bluuebunny/crossref_metadata_2025 huggingface dataset:
Oscillation between identities and Subjective psychological health objectives among an informed audience in therapeutic patient education
Authors: Roussel Sandrine , Deccache Alain , Frenay Mariane
Published: May 2018

Introduction: The implementation of Therapeutic Patient Education (TPE) remains a challenge. An exploratory study highlighted two tendencies among practitioners of TPE, which could hamper this implementation: an oscillation between identities (as caregivers versus as educators) and an inclination towards subjective psychological health objectives. Objectives: To verify whether these tendencies can be observed among an informed audience in TPE. Next, to explore the variables associated with one or other of these tendencies. Method: A quantitative cross-sectional survey by a self-administered questionnaire was carried out among 90 French-speaking healthcare professionals. Statistical analyses (chi-square, logistic regression) were then conducted. Results: Sixty percent of respondents displayed identity oscillation, which was found to be linked to task oscillation, patient curability, scepticism towards medicine and practising in France. Fifty-six percent pursued subjective psychological health objectives, which was found to be associated with health behaviour objectives and a locus of power in the healthcare relationship distinct from those seen in the pre-existing health models (biomedical, global). This tendency seems to constitute an alternative model of TPE. Discussion & conclusion: Identity oscillation and subjective psychological health objectives can be both observed. This study stresses the need to deliberate on the form(s) of TPE that is/are desired.
Updates on Translational Research on Prevention of Polyps and Colorectal Cancer
Authors: Stoffel Elena
Published: May 2018

Morbidity and mortality from colorectal cancer (CRC) can be effectively reduced through early detection and prevention. To date, strategies for managing CRC risk have focused primarily on secondary prevention, through screening asymptomatic individuals for colorectal neoplasia. In the United States, implementation of screening among individuals age ≥50 has led to not only decreased CRC-related mortality but also reduced CRC incidence through colonoscopic removal of precancerous polyps. In contrast to screening's endpoint of early detection, the goal of primary prevention of CRC is to arrest and/or reverse colorectal carcinogenesis. Observational studies and randomized clinical trials continue to examine effects of specific pharmacologic agents (chemoprevention) and dietary interventions on development of advanced colorectal neoplasia. This review will present an overview of strategies for primary and secondary prevention of CRC, including endoscopic, pharmacologic, and dietary interventions.
Timing of ECMO Initiation Impacts Survival in Influenza-Associated ARDS
Authors: Steimer Desiree , Hernandez Omar , Mason David , Schwartz Gary
Published: May 2018

In the past decade, extracorporeal membrane oxygenation (ECMO) has emerged as an innovative therapy for influenza-associated acute respiratory distress syndrome (ARDS). Despite its promising results, the ideal timing of ECMO initiation for these patients remains unclear. Retrospective analysis of a single institution experience with venovenous ECMO for influenza-induced ARDS was performed. Twenty-one patients were identified and categorized into early (0–2 days), standard (3–6 days), or late (more than 7 days) cannulation cohorts. Patients cannulated within 48 hours of admission had 80% survival rate at 90 days. Comparatively, the standard and late cannulation cohorts had an observed 90-day survival rate of 60 and 16.7%, respectively.
Benefits and Risks of Prophylactic Cerebrospinal Fluid Catheter and Evoked Potential Monitoring in Symptomatic Spinal Cord Ischemia Low-Risk Thoracic Endovascular Aortic Repair
Authors: Maier Sven , Shcherbakova Maria , Beyersdorf Friedhelm , Benk Christoph , Kari Fabian Alexander , Siepe Matthias , Czerny Martin , Rylski Bartosz
Published: May 2018

Background To assess risks and benefits of a standardized strategy to prevent symptomatic spinal cord ischemia (SSCI) after thoracic endovascular repair (TEVAR) using routine cerebrospinal fluid (CSF) catheter placement and evoked potential (EP) monitoring.

Methods One hundred and ninety-five patients underwent 223 SSCI low-risk TEVAR procedures between 1998 and 2014. CSF catheter was used to measure CSF pressure and drain CSF if necessary throughout the procedure and up to 24 hours thereafter. EPs were used to monitor spinal cord integrity throughout the procedure.

Results Underlying pathologies included descending thoracic aortic aneurysm in 115 (52%), type B aortic dissection in 85 (38%), traumatic aortic rupture in 16 (7%), and others in 7 (3%) patients. CSF catheter was inserted before TEVAR in 116 procedures (52%). Active CSF draining was required in 29 patients (25%). The CSF catheter caused no major and 11 (10%) minor complications. EP were monitored during 88 (40%) procedures. We observed a reduction in the amplitude, prolonged latencies, or complete signal loss in nine procedures. There were no EP monitoring-related complications. SSCI incidence was higher in patients without CSF drainage (0.8% vs 4.7%, p = 0.031).

Conclusion Use of CSF drainage is associated with a significant lower incidence of SSCI after SSCI low-risk TEVAR than nonuse, whereas the complication rate associated with CSF drainage insertion or removal is very low. Routine EP monitoring is a useful tool to detect immediate arterial inflow obstruction to the spinal cord. The combination of these two methods serves as a safe and reliable standardized strategy in reducing the incidence of SSCI to a minimum.
The Feasibility of Thoracoscopic Left Pneumonectomy
Authors: Xu Hao , Zhang Linyou
Published: May 2018

Objective In this study, we describe our experience with video-assisted thoracoscopic surgery (VATS) left pneumonectomy as a treatment for advanced malignant and benign diseases.

Methods Patients who underwent VATS left pneumonectomy in our clinic between October 2013 and August 2017 were retrospectively evaluated. VATS pneumonectomy was successfully completed in 46 patients. We reviewed and analyzed the characteristics of the patients in addition to intraoperative parameters, chest tube duration, length of hospital stay, morbidity, and mortality.

Results A total of 46 patients underwent VATS left pneumonectomy. Of these, 43 patients had malignant tumors and 3 patients had destroyed lung. The histologic types were squamous cell carcinoma in 24 patients, adenocarcinoma in 11, large cell carcinoma in 2, sarcomatoid carcinoma in 1, follicular dendritic cell sarcoma in 1, and small cell carcinoma in 4. Primary lung cancers were classified as stage IA1 in 2 patients, IA2 in 2, IA3 in 1, IB in 3, IIA in 3, IIB in 11, IIIA in 18, and IIIB in 3. The mean operation time was 160.54 ± 43.44 minutes, and the mean blood loss was 401.09 ± 284.32 mL. There was no perioperative mortality and no secretion retention and bronchopleural fistula. Arrhythmia was found in three patients. Pneumonia was found in four patients. The median follow-up time in this cohort was 25 months. A total of 15 patients (34.8%) developed recurrent diseases, 12 developed distant or multiple metastasis, and 3 developed locoregional recurrence.

Conclusion VATS pneumonectomy is a safe, feasible treatment for complicated diseases that induces acceptable damage and has lower morbidity.
Lung Ultrasound Findings in Congenital Pulmonary Airway Malformation
Authors: Mokhtari Mostafa , Durand Philippe , Raimondi Francesco , Migliaro Fiorella , Letourneau Alexandra , Tissières Pierre , De Luca Daniele , Yousef Nadya
Published: May 2018

Background and Objective Congenital pulmonary airway malformation (CPAM) is a group of rare congenital malformations of the lung and airways. Lung ultrasound (LU) is increasingly used to diagnose neonatal respiratory diseases since it is quick, easy to learn, and radiation-free, but no formal data exist for congenital lung malformations. We aimed to describe LU findings in CPAM neonates needing neonatal intensive care unit (NICU) admission and to compare them with a control population.

Methods A retrospective review of CPAM cases from three tertiary academic NICUs over 3 years (2014–2016) identified five patients with CPAM who had undergone LU examination. LU was compared with chest radiograms and computed tomography (CT) scans that were used as references.

Results CPAM lesions were easily identified and corresponded well with CT scans; they varied from a single large cystic lesion, multiple hypoechoic lesions, and/or consolidation. The first two LU findings have not been described in other respiratory conditions and were not found in controls.

Conclusion We provide the first description of LU findings in neonates with CPAM. LU may be used to confirm antenatally diagnosed CPAM and to suspect CPAM in infants with respiratory distress if cystic lung lesions are revealed. Further studies are necessary to define the place of LU in the management of CPAM.
Oral Epignathus with Maxilla Duplication: Report of a Rare Case
Authors: Tunes Roberto S. , Cavalcanti Gabriel Z. , Squarisi José Mauro O. , Patrocinio Lucas G.
Published: May 2018

Epignathus is a rare congenital oropharyngeal teratoma that arises from the oropharynx, especially the sphenoid, palatine, and ethmoid bones. Teratomas are benign tumors containing cells from ectodermal, mesodermal, and endodermal layers. The incidence of epignathus is between 1:35,000 and 1:200,000 live births with a female predominance. We reported an uncommon case of epignathus in a female newborn baby with an ill-defined oral mass protruding through a cleft in the hard palate. Computed tomography scan showed a contrast-enhanced solid mass with areas of calcification simulating a unique case of maxilla duplication. Surgery was performed, the mass was excised successfully, and microscopic analysis confirmed the diagnosis of mature teratoma. The patient evolved with good general health and showed no clinical signs of recurrence. Although epignathus is a rare condition, it should be diagnosed in the fetus as early as possible, especially to avoid fatal airway obstruction. In such cases, the treatment option is exclusively surgical, and complete resection is curative in most cases during the early neonatal period.
Grain boundary-dominated electrical conduction and anomalous optical-phonon behaviour near the Neel temperature in YFeO3 ceramics
Authors: Raut Subhajit , Babu P. D , Sharma R. K. , Pattanayak Ranjit , Panigrahi Simanchalo
Published: May 2018

We investigated the anomalous behaviour in the dielectric properties, occurring nearly at room temperature and at elevated temperatures (near the Neel temperature TN) of the polycrystalline samples of YFeO3 (YFO) ceramics. On the prepared YFO ceramics, the magnetic measurements showed the Neel temperature of YFO to be 650 K, below which the compound exhibited the weak ferromagnetic behaviour. X-ray photoelectron spectroscopy (XPS) shows the presence of Fe ions (Fe2+ and Fe3+ states) and also revealed the formation of the oxygen vacancies. The frequency dependence of the complex dielectric constant within the frequency domain of 100 Hz–1 MHz shows the presence of grain dominated dielectric relaxation over the thermal window of 300–373 K. The activation energy Eact.ε=0.611eV extracted from the imaginary permittivity spectrum indicates the involvement of oxygen vacancies in the relaxation process. Above 493 K, the ac conductivity, complex impedance, and modulus studies revealed appreciable conduction and relaxation processes occurring in YFO ceramics with respective activation energies Eact.σ=1.362eV and Eact.Z=1.345eV, which suggests that the oxygen vacancies are also involved for the anomalous behaviour of the dielectric constant at elevated temperatures. The temperature dependent Raman spectroscopic measurements within the thermal window of 298–698 K showed anomalous variations of the line widths and frequencies of several Raman active modes above 473 K up to the vicinity of TN pointing towards the presence of admixtures of the electron-phonon and spin-phonon coupling in the system. A further study on the thermal variation of the B2g(4) mode frequency with [M(T)/MS]2 shows the occurrence of strong spin–phonon (s-p) coupling, while the line shape shows the presence of the Fano asymmetry, suggesting spin dependent electron-phonon (e-p) coupling in the system below TN.
Optimal scheme of star observation of missile-borne inertial navigation system/stellar refraction integrated navigation
Authors: Lu Jiazhen , Yang Lie
Published: May 2018

To achieve accurate and completely autonomous navigation for spacecraft, inertial/celestial integrated navigation gets increasing attention. In this study, a missile-borne inertial/stellar refraction integrated navigation scheme is proposed. Position Dilution of Precision (PDOP) for stellar refraction is introduced and the corresponding equation is derived. Based on the condition when PDOP reaches the minimum value, an optimized observation scheme is proposed. To verify the feasibility of the proposed scheme, numerical simulation is conducted. The results of the Extended Kalman Filter (EKF) and Unscented Kalman Filter (UKF) are compared and impact factors of navigation accuracy are studied in the simulation. The simulation results indicated that the proposed observation scheme has an accurate positioning performance, and the results of EKF and UKF are similar.
Circulation of spoof surface plasmon polaritons: Implementation and verification
Authors: Pan Junwei , Wang Jiafu , Qiu Tianshuo , Pang Yongqiang , Li Yongfeng , Zhang Jieqiu , Qu Shaobo
Published: May 2018

In this letter, we are dedicated to implementation and experimental verification of broadband circulator for spoof surface plasmon polaritons (SSPPs). For the ease of fabrication, a circulator operating in X band was firstly designed. The comb-like transmission lines (CL-TLs), a typical SSPP structure, are adopted as the three branches of the Y-junction. To enable broadband coupling of SSPP, a transition section is added on each end of the CL-TLs. Through such a design, the circulator can operate under the sub-wavelength SSPP mode in a broad band. The simulation results show that the insertion loss is less than 0.5dB while the isolation and return loss are higher than 20dB in 9.4-12.0GHz. A prototype was fabricated and measured. The experimental results are consistent with the simulation results and verify the broadband circulation performance in X band.
Note: Evaluation of microfracture strength of diamond materials using nano-polycrystalline diamond spherical indenter
Authors: Sumiya H. , Hamaki K. , Harano K.
Published: May 2018

Ultra-hard and high-strength spherical indenters with high precision and sphericity were successfully prepared from nanopolycrystalline diamond (NPD) synthesized by direct conversion sintering from graphite under high pressure and high temperature. It was shown that highly accurate and stable microfracture strength tests can be performed on various super-hard diamond materials by using the NPD spherical indenters. It was also verified that this technique enables quantitative evaluation of the strength characteristics of single crystal diamonds and NPDs which have been quite difficult to evaluate.
Membrane isolation of repeated-use sweat stimulants for mitigating both direct dermal contact and sweat dilution
Authors: Simmers P. , Yuan Y. , Sonner Z. , Heikenfeld J.
Published: May 2018

With the device integration of sweat stimulation, sweat becomes a stronger candidate for non-invasive continuous biochemical sensing. However, sweat stimulants are cholinergenic agents and non-selective to just the sweat glands, and so, direct placement of sweat stimulants poses additional challenges in the possibility for uncontrollable transport of the stimulant into the body and challenges in contamination of the sweat sample. Reported here is membrane isolation of repeated-use sweat stimulants for mitigating direct dermal contact, dilution of the sweat stimulant, and contamination of the sweat sample. The membrane dramatically reduces passive diffusion of the sweat stimulant carbachol by roughly two orders of magnitude, while still allowing repeated sweat stimulation by iontophoretic delivery of the carbachol through the membrane and into the skin. Both in-vivo and in-vitro validation reveal feasibility for reliable integration of sweat stimulants within a wearable device for use periods of 24 h or more. In addition, advanced topics and confounding issues such as stimulant gel design, osmotic pressure, and ionic impurities are speculatively and theoretically discussed.
Non-steric-zipper models for pathogenic α-synuclein conformers
Authors: Schuman Brock , Won Amy , Brand-Arzamendi Koroboshka , Koprich James B. , Wen Xiao-Yan , Howson Patrick A. , Brotchie Jonathan M. , Yip Christopher M.
Published: May 2018

Parkinson's disease neurodegenerative brain tissue exhibits two biophysically distinct α-synuclein fiber isoforms—single stranded fibers that appear to be steric-zippers and double-stranded fibers with an undetermined structure. Herein, we describe a β-helical homology model of α-synuclein that exhibits stability in probabilistic and Monte Carlo simulations as a candidate for stable prional dimer conformers in equilibrium with double-stranded fibers and cytotoxic pore assemblies. Molecular models of β-helical pore assemblies are consistent with α-synucleinA53T transfected rat immunofluorescence epitope maps. Atomic force microscopy reveals that α-synuclein peptides aggregate into anisotropic fibrils lacking the density or circumference of a steric-zipper. Moreover, fibrillation was blocked by mutations designed to hinder β-helical but not steric-zipper conformations. β-helical species provide a structural basis for previously described biophysical properties that are incompatible with a steric-zipper, provide pathogenic mechanisms for familial human α-synuclein mutations, and offer a direct cytotoxic target for therapeutic development.
PIEZO channel protein naturally expressed in human breast cancer cell MDA-MB-231 as probed by atomic force microscopy
Authors: Weng Yuanqi , Yan Fei , Chen Runkang , Qian Ming , Ou Yun , Xie Shuhong , Zheng Hairong , Li Jiangyu
Published: May 2018

Mechanical stimuli drives many physiological processes through mechanically activated channels, and the recent discovery of PIEZO channel has generated great interests in its mechanotransduction. Many previous researches investigated PIEZO proteins by transcribing them in cells that originally have no response to mechanical stimulation, or by forming PIEZO-combined complexes in vitro, and few studied PIEZO protein’s natural characteristics in cells. In this study we show that MDA-MB-231, a malignant cell in human breast cancer cell line, expresses the mechanosensitive behavior of PIEZO in nature without extra treatment, and we report its characteristics in response to localized mechanical stimulation under an atomic force microscope, wherein a correlation between the force magnitude applied and the channel opening probability is observed. The results on PIEZO of MDA-MB-231 can help establish a basis of preventing and controlling of human breast cancer cell via mechanical forces.
Derivation of the threshold condition for the ion temperature gradient mode with an inverted density profile from a simple physics picture
Authors: Jhang Hogun
Published: May 2018

We show that the threshold condition for the toroidal ion temperature gradient (ITG) mode with an inverted density profile can be derived from a simple physics argument. The key in this picture is that the density inversion reduces the ion compression due to the ITG mode and the electron drift motion mitigates the poloidal potential build-up. This condition reproduces the same result that has been reported from a linear gyrokinetic calculation [T. S. Hahm and W. M. Tang, Phys. Fluids B 1, 1185 (1989)]. The destabilizing role of trapped electrons in toroidal geometry is easily captured in this picture.
A current transient method for trap analysis in BiFeO3 thin films
Authors: Zhu Hui , Yang Ying , Meng Xiao , Jiang Anquan , Bai Zilong , Zheng Xiang , Jin Lei , Wang Chen , Feng Shiwei
Published: May 2018

We present a method to study the trap characteristics in BiFeO3 thin films, which display a resistance switching effect caused by trapping/detrapping of charge carriers. The method consists of measuring the current transients for the detrapping of charge carriers from trap sites and subsequent analysis of the time constant from the current transient curve. Using this method, the energy level of the traps was identified to be 0.71 ± 0.06 eV. The parameters of the trapping pulses (voltage and time duration) were found to affect the time constant, indicating a close relationship between the escape frequency of the charge carriers and the structure ordering caused by polarization and the filling of the traps.
Optical characterization and bandgap engineering of flat and wrinkle-textured FA0.83Cs0.17Pb(I1–xBrx)3 perovskite thin films
Authors: Tejada A. , Braunger S. , Korte L. , Albrecht S. , Rech B. , Guerra J. A.
Published: May 2018

The complex refractive indices of formamidinium cesium lead mixed-halide [FA0.83Cs0.17Pb(I1– xBrx)3] perovskite thin films of compositions ranging from x = 0 to 0.4, with both flat and wrinkle-textured surface topographies, are reported. The films are characterized using a combination of variable angle spectroscopic ellipsometry and spectral transmittance in the wavelength range of 190 nm to 850 nm. Optical constants, film thicknesses and roughness layers are obtained point-by-point by minimizing a global error function, without using optical dispersion models, and including topographical information supplied by a laser confocal microscope. To evaluate the bandgap engineering potential of the material, the optical bandgaps and Urbach energies are then accurately determined by applying a band fluctuation model for direct semiconductors, which considers both the Urbach tail and the fundamental band-to-band absorption region in a single equation. With this information, the composition yielding the optimum bandgap of 1.75 eV for a Si-perovskite tandem solar cell is determined.
Piezoelectric performance enhancement of Pb(Mg1/3Nb2/3)O3-0.25PbTiO3 crystals by alternating current polarization for ultrasonic transducer
Authors: Xu Jialin , Deng Hao , Zeng Zhou , Zhang Zhang , Zhao Kunyu , Chen Jianwei , Nakamori Nami , Wang Feifei , Ma Jinpeng , Li Xiaobing , Luo Haosu
Published: May 2018

The [001]-oriented Pb(Mg1/3Nb2/3)O3-0.25PbTiO3(PMN-0.25PT) single crystal has been poled by alternating current polarization (ACP). The piezoelectric, dielectric, and electromechanical properties of PMN-0.25PT crystals were investigated with the variations of the electric field, polarization frequency, and cycles. For the piezoelectric performance of the PMN-0.25PT crystal, the optimum ACP condition was obtained under the electric field of 12–18 kV/cm in the frequency range of 20–40 Hz and after 20 cycles. It gives the crystals an increase by 40% from 1220 pC/N to 1730 pC/N in the piezoelectric coefficient compared with traditional direct current polarization. The patterns of the periodic stripe nanodomains under different polarization conditions were revealed by piezoresponse force microscopy. The enhancement of the piezoelectric performance is attributed to the high density of these domain walls. This work indicates that ACP is an effective way to modify the piezoelectric performance of PMN-0.25PT crystals and make it a promising candidate for sensors and transducers.
A leap in precision for diamond-defect NMR
Authors: Smart Ashley G.
Published: May 2018

The technique’s spectral resolution is now sharp enough to reveal a molecule’s unique chemical fingerprint.
The origins ofPhysics Today
Authors: Kaiser David
Published: May 2018

In 1945 leaders of the American Institute of Physics conceived a bold experiment: a magazine that would help unify an increasingly balkanized discipline.
An insight into the downstream analysis of RB gene in F1 RB potato lines imparting field resistance to late blight
Authors: Sundaresha S. , Sharma Sanjeev , Shandil Rajesh K. , Sharma Sadhana , Thakur Vandana , Bhardwaj Vinay , Kaushik Surinder K. , Singh Bir Pal , Chakrabarti Swarup K.
Published: May 2018

Earlier studies have shown that level of late blight resistance conferred by the classical R gene (RB Rpi-blb1) is dependent on genetic background of the recipient genotype. This was revealed in the analysis of late blight response that belonged to a group of F1 progeny obtained from the cross between Kufri Jyoti and SP951, which showed wide variation in late blight resistance response in spite of possessing the same RB gene. The global gene expression pattern in the RB potato lines was studied in response to late blight infection using cDNA microarray analysis to reveal the background effect. Leaf samples were collected at 0, 24, 72 and 120 h post inoculation (hpi) with Phytophthora infestans for gene expression analysis using 61031 gene sequences. Significantly upregulated (1477) and downregulated (4245) genes common in the RB-transgenic F1 lines at 24 and 72 hpi were classified into several categories based on GO identifiers and majority of genes were assigned putative biological functions. Highest expression of an NBS-LRR along with protease, pectin esterase inhibitors, chaperones and reactive oxygen species genes were observed which affirmed a significant role of these categories in the defence response of RB-KJ lines. Results suggest that the immune priming of plant receptors are likely to be involved in stability and functionality of RB to induce resistance against P. infestans. This study is important for effective deployment of RB gene in the host background and contributes immensely to scientific understanding of R gene interaction with host protein complexes to regulate defence system in plants.
Negative effects of oxidative stress in bovine spermatozoa on in vitro development and DNA integrity of embryos
Authors: Bittner L. , Wyck S. , Herrera C. , Siuda M. , Wrenzycki C. , van Loon B. , Bollwein H.
Published: May 2018

Oxidative stress in spermatozoa has effects on subsequent embryo development. The aim of the present study was to elucidate whether sperm oxidative stress results in increased DNA damage in the embryo. To this end, bovine spermatozoa were incubated for 1 h at 37°C without or with 100 µM H2O2, resulting in non-oxidised (NOX-S) and oxidised (OX-S) spermatozoa respectively. Non-incubated spermatozoa served as the control group (CON-S). After IVF, developmental rates 30, 46 and 60 h and 7 days after IVF were assessed. DNA damage was analysed in embryos using the comet assay and a DNA damage marker (γH2AX immunostaining); the apoptotic index was determined in blastocysts. Exposure of spermatozoa to H2O2 induced a significant amount of sperm chromatin damage. The use of OX-S in IVF resulted in significantly reduced cleavage and blastocyst rates compared with the use of CON-S and NOX-S. Furthermore, in embryos resulting from the use of OX-S, a developmental delay was evident 30 and 46 h after IVF. γH2AX immunostaining was lower in blastocysts than in early embryos. In blastocysts, the comet and apoptotic indices were significantly higher in embryos resulting from the use of OX-S than CON-S and NOX-S. In conclusion, oxidative stress in spermatozoa induces developmental abnormalities and is a source of DNA damage in the resulting embryos.
Robustness of adult female survival maintains a high-density sika deer (Cervus nippon) population following the initial irruption
Authors: Ueno M. , Iijima H. , Takeshita K. , Takahashi H. , Yoshida T. , Uehara H. , Igota H. , Matsuura Y. , Ikeda T. , Azumaya M. , Kaji K.
Published: May 2018

Context Irruption of large herbivore populations is characterised by three distinct phases: (1) an exponential increase in population to a peak abundance; (2) a population crash; and (3) a second increase to another population peak, typically lower than the first peak of abundance. However, there has been little study of age- and sex-specific factors that affect the post-initial irruption interactions with food sources. Aims We aimed to investigate annual survival rates of sika deer (Cervus nippon Temminck, 1838) in the sequent irruption of a population on Nakanoshima Island, Lake Toya, Japan, with a chronically high density during the period 2002–12. Methods Survival monitoring data were obtained for 219 individuals (93 males and 126 females) using radio-collars. Annual survival was quantified, and related factors, i.e. deer abundance and winter severity, were determined by model selection using Akaike information criterion values. Key Results The results showed that annual survival rates across sexes and age classes (fawn, yearling, prime-aged, old) decreased with increasing population density, snow depth and winter precipitation. Winter severity had a greater effect on adult survival than density regulation. Nevertheless, female adult survival was maintained at a high level, with a mean of 0.84 (95% CI: 0.80–0.88). Key conclusions Robust survival rates for adult females might contribute to the maintenance of a high-density sika deer population in the post-initial irruption. Implications We suggest that in the absence of predation and hunting, sika deer population is not able to self-regulate to the density level that avoids an irreversible impact on plants.
The ongoing invasion of translocated sleepy cod (Oxyeleotris lineolata) in the Lake Eyre Basin, central Australia
Authors: Sternberg David , Cockayne Bernie
Published: May 2018

Context Present-day distribution records show that Oxyeleotris lineolata (sleepy cod) has colonised many ephemeral streams and refugial waterholes of the Cooper Creek catchment in the Lake Eyre Basin within a decade of the first record or capture. When introduced to new habitats outside its natural range, this species is considered to be a serious conservation risk to native fish species. Aims The present study aims to document the transport, establishment, colonisation and integration of O. lineolata in the Lake Eyre Basin, and quantify its impact on native fish assemblages. Methods Fish samples were taken annually in 21 waterholes between 2011 and 2016, by using a combination of single- and double-winged fyke nets. We collected novel diet and life-history information from 242 O. lineolata individuals across their known distribution. Key results Abundance, length distribution and life-history information suggested a ‘colonising front’ moving downstream, across state jurisdictional boundaries and into the Coongie Lakes Ramsar site. Oxyeleotris lineolata diet is most similar to that of two native generalist invertivore–piscivores and preys on several native fish species. With a derived longevity in excess of 15 years and a life-history strategy that combines batch spawning, high fecundity and parental care (i.e. high juvenile survivorship), there is real potential for O. lineolata to dominate fish assemblages in waterholes that provide refuge for native fishes during dry periods. Conclusions The present study showed that O. lineolata has the potential to negatively influence native fish assemblages through both competition and predation in refugial waterholes. Eradication of O. lineolata from the Cooper Creek catchment in central Australia is highly unlikely, given its widespread distribution, the remoteness of the receiving landscape and a current lack of resources to monitor spread and attempt eradication at the moving front of the Cooper Creek population. Implications Achieving greater awareness of the potential impacts of introducing or spreading non-native species is an important first step towards preserving the native fish fauna of the Lake Eyre Basin. Further research is warranted to fully understand the current and potential future distribution of O. lineolata in the basin, its biological and ecological requirements, and influence on native fish species and assemblages.
Vagises’ Virtuous Hand: An Unforeseen Note on Plutarch,Life of Crassus18, 3
Authors: Courtieu Gilles
Published: May 2018

When Crassus met the Parthian ambassador Vagises on the eve of his disastrous expedition ending at the Battle of Carrhae in 53 BC, Vagises mocked his boldness and showed the palm of his hand, on which, according to him, no hair would ever grow unless the Roman were to reach Mesopotamia, the heart of Parthian empire. This bizarre gesture and statement, usually assumed to be frivolous, can only be understood in the context of Zoroastrian sexual and cathartic ethics, which of course no Roman or Greek could understand. The source of this information therefore could not have been Plutarch, but rather someone conversant with Persian culture, from either Parthian or Armenian stock.
Protein threading using residue co-variation and deep learning
Authors: Zhu Jianwei , Wang Sheng , Bu Dongbo , Xu Jinbo
Published: May 2018

Motivation

Template-based modeling, including homology modeling and protein threading, is a popular method for protein 3D structure prediction. However, alignment generation and template selection for protein sequences without close templates remain very challenging.

Results

We present a new method called DeepThreader to improve protein threading, including both alignment generation and template selection, by making use of deep learning (DL) and residue co-variation information. Our method first employs DL to predict inter-residue distance distribution from residue co-variation and sequential information (e.g. sequence profile and predicted secondary structure), and then builds sequence-template alignment by integrating predicted distance information and sequential features through an ADMM algorithm. Experimental results suggest that predicted inter-residue distance is helpful to both protein alignment and template selection especially for protein sequences without very close templates, and that our method outperforms currently popular homology modeling method HHpred and threading method CNFpred by a large margin and greatly outperforms the latest contact-assisted protein threading method EigenTHREADER.

Availability and implementation

http://raptorx.uchicago.edu/

Supplementary information

Supplementary data are available at Bioinformatics online.
Modeling one thousand intron length distributions with fitild
Authors: Gotoh Osamu
Published: May 2018

Motivation

Intron length distribution (ILD) is a specific feature of a genome that exhibits extensive species-specific variation. Whereas ILD contributes to up to 30% of the total information content for intron recognition in some species, rendering it an important component of computational gene prediction, very few studies have been conducted to quantitatively characterize ILDs of various species.

Results

We developed a set of computer programs (fitild, compild, etc.) to build statistical models of ILDs and compare them with one another. Each ILD of more than 1000 genomes was fitted with fitild to a statistical model consisting of one, two, or three components of Frechet distributions. Several measures of distances between ILDs were calculated by compild. A theoretical model was presented to better understand the origin of the observed shape of an ILD.

Availability and implementation

The C++ source codes are available at https://github.com/ogotoh/fitild.git/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks
Authors: Pan Xiaoyong , Shen Hong-Bin
Published: May 2018

Motivation

RNA-binding proteins (RBPs) take over 5–10% of the eukaryotic proteome and play key roles in many biological processes, e.g. gene regulation. Experimental detection of RBP binding sites is still time-intensive and high-costly. Instead, computational prediction of the RBP binding sites using patterns learned from existing annotation knowledge is a fast approach. From the biological point of view, the local structure context derived from local sequences will be recognized by specific RBPs. However, in computational modeling using deep learning, to our best knowledge, only global representations of entire RNA sequences are employed. So far, the local sequence information is ignored in the deep model construction process.

Results

In this study, we present a computational method iDeepE to predict RNA–protein binding sites from RNA sequences by combining global and local convolutional neural networks (CNNs). For the global CNN, we pad the RNA sequences into the same length. For the local CNN, we split a RNA sequence into multiple overlapping fixed-length subsequences, where each subsequence is a signal channel of the whole sequence. Next, we train deep CNNs for multiple subsequences and the padded sequences to learn high-level features, respectively. Finally, the outputs from local and global CNNs are combined to improve the prediction. iDeepE demonstrates a better performance over state-of-the-art methods on two large-scale datasets derived from CLIP-seq. We also find that the local CNN runs 1.8 times faster than the global CNN with comparable performance when using GPUs. Our results show that iDeepE has captured experimentally verified binding motifs.

Availability and implementation

https://github.com/xypan1232/iDeepE

Supplementary information

Supplementary data are available at Bioinformatics online.
Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids
Authors: Dorier Julien , Goundaroulis Dimos , Benedetti Fabrizio , Stasiak Andrzej
Published: May 2018

The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluating the entanglement of open curves without the need to close them, using the recent concept of knotoids which is a generalization of the classical knot theory to open curves. Knoto-ID can analyse the global topology of the full chain as well as the local topology by exhaustively studying all subchains or only determining the knotted core. Knoto-ID permits to localize topologically non-trivial protein folds that are not detected by informatics tools detecting knotted protein folds.

Availability and implementation

Knoto-ID is written in C++ and includes R (www.R-project.org) scripts to generate plots of projections maps, fingerprint matrices and disk matrices. Knoto-ID is distributed under the GNU General Public License (GPL), version 2 or any later version and is available at https://github.com/sib-swiss/Knoto-ID. A binary distribution for Mac OS X, Linux and Windows with detailed user guide and examples can be obtained from https://www.vital-it.ch/software/Knoto-ID.
Improved enzyme annotation with EC-specific cutoffs using DETECT v2
Authors: Nursimulu Nirvana , Xu Leon L , Wasmuth James D , Krukov Ivan , Parkinson John
Published: May 2018

We present DETECT v2—an enzyme annotation tool which considers the effect of sequence diversity when assigning enzymatic function [as an Enzyme Commission (EC) number] to a protein sequence. In addition to capturing more enzyme classes than the previous version, we now provide EC-specific cutoffs that greatly increase precision and recall of assignments and show its performance in the context of pathways.

Availability and implementation

https://github.com/ParkinsonLab/DETECT-v2

Supplementary information

Supplementary data are available at Bioinformatics online.
polymapR—linkage analysis and genetic map construction from F1 populations of outcrossing polyploids
Authors: Bourke Peter M , van Geest Geert , Voorrips Roeland E , Jansen Johannes , Kranenburg Twan , Shahin Arwa , Visser Richard G F , Arens Paul , Smulders Marinus J M , Maliepaard Chris
Published: May 2018

Motivation

Polyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.

Results

polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.

Availability and implementation

polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR.

Supplementary information

Supplementary data are available at Bioinformatics online.
AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs
Authors: Gorjanc Gregor , Hickey John M
Published: May 2018

AlphaMate is a flexible program that optimizes selection, maintenance of genetic diversity and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimization of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic. The optimization can maximize genetic gain, minimize group coancestry, minimize inbreeding of individual matings, or maximize genetic gain for a given increase in group coancestry or inbreeding. Users provide a list of candidate individuals with associated gender and selection criteria information (if applicable) and coancestry matrix. Selection criteria and coancestry matrix can be based on pedigree or genome-wide markers. Additional individual or mating specific information can be included to enrich optimization objectives. An example of rapid recurrent genomic selection in wheat demonstrates how AlphaMate can double the efficiency of converting genetic diversity into genetic gain compared to truncation selection. Another example demonstrates the use of genome editing to expand the gain-diversity frontier.

Availability and implementation

Executable versions of AlphaMate for Windows, Mac and Linux platforms are available at http://www.AlphaGenes.roslin.ed.ac.uk/AlphaMate.
Health in All Policies (HiAP) governance: lessons from network governance
Authors: Khayatzadeh-Mahani Akram , Ruckert Arne , Labonté Ronald , Kenis Patrick , Akbari-Javar Mohammad Reza
Published: May 2018

The Health in All Policies (HiAP) approach requires formal and sustained governance structures and mechanisms to ensure that the policies of various non-health sectors maximize positive and minimize negative impacts on population health. In this paper, we demonstrate the usefulness of a network perspective in understanding and contributing to the effectiveness of HiAP. We undertook an exploratory, qualitative case study of a HiAP structure in Iran, the Kerman province Council of Health and Food Security (CHFS) with diverse members from health and non-health sectors. We analyzed relevant policy texts and interviewed 32 policy actors involved in the CHFS. Data were analyzed using within-case analysis and constant comparative methodology. Our findings suggest that CHFS governance from a network perspective drew in practice on elements of two competing network governance modes: the network administrative organization (NAO) and the lead organization mode. Our results also show that a shift from a hierarchical and market-based mode of interaction to a network logic within CHFS has not yet taken place. In addition, CHFS suffers from large membership and an inability to address complex ‘wicked problems’, as well as low trust, legitimacy and goal consensus among its members. Drawing on other HiAP studies and commentaries, insights from organization network theory, and in-depth findings from our case study, we conclude that a NAO may be the most effective mode of governance for tackling complex social problems in HiAP structures. Since similar studies are limited, and our single case study may not be transferable across all contexts, we suggest that further research be undertaken to explore HiAP structures from a network perspective in different institutional and cultural settings. With increasing emphasis given to HiAP approaches in national and international health policy discourse, it is important that comparative knowledge about the effectiveness of HiAP governance arrangements be developed.
Mitochondrial DNA Is a Pro-Inflammatory Damage-Associated Molecular Pattern Released During Active IBD
Authors: Boyapati Ray K , Dorward David A , Tamborska Arina , Kalla Rahul , Ventham Nicholas T , Doherty Mary K , Whitfield Philip D , Gray Mohini , Loane Joseph , Rossi Adriano G , Satsangi Jack , Ho Gwo-tzer
Published: May 2018

Background

Due to common evolutionary origins, mitochondrial DNA (mtDNA) shares many similarities with immunogenic bacterial DNA. MtDNA is recognized as a pro-inflammatory damage-associated molecular pattern (DAMP) with a pathogenic role in several inflammatory diseases. We hypothesised that mtDNA is released during active disease, serving as a key pro-inflammatory factor in inflammatory bowel disease (IBD).

Methods

Between 2014 and 2015, we collected plasma separated within 2 hours of sampling from 97 prospectively recruited IBD patients (67 ulcerative colitis [UC] and 30 Crohn’s disease [CD]) and 40 non-IBD controls. We measured circulating mtDNA using quantitative polymerase chain reaction (amplifying mitochondria COXIII/ND2 genes) and also in mouse colitis induced by dextran sulfate-sodium (DSS). We used a mass spectometry approach to detect free plasma mitochondrial formylated peptides. Furthermore, we examined for mitochondrial damage using electron microscopy (EM) and TLR9 expression, the target for mtDNA, in human intestinal IBD mucosa.

Results

Plasma mtDNA levels were increased in UC and CD (both P < 0.0001) compared with non-IBD controls. These levels were significantly correlated to blood (C-reactive protein, albumin, white cell count), clinical and endoscopic markers of severity, and disease activity. In active UC, we identified 5 mitochondrial formylated peptides (the most abundant being fMMYALF with known chemoattractant function) in plasma. We observed mitochondrial damage in inflamed UC mucosa and significantly higher fecal MtDNA levels (vs non-IBD controls [P < 0.0001]), which supports gut mucosal mitochondrial DAMP release as the primary source. In parallel, plasma mtDNA levels increased during induction of acute DSS colitis and were associated with more severe colitis (P < 0.05). In active IBD, TLR9+ lamina propria inflammatory cells were significantly higher in UC and CD compared with controls (P < 0.05).

Conclusions

We present the first evidence to show that mtDNA is released during active IBD. MtDNA is a potential mechanistic biomarker, and our data point to mtDNA-TLR9 as a therapeutic target in IBD.