bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic dc voltage regulation of split‐capacitor DSTATCOM for power quality improvement
Authors: Myneni Hareesh , Siva Kumar Ganjikunta , Sreenivasarao Dharmavarapu
Published: August 2017

A distribution static compensator (DSTATCOM) is used for power quality improvement in the distribution system. In the conventional DSTATCOM, the dc voltage is kept constant and it is selected based on rated reactive load. Under light load or reduced load conditions, the compensator works perfectly even though the dc voltage is reduced from its rated value. Maintaining the dc voltage constant under reduced or light load conditions leads to unnecessary voltage stress across the switching devices. Therefore, in this study, a simple dynamic dc voltage regulation is proposed to reduce the voltage stress across switching devices under the reduced load conditions. The proposed algorithm optimises the value of dc voltage based on reactive load without compromising the performance of the DSTATCOM. To validate the proposed method, simulation and experimental studies were carried out on the three‐phase two‐level split‐capacitor DSTATCOM for harmonic mitigation, reactive power compensation and load balancing.
Case study on the effectiveness of gear fault diagnosis technique for gear tooth defects under fluctuating speed
Authors: Sharma Vikas , Parey Anand
Published: August 2017

Gears are very reliable parts of wind turbines and normally contribute for more than 5 years without failure when operated under fluctuating speed conditions. This case study presents the effectiveness of gear fault diagnosis techniques to highlight cracked tooth, chipped tooth and missing tooth gear under fluctuating speed conditions. Various measuring parameters such as overall vibration acceleration and envelope‐detected acceleration were calculated for vibration signal, and sound intensity and sound pressure were calculated for acoustic signal. A statistical indicator kurtosis was also calculated for both vibration signal and acoustic signal. These measuring parameters were then compared with showing the fault detection capability of techniques employed under fluctuating speed and also under different loading conditions. The detection of faults by kurtosis of acoustic signal is found most efficient. For low load conditions, envelope‐detected acceleration of vibration signal can also support fault diagnosis under fluctuating speed conditions.
Recursive instrumental variable method for locating a scanning emitter by a single observer using time of interception
Authors: Zhang Yifei , Zhang Min , Guo Fucheng
Published: August 2017

The recursive solution to passive localisation of a scanning emitter using time of interception (TOI) by a single moving observer is investigated in this study. First, the correlated measurement noise in the traditional pseudo‐linear model for the scanning emitter localisation is decoupled by introducing the first noise corrupted direction of arrival as a nuisance parameter. A recursive pseudo‐linear least square (RPLS) estimator is then developed by transforming the TOI of the scanning emitter into the direction difference of arrival model. However, there is bias in this method due to the correlation between the measurement matrix and the noise. To reduce the bias, the instrumental variable (IV) method is used, and two recursive IV (RIV) estimators, forgetting factor based RIV (F2RIV) and Taylor series expansion based RIV (TSRIV), are proposed. It approximates the IV matrix recursively using the Taylor series expansion in the TSRIV estimator. Simulations show that the TSRIV estimator alleviates the bias compared with the RPLS estimator dramatically and can reach the Cramer–Rao lower bound at moderate measurement noise levels. Moreover, it is more stable and has shorter convergence time than the F2RIV estimator.
Polarized radiative transfer modeling of warped and clumpy dusty tori
Authors: Marin F. , Schartmann M.
Published: August 2017

Context.Active galactic nuclei (AGN) are anisotropic objects surrounded by an optically thick equatorial medium whose true geometry still defies observers.

Aims.We aim to explore the optical scattering-induced polarization that emerges from clumpy and warped dusty tori to check whether they can fit the unified model predictions.

Methods.We ran polarized radiative transfer simulations in a set of warped and non-warped clumpy tori to explore the differences induced by distorted dust distributions. We then included warped tori in a more complex model representative of an AGN to check, using polarimetry and imaging methods, whether warps can reproduce the expected polarization dichotomy between Seyfert-I and Seyfert-II AGN.

Results.The main results from our simulations highlight that isolated warped structures imprint the polarization degree and angle with distinctive signatures at Seyfert-I orientations. Included in an AGN model, the signatures of warps are easily (but not always) washed out by multiple scattering in a clumpy environment. Imaging polarimetry may help to detect warped tori, but we prove that warps can exist in AGN circumnuclear regions without contradicting observations.

Conclusions.Two warped tori with a non-significant difference in geometry in terms of photometry or spectroscopy can have entirely different signatures in polarimetry. Testing the geometry of any alternative model to the usual dusty torus using polarized radiative transfer is a necessary approach to verify or reject a hypothesis.
Medical Termination of Delayed Miscarriage: Four-Year Experience with an Outpatient Protocol
Authors: Lyra Joana , Cavaco-Gomes João , Moucho Marina , Montenegro Nuno
Published: August 2017

Purpose To evaluate the efficacy of an outpatient protocol with vaginal misoprostol to treat delayed miscarriage.

Methods Retrospective analysis of prospectively collected data on women medically treated for missed abortion with an outpatient protocol. The inclusion criteria were: ultrasound-based diagnosis of missed abortion with less than 10 weeks; no heavy bleeding, infection, inflammatory bowel disease or misoprostol allergy; no more than 2 previous spontaneous abortions; the preference of the patient regarding the medical management. The protocol consisted of: 1) a single dose of 800 µg of misoprostol administered intravaginally at the emergency department, after which the patients were discharged home; 2) clinical and ultrasonographic evaluation 48 hours later – if the intrauterine gestational sac was still present, the application of 800 µg of vaginal misoprostol was repeated, and the patients were discharged home; 3) clinical and ultrasonography evaluation 7 days after the initiation of the protocol – if the intrauterine gestational sac was still present, surgical management was proposed. The protocol was introduced in January 2012. Every woman received oral analgesia and written general recommendations. We also gave them a paper form to be presented and filled out at each evaluation.

Results Complete miscarriage with misoprostol occurred in 340 women (90.2%). Surgery was performed in 37 (9.8%) patients, representing the global failure rate of the protocol. Miscarriage was completed after the first misoprostol administration in 208 (55.2%) women, with a success rate after the second administration of 78.1% (132/169). The average age of the women with complete resolution using misoprostol was superior to the average age of those who required surgery (33.99 years versus 31.74 years; p = 0.031). Based on the ultrasonographic findings in the first evaluation, the women diagnosed with fetal loss achieved greater success rates compared with those diagnosed with empty sac (p = 0.049).

Conclusions We conclude this is an effective and safe option in the majority of delayed miscarriage cases during the first trimester, reducing surgical procedures and their consequences.
Cerebral Microdialysis: Going Deep into Brain Biochemistry for a Better Understanding of Pathomechanisms of Acute Brain Injury
Authors: Gupta Deepak , Mazzeo Anna
Published: August 2017

Patients with traumatic brain injury (TBI) have variable outcomes subject to intracranial hypertension, ischemia, hypotension, and various biochemical alterations. Multimodality neurointensive monitoring is standard of care for decision making in all severe TBI cases at present in most neurotrauma units. Neuromonitoring tools, such as cerebral microdialysis, may contribute to understanding the pathomechanisms of acute brain injury, provide an early warning of secondary cerebral deterioration (therapeutic window of opportunity), and help in selecting the patients most suitable to benefit from this very invasive surgical rescue therapy. Cerebral microdialysis can be used as a measure of the effect of decompressive craniectomy on neurochemistry derangement and brain energy crisis jeopardizing the injured brain. Present review discusses the cerebral microdialysis, its usefulness, and role in prognostication of severe TBIs, especially in patients post-decompressive craniectomy. The authors also discuss the current consensus guidelines on usage of cerebral microdialysis in TBI patients.
Die Progression der Nierenerkrankung – wie ist sie zu verhindern?
Authors: Schneider Markus , Hilgers Karl
Published: August 2017

End stage chronic kidney disease (CKD) requiring renal replacement therapy is related to poor quality of life and high mortality. Thus, slowing the progression of CKD is an important purpose of therapy. Some general therapeutic approaches aim to slow the decline of renal function and they can be applied in all patients with CKD – irrespective of the underlying cause of CKD. A key intervention is lowering blood pressure (target: ≤ 140/90 mmHg, and in patients with albuminuria ≤ 130/80 mmHg). Inhibitors of the renin angiotensin system preferentially should be used in case of albuminuria, depending on the diabetic status and the level of albuminuria: in diabetics with albuminuria ≥ 30 mg/d, in non-diabetics with albuminuria > 300 mg/d. Mineralocorticoid receptor blockers and endothelin receptors blockers promise novel anti-proteinuric strategies – but still validation of their positive effects on retarding CKD progression is necessary. In patients with diabetic kidney disease, glycemic control aiming for an HbA1c of ≈ 7.0 % has been established to slow CKD progression. Furthermore, SGLT-2 inhibition with empagliflozin may be considered as a new therapeutic approach that provides additional cardiovascular and renal protection. Finally, recent studies suggest: correction of metabolic acidosis and avoidance of episodes of acute renal failure may provide protection against the progression of CKD.
Granuloma anulare als mögliche kutane Paraneoplasie
Authors: Troyanova-Slavkova S. , Seidl C. , Schaarschmidt E. , Werner W. , Kowalzick L.
Published: August 2017

Die paraneoplastische Variante des Granuloma anulare (GA) ist eine seltene kutane Manifestation einer zugrunde liegenden Malignität, die am häufigsten ein systemisches Lymphom ist. Wir berichten über den Fall eines Patienten mit Urothelkarzinom des Ureters und ca. 2 Jahre später mit Rezidiv-Urothelkarzinom der Harnblase mit disseminiertem und therapierefraktärem GA. Das GA trat nahezu gleichzeitig mit dem Urothelkarzinom auf, nach der Tumorentfernung bildete es sich etwas zurück und verschlechterte sich erneut bei dem Rezidiv des Karzinoms. Die enge zeitliche Korrelation der klinischen Verläufe dieser beiden Krankheiten weist darauf hin, dass ihre Koexistenz mehr als ein zufälliger Befund ist. Dieser Fall hebt hervor, wie wichtig es ist, ein paraneoplastisches GA auszuschließen, besonders in Fällen, in denen die Hautmanifestationen umfangreich und resistent gegen die Behandlung sind.
Epileptic Seizures Under Antidepressive Drug Treatment: Systematic Review
Authors: Steinert Tilman , Fröscher Walter
Published: August 2017

Objective This paper is a systematic review on seizures under treatment with substances licensed for major depression.

Method Systematic review protocol is available in PROSPERO registration number CRD42016034010. Twenty-five substances were selected according to frequencies of prescriptions and publications. A PubMed search was conducted with “substance name” and “seizure.”

Results A total of 2291 articles were screened, out of which 164 fulfilled inclusion criteria. Data synthesis was possible only to a limited extent due to heterogeneity of included patients, observation periods, methods, and outcomes. Evidence for an at most moderate, but still low, risk (>0.1% under regular doses) was found highest for clomipramine, followed by quetiapine, amitriptyline, venlafaxine, citalopram, sertraline, trazodone, mirtazapine, paroxetine, bupropion, and escitalopram. For fluoxetine and duloxetine, the risk seems to be negligible. For the other, mostly newer, substances, sufficient evidence was not available. An increased risk for lithium, as reported in many reviews and textbooks, could not be confirmed.

Conclusions Antidepressive treatment is rather safe in terms of risk of seizures and also can be generally recommended in the treatment of patients with epilepsy.
The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces
Authors: Aviat Félix , Lagardère Louis , Piquemal Jean-Philip
Published: August 2017

In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180–190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered “non-iterative.” This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.
A comparative study of different methods for calculating electronic transition rates
Authors: Kananenka Alexei A. , Sun Xiang , Schubert Alexander , Dunietz Barry D. , Geva Eitan
Published: August 2017

We present a comprehensive comparison of the following mixed quantum-classical methods for calculating electronic transition rates: (1) nonequilibrium Fermi’s golden rule, (2) mixed quantum-classical Liouville method, (3) mean-field (Ehrenfest) mixed quantum-classical method, and (4) fewest switches surface-hopping method (in diabatic and adiabatic representations). The comparison is performed on the Garg-Onuchic-Ambegaokar benchmark charge-transfer model, over a broad range of temperatures and electronic coupling strengths, with different nonequilibrium initial states, in the normal and inverted regimes. Under weak to moderate electronic coupling, the nonequilibrium Fermi’s golden rule rates are found to be in good agreement with the rates obtained via the mixed quantum-classical Liouville method that coincides with the fully quantum-mechanically exact results for the model system under study. Our results suggest that the nonequilibrium Fermi’s golden rule can serve as an inexpensive yet accurate alternative to Ehrenfest and the fewest switches surface-hopping methods.
Terahertz radiation enhanced emission of fluorescence from elongated plasmas and microplasmas in the counter-propagating geometry
Authors: Buccheri Fabrizio , Liu Kang , Zhang Xi-Cheng
Published: August 2017

Remote sensing is one of the major challenges for Terahertz (THz) radiation applications, due to the THz wave attenuation by the atmosphere water vapor during its propagation. THz-Radiation-Enhanced-Emission-of-Fluorescence (REEF) is a THz air-photonics technique that has the potential to bypass this issue, by having the sought-after THz spectral fingerprints carried from the target to the operator by ultraviolet light, which experiences low absorption in the atmosphere. This technique has been previously demonstrated when the THz radiation and the laser excitation are focused collinearly, namely, the co-propagating geometry. However, the co-propagating geometry is not a favorable configuration for practical stand-off detection. Therefore, further exploration on alternative sensing geometries is still required. Herein, we report the interaction of broadband THz radiation with plasmas induced by a counter-propagating laser beam, which is a more desirable geometry for remote sensing. We have found that in the counter-propagating geometry, the maximum amplitude of the REEF signal is comparable to that in the co-propagating case, whereas the time resolved REEF trace significantly changes. By performing the study with different plasmas, we observed that in the counter-propagating geometry, the shape of the REEF trace depends strongly on the plasma length and electron density. A theoretical model suggesting that the densest volume of the plasma does not contribute to the fluorescence enhancement is proposed to reproduce the experimental measurements. Our results further the understanding of the THz-plasma interaction and highlight the potential of the THz-REEF technique in plasma diagnostic applications.
Hundred joules plasma focus device as a potential pulsed source for in vitro cancer cell irradiation
Authors: Jain J. , Moreno J. , Andaur R. , Armisen R. , Morales D. , Marcelain K. , Avaria G. , Bora B. , Davis S. , Pavez C. , Soto L.
Published: August 2017

Plasma focus devices may arise as useful source to perform experiments aimed to study the effects of pulsed radiation on human cells in vitro. In the present work, a table top hundred joules plasma focus device, namely “PF-400J”, was adapted to irradiate colorectal cancer cell line, DLD-1. For pulsed x-rays, the doses (energy absorbed per unit mass, measured in Gy) were measured using thermoluminescence detectors (TLD-100 dosimeters). The neutron fluence and the average energy were used to estimate the pulsed neutron doses. Fifty pulses of x-rays (0.12 Gy) and fifty pulses of neutrons (3.5 μGy) were used to irradiate the cancer cells. Irradiation-induced DNA damage and cell death were assessed at different time points after irradiation. Cell death was observed using pulsed neutron irradiation, at ultralow doses. Our results indicate that the PF-400J can be used for in vitro assessment of the effect of pulsed radiation in cancer cell research.
Neural network based coupled diabatic potential energy surfaces for reactive scattering
Authors: Lenzen Tim , Manthe Uwe
Published: August 2017

An approach for the construction of vibronically coupled potential energy surfaces describing reactive collisions is proposed. The scheme utilizes neural networks to obtain the elements of the diabatic potential energy matrix. The training of the neural network employs a diabatization by the Ansatz approach and is solely based on adiabatic electronic energies. Furthermore, no system-specific symmetry consideration is required. As the first example, the H2+Cl→H+HCl reaction, which shows a conical intersection in the entrance channel, is studied. The capability of the approach to accurately reproduce the adiabatic reference energies is investigated. The accuracy of the fit is found to crucially depend on the number of data points as well as the size of the neural network. 5000 data points and a neural network with two hidden layers and 40 neurons in each layer result in a fit with a root mean square error below 1 meV for the relevant geometries. The coupled diabatic potential energies are found to vary smoothly with the coordinates, but the conical intersection is erroneously represented as a very weakly avoided crossing. This shortcoming can be avoided if symmetry constraints for the coupling potential are incorporated into the neural network design.
Turbulent boundary layer over a divergent convergent superhydrophobic surface
Authors: Jalalabadi Razieh , Hwang Jinyul , Nadeem Muhammad , Yoon Min , Sung Hyung Jin
Published: August 2017

A direct numerical simulation of a spatially developing turbulent boundary layer over a divergent and convergent superhydrophobic surface (SHS) was performed over the range 800 < Reθ < 1200. The surface patterns were aligned along the streamwise direction. The SHS was modeled as a pattern of free-slip and no-slip surfaces. The gas fraction of the divergent and convergent SHS was the same as that for the straight SHS for a given slip area. The divergent and convergent SHS gave 21% more drag reduction than the straight SHS. Although the maximum value of the streamwise slip velocity was larger over the divergent and convergent SHS, the average slip velocity (Uslip/U∞) was larger over the straight SHS. The greater drag reduction was attributed to the manipulation of the secondary flow in the y–z plane and the changes in the turbulence structure. The streamwise vortices generated by the secondary flow over the divergent and convergent SHS were diminished which reduced drag relative to the flow over the straight SHS. The ejection and sweep motions were weak, and the vortical structure was attenuated near the wall over the divergent and convergent SHS. The skin friction contributions were explored using the velocity–vorticity correlation. The vortex stretching contribution dominated the skin friction budget. The reduced skin friction over the divergent and convergent SHS resulted mainly from reduced vortex stretching.
Groynes: a factor modifying the occurrence of dragonfly larvae (Odonata) on a large lowland river
Authors: Buczyński P. , Szlauer-Łukaszewska A. , Tończyk G. , Buczyńska E.
Published: August 2017

The regulation of rivers and their valleys has had a strong, negative influence on the maintenance of their original biota. Nevertheless, some hydro-engineering works conducted along already regulated rivers may be beneficial, creating habitats for endangered species and assemblages. Such works include the construction of groynes. We analysed this effect on the occurrence of dragonfly larvae along middle and lower stretches of the Oder, where groynes were built over a distance of 306km, creating an area of uniform habitat. We demonstrated that the presence of groynes increased not only the abundance of dragonfly larvae, but also the species richness and diversity of these insects. Habitats were recreated for assemblages typical of a river with highly diverse habitat conditions, from typically riverine assemblages to those occurring in oxbow lakes, also endangered by regulations. The fauna along the stretches with groynes was richer and more valuable than that along the stretches without groynes, achieving values approaching those obtained from modelled unregulated rivers. This can be put down to greater habitat heterogeneity and groyne-reduced levels of waves produced by ships. The presence of groynes provides the key to the restoration or stabilisation of the populations of certain species and to renaturalisation processes.
Current knowledge of the behavioural ecology of Lumholtz’s tree-kangaroo (Dendrolagus lumholtzi)
Authors: Heise-Pavlov Sigrid
Published: August 2017

Behavioural ecology increasingly contributes to effective species conservation. It provides a better understanding of habitat requirements and landscape use of a species. In this review the current knowledge of the behavioural ecology of the Lumholtz’s tree-kangaroo (Dendrolagus lumholtzi) is summarised. It describes how the species utilises a structurally diverse environment such as rainforest with respect to its climbing abilities and the consumption of partly toxic rainforest foliage. It presents the latest findings on the use of non-rainforest habitats by this species, how it copes with highly fragmented landscapes within its distribution and the evolutionary bases of its antipredatory behaviours. Available information on home ranges of D. lumholtzi in various habitats is compiled and supplemented by our sparse knowledge of conspecific interactions of this species. The review shows how limited our current knowledge on the behavioural ecology of this species is, and how this knowledge should be integrated into conservation efforts for this species, and aims at encouraging more research in this field.
MicroRNA expression in bovine preimplantation embryos
Authors: Berg Debra K. , Pfeffer Peter L.
Published: August 2017

We profiled 98 mature microRNAs (miRNAs) using a stem-loop reverse transcription polymerase chain reaction assay array based on human miRNAs. We demonstrated that one, but not two, base-pair changes in the miRNA recognition sequence at the 3′ end only marginally affected copy number estimates. Absolute levels of miRNAs were measured in matured cattle oocytes, eight-cell embryos and normal and parthenogenetic blastocysts and Day-14 trophoblast. Most miRNA concentrations were below the expected functional threshold required for effective repression of moderately to highly abundant target RNA. In oocytes and peri-embryonic genome activation embryos, miRNA 320, a member of the Dgcr8/Drosha-independent class of miRNAs, was expressed at greater than 1000 copies per embryo. miRNAs were more abundant at the eight-cell than the oocyte stage. miRNA concentrations per cell increased from the eight-cell to the blastocyst stage. Both the number of miRNA species and their expression levels were reduced in trophoblast tissue at Day 14. The parthenogenetic samples were more related in their miRNA expression profiles to each other than to their wild-type (in vitro-produced cultured) counterparts. miRNAs 299 and 323, which have been shown to be maternally expressed in other species, were also more than 4-fold overexpressed in the cattle parthenogenetic samples.
Patterns of human–crocodile conflict in Queensland: a review of historical estuarine crocodile (Crocodylus porosus) management
Authors: Brien M. L. , Gienger C. M. , Browne C. A. , Read M. A. , Joyce M. J. , Sullivan S.
Published: August 2017

Context
In Queensland, the management of estuarine crocodiles (Crocodylus porosus) by the government is important for ensuring public safety, especially along the populated east coast, where there is a large human population.

Aims
The present study aimed to determine historical, temporal and spatial patterns of human–crocodile conflict in Queensland.

Methods
The study used Queensland Government records of estuarine crocodile attacks (1971–2015), sightings by the general public (2003–2015), and removals and relocations for management purposes (1985–2015) to develop General Linear Models describing historical, temporal and spatial patterns.

Key results
The highest number of attacks, sightings, removals and relocations occurred along the populated east coast between Townsville and the Daintree during wet season months (November–February). There have been 35 crocodile attacks in Queensland since 1971 (total 0.8 per year; fatal 0.3 per year), mostly involving local people or regular visitors (77.1%), specifically adult males (71.4%; mean age 44). There has been an increase in the rate of crocodile attacks over time, with an average of 1.3 per year since 1996, most of which were non-fatal (84%). The number of crocodile sightings has been increasing annually (with a mean of 348 per year since 2011), while the number of crocodiles removed or relocated for management purposes (n = 608) has fluctuating widely each year (range 1–57).

Conclusions
The level of human–crocodile conflict in Queensland is increasing, and this is likely to be a consequence of increasing human and crocodile populations. While conflict is highest during the wet season, estuarine crocodiles pose a threat to public safety year round.

Implications
With the increase in conflict, the ongoing management of estuarine crocodiles, through targeted removals in and around areas of higher human habitation and through education, is essential for ensuring public safety into the future.
The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene
Authors: Lister Nicholas , Shevchenko Galina , Walshe James L. , Groen Jessica , Johnsson Per , Vidarsdóttir Linda , Grander Dan , Ataide Sandro F. , Morris Kevin V.
Published: August 2017

Significance

In recent years, noncoding RNA transcripts have been found to interact with genes and modulate their ability to be transcribed and made into protein. Here we uncover many of the mechanistic underpinnings involved in how noncoding RNAs control gene transcription. Notably, we find that noncoding RNA control of gene transcription is based on a combination of structural and sequence components of the noncoding RNA and targeted gene. Collectively, the observations presented here suggest that a much more complex and vibrant RNA regulatory world is operative in gene expression and evolution of the genome.
Role for the EWS domain of EWS/FLI in binding GGAA-microsatellites required for Ewing sarcoma anchorage independent growth
Authors: Johnson Kirsten M. , Mahler Nathan R. , Saund Ranajeet S. , Theisen Emily R. , Taslim Cenny , Callender Nathan W. , Crow Jesse C. , Miller Kyle R. , Lessnick Stephen L.
Published: August 2017

Significance

Ewing sarcoma is a pediatric bone malignancy driven by the fusion protein EWS/FLI. EWS/FLI mediates oncogenesis through its role as an aberrant transcription factor, but little is known about molecular mechanisms underlying this function. We demonstrate in Ewing sarcoma cells that EWS/FLI activates gene targets through binding at associated GGAA-microsatellites, and these repetitive sequences are necessary for Ewing sarcoma cell proliferation and anchorage-independent growth. Furthermore, we show a previously unknown role for the EWS portion of the fusion protein as critical in binding at EWS/FLI targets. Understanding the mechanism of EWS/FLI transcriptional regulation is imperative to expose novel, targetable biology to inhibit its function. Additionally, these insights provide a useful model for understanding the molecular complexities of other pediatric cancers.
A-to-I RNA editing is developmentally regulated and generally adaptive for sexual reproduction in
Neurospora crassa
Authors: Liu Huiquan , Li Yang , Chen Daipeng , Qi Zhaomei , Wang Qinhu , Wang Jianhua , Jiang Cong , Xu Jin-Rong
Published: August 2017

Significance

This study systematically identified adenosine to inosine (A-to-I) editing sites in
Neurospora crassa
and showed the existence of stage-specific editing events at different sexual stages. Unlike in humans, fungal A-to-I editing mainly occurred in coding regions and caused nonsynonymous changes that significantly increased proteome complexity. In general, nonsynonymous editing sites in
Neurospora
are adaptive and favored by positive selection. RNA editing enables stage-specific functions or expression of proteins important for different sexual developmental processes. Some editing events are well conserved and may affect genes important for other genetic and epigenetic phenomena occurring during sexual reproduction. Overall, our results provide insights into the complex regulation of sexual development and reveal the role of A-to-I editing for adaptive evolution in
Neurospora.
Affinity of IDPs to their targets is modulated by ion-specific changes in kinetics and residual structure
Authors: Wicky Basile I. M. , Shammas Sarah L. , Clarke Jane
Published: August 2017

Significance

Intrinsically disordered proteins (IDPs) rapidly exchange between conformations of marginal stability. These transient structures are much more sensitive to solution conditions than ordered proteins. Here we reveal that coupled folding and binding of IDPs are affected by the presence of different common salts beyond simple electrostatic effects, such that their affinities are ion-specific, and occur at physiological concentrations. We demonstrate that the phenomenon is rooted in the structural sensitivity of IDPs to co-solutes, which in turn affects binding rates and affinities. We suggest that the sensitivity of coupled folding and binding reactions to the environment might be a functional consequence of protein disorder. Considering the role of ions in biology, it might be a regulatory mechanism of physiological significance.
Injection of T3SS effectors not resulting in invasion is the main targeting mechanism of
Shigella
toward human lymphocytes
Authors: Pinaud Laurie , Samassa Fatoumata , Porat Ziv , Ferrari Mariana L. , Belotserkovsky Ilia , Parsot Claude , Sansonetti Philippe J. , Campbell-Valois François-Xavier , Phalipon Armelle
Published: August 2017

Significance

Invasion of human intestinal epithelial cells resulting from the delivery of bacterial effectors into the host cell cytoplasm via a type III secretion system (T3SS) is the hallmark of
Shigella
, the causal agent of bacillary dysentery. Here, we provide evidence that human lymphocytes are mainly targeted by injection of T3SS effectors not resulting in cell invasion. These findings highlight the diversity of mechanisms triggered by
Shigella
to enlarge the panel of targeted cells and thus counteract host immunity, including adaptive immune responses. The potential impact of these data on vaccine design, in particular for live-attenuated vaccine candidates, deserves further investigation.
Amorphous calcium carbonate particles form coral skeletons
Authors: Mass Tali , Giuffre Anthony J. , Sun Chang-Yu , Stifler Cayla A. , Frazier Matthew J. , Neder Maayan , Tamura Nobumichi , Stan Camelia V. , Marcus Matthew A. , Gilbert Pupa U. P. A.
Published: August 2017

Significance

Whether coral skeleton crystals grow by attachment of ions from solution or particles from tissue determines (
i
) corals’ growth rate, (
ii
) how they survive acidifying oceans, and (
iii
) the isotopes in the crystals used for reconstructing ancient temperatures. Our data show that two amorphous precursors exist, one hydrated and one dehydrated amorphous calcium carbonate; that these are formed in the tissue as ∼400-nm particles; and that they attach to the surface of coral skeletons, remain amorphous for hours, and finally crystallize into aragonite. Since these particles are formed inside tissue, coral skeleton growth may be less susceptible to ocean acidification than previously assumed. Coral bleaching and postmortem dissolution of the skeleton will occur, but a calcification crisis may not.
Seed dispersal increases local species richness and reduces spatial turnover of tropical tree seedlings
Authors: Wandrag Elizabeth M. , Dunham Amy E. , Duncan Richard P. , Rogers Haldre S.
Published: August 2017

Significance

Dispersal is considered a key process underlying the high spatial diversity of tropical forests, with the seeds of most tropical tree species dispersed by vertebrates, particularly birds. Although it has proven very difficult to quantify the contribution of dispersal to tree species diversity, it is increasingly important to do so in the face of global declines in vertebrate disperser populations. We show that the complete loss of native seed dispersers on the island of Guam is having a major impact on tree seedling regeneration in canopy gaps, leading to species-poor and spatially aggregated seedling communities. These pronounced changes in patterns of seedling regeneration highlight the importance of dispersal in maintaining patterns of diversity in tropical forests.
Feeding Ecology of Pacific Sand Lance in the San Juan Archipelago
Authors: Sisson Nicholas B. , Baker Matthew R.
Published: August 2017

Forage fishes such as Pacific Sand Lance Ammodytes personatus are a crucial link between lower and upper elements in marine food webs, as they transfer energy from plankton to higher trophic levels. Despite their importance to marine food webs, little is known about the population structure and feeding ecology of Pacific Sand Lance. In this study, we examined the population density and diet composition of Pacific Sand Lance as well as feeding patterns and movement in response to tidal, diel, and seasonal cycles in a prominent sand wave field in the San Juan Channel, Washington. A generalized linear model was applied to account for the corresponding effects of tidal, diel, and seasonal trends as well as habitat affinity related to substrate type. We showed that fish distributions were predominantly driven by sediment type and that time of day had a significant influence on foraging behavior with distinct crepuscular feeding patterns. Our results also provide evidence for the cessation of feeding over the fall transition and the onset of a winter dormant period, as observed by increased densities of fish within the sand wave field (177%), a marked increase in the number of empty stomachs (511%), and a significant decrease in condition factor. These trends correspond with the expectations that Pacific Sand Lances exhibit a winter dormant phase and burrow in sediments throughout the winter months to conserve energy and reduce predation risk during periods of low productivity. We anticipate our study to be a starting point for understanding the foraging ecology of the Pacific Sand Lance, particularly in the San Juan Archipelago and Salish Sea. The results of this study may improve the understanding of Pacific Sand Lance habitat and availability to pelagic predators, inform fisheries management, and increase the resolution of marine food web models.
RUCS: rapid identification of PCR primers for unique core sequences
Authors: Thomsen Martin Christen Frølund , Hasman Henrik , Westh Henrik , Kaya Hülya , Lund Ole
Published: August 2017

Motivation

Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs for the targets in silico.

Results

Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5–20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin resistance gene. Three of the predicted pairs were chosen for experimental validation using PCR and gel electrophoresis. All three pairs successfully produced an amplicon with the target length for the samples containing mcr-1 and no amplification products were produced for the negative samples. The novel methods presented in this manuscript can reduce the time needed to identify target sequences, and provide a quick virtual PCR validation to eliminate time wasted on ambiguously binding primers.

Availability and implementation

Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. Web service is freely available on https://cge.cbs.dtu.dk/services/RUCS.

Supplementary information

Supplementary data are available at Bioinformatics online.
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis
Authors: Singer Jochen , Ruscheweyh Hans-Joachim , Hofmann Ariane L , Thurnherr Thomas , Singer Franziska , Toussaint Nora C , Ng Charlotte K Y , Piscuoglio Salvatore , Beisel Christian , Christofori Gerhard , Dummer Reinhard , Hall Michael N , Krek Wilhelm , Levesque Mitchell P , Manz Markus G , Moch Holger , Papassotiropoulos Andreas , Stekhoven Daniel J , Wild Peter , Wüst Thomas , Rinn Bernd , Beerenwinkel Niko
Published: August 2017

Motivation

Next-generation sequencing is now an established method in genomics, and massive amounts of sequencing data are being generated on a regular basis. Analysis of the sequencing data is typically performed by lab-specific in-house solutions, but the agreement of results from different facilities is often small. General standards for quality control, reproducibility and documentation are missing.

Results

We developed NGS-pipe, a flexible, transparent and easy-to-use framework for the design of pipelines to analyze whole-exome, whole-genome and transcriptome sequencing data. NGS-pipe facilitates the harmonization of genomic data analysis by supporting quality control, documentation, reproducibility, parallelization and easy adaptation to other NGS experiments.

Availability and implementation

https://github.com/cbg-ethz/NGS-pipe
A hybrid clustering and ranking method for best positioned logistics distribution centre in Balkan Peninsula
Authors: Simić Dragan , Ilin Vladimir , Svirčević Vasa , Simić Svetlana
Published: August 2017

Facility location decisions are critical in strategic planning for a wide range of operational and logistical decisions. Facility location problem with focus on logistics distribution centre (LDC) in Balkan Peninsula (BP) is discussed in this article. Methodological hybrid genetic algorithm, Analytical Hierarchy Process, and fuzzy c-means method is proposed here and it is shown how such a model can be of assistance in analysing a multi criteria decision-making problem. This research represents continuation of three existing studies. The experimental results in our research could be well compared with other official results of the feasibility study of the LDC located in BP.
Cervical Alignment Changes in Patients Developing Proximal Junctional Kyphosis Following Surgical Correction of Adult Spinal Deformity
Authors: Passias Peter G , Horn Samantha R , Jalai Cyrus M , Ramchandran Subaraman , Poorman Gregory W , Kim Han Jo , Smith Justin S , Sciubba Daniel , Soroceanu Alexandra , Ames Christopher P , Hamilton D Kojo , Eastlack Robert , Burton Douglas , Gupta Munish , Bess Shay , Lafage Virginie , Schwab Frank
Published: August 2017

BACKGROUND

Proximal junctional kyphosis (PJK) following adult spinal deformity (ASD) surgery is a well-documented complication, but associations between radiographic PJK and cervical malalignment onset remain unexplored.

OBJECTIVE

To study cervical malalignment in ASD surgical patients that develop PJK.

METHODS

Retrospective review of prospective multicenter database. Inclusion: primary ASD patients (≥5 levels fused, upper instrumented vertebra [UIV] at T2 or above, and 1-yr minimum follow-up) without baseline cervical deformity (CD), defined as ≥2 of the following criteria: T1 slope minus cervical lordosis < 20°, cervical sagittal vertical axis < 4 cm, C2-C7 cervical lordosis < 10°. PJK presence (<10° change in UIV and UIV + 2 kyphosis) and angle were identified 1 yr postoperative. Propensity score matching between PJK and nonPJK groups controlled for baseline alignment. Preoperative and 1-yr postoperative cervical alignment were compared between PJK and nonPJK patients.

RESULTS

One hundred sixty-three patients without baseline CD (54.9 yr, 83.9% female) were included. PJK developed in 60 (36.8%) patients, with 27 (45%) having UIV above T7. PJK patients had significantly greater baseline T1 slope in unmatched and propensity score matching comparisons (P < .05). At 1 yr postoperative, PJK patients had significantly higher T1 slope (P < .001), C2-T3 Cobb (P = .04), and C2-T3 sagittal vertical axis (P = .02). New-onset CD rate in PJK patients was 15%, and 16.5% in nonPJK patients (P > .05). Increased PJK magnitude was associated with increasing T1 slope and C2-T3 SVA (P < .05).

CONCLUSION

Patients who develop PJK following surgical correction of ASD have a 15% incidence of development of new-onset CD. Patients developing PJK following surgical correction of ASD tend to have an increased preoperative T1 slope. Increased progression of C2-T3 Cobb angle and C2-T3 SVA are associated with development of PJK following surgical correction of thoracolumbar deformity.
A Destructive Leaf Spot and Blight Caused byAlternaria kareliniaesp. nov. on a Sand-Stabilizing Plant, Caspian Sea Karelinia
Authors: Xu Biao , Song Jiage , Xi Pinggen , Li Minhui , Hsiang Tom , Jiang Zide
Published: August 2017

Leaf spots and stem lesions causing widespread mortality of Caspian Sea karelinia (Karelinia caspia) were observed in desert regions of Xinjiang Uyghur Autonomous Region, China. Fifteen samples were collected from five widely distributed counties of Tarim and Junggar Basins in 2016. The pathogen was identified using morphological observations and phylogenetic analyses based on combined partial sequences from seven genes (Alt a 1, ATPase, calmodulin, glyceraldehyde 3-phosphate dehydrogenase, internal transcribed spacer, RNA polymerase II, and translation elongation factor 1), and placed as a new species: Alternaria kareliniae sp. nov. in section Dianthicola. The fungus has a small conidium (24.3 to) 29.1 to 64.8 (to 75.8) by (9.3 to) 12.4 to 16.5 (to 21.7) μm with a long beak (130 to) 183.9 to 350.4 (to 378.2) μm, as well as four to eight transverse septa, which differs significantly from other species of Alternaria section Dianthicola. On potato carrot agar, it grew significantly more slowly than others of this section. Pathogenicity tests showed that the fungus could infect leaves and stems of K. caspia and cause the same symptoms as those observed in the field. The fungus was reisolated from inoculated leaves and stems of the host. The disease in desert regions appears to be increasing, and it may have future negative implications for desert ecology in these areas. Future research should concentrate on elucidating the disease cycle and disease management alternatives.
Sex-Related Differences in the Developmental Morphology of the Atlas
Authors: Asukai Mitsuru , Fujita Tomotada , Suzuki Daisuke , Nishida Tatsuya , Ohishi Tsuyoshi , Matsuyama Yukihiro
Published: August 2017

Study Design.

A retrospective study.

Objective.

To elucidate sex-related differences in the age at synchondroses closure, the normative size of the atlas, and the ossification patterns of the atlas in Japanese children.

Summary of Background Data.

The atlas develops from three ossification centers during childhood. The anterior and posterior synchondroses, which are separate ossification centers, mimic fracture lines on computed tomography (CT). Sex-related differences of age dependent morphological changes of the atlas in a large sample size have not been reported.

Methods.

This study analyzed data of 688 subjects (449 boys) between 0 and 18 years old who underwent CT examination of the head and/or neck between January 2010 and July 2016. The age at synchondroses closure, anteroposterior outer, inner, and spinal canal widths of the atlas, and variations of the ossification centers were examined.

Results.

Anterior synchondroses closed by 10 years in boys and by 7 years in girls. Significant earlier closure of anterior synchondroses was observed in girls than in boys (P < 0.05 at 4 and 5 years old). Posterior synchondrosis closed by 6 years in boys and by 5 years in girls. The outer, inner, and spinal canal widths increased up to 10 to 15 years in both sexes, although all three parameters in girls peaked 3 years earlier than those in boys. All parameters in boys were significantly larger than those in girls, except in the 10- to 12-year-old age category. Two or more ossification centers in the anterior arch were observed in 18.3% subjects, and 6% had midline ossification centers in the posterior arch of the atlas.

Conclusion.

Distinct sex-related differences in the age at anterior synchondroses closure and the size of the atlas were observed in Japanese children. Knowledge of morphological features of the atlas could help distinguish fractures from synchondroses.

Level of Evidence: 3