bluuebunny/crossref_metadata_2025 huggingface dataset:
The Late Pleistocene-Holocene African Humid Period as Evident in Lakes
Authors: Holmes Jonathan , Hoelzmann Philipp
Published: April 2017

From the end of the last glacial stage until the mid-Holocene, large areas of arid and semi-arid North Africa were much wetter than present, during the interval that is known as the African Humid Period (AHP). During this time, large areas were characterized by a marked increase in precipitation, an expansion of lakes, river systems, and wetlands, and the spread of grassland, shrub land, and woodland vegetation into areas that are currently much drier. Simulations with climate models indicate that the AHP was the result of orbitally forced increase in northern hemisphere summer insolation, which caused the intensification and northward expansion of the boreal summer monsoon. However, feedbacks from ocean circulation, land-surface cover, and greenhouse gases were probably also important.

Lake basins and their sediment archives have provided important information about climate during the AHP, including the overall increases in precipitation and in rates, trajectories, and spatial variations in change at the beginning and the end of the interval. The general pattern is one of apparently synchronous onset of the AHP at the start of the Bølling-Allerød interstadial around 14,700 years ago, although wet conditions were interrupted by aridity during the Younger Dryas stadial. Wetter conditions returned at the start of the Holocene around 11,700 years ago covering much of North Africa and extended into parts of the southern hemisphere, including southeastern Equatorial Africa. During this time, the expansion of lakes and of grassland or shrub land vegetation over the area that is now the Sahara desert, was especially marked. Increasing aridity through the mid-Holocene, associated with a reduction in northern hemisphere summer insolation, brought about the end of the AHP by around 5000–4000 years before present. The degree to which this end was abrupt or gradual and geographically synchronous or time transgressive, remains open to debate. Taken as a whole, the lake sediment records do not support rapid and synchronous declines in precipitation and vegetation across the whole of North Africa, as some model experiments and other palaeoclimate archives have suggested. Lake sediments from basins that desiccated during the mid-Holocene may have been deflated, thus providing a misleading picture of rapid change. Moreover, different proxies of climate or environment may respond in contrasting ways to the same changes in climate. Despite this, there is evidence of rapid (within a few hundred years) termination to the AHP in some regions, with clear signs of a time-transgressive response both north to south and east to west, pointing to complex controls over the mid-Holocene drying of North Africa.
Wound Culture
Authors: Seltzer Mark
Published: April 2017

The concept of a “wound culture” was introduced, in the later 1990s, to provide an alternative description of contemporary society, and, more exactly, to set out an alternative account of the modern and contemporary forms of crime and violence, and the forms of media and institutions, proper to this type of world. In short, the concept redescribed new species and scenes of death and life in a public culture in which addictive and spectacular bodily violence has become public spectacle. Moreover, the paradoxes of self-amplified violence make visible wound culture’s autotropic, or self-turned, character. They raise the question of how we live in, and with, autotropic violence, and how such a world renders its own reality comprehensible to itself. Self-torn forms of life and death become perspicuous, and appear on countless stages throughout our self-reporting world. These are some of the forms though which wounds communicate, and some of the modes in which wound culture itself becomes a medium.
Incarceration Rates in an International Perspective
Authors: Mauer Marc
Published: April 2017

A nation’s rate of incarceration is the number of people incarcerated as a proportion of its total population. Internationally, there is broad variation in the degree to which nations incarcerate their citizens, with a nearly 40-fold difference between the highest and lowest rates. The incarceration rate is often interpreted as a measurement of the degree of punitiveness in a society, although it is an imperfect measurement. Factors that may influence these rates include rates of serious crime, law enforcement and prosecutorial decision making, scale of prison admissions, length of time served in prison, and other means of social control in a society.

Emerging scholarship is exploring the broader societal factors contributing to a nation’s rate of incarceration. These studies explore policy initiatives to prioritize incarceration as a means of crime control, degree of inequality in a society, racial assumptions about crime, and the cultural values of a nation. With the rise of mass incarceration in the United States, a body of research has developed that is assessing the limited public safety benefits and collateral effects of these developments. These counterproductive effects include impacts on family formation and parenting in high-incarceration communities, rates of civic engagement, and the fraying of community bonds and informal social control.
Nordic Noir
Authors: Hill Annette , Turnbull Susan
Published: April 2017

Nordic noir is an emerging crime genre that draws on crime fiction, feature film, and television drama. The term Nordic noir is associated with a region (Scandinavia), with a mood (gloomy and bleak), with a look (dark and grim), and with strong characters and a compelling narrative. Such is the popularity of Nordic noir as a brand for crime that it can also, and somewhat confusingly, be associated with disparate, bleak dramas set in particular locations outside the Scandinavian region (Sweden, Denmark, Norway, Iceland, and Finland), such as Wales, Italy, France, Mexico, and the United States. As such, Nordic noir is a global brand that attracts transnational audiences, and at the same time, it is a genre that offers a specific style of storytelling that has the look and feel of a regional, moody, and compelling crime narrative.

The approach to Nordic noir taken in this article analyzes the genre as multidimensional, involving production and institutional contexts, creative practices, and the practices of audiences and fans. The research uses empirical and theoretical analysis drawing on genre analysis, as well as production and audience studies, including qualitative interviews and participant observations with executive and creative producers, viewers, and fans. Nordic noir is not a fixed genre; rather, it is in a constant process of iteration as it mutates, hybridizes and migrates from one location to another, where it may be received and understood in different ways. The concept of “genre work” is useful in helping to capture and critically analyze Nordic noir from multiple perspectives, taking into account the complex ways in which this genre is a cocreation between industries and audiences. This is particularly evident in the case of the Danish-Swedish coproduction Broen/Bron/The Bridge (2011), which provides an illuminating case study of these processes at work. It is this constantly ongoing notion of genre work that illuminates the fluidity of Nordic noir, where its meaning and symbolic power is cocreated by institutions, producers, and audiences.
Slavery at the Cape
Authors: Worden Nigel
Published: April 2017

Slavery was a mainstay of the labor force of the Cape Colony between its foundation by the Dutch East India Company (VOC) in 1652 and abolition in 1834, by which date the Cape was under British rule. Slaves were transported to the Cape from a wide range of areas in the Indian Ocean world, including South and Southeast Asia, Madagascar, and Mozambique. Some were owned by the VOC and labored on the Company farms, outposts, and docks. The majority were sold to settlers and worked as domestic servants in Cape Town or as laborers on the grain, wine, and pastoral farms of the Cape interior.

Throughout the 18th century slaves outnumbered settlers. Although there were few major revolts, individual resistance was widespread and desertion common. Some runaways joined indigenous groups in the Cape interior, while others formed more isolated maroon communities. Toward the end of the 18th century some slaves claimed individual rights, reflecting the influence of wider revolutionary movements in the Atlantic world. A revolutionary uprising took place in 1808, shortly after the abolition of the slave trade and the takeover of the colony by the British.

In the early 19th century slave resentment continued to grow, especially as a boom in wine production increased labor demands. In the 1820s and early 1830s abolitionist voices were heard in the colony, and slavery was ended at the same time as that in the British Caribbean and Mauritius. Unlike these other British colonies, Cape slaves largely continued to work as farm laborers, and their living and working conditions produced the continued impoverishment of farmworkers in the western Cape region.

Slaves played an important part in the creation of a distinctive creolized Cape culture, notably in the development of the Afrikaans language and Cape musical and culinary traditions. They were also responsible for the growth of Islam in Cape Town and its hinterland, which took a distinctive form influenced by its Southeast Asian origins.
Glacier Retreat and Glacial Lake Outburst Floods (GLOFs)
Authors: Emmer Adam
Published: April 2017

Glacier retreat is considered to be one of the most obvious manifestations of recent and ongoing climate change in the majority of glacierized alpine and high-latitude regions throughout the world. Glacier retreat itself is both directly and indirectly connected to the various interrelated geomorphological/hydrological processes and changes in hydrological regimes. Various types of slope movements and the formation and evolution of lakes are observed in recently deglaciated areas. These are most commonly glacial lakes (ice-dammed, bedrock-dammed, or moraine-dammed lakes).

“Glacial lake outburst flood” (GLOF) is a phrase used to describe a sudden release of a significant amount of water retained in a glacial lake, irrespective of the cause. GLOFs are characterized by extreme peak discharges, often several times in excess of the maximum discharges of hydrometeorologically induced floods, with an exceptional erosion/transport potential; therefore, they can turn into flow-type movements (e.g., GLOF-induced debris flows). Some of the Late Pleistocene lake outburst floods are ranked among the largest reconstructed floods, with peak discharges of up to 107 m3/s and significant continental-scale geomorphic impacts. They are also considered capable of influencing global climate by releasing extremely high amounts of cold freshwater into the ocean. Lake outburst floods associated with recent (i.e., post-Little Ice Age) glacier retreat have become a widely studied topic from the perspective of the hazards and risks they pose to human society, and the possibility that they are driven by anthropogenic climate change.

Despite apparent regional differences in triggers (causes) and subsequent mechanisms of lake outburst floods, rapid slope movement into lakes, producing displacement waves leading to dam overtopping and eventually dam failure, is documented most frequently, being directly (ice avalanche) and indirectly (slope movement in recently deglaciated areas) related to glacial activity and glacier retreat. Glacier retreat and the occurrence of GLOFs are, therefore, closely tied, because glacier retreat is connected to: (a) the formation of new, and the evolution of existing, lakes; and (b) triggers of lake outburst floods (slope movements).
Positive Emotion
Authors: Black Jessica M.
Published: April 2017

Scientific findings from social sciences, neurobiology, endocrinology, and immunology highlight the adaptive benefits of positive emotion and activity to both mental and physical health. Positive activity, such as engagement with music and exercise, can also contribute to favorable health outcomes. This article reviews scientific evidence of the adaptive benefits of positive emotion and activity throughout the life course, with examples drawn from the fetal environment through late adulthood. Specifically, the text weaves together theory and empirical findings from an interdisciplinary literature to describe how positive emotion and activity help to build important cognitive, social, and physical resources throughout the life course.
Catalyzing Interdisciplinary Research and Training: Initial Outcomes and Evolution of the Affinity Research Collaboratives Model
Authors: Ravid Katya , Seta Francesca , Center David , Waters Gloria , Coleman David
Published: April 2017

Team science has been recognized as critical to solving increasingly complex biomedical problems and advancing discoveries in the prevention, diagnosis, and treatment of human disease. In 2009, the Evans Center for Interdisciplinary Biomedical Research (ECIBR) was established in the Department of Medicine at Boston University School of Medicine as a new organizational paradigm to promote interdisciplinary team science. The ECIBR is made up of affinity research collaboratives (ARCs), consisting of investigators from different departments and disciplines who come together to study biomedical problems that are relevant to human disease and not under interdisciplinary investigation at the university. Importantly, research areas are identified by investigators according to their shared interests. ARC proposals are evaluated by a peer review process, and collaboratives are funded annually for up to three years.

Initial outcomes of the first 12 ARCs show the value of this model in fostering successful biomedical collaborations that lead to publications, extramural grants, research networking, and training. The most successful ARCs have been developed into more sustainable organizational entities, including centers, research cores, translational research projects, and training programs.

To further expand team science at Boston University, the Interdisciplinary Biomedical Research Office was established in 2015 to more fully engage the entire university, not just the medical campus, in interdisciplinary research using the ARC mechanism. This approach to promoting team science may be useful to other academic organizations seeking to expand interdisciplinary research at their institutions.
Canadian National Guidelines and Recommendations for Integrating Career Advising Into Medical School Curricula
Authors: Howse Kelly , Harris June , Dalgarno Nancy
Published: April 2017

Career planning, decision making about specialty choice, and preparation for residency matching are significant sources of stress for medical students. Attempts have been made to structure and formalize career advising by including it in accreditation standards. There is an expressed need for national guidelines on career advising for medical students. The Future of Medical Education in Canada Postgraduate (FMEC PG) Implementation Project was created to ensure Canadian medical trainees receive the best education possible. From this, a diverse sub-working group (SWG), representing different Canadian regions, was formed to review career advising processes across the country. The SWG developed, through a modified formal consensus methodology, a strategy for medical student career advising that is adaptable to all schools in alignment with existing accreditation standards. The SWG outlined five guiding principles and five essential elements for Canadian universities offering an MD degree with recommendations on how to integrate the elements into each school’s career advising system. The five essential elements are a structured approach to career advising, information about available career options, elective guidance, preparation for residency applications, and social accountability. This Perspective endorses the view of the FMEC PG Implementation Project that national guidelines are important to ensure Canadian medical schools are consistently meeting accreditation standards by providing reliable and quality career advising to all medical students. The SWG’s position, based on national and provincial feedback, is that these guidelines will stimulate discourse and action regarding the requirements and processes to carry out these recommendations nationwide and share across borders.
Why Health Insurance Matters—and Why Research Evidence Should Too
Authors: Sommers Benjamin D.
Published: April 2017

In the current debate over the future of the Affordable Care Act (ACA), research evidence on the impact of the law and the effects of health insurance coverage in general is critical. Studies of health insurance expansion over the past decade have demonstrated that coverage expansions can produce significant reductions in mortality—particularly among minorities, those living in poorer areas, and those with chronic conditions potentially treatable with timely medical care. More recent studies of the ACA in particular demonstrate that the law has produced historically large reductions in the uninsured rate, with resulting improvements in access to care, perceived quality of care, and self-reported health. Yet much of the general public and many policy makers remain unaware of this evidence. Researchers and clinicians in academic medicine have a role to play in ensuring that critically important health policy decisions are made using rigorous evidence to best protect the interests of our patients.
Absence of Ulnar Artery Inflow Detected by Allen’s Test Prior to Radial Forearm Free Flap
Authors: Taylor Benjamin A. , Alzahrani Faisal , Levi Eric , Taylor S. Mark , Rigby Matthew H. , Trites Jonathan , Hart Robert D.
Published: April 2017

Radial forearm free flaps are commonly used for soft-tissue reconstruction after resection of head and neck cancer. It is perfused by the radial artery, leaving the ulnar artery for perfusion of the hand and digits. The absence of distal ulnar artery and associated superficial palmar arch, however, has not been reported in cadaveric dissection. We report a case of unilateral ulnar artery flow absence, detected by Allen’s test, during preoperative preparation for a radial forearm free flap. Based on the simplicity, safety, and ease, we recommend Allen’s test to be performed preoperatively on every patient for whom such a flap is a consideration.
A Pilot Randomized Trial on Safety and Efficacy of a Novel Topical Combined Inhibitor of Janus Kinase 1/3 and Spleen Tyrosine Kinase for GVHD-Associated Ocular Surface Disease
Authors: Kheirkhah Ahmad , Di Zazzo Antonio , Satitpitakul Vannarut , Fernandez Merle , Magilavy Daniel , Dana Reza
Published: April 2017

Purpose:

Janus kinase (JAK) and spleen tyrosine kinase (SYK) play critical functions in T-cell activation and in inflammation. Because of their antiinflammatory effects, JAK and SYK inhibitors have recently been evaluated in several immunopathogenic disorders. This pilot study was designed to assess the safety and efficacy of a topical combined JAK/SYK inhibitor, R348, ophthalmic solution for treatment of ocular surface disease in graft-versus-host disease (GVHD).

Methods:

This phase 2, double-masked, randomized, pilot trial included 30 patients with ocular surface disease due to GVHD who were randomized to receive topical 0.5% R348, 0.2% R348, or vehicle, twice daily for 12 weeks. Before and after treatment, a comprehensive ophthalmic evaluation was performed, which included Ocular Surface Disease Index (OSDI) questionnaire, Ocular Comfort Index questionnaire, corneal fluorescein staining, conjunctival lissamine green staining, and Schirmer test with anesthesia. Changes in these parameters were compared between the 3 groups.

Results:

The mean decrease in total corneal fluorescein staining at 12 weeks after treatment was higher in the 0.5% R348 group (−6.0 ± 3.9, NEI scoring) compared with the vehicle (−2.1 ± 2.6, P = 0.045) or the 0.2% R348 group (−4.1 ± 3.6, P = 0.34). However, there were no significant differences among the groups in terms of treatment-induced changes in OSDI, Ocular Comfort Index, conjunctival lissamine green staining, or Schirmer scores. R348 eye drops were well tolerated.

Conclusions:

This pilot study indicates that 0.5% R348 JAK/SYK inhibitor ophthalmic solution is well tolerated and may have some therapeutic efficacy in treating ocular GVHD. Larger trials are required to derive more definitive data.
Candidate genes mediating magnetoreception in rainbow trout (
Oncorhynchus mykiss
)
Authors: Fitak Robert R. , Wheeler Benjamin R. , Ernst David A. , Lohmann Kenneth J. , Johnsen Sönke
Published: April 2017

Diverse animals use Earth's magnetic field in orientation and navigation, but little is known about the molecular mechanisms that underlie magnetoreception. Recent studies have focused on two possibilities: (i) magnetite-based receptors; and (ii) biochemical reactions involving radical pairs. We used RNA sequencing to examine gene expression in the brain of rainbow trout (
Oncorhynchus mykiss
) after exposure to a magnetic pulse known to disrupt magnetic orientation behaviour. We identified 181 differentially expressed genes, including increased expression of six copies of the
frim
gene, which encodes a subunit of the universal iron-binding and trafficking protein ferritin. Functions linked to the oxidative effects of free iron (e.g. oxidoreductase activity, transition metal ion binding, mitochondrial oxidative phosphorylation) were also affected. These results are consistent with the hypothesis that a magnetic pulse alters or damages magnetite-based receptors and/or other iron-containing structures, which are subsequently repaired or replaced through processes involving ferritin. Additionally, some genes that function in the development and repair of photoreceptive structures (e.g.
crggm3
,
purp
,
prl
,
gcip
,
crabp1
and
pax6
) were also differentially expressed, raising the possibility that a magnetic pulse might affect structures and processes unrelated to magnetite-based magnetoreceptors.
Preservation of protein expression systems at elevated temperatures for portable therapeutic production
Authors: Karig David K. , Bessling Seneca , Thielen Peter , Zhang Sherry , Wolfe Joshua
Published: April 2017

Many biotechnology capabilities are limited by stringent storage needs of reagents, largely prohibiting use outside of specialized laboratories. Focusing on a large class of protein-based biotechnology applications, we address this issue by developing a method for preserving cell-free protein expression systems for months above room temperature. Our approach realizes unprecedented long-term stability at elevated temperatures by leveraging the sugar alcohol trehalose, a simple, low-cost, open-air drying step, and strategic separation of reaction components during drying. The resulting preservation capacity enables efficient production of a wide range of on-demand proteins under adverse conditions, for instance during emergency outbreaks or in remote locations. To demonstrate application potential, we use cell-free reagents subjected to months of exposure at 37°C and atmospheric conditions to produce sufficient concentrations of a pyocin protein to kill
Pseudomonas aeruginosa
, a troublesome pathogen for traumatic and burn wound injuries. Our work makes possible new biotechnology applications that demand ruggedness and scalability.
Alteration of cerebrovascular haemodynamic patterns due to atrial fibrillation: an
in silico
investigation
Authors: Scarsoglio S. , Saglietto A. , Anselmino M. , Gaita F. , Ridolfi L.
Published: April 2017

There has recently been growing evidence that atrial fibrillation (AF), the most common cardiac arrhythmia, is independently associated with the risk of dementia. This represents a very recent frontier with high social impact for the number of individuals involved and for the expected increase in AF incidence in the next 40 years. Although a number of potential haemodynamic processes, such as microembolisms, altered cerebral blood flow, hypoperfusion and microbleeds, arise as connecting links between the two pathologies, the causal mechanisms are far from clear. An
in silico
approach is proposed that combines in sequence two lumped-parameter schemes, for the cardiovascular system and the cerebral circulation. The systemic arterial pressure is obtained from the cardiovascular system and used as the input for the cerebral circulation, with the aim of studying the role of AF on the cerebral haemodynamics with respect to normal sinus rhythm (NSR), over a 5000 beat recording. In particular, the alteration of the haemodynamic (pressure and flow rate) patterns in the microcirculation during AF is analysed by means of different statistical tools, from correlation coefficients to autocorrelation functions, crossing times, extreme values analysis and multivariate linear regression models. A remarkable signal alteration, such as a reduction in signal correlation (NSR, about 3 s; AF, less than 1 s) and increased probability (up to three to four times higher in AF than in NSR) of extreme value events, emerges for the peripheral brain circulation. The described scenario offers a number of plausible cause–effect mechanisms that might explain the occurrence of critical events and the haemodynamic links relating to AF and dementia.
Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems
Authors: Ruiz-Mirazo Kepa , Briones Carlos , de la Escosura Andrés
Published: April 2017

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided.
Using Fisher information to assess stability in the performance of public transportation systems
Authors: Ahmad Nasir , Derrible Sybil , Cabezas Heriberto
Published: April 2017

Public transportation systems (PTS) are large and complex systems that consist of many modes operated by different agencies to service entire regions. Assessing their performance can therefore be difficult. In this work, we use concepts of Fisher information (FI) to analyse the stability in the performance of PTS in the 372 US urbanized areas (UZA) reported by the National Transit Database. The key advantage of FI is its ability to handle multiple variables simultaneously to provide information about overall trends of a system. It can therefore detect whether a system is stable or heading towards instability, and whether any regime shifts have occurred or are approaching. A regime shift is a fundamental change in the dynamics of the system, e.g. major and lasting change in service. Here, we first provide a brief background on FI and then compute and analyse FI for all US PTS using monthly data from 2002 to 2016; datasets include unlinked passenger trips (i.e. demand) and vehicle revenue miles (i.e. supply). We detect eight different patterns from the results. We find that most PTS are seeking stability, although some PTS have gone through regime shifts. We also observe that several PTS have consistently decreasing FI results, which is a cause for concern. FI results with detailed explanations are provided for eight major UZA.
Reproductive seasonality, sex ratio and philopatry in Argentina's common vampire bats
Authors: Delpietro H. A. , Russo R. G. , Carter G. G. , Lord R. D. , Delpietro G. L.
Published: April 2017

Common vampire bats (Desmodus rotundus) are a key rabies vector in South America. Improved management of this species requires long-term, region-specific information. To investigate patterns of demography and dispersal, we analysed 13 642 captures of common vampire bats in Northern Argentina from the period 1969–2004. In contrast with findings from more tropical regions, we found reproductive seasonality with peak pregnancy in September and peak lactation in February. Curiously, sex ratios were consistently male-biased both in maternity roosts and at foraging sites. Males comprised 57% of 9509 adults caught at night, 57% of 1078 juveniles caught at night, 57% of 603 juveniles caught in roosts during the day, and 55% of 103 newborns and mature fetuses. Most observed roosts were in man-made structures. Movements of 1.5–54 km were most frequent in adult males, followed by young males, adult females and young females. At night, males visited maternity roosts, and non-pregnant, non-lactating females visited bachelor roosts. Males fed earlier in the night. Finally, we report new longevity records for free-ranging vampire bats: 16 and 17 years of age for a female and male, respectively. Our results are consistent with model predictions that sex-biased movements might play a key role in rabies transmission between vampire bat populations.
An RGB colour image steganography scheme using overlapping block-based pixel-value differencing
Authors: Prasad Shiv , Pal Arup Kumar
Published: April 2017

This paper presents a steganographic scheme based on the RGB colour cover image. The secret message bits are embedded into each colour pixel sequentially by the pixel-value differencing (PVD) technique. PVD basically works on two consecutive non-overlapping components; as a result, the straightforward conventional PVD technique is not applicable to embed the secret message bits into a colour pixel, since a colour pixel consists of three colour components, i.e. red, green and blue. Hence, in the proposed scheme, initially the three colour components are represented into two overlapping blocks like the combination of red and green colour components, while another one is the combination of green and blue colour components, respectively. Later, the PVD technique is employed on each block independently to embed the secret data. The two overlapping blocks are readjusted to attain the modified three colour components. The notion of overlapping blocks has improved the embedding capacity of the cover image. The scheme has been tested on a set of colour images and satisfactory results have been achieved in terms of embedding capacity and upholding the acceptable visual quality of the stego-image.
The chinchilla as a novel animal model of pregnancy
Authors: Mikkelsen Emmeli , Lauridsen Henrik , Nielsen Per Mose , Qi Haiyun , Nørlinger Thomas , Andersen Maria Dahl , Uldbjerg Niels , Laustsen Christoffer , Sandager Puk , Pedersen Michael
Published: April 2017

Several parameters are important when choosing the most appropriate animal to model human obstetrics, including gestation period, number of fetuses per gestation and placental structure. The domesticated long-tailed chinchilla (Chinchilla lanigera) is a well-suited and appropriate animal model of pregnancy that often will carry only one offspring and has a long gestation period of 105–115 days. Furthermore, the chinchilla placenta is of the haemomonochorial labyrinthine type and is therefore comparable to the human villous haemomonochorial placenta. This proof-of-concept study demonstrated the feasibility in laboratory settings, and demonstrated the potential of the pregnant chinchilla as an animal model for obstetric research and its potential usefulness for non-invasive measurements in the placenta. We demonstrate measurements of the placental and fetal metabolism (demonstratedin vivoby hyperpolarized MRI andin vitroby qPCR analyses), placental vessels (demonstratedex vivoby contrast-enhanced CT angiography) and overall anatomy (demonstratedin vivoby whole-body CT).
Aggressive behaviours, food deprivation and the
foraging
gene
Authors: Wang Silu , Sokolowski Marla B.
Published: April 2017

A pleiotropic gene governs multiple traits, which might constrain the evolution of complexity due to conflicting selection on these traits. However, if the pleiotropic effect is modular, then this can facilitate synergistic responses to selection on functionally related traits, thereby leveraging the evolution of complexity. To understand the evolutionary consequence of pleiotropy, the relation among functionally different traits governed by the same gene is key. We examined a pleiotropic function of the
foraging
(
for
) gene with its rover and sitter allelic variants in fruit fly,
Drosophila melanogaster
. We measured
for
's effect on adult male aggressive behaviours and whether this effect was shaped by
for
's known role in food-related traits. Rover exhibited higher levels of offensive behaviour than sitters and s2, a sitter-like mutant on rover genetic background. With a Markov chain model, we estimated the rate of aggression escalation, and found that the rover pattern of aggressive escalation more rapidly intensified fights. Subsequent analysis revealed that this was not caused by
for
's effect on food-related traits, suggesting that
for
might directly regulate aggressive behaviours. Food deprivation did not elevate aggression, but reduced intermediate-level aggressive behaviours. Aggression and other foraging-related behaviour might comprise a synergistic trait module underlaid by this pleiotropic gene.
Comparative behavioural observations demonstrate the ‘cleaner’ shrimp
Periclimenes yucatanicus
engages in true symbiotic cleaning interactions
Authors: Titus Benjamin M. , Vondriska Clayton , Daly Marymegan
Published: April 2017

Cleaner shrimps are ecologically important members of coral reef communities, but for many species, cleaner status (i.e. dedicated, facultative and mimic), clientele and ecological role remain unverified or described. On Caribbean coral reefs, the spotted ‘cleaner’ shrimp
Periclimenes yucatanicus
forms symbioses with sea anemones that may serve as cleaning stations for reef fishes. The status of this species as a cleaner is ambiguous: only a single
in situ
cleaning interaction has been reported, and in the only test of its efficacy as a cleaner, it did not effectively reduce parasite loads from surgeonfish. It has subsequently been hypothesized by other authors to be a cleaner mimic. We conduct a comparative investigation of cleaning behaviour between
P. yucatanicus
and the ecologically similar, closely related, dedicated cleaner shrimp
Ancylomenes pedersoni
in Curacao, Netherlands Antilles. We provide the first detailed field observations on cleaning behaviour for
P. yucatanicus
and test multiple behavioural expectations surrounding mimicry in cleaning symbioses. We found that
P. yucatanicus
regularly signals its availability to clean, client fishes visit regularly and the shrimp does engage in true symbiotic cleaning interactions, but these are brief and our video reflects a species that appears hesitant to engage posing clients. In comparison to
A. pedersoni
,
P. yucatanicus
stations had significantly fewer total visits and cleans, and 50% of all cleaning interactions at
P. yucatanicus
stations were shorter than 10 s in total duration. Our behavioural observations confirm that
P. yucatanicus
is a true cleaner shrimp; we reject the hypothesis of mimicry. However, investigation is needed to confirm whether this species is a dedicated or facultative cleaner. We hypothesize that
P. yucatanicus
has a specialized ecological role as a cleaner species, compared to
A. pedersoni
.
Reduced-order modelling of parameter-dependent, linear and nonlinear dynamic partial differential equation models
Authors: Shah A. A. , Xing W. W. , Triantafyllidis V.
Published: April 2017

In this paper, we develop reduced-order models for dynamic, parameter-dependent, linear and nonlinear partial differential equations using proper orthogonal decomposition (POD). The main challenges are to accurately and efficiently approximate the POD bases for new parameter values and, in the case of nonlinear problems, to efficiently handle the nonlinear terms. We use a Bayesian nonlinear regression approach to learn the snapshots of the solutions and the nonlinearities for new parameter values. Computational efficiency is ensured by using manifold learning to perform the emulation in a low-dimensional space. The accuracy of the method is demonstrated on a linear and a nonlinear example, with comparisons with a global basis approach.
Uncertainty quantification and optimal decisions
Authors: Farmer C. L.
Published: April 2017

A mathematical model can be analysed to construct policies for action that are close to optimal for the model. If the model is accurate, such policies will be close to optimal when implemented in the real world. In this paper, the different aspects of an ideal workflow are reviewed: modelling, forecasting, evaluating forecasts, data assimilation and constructing control policies for decision-making. The example of the oil industry is used to motivate the discussion, and other examples, such as weather forecasting and precision agriculture, are used to argue that the same mathematical ideas apply in different contexts. Particular emphasis is placed on (i) uncertainty quantification in forecasting and (ii) how decisions are optimized and made robust to uncertainty in models and judgements. This necessitates full use of the relevant data and by balancing costs and benefits into the long term may suggest policies quite different from those relevant to the short term.
Social learning and the demise of costly cooperation in humans
Authors: Burton-Chellew Maxwell N. , El Mouden Claire , West Stuart A.
Published: April 2017

Humans have a sophisticated ability to learn from others, termed social learning, which has allowed us to spread over the planet, construct complex societies, and travel to the moon. It has been hypothesized that social learning has played a pivotal role in making human societies cooperative, by favouring cooperation even when it is not favoured by genetical selection. However, this hypothesis lacks direct experimental testing, and the opposite prediction has also been made, that social learning disfavours cooperation. We experimentally tested how different aspects of social learning affect the level of cooperation in public-goods games. We found that: (i) social information never increased cooperation and usually led to decreased cooperation; (ii) cooperation was lowest when individuals could observe how successful individuals behaved; and (iii) cooperation declined because individuals preferred to copy successful individuals, who cooperated less, rather than copy common behaviours. Overall, these results suggest that individuals use social information to try and improve their own success, and that this can lead to lower levels of cooperation.
Breaking the cipher: ant eavesdropping on the variational trail pheromone of its termite prey
Authors: Wen Xiao-Lan , Wen Ping , Dahlsjö Cecilia A. L. , Sillam-Dussès David , Šobotník Jan
Published: April 2017

Predators may eavesdrop on their prey using innate signals of varying nature. In regards to social prey, most of the prey signals are derived from social communication and may therefore be highly complex. The most efficient predators select signals that provide the highest benefits. Here, we showed the use of eusocial prey signals by the termite-raiding ant
Odontoponera transversa
.
O. transversa
selected the trail pheromone of termites as kairomone in several species of fungus-growing termites (Termitidae: Macrotermitinae:
Odontotermes yunnanensis
,
Macrotermes yunnanensis
,
Ancistrotermes dimorphus
). The most commonly predated termite,
O. yunnanensis,
was able to regulate the trail pheromone component ratios during its foraging activity. The ratio of the two trail pheromone compounds was correlated with the number of termites in the foraging party. (3
Z
)-Dodec-3-en-1-ol (DOE) was the dominant trail pheromone component in the initial foraging stages when fewer termites were present. Once a trail was established, (3
Z,6Z
)-dodeca-3,6-dien-1-ol (DDE) became the major recruitment component in the trail pheromone and enabled mass recruitment of nest-mates to the food source. Although the ants could perceive both components, they revealed stronger behavioural responses to the recruitment component, DDE, than to the common major component, DOE. In other words, the ants use the trail pheromone information as an indication of suitable prey abundance, and regulate their behavioural responses based on the changing trail pheromone component. The eavesdropping behaviour in ants therefore leads to an arms race between predator and prey where the species specific production of trail pheromones in termites is targeted by predatory ant species.
Spiders in caves
Authors: Mammola Stefano , Isaia Marco
Published: April 2017

World experts of different disciplines, from molecular biology to macro-ecology, recognize the value of cave ecosystems as ideal ecological and evolutionary laboratories. Among other subterranean taxa, spiders stand out as intriguing model organisms for their ecological role of top predators, their unique adaptations to the hypogean medium and their sensitivity to anthropogenic disturbance. As the description of the first eyeless spider (
Stalita taenaria
), an array of papers on subterranean spider biology, ecology and evolution has been published, but a comprehensive review on these topics is still lacking. We provide a general overview of the spider families recorded in hypogean habitats worldwide, we review the different adaptations of hypogean spiders to subterranean life, and we summarize the information gathered so far about their origin, population structure, ecology and conservation status. Finally, we point out the limits of the knowledge we currently have regarding hypogean spiders, aiming to stimulate future research.
Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases
Authors: Gundogdu Aycan , Nalbantoglu Ufuk
Published: April 2017

A short while ago, the human genome and microbiome were analysed simultaneously for the first time as a multi-omic approach. The analyses of heterogeneous population cohorts showed that microbiome components were associated with human genome variations. In-depth analysis of these results reveals that the majority of those relationships are between immune pathways and autoimmune disease-associated microbiome components. Thus, it can be hypothesized that autoimmunity may be associated with homeostatic disequilibrium of the human-microbiome interactome. Further analysis of human genome–human microbiome relationships in disease contexts with tailored systems biology approaches may yield insights into disease pathogenesis and prognosis.
Quantification of cancer cell migration with an integrated experimental-computational pipeline
Authors: Juarez Edwin F. , Garri Carolina , Ghaffarizadeh Ahmadreza , Macklin Paul , Kani Kian
Published: April 2017

We describe an integrated experimental-computational pipeline for quantifying cell migrationin vitro.This pipeline is robust to image noise, open source, and user friendly. The experimental component uses the Oris cell migration assay (Platypus Technologies) to create migration regions. The computational component of the pipeline creates masks in Matlab (MathWorks) to cell-covered regions, uses a genetic algorithm to automatically select the migration region, and outputs a metric to quantify the migration of cells. In this work we demonstrate the utility of our pipeline by quantifying the effects of a drug (Taxol) and of the secreted Anterior Gradient 2 (sAGR2) protein in the migration of MDA-MB-231 cells (a breast cancer cell line). In particular, we show that blocking sAGR2 reduces migration of MDA-MB-231 cells.
Escalation of Memory Length in Finite Populations
Authors: Harrington Kyle , Pollack Jordan
Published: April 2017

The escalation of complexity is a commonly cited benefit of coevolutionary systems, but computational simulations generally fail to demonstrate this capacity to a satisfactory degree. We draw on a macroevolutionary theory of escalation to develop a set of criteria for coevolutionary systems to exhibit escalation of strategic complexity. By expanding on a previously developed model of the evolution of memory length for cooperative strategies by Kristian Lindgren, we resolve previously observed limitations to the escalation of memory length. We present long-term coevolutionary simulations showing that larger population sizes tend to support greater escalation of complexity than smaller population sizes. Additionally, escalation is sensitive to perturbation during transitions of complexity. In whole, a long-standing counter-argument to the ubiquitous nature of coevolution is resolved, suggesting that the escalation of coevolutionary arms races can be harnessed by computational simulations.
Parameter estimation in mathematical models of viral infections using R
Authors: Nguyen Van Kinh , Hernandez-Vargas Esteban A.
Published: April 2017

In recent years, mathematical modeling approaches have played a central role to understand and to quantify mechanisms in different viral infectious diseases. In this approach, biological-based hypotheses are expressed via mathematical relations and then tested based on empirical data. The simulation results can be used to either identify underlying mechanisms, provide predictions on infection outcomes, or evaluate the efficacy of a treatment.

Conducting parameter estimation for mathematical models is not an easy task. Here we detail an approach to conduct parameter estimation and to evaluate the results using the free software R. The method is applicable to influenza virus dynamics at different complexity levels, widening experimentalists capabilities in understanding their data. The parameter estimation approach presented here can be also applied to other viral infections or biological applications.
High-resolution single-cell sequencing of malaria parasites
Authors: Trevino Simon G. , Nkhoma Standwell C. , Nair Shalini , Daniel Benjamin J. , Moncada Karla , Khoswe Stanley , Banda Rachel L. , Nosten François , Cheeseman Ian H.
Published: April 2017

Single-cell genomics is a powerful tool for determining the genetic structure of complex communities of unicellular organisms. Patients infected with the malaria-causing parasite,Plasmodium falciparum, often carry multiple, genetically distinct parasites. Little is known about the diversity and relatedness of these lineages. We have developed an improved single-cell genomics protocol to reconstruct individual haplotypes from infections, a necessary step in uncovering parasite ecology within the host. This approach captures singly-infected red blood cells (iRBCs) by fluorescence-activated cell sorting (FACS) prior to whole genome amplification (WGA) and whole genome sequencing (WGS). Here, we demonstrate that parasites in late cell cycle stages, which contain increased DNA content, are far superior templates for generating high quality genomic data. Targeting of these cells routinely generates near-complete capture of the 23MbP. falciparumgenome (mean breadth of coverage 90.7%) at high efficiency. We used this approach to analyze the genomes of 48 individual cells from a polyclonal malaria infection sampled in Chikhwawa, Malawi. This comprehensive dataset enabled high-resolution estimation of the clonality and the relatedness of parasite haplotypes within the infection, long-standing problems in malaria biology.