bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations
Authors: Fuentes‐Pardo Angela P. , Ruzzante Daniel E.
Published: July 2017

Whole‐genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled‐individual DNA (Pool‐seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
Structure and stability of genetic variance–covariance matrices: A Bayesian sparse factor analysis of transcriptional variation in the three‐spined stickleback
Authors: Siren J. , Ovaskainen O. , Merilä J.
Published: July 2017

The genetic variance–covariance matrix (G) is a quantity of central importance in evolutionary biology due to its influence on the rate and direction of multivariate evolution. However, the predictive power of empirically estimated G‐matrices is limited for two reasons. First, phenotypes are high‐dimensional, whereas traditional statistical methods are tuned to estimate and analyse low‐dimensional matrices. Second, the stability of G to environmental effects and over time remains poorly understood. Using Bayesian sparse factor analysis (BSFG) designed to estimate high‐dimensional G‐matrices, we analysed levels variation and covariation in 10,527 expressed genes in a large (n = 563) half‐sib breeding design of three‐spined sticklebacks subject to two temperature treatments. We found significant differences in the structure of G between the treatments: heritabilities and evolvabilities were higher in the warm than in the low‐temperature treatment, suggesting more and faster opportunity to evolve in warm (stressful) conditions. Furthermore, comparison of G and its phenotypic equivalent P revealed the latter is a poor substitute of the former. Most strikingly, the results suggest that the expected impact of G on evolvability—as well as the similarity among G‐matrices—may depend strongly on the number of traits included into analyses. In our results, the inclusion of only few traits in the analyses leads to underestimation in the differences between the G‐matrices and their predicted impacts on evolution. While the results highlight the challenges involved in estimating G, they also illustrate that by enabling the estimation of large G‐matrices, the BSFG method can improve predicted evolutionary responses to selection.
A unique invertase is important for sugar absorption of an obligate biotrophic pathogen during infection
Authors: Chang Qing , Liu Jie , Lin Xiaohong , Hu Shoujun , Yang Yang , Li Dan , Chen Liyang , Huai Baoyu , Huang Lili , Voegele Ralf T. , Kang Zhensheng
Published: July 2017

An increased invertase activity in infected plant tissue has been observed in many plant–pathogen interactions. However, the origin of this increased invertase activity (plant and/or pathogen) is still under debate. In addition, the role of pathogen invertases in the infection process is also unclear.

We identified and cloned a gene with homology to invertases from Puccinia striiformis f. sp. tritici (Pst). Transcript levels of PsINV were analyzed by quantitative reverse transcription PCR in both compatible and incompatible Pst–wheat interactions . Function of the gene product was confirmed by heterologous expression, and its function in Pst infection was analyzed by host‐induced gene silencing (HIGS).

Pst abundantly secretes invertase during its invasion attempts whether in a compatible or incompatible interaction with wheat. Further research into the different domains of this protein indicated that the rust‐specific sequence contributes to a higher efficiency of sucrose hydrolysis. With PsINV silenced by HIGS during the infection process, growth of Pst is inhibited and conidial fructification incomplete. Finally, pathogenicity of Pst is impaired and spore yield significantly reduced.

Our results clearly demonstrate that this Pst invertase plays a pivotal role in this plant–pathogen interaction probably by boosting sucrose hydrolysis to secure the pathogen's sugar absorption.
Oil rent, the Rentier State/Resource Curse Narrative and the GCC Countries
Authors: Rutledge Emilie
Published: July 2017

Despite the fact that ‘rent’ underpins both Rentier State (RS) and Resource Curse (RC) theses, external factors that help shape perceptions of it and determine its value, are rarely factored in. The purpose of this article is to suggest reasons for this shortcoming and, with particular reference to the ‘archetypal candidate’ Gulf Cooperation Council countries, question the utility per se of the RS/RC paradigm (RS outcomes can only manifest within RC contexts). To explain the default and long‐standing utilisation of the construct across the social sciences—in spite of the frequent need to detour around contrary data—this paper points firstly to the way in which rent is now popularly perceived (from logically grounded, to excessively unwarranted) and secondly, to the fact that ‘oil’ lies at the paradigm's heart. It is a commodity that various Western polities once had unfettered control over; no other depletable natural resource in the past century has held such global economic significance (external actors clearly have a vested interest). Lastly, to underscore the need for a reappraisal of the RS/RC analytical framework, some data are presented that demonstrate that the GCC countries have not, comparatively speaking, suffered the deleterious consequences that the paradigm stipulates.
Impact of timing of recurrence following catheter ablation of scar‐related ventricular tachycardia on subsequent mortality
Authors: Muser Daniele , Mendelson Todd , Fahed Joe , Liang Jackson J. , Castro Simon A. , Zado Erica , Marchlinski Francis E. , Santangeli Pasquale
Published: July 2017

Background

Catheter ablation (CA) has an established role in scar‐related ventricular tachycardia (VT), but the risk of recurrences is substantial and the appropriate intensity of postablation monitoring unknown. The implication of timing of postablation VT recurrence has not been adequately investigated.

Methods

We studied 120 consecutive patients with scar‐related VT (age 60 ± 15 years, left ventricular ejection fraction 39 ± 16%, 52% ischemic etiology) with at least 2 years of follow‐up. Timing of VT recurrence was classified as very early (<1 month), early (1–6 months), or late (>6 months).

Results

At 24 months follow‐up, 53 (44%) patients had recurrent VT, with eight (15%) having very early recurrence, 17 (32%) early recurrence, and 28 (53%) late recurrence. Mortality rates at 2 years were significantly higher in patients with very early VT recurrence (38%) compared to those with early (12%), late (7%), and no (3%) recurrences (log‐rank P < 0.001). Very early VT recurrence was associated with an increased risk of death (odds ratio = 5.68, 95% confidence interval = 1.06–30.62, P = 0.04), while recurrent VT beyond 6 months was not associated with increased risk of mortality (P = 0.94).

Conclusions

Timing of VT recurrence following CA of scar‐related VT impacts subsequent risk of mortality. Patients experiencing VT recurrence within 1–6 months from the procedure are at particularly high risk. These data support the importance of intense postablation monitoring for at least 6 months after the procedure to identify patients with early VT recurrence who may benefit from additional therapeutic interventions to improve outcomes.
Epicardial ablation of tachyarrhythmia in children: Experience at two academic centers
Authors: Upadhyay Shailendra , Walsh Edward P. , Cecchin Frank , Triedman John K. , Villafane Juan , Saul J. Philip
Published: July 2017

Background

Experience with percutaneous epicardial ablation of tachyarrhythmia in pediatrics is limited. This case series addresses the feasibility, safety, and complications of the procedure in children.

Methods

A total of nine patients underwent 10 epicardial ablation procedures from 2002 to 2013 at two academic centers. Activation mapping was performed in all cases, and electroanatomic map was utilized in nine of the 10 procedures. Patients had undergone one to three failed endocardial catheter ablations in addition to medical management, and all had symptoms, a high‐risk accessory pathway (AP), aborted cardiac arrest with Wolff‐Parkinson‐White syndrome (WPW), or ventricular dysfunction. A standard epicardial approach was used for access in all cases, using a 7‐ or 8‐ Fr sheath. Epicardial ablation modality was radiofrequency (RF) in seven, cryoablation (CRYO) in one, and CRYO plus RF in one.

Results

Median age was 14 (range 8–19) years. Indications: drug refractory ectopic atrial tachycardia (one), ventricular tachycardia (VT) (five), high‐risk AP (two), and aborted cardiac arrest from WPW – (one). Epicardial ablation was not performed in one case despite access due to an inability to maneuver the catheter around a former pericardial scar. VT foci included the right ventricular outflow tract septum, high posterior left ventricle (LV), LV outflow tract, postero‐basal LV, and scar from previous rhabdomyoma surgery. WPW foci were in the area of the posterior septum and coronary sinus in all three cases. Overall procedural success was 70% (7/10), with epicardial ablation success in five and endocardial ablation success after epicardial mapping in two. The VT focus was close to the left anterior descending coronary artery in one of the unsuccessful cases in which both RF and CRYO were used. There was one recurrence after a successful epicardial VT ablation, which was managed with a second successful epicardial procedure. There were no other recurrences at more than 1 year of follow‐up. Complications were minimal, with one case of inadvertent pleural access requiring no specific therapy. No pericarditis or effusion was seen in any of the patients who underwent epicardial ablation.

Conclusion

Epicardial ablation in pediatric patients can be performed with low complications and acceptable success. It can be considered for a spectrum of tachycardia mechanisms after failed endocardial ablation attempts and suspected epicardial foci. Success and recurrence may be related to foci in proximity to the epicardial coronaries, pericardial scar, or a distant location from the closest epicardial location. Repeat procedures may be necessary.
Translating policy transparency into policy understanding and policy support: Evidence from a survey experiment
Authors: Porumbescu Gregory , Bellé Nicola , Cucciniello Maria , Nasi Greta
Published: July 2017

While transparency is viewed as a means of improving citizen understanding of public policies and eliciting policy support, there are few empirical assessments of these relationships. We address this gap in the literature using an experimental design. We predict that exposure to less detailed policy information improves policy understanding, and that this effect varies according to presentation format. Further, we predict that policy understanding will correspond to greater policy support. Using a nationally representative panel of US citizens we find that exposure to detailed policy information decreases policy understanding and that the effect varies by presentation format. In addition, policy understanding is negatively associated with policy support. These findings culminate in a positive indirect effect—increasing detail reduces understanding, which in turn is negatively associated with policy support. However, interestingly, policy support was highest among those who felt they understood the policy best, yet possessed the lowest levels of actual understanding.
A meta‐analysis on growth, physiological, and biochemical responses of woody species to ground‐level ozone highlights the role of plant functional types
Authors: Li Pin , Feng Zhaozhong , Catalayud Vicent , Yuan Xiangyang , Xu Yansen , Paoletti Elena
Published: July 2017

The carbon‐sink strength of temperate and boreal forests at midlatitudes of the northern hemisphere is decreased by ozone pollution, but knowledge on subtropical evergreen broadleaved forests is missing. Taking the dataset from Chinese studies covering temperate and subtropical regions, effects of elevated ozone concentration ([O3]) on growth, biomass, and functional leaf traits of different types of woody plants were quantitatively evaluated by meta‐analysis. Elevated mean [O3] of 116 ppb reduced total biomass of woody plants by 14% compared with control (mean [O3] of 21 ppb). Temperate species from China were more sensitive to O3 than those from Europe and North America in terms of photosynthesis and transpiration. Significant reductions in chlorophyll content, chlorophyll fluorescence parameters, and ascorbate peroxidase induced significant injury to photosynthesis and growth (height and diameter). Importantly, subtropical species were significantly less sensitive to O3 than temperate ones, whereas deciduous broadleaf species were significantly more sensitive than evergreen broadleaf and needle‐leaf species. These findings suggest that carbon‐sink strength of Chinese forests is reduced by present and future [O3] relative to control (20–40 ppb). Given that (sub)‐tropical evergreen broadleaved species dominate in Chinese forests, estimation of the global carbon‐sink constraints due to [O3] should be re‐evaluated.
Neonatal perforated appendicitis in incarcerated inguinal hernia in the differential diagnosis of testis torsion
Authors: Erginel Basak , Soysal Feryal Gun , Celik Alaaddin , Salman Tansu
Published: July 2017

Appendicitis in newborns is uncommon and difficult to diagnose. Reports on neonatal appendicitis subsequent to inguinal hernia incarceration are exceptionally rare. We present the case of a 26‐day‐old infant with perforated appendicitis due to incarceration of a right inguinal hernia, mimicking right testicular torsion.
Commentary: Some Practical Considerations Concerning Public Debt Issuance
Authors: Bell Michael J.
Published: July 2017

Related Content: Liu, Moldogaziev, and Mikesell (PAR September/October 2017)
Transparency in multilateral climate politics: Furthering (or distracting from) accountability?
Authors: Gupta Aarti , van Asselt Harro
Published: July 2017

This article analyzes the interplay between transparency and accountability in multilateral climate politics. The 2015 Paris Agreement calls for a “pledge‐and‐review” approach to collective climate action with an “enhanced transparency framework” as a key pillar of the Agreement. By making visible who is doing what, transparency is widely assumed to be vital to holding countries to account and building trust. We explore whether transparency is generating such effects in this context, by developing and applying an analytical framework to examine the link between transparency and accountability. We find that the scope and practices of climate transparency reflect (rather than necessarily reduce) broader conflicts over who should be held to account to whom and about what, with regard to responsibility and burden sharing for ambitious climate action. We conclude that the relationship between transparency and accountability is less straightforward than assumed, and that the transformative promise of transparency needs to be reconsidered in this light.
Congressional Attention and Opportunity Structures: The Select Energy Independence and Global Warming Committee
Authors: Lewallen Jonathan
Published: July 2017

This article examines the role that overlapping committee jurisdictions play in fostering or hindering attention to environmental and energy issues in the U.S. Congress. The Select Energy Independence and Global Warming Committee, created by House Democrats in , and its chairman Rep. Ed Markey took advantage of opportunities within the existing jurisdictional arrangement to increase attention to these issues despite lacking any legislative authority. Data from the 110th and 111th Congresses show that the Select Committee held more hearings on climate change and alternative energy, and on environmental and energy policy generally, than any other committee. The committee also increased the range of sources informing debate on these issues by calling different witnesses than other committees. These findings have important implications for the relationship between institutional structure and agendas and for Congress' policy‐making role on energy and the environment.
The Foreseeable Harms of Trump's Global Gag Rule
Authors: Bingenheimer Jeffrey B. , Skuster Patty
Published: July 2017

As one of his first acts as President of the United States, Donald Trump signed an executive order reinstating a version of the global gag rule. Under this rule, US grantees are barred from receiving global health funding if they engage in abortion‐related work: not only abortion services, but also abortion referrals and counseling or advocacy for the liberalization of abortion laws. Critics of the Trump global gag rule generally raise three classes of objections: (1) that the rule fails to accomplish its presumed objective of reducing the number of abortions; (2) that it negatively affects the health and well‐being of individuals and populations in affected countries; and (3) that it interferes with governments’ ability to meet their international obligations. In this commentary, we examine the scientific and policy bases for these criticisms.
Benedictine Monastic Communitas in Wartime Central Vietnam (1954–75)
Authors: Jammes Jeremy
Published: July 2017

This article focuses on the question of the establishment of a Catholic monastic tradition, shaped by its Western creation and subsequent exportation to an Asian society. In 1954 the French Benedictine Congregation of St. Bathilde of Vanves founded a monastery in Central Vietnam. The circumstances of the Vietnam war, coupled with a holistic implementation plan instigated by the nuns, enabled the establishment of a small, but sedentary and durable, community, organised within Benedictine structures involving a girls’ hostel, plantation agriculture and catechism instruction. Choosing a life of self‐denial alongside the indigenous people, they eventually formed a ‘Benedictine community village’, implementing a non‐monastic but austere and disciplined life. However, these Benedictine nuns continuously self‐transformed and re‐defined themselves vis‐à‐vis their ‘spiritual tradition’. The pursuit of a life of interiority produced a form of rupture with older forms of evangelisation and with established clergy, reflecting the way in which these nuns conceived their alternative role in the Benedictine tradition. I interrogate here the Benedictine ascetic form and the place given by the Order to new alternative subjectivities.
An open task to promote students to create statistical concepts through modelling
Authors: Albarracín Lluís , Aymerich Àngels , Gorgorió Núria
Published: July 2017

This article reports on the solutions of a group of 22 students, aged 15/16 years old, when facing a statistical modelling activity. They were given the salary lists of 5 companies and were asked what could be said about their salary structure; no hint was given. The results show that students not only used a wide range of data concepts and procedures but also developed their own criteria to measure dispersion.
The LexA transcription factor regulates fatty acid biosynthetic genes in the cyanobacterium Synechocystis sp. PCC 6803
Authors: Kizawa Ayumi , Kawahara Akihito , Takashima Kosuke , Takimura Yasushi , Nishiyama Yoshitaka , Hihara Yukako
Published: July 2017

Specific transcription factors have been identified in various heterotrophic bacterial species that regulate the sets of genes required for fatty acid metabolism. Here, we report that expression of the fab genes, encoding fatty acid biosynthetic enzymes, is regulated by the global regulator LexA in the photoautotrophic cyanobacterium Synechocystis sp. PCC 6803. Sll1626, an ortholog of the well‐known LexA repressor involved in the SOS response in heterotrophic bacteria, was isolated from crude extracts of Synechocystis by DNA affinity chromatography, reflecting its binding to the upstream region of the acpP‐fabF and fabI genes. An electrophoresis mobility shift assay revealed that the recombinant LexA protein can bind to the upstream region of each fab gene tested (fabD, fabH, fabF, fabG, fabZ and fabI). Quantitative RT‐PCR analysis of the wild type and a lexA‐disrupted mutant strain suggested that LexA acts as a repressor of the fab genes involved in initiation of fatty acid biosynthesis (fabD, fabH and fabF) and the first reductive step in the subsequent elongation cycle (fabG) under normal growth conditions. Under nitrogen‐depleted conditions, downregulation of fab gene expression is partly achieved through an increase in LexA‐repressing activity. In contrast, under phosphate‐depleted conditions, fab gene expression is upregulated, probably due to the loss of repression by LexA. We further demonstrate that elimination of LexA largely increases the production of fatty acids in strains modified to secrete free fatty acids.
A generalized scheme based on shifted Jacobi polynomials for numerical simulation of coupled systems of multi-term fractional-order partial differential equations
Authors: Shah Kamal , Khalil Hammad , Khan Rahmat Ali
Published: July 2017

Due to the increasing application of fractional calculus in engineering and biomedical processes, we analyze a new method for the numerical simulation of a large class of coupled systems of fractional-order partial differential equations. In this paper, we study shifted Jacobi polynomials in the case of two variables and develop some new operational matrices of fractional-order integrations as well as fractional-order differentiations. By the use of these operational matrices, we present a new and easy method for solving a generalized class of coupled systems of fractional-order partial differential equations subject to some initial conditions. We convert the system under consideration to a system of easily solvable algebraic equation without discretizing the system, and obtain a highly accurate solution. Also, the proposed method is compared with some other well-known differential transform methods. The proposed method is computer oriented. We useMatLabto perform the necessary calculation. The next two parts will appear soon.
The role of T‐type calcium channels in the subiculum: to burst or not to burst?
Authors: Joksimovic Srdjan M. , Eggan Pierce , Izumi Yukitoshi , Joksimovic Sonja Lj. , Tesic Vesna , Dietz Robert M. , Orfila James E. , DiGruccio Michael R. , Herson Paco S. , Jevtovic‐Todorovic Vesna , Zorumski Charles F. , Todorovic Slobodan M.
Published: July 2017

Key points

Pharmacological, molecular and genetic data indicate a prominent role of low‐voltage‐activated T‐type calcium channels (T‐channels) in the firing activity of both pyramidal and inhibitory interneurons in the subiculum.

Pharmacological inhibition of T‐channels switched burst firing with lower depolarizing stimuli to regular spiking, and fully abolished hyperpolarization‐induced burst firing.

Our molecular studies showed that CaV3.1 is the most abundantly expressed isoform of T‐channels in the rat subiculum.

Consistent with this finding, both regular‐spiking and burst firing patterns were profoundly depressed in the mouse with global deletion of CaV3.1 isoform of T‐channels.

Selective inhibition of T‐channels and global deletion of CaV3.1 channels completely suppressed development of long‐term potentiation (LTP) in the CA1–subiculum, but not in the CA3–CA1 pathway.

Several studies suggest that voltage‐gated calcium currents are involved in generating high frequency burst firing in the subiculum, but the exact nature of these currents remains unknown. Here, we used selective pharmacology, molecular and genetic approaches to implicate Cav3.1‐containing T‐channels in subicular burst firing, in contrast to several previous reports discounting T‐channels as major contributors to subicular neuron physiology. Furthermore, pharmacological antagonism of T‐channels, as well as global deletion of CaV3.1 isoform, completely suppressed development of long‐term potentiation (LTP) in the CA1–subiculum, but not in the CA3–CA1 pathway. Our results indicate that excitability and synaptic plasticity of subicular neurons relies heavily on T‐channels. Hence, T‐channels may be a promising new drug target for different cognitive deficits.
Reliable Finite-Time Robust Control for Sampled-Data Mechanical Systems Under Stochastic Actuator Failures
Authors: Xu Shidong , Sun Guanghui , Liu Jianxing , Li Zhan
Published: July 2017

This paper considers the problem of reliable finite-time robust control for uncertain mechanical systems with stochastic actuator failures and aperiodic sampling. A novel model of actuator failure capable of depicting various faulty modes is developed on the basis of homogenous Markov variable. To guarantee the finite-time stability (FTS) and boundedness, a novel fault-tolerant switching controller is developed by virtue of Lyapunov–Krasovskii functional and stochastic analysis technique, simultaneously, the finite-time H∞ performance is also ensured to attenuate the mechanical vibration caused by external disturbances. With convex optimization algorithm, the anticipated controller can be procured by solving a set of linear matrix inequalities (LMIs). Finally, two practical examples of mechanical systems, one of which is governed by lumped parameters and the other is described by distributed parameters, are proposed to prove the effectiveness of the theoretical developments of this study.
Experimental Study on Contact Force in a Slewing Bearing
Authors: Chen Guanci , Wen Ge , Xiao Zhengming , San Hongjun
Published: July 2017

Measuring and verification of contact force in a rolling element bearing is a big problem. In this study, a new measuring method for contact force in a large-scale ball bearing is developed. The idea is to measure the deformation under the ball–race contact by displacement sensor at first, and the displacement of the end face of load bearing ring is also measured to determine the contact angle of ball–race contact. Then, the corresponding theory is developed to calculate the contact angle of ball–race contact by the displacement of the end face of load bearing ring. At last, the ball–race contact force is determined by accurately calculating through finite element method (FEM). Results show that the relation between contact force and deformation of measuring surface which is under ball–race contact is linear. The position of ball greatly affects the contact angle of ball–race contact. The contact angle of the ball which is near the arm of force is larger than that of the ball which is far from the arm of force. On the contrary, the measuring deformation of ball–race contact that is near the arm of force is less than that of ball–race contact that is far from the arm of force. The method developed here is only suitable for large-scale rolling element bearing because of the size constraint of the sensor.
Tribological, Mechanical, and Microstructural of Multiwalled Carbon Nanotubes/Short Carbon Fiber Epoxy Composites
Authors: Gbadeyan O. J. , Kanny Krishnan , Turup Pandurangan Mohan
Published: July 2017

In the present work, composites were developed with novel combination of particular fillers and fibers for an automotive brake system. The influence of short carbon fiber (SCF) on wear rate, coefficient of friction (CoF), modulus, compressive strength, hardness, and surface morphology of worn surface were examined. This investigation confirmed that 0.1% multiwalled carbon nanotubes (MWCNTs) reduced wear rate, CoF for all combinations of composite with carbon fiber. Results indicate that 0.1% (MWCNTs) and 10% SCF-filled composite had superior properties. This performance may be attributed to the uniform dispersion of fiber and the synergistic effect of SCF and MWCNTs, acting in concert that formed a more stable structure resulting in a high strength, stiffness, tougher, and high-heat absorption. Scanning electron microscopy (SEM) microstructure subsequently performed show change in structural development with a corresponding increase of the incorporation of SCF and MWCNTs, which eventually explained the improved properties of composite.
On the Source of the Systematic Error of the Pressure Measurement Film Applied to Wheel–Rail Normal Contact Measurements
Authors: Lekue Jagoba , Dörner Florian , Schindler Christian
Published: July 2017

This paper presents research activities regarding the systematic error of the pressure measurement film when measuring the area of the wheel–rail contact. In particular, an explanation for the different error values shown by the different film types was sought. A finite element model was created based on the assumption that not only the film, but also the microcapsules on top of it alter the results. The performance of the existing film models was enhanced by defining microcapsules with element failure and deletion behaviors. The new model was capable of reproducing the trend shown by the systematic error in the experiments. The simulation results confirmed that the measurement error of a certain film type is not only caused by the film itself, but also depends on the failure pressure and especially the diameter of the capsules.
Finite Element Modeling and Experimental Study of Burr Formation in Drilling Processes
Authors: Efstathiou Chara , Vakondios Dimitrios , Lyronis Antonios , Sofiakis Konstantinos , Antoniadis Aristomenis
Published: July 2017

Drilling is among the most significant manufacturing processes since it is widely used in the production of almost any product or part. Research in drilling processes and investigation of the phenomena that occur during the process is of great interest, given the fact that drilling is mainly applied at the final stages of the production process, thus it can greatly affect the total manufacturing cost. In the context of this study, a finite element model to simulate drilling and burr formation both on entrance and exit surface of the workpiece, was created. Simulation was implemented for the investigation of several combinations of cutting conditions, namely cutting speed and feed rate and the model was validated with a series of drilling experiments monitored by a high-speed camera.
Review Article: Tunneling-based graphene electronics: Methods and examples
Authors: Katkov Vsevolod L. , Osipov Vladimir A.
Published: July 2017

The authors present an overview of the main theoretical approaches used to describe tunnel processes in graphene nanoelectronics. Two currently central theoretical methods of calculating tunnel current, the Bardeen tunneling Hamiltonian approach and the method of nonequilibrium Green's functions, are reviewed in a pedagogical fashion. Several examples are used to illustrate the specific features of the methods. An application of both methods to the analysis of current flow in graphene tunnel field-effect transistors is discussed.
Cyclic Cl2/H2 quasi-atomic layer etching approach for TiN and TaN patterning using organic masks
Authors: Marchack Nathan , Papalia John M. , Engelmann Sebastian , Joseph Eric A.
Published: July 2017

A plasma-enhanced cyclic etch process utilizing sequential cycles of Cl2 (deposition) and He/H2 (etch) chemistries separated by purge steps was used to pattern TiN and TaN lines using an organic planarization layer mask at a 100 nm critical dimension and a 200 nm pitch. Etch rates (ERs) were found to vary from 3.5 to 7 nm per cycle for TaN and 5–7.3 nm per cycle for TiN, depending on the addition of H2 to the etch step. The cyclic etch process displayed several key advantages over a continuous wave plasma process, such as no residual material in TiN patterning and reduced veiling due to redeposition in the TaN features. Analysis of the optical emission spectra collected indicated a key mechanistic difference between etching of the two materials, with TiN etching mainly controlled by the residence time of Cl species and TaN etching rate-limited by physical bombardment to facilitate Ta-Cl formation. Tailoring of the feature profiles and control of the etch rate per cycle (ER/cycle) were demonstrated through manipulation of the Cl and H2 residence times.
Self-catalyst assisted and catalyst-free epitaxial growth of InAs on Ge (111): Role of substrate surface and evolution of polytypism
Authors: Pal Suparna , Mukherjee Chandrachur , Sathe Vasant G. , Kumar Ravi , Tiwari Pragya , Dixit Vijay Kumar , Sharma Tarun Kumar
Published: July 2017

In the present work, the authors report on the role of a self-catalyst (indium) and a substrate surface in various growth mechanisms and the crystalline structure of InAs nucleating layers on Ge (111) using metal organic vapor phase epitaxy. This study opens up the possibility of direct integration of InAs with Ge (111) substrates for next generation optoelectronic and microelectronic device applications. Different nucleation modes like droplet-epitaxy (DE), Volmer–Weber (VW), and Frank–Van der Merwe (FM) modes are observed in various growth windows. DE and FM modes are the dominating nucleation modes at lower growth temperature (400–470 °C) with the assistance of indium catalysts, while the VW mode dominates at higher growth temperature (470–540 °C). Three dimensional faceted structures are formed with varying densities in the overall growth temperature range of 400–540 °C, which is attributed to various factors like surface strain of the indium adatom covered Ge (111) surface, indium surface diffusion, and twin defect formation. High resolution x-ray diffraction identifies the twin formation at low growth temperature. Raman mapping reveals that InAs nano-/microstructures grow with a zinc blende-wurtzite polytypic crystal structure at higher growth temperature and arsenic-rich conditions. A comparison is made on the growth modes, morphology, and polytypism in InAs nanostructures, which are grown on Ge (111) and Si (111) substrates under identical conditions. Low surface diffusivity of indium on the Ge substrate and InAs/Ge interface energy are proposed as the main factors for the inhibition of anisotropic axial growth of InAs on Ge via the vapor-liquid-solid mode, while they succeed on the Si substrate.
Theoretical prediction and experimental measurement of isothermal extrudate swell of monodisperse and bidisperse polystyrenes
Authors: Robertson Ben , Thompson Richard L. , McLeish Tom C. B. , Robinson Ian
Published: July 2017

This paper describes the theoretical prediction, finite element simulation, and experimental studies of extrudate swell in monodisperse and bidisperse polystyrenes. We present a molecular approach to understanding extrudate swell using the tube-model-based Rolie-Poly constitutive equation within a Lagrangian finite element solver. This yields theoretical predictions of swelling which show a close universality: The molecular weight dependence of the swelling can be removed when the flow speed is scaled by the Rouse Weissenberg number. The roles that both chain orientation and stretch play in determining extrudate swell are clearly identifiable from plots of swelling ratio against each Weissenberg number. We also present isothermal extrusion experiments on the same polymers and can obtain good predictions well into the strong chain stretching regime. The predictions for swelling ratios match those from experiments up to Rouse Weissenberg numbers of ∼7, above which swelling is overpredicted by the Rolie-Poly equation.
Inflamm-vestigating inflamm-aging
Authors: Dupnik Kathryn
Published: July 2017

Monocytes from elderly people respond differently to pattern recognition receptor engagement than monocytes from younger adults.
Comfy wirewear
Authors: King Kevin R.
Published: July 2017

Nanomesh fabrication creates breathable, stretchable, comfortable, inflammation-free, on-skin conductors without residual polymeric support for wearable biosensors.
Interferon with antitumor immunity
Authors: Scharschmidt Tiffany C.
Published: July 2017

IFN-γ directs homeostatic differentiation of tissue APCs but may subvert aspects of tumor immune surveillance.
AID-ing Signaling in
Toxoplasma gondii
Authors: Kim Kami
Published: July 2017

The cyclic GMP-dependent protein kinase (PKG) of apicomplexan parasites is essential for secretion of micronemes and host cell invasion and egress. Both kinase specificity and localization can determine which substrates are phosphorylated. The functions of plasma membrane and cytosolic PKG isoforms of
Toxoplasma gondii
were unknown because of difficulties precisely manipulating expression of essential genes. Brown et al. (K. M. Brown, S. Long, and L. D. Sibley, mBio 8:e00375-17,
https://doi.org/10.1128/mBio.00375-17
) adapted the auxin-inducible degron (AID) system for conditional expression of
T. gondii
proteins. AID, in combination with clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 gene editing, facilitated creation of a panel of PKG mutants to demonstrate that the membrane association via acylation of PKG is critical for its essential functions in tachyzoites. The cytosolic form of PKG is not sufficient for viability and is dispensable. These studies illuminate a critical role for targeting of kinase complexes for parasite viability. The AID system enables rapid, conditional regulation of protein expression that expands the molecular toolbox of
T. gondii
.
Clostridium difficile
Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes
Authors: Jenior Matthew L. , Leslie Jhansi L. , Young Vincent B. , Schloss Patrick D.
Published: July 2017

Infection by the bacterium
Clostridium difficile
causes an inflammatory diarrheal disease which can become life threatening and has grown to be the most prevalent nosocomial infection. Susceptibility to
C. difficile
infection is strongly associated with previous antibiotic treatment, which disrupts the gut microbiota and reduces its ability to prevent colonization. In this study, we demonstrated that
C. difficile
altered pathogenesis between hosts pretreated with antibiotics from separate classes and exploited different nutrient sources across these environments. Our metabolite score calculation also provides a platform to study nutrient requirements of pathogens during an infection. Our results suggest that
C. difficile
colonization resistance is mediated by multiple groups of bacteria competing for several subsets of nutrients and could explain why total reintroduction of competitors through fecal microbial transplant currently is the most effective treatment for recurrent CDI. This work could ultimately contribute to the identification of targeted, context-dependent measures that prevent or reduce
C. difficile
colonization, including pre- and probiotic therapies.
Human bone marrow mesenchymal stem cells suppress the proliferation of hepatic stellate cells by inhibiting the ubiquitination of p27
Authors: Wang Liang , Bai Guang , Chen Fei
Published: July 2017

Bone marrow mesenchymal stem cells (BMSCs) have considerable therapeutic potential for the treatment of end-stage liver disease. Previous studies have demonstrated that BMSCs secrete growth factors and cytokines that inactivate hepatic stellate cells (HSCs), which inhibited the progression of hepatic fibrosis. The aim of this study was to determine the mechanism by which BMSCs suppress the function of HSCs in fibrosis. Our results showed that co-culture of BMSCs and HSCs induced cell cycle arrest at the G10/G1 phase and cell apoptosis of HSCs, which finally inhibited the cell proliferation of HSCs. Consistent with the cell cycle arrest, co-culture of BMSCs and HSCs increased the abundance of the cell cycle protein p27. Mechanistically, we further uncovered that following the co-culture with BMSCs, the expression level of the E3 ligase S-phase kinase-associated protein 2 (SKP2) that is responsible for the ubiquitination of p27 was decreased, which attenuated the ubiquitination of p27 and increased the stability of p27 in HSCs. Collectively, our results indicated the potential involvement of the SKP2–p27 axis for the inhibitory effect of BSMCs on the cell proliferation of HSCs.
Employing contact metamorphism to assess the conditions of pluton emplacement and timing of recrystallization in southwestern Kellys Mountain, Cape Breton Island, Nova Scotia
Authors: Shawwa Nabil A. , Raeside Robert P. , McMullin David W.A. , McFarlane Christopher R.M.
Published: July 2017

At Kellys Mountain, Cape Breton Island, Nova Scotia, the late Neoproterozoic Glen Tosh formation (a low-grade metapsammite–metapelite unit of the George River Metamorphic Suite) has been intruded by diorite, granodiorite, and granite plutons, and the diorite hosts a narrow contact metamorphic aureole. New mapping and sampling in the contact aureole reveals that the metasedimentary rocks have reached amphibolite-facies metamorphism resulting in the development of neoformed biotite, muscovite, cordierite, ilmenite, garnet, andalusite, sillimanite, monazite, and spinel within the meta-pelite, a mineral assemblage also found in the Kellys Mountain Gneiss as a result of low-pressure regional metamorphism. Neoformed minerals and the disappearance of foliation defines a contact metamorphic aureole within 300 m of the pluton contacts. Petrographic and microprobe analyses of equilibrium assemblages in metapelitic units of the contact aureole yielded metamorphic pressures of 250 MPa, implying an intrusion depth of ∼9 km, with temperatures ranging from 365 to 590 °C. The presence of earlier-formed andalusite and garnet indicates the rocks may have initially undergone a low-pressure regional metamorphic event prior to contact metamorphism. Monazite in the contact aureole was dated using in-situ U–Pb methods and yielded an age of 480.9 ± 3.7 Ma, interpreted as the time of formation of the contact metamorphic aureole.
Quasi-periodic solutions of the Belov–Chaltikian lattice hierarchy
Authors: Geng Xianguo , Zeng Xin
Published: July 2017

Utilizing the characteristic polynomial of Lax matrix for the Belov–Chaltikian (BC) lattice hierarchy associated with a [Formula: see text] discrete matrix spectral problem, we introduce a trigonal curve with three infinite points, from which we establish the associated Dubrovin-type equations. The essential properties of the Baker–Akhiezer function and the meromorphic function are discussed, that include their asymptotic behavior near three infinite points on the trigonal curve and the divisor of the meromorphic function. The Abel map is introduced to straighten out the continuous flow and the discrete flow in the Jacobian variety, from which the quasi-periodic solutions of the entire BC lattice hierarchy are obtained in terms of the Riemann theta function.
Ultrasonic wave generation in two-band organic conductors due to thermoelectric effect
Authors: Krstovska Danica
Published: July 2017

A linear thermoelectric generation of a longitudinal ultrasonic wave in organic conductors with two conducting channels, quasi-one dimensional (q1D) and quasi-two dimensional (q2D), is investigated theoretically. The magnetic field and temperature dependences of the amplitude of generated through Nernst effect wave in [Formula: see text]-(BEDT-TTF)2KHg(SCN)4 for two boundary conditions, isothermal and adiabatic are obtained. Findings show a preference of one type of a boundary over another in the wave generation and propagation depending on the magnetic field strength and temperature. At lower temperatures and above B[Formula: see text]=[Formula: see text]4 T, the wave amplitude for adiabatic boundary is smaller compared to the one for isothermal boundary although there is a heat flux through the conductor’s surface in the latter. Both the q1D and q2D charge carriers contribute to the observation of the effect but with different magnitude due to the different drift velocity along the direction of wave propagation.
Carrier effective masses and thermoelectric properties of novel Ag3AuSe2 and Ag3AuTe2 compounds
Authors: Faizan M. , Ullah Hayat , Khan S. H. , Ramay Shahid M. , Qaid Salem A. S. , Mahmood Asif , Ali Manzar
Published: July 2017

The carrier effective masses as well as thermoelectric and electronic properties of ternary chalcogenides compounds of the form Ag3AuX2(X = Se, Te) have been studied using first-principles method based on density functional theory. For the treatment of exchange-correlation energy, we have used the generalized gradient approximation (GGA) by Perdew, Burke and Ernzerhof (PBE-GGA) and Wu–Cohen (WU-GGA) schemes. Both the compounds (Ag3AuSe2 and Ag3AuTe2) are direct bandgap semiconductors. The p-type nature of these compounds is confirmed by the effective mass calculations. In thermoelectric measurements, different parameters (electrical conductivity, carrier concentration, Seebeck coefficient, thermal conductivity and thermoelectric power) are calculated. It is found that all these parameters increase with the increase in temperature for both the compounds. The obtained results for these compounds such as the direct bandgap nature and their high value of the thermoelectric power make them valuable candidates for different device applications.
Lump-type solutions for the (4+1)-dimensional Fokas equation via symbolic computations
Authors: Cheng Li , Zhang Yi
Published: July 2017

Based on the Hirota bilinear form, two classes of lump-type solutions of the (4[Formula: see text]+[Formula: see text]1)-dimensional nonlinear Fokas equation, rationally localized in almost all directions in the space are obtained through a direct symbolic computation with Maple. The resulting lump-type solutions contain free parameters. To guarantee the analyticity and rational localization of the solutions, the involved parameters need to satisfy certain constraints. A few particular lump-type solutions with special choices of the involved parameters are given.