bluuebunny/crossref_metadata_2025 huggingface dataset:
Intranasal Fentanyl as a Pain Management Modality During Dressing Changes in the Outpatient Setting
Authors: Nederveld Cindy , Barron Avery , Porter Austin , Recicar John
Published: May 2017

Objective

The purpose of this study was to compare the effectiveness of intranasal (IN) fentanyl versus an oral opioid for managing pain during a pediatric burn dressing change in the outpatient setting.

Methods

Previously healthy children with burn injuries who underwent dressing changes in the outpatient setting were prospectively enrolled in a comparative trial. The patients were matched based on demographics, burn size, and location. The patients were divided into two treatment groups: One group received IN fentanyl immediately before their dressing change, whereas the other group received an oral opioid 30 minutes before their burn clinic visit. Revised Face, Legs, Activity, Cry, Consolability (rFLACC) pain scores were calculated to assess effectiveness.

Results

Sixty-four patients were included (n= 32 per group). rFLACC scores for children who received IN fentanyl decreased from 5.06 ± 2.5 during treatment to 0.50 ± 0.14 after treatment (p< .0001). Similarly, rFLACC scores for children who received an oral opioid decreased from 6.47 ± 2.3 during treatment to 1.19 ± 1.9 after treatment (p< .0001). There was no significant difference in the average rFLACC pain scores of the two groups (p> .05).

Conclusion

IN fentanyl and oral opioid are equally effective for managing pain associated with burn dressing changes in the outpatient setting. However, IN fentanyl showed a more rapid onset of action and provided a more reliable form of pain control.
Everyday Life After Colon Cancer
Authors: Stuhlfauth Susanne , Melby Line , Hellesø Ragnhild
Published: May 2017

Background:

There is little research regarding how everyday life is affected by colon cancer treatment. Few studies exist that exclusively examine patients with Dukes C colon cancer. Most studies include other types of bowel cancer and different stages.

Objectives:

The aims of this study were to explore and describe how colon cancer survivors experience everyday life in general and sexuality in particular after treatment of Dukes C colon cancer.

Methods:

The study is exploratory and descriptive and uses semistructured interviews to collect data. Nine participants were interviewed regarding their everyday lives up until 2 years after concluded treatment. The analysis was done using Graneheim and Lundman’s method of content-analysis.

Results:

Bodily changes are a consequence of colon cancer. Exhaustion, colon problems, and visible bodily changes are some of the challenges that survivors are faced with. Socializing with friends was different, and work had to be facilitated. Social networks proved to be a good support, and spouses were considered to be the most important source of social support. Sexual challenges were experienced by men and women alike.

Conclusion:

Participants experience changes in day-to-day life after cancer treatment. Social networks and the participants’ own coping strategies are key to shaping everyday life after treatment.

Implication for Practice:

It is crucial that healthcare professionals have a holistic view of patients. Both partners and physical activity were identified as an integral part of coping. Seniors are often less active, and some have lost their spouses, it is therefore especially important to examine this demographic. A survey before and after treatment can help optimize rehabilitation.
Staring at My Body
Authors: Chuang Li-Yu , Hsu Yu-Yun , Yin Shu-Yuan , Shu Bih-Ching
Published: May 2017

Background:

Breast cancer takes time for its survivors after a mastectomy to adjust to their changed bodies. There are limited studies about the process of how those survivors accept the changes of their bodies and how they reestablish their new selves.

Objective:

The aim of this study was to understand the perception of body from women diagnosed with breast cancer more than 5 years previously and whose treatment included a mastectomy.

Methods:

A phenomenological method was applied to this study. Women who received a mastectomy at least 5 years previously were invited to participate. Eight participants were recruited from southern Taiwan.

Results:

Twenty transcripts were obtained and analyzed using Colaizzi’s method. Three themes were obtained from the data analysis: “restoration of the body image,” “abandonment of objectification,” and “redefinition of self.” Subthemes were also identified and described.

Conclusion:

The results indicate that women with breast cancer have embodied the recovering experience to a new self and have adapted to identify their new bodies. They overcome being a female body with an absent breast(s) by discovering the value of their existence and being free from self-objectification.

Implications for Practice:

This study contributes to the understanding of the perception of body in long-term breast cancer survivors, which reflects the process of adjusting to the loss of a breast/breasts to reconstructing a new body experience. Health professionals could help and encourage women undergoing a mastectomy to engage in self-recovery by searching for and affirming self-value.
The Differences in Preference for Truth-telling of Patients With Cancer of Different Genders
Authors: Chen Shih-Ying , Wang Hung-Ming , Tang Woung-Ru
Published: May 2017

Background:

Patients' personality traits, especially age, gender, and cancer stage, tend to affect doctors' truth-telling methods. However, there is a lack of studies investigating the influence of patients' gender on truth-telling, especially for Asian cultures.

Objective:

The aims of this study were to qualitatively investigate the differences in preferences for truth-telling for patients with cancer of different genders and explore patients' preferences for decision making.

Methods:

For this descriptive qualitative study, in-depth interviews were conducted with 20 patients with cancer (10 men and 10 women) using a semistructured interview guide. All interviews were audiotaped and transcribed verbatim. Data collection and analysis occurred concurrently; content analysis developed categories and themes.

Results:

Data analysis revealed 2 themes: (1) similar gender preferences for truth-telling and decision making: knowledge of their medical condition, direct and frank truthfulness, and assistance in decision making for subsequent treatment programs, and (2) preferences in truth-telling that differed by gender: women wanted family members present for confirmation of diagnosis, whereas men did not; men preferred truth-telling for only key points of their cancer, whereas women wanted detailed information; and men did not want to know their survival period, whereas women wanted this information.

Conclusions:

Our study revealed similar gender preferences for truth-telling regarding knowledge and decision making; however, preferences differed for family support, scope of information, and survival time.

Implications for Practice:

These findings can serve as a reference for nurses and other healthcare personnel when implementing truth-telling for patients given a diagnosis of cancer. Strategies can be targeted for specific preferences of men and women.
Implementation of a Modified Bedside Handoff for a Postpartum Unit
Authors: Wollenhaup Christine A. , Stevenson Eleanor L. , Thompson Julie , Gordon Helen A. , Nunn Gloria
Published: May 2017

The most frequent cause of sentinel events is poor communication during the nurse-to-nurse handoff process. Standardized methods of handoff do not fit in every patient care setting. The aims of this quality improvement project were to successfully implement a modified bedside handoff model, with some report outside and some inside the patient's room, in a postpartum unit. A structured educational module and champion nurses were used. The new model was evaluated based on the change in compliance, patient satisfaction, and nursing satisfaction. Two months after implementation, there was an increase in nursing compliance in completing all aspects of the model as well as an increase in both patient and staff satisfactions of the process. Replicating this project may help other specialty units adhere to safety recommendations for handoff report.
The Colorado Collaborative for Nursing Research
Authors: Sousa Karen H. , Reeder Blaine , Bondy Jessica , Ozkaynak Mustafa , Weiss Jason
Published: May 2017

Nurse leaders lack timely access to trended electronic health record (EHR) data to drive decision making. Robust nurse-sensitive patient outcome data are difficult to locate in EHRs and largely absent across entities. The Colorado Collaborative for Nursing Research is currently testing a federated data system to get nurse leaders the information they need, when they need it.
Mechanical evidence that flamingos can support their body on one leg with little active muscular force
Authors: Chang Young-Hui , Ting Lena H.
Published: May 2017

Flamingos (Phoenicopteridae) often stand and sleep on one leg for long periods, but it is unknown how much active muscle contractile force they use for the mechanical demands of standing on one leg: body weight support and maintaining balance. First, we demonstrated that flamingo cadavers could passively support body weight on one leg without
any
muscle activity while adopting a stable, unchanging, joint posture resembling that seen in live flamingos. By contrast, the cadaveric flamingo could not be stably held in a two-legged pose, suggesting a greater necessity for active muscle force to stabilize two-legged versus one-legged postures. Our results suggest that flamingos engage a passively engaged gravitational stay apparatus (proximally located) for weight support during one-legged standing. Second, we discovered that live flamingos standing on one leg have markedly reduced body sway during quiescent versus alert behaviours, with the point of force application directly under the distal joint, reducing the need for muscular joint torque. Taken together, our results highlight the possibility that flamingos stand for long durations on one leg without exacting high muscular forces and, thus, with little energetic expenditure.
How does environment influence fighting? The effects of tidal flow on resource value and fighting costs in sea anemones
Authors: Palaoro Alexandre V. , Velasque Mariana , Santos Sandro , Briffa Mark
Published: May 2017

An animal's decision to enter into a fight depends on the interaction between perceived resource value (V) and fighting costs (C). Both could be altered by predictable environmental fluctuations. For intertidal marine animals, such as the sea anemone
Actinia equina
, exposure to high flow during the tidal cycle may increase V by bringing more food. It may also increase C via energy expenditure needed to attach to the substrate. We asked whether simulated tidal cycles would alter decisions in fighting
A. equina
. We exposed some individuals to still water and others to simulated tidal cycles. To gain insights into V, we measured their startle responses before and after exposure to the treatments, before staging dyadic fights. Individuals exposed to flow present shorter startle responses, suggesting that flowing water indicates high V compared with still water. A higher probability of winning against no-flow individuals and longer contests between flow individuals suggests that increased V increases persistence. However, encounters between flow individuals were less likely to escalate, suggesting that C is not directly related to V. Therefore, predictable environmental cycles alter V and C, but in complex ways.
Social bet-hedging in vampire bats
Authors: Carter Gerald G. , Farine Damien R. , Wilkinson Gerald S.
Published: May 2017

Helping kin or nonkin can provide direct fitness benefits, but helping kin also benefits indirect fitness. Why then should organisms invest in cooperative partnerships with nonkin, if kin relationships are available and more beneficial? One explanation is that a kin-limited support network is too small and risky. Even if additional weaker partnerships reduce immediate net cooperative returns, individuals extending cooperation to nonkin can maintain a larger social network which reduces the potential costs associated with losing a primary cooperation partner. Just as financial or evolutionary bet-hedging strategies can reduce risk, investing inquantityof social relationships at the expense of relationshipquality(‘social bet-hedging’) can reduce the risks posed by unpredictable social environments. Here, we provide evidence for social bet-hedging in food-sharing vampire bats. When we experimentally removed a key food-sharing partner, females that previously fed a greater number of unrelated females suffered a smaller reduction in food received. Females that invested in more nonkin bonds did not do better under normal conditions, but they coped better with partner loss. Hence, loss of a key partner revealed the importance of weaker nonkin bonds. Social bet-hedging can have important implications for social network structure by influencing how individuals form relationships.
Inferring stratified parasitoid dispersal mechanisms and parameters from coarse data using mathematical and Bayesian methods
Authors: Strickland Christopher , Kristensen Nadiah P. , Miller Laura
Published: May 2017

Biological invasions have movement at the core of their success. However, due to difficulties in collecting data, medium- and long-distance dispersal of small insects has long been poorly understood and likely to be underestimated. The agricultural release of parasitic hymenoptera, a group of wasps that are critical for biological pest control, represents a rare opportunity to study the spread of insects on multiple spatial scales. As these insects are typically less than 1 mm in size and are challenging to track individually, a first-time biocontrol release will provide a known spatial position and time of initial release for all individuals that are subsequently collected. In this paper, we develop and validate a new mathematical model for parasitoid wasp dispersal from point release, as in the case of biocontrol. The model is derived from underlying stochastic processes but is fully deterministic and admits an analytical solution. Using a Bayesian framework, we then fit the model to an Australian dataset describing the multi-scale wind-borne dispersal pattern ofEretmocerus hayatiZolnerowich & Rose (Hymenoptera: Aphelinidae). Our results confirm that both local movements and long-distance wind dispersal are significant to the movement of parasitoids. The model results also suggest that low velocity winds are the primary indicator of dispersal direction on the field scale shortly after release, and that average wind data may be insufficient to resolve long-distance movement given inherent nonlinearities and heterogeneities in atmospheric flows. The results highlight the importance of collecting wind data when developing models to predict the spread of parasitoids and other tiny organisms.
Multi-cored vortices support function of slotted wing tips of birds in gliding and flapping flight
Authors: KleinHeerenbrink Marco , Johansson L. Christoffer , Hedenström Anders
Published: May 2017

Slotted wing tips of birds are commonly considered an adaptation to improve soaring performance, despite their presence in species that neither soar nor glide. We used particle image velocimetry to measure the airflow around the slotted wing tip of a jackdaw (Corvus monedula) as well as in its wake during unrestrained flight in a wind tunnel. The separated primary feathers produce individual wakes, confirming a multi-slotted function, in both gliding and flapping flight. The resulting multi-cored wingtip vortex represents a spreading of vorticity, which has previously been suggested as indicative of increased aerodynamic efficiency. Considering benefits of the slotted wing tips that are specific to flapping flight combined with the wide phylogenetic occurrence of this configuration, we propose the hypothesis that slotted wings evolved initially to improve performance in powered flight.
Fundamentals of soft robot locomotion
Authors: Calisti M. , Picardi G. , Laschi C.
Published: May 2017

Soft robotics and its related technologies enable robot abilities in several robotics domains including, but not exclusively related to, manipulation, manufacturing, human–robot interaction and locomotion. Although field applications have emerged for soft manipulation and human–robot interaction, mobile soft robots appear to remain in the research stage, involving the somehow conflictual goals of having a deformable body and exerting forces on the environment to achieve locomotion. This paper aims to provide a reference guide for researchers approaching mobile soft robotics, to describe the underlying principles of soft robot locomotion with its pros and cons, and to envisage applications and further developments for mobile soft robotics.
Phosphatase UBLCP1 controls proteasome assembly
Authors: Sun Shuangwu , Liu Sisi , Zhang Zhengmao , Zeng Wang , Sun Chuang , Tao Tao , Lin Xia , Feng Xin-Hua
Published: May 2017

Ubiquitin-like domain-containing C-terminal domain phosphatase 1 (UBLCP1), an FCP/SCP phosphatase family member, was identified as the first proteasome phosphatase. UBLCP1 binds to proteasome subunit Rpn1 and dephosphorylates the proteasome
in vitro
. However, it is still unclear which proteasome subunit(s) are the
bona fide
substrate(s) of UBLCP1 and the precise mechanism for proteasome regulation remains elusive. Here, we show that UBLCP1 selectively binds to the 19S regulatory particle (RP) through its interaction with Rpn1, but not the 20S core particle (CP) or the 26S proteasome holoenzyme. In the RP, UBLCP1 dephosphorylates the subunit Rpt1, impairs its ATPase activity, and consequently disrupts the 26S proteasome assembly, yet it has no effects on the RP assembly from precursor complexes. The Rpn1-binding and phosphatase activities of UBLCP1 are essential for its function on Rpt1 dephosphorylation and proteasome activity both
in vivo
and
in vitro
. Our study establishes the essential role of the UBLCP1/Rpn1/Rpt1 complex in regulating proteasome assembly.
A single migrant enhances the genetic diversity of an inbred puma population
Authors: Gustafson Kyle D. , Vickers T. Winston , Boyce Walter M. , Ernest Holly B.
Published: May 2017

Migration is essential for maintaining genetic diversity among populations, and pumas (Puma concolor) provide an excellent model for studying the genetic impacts of migrants on populations isolated by increasing human development. In densely populated southern California, USA, puma populations on the east and west side of interstate highway 15 (I-15) have become fragmented into a small inbred population on the west side (Santa Ana Mountains) and a relatively larger, more diverse population on the east side (Eastern Peninsular Range). From 146 sampled pumas, genetic analyses indicate seven pumas crossed I-15 over the last 15 years, including four males from west to east, and three males from east to west. However, only a single migrant (named M86) was detected to have produced offspring and contribute to gene flow across the I-15 barrier.Prior to the M86 migration, the Santa Ana population exhibited inbreeding and had significantly lower genetic diversity than the Eastern Peninsular Range population. After M86 emigrated, he sired 11 offspring with Santa Ana females, decreasing inbreeding measures and raising heterozygosity to levels similar to pumas in the Eastern Peninsular Range. The emigration of M86 also introduced new alleles into the Santa Ana population, although allelic richness still remained significantly lower than the Eastern Peninsular population. Our results clearly show the benefit of a single migrant to the genetics of a small, isolated population. However, ongoing development and habitat loss on both sides of I-15 will increasingly strengthen the barrier to successful migration. Further monitoring, and potential human intervention, including minimizing development effects on connectivity, adding or improving freeway crossing structures, or animal translocation, may be needed to ensure adequate gene flow and long-term persistence of the Santa Ana puma population.
Does behaviour affect the dispersal of flatback post-hatchlings in the Great Barrier Reef?
Authors: Wildermann Natalie , Critchell Kay , Fuentes Mariana M. P. B. , Limpus Colin J. , Wolanski Eric , Hamann Mark
Published: May 2017

The ability of individuals to actively control their movements, especially during the early life stages, can significantly influence the distribution of their population. Most marine turtle species develop oceanic foraging habitats during different life stages. However, flatback turtles (Natator depressus) are endemic to Australia and are the only marine turtle species with an exclusive neritic development. To explain the lack of oceanic dispersal of this species, we predicted the dispersal of post-hatchlings in the Great Barrier Reef (GBR), Australia, using oceanographic advection-dispersal models. We included directional swimming in our models and calibrated them against the observed distribution of post-hatchling and adult turtles. We simulated the dispersal of green and loggerhead turtles since they also breed in the same region. Our study suggests that the neritic distribution of flatback post-hatchlings is favoured by the inshore distribution of nesting beaches, the local water circulation and directional swimming during their early dispersal. This combination of factors is important because, under the conditions tested, if flatback post-hatchlings were entirely passively transported, they would be advected into oceanic habitats after 40 days. Our results reinforce the importance of oceanography and directional swimming in the early life stages and their influence on the distribution of a marine turtle species.
First empirical evidence of naturally occurring androgenesis in vertebrates
Authors: Morgado-Santos Miguel , Carona Sara , Vicente Luís , Collares-Pereira Maria João
Published: May 2017

Androgenesis among vertebrates is considered a rare phenomenon, with some cases reported so far, but linked to experiments involving gamete manipulation (artificial androgenesis). Herein, we report the first empirical evidence of the natural occurrence of spontaneous androgenesis in a vertebrate, theSqualius alburnoidesallopolyploid complex. A genetically screened random sample of a natural population was allowed to reproduce in an isolated pond without any human interference, and the viable offspring obtained was later analysed for paternity. Both nuclear and mitochondrial markers showed that the only allodiploid fish found among all the allotriploid offspring was androgenetically produced by an allodiploid male. This specimen had no female nuclear genomic input, and the sequence of the mitochondrial fragment examined differed from that of the male progenitor, matching one of the parental females available in the pond, probably the mother. The possible role of androgenesis in the reproductive dynamics of this highly successful vertebrate complex is discussed.
Oilbirds produce echolocation signals beyond their best hearing range and adjust signal design to natural light conditions
Authors: Brinkløv Signe , Elemans Coen P. H. , Ratcliffe John M.
Published: May 2017

Oilbirds are active at night, foraging for fruits using keen olfaction and extremely light-sensitive eyes, and echolocate as they leave and return to their cavernous roosts. We recorded the echolocation behaviour of wild oilbirds using a multi-microphone array as they entered and exited their roosts under different natural light conditions. During echolocation, the birds produced click bursts (CBs) lasting less than 10 ms and consisting of a variable number (2–8) of clicks at 2–3 ms intervals. The CBs have a bandwidth of 7–23 kHz at −6 dB from signal peak frequency. We report on two unique characteristics of this avian echolocation system. First, oilbirds reduce both the energy and number of clicks in their CBs under conditions of clear, moonlit skies, compared with dark, moonless nights. Second, we document a frequency mismatch between the reported best frequency of oilbird hearing (approx. 2 kHz) and the bandwidth of their echolocation CBs. This unusual signal-to-sensory system mismatch probably reflects avian constraints on high-frequency hearing but may still allow oilbirds fine-scale, close-range detail resolution at the upper extreme (approx. 10 kHz) of their presumed hearing range. Alternatively, oilbirds, by an as-yet unknown mechanism, are able to hear frequencies higher than currently appreciated.
What makes specialized food-caching mountain chickadees successful city slickers?
Authors: Kozlovsky Dovid Y. , Weissgerber Emily A. , Pravosudov Vladimir V.
Published: May 2017

Anthropogenic environments are a dominant feature of the modern world; therefore, understanding which traits allow animals to succeed in these urban environments is especially important. Overall, generalist species are thought to be most successful in urban environments, with better general cognition and less neophobia as suggested critical traits. It is less clear, however, which traits would be favoured in urban environments in highly specialized species. Here, we compared highly specialized food-caching mountain chickadees living in an urban environment (Reno, NV, USA) with those living in their natural environment to investigate what makes this species successful in the city. Using a ‘common garden’ paradigm, we found that urban mountain chickadees tended to explore a novel environment faster and moved more frequently, were better at novel problem-solving, had better long-term spatial memory retention and had a larger telencephalon volume compared with forest chickadees. There were no significant differences between urban and forest chickadees in neophobia, food-caching rates, spatial memory acquisition, hippocampus volume, or the total number of hippocampal neurons. Our results partially support the idea that some traits associated with behavioural flexibility and innovation are associated with successful establishment in urban environments, but differences in long-term spatial memory retention suggest that even this trait specialized for food-caching may be advantageous. Our results highlight the importance of environmental context, species biology, and temporal aspects of invasion in understanding how urban environments are associated with behavioural and cognitive phenotypes and suggest that there is likely no one suite of traits that makes urban animals successful.
Fin-fold development in paddlefish and catshark and implications for the evolution of the autopod
Authors: Tulenko Frank J. , Massey James L. , Holmquist Elishka , Kigundu Gabriel , Thomas Sarah , Smith Susan M. E. , Mazan Sylvie , Davis Marcus C.
Published: May 2017

The evolutionary origin of the autopod involved a loss of the fin-fold and associated dermal skeleton with a concomitant elaboration of the distal endoskeleton to form a wrist and digits. Developmental studies, primarily from teleosts and amniotes, suggest a model for appendage evolution in which a delay in the AER-to-fin-fold conversion fuelled endoskeletal expansion by prolonging the function of AER-mediated regulatory networks. Here, we characterize aspects of paired fin development in the paddlefishPolyodon spathula(a non-teleost actinopterygian) and catsharkScyliorhinus canicula(chondrichthyan) to explore aspects of this model in a broader phylogenetic context. Our data demonstrate that in basal gnathostomes, the autopod markerHoxA13co-localizes with the dermoskeleton componentAnd1to mark the position of the fin-fold, supporting recent work demonstrating a role forHoxA13in zebrafish fin ray development. Additionally, we show that in paddlefish, the proximal fin and fin-fold mesenchyme share a common mesodermal origin, and that components of the Shh/LIM/Gremlin/Fgf transcriptional network critical to limb bud outgrowth and patterning are expressed in the fin-fold with a profile similar to that of tetrapods. Together these data draw contrast with hypotheses of AER heterochrony and suggest that limb-specific morphologies arose through evolutionary changes in the differentiation outcome of conserved early distal patterning compartments.
Courtship song preferences in female zebra finches are shaped by developmental auditory experience
Authors: Chen Yining , Clark Oliver , Woolley Sarah C.
Published: May 2017

The performance of courtship signals provides information about the behavioural state and quality of the signaller, and females can use such information for social decision-making (e.g. mate choice). However, relatively little is known about the degree to which the perception of and preference for differences in motor performance are shaped by developmental experiences. Furthermore, the neural substrates that development could act upon to influence the processing of performance features remains largely unknown. In songbirds, females use song to identify males and select mates. Moreover, female songbirds are often sensitive to variation in male song performance. Consequently, we investigated how developmental exposure to adult male song affected behavioural and neural responses to song in a small, gregarious songbird, the zebra finch. Zebra finch males modulate their song performance when courting females, and previous work has shown that females prefer the high-performance, female-directed courtship song. However, unlike females allowed to hear and interact with an adult male during development, females reared without developmental song exposure did not demonstrate behavioural preferences for high-performance courtship songs. Additionally, auditory responses to courtship and non-courtship song were altered in adult females raised without developmental song exposure. These data highlight the critical role of developmental auditory experience in shaping the perception and processing of song performance.
Memory, not just perception, plays an important role in terrestrial mammalian migration
Authors: Bracis Chloe , Mueller Thomas
Published: May 2017

One of the key questions regarding the underlying mechanisms of mammalian land migrations is how animals select where to go. Most studies assume perception of resources as the navigational mechanism. The possible role of memory that would allow forecasting conditions at distant locations and times based on information about environmental conditions from previous years has been little studied. We study migrating zebra in Botswana using an individual-based simulation model, where perceptually guided individuals use currently sensed resources at different perceptual ranges, while memory-guided individuals use long-term averages of past resources to forecast future conditions. We compare simulated individuals guided by perception or memory on resource landscapes of remotely sensed vegetation data to trajectories of GPS-tagged zebras. Our results show that memory provides a clear signal that best directs migrants to their destination compared to perception at even the largest perceptual ranges. Zebras modelled with memory arrived two to four times, or up to 100 km, closer to the migration destination than those using perception. We suggest that memory in addition to perception is important for directing ungulate migration. Furthermore, our findings are important for the conservation of migratory mammals, as memory informing direction suggests migration routes could be relatively inflexible.
Spatial patterns of Anchoveta (
Engraulis ringens
) eggs and larvae in relation to
p
CO
2
in the Peruvian upwelling system
Authors: Shen Sara G. , Thompson Andrew R. , Correa Jonathan , Fietzek Peer , Ayón Patricia , Checkley David M.
Published: May 2017

Large and productive fisheries occur in regions experiencing or projected to experience ocean acidification. Anchoveta (
Engraulis ringens
) constitute the world's largest single-species fishery and live in one of the ocean's highest
p
CO
2
regions. We investigated the relationship of the distribution and abundance of Anchoveta eggs and larvae to natural gradients in
p
CO
2
in the Peruvian upwelling system. Eggs and larvae, zooplankton, and data on temperature, salinity, chlorophyll
a
and
p
CO
2
were collected during a cruise off Peru in 2013.
p
CO
2
ranged from 167–1392 µatm and explained variability in egg presence, an index of spawning habitat. Zooplankton abundance explained variability in the abundance of small larvae. Within the main spawning and larva habitats (6–10°S), eggs were found in cool, low-salinity, and both extremely low (less than 200 µatm) and high (more than 900 µatm)
p
CO
2
waters, and larvae were collected in warmer, higher salinity, and moderate (400–600 µatm)
p
CO
2
waters. Our data support the hypothesis that Anchoveta preferentially spawned at high
p
CO
2
and these eggs had lower survival. Enhanced understanding of the influence of
p
CO
2
on Anchoveta spawning and larva mortality, together with
p
CO
2
measurements, may enable predictions of ocean acidification effects on Anchoveta and inform adaptive fisheries management.
Positive social behaviours are induced and retained after oxytocin manipulations mimicking endogenous concentrations in a wild mammal
Authors: Robinson Kelly J. , Twiss Sean D. , Hazon Neil , Moss Simon , Pomeroy Patrick P.
Published: May 2017

The neuropeptide hormone oxytocin modulates numerous social and parental behaviours across a wide range of species, including humans. We conducted manipulation experiments on wild grey seals (
Halichoerus grypus
) to determine whether oxytocin increases proximity-seeking behaviour, which has previously been correlated with endogenous oxytocin concentrations in wild seal populations. Pairs of seals that had never met previously were given intravenous injections of 0.41 µg kg
−1
oxytocin or saline and were observed for 1 h post-manipulation. The dose was designed to mimic endogenous oxytocin concentrations during the observation period, and is one of the lowest doses used to manipulate behaviour to date. Seals given oxytocin spent significantly more time in close proximity to each other, confirming that oxytocin causes conspecifics to seek others out and remain close to one another. Aggressive and investigative behaviours also significantly fell after oxytocin manipulations. Despite using a minimal oxytocin dose, pro-social behavioural changes unexpectedly persisted for 2 days despite rapid dose clearance from circulation post-injection. This study verifies that oxytocin promotes individuals staying together, demonstrating how the hormone can form positive feedback loops of oxytocin release following conspecific stimuli, increased motivation to remain in close proximity and additional oxytocin release from stimuli received while in close proximity.
Maintaining mimicry diversity: optimal warning colour patterns differ among microhabitats in Amazonian clearwing butterflies
Authors: Willmott Keith R. , Robinson Willmott Julia C. , Elias Marianne , Jiggins Chris D.
Published: May 2017

Mimicry is one of the best-studied examples of adaptation, and recent studies have provided new insights into the role of mimicry in speciation and diversification. Classical Müllerian mimicry theory predicts convergence in warning signal among protected species, yet tropical butterflies are exuberantly diverse in warning colour patterns, even within communities. We tested the hypothesis that microhabitat partitioning in aposematic butterflies and insectivorous birds can lead to selection for different colour patterns in different microhabitats and thus help maintain mimicry diversity. We measured distribution across flight height and topography for 64 species of clearwing butterflies (Ithomiini) and their co-mimics, and 127 species of insectivorous birds, in an Amazon rainforest community. For the majority of bird species, estimated encounter rates were non-random for the two most abundant mimicry rings. Furthermore, most butterfly species in these two mimicry rings displayed the warning colour pattern predicted to be optimal for anti-predator defence in their preferred microhabitats. These conclusions were supported by a field trial using butterfly specimens, which showed significantly different predation rates on colour patterns in two microhabitats. We therefore provide the first direct evidence to support the hypothesis that different mimicry patterns can represent stable, community-level adaptations to differing biotic environments.
Open Hardware for neuro-prosthesis research: A study about a closed-loop multi-channel system for electrical surface stimulations and measurements
Authors: Rotermund David , Ernst Udo A. , Pawelzik Klaus R.
Published: May 2017

1

Recent progress in neuro-prosthetic technology gives rise to the hope that in the future blind people might regain some degree of visual perception. It was shown that electrically stimulating the brain can be used to produce simple visual impressions of light blobs (phosphenes). However, this perception is very far away from natural sight. For developing the next generation of visual prostheses, real-time closed-loop stimulators which measure the actual neuronal activities and on this basis determine the required stimulation pattern. This leads to the challenge to design a system that can produce arbitrary stimulation-patterns with up to ±70V and with up to 25mA while measuring neuronal signals with amplitudes in the order of mV. Furthermore, the interruption of the measurement by stimulation must be as short as possible and the system needs to scale to hundreds of electrodes. We discuss how such a system and especially its current pumps and input protection need to be designed and which problems arise. We condense our findings into an example design for which we provide all design files (boards, firmwares and software) as open-source. This is a first step in taking the existing open-sourcewww.open-ephys.orgrecording system and converting it into a closed-loop experimental setup for neuro-prosthetic research.
Association Mapping from Sequencing Reads UsingK-mers
Authors: Rahman Atif , Hallgrímsdóttir Ingileif , Eisen Michael B. , Pachter Lior
Published: May 2017

Genome wide association studies (GWAS) rely on microarrays, or more recently mapping of whole-genome sequencing reads, to genotype individuals. The reliance on prior sequencing of a reference genome for the organism on which the association study is to be performed limits the scope of association studies, and also precludes the identification of differences between cases and controls outside of the reference. We present an alignment free method for association studies that is based on counting k-mers in sequencing reads, testing for associations directly between k-mers and the trait of interest, and local assembly of the statistically significant k-mers to identify sequence differences. Results with simulated data and an analysis of the 1000 genomes data provide a proof of principle for the approach. In a pairwise comparison of the Toscani in Italia (TSI) and the Yoruba in Ibadan, Nigeria (YRI) populations we find that sequences identified by our method largely agree with results obtained using standard GWAS based on variant calling from mapped reads. However unlike standard GWAS, we find that our method identifies associations with structural variations and sites not present in the reference genome revealing sequences absent from the human reference genome. We also analyze data from the Bengali from Bangladesh (BEB) population to explore possible genetic basis of high rate of mortality due to cardiovascular diseases (CVD) among South Asians and find significant differences in frequencies of a number of non-synonymous variants in genes linked to CVDs between BEB and TSI samples, including the site rs1042034, which has been associated with higher risk of CVDs previously, and the nearby rs676210 in theApolipoprotein B (ApoB)gene.

Author Summary

We present a method for associating regions in genomes to traits or diseases. The method is based on finding differences in frequencies of short strings of letters in sequencing reads and do not require reads to be aligned to a reference genome. This makes it applicable to study of organisms with no or incomplete reference genomes. We test our method with simulated data and sequencing data from the 1000 genomes project and find agreement with the conventional approach based on alignment to a reference genome. In addition, our method finds associations with sequences not in reference genomes and reveals sequences missing from the human reference genome. We also explore high rates of mortality due to cardiovascular diseases among South Asians and find prevalence of variations in genes associated with heart diseases in samples from the Bengali from Bangladesh population including one that has been reported to be associated with early onset of cardiovascular diseases.
Hormone-dependent control of developmental timing through regulation of chromatin accessibility
Authors: Uyehara Christopher M. , Nystrom Spencer L. , Niederhuber Matthew J. , Leatham-Jensen Mary , Ma Yiqin , Buttitta Laura A. , McKay Daniel J.
Published: May 2017

Specification of tissue identity during development requires precise coordination of gene expression in both space and time. Spatially, master regulatory transcription factors are required to control tissue-specific gene expression programs. However, the mechanisms controlling how tissue-specific gene expression changes over time are less well understood. Here, we show that hormone-induced transcription factors control temporal gene expression by regulating the accessibility of DNA regulatory elements. Using the Drosophila wing, we demonstrate that temporal changes in gene expression are accompanied by genome-wide changes in chromatin accessibility at temporal-specific enhancers. We also uncover a temporal cascade of transcription factors following a pulse of the steroid hormone ecdysone such that different times in wing development can be defined by distinct combinations of hormone-induced transcription factors. Finally, we show that the ecdysone-induced transcription factor E93 controls temporal identity by directly regulating chromatin accessibility across the genome. Notably, we found that E93 controls enhancer activity through three different modalities, including promoting accessibility of late-acting enhancers and decreasing accessibility of early-acting enhancers. Together, this work supports a model in which an extrinsic signal triggers an intrinsic transcription factor cascade that drives development forward in time through regulation of chromatin accessibility.
Validation of experimental charge-density refinement strategies: when do we overfit?
Authors: Krause Lennard , Niepötter Benedikt , Schürmann Christian J. , Stalke Dietmar , Herbst-Irmer Regine
Published: May 2017

A cross-validation method is supplied to judge between various strategies in multipole refinement procedures. Its application enables straightforward detection of whether the refinement of additional parameters leads to an improvement in the model or an overfitting of the given data. For all tested data sets it was possible to prove that the multipole parameters of atoms in comparable chemical environments should be constrained to be identical. In an automated approach, this method additionally delivers parameter distributions ofkdifferent refinements. These distributions can be used for further error diagnostics,e.g.to detect erroneously defined parameters or incorrectly determined reflections. Visualization tools show the variation in the parameters. These different refinements also provide rough estimates for the standard deviation of topological parameters.
Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation
Authors: Martin-Garcia Jose M. , Conrad Chelsie E. , Nelson Garrett , Stander Natasha , Zatsepin Nadia A. , Zook James , Zhu Lan , Geiger James , Chun Eugene , Kissick David , Hilgart Mark C. , Ogata Craig , Ishchenko Andrii , Nagaratnam Nirupa , Roy-Chowdhury Shatabdi , Coe Jesse , Subramanian Ganesh , Schaffer Alexander , James Daniel , Ketwala Gihan , Venugopalan Nagarajan , Xu Shenglan , Corcoran Stephen , Ferguson Dale , Weierstall Uwe , Spence John C. H. , Cherezov Vadim , Fromme Petra , Fischetti Robert F. , Liu Wei
Published: May 2017

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2Aadenosine receptor (A2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suitesCheetahandCrystFELenabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
Grazing-incidence small-angle X-ray scattering (GISAXS) on small periodic targets using large beams
Authors: Pflüger Mika , Soltwisch Victor , Probst Jürgen , Scholze Frank , Krumrey Michael
Published: May 2017

Grazing-incidence small-angle X-ray scattering (GISAXS) is often used as a versatile tool for the contactless and destruction-free investigation of nanostructured surfaces. However, due to the shallow incidence angles, the footprint of the X-ray beam is significantly elongated, limiting GISAXS to samples with typical target lengths of several millimetres. For many potential applications, the production of large target areas is impractical, and the targets are surrounded by structured areas. Because the beam footprint is larger than the targets, the surrounding structures contribute parasitic scattering, burying the target signal. In this paper, GISAXS measurements of isolated as well as surrounded grating targets in Si substrates with line lengths from 50 µm down to 4 µm are presented. For the isolated grating targets, the changes in the scattering patterns due to the reduced target length are explained. For the surrounded grating targets, the scattering signal of a 15 µm × 15 µm target grating structure is separated from the scattering signal of 100 µm × 100 µm nanostructured surroundings by producing the target with a different orientation with respect to the predominant direction of the surrounding structures. As virtually all lithographically produced nanostructures have a predominant direction, the described technique allows GISAXS to be applied in a range of applications,e.g. for characterization of metrology fields in the semiconductor industry, where up to now it has been considered impossible to use this method due to the large beam footprint.