bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poor Cardiorespiratory Fitness Is a Risk Factor for Sepsis in Patients Awaiting Liver Transplantation
Authors: Wallen Matthew P. , Woodward Aidan J. , Hall Adrian , Skinner Tina L. , Coombes Jeff S. , Macdonald Graeme A. 
Published: July 2018

Background.
Patients with advanced liver disease are at increased risk of infection and other complications. A significant proportion of patients also have poor fitness and low muscle mass. The primary aim of this study was to investigate if cardiorespiratory fitness and body composition are risk factors for sepsis and other complications of advanced liver disease.

Methods.
Patients being listed for liver transplantation underwent cardiopulmonary exercise testing to determine ventilatory threshold (VT). Computed tomography was used to measure skeletal muscle and subcutaneous and visceral adipose tissue indexes. All unplanned hospital admissions, deaths or delistings before transplantation were recorded.

Results.
Eighty-two patients (aged 55.1 [50.6–59.4] years, median (interquartile range); male 87%] achieved a median VT of 11.7 (9.7–13.4) mL·kg−1·min−1. Their median model of end-stage liver disease, incorporating serum sodium score was 18 (14–22); and 37 had hepatocellular carcinoma. There were 50 admissions in 31 patients; with 16 admissions for sepsis in 13 patients. Patients with sepsis had a significantly lower VT (sepsis, 9.5 [7.8–11.9]; no sepsis, 11.8 [10.5–13.8] mL·kg−1·min−1; P = 0.003]. No body composition variables correlated with sepsis, nor were there any significant associations between VT and unplanned admissions for other indications. Multivariate logistic regression demonstrated that VT was independently associated with a diagnosis of sepsis (P = 0.03). Poisson regression revealed that VT was a significant predictor for the number of septic episodes (P = 0.02); independent of age, model of end-stage liver disease, incorporating serum sodium score, hepatocellular carcinoma diagnosis, presence of ascites, and β-blocker use.

Conclusions.
Poor cardiorespiratory fitness is an independent risk factor for the development of sepsis in advanced liver disease.
No Evidence for Cross-reactivity of Virus-specific Antibodies With HLA Alloantigens
Authors: Heidt Sebastiaan , Feltkamp Mariet C. , Karahan Gonca E , de Brouwer Caroline S. , Langerak-Langerak Janneke , Mulder Arend , Claas Frans H.J. 
Published: July 2018

Background
Antibodies directed against HLA can develop through pregnancy, blood transfusions, or organ transplants. Anecdotal evidence suggests that virus-specific antibodies may have the capacity to cross-react with HLA, a phenomenon called heterologous immunity, which is well described for T-cell alloreactivity.

Methods
To determine whether antibody cross-reactivity between viral antigens and HLA is common, we tested 51 virus-specific human monoclonal antibodies (mAbs) specific for human immunodeficiency virus, varicella zoster virus, cytomegalovirus, and parvovirus, for reactivity against HLA class I and class II in single-antigen bead assays. In addition, we tested the reactivity of 41 HLA-specific human mAbs against common viral antigens of cytomegalovirus, varicella zoster virus, human immunodeficiency virus, Epstein-Barr virus, and BK polyomavirus.

Results
No cross-reactivity of any of the virus-specific mAbs with either HLA class I or class II molecules, as well as no cross-reactivity of any of the HLA-specific mAbs with any of the viral antigens was observed.

Conclusions
These findings indicate that the frequency of cross-reactivity on the antibody level between viral antigens and HLA, if present at all, is low. The emergence of HLA antibodies upon viral infection or vaccination is therefore probably due to bystander activation of dormant HLA-specific memory B cells.
Occurrence and variability of tactile interactions between wild American crows and dead conspecifics
Authors: Swift Kaeli , Marzluff John M. 
Published: July 2018

Observations of some mammals and birds touching their dead provoke questions about the motivation and adaptive value of this potentially risky behaviour. Here, we use controlled experiments to determine if tactile interactions are characteristic of wild American crow responses to dead crows, and what the prevalence and nature of tactile interactions suggests about their motivations. In Experiment 1, we test if food or information acquisition motivates contact by presenting crows with taxidermy-prepared dead crows, and two species crows are known to scavenge: dead pigeons and dead squirrels. In Experiment 2, we test if territoriality motivates tactile interactions by presenting crows with taxidermy crows prepared to look either dead or upright and life-like. In Experiment 1, we find that crows are significantly less likely to make contact but more likely to alarm call and recruit other birds in response to dead crows than to dead pigeons and squirrels. In addition, we find that aggressive and sexual encounters with dead crows are seasonally biased. These findings are inconsistent with feeding or information acquisition-based motivation. In Experiment 2, we find that crows rarely dive-bomb and more often alarm call and recruit other crows to dead than to life-like crows, behaviours inconsistent with responses given to live intruders. Consistent with a danger response hypothesis, our results show that alarm calling and neighbour recruitment occur more frequently in response to dead crows than other stimuli, and that touching dead crows is atypical. Occasional contacts, which take a variety of aggressive and sexual forms, may result from an inability to mediate conflicting stimuli.
This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
Comparative thanatology, an integrative approach: exploring sensory/cognitive aspects of death recognition in vertebrates and invertebrates
Authors: Gonçalves André , Biro Dora 
Published: July 2018

Evolutionary thanatology benefits from broad taxonomic comparisons of non-human animals' responses to death. Furthermore, exploring the sensory and cognitive bases of these responses promises to allow classification of the underlying mechanisms on a spectrum from phylogenetically ancient to more derived traits. We draw on studies of perception and cognition in invertebrate and vertebrate taxa (with a focus on arthropods, corvids, proboscids, cetaceans and primates) to explore the cues that these animals use to detect life and death in others, and discuss proximate and ultimate drivers behind their capacities to do so. Parallels in thanatological behaviour exhibited by the last four taxa suggest similar sensory–cognitive processing rules for dealing with corpses, the evolution of which may have been driven by complex social environments. Uniting these responses is a phenomenon we term ‘animacy detection malfunction’, whereupon the corpse, having both animate and inanimate attributes, creates states of fear/curiosity manifested as approach/avoidance behaviours in observers. We suggest that integrating diverse lines of evidence (including the ‘uncanny valley’ effect originating from the field of robotics) provides a promising way to advance the field, and conclude by proposing avenues for future research.This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
The Late Upper Palaeolithic and earliest Mesolithic evidence of burials in Europe
Authors: Orschiedt Jörg 
Published: July 2018

Burials of the Late Palaeolithic (14 000–11 600 cal years before present, henceforth BP) are a rare phenomenon in Europe. Several sites possess burials of single and double individuals. As with the preceding Magdalenian, the burial of more than two individuals in the same grave cutting seems to be unusual, but does occur occasionally. The deposition of isolated and disarticulated human remains with or without cut marks seems additionally to belong to the Magdalenian context. In the final Palaeolithic phase (13 000–11 600 cal years BP) there is evidence for cemetery-like clusters of burials, which contrast to the Magdalenian evidence, instead showing some similarities with the succeeding Mesolithic. The earliest Mesolithic burials 11 600–10 500 cal BP) are a very rare phenomenon, covering a short time span between the beginning of the Preboreal and the beginning of the Boreal phase of the early Holocene. Here the evidence includes single inhumations, cemetery-like structures and a number of isolated human remains. Caves and rock shelters were the most common places for inhumations in both the final Palaeolithic and the early Mesolithic. Although the number of sites with a chronological continuity from the LUP to the Early Mesolithic burial is low, several aspects indicate a general continuity in burial patterns over this period. Apart from this continuity, the Mesolithic burials in general seem to represent a new level of diversity in burial practices.
This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
Children's understanding of death: from biology to religion
Authors: Harris Paul L. 
Published: July 2018

Young children construct a biological conception of death, recognizing that death terminates mental and bodily processes. Despite this recognition, many children are receptive to an alternative conception of death, which affirms that the deceased has an afterlife elsewhere. A plausible interpretation of children's receptivity to this alternative conception is that human beings, including young children, are naturally disposed to remember and keep in mind individuals to whom they are attached even when those individuals leave and are absent for extended periods. This disposition is reflected in the pervasive tendency to talk about death as a departure rather than a terminus. It also enables the living to sustain their ties to the dead, even if, in the case of death, the departure is permanent rather than temporary. Linguistic and developmental evidence for these claims is reviewed. Possible biological origins and implications for archaeological research are also discussed.
This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
Hominin evolutionary thanatology from the mortuary to funerary realm: the palaeoanthropological bridge between chemistry and culture
Authors: Pettitt Paul 
Published: July 2018

Palaeoanthropology, or more precisely Palaeolithic archaeology, offers the possibility of bridging the gap between mortuary activities that can be observed in the wider animal community and which relate to chemistry and emotion; to the often-elaborate systems of rationalization and symbolic contextualisation that are characteristic of recently observable societies. I draw on ethological studies to provide a core set of mortuary behaviours one might expect hominoids to inherit, and on anthropological observations to explore funerary activity represented in the Middle and Upper Palaeolithic, in order to examine how a distinctly human set of funerary behaviours arose from a more widespread set of mortuary behaviours. I suggest that the most profound innovation of the hominins was the incorporation of places into the commemoration of the dead, and propose a falsifiable mechanism for why this came about; and I suggest that the pattern of the earliest burials fits with modern hunter–gatherer belief systems about death, and how these vary by social complexity. Finally, I propose several research questions pertaining to the social context of funerary practices, suggesting how a hominin evolutionary thanatology may contribute not only to our understanding of human behavioural evolution, but to a wider thanatology of the animal kingdom.This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
Saccharomyces cerevisiae adapted to grow in the presence of low-dose rapamycin exhibit altered amino acid metabolism
Authors: Dikicioglu Duygu , Eke Elif Dereli , Eraslan Serpil , Oliver Stephen G , Kirdar Betul 
Published: July 2018

ABSTRACTRapamycin is a potent inhibitor of the highly conserved TOR kinase, the nutrient-sensitive controller of growth and aging. It has been utilised as a chemotherapeutic agent due to its anti-proliferative properties and as an immunosuppressive drug, and is also known to extend lifespan in a range of eukaryotes from yeast to mammals. However, the mechanisms through which eukaryotic cells adapt to sustained exposure to rapamycin have not yet been thoroughly investigated. Here, S. cerevisiae response to long-term rapamycin exposure was investigated by identifying the physiological, transcriptomic and metabolic differences observed for yeast populations inoculated into low-dose rapamycin-containing environment. The effect of oxygen availability and acidity of extracellular environment on this response was further deliberated by controlling or monitoring the dissolved oxygen level and pH of the culture. Yeast populations grown in the presence of rapamycin reached higher cell densities complemented by an increase in their chronological lifespan, and these physiological adaptations were associated with a rewiring of the amino acid metabolism, particularly that of arginine. The ability to synthesise amino acids emerges as the key factor leading to the major mechanistic differences between mammalian and microbial TOR signalling pathways in relation to nutrient recognition. Furthermore, oxygen levels and extracellular acidity of the culture were observed to conjointly affect yeast populations, virtually acting as coupled physiological effectors; cells were best adapted when maximal oxygenation of the culture was maintained in slightly acidic pH, any deviation necessitated more extensive readjustment to additional stress factors.
How do your genetics compare to the world’s elite marathoners?
Authors: Sims Gregory E. , Zeng Xiang-pei , Falk Jeffrey , Nova Michael 
Published: July 2018

AbstractPathway OME (Formerly Pathway Genomics, http://www.pathway.com) has identified a unique set of genetic traits associated with endurance, anxiety and likelihood of hamstring/Achilles injuries in an elite set of marathon runners. To date, this is the largest database of elite marathon athletes to ever have their exomes sequenced. Proprietary SportIQ Artificial Intelligence (AI) algorithms were developed and used to compare genetic traits in these 1,119 elite marathon runners to a normal population enabling us to develop a ‘Marathon Runner’ profile to assist athletes in training to compete and achieve their athletic goals. Athlete’s whose genetic profiles differ significantly from the “Marathon Runner” profile will gain additional insights on the specific training necessary to prepare their muscles for the demanding conditions of long distance running.
Early life stress impairs postnatal oligodendrogenesis and adult emotional behaviour through activity-dependent mechanisms
Authors: Teissier A. , Le Magueresse C. , Olusakin J. , Andrade da Costa B. L. S. , De Stasi A. M. , Bacci A. , Kawasawa Y. , Vaidya V. A. , Gaspar P. 
Published: July 2018

ABSTRACTExposure to stress during early life (infancy/childhood) has long-term effects on the structure and function of the prefrontal cortex (PFC) and increases the risk for adult depression and anxiety disorders. However, little is known about the molecular and cellular mechanisms of these effects. Here we focused on changes induced by chronic maternal separation during the first two weeks of postnatal life. Unbiased mRNA expression profiling in the medial PFC (mPFC) of maternally separated (MS) pups identified an increased expression of myelin-related genes and a decreased expression of immediate early genes. Oligodendrocyte lineage markers and birthdating experiments indicated a precocious oligodendrocyte differentiation in the mPFC at P15, leading to a depletion of the oligodendrocyte progenitor pool in MS adults. We tested the role of neuronal activity in oligodendrogenesis, using designed receptors exclusively activated by designed drugs (DREADDs) techniques. hM4Di or hM3Dq constructs were transfected into mPFC neurons using fast-acting AAV8 viruses. Reduction of mPFC neuron excitability during the first two postnatal weeks caused a premature differentiation of oligodendrocytes similar to the MS pups, while chemogenetic activation normalized it in the MS animals. Bidirectional manipulation of neuron excitability in the mPFC during the P2-P14 period had long lasting effects on adult emotional behaviours and on temporal object recognition: hM4Di mimicked MS effects, while hM3Dq prevented the pro-depressive effects and short term memory impairment of MS. Thus, our results identify neuronal activity as a critical target of early life stress and demonstrate its function in controlling both postnatal oligodendrogenesis and adult mPFC-related behaviors.
Simultaneous production of diverse neuronal subtypes during early corticogenesis
Authors: Magrinelli E. , Wagener R. J. , Jabaudon D. 
Published: July 2018

AbstractThe circuits of the neocortex are composed of a broad diversity of neuronal cell types, which can be distinguished by their laminar location, molecular identity, and connectivity. During embryogenesis, successive generations of glutamatergic neurons are sequentially born from progenitors located in germinal zones below the cortex. In this process, the earliest-born generations of neurons differentiate to reside in deep layers, while later-born daughter neurons reside in more superficial layers. Although the aggregate competence of progenitors to produce successive subtypes of neurons progresses as corticogenesis proceeds, a fine-grained temporal understanding of how neuronal subtypes are sequentially produced is still missing. Here, we use FlashTag, a high temporal resolution labeling approach, to follow the fate of the simultaneously-born daughter neurons of ventricular zone progenitors at multiple stages of corticogenesis. Our findings reveal a bimodal regulation in the diversity of neurons being produced at single time points of corticogenesis. Initially, distinct subtypes of deep-layer neurons are simultaneously produced, as defined by their laminar location, molecular identity and connectivity. Later on, instead, instantaneous neuronal production is homogeneous and the distinct superficial-layer neurons subtypes are sequentially produced. These findings suggest that early-born, deep-layer neurons have a less determined fate potential than later-born superficial layer neurons, which may reflect the progressive implementation of pre-and/or post-mitotic mechanisms controlling neuronal fate reliability.
The trichotomy of pneumococcal infection outcomes
Authors: Almocera Alexis Erich S. , Hernandez-Mejia Gustavo , Parra-Rojas César , Hernandez-Vargas Esteban A. 
Published: July 2018

AbstractThe successful elimination of bacteria such as Streptococcus pneumoniae from a host involves the coordination between different parts of the immune system. Previous studies have explored the effects of the initial pneumococcal load (bacterial dose) on different representations of innate immunity, finding that pathogenic outcomes can vary with the size of the bacterial dose. However, others yield support to the notion of dose-independent factors contributing to bacterial clearance. In this paper, we seek to provide a deeper understanding of the immune responses associated to the pneumococcus. To this end, we formulate a model that realizes an abstraction of the innate-regulatory immune host response. Stability and bifurcation analyses of the model reveal the following trichotomy of pneumococcal outcomes determined by the bifurcation parameters: (i) dose-independent clearance; (ii) dose-independent persistence; and (iii) dose-limited clearance. Bistability, where the bacteria-free equilibrium co-stabilizes with the most substantial steady-state bacterial load is the specific result behind dose-limited clearance. The trichotomy of pneumococcal outcomes here described integrates all previously observed bacterial fates into a unified framework.
Novel cytonuclear combinations modify Arabidopsis seed physiology and vigor
Authors: Boussardon Clément , Martin-Magniette Marie-Laure , Godin Béatrice , Benamar Abdelilah , Vittrant Benjamin , Citerne Sylvie , Mary-Huard Tristan , Macherel David , Rajjou Loïc , Budar Françoise 
Published: July 2018

AbstractThe influence of intraspecific variation in cytoplasmic genomes and cytonuclear interactions on key seed traits that can impact adaptation and agriculture has not been thoroughly explored, so far. Here, dormancy, germination performance and longevity of seeds have been assessed in Arabidopsis plants with novel cytonuclear combinations that disrupt coadaptation between natural variants of nuclear and cytoplasmic genomes. Although all three traits were affected by cytonuclear reshuffling, the sensitivity of seed traits to cytoplasmic change was dependent on the nuclear background. Both deleterious and, more surprisingly, favorable effects of novel cytonuclear combinations (in comparison with the nuclear parent) were observed, suggesting suboptimal genetic combinations exist in natural populations for these traits. Significant changes on dormancy and germination performance due to specific cytonuclear interacting combinations mainly occurred in opposite directions, in accordance with the previously proposed ‘dormancy continuum’. Consistently, reduced sensitivity to exogenous ABA and faster endogenous ABA decay during germination were observed in a novel cytonuclear combination that also exhibited enhanced longevity and better germination performance, compared to its natural nuclear parent. Cytoplasmic genomes, therefore, represent an additional resource of natural variation for breeding seed vigor traits.Issue sectionGrowth and developmentHighlightNatural variation in Arabidopsis organelles and cytonuclear interactions influence seed dormancy, longevity and germination performance. Enhanced seed vigor was obtained through the creation of novel cytonuclear combinations.
ATG13 dynamics in non-selective autophagy and mitophagy: insights from live imaging studies and mathematical modelling
Authors: Pezze Piero Dalle , Karanasios Eleftherios , Kandia Varvara , Manifava Maria , Walker Simon A. , Le Novère Nicolas Gambardella , Ktistakis Nicholas T. 
Published: July 2018

AbstractDuring autophagy, the ULK complex nucleates autophagic precursors which give rise to autophagosomes. We analysed by live imaging and mathematical modelling translocation of ATG13 (part of ULK complex) to autophagic puncta in starvation-induced autophagy and ivermectin-induced mitophagy. In non-selective autophagy, the intensity and duration of ATG13 translocation approximated a normal distribution whereas wortmannin reduced this and shifted to a log-normal distribution. During mitophagy, multiple translocations of ATG13, with increasing time between peaks were observed. We hypothesised that these multiple translocations arise because engulfment of mitochondrial fragments requires successive nucleations of multiple phagophores on the same target, and a mathematical model based on this idea reproduced the oscillatory behaviour. Significantly, model and experimental data were also in agreement that the number of ATG13 translocations is directly proportional to the diameter of the targeted mitochondrial fragments. Our data provide novel insights into the early dynamics of selective and non-selective autophagy.