bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-term Results After Extensive Soft Tissue Release in Very Severe Congenital Clubfeet
Authors: Alkar Fanny , Louahem Djamel , Bonnet Frédérique , Patte Karine , Delpont Marion , Cottalorda Jérôme
Published: December 2015

Background:

The purpose of this study was to determine the long-term results, at an average follow-up of 22 years, in 66 patients (105 clubfeet) with very severe congenital idiopathic clubfeet according to the Dimeglio-Bensahel scale.

Methods:

Patients were treated with an extensive soft tissue release in infancy. Results of the treatment were assessed according to the 100-point system of Ghanem-Seringe. At the latest follow-up, all participants were evaluated with regard to pain and the overall function of the lower extremities. At the latest follow-up, anteroposterior and lateral radiographs of the affected foot and the contralateral normal foot, when applicable, were performed.

Results:

In total, 92% of the patients were satisfied. The mean functional score of Ghanem-Seringe was 70.4 points. No foot had an excellent result, 19 feet had a good result, 16 had a fair result, and 70 had a poor result. A total of 86 feet were painful after strenuous activities or during walking. Eleven patients walked with a limp. In total, 82 feet were stiff. Ankle dorsiflexion and plantar flexion averaged 4.0±4.5 degrees and 19.9±10.7 degrees. Bone deformations such as flattening of the talar dome were observed in 93 feet. Among these feet, the Ghanem score was significantly lower (P<0.05). Necrosis of the navicular was present in 28 feet and subluxation in 82 feet. In total, 32 feet had moderate osteoarthritis.

Discussion:

Results revealed that despite anatomically and radiologically imperfect clubfeet, most patients demonstrated satisfaction. Satisfaction was not significantly correlated with residual deformity, but with the sensation of a normal gait by the patient and the high initial Dimeglio-Bensahel score. Female patients were significantly less satisfied than male patients because they were more constrained in their social life than boys. Their main dissatisfaction was the atrophy of the calf. We noted several residual deformations. Plantar release seems to contribute to the high rate of overcorrection in our series. Extensive posterolateral and plantar releases in very severe clubfeet was responsible for sequelae, morphologic, anatomic, and functional, especially in adulthood. Deterioration of results over time was confirmed by our series.

Level of Evidence:

Level IV.
The Fate of the Iliopsoas Muscle in Long-term Follow-up After Open Reduction With a Medial Approach in Developmental Dysplasia of the Hip. Part 2: Isokinetic Muscle Strength Evaluation
Authors: Yilmaz Serdar , Aksahin Ertugrul , Ersoz Murat , Bicimoglu Ali
Published: December 2015

Background:

The impact on long-term weakness of hip flexion of complete iliopsoas tenotomy during open reduction of developmental hip dysplasia with a medial approach has not yet been fully clarified. The purpose of this study was to investigate the isokinetic muscle strength (IMS) of hip flexor and extensor muscles in these patients and also to analyze the effect of spontaneous reattachment of the iliopsoas muscle on IMS measurements.

Methods:

The study included 20 patients. Earlier magnetic resonance imaging examination of all the patients revealed spontaneous reattachment of the iliopsoas in 18 (90%) patients. IMS measurements were performed at 60 and 150 degrees/s. The peak torque, total work (TW), average power (AP), work fatigue, and agonist to antagonist muscle ratio of the operated and nonoperated hips were recorded separately for flexors and extensors. The effect of iliopsoas reattachment on IMS was also evaluated.

Results:

The mean follow-up period was 16.65±2.16 (13 to 20) years. Total work (P=0.013) and average power (P=0.009) of the flexor muscles and work fatigue of the extensor muscles (P=0.030) of the operated hip were significantly decreased when compared with the nonoperated hips at 150 degrees/s. There was no significant difference between the flexor muscles of the operated and nonoperated hips (P<0.05) at 60 degrees/s and extensor muscles (P<0.05) at 150 degrees/s. In addition, patients without reattachment had lower IMS in the operated hips.

Discussion:

Flexor muscle strength was decreased in the operated hip against low resistance in long-term follow-up after iliopsoas tenotomy. This may reflect that hip muscle strength was decreased after prolonged activities such as sports. However, in forceful activities flexor muscle strength was retained due to iliopsoas reattachment. On the basis of this study we thought that spontaneous reattachment of the iliopsoas tendon substantially preserves muscle strength. Nonetheless possible efforts should be made to surgically reattach the psoas tendon to preserve strength of the muscle.

Level of Evidence:

Therapeutic level IV.
Liposome Bupivacaine for Postsurgical Analgesia in Patients Undergoing Robotically Assisted Cardiac Surgery
Authors: Balkhy Husam H. , Arnsdorf Susan , Krienbring Dorothy , Urban John
Published: December 2015

Objective

Despite the advantages of robotically assisted cardiac surgery over conventional open sternotomy, robotically assisted surgery may be associated with substantial postsurgical pain arising from multiple incisions and access ports. This single-site, retrospective chart review evaluated the impact of liposome bupivacaine compared with bupivacaine HCl on postsurgical pain management in patients undergoing robotically assisted endoscopic cardiac surgery.

Methods

Sequential patient cohorts undergoing robotically assisted cardiac surgery received either 0.25% bupivacaine HCl (100 mg in 40 mL, n = 30) or liposome bupivacaine (266 mg in 20 mL, expanded to 40 mL with 0.9% sterile normal saline, n = 30) intraoperatively via equal-volume infiltration across port sites. Outcome measures, collected from the day of surgery through postoperative day 3, were daily and total use of opioid analgesics (converted to morphine equivalents), pain intensity (11-point numeric rating scale), and incidence of postoperative nausea and vomiting.

Results

Median length of hospital stay was 4 days in the liposome bupivacaine group and 3 days in the bupivacaine HCl group. Patients receiving liposome bupivacaine had numerically lower mean pain scores (at six of seven time points), reduced mean opioid consumption, and a reduced incidence of postoperative nausea and vomiting compared with those receiving bupivacaine HCl, although none of the differences reached statistical significance.

Conclusions

Results from this small retrospective, observational study suggest that liposome bupivacaine may improve postsurgical pain relief and reduce postsurgical opioid consumption, in comparison with bupivacaine HCl, in patients undergoing robotically assisted cardiac surgery. Larger prospective studies of liposome bupivacaine in this setting are warranted.
Cognitive and Affective Symptoms Experienced by Cancer Patients Receiving High-Dose Intravenous Interleukin 2 Therapy
Authors: Mann Tara K. , Dail Robin B. , Bailey Donald E.
Published: December 2015

Background:

Alterations in cognitive/affective functioning are among the most challenging adverse effects experienced by 80% of patients with metastatic melanoma and metastatic renal cell carcinoma undergoing high-dose interleukin 2 (IL-2) therapy.

Objective:

The purpose of this literature review is to describe what is known about IL-2–induced cognitive/affective symptoms, their prevalence, and level of severity and synthesize findings to determine areas for future research to address symptom management challenges. This review describes the IL-2 patient experience and the pathophysiology leading to these changes.

Methods:

An online electronic search using PubMed was performed to identify relevant literature published between 1992 and 2015. Of the original 113 articles, information was extracted from 9 articles regarding cognitive symptoms, affective symptoms, sample size, research design, reliability, and validity.

Results:

Our review suggests that the trajectories, breadth, and depth of cognitive/affective symptoms have yet to be described. Despite intervention studies designed to address the psychosocial complications of IL-2, an understanding of the level of altered cognitive/affective symptoms experienced by IL-2 patients remains unclear.

Conclusion:

Our literature review reveals a lack of standardization when assessing, reporting, and managing cognitive/affective symptoms. Patients/family members have reported cognitive/affective symptoms to be the most alarming and difficult symptoms, yet these symptoms are not adequately screened for, and patients were not informed about potential changes.

Implications for Practice:

Assessing patients for cognitive/affective alterations is important to reduce anxiety while improving outcomes. Education about the illness trajectory (what to expect during/after treatment) can help care partners/patients set realistic shared expectations and increase coping.
Involvement of the avian song system in reproductive behaviour
Authors: Wild J. Martin , Botelho João F.
Published: December 2015

The song system of songbirds consists of an interconnected set of forebrain nuclei that has traditionally been regarded as dedicated to the learning and production of song. Here, however, we suggest that the song system could also influence muscles used in reproductive behaviour, such as the cloacal sphincter muscle. We show that the same medullary nucleus, retroambigualis (RAm), that projects upon spinal motoneurons innervating expiratory muscles (which provide the pressure head for vocalization) and upon vocal motoneurons for respiratory–vocal coordination also projects upon cloacal motoneurons. Furthermore, RAm neurons projecting to sacral spinal levels were shown to receive direct projections from nucleus robustus arcopallialis (RA) of the forebrain song system. Thus, by indicating a possible disynaptic relationship between RA and motoneurons innervating the reproductive organ, in both males and females, these results potentially extend the role of the song system to include consummatory as well as appetitive aspects of reproductive behaviour.
Is the scaling of swim speed in sharks driven by metabolism?
Authors: Jacoby David M. P. , Siriwat Penthai , Freeman Robin , Carbone Chris
Published: December 2015

The movement rates of sharks are intrinsically linked to foraging ecology, predator–prey dynamics and wider ecosystem functioning in marine systems. During ram ventilation, however, shark movement rates are linked not only to ecological parameters, but also to physiology, as minimum speeds are required to provide sufficient water flow across the gills to maintain metabolism. We develop a geometric model predicting a positive scaling relationship between swim speeds in relation to body size and ultimately shark metabolism, taking into account estimates for the scaling of gill dimensions. Empirical data from 64 studies (26 species) were compiled to test our model while controlling for the influence of phylogenetic similarity between related species. Our model predictions were found to closely resemble the observed relationships from tracked sharks, providing a means to infer mobility in particularly intractable species.
Landmark-free geometric methods in biological shape analysis
Authors: Koehl Patrice , Hass Joel
Published: December 2015

In this paper, we propose a new approach for computing a distance between two shapes embedded in three-dimensional space. We take as input a pair of triangulated genus zero surfaces that are topologically equivalent to spheres with no holes or handles, and construct a discrete conformal mapfbetween the surfaces. The conformal map is chosen to minimize a symmetric deformation energyEsd(f) which we introduce. This measures the distance offfrom an isometry, i.e. a non-distorting correspondence. We show that the energy of the minimizing map gives a well-behaved metric on the space of genus zero surfaces. In contrast to most methods in this field, our approach does not rely on any assignment of landmarks on the two surfaces. We illustrate applications of our approach to geometric morphometrics using three datasets representing the bones and teeth of primates. Experiments on these datasets show that our approach performs remarkably well both in shape recognition and in identifying evolutionary patterns, with success rates similar to, and in some cases better than, those obtained by expert observers.
Grand challenges in space synthetic biology
Authors: Menezes Amor A. , Montague Michael G. , Cumbers John , Hogan John A. , Arkin Adam P.
Published: December 2015

Space synthetic biology is a branch of biotechnology dedicated to engineering biological systems for space exploration, industry and science. There is significant public and private interest in designing robust and reliable organisms that can assist on long-duration astronaut missions. Recent work has also demonstrated that such synthetic biology is a feasible payload minimization and life support approach as well. This article identifies the challenges and opportunities that lie ahead in the field of space synthetic biology, while highlighting relevant progress. It also outlines anticipated broader benefits from this field, because space engineering advances will drive technological innovation on Earth.
Biomechanical rupture risk assessment of abdominal aortic aneurysms based on a novel probabilistic rupture risk index
Authors: Polzer Stanislav , Gasser T. Christian
Published: December 2015

A rupture risk assessment is critical to the clinical treatment of abdominal aortic aneurysm (AAA) patients. The biomechanical AAA rupture risk assessment quantitatively integrates many known AAA rupture risk factors but the variability of risk predictions due to model input uncertainties remains a challenging limitation. This study derives a probabilistic rupture risk index (PRRI). Specifically, the uncertainties in AAA wall thickness and wall strength were considered, and wall stress was predicted with a state-of-the-art deterministic biomechanical model. The discriminative power of PRRI was tested in a diameter-matched cohort of ruptured (
n
= 7) and intact (
n
= 7) AAAs and compared to alternative risk assessment methods. Computed PRRI at 1.5 mean arterial pressure was significantly (
p
= 0.041) higher in ruptured AAAs (20.21(s.d. 14.15%)) than in intact AAAs (3.71(s.d. 5.77)%). PRRI showed a high sensitivity and specificity (discriminative power of 0.837) to discriminate between ruptured and intact AAA cases. The underlying statistical representation of stochastic data of wall thickness, wall strength and peak wall stress had only negligible effects on PRRI computations. Uncertainties in AAA wall stress predictions, the wide range of reported wall strength and the stochastic nature of failure motivate a probabilistic rupture risk assessment. Advanced AAA biomechanical modelling paired with a probabilistic rupture index definition as known from engineering risk assessment seems to be superior to a purely deterministic approach.
Prey should hide more randomly when a predator attacks more persistently
Authors: Gal Shmuel , Alpern Steve , Casas Jérôme
Published: December 2015

When being searched for and then (if found) pursued by a predator, a prey animal has a choice between choosing very randomly among hiding locations so as to be hard to find or alternatively choosing a location from which it is more likely to successfully flee if found. That is, the prey can choose to be hard to find or hard to catch, if found. In our model, capture of prey requires both finding it and successfully pursuing it. We model this dilemma as a zero-sum repeated game between predator and prey, with the eventual capture probability as the pay-off to the predator. We find that the more random hiding strategy is better when the chances of repeated pursuit, which are known to be related to area topography, are high. Our results extend earlier results of Gal and Casas, where there was at most only a single pursuit. In that model, hiding randomly was preferred by the prey when the predator has only a few looks. Thus, our new multistage model shows that the effect of more potential looks is opposite. Our results can be viewed as a generalization of search games to the repeated game context and are in accordance with observed escape behaviour of different animals.
The miR-302/367 cluster: a comprehensive update on its evolution and functions
Authors: Gao Zeqian , Zhu Xueliang , Dou Yongxi
Published: December 2015

microRNAs are a subclass of small non-coding RNAs that fine-tune the regulation of gene expression at the post-transcriptional level. The miR-302/367 cluster, generally consisting of five members, miR-367, miR-302d, miR-302a, miR-302c and miR-302b, is ubiquitously distributed in vertebrates and occupies an intragenic cluster located in the gene
La-related protein 7
(
LARP7
). The cluster was demonstrated to play an important role in diverse biological processes, such as the pluripotency of human embryonic stem cells (hESCs), self-renewal and reprogramming. This paper provides an overview of the mir-302/367 cluster, discusses our current understanding of the cluster's evolutionary history and transcriptional regulation and reviews the literature surrounding the cluster's roles in cell cycle regulation, epigenetic regulation and different cellular signalling pathways.
High-content screening identifies a role for Na
+
channels in insulin production
Authors: Szabat Marta , Modi Honey , Ramracheya Reshma , Girbinger Vroni , Chan Forson , Lee Jason T. C. , Piske Micah , Kamal Sepehr , Carol Yang Yu Hsuan , Welling Andrea , Rorsman Patrik , Johnson James D.
Published: December 2015

Insulin production is the central feature of functionally mature and differentiated pancreatic
β
-cells. Reduced insulin transcription and dedifferentiation have been implicated in type 2 diabetes, making drugs that could reverse these processes potentially useful. We have previously established ratiometric live-cell imaging tools to identify factors that increase insulin promoter activity and promote
β
-cell differentiation. Here, we present a single vector imaging tool with eGFP and mRFP, driven by the
Pdx1
and
Ins1
promoters, respectively, targeted to the nucleus to enhance identification of individual cells in a high-throughput manner. Using this new approach, we screened 1120 off-patent drugs for factors that regulate
Ins1
and
Pdx1
promoter activity in MIN6
β
-cells. We identified a number of compounds that positively modulate
Ins1
promoter activity, including several drugs known to modulate ion channels. Carbamazepine was selected for extended follow-up, as our previous screen also identified this use-dependent sodium channel inhibitor as a positive modulator of
β
-cell survival. Indeed, carbamazepine increased
Ins1
and
Ins2
mRNA in primary mouse islets at lower doses than were required to protect
β
-cells. We validated the role of sodium channels in insulin production by examining Nav1.7 (
Scn9a
) knockout mice and remarkably islets from these animals had dramatically elevated insulin content relative to wild-type controls. Collectively, our experiments provide a starting point for additional studies aimed to identify drugs and molecular pathways that control insulin production and
β
-cell differentiation status. In particular, our unbiased screen identified a novel role for a
β
-cell sodium channel gene in insulin production.
Clover root exudate produces male-biased sex ratios and accelerates male metamorphic timing in wood frogs
Authors: Lambert Max R.
Published: December 2015

In amphibians, abnormal metamorph sex ratios and sexual development have almost exclusively been considered in response to synthetic compounds like pesticides or pharmaceuticals. However, endocrine-active plant chemicals (i.e. phytoestrogens) are commonly found in agricultural and urban waterways hosting frog populations with deviant sexual development. Yet the effects of these compounds on amphibian development remain predominantly unexplored. Legumes, like clover, are common in agricultural fields and urban yards and exude phytoestrogen mixtures from their roots. These root exudates serve important ecological functions and may also be a source of phytoestrogens in waterways. I show that clover root exudate produces male-biased sex ratios and accelerates male metamorphosis relative to females in low and intermediate doses of root exudate. My results indicate that root exudates are a potential source of contaminants impacting vertebrate development and that humans may be cultivating sexual abnormalities in wildlife by actively managing certain plant species.
No early gender effects on energetic status and life history in a salmonid
Authors: Régnier Thomas , Labonne Jacques , Chat Joëlle , Yano Ayaka , Guiguen Yann , Bolliet Valérie
Published: December 2015

Throughout an organism's early development, variations in physiology and behaviours may have long lasting consequences on individual life histories. While a large part of variation in critical life-history transitions remains unexplained, a significant proportion may be caused by early gender effects as part of gender-specific life histories shaped by sexual selection. In this study, we investigated the presence of early gender effects on the timing of emergence from gravel and the energetic status of brown trout (
Salmo trutta
) early stages. To investigate this question, individual measures of emergence timing, metabolic rate and energetic content were coupled for the first time with the use of a recent genetic marker for
sdY
(sexually dimorphic on the Y-chromosome), a master sex-determining gene. Our results show that gender does not influence the energetic content of emerging juveniles or their emergence timing. These findings suggest that gender differences may appear later throughout salmonid life history and that selective pressures associated with the critical period of emergence from gravel may shape early life-history traits similarly in both males and females.
Comparing and modelling land use organization in cities
Authors: Lenormand Maxime , Picornell Miguel , Cantú-Ros Oliva G. , Louail Thomas , Herranz Ricardo , Barthelemy Marc , Frías-Martínez Enrique , San Miguel Maxi , Ramasco José J.
Published: December 2015

The advent of geolocated information and communication technologies opens the possibility of exploring how people use space in cities, bringing an important new tool for urban scientists and planners, especially for regions where data are scarce or not available. Here we apply a functional network approach to determine land use patterns from mobile phone records. The versatility of the method allows us to run a systematic comparison between Spanish cities of various sizes. The method detects four major land use types that correspond to different temporal patterns. The proportion of these types, their spatial organization and scaling show a strong similarity between all cities that breaks down at a very local scale, where land use mixing is specific to each urban area. Finally, we introduce a model inspired by Schelling's segregation, able to explain and reproduce these results with simple interaction rules between different land uses.
First evidence of hybridization between golden jackal (Canis aureus) and domestic dog (Canis familiaris) as revealed by genetic markers
Authors: Galov Ana , Fabbri Elena , Caniglia Romolo , Arbanasić Haidi , Lapalombella Silvana , Florijančić Tihomir , Bošković Ivica , Galaverni Marco , Randi Ettore
Published: December 2015

Interspecific hybridization is relatively frequent in nature and numerous cases of hybridization between wild canids and domestic dogs have been recorded. However, hybrids between golden jackals (Canis aureus) and other canids have not been described before. In this study, we combined the use of biparental (15 autosomal microsatellites and three major histocompatibility complex (MHC) loci) and uniparental (mtDNA control region and a Y-linkedZfyintron) genetic markers to assess the admixed origin of three wild-living canids showing anomalous phenotypic traits. Results indicated that these canids were hybrids between golden jackals and domestic dogs. One of them was a backcross to jackal and another one was a backcross to dog, confirming that golden jackal–domestic dog hybrids are fertile. The uniparental markers showed that the direction of hybridization, namely females of the wild species hybridizing with male domestic dogs, was common to most cases of canid hybridization. A melanistic 3bp-deletion at theKlocus (β-defensin CDB103 gene), that was absent in reference golden jackal samples, but was found in a backcross to jackal with anomalous black coat, suggested its introgression from dogs via hybridization. Moreover, we demonstrated that MHC sequences, although rarely used as markers of hybridization, can be also suitable for the identification of hybrids, as long as haplotypes are exclusive for the parental species.
A new Early Oligocene toothed ‘baleen’ whale (Mysticeti: Aetiocetidae) from western North America: one of the oldest and the smallest
Authors: Marx Felix G. , Tsai Cheng-Hsiu , Fordyce R. Ewan
Published: December 2015

Archaic toothed mysticetes represent the evolutionary transition from raptorial to bulk filter feeding in baleen whales. Aetiocetids, in particular, preserve an intermediate morphological stage in which teeth functioned alongside a precursor of baleen, the hallmark of all modern mysticetes. To date, however, aetiocetids are almost exclusively Late Oligocene and coeval with both other toothed mysticetes and fully fledged filter feeders. By contrast, reports of cetaceans from the Early Oligocene remain rare, leaving the origins of aetiocetids, and thus of baleen, largely in the dark. Here, we report a new aetiocetid,Fucaia buelli, from the earliest Oligocene (ca33–31 Ma) of western North America. The new material narrows the temporal gap between aetiocetids and the oldest known mysticete,Llanocetus(ca34 Ma). The specimen preserves abundant morphological detail relating to the phylogenetically informative ear bones (otherwise poorly documented in this family), the hyoid apparatus and much of the (heterodont) dentition.Fucaiacomprises some of the smallest known mysticetes, comparable in size with the smallest odontocetes. Based on their phylogenetic relationships and dental and mandibular morphology, including tooth wear patterns, we propose that aetiocetids were suction-assisted raptorial feeders and interpret this strategy as a crucial, intermediary step, enabling the transition from raptorial to filter feeding. Following this line of argument, a combination of raptorial and suction feeding would have been ancestral to all toothed mysticetes, and possibly even baleen whales as a whole.
Across-shelf distribution of blue mussel larvae in the northern Gulf of Maine: consequences for population connectivity and a species range boundary
Authors: Yund Philip O. , Tilburg Charles E. , McCartney Michael A.
Published: December 2015

Studies of population connectivity have largely focused on along-shelf, as opposed to across-shelf, processes. We hypothesized that a discontinuity in across-shelf mixing caused by the divergence of the Eastern Maine Coastal Current (EMCC) from shore acts as an ecological barrier to the supply of mussel larvae to the coast. Existing data on the relative abundance of two congeneric blue mussels,
Mytilus edulis
and
M. trossulus
, were analysed to quantify the association of
M. trossulus
with the colder temperature signal of the EMCC and generate larval distribution predictions. We then sampled the across-shelf distribution of larvae along two transects during 2011. Larvae were identified using restriction digests of PCR amplicons from the mitochondrial 16S rDNA.
Mytilus edulis
larvae were consistently abundant on either the inshore and offshore transect ends, but not homogeneously distributed across the shelf, while
M. trossulus
larvae were less common throughout the study area. The divergence of the EMCC from shore appears to create a break in the connectivity of
M. edulis
populations by isolating those inshore of the EMCC from upstream larval sources. Across-shelf transport processes can thus produce connectivity patterns that would not be predicted solely on the basis of along-shelf processes.
Oviposition preference of cabbage white butterflies in the framework of costs and benefits of interspecific herbivore associations
Authors: Shiojiri Kaori , Sabelis Maurice , Takabayashi Junji
Published: December 2015

When deciding where to oviposit, herbivorous insects consider: (i) the plant’s value as a food source, (ii) the risks of competing with con- and heterospecific herbivores, and (iii) the risks of parasitism and predation on the host plant. The presence of con- and/or heterospecific competitors would further affect the oviposition preference, because the preceding herbivores induce direct/indirect defences in plants against forthcoming herbivores, and thereby alter oviposition decisions. In previous studies, the abovementioned factors have not been studied in an integrative manner. We performed here a case study of this by assessing the oviposition preferences of a small white butterfly,
Pieris rapae
, for plants occupied by combinations of conspecific larvae, heterospecific larvae (
Plutella xylostella
), specialist parasitoids of
Pi. rapae
(
Cotesia glomerata
) and generalist predators (ants). We previously reported that the females showed equal preference for
Pl. xylostella
-infested and uninfested plants. Here, we showed that
Pi. rapae
females preferred uninfested plants to conspecific-infested ones, and
Pl. xylostella
-infested plants to
Pi. rapae
-infested ones. We discuss these oviposition preferences of
Pi. rapae
females in the framework of costs and benefits of interspecific herbivore associations from the above point of view.
On an atom with a magnetic quadrupole moment subject to harmonic and linear confining potentials
Authors: Fonseca I. C. , Bakke Knut
Published: December 2015

The quantum dynamics of an atom with a magnetic quadrupole moment that interacts with an external field subject to harmonic and linear confining potentials is investigated. It is shown that the interaction between the magnetic quadrupole moment and an electric field gives rise to an analogue of the Coulomb potential and, by confining this atom to harmonic and linear confining potentials, a quantum effect characterized by the dependence of the angular frequency on the quantum numbers of the system is obtained. In particular, it is shown that the possible values of the angular frequency associated with the ground state of the system are determined by a third-degree algebraic equation.
A control algorithm for nonlinear offshore structural dynamical systems
Authors: Manikandan R. , Saha Nilanjan
Published: December 2015

A reasonable knowledge about the response of nonlinear offshore structural systems under environmental loads is necessary but challenging. This is due to the coupling of internal forces along with external excitations. In this paper, a mathematical model of nonlinear offshore systems is studied with the intention of keeping the response close to the desired one. This is achieved using a novel sub-optimal control mechanism derived from nonlinear quadratic regulator (NQR) theory. Herein, two linearized functions of nonlinear motions—displacement and velocity—are introduced such that the parametrization of the state-dependent system matrices is obtained. By doing so, the system becomes conditioned only on the present state and therefore one needs to solve only an algebraic state-dependent Riccati problem. This results in a control law which may either be partial or full rank for the dynamical system depending on measurable states. The performance of the controller is compared with conventional NQR. The performance of the proposed control strategy is illustrated through a range of models of nonlinear offshore problems. The motions (generalized displacements and velocities) show that the proposed controller was not only able to restrict the undesirable behaviour but also provide means of shaping the transient performance.
Ultrafast thermomechanical responses of a copper film under femtosecond laser trains: a molecular dynamics study
Authors: Qi-lin Xiong , Li Zhenhuan , Xiao-geng Tian
Published: December 2015

Using molecular dynamics (MD) simulation, the ultrafast thermomechanical coupling responses of an immense homogeneous, isotropic copper film with the thickness of 1 μm, which is irradiated by various ultra-short laser pulse trains, are investigated. For the same energy injection, the effect of laser pulse trains is studied and it is observed from the numerical results that the pulse train technology may improve the ultrafast thermomechanical responses of the film significantly. By thoroughly analysing temperature, stress and displacement (strain) of the film, the thermomechanical coupling characteristics between stress, displacement (strain) and temperature are presented perfectly at the atomic scale. It is found that the lattice temperature of the region under tensile stress (or compressive stress) is lower (or higher) than the lattice temperature of the surrounding region, and the positive and negative strain (tensile or compressive) is related to tensile and compressive stress very well.
Preys’ exploitation of predators’ fear: when the caterpillar plays the Gruffalo
Authors: Castellano Sergio , Cermelli Paolo
Published: December 2015

Alike the little mouse of the Gruffalo's tale, many harmless preys use intimidating deceptive signals as anti-predator strategies. For example, several caterpillars display eyespots and face-like colour patterns that are thought to mimic the face of snakes as deterrents to insectivorous birds. We develop a theoretical model to investigate the hypothesis that these defensive strategies exploit adaptive cognitive biases of birds, which make them much more likely to confound caterpillars with snakes than vice versa. By focusing on the information-processing mechanisms of decision-making, the model assumes that, during prey assessment, the bird accumulates noisy evidence supporting either the snake-escape or the caterpillar-attack motor responses, which compete against each other for execution. Competition terminates when the evidence for either one of the responses reaches a critical threshold. This model predicts a strong asymmetry and a strong negative correlation between the prey- and the predator-decision thresholds, which increase with the increasing risk of snake predation and assessment uncertainty. The threshold asymmetry causes an asymmetric distribution of false-negative and false-positive errors in the snake–caterpillar decision plane, which makes birds much more likely to be deceived by the intimidating signals of snake-mimicking caterpillars than by the alluring signals of caterpillar-mimicking snakes.
Freezing behaviour facilitates bioelectric crypsis in cuttlefish faced with predation risk
Authors: Bedore Christine N. , Kajiura Stephen M. , Johnsen Sönke
Published: December 2015

Cephalopods, and in particular the cuttlefishSepia officinalis, are common models for studies of camouflage and predator avoidance behaviour. Preventing detection by predators is especially important to this group of animals, most of which are soft-bodied, lack physical defences, and are subject to both visually and non-visually mediated detection. Here, we report a novel cryptic mechanism inS. officinalisin which bioelectric cues are reduced via a behavioural freeze response to a predator stimulus. The reduction of bioelectric fields created by the freeze-simulating stimulus resulted in a possible decrease in shark predation risk by reducing detectability. The freeze response may also facilitate other non-visual cryptic mechanisms to lower predation risk from a wide range of predator types.
A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells
Authors: Tichon Ailone , Gil Noa , Lubelsky Yoav , Havkin Solomon Tal , Lemze Doron , Itzkovitz Shalev , Stern-Ginossar Noam , Ulitsky Igor
Published: December 2015

Thousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionary conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD – an abundant and highly conserved cytoplasmic lncRNA. Most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two Pumilio homologs in mammals. Through binding to PUM1 and PUM2, NORAD modulates the mRNA levels of their targets, which are enriched for genes involved in chromosome segregation during cell division. Our results suggest that some cytoplasmic lncRNAs function by modulating the activities of RNA binding proteins, an activity which positions them at key junctions of cellular signaling pathways.
TopHat-Recondition: A post-processor for TopHat unmapped reads
Authors: Brueffer Christian , Saal Lao H
Published: December 2015

TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat.

Availability and implementation:

TopHat-Recondition is implemented in Python using the Pysam library and is freely available under a 2-clause BSD license on GitHub:https://github.com/cbrueffer/tophat-recondition.

Contact:christian.brueffer@med.lu.se,lao.saal@med.lu.se
Empirical evidence for heterozygote advantage in adapting diploid populations ofSaccharomyces cerevisiae
Authors: Sellis Diamantis , Kvitek Daniel J. , Dunn Barbara , Sherlock Gavin , Petrov Dmitri A.
Published: December 2015

Adaptation in diploids is predicted to proceed via mutations that are at least partially dominant in fitness. Recently we argued that many adaptive mutations might also be commonlyoverdominantin fitness. Natural (directional) selection acting on overdominant mutations should drive them into the population but then, instead of bringing them to fixation, should maintain them as balanced polymorphisms via heterozygote advantage. If true, this would make adaptive evolution in sexual diploids differ drastically from that of haploids. Unfortunately, the validity of this prediction has not yet been tested experimentally. Here we performed 4 replicate evolutionary experiments with diploid yeast populations (Saccharomyces cerevisiae) growing in glucose-limited continuous cultures. We sequenced 24 evolved clones and identified initial adaptive mutations in all four chemostats. The first adaptive mutations in all four chemostats were three CNVs, all of which proved to be overdominant in fitness. The fact that fitness overdominant mutations were always the first step in independent adaptive walks strongly supports the prediction that heterozygote advantage can arise as a common outcome of directional selection in diploids and demonstrates that overdominance of de novo adaptive mutations in diploids is not rare.
Integrating basin modeling with seismic technology and rock physics
Authors: Kawai Wisam Al , Mukerji Tapan
Published: December 2015

We explore the link between basin modelling and seismic inversion by applying different rock physics models. This study uses the E‐Dragon II data in the Gulf of Mexico. To investigate the impact of different rock physics models on the link between basin modelling and seismic inversion, we first model relationships between seismic velocities and both (1) porosity and (2) effective stress for well‐log data using published rock physics models. Then, we build 1D basin models to predict seismic velocities derived from basin modelling with different rock physics models, in a comparison with average sonic velocities measured in the wells. Finally, we examine how basin modelling outputs can be used to aid seismic inversion by providing constraints for the background low‐frequency model. For this, we run different scenarios of inverting near angle partial stack seismic data into elastic impedances to test the impact of the background model on the quality of the inversion results. The results of the study suggest that the link between basin modelling and seismic technology is a two‐way interaction in terms of potential applications, and the key to refine it is establishing a rock physics models that properly describes changes in seismic signatures reflecting changes in rock properties.
Wavelet‐based cepstrum decomposition of seismic data and its application in hydrocarbon detection
Authors: Xue Ya‐juan , Cao Jun‐xing , Tian Ren‐fei , Du Hao‐kun , Yao Yao
Published: December 2015

How to use cepstrum analysis for reservoir characterization and hydrocarbon detection is an initial question of great interest to exploration seismologists. In this paper, wavelet‐based cepstrum decomposition is proposed as a valid technology for enhancing geophysical responses in specific frequency bands, in the same way as traditional spectrum decomposition methods do. The calculation of wavelet‐based cepstrum decomposition, which decomposes the original seismic volume into a series of common quefrency volumes, employs a sliding window to move over each seismic trace sample by sample. The key factor in wavelet‐based cepstrum decomposition is the selection of the sliding‐window length as it limits the frequency ranges of the common quefrency section. Comparison of the wavelet‐based cepstrum decomposition with traditional spectrum decomposition methods, such as short‐time Fourier transform and wavelet transform, is conducted to demonstrate the effectiveness of the wavelet‐based cepstrum decomposition and the relation between these two technologies. In hydrocarbon detection, seismic amplitude anomalies are detected using wavelet‐based cepstrum decomposition by utilizing the first and second common quefrency sections. This reduces the burden of needing dozens of seismic volumes to represent the response to different mono‐frequency sections in the interpretation of spectrum decomposition in conventional spectrum decomposition methods. The model test and the application of real data acquired from the Sulige gas field in the Ordos Basin, China, confirm the effectiveness of the seismic amplitude anomaly section using wavelet‐based cepstrum decomposition for discerning the strong amplitude anomalies at a particular quefrency buried in the broadband seismic response. Wavelet‐based cepstrum decomposition provides a new method for measuring the instantaneous cepstrum properties of a reservoir and offers a new field of processing and interpretation of seismic reflection data.
Modified image algorithm to simulate seismic channel waves in 3D tunnel model with rugged free surfaces
Authors: Li Hui , Zhu Peimin , Ji Guangzhong , Zhang Qiang
Published: December 2015

The existence of rugged free‐surface three‐dimensional tunnel conditions in the coal seams, caused either by geological or mining processes, will inevitably influence wave propagation characteristics when the seismic waves go through the coal mines. Thus, a modified image algorithm has been developed to account for seismic channel waves propagating through this complicated topography with irregular free surfaces. Moreover, the seismic channel waves commonly exhibit damped and dispersive signatures, which is not only because of their own unique sandwich geometry of rock–coal–rock but also because of the viscoelastic behavior of coal. Considering the complexity of programming in three‐dimensional tunnel models with rugged free surfaces, an optimized vacuum grid search algorithm, enabling to model highly irregular topography and to compute efficiently, is also proposed when using high‐order staggered finite‐difference scheme to simulate seismic channel wave propagations in viscoelastic media. The numerical simulations are implemented to investigate the accuracy and stability of the method and the impact of coal's viscoelastic behavior on seismic channel wave propagation characteristics. The results indicate that the automatic vacuum grid search algorithm can be easily merged into high‐order staggered finite‐difference scheme, which can efficiently be applied to calculate three‐dimensional tunnel models with rugged free surfaces in the viscoelastic media. The simulation also suggests that the occurrence of a three‐dimensional tunnel with free surfaces has a remarkable influence on the seismic channel wave propagation characteristics and elastic energy distribution.
Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla
Authors: Schmidt Marian L. , White Jeffrey D. , Denef Vincent J.
Published: December 2015

Despite their homogeneous appearance, aquatic systems harbour heterogeneous habitats resulting from nutrient gradients, suspended particulate matter and stratification. Recent reports suggest phylogenetically conserved habitat preferences among bacterioplankton, particularly for particle‐associated (PA) and free‐living (FL) habitats. Here, we show that independent of lake nutrient level and layer, PA and FL abundance‐weighted bacterial community composition (BCC) differed and that inter‐lake BCC varied more for PA than for FL fractions. In low‐nutrient lakes, BCC differences between PA and FL fractions were larger than those between lake layers. The reverse was true for high‐nutrient lakes. Nutrient level affected BCC more in hypolimnia than in epilimnia, likely due to hypolimnetic hypoxia in high‐nutrient lakes. In line with previous reports, we observed within‐phylum operational taxonomic unit (OTU) habitat preference conservation, although not for all phyla, including the phylum with the highest average relative abundance across all habitats (Bacteroidetes). Consistent phylum‐level habitat preferences may indicate that the functional traits that underpin ecological adaptation of freshwater bacteria to lake habitats can be phylogenetically conserved, although the levels of conservation are phylum dependent. Resolving taxa preferences for freshwater habitats sets the stage for identification of traits that underpin habitat specialization and associated functional traits that influence differences in biogeochemical cycling across freshwater lake habitats.