bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social relationships and death-related behaviour in aquatic mammals: a systematic review
Authors: Reggente Melissa A. L. V. , Papale Elena , McGinty Niall , Eddy Lavinia , de Lucia Giuseppe Andrea , Bertulli Chiara Giulia 
Published: July 2018

Some aquatic mammals appear to care for their dead, whereas others abandon their live offspring when conditions are unfavourable. This incredible variety in behaviours suggests the importance of comparing and contrasting mechanisms driving death-related behaviours among these species. We reviewed 106 cases of aquatic mammals (81 cetaceans and 25 non-cetaceans) reacting to a death event, and extrapolated ‘participant’ (age class,sex,relationshipanddecomposition) and ‘social’ characteristics (escorting,calf dependence,alloparental care,herdinganddispersal patterns) from published and unpublished literature. A multiple correspondence analysis (MCA) was performed to explore the relationships between these characteristics and death-related behaviours, with species clustered based on MCA scores. Results showed that both cetaceans and non-cetaceans react to death but in different ways. Non-cetaceans, characterized by a short maternal investment, were observed to protect the dead (defending it from external attacks), while cetaceans spent much longer with their offspring and display carrying (hauling, spinning, mouthing with the carcass and diving with it) and breathing-related (lifting and sinking the carcass) activities with the dead generally in association with other conspecifics. Our work emphasizes the need of increased documentation of death-related cases around the world to improve our understanding of aquatic mammals and their responses to death.This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
The lure of death: suicide and human evolution
Authors: Humphrey Nicholas 
Published: July 2018

At some point in evolutionary history, human beings came to understand, as no non-human animals do, that death brings to an end a person's bodily and mental presence in the world. A potentially devastating consequence was that individuals, seeking to escape physical or mental pain, might choose to kill themselves.
This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
The moral standing of the dead
Authors: Luper Steven 
Published: July 2018

In choosing to do certain things, we appear to presuppose that we can act in the interests the dead, and that we have a duty to do so. For example, some of us go to great lengths to carry out their final wishes. Given that the dead no longer exist, however, it seems that nothing can be good or badforthem: they lack prudential interests. In that case, it is hard to see how we could owe them anything. They seem to lack moral standing altogether. In this essay, I will rebut this line of thought. I will claim that in some cases things that happen after people die are indeed good or bad for them. Their interests can still be advanced or hindered, so the dead have moral standing.This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
Changing relationship between the dead and the living in Japanese prehistory
Authors: Matsumoto Naoko 
Published: July 2018

The aim of this paper is to propose a new insight on the changing burial practice by regarding it as a part of the cognitive system for maintaining complex social relationships. Development of concentrated burials and their transformation in Japanese prehistory are examined to present a specific case of the changing relationship between the dead and the living to highlight the significance of the dead in sociocultural evolution. The essential feature of the burial practices observed at Jomon sites is the centrality of the dead and their continuous presence in the kinship system. The mortuary practices discussed in this paper represent a close relationship between the dead and the living in the non-hierarchical complex society, in which the dead were not detached from the society, but kept at its core, as a materialized reference of kin networks.
This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
Speaking of death
Authors: Husband E. Matthew 
Published: July 2018

As a human-specific trait, language offers a unique window on human cognition. Grammatical constraints on the ways we speak about events, for instance, have long been thought to reveal the representational formats that our minds impose on the ways that we think about events. In recent research, verbs that name events of death have stood out as key counterexamples to standard theories of the grammatical constraints on possible verbs. The special status of these thanatological verbs raises two important questions: why, given the vast number of verbs in any language, is it that verbs of death hold this special status, and what do they tell us about the restrictions on the representational format for possible verbs? This paper reexamines the evidence coming from verbs of death, confirming that they are counterexamples to standard theories, but that their behaviour suggests a more revealing constraint on our mental representations—that our minds impose strict restrictions on the format of asserted meaning. Thus, the constraints on linguistic representation and the human mind offer a unique perspective on the mental representations of thanatological phenomena.This article is part of the theme issue ‘Evolutionary thanatology: impacts of the dead on the living in humans and other animals’.
Gfi1-expressing Paneth cells revert to stem cells following intestinal injury
Authors: Chen Min-Shan , Lo Yuan-Hung , Butkus Joann , Zou Winnie , Tseng Yu-Jung , Jen Hsin-I , Patel Shreena , Groves Andrew , Estes Mary , Sahin Ergun , Frey Mark , Dempsey Peter , Shroyer Noah 
Published: July 2018

AbstractBackground＆AimChemotherapy drugs harm rapidly dividing normal healthy cells such as those lining the gastrointestinal tract, causing morbidity and mortality that complicates medical treatment modalities. Growth Factor-Independent 1 (GFI1) is a zinc finger transcriptional repressor implicated in the differentiation of secretory precursors into Paneth and goblet cells in the intestinal epithelium. We hypothesize that stimulating the reversion of Gfi1+ secretory cells into stem cells will improve intestinal epithelial regeneration and mitigate injury.MethodsGfi1 reporter mice (Gfi1cre/+; ROSA26 LSL-YFP) were treated with Doxorubicin, radiation, anti-CD3 antibody, and rotavirus to induce intestinal injury. Mice and intestinal organoids (enteroids) were used to investigate cellular repair mechanisms following injury.ResultsUnder homeostatic conditions, Gfi1-lineage cells are Paneth and goblet cells, which were non-proliferative and not part of the stem cell pool. After injury, Gfi1+ secretory cells can re-enter the cell cycle and give rise to all cell lineages of the intestinal epithelium including stem cells. Reversion of Gfi1-lineage cells was observed in other injury model systems, including irradiation and anti-CD3 treatment, but not in ISC-sparing rotavirus infection. Our results also demonstrated that PI3kinase/AKT activation improved cell survival, and elevated WNT signaling increased the efficiency of Gfi1+ cell reversion upon injury.ConclusionsThese findings indicate that Gfi1+ secretory cells display plasticity and reacquire stemness following severe damage. Moreover, PI3kinase/AKT and WNT are key regulators involved in injury-induced regeneration. Our studies identified potential therapeutic intervention strategies to mitigate the adverse effects of chemotherapy-induced damage to normal tissues and improve the overall effectiveness of cancer chemotherapy.
Speed breeding in growth chambers and glasshouses for crop breeding and model plant research
Authors: Ghosh Sreya , Watson Amy , Gonzalez-Navarro Oscar E. , Ramirez-Gonzalez Ricardo H. , Yanes Luis , Mendoza-Suárez Marcela , Simmonds James , Wells Rachel , Rayner Tracey , Green Phon , Hafeez Amber , Hayta Sadiye , Melton Rachel E. , Steed Andrew , Sarkar Abhimanyu , Carter Jeremy , Perkins Lionel , Lord John , Tester Mark , Osbourn Anne , Moscou Matthew J. , Nicholson Paul , Harwood Wendy , Martin Cathie , Domoney Claire , Uauy Cristobal , Hazard Brittany , Wulff Brande B. H. , Hickey Lee T. 
Published: July 2018

1.AbstractTo meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in crop breeding. One way this can be achieved is through “speed breeding” (SB), which shortens the breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carried out in a number of ways, one of which involves extending the duration of a plant’s daily exposure to light (photoperiod) combined with early seed harvest in order to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. Here we present glasshouse and growth chamber-based SB protocols with supporting data from experimentation with several crop species. These protocols describe the growing conditions, including soil media composition, lighting, temperature and spacing, which promote rapid growth of spring and winter bread wheat, durum wheat, barley, oat, various members of the Brassica family, chickpea, pea, grasspea, quinoa and the model grass Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale-up plant numbers for single seed descent (SSD) purposes. Conversely, instructions on how to perform SB on a small-scale by creating a benchtop SB growth cabinet that enables optimization of parameters at a low cost are provided. We also outline the procedure for harvesting and germinating premature wheat, barley and pea seed to reduce generation time. Finally, we provide troubleshooting suggestions to avoid potential pitfalls.
Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks
Authors: Hodzic Ermin , Shrestha Raunak , Zhu Kaiyuan , Cheng Kuoyuan , Collins Colin C. , Cenk Sahinalp S. 
Published: July 2018

AbstractBackgroundAdvances in large scale tumor sequencing have lead to an understanding that there are combinations of genomic and transcriptomic alterations speciflc to tumor types, shared across many patients. Unfortunately, computational identiflcation of functionally meaningful shared alteration patterns, impacting gene/protein interaction subnetworks, has proven to be challenging.FindingsWe introduce a novel combinatorial method, cd-CAP, for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples. Our method differentiates distinct alteration types associated with each gene (rather than relying on binary information of a gene being altered or not), and simultaneously detects multiple alteration proflle conserved subnetworks.ConclusionsIn a number of The Cancer Genome Atlas (TCGA) data sets, cd-CAP identifled large biologically signiflcant subnetworks with conserved alteration patterns, shared across many tumor samples.
Dynamic plant height QTL revealed in maize through remote sensing phenotyping using a high-throughput unmanned aerial vehicle (UAV)
Authors: Wang Xiaqing , Zhang Ruyang , Han Liang , Yang Hao , Song Wei , Liu Xiaolei , Sun Xuan , Luo Meijie , Chen Kuan , Zhang Yunxia , Yang Guijun , Zhao Yanxin , Zhao Jiuran 
Published: July 2018

AbstractPlant height is the key factor for plant architecture, biomass and yield in maize (Zea mays). In this study, plant height was investigated using unmanned aerial vehicle high-throughput phenotypic platforms (UAV-HTPPs) for maize diversity inbred lines at four important growth stages. Using an automated pipeline, we extracted accurate plant heights. We found that in temperate regions, from sowing to the jointing period, the growth rate for temperate maize was faster than tropical maize. However, from jointing to flowering stage, tropical maize maintained a vigorous growth state, and finally resulted in a taller plant than temperate lines. Genome-wide association study for temperate, tropical and both groups identified a total of 238 quantitative trait locus (QTLs) for the 16 plant height related traits over four growth periods. And, we found that plant height at different stages were controlled by different genes, for example, PIN1 controlled plant height at the early stage and PIN11 at the flowering stages. In this study, the plant height data collected by the UAV-HTTPs were credible and the genetic mapping power is high, indicating that the application of this UAV-HTTPs into the study of plant height will have great prospects.HighlightWe used UAV-based sensing platform to investigate plant height over 4 growth stages for different maize populations, and detected numbers of reliable QTLs using GWAS.
Drug-target binding quantitatively predicts optimal antibiotic dose levels
Authors: Clarelli Fabrizio , Palmer Adam , Singh Bhupender , Storflor Merete , Lauksund Silje , Cohen Ted , Abel Sören , zur Wiesch Pia Abel 
Published: July 2018

AbstractCombatting antibiotic resistance will require both new antibiotics and strategies to preserve the effectiveness of existing drugs. Both approaches would benefit from predicting optimal dosing of antibiotics based on drug-target binding parameters that can be measured early in drug development and that can change when bacteria become resistant. This would avoid the currently frequently employed trial-and-error approaches and might reduce the number of antibiotic candidates that fail late in drug development.Here, we describe a computational model (COMBAT-COmputational Model of Bacterial Antibiotic Target-binding) that leverages accessible biochemical parameters to quantitatively predict antibiotic dose-response relationships. We validate our model with MICs of a range of quinolone antibiotics in clinical isolates demonstrating that antibiotic efficacy can be predicted from drug-target binding (R2 > 0.9). To further challenge our approach, we do not only predict antibiotic efficacy from biochemical parameters, but also do the reverse: estimate the magnitude of changes in drug-target binding based on antibiotic dose-response curves. We experimentally demonstrate that changes in drug-target binding can be predicted from antibiotic dose-response curves with 92-94 % accuracy by exposing bacteria overexpressing target molecules to ciprofloxacin. To test the generality of COMBAT, we apply it to a different antibiotic class, the beta-lactam ampicillin, and can again predict binding parameters from dose-response curves with 90 % accuracy. We then apply COMBAT to predict antibiotic concentrations that can select for resistance due to novel resistance mutations.Our goal here is dual: First, we address a fundamental biological question and demonstrate that drug-target binding determines bacterial response to antibiotics, although antibiotic action involves many additional effects downstream of drug-target binding. Second, we create a tool that can help accelerate drug development by predicting optimal dosing and preserve the efficacy of existing antibiotics by predicting optimal treatment for possible resistant mutants.
Predicting the Outcomes of New Short-Course Regimens for Multi-Drug Resistant Tuberculosis Using Intrahost and Pharmacokinetic-Pharmacodynamic Modelling
Authors: Doan Tan N , Cao Pengxing , Emeto Theophilus I , McCaw James M , McBryde Emma S 
Published: July 2018

ABSTRACTShort-course regimens for multi-drug resistant tuberculosis (MDR-TB) are urgently needed. Limited data suggest that the new drug, bedaquiline (BDQ), may have the potential to shorten MDR-TB treatment to less than six months when used in conjunction with standard anti-TB drugs. However, the feasibility of BDQ in shortening MDR-TB treatment duration remains to be established. Mathematical modelling provides a platform to investigate different treatment regimens and predict their efficacy. We developed a mathematical model to capture the immune response to TB inside a human host environment. This model was then combined with a pharmacokinetic-pharmacodynamic model to simulate various short-course BDQ-containing regimens. Our modelling suggests that BDQ could reduce MDR-TB treatment duration to just 18 weeks (four months) while still maintaining a very high treatment success rate (100% for daily BDQ for two weeks, or 95% for daily BDQ for one week during the intensive phase). The estimated time to bacterial clearance of these regimens ranges from 27 to 33 days. Our findings provide the justification for empirical evaluation of short-course BDQ-containing regimens. If short-course BDQ-containing regimens are found to improve outcomes then we anticipate clear cost-savings and a subsequent improvement in the efficiency of national TB programs.
Parallel Evolution in the Emergence of Highly Pathogenic Avian Influenza A Viruses
Authors: Escalera-Zamudio Marina , Golden Michael , Gutiérrez Bernardo , Thézé Julien , Keown Jeremy Russell , Carrique Loic , Bowden Thomas A. , Pybus Oliver G. 
Published: July 2018

ABSTRACTParallel molecular evolution and adaptation are important phenomena commonly observed in viruses. Here we exploit parallel molecular evolution to understand virulence evolution in avian influenza viruses (AIV). Highly-pathogenic AIVs independently evolve from low-pathogenic ancestors via acquisition of a polybasic cleavage sites (pCS). Why some AIV lineages but not others evolve in this way is unknown. We hypothesise that the parallel emergence of highly-pathogenic AIV may be facilitated by permissive or compensatory mutations occurring across the AIV genome. We combined phylogenetic, statistical and structural approaches to discover parallel mutations in AIV genomes associated with the highly-pathogenic phenotype. Parallel mutations were screened using a new statistical test of mutation-phenotype association and further evaluated in the contexts of positive selection and protein function. The mutational panel we present reveals new links between virulence evolution and other viral traits and raises the possibility of predicting aspects of AIV evolution.
The integration of visual and target signals in V4 and IT during visual object search
Authors: Roth Noam , Rust Nicole C. 
Published: July 2018

ABSTRACTSearching for a specific visual object requires our brain to compare the items in view with a remembered representation of the sought target to determine whether a target match is present. This comparison is thought to be implemented, in part, via the combination of top-down modulations reflecting target identity with feed-forward visual representations. However, it remains unclear whether top-down signals are integrated at a single locus within the ventral visual pathway (e.g. V4) or at multiple stages (e.g. both V4 and inferotemporal cortex, IT). To investigate, we recorded neural responses in V4 and IT as rhesus monkeys performed a task that required them to identify when a target object appeared across variation in position, size and background context. We found non-visual, task-specific signals in both V4 and IT. To evaluate whether V4 was the only locus for the integration of top-down signals, we evaluated several feed-forward accounts of processing from V4 to IT, including a model in which IT preferentially sampled from the best V4 units and a model that allowed for nonlinear IT computation. IT task-specific modulation was not accounted for by any of these feed-forward descriptions, suggesting that during object search, top-down signals are integrated directly within IT.NEW & NOTEWORTHYTo find specific objects, the brain must integrate top-down, target-specific signals with visual information about objects in view. However, the exact route of this integration in the ventral visual pathway is unclear. In the first study to systematically compare V4 and IT during an invariant object search task, we demonstrate that top-down signals found in IT cannot be described as being inherited from V4, but rather must be integrated directly within IT itself.
Characterisation of morphological differences in well-differentiated nasal epithelial cell cultures from preterm and term infants at birth and one-year
Authors: Groves Helen E. , Guo-Parke Hong , Broadbent Lindsay , Shields Michael D. , Power Ultan F. 
Published: July 2018

AbstractBackgroundInnate immune responses of airway epithelium are important defences against respiratory pathogens and allergens. Newborn infants are at greater risk of severe respiratory infections compared to older infants. However, very little is known regarding human neonatal airway epithelium immune responses and whether age-related morphological and/or innate immune changes contribute to the development of airway disease.MethodsWe collected nasal epithelial cells from 41 newborn infants (23 term, 18 preterm) within 5 days of birth. Repeat sampling was achieved for 24 infants (13 term, 11 preterm) at a median age of 12.5 months. Morphologically and physiologically authentic well-differentiated primary paediatric nasal epithelial cell (WD-PNEC) cultures were generated and characterised using light microscopy and immunofluorescence.ResultsWD-PNEC cultures were established for 15/23 (65%) term and 13/18 (72%) preterm samples at birth, and 9/13 (69%) term and 8/11 (73%) preterm samples at one-year. Newborn and infant WD-PNEC cultures demonstrated extensive cilia coverage, mucous production and tight junction integrity. Newborn WD-PNECs took significantly longer to reach full differentiation and were noted to have much greater proportions of goblet cells compared to one-year repeat WD-PNECs. No differences were evident in ciliated/goblet cell proportions between term- and preterm-derived WD-PNECs at birth or one-year old.ConclusionWD-PNEC culture generation from newborn infants is feasible and represents a powerful and exciting opportunity to study differential innate immune responses in human airway epithelium very early in life.
Computational metabolomics hints at the relevance of glutamine metabolism in breast cancer
Authors: Trilla-Fuertes Lucía , Gámez-Pozo Angelo , López-Camacho Elena , Prado-Vázquez Guillermo , Zapater-Moros Andrea , López-Vacas Rocío , Arevalillo Jorge M , Díaz-Almirón Mariana , Navarro Hilario , Maín Paloma , Espinosa Enrique , Zamora Pilar , Fresno Vara Juan Ángel 
Published: July 2018

AbstractMetabolomics has a great potential in the development of new biomarkers in cancer. In this study, metabolomics and gene expression data from breast cancer tumor samples were analyzed, using (1) probabilistic graphical models to define associations using quantitative data without othera prioriinformation; and (2) Flux Balance Analysis and flux activities to characterize differences in metabolic pathways. On the one hand, both analyses highlighted the importance of glutamine in breast cancer. Moreover, cell experiments showed that treating breast cancer cells with drugs targeting glutamine metabolism significantly affects cell viability. On the other hand, these computational methods suggested some hypotheses and have demonstrated their utility in the analysis of metabolomics data and in associating metabolomics with patient’s clinical outcome.