bluuebunny/crossref_metadata_2025 huggingface dataset:
Multimodal Metaphor and Metonymy in Advertising
Authors: Pérez Sobrino Paula
Published: July 2017

Metaphor and metonymy appeal to us because they evoke mental images in unique but still recognisable ways. The potential for figurative thought exists in everyone, and it pervades our everyday social interactions. In particular, advertising offers countless opportunities to explore the way in which people think creatively through metaphor and metonymy. The thorough analysis of a corpus of 210 authentic printed advertisements shows the central role of multimodal metaphor, metonymy, and their patterns of interaction, at the heart of advertising campaigns. This book is the first in-depth research monograph to bring together qualitative and quantitative evidence of metaphor-metonymy combinations in real multimodal discourse. It combines detailed case study analyses with corpus-based analysis and psycholinguistic enquiry to provide the reader with a prismatic approach to the topic of figurative language in multimodal advertising. Besides its theoretical contribution to the field of multimodal figurative language, this monograph has a wide number of practical applications due to its focus on advertising and the communicative impact of creative messages on consumers. This book will pave the way for further qualitative and quantitative research on the ways in which figurative language shapes multimodal discourse, and how it relates to our everyday creative thinking.
Negative scope, temporality, fixedness, and right- and left-branching
Authors: Ono Tsuyoshi , Thompson Sandra
Published: July 2017

‘Negative scope’ concerns what it is that is negated in an utterance with a negative morpheme. With English and Japanese conversational data, we show that for an English speaker, calculating negative scope requires that recipients incrementally keep track of all the material in the clause that follows the negative morpheme, which comes early in the clause. In contrast, the negative morpheme comes late in the clause in Japanese; thus it would seem that recipients need to hold in memory all the material in the clause preceding the negative until the negative morpheme is produced. Several features of Japanese grammar, however, suggest that this characterization is not accurate. We argue that prosody, grammar, cognition, processing, and fixedness all interact with the grammar of clause organization to afford quite different real-time processing strategies for calculating the assignment of negative scope in languages with different ‘word order’ norms.
Agreement with the internal possessor in Chimane*
Authors: Ritchie Sandy
Published: July 2017

The paper examines a type of clausal construction in Chimane (or Tsimane’, unclassified, Bolivia) in which possessors which are apparently internal to patient- or recipient-like possessive phrases can control object agreement on the verb. Various aspects of the construction point to an analysis in which the internal possessor is doubled by an external representation or ‘proxy’ in the clause which mediates the agreement relation between the possessor and the verb. The construction bears some resemblance to external possessor constructions, albeit with the added complication that the possessor itself remains internal to the possessive phrase while its argument function is borne by the external proxy. The paper examines features of the construction and contrasts it with similar or related phenomena which have been identified in other languages.
Production of a novel wheat gluten hydrolysate containing dipeptidyl peptidase-IV inhibitory tripeptides using ginger protease
Authors: Taga Yuki , Hayashida Osamu , Kusubata Masashi , Ogawa-Goto Kiyoko , Hattori Shunji
Published: July 2017

Wheat gluten is a Pro-rich protein complex comprising glutenins and gliadins. Previous studies have reported that oral intake of enzymatic hydrolysates of gluten has beneficial effects, such as suppression of muscle injury and improvement of hepatitis. Here, we utilized ginger protease that preferentially cleaves peptide bonds with Pro at the P2 position to produce a novel type of wheat gluten hydrolysate. Ginger protease efficiently hydrolyzed gluten, particularly under weak acidic conditions, to peptides with an average molecular weight of <600 Da. In addition, the gluten hydrolysate contained substantial amounts of tripeptides, including Gln-Pro-Gln, Gln-Pro-Gly, Gln-Pro-Phe, Leu-Pro-Gln, and Ser-Pro-Gln (e.g. 40.7 mg/g at pH 5.2). These gluten-derived tripeptides showed high inhibitory activity on dipeptidyl peptidase-IV with IC50 values of 79.8, 70.9, 71.7, 56.7, and 78.9 μM, respectively, suggesting that the novel gluten hydrolysate prepared using ginger protease can be used as a functional food for patients with type 2 diabetes.
ISEScan: automated identification of insertion sequence elements in prokaryotic genomes
Authors: Xie Zhiqun , Tang Haixu
Published: July 2017

Motivation

The insertion sequence (IS) elements are the smallest but most abundant autonomous transposable elements in prokaryotic genomes, which play a key role in prokaryotic genome organization and evolution. With the fast growing genomic data, it is becoming increasingly critical for biology researchers to be able to accurately and automatically annotate ISs in prokaryotic genome sequences. The available automatic IS annotation systems are either providing only incomplete IS annotation or relying on the availability of existing genome annotations. Here, we present a new IS elements annotation pipeline to address these issues.

Results

ISEScan is a highly sensitive software pipeline based on profile hidden Markov models constructed from manually curated IS elements. ISEScan performs better than existing IS annotation systems when tested on prokaryotic genomes with curated annotations of IS elements. Applying it to 2784 prokaryotic genomes, we report the global distribution of IS families across taxonomic clades in Archaea and Bacteria.

Availability and implementation

ISEScan is implemented in Python and released as an open source software at https://github.com/xiezhq/ISEScan.

Supplementary information

Supplementary data are available at Bioinformatics online.
nandb—number and brightness in R with a novel automatic detrending algorithm
Authors: Nolan Rory , Alvarez Luis A J , Elegheert Jonathan , Iliopoulou Maro , Jakobsdottir G Maria , Rodriguez-Muñoz Marina , Aricescu A Radu , Padilla-Parra Sergi
Published: July 2017

An R package for performing number and brightness image analysis, with the implementation of a novel automatic detrending algorithm.

Availability and implementation

Available at https://github.com/rorynolan/nandb for all platforms.

Contact

rnolan@well.ox.ac.uk or spadilla@well.ox.ac.uk

Supplementary information

Supplementary data are available at Bioinformatics online.
powsimR: power analysis for bulk and single cell RNA-seq experiments
Authors: Vieth Beate , Ziegenhain Christoph , Parekh Swati , Enard Wolfgang , Hellmann Ines
Published: July 2017

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

Availability and implementation

The R package and associated tutorial are freely available at https://github.com/bvieth/powsimR.

Supplementary information

Supplementary data are available at Bioinformatics online.
Defending the IASP Definition of Pain
Authors: Aydede Murat
Published: July 2017

The official definition of ‘pain’ by the International Association for the Study of Pain (IASP) hasn’t seen much revision since its publication in 1979. There have been various criticisms of the definition in the literature from different quarters. In my view, most of these criticisms depend on misunderstandings or on uncharitable interpretations. My aim is to go over the definition, clarify some potential ambiguities, and argue that these criticisms don’t cut much ice. At the end, I will present a few slightly reworded versions of the definition that I claim are more felicitous and capture the original intended meaning by the members of the taxonomic committee in a much better and transparent way that avoids all the major extant criticisms in the literature.
A National Longitudinal Survey of Medical Students’ Intentions to Practice Among the Underserved
Authors: O’Connell Thomas F. , Ham Sandra A. , Hart Theodore G. , Curlin Farr A. , Yoon John D.
Published: July 2017

Purpose

To explore students’ intentions to practice in medically underserved areas.

Method

In January 2011, 960 third-year medical students from 24 MD-granting U.S. medical schools were invited to participate in a survey on their intention to practice in a medically underserved area. A follow-up survey was sent to participants in September 2011. Covariates included student demographics, medical school characteristics, environmental exposures, work experiences, sense of calling, and religious characteristics.

Results

Adjusted response rates were 564/919 (61.4%, first survey) and 474/564 (84.0%, follow-up survey). Among fourth-year medical students, an estimated 34.3% had an intention to practice among the underserved. In multivariate logistic regression modeling, predictors for intentions to practice among the underserved included growing up in an underserved setting (odds ratio [OR] range: 2.96–4.81), very strong sense of calling (OR range: 1.86–3.89), and high medical school social mission score (in fourth year: OR = 2.34 [95% confidence interval (CI), 1.31–4.21]). International experience was associated with favorable change of mind in the fourth year (OR = 2.86 [95% CI, 1.13–7.24]). High intrinsic religiosity was associated with intentions to practice primary care in underserved settings (in fourth year: OR = 2.29 [95% CI = 1.13–4.64]).

Conclusions

Growing up in medically underserved settings, work experience in religiously affiliated organizations, very strong sense of calling, and high medical school social mission score were associated with intentions to practice in underserved areas. Lack of formative educational experiences may dissuade students from considering underserved practice.
Cantonese Tone Perception for Children Who Use a Hearing Aid and a Cochlear Implant in Opposite Ears
Authors: Mok Mansze , Holt Colleen M. , Lee Kathy Y. S. , Dowell Richard C. , Vogel Adam P.
Published: July 2017

Objectives:

The ability to recognize tones is vital for speech perception in tonal languages. Cantonese has six tones, which are differentiated almost exclusively by pitch cues (tones 1 to 6). The differences in pitch contours among the tones are subtle, making Cantonese a challenging language for cochlear implant users. The addition of a hearing aid has been shown to improve speech perception in nontonal languages and in Mandarin Chinese. This study (1) investigates the Cantonese tone perception ability of children who use a cochlear implant and a hearing aid in opposite ears; (2) evaluates the effect of varying pitch height and pitch contour cues on Cantonese tone perception for these children; and (3) compares the Cantonese tone perception ability for using a hearing aid and a cochlear implant together versus an implant alone.

Design:

Eight native Cantonese speaking children using a cochlear implant and a hearing aid in opposite ears were assessed for tone perception and word identification. The tone perception test involved discriminating and ranking tone pairs from natural and artificially manipulated Cantonese tones with various pitch heights and/or pitch contours. The word identification test involved identifying Cantonese words in a four-alternative forced-choice task. All tests were performed in two device conditions: (1) cochlear implant and hearing aid together and (2) implant alone.

Results:

Seven of the 8 subjects performed significantly above chance in both tests using the cochlear implant alone. Results showed that both pitch height and/or pitch direction were important perceptual cues for implant users. Perception for some tones was improved by increasing the pitch height differences between the tones. The ability to discriminate and rank the tone 2/tone 5 contrast and the tone 4/tone 6 contrast was poor, as the tones in these contrasts are similar in pitch contours and onset frequencies. No significant improvement was observed after artificially increasing the pitch offset differences between the tones in the tone 2/tone 5 and the tone 4/tone 6 contrasts. Tone perception results were significantly better with the addition of the hearing aid in the nonimplanted ear compared with using the implant alone; however, word identification results were not significantly different between using the implant alone and using both the hearing aid and the implant together. None of the subjects performed worse in tone perception or in word identification when the hearing aid was added.

Conclusions:

Reduced ability to perceive pitch contour cues, even when artificially exaggerated, may explain some of the difficulties in Cantonese word recognition for implant users. The addition of a contralateral hearing aid could be beneficial for Cantonese tone perception for some individuals with a unilateral implant. The results encouraged Cantonese speakers to trial a hearing aid in the nonimplanted ear when using a cochlear implant.
High-Frequency Distortion-Product Otoacoustic Emission Repeatability in a Patient Population
Authors: Dreisbach Laura , Zettner Erika , Chang Liu Margaret , Meuel Fernhoff Caitlin , MacPhee Imola , Boothroyd Arthur
Published: July 2017

Objectives:

Distortion-product otoacoustic emissions (DPOAEs) are repeatable over time at lower frequencies (≤8 kHz) and higher frequencies (>8 kHz) in healthy, normal-hearing subjects. The purpose of this study was to examine the repeatability of DPOAEs measured with high-frequency (HF) stimuli in a patient population. It was hypothesized that HF DPOAEs would be repeatable over four trials.

Design:

DPOAEs were measured in 40 cystic fibrosis (CF) patients (17 females and 23 males) with measurable behavioral thresholds and present DPOAEs for at least 2 of the high frequencies tested (8 to 16 kHz). A depth-compensated simulator sound pressure level (SPL) method of calibration was utilized. Each patient attended four trials, in which a complete set of data were collected. At each trial, three different DPOAE paradigms were completed. First, a discrete frequency sweep was measured between 8 and 16 kHz with a ratio (f
2/f
1) of 1.2 and levels of 65/50 dB SPL for L
1/L
2. Next, ratio and level sweeps were obtained at the two highest frequencies with a present DPOAE determined from the discrete frequency sweep, and the results were used to calculate DPOAE group delay and DPOAE detection thresholds, respectively. Ratio sweeps were collected with f
2/f
1 varied from 1.1 to 1.3 and stimulus levels of 60/45 dB SPL (L
1/L
2). Level sweeps were collected with an f
2/f
1 of 1.22 and L
2 = 50 and L
1 varied between 20 and 70 dB SPL. Differences and correlations between trials, SE of the measurement, and confidence intervals were calculated, as well as a repeated-measures analysis of variance.

Results:

DPOAE response and behavioral threshold variability in CF patients were not significantly different across four trials. It can be expected in 95% of CF patients that differences between trials of DPOAE levels, group delay, and detection thresholds and behavioral thresholds are less than 6.26 dB, 0.87 msec, 9.34 dB, and 9.60 dB, respectively.

Conclusions:

HF DPOAEs were repeatable across four test trials for all three paradigms measured in a group of CF patients. These results are encouraging for the measurement of HF DPOAEs to be monitored in those exposed to ototoxic agents.
Immunotherapy-based combinations: current status and perspectives
Authors: de Miguel-Luken María J. , Mansinho André , Boni Valentina , Calvo Emiliano
Published: July 2017

Purpose of review

Since the approval of ipilimumab, different immune checkpoint inhibitors, vaccines and costimulatory agonists have been developed with success, improving patient's survival in a number of different tumour types. However, immunotherapy results in durable responses but only in a fraction of patients. In order to improve this, combination of different immune agents is currently being attempted in the clinic with the potential of becoming one day the next wave of immune treatments available for our cancer patients.

Recent findings

Combinatory regimens may have synergistic effects by acting at different points of the cancer immune cycle, from initiation and propagation of anticancer immunity, to stimulation of neoantigen presentation and priming, promotion of trafficking of immune cells to access the tumour and, finally, cancer-cell recognition and killing.

In this article, the most relevant combination strategies that are currently under research are reviewed, as they are expected to become a new standard of care in the near future.
Height and risk of colorectal cancer: a meta-analysis
Authors: Song Xinyuan , Gong Xiuzhen , Zhang Tong , Jiang Wenjie
Published: July 2017

Several epidemiological studies have investigated the relationship between height and risk of colorectal cancer (CRC), but the results were inconsistent. Thus, a meta-analysis of observational studies was carried out to clarify this association. A literature search was performed in PubMed and Web of Science databases for all relevant studies up to 25 May 2016. The random-effects model was used to calculate the pooled relative risks (RRs) and restricted cubic spline model was adopted for the dose–response analysis. A total of 31 studies involving 13 077 848 participants with 93 818 cases were included. The pooled RR (95% confidence interval) of CRC for the highest versus the lowest category of height was 1.25 (1.18–1.32); the pooled RR was 1.32 (1.22–1.43) for colon cancer and 1.12 (1.05–1.19) for rectal cancer for the highest versus the lowest category of height. A nonlinear relationship was found between height and the risk of CRC in the dose–response analysis (P
nonlinearity=0.0024). This meta-analysis indicates that height is associated with an increased risk of CRC.
Is there an association between trends in alcohol consumption and cancer mortality? Findings from a multicountry analysis
Authors: Schwartz Naomi , Nishri Diane , Chin Cheong Sandrene , Giesbrecht Norman , Klein-Geltink Julie
Published: July 2017

The aim of this analysis is to examine long-term trends in alcohol consumption and associations with lagged data on specific types of cancer mortality, and indicate policy implications. Data on per capita annual sales of pure alcohol; mortality for three alcohol-related cancers – larynx, esophageal, and lip, oral cavity, and pharynx; and per capita consumption of tobacco products were extracted at the country level. The Unobservable Components Model was used for this time-series analysis to examine the temporal association between alcohol consumption and cancer mortality, using lagged data, from 17 countries. Statistically significant associations were observed between alcohol sales and cancer mortality, in the majority of countries examined, which remained after controlling for tobacco use (P<0.05). Significant associations were observed in countries with increasing, decreasing, or stable trends in alcohol consumption and corresponding lagged trends in alcohol-related cancer mortality. Curtailing overall consumption has potential benefits in reducing a number of harms from alcohol, including cancer mortality. Future research and surveillance are needed to investigate, monitor, and quantify the impact of alcohol control policies on trends in cancer mortality.
Coagulation Profile Is Not a Predictor of Acute Cerebrovascular Events in Pediatric Extracorporeal Membrane Oxygenation Patients
Authors: Anton-Martin Pilar , Journeycake Janna , Modem Vinai , Golla Sailaja , Raman Lakshmi , Tweed Jefferson , Darnell-Bowens Cindy
Published: July 2017

We performed a retrospective matched case–control study evaluating whether the traditional coagulation profile predicts cerebrovascular events in children on extracorporeal membrane oxygenation (ECMO) in a 71 bed intensive care unit at a tertiary children’s hospital. Between 2009 and 2014, 241 neonates and children were initiated on ECMO. The cumulative 5 year incidence of intracranial hemorrhage and infarct was 9.2% and 7.9%, respectively. Thirty-six cases were individually matched 1:1 with control subjects based on age, primary diagnosis, ECMO type, cannulation site, and the presence of pre-ECMO coagulopathy. In-hospital mortality was higher among the cases compared with control subjects (78 vs. 22%, p < 0.01). The median laboratory values that assisted with heparin anticoagulation monitoring (activated clotting time, partial thromboplastin time, and antifactor Xa) and the laboratory data that assisted with blood product administration (platelet count, prothrombin time, fibrinogen, and d-dimer) during the 24 and 72 hour periods before the cerebrovascular event did not show any significant difference between the hemorrhage group and their controls or between the infarct group and their controls. The traditional coagulation profile did not predict acute cerebrovascular events in our cohort. Other markers of neurologic injury on ECMO are yet to be elucidated. Prospective studies to determine better predictors of cerebrovascular complications in pediatric ECMO patients are required.
Current use of MRI in patients with liver metastatic colorectal cancer: a population-based study
Authors: Pech Laurianne , Cercueil Jean-Pierre , Jooste Valérie , Krause Denis , Facy Olivier , Bouvier Anne-Marie
Published: July 2017

Background

Liver MRI is recommended as the preoperative imaging strategy in liver metastatic colorectal cancers.

Objective

The aim of the study was to assess for the first time the use of liver MRI in a French population-based cancer registry.

Patients and methods

All liver-only metastatic colorectal cancers resected for their primary tumour diagnosed between 2009 and 2013 were included. Nonconditional logistic regression was used to search for associations between the MRI order and the characteristics of patients and tumours.

Results

The primary tumour and liver metastases were resected for cure in 30% (69/233) of cases, and in 72% of these liver MRI was performed before resection of the liver metastases. Preoperative MRI ordering was not significantly higher in patients younger than 70 years when compared with that in older patients. Among patients who did not undergo resection of their liver metastasis, 22% had undergone a liver MRI. After adjustment for comorbidities, the probability of having undergone an MRI was higher for patients managed in the university hospital (P=0.004) and lower in those managed in nonuniversity hospitals (P=0.002) compared with the mean of odds for all facilities. Patients more than or equal to 70 years were 2.4 times less likely than younger patients to undergo an MRI (P=0.043).

Conclusion

Liver MRI was underused in patients with colorectal liver-only synchronous metastasis undergoing curative resection for metastases and in elderly patients.
Pediatric Minoxidil Exposures Reported to Texas Poison Centers
Authors: Forrester Mathias B.
Published: July 2017

Objectives

It has been suggested that ingestion of even small amounts of minoxidil by young children may result in serious adverse effects. The intent of this study was to describe pediatric minoxidil exposures reported to a statewide poison center system.

Methods

Cases were minoxidil exposures among patients 5 years or younger reported to Texas poison centers during 2000 to 2014. The distribution by various demographic and clinical factors was determined.

Results

Of 125 total cases, 58% were male and 78% aged 1 to 2 years. Ingestion alone was reported in 92% of the exposures. Ninety-eight percent of the exposures were unintentional, and 94% occurred at the patient's own residence. Sixty-two percent of the patients were managed on site. The outcome was not serious (no effect, minor effect, not followed [nontoxic], not followed [minimal effects]) in 88% of the exposures. The most common adverse effect was vomiting, reported in 8% of the exposures. The most common treatments were dilution/irrigation/wash (53%), activated charcoal (18%), food/snack (17%), and intravenous fluids (8%).

Conclusions

Few pediatric minoxidil exposures were reported to Texas poison centers. Of these exposures, most involved ingestion, were unintentional, and involved patients who were male and aged 1 to 2 years. Although it has been suggested that pediatric minoxidil ingestions might result in serious adverse effects, this study suggests that most pediatric minoxidil exposures reported to poison centers are not likely to have serious outcomes and may be managed at home.
A Case of Lenticulostriate Stroke Due to Minor Closed Head Injury in a 2-Year-Old Child
Authors: Fidan Emin , Cummings Dana D. , Manole Mioara D.
Published: July 2017

Objective

Cerebral infarction due to minor head injury is rare. Mineralizing angiopathy is considered a predisposing factor for lenticulostriate stroke after minor closed head injury. This entity is characterized by infarction of the basal ganglia and most often occurs in young children, from infancy to 2 years of age. Symptoms usually occur immediately after the injury.

Methods and Results

We present the case of a previously healthy 2-year-old female child presenting with right facial hemiparesis and aphasia, along with right arm and leg weakness that occurred immediately after a fall from the couch onto a carpeted floor. A brain computed tomography scan revealed small and linear calcifications of the basal ganglia and subcortical frontoparietal area, in the absence of signs of intracranial hemorrhage. Brain magnetic resonance imaging with stroke protocol revealed restriction of water diffusion in the left basal ganglia on diffusion-weighted imaging sequences as well as apparent diffusion coefficient sequences, suggesting an acute infarct of the left basal ganglia within the distribution of the lenticulostriate vessels. The patient was treated with aspirin and conservative management and had gradual improvement over the next few days, with full recovery of the aphasia, facial nerve function, and arm and leg mobility, within 2 months.

Conclusions

Some infants can present with the onset of stroke-like symptoms after minor head injuries. Presence of linear calcifications of the basal ganglia noticed on brain computed tomography in many of these patients suggests that mineralizing angiopathy may be a predisposing factor for lenticulostriate stroke after minor closed head injury in infants. Brain magnetic resonance imaging to further delineate possible cerebral infarction is indicated.
Burn Trauma Acutely Increases the Respiratory Capacity and Function of Liver Mitochondria
Authors: Bohanon Fredrick J. , Nunez Lopez Omar , Herndon David N. , Wang Xiaofu , Bhattarai Nisha , Ayadi Amina E. , Prasai Anesh , Jay Jayson W. , Rojas-Khalil Yesenia , Toliver-Kinsky Tracy E. , Finnerty Celeste C. , Radhakrishnan Ravi S. , Porter Craig
Published: July 2017

Background:

A complete understanding of the role of the liver in burn-induced hypermetabolism is lacking. We investigated the acute effect of severe burn trauma on liver mitochondrial respiratory capacity and coupling control as well as the signaling events underlying these alterations.

Methods:

Male BALB/c mice (8–12 weeks) received full-thickness scald burns on ∼30% of the body surface. Liver tissue was harvested 24 h postinjury. Mitochondrial respiration was determined by high-resolution respirometry. Citrate synthase activity was determined as a proxy of mitochondrial density. Male Sprague-Dawley rats received full-thickness scald burns to ∼60% of the body surface. Serum was collected 24 h postinjury. HepG2 cells were cultured with serum-enriched media from either sham- or burn-treated rats. Protein levels were analyzed via western blot.

Results:

Mass-specific (P = 0.01) and mitochondrial-specific (P = 0.01) respiration coupled to ATP production significantly increased in the liver after burn. The respiratory control ratio for ADP (P = 0.04) and the mitochondrial flux control ratio (P = 0.03) were elevated in the liver of burned animals. Complex III and Complex IV protein abundance in the liver increased after burn by 17% and 14%, respectively. Exposure of HepG2 cells to serum from burned rats increased the pAMPKα:AMPKα ratio (P < 0.001) and levels of SIRT1 (P = 0.01), Nrf2 (P < 0.001), and PGC1α (P = 0.02).

Conclusions:

Severe burn trauma augments respiratory capacity and function of liver mitochondria, adaptations that augment ATP production. This response may be mediated by systemic factors that activate signaling proteins responsible for regulating cellular energy metabolism and mitochondrial biogenesis.
Chronic Critical Illness and Persistent Inflammation: What can we Learn from the Elderly, Injured, Septic, and Malnourished?
Authors: Nomellini Vanessa , Kaplan Lewis J. , Sims Carrie A. , Caldwell Charles C.
Published: July 2017

Patients in the intensive care unit (ICU) who develop chronic critical illness significantly stress the clinical capacity and financial resources of healthcare systems. Although vast improvements have been made in critical care management, outcomes for this ICU subset remain poor. A hallmark for patients who progress to chronic critical illness is the development of persistent inflammation and immunosuppression. The risk factors associated with the development of chronic critical illness include increased age, medical comorbidities, severe injury, septic shock, and malnutrition. Interestingly, each of these clinical states bears strikingly similar immune defects, often resulting in the activation of a persistent inflammatory state. Strategies aimed at the prevention or early recognition of this state of immune compromise may help improve outcomes for these individuals and minimize the number who progress to chronic critical illness. This review explores the current knowledge regarding the immune defects associated with the development of persistent inflammation, the ways in which it can manifest clinically, attempted therapeutic interventions to date, and future insights into improving outcomes for this patient population.
Dynamic modulation of sociality and aggression: an examination of plasticity within endocrine and neuroendocrine systems
Authors: Kelly Aubrey M. , Vitousek Maren N.
Published: July 2017

Endocrine and neuroendocrine systems are key mediators of behavioural plasticity and allow for the ability to shift social behaviour across dynamic contexts. These systems operate across timescales, modulating both rapid responses to environmental changes and developmental plasticity in behavioural phenotypes. Thus, not only do endocrine systems mediate behavioural plasticity, but also the systems themselves exhibit plasticity in functional capabilities. This flexibility at both the mechanistic and behavioural levels can be crucial for reproduction and survival. Here, we discuss how plasticity in nonapeptide and steroid actions may influence the expression of, and allow rapid shifts between, sociality and aggression—behavioural shifts that can be particularly important for social interactions. Recent findings of overlap in the mechanisms that modulate social and aggressive behaviour suggest the potential for a mechanistic continuum between these behaviours. We briefly discuss the potential for a sociality–aggression continuum and novel techniques that will enable probing of the functional connectivity of social behaviours. From an evolutionary perspective, we suggest that plasticity in endocrine and neuroendocrine mechanisms of behaviour may be important targets of selection, and discuss the conditions under which we would predict selection to have resulted in differences in endocrine plasticity across species that differ in social organization.

This article is part of the themed issue ‘Physiological determinants of social behaviour in animals’.
Why are there so many explanations for primate brain evolution?
Authors: Dunbar R. I. M. , Shultz Susanne
Published: July 2017

The question as to why primates have evolved unusually large brains has received much attention, with many alternative proposals all supported by evidence. We review the main hypotheses, the assumptions they make and the evidence for and against them. Taking as our starting point the fact that every hypothesis has sound empirical evidence to support it, we argue that the hypotheses are best interpreted in terms of a framework of evolutionary causes (selection factors), consequences (evolutionary windows of opportunity) and constraints (usually physiological limitations requiring resolution if large brains are to evolve). Explanations for brain evolution in birds and mammals generally, and primates in particular, have to be seen against the backdrop of the challenges involved with the evolution of coordinated, cohesive, bonded social groups that require novel social behaviours for their resolution, together with the specialized cognition and neural substrates that underpin this. A crucial, but frequently overlooked, issue is that fact that the evolution of large brains required energetic, physiological and time budget constraints to be overcome. In some cases, this was reflected in the evolution of ‘smart foraging’ and technical intelligence, but in many cases required the evolution of behavioural competences (such as coalition formation) that required novel cognitive skills. These may all have been supported by a domain-general form of cognition that can be used in many different contexts.

This article is part of the themed issue ‘Physiological determinants of social behaviour in animals’.
Synchronization of Hes1 oscillations coordinate and refine condensation formation and patterning of the avian limb skeleton
Authors: Bhat Ramray , Glimm Tilmann , Linde-Medina Marta , Cui Cheng , Newman Stuart A.
Published: July 2017

The tetrapod appendicular skeleton is initiated as spatially patterned mesenchymal condensations. The size and spacing of these condensations in avian limb buds are mediated by a reaction-diffusion-adhesion network consisting of galectins Gal-1A, Gal-8 and their cell surface receptors. In cell cultures, the appearance of condensations is synchronized across distances greater than the characteristic wavelength of their spatial pattern. We explored the possible role of observed oscillations of the transcriptional co-regulator Hes1 in this phenomenon. Treatment of micromass cultures with DAPT, a γ-secretase inhibitor, damped Hes1 oscillations, elevated Gal-1A and -8 mRNA levels, and led to irregularly-sized and fused condensations. In developing limb buds, DAPT led to spatially non-uniform Hes1 expression and fused and misshapen digits. Periodicity in adhesive response to Gal-1A, a plausible Hes1-dependent function, was added to a previously tested mathematical model for condensation patterning by the two-galectin network. The enhanced model predicted regularization of patterning due to synchronization of Hes1 oscillations and resulting spatiotemporal coordination of its expression. The model also predicted changes in galectin expression and patterning in response to suppression of Hes1 expression, which were confirmed in in vitro experiments. Our results indicate that the two-galectin patterning network is regulated by Hes1 dynamics, the synchronization of which refines and regularizes limb skeletogenesis.
Reliability of fMRI time series: Similarity of neural processing during movie viewing
Authors: Schmälzle Ralf , Imhof Martin A. , Grall Clare , Flaisch Tobias , Schupp Harald T.
Published: July 2017

Despite its widespread use in neuroscience, the reliability of fMRI remains insufficiently understood. One powerful way to tap into aspects of fMRI reliability is via the inter-subject correlation (ISC) approach, which exposes different viewers to the same time-locked naturalistic stimulus and assesses the similarity of neural time series. Here we examined the correlations of fMRI time series from 24 participants who watched the same movie clips across three repetitions. This enabled us to examine inter-subject correlations, intra-subject correlations, and correlations between aggregated time series, which we link to the notions of inter-rater reliability, stability, and consistency. In primary visual cortex we found average pairwise inter-subject correlations of aboutr= 0.3, and intra-subject correlations of similar magnitude. Aggregation across subjects increased inter-subject (inter-group) correlations tor= 0.87, and additional intra-subject averaging before cross-subject aggregation yielded correlations ofr= 0.93. Computing the same analyses for parietal (visuospatial network) and cingulate cortices (saliency network) revealed a gradient of decreasing ISC from primary visual to higher visual to post-perceptual regions. These latter regions also benefitted most from the increased reliability due to aggregation. We discuss theoretical and practical implications of this link between neural process similarity and psychometric conceptions of inter-rater reliability, stability, and internal consistency.
PHASIS: A computational suite forde novodiscovery and characterization of phased, siRNA-generating loci and their miRNA triggers
Authors: Kakrana Atul , Li Pingchuan , Patel Parth , Hammond Reza , Anand Deepti , Mathioni Sandra M. , Meyers Blake C.
Published: July 2017

Phased, secondary siRNAs (phasiRNAs) are found widely in plants, from protein-coding transcripts and long, non-coding RNAs; animal piRNAs are also phased. Integrated methods characterizing“PHAS”loci are unavailable, and existing methods are quite limited and inefficient in handling large volumes of sequencing data. ThePHASISsuite described here provides complete tools for the computational characterization ofPHASloci, with an emphasis on plants, in which these loci are numerous. Benchmarked comparisons demonstrate thatPHASISis sensitive, highly scalable and fast. Importantly,PHASISeliminates the requirement of a sequenced genome and PARE/degradome data for discovery of phasiRNAs and their miRNA triggers.
Light-dependent decomposition of FICZ, an endogenous ligand of the aryl hydrocarbon receptor
Authors: Zhang Cunyu , Creech Katrina L. , Zuercher William J. , Willson Timothy M.
Published: July 2017

An efficient and scalable synthesis of 6-formylindolo[3,2-b]carbazole (FICZ) has been developed to provide large quantities of this physiologically important ligand of the aryl hydrocarbon receptor. Photo-decomposition of FICZ revealed a new non-enzymatic light-assisted mechanism for its conversion to a biologically less active quinone. The light-dependent synthesis and decomposition of FICZ makes it a candidate hormone to link sun exposure to regulation of biological pathways in peripheral tissues.
The first near-complete assembly of the hexaploid bread wheat genome,Triticum aestivum
Authors: Zimin Aleksey V. , Puiu Daniela , Hall Richard , Kingan Sarah , Clavijo Bernardo J. , Salzberg Steven L.
Published: July 2017

Common bread wheat,Triticum aestivum, has one of the most complex genomes known to science, with 6 copies of each chromosome, enormous numbers of near-identical sequences scattered throughout, and an overall size of more than 15 billion bases. Multiple past attempts to assemble the genome have failed. Here we report the first successful assembly ofT. aestivum, using deep sequencing coverage from a combination of short Illumina reads and very long Pacific Biosciences reads. The final assembly contains 15,344,693,583 bases and has a weighted average (N50) contig size of of 232,659 bases. This represents by far the most complete and contiguous assembly of the wheat genome to date, providing a strong foundation for future genetic studies of this important food crop. We also report how we used the recently published genome ofAegilops tauschii, the diploid ancestor of the wheat D genome, to identify 4,179,762,575 bp ofT. aestivumthat correspond to its D genome components.
Affiliative social relationships and coccidian oocyst excretion in a cooperatively breeding bird species
Authors: Wascher Claudia A.F. , Canestrari Daniela , Baglione Vittorio
Published: July 2017

In group living animals, behavioural interactions with conspecifics strongly modulate an individual’s physiological stress response. Stable social relationships may reduce an individual’s stress response, which in turn can affect the immune system and health. Ultimately, positive health effects of stable social bonds may contribute to maintain group living. We investigated whether, in cooperatively breeding carrion crows (Corvus corone), the quality of social relationships correlates with coccidian oocyst and nematode eggs excretion. We repeatably collected behavioural data on dyadic social interactions and individual droppings to quantify parasite eggs and oocysts from 36 individuals in a captive population of carrion crows in northern Spain. Individuals with strong social bonds, living with more relatives and in larger groups excreted a significantly smaller proportion of droppings containing coccidian oocysts. The probability to excrete droppings containing nematode eggs was not affected by social factors. The relationship between social interactions and coccidian oocyst excretion is consistent with the idea that high quality social relationships can positively affects individual’s health, setting the stage for the evolution of stable social living.
Is obesity a genetic disease? Human obese transcriptome analysis in monozygotic twins
Authors: Font-Clos Francesc , Zapperi Stefano , La Porta Caterina A.M.
Published: July 2017

Obesity is a pandemic disease with a critical increase in childhood. An important unanswered question is to understand if this disease is due to genetic causes or to the life-style of the subjects. To address this question, we have analyzed if monozygotic twins show the same robust transcriptomic signature (5σ, as for the Higgs Boson) that we have recently revealed in obese subjects. Our results show that our signature correlates with BMI in paired transcriptomes of monozygotic twins, suggesting that the signature does not reflect underlying genetic causes.
Cas Adaptor Proteins Coordinate Sensory Axon Fasciculation
Authors: Vahedi-Hunter Tyler A. , Riccomagno Martin M.
Published: July 2017

Development of complex neural circuits like the peripheral somatosensory system requires intricate mechanisms to ensure axons make proper connections. While much is known about ligand-receptor pairs required for dorsal root ganglion (DRG) axon guidance, very little is known about the cytoplasmic effectors that mediate cellular responses triggered by these guidance cues. Here we show that members of the Cas family of cytoplasmic signaling adaptors are highly phosphorylated in central projections of the DRG as they enter the spinal cord. Furthermore, we provide genetic evidence that Cas proteins act DRG-autonomously to promote fasciculation of sensory projections. These data establish an evolutionarily conserved requirement for Cas adaptor proteins during peripheral nervous system axon pathfinding. They also provide insight into the interplay between axonal fasciculation and adhesion to the substrate.
Deep convolutional and recurrent neural networks for cell motility discrimination and prediction
Authors: Kimmel Jacob C. , Brack Andrew S. , Marshall Wallace F.
Published: July 2017

Cells in culture display diverse motility behaviors that may reflect differences in cell state and function, providing motivation to discriminate between different motility behaviors. Current methods to do so rely upon manual feature engineering. However, the types of features necessary to distinguish between motility behaviors can vary greatly depending on the biological context, and it is not always clear which features may be most predictive in each setting for distinguishing particular cell types or disease states. Convolutional neural networks (CNNs) are machine learning models allowing for relevant features to be learned directly from spatial data. Similarly, recurrent neural networks (RNNs) are a class of models capable of learning long term temporal dependencies. Given that cell motility is inherently spacio-temporal data, we present an approach utilizing both convolutional and long- short-term memory (LSTM) recurrent neural network units to analyze cell motility data. These RNN models provide accurate classification of simulated motility and experimentally measured motility from multiple cell types, comparable to results achieved with hand-engineered features. The variety of cell motility differences we can detect suggests that the algorithm is generally applicable to additional cell types not analyzed here. RNN autoencoders based on the same architecture are capable of learning motility features in an unsupervised manner and capturing variation between myogenic cells in the latent space. Adapting these RNN models to motility prediction, RNNs are capable of predicting muscle stem cell motility from past tracking data with performance superior to standard motion prediction models. This advance in cell motility prediction may be of practical utility in cell tracking applications.
Organizational culture: a foundational perspective
Authors: Pietersen Charlotte
Published: July 2017

Purpose

The purpose of this paper is to perform a typological analysis of research orientations in the field of organizational culture (OC) in order to provide a broad, original perspective on the nature of research in this field, beyond the current quantitative/qualitative dichotomy.

Design/methodology/approach

Documentary analysis, consisting of a content analysis of an appropriate and conceptually convenient selection of 200 source publications, was conducted. The analysis was performed in terms of four fundamental knowledge orientations and methodologies.

Findings

An analysis and description of the chosen set of examples for each of the four types of knowledge showed that, as with other areas in the field of organizational behavior and management (and also other scholarly disciplines), the typology finds clear expression in the area of OC.

Research limitations/implications

In view of the aim and originality of the present paper, the sample size employed is not a worrying factor as sufficient and clear examples of each of the four basic types of research orientations have been provided. It is recommended that the broadly applicable knowledge (and by implication research) orientations that were introduced here, be considered by OC researchers. The analysis of fundamental approaches to research provides an inclusive perspective on the nature of different ways of studying and understanding OC. This should assist in expanding both scholarly and practitioner horizons. It is concluded that the analysis of research in the field of OC in terms of fundamental types of human knowledge provides a unique and expanded view on research in this area.

Practical implications

All stakeholders in the field of human resource management could benefit from taking cognizance of a broader perspective of knowledge development in the field of OC. The four-fold framework could also be utilized as a valuable source for restructuring and teaching of research methodology programs and courses in institutions of higher education, especially concerning the general need for greater attention to: theoretical (type I), and evaluation (type IV) research in management and organizational behavior.

Originality/value

The analysis of fundamental knowledge orientations provides an original and encompassing perspective on the nature of different approaches to the study and understanding of OC.