bluuebunny/crossref_metadata_2025 huggingface dataset:
An Automated Segmentation of R2* Iron-Overloaded Liver Images Using a Fuzzy C-Mean Clustering Scheme
Authors: Saiviroonporn Pairash , Korpraphong Pornpim , Viprakasit Vip , Krittayaphong Rungroj
Published: February 2018

Objectives

The objectives of this study were to develop and test an automated segmentation of R2* iron-overloaded liver images using fuzzy c-mean (FCM) clustering and to evaluate the observer variations.

Materials and Methods

Liver R2* images and liver iron concentration (LIC) maps of 660 thalassemia examinations were randomly separated into training (70%) and testing (30%) cohorts for development and evaluation purposes, respectively. Two-dimensional FCM used R2* images, and the LIC map was implemented to segment vessels from the parenchyma. Two automated FCM variables were investigated using new echo time and membership threshold selection criteria based on the FCM centroid distance and LIC levels, respectively. The new method was developed on a training cohort and compared with manual segmentation for segmentation accuracy and to a previous semiautomated method, and a semiautomated scheme was suggested to improve unsuccessful results. The automated variables found from the training cohort were assessed for their effectiveness in the testing cohort, both quantitatively and qualitatively (the latter by 2 abdominal radiologists using a grading method, with evaluations of observer variations). A segmentation error of less than 30% was considered to be a successful result in both cohorts, whereas, in the testing cohort, a good grade obtained from satisfactory automated results was considered a success.

Results

The centroid distance method has a segmentation accuracy comparable with the previous-best, semiautomated method. About 94% and 90% of the examinations in the training and testing cohorts were automatically segmented out successfully, respectively. The failed examinations were successfully segmented out with thresholding adjustment (3% and 8%) or by using alternative results from the previous 1-dimensional FCM method (3% and 2%) in the training and testing cohorts, respectively. There were no failed segmentation examinations in either cohort. The intraobserver and interobserver variabilities were found to be in substantial agreement.

Conclusions

Our new method provided a robust automated segmentation outcome with a high ease of use for routine clinical application.
Teaching Vaginal Hysterectomy via Simulation: Creation and Validation of the Objective Skills Assessment Tool for Simulated Vaginal Hysterectomy on a Task Trainer and Performance Among Different Levels of Trainees
Authors: Malacarne D.R. , Escobar C.M. , Lam C.J. , Ferrante K.L. , Szyld D. , Lerner Veronica T.
Published: February 2018

Objectives

The use of simulation-based education to train surgeons is widely accepted. Although many authors describe the use of an Objective Skills Assessment Test (OSAT) to assess performance of various surgical procedures, there is a paucity of research on use of this modality to evaluate vaginal surgery skills. We created a vaginal hysterectomy procedure-specific checklist (PSC) to complete the OSAT (which is composed of a PSC and a global rating scale [GRS]). The primary objective of this study is to evaluate the performance of a novel evaluation strategy for vaginal hysterectomy using an OSAT combining PSC and GRS.

Methods

This is a descriptive prospective study from a single institution. After orientation to the model, participants were filmed performing vaginal hysterectomy. A blinded grader scored each subject using the PSC and GRS.

Results

Medical students, residents, fellows, and attendings performed vaginal hysterectomy on a simulated model. Mean PSC and GRS scores increased significantly with surgeon level of experience (P < 0.001). Procedure-specific checklist scores significantly correlated with GRS scores (P < 0.001).

Conclusions

The vaginal hysterectomy model and PSC have been studied across different surgeon levels using OSATs. Training programs should consider using this low-cost task trainer as a teaching tool.
Red tides: Mass casualty and whole blood at sea
Authors: Miller Benjamin T. , Lin Andrew H. , Clark Susan C. , Cap Andrew P. , Dubose Joseph J.
Published: February 2018

BACKGROUND

The U.S. Navy’s casualty-receiving ships provide remote damage control resuscitation platforms to treat injured combatants deployed afloat and ashore. We report a significant mass casualty incident aboard the USS Bataan, and the most warm fresh whole blood (WFWB) transfused at sea for traumatic hemorrhagic shock since the Vietnam War.

METHODS

Casualty-receiving ships have robust medical capabilities, including a frozen blood bank with packed red blood cells (pRBC) and fresh frozen plasma (FFP). The blood supply can be augmented with WFWB collected from a “walking blood bank.”

RESULTS

Following a helicopter crash, six patients were transported by MV-22 Osprey to the USS Bataan. Patient 1 had a pelvic fracture, was managed with a pelvic binder, and received 4 units of pRBC, 2 units of FFP, and 6 units of WFWB. Patient 2, with a comminuted tibia and fibula fracture, underwent lower extremity four-compartment fasciotomy, and received 4 units of WFWB. Patient 3 underwent several procedures, including left anterior thoracotomy, aortic cross-clamping, exploratory laparotomy, small bowel resection, and tracheostomy. He received 8 units of pRBC, 8 units of FFP, and 28 units of WFWB. Patients 4 and 5 had suspected spine injuries and were managed nonoperatively. Patient 6, with open tibia and fibula fractures, underwent lower extremity four-compartment fasciotomy with tibia external fixation and received 1 unit of WFWB. All patients survived aeromedical evacuation to a role 4 medical facility and subsequent transfer to local hospitals.

CONCLUSION

Maritime military mass casualty incidents are challenging, but the U.S. Navy’s casualty-receiving ships are ready to perform remote damage control resuscitation at sea. Activation of the ship’s walking blood bank to transfuse WFWB is essential for hemostatic resuscitations afloat.

LEVEL OF EVIDENCE

Study type: case series, level V.
Stability of Early EEG Background Patterns After Pediatric Cardiac Arrest
Authors: Abend Nicholas S. , Xiao Rui , Kessler Sudha Kilaru , Topjian Alexis A.
Published: February 2018

Purpose:

We aimed to determine whether EEG background characteristics remain stable across discrete time periods during the acute period after resuscitation from pediatric cardiac arrest.

Methods:

Children resuscitated from cardiac arrest underwent continuous conventional EEG monitoring. The EEG was scored in 12-hour epochs for up to 72 hours after return of circulation by an electroencephalographer using a Background Category with 4 levels (normal, slow-disorganized, discontinuous/burst-suppression, or attenuated-featureless) or 2 levels (normal/slow-disorganized or discontinuous/burst-suppression/attenuated-featureless). Survival analyses and mixed-effects ordinal logistic regression models evaluated whether the EEG remained stable across epochs.

Results:

EEG monitoring was performed in 89 consecutive children. When EEG was assessed as the 4-level Background Category, 30% of subjects changed category over time. Based on initial Background Category, one quarter of the subjects changed EEG category by 24 hours if the initial EEG was attenuated-featureless, by 36 hours if the initial EEG was discontinuous or burst-suppression, by 48 hours if the initial EEG was slow-disorganized, and never if the initial EEG was normal. However, regression modeling for the 4-level Background Category indicated that the EEG did not change over time (odds ratio = 1.06, 95% confidence interval = 0.96–1.17, P = 0.26). Similarly, when EEG was assessed as the 2-level Background Category, 8% of subjects changed EEG category over time. However, regression modeling for the 2-level category indicated that the EEG did not change over time (odds ratio = 1.02, 95% confidence interval = 0.91–1.13, P = 0.75).

Conclusions:

The EEG Background Category changes over time whether analyzed as 4 levels (30% of subjects) or 2 levels (8% of subjects), although regression analyses indicated that no significant changes occurred over time for the full cohort. These data indicate that the Background Category is often stable during the acute 72 hours after pediatric cardiac arrest and thus may be a useful EEG assessment metric in future studies, but that some subjects do have EEG changes over time and therefore serial EEG assessments may be informative.
Comparative dynamics of microglial and glioma cell motility at the infiltrative margin of brain tumours
Authors: Juliano Joseph , Gil Orlando , Hawkins-Daarud Andrea , Noticewala Sonal , Rockne Russell C. , Gallaher Jill , Massey Susan Christine , Sims Peter A. , Anderson Alexander R. A. , Swanson Kristin R. , Canoll Peter
Published: February 2018

Microglia are a major cellular component of gliomas, and abundant in the centre of the tumour and at the infiltrative margins. While glioma is a notoriously infiltrative disease, the dynamics of microglia and glioma migratory patterns have not been well characterized. To investigate the migratory behaviour of microglia and glioma cells at the infiltrative edge, we performed two-colour time-lapse fluorescence microscopy of brain slices generated from a platelet-derived growth factor-B (PDGFB)-driven rat model of glioma, in which glioma cells and microglia were each labelled with one of two different fluorescent markers. We used mathematical techniques to analyse glioma cells and microglia motility with both single cell tracking and particle image velocimetry (PIV). Our results show microglia motility is strongly correlated with the presence of glioma, while the correlation of the speeds of glioma cells and microglia was variable and weak. Additionally, we showed that microglia and glioma cells exhibit different types of diffusive migratory behaviour. Microglia movement fit a simple random walk, while glioma cell movement fits a super diffusion pattern. These results show that glioma cells stimulate microglia motility at the infiltrative margins, creating a correlation between the spatial distribution of glioma cells and the pattern of microglia motility.
On the diverse roles of fluid dynamic drag in animal swimming and flying
Authors: Godoy-Diana R. , Thiria B.
Published: February 2018

Questions of energy dissipation or friction appear immediately when addressing the problem of a body moving in a fluid. For the most simple problems, involving a constant steady propulsive force on the body, a straightforward relation can be established balancing this driving force with a skin friction or form drag, depending on the Reynolds number and body geometry. This elementary relation closes the full dynamical problem and sets, for instance, average cruising velocity or energy cost. In the case of finite-sized and time-deformable bodies though, such as flapping flyers or undulatory swimmers, the comprehension of driving/dissipation interactions is not straightforward. The intrinsic unsteadiness of the flapping and deforming animal bodies complicates the usual application of classical fluid dynamic forces balance. One of the complications is because the shape of the body is indeed changing in time, accelerating and decelerating perpetually, but also because the role of drag (more specifically the role of the local drag) has two different facets, contributing at the same time to global dissipation and to driving forces. This causes situations where a strong drag is not necessarily equivalent to inefficient systems. A lot of living systems are precisely using strong sources of drag to optimize their performance. In addition to revisiting classical results under the light of recent research on these questions, we discuss in this review the crucial role of drag from another point of view that concerns the fluid–structure interaction problem of animal locomotion. We consider, in particular, the dynamic subtleties brought by the quadratic drag that resists transverse motions of a flexible body or appendage performing complex kinematics, such as the phase dynamics of a flexible flapping wing, the propagative nature of the bending wave in undulatory swimmers, or the surprising relevance of drag-based resistive thrust in inertial swimmers.
Tailoring drug release rates in hydrogel-based therapeutic delivery applications using graphene oxide
Authors: Puvirajesinghe T. M. , Zhi Z. L. , Craster R. V. , Guenneau S.
Published: February 2018

Graphene oxide (GO) is increasingly used for controlling mass diffusion in hydrogel-based drug delivery applications. On the macro-scale, the density of GO in the hydrogel is a critical parameter for modulating drug release. Here, we investigate the diffusion of a peptide drug through a network of GO membranes and GO-embedded hydrogels, modelled as porous matrices resembling both laminated and ‘house of cards’ structures. Our experiments use a therapeutic peptide and show a tunable nonlinear dependence of the peptide concentration upon time. We establish models using numerical simulations with a diffusion equation accounting for the photo-thermal degradation of fluorophores and an effective percolation model to simulate the experimental data. The modelling yields an interpretation of the control of drug diffusion through GO membranes, which is extended to the diffusion of the peptide in GO-embedded agarose hydrogels. Varying the density of micron-sized GO flakes allows for fine control of the drug diffusion. We further show that both GO density and size influence the drug release rate. The ability to tune the density of hydrogel-like GO membranes to control drug release rates has exciting implications to offer guidelines for tailoring drug release rates in hydrogel-based therapeutic delivery applications.
A simple route to a novel acid-sensitive 20(
S
)-
O
-linked camptothecin norcantharidin acid ester derivative
Authors: Zhao Changkuo , Wang Xianheng , Yang Fuhong , Gao Lei , Wang Yuhe
Published: February 2018

A facile synthetic method was developed for a novel acid-sensitive camptothecin norcantharidin acid ester derivative
I
. The total yield can reach 71%. This method provides several advantages, including high yield and simple working procedure for the synthesis of analogues. The new synthetic compound
I
has been shown to exhibit better solubility and similar activity against tumour cell lines.
Photophysical studies on curcumin-sophorolipid nanostructures: applications in quorum quenching and imaging
Authors: Vasudevan Sahana , Prabhune Asmita A.
Published: February 2018

Sophorolipid biosurfactants are biodegradable, less toxic and FDA approved. The purified acidic form of sophorolipid is stimuli-responsive with self-assembling properties and used for solubilizing hydrophobic drugs. This study encapsulated curcumin (CU) with acidic sophorolipid (ASL) micelles and analysed using photophysical studies like UV-visible spectroscopy, photoluminescence (PL) spectroscopy and time-correlated single photon counting (TCSPC). TEM images have revealed ellipsoid micelles of approximately 100 nm size and were confirmed by dynamic light scattering. The bacterial fluorescence uptake studies showed the uptake of formed CUASL nanostructures into both Gram-positive and Gram-negative bacteria. They also showed quorum quenching activity against
Pseudomonas aeruginosa
. The results have demonstrated this system has potential theranostic applications.
Removal of cadmium from aqueous solutions using industrial coal fly ash-nZVI
Authors: Ma Lixia , Wei Qi , Chen Yueqin , Song Qiuyang , Sun Conghui , Wang Zhiqiang , Wu Guanghong
Published: February 2018

Batch experiments were conducted to test the effects of various solution properties, such as pH, temperature, initial concentration and anoxic and aerobic atmosphere, on Cd removal by nanoscale zerovalent iron (nZVI) supported on industrial coal fly ash. Cd (II) could be removed by adsorption on fly ash-nZVI in a very short time (5 min) with high removal rates (greater than 99.9%) over a wide range of concentration (5–100 mg l
−1
). Cd (II) was physically adsorbed on the surface of fly ash-nZVI. The preparation of fly ash-nZVI can incorporate the use of waste media, making the overall adsorbent more removal efficient and low cost.
Topological, chemical and electro-optical characteristics of riboflavin-doped artificial and natural DNA thin films
Authors: Gnapareddy Bramaramba , Dugasani Sreekantha Reddy , Son Junyoung , Park Sung Ha
Published: February 2018

DNA is considered as a useful building bio-material, and it serves as an efficient template to align functionalized nanomaterials. Riboflavin (RF)-doped synthetic double-crossover DNA (DX-DNA) lattices and natural salmon DNA (SDNA) thin films were constructed using substrate-assisted growth and drop-casting methods, respectively, and their topological, chemical and electro-optical characteristics were evaluated. The critical doping concentrations of RF ([RF]C, approx. 5 mM) at given concentrations of DX-DNA and SDNA were obtained by observing the phase transition (from crystalline to amorphous structures) of DX-DNA and precipitation of SDNA in solution above [RF]C. [RF]Care verified by analysing the atomic force microscopy images for DX-DNA and current, absorbance and photoluminescence (PL) for SDNA. We study the physical characteristics of RF-embedded SDNA thin films, using the Fourier transform infrared spectrum to understand the interaction between the RF and DNA molecules, current to evaluate the conductance, absorption to understand the RF binding to the DNA and PL to analyse the energy transfer between the RF and DNA. The current and UV absorption band of SDNA thin films decrease up to [RF]Cfollowed by an increase above [RF]C. By contrast, the PL intensity illustrates the reverse trend, as compared to the current and UV absorption behaviour as a function of the varying [RF]. Owing to the intense PL characteristic of RF, the DNA lattices and thin films with RF might offer immense potential to develop efficient bio-sensors and useful bio-photonic devices.
Songbird dynamics under the sea: acoustic interactions between humpback whales suggest song mediates male interactions
Authors: Cholewiak Danielle M. , Cerchio Salvatore , Jacobsen Jeff K. , Urbán-R. Jorge , Clark Christopher W.
Published: February 2018

The function of song has been well studied in numerous taxa and plays a role in mediating both intersexual and intrasexual interactions. Humpback whales are among few mammals who sing, but the role of sexual selection on song in this species is poorly understood. While one predominant hypothesis is that song mediates male–male interactions, the mechanism by which this may occur has never been explored. We applied metrics typically used to assess songbird interactions to examine song sequences and movement patterns of humpback whale singers. We found that males altered their song presentation in the presence of other singers; focal males increased the rate at which they switched between phrase types (
p
 = 0.005), and tended to increase the overall evenness of their song presentation (
p
 = 0.06) after a second male began singing. Two-singer dyads overlapped their song sequences significantly more than expected by chance. Spatial analyses revealed that change in distance between singers was related to whether both males kept singing (
p
 = 0.012), with close approaches leading to song cessation. Overall, acoustic interactions resemble known mechanisms of mediating intrasexual interactions in songbirds. Future work should focus on more precisely resolving how changes in song presentation may be used in competition between singing males.
Coupled electro-thermal field in a high current electrolysis cell or liquid metal batteries
Authors: Sun Ze , Cai Liwei , Ni Haiou , Lu Gui-Min , Yu Jian-Guo
Published: February 2018

Coupled electro-thermal field exists widely in chemical batteries and electrolysis industry. In this study, a three-dimensional numerical model, which is based on the finite-element software ANSYS, has been built to simulate the electro-thermal field in a magnesium electrolysis cell. The adjustment of the relative position of the anode and cathode can change the energy consumption of the magnesium electrolysis process significantly. Besides, the current intensity has a nonlinear effect on heat balance, and the effects of heat transfer coefficients, electrolysis and air temperature on the heat balance have been released to maintain the thermal stability in a magnesium electrolysis cell. The relationship between structure as well as process parameters and electro-thermal field has been obtained and the simulation results can provide experience for the scale-up design in liquid metal batteries.
Orientation-dependent structural and photocatalytic properties of LaCoO
3
epitaxial nano-thin films
Authors: Zhang Yan-ping , Liu Hai-feng , Hu Hai-long , Xie Rui-shi , Ma Guo-hua , Huo Ji-chuan , Wang Hai-bin
Published: February 2018

LaCoO
3
epitaxial films were grown on (100), (110) and (111) oriented LaAlO
3
substrates by the polymer-assisted deposition method. Crystal structure measurement and cross-section observation indicate that all the LaCoO
3
films are epitaxially grown in accordance with the orientation of LaAlO
3
substrates, with biaxial compressive strain in the
ab
plane. Owing to the different strain directions of CoO
6
octahedron, the mean Co–O bond length increases by different amounts in (100), (110) and (111) oriented films compared with that of bulk LaCoO
3
, and the (100) oriented LaCoO
3
has the largest increase. Photocatalytic degradation of methyl orange indicates that the order of photocatalytic activity of the three oriented films is (100) > (111) > (110). Combined with analysis of electronic nature and band structure for LaCoO
3
films, it is found that the change of the photocatalytic activity is closely related to the crystal field splitting energy of Co
3+
and Co–O binding energy. The increase in the mean Co–O bond length will decrease the crystal field splitting energy of Co
3+
and Co–O binding energy and further reduce the value of band gap energy, thus improving the photocatalytic activity. This may also provide a clue for expanding the visible-light-induced photocatalytic application of LaCoO
3
.
Integrating viscoelastic mass spring dampers into position-based dynamics to simulate soft tissue deformation in real time
Authors: Xu Lang , Lu Yuhua , Liu Qian
Published: February 2018

We propose a novel method to simulate soft tissue deformation for virtual surgery applications. The method considers the mechanical properties of soft tissue, such as its viscoelasticity, nonlinearity and incompressibility; its speed, stability and accuracy also meet the requirements for a surgery simulator. Modifying the traditional equation for mass spring dampers (MSD) introduces nonlinearity and viscoelasticity into the calculation of elastic force. Then, the elastic force is used in the constraint projection step for naturally reducing constraint potential. The node position is enforced by the combined spring force and constraint conservative force through Newton's second law. We conduct a comparison study of conventional MSD and position-based dynamics for our new integrating method. Our approach enables stable, fast and large step simulation by freely controlling visual effects based on nonlinearity, viscoelasticity and incompressibility. We implement a laparoscopic cholecystectomy simulator to demonstrate the practicality of our method, in which liver and gallbladder deformation can be simulated in real time. Our method is an appropriate choice for the development of real-time virtual surgery applications.
Isospectrals of non-uniform Rayleigh beams with respect to their uniform counterparts
Authors: Bhat K Srivatsa , Ganguli Ranjan
Published: February 2018

In this paper, we look for non-uniform Rayleigh beams isospectral to a given uniform Rayleigh beam. Isospectral systems are those that have the same spectral properties, i.e. the same free vibration natural frequencies for a given boundary condition. A transformation is proposed that converts the fourth-order governing differential equation of non-uniform Rayleigh beam into a uniform Rayleigh beam. If the coefficients of the transformed equation match with those of the uniform beam equation, then the non-uniform beam is isospectral to the given uniform beam. The boundary-condition configuration should be preserved under this transformation. We present the constraints under which the boundary configurations will remain unchanged. Frequency equivalence of the non-uniform beams and the uniform beam is confirmed by the finite-element method. For the considered cases, examples of beams having a rectangular cross section are presented to show the application of our analysis.
Study on the optimization of the deposition rate of planetary GaN-MOCVD films based on CFD simulation and the corresponding surface model
Authors: Li Jian , Fei Ze-yuan , Xu Yi-feng , Wang Jie , Fan Bing-feng , Ma Xue-jin , Wang Gang
Published: February 2018

Metal-organic chemical vapour deposition (MOCVD) is a key technique for fabricating GaN thin film structures for light-emitting and semiconductor laser diodes. Film uniformity is an important index to measure equipment performance and chip processes. This paper introduces a method to improve the quality of thin films by optimizing the rotation speed of different substrates of a model consisting of a planetary with seven 6-inch wafers for the planetary GaN-MOCVD. A numerical solution to the transient state at low pressure is obtained using computational fluid dynamics. To evaluate the role of the different zone speeds on the growth uniformity, single factor analysis is introduced. The results show that the growth rate and uniformity are strongly related to the rotational speed. Next, a response surface model was constructed by using the variables and the corresponding simulation results. The optimized combination of the matching of different speeds is also proposed as a useful reference for applications in industry, obtained by a response surface model and genetic algorithm with a balance between the growth rate and the growth uniformity. This method can save time, and the optimization can obtain the most uniform and highest thin film quality.
Therapeutic target discovery using Boolean network attractors: improvements of kali
Authors: Poret Arnaud , Guziolowski Carito
Published: February 2018

In a previous article, an algorithm for identifying therapeutic targets in Boolean networks modelling pathological mechanisms was introduced. In the present article, the improvements made on this algorithm, named kali, are described. These improvements are (i) the possibility to work on asynchronous Boolean networks, (ii) a finer assessment of therapeutic targets and (iii) the possibility to use multivalued logic. kali assumes that the attractors of a dynamical system, such as a Boolean network, are associated with the phenotypes of the modelled biological system. Given a logic-based model of pathological mechanisms, kali searches for therapeutic targets able to reduce the reachability of the attractors associated with pathological phenotypes, thus reducing their likeliness. kali is illustrated on an example network and used on a biological case study. The case study is a published logic-based model of bladder tumorigenesis from which kali returns consistent results. However, like any computational tool, kali can predict but cannot replace human expertise: it is a supporting tool for coping with the complexity of biological systems in the field of drug discovery.
A time-domain method for prediction of noise radiated from supersonic rotating sources in a moving medium
Authors: Huang Zhongjie , Siozos-Rousoulis Leonidas , De Troyer Tim , Ghorbaniasl Ghader
Published: February 2018

This paper presents a time-domain method for noise prediction of supersonic rotating sources in a moving medium. The proposed approach can be interpreted as an extensive time-domain solution for the convected permeable Ffowcs Williams and Hawkings equation, which is capable of avoiding the Doppler singularity. The solution requires special treatment for construction of the emission surface. The derived formula can explicitly and efficiently account for subsonic uniform constant flow effects on radiated noise. Implementation of the methodology is realized through the Isom thickness noise case and high-speed impulsive noise prediction from helicopter rotors.
A generalized sound extrapolation method for turbulent flows
Authors: Zhong Siyang , Zhang Xin
Published: February 2018

Sound extrapolation methods are often used to compute acoustic far-field directivities using near-field flow data in aeroacoustics applications. The results may be erroneous if the volume integrals are neglected (to save computational cost), while non-acoustic fluctuations are collected on the integration surfaces. In this work, we develop a new sound extrapolation method based on an acoustic analogy using Taylor’s hypothesis (Taylor 1938
Proc. R. Soc. Lon. A
164
, 476–490. (
doi:10.1098/rspa.1938.0032
)). Typically, a convection operator is used to filter out the acoustically inefficient components in the turbulent flows, and an acoustics dominant indirect variable

D

c

p
′

is solved. The sound pressure
p
′ at the far field is computed from

D

c

p
′

based on the asymptotic properties of the Green’s function. Validations results for benchmark problems with well-defined sources match well with the exact solutions. For aeroacoustics applications: the sound predictions by the aerofoil–gust interaction are close to those by an earlier method specially developed to remove the effect of vortical fluctuations (Zhong & Zhang 2017
J. Fluid Mech.
820
, 424–450. (
doi:10.1017/jfm.2017.219
)); for the case of vortex shedding noise from a cylinder, the off-body predictions by the proposed method match well with the on-body Ffowcs-Williams and Hawkings result; different integration surfaces yield close predictions (of both spectra and far-field directivities) for a co-flowing jet case using an established direct numerical simulation database. The results suggest that the method may be a potential candidate for sound projection in aeroacoustics applications.
Quantitative analysis of the complete larval settlement process confirms Crisp's model of surface selectivity by barnacles
Authors: Aldred Nick , Alsaab Ahmad , Clare Anthony S.
Published: February 2018

For barnacle cypris larvae at the point of settlement, selection of an appropriate surface is critical. Since post-settlement relocation is usually impossible, barnacles have evolved finely tuned surface-sensing capabilities to identify suitable substrata, and a temporary adhesion system for extensive surface exploration. The pattern of exploratory behaviour appears complex and may last for several hours, imposing significant barriers to quantitative measurement. Here, we employ a novel tracking system that enables simultaneous analysis of the larval body movement of multiple individuals over their entire planktonic phase. For the first time, to our knowledge, we describe quantitatively the complete settlement process of cyprids as they explore and select surfaces for attachment. We confirm the ‘classic’ behaviours of wide searching, close searching and inspection that comprise a model originally proposed by Prof. Dennis Crisp FRS. Moreover, a short-term assay of cyprid body movement has identified inspection behaviour as the best indicator of propensity to settle, with more inspection-related movements occurring in conditions that also promote higher settlement. More than half a century after the model was first proposed by Crisp, there exists a precise method for quantifying cyprid settlement behaviour in wide-ranging investigations of barnacle ecology and applied studies of fouling management.
Wound treatment and selective help in a termite-hunting ant
Authors: Frank Erik T. , Wehrhahn Marten , Linsenmair K. Eduard
Published: February 2018

Open wounds are a major health risk in animals, with species prone to injuries likely developing means to reduce these risks. We therefore analysed the behavioural response towards open wounds on the social and individual level in the termite group-hunting ant
Megaponera analis
. During termite raids, some ants get injured by termite soldiers (biting off extremities), after the fight injured ants get carried back to the nest by nest-mates. We observed treatment of the injury by nest-mates inside the nest through intense allogrooming at the wound. Lack of treatment increased mortality from 10% to 80% within 24 h, most likely due to infections. Wound clotting occurred extraordinarily fast in untreated injured individuals, within 10 min. Furthermore, heavily injured ants (loss of five extremities) were not rescued or treated; this was regulated not by the helper but by the unresponsiveness of the injured ant. Interestingly, lightly injured ants behaved ‘more injured’ near nest-mates. We show organized social wound treatment in insects through a multifaceted help system focused on injured individuals. This was not only limited to selective rescuing of lightly injured individuals by carrying them back (thus reducing predation risk), but, moreover, included a differentiated treatment inside the nest.
The influence of the few: a stable ‘oligarchy’ controls information flow in house-hunting ants
Authors: Richardson Thomas O. , Mullon Charles , Marshall James A. R. , Franks Nigel R. , Schlegel Thomas
Published: February 2018

Animals that live together in groups often face difficult choices, such as which food resource to exploit, or which direction to flee in response to a predator. When there are costs associated with deadlock or group fragmentation, it is essential that the group achieves a consensus decision. Here, we study consensus formation in emigrating ant colonies faced with a binary choice between two identical nest-sites. By individually tagging each ant with a unique radio-frequency identification microchip, and then recording all ant-to-ant ‘tandem runs’—stereotyped physical interactions that communicate information about potential nest-sites—we assembled the networks that trace the spread of consensus throughout the colony. Through repeated emigrations, we show that both the order in which these networks are assembled and the position of each individual within them are consistent from emigration to emigration. We demonstrate that the formation of the consensus is delegated to an influential but exclusive minority of highly active individuals—an ‘oligarchy’—which is further divided into two subgroups, each specialized upon a different tandem running role. Finally, we show that communication primarily occurs between subgroups not within them, and further, that such between-group communication is more efficient than within-group communication.
Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes
Authors: Marburger Sarah , Alexandrou Markos A. , Taggart John B. , Creer Simon , Carvalho Gary , Oliveira Claudio , Taylor Martin I.
Published: February 2018

Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.
Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231
Authors: Baptista Rodrigo P. , Reis-Cunha Joao Luis , DeBarry Jeremy D. , Chiari Egler , Kissinger Jessica C. , Bartholomeu Daniella C. , Macedo Andrea M.
Published: February 2018

Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature. Only three of six recognized discrete typing units (DTUs) of the parasite have their draft genomes published and therefore genome evolution analyses in the taxon are limited. In this study, we developed a computational workflow to assemble highly repetitive genomes via a combination of de novo and reference-based assembly strategies to better overcome the intrinsic limitations of each, based on Illumina reads. The highly repetitive genome of the human-infecting parasite T. cruzi 231 strain was used as a test subject. The combined-assembly approach shown in this study benefits from the reference-based assembly ability to resolve highly repetitive sequences and from the de novo capacity to assemble genome-specific regions, improving the quality of the assembly. The acceptable confidence obtained by analyzing our results showed that our combined approach is an attractive option to assemble highly repetitive genomes with NGS short reads. Phylogenomic analysis including the 231 strain, the first representative of DTU III whose genome was sequenced, was also performed and provides new insights into T. cruzi genome evolution.
Information synergy: adding unambiguous quality information rescues social information use in ants
Authors: Czaczkes Tomer J. , Beckwith John J. , Horsch Anna-Lena
Published: February 2018

Animals have access to many alternative information sources when making decisions, such as private information (e.g. memory) and social information. Social insects make extensive use of social information. However, when intentional social information (e.g. pheromone trails in ants) conflicts with private information (e.g. route memories), insects often follow their private information. Why is this? We propose that an asymmetry in the type of information provided by these two information sources drives the neglect of social information: In ants, workers with certain information about the quality of a food source (memory) ignore valuable social information (pheromone trails) because the pheromone trails encode only a very ambiguous measure of food quality. This leads to a testable hypothesis: the addition of unambiguous quality information should rescue social information following. To test this, we trained ants to a poor quality (0.25M sucrose) food source, and then provided an alternative path along with either 1) no information, 2) a pheromone trail, 3) a 0.2μl 1.5M sucrose droplet, providing unambiguous quality information, or 4) both a trail and a droplet. When either no or only one information source was provided (1-3), most ants (60-75%) continued following their own memory. However, the addition of unambiguous quality information (4) rescued trail following: when both a trail and a droplet were provided, 75% of ants followed the trail. In further experiments, we show that quality information gleaned from direct contact with fed nestmates produced similar effects. Using florescence microscopy, we demonstrate that food (and information) flows from fed workers to outgoing foragers, explaining the frequent contacts on trails. We propose that the type of information an information source can convey, and its ambiguity, is a strong driver of which source of information is attended to.
Exploring the relationship between altmetrics and traditional measures of dissemination in health professions education
Authors: Maggio Lauren A. , Leroux Todd C. , Meyer Holly S. , Artino Anthony R.
Published: February 2018

Researchers, funders, and institutions are interested in understanding and quantifying research dissemination and impact, particularly related to communicating with the public. Traditionally, citations have been a primary impact measure; however, citations can be slow to accrue and focus on academic use. Recently altmetrics, which track alternate dissemination forms (e.g., social media) have been suggested as a complement to citation-based metrics. This study examines the relationship between altmetrics and traditional measures: journal article citations and access counts.

The researchers queried Web of Science and Altmetric Explorer for articles published in HPE journals between 2013-2015. They identified 2,486 articles with altmetrics. Data were analyzed using negative binomial and linear regression models.

Blogging was associated with the greatest increase in citations (13% increase), whereas Tweets (1.2%) and Mendeley (1%) were associated with smaller increases. Journal impact factor (JIF) was associated with a 21% increase in citations. Publicly accessible articles were associated with a 19% decrease, but the interactive effect between accessible articles and JIF was associated with a 12% increase. When examining access counts, publicly accessible articles had an increase of 170 access counts whereas blogging was associated with a decrease of 87 accesses.

This study suggests that several altmetrics outlets are positively associated with citations, and that public accessibility, holding all other independent variables constant, is positively related to article access. Given the scientific community’s evolving focus on dissemination—including to the public—these findings have implications for stakeholders, providing insight into the factors that may improve citations and access of articles.
Segmenting accelerometer data from daily life with unsupervised machine learning
Authors: van Kuppevelt Dafne , Heywood Joe , Hamer Mark , Sabia Séverine , Fitzsimons Emla , van Hees Vincent
Published: February 2018

Purpose:

Accelerometers are increasingly used to obtain valuable descriptors of physical activity for health research. The cut-points approach to segment accelerometer data is widely used in physical activity research but requires resource expensive calibration studies and does not make it easy to explore the information that can be gained for a variety of raw data metrics. To address these limitations, we present a data-driven approach for segmenting and clustering the accelerometer data using unsupervised machine learning.

Methods:

The data used came from five hundred fourteen-year-old participants from the Millennium cohort study who wore an accelerometer (GENEActiv) on their wrist on one weekday and one weekend day. A Hidden Semi-Markov Model (HSMM), configured to identify a maximum of ten behavioral states from five second averaged acceleration with and without addition of x, y, and z-angles, was used for segmenting and clustering of the data. A cut-points approach was used as comparison.

Results:

Time spent in behavioral states with or without angle metrics constituted eight and five principal components to reach 95% explained variance, respectively; in comparison four components were identified with the cut-points approach. In the HSMM with acceleration and angle as input, the distributions for acceleration in the states showed similar groupings as the cut-points categories, while more variety was seen in the distribution of angles.

Conclusion:

Our unsupervised classification approach learns a construct of human behavior based on the data it observes, without the need for resource expensive calibration studies, has the ability to combine multiple data metrics, and offers a higher dimensional description of physical behavior. States are interpretable from the distributions of observations and by their duration.
MasterPATH: network analysis of functional genomics screening data
Authors: Rubanova Natalia , Polesskaya Anna , Campalans Anna , Pinna Guillaume , Kropp Jeremie , Harel-Bellan Annick , Morozova Nadya
Published: February 2018

Functional genomics employs several experimental techniques to investigate gene functions. These techniques such as loss-of-function screening and transcriptome profiling performed in a high-throughput manner give as result a list of genes involved in the biological process of interest. There exist several computational methods for analysis and interpretation of the list. The most widespread methods aim at investigation of biological processes significantly represented in the list or at extracting significantly represented subnetworks. Here we present a new exploratory network analysis method that employs the shortest path approach and centrality measure to uncover members of active molecular pathways leading to the studied phenotype based on the results of functional genomics screening data. We present the method and we demonstrate what data can be retrieved by its application to the terminal muscle differentiation miRNA loss-of-function screening and transcriptomic profiling data and to the ‘druggable’ loss-of-function RNAi screening data of the DNA repair process.
Two novel strains of Torulaspora delbrueckii isolated from the honey bee microbiome and their use in honey fermentation
Authors: Barry Joseph P. , Metz Mindy S. , Hughey Justin , Quirk Adam , Bochman Matthew L.
Published: February 2018

Yeasts are ubiquitous microbes found in virtually all environments. Many yeast species can ferment sugar into ethanol and CO2, and humans have taken advantage of these characteristics to produce fermented beverages for thousands of years. As a naturally abundant source of fermentable sugar, honey has had a central role in such fermentations since Neolithic times. However, as beverage fermentation has become industrialized, the processes have been streamlined, including the narrow and almost exclusive usage of yeasts in the genus Saccharomyces for fermentation. We set out to identify wild honey- or honey bee-related yeasts that can be used in honey fermentation. Here, we isolated two strains of Torulaspora delbrueckii from the gut of a locally collected honey bee. Both strains were able to ferment honey sugar into mead but failed to metabolize more than a modest amount of wort sugar in trial beer fermentations. Further, the meads fermented by the T. delbrueckii strains displayed better sensory characteristics than mead fermented by a champagne yeast. The combination of T. delbrueckii and champagne yeast strains was also able to rapidly ferment honey at an industrial scale. Thus, wild yeasts represent a largely untapped reservoir for the introduction of desirable sensory characteristics in fermented beverages such as mead.