw up appropriate mechanisms for the allocation of emission reduction responsibilities according to conditions in various regions, with emphasis on the local cropping patterns. There is a trade-off between reducing carbon emission and increasing crop yields.

Originality/value

This study calculates agricultural MAC by using the shadow price approach, taking agricultural carbon emissions as undesired environmental output. The study also provides a reference emission right price and provides guidance to make use of cropping structure adjustment and optimization for exploring the emission reduction strategy.
Technology adoption among farmers in Jilin Province, China
Authors: Zheng Shi , Wang Zhigang , Wachenheim Cheryl Joy
Published: August 2018

Purpose

The purpose of this paper is to investigate factors influencing intent to adopt unmanned aerial vehicles for use in agricultural operations in Jilin Province, China.

Design/methodology/approach

This paper uses probit analysis to estimate the influence of factors on intent to adopt unmanned aerial vehicles for plant protection application operations in Jilin Province, China based on the Technology Acceptance Model.

Findings

UAV technology is acceptable to most participating farmers. Gender (male), agricultural income ratio, understanding of new technology, perceived ease-of-use and perceived usefulness have a positive relationship with farmers’ willingness to adopt UAVs.

Practical implications

For application, crop monitoring and other farm operations, UAVs have clear advantages. There remain challenges associated with the development of applicable technology and facilitating adoption among farmers. Understanding factors affecting adoption will contribute to the latter, and brings forth the following recommendations: conduct research on the cost effectiveness of UAVs for agriculture; accelerate development of the information service system; and increase financial support.

Originality/value

This paper is among the first to consider adoption intent among Chinese farmers of use of UAVs for agricultural operations.